Query psy11065
Match_columns 138
No_of_seqs 188 out of 1077
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 17:09:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11065.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11065hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1676|consensus 99.8 4.2E-18 9.1E-23 144.5 12.6 111 5-123 196-308 (600)
2 cd02396 PCBP_like_KH K homolog 99.6 1E-15 2.2E-20 96.9 7.5 63 47-109 2-64 (65)
3 cd02393 PNPase_KH Polynucleoti 99.6 7.5E-15 1.6E-19 92.1 7.5 60 44-110 1-61 (61)
4 KOG1676|consensus 99.5 4.3E-14 9.3E-19 120.3 11.0 109 3-121 107-216 (600)
5 cd02394 vigilin_like_KH K homo 99.5 1.7E-14 3.7E-19 90.1 5.8 61 47-110 2-62 (62)
6 PF00013 KH_1: KH domain syndr 99.5 2E-14 4.4E-19 89.2 4.9 60 46-109 1-60 (60)
7 cd00105 KH-I K homology RNA-bi 99.5 2E-13 4.4E-18 85.0 7.6 62 47-109 2-63 (64)
8 KOG2192|consensus 99.4 5.4E-12 1.2E-16 99.5 9.5 102 12-117 284-386 (390)
9 KOG2191|consensus 99.4 5.8E-12 1.3E-16 101.4 9.8 78 45-122 39-118 (402)
10 smart00322 KH K homology RNA-b 99.3 2.8E-11 6E-16 74.9 9.0 67 44-113 2-68 (69)
11 cd02395 SF1_like-KH Splicing f 99.3 8.6E-12 1.9E-16 88.1 7.0 83 54-137 15-117 (120)
12 KOG2190|consensus 99.3 4.3E-11 9.3E-16 101.6 11.4 74 44-117 137-210 (485)
13 PF13014 KH_3: KH domain 99.2 3.3E-11 7.2E-16 70.2 5.5 43 55-97 1-43 (43)
14 KOG2191|consensus 99.1 1.2E-10 2.7E-15 93.8 7.7 74 45-118 132-207 (402)
15 TIGR03665 arCOG04150 arCOG0415 99.1 6.2E-10 1.3E-14 83.0 9.2 104 4-130 50-162 (172)
16 KOG0119|consensus 99.1 1E-09 2.2E-14 92.3 10.8 118 10-137 113-254 (554)
17 KOG2193|consensus 99.1 1.1E-10 2.4E-15 96.8 4.4 74 43-116 409-482 (584)
18 TIGR03665 arCOG04150 arCOG0415 99.0 3.3E-10 7.2E-15 84.5 5.5 61 49-115 2-65 (172)
19 PRK13763 putative RNA-processi 99.0 6.8E-10 1.5E-14 83.4 7.0 64 45-114 3-70 (180)
20 PRK13763 putative RNA-processi 99.0 2.1E-09 4.5E-14 80.8 9.5 54 54-115 104-157 (180)
21 KOG2193|consensus 99.0 8.7E-10 1.9E-14 91.5 6.8 78 43-120 197-274 (584)
22 TIGR02696 pppGpp_PNP guanosine 98.9 2.3E-09 5.1E-14 94.4 7.8 95 5-115 547-642 (719)
23 TIGR03591 polynuc_phos polyrib 98.9 2.6E-09 5.7E-14 94.2 5.8 96 5-118 519-618 (684)
24 KOG2192|consensus 98.8 6.7E-09 1.5E-13 82.2 5.0 80 40-119 118-197 (390)
25 COG1185 Pnp Polyribonucleotide 98.6 5.8E-08 1.2E-12 84.7 6.4 106 4-123 519-624 (692)
26 KOG1588|consensus 98.6 4.1E-07 8.9E-12 71.5 10.5 93 42-137 89-210 (259)
27 PLN00207 polyribonucleotide nu 98.6 3.7E-08 8E-13 88.6 4.8 103 5-121 653-756 (891)
28 KOG2190|consensus 98.5 2.6E-07 5.6E-12 78.8 7.6 70 45-115 43-121 (485)
29 KOG0336|consensus 98.3 7.8E-07 1.7E-11 74.5 5.1 70 45-118 47-116 (629)
30 PRK11824 polynucleotide phosph 98.3 3.3E-07 7.2E-12 81.2 3.0 99 5-118 522-621 (693)
31 KOG1067|consensus 98.3 1.2E-06 2.6E-11 75.4 5.4 101 4-120 564-665 (760)
32 COG1094 Predicted RNA-binding 98.0 2.6E-05 5.7E-10 59.1 6.5 54 55-116 112-165 (194)
33 PRK04163 exosome complex RNA-b 97.9 2.8E-05 6.1E-10 60.7 6.6 66 47-119 147-213 (235)
34 KOG2814|consensus 97.9 2.4E-05 5.2E-10 63.5 5.5 71 45-117 57-127 (345)
35 COG5176 MSL5 Splicing factor ( 97.8 7.1E-05 1.5E-09 57.6 6.3 92 45-136 148-263 (269)
36 PRK12704 phosphodiesterase; Pr 97.6 0.00022 4.8E-09 61.6 7.5 67 45-117 210-278 (520)
37 TIGR03319 YmdA_YtgF conserved 97.6 0.00021 4.5E-09 61.6 7.3 67 45-117 204-272 (514)
38 PRK00106 hypothetical protein; 97.6 0.00026 5.6E-09 61.3 7.5 67 45-117 225-293 (535)
39 cd02134 NusA_KH NusA_K homolog 97.5 0.00019 4.2E-09 44.6 4.6 36 45-80 25-60 (61)
40 KOG2113|consensus 97.4 0.00021 4.6E-09 57.9 4.9 66 42-111 23-88 (394)
41 COG1094 Predicted RNA-binding 97.2 0.0013 2.9E-08 49.9 6.9 63 45-113 8-75 (194)
42 COG1097 RRP4 RNA-binding prote 96.9 0.0029 6.2E-08 49.6 6.0 62 47-115 148-210 (239)
43 KOG2113|consensus 96.7 0.002 4.3E-08 52.3 3.8 95 8-106 78-173 (394)
44 KOG2279|consensus 96.7 0.0011 2.4E-08 57.1 2.5 75 43-118 138-212 (608)
45 PRK12705 hypothetical protein; 96.7 0.0029 6.2E-08 54.6 4.8 68 45-117 198-266 (508)
46 PRK00468 hypothetical protein; 96.6 0.0029 6.4E-08 41.1 3.6 30 45-74 30-59 (75)
47 PRK02821 hypothetical protein; 96.6 0.0024 5.3E-08 41.7 3.0 31 45-75 31-61 (77)
48 KOG2279|consensus 96.5 0.0017 3.7E-08 56.0 2.4 71 43-115 66-136 (608)
49 COG1837 Predicted RNA-binding 96.3 0.0056 1.2E-07 39.9 3.4 29 45-73 30-58 (76)
50 PRK01064 hypothetical protein; 96.0 0.0089 1.9E-07 39.2 3.3 30 45-74 30-59 (78)
51 KOG4369|consensus 95.8 0.0024 5.1E-08 59.6 -0.0 75 44-118 1339-1413(2131)
52 KOG2208|consensus 95.8 0.026 5.7E-07 50.9 6.5 71 45-118 347-417 (753)
53 PRK08406 transcription elongat 95.7 0.019 4E-07 41.6 4.3 38 45-82 32-69 (140)
54 PF13083 KH_4: KH domain; PDB: 95.5 0.0091 2E-07 38.0 1.9 32 45-76 29-60 (73)
55 PRK08406 transcription elongat 95.4 0.017 3.7E-07 41.7 3.2 38 45-82 99-136 (140)
56 cd02409 KH-II KH-II (K homolo 95.1 0.049 1.1E-06 33.1 4.2 34 45-78 25-58 (68)
57 COG1855 ATPase (PilT family) [ 94.4 0.041 8.9E-07 47.3 3.3 41 45-85 486-526 (604)
58 PF07650 KH_2: KH domain syndr 94.4 0.033 7.1E-07 35.7 2.2 35 45-79 25-59 (78)
59 cd02410 archeal_CPSF_KH The ar 94.3 0.2 4.3E-06 36.5 6.3 66 5-84 50-115 (145)
60 PF14611 SLS: Mitochondrial in 94.2 0.37 8.1E-06 36.4 8.0 71 46-122 27-97 (210)
61 TIGR01952 nusA_arch NusA famil 94.1 0.099 2.2E-06 37.9 4.4 37 46-82 34-70 (141)
62 KOG2208|consensus 94.0 0.095 2.1E-06 47.4 5.0 90 2-114 397-487 (753)
63 TIGR01952 nusA_arch NusA famil 93.8 0.062 1.4E-06 39.0 2.9 39 44-82 99-137 (141)
64 KOG3273|consensus 93.8 0.036 7.7E-07 42.7 1.7 67 54-132 178-244 (252)
65 cd02414 jag_KH jag_K homology 93.8 0.073 1.6E-06 34.3 2.9 36 45-80 24-59 (77)
66 PF13184 KH_5: NusA-like KH do 93.7 0.061 1.3E-06 34.3 2.4 38 46-83 4-47 (69)
67 PRK13764 ATPase; Provisional 93.4 0.076 1.6E-06 46.9 3.3 41 45-85 481-521 (602)
68 cd02413 40S_S3_KH K homology R 93.4 0.13 2.7E-06 33.8 3.5 38 43-80 28-65 (81)
69 KOG2874|consensus 92.7 0.3 6.6E-06 39.4 5.4 52 56-115 160-211 (356)
70 COG0195 NusA Transcription elo 92.1 0.18 4E-06 38.3 3.4 37 46-82 143-179 (190)
71 TIGR01953 NusA transcription t 91.6 0.27 5.8E-06 40.6 4.1 38 45-82 301-338 (341)
72 PRK12328 nusA transcription el 91.1 0.28 6.2E-06 40.9 3.8 40 45-84 308-347 (374)
73 PRK06418 transcription elongat 91.0 0.55 1.2E-05 35.0 4.9 38 45-83 61-98 (166)
74 cd02412 30S_S3_KH K homology R 89.9 0.34 7.3E-06 33.4 2.8 32 45-76 61-92 (109)
75 PRK12327 nusA transcription el 89.5 0.48 1E-05 39.4 3.9 40 45-84 303-342 (362)
76 cd02411 archeal_30S_S3_KH K ho 89.0 0.53 1.1E-05 30.9 3.1 30 45-74 38-67 (85)
77 PRK09202 nusA transcription el 88.6 0.44 9.5E-06 40.9 3.2 39 45-83 302-340 (470)
78 COG1782 Predicted metal-depend 88.5 1.4 3E-05 38.6 6.0 66 5-84 73-138 (637)
79 COG0092 RpsC Ribosomal protein 88.1 0.49 1.1E-05 37.0 2.9 40 43-82 49-95 (233)
80 TIGR03675 arCOG00543 arCOG0054 87.7 1.3 2.9E-05 39.3 5.7 67 5-85 67-133 (630)
81 PRK12329 nusA transcription el 87.0 0.68 1.5E-05 39.5 3.3 38 45-82 335-372 (449)
82 COG0195 NusA Transcription elo 86.3 1 2.2E-05 34.2 3.7 38 46-83 77-114 (190)
83 TIGR00436 era GTP-binding prot 80.3 2.8 6E-05 32.8 4.1 29 45-73 221-250 (270)
84 TIGR01008 rpsC_E_A ribosomal p 79.5 2.4 5.2E-05 32.3 3.4 32 43-74 36-67 (195)
85 CHL00048 rps3 ribosomal protei 78.4 2.8 6.1E-05 32.4 3.5 32 43-74 64-95 (214)
86 PRK15494 era GTPase Era; Provi 76.3 4.2 9E-05 33.2 4.1 36 45-80 273-317 (339)
87 PRK00089 era GTPase Era; Revie 75.2 4.7 0.0001 31.6 4.1 36 45-80 226-270 (292)
88 PRK04191 rps3p 30S ribosomal p 75.0 3.7 8E-05 31.5 3.3 30 46-75 41-70 (207)
89 PTZ00084 40S ribosomal protein 74.7 3.5 7.7E-05 32.0 3.1 31 44-74 43-73 (220)
90 COG1702 PhoH Phosphate starvat 73.9 11 0.00025 31.2 6.0 57 52-116 22-80 (348)
91 COG1159 Era GTPase [General fu 71.2 6.6 0.00014 31.9 4.0 27 47-73 231-258 (298)
92 PRK12327 nusA transcription el 69.3 5.1 0.00011 33.4 3.1 29 54-82 245-274 (362)
93 COG1847 Jag Predicted RNA-bind 68.3 4.4 9.6E-05 31.3 2.3 62 7-80 65-126 (208)
94 TIGR01953 NusA transcription t 67.3 5.6 0.00012 32.8 2.9 29 54-82 243-272 (341)
95 PRK12329 nusA transcription el 65.8 5.3 0.00012 34.2 2.5 29 54-82 277-306 (449)
96 TIGR01009 rpsC_bact ribosomal 65.7 7.3 0.00016 30.0 3.1 31 44-74 61-91 (211)
97 PRK12328 nusA transcription el 62.0 6.1 0.00013 33.1 2.2 29 54-82 251-280 (374)
98 PRK09202 nusA transcription el 60.0 7.6 0.00016 33.5 2.5 29 54-82 245-274 (470)
99 PRK00310 rpsC 30S ribosomal pr 57.8 12 0.00027 29.2 3.1 31 44-74 61-91 (232)
100 PF03958 Secretin_N: Bacterial 54.9 35 0.00076 21.2 4.5 34 73-112 43-76 (82)
101 COG5166 Uncharacterized conser 51.1 10 0.00022 33.4 1.8 39 44-82 448-486 (657)
102 KOG4369|consensus 50.6 14 0.0003 35.9 2.6 71 46-117 782-852 (2131)
103 cd07055 BMC_like_2 Bacterial M 50.5 57 0.0012 20.3 4.6 38 72-111 21-59 (61)
104 KOG1423|consensus 49.5 21 0.00046 29.6 3.4 32 44-75 327-359 (379)
105 PF09869 DUF2096: Uncharacteri 49.0 76 0.0016 23.7 5.9 54 45-112 113-166 (169)
106 PF02749 QRPTase_N: Quinolinat 48.2 74 0.0016 20.6 5.6 53 63-115 32-86 (88)
107 cd07049 BMC_EutL_repeat1 ethan 45.4 85 0.0018 21.6 5.3 46 71-116 46-100 (103)
108 PF14611 SLS: Mitochondrial in 42.5 1.4E+02 0.0031 22.2 8.2 49 63-114 114-164 (210)
109 COG0331 FabD (acyl-carrier-pro 39.9 1E+02 0.0023 25.0 6.0 54 56-113 133-188 (310)
110 COG4010 Uncharacterized protei 39.8 1.4E+02 0.003 22.0 6.0 43 65-114 126-168 (170)
111 PRK07428 nicotinate-nucleotide 38.8 2.1E+02 0.0045 23.1 9.2 66 48-115 44-113 (288)
112 COG0490 Putative regulatory, l 38.8 90 0.0019 23.2 5.0 61 45-109 86-157 (162)
113 PF09383 NIL: NIL domain; Int 29.3 94 0.002 19.2 3.4 48 64-111 16-68 (76)
114 PF02080 TrkA_C: TrkA-C domain 28.5 65 0.0014 19.2 2.5 45 64-108 14-69 (71)
115 smart00877 BMC Bacterial micro 27.9 1.3E+02 0.0028 19.0 3.9 45 68-114 18-62 (75)
116 PF07837 FTCD_N: Formiminotran 27.3 2E+02 0.0043 21.7 5.3 52 61-114 12-69 (178)
117 PF10369 ALS_ss_C: Small subun 26.1 1.8E+02 0.0038 18.3 4.4 40 65-110 17-57 (75)
118 cd07045 BMC_CcmK_like Carbon d 25.2 1.7E+02 0.0037 19.0 4.1 45 69-115 19-63 (84)
119 TIGR03131 malonate_mdcH malona 24.5 3.4E+02 0.0073 21.1 6.5 48 58-111 125-172 (295)
120 PF00936 BMC: BMC domain; Int 23.6 2E+02 0.0043 18.1 5.1 46 68-115 19-64 (75)
121 COG1117 PstB ABC-type phosphat 22.1 45 0.00097 26.4 1.0 22 45-66 24-45 (253)
No 1
>KOG1676|consensus
Probab=99.77 E-value=4.2e-18 Score=144.46 Aligned_cols=111 Identities=34% Similarity=0.515 Sum_probs=90.0
Q ss_pred hHHHHHHHHHHHhhcC--CCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 5 EFQQSRRWQQGIGRNN--DNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 5 ~~~~ak~~v~~i~~~~--~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
