Query psy17938
Match_columns 307
No_of_seqs 144 out of 986
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 18:09:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17938.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17938hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14910 MMS22L_N: S-phase gen 100.0 4.7E-43 1E-47 359.1 5.9 148 141-290 366-525 (704)
2 COG0092 RpsC Ribosomal protein 100.0 1.9E-39 4.1E-44 297.7 14.2 139 2-154 9-166 (233)
3 PTZ00084 40S ribosomal protein 100.0 2.7E-39 5.9E-44 295.7 14.7 146 1-159 7-164 (220)
4 TIGR01008 rpsC_E_A ribosomal p 100.0 2E-38 4.4E-43 285.5 15.3 139 1-153 1-151 (195)
5 PRK04191 rps3p 30S ribosomal p 100.0 1E-36 2.3E-41 276.3 14.6 139 1-153 3-153 (207)
6 CHL00048 rps3 ribosomal protei 100.0 6.5E-33 1.4E-37 252.8 15.1 142 5-158 33-187 (214)
7 TIGR01009 rpsC_bact ribosomal 100.0 1.6E-31 3.5E-36 243.1 14.1 135 5-154 29-176 (211)
8 PRK00310 rpsC 30S ribosomal pr 100.0 1.3E-30 2.8E-35 240.3 14.0 133 6-153 30-175 (232)
9 KOG3181|consensus 99.9 1.4E-23 3.1E-28 188.8 10.3 127 2-140 8-142 (244)
10 cd02413 40S_S3_KH K homology R 99.8 1.5E-20 3.3E-25 148.1 10.7 80 9-88 1-80 (81)
11 cd02411 archeal_30S_S3_KH K ho 99.8 3.9E-20 8.4E-25 146.0 10.0 85 1-87 1-85 (85)
12 cd02412 30S_S3_KH K homology R 99.7 3.2E-17 7E-22 135.1 9.7 82 5-88 28-109 (109)
13 PF07650 KH_2: KH domain syndr 99.6 8.3E-15 1.8E-19 112.7 7.2 77 14-90 1-78 (78)
14 cd02409 KH-II KH-II (K homolo 98.9 1.3E-08 2.8E-13 74.0 8.0 65 16-82 1-67 (68)
15 PF00189 Ribosomal_S3_C: Ribos 97.9 6.1E-06 1.3E-10 65.3 2.0 44 98-153 1-58 (85)
16 smart00322 KH K homology RNA-b 97.5 8.3E-05 1.8E-09 52.9 3.4 67 38-104 3-69 (69)
17 cd02414 jag_KH jag_K homology 97.0 0.0034 7.3E-08 48.6 7.1 66 17-82 2-71 (77)
18 PF13083 KH_4: KH domain; PDB: 96.8 0.0018 3.9E-08 49.3 3.9 69 13-81 2-72 (73)
19 PRK01064 hypothetical protein; 95.9 0.11 2.3E-06 41.2 9.6 54 31-84 21-76 (78)
20 COG1847 Jag Predicted RNA-bind 95.0 0.085 1.9E-06 48.9 7.3 127 9-136 61-205 (208)
21 cd02134 NusA_KH NusA_K homolog 94.6 0.072 1.6E-06 39.6 4.8 53 16-68 2-55 (61)
22 PRK02821 hypothetical protein; 94.4 0.57 1.2E-05 37.0 9.6 52 30-84 21-74 (77)
23 COG1159 Era GTPase [General fu 93.7 0.44 9.6E-06 46.4 9.3 77 4-83 189-278 (298)
24 PRK08406 transcription elongat 93.4 0.095 2.1E-06 45.4 4.0 61 13-73 72-134 (140)
25 cd02410 archeal_CPSF_KH The ar 93.2 0.27 5.9E-06 43.3 6.4 85 13-111 52-137 (145)
26 PRK00468 hypothetical protein; 92.6 1.4 3E-05 34.6 9.0 52 31-82 21-74 (75)
27 TIGR00436 era GTP-binding prot 91.3 1 2.2E-05 41.8 8.3 74 4-82 181-267 (270)
28 PRK15494 era GTPase Era; Provi 91.1 1.7 3.6E-05 42.3 9.8 78 4-84 233-323 (339)
29 COG1837 Predicted RNA-binding 90.7 2.4 5.1E-05 33.7 8.5 52 31-82 19-74 (76)
30 PRK00089 era GTPase Era; Revie 90.5 2 4.4E-05 40.0 9.4 80 5-87 189-279 (292)
31 COG1782 Predicted metal-depend 86.6 5.2 0.00011 42.1 10.0 59 24-95 87-145 (637)
32 TIGR01952 nusA_arch NusA famil 85.3 1.1 2.3E-05 39.2 3.8 60 14-73 74-135 (141)
33 TIGR03675 arCOG00543 arCOG0054 83.0 9.2 0.0002 40.7 10.3 84 14-111 70-154 (630)
34 cd02393 PNPase_KH Polynucleoti 77.1 2.3 4.9E-05 31.5 2.5 28 39-66 3-30 (61)
35 PRK06418 transcription elongat 74.5 5.6 0.00012 35.8 4.8 56 12-68 32-90 (166)
36 PF13014 KH_3: KH domain 72.7 2.8 6E-05 28.6 1.9 16 50-65 3-18 (43)
37 cd00105 KH-I K homology RNA-bi 65.1 7 0.00015 27.8 2.8 27 41-67 3-29 (64)
38 cd02396 PCBP_like_KH K homolog 63.4 6.2 0.00013 29.1 2.3 27 40-66 2-28 (65)
39 PF00013 KH_1: KH domain syndr 62.4 3.2 7E-05 29.8 0.6 28 40-67 2-29 (60)
40 TIGR01953 NusA transcription t 61.0 17 0.00037 36.0 5.5 60 15-81 277-337 (341)
41 PRK12328 nusA transcription el 60.6 20 0.00043 36.2 5.9 65 15-86 285-349 (374)
42 PRK09202 nusA transcription el 60.6 17 0.00037 37.5 5.6 50 15-64 279-328 (470)
43 cd02394 vigilin_like_KH K homo 58.3 7.8 0.00017 27.9 2.0 27 41-67 3-29 (62)
44 COG4604 CeuD ABC-type enteroch 57.0 43 0.00092 32.0 7.0 71 38-110 18-89 (252)
45 PRK12327 nusA transcription el 54.7 23 0.00049 35.5 5.2 60 15-81 279-339 (362)
46 COG0195 NusA Transcription elo 52.9 33 0.00072 31.4 5.6 63 14-83 117-180 (190)
47 PF14480 DNA_pol3_a_NI: DNA po 48.5 82 0.0018 23.5 6.4 57 20-82 18-74 (76)
48 PRK08406 transcription elongat 48.2 27 0.00058 30.3 4.0 43 23-67 19-61 (140)
49 KOG2191|consensus 46.2 30 0.00066 34.8 4.5 55 10-67 104-161 (402)
50 PF03780 Asp23: Asp23 family; 46.0 49 0.0011 26.2 5.0 58 28-85 47-107 (108)
51 TIGR03665 arCOG04150 arCOG0415 44.6 15 0.00032 32.6 2.0 63 44-113 4-72 (172)
52 PF13184 KH_5: NusA-like KH do 42.8 19 0.00042 27.6 2.1 31 38-68 3-38 (69)
53 PRK12329 nusA transcription el 42.4 39 0.00086 34.9 4.8 48 15-62 311-359 (449)
54 TIGR01952 nusA_arch NusA famil 41.9 31 0.00067 30.2 3.4 43 22-65 18-60 (141)
55 TIGR03112 6_pyr_pter_rel 6-pyr 41.7 1E+02 0.0022 25.8 6.4 61 39-108 28-91 (113)
56 COG1534 Predicted RNA-binding 39.2 85 0.0018 26.1 5.4 52 45-103 15-69 (97)
57 COG1855 ATPase (PilT family) [ 38.4 46 0.001 35.1 4.6 54 8-65 459-513 (604)
58 PRK13764 ATPase; Provisional 37.3 60 0.0013 34.7 5.4 54 9-65 455-508 (602)
59 COG0195 NusA Transcription elo 37.0 68 0.0015 29.4 5.0 54 15-68 48-106 (190)
60 PF13653 GDPD_2: Glycerophosph 35.3 25 0.00053 23.2 1.4 17 106-122 10-26 (30)
61 TIGR01953 NusA transcription t 35.2 1.6E+02 0.0034 29.3 7.6 62 13-80 200-270 (341)
62 COG0779 Uncharacterized protei 34.2 3.4E+02 0.0073 24.2 9.0 87 11-112 6-97 (153)
63 KOG2192|consensus 33.4 35 0.00076 33.5 2.7 34 38-71 48-81 (390)
64 COG1302 Uncharacterized protei 32.9 2.8E+02 0.006 24.2 7.8 65 19-89 44-118 (131)
65 PF09462 Mus7: Mus7/MMS22 fami 32.6 1.3E+02 0.0028 32.0 6.9 115 159-290 71-201 (614)
66 PRK12327 nusA transcription el 32.3 1.6E+02 0.0034 29.7 7.1 56 13-68 202-266 (362)
67 PRK09509 fieF ferrous iron eff 31.8 1.5E+02 0.0033 28.1 6.7 72 11-84 214-286 (299)
68 TIGR00253 RNA_bind_YhbY putati 31.3 1.3E+02 0.0028 24.7 5.3 52 45-103 14-68 (95)
69 PRK12328 nusA transcription el 30.5 1.7E+02 0.0037 29.7 7.1 56 13-68 208-272 (374)
70 TIGR03675 arCOG00543 arCOG0054 30.2 77 0.0017 33.9 4.8 53 14-71 3-56 (630)
71 PF00724 Oxidored_FMN: NADH:fl 30.0 34 0.00074 33.3 2.0 57 107-165 153-215 (341)
72 PRK13763 putative RNA-processi 29.8 56 0.0012 29.2 3.3 67 40-113 5-78 (180)
73 PRK13763 putative RNA-processi 28.4 70 0.0015 28.6 3.6 59 48-112 105-163 (180)
74 PLN02411 12-oxophytodienoate r 28.0 33 0.00072 34.3 1.6 56 108-165 170-231 (391)
75 KOG2192|consensus 25.9 27 0.00059 34.3 0.6 39 35-73 120-158 (390)
76 COG1902 NemA NADH:flavin oxido 25.4 46 0.001 33.3 2.1 57 107-165 153-215 (363)
77 COG2344 AT-rich DNA-binding pr 24.7 3.5E+02 0.0076 25.5 7.4 87 13-121 69-175 (211)
78 PRK05090 hypothetical protein; 24.6 3.9E+02 0.0085 21.9 7.0 40 56-95 44-91 (95)
79 PRK10343 RNA-binding protein Y 24.2 1.9E+02 0.0041 23.8 5.1 52 45-103 16-70 (97)
80 KOG1423|consensus 24.1 2.9E+02 0.0062 28.0 7.2 42 38-82 326-374 (379)
81 COG1942 Uncharacterized protei 24.0 1.2E+02 0.0026 23.5 3.7 47 42-88 4-50 (69)
82 PRK10605 N-ethylmaleimide redu 23.7 48 0.001 32.8 1.8 57 107-165 163-225 (362)
83 COG1094 Predicted RNA-binding 23.4 1.2E+02 0.0026 28.2 4.1 58 49-112 113-170 (194)
84 PF01545 Cation_efflux: Cation 22.2 2.5E+02 0.0054 25.7 6.1 64 9-72 204-269 (284)
85 PF14698 ASL_C2: Argininosucci 22.0 70 0.0015 24.4 2.0 22 90-114 2-23 (70)
86 PRK12329 nusA transcription el 21.4 2.8E+02 0.006 28.9 6.7 61 14-80 228-304 (449)
87 cd00554 MECDP_synthase MECDP_s 21.1 2.3E+02 0.0051 25.2 5.4 42 38-84 91-132 (153)
88 PF14552 Tautomerase_2: Tautom 20.8 83 0.0018 24.9 2.3 54 33-87 23-76 (82)
89 KOG1676|consensus 20.8 63 0.0014 34.6 2.0 27 39-65 140-166 (600)
90 COG1782 Predicted metal-depend 20.3 1.2E+02 0.0026 32.4 3.9 56 13-73 8-64 (637)
91 PRK09202 nusA transcription el 20.3 3E+02 0.0065 28.6 6.8 62 13-80 202-272 (470)
92 KOG1676|consensus 20.1 78 0.0017 33.9 2.5 27 39-65 231-257 (600)
No 1
>PF14910 MMS22L_N: S-phase genomic integrity recombination mediator, N-terminal
Probab=100.00 E-value=4.7e-43 Score=359.12 Aligned_cols=148 Identities=28% Similarity=0.362 Sum_probs=138.9
Q ss_pred ecCC--CcccceEeeehhHHHHhhcCCCCccchhhhhhhhhhccCCCccccccccccccccccccccHHHHHHHHhhccc
Q psy17938 141 HQCP--GCRELRIILTFLDSIVSLKEVCKPDIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMIS 218 (307)
Q Consensus 141 ar~e--~~~e~~i~l~~l~~i~~~w~~~~~~~v~~LWeyfsK~Lns~F~~~~~~l~~~~~~~~~~~s~l~~~~~c~~~~~ 218 (307)
+.+. .|+++||.|.++.|+.++|+| |+++|++|||||||||||||++||+|++++.+++|||.+++|.+++||++.+
T Consensus 366 ~~q~~~~EeqlRm~L~c~l~L~~~W~p-n~~iv~~LWEYfsK~LNssF~v~~~~l~~L~~i~kS~~~~le~~~~~c~~~~ 444 (704)
T PF14910_consen 366 NSQDGILEEQLRMYLHCCLPLCQWWEP-NTDIVTILWEYFSKNLNSSFSVPWLGLKGLACICKSPLSMLEQAKSCCSPQQ 444 (704)
T ss_pred ccCCcccHHHHHHHHHHHHHHHhhcCC-ChHHHHHHHHHHHhhcCCCCccCccchhhhhhhcCCHHHHHHHHHHHhCCCc
Confidence 4444 899999999999999888888 9999999999999999999999999999999999999999999999999999
Q ss_pred cchhccCCchhHHHHHHHHHHHHhhc--ccCcccccccccc-cCCCCc-------hhhHHHHHHHHHHHHHHhccccccc
Q psy17938 219 STRIQKNEENSYTLFLRMLGIYLLKY--NHEQRIWNQVKGL-KSPFTP-------AVGYYYYYCGQILLSVYTASFHFNC 288 (307)
Q Consensus 219 ~~~~~~~~~~Sy~~FL~iLa~~l~~~--~~~~~~w~qikgR-yskf~~-------e~gl~nf~~lfl~la~~~~~~~~~~ 288 (307)
.+++++ ++|||+|||++||+|||+. +++++||+||||| |||||| |+|||||++||||||.+||.-...+
T Consensus 445 ~~~L~~-~~sSf~iFL~lLa~~lk~~~~~~~~~~wkQiKGRIYSKF~~kKm~ELtE~GL~Nf~~LFLtLa~~ad~eDvas 523 (704)
T PF14910_consen 445 HDDLYK-SESSFHIFLRLLAKMLKKLYSNSGPHPWKQIKGRIYSKFSQKKMEELTEVGLYNFISLFLTLASVADFEDVAS 523 (704)
T ss_pred cccccc-ccCcHHHHHHHHHHHHHHHHhcCCCChHHHhcCeehhhcCHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence 888998 9999999999999999973 5789999999999 999999 9999999999999999999888777
Q ss_pred hh
Q psy17938 289 RY 290 (307)
Q Consensus 289 ~~ 290 (307)
|.
