Query psy986
Match_columns 71
No_of_seqs 115 out of 400
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 21:27:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy986.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/986hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1837 Predicted RNA-binding 99.4 1.9E-13 4.1E-18 86.3 2.9 37 3-39 28-64 (76)
2 PRK00468 hypothetical protein; 99.4 1.7E-13 3.8E-18 85.6 2.2 37 4-40 29-65 (75)
3 PRK02821 hypothetical protein; 99.3 1.3E-12 2.9E-17 82.2 2.4 34 4-37 30-63 (77)
4 PRK01064 hypothetical protein; 98.9 5.6E-10 1.2E-14 70.3 2.0 37 4-40 29-65 (78)
5 cd00105 KH-I K homology RNA-bi 98.4 8.5E-07 1.8E-11 50.3 4.9 36 7-43 2-37 (64)
6 PF13083 KH_4: KH domain; PDB: 98.3 1.2E-07 2.7E-12 56.9 0.7 35 5-39 29-63 (73)
7 cd02396 PCBP_like_KH K homolog 98.2 2.9E-06 6.4E-11 49.9 4.8 38 7-45 2-39 (65)
8 cd02393 PNPase_KH Polynucleoti 98.1 4.9E-06 1.1E-10 49.1 3.5 36 6-42 3-38 (61)
9 PF00013 KH_1: KH domain syndr 98.0 2.3E-06 4.9E-11 48.9 1.1 37 7-44 2-38 (60)
10 cd02134 NusA_KH NusA_K homolog 98.0 6.3E-06 1.4E-10 48.7 2.9 30 6-35 26-55 (61)
11 cd02394 vigilin_like_KH K homo 97.9 1.4E-05 3.1E-10 45.9 3.8 36 7-43 2-37 (62)
12 smart00322 KH K homology RNA-b 97.9 1.2E-05 2.5E-10 44.4 3.0 38 4-42 2-39 (69)
13 PF13014 KH_3: KH domain 97.6 9.2E-05 2E-09 40.5 3.6 28 15-43 1-28 (43)
14 cd02414 jag_KH jag_K homology 97.4 0.00011 2.4E-09 44.7 2.0 32 7-38 26-57 (77)
15 PRK08406 transcription elongat 97.3 0.00016 3.5E-09 49.2 2.7 30 7-36 101-130 (140)
16 TIGR03665 arCOG04150 arCOG0415 96.8 0.00063 1.4E-08 47.1 1.6 34 9-43 2-35 (172)
17 cd02409 KH-II KH-II (K homolo 96.8 0.0018 3.9E-08 36.3 3.1 33 5-37 25-57 (68)
18 PRK13763 putative RNA-processi 96.7 0.0014 3.1E-08 45.7 2.8 38 4-42 2-39 (180)
19 TIGR02696 pppGpp_PNP guanosine 96.0 0.0064 1.4E-07 51.1 3.2 36 6-42 579-614 (719)
20 PRK13764 ATPase; Provisional 96.0 0.01 2.2E-07 48.8 4.1 40 6-46 482-521 (602)
21 TIGR03591 polynuc_phos polyrib 95.9 0.0049 1.1E-07 50.8 2.2 35 7-42 553-587 (684)
22 cd02395 SF1_like-KH Splicing f 95.9 0.007 1.5E-07 40.3 2.5 30 14-44 15-44 (120)
23 TIGR03319 YmdA_YtgF conserved 95.8 0.01 2.2E-07 47.6 3.6 33 3-35 202-235 (514)
24 PRK12704 phosphodiesterase; Pr 95.7 0.012 2.6E-07 47.3 3.5 33 3-35 208-241 (520)
25 KOG1676|consensus 95.7 0.01 2.2E-07 49.3 3.1 41 6-47 231-271 (600)
26 PRK00106 hypothetical protein; 95.6 0.012 2.7E-07 47.8 3.4 33 3-35 223-256 (535)
27 KOG2190|consensus 95.6 0.011 2.4E-07 47.5 3.1 38 6-44 139-176 (485)
28 TIGR03665 arCOG04150 arCOG0415 95.4 0.0099 2.1E-07 41.2 1.8 22 15-36 99-120 (172)
29 TIGR01952 nusA_arch NusA famil 95.2 0.016 3.5E-07 39.8 2.4 30 6-35 101-130 (141)
30 PRK12705 hypothetical protein; 95.0 0.014 3.1E-07 47.1 2.0 39 3-42 196-235 (508)
31 PRK08406 transcription elongat 94.9 0.023 5E-07 38.6 2.6 34 8-42 35-68 (140)
32 KOG2193|consensus 94.9 0.017 3.8E-07 47.3 2.1 37 5-42 493-529 (584)
33 PLN00207 polyribonucleotide nu 94.4 0.014 3E-07 50.1 0.6 37 6-42 686-722 (891)
34 TIGR01952 nusA_arch NusA famil 94.4 0.049 1.1E-06 37.4 3.2 36 6-42 34-69 (141)
35 COG1855 ATPase (PilT family) [ 94.2 0.034 7.4E-07 46.0 2.4 39 7-46 488-526 (604)
36 PF07650 KH_2: KH domain syndr 94.0 0.025 5.3E-07 33.8 1.0 29 7-35 27-55 (78)
37 PRK13763 putative RNA-processi 94.0 0.03 6.5E-07 39.1 1.5 22 15-36 105-126 (180)
38 PRK11824 polynucleotide phosph 93.7 0.022 4.7E-07 47.0 0.4 35 7-42 556-590 (693)
39 KOG2192|consensus 93.4 0.11 2.4E-06 40.8 3.8 40 6-46 316-355 (390)
40 COG0195 NusA Transcription elo 92.9 0.069 1.5E-06 38.3 1.9 36 6-42 143-178 (190)
41 KOG2190|consensus 91.4 0.19 4.2E-06 40.4 3.0 41 5-46 338-378 (485)
42 PF13184 KH_5: NusA-like KH do 90.8 0.15 3.2E-06 31.1 1.5 39 8-46 6-49 (69)
43 KOG1676|consensus 90.4 0.14 3.1E-06 42.7 1.4 38 6-44 319-356 (600)
44 COG0195 NusA Transcription elo 90.0 0.37 8E-06 34.6 3.1 36 6-42 77-112 (190)
45 COG1094 Predicted RNA-binding 89.8 0.2 4.3E-06 36.5 1.6 22 15-36 112-133 (194)
46 KOG2191|consensus 89.7 0.3 6.6E-06 38.9 2.7 37 6-43 133-169 (402)
47 PRK06418 transcription elongat 89.5 0.37 8E-06 34.1 2.7 33 8-42 64-96 (166)
48 PRK04163 exosome complex RNA-b 88.1 0.24 5.2E-06 35.8 1.0 29 7-35 147-175 (235)
49 cd02412 30S_S3_KH K homology R 87.4 0.6 1.3E-05 30.1 2.5 29 8-36 64-92 (109)
50 PRK12328 nusA transcription el 86.9 1.1 2.4E-05 35.4 4.1 41 6-47 309-351 (374)
51 COG1185 Pnp Polyribonucleotide 86.7 0.48 1E-05 40.2 2.2 36 6-42 553-588 (692)
52 cd02411 archeal_30S_S3_KH K ho 86.1 0.78 1.7E-05 28.3 2.4 28 9-36 42-69 (85)
53 KOG2193|consensus 85.8 0.45 9.7E-06 39.3 1.6 36 8-44 414-449 (584)
54 PRK12327 nusA transcription el 85.8 0.62 1.3E-05 36.3 2.2 37 6-43 304-340 (362)
55 KOG2192|consensus 85.6 0.33 7.1E-06 38.2 0.7 35 6-41 124-158 (390)
56 TIGR01953 NusA transcription t 84.4 0.73 1.6E-05 35.5 2.1 36 6-42 302-337 (341)
57 PRK09202 nusA transcription el 83.5 0.7 1.5E-05 37.1 1.7 36 6-42 303-338 (470)
58 COG1847 Jag Predicted RNA-bind 81.9 0.78 1.7E-05 33.8 1.3 34 7-40 93-126 (208)
59 cd02413 40S_S3_KH K homology R 81.3 1.7 3.6E-05 27.1 2.5 28 9-36 34-61 (81)
60 PRK00089 era GTPase Era; Revie 80.6 1.1 2.3E-05 32.0 1.6 30 6-35 227-257 (292)
61 PRK12329 nusA transcription el 80.0 1.3 2.8E-05 35.9 2.1 29 7-35 337-365 (449)
62 KOG0336|consensus 78.3 0.55 1.2E-05 39.0 -0.5 26 7-32 49-74 (629)
63 KOG2191|consensus 78.0 3 6.4E-05 33.5 3.5 38 8-46 42-79 (402)
64 TIGR00436 era GTP-binding prot 76.1 1.8 4E-05 30.9 1.7 30 6-35 222-252 (270)
65 KOG1588|consensus 75.0 1.6 3.5E-05 33.1 1.2 22 14-35 107-128 (259)
66 PRK15494 era GTPase Era; Provi 71.1 2.7 5.9E-05 31.5 1.6 30 6-35 274-304 (339)
67 KOG2814|consensus 68.9 1.7 3.6E-05 34.3 0.1 38 7-45 59-96 (345)
68 PRK04191 rps3p 30S ribosomal p 63.8 6.5 0.00014 28.3 2.3 28 9-36 44-71 (207)
69 COG0092 RpsC Ribosomal protein 63.5 6.4 0.00014 29.5 2.3 32 11-42 57-94 (233)
70 KOG0394|consensus 62.1 5.2 0.00011 29.7 1.6 18 50-67 111-128 (210)
71 KOG2113|consensus 61.2 6.6 0.00014 31.4 2.1 31 5-35 26-56 (394)
72 KOG2279|consensus 53.2 4.4 9.5E-05 34.1 -0.0 32 5-36 140-171 (608)
73 KOG2208|consensus 48.6 20 0.00043 30.5 3.1 37 6-42 421-457 (753)
74 PRK12327 nusA transcription el 46.7 18 0.0004 28.2 2.5 30 14-43 245-274 (362)
75 COG1094 Predicted RNA-binding 46.4 27 0.00059 25.5 3.2 31 5-35 8-38 (194)
76 COG5176 MSL5 Splicing factor ( 46.2 19 0.0004 27.5 2.4 32 13-44 162-194 (269)
77 TIGR01953 NusA transcription t 46.2 20 0.00043 27.7 2.5 30 14-43 243-272 (341)
78 COG1159 Era GTPase [General fu 46.1 15 0.00032 28.4 1.9 28 7-34 231-259 (298)
79 TIGR01008 rpsC_E_A ribosomal p 44.7 22 0.00047 25.6 2.5 28 9-36 42-69 (195)
80 cd03710 BipA_TypA_C BipA_TypA_ 43.4 11 0.00024 22.4 0.7 18 4-21 3-20 (79)
81 CHL00048 rps3 ribosomal protei 42.7 24 0.00052 25.6 2.4 26 10-35 71-96 (214)
82 PRK09202 nusA transcription el 42.3 22 0.00048 28.7 2.4 32 15-46 246-277 (470)
83 smart00838 EFG_C Elongation fa 41.7 8.6 0.00019 23.0 -0.0 21 1-21 1-22 (85)
84 PF15299 ALS2CR8: Amyotrophic 40.0 19 0.00041 25.8 1.6 16 54-69 23-38 (225)
85 PTZ00084 40S ribosomal protein 39.7 29 0.00062 25.6 2.4 27 10-36 49-75 (220)
86 PRK12329 nusA transcription el 38.7 28 0.00061 28.4 2.5 29 14-42 277-305 (449)
87 PF00679 EFG_C: Elongation fac 37.8 9.4 0.0002 23.1 -0.3 21 1-21 2-23 (89)
88 PRK12328 nusA transcription el 37.4 27 0.00058 27.8 2.1 30 14-43 251-280 (374)
89 TIGR01009 rpsC_bact ribosomal 36.2 36 0.00079 24.5 2.5 28 9-36 66-93 (211)