+||+||.||.+|++.- ..++ +.++.+++.+ ...+.++.||..+||.||||+|++||+|+.+||+||+|.+
T Consensus 196 ~ve~a~~lV~dil~e~~~~~~g---~~~~~g~~~g-----~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp 267 (600)
T KOG1676|consen 196 KVEQAKQLVADILREEDDEVPG---SGGHAGVRGG-----GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP 267 (600)
T ss_pred HHHHHHHHHHHHHHhcccCCCc---cccccCcCcc-----ccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec
Confidence 6899999999999952 2221 1122222211 1238999999999999999999999999999999999999
Q ss_pred CCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCC
Q psy11065 83 MREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSG 123 (138)
Q Consensus 83 ~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~ 123 (138)
++++.+-+|.+.|.|++++|.+|.++|.+||++......++
T Consensus 268 Dd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~~~~~ 308 (600)
T KOG1676|consen 268 DDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAGAGGG 308 (600)
T ss_pred CCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 88754449999999999999999999999999998885443
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=99.64 E-value=1e-15 Score=96.94 Aligned_cols=63 Identities=35% Similarity=0.617 Sum_probs=58.1
Q ss_pred EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHH
Q psy11065 47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI 109 (138)
Q Consensus 47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I 109 (138)
++|.||.+.+|.|||++|++|++|+++|||+|.+.+...+.+.+|+++|.|+++++..|..+|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 689999999999999999999999999999999998765344489999999999999999987
No 3
>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=99.58 E-value=7.5e-15 Score=92.11 Aligned_cols=60 Identities=28% Similarity=0.483 Sum_probs=54.8
Q ss_pred ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecC-HHHHHHHHHHHH
Q psy11065 44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGS-PDQVQEARARIE 110 (138)
Q Consensus 44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~-~e~i~~A~~~I~ 110 (138)
|....+.||.+++|.|||++|++|++|+++|||+|.|++ ++.|+|.|+ +++++.|+++|+
T Consensus 1 P~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred CeEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-------CCEEEEEeCCHHHHHHHHHHhC
Confidence 467899999999999999999999999999999999987 356999998 999999999873
No 4
>KOG1676|consensus
Probab=99.55 E-value=4.3e-14 Score=120.27 Aligned_cols=109 Identities=21% Similarity=0.378 Sum_probs=90.4
Q ss_pred chhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 3 SIEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 3 ~~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
++.|+.||.|+.++++... ...+|.+..+. ..++.+|.||.+++|+||||+|+|||+|++.|||++.+..
T Consensus 107 pe~v~~aK~li~evv~r~~---~~~~~~~~q~~-------~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iq 176 (600)
T KOG1676|consen 107 PENVEVAKQLIGEVVSRGR---PPGGFPDNQGS-------VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQ 176 (600)
T ss_pred cccHHHHHHhhhhhhhccC---CCCCccccCCc-------cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEe
Confidence 6789999999999998765 33444444442 2489999999999999999999999999999999999888
Q ss_pred CCCCCCC-CcEEEEecCHHHHHHHHHHHHHHHHhhhhccC
Q psy11065 83 MREDDPS-DRRCMLSGSPDQVQEARARIEELIDSVMVEQF 121 (138)
Q Consensus 83 ~~~~~~~-~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~ 121 (138)
+....++ .+.+.|+|++++|+.|+.||.++|++.....+
T Consensus 177 d~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~ 216 (600)
T KOG1676|consen 177 DGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVP 216 (600)
T ss_pred cCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCC
Confidence 7764432 78899999999999999999999997444433
No 5
>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=99.53 E-value=1.7e-14 Score=90.09 Aligned_cols=61 Identities=28% Similarity=0.498 Sum_probs=55.9
Q ss_pred EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHH
Q psy11065 47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIE 110 (138)
Q Consensus 47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~ 110 (138)
.++.||.++++.|||++|++|++|+++|||+|++++...+ ++.|+|.|+++++..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~---~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSK---SDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCC---CCEEEEEcCHHHHHHHHHHhC
Confidence 5899999999999999999999999999999999986532 789999999999999998873
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=99.51 E-value=2e-14 Score=89.20 Aligned_cols=60 Identities=37% Similarity=0.596 Sum_probs=54.8
Q ss_pred EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHH
Q psy11065 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI 109 (138)
Q Consensus 46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I 109 (138)
|.+|.||.+.+++|||++|++|++|+++|||+|.++++. ....++|.|+++++..|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~----~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD----ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT----EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC----CcEEEEEEeCHHHHHHHHhhC
Confidence 578999999999999999999999999999999998752 156899999999999999987
No 7
>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=99.48 E-value=2e-13 Score=85.03 Aligned_cols=62 Identities=35% Similarity=0.669 Sum_probs=56.1
Q ss_pred EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHH
Q psy11065 47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARI 109 (138)
Q Consensus 47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I 109 (138)
.++.||.+++++|||++|++|++|+++|||+|.|++.... ..++.+++.|+.+++..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~-~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSG-SEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCC-CCceEEEEEcCHHHHHHHHHHh
Confidence 5899999999999999999999999999999999886542 3389999999999999999887
No 8
>KOG2192|consensus
Probab=99.35 E-value=5.4e-12 Score=99.50 Aligned_cols=102 Identities=26% Similarity=0.413 Sum_probs=77.5
Q ss_pred HHHHHhhcC-CCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCC
Q psy11065 12 WQQGIGRNN-DNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSD 90 (138)
Q Consensus 12 ~v~~i~~~~-~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~ 90 (138)
|.+.|-.++ +.|++.+++..+..|..|. .-.+.++.||.+.-|.||||+|..|++|++++||.|.|+++.+..+ +
T Consensus 284 wqmaYePQgGs~ydysyAG~~GsYGdlGG---PitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGse-d 359 (390)
T KOG2192|consen 284 WQMAYEPQGGSGYDYSYAGGYGSYGDLGG---PITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSE-D 359 (390)
T ss_pred cccccCCCCCCCCCccccccccccCCCCC---ceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCC-c
Confidence 344444433 3445555444443443331 1256789999999999999999999999999999999988665545 9
Q ss_pred cEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065 91 RRCMLSGSPDQVQEARARIEELIDSVM 117 (138)
Q Consensus 91 r~i~i~G~~e~i~~A~~~I~~ii~~~~ 117 (138)
|+++|+|+.++|+.|+.+++..++.-.
T Consensus 360 rIitItGTqdQIqnAQYLlQn~Vkq~r 386 (390)
T KOG2192|consen 360 RIITITGTQDQIQNAQYLLQNSVKQYR 386 (390)
T ss_pred eEEEEeccHHHHhhHHHHHHHHHHhhh
Confidence 999999999999999999999888443
No 9
>KOG2191|consensus
Probab=99.35 E-value=5.8e-12 Score=101.39 Aligned_cols=78 Identities=29% Similarity=0.532 Sum_probs=72.4
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCC--CcEEEEecCHHHHHHHHHHHHHHHHhhhhccCC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPS--DRRCMLSGSPDQVQEARARIEELIDSVMVEQFS 122 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~--~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g 122 (138)
..++|+||...+|.||||+|++|.++|++|||+|++.+..+..|+ +|+|.|.|+.+.+....++|.+.|++..+..-+
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~k 118 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVAK 118 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhcC
Confidence 789999999999999999999999999999999999998876665 999999999999999999999999997766555
No 10
>smart00322 KH K homology RNA-binding domain.
Probab=99.31 E-value=2.8e-11 Score=74.91 Aligned_cols=67 Identities=34% Similarity=0.631 Sum_probs=59.9
Q ss_pred ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065 44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELI 113 (138)
Q Consensus 44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii 113 (138)
..+.++.||...++.+||++|++|++|++.|+++|.+..... ....+.+.|+++++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~---~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS---EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC---CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 357899999999999999999999999999999999977543 2688999999999999999998765
No 11
>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=99.30 E-value=8.6e-12 Score=88.14 Aligned_cols=83 Identities=24% Similarity=0.406 Sum_probs=61.7
Q ss_pred CccceeeccCcHHHHHHHHHhCCeEEEecCCC------------------CCCCCcEEEEecC--HHHHHHHHHHHHHHH
Q psy11065 54 AAVGVVIGKGGDMIKKLQNETGARVQFVQMRE------------------DDPSDRRCMLSGS--PDQVQEARARIEELI 113 (138)
Q Consensus 54 ~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~------------------~~~~~r~i~i~G~--~e~i~~A~~~I~~ii 113 (138)
.++|.|||++|++||+|+++|||+|.|..... ..+ .++.+.+-+ .+++.+|+.+|+.++
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~ep-lhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEP-LHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCC-cEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 57899999999999999999999999987521 111 344555556 799999999999999
Q ss_pred HhhhhccCCCCcccchhhhhcccC
Q psy11065 114 DSVMVEQFSGANFDKLRSTVLANR 137 (138)
Q Consensus 114 ~~~~~~~~g~~~~~~l~~~~~~~~ 137 (138)
.........--.-.+|+++++.|-
T Consensus 94 ~~~~~~~~~~~k~~ql~~la~~nG 117 (120)
T cd02395 94 KPAIEGGNDELKREQLRELALLNG 117 (120)
T ss_pred ccCCCccchHHHHHHHHHHHHhcc
Confidence 955444112223458888888773
No 12
>KOG2190|consensus
Probab=99.27 E-value=4.3e-11 Score=101.65 Aligned_cols=74 Identities=31% Similarity=0.512 Sum_probs=69.9
Q ss_pred ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065 44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117 (138)
Q Consensus 44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~ 117 (138)
+.+.+|+||...+|.||||+|+.||+|+++|||+|.|..+..+..++|.|+|.|.+++|.+|...|...|.+..