T Consensus 524 r~ 525 (704)
T PF14910_consen 524 RV 525 (704)
T ss_pred HH
Confidence 64
No 2
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-39 Score=297.68 Aligned_cols=139 Identities=32% Similarity=0.386 Sum_probs=133.7
Q ss_pred cccchhhh------hHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCC
Q psy17938 2 SAKFVADG------VFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFAD 75 (307)
Q Consensus 2 ~kkfI~d~------~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~ 75 (307)
++.|.+++ ..|.+|||||.+++.+||||+|+|+|+|++++|+|||+|||++||++|++|++|++.|+++++.+
T Consensus 9 srwfa~~~~~~~~l~ed~kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~- 87 (233)
T COG0092 9 SRWFANKKEYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE- 87 (233)
T ss_pred hhhccccccchHHHHHHHHHHHHHHHHHHhCCcceEEEEecCCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCC-
Confidence 57899999 99999999999999999999999999999999999999999999999999999999999999864
Q ss_pred CeEEEEEEEecCCCcCHHHHHHHHHHHHHcChhhhhhh--------hcCCceeEEeeeccceeeEEEeeeeee-----ec
Q psy17938 76 GAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYP--------AIDAQYCSLLAQFGWSILILVVAVGTL-----HQ 142 (307)
Q Consensus 76 ~kI~I~I~eVknP~l~A~lLAe~IA~QLE~Rv~FRRAM--------kaGAkGIKI~~~~~~~~~~~~~~sgrl-----ar 142 (307)
++.|+|.||++|++||+++|++||+|||+|++||||| ++|||||||+ ||||| ||
T Consensus 88 -~v~I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGAkGiki~------------vSGRL~GaeiAR 154 (233)
T COG0092 88 -NVQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQ------------VSGRLGGAEIAR 154 (233)
T ss_pred -CceEEEEEcCCCCcCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcCCceeEEE------------EecccchHHHHh
Confidence 7888899999999999999999999999999999975 8999999999 99999 99
Q ss_pred CCCcccceEeee
Q psy17938 143 CPGCRELRIILT 154 (307)
Q Consensus 143 ~e~~~e~~i~l~ 154 (307)
+|.|.|++++|-
T Consensus 155 ~E~y~eG~vplh 166 (233)
T COG0092 155 TEKYREGRVPLH 166 (233)
T ss_pred HHHHhcceeEcc
Confidence 999999999993
No 3
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=100.00 E-value=2.7e-39 Score=295.66 Aligned_cols=146 Identities=61% Similarity=0.926 Sum_probs=138.9
Q ss_pred CcccchhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q psy17938 1 MSAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIEL 80 (307)
Q Consensus 1 ~~kkfI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I 80 (307)
++|+||+||+++++|||||++++.+||||+|+|+|+++.++|+|||++||++||++|+++++|++.|++.+++++++|+|
T Consensus 7 ~~k~fi~~~~~~~~~re~l~k~~~~agis~ieI~Rt~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~~~~~~i~i 86 (220)
T PTZ00084 7 KKRKFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEGKVEL 86 (220)
T ss_pred hhhHHHHcchhhHHHHHHHHHHHHHCCcceEEEEEcCCcEEEEEEECCCccEEcCCchHHHHHHHHHHHHhCCCCceEEE
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999988899999
Q ss_pred EEEEecCCCcCHHHHHHHHHHHHHcChhhhhhh--------hcCCceeEEeeeccceeeEEEeeeeee----ecCCCccc
Q psy17938 81 YAEKVATRGLCAIAQAESLRYKLIGGLAVRRYP--------AIDAQYCSLLAQFGWSILILVVAVGTL----HQCPGCRE 148 (307)
Q Consensus 81 ~I~eVknP~l~A~lLAe~IA~QLE~Rv~FRRAM--------kaGAkGIKI~~~~~~~~~~~~~~sgrl----ar~e~~~e 148 (307)
++.||++|+++|.++|++||+|||+|+|||||| ++||+||||+ +|||| ||+|.+.|
T Consensus 87 ~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGakGikI~------------iSGRL~~EiARtE~~~e 154 (220)
T PTZ00084 87 FAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVI------------VSGKLRAQRAKSMKFRD 154 (220)
T ss_pred EEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCCceEEEE------------EccchhhHHHHhhHhhc
Confidence 999999999999999999999999999999975 8999999999 99999 99999999
Q ss_pred ceEeeehhHHH
Q psy17938 149 LRIILTFLDSI 159 (307)
Q Consensus 149 ~~i~l~~l~~i 159 (307)
+|| |--++|.
T Consensus 155 GrV-l~Tg~~~ 164 (220)
T PTZ00084 155 GYM-ISTGQPK 164 (220)
T ss_pred cEE-EecCchH
Confidence 999 7443333
No 4
>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=100.00 E-value=2e-38 Score=285.47 Aligned_cols=139 Identities=39% Similarity=0.539 Sum_probs=133.3
Q ss_pred CcccchhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q psy17938 1 MSAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIEL 80 (307)
Q Consensus 1 ~~kkfI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I 80 (307)
++|+||+||+++.+|||||.+++.+||||+|||+|+++.++|+|||++||.+||++|+++++|++.|++.++. .+++|
T Consensus 1 ~~kkfi~~~~~~~~ire~l~k~~~~agis~ieI~r~~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~--~~~~I 78 (195)
T TIGR01008 1 IERKFVAEGLKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGL--ENPQI 78 (195)
T ss_pred CcEehHhcchHHHHHHHHHHHHHHhCCeeEEEEEEcCCcEEEEEEECCCceEECCCchHHHHHHHHHHHHhCC--CceEE
Confidence 5799999999999999999999999999999999999999999999999999999999999999999999975 36889
Q ss_pred EEEEecCCCcCHHHHHHHHHHHHHcChhhhhhh--------hcCCceeEEeeeccceeeEEEeeeeee----ecCCCccc
Q psy17938 81 YAEKVATRGLCAIAQAESLRYKLIGGLAVRRYP--------AIDAQYCSLLAQFGWSILILVVAVGTL----HQCPGCRE 148 (307)
Q Consensus 81 ~I~eVknP~l~A~lLAe~IA~QLE~Rv~FRRAM--------kaGAkGIKI~~~~~~~~~~~~~~sgrl----ar~e~~~e 148 (307)
++.||++|+++|.++|++||+|||+|+|||||| ++||+||||+ +|||| ||+|.|.|
T Consensus 79 ~v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGakGikI~------------iSGRL~GeiARtE~~~e 146 (195)
T TIGR01008 79 DVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVT------------ISGKLTGERARTEKFAA 146 (195)
T ss_pred EEEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCceEEEE------------Ecccccchhhhhhheec
Confidence 999999999999999999999999999999975 8999999999 99999 99999999
Q ss_pred ceEee
Q psy17938 149 LRIIL 153 (307)
Q Consensus 149 ~~i~l 153 (307)
++++.
T Consensus 147 G~v~~ 151 (195)
T TIGR01008 147 GYLKH 151 (195)
T ss_pred cEEec
Confidence 99944
No 5
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=100.00 E-value=1e-36 Score=276.27 Aligned_cols=139 Identities=32% Similarity=0.453 Sum_probs=132.5
Q ss_pred CcccchhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q psy17938 1 MSAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIEL 80 (307)
Q Consensus 1 ~~kkfI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I 80 (307)
++|+||+||+.+.+||+||.+.+.+|||++|+|+|+++.++|+||+++||++||++|+++++|++.|++.++.. ++.|
T Consensus 3 ~~~~fi~~~~~~~~irefi~~~~~~AgIs~IeI~Rt~~~i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~~~~--~v~I 80 (207)
T PRK04191 3 IEKKFVEEGLKKVMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGLE--NPQI 80 (207)
T ss_pred hhhHHHHcchHHHHHHHHHHhhhhhcceeEEEEEEcCCcEEEEEEECCCCeEECCCchhHHHHHHHHHHHhCCC--ceeE
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999653 5788
Q ss_pred EEEEecCCCcCHHHHHHHHHHHHHcChhhhhhh--------hcCCceeEEeeeccceeeEEEeeeeee----ecCCCccc
Q psy17938 81 YAEKVATRGLCAIAQAESLRYKLIGGLAVRRYP--------AIDAQYCSLLAQFGWSILILVVAVGTL----HQCPGCRE 148 (307)
Q Consensus 81 ~I~eVknP~l~A~lLAe~IA~QLE~Rv~FRRAM--------kaGAkGIKI~~~~~~~~~~~~~~sgrl----ar~e~~~e 148 (307)
++.||++|+++|.++|++||+|||+|++||||| ++||+||||+ +|||| ||+|.|+|
T Consensus 81 ~v~ev~~p~~~a~~vA~~ia~qLe~r~~fRra~k~~i~~~~~agakGiki~------------iSGrL~Ge~AR~e~~~e 148 (207)
T PRK04191 81 DVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVEII------------ISGKLTGERARTEKFTE 148 (207)
T ss_pred EEEEEeCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCeeEEEE------------EccccchHHHHhhhhhc
Confidence 899999999999999999999999999999964 8999999999 99999 99999999
Q ss_pred ceEee
Q psy17938 149 LRIIL 153 (307)
Q Consensus 149 ~~i~l 153 (307)
+|++.
T Consensus 149 G~v~~ 153 (207)
T PRK04191 149 GYIKK 153 (207)
T ss_pred ceEec
Confidence 99954
No 6
>CHL00048 rps3 ribosomal protein S3
Probab=100.00 E-value=6.5e-33 Score=252.77 Aligned_cols=142 Identities=20% Similarity=0.223 Sum_probs=133.3
Q ss_pred chhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q psy17938 5 FVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK 84 (307)
Q Consensus 5 fI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~e 84 (307)
+.+|.+++..|+|||.+++.+|||++|+|+|+++.++|+||+++||.+||++|+++++|++.|++.++..+++++|++.|
T Consensus 33 l~eD~~ir~~i~~~l~~~~~~agis~i~I~r~~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~k~~~~~~~~i~I~v~e 112 (214)
T CHL00048 33 LQEDKKIRDCIKNYVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLLIERKGRGIEELQINLQKELNSVNRKLNINITE 112 (214)
T ss_pred HHHHHHHHHHHHHHHHhhhhhCCeeEEEEEEcCCeEEEEEEECCCceEECCCcHhHHHHHHHHHHHhCCCCceEEEEEEE
Confidence 46889999999999999999999999999999999999999999999999999999999999999998777789999999
Q ss_pred ecCCCcCHHHHHHHHHHHHHcChhhhhhh--------hcCCceeEEeeeccceeeEEEeeeeee-----ecCCCcccceE
Q psy17938 85 VATRGLCAIAQAESLRYKLIGGLAVRRYP--------AIDAQYCSLLAQFGWSILILVVAVGTL-----HQCPGCRELRI 151 (307)
Q Consensus 85 VknP~l~A~lLAe~IA~QLE~Rv~FRRAM--------kaGAkGIKI~~~~~~~~~~~~~~sgrl-----ar~e~~~e~~i 151 (307)
|++|+++|.++|++||+|||+|++||||| ++||+||||+ +|||| ||+|.++++++
T Consensus 113 v~~p~~~A~~iA~~ia~~Le~r~~fRra~~~~i~~~~~~ga~GikI~------------iSGRL~Gae~AR~e~~~~G~v 180 (214)
T CHL00048 113 VKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQ------------ISGRLNGAEIARVEWIREGRV 180 (214)
T ss_pred ecCCCcCHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHhCCcEEEEE------------EecccCccchheEEEEeccee
Confidence 99999999999999999999999999975 8899999999 99999 99999999999
Q ss_pred eeehhHH
Q psy17938 152 ILTFLDS 158 (307)
Q Consensus 152 ~l~~l~~ 158 (307)
+|--|+.