90 KOG0119|consensus 33.6 32 0.00068 28.9 2.0 27 14-40 153-180 (554)
91 cd02410 archeal_CPSF_KH The ar 33.5 36 0.00078 23.9 2.0 29 8-36 79-107 (145)
92 KOG1423|consensus 32.1 49 0.0011 26.6 2.8 31 4-34 327-358 (379)
93 smart00059 FN2 Fibronectin typ 31.5 42 0.0009 19.3 1.8 17 52-68 4-20 (49)
94 cd03709 lepA_C lepA_C: This fa 31.1 18 0.00039 21.6 0.2 18 4-21 3-20 (80)
95 cd00062 FN2 Fibronectin Type I 28.8 57 0.0012 18.6 2.0 16 53-68 4-19 (48)
96 KOG2279|consensus 27.9 47 0.001 28.2 2.2 32 5-36 68-99 (608)
97 KOG4369|consensus 25.0 34 0.00073 32.3 0.9 35 7-42 1342-1376(2131)
98 KOG4277|consensus 25.0 36 0.00079 27.6 1.0 45 22-66 116-163 (468)
99 cd04096 eEF2_snRNP_like_C eEF2 24.4 30 0.00064 20.3 0.3 18 4-21 3-20 (80)
100 KOG3273|consensus 23.7 17 0.00036 27.6 -1.1 17 15-31 179-195 (252)
101 KOG3387|consensus 21.3 49 0.0011 23.0 1.0 14 52-65 72-85 (131)
102 PF08477 Miro: Miro-like prote 20.5 73 0.0016 18.8 1.5 11 56-66 107-117 (119)
103 cd04097 mtEFG1_C mtEFG1_C: C-t 20.5 30 0.00066 20.3 -0.2 18 4-21 3-20 (78)
104 PRK13601 putative L7Ae-like ri 20.1 20 0.00044 22.4 -1.1 51 14-66 4-59 (82)
No 1
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=99.39 E-value=1.9e-13 Score=86.29 Aligned_cols=37 Identities=38% Similarity=0.427 Sum_probs=34.4
Q ss_pred ceeeeeeeeCCCccCcccccCchhHHHHHhhhceeEE
Q psy986 3 EYSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRV 39 (71)
Q Consensus 3 Ef~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~i 39 (71)
.+..++|.|+++|+||+|||+||+||||||++.+++.
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~ 64 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGS 64 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHHHHHhcc
Confidence 3678999999999999999999999999999999876
No 2
>PRK00468 hypothetical protein; Provisional
Probab=99.38 E-value=1.7e-13 Score=85.58 Aligned_cols=37 Identities=35% Similarity=0.419 Sum_probs=34.1
Q ss_pred eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEe
Q psy986 4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVK 40 (71)
Q Consensus 4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~ik 40 (71)
+..+.|.|+++|+||||||+||+|+||||++++++.+
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~aaa~k 65 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIK 65 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHHHHHHHhc
Confidence 5678999999999999999999999999999988655
No 3
>PRK02821 hypothetical protein; Provisional
Probab=99.29 E-value=1.3e-12 Score=82.20 Aligned_cols=34 Identities=24% Similarity=0.358 Sum_probs=32.0
Q ss_pred eeeeeeeeCCCccCcccccCchhHHHHHhhhcee
Q psy986 4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV 37 (71)
Q Consensus 4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~ 37 (71)
.....|.|+++|+||+|||+||+|+|||++++++
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~ 63 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI 63 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh
Confidence 5678999999999999999999999999999987
No 4
>PRK01064 hypothetical protein; Provisional
Probab=98.91 E-value=5.6e-10 Score=70.34 Aligned_cols=37 Identities=32% Similarity=0.375 Sum_probs=33.2
Q ss_pred eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEe
Q psy986 4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVK 40 (71)
Q Consensus 4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~ik 40 (71)
+..+.+.|+++|+|++|||+|++|+|||+++++++.+
T Consensus 29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~~~~~ 65 (78)
T PRK01064 29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASR 65 (78)
T ss_pred EEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhh
Confidence 5678899999999999999999999999999887543
No 5
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.40 E-value=8.5e-07 Score=50.29 Aligned_cols=36 Identities=44% Similarity=0.841 Sum_probs=31.6
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~ 43 (71)
..+.||++.+|++||++|+++++|+..+++ .+.+..
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~-~I~i~~ 37 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGA-KIKIPD 37 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCC-EEEEcC
Confidence 578999999999999999999999999975 566663
No 6
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=98.35 E-value=1.2e-07 Score=56.87 Aligned_cols=35 Identities=14% Similarity=0.279 Sum_probs=31.3
Q ss_pred eeeeeeeCCCccCcccccCchhHHHHHhhhceeEE
Q psy986 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRV 39 (71)
Q Consensus 5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~i 39 (71)
....+.++.+|.|++|||+|++++||+++++++.-
T Consensus 29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~ 63 (73)
T PF13083_consen 29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAAN 63 (73)
T ss_dssp TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHH
T ss_pred eEEEEEECCCccceEECCCCeeHHHHHHHHHHHHH
Confidence 45678999999999999999999999999988753
No 7
>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=98.23 E-value=2.9e-06 Score=49.85 Aligned_cols=38 Identities=32% Similarity=0.629 Sum_probs=33.2
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCC
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN 45 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~ 45 (71)
..+.||.+.+|++|||+|.+++.|++.+|+ .+++..++
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga-~I~i~~~~ 39 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGA-KIRVSKSV 39 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCC-EEEEcCCC
Confidence 468899999999999999999999999987 68887443
No 8
>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=98.07 E-value=4.9e-06 Score=49.08 Aligned_cols=36 Identities=33% Similarity=0.744 Sum_probs=31.8
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
-..+.||++.+|++|||+|.+|+.|++.+++- ++++
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~-I~i~ 38 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVK-IDIE 38 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCE-EEeC
Confidence 35789999999999999999999999999865 6665
No 9
>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=98.00 E-value=2.3e-06 Score=48.95 Aligned_cols=37 Identities=46% Similarity=0.859 Sum_probs=32.9
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~ 44 (71)
..+.||++++|++||++|++++.|+..+++. +.++.+
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~-I~i~~~ 38 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEETGVK-IQIPDD 38 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHHTSE-EEEEST
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhcCeE-EEEcCC
Confidence 5789999999999999999999999999865 888643
No 10
>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=97.99 E-value=6.3e-06 Score=48.67 Aligned_cols=30 Identities=27% Similarity=0.452 Sum_probs=27.6
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
...+.|+++++|++|||+|++|+.++.+++
T Consensus 26 ~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~ 55 (61)
T cd02134 26 RARVVVPDDQLGLAIGKGGQNVRLASKLLG 55 (61)
T ss_pred EEEEEECcccceeeECCCCHHHHHHHHHHC
Confidence 456889999999999999999999999887
No 11
>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=97.94 E-value=1.4e-05 Score=45.86 Aligned_cols=36 Identities=31% Similarity=0.716 Sum_probs=31.1
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~ 43 (71)
..+.||++.+|.+||++|.+|+.|++..+ +.+.+..