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLENP 210 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHhcC
Confidence 58999999999999999999999999999999999999987777779999999999999999999999998854
No 13
>PF13014 KH_3: KH domain
Probab=99.22 E-value=3.3e-11 Score=70.24 Aligned_cols=43 Identities=40% Similarity=0.699 Sum_probs=37.6
Q ss_pred ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec
Q psy11065 55 AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG 97 (138)
Q Consensus 55 ~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G 97 (138)
++|+|||++|++|++|+++|+|+|+|++...+.+.++.|+|.|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 4799999999999999999999999999554555589999987
No 14
>KOG2191|consensus
Probab=99.15 E-value=1.2e-10 Score=93.78 Aligned_cols=74 Identities=31% Similarity=0.511 Sum_probs=63.7
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCC--CCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRED--DPSDRRCMLSGSPDQVQEARARIEELIDSVMV 118 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~--~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~ 118 (138)
..+++.||+...|.||||+|.+||.|+++++|.|+|.+..+. ..-+|++++.|++++..+|+++|.+.|.++.+
T Consensus 132 kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 132 KQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred ceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence 458899999999999999999999999999999999842221 11289999999999999999999999887654
No 15
>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=99.10 E-value=6.2e-10 Score=83.03 Aligned_cols=104 Identities=23% Similarity=0.364 Sum_probs=72.7
Q ss_pred hhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecC---------CccceeeccCcHHHHHHHHHh
Q psy11065 4 IEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPK---------AAVGVVIGKGGDMIKKLQNET 74 (138)
Q Consensus 4 ~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~---------~~vg~IIGk~G~~Ik~I~~~T 74 (138)
..+.+|+++++++...-+ ...++.- - ........+.|+. ..+|+|||++|++++.|+..|
T Consensus 50 ~~i~kA~~~I~~i~~gf~---~e~A~~l--~------gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t 118 (172)
T TIGR03665 50 LAVMKAREVVKAIGRGFS---PEKALKL--L------DDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELT 118 (172)
T ss_pred HHHHHHHHHHHHHHcCCC---HHHHHHh--c------CCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHH
Confidence 468899999999877521 0000000 0 0011223455554 368999999999999999999
Q ss_pred CCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCCCcccchh
Q psy11065 75 GARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDKLR 130 (138)
Q Consensus 75 ga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~~~~~~l~ 130 (138)
||+|.|++ ..|.|.|++++++.|+++|.+++... ..+..|..|+
T Consensus 119 ~~~i~i~~--------~~v~i~G~~~~~~~A~~~i~~li~~~----~~~~vy~~l~ 162 (172)
T TIGR03665 119 GVSISVYG--------KTVGIIGDPEQVQIAREAIEMLIEGA----PHGTVYKFLE 162 (172)
T ss_pred CCeEEEcC--------CEEEEECCHHHHHHHHHHHHHHHcCC----CChhHHHHHH
Confidence 99999964 46999999999999999999999433 2334455553
No 16
>KOG0119|consensus
Probab=99.09 E-value=1e-09 Score=92.30 Aligned_cols=118 Identities=22% Similarity=0.273 Sum_probs=88.4
Q ss_pred HHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecC------CccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065 10 RRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPK------AAVGVVIGKGGDMIKKLQNETGARVQFVQM 83 (138)
Q Consensus 10 k~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~------~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~ 83 (138)
.++|.+++..+..|.....|.... ....++.||. ++||+|||..|.|.|+|+++|||||.|--.
T Consensus 113 ~e~I~~~lk~nP~fkpP~DYk~p~----------~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGk 182 (554)
T KOG0119|consen 113 HEIIEEILKLNPGFKPPADYKPPA----------KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGK 182 (554)
T ss_pred HHHHHHHHHhCcCCCCCcccCccc----------ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecc
Confidence 467888888888887777774332 2456777765 589999999999999999999999999651
Q ss_pred C------------C--CC--CCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCCCcc--cchhhhhcccC
Q psy11065 84 R------------E--DD--PSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANF--DKLRSTVLANR 137 (138)
Q Consensus 84 ~------------~--~~--~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~~~~--~~l~~~~~~~~ 137 (138)
. . +. ..-++.+.+-+.|.|++|+++|+.+|.+...-..+..+. -+|||++-+|.
T Consensus 183 gSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNg 254 (554)
T KOG0119|consen 183 GSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNG 254 (554)
T ss_pred ccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCC
Confidence 1 0 00 003556666788999999999999999966666665443 48999998874
No 17
>KOG2193|consensus
Probab=99.07 E-value=1.1e-10 Score=96.76 Aligned_cols=74 Identities=31% Similarity=0.492 Sum_probs=66.7
Q ss_pred cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV 116 (138)
Q Consensus 43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~ 116 (138)
....+++.||...||.|||++|.+||.|...+||.|.|.+..-++..+|.|+|+|++++..+|+..|...|++.
T Consensus 409 e~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEe 482 (584)
T KOG2193|consen 409 EQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEE 482 (584)
T ss_pred chhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhh
Confidence 45678999999999999999999999999999999999887766555999999999999999999997777664
No 18
>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=99.04 E-value=3.3e-10 Score=84.47 Aligned_cols=61 Identities=28% Similarity=0.506 Sum_probs=54.5
Q ss_pred EEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEE---ecCHHHHHHHHHHHHHHHHh
Q psy11065 49 VCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCML---SGSPDQVQEARARIEELIDS 115 (138)
Q Consensus 49 i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i---~G~~e~i~~A~~~I~~ii~~ 115 (138)
+.||.+++|.|||++|++|+.|+++|||+|+++++ +..|.| +++++++.+|+++|..+...
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~------~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE------TGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC------CceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 67999999999999999999999999999999874 234666 89999999999999998773
No 19
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.04 E-value=6.8e-10 Score=83.38 Aligned_cols=64 Identities=25% Similarity=0.432 Sum_probs=57.4
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEE----ecCHHHHHHHHHHHHHHHH
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCML----SGSPDQVQEARARIEELID 114 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i----~G~~e~i~~A~~~I~~ii~ 114 (138)
....+.||.++++.|||++|++|+.|+++|||+|+++++ +..|.| +++++++++|+++|++++.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE------TGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC------CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 467899999999999999999999999999999999874 234555 5899999999999999988
No 20
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.03 E-value=2.1e-09 Score=80.79 Aligned_cols=54 Identities=31% Similarity=0.550 Sum_probs=48.5
Q ss_pred CccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065 54 AAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS 115 (138)
Q Consensus 54 ~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~ 115 (138)
..+|+|||++|++++.|++.|||+|.|.+ +.+.+.|++++++.|++.|..++..
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~--------~~v~i~G~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYG--------KTVAIIGDPEQVEIAREAIEMLIEG 157 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcC--------CEEEEEeCHHHHHHHHHHHHHHHcC
Confidence 36899999999999999999999999974 2388889999999999999999843
No 21
>KOG2193|consensus
Probab=99.00 E-value=8.7e-10 Score=91.49 Aligned_cols=78 Identities=22% Similarity=0.379 Sum_probs=69.8
Q ss_pred cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhcc
Q psy11065 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQ 120 (138)
Q Consensus 43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~ 120 (138)
..-.++++||..++|.||||.|.|||.|.+.|.|+|++....+....++.+++.+++|...+|+.+|.+++.......
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~ 274 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDD 274 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccchHHHHHHHHHHHHHhhhcc
Confidence 346789999999999999999999999999999999998876655559999999999999999999999998766543
No 22
>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=98.94 E-value=2.3e-09 Score=94.41 Aligned_cols=95 Identities=24% Similarity=0.319 Sum_probs=73.9
Q ss_pred hHHHHHHHHHHHhhcCCC-CCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065 5 EFQQSRRWQQGIGRNNDN-FGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM 83 (138)
Q Consensus 5 ~~~~ak~~v~~i~~~~~~-~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~ 83 (138)
.+++|++-...|++-... .. .+ ...+...|....+.||+++++.|||++|++||.|+++|||+|+|.++
T Consensus 547 aL~~A~~g~~~Il~~m~~al~-------~p---~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~ 616 (719)
T TIGR02696 547 ALKQARDARLAILDVMAEAID-------TP---DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD 616 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHh-------Cc---cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC
Confidence 456777776666653311 10 00 13445578999999999999999999999999999999999999872
Q ss_pred CCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065 84 REDDPSDRRCMLSGSPDQVQEARARIEELIDS 115 (138)
Q Consensus 84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~ 115 (138)
..+.+...+.+++++|+++|+.++..
T Consensus 617 ------G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 617 ------GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ------cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 45566667999999999999999994
No 23
>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=98.88 E-value=2.6e-09 Score=94.23 Aligned_cols=96 Identities=18% Similarity=0.230 Sum_probs=74.9
Q ss_pred hHHHHHHHHHHHhhcC----CCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEE
Q psy11065 5 EFQQSRRWQQGIGRNN----DNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF 80 (138)
Q Consensus 5 ~~~~ak~~v~~i~~~~----~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I 80 (138)
.+++|++-..+|++.. ..+ ....+...|...++.||+++++.|||++|++||.|+++|||+|.|
T Consensus 519 al~~a~~~~~~I~~~m~~~l~~~------------~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i 586 (684)
T TIGR03591 519 ALEQAKEGRLHILGEMNKVISEP------------RAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDI 586 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhh------------hccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEE
Confidence 4567777777766532 111 112344577999999999999999999999999999999999999
Q ss_pred ecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065 81 VQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV 118 (138)
Q Consensus 81 ~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~ 118 (138)
.++ ..+.....+.+.+.+|.++|..+..+.+.
T Consensus 587 ~dd------G~V~i~~~~~~~~~~a~~~I~~~~~~~~~ 618 (684)
T TIGR03591 587 EDD------GTVKIAASDGEAAEAAIKMIEGITAEPEV 618 (684)
T ss_pred ecC------eEEEEEECcHHHHHHHHHHHHhhhccccc
Confidence 873 45666677899999999999999776443
No 24
>KOG2192|consensus
Probab=98.80 E-value=6.7e-09 Score=82.15 Aligned_cols=80 Identities=23% Similarity=0.351 Sum_probs=73.0
Q ss_pred CCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhc
Q psy11065 40 WEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVE 119 (138)
Q Consensus 40 ~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~ 119 (138)
..+.|..++++|+.+..|.|||++|+.||+|++...+++.|-..+.+.+++|++.+.|.+..|..+++.|.++|.+..-+
T Consensus 118 ~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pik 197 (390)
T KOG2192|consen 118 QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIK 197 (390)
T ss_pred CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcC
Confidence 45667899999999999999999999999999999999999999988888999999999999999999999998875443
No 25
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.64 E-value=5.8e-08 Score=84.73 Aligned_cols=106 Identities=18% Similarity=0.224 Sum_probs=80.6
Q ss_pred hhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065 4 IEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM 83 (138)
Q Consensus 4 ~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~ 83 (138)
.++.|||+....|+.....- -.......+..+|...++.|+++++..+||++|++|++|.++||++|+|.++
T Consensus 519 ~AL~QAk~aRlhIL~~M~~a--------i~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd 590 (692)
T COG1185 519 KALEQAKGARLHILIVMNEA--------ISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD 590 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHH--------HhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC
Confidence 46789999999988843110 0000113344577899999999999999999999999999999999999852
Q ss_pred CCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCC
Q psy11065 84 REDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSG 123 (138)
Q Consensus 84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~ 123 (138)
.++.+.+-+.+.+.+|+++|+.++++.+..+..-
T Consensus 591 ------Gtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~ 624 (692)
T COG1185 591 ------GTVKIAASDGESAKKAKERIEAITREVEVGEVYE 624 (692)
T ss_pred ------CcEEEEecchHHHHHHHHHHHHHHhhcccccEEE
Confidence 2344445566899999999999999887765443
No 26
>KOG1588|consensus
Probab=98.63 E-value=4.1e-07 Score=71.53 Aligned_cols=93 Identities=22% Similarity=0.298 Sum_probs=65.8
Q ss_pred ccceEEEEEecCC------ccceeeccCcHHHHHHHHHhCCeEEEecCCC-------------------CCCCCcEEEEe
Q psy11065 42 VTWEVIQVCVPKA------AVGVVIGKGGDMIKKLQNETGARVQFVQMRE-------------------DDPSDRRCMLS 96 (138)
Q Consensus 42 ~~~~~~~i~IP~~------~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~-------------------~~~~~r~i~i~ 96 (138)
+-..+.+|.||.. +||+|+|+.|.++|+|+++|+|+|.|--... ..+-...|...
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~ 168 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE 168 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence 3447788888876 8999999999999999999999999954321 11113445556
Q ss_pred cCHHHH----HHHHHHHHHHHHhhhhccCCCCcccchhhhhcccC
Q psy11065 97 GSPDQV----QEARARIEELIDSVMVEQFSGANFDKLRSTVLANR 137 (138)
Q Consensus 97 G~~e~i----~~A~~~I~~ii~~~~~~~~g~~~~~~l~~~~~~~~ 137 (138)
.++.-+ ..|.+.|+.+|.......- ..++||+++..|.