T Consensus 181 pl~tl~a 187 (214)
T CHL00048 181 PLQTLRA 187 (214)
T ss_pred ECCcchh
Confidence 8744443
No 7
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=99.97 E-value=1.6e-31 Score=243.14 Aligned_cols=135 Identities=22% Similarity=0.266 Sum_probs=126.4
Q ss_pred chhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q psy17938 5 FVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK 84 (307)
Q Consensus 5 fI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~e 84 (307)
|-+-=..|.+|||||.+++.+|||++|||+|+++.++|+||+++||.+||++|+++++|++.|++.++ .+++|++.+
T Consensus 29 Y~~~l~eD~~IR~~i~k~~~~agis~IeI~rt~~~i~I~I~~~~pg~vIG~~g~~i~~l~~~l~~~~~---~~~~i~v~~ 105 (211)
T TIGR01009 29 YAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKKGSEIEKLRKDLQKLTG---KEVQINIAE 105 (211)
T ss_pred hHHHHHHHHHHHHHHHHHhhhCCcceEEEEEcCCceEEEEEeCCCcceeCCCchHHHHHHHHHHHHhC---CceEEEEEE
Confidence 33444679999999999999999999999999999999999999999999999999999999999996 478999999
Q ss_pred ecCCCcCHHHHHHHHHHHHHcChhhhhh--------hhcCCceeEEeeeccceeeEEEeeeeee-----ecCCCcccceE
Q psy17938 85 VATRGLCAIAQAESLRYKLIGGLAVRRY--------PAIDAQYCSLLAQFGWSILILVVAVGTL-----HQCPGCRELRI 151 (307)
Q Consensus 85 VknP~l~A~lLAe~IA~QLE~Rv~FRRA--------MkaGAkGIKI~~~~~~~~~~~~~~sgrl-----ar~e~~~e~~i 151 (307)
|++|+++|.++|++||+|||+|++|||| |++||+||||+ +|||| ||+|.+.++++
T Consensus 106 v~~p~~~a~~iA~~ia~~Le~~~~fRr~~~~~i~~~~~~g~~GikI~------------isGRl~g~e~Ar~e~~~~G~v 173 (211)
T TIGR01009 106 VKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQ------------VSGRLGGAEIARTEWYKEGRV 173 (211)
T ss_pred ecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCCcEEEEE------------EecccCchhhhheeeeeeCcc
Confidence 9999999999999999999999999996 48999999999 99999 99999999999
Q ss_pred eee
Q psy17938 152 ILT 154 (307)
Q Consensus 152 ~l~ 154 (307)
+|-
T Consensus 174 pl~ 176 (211)
T TIGR01009 174 PLH 176 (211)
T ss_pred Ccc
Confidence 763
No 8
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=99.97 E-value=1.3e-30 Score=240.26 Aligned_cols=133 Identities=25% Similarity=0.262 Sum_probs=125.5
Q ss_pred hhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEe
Q psy17938 6 VADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKV 85 (307)
Q Consensus 6 I~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eV 85 (307)
-+-=..|.+|||||.+++.+|||++|+|+|+++.++|+||+++||++||++|+++++|++.|++.++ .+++|++.||
T Consensus 30 ~~~L~eD~~IRe~i~k~~~~agis~IeI~R~~~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~~~~~---~~~~i~v~ev 106 (232)
T PRK00310 30 ADLLHEDLKIRKFLKKKLKKAGVSRIEIERPAKRVRVTIHTARPGIVIGKKGAEIEKLRKELEKLTG---KPVQINIVEV 106 (232)
T ss_pred HHHHHHHHHHHHHHHHhHhhCceeEEEEEEcCCeEEEEEEECCCccccCCCcHHHHHHHHHHHHHhC---CceEEEEEEe
Confidence 3344678999999999999999999999999999999999999999999999999999999999995 4788999999
Q ss_pred cCCCcCHHHHHHHHHHHHHcChhhhhhh--------hcCCceeEEeeeccceeeEEEeeeeee-----ecCCCcccceEe
Q psy17938 86 ATRGLCAIAQAESLRYKLIGGLAVRRYP--------AIDAQYCSLLAQFGWSILILVVAVGTL-----HQCPGCRELRII 152 (307)
Q Consensus 86 knP~l~A~lLAe~IA~QLE~Rv~FRRAM--------kaGAkGIKI~~~~~~~~~~~~~~sgrl-----ar~e~~~e~~i~ 152 (307)
++|+++|.++|++||+|||+|++||||| ++||+||||+ +|||| ||+|.+.+++|+
T Consensus 107 ~~p~~~a~~iA~~ia~~Le~r~~fRr~~~~~i~~~~~~g~~GikI~------------isGRl~g~e~Ar~e~~~~G~vp 174 (232)
T PRK00310 107 KKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKVQ------------VSGRLGGAEIARTEWYREGRVP 174 (232)
T ss_pred cCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCcEEEEE------------EcCCCCcceeeeEEEeeecccc
Confidence 9999999999999999999999999964 8899999999 99999 999999999998
Q ss_pred e
Q psy17938 153 L 153 (307)
Q Consensus 153 l 153 (307)
|
T Consensus 175 l 175 (232)
T PRK00310 175 L 175 (232)
T ss_pred c
Confidence 7
No 9
>KOG3181|consensus
Probab=99.90 E-value=1.4e-23 Score=188.81 Aligned_cols=127 Identities=77% Similarity=1.143 Sum_probs=124.2
Q ss_pred cccchhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEE
Q psy17938 2 SAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY 81 (307)
Q Consensus 2 ~kkfI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~ 81 (307)
.+||+.||+++++++|||.+++.+.|||++|.+-||.+++|+|.+++|..++|.+|.+|++|+...||+|+..+..|+++
T Consensus 8 krkfv~dGvf~AELnef~treLaedGySgvEvRvtptr~eiIi~atrtq~vlGEkgrRirelt~lvqkRf~f~~~svely 87 (244)
T KOG3181|consen 8 KRKFVADGVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKFPEGSVELY 87 (244)
T ss_pred hhhhhhcchhHHHHHHHHHHHHHhcCcCceEEEeeccceeEEEEecchhhhhhhcchhHHHHHHHHHHhcCCCCCcEEEe
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCcCHHHHHHHHHHHHHcChhhhhh--------hhcCCceeEEeeeccceeeEEEeeeeee
Q psy17938 82 AEKVATRGLCAIAQAESLRYKLIGGLAVRRY--------PAIDAQYCSLLAQFGWSILILVVAVGTL 140 (307)
Q Consensus 82 I~eVknP~l~A~lLAe~IA~QLE~Rv~FRRA--------MkaGAkGIKI~~~~~~~~~~~~~~sgrl 140 (307)
+++|.+++++|..+|++++++|-...++||| |.+|||||.|. |||.|
T Consensus 88 aEkV~~rGLcAiaQaeslryKllgGlavRRA~ygvlr~vmesgAkGcevi------------VSGKL 142 (244)
T KOG3181|consen 88 AEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVI------------VSGKL 142 (244)
T ss_pred hhhhhccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHccCCccEEE------------Eeccc
Confidence 9999999999999999999999999999995 79999999999 99999
No 10
>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=99.84 E-value=1.5e-20 Score=148.14 Aligned_cols=80 Identities=83% Similarity=1.219 Sum_probs=77.5
Q ss_pred hhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCC
Q psy17938 9 GVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATR 88 (307)
Q Consensus 9 ~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP 88 (307)
|+++++||+||++++.+||||+|||+|+++.++|+|||++||++||++|+++++|++.|++.|++++++|++.+++|.+.
T Consensus 1 ~~~~~~Ire~l~k~~~~agis~IeI~Rt~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~~i~v~~~~v~~~ 80 (81)
T cd02413 1 GVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEGSVELYAEKVANR 80 (81)
T ss_pred CchhHHHHHHHHHHHHhCCeeeEEEEEcCCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCCeEEEEEEEcccC
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999875
No 11
>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=99.82 E-value=3.9e-20 Score=146.04 Aligned_cols=85 Identities=39% Similarity=0.660 Sum_probs=80.3
Q ss_pred CcccchhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q psy17938 1 MSAKFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIEL 80 (307)
Q Consensus 1 ~~kkfI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I 80 (307)
|+|+|++||+.+.+||+|+++.+..||||+|+|+|+++.++|+|||++||.+||++|+++++|++.|++.++. .++.|
T Consensus 1 ~~~~~~~~~~~~~~Ir~fl~~~~~~agIs~IeI~r~~~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l~k~~~~--~~v~I 78 (85)
T cd02411 1 VERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGL--ENPQI 78 (85)
T ss_pred CeEeHHhcchHHHHHHHHHHhhhhhCcccEEEEEEcCCcEEEEEEECCCCceECCCchhHHHHHHHHHHHhCC--CCceE
Confidence 6799999999999999999999999999999999999999999999999999999999999999999999964 47888
Q ss_pred EEEEecC
Q psy17938 81 YAEKVAT 87 (307)
Q Consensus 81 ~I~eVkn 87 (307)
++.||++
T Consensus 79 ~v~ev~~ 85 (85)
T cd02411 79 DVQEVEN 85 (85)
T ss_pred EEEEecC
Confidence 8899875
No 12
>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=99.72 E-value=3.2e-17 Score=135.11 Aligned_cols=82 Identities=22% Similarity=0.325 Sum_probs=75.2
Q ss_pred chhhhhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q psy17938 5 FVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK 84 (307)
Q Consensus 5 fI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~e 84 (307)
|-+-=..|.+|||||.+.+.+|||++|+|+|+++.++|+|||++||++||++|+++++|++.|++.+++ .++.|+|.|
T Consensus 28 y~~~l~ed~~IR~yL~k~~~~agis~I~I~R~~~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~~~~--~~~~I~V~e 105 (109)
T cd02412 28 YAELLHEDLKIRKFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIEKLRKELQKLLGN--KKVRINIVE 105 (109)
T ss_pred hHHHHHhHHHHHHHHHHHHhhCCccEEEEEEcCCCEEEEEEeCCCCcccCCchHHHHHHHHHHHHHhCC--CceEEEEEE
Confidence 334446789999999999999999999999999999999999999999999999999999999999964 478899999
Q ss_pred ecCC
Q psy17938 85 VATR 88 (307)
Q Consensus 85 VknP 88 (307)
|++|
T Consensus 106 v~~P 109 (109)
T cd02412 106 VKKP 109 (109)
T ss_pred ecCC
Confidence 9998
No 13
>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=99.56 E-value=8.3e-15 Score=112.74 Aligned_cols=77 Identities=29% Similarity=0.434 Sum_probs=72.7
Q ss_pred HHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC-CCCCeEEEEEEEecCCCc
Q psy17938 14 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK-FADGAIELYAEKVATRGL 90 (307)
Q Consensus 14 kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~-~~~~kI~I~I~eVknP~l 90 (307)
+||+|+.+++..+|+++++|+|+++.+.|++++++||++||++|+++++|++.+++.+. ..+++|.+++.+|++|++
T Consensus 1 eI~~~l~~~~~~~~~~~i~I~r~~~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~~~~~~~V~l~v~~V~~~~~ 78 (78)
T PF07650_consen 1 EIRYFLFKEIKKAGISDIEIERTPDQIIIVIKASQPGIVIGKKGSNIKKIREELRKELEKLLNKKVFLNVVKVKKPWR 78 (78)
T ss_dssp HHHHHHHHHTTTTTEEEEEEEESSSEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHHHHCSSSEEEEEEEESSCGG
T ss_pred ChhhhHHhhhhhccCceEEEEEcCCeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHhhcCCCcEEEEEEEecCCCC
Confidence 68999999999999999999999999999999999999999999999999999999995 457899999999999964
No 14
>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=98.86 E-value=1.3e-08 Score=74.03 Aligned_cols=65 Identities=43% Similarity=0.641 Sum_probs=58.3
Q ss_pred HHHHHHhhccCCeeeeEEEEcCCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q psy17938 16 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATR--TQNVLGDKGRRIRELTSVVQKRFKFADGAIELYA 82 (307)
Q Consensus 16 Refl~k~l~~AGIs~IeI~Rt~~~I~I~I~tar--Pg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I 82 (307)
|+|+.+.+..+|+++|+|+++++...+.+++.+ ||.+||++|+++++++..+++.+ .++++.|++
T Consensus 1 r~~l~~~~~~~~i~~i~i~~~~~~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~--~~~~~~i~v 67 (68)
T cd02409 1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL--RKKRVKIDV 67 (68)
T ss_pred ChHHHHHHHHCCCCeEEEEEcCCcEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc--CCCceEEEE
Confidence 588999999999999999999888999999999 99999999999999999999998 356666654
No 15
>PF00189 Ribosomal_S3_C: Ribosomal protein S3, C-terminal domain; InterPro: IPR001351 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S3 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S3 is known to be involved in the binding of initiator Met-tRNA. This family of ribosomal proteins includes S3 from bacteria, algae and plant chloroplast, cyanelle, archaebacteria, plant mitochondria, vertebrates, insects, Caenorhabditis elegans and yeast []. This entry is the C-terminal domain.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_C 2XZM_C 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C ....
Probab=97.88 E-value=6.1e-06 Score=65.30 Aligned_cols=44 Identities=18% Similarity=0.152 Sum_probs=38.4
Q ss_pred HHHHHHHcChhhhhh---------hhcCCceeEEeeeccceeeEEEeeeeee-----ecCCCcccceEee
Q psy17938 98 SLRYKLIGGLAVRRY---------PAIDAQYCSLLAQFGWSILILVVAVGTL-----HQCPGCRELRIIL 153 (307)
Q Consensus 98 ~IA~QLE~Rv~FRRA---------MkaGAkGIKI~~~~~~~~~~~~~~sgrl-----ar~e~~~e~~i~l 153 (307)
+|+++||++.+|||+ |.+||+||||+ +|||| ||++-++.+.+.+
T Consensus 1 ~i~~~l~k~~~~r~~i~~~~~~i~~~~~~~GikI~------------isGRl~g~~rar~~~~~~G~i~~ 58 (85)
T PF00189_consen 1 FIAQKLEKRISFRRIIKKIIRRIMMNKGIKGIKIQ------------ISGRLNGAERARTEKFKKGKISL 58 (85)
T ss_dssp HHHHHHHTTSTHHHHHHHHHHHHHHCTTSSEEEEE------------EESSGGGTSSSEEEEEEEESSSS
T ss_pred ChHHHHhcCcHHHHHHHHHHHHHHhhcccceEEEE------------EeecCCCCccceEEEEECCCCcc
Confidence 589999999999995 46799999999 99999 7788888888754
No 16
>smart00322 KH K homology RNA-binding domain.