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g-~~I~i~~ 37 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETG-VKIRFPD 37 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhC-CEEEcCC
Confidence 57899999999999999999999999886 4466653
No 12
>smart00322 KH K homology RNA-binding domain.
Probab=97.92 E-value=1.2e-05 Score=44.38 Aligned_cols=38 Identities=32% Similarity=0.603 Sum_probs=32.5
Q ss_pred eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
.....+.||.+.+|.+||++|.++++|+..++ +.+.+.
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~-~~i~~~ 39 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETG-VKIDIP 39 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHC-CEEEEC
Confidence 35678999999999999999999999999986 445554
No 13
>PF13014 KH_3: KH domain
Probab=97.63 E-value=9.2e-05 Score=40.46 Aligned_cols=28 Identities=39% Similarity=0.835 Sum_probs=24.7
Q ss_pred ccCcccccCchhHHHHHhhhceeEEeecC
Q psy986 15 LVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43 (71)
Q Consensus 15 dvGKVIGk~Gr~ikaIr~~~~a~~iki~~ 43 (71)
.+|.+||++|.+|+.|++.++ +.|+|..
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg-~~I~i~~ 28 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETG-AKIQIPP 28 (43)
T ss_pred CcCeEECCCChHHHHHHHHhC-cEEEECC
Confidence 479999999999999999988 5688875
No 14
>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=97.38 E-value=0.00011 Score=44.74 Aligned_cols=32 Identities=19% Similarity=0.400 Sum_probs=28.5
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeE
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVR 38 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~ 38 (71)
..+.+..++.|++|||+|+++.||..++..+.
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 36889999999999999999999999888653
No 15
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.34 E-value=0.00016 Score=49.20 Aligned_cols=30 Identities=30% Similarity=0.362 Sum_probs=27.0
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhce
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
..+.|+++++|+.|||+|+++++++.+++-
T Consensus 101 ~~V~V~~~d~g~aIGK~G~ni~la~~L~~~ 130 (140)
T PRK08406 101 AYVEVAPEDKGIAIGKNGKNIERAKDLAKR 130 (140)
T ss_pred EEEEECccccchhhCCCCHHHHHHHHHhCC
Confidence 457899999999999999999999988763
No 16
>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=96.82 E-value=0.00063 Score=47.14 Aligned_cols=34 Identities=32% Similarity=0.753 Sum_probs=30.1
Q ss_pred eeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43 (71)
Q Consensus 9 l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~ 43 (71)
+.||++-+|.+||++|++|+.|...+++- ++++.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~-I~Id~ 35 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVK-LDIDS 35 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcE-EEEEc
Confidence 68999999999999999999999999854 77763
No 17
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=96.79 E-value=0.0018 Score=36.27 Aligned_cols=33 Identities=30% Similarity=0.345 Sum_probs=27.5
Q ss_pred eeeeeeeCCCccCcccccCchhHHHHHhhhcee
Q psy986 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVV 37 (71)
Q Consensus 5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~ 37 (71)
....+.+++.+.|.+|||+|++++++..+++..
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~ 57 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKL 57 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHH
Confidence 344677777799999999999999999888743
No 18
>PRK13763 putative RNA-processing protein; Provisional
Probab=96.70 E-value=0.0014 Score=45.73 Aligned_cols=38 Identities=32% Similarity=0.702 Sum_probs=33.2
Q ss_pred eeeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 4 YSEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 4 f~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
+....+.||++-+|.+||++|.+|++|.+..++ .++++
T Consensus 2 ~~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~-~I~i~ 39 (180)
T PRK13763 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGV-KLEID 39 (180)
T ss_pred CceEEEEcCHHHhhhHhccchhHHHHHHHHHCc-EEEEE
Confidence 356789999999999999999999999999974 47776
No 19
>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=95.98 E-value=0.0064 Score=51.06 Aligned_cols=36 Identities=33% Similarity=0.713 Sum_probs=31.8
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
.+.+++|++.+|.+||.+|++|++|.+..|+- |+|+
T Consensus 579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~-Idi~ 614 (719)
T TIGR02696 579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAE-ISIE 614 (719)
T ss_pred eEEEEeChHHhhheeCCCcHhHHHHHHHHCCE-EEEe
Confidence 36789999999999999999999999999854 6666
No 20
>PRK13764 ATPase; Provisional
Probab=95.95 E-value=0.01 Score=48.81 Aligned_cols=40 Identities=33% Similarity=0.541 Sum_probs=33.3
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e 46 (71)
.-.+.||+.+++++|||+|+.|..|...+| +.++|...+|
T Consensus 482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~-~~i~v~~~~~ 521 (602)
T PRK13764 482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLG-IDIDVRPLDE 521 (602)
T ss_pred eEEEEEChhhhhHHhccCcchHHHHHHHhC-CceEEEEccc
Confidence 456899999999999999999999999998 4566654444
No 21
>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=95.93 E-value=0.0049 Score=50.75 Aligned_cols=35 Identities=31% Similarity=0.708 Sum_probs=31.2
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
+.++||++.+|++||++|++|++|.+..|+- |+|+
T Consensus 553 ~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~-I~i~ 587 (684)
T TIGR03591 553 ETIKINPDKIRDVIGPGGKVIREITEETGAK-IDIE 587 (684)
T ss_pred EEEecCHHHHHhhcCCCcHHHHHHHHHHCCE-EEEe
Confidence 5789999999999999999999999988854 6665
No 22
>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=95.89 E-value=0.007 Score=40.35 Aligned_cols=30 Identities=27% Similarity=0.689 Sum_probs=26.1
Q ss_pred CccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986 14 NLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44 (71)
Q Consensus 14 ~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~ 44 (71)
+.+|++||.+|+++|.|.+..++- |.|.++
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~k-I~Irg~ 44 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAK-ISIRGK 44 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCE-EEEecC
Confidence 679999999999999999999954 777754
No 23
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.81 E-value=0.01 Score=47.56 Aligned_cols=33 Identities=27% Similarity=0.642 Sum_probs=27.0
Q ss_pred ceeeeeeeeCCC-ccCcccccCchhHHHHHhhhc
Q psy986 3 EYSEESLQVPRN-LVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 3 Ef~e~~l~V~~~-dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
|.+...|.+|.+ ..||+|||.||+|+++-+..|
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tg 235 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTG 235 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhC
Confidence 456677888884 569999999999999976666
No 24
>PRK12704 phosphodiesterase; Provisional
Probab=95.70 E-value=0.012 Score=47.25 Aligned_cols=33 Identities=27% Similarity=0.629 Sum_probs=26.7
Q ss_pred ceeeeeeeeCC-CccCcccccCchhHHHHHhhhc
Q psy986 3 EYSEESLQVPR-NLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 3 Ef~e~~l~V~~-~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
|.+...+.+|. +..||+|||.||+|+++-...|
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tg 241 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTG 241 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhC
Confidence 45667788888 4569999999999999976665
No 25
>KOG1676|consensus
Probab=95.69 E-value=0.01 Score=49.26 Aligned_cols=41 Identities=32% Similarity=0.794 Sum_probs=36.4
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCCC
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNEP 47 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e~ 47 (71)
...+.||+.-||-||||+|.+||.|-...| ++|.|..|+++
T Consensus 231 ~~~V~VPr~~VG~IIGkgGE~IKklq~etG-~KIQfkpDd~p 271 (600)
T KOG1676|consen 231 TREVKVPRSKVGIIIGKGGEMIKKLQNETG-AKIQFKPDDDP 271 (600)
T ss_pred eeEEeccccceeeEEecCchHHHHHhhccC-ceeEeecCCCC
Confidence 457899999999999999999999988877 68888888885
No 26
>PRK00106 hypothetical protein; Provisional
Probab=95.64 E-value=0.012 Score=47.79 Aligned_cols=33 Identities=30% Similarity=0.677 Sum_probs=27.5
Q ss_pred ceeeeeeeeCC-CccCcccccCchhHHHHHhhhc
Q psy986 3 EYSEESLQVPR-NLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 3 Ef~e~~l~V~~-~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
|.+...+.+|. +..||+|||.||+|+++-+..|
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tG 256 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTG 256 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhC
Confidence 45667788888 4569999999999999987776
No 27
>KOG2190|consensus
Probab=95.61 E-value=0.011 Score=47.45 Aligned_cols=38 Identities=37% Similarity=0.742 Sum_probs=33.4
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~ 44 (71)
.-.|-||.+.+|=+|||+|..||.||+..+ +.+++.+|
T Consensus 139 ~~RLlVp~sq~GslIGK~G~~Ik~Ire~Tg-A~I~v~~~ 176 (485)
T KOG2190|consen 139 TCRLLVPSSQVGSLIGKGGSLIKEIREETG-AKIRVSSD 176 (485)
T ss_pred EEEEEechhheeeeeccCcHHHHHHHHhcC-ceEEecCC
Confidence 356889999999999999999999999955 68888876
No 28
>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=95.38 E-value=0.0099 Score=41.17 Aligned_cols=22 Identities=32% Similarity=0.682 Sum_probs=20.5
Q ss_pred ccCcccccCchhHHHHHhhhce
Q psy986 15 LVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 15 dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
..|++||++|+++++|-+.+++
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~ 120 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGV 120 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCC
Confidence 6999999999999999998885
No 29
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=95.20 E-value=0.016 Score=39.81 Aligned_cols=30 Identities=23% Similarity=0.282 Sum_probs=26.4
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
...+.||+++.|..|||+|+.++-.+.+++
T Consensus 101 ~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~ 130 (141)
T TIGR01952 101 VAYVEVHPRDKGIAIGKGGKNIERAKELAK 130 (141)
T ss_pred EEEEEEChhhhhhhhCCCchhHHHHHHHhc
Confidence 456889999999999999999998887765
No 30