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~P~~e~~d---k~~QL~ELa~lng 210 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLVPDHEDED---KREQLRELAILNG 210 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCCCch---HHHHHHHHhhcCC
Confidence 666433 3577777777665544443 5789999999885
No 27
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.62 E-value=3.7e-08 Score=88.64 Aligned_cols=103 Identities=16% Similarity=0.163 Sum_probs=77.9
Q ss_pred hHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCe-EEEecC
Q psy11065 5 EFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGAR-VQFVQM 83 (138)
Q Consensus 5 ~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~-I~I~~~ 83 (138)
.+++|++-...|++....- -...-..++...|....+.||+++++.|||++|++||.|+++||++ |+|.++
T Consensus 653 AL~~A~~g~~~Il~~M~~~--------i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd 724 (891)
T PLN00207 653 ALLQAKDGRKHILAEMSKC--------SPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD 724 (891)
T ss_pred HHHHHHHHHHHHHHHHHHH--------HhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC
Confidence 4678888887777633111 0000112344577999999999999999999999999999999999 999772
Q ss_pred CCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccC
Q psy11065 84 REDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQF 121 (138)
Q Consensus 84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~ 121 (138)
..+.++.-+.+++++|+++|+.++.+.+....
T Consensus 725 ------g~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~i 756 (891)
T PLN00207 725 ------GTVKITAKDLSSLEKSKAIISSLTMVPTVGDI 756 (891)
T ss_pred ------eeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcE
Confidence 45666667999999999999999987554433
No 28
>KOG2190|consensus
Probab=98.54 E-value=2.6e-07 Score=78.82 Aligned_cols=70 Identities=24% Similarity=0.388 Sum_probs=61.5
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec---------CHHHHHHHHHHHHHHHHh
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG---------SPDQVQEARARIEELIDS 115 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G---------~~e~i~~A~~~I~~ii~~ 115 (138)
.+++++++...+|.||||+|..||+|+++|.++|.|.+.....+ +|++++.| ..+++.+|.++|-....+
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~-eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCP-ERIITITGNRVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCC-cceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence 44799999999999999999999999999999998887644334 99999999 999999999999777663
No 29
>KOG0336|consensus
Probab=98.32 E-value=7.8e-07 Score=74.54 Aligned_cols=70 Identities=27% Similarity=0.405 Sum_probs=62.0
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV 118 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~ 118 (138)
....|.|..++||.|||++|++||.||..|+++|+|.+.. + +..|+|-|...--.+|+..|...+...+.
T Consensus 47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~-e~kv~ifg~~~m~~kaka~id~~~~k~e~ 116 (629)
T KOG0336|consen 47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---L-EVKVTIFGINHMRKKAKASIDRGQDKDER 116 (629)
T ss_pred CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---c-eeEEEEechHHHHHHHHhhHhhhhhhhhh
Confidence 5578889999999999999999999999999999998743 2 78899999999889999999988887665
No 30
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.32 E-value=3.3e-07 Score=81.17 Aligned_cols=99 Identities=19% Similarity=0.293 Sum_probs=72.3
Q ss_pred hHHHHHHHHHHHhhcCC-CCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065 5 EFQQSRRWQQGIGRNND-NFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM 83 (138)
Q Consensus 5 ~~~~ak~~v~~i~~~~~-~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~ 83 (138)
.+++|++-...|++... ....+ -.......|....+.||.++++.+||++|++||.|.++||++|++.++
T Consensus 522 al~~a~~g~~~I~~~M~~aI~~~---------r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~ 592 (693)
T PRK11824 522 ALEQAKEGRLHILGKMNEAISEP---------RAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD 592 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCC---------hhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC
Confidence 35677777777766331 11000 011233456788999999999999999999999999999999988652
Q ss_pred CCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065 84 REDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV 118 (138)
Q Consensus 84 ~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~ 118 (138)
..+....-+.+.+++|+++|+.++.+.+.
T Consensus 593 ------G~v~i~~~~~~~~~~a~~~I~~~~~~~~v 621 (693)
T PRK11824 593 ------GTVKIAATDGEAAEAAKERIEGITAEPEV 621 (693)
T ss_pred ------ceEEEEcccHHHHHHHHHHHHHhcccCcC
Confidence 34555566889999999999999876443
No 31
>KOG1067|consensus
Probab=98.28 E-value=1.2e-06 Score=75.42 Aligned_cols=101 Identities=23% Similarity=0.240 Sum_probs=79.9
Q ss_pred hhHHHHHHHHHHHhhcCC-CCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 4 IEFQQSRRWQQGIGRNND-NFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 4 ~~~~~ak~~v~~i~~~~~-~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
.++++|++...+|++... +...+.+ ......|...++.++++++..+||++|...|+|+.+||+.-++++
T Consensus 564 eal~~a~~ar~~Il~~m~k~i~~Pr~---------~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vDe 634 (760)
T KOG1067|consen 564 EALQKAREARLQILDIMEKNINSPRG---------SDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVDE 634 (760)
T ss_pred HHHHhhhHHHHHHHHHHHhhcCCccc---------CccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeecC
Confidence 357888888888888542 2211111 122445689999999999999999999999999999997777765
Q ss_pred CCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhcc
Q psy11065 83 MREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQ 120 (138)
Q Consensus 83 ~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~ 120 (138)
+.+-+++-++.++++|+++|..++..++.++
T Consensus 635 -------~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~ 665 (760)
T KOG1067|consen 635 -------GTFSIFAPTQAAMEEAKEFIDGIIKDDQVQD 665 (760)
T ss_pred -------ceEEEEecCHHHHHHHHHHHHHHhcCccccc
Confidence 6778889999999999999999999877663
No 32
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.96 E-value=2.6e-05 Score=59.12 Aligned_cols=54 Identities=26% Similarity=0.440 Sum_probs=48.8
Q ss_pred ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhh
Q psy11065 55 AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSV 116 (138)
Q Consensus 55 ~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~ 116 (138)
..|+|||++|.|.+.|++-|+|.|.|.. ..|.|.|.++++..|++.|..++.-.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g--------~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG--------KTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC--------cEEEEecChhhhHHHHHHHHHHHcCC
Confidence 4699999999999999999999999975 46889999999999999999998743
No 33
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.94 E-value=2.8e-05 Score=60.67 Aligned_cols=66 Identities=26% Similarity=0.309 Sum_probs=55.2
Q ss_pred EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEe-cCHHHHHHHHHHHHHHHHhhhhc
Q psy11065 47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLS-GSPDQVQEARARIEELIDSVMVE 119 (138)
Q Consensus 47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~-G~~e~i~~A~~~I~~ii~~~~~~ 119 (138)
..+.||..+++.+||++|.+|+.|.+.|+++|.|.. +-.|+|. .+.+.+..|+.+|+.+-++....
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~ 213 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-------NGRIWIKGPDEEDEEIAIEAIKKIEREAHTS 213 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-------CcEEEEeeCCHHHHHHHHHHHHHHHhhhhcc
Confidence 789999999999999999999999999999999976 2345555 56779999999998886665443
No 34
>KOG2814|consensus
Probab=97.89 E-value=2.4e-05 Score=63.47 Aligned_cols=71 Identities=28% Similarity=0.315 Sum_probs=61.3
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~ 117 (138)
-...+.++...++.|||+.|.|.++|+++|+|+|.++.+... . +.++.+.+..++|.+|.+.|..+|.+..
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n-~-~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN-K-EEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC-c-ceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 345788999999999999999999999999999999986532 1 5666677799999999999999998876
No 35
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.79 E-value=7.1e-05 Score=57.56 Aligned_cols=92 Identities=18% Similarity=0.205 Sum_probs=64.1
Q ss_pred eEEEEEecC------CccceeeccCcHHHHHHHHHhCCeEEEecCCCCC--------C-C-------CcEEEEecCHHHH
Q psy11065 45 EVIQVCVPK------AAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD--------P-S-------DRRCMLSGSPDQV 102 (138)
Q Consensus 45 ~~~~i~IP~------~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~--------~-~-------~r~i~i~G~~e~i 102 (138)
.+.++.||. .+||+|||+.|.|+|+++..|+|+|-|-.....- + . -+..+...+.+.+
T Consensus 148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki 227 (269)
T COG5176 148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKI 227 (269)
T ss_pred ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhH
Confidence 345666664 5899999999999999999999999995432110 0 0 1234445566778
Q ss_pred HHHHHHHHHHHHhhhhccCCCCccc--chhhhhccc
Q psy11065 103 QEARARIEELIDSVMVEQFSGANFD--KLRSTVLAN 136 (138)
Q Consensus 103 ~~A~~~I~~ii~~~~~~~~g~~~~~--~l~~~~~~~ 136 (138)
.+++..+..+|.+...-..|.-+.. +||.++-+|
T Consensus 228 ~~~ik~~~n~I~~a~~~PeGqnDlkR~qlr~la~ln 263 (269)
T COG5176 228 CRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLN 263 (269)
T ss_pred HHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHhc
Confidence 8888888888888777766654443 677666554
No 36
>PRK12704 phosphodiesterase; Provisional
Probab=97.61 E-value=0.00022 Score=61.57 Aligned_cols=67 Identities=30% Similarity=0.433 Sum_probs=54.0
Q ss_pred eEEEEEecCC-ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhhh
Q psy11065 45 EVIQVCVPKA-AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSVM 117 (138)
Q Consensus 45 ~~~~i~IP~~-~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~~ 117 (138)
....+.+|++ +-|+|||+.|.||+.++.-||+.|.|++.++ +|++++ +|-.-+.|...++.++.+..
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp~------~v~ls~~~~~rre~a~~~l~~l~~dg~ 278 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPE------AVILSGFDPIRREIARLALEKLVQDGR 278 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCCC------eEEEecCChhhHHHHHHHHHHHHhcCC
Confidence 5667888984 5599999999999999999999999987532 466776 77666788888888877654
No 37
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.61 E-value=0.00021 Score=61.62 Aligned_cols=67 Identities=31% Similarity=0.445 Sum_probs=54.6
Q ss_pred eEEEEEecCC-ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhhh
Q psy11065 45 EVIQVCVPKA-AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSVM 117 (138)
Q Consensus 45 ~~~~i~IP~~-~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~~ 117 (138)
....+.+|++ +-|+|||+.|.||+.++.-||+.|.|++.++ .|++++ +|---+.|+..++.++.+..
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~------~v~ls~fdp~rreia~~~l~~li~dgr 272 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPE------AVILSGFDPVRREIARMALEKLIQDGR 272 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCC------eEEecCCchHHHHHHHHHHHHHHHcCC
Confidence 5667889995 5599999999999999999999999987532 466666 78777888888888887643
No 38
>PRK00106 hypothetical protein; Provisional
Probab=97.58 E-value=0.00026 Score=61.28 Aligned_cols=67 Identities=31% Similarity=0.445 Sum_probs=55.2
Q ss_pred eEEEEEecCC-ccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEec-CHHHHHHHHHHHHHHHHhhh
Q psy11065 45 EVIQVCVPKA-AVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSG-SPDQVQEARARIEELIDSVM 117 (138)
Q Consensus 45 ~~~~i~IP~~-~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~~ 117 (138)
....+.+|++ +-|+|||+-|.||+.++.-||+.|.|++.++ .|++++ +|---+.|+..++.++.+..
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~------~v~lS~fdpvRReiAr~~le~Li~dgr 293 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPE------VVVLSGFDPIRREIARMTLESLIKDGR 293 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCC------eEEEeCCChHHHHHHHHHHHHHHHcCC
Confidence 5677889994 5599999999999999999999999987543 356666 88888888888888887643
No 39
>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=97.54 E-value=0.00019 Score=44.64 Aligned_cols=36 Identities=28% Similarity=0.593 Sum_probs=33.8
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEE
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF 80 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I 80 (138)
....+.||.+.+|..|||+|.+|+.+++.++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578999999999999999999999999999988876
No 40
>KOG2113|consensus
Probab=97.44 E-value=0.00021 Score=57.88 Aligned_cols=66 Identities=24% Similarity=0.291 Sum_probs=58.4
Q ss_pred ccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHH
Q psy11065 42 VTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEE 111 (138)
Q Consensus 42 ~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ 111 (138)
+...++.+.+|...++.|.|++|.+||.|+.+|.++|.-+.... +-++.++|.++.+..|+.-|..