Probab=97.54 E-value=8.3e-05 Score=52.86 Aligned_cols=67 Identities=15% Similarity=0.174 Sum_probs=52.5
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHH
Q psy17938 38 ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLI 104 (307)
Q Consensus 38 ~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~A~lLAe~IA~QLE 104 (307)
..++|.|+...|+.+||++|+++++|++.....+...+..-...+..|..|..++...++.|.++++
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 4678889999999999999999999998887655433322134557888888889999888888764
No 17
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=96.98 E-value=0.0034 Score=48.58 Aligned_cols=66 Identities=20% Similarity=0.241 Sum_probs=51.7
Q ss_pred HHHHHhhccCCee-eeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC---CCeEEEEE
Q psy17938 17 EFLTRELAEDGYS-GVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFA---DGAIELYA 82 (307)
Q Consensus 17 efl~k~l~~AGIs-~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~---~~kI~I~I 82 (307)
+|+++-+...|+. .|++....+.+.+.|....+|.+||++|+.++.|+..+...++.. ..+|.|++
T Consensus 2 ~~L~~il~~mg~~~~v~~~~~~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~~~~~~~~v~lDv 71 (77)
T cd02414 2 EFLEEVLELMGIEADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNRNTGEYVRITLDV 71 (77)
T ss_pred hHHHHHHHHcCCCcEEEEEecCCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhhccCCceEEEEEC
Confidence 5777777777763 477777888999999999999999999999999999888777532 23455543
No 18
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=96.76 E-value=0.0018 Score=49.31 Aligned_cols=69 Identities=14% Similarity=0.173 Sum_probs=46.6
Q ss_pred HHHHHHHHHhhccCCeeeeEEE--EcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEE
Q psy17938 13 AELDEFLTRELAEDGYSGVEIR--FTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY 81 (307)
Q Consensus 13 ~kIRefl~k~l~~AGIs~IeI~--Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~ 81 (307)
..+++|+..-+...+=-.|++. ...+.+.+.+....+|.+||++|+.++.|+..+....+-.+.++.|.
T Consensus 2 e~l~~~l~~l~~~~~~v~v~~~~~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~~v~ 72 (73)
T PF13083_consen 2 EFLEDFLKNLVDKPMDVEVTIEIEEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAANKHGKRVRVE 72 (73)
T ss_dssp ---HHHHHHHHHHTT--EEEEEEETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHHHT-SS-EEE
T ss_pred chHHHHHHHHhCCcCeEEEEEEEcCCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHHHhCCCEEEEe
Confidence 4567777777643332234444 45679999999999999999999999999998887775444455543
No 19
>PRK01064 hypothetical protein; Provisional
Probab=95.88 E-value=0.11 Score=41.24 Aligned_cols=54 Identities=9% Similarity=0.162 Sum_probs=42.2
Q ss_pred eEEEEcCCeEEEEEEeccc--ceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q psy17938 31 VEIRFTPARTEIIIMATRT--QNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK 84 (307)
Q Consensus 31 IeI~Rt~~~I~I~I~tarP--g~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~e 84 (307)
|+-......+.+.+++... |.+||++|++++.++..+.....-.+.++.+.+.+
T Consensus 21 V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~~~~~~~~rv~leI~~ 76 (78)
T PRK01064 21 IKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIME 76 (78)
T ss_pred EEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhhCCCEEEEEEec
Confidence 4544445677888888776 88999999999999999988776556778877665
No 20
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=95.01 E-value=0.085 Score=48.89 Aligned_cols=127 Identities=13% Similarity=0.060 Sum_probs=85.8
Q ss_pred hhHHHHHHHHHHHhhccCCeee-eEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC---CCeEEEEEEE
Q psy17938 9 GVFRAELDEFLTRELAEDGYSG-VEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFA---DGAIELYAEK 84 (307)
Q Consensus 9 ~~i~~kIRefl~k~l~~AGIs~-IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~---~~kI~I~I~e 84 (307)
..+..++.+|+..-+..-|++- |.+....+.+.+.|....+|.+||++|+.++.|+...+-.++.. ..+|.+++..
T Consensus 61 ~~~~~~~~~~L~ell~~m~~~~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~ 140 (208)
T COG1847 61 EKIAQEAKDYLEELLELMDFEVTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGD 140 (208)
T ss_pred hHHHHHHHHHHHHHHHHhCCceEEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhh
Confidence 3467889999999998887654 88888899999999999999999999999999998777666532 2356666544
Q ss_pred ecCC-CcCHHHHHHHHHHHH-H--------cChhhhh-hh---hcCCceeEEeeeccceeeEEEee
Q psy17938 85 VATR-GLCAIAQAESLRYKL-I--------GGLAVRR-YP---AIDAQYCSLLAQFGWSILILVVA 136 (307)
Q Consensus 85 VknP-~l~A~lLAe~IA~QL-E--------~Rv~FRR-AM---kaGAkGIKI~~~~~~~~~~~~~~ 136 (307)
-..+ .-.=..+|+.+|.|. + -..||-| .+ =+.-.|+++- .+|-.|-=-|+|
T Consensus 141 yRerR~e~L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~~~~~V~T~-SeG~ep~R~vVV 205 (208)
T COG1847 141 YRERRKETLIKLAERAAERVLETGRSVELEPMPPFERKIVHTALSANPGVETY-SEGEEPNRRVVV 205 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHHhcCCccee-ecCCCCceEEEE
Confidence 3322 112345677777665 2 2234433 22 2366777776 444444444443
No 21
>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=94.61 E-value=0.072 Score=39.62 Aligned_cols=53 Identities=15% Similarity=0.315 Sum_probs=44.1
Q ss_pred HHHHHHhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHHH
Q psy17938 16 DEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRELTSVVQ 68 (307)
Q Consensus 16 Refl~k~l~~AGIs~IeI~Rt-~~~I~I~I~tarPg~IIGr~G~~IkkL~~~Lq 68 (307)
.+|+.+-+.-+.+.+|++... .+.+.|.+....-|..||++|++++.+++.+.
T Consensus 2 ~~~i~n~~~p~~i~~V~~~~~~~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~ 55 (61)
T cd02134 2 AEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLG 55 (61)
T ss_pred HHHHHHhcCcccceEEEEecCCCcEEEEEECcccceeeECCCCHHHHHHHHHHC
Confidence 467777777888999988765 47888888888899999999999988887665
No 22
>PRK02821 hypothetical protein; Provisional
Probab=94.39 E-value=0.57 Score=37.04 Aligned_cols=52 Identities=15% Similarity=0.196 Sum_probs=40.0
Q ss_pred eeEEEEcCCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q psy17938 30 GVEIRFTPARTEIIIMATR--TQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK 84 (307)
Q Consensus 30 ~IeI~Rt~~~I~I~I~tar--Pg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~e 84 (307)
.|+.+...+.+.+.|+++. -|.+||++|..++.++..+.-. .++++.+.+.+
T Consensus 21 ~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~leI~~ 74 (77)
T PRK02821 21 RVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI---GGRGVRVDVVD 74 (77)
T ss_pred EEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh---cCCeEEEEEEe
Confidence 3555555667777777755 4679999999999999999877 46788887765
No 23
>COG1159 Era GTPase [General function prediction only]
Probab=93.66 E-value=0.44 Score=46.41 Aligned_cols=77 Identities=23% Similarity=0.375 Sum_probs=55.9
Q ss_pred cchhhhhHHHHHHHHHHHhhccCCeeeeEEEEcC------CeEEEEEEeccc---ceeeccCcccHHHH----HHHHHHH
Q psy17938 4 KFVADGVFRAELDEFLTRELAEDGYSGVEIRFTP------ARTEIIIMATRT---QNVLGDKGRRIREL----TSVVQKR 70 (307)
Q Consensus 4 kfI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~------~~I~I~I~tarP---g~IIGr~G~~IkkL----~~~LqK~ 70 (307)
+|+.-.++++++=.++..+++.+ ..|||++.. ..|.-.|+++|. |++||++|+.|+++ +.++++.
T Consensus 189 rf~~aEiiREk~~~~l~eElPhs--v~VeIe~~~~~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l 266 (298)
T COG1159 189 RFLAAEIIREKLLLLLREELPHS--VAVEIEEFEEREKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKL 266 (298)
T ss_pred HHHHHHHHHHHHHHhcccccCce--EEEEEEEEEecCCCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHH
Confidence 57777888888888988888765 347777642 256667787654 68999999999776 5678888
Q ss_pred hCCCCCeEEEEEE
Q psy17938 71 FKFADGAIELYAE 83 (307)
Q Consensus 71 ~~~~~~kI~I~I~ 83 (307)
|+. +..+++.|.
T Consensus 267 ~~~-kV~L~L~VK 278 (298)
T COG1159 267 LGC-KVYLELWVK 278 (298)
T ss_pred hCC-ceEEEEEEE
Confidence 864 344555544
No 24
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=93.45 E-value=0.095 Score=45.44 Aligned_cols=61 Identities=15% Similarity=0.315 Sum_probs=49.0
Q ss_pred HHHHHHHHHhhccCCeeeeEEEEcC--CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q psy17938 13 AELDEFLTRELAEDGYSGVEIRFTP--ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 73 (307)
Q Consensus 13 ~kIRefl~k~l~~AGIs~IeI~Rt~--~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~ 73 (307)
....+|+.+-+..+++.+++|.... ..+.|.+.-..-|..||++|++++.++..+.+.++.
T Consensus 72 ~d~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 72 DDPEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred CCHHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 3467899999999999999995443 345666667777889999999999999988888764
No 25
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=93.22 E-value=0.27 Score=43.31 Aligned_cols=85 Identities=25% Similarity=0.301 Sum_probs=58.0
Q ss_pred HHHHHHHHHhhc-cCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcC
Q psy17938 13 AELDEFLTRELA-EDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLC 91 (307)
Q Consensus 13 ~kIRefl~k~l~-~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~ 91 (307)
.+-++.+.+-.. +||+.+ |...++.=+|+|++.+||+++|++|..+.++.. ..|. ....+..|-+.
T Consensus 52 e~A~~~I~~ivP~ea~i~d--i~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~----~tgW-------~p~vvRtpPi~ 118 (145)
T cd02410 52 EEAIKIILEIVPEEAGITD--IYFDDDTGEVIIEAEKPGLVIGKGGSTLREITR----ETGW-------APKVVRTPPIQ 118 (145)
T ss_pred HHHHHHHHHhCCCccCcee--eEecCCCcEEEEEEcCCeEEEecCchhHHHHHH----HhCC-------eeEEEecCCCC
Confidence 344556666554 578855 455667778999999999999999988877654 5554 22346777777
Q ss_pred HHHHHHHHHHHHHcChhhhh
Q psy17938 92 AIAQAESLRYKLIGGLAVRR 111 (307)
Q Consensus 92 A~lLAe~IA~QLE~Rv~FRR 111 (307)
+..+ +.|++-|-+-...|+
T Consensus 119 S~ti-~~ir~~l~~~~~eR~ 137 (145)
T cd02410 119 SRTV-KSIRRFLRREREERK 137 (145)
T ss_pred cHHH-HHHHHHHHHhHHHHH
Confidence 7765 556666666666665
No 26
>PRK00468 hypothetical protein; Provisional
Probab=92.56 E-value=1.4 Score=34.60 Aligned_cols=52 Identities=13% Similarity=0.133 Sum_probs=37.3
Q ss_pred eEEEEcCCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q psy17938 31 VEIRFTPARTEIIIMATR--TQNVLGDKGRRIRELTSVVQKRFKFADGAIELYA 82 (307)
Q Consensus 31 IeI~Rt~~~I~I~I~tar--Pg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I 82 (307)
|+.....+.+.+.++++. -|.+||++|..++.|+..+.-.-...+.++.+.|
T Consensus 21 V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~leI 74 (75)
T PRK00468 21 VNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVEI 74 (75)
T ss_pred EEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHHHHHhcCCCEEEEEE
Confidence 444445567777777764 4679999999999999999866544456666654
No 27
>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=91.34 E-value=1 Score=41.84 Aligned_cols=74 Identities=18% Similarity=0.319 Sum_probs=48.1
Q ss_pred cchhhhhHHHHHHHHHHHhhccCCeeeeEEEE---cC---CeEEEEEEeccc---ceeeccCcccHHHH----HHHHHHH
Q psy17938 4 KFVADGVFRAELDEFLTRELAEDGYSGVEIRF---TP---ARTEIIIMATRT---QNVLGDKGRRIREL----TSVVQKR 70 (307)
Q Consensus 4 kfI~d~~i~~kIRefl~k~l~~AGIs~IeI~R---t~---~~I~I~I~tarP---g~IIGr~G~~IkkL----~~~LqK~ 70 (307)
+|+-..++++++=+++.++++-+-- ++|+. .+ ..|...|++.|+ +++||++|+.|+++ +.+|++.
T Consensus 181 ~~~~~e~ire~~~~~~~~e~p~~~~--~~~~~~~~~~~~~~~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~~~ 258 (270)
T TIGR00436 181 RFKISEIIREKIIRYTKEEIPHSVR--VEIERKSFNEKGLLKIHALISVERESQKKIIIGKNGSMIKAIGIAARKDILEL 258 (270)
T ss_pred HHHHHHHHHHHHHHhcccccCceEE--EEEEEEEECCCCeEEEEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHHHH
Confidence 3455566666666666666654422 33333 22 258888999887 57999999999776 5667777
Q ss_pred hCCCCCeEEEEE
Q psy17938 71 FKFADGAIELYA 82 (307)
Q Consensus 71 ~~~~~~kI~I~I 82 (307)
|+ .+|.+.+
T Consensus 259 ~~---~~v~l~l 267 (270)
T TIGR00436 259 FD---CDVFLEL 267 (270)
T ss_pred hC---CCEEEEE
Confidence 75 4555543
No 28
>PRK15494 era GTPase Era; Provisional
Probab=91.10 E-value=1.7 Score=42.30 Aligned_cols=78 Identities=23% Similarity=0.367 Sum_probs=52.6
Q ss_pred cchhhhhHHHHHHHHHHHhhccCCeeeeEEEEc---C---CeEEEEEEecccc---eeeccCcccHHHH----HHHHHHH
Q psy17938 4 KFVADGVFRAELDEFLTRELAEDGYSGVEIRFT---P---ARTEIIIMATRTQ---NVLGDKGRRIREL----TSVVQKR 70 (307)
Q Consensus 4 kfI~d~~i~~kIRefl~k~l~~AGIs~IeI~Rt---~---~~I~I~I~tarPg---~IIGr~G~~IkkL----~~~LqK~ 70 (307)
+|+--.+++++|=+++.++++-+- .|+|+.- . ..|...|++.|++ ++||++|+.|+++ +.+|++.