>PRK12705 hypothetical protein; Provisional
Probab=95.03 E-value=0.014 Score=47.12 Aligned_cols=39 Identities=28% Similarity=0.624 Sum_probs=28.9
Q ss_pred ceeeeeeeeCCC-ccCcccccCchhHHHHHhhhceeEEeec
Q psy986 3 EYSEESLQVPRN-LVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 3 Ef~e~~l~V~~~-dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
|.+...+..|.+ ..||+|||.||.|+++-...|+ .+-|+
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGv-dliid 235 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGV-DLIID 235 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCC-ceEec
Confidence 445566777774 5699999999999999877774 33343
No 31
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=94.92 E-value=0.023 Score=38.62 Aligned_cols=34 Identities=24% Similarity=0.417 Sum_probs=28.2
Q ss_pred eeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
.+-|++.++|..||++|..||+|.++++- .+++-
T Consensus 35 i~vV~~~~vG~~IG~~G~rI~~i~e~lge-kIdVv 68 (140)
T PRK08406 35 IFVVKEGDMGLAIGKGGENVKRLEEKLGK-DIELV 68 (140)
T ss_pred EEEEeCCCccccCCcCchHHHHHHHHhCC-ceEEE
Confidence 45678999999999999999999888763 56653
No 32
>KOG2193|consensus
Probab=94.86 E-value=0.017 Score=47.27 Aligned_cols=37 Identities=30% Similarity=0.606 Sum_probs=31.2
Q ss_pred eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
+|-+++||..-.||||||+|++.+.+-.+.+| .+.|-
T Consensus 493 lethirVPs~~aGRvIGKGGktVnELQnlt~A-eV~vP 529 (584)
T KOG2193|consen 493 LETHIRVPSSAAGRVIGKGGKTVNELQNLTSA-EVVVP 529 (584)
T ss_pred eeeeeeccchhhhhhhccccccHHHHhccccc-eEEcc
Confidence 56789999999999999999999999887775 34443
No 33
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=94.40 E-value=0.014 Score=50.12 Aligned_cols=37 Identities=22% Similarity=0.489 Sum_probs=32.9
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
...++||++.+|.+||.+|++|++|.+-.++-.++++
T Consensus 686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~ 722 (891)
T PLN00207 686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ 722 (891)
T ss_pred eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC
Confidence 3578999999999999999999999999987766665
No 34
>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=94.40 E-value=0.049 Score=37.40 Aligned_cols=36 Identities=19% Similarity=0.362 Sum_probs=29.4
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
.-.+-|.+.++|..||++|..||+++++.|- .+++-
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~ge-kIdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGK-SIELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCC-eeEEE
Confidence 3456789999999999999999999887773 55553
No 35
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=94.22 E-value=0.034 Score=46.03 Aligned_cols=39 Identities=36% Similarity=0.647 Sum_probs=31.9
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e 46 (71)
..+.||+.+++++|||+|+.|+.|...+| ..+++..-++
T Consensus 488 avv~vpe~~i~~vigk~g~~i~~ie~klg-i~I~v~~~e~ 526 (604)
T COG1855 488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLG-IKIDVKPLEE 526 (604)
T ss_pred EEEEeCHHHhhHHhhcccchHHHHHHHhC-CceEEEEccc
Confidence 56899999999999999999999999988 4555543333
No 36
>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=94.04 E-value=0.025 Score=33.82 Aligned_cols=29 Identities=28% Similarity=0.367 Sum_probs=24.6
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
-.+.+..+..|.+||++|+.++.|++.++
T Consensus 27 ~~i~i~~~~~~ivIGk~G~~ik~i~~~~~ 55 (78)
T PF07650_consen 27 IIIVIKASQPGIVIGKKGSNIKKIREELR 55 (78)
T ss_dssp EEEEEEESSHHHHHTGGGHHHHHHHHHHH
T ss_pred EEEEEeCCCccHhHHhhhHHHHHHHHHHH
Confidence 45667788999999999999999987665
No 37
>PRK13763 putative RNA-processing protein; Provisional
Probab=94.02 E-value=0.03 Score=39.08 Aligned_cols=22 Identities=32% Similarity=0.682 Sum_probs=20.3
Q ss_pred ccCcccccCchhHHHHHhhhce
Q psy986 15 LVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 15 dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
-.|++||++|+++++|-+.+++
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~ 126 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGV 126 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCc
Confidence 5899999999999999988885
No 38
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=93.72 E-value=0.022 Score=47.02 Aligned_cols=35 Identities=34% Similarity=0.795 Sum_probs=30.9
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
..+++|++.+|.+||.+|++|++|.+..++ .++++
T Consensus 556 ~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~-~idi~ 590 (693)
T PRK11824 556 ETIKIPPDKIRDVIGPGGKTIREITEETGA-KIDIE 590 (693)
T ss_pred eeecCCHHHHHHHhcCCchhHHHHHHHHCC-ccccC
Confidence 467889999999999999999999999988 56654
No 39
>KOG2192|consensus
Probab=93.43 E-value=0.11 Score=40.82 Aligned_cols=40 Identities=35% Similarity=0.663 Sum_probs=33.5
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e 46 (71)
.-.+.+|.++-|-+|||+|..|+.||.-+|| .|+++-.-|
T Consensus 316 TaQvtip~dlggsiigkggqri~~ir~esGA-~Ikideple 355 (390)
T KOG2192|consen 316 TAQVTIPKDLGGSIIGKGGQRIKQIRHESGA-SIKIDEPLE 355 (390)
T ss_pred eeeEecccccCcceecccchhhhhhhhccCc-eEEecCcCC
Confidence 4578899999999999999999999999885 677764333
No 40
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=92.87 E-value=0.069 Score=38.33 Aligned_cols=36 Identities=25% Similarity=0.399 Sum_probs=29.9
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
...+.||+++.+++|||+|+.++.+..+.| ..++|.
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg-~~i~I~ 178 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTG-WEIDIE 178 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhC-CEEEEE
Confidence 467889999999999999999999988877 344444
No 41
>KOG2190|consensus
Probab=91.45 E-value=0.19 Score=40.43 Aligned_cols=41 Identities=37% Similarity=0.644 Sum_probs=34.0
Q ss_pred eeeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46 (71)
Q Consensus 5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e 46 (71)
....+.||.+++|-+|||+|+.|..||...| +.|+|...++
T Consensus 338 v~~~l~vps~~igciiGk~G~~iseir~~tg-A~I~I~~~~~ 378 (485)
T KOG2190|consen 338 VTQRLLVPSDLIGCIIGKGGAKISEIRQRTG-ASISILNKEE 378 (485)
T ss_pred eeeeeccCccccceeecccccchHHHHHhcC-CceEEccccc
Confidence 3467899999999999999999999998887 4667764444
No 42
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=90.84 E-value=0.15 Score=31.08 Aligned_cols=39 Identities=23% Similarity=0.359 Sum_probs=28.4
Q ss_pred eeeeCCCc-----cCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986 8 SLQVPRNL-----VGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46 (71)
Q Consensus 8 ~l~V~~~d-----vGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e 46 (71)
.+-|...+ +|..||++|..|++|...++--.+++-..++
T Consensus 6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s~ 49 (69)
T PF13184_consen 6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYSD 49 (69)
T ss_dssp EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--S
T ss_pred EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcCC
Confidence 34566677 9999999999999999999767787754333
No 43
>KOG1676|consensus
Probab=90.41 E-value=0.14 Score=42.65 Aligned_cols=38 Identities=32% Similarity=0.595 Sum_probs=32.2
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~ 44 (71)
+..+.||.+-+|=||||+|.+||.|-+.+|| .|-...+
T Consensus 319 ~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA-~~el~r~ 356 (600)
T KOG1676|consen 319 QFYMKVPADKCGLVIGRGGETIKQINQQSGA-RCELSRQ 356 (600)
T ss_pred eEEEeccccccccccCCCccchhhhcccCCc-cccccCC
Confidence 6678999999999999999999999999995 4444444
No 44
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=89.97 E-value=0.37 Score=34.61 Aligned_cols=36 Identities=25% Similarity=0.396 Sum_probs=30.4
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
.....+..+.||..||++|..++++...++ =.|+|-
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLg-ekIdVV 112 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELG-EKIDVV 112 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhC-CceEEE
Confidence 345667778899999999999999999999 777774
No 45
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=89.77 E-value=0.2 Score=36.54 Aligned_cols=22 Identities=32% Similarity=0.753 Sum_probs=19.7
Q ss_pred ccCcccccCchhHHHHHhhhce
Q psy986 15 LVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 15 dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
-.||+||++|+|-++|-.+.++
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~ 133 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGV 133 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCC
Confidence 3799999999999999988875
No 46
>KOG2191|consensus
Probab=89.67 E-value=0.3 Score=38.93 Aligned_cols=37 Identities=32% Similarity=0.595 Sum_probs=31.9
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~ 43 (71)
+-.+-||..-.|-+|||+|-+||+|++.+++ .|+|++
T Consensus 133 qikivvPNstag~iigkggAtiK~~~Eqsga-~iqisP 169 (402)
T KOG2191|consen 133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGA-WIQISP 169 (402)
T ss_pred eeEEeccCCcccceecCCcchHHHHHHhhCc-ceEecc
Confidence 3567899999999999999999999999985 566664
No 47
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=89.49 E-value=0.37 Score=34.14 Aligned_cols=33 Identities=30% Similarity=0.433 Sum_probs=27.2
Q ss_pred eeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
.+-|.+.+ |..|||+|.+++++...+|- .+++-
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk-~VevV 96 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGK-KVRVV 96 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCC-cEEEE
Confidence 35577889 99999999999999999985 55553
No 48
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=88.08 E-value=0.24 Score=35.83 Aligned_cols=29 Identities=28% Similarity=0.531 Sum_probs=25.4
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
..++||++.++++||++|.+++.|-...+
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~ 175 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETG 175 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhC
Confidence 35899999999999999999999986654
No 49
>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=87.38 E-value=0.6 Score=30.12 Aligned_cols=29 Identities=21% Similarity=0.321 Sum_probs=23.0
Q ss_pred eeeeCCCccCcccccCchhHHHHHhhhce
Q psy986 8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
.+.+.-+..|.+||++|+.+++++..+..