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e----ePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE----EPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC----CCcceeccCchhHHHHhhcCcc
Confidence 35688999999999999999999999999999999998876544 4588899999999999988865
No 41
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.24 E-value=0.0013 Score=49.91 Aligned_cols=63 Identities=24% Similarity=0.411 Sum_probs=53.3
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEe-----cCHHHHHHHHHHHHHHH
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLS-----GSPDQVQEARARIEELI 113 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~-----G~~e~i~~A~~~I~~ii 113 (138)
....+.||.+.++.+||+.|++.+.|.+.++++|.++... ..++|. .+|-.+++|.++|+.+-
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~------~~V~i~~~~~t~Dp~~~~ka~d~VkAIg 75 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKT------GSVTIRTTRKTEDPLALLKARDVVKAIG 75 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCC------CeEEEEecCCCCChHHHHHHHHHHHHHh
Confidence 4567999999999999999999999999999999998743 334443 37889999999998874
No 42
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.89 E-value=0.0029 Score=49.56 Aligned_cols=62 Identities=27% Similarity=0.390 Sum_probs=50.9
Q ss_pred EEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHH-HHHHHHHHHHHHHh
Q psy11065 47 IQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQ-VQEARARIEELIDS 115 (138)
Q Consensus 47 ~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~-i~~A~~~I~~ii~~ 115 (138)
.-+.||+.+|.++||++|+.++-|.+.|+|+|-+.. +-.|++.+..+. ...|...|..+-.+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-------NG~IWV~~~~~~~e~~~~~aI~~ie~e 210 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-------NGRIWVDGENESLEELAIEAIRKIERE 210 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-------CCEEEecCCCcchHHHHHHHHHHHhhh
Confidence 578999999999999999999999999999999987 456888887773 55566666555444
No 43
>KOG2113|consensus
Probab=96.68 E-value=0.002 Score=52.34 Aligned_cols=95 Identities=26% Similarity=0.370 Sum_probs=73.0
Q ss_pred HHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCC
Q psy11065 8 QSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDD 87 (138)
Q Consensus 8 ~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~ 87 (138)
-+++..+||.....+|+-..+.++..++-.++..+...+....+|...+|.|.|..|.+|+.|++.++..|.-.-...
T Consensus 78 dv~~aRrei~saaeH~~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~-- 155 (394)
T KOG2113|consen 78 DVRRARREIPSAAEHFGLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCG-- 155 (394)
T ss_pred hHHHHhhcCccccceeeeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccCC--
Confidence 344555677777777876666666666666667778889999999999999999999999999999999886654332
Q ss_pred CCCcEEEEecCHHH-HHHHH
Q psy11065 88 PSDRRCMLSGSPDQ-VQEAR 106 (138)
Q Consensus 88 ~~~r~i~i~G~~e~-i~~A~ 106 (138)
+.++.+.|-+.. +++|.
T Consensus 156 --~~Vf~Vtg~~~nC~kra~ 173 (394)
T KOG2113|consen 156 --EPVFCVTGAPKNCVKRAR 173 (394)
T ss_pred --CceEEEecCCcchhhhcc
Confidence 567888887766 45554
No 44
>KOG2279|consensus
Probab=96.67 E-value=0.0011 Score=57.06 Aligned_cols=75 Identities=27% Similarity=0.365 Sum_probs=63.1
Q ss_pred cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV 118 (138)
Q Consensus 43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~ 118 (138)
.+....+.+|...++.|+|++|.+++.|+..++++|.++.+..... .+...|.+.......|+.++.+.+.+.+.
T Consensus 138 ~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~-~~~~~i~~qqk~~~~a~~~~~~~~~edee 212 (608)
T KOG2279|consen 138 TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGL-SRLIKISGQQKEVAAAKHLILEKVSEDEE 212 (608)
T ss_pred Ccccccccchhhhcccccccchhhhcchhccccccccccccccccc-ccceecccccchHHHHHhhhhccccchhH
Confidence 4467889999999999999999999999999999999988643333 67888888888888999999887776544
No 45
>PRK12705 hypothetical protein; Provisional
Probab=96.65 E-value=0.0029 Score=54.60 Aligned_cols=68 Identities=26% Similarity=0.346 Sum_probs=49.9
Q ss_pred eEEEEEecCCcc-ceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065 45 EVIQVCVPKAAV-GVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117 (138)
Q Consensus 45 ~~~~i~IP~~~v-g~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~ 117 (138)
....+.+|++.+ |+|||+-|.||+.++..||+.|.|++.++ .++...=+|.--+.|...+..++.+..
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~-----~V~ls~fdp~rreia~~~l~~Li~dgr 266 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTPE-----AVVISSFNPIRREIARLTLEKLLADGR 266 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCcc-----chhhcccCccchHHHHHHHHHHHhcCC
Confidence 556778888555 99999999999999999999999987543 233333366666667666766665543
No 46
>PRK00468 hypothetical protein; Provisional
Probab=96.60 E-value=0.0029 Score=41.12 Aligned_cols=30 Identities=27% Similarity=0.489 Sum_probs=26.8
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T 74 (138)
..+++.+.++.+|.||||+|.+|+.|+.--
T Consensus 30 ~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 30 VILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred EEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 678899999999999999999999997543
No 47
>PRK02821 hypothetical protein; Provisional
Probab=96.57 E-value=0.0024 Score=41.72 Aligned_cols=31 Identities=29% Similarity=0.500 Sum_probs=27.8
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETG 75 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tg 75 (138)
..+++.+.++.+|.||||+|.+|+.|+.--.
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 6789999999999999999999999986544
No 48
>KOG2279|consensus
Probab=96.49 E-value=0.0017 Score=56.00 Aligned_cols=71 Identities=32% Similarity=0.523 Sum_probs=58.6
Q ss_pred cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS 115 (138)
Q Consensus 43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~ 115 (138)
.....++.||.+.|.+++|+.|.+|+.|++.|++||.+..+.-+ .+++-++.|-+.++..|...+..++..
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g--~e~~~~~~~~p~~v~~a~a~~~~~~~~ 136 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG--DERVLLISGFPVQVCKAKAAIHQILTE 136 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC--cccchhhccCCCCCChHHHHHHHHHhc
Confidence 45788999999999999999999999999999999999775433 266666777888888888887666544
No 49
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=96.29 E-value=0.0056 Score=39.93 Aligned_cols=29 Identities=31% Similarity=0.480 Sum_probs=26.3
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHH
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNE 73 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~ 73 (138)
...++.+.++.+|.||||+|.+|+.|+.-
T Consensus 30 ~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 30 VTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred EEEEEEECcccccceecCCChhHHHHHHH
Confidence 67889999999999999999999999753
No 50
>PRK01064 hypothetical protein; Provisional
Probab=95.99 E-value=0.0089 Score=39.15 Aligned_cols=30 Identities=30% Similarity=0.522 Sum_probs=27.0
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T 74 (138)
..+++.+..+..|.+|||+|.+|+.|+.-.
T Consensus 30 ~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 30 IIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred EEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 678899999999999999999999998743
No 51
>KOG4369|consensus
Probab=95.81 E-value=0.0024 Score=59.55 Aligned_cols=75 Identities=25% Similarity=0.241 Sum_probs=63.8
Q ss_pred ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065 44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV 118 (138)
Q Consensus 44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~ 118 (138)
...-++.+|.....+|||++|.+|+.++.-||+.|.|.+-...+-.+|.+.+.|.++....|...|...|.+...
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv 1413 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDV 1413 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCc
Confidence 355677899999999999999999999999999999988544443489999999999999999999877776443
No 52
>KOG2208|consensus
Probab=95.78 E-value=0.026 Score=50.90 Aligned_cols=71 Identities=20% Similarity=0.407 Sum_probs=62.9
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhh
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMV 118 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~ 118 (138)
....+.|-++.+..|+||+|.+|.+|++++.|.|.+...... ...+.+.+....+.+|.+.|+.++.+...
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~---~~~v~~~~~~~~~~ka~~~v~~~~~ei~n 417 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSN---NKKVVITGVSANDEKAVEDVEKIIAEILN 417 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCC---CCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence 567889999999999999999999999999999999884433 67889999999999999999988888766
No 53
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=95.70 E-value=0.019 Score=41.57 Aligned_cols=38 Identities=32% Similarity=0.685 Sum_probs=34.6
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
....+.|+...+|..||++|++|+.|++..|-+|.|-.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 46788889999999999999999999999999998866
No 54
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=95.51 E-value=0.0091 Score=38.04 Aligned_cols=32 Identities=31% Similarity=0.436 Sum_probs=28.2
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGA 76 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga 76 (138)
..+.+.+..+..|.||||.|.+++.||.-.+.
T Consensus 29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred eEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 57889999999999999999999999876543
No 55
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=95.38 E-value=0.017 Score=41.74 Aligned_cols=38 Identities=24% Similarity=0.349 Sum_probs=33.9
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
....+.|+.+..|.+|||+|.|++.++.-++-++.|.+
T Consensus 99 ~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~~ 136 (140)
T PRK08406 99 KVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDIDD 136 (140)
T ss_pred EEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCeE
Confidence 45677899999999999999999999999999887754
No 56
>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=95.07 E-value=0.049 Score=33.11 Aligned_cols=34 Identities=32% Similarity=0.425 Sum_probs=27.3
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeE
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARV 78 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I 78 (138)
....+.+.....|.+||++|.+|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4455666665689999999999999999998554
No 57
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=94.37 E-value=0.041 Score=47.30 Aligned_cols=41 Identities=32% Similarity=0.531 Sum_probs=36.8
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE 85 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~ 85 (138)
....+.||...++.+|||+|.+|++|++..|.+|.+.....
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 45788999999999999999999999999999999976443
No 58
>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=94.37 E-value=0.033 Score=35.75 Aligned_cols=35 Identities=31% Similarity=0.560 Sum_probs=29.4
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEE
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQ 79 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~ 79 (138)
....+.+.....+.|||++|++|++|.+...-.+.
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 55788889999999999999999999887765553
No 59
>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=94.30 E-value=0.2 Score=36.55 Aligned_cols=66 Identities=20% Similarity=0.304 Sum_probs=48.5
Q ss_pred hHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065 5 EFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR 84 (138)
Q Consensus 5 ~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~ 84 (138)
+=+.|++.+.+++..-.+..+- +. .+.+-++.|-.++-|.+||++|.++++|..+||-+-.|-+.+
T Consensus 50 ~~e~A~~~I~~ivP~ea~i~di--~F------------d~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 50 PPEEAIKIILEIVPEEAGITDI--YF------------DDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred CHHHHHHHHHHhCCCccCceee--Ee------------cCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 4478999999988643222000 00 113448888889999999999999999999999988887744
No 60
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.17 E-value=0.37 Score=36.44 Aligned_cols=71 Identities=15% Similarity=0.372 Sum_probs=60.5
Q ss_pred EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCC
Q psy11065 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFS 122 (138)
Q Consensus 46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g 122 (138)
...+.++....-.+...+|..++.|....||+|.+..+ ...+.|+|+...+..+...|.+++.........
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~------~~~i~I~g~k~~~~~i~~~i~~~l~~i~~~~i~ 97 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS------ENRIRITGTKSTAEYIEASINEILSNIRTEEID 97 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC------CcEEEEEccHHHHHHHHHHHHHHHhhcEEEEEe
Confidence 35666678888999999999999998888999999874 567999999999999999999999887665433
No 61
>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=94.08 E-value=0.099 Score=37.90 Aligned_cols=37 Identities=27% Similarity=0.630 Sum_probs=33.9
Q ss_pred EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
..-|.|....+|..||++|++|+.|++..|-+|.|-.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 5778899999999999999999999999999998865
No 62
>KOG2208|consensus
Probab=93.98 E-value=0.095 Score=47.39 Aligned_cols=90 Identities=16% Similarity=0.193 Sum_probs=61.7
Q ss_pred cchhHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhC-CeEEE
Q psy11065 2 CSIEFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETG-ARVQF 80 (138)
Q Consensus 2 ~~~~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tg-a~I~I 80 (138)
++-.+++|.+.++.+...-.+- .....+.||...+..+||.+|..|..|..+++ ..|..
T Consensus 397 ~~~~~~ka~~~v~~~~~ei~n~--------------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f 456 (753)
T KOG2208|consen 397 VSANDEKAVEDVEKIIAEILNS--------------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKF 456 (753)
T ss_pred cccchhHHHHHHHHHHHhhhcc--------------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEec
Confidence 4556788888888877754330 24678999999999999999999999999999 55555
Q ss_pred ecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHH
Q psy11065 81 VQMREDDPSDRRCMLSGSPDQVQEARARIEELID 114 (138)
Q Consensus 81 ~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~ 114 (138)
...... ....++.+....+..+..+...+..
T Consensus 457 ~~~~~~---~~~~~~~~~~~dv~~~~~~~~~~~~ 487 (753)
T KOG2208|consen 457 QNNNNS---SDMVTIRGISKDVEKSVSLLKALKA 487 (753)
T ss_pred CCCCcc---cccceEeccccccchhHHHHHhhhh
Confidence 443322 3445556655555555555444444
No 63
>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=93.83 E-value=0.062 Score=38.96 Aligned_cols=39 Identities=26% Similarity=0.317 Sum_probs=34.4
Q ss_pred ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
.....+.||.+..+..|||+|.|++...+-++-++.|.+
T Consensus 99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~~ 137 (141)
T TIGR01952 99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDIDD 137 (141)
T ss_pred CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCeE
Confidence 356778899999999999999999999999998887754
No 64
>KOG3273|consensus
Probab=93.82 E-value=0.036 Score=42.65 Aligned_cols=67 Identities=25% Similarity=0.410 Sum_probs=54.5
Q ss_pred CccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhhhccCCCCcccchhhh
Q psy11065 54 AAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVMVEQFSGANFDKLRST 132 (138)
Q Consensus 54 ~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~~~~~g~~~~~~l~~~ 132 (138)
..+|+|+|++|+|--.|+..|.++|.+.+ .-|.|-|.-+.+..|+..|..+|.- ...|-.|..||..