T Consensus 233 ~~~~~eiiRe~~~~~~~~EiP~~~--~v~i~~~~~~~~~~~~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~ 310 (339)
T PRK15494 233 RFIAAEITREQLFLNLQKELPYKL--TVQTEKWEDLKDKSVKINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERF 310 (339)
T ss_pred HHHHHHHHHHHHHhhCCcccCceE--EEEEEEEEEcCCCeEEEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHH
Confidence 456667777777777777776442 2444432 2 2578899998886 7999999999776 5677778
Q ss_pred hCCCCCeEEEEEEE
Q psy17938 71 FKFADGAIELYAEK 84 (307)
Q Consensus 71 ~~~~~~kI~I~I~e 84 (307)
|+. +..+++.|..
T Consensus 311 ~~~-~v~l~l~Vkv 323 (339)
T PRK15494 311 FGF-PVHLFLFVKV 323 (339)
T ss_pred hCC-CeEEEEEEEE
Confidence 864 3344555443
No 29
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=90.69 E-value=2.4 Score=33.66 Aligned_cols=52 Identities=13% Similarity=0.190 Sum_probs=35.9
Q ss_pred eEEEEc--CCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q psy17938 31 VEIRFT--PARTEIIIMATR--TQNVLGDKGRRIRELTSVVQKRFKFADGAIELYA 82 (307)
Q Consensus 31 IeI~Rt--~~~I~I~I~tar--Pg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I 82 (307)
+.+... ...+.+.++++. -|-+|||+|..++.|+..|.-.-.-.++++.|.+
T Consensus 19 v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~~~~~~v~i~i 74 (76)
T COG1837 19 VRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGSKDSKRVVVEI 74 (76)
T ss_pred eEEEEEecCCeEEEEEEECcccccceecCCChhHHHHHHHHHHhcccCceEEEEEe
Confidence 444443 456666666655 4679999999999999999866553455666544
No 30
>PRK00089 era GTPase Era; Reviewed
Probab=90.47 E-value=2 Score=39.96 Aligned_cols=80 Identities=24% Similarity=0.322 Sum_probs=47.8
Q ss_pred chhhhhHHHHHHHHHHHhhccCCeeeeEEEE----cCCeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCC
Q psy17938 5 FVADGVFRAELDEFLTRELAEDGYSGVEIRF----TPARTEIIIMATRTQ---NVLGDKGRRIREL----TSVVQKRFKF 73 (307)
Q Consensus 5 fI~d~~i~~kIRefl~k~l~~AGIs~IeI~R----t~~~I~I~I~tarPg---~IIGr~G~~IkkL----~~~LqK~~~~ 73 (307)
|.-..++++++-+++.++++-+- .|+|+. ....|...|++.++. ++||++|+.|+++ +..|++.|+.
T Consensus 189 ~~~~EiiRe~~~~~l~~e~p~~~--~v~~~~~~~~~~~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~ 266 (292)
T PRK00089 189 FLAAEIIREKLLRLLGDELPYSV--AVEIEKFEERGLVRIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGK 266 (292)
T ss_pred HHHHHHHHHHHHhhCCccCCceE--EEEEEEEEECCeEEEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCC
Confidence 34444555555555555555331 133332 224578889998874 7999999999776 5667778853
Q ss_pred CCCeEEEEEEEecC
Q psy17938 74 ADGAIELYAEKVAT 87 (307)
Q Consensus 74 ~~~kI~I~I~eVkn 87 (307)
+-.+++.|..-++
T Consensus 267 -~v~l~l~vkv~~~ 279 (292)
T PRK00089 267 -KVFLELWVKVKKG 279 (292)
T ss_pred -CEEEEEEEEECCC
Confidence 3344555444433
No 31
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=86.62 E-value=5.2 Score=42.14 Aligned_cols=59 Identities=29% Similarity=0.401 Sum_probs=43.2
Q ss_pred ccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHH
Q psy17938 24 AEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQ 95 (307)
Q Consensus 24 ~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~A~lL 95 (307)
.+|||++ |.-..+.=+|.|.+.+||.+||++|+..+++.. ..+.. ...+..|-+....+
T Consensus 87 ~ea~i~~--i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~----~tgW~-------p~ivR~PPi~S~ti 145 (637)
T COG1782 87 EEAGITD--IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITA----ETGWA-------PKIVRTPPIQSRTI 145 (637)
T ss_pred cccCcee--EEecCCCceEEEEecCCceEEecCchHHHHHHH----HhCCc-------ceeeecCCCchhhH
Confidence 3688876 666788889999999999999999988776654 44441 23366676666655
No 32
>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=85.34 E-value=1.1 Score=39.24 Aligned_cols=60 Identities=15% Similarity=0.278 Sum_probs=44.4
Q ss_pred HHHHHHHHhhccCCeeeeEEEEcC--CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q psy17938 14 ELDEFLTRELAEDGYSGVEIRFTP--ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 73 (307)
Q Consensus 14 kIRefl~k~l~~AGIs~IeI~Rt~--~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~ 73 (307)
-+.+|+.+.+.-|.+.+|.+...+ ....|.+.-..-+..||++|++++...+.+...++.
T Consensus 74 D~~~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 74 NLEEFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred CHHHHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 467899999999999999886532 234455555667789999999997777766655543
No 33
>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=82.99 E-value=9.2 Score=40.73 Aligned_cols=84 Identities=25% Similarity=0.320 Sum_probs=54.5
Q ss_pred HHHHHHHHhhc-cCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCH
Q psy17938 14 ELDEFLTRELA-EDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCA 92 (307)
Q Consensus 14 kIRefl~k~l~-~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~A 92 (307)
+-+|.+.+-.. +||+. +|.-.++.=+|.|.+.+||.+||++|..++++.. ..|. ....+..|-+.+
T Consensus 70 ~~~~~i~~~~~~~~~~~--~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~----~~~w-------~~~~~~~~~~~~ 136 (630)
T TIGR03675 70 EAIEKIKEIVPEEAGIT--DIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITA----ETGW-------TPKVVRTPPIES 136 (630)
T ss_pred HHHHHHHHhCCCcCCce--eEEecCCCceEEEEEcCCeEEEecCcchHHHHHH----HhCC-------eeeEEecCCCCc
Confidence 34455555443 57885 4555677788999999999999999988877654 4544 223467777777
Q ss_pred HHHHHHHHHHHHcChhhhh
Q psy17938 93 IAQAESLRYKLIGGLAVRR 111 (307)
Q Consensus 93 ~lLAe~IA~QLE~Rv~FRR 111 (307)
..+ +.|++-|.+-...|+
T Consensus 137 ~~~-~~~~~~~~~~~~~r~ 154 (630)
T TIGR03675 137 KTI-KNIREYLRSESEERK 154 (630)
T ss_pred HHH-HHHHHHHHHhHHHHH
Confidence 655 344444444444444
No 34
>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=77.10 E-value=2.3 Score=31.51 Aligned_cols=28 Identities=18% Similarity=0.406 Sum_probs=22.4
Q ss_pred eEEEEEEecccceeeccCcccHHHHHHH
Q psy17938 39 RTEIIIMATRTQNVLGDKGRRIRELTSV 66 (307)
Q Consensus 39 ~I~I~I~tarPg~IIGr~G~~IkkL~~~ 66 (307)
...+.|-..+-|.+||++|+.+++|++.
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~ 30 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEE 30 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHH
Confidence 3456677788899999999999887764
No 35
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=74.53 E-value=5.6 Score=35.80 Aligned_cols=56 Identities=13% Similarity=0.216 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhhccCCeeeeEEEEc---CCeEEEEEEecccceeeccCcccHHHHHHHHH
Q psy17938 12 RAELDEFLTRELAEDGYSGVEIRFT---PARTEIIIMATRTQNVLGDKGRRIRELTSVVQ 68 (307)
Q Consensus 12 ~~kIRefl~k~l~~AGIs~IeI~Rt---~~~I~I~I~tarPg~IIGr~G~~IkkL~~~Lq 68 (307)
|.++-+-|-+...+..+++++..+. .|.+-+.+..+. |..||++|+++++|++.|-
T Consensus 32 dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lg 90 (166)
T PRK06418 32 DVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGP-RIPIGKGGKIAKALSRKLG 90 (166)
T ss_pred ehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCC-cccccccchHHHHHHHHhC
Confidence 3445455544434444566666665 577777777777 8999999999988887654
No 36
>PF13014 KH_3: KH domain
Probab=72.73 E-value=2.8 Score=28.60 Aligned_cols=16 Identities=25% Similarity=0.636 Sum_probs=14.1
Q ss_pred ceeeccCcccHHHHHH
Q psy17938 50 QNVLGDKGRRIRELTS 65 (307)
Q Consensus 50 g~IIGr~G~~IkkL~~ 65 (307)
|.+||++|+.|++|++
T Consensus 3 g~iIG~~G~~I~~I~~ 18 (43)
T PF13014_consen 3 GRIIGKGGSTIKEIRE 18 (43)
T ss_pred CeEECCCChHHHHHHH
Confidence 6799999999988875
No 37
>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=65.06 E-value=7 Score=27.78 Aligned_cols=27 Identities=15% Similarity=0.445 Sum_probs=21.2
Q ss_pred EEEEEecccceeeccCcccHHHHHHHH
Q psy17938 41 EIIIMATRTQNVLGDKGRRIRELTSVV 67 (307)
Q Consensus 41 ~I~I~tarPg~IIGr~G~~IkkL~~~L 67 (307)
+|.|-...-+.+||++|+.+++|++.-
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s 29 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREET 29 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHH
Confidence 455566677899999999999888753
No 38
>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=63.38 E-value=6.2 Score=29.11 Aligned_cols=27 Identities=15% Similarity=0.486 Sum_probs=21.7
Q ss_pred EEEEEEecccceeeccCcccHHHHHHH
Q psy17938 40 TEIIIMATRTQNVLGDKGRRIRELTSV 66 (307)
Q Consensus 40 I~I~I~tarPg~IIGr~G~~IkkL~~~ 66 (307)
+++.|-...-|.+||++|..+++|++.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~ 28 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREE 28 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHH
Confidence 456666677789999999999988864
No 39
>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=62.42 E-value=3.2 Score=29.77 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=22.0
Q ss_pred EEEEEEecccceeeccCcccHHHHHHHH
Q psy17938 40 TEIIIMATRTQNVLGDKGRRIRELTSVV 67 (307)
Q Consensus 40 I~I~I~tarPg~IIGr~G~~IkkL~~~L 67 (307)
.+|.|....-|.+||++|+++++|++.-
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t 29 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEET 29 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHH
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhc
Confidence 4566677777899999999998877643
No 40
>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=61.01 E-value=17 Score=36.01 Aligned_cols=60 Identities=18% Similarity=0.265 Sum_probs=43.7
Q ss_pred HHHHHHHhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEE
Q psy17938 15 LDEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY 81 (307)
Q Consensus 15 IRefl~k~l~~AGIs~IeI~Rt-~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~ 81 (307)
..+|+.+.+.-|.+.+|+|... .....|.+--..-+..||++|++++. ...| . .++|+|.
T Consensus 277 ~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~l-a~~l---~---g~~IdI~ 337 (341)
T TIGR01953 277 PAEFIANALSPAKVISVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRL-ASKL---T---GWNIDVK 337 (341)
T ss_pred HHHHHHHhcCCceEEEEEEEcCCCcEEEEEEChHHcchhhcCCChhHHH-HHHH---h---CCEEEEE
Confidence 5689999999999999987443 35667766667778899999999943 3333 3 3567764
No 41
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=60.65 E-value=20 Score=36.20 Aligned_cols=65 Identities=23% Similarity=0.302 Sum_probs=47.2
Q ss_pred HHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEec
Q psy17938 15 LDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVA 86 (307)
Q Consensus 15 IRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVk 86 (307)
..+|+.+.+.-|.+.+|.+........|++--..-+..||++|++++. ...| . .++|+|.-.+-+
T Consensus 285 ~~~fI~Nal~Pa~V~~V~i~~~~~~~~V~V~~~qlslAIGk~GqNvrL-A~~L---t---GwkIDI~s~~~~ 349 (374)
T PRK12328 285 PEIFIARALAPAIISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRL-ASML---T---GYEIELNEIGSK 349 (374)
T ss_pred HHHHHHHhCCCceeeEEEEcCCCcEEEEEEChHHhhhhhcCCChhHHH-HHHH---h---CCEEEEEECCCC
Confidence 468999999999999998874456677777777778899999999943 3323 3 467777554444
No 42
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=60.55 E-value=17 Score=37.55 Aligned_cols=50 Identities=14% Similarity=0.297 Sum_probs=42.5
Q ss_pred HHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHH
Q psy17938 15 LDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELT 64 (307)
Q Consensus 15 IRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~ 64 (307)
..+|+.+.+..|.+.+|.+......+.|.+.-..-+..||++|++++...