T Consensus 64 ~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 64 EVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 34455556899999999999999987764
No 50
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=86.88 E-value=1.1 Score=35.41 Aligned_cols=41 Identities=24% Similarity=0.329 Sum_probs=32.4
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEee--cCCCCC
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKI--EGDNEP 47 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki--~~~~e~ 47 (71)
.-.+.||+++.+..|||+|+.++-.+.+.|- .++| -++.|+
T Consensus 309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGw-kIDI~s~~~~~~ 351 (374)
T PRK12328 309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGY-EIELNEIGSKEN 351 (374)
T ss_pred EEEEEEChHHhhhhhcCCChhHHHHHHHhCC-EEEEEECCCCcc
Confidence 3468899999999999999999999888884 4444 445554
No 51
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=86.71 E-value=0.48 Score=40.18 Aligned_cols=36 Identities=31% Similarity=0.669 Sum_probs=30.6
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
.+.++++++-++-+||++|++|++|.+..|+ .|.|+
T Consensus 553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~-~Idie 588 (692)
T COG1185 553 IETIKIDPDKIRDVIGPGGKTIKAITEETGV-KIDIE 588 (692)
T ss_pred eEEEccCHHHHhhccCCcccchhhhhhhhCc-EEEec
Confidence 4678999999999999999999999988874 45555
No 52
>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=86.13 E-value=0.78 Score=28.26 Aligned_cols=28 Identities=25% Similarity=0.447 Sum_probs=22.3
Q ss_pred eeeCCCccCcccccCchhHHHHHhhhce
Q psy986 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 9 l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
+.+.-..-|.+||++|+.++.++..+..
T Consensus 42 V~I~t~~pg~iIGk~G~~I~~l~~~l~k 69 (85)
T cd02411 42 ITIYAERPGMVIGRGGKNIRELTEILET 69 (85)
T ss_pred EEEEECCCCceECCCchhHHHHHHHHHH
Confidence 3344478899999999999999987753
No 53
>KOG2193|consensus
Probab=85.84 E-value=0.45 Score=39.29 Aligned_cols=36 Identities=31% Similarity=0.591 Sum_probs=29.7
Q ss_pred eeeeCCCccCcccccCchhHHHHHhhhceeEEeecCC
Q psy986 8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGD 44 (71)
Q Consensus 8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~ 44 (71)
.+-||...+|-+|||+|..||.|..-.| +.|||...
T Consensus 414 ~~fiP~~~vGAiIGkkG~hIKql~Rfag-ASiKIapp 449 (584)
T KOG2193|consen 414 RMFIPAQAVGAIIGKKGQHIKQLSRFAG-ASIKIAPP 449 (584)
T ss_pred eeeccHHHHHHHHhhcchhHHHHHHhcc-ceeeecCC
Confidence 5678999999999999999999876666 57788743
No 54
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=85.77 E-value=0.62 Score=36.27 Aligned_cols=37 Identities=22% Similarity=0.364 Sum_probs=30.2
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeecC
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~ 43 (71)
.-.+.||+++.+..|||+|+.++--..+.|- .++|..
T Consensus 304 ~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~-~idi~s 340 (362)
T PRK12327 304 AARVVVPDYQLSLAIGKEGQNARLAARLTGW-KIDIKS 340 (362)
T ss_pred EEEEEEChhhcchhhcCCChhHHHHHHHHCC-eeeEEE
Confidence 3568899999999999999999998888774 355543
No 55
>KOG2192|consensus
Probab=85.60 E-value=0.33 Score=38.20 Aligned_cols=35 Identities=40% Similarity=0.682 Sum_probs=28.7
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEee
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKI 41 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki 41 (71)
|-.+-|+++..|-+||+||.-||.+|++-.| +.||
T Consensus 124 e~rllihqs~ag~iigrngskikelrekcsa-rlki 158 (390)
T KOG2192|consen 124 ELRLLIHQSLAGGIIGRNGSKIKELREKCSA-RLKI 158 (390)
T ss_pred hhhhhhhhhhccceecccchhHHHHHHhhhh-hhhh
Confidence 4456789999999999999999999998763 4444
No 56
>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=84.39 E-value=0.73 Score=35.53 Aligned_cols=36 Identities=19% Similarity=0.407 Sum_probs=29.6
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
.-.+.||+++.+..|||+|+.++-.+.+.| ..++|-
T Consensus 302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g-~~IdI~ 337 (341)
T TIGR01953 302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTG-WNIDVK 337 (341)
T ss_pred EEEEEEChHHcchhhcCCChhHHHHHHHhC-CEEEEE
Confidence 356889999999999999999998887777 345554
No 57
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=83.54 E-value=0.7 Score=37.05 Aligned_cols=36 Identities=25% Similarity=0.442 Sum_probs=30.0
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
...+-||+++++..|||+|++++-.+.+.|- .++|-
T Consensus 303 ~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~-~idi~ 338 (470)
T PRK09202 303 SADVVVPDDQLSLAIGKNGQNVRLASKLTGW-KIDIM 338 (470)
T ss_pred EEEEEECcchHHHhhCCCCeeHHHHHHHHCC-eEEEE
Confidence 4568899999999999999999999888874 35554
No 58
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=81.92 E-value=0.78 Score=33.83 Aligned_cols=34 Identities=18% Similarity=0.331 Sum_probs=27.7
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEe
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVK 40 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~ik 40 (71)
..+++.-++.|++||++|++.+|+--+..++.-+
T Consensus 93 v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 93 VVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3566777889999999999999999887776444
No 59
>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=81.28 E-value=1.7 Score=27.07 Aligned_cols=28 Identities=21% Similarity=0.369 Sum_probs=21.9
Q ss_pred eeeCCCccCcccccCchhHHHHHhhhce
Q psy986 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 9 l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
+.+.-..-|-+||++|+.++.++..+..
T Consensus 34 I~I~tarPg~vIG~~G~~i~~L~~~L~k 61 (81)
T cd02413 34 IIIRATRTQNVLGEKGRRIRELTSLVQK 61 (81)
T ss_pred EEEEeCCCceEECCCchhHHHHHHHHHH
Confidence 3444455699999999999999987653
No 60
>PRK00089 era GTPase Era; Reviewed
Probab=80.59 E-value=1.1 Score=32.01 Aligned_cols=30 Identities=27% Similarity=0.492 Sum_probs=22.2
Q ss_pred eeeeeeC-CCccCcccccCchhHHHHHhhhc
Q psy986 6 EESLQVP-RNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 6 e~~l~V~-~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
+-.|.|. ++..+=||||+|+.|++|.+.+.
T Consensus 227 ~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar 257 (292)
T PRK00089 227 EATIYVERDSQKGIIIGKGGAMLKKIGTEAR 257 (292)
T ss_pred EEEEEEccCCceeEEEeCCcHHHHHHHHHHH
Confidence 3445554 45678899999999999986554
No 61
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=80.02 E-value=1.3 Score=35.86 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=25.5
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
-.+.||+++.+..|||+|++++--..+.|
T Consensus 337 a~V~V~~~qlslAIGK~GqNvrLAs~Ltg 365 (449)
T PRK12329 337 AHVLVPPDQLSLAIGKEGQNVRLAARLTG 365 (449)
T ss_pred EEEEEChHhcchhhcCCChhHHHHHHHHC
Confidence 46899999999999999999988776665
No 62
>KOG0336|consensus
Probab=78.35 E-value=0.55 Score=38.99 Aligned_cols=26 Identities=35% Similarity=0.650 Sum_probs=22.3
Q ss_pred eeeeeCCCccCcccccCchhHHHHHh
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVD 32 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~ 32 (71)
.++.+..+.||+|||++|..|+.|-.