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVlad--------~kIHiLG~~~niriAR~avcsLIlG----sppgkVy~~LR~v 244 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLAD--------SKIHILGAFQNIRIARDAVCSLILG----SPPGKVYGNLRNV 244 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEecC--------ceEEEeecchhhHHHHHhhHhhhcc----CCchhHHHHHHHH
Confidence 46899999999999999999999999875 3588889999999999999888763 2233467777754
No 65
>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=93.79 E-value=0.073 Score=34.30 Aligned_cols=36 Identities=22% Similarity=0.427 Sum_probs=29.6
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEE
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF 80 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I 80 (138)
....+.|..+..|.+|||.|.++..||--++.-++-
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 356788888999999999999999999877655443
No 66
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=93.66 E-value=0.061 Score=34.28 Aligned_cols=38 Identities=34% Similarity=0.574 Sum_probs=29.3
Q ss_pred EEEEEecCCc-----cceeeccCcHHHHHHHHHh-CCeEEEecC
Q psy11065 46 VIQVCVPKAA-----VGVVIGKGGDMIKKLQNET-GARVQFVQM 83 (138)
Q Consensus 46 ~~~i~IP~~~-----vg~IIGk~G~~Ik~I~~~T-ga~I~I~~~ 83 (138)
...+-|-... +|..||++|..|+.|+++. |-+|.|-.-
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 3455666666 8999999999999999999 899988763
No 67
>PRK13764 ATPase; Provisional
Probab=93.39 E-value=0.076 Score=46.88 Aligned_cols=41 Identities=34% Similarity=0.565 Sum_probs=37.2
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMRE 85 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~ 85 (138)
....+.||...++.+|||+|.+|++|++..|.+|.|....+
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 56789999999999999999999999999999999976443
No 68
>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=93.35 E-value=0.13 Score=33.83 Aligned_cols=38 Identities=21% Similarity=0.315 Sum_probs=31.6
Q ss_pred cceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEE
Q psy11065 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF 80 (138)
Q Consensus 43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I 80 (138)
++...++.|-...-|.|||++|++|++|++.-.-...+
T Consensus 28 t~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 28 TPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred cCCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 34568899999999999999999999998877655555
No 69
>KOG2874|consensus
Probab=92.70 E-value=0.3 Score=39.40 Aligned_cols=52 Identities=19% Similarity=0.252 Sum_probs=43.2
Q ss_pred cceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065 56 VGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS 115 (138)
Q Consensus 56 vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~ 115 (138)
.-++||++|.|+|.|+=-|.|.|-|.. ..|.+.|.-..+..+...+.+.+..
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVqG--------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQG--------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEeeC--------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 467999999999999999999999864 3577788888888888887777654
No 70
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=92.11 E-value=0.18 Score=38.28 Aligned_cols=37 Identities=30% Similarity=0.482 Sum_probs=34.8
Q ss_pred EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
...+.||.+..+..|||+|.+++-+.+-||-++.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 6778899999999999999999999999999999976
No 71
>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=91.57 E-value=0.27 Score=40.59 Aligned_cols=38 Identities=26% Similarity=0.469 Sum_probs=35.5
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
....+.||.+..+..|||+|.|++-..+-||.+|.|..
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 46788999999999999999999999999999999976
No 72
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=91.13 E-value=0.28 Score=40.92 Aligned_cols=40 Identities=20% Similarity=0.205 Sum_probs=36.5
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR 84 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~ 84 (138)
....+.||.+..+..|||+|.|++-..+-||.+|+|..-.
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 5678899999999999999999999999999999997643
No 73
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=90.97 E-value=0.55 Score=35.00 Aligned_cols=38 Identities=29% Similarity=0.568 Sum_probs=32.9
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM 83 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~ 83 (138)
..+-|.|.... |.-||++|.+++.+++..|-+|.+-..
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 35677777777 999999999999999999999998764
No 74
>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=89.93 E-value=0.34 Score=33.36 Aligned_cols=32 Identities=34% Similarity=0.567 Sum_probs=26.7
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGA 76 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga 76 (138)
..+++.|-...-|.|||++|++|++|++....
T Consensus 61 ~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 61 DRVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CCEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 45788888889999999999999998776543
No 75
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=89.52 E-value=0.48 Score=39.41 Aligned_cols=40 Identities=23% Similarity=0.354 Sum_probs=36.6
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR 84 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~ 84 (138)
....+.||.+..+..|||+|.|++--.+-||.+|.|....
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 5688899999999999999999999999999999997743
No 76
>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=89.05 E-value=0.53 Score=30.86 Aligned_cols=30 Identities=30% Similarity=0.457 Sum_probs=24.2
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T 74 (138)
...++.|....-|.+||++|.+|++|++.-
T Consensus 38 ~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 38 LGTQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred CcEEEEEEECCCCceECCCchhHHHHHHHH
Confidence 346777777899999999999998877654
No 77
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=88.64 E-value=0.44 Score=40.95 Aligned_cols=39 Identities=23% Similarity=0.437 Sum_probs=36.1
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM 83 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~ 83 (138)
....+.||.+..+..|||+|.|++...+-||.+|.|...
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 477889999999999999999999999999999999764
No 78
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=88.52 E-value=1.4 Score=38.55 Aligned_cols=66 Identities=23% Similarity=0.351 Sum_probs=48.1
Q ss_pred hHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065 5 EFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR 84 (138)
Q Consensus 5 ~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~ 84 (138)
+-++|++.+.+++..-.+..+- -| ...+-++.|-..+-|.+|||+|++.++|.++||-.-.|-+.+
T Consensus 73 ~~e~A~~~I~eivP~ea~i~~i-~F-------------d~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P 138 (637)
T COG1782 73 PPEEARKIILEIVPEEAGITDI-YF-------------DDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP 138 (637)
T ss_pred CHHHHHHHHHHhCccccCceeE-Ee-------------cCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence 4578899999988644322110 00 113458888999999999999999999999999877776644
No 79
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=88.10 E-value=0.49 Score=37.05 Aligned_cols=40 Identities=33% Similarity=0.436 Sum_probs=30.8
Q ss_pred cceEEEEEecCCccceeeccCcHHHHHHHH----HhCC---eEEEec
Q psy11065 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQN----ETGA---RVQFVQ 82 (138)
Q Consensus 43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~----~Tga---~I~I~~ 82 (138)
+|...++.|....-|.|||++|++|++|++ .+|. .|+|.+
T Consensus 49 ~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~i~E 95 (233)
T COG0092 49 TPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQINIEE 95 (233)
T ss_pred cCCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEEEEE
Confidence 466788899999999999999999987655 4554 345544
No 80
>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=87.72 E-value=1.3 Score=39.34 Aligned_cols=67 Identities=21% Similarity=0.285 Sum_probs=49.5
Q ss_pred hHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCC
Q psy11065 5 EFQQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMR 84 (138)
Q Consensus 5 ~~~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~ 84 (138)
+-+.|++.+.+++..-.+..+-+ | .+.+-++.|-..+-|.||||+|.++++|.++||-+-.|.+.+
T Consensus 67 ~~~~~~~~i~~~~~~~~~~~~~~-f-------------~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 67 PPEEAIEKIKEIVPEEAGITDIY-F-------------DDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred CHHHHHHHHHHhCCCcCCceeEE-e-------------cCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 45789999999886443220000 0 123458889999999999999999999999999988887754
Q ss_pred C
Q psy11065 85 E 85 (138)
Q Consensus 85 ~ 85 (138)
.
T Consensus 133 ~ 133 (630)
T TIGR03675 133 P 133 (630)
T ss_pred C
Confidence 3
No 81
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=86.97 E-value=0.68 Score=39.52 Aligned_cols=38 Identities=24% Similarity=0.398 Sum_probs=35.3
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
....+.||.+..+..|||+|.|++--.+-||.+|.|..
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 45788999999999999999999999999999999976
No 82
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=86.32 E-value=1 Score=34.21 Aligned_cols=38 Identities=32% Similarity=0.545 Sum_probs=31.9
Q ss_pred EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecC
Q psy11065 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQM 83 (138)
Q Consensus 46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~ 83 (138)
...+.+-.+.+|..||++|.+|+.|+++.|-+|.|-.-
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~ 114 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW 114 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe
Confidence 35556667788999999999999999999988888653
No 83
>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=80.30 E-value=2.8 Score=32.81 Aligned_cols=29 Identities=28% Similarity=0.436 Sum_probs=21.6
Q ss_pred eEEEEEecCCcc-ceeeccCcHHHHHHHHH
Q psy11065 45 EVIQVCVPKAAV-GVVIGKGGDMIKKLQNE 73 (138)
Q Consensus 45 ~~~~i~IP~~~v-g~IIGk~G~~Ik~I~~~ 73 (138)
....+.|+.+.. +.|||++|++||+|..+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 455666665544 88999999999887644
No 84
>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=79.54 E-value=2.4 Score=32.33 Aligned_cols=32 Identities=31% Similarity=0.419 Sum_probs=26.2
Q ss_pred cceEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74 (138)
Q Consensus 43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T 74 (138)
++...++.|....-|.|||++|..|++|++.-
T Consensus 36 ~~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 36 TPLGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cCCcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 34567888888899999999999998876553
No 85
>CHL00048 rps3 ribosomal protein S3
Probab=78.42 E-value=2.8 Score=32.35 Aligned_cols=32 Identities=25% Similarity=0.296 Sum_probs=26.4
Q ss_pred cceEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065 43 TWEVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74 (138)
Q Consensus 43 ~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T 74 (138)
++...++.|-...-|.|||++|.+|++|++.-
T Consensus 64 ~~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 64 KIDLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred cCCeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 34567888888889999999999999887655
No 86
>PRK15494 era GTPase Era; Provisional
Probab=76.32 E-value=4.2 Score=33.20 Aligned_cols=36 Identities=22% Similarity=0.367 Sum_probs=25.1
Q ss_pred eEEEEEecCCcc-ceeeccCcHHHHHHH--------HHhCCeEEE
Q psy11065 45 EVIQVCVPKAAV-GVVIGKGGDMIKKLQ--------NETGARVQF 80 (138)
Q Consensus 45 ~~~~i~IP~~~v-g~IIGk~G~~Ik~I~--------~~Tga~I~I 80 (138)
....+.|+.+.. +.|||++|++||+|. +-.+++|.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 445666766544 889999999998764 445665554
No 87
>PRK00089 era GTPase Era; Reviewed
Probab=75.23 E-value=4.7 Score=31.65 Aligned_cols=36 Identities=33% Similarity=0.603 Sum_probs=23.9
Q ss_pred eEEEEEecCCc-cceeeccCcHHHHHHH--------HHhCCeEEE
Q psy11065 45 EVIQVCVPKAA-VGVVIGKGGDMIKKLQ--------NETGARVQF 80 (138)
Q Consensus 45 ~~~~i~IP~~~-vg~IIGk~G~~Ik~I~--------~~Tga~I~I 80 (138)
....+.|..+. -+.|||++|++||+|. +-.+++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 34455555443 4889999999998765 445666554
No 88
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=74.96 E-value=3.7 Score=31.51 Aligned_cols=30 Identities=27% Similarity=0.465 Sum_probs=24.2
Q ss_pred EEEEEecCCccceeeccCcHHHHHHHHHhC
Q psy11065 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETG 75 (138)
Q Consensus 46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tg 75 (138)
..++.|-...-|.+||++|++|+++++.-.
T Consensus 41 ~i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 41 GTRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred cEEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 466777778899999999999988776543
No 89
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=74.72 E-value=3.5 Score=32.03 Aligned_cols=31 Identities=16% Similarity=0.193 Sum_probs=25.6
Q ss_pred ceEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065 44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74 (138)
Q Consensus 44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T 74 (138)
+...++.|....-|.|||++|..|++|++.-
T Consensus 43 ~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 43 PIRTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred CCcEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 4557888888889999999999998876654
No 90
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=73.92 E-value=11 Score=31.20 Aligned_cols=57 Identities=16% Similarity=0.173 Sum_probs=46.7
Q ss_pred cCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHH--HHHHhh
Q psy11065 52 PKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIE--ELIDSV 116 (138)
Q Consensus 52 P~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~--~ii~~~ 116 (138)
+....-.+.|+.+.+++.|++.+|+.|... .+.+.|.|+...+..|...+. .++...
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r--------G~~~~i~g~~~~v~~A~~~l~~l~~~~~~ 80 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR--------GEAVRIIGARPLVDVATRVLLTLELLAEV 80 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC--------CceEEEEechHHHHHHHHHHhHHHHHHHH
Confidence 467778999999999999999999988664 356889999779999998888 554443
No 91
>COG1159 Era GTPase [General function prediction only]
Probab=71.16 E-value=6.6 Score=31.93 Aligned_cols=27 Identities=37% Similarity=0.705 Sum_probs=19.3
Q ss_pred EEEEecCCc-cceeeccCcHHHHHHHHH
Q psy11065 47 IQVCVPKAA-VGVVIGKGGDMIKKLQNE 73 (138)
Q Consensus 47 ~~i~IP~~~-vg~IIGk~G~~Ik~I~~~ 73 (138)
..+.|+.+. -+.|||++|++||+|-..