T Consensus 279 ~~~fi~nal~pa~v~~v~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~ 328 (470)
T PRK09202 279 PAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGKNGQNVRLAS 328 (470)
T ss_pred HHHHHHHhCCCCEEEEEEEeCCCCEEEEEECcchHHHhhCCCCeeHHHHH
Confidence 56899999999999999887777788888888888899999999995444
No 43
>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=58.26 E-value=7.8 Score=27.93 Aligned_cols=27 Identities=26% Similarity=0.427 Sum_probs=20.0
Q ss_pred EEEEEecccceeeccCcccHHHHHHHH
Q psy17938 41 EIIIMATRTQNVLGDKGRRIRELTSVV 67 (307)
Q Consensus 41 ~I~I~tarPg~IIGr~G~~IkkL~~~L 67 (307)
++.|-...=+.+||++|+++++|++.-
T Consensus 3 ~i~Vp~~~~~~iIG~~G~~i~~i~~~~ 29 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGSNIRKIMEET 29 (62)
T ss_pred EEEeCHHHhhhccCCCCCcHHHHHHHh
Confidence 344445556789999999999988743
No 44
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=56.98 E-value=43 Score=31.96 Aligned_cols=71 Identities=17% Similarity=0.201 Sum_probs=57.0
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHH-HHHcChhhh
Q psy17938 38 ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRY-KLIGGLAVR 110 (307)
Q Consensus 38 ~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~A~lLAe~IA~-QLE~Rv~FR 110 (307)
+.+.+.|..+.--.+||.+|++...|-..+...++.+..+|.|+=.++.+- +...+|+.++- +=|+-..-|
T Consensus 18 ~~isl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~~d~G~i~i~g~~~~~~--~s~~LAk~lSILkQ~N~i~~r 89 (252)
T COG4604 18 DDVSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKKDSGEITIDGLELTST--PSKELAKKLSILKQENHINSR 89 (252)
T ss_pred ccceeeecCCceeEEECCCCccHHHHHHHHHHhccccCceEEEeeeecccC--ChHHHHHHHHHHHhhchhhhe
Confidence 567778888888899999999999999999999998888999988888875 78888888873 333433333
No 45
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=54.72 E-value=23 Score=35.51 Aligned_cols=60 Identities=17% Similarity=0.285 Sum_probs=42.8
Q ss_pred HHHHHHHhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEE
Q psy17938 15 LDEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELY 81 (307)
Q Consensus 15 IRefl~k~l~~AGIs~IeI~Rt-~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~ 81 (307)
..+|+.+.+.-|.+.+|+|... .....|.+--..-+..||++|++++ |...|. .++++|.
T Consensus 279 ~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~-la~~L~------~~~idi~ 339 (362)
T PRK12327 279 PAEFVANALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNAR-LAARLT------GWKIDIK 339 (362)
T ss_pred HHHHHHHhCCCceEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHH-HHHHHH------CCeeeEE
Confidence 5689999999999999988432 2456666666777889999999994 333333 3556654
No 46
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=52.90 E-value=33 Score=31.42 Aligned_cols=63 Identities=16% Similarity=0.227 Sum_probs=45.7
Q ss_pred HHHHHHHHhhccCCeeeeEEEEcCC-eEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEE
Q psy17938 14 ELDEFLTRELAEDGYSGVEIRFTPA-RTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAE 83 (307)
Q Consensus 14 kIRefl~k~l~~AGIs~IeI~Rt~~-~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~ 83 (307)
...+|+.+.+..|.+.+|.+.-..+ ...|.+.-..-+..||++|++++..++ .. .++++|...
T Consensus 117 d~~~fI~nal~Pa~v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~----Lt---g~~i~I~~~ 180 (190)
T COG0195 117 DPAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQ----LT---GWEIDIETI 180 (190)
T ss_pred CHHHHHHHhcCcceEeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHH----Hh---CCEEEEEeh
Confidence 3568888899899999999987433 566667777778999999999855443 22 356666443
No 47
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=48.47 E-value=82 Score=23.55 Aligned_cols=57 Identities=9% Similarity=0.114 Sum_probs=42.0
Q ss_pred HHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q psy17938 20 TRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYA 82 (307)
Q Consensus 20 ~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I 82 (307)
...+.++.|.+|.+.+..+..++.+.. |..+ .-+.+..+.+.|++.|+. ..+|++.+
T Consensus 18 ~~~f~~~~I~kv~v~k~~~~w~f~l~~--~~~l---~~~~~~~~~~~l~~~F~~-ia~v~~~i 74 (76)
T PF14480_consen 18 NPLFEDAEIEKVTVHKKSRKWRFHLSS--PHIL---PFEVYQKFEEKLKKQFSH-IAKVELII 74 (76)
T ss_pred hhhhcccEEEEEEEEccCCEEEEEEEe--CCcC---CHHHHHHHHHHHHHHhCC-cCeEEEEE
Confidence 445678889999999999988886554 4444 345679999999999864 23666654
No 48
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=48.19 E-value=27 Score=30.30 Aligned_cols=43 Identities=12% Similarity=0.222 Sum_probs=31.2
Q ss_pred hccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHH
Q psy17938 23 LAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 67 (307)
Q Consensus 23 l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~L 67 (307)
+.++..-++-+ ..+.+.+.+.....|..+|++|++++.+++.+
T Consensus 19 ~t~~~~~dc~~--d~~~vi~vV~~~~vG~~IG~~G~rI~~i~e~l 61 (140)
T PRK08406 19 ITGATVKDCII--DDDRIIFVVKEGDMGLAIGKGGENVKRLEEKL 61 (140)
T ss_pred HhCCCceEEEE--eCCEEEEEEeCCCccccCCcCchHHHHHHHHh
Confidence 33444444333 23888888888899999999999999986543
No 49
>KOG2191|consensus
Probab=46.18 E-value=30 Score=34.77 Aligned_cols=55 Identities=15% Similarity=0.215 Sum_probs=34.9
Q ss_pred hHHHHHHHHHHHhhccCCeeeeEEEEcCCe---EEEEEEecccceeeccCcccHHHHHHHH
Q psy17938 10 VFRAELDEFLTRELAEDGYSGVEIRFTPAR---TEIIIMATRTQNVLGDKGRRIRELTSVV 67 (307)
Q Consensus 10 ~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~---I~I~I~tarPg~IIGr~G~~IkkL~~~L 67 (307)
.|-+||||-.... +++.++.=.|++++ |+|.+=..--|.+||++|..|+.++++-
T Consensus 104 fI~dKire~p~~~---~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqs 161 (402)
T KOG2191|consen 104 FIADKIREKPQAV---AKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQS 161 (402)
T ss_pred HHHHHHHHhHHhh---cCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhh
Confidence 3445566654422 34444533555654 5566666677899999999999887743
No 50
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=46.04 E-value=49 Score=26.21 Aligned_cols=58 Identities=10% Similarity=0.156 Sum_probs=34.3
Q ss_pred eeeeEEEEc-CCeEEEEEEeccc-ceeeccCcccH-HHHHHHHHHHhCCCCCeEEEEEEEe
Q psy17938 28 YSGVEIRFT-PARTEIIIMATRT-QNVLGDKGRRI-RELTSVVQKRFKFADGAIELYAEKV 85 (307)
Q Consensus 28 Is~IeI~Rt-~~~I~I~I~tarP-g~IIGr~G~~I-kkL~~~LqK~~~~~~~kI~I~I~eV 85 (307)
-.+|.++.. .+.+.|.+++.-. |.=+-.-.+.+ +++++.+++.+++.-..|+|.+..|
T Consensus 47 ~~~v~v~~~~~~~i~v~l~v~v~~g~~i~~v~~~iq~~V~~~v~~~tg~~v~~V~V~V~~v 107 (108)
T PF03780_consen 47 SKGVKVEVDEDGGITVDLHVVVEYGVNIPEVAEEIQEKVKEAVEEMTGIEVSEVNVHVEDV 107 (108)
T ss_pred CCCeEEEEccCcceEEEEEEEEECCccHHHHHHHHHHHHHHHHHHHHCCeeEEEEEEEEec
Confidence 455777766 6777777665321 11111112222 5677777778887667888887765
No 51
>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=44.61 E-value=15 Score=32.61 Aligned_cols=63 Identities=14% Similarity=0.209 Sum_probs=44.6
Q ss_pred EEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE----EEe--cCCCcCHHHHHHHHHHHHHcChhhhhhh
Q psy17938 44 IMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYA----EKV--ATRGLCAIAQAESLRYKLIGGLAVRRYP 113 (307)
Q Consensus 44 I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I----~eV--knP~l~A~lLAe~IA~QLE~Rv~FRRAM 113 (307)
|-..+-|.+||++|+.+++|++. ++. +|+++- ..| ..++.++..-|..+...+....+...|+
T Consensus 4 Ip~~kig~vIG~gG~~Ik~I~~~----tgv---~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~ 72 (172)
T TIGR03665 4 IPKDRIGVLIGKGGETKKEIEER----TGV---KLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKAL 72 (172)
T ss_pred CCHHHhhhHhCCchhHHHHHHHH----hCc---EEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 34456688999999999887764 433 344332 244 4566688899999999888877777776
No 52
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=42.84 E-value=19 Score=27.62 Aligned_cols=31 Identities=23% Similarity=0.501 Sum_probs=24.5
Q ss_pred CeEEEEEEecc-----cceeeccCcccHHHHHHHHH
Q psy17938 38 ARTEIIIMATR-----TQNVLGDKGRRIRELTSVVQ 68 (307)
Q Consensus 38 ~~I~I~I~tar-----Pg~IIGr~G~~IkkL~~~Lq 68 (307)
+++.|.+.... -|..+|.+|++++.+.+.|.
T Consensus 3 ~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~ 38 (69)
T PF13184_consen 3 NRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELN 38 (69)
T ss_dssp TEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTT
T ss_pred ceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhC
Confidence 56777788777 57899999999999888764
No 53
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=42.40 E-value=39 Score=34.95 Aligned_cols=48 Identities=10% Similarity=0.255 Sum_probs=37.5
Q ss_pred HHHHHHHhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHH
Q psy17938 15 LDEFLTRELAEDGYSGVEIRFT-PARTEIIIMATRTQNVLGDKGRRIRE 62 (307)
Q Consensus 15 IRefl~k~l~~AGIs~IeI~Rt-~~~I~I~I~tarPg~IIGr~G~~Ikk 62 (307)
..+|+.+.+.-|.+.+|.|... .....|++--..-+..||++|++++.
T Consensus 311 p~~fI~NaLsPA~V~~V~i~~~~~k~a~V~V~~~qlslAIGK~GqNvrL 359 (449)
T PRK12329 311 PATYIANALSPARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRL 359 (449)
T ss_pred HHHHHHHhcCCceeeEEEEEcCCCcEEEEEEChHhcchhhcCCChhHHH
Confidence 4689999999999999987442 34566777777778899999999943
No 54
>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=41.86 E-value=31 Score=30.17 Aligned_cols=43 Identities=12% Similarity=0.232 Sum_probs=30.5
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHH
Q psy17938 22 ELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTS 65 (307)
Q Consensus 22 ~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~ 65 (307)
.+.++..-++.+.-.. ++-..+..+..|..+|++|++++.+++
T Consensus 18 ~~t~~~~~dc~~d~~~-riifvV~~g~vG~~IG~~G~rIk~i~e 60 (141)
T TIGR01952 18 DMTGATVVDCLIDDRN-RVVFVVKEGEMGAAIGKGGENVKRLEE 60 (141)
T ss_pred HHhCCceEEEEecCCc-EEEEEEcCCCccccCCCCchHHHHHHH
Confidence 4455666666654332 666667777889999999999999853
No 55
>TIGR03112 6_pyr_pter_rel 6-pyruvoyl tetrahydropterin synthase-related domain. Members of this family are small proteins, or small domains of larger proteins, that occur in certain Firmicutes in the same regions as members of families TIGR03110 and TIGR03111. Members of TIGR03110 resemble exosortase, a proposed protein sorting transpeptidase (see TIGR02602). TIGR03111 represents a small clade among the group 2 glycosyltransferases. Members of the current protein family resemble eukaryotic known and prokaryotic predicted 6-pyruvoyl tetrahydropterin synthases.
Probab=41.73 E-value=1e+02 Score=25.80 Aligned_cols=61 Identities=10% Similarity=0.121 Sum_probs=36.5
Q ss_pred eEEEEEEecccceeeccCcccHHHHHHHHHHHhC-CCCCeEEEEEEEec--CCCcCHHHHHHHHHHHHHcChh
Q psy17938 39 RTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFK-FADGAIELYAEKVA--TRGLCAIAQAESLRYKLIGGLA 108 (307)
Q Consensus 39 ~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~-~~~~kI~I~I~eVk--nP~l~A~lLAe~IA~QLE~Rv~ 108 (307)
.++|+|.....|+ + ....|++.+++... ++.+.++ ++.... +| .|..||..|.++|..+.+
T Consensus 28 ~vev~v~g~~~g~-v-----Df~~lk~~l~~v~~~~DH~~LN-dv~~f~~~~P--TaEniA~~i~~~l~~~l~ 91 (113)
T TIGR03112 28 EITIFVIKKEDKF-I-----LFNDVEKKVEKYLKPYQNKYLN-DLEPFDKINP--TLENIGDYFFDEIKKLLK 91 (113)
T ss_pred EEEEEEEecCCeE-E-----EHHHHHHHHHHHHHcCCCceec-cCCccCCCCC--CHHHHHHHHHHHHHHhhc
Confidence 5566665444343 2 35566665555443 1233333 444443 56 899999999999998875
No 56
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=39.19 E-value=85 Score=26.09 Aligned_cols=52 Identities=17% Similarity=0.186 Sum_probs=34.4
Q ss_pred EecccceeeccCccc---HHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHH
Q psy17938 45 MATRTQNVLGDKGRR---IRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKL 103 (307)
Q Consensus 45 ~tarPg~IIGr~G~~---IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~A~lLAe~IA~QL 103 (307)
|..+|-+.||++|-. ++++.+.|+.+= -|.| ....+-.-+...+|+.|+++.