T Consensus 49 lcf~iks~mvg~vigrggskik~iq~ 74 (629)
T KOG0336|consen 49 LCFSIKSEMVGKVIGRGGSKIKRIQN 74 (629)
T ss_pred hhhhhhhhhhheeeccCcchhhhhhc
Confidence 35677889999999999999999873
No 63
>KOG2191|consensus
Probab=78.01 E-value=3 Score=33.47 Aligned_cols=38 Identities=26% Similarity=0.633 Sum_probs=31.4
Q ss_pred eeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986 8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46 (71)
Q Consensus 8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e 46 (71)
.+-||..-.|-||||+|.+|..+....+ ++|+.+...|
T Consensus 42 kvLips~AaGsIIGKGG~ti~~lqk~tg-ariklSks~d 79 (402)
T KOG2191|consen 42 KVLIPSYAAGSIIGKGGQTIVQLQKETG-ARIKLSKSKD 79 (402)
T ss_pred EEEeecccccceeccchHHHHHHHhccC-cEEEeccccc
Confidence 4668999999999999999999987777 5777775544
No 64
>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=76.09 E-value=1.8 Score=30.85 Aligned_cols=30 Identities=27% Similarity=0.343 Sum_probs=21.9
Q ss_pred eeeeeeC-CCccCcccccCchhHHHHHhhhc
Q psy986 6 EESLQVP-RNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 6 e~~l~V~-~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
.-.+.|. ++..|=||||+|+.|+.|.+.+.
T Consensus 222 ~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar 252 (270)
T TIGR00436 222 HALISVERESQKKIIIGKNGSMIKAIGIAAR 252 (270)
T ss_pred EEEEEECcCCceeEEEcCCcHHHHHHHHHHH
Confidence 3345555 35678899999999999986544
No 65
>KOG1588|consensus
Probab=74.95 E-value=1.6 Score=33.14 Aligned_cols=22 Identities=27% Similarity=0.809 Sum_probs=18.9
Q ss_pred CccCcccccCchhHHHHHhhhc
Q psy986 14 NLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 14 ~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
++|||++|-+|++++.+-.-.+
T Consensus 107 NFVGRILGPrGnSlkrLe~eTg 128 (259)
T KOG1588|consen 107 NFVGRILGPRGNSLKRLEEETG 128 (259)
T ss_pred ccccccccCCcchHHHHHHHHC
Confidence 5899999999999999875554
No 66
>PRK15494 era GTPase Era; Provisional
Probab=71.05 E-value=2.7 Score=31.49 Aligned_cols=30 Identities=37% Similarity=0.502 Sum_probs=22.1
Q ss_pred eeeeeeCC-CccCcccccCchhHHHHHhhhc
Q psy986 6 EESLQVPR-NLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 6 e~~l~V~~-~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
+-.|.|.+ +..|=||||+|+.||.|.+.+.
T Consensus 274 ~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar 304 (339)
T PRK15494 274 NQVIVVSRESYKTIILGKNGSKIKEIGAKSR 304 (339)
T ss_pred EEEEEECCCCceeEEEcCCcHHHHHHHHHHH
Confidence 34455554 5678899999999999986543
No 67
>KOG2814|consensus
Probab=68.92 E-value=1.7 Score=34.35 Aligned_cols=38 Identities=21% Similarity=0.441 Sum_probs=28.6
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEeecCCC
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIEGDN 45 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~ 45 (71)
.++.|++...|.+||++|++-+.|+.-.+ ..+.+..+.
T Consensus 59 ~si~v~s~~~~~lig~~g~trkkle~Etq-~~i~lp~p~ 96 (345)
T KOG2814|consen 59 SSILVRSSFIGWLIGKQGKTRKKLEEETQ-TNIFLPRPN 96 (345)
T ss_pred hhhhhhHHHhhhhhcccchHHHHHHHhhc-cceEccCCC
Confidence 36789999999999999999999985544 234444333
No 68
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=63.79 E-value=6.5 Score=28.26 Aligned_cols=28 Identities=25% Similarity=0.427 Sum_probs=22.1
Q ss_pred eeeCCCccCcccccCchhHHHHHhhhce
Q psy986 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 9 l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
+.+.-.+-|-+||++|+.++.++..+.-
T Consensus 44 I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 44 ITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 3344477899999999999999877654
No 69
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=63.47 E-value=6.4 Score=29.51 Aligned_cols=32 Identities=31% Similarity=0.464 Sum_probs=23.3
Q ss_pred eCCCccCcccccCchhHHHHHhhhc----e--eEEeec
Q psy986 11 VPRNLVGKVIGKNGRIIQEIVDKSG----V--VRVKIE 42 (71)
Q Consensus 11 V~~~dvGKVIGk~Gr~ikaIr~~~~----a--~~iki~ 42 (71)
+.-.--|-||||+|+.|+.|+..+. . +.++|.
T Consensus 57 I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~i~ 94 (233)
T COG0092 57 IHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQINIE 94 (233)
T ss_pred EEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEEEE
Confidence 3345568999999999999986554 3 555654
No 70
>KOG0394|consensus
Probab=62.07 E-value=5.2 Score=29.74 Aligned_cols=18 Identities=22% Similarity=0.654 Sum_probs=14.7
Q ss_pred CCCCCCCccceEEeeeEE
Q psy986 50 TLPREEGQVPFMVLTKTV 67 (71)
Q Consensus 50 ~~~~~~~~vpF~~vGt~~ 67 (71)
+.|.+..++|||++|.|+
T Consensus 111 a~~~~Pe~FPFVilGNKi 128 (210)
T KOG0394|consen 111 ASPQDPETFPFVILGNKI 128 (210)
T ss_pred cCCCCCCcccEEEEcccc
Confidence 345677899999999986
No 71
>KOG2113|consensus
Probab=61.18 E-value=6.6 Score=31.41 Aligned_cols=31 Identities=29% Similarity=0.552 Sum_probs=27.1
Q ss_pred eeeeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
.-++++||-+.++-+.|++|-.|+++|.+-.
T Consensus 26 vt~sv~vps~~v~~ivg~qg~kikalr~KTq 56 (394)
T KOG2113|consen 26 VTESVEVPSEHVAEIVGRQGCKIKALRAKTQ 56 (394)
T ss_pred cceeeecCcccceeecccCccccchhhhhhc
Confidence 3568999999999999999999999996544
No 72
>KOG2279|consensus
Probab=53.24 E-value=4.4 Score=34.12 Aligned_cols=32 Identities=41% Similarity=0.760 Sum_probs=27.9
Q ss_pred eeeeeeeCCCccCcccccCchhHHHHHhhhce
Q psy986 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
...+++||....|+++|++|-+++.|+.-+++
T Consensus 140 vk~~lsvpqr~~~~i~grgget~~si~~ss~a 171 (608)
T KOG2279|consen 140 VSEQLSVPQRSVGRIIGRGGETIRSICKSSGA 171 (608)
T ss_pred ccccccchhhhcccccccchhhhcchhccccc
Confidence 35678999999999999999999999966654
No 73
>KOG2208|consensus
Probab=48.55 E-value=20 Score=30.51 Aligned_cols=37 Identities=32% Similarity=0.619 Sum_probs=32.4
Q ss_pred eeeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 6 EESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 6 e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
++.+++|.....++||.+|+.|++|....+-+.++..
T Consensus 421 ~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~ 457 (753)
T KOG2208|consen 421 KEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQ 457 (753)
T ss_pred cceeecCccchhhhhccccccHHHHHhhcCcEEEecC
Confidence 5789999999999999999999999998887555554
No 74
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=46.74 E-value=18 Score=28.22 Aligned_cols=30 Identities=23% Similarity=0.403 Sum_probs=24.5
Q ss_pred CccCcccccCchhHHHHHhhhceeEEeecC
Q psy986 14 NLVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43 (71)
Q Consensus 14 ~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~ 43 (71)
+-||-.||++|..|++|...++-=.|+|-.
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 348999999999999999888666666643
No 75
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=46.44 E-value=27 Score=25.51 Aligned_cols=31 Identities=35% Similarity=0.746 Sum_probs=25.9
Q ss_pred eeeeeeeCCCccCcccccCchhHHHHHhhhc
Q psy986 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
..+.+.+|++-+|-+||+.|.+-+.|-...+
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~ 38 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTG 38 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcC
Confidence 3445999999999999999999999876553
No 76
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=46.18 E-value=19 Score=27.54 Aligned_cols=32 Identities=25% Similarity=0.504 Sum_probs=26.1
Q ss_pred CCccCcccccCchhHHHHHhhhce-eEEeecCC
Q psy986 13 RNLVGKVIGKNGRIIQEIVDKSGV-VRVKIEGD 44 (71)
Q Consensus 13 ~~dvGKVIGk~Gr~ikaIr~~~~a-~~iki~~~ 44 (71)
-++||=+||..|+|.+.+-.++++ ++|+=.+.
T Consensus 162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gs 194 (269)
T COG5176 162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS 194 (269)
T ss_pred cceeEEEecCCcchHHHHHHHhCCeEEEecccc
Confidence 368999999999999999999987 36665543
No 77
>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=46.17 E-value=20 Score=27.74 Aligned_cols=30 Identities=27% Similarity=0.387 Sum_probs=25.0
Q ss_pred CccCcccccCchhHHHHHhhhceeEEeecC
Q psy986 14 NLVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43 (71)
Q Consensus 14 ~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~ 43 (71)
+=||-.||++|..|++|...++-=.|+|-.
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 348999999999999999888766777744
No 78
>COG1159 Era GTPase [General function prediction only]
Probab=46.07 E-value=15 Score=28.43 Aligned_cols=28 Identities=36% Similarity=0.591 Sum_probs=21.1
Q ss_pred eeeeeCC-CccCcccccCchhHHHHHhhh
Q psy986 7 ESLQVPR-NLVGKVIGKNGRIIQEIVDKS 34 (71)
Q Consensus 7 ~~l~V~~-~dvGKVIGk~Gr~ikaIr~~~ 34 (71)
-.+.|++ +..|=+|||+|..+|+|-..+
T Consensus 231 a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 231 ATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 3455655 568899999999999986443
No 79
>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=44.74 E-value=22 Score=25.64 Aligned_cols=28 Identities=32% Similarity=0.465 Sum_probs=21.2
Q ss_pred eeeCCCccCcccccCchhHHHHHhhhce
Q psy986 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 9 l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
+.+.-.--|-+||++|+.++.++..+..