T Consensus 231 a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 231 ATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEecCCccceEECCCcHHHHHHHHH
Confidence 345565544 489999999999876443
No 92
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=69.32 E-value=5.1 Score=33.40 Aligned_cols=29 Identities=21% Similarity=0.565 Sum_probs=25.7
Q ss_pred CccceeeccCcHHHHHHHHHh-CCeEEEec
Q psy11065 54 AAVGVVIGKGGDMIKKLQNET-GARVQFVQ 82 (138)
Q Consensus 54 ~~vg~IIGk~G~~Ik~I~~~T-ga~I~I~~ 82 (138)
+-+|..||++|.+|+.|.++. |-+|.|-.
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 467999999999999999998 88898855
No 93
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=68.28 E-value=4.4 Score=31.26 Aligned_cols=62 Identities=18% Similarity=0.203 Sum_probs=44.1
Q ss_pred HHHHHHHHHHhhcCCCCCCCcCCCCCCCCCCCCCCccceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEE
Q psy11065 7 QQSRRWQQGIGRNNDNFGNMREFNENGDGRGGMWEVTWEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQF 80 (138)
Q Consensus 7 ~~ak~~v~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I 80 (138)
++++++|.+++...+ +...-.. ......+.+.|..+..+.+||+.|+++..||--+++-++-
T Consensus 65 ~~~~~~L~ell~~m~-~~~~i~v-----------~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 65 QEAKDYLEELLELMD-FEVTITV-----------SEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred HHHHHHHHHHHHHhC-CceEEEE-----------eecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 788999999888543 1100000 0012567888888889999999999999999888766655
No 94
>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=67.31 E-value=5.6 Score=32.84 Aligned_cols=29 Identities=24% Similarity=0.619 Sum_probs=25.8
Q ss_pred CccceeeccCcHHHHHHHHHh-CCeEEEec
Q psy11065 54 AAVGVVIGKGGDMIKKLQNET-GARVQFVQ 82 (138)
Q Consensus 54 ~~vg~IIGk~G~~Ik~I~~~T-ga~I~I~~ 82 (138)
+-+|..||++|.+|+.|.++. |-+|.|-.
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 467999999999999999998 78898865
No 95
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=65.75 E-value=5.3 Score=34.22 Aligned_cols=29 Identities=31% Similarity=0.623 Sum_probs=25.7
Q ss_pred CccceeeccCcHHHHHHHHHh-CCeEEEec
Q psy11065 54 AAVGVVIGKGGDMIKKLQNET-GARVQFVQ 82 (138)
Q Consensus 54 ~~vg~IIGk~G~~Ik~I~~~T-ga~I~I~~ 82 (138)
+-+|..||++|.+|+.|.++. |-+|.|-.
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 467999999999999999998 78888855
No 96
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=65.71 E-value=7.3 Score=29.99 Aligned_cols=31 Identities=39% Similarity=0.591 Sum_probs=25.3
Q ss_pred ceEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065 44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74 (138)
Q Consensus 44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T 74 (138)
+...++.|-...-+.|||++|..|++|++.-
T Consensus 61 ~~~i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 61 ADKIRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred CCceEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 3457788888888999999999998887543
No 97
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=61.97 E-value=6.1 Score=33.12 Aligned_cols=29 Identities=21% Similarity=0.496 Sum_probs=25.8
Q ss_pred CccceeeccCcHHHHHHHHHh-CCeEEEec
Q psy11065 54 AAVGVVIGKGGDMIKKLQNET-GARVQFVQ 82 (138)
Q Consensus 54 ~~vg~IIGk~G~~Ik~I~~~T-ga~I~I~~ 82 (138)
+-+|..||++|.+|+.|.++. |-+|.|-.
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~ 280 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIE 280 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEE
Confidence 567999999999999999998 88898865
No 98
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=60.01 E-value=7.6 Score=33.48 Aligned_cols=29 Identities=28% Similarity=0.607 Sum_probs=25.5
Q ss_pred CccceeeccCcHHHHHHHHHh-CCeEEEec
Q psy11065 54 AAVGVVIGKGGDMIKKLQNET-GARVQFVQ 82 (138)
Q Consensus 54 ~~vg~IIGk~G~~Ik~I~~~T-ga~I~I~~ 82 (138)
+-+|..||++|.+|+.|.++. |-+|.|-.
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~ 274 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIIL 274 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEE
Confidence 357999999999999999998 78898855
No 99
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=57.85 E-value=12 Score=29.17 Aligned_cols=31 Identities=39% Similarity=0.563 Sum_probs=25.0
Q ss_pred ceEEEEEecCCccceeeccCcHHHHHHHHHh
Q psy11065 44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNET 74 (138)
Q Consensus 44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~T 74 (138)
+..+++.|-...-+.|||++|..|++|++.-
T Consensus 61 ~~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 61 AKRVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred CCeEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 3557777777888999999999998877654
No 100
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=54.89 E-value=35 Score=21.22 Aligned_cols=34 Identities=18% Similarity=0.428 Sum_probs=25.8
Q ss_pred HhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHH
Q psy11065 73 ETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEEL 112 (138)
Q Consensus 73 ~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~i 112 (138)
..+.+|..++. ...+++.|+++.+.....+|..+
T Consensus 43 ~~~~~i~~d~~------tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 43 SSSGRIVADER------TNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp HTTTEEEEECT------TTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCCeEEEEECC------CCEEEEEeCHHHHHHHHHHHHHH
Confidence 34557776653 45688889999999999988765
No 101
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=51.07 E-value=10 Score=33.36 Aligned_cols=39 Identities=18% Similarity=0.258 Sum_probs=35.0
Q ss_pred ceEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEec
Q psy11065 44 WEVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQ 82 (138)
Q Consensus 44 ~~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~ 82 (138)
|..+.+.||...+..|||-+|..|+++....++.|+...
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n 486 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKN 486 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhh
Confidence 467889999999999999999999999999999887754
No 102
>KOG4369|consensus
Probab=50.58 E-value=14 Score=35.89 Aligned_cols=71 Identities=13% Similarity=0.056 Sum_probs=57.4
Q ss_pred EEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHhhh
Q psy11065 46 VIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDSVM 117 (138)
Q Consensus 46 ~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~~~ 117 (138)
.++...+..++.+||+..+..|+-++.-+++++.|+...+- ..++.+++.+.......+.-+|...+++..
T Consensus 782 niehrdkkgf~plImaatagh~tvV~~llk~ha~veaQsdr-tkdt~lSlacsggr~~vvelLl~~gankeh 852 (2131)
T KOG4369|consen 782 NIEHRDKKGFVPLIMAATAGHITVVQDLLKAHADVEAQSDR-TKDTMLSLACSGGRTRVVELLLNAGANKEH 852 (2131)
T ss_pred cccccccccchhhhhhcccCchHHHHHHHhhhhhhhhhccc-ccCceEEEecCCCcchHHHHHHHhhccccc
Confidence 46888999999999999999999999999999999765443 238999999888777777777766655543
No 103
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=50.48 E-value=57 Score=20.31 Aligned_cols=38 Identities=24% Similarity=0.181 Sum_probs=24.0
Q ss_pred HHhCCeEEEecCCCCCCC-CcEEEEecCHHHHHHHHHHHHH
Q psy11065 72 NETGARVQFVQMREDDPS-DRRCMLSGSPDQVQEARARIEE 111 (138)
Q Consensus 72 ~~Tga~I~I~~~~~~~~~-~r~i~i~G~~e~i~~A~~~I~~ 111 (138)
+.+++.| ++..... |. ...+.|.|+..+++.|.+.|++
T Consensus 21 Kaa~V~i-~d~f~gC-Pq~~~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 21 KASGVFV-SDIFGSC-PQHMITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred hccCeEE-EEecCCC-CCceEEEEEEecHHHHHHHHHHHhh
Confidence 4455666 4433221 21 3455689999999999888764
No 104
>KOG1423|consensus
Probab=49.47 E-value=21 Score=29.62 Aligned_cols=32 Identities=28% Similarity=0.580 Sum_probs=24.7
Q ss_pred ceEEEEEecCCcc-ceeeccCcHHHHHHHHHhC
Q psy11065 44 WEVIQVCVPKAAV-GVVIGKGGDMIKKLQNETG 75 (138)
Q Consensus 44 ~~~~~i~IP~~~v-g~IIGk~G~~Ik~I~~~Tg 75 (138)
....++.+|.... ..|||++|..|++|-.+-+
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 4667788887665 6778999999999876543
No 105
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=49.03 E-value=76 Score=23.75 Aligned_cols=54 Identities=17% Similarity=0.383 Sum_probs=41.9
Q ss_pred eEEEEEecCCccceeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHH
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEEL 112 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~i 112 (138)
.+.++.+|....- +.+.+|.+-.|+-+...+ +..|.|.|+.+.|..|..-+..+
T Consensus 113 ~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efee-------~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 113 ETIRVKLKKPIQE-------ERLQEISEWHGVIFEFEE-------DDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred eeEEEecCccchH-------HHHHHHHHHhceeEEecC-------CcEEEEeccHHHHHHHHHHHHHH
Confidence 5667777766542 667899999999998833 45699999999999998776544
No 106
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=48.21 E-value=74 Score=20.58 Aligned_cols=53 Identities=15% Similarity=0.283 Sum_probs=40.3
Q ss_pred CcHHHHHHHHHhCCeEEEecCCCC--CCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065 63 GGDMIKKLQNETGARVQFVQMRED--DPSDRRCMLSGSPDQVQEARARIEELIDS 115 (138)
Q Consensus 63 ~G~~Ik~I~~~Tga~I~I~~~~~~--~~~~r~i~i~G~~e~i~~A~~~I~~ii~~ 115 (138)
+=.-..++-+..++++........ .+++.++.+.|+..++..|.+.+..++..
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 445667888888988877643322 24589999999999999999999988763
No 107
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=45.39 E-value=85 Score=21.57 Aligned_cols=46 Identities=15% Similarity=0.216 Sum_probs=33.2
Q ss_pred HHHhCCeEEEecCCC--------CCCCCcEEEEec-CHHHHHHHHHHHHHHHHhh
Q psy11065 71 QNETGARVQFVQMRE--------DDPSDRRCMLSG-SPDQVQEARARIEELIDSV 116 (138)
Q Consensus 71 ~~~Tga~I~I~~~~~--------~~~~~r~i~i~G-~~e~i~~A~~~I~~ii~~~ 116 (138)
-+.++++|-..++.. +.+++-+++|.| ++..+..|.+.+.+.+.+.
T Consensus 46 tKaa~vev~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 46 TKAAEVEVVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred hhhcCeEEEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhcc
Confidence 356788887777541 113355777999 9999999999988887653
No 108
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=42.45 E-value=1.4e+02 Score=22.22 Aligned_cols=49 Identities=12% Similarity=0.131 Sum_probs=36.8
Q ss_pred CcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEe--cCHHHHHHHHHHHHHHHH
Q psy11065 63 GGDMIKKLQNETGARVQFVQMREDDPSDRRCMLS--GSPDQVQEARARIEELID 114 (138)
Q Consensus 63 ~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~--G~~e~i~~A~~~I~~ii~ 114 (138)
....++.|++.|++.|...++... ..+..+. -....+..|+.++...+.