T Consensus 15 h~l~piv~IGk~Glte~vi~Ei~~aL~~re-----LIKV--kvl~~~~edr~eia~~l~~~~ 69 (97)
T COG1534 15 HHLKPIVQIGKNGLTEGVIKEIDRALEARE-----LIKV--KVLQNAREDKKEIAEALAEET 69 (97)
T ss_pred ccCCceEEecCCccCHHHHHHHHHHHHhCC-----cEEE--EeeccchhhHHHHHHHHHHHh
Confidence 778899999999843 677777777432 2333 335555447777777777654
No 57
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=38.42 E-value=46 Score=35.12 Aligned_cols=54 Identities=22% Similarity=0.378 Sum_probs=37.8
Q ss_pred hhhHHHHHHHHHHHhhccCCeeeeEEEEcC-CeEEEEEEecccceeeccCcccHHHHHH
Q psy17938 8 DGVFRAELDEFLTRELAEDGYSGVEIRFTP-ARTEIIIMATRTQNVLGDKGRRIRELTS 65 (307)
Q Consensus 8 d~~i~~kIRefl~k~l~~AGIs~IeI~Rt~-~~I~I~I~tarPg~IIGr~G~~IkkL~~ 65 (307)
.++...+|.+.+++.+.. +++++-.. ....|.+.-..-+.+||++|+++++|.+
T Consensus 459 ~~~a~~~i~~~i~r~~p~----~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~ 513 (604)
T COG1855 459 LKLAEEEIEREIKRYLPG----DVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEK 513 (604)
T ss_pred hHHHHHHHHHHHHHhCCC----CceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHH
Confidence 456677888888888765 44555443 4566655555667899999999988664
No 58
>PRK13764 ATPase; Provisional
Probab=37.33 E-value=60 Score=34.73 Aligned_cols=54 Identities=20% Similarity=0.395 Sum_probs=36.2
Q ss_pred hhHHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHH
Q psy17938 9 GVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTS 65 (307)
Q Consensus 9 ~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~ 65 (307)
.+...+|.+-+.+.. .|...+++. ..+...|.|--.--+.+||++|++|+++.+
T Consensus 455 ~~~~~~~~~~~~~~~--~~~~~~~~~-~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~ 508 (602)
T PRK13764 455 RLAEKEIEREIKRYL--PGPVEVEVV-SDNKAVVYVPEKDIPKVIGKGGKRIKKIEK 508 (602)
T ss_pred HHHHHHHHHHHHHhc--CCceEEEEe-cCCeEEEEEChhhhhHHhccCcchHHHHHH
Confidence 344566666666666 556667776 455666655445556799999999987665
No 59
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=37.04 E-value=68 Score=29.43 Aligned_cols=54 Identities=17% Similarity=0.343 Sum_probs=31.2
Q ss_pred HHHHHHHhhccCCeeeeEEEEcCCe----EEEEEEeccc-ceeeccCcccHHHHHHHHH
Q psy17938 15 LDEFLTRELAEDGYSGVEIRFTPAR----TEIIIMATRT-QNVLGDKGRRIRELTSVVQ 68 (307)
Q Consensus 15 IRefl~k~l~~AGIs~IeI~Rt~~~----I~I~I~tarP-g~IIGr~G~~IkkL~~~Lq 68 (307)
+.+.+.-++.+-.=+-++|..-.+- +.+.+-..-| |..+|++|++++.+++.|.
T Consensus 48 ~~~L~~~evpEi~~g~i~ik~i~rd~r~av~~~~~~~d~vG~~iG~~G~rvk~i~~eLg 106 (190)
T COG0195 48 LEKLFEIEVPEIGDGVIEIKCVARDPRAAVVSNVVKIDPVGACIGKRGSRVKAVSEELG 106 (190)
T ss_pred HHHHHHhhcccccCCcEEEEEEEeccccceEEeecCcCchhhhccCCChHHHHHHHHhC
Confidence 3344444554443334555554311 3333333334 8899999999999888765
No 60
>PF13653 GDPD_2: Glycerophosphoryl diester phosphodiesterase family; PDB: 3RLG_A 2F9R_B 1XX1_A 3RLH_A.
Probab=35.30 E-value=25 Score=23.17 Aligned_cols=17 Identities=6% Similarity=-0.109 Sum_probs=13.5
Q ss_pred ChhhhhhhhcCCceeEE
Q psy17938 106 GLAVRRYPAIDAQYCSL 122 (307)
Q Consensus 106 Rv~FRRAMkaGAkGIKI 122 (307)
...+|.+|.+|+.||-+
T Consensus 10 ~~~~~~~l~~GVDgI~T 26 (30)
T PF13653_consen 10 PASWRELLDLGVDGIMT 26 (30)
T ss_dssp HHHHHHHHHHT-SEEEE
T ss_pred HHHHHHHHHcCCCEeeC
Confidence 45789999999999976
No 61
>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=35.18 E-value=1.6e+02 Score=29.33 Aligned_cols=62 Identities=26% Similarity=0.391 Sum_probs=44.3
Q ss_pred HHHHHHHHHhhccCCeeeeEE---EEcC-CeEEEEEEecccc-----eeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q psy17938 13 AELDEFLTRELAEDGYSGVEI---RFTP-ARTEIIIMATRTQ-----NVLGDKGRRIRELTSVVQKRFKFADGAIEL 80 (307)
Q Consensus 13 ~kIRefl~k~l~~AGIs~IeI---~Rt~-~~I~I~I~tarPg-----~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I 80 (307)
..+++.|..+.++-.=+-|+| -|-| .+++|-+++..|+ ..+|.+|.+++.+.+.|. +.+|+|
T Consensus 200 ~~v~~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~------ge~Idi 270 (341)
T TIGR01953 200 EFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELN------GEKIDI 270 (341)
T ss_pred HHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhC------CCeEEE
Confidence 456777777776542222444 5555 7999999998875 589999999999888774 355555
No 62
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.21 E-value=3.4e+02 Score=24.16 Aligned_cols=87 Identities=15% Similarity=0.208 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHhhccCCeee--eEEEEcCCeEEEEEEecccceeeccCcccH---HHHHHHHHHHhCCCCCeEEEEEEEe
Q psy17938 11 FRAELDEFLTRELAEDGYSG--VEIRFTPARTEIIIMATRTQNVLGDKGRRI---RELTSVVQKRFKFADGAIELYAEKV 85 (307)
Q Consensus 11 i~~kIRefl~k~l~~AGIs~--IeI~Rt~~~I~I~I~tarPg~IIGr~G~~I---kkL~~~LqK~~~~~~~kI~I~I~eV 85 (307)
+..++.+.++.-+...|+.= |++.+....-.+-|++.+|| |-.+ +++.+.+.-.+..+++-..=+..||
T Consensus 6 ~~~~v~~liep~~~~lG~ELv~ve~~~~~~~~~lrI~id~~g------~v~lddC~~vSr~is~~LD~edpi~~~Y~LEV 79 (153)
T COG0779 6 ITEKVTELIEPVVESLGFELVDVEFVKEGRDSVLRIYIDKEG------GVTLDDCADVSRAISALLDVEDPIEGAYFLEV 79 (153)
T ss_pred hHHHHHHHHHHhHhhcCcEEEEEEEEEcCCCcEEEEEeCCCC------CCCHHHHHHHHHHHHHHhccCCcccccEEEEe
Confidence 55678888888888888765 55555554566666777773 3344 6777788888865555556778999
Q ss_pred cCCCcCHHHHHHHHHHHHHcChhhhhh
Q psy17938 86 ATRGLCAIAQAESLRYKLIGGLAVRRY 112 (307)
Q Consensus 86 knP~l~A~lLAe~IA~QLE~Rv~FRRA 112 (307)
..|+++ ..|.+-..|+|.
T Consensus 80 SSPGld---------RpL~~~~~f~r~ 97 (153)
T COG0779 80 SSPGLD---------RPLKTAEHFARF 97 (153)
T ss_pred eCCCCC---------CCcCCHHHHHHh
Confidence 999886 334444556654
No 63
>KOG2192|consensus
Probab=33.45 E-value=35 Score=33.53 Aligned_cols=34 Identities=18% Similarity=0.384 Sum_probs=27.0
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHh
Q psy17938 38 ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRF 71 (307)
Q Consensus 38 ~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~ 71 (307)
-.++|-+..-..|.|||++|++|+.|+.+..-..
T Consensus 48 ~e~ril~~sk~agavigkgg~nik~lr~d~na~v 81 (390)
T KOG2192|consen 48 VELRILLQSKNAGAVIGKGGKNIKALRTDYNASV 81 (390)
T ss_pred eeEEEEEecccccceeccccccHHHHhhhcccee
Confidence 3567777888899999999999999988654433
No 64
>COG1302 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.92 E-value=2.8e+02 Score=24.18 Aligned_cols=65 Identities=12% Similarity=0.179 Sum_probs=42.2
Q ss_pred HHHhhccCCeee-eEEEEcCCe-EEEEEEecccceeeccCcccH--------HHHHHHHHHHhCCCCCeEEEEEEEecCC
Q psy17938 19 LTRELAEDGYSG-VEIRFTPAR-TEIIIMATRTQNVLGDKGRRI--------RELTSVVQKRFKFADGAIELYAEKVATR 88 (307)
Q Consensus 19 l~k~l~~AGIs~-IeI~Rt~~~-I~I~I~tarPg~IIGr~G~~I--------kkL~~~LqK~~~~~~~kI~I~I~eVknP 88 (307)
+.+.+.+.++++ +.++...+. +.|.+|+.-+ =|..| +.++..+++..++.-..|+|++.-|.-|
T Consensus 44 ~~e~l~~~n~~kGV~Ve~~~~~~v~VDvyi~v~------YGv~IpeVa~~Iq~~V~~~v~~mtgl~v~~VNV~V~gV~~~ 117 (131)
T COG1302 44 LTEKLGKENVTKGVKVEVGEDQSVAVDVYIIVE------YGVKIPEVAENIQERVKEEVENMTGLKVVEVNVHVVGVKVK 117 (131)
T ss_pred HHHHhCccccCCCeEEEecCCCcEEEEEEEEEe------cCCchHHHHHHHHHHHHHHHHHhhCCceEEEEEEEEEeEec
Confidence 334445556654 889886554 8887776332 24444 5566777778888767888888777655
Q ss_pred C
Q psy17938 89 G 89 (307)
Q Consensus 89 ~ 89 (307)
.
T Consensus 118 k 118 (131)
T COG1302 118 K 118 (131)
T ss_pred C
Confidence 3
No 65
>PF09462 Mus7: Mus7/MMS22 family; InterPro: IPR019021 Methyl methanesulphonate-sensitivity protein 22 (MMS22), along with MMS1, is involved in protection against replication-dependent DNA damage. MMS22 may act by restoring active replication forks, repairing unusual DNA structures, and/or preventing aberrant DNA rearrangement at arrested replication forks, including the repair of double-stranded DNA breaks created by the cleavage reaction of topoisomerase II [].
Probab=32.64 E-value=1.3e+02 Score=32.02 Aligned_cols=115 Identities=17% Similarity=0.187 Sum_probs=69.6
Q ss_pred HHhhcCCCCc-cchhhhhhhhhhccCCCccccccccccccccccccccHHHHHHHHhhccccchhccCCchhHHHHHHHH
Q psy17938 159 IVSLKEVCKP-DIIIALWEYFHKRLNSNFVLKSMPFAYTLSCLNSNRSVLEVLTHVEQMISSTRIQKNEENSYTLFLRML 237 (307)
Q Consensus 159 i~~~w~~~~~-~~v~~LWeyfsK~Lns~F~~~~~~l~~~~~~~~~~~s~l~~~~~c~~~~~~~~~~~~~~~Sy~~FL~iL 237 (307)
.++-|++... +++..|-|.|.+|==..|.- +.. .++|. .+++--...+. .. .+.++.||+||.+|
T Consensus 71 L~~~w~W~~~~~ii~~l~d~F~~r~f~nl~~--E~~------~~~P~----fl~~l~~~~~l-~~-~~~d~~F~iFLklL 136 (614)
T PF09462_consen 71 LISRWGWRICEPIILQLFDFFKSRKFANLRN--EEV------YDSPS----FLEQLDTRPSL-EI-EPKDTCFHIFLKLL 136 (614)
T ss_pred HhhccCCCCchHHHHHHHHHHhhcccCCCCc--ccc------cCCch----HHHhcccCCCc-CC-CCCCcHHHHHHHHH
Confidence 3777877333 78889999999993223321 110 11122 22222222221 12 33667999999999
Q ss_pred HHHHhhc---cc--Ccc--cccccc--cc-cCCCCc-----hhhHHHHHHHHHHHHHHhccccccchh
Q psy17938 238 GIYLLKY---NH--EQR--IWNQVK--GL-KSPFTP-----AVGYYYYYCGQILLSVYTASFHFNCRY 290 (307)
Q Consensus 238 a~~l~~~---~~--~~~--~w~qik--gR-yskf~~-----e~gl~nf~~lfl~la~~~~~~~~~~~~ 290 (307)
|..++.. .. ..+ .|+=++ +| |.|=.| -.-|.|=+.|.++|+-.+.. +||.
T Consensus 137 ~~~~~~L~~~~~~~~i~~lv~Rl~P~~~~~y~k~~~~~~~dl~aL~Nh~~Ll~~L~~~sp~---~~r~ 201 (614)
T PF09462_consen 137 ALAISGLRQLYDSKKIRNLVSRLLPNHGRQYPKEQPIHQRDLAALRNHHNLLCTLYWASPP---NLRP 201 (614)
T ss_pred HHHHHHHHhcchhHHHHHHHHHHcCCCCcccCCCCCcchHHHHHHHhHHHHHHHHHHHCCc---chhh
Confidence 9988764 21 111 454433 55 776665 56799999999999988874 5664
No 66
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=32.33 E-value=1.6e+02 Score=29.66 Aligned_cols=56 Identities=23% Similarity=0.367 Sum_probs=41.4
Q ss_pred HHHHHHHHHhhccCCeeeeEEE---EcC-CeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q psy17938 13 AELDEFLTRELAEDGYSGVEIR---FTP-ARTEIIIMATRTQ-----NVLGDKGRRIRELTSVVQ 68 (307)
Q Consensus 13 ~kIRefl~k~l~~AGIs~IeI~---Rt~-~~I~I~I~tarPg-----~IIGr~G~~IkkL~~~Lq 68 (307)
..+++.|..+.++-.=+-|+|. |-| .+++|-+++..|+ ..||.+|.+++.+.+.|.
T Consensus 202 ~~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~ 266 (362)
T PRK12327 202 GLVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELK 266 (362)
T ss_pred HHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhC
Confidence 4567777777765433335554 555 7999999998875 589999999999888774
No 67
>PRK09509 fieF ferrous iron efflux protein F; Reviewed
Probab=31.76 E-value=1.5e+02 Score=28.09 Aligned_cols=72 Identities=14% Similarity=0.116 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHhhccCCeeeeEEEEcCCeEEEEEEeccccee-eccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q psy17938 11 FRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNV-LGDKGRRIRELTSVVQKRFKFADGAIELYAEK 84 (307)
Q Consensus 11 i~~kIRefl~k~l~~AGIs~IeI~Rt~~~I~I~I~tarPg~I-IGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~e 84 (307)
...+|++-+.+.-.-.++.++.+.+..+...|++|..-|+.+ +.+--+-.+++++.|++.++. ..+.|.++.