T Consensus 42 I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 42 VIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred EEEEECCCceEECCCchHHHHHHHHHHH
Confidence 3344445699999999999999877654
No 80
>cd03710 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secreti
Probab=43.43 E-value=11 Score=22.39 Aligned_cols=18 Identities=33% Similarity=0.549 Sum_probs=15.7
Q ss_pred eeeeeeeeCCCccCcccc
Q psy986 4 YSEESLQVPRNLVGKVIG 21 (71)
Q Consensus 4 f~e~~l~V~~~dvGKVIG 21 (71)
+.+-+|.||.+.+|+|++
T Consensus 3 i~~v~I~~P~~~~g~V~~ 20 (79)
T cd03710 3 IEELTIDVPEEYSGAVIE 20 (79)
T ss_pred EEEEEEEeCchhhHHHHH
Confidence 466789999999999987
No 81
>CHL00048 rps3 ribosomal protein S3
Probab=42.71 E-value=24 Score=25.56 Aligned_cols=26 Identities=19% Similarity=0.195 Sum_probs=20.3
Q ss_pred eeCCCccCcccccCchhHHHHHhhhc
Q psy986 10 QVPRNLVGKVIGKNGRIIQEIVDKSG 35 (71)
Q Consensus 10 ~V~~~dvGKVIGk~Gr~ikaIr~~~~ 35 (71)
.+--..-|-+||++|+.++.+++.+.
T Consensus 71 ~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 71 IIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred EEEECCCceEECCCcHhHHHHHHHHH
Confidence 33344568999999999999998774
No 82
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=42.28 E-value=22 Score=28.66 Aligned_cols=32 Identities=28% Similarity=0.355 Sum_probs=25.7
Q ss_pred ccCcccccCchhHHHHHhhhceeEEeecCCCC
Q psy986 15 LVGKVIGKNGRIIQEIVDKSGVVRVKIEGDNE 46 (71)
Q Consensus 15 dvGKVIGk~Gr~ikaIr~~~~a~~iki~~~~e 46 (71)
=||-.||++|..||+|..-++-=.|.|-..++
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~ 277 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSD 277 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCC
Confidence 38999999999999999888766777754333
No 83
>smart00838 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
Probab=41.70 E-value=8.6 Score=22.99 Aligned_cols=21 Identities=38% Similarity=0.708 Sum_probs=17.6
Q ss_pred Ccc-eeeeeeeeCCCccCcccc
Q psy986 1 MLE-YSEESLQVPRNLVGKVIG 21 (71)
Q Consensus 1 ~LE-f~e~~l~V~~~dvGKVIG 21 (71)
+|| +.+-.|.+|.+.+|+|++
T Consensus 1 llEPi~~~~I~~p~~~~g~v~~ 22 (85)
T smart00838 1 LLEPIMKVEVTVPEEYMGDVIG 22 (85)
T ss_pred CcCCEEEEEEEeCHHHHHHHHH
Confidence 466 788899999999998875
No 84
>PF15299 ALS2CR8: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Probab=40.05 E-value=19 Score=25.83 Aligned_cols=16 Identities=25% Similarity=0.656 Sum_probs=13.2
Q ss_pred CCCccceEEeeeEEEE
Q psy986 54 EEGQVPFMVLTKTVYR 69 (71)
Q Consensus 54 ~~~~vpF~~vGt~~~~ 69 (71)
...-+||++.|+.+|.
T Consensus 23 p~dgiPFi~~g~~~~~ 38 (225)
T PF15299_consen 23 PFDGIPFIIIGTKVYE 38 (225)
T ss_pred cCCCCCeEEeeceEEE
Confidence 3456899999999986
No 85
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=39.68 E-value=29 Score=25.56 Aligned_cols=27 Identities=22% Similarity=0.331 Sum_probs=20.6
Q ss_pred eeCCCccCcccccCchhHHHHHhhhce
Q psy986 10 QVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 10 ~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
.+.-.--|-+||++|..++.++..+..
T Consensus 49 ~I~tarPg~vIG~~G~~i~~l~~~L~k 75 (220)
T PTZ00084 49 IIRATRTREVLGDKGRRIRELTSLLQK 75 (220)
T ss_pred EEEECCCccEEcCCchHHHHHHHHHHH
Confidence 333444699999999999999877653
No 86
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=38.66 E-value=28 Score=28.38 Aligned_cols=29 Identities=28% Similarity=0.449 Sum_probs=24.0
Q ss_pred CccCcccccCchhHHHHHhhhceeEEeec
Q psy986 14 NLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 14 ~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
+=||-.||++|..|++|...++-=.|+|-
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI 305 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVI 305 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEE
Confidence 34899999999999999988866666664
No 87
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=37.81 E-value=9.4 Score=23.15 Aligned_cols=21 Identities=38% Similarity=0.659 Sum_probs=17.8
Q ss_pred Ccc-eeeeeeeeCCCccCcccc
Q psy986 1 MLE-YSEESLQVPRNLVGKVIG 21 (71)
Q Consensus 1 ~LE-f~e~~l~V~~~dvGKVIG 21 (71)
+|| +...+|.+|.+..|+|+.
T Consensus 2 LlEP~~~~~I~~p~~~~g~v~~ 23 (89)
T PF00679_consen 2 LLEPIMSVEISVPEEYLGKVIS 23 (89)
T ss_dssp EEEEEEEEEEEEEGGGHHHHHH
T ss_pred EECCEEEEEEEECHHHHHHHHH
Confidence 356 788899999999999885
No 88
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=37.42 E-value=27 Score=27.76 Aligned_cols=30 Identities=13% Similarity=0.236 Sum_probs=25.0
Q ss_pred CccCcccccCchhHHHHHhhhceeEEeecC
Q psy986 14 NLVGKVIGKNGRIIQEIVDKSGVVRVKIEG 43 (71)
Q Consensus 14 ~dvGKVIGk~Gr~ikaIr~~~~a~~iki~~ 43 (71)
+=||-.||++|..|++|...++-=.|+|-.
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~ 280 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIE 280 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEE
Confidence 348999999999999999888766777743
No 89
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=36.20 E-value=36 Score=24.53 Aligned_cols=28 Identities=25% Similarity=0.351 Sum_probs=21.5
Q ss_pred eeeCCCccCcccccCchhHHHHHhhhce
Q psy986 9 LQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 9 l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
|.+....-|-+||++|+.++.++..+..
T Consensus 66 I~I~~~~pg~vIG~~g~~i~~l~~~l~~ 93 (211)
T TIGR01009 66 VTIHTARPGIVIGKKGSEIEKLRKDLQK 93 (211)
T ss_pred EEEEeCCCcceeCCCchHHHHHHHHHHH
Confidence 4444555699999999999999877643
No 90
>KOG0119|consensus
Probab=33.57 E-value=32 Score=28.91 Aligned_cols=27 Identities=26% Similarity=0.639 Sum_probs=22.8
Q ss_pred CccCcccccCchhHHHHHhhhce-eEEe
Q psy986 14 NLVGKVIGKNGRIIQEIVDKSGV-VRVK 40 (71)
Q Consensus 14 ~dvGKVIGk~Gr~ikaIr~~~~a-~~ik 40 (71)
++||=+||.+|+|-|.+-...+| +.|+
T Consensus 153 NFvGLiiGPRG~TqK~lE~etgAKI~IR 180 (554)
T KOG0119|consen 153 NFVGLIIGPRGNTQKRLERETGAKIAIR 180 (554)
T ss_pred ceeEEEecCCccHHHHHHHHhCCeEEEe
Confidence 67999999999999999988886 2444
No 91
>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=33.47 E-value=36 Score=23.86 Aligned_cols=29 Identities=31% Similarity=0.522 Sum_probs=21.9
Q ss_pred eeeeCCCccCcccccCchhHHHHHhhhce
Q psy986 8 SLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 8 ~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
++.+--+--|.+|||+|.+++.|-...|=
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW 107 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGW 107 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCC
Confidence 34444556799999999999888766663
No 92
>KOG1423|consensus
Probab=32.09 E-value=49 Score=26.60 Aligned_cols=31 Identities=29% Similarity=0.536 Sum_probs=25.3
Q ss_pred eeeeeeeeCCCccCcc-cccCchhHHHHHhhh
Q psy986 4 YSEESLQVPRNLVGKV-IGKNGRIIQEIVDKS 34 (71)
Q Consensus 4 f~e~~l~V~~~dvGKV-IGk~Gr~ikaIr~~~ 34 (71)
|++-++.+|..--+|+ |||+|..|..|-+.+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a 358 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRA 358 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHH
Confidence 7788899999888885 799999998875443
No 93
>smart00059 FN2 Fibronectin type 2 domain. One of three types of internal repeat within the plasma protein, fibronectin. Also occurs in coagulation factor XII, 2 type IV collagenases, PDC-109, and cation-independent mannose-6-phosphate and secretory phospholipase A2 receptors. In fibronectin, PDC-109, and the collagenases, this domain contributes to collagen-binding function.