T Consensus 114 ~~~~l~~i~~~t~~~ie~~~~~~~---~~i~~~~~~~~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 114 TPDLLEEIQKLTNVYIEKNPDGNK---LKISWLASPENEKRADRAKRLLLWALD 164 (210)
T ss_pred cHHHHHHHHHHHcEEEEECCCCCe---EEEEEEeeccccchHHHHHHHHHHhcc
Confidence 467889999999999998775332 2233333 677889999999988885
No 109
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=39.93 E-value=1e+02 Score=25.03 Aligned_cols=54 Identities=17% Similarity=0.320 Sum_probs=41.7
Q ss_pred cceeeccCcHHHHHHHHHhCCe--EEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHH
Q psy11065 56 VGVVIGKGGDMIKKLQNETGAR--VQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELI 113 (138)
Q Consensus 56 vg~IIGk~G~~Ik~I~~~Tga~--I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii 113 (138)
...|+|---+.|.++.++..-. |.+...+. ...+.|+|+++++++|...+++.=
T Consensus 133 Maav~gl~~e~v~~~~~~~~~~~~v~iaN~N~----~~QiVIsG~~~ale~a~~~~~~~g 188 (310)
T COG0331 133 MAAVLGLDDEQVEKACEEAAQGTVVEIANYNS----PGQIVISGTKEALEKAAEILKEAG 188 (310)
T ss_pred HHHHcCCCHHHHHHHHHHhccCCeEEEeeeCC----CCcEEEECCHHHHHHHHHHHHHhh
Confidence 4566677888899998888754 66655433 477999999999999998887765
No 110
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.82 E-value=1.4e+02 Score=22.03 Aligned_cols=43 Identities=16% Similarity=0.341 Sum_probs=35.8
Q ss_pred HHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHH
Q psy11065 65 DMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELID 114 (138)
Q Consensus 65 ~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~ 114 (138)
+.++.|.+-.|+-|.... ...+.|.|+.+.|.+|..-|..+-+
T Consensus 126 eRlqDi~E~hgvIiE~~E-------~D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE-------YDLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEeee-------ccEEEEeccHHHHHHHHHHHHHHHh
Confidence 677889999999988874 5689999999999999988876643
No 111
>PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=38.80 E-value=2.1e+02 Score=23.08 Aligned_cols=66 Identities=14% Similarity=0.097 Sum_probs=44.7
Q ss_pred EEEecCCccceeeccCcHHHHHHHHHhCCeEEEe----cCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065 48 QVCVPKAAVGVVIGKGGDMIKKLQNETGARVQFV----QMREDDPSDRRCMLSGSPDQVQEARARIEELIDS 115 (138)
Q Consensus 48 ~i~IP~~~vg~IIGk~G~~Ik~I~~~Tga~I~I~----~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~ 115 (138)
+..+-...-+.+ .+-....+|-+..++++.+. +...-.+++.++.+.|+..++..+.+.+..++.-
T Consensus 44 ~~~i~ar~~gv~--~G~~~a~~i~~~~~~~~~~~~~~~dG~~v~~g~~i~~~~G~a~~ll~~eR~~lN~l~~ 113 (288)
T PRK07428 44 QAKWIAKESGVI--AGLPIAARVFQLLDPQVSFTPLVAEGAACESGQVVAEIEGPLDALLMGERVALNLAMR 113 (288)
T ss_pred EEEEEecCCeEE--ECHHHHHHHHHHcCCcEEEEEEcCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 334433444444 34456678888999777632 2222235588999999999999999888888764
No 112
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=38.77 E-value=90 Score=23.21 Aligned_cols=61 Identities=23% Similarity=0.373 Sum_probs=36.5
Q ss_pred eEEEEEecCCccceeeccC-cHHHHHHHHHhCCeE-EEecCCC----CCCC-----CcEEEEecCHHHHHHHHHHH
Q psy11065 45 EVIQVCVPKAAVGVVIGKG-GDMIKKLQNETGARV-QFVQMRE----DDPS-----DRRCMLSGSPDQVQEARARI 109 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~-G~~Ik~I~~~Tga~I-~I~~~~~----~~~~-----~r~i~i~G~~e~i~~A~~~I 109 (138)
...++++-.... ++||. |.+ +|.+.|||.| -|-++.+ |.|. ...+.+.|+...+.+++.+.
T Consensus 86 ~~~~~~i~~~s~--~~GksiGdl--~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~ 157 (162)
T COG0490 86 IIEWFKIEAGSP--FIGKTIGDL--NIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFL 157 (162)
T ss_pred hheeeeeecCCc--ccCcchhhc--ccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHh
Confidence 445555543332 55554 444 6889999986 3433221 1111 56788889988888877654
No 113
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=29.31 E-value=94 Score=19.20 Aligned_cols=48 Identities=21% Similarity=0.263 Sum_probs=32.7
Q ss_pred cHHHHHHHHHhCCeEEEecCCCCC-----CCCcEEEEecCHHHHHHHHHHHHH
Q psy11065 64 GDMIKKLQNETGARVQFVQMREDD-----PSDRRCMLSGSPDQVQEARARIEE 111 (138)
Q Consensus 64 G~~Ik~I~~~Tga~I~I~~~~~~~-----~~~r~i~i~G~~e~i~~A~~~I~~ 111 (138)
.--|.++.++++..++|-...-.. -+.=++.+.|+.+++++|.+.+.+
T Consensus 16 ~piis~l~~~~~v~~nIl~g~i~~i~~~~~G~l~l~l~g~~~~~~~a~~~L~~ 68 (76)
T PF09383_consen 16 EPIISQLIREFGVDVNILHGNIEEIQGTPFGILILELPGDDEEIEKAIAYLRE 68 (76)
T ss_dssp SCHHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHH
T ss_pred chHHHHHHHHhCCCEEEEEEEeEEcCCeeEEEEEEEEECCHHHHHHHHHHHHH
Confidence 456789999999999887643211 113456688999999999887765
No 114
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=28.54 E-value=65 Score=19.23 Aligned_cols=45 Identities=20% Similarity=0.367 Sum_probs=29.2
Q ss_pred cHHHHH--HHHHhCCeEE-EecCC---CCCCC-----CcEEEEecCHHHHHHHHHH
Q psy11065 64 GDMIKK--LQNETGARVQ-FVQMR---EDDPS-----DRRCMLSGSPDQVQEARAR 108 (138)
Q Consensus 64 G~~Ik~--I~~~Tga~I~-I~~~~---~~~~~-----~r~i~i~G~~e~i~~A~~~ 108 (138)
|.+|++ +.+.+++.|- |.++. .+.+. ...+.+.|+++.+.++.++
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~ 69 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFREL 69 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHH
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHh
Confidence 567777 7777788763 32221 01111 6778899999999888765
No 115
>smart00877 BMC Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.
Probab=27.90 E-value=1.3e+02 Score=18.97 Aligned_cols=45 Identities=9% Similarity=0.011 Sum_probs=30.4
Q ss_pred HHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHH
Q psy11065 68 KKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELID 114 (138)
Q Consensus 68 k~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~ 114 (138)
....+..++++---+... ++.-.+.+.|+..+++.|.+...+...
T Consensus 18 D~a~KaA~V~l~~~~~~~--~g~~~~~v~Gdvs~V~~Av~a~~~~~~ 62 (75)
T smart00877 18 DAALKAANVELVGYESIG--GGKVTVIITGDVAAVRAAVEAGLEAAE 62 (75)
T ss_pred HHHhhhcCcEEEEEEecC--CCEEEEEEEEcHHHHHHHHHHHHHHHh
Confidence 345566677654333322 235677899999999999888877664
No 116
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=27.32 E-value=2e+02 Score=21.67 Aligned_cols=52 Identities=19% Similarity=0.374 Sum_probs=31.8
Q ss_pred ccCcHHHHHHHHHhC----Ce-EEEecCCCCCCCCcEEEEecCHHHHHH-HHHHHHHHHH
Q psy11065 61 GKGGDMIKKLQNETG----AR-VQFVQMREDDPSDRRCMLSGSPDQVQE-ARARIEELID 114 (138)
Q Consensus 61 Gk~G~~Ik~I~~~Tg----a~-I~I~~~~~~~~~~r~i~i~G~~e~i~~-A~~~I~~ii~ 114 (138)
|+.-+.|..|.+... ++ +++..+.+.+ -.++|+.|+++.+.. |..++...+.
T Consensus 12 gR~~~~ie~I~~a~~~~~gv~ll~~~~D~~~N--Rsv~T~vG~p~~v~~a~~~~~~~A~~ 69 (178)
T PF07837_consen 12 GRDKEVIEAIAKAARNVPGVKLLDVFSDADYN--RSVITLVGEPEAVAEAAFAAIRKALE 69 (178)
T ss_dssp SSSHHHHHHHHHHCCTSTTEEEEEEEEETTTT--EEEEEEEE-HHHHHHHHHHHHHHHHC
T ss_pred CCCHHHHHHHHHHHHcCCCCEEEecCCCCCCC--CCeEEEeeChHHHHHHHHHHHHHHHH
Confidence 666777777776554 34 4555544442 467889999998865 4555555444
No 117
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=26.15 E-value=1.8e+02 Score=18.34 Aligned_cols=40 Identities=18% Similarity=0.222 Sum_probs=28.3
Q ss_pred HHHHHHHHHhCCeE-EEecCCCCCCCCcEEEEecCHHHHHHHHHHHH
Q psy11065 65 DMIKKLQNETGARV-QFVQMREDDPSDRRCMLSGSPDQVQEARARIE 110 (138)
Q Consensus 65 ~~Ik~I~~~Tga~I-~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~ 110 (138)
..|.+|.+.++++| ++.++ .-++.++|+++.+....+++.
T Consensus 17 ~ei~~l~~~f~a~ivd~~~~------~~iie~tG~~~kid~fi~~l~ 57 (75)
T PF10369_consen 17 SEILQLAEIFRARIVDVSPD------SIIIELTGTPEKIDAFIKLLK 57 (75)
T ss_dssp HHHHHHHHHTT-EEEEEETT------EEEEEEEE-HHHHHHHHHHST
T ss_pred HHHHHHHHHhCCEEEEECCC------EEEEEEcCCHHHHHHHHHHhh
Confidence 56788999999986 34331 467889999999988777654
No 118
>cd07045 BMC_CcmK_like Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). Potential functional differences between the two types are not yet fully understood. In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carbox
Probab=25.23 E-value=1.7e+02 Score=18.97 Aligned_cols=45 Identities=7% Similarity=-0.057 Sum_probs=30.7
Q ss_pred HHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065 69 KLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS 115 (138)
Q Consensus 69 ~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~ 115 (138)
.+-+...+.+---+.. .++...+.++|+..+|+.|.+...+...+
T Consensus 19 ~~lKaA~V~l~~~~~~--~~gk~~vii~GdvsaV~~Av~a~~~~~~~ 63 (84)
T cd07045 19 AALKAANVTLVGYEKV--GGGLVTVKITGDVAAVKAAVEAGAAAAER 63 (84)
T ss_pred HHhhhCCeEEEEEEec--CCcEEEEEEEEcHHHHHHHHHHHHHHHhc
Confidence 3445566665433333 23367788999999999998888776654
No 119
>TIGR03131 malonate_mdcH malonate decarboxylase, epsilon subunit. Members of this protein family are the epsilon subunit of malonate decarboxylase. This subunit has malonyl-CoA/dephospho-CoA acyltransferase activity. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. The epsilon subunit is closely related to the malonyl CoA-acyl carrier protein (ACP) transacylase family described by TIGR00128, but acts on an ACP subunit of malonate decarboxylase that has an unusual coenzyme A derivative as its prothetic group.
Probab=24.54 E-value=3.4e+02 Score=21.07 Aligned_cols=48 Identities=13% Similarity=0.254 Sum_probs=32.7
Q ss_pred eeeccCcHHHHHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHH
Q psy11065 58 VVIGKGGDMIKKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEE 111 (138)
Q Consensus 58 ~IIGk~G~~Ik~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ 111 (138)
.++|-.-+.+.++-+++++.|..... .+.++|+|+++.+....+.++.
T Consensus 125 av~~~~~~~~~~~l~~~~v~ia~~Ns------p~~~visG~~~~l~~l~~~l~~ 172 (295)
T TIGR03131 125 AVLGLDLAAVEALIAKHGVYLAIINA------PDQVVIAGSRAALRAVAELARA 172 (295)
T ss_pred EEeCCCHHHHHHHHHHcCEEEEEEcC------CCCEEEECCHHHHHHHHHHHHh
Confidence 34566666777777777655554432 3569999999999888776543
No 120
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=23.58 E-value=2e+02 Score=18.06 Aligned_cols=46 Identities=11% Similarity=0.123 Sum_probs=32.4
Q ss_pred HHHHHHhCCeEEEecCCCCCCCCcEEEEecCHHHHHHHHHHHHHHHHh
Q psy11065 68 KKLQNETGARVQFVQMREDDPSDRRCMLSGSPDQVQEARARIEELIDS 115 (138)
Q Consensus 68 k~I~~~Tga~I~I~~~~~~~~~~r~i~i~G~~e~i~~A~~~I~~ii~~ 115 (138)
....+.+++++---+... ++...+.+.|+..+|+.|.+...+...+
T Consensus 19 D~alKaa~V~l~~~~~~~--~g~~~~~i~G~vs~V~~Av~a~~~~~~~ 64 (75)
T PF00936_consen 19 DAALKAANVELVEIELIC--GGKVTVIITGDVSAVKAAVDAAEEAAGK 64 (75)
T ss_dssp HHHHHHSSEEEEEEEEES--TTEEEEEEEESHHHHHHHHHHHHHHHHH
T ss_pred HHHhhcCCEEEEEEEecC--CCeEEEEEEECHHHHHHHHHHHHHHHhh
Confidence 445566777653333222 3367788999999999999998887765
No 121
>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=22.13 E-value=45 Score=26.41 Aligned_cols=22 Identities=32% Similarity=0.445 Sum_probs=19.2
Q ss_pred eEEEEEecCCccceeeccCcHH
Q psy11065 45 EVIQVCVPKAAVGVVIGKGGDM 66 (138)
Q Consensus 45 ~~~~i~IP~~~vg~IIGk~G~~ 66 (138)
..+.+.||...|-.+||+.|+-
T Consensus 24 ~~i~l~i~~~~VTAlIGPSGcG 45 (253)
T COG1117 24 KDINLDIPKNKVTALIGPSGCG 45 (253)
T ss_pred ccCceeccCCceEEEECCCCcC
Confidence 4478999999999999999964
Done!