Probab=31.53 E-value=42 Score=19.32 Aligned_cols=17 Identities=24% Similarity=0.196 Sum_probs=13.0
Q ss_pred CCCCCccceEEeeeEEE
Q psy986 52 PREEGQVPFMVLTKTVY 68 (71)
Q Consensus 52 ~~~~~~vpF~~vGt~~~ 68 (71)
..+..+.||+|-|+.-+
T Consensus 4 ~g~~C~FPF~y~g~~Y~ 20 (49)
T smart00059 4 DGEPCVFPFIYNGKKYH 20 (49)
T ss_pred CCCceECCEEECCEEEc
Confidence 34667899999998654
No 94
>cd03709 lepA_C lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits significant homology to elongation factors (EFs) Tu and G. The function(s) of the proteins in this family are unknown. The N-terminal domain of LepA is homologous to a domain of similar size found in initiation factor 2 (IF2), and in EF-Tu and EF-G (factors required for translation in Escherichia coli). Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including S. cerevisiae GUF1) originated within the bacterial LepA family. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=31.13 E-value=18 Score=21.64 Aligned_cols=18 Identities=11% Similarity=0.534 Sum_probs=15.4
Q ss_pred eeeeeeeeCCCccCcccc
Q psy986 4 YSEESLQVPRNLVGKVIG 21 (71)
Q Consensus 4 f~e~~l~V~~~dvGKVIG 21 (71)
+.+-.|.||.+.+|.|++
T Consensus 3 i~~v~i~vP~e~~G~V~~ 20 (80)
T cd03709 3 FVKATIITPSEYLGAIME 20 (80)
T ss_pred EEEEEEEeCHHhhHHHHH
Confidence 456789999999999887
No 95
>cd00062 FN2 Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. Fibronectin is composed of 3 types of modules, FN1,FN2 and FN3. The collagen binding domain contains four FN1 and two FN2 repeats.
Probab=28.79 E-value=57 Score=18.60 Aligned_cols=16 Identities=19% Similarity=0.090 Sum_probs=12.4
Q ss_pred CCCCccceEEeeeEEE
Q psy986 53 REEGQVPFMVLTKTVY 68 (71)
Q Consensus 53 ~~~~~vpF~~vGt~~~ 68 (71)
.+..+.||+|-|+.-+
T Consensus 4 g~~C~FPF~y~g~~y~ 19 (48)
T cd00062 4 GAPCVFPFIYRGKWYH 19 (48)
T ss_pred CCccCCCEEECCEEEc
Confidence 4567899999998654
No 96
>KOG2279|consensus
Probab=27.89 E-value=47 Score=28.21 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=27.9
Q ss_pred eeeeeeeCCCccCcccccCchhHHHHHhhhce
Q psy986 5 SEESLQVPRNLVGKVIGKNGRIIQEIVDKSGV 36 (71)
Q Consensus 5 ~e~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a 36 (71)
.+.+..|+.+.+=.++||+|..|+.+++..++
T Consensus 68 v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~a 99 (608)
T KOG2279|consen 68 IEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGA 99 (608)
T ss_pred eeeeEeecccceeeeeccccCCcchhhccccc
Confidence 34577899999999999999999999988774
No 97
>KOG4369|consensus
Probab=24.97 E-value=34 Score=32.27 Aligned_cols=35 Identities=20% Similarity=0.311 Sum_probs=26.8
Q ss_pred eeeeeCCCccCcccccCchhHHHHHhhhceeEEeec
Q psy986 7 ESLQVPRNLVGKVIGKNGRIIQEIVDKSGVVRVKIE 42 (71)
Q Consensus 7 ~~l~V~~~dvGKVIGk~Gr~ikaIr~~~~a~~iki~ 42 (71)
..+++|-.-.-||||++|.+++|+|.--|+. +.++
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~-iele 1376 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGAL-IELE 1376 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceE-Eehh
Confidence 3466777778999999999999999766654 3443
No 98
>KOG4277|consensus
Probab=24.95 E-value=36 Score=27.56 Aligned_cols=45 Identities=22% Similarity=0.171 Sum_probs=30.3
Q ss_pred cCchhHHHHHhhhcee-EEeecCCCCCCCC--CCCCCCccceEEeeeE
Q psy986 22 KNGRIIQEIVDKSGVV-RVKIEGDNEPQPT--LPREEGQVPFMVLTKT 66 (71)
Q Consensus 22 k~Gr~ikaIr~~~~a~-~iki~~~~e~~~~--~~~~~~~vpF~~vGt~ 66 (71)
|+||.-.+|..-..-+ +.-|+.-+|+|.- .....+++-|+|+||-
T Consensus 116 RG~R~Kd~iieFAhR~a~aiI~pi~enQ~~fehlq~Rhq~ffVf~Gtg 163 (468)
T KOG4277|consen 116 RGGREKDAIIEFAHRCAAAIIEPINENQIEFEHLQARHQPFFVFFGTG 163 (468)
T ss_pred CCCccHHHHHHHHHhcccceeeecChhHHHHHHHhhccCceEEEEeCC
Confidence 5688888888766544 3334555665533 3456678999999985
No 99
>cd04096 eEF2_snRNP_like_C eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=24.36 E-value=30 Score=20.31 Aligned_cols=18 Identities=28% Similarity=0.410 Sum_probs=15.3
Q ss_pred eeeeeeeeCCCccCcccc
Q psy986 4 YSEESLQVPRNLVGKVIG 21 (71)
Q Consensus 4 f~e~~l~V~~~dvGKVIG 21 (71)
+.+-+|.+|.+.+|+|++
T Consensus 3 i~~~~I~~p~~~~g~V~~ 20 (80)
T cd04096 3 IYLVEIQCPEDALGKVYS 20 (80)
T ss_pred EEEEEEEEcHHHhhHHHH
Confidence 466789999999999886
No 100
>KOG3273|consensus
Probab=23.69 E-value=17 Score=27.64 Aligned_cols=17 Identities=29% Similarity=0.585 Sum_probs=14.9
Q ss_pred ccCcccccCchhHHHHH
Q psy986 15 LVGKVIGKNGRIIQEIV 31 (71)
Q Consensus 15 dvGKVIGk~Gr~ikaIr 31 (71)
-+||++||+|++--+|-
T Consensus 179 AIGRiaGk~GkTkfaIE 195 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIE 195 (252)
T ss_pred HHHHhhcCCCcceeeee
Confidence 48999999999988875
No 101
>KOG3387|consensus
Probab=21.30 E-value=49 Score=23.03 Aligned_cols=14 Identities=21% Similarity=0.506 Sum_probs=11.5
Q ss_pred CCCCCccceEEeee
Q psy986 52 PREEGQVPFMVLTK 65 (71)
Q Consensus 52 ~~~~~~vpF~~vGt 65 (71)
-|++..|||+||=.
T Consensus 72 LcedknVp~v~Vps 85 (131)
T KOG3387|consen 72 LCEDKNVPYVFVPS 85 (131)
T ss_pred HhhccCCceEEeec
Confidence 47888999999854
No 102
>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.
Probab=20.53 E-value=73 Score=18.83 Aligned_cols=11 Identities=9% Similarity=0.522 Sum_probs=8.3
Q ss_pred CccceEEeeeE
Q psy986 56 GQVPFMVLTKT 66 (71)
Q Consensus 56 ~~vpF~~vGt~ 66 (71)
..+|.+++||+
T Consensus 107 ~~~piilv~nK 117 (119)
T PF08477_consen 107 KNIPIILVGNK 117 (119)
T ss_dssp SCSEEEEEEE-
T ss_pred CCCCEEEEEec
Confidence 34899999987
No 103
>cd04097 mtEFG1_C mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (desig
Probab=20.49 E-value=30 Score=20.29 Aligned_cols=18 Identities=28% Similarity=0.547 Sum_probs=14.9
Q ss_pred eeeeeeeeCCCccCcccc
Q psy986 4 YSEESLQVPRNLVGKVIG 21 (71)
Q Consensus 4 f~e~~l~V~~~dvGKVIG 21 (71)
+.+-+|.+|.+.+|+|++
T Consensus 3 i~~~~I~~p~~~~g~v~~ 20 (78)
T cd04097 3 IMKVEVTAPTEFQGNVIG 20 (78)
T ss_pred EEEEEEEecHHHHHHHHH
Confidence 456789999999998875
No 104
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=20.09 E-value=20 Score=22.38 Aligned_cols=51 Identities=18% Similarity=0.182 Sum_probs=29.7
Q ss_pred CccCcccccCchhHHHHHhhhcee-EEeecCCCCCC--CC--CCCCCCccceEEeeeE
Q psy986 14 NLVGKVIGKNGRIIQEIVDKSGVV-RVKIEGDNEPQ--PT--LPREEGQVPFMVLTKT 66 (71)
Q Consensus 14 ~dvGKVIGk~Gr~ikaIr~~~~a~-~iki~~~~e~~--~~--~~~~~~~vpF~~vGt~ 66 (71)
+..||++-=.-.+.++|+. +-+ -+=+..|-.+. .. .-++...|||++.+|+
T Consensus 4 ~~~GKlv~G~~~vlkaIk~--gkakLViiA~Da~~~~~k~i~~~c~~~~Vpv~~~~t~ 59 (82)
T PRK13601 4 DCPSKRVVGAKQTLKAITN--CNVLQVYIAKDAEEHVTKKIKELCEEKSIKIVYIDTM 59 (82)
T ss_pred ccCccEEEchHHHHHHHHc--CCeeEEEEeCCCCHHHHHHHHHHHHhCCCCEEEeCCH
Confidence 4578887755678899974 333 33333222211 11 1245678999999875
Done!