T Consensus 214 ~~~~I~~~i~~~~~v~~v~~l~~~~~G~~~~v~v~i~v~~~~~~~e~h~i~~~ie~~l~~~~~~--~~v~ihveP 286 (299)
T PRK09509 214 ERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQLHLEMEDNLPLVQAHMIADQVEQALLRRFPG--SDVIIHQDP 286 (299)
T ss_pred HHHHHHHHHHhCCCCcCceeeeeEeeCCeEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHhCCC--CEEEEEeCC
Confidence 456677766553233467788888888878888888776543 222222246677777776652 345555443
No 68
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=31.31 E-value=1.3e+02 Score=24.69 Aligned_cols=52 Identities=17% Similarity=0.191 Sum_probs=32.9
Q ss_pred EecccceeeccCccc---HHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHH
Q psy17938 45 MATRTQNVLGDKGRR---IRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKL 103 (307)
Q Consensus 45 ~tarPg~IIGr~G~~---IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~A~lLAe~IA~QL 103 (307)
|--+|-+.||++|-. ++++.+.|+++= =|.|.+ .++-..+..-+|+.|+++.
T Consensus 14 h~l~p~v~IGK~Glt~~vi~ei~~aL~~hE-----LIKVkv--l~~~~~~~~e~a~~i~~~~ 68 (95)
T TIGR00253 14 HHLKPVVLVGKNGLTEGVIKEIEQALEHRE-----LIKVKV--ATEDREDKTLIAEALVKET 68 (95)
T ss_pred CCCCCeEEECCCCCCHHHHHHHHHHHHhCC-----cEEEEe--cCCChhHHHHHHHHHHHHH
Confidence 567888999999854 577777777533 233432 4554455666666666554
No 69
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=30.52 E-value=1.7e+02 Score=29.65 Aligned_cols=56 Identities=23% Similarity=0.341 Sum_probs=41.3
Q ss_pred HHHHHHHHHhhccCCeeeeEE---EEcC-CeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q psy17938 13 AELDEFLTRELAEDGYSGVEI---RFTP-ARTEIIIMATRTQ-----NVLGDKGRRIRELTSVVQ 68 (307)
Q Consensus 13 ~kIRefl~k~l~~AGIs~IeI---~Rt~-~~I~I~I~tarPg-----~IIGr~G~~IkkL~~~Lq 68 (307)
..+++.|..+.++-.=+-||| -|-| .+++|-+++.-|+ ..||.+|.+++.+.+.|.
T Consensus 208 ~~v~~Lfe~EVPEI~dG~VeIk~IARepG~RtKVAV~S~d~~iDPvGacIG~~G~rI~~I~~eL~ 272 (374)
T PRK12328 208 KFLEALLELEVPEIKDGEVIIIHSARIPGERAKVALFSNNPNIDPIGATVGVKGVRINAVSKELN 272 (374)
T ss_pred HHHHHHHHHhCccccCCeEEEEEEeccCcceeEEEEEcCCCCCChHHhhcCCCcchHHHHHHHhC
Confidence 356777777777543233554 4555 7999999998885 589999999999888774
No 70
>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=30.22 E-value=77 Score=33.93 Aligned_cols=53 Identities=23% Similarity=0.383 Sum_probs=37.9
Q ss_pred HHHHHHHHhhc-cCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHh
Q psy17938 14 ELDEFLTRELA-EDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRF 71 (307)
Q Consensus 14 kIRefl~k~l~-~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~ 71 (307)
+|++=+.+.+. ++.|++||.+ +-+|.|||-.|..+..+ |.-+++|.+.|+|+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~e----gp~~~~~~~~~~~~~~~-~~~~~~~~~~~~~r~ 56 (630)
T TIGR03675 3 EIKEIINELLPKDIKITDVEFE----GPELVIYTKNPELFAKD-DDLVKELAKKLRKRI 56 (630)
T ss_pred HHHHHHHHhCCCCCeEEEEEEe----CCeEEEEeCCHHHhccc-hHHHHHHHHHhhceE
Confidence 34555555564 6789999986 67899999999887654 456677777777654
No 71
>PF00724 Oxidored_FMN: NADH:flavin oxidoreductase / NADH oxidase family; InterPro: IPR001155 The TIM-barrel fold is a closed barrel structure composed of an eight-fold repeat of beta-alpha units, where the eight parallel beta strands on the inside are covered by the eight alpha helices on the outside []. It is a widely distributed fold which has been found in many enzyme families that catalyse completely unrelated reactions []. The active site is always found at the C-terminal end of this domain. Proteins in this entry are a variety of NADH:flavin oxidoreductase/NADH oxidase enzymes, found mostly in bacteria or fungi, that contain a TIM-barrel fold. They commonly use FMN/FAD as cofactor and include: dimethylamine dehydrogenase trimethylamine dehydrogenase 12-oxophytodienoate reductase NADPH dehydrogenase NADH oxidase ; GO: 0010181 FMN binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3GKA_B 3P67_A 3F03_K 2ABA_A 1VYR_A 1GVO_A 3KFT_B 3P8I_A 1GVQ_A 3P74_A ....
Probab=29.96 E-value=34 Score=33.25 Aligned_cols=57 Identities=14% Similarity=0.130 Sum_probs=32.2
Q ss_pred hhhhhhhhcCCceeEEeeeccceeeEEEeeeeee-ecCCCc-----ccceEeeehhHHHHhhcCC
Q psy17938 107 LAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTL-HQCPGC-----RELRIILTFLDSIVSLKEV 165 (307)
Q Consensus 107 v~FRRAMkaGAkGIKI~~~~~~~~~~~~~~sgrl-ar~e~~-----~e~~i~l~~l~~i~~~w~~ 165 (307)
.+-|||.+||..||.|.|+.||= ..=..|-.- .|+--| ...|..+-.++-|...-.+
T Consensus 153 ~AA~~A~~AGfDGVEIH~ahGyL--l~qFLSp~~N~RtDeYGGs~ENR~Rf~~Eii~aIr~~vg~ 215 (341)
T PF00724_consen 153 QAARRAKEAGFDGVEIHAAHGYL--LSQFLSPLTNRRTDEYGGSLENRARFLLEIIEAIREAVGP 215 (341)
T ss_dssp HHHHHHHHTT-SEEEEEESTTSH--HHHHHSTTT---SSTTSSSHHHHHHHHHHHHHHHHHHHTG
T ss_pred HHHHHHHHhccCeEeecccchhh--hhheeeeccCCCchhhhhhhchhhHHHHHHHHHHHHHhcC
Confidence 46688999999999999888872 112222222 444443 3345555555665554444
No 72
>PRK13763 putative RNA-processing protein; Provisional
Probab=29.84 E-value=56 Score=29.21 Aligned_cols=67 Identities=16% Similarity=0.213 Sum_probs=45.9
Q ss_pred EEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEE----Eec---CCCcCHHHHHHHHHHHHHcChhhhhh
Q psy17938 40 TEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAE----KVA---TRGLCAIAQAESLRYKLIGGLAVRRY 112 (307)
Q Consensus 40 I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~----eVk---nP~l~A~lLAe~IA~QLE~Rv~FRRA 112 (307)
..+.|-..+-|.+||++|+.++.|++. ++. +|+++-. .|. .++.++..-|..+.+.+-...+...|
T Consensus 5 ~~i~IP~~kig~iIG~gGk~Ik~I~e~----tg~---~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~~e~A 77 (180)
T PRK13763 5 EYVKIPKDRIGVLIGKKGETKKEIEER----TGV---KLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSPEKA 77 (180)
T ss_pred EEEEcCHHHhhhHhccchhHHHHHHHH----HCc---EEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCHHHH
Confidence 345566678889999999999887764 432 2333222 233 56668888899998888887666666
Q ss_pred h
Q psy17938 113 P 113 (307)
Q Consensus 113 M 113 (307)
+
T Consensus 78 ~ 78 (180)
T PRK13763 78 L 78 (180)
T ss_pred H
Confidence 5
No 73
>PRK13763 putative RNA-processing protein; Provisional
Probab=28.42 E-value=70 Score=28.62 Aligned_cols=59 Identities=12% Similarity=0.175 Sum_probs=33.5
Q ss_pred ccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChhhhhh
Q psy17938 48 RTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRY 112 (307)
Q Consensus 48 rPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~A~lLAe~IA~QLE~Rv~FRRA 112 (307)
.-|.+||++|+.++.|++.-.-.+...+..|.| +-+| +..-.|......|-+..+--+|
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~i----~G~~--~~~~~A~~~I~~li~g~~~~~~ 163 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVAI----IGDP--EQVEIAREAIEMLIEGAPHGTV 163 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCCEEEE----EeCH--HHHHHHHHHHHHHHcCCCcHHH
Confidence 467899999988877665433322222333222 3344 5666666666666555444444
No 74
>PLN02411 12-oxophytodienoate reductase
Probab=28.00 E-value=33 Score=34.31 Aligned_cols=56 Identities=13% Similarity=0.121 Sum_probs=44.2
Q ss_pred hhhhhhhcCCceeEEeeeccceeeEEEeeeeee-ecCCCc-----ccceEeeehhHHHHhhcCC
Q psy17938 108 AVRRYPAIDAQYCSLLAQFGWSILILVVAVGTL-HQCPGC-----RELRIILTFLDSIVSLKEV 165 (307)
Q Consensus 108 ~FRRAMkaGAkGIKI~~~~~~~~~~~~~~sgrl-ar~e~~-----~e~~i~l~~l~~i~~~w~~ 165 (307)
+-+||++||..||.|.|+.|| |..-..|-.. .|+--| ...|..+-.++-|-...++
T Consensus 170 AA~rA~~AGFDGVEIH~AhGY--Ll~QFLSp~tN~RtDeYGGSlENR~RF~lEIi~aVr~~vg~ 231 (391)
T PLN02411 170 AALNAIRAGFDGIEIHGAHGY--LIDQFLKDGINDRTDEYGGSIENRCRFLMQVVQAVVSAIGA 231 (391)
T ss_pred HHHHHHHcCCCEEEEccccch--HHHHhCCCccCCCCCcCCCCHHHHhHHHHHHHHHHHHHcCC
Confidence 568899999999999999999 5555566655 666655 5778888888999888876
No 75
>KOG2192|consensus
Probab=25.95 E-value=27 Score=34.27 Aligned_cols=39 Identities=23% Similarity=0.497 Sum_probs=32.5
Q ss_pred EcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q psy17938 35 FTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 73 (307)
Q Consensus 35 Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~ 73 (307)
|.|-.++.-||-.-.|.+|||+|..|++|++.-.-+++.
T Consensus 120 ~~pce~rllihqs~ag~iigrngskikelrekcsarlki 158 (390)
T KOG2192|consen 120 PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKI 158 (390)
T ss_pred CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhh
Confidence 344566778899999999999999999999988877754
No 76
>COG1902 NemA NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]
Probab=25.43 E-value=46 Score=33.25 Aligned_cols=57 Identities=14% Similarity=0.150 Sum_probs=44.6
Q ss_pred hhhhhhhhcCCceeEEeeeccceeeEEEeeeeee-ecCCCcc-----cceEeeehhHHHHhhcCC
Q psy17938 107 LAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTL-HQCPGCR-----ELRIILTFLDSIVSLKEV 165 (307)
Q Consensus 107 v~FRRAMkaGAkGIKI~~~~~~~~~~~~~~sgrl-ar~e~~~-----e~~i~l~~l~~i~~~w~~ 165 (307)
-+-|||.+||..||+|.|+.|| |+.=..|-+- .|+--|- ..|..+-.++-+..-|.+
T Consensus 153 ~AA~rA~~AGFDgVEIH~AhGY--Li~qFlsp~tN~RtD~YGGSlENR~Rf~~EVv~aVr~~vg~ 215 (363)
T COG1902 153 RAARRAKEAGFDGVEIHGAHGY--LLSQFLSPLTNKRTDEYGGSLENRARFLLEVVDAVREAVGA 215 (363)
T ss_pred HHHHHHHHcCCCEEEEeeccch--HHHHhcCCccCCCCCccCCcHHHHHHHHHHHHHHHHHHhCC
Confidence 4667889999999999999996 4444455555 7776665 677777889999999999
No 77
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=24.70 E-value=3.5e+02 Score=25.48 Aligned_cols=87 Identities=18% Similarity=0.174 Sum_probs=49.3
Q ss_pred HHHHHHHHHhhccCCeeeeEEEEc--------------CCeEEE-EEEecccceeeccCcc-----cHHHHHHHHHHHhC
Q psy17938 13 AELDEFLTRELAEDGYSGVEIRFT--------------PARTEI-IIMATRTQNVLGDKGR-----RIRELTSVVQKRFK 72 (307)
Q Consensus 13 ~kIRefl~k~l~~AGIs~IeI~Rt--------------~~~I~I-~I~tarPg~IIGr~G~-----~IkkL~~~LqK~~~ 72 (307)
..+++||.+.+......++-|-=- .++++| -++=..|. .||++=. ++++|.+.+++.
T Consensus 69 ~~L~~ff~~~Lg~~~~tnviiVG~GnlG~All~Y~f~~~~~~~iv~~FDv~~~-~VG~~~~~v~V~~~d~le~~v~~~-- 145 (211)
T COG2344 69 KYLRDFFDDLLGQDKTTNVIIVGVGNLGRALLNYNFSKKNGMKIVAAFDVDPD-KVGTKIGDVPVYDLDDLEKFVKKN-- 145 (211)
T ss_pred HHHHHHHHHHhCCCcceeEEEEccChHHHHHhcCcchhhcCceEEEEecCCHH-HhCcccCCeeeechHHHHHHHHhc--
Confidence 467888888887666555555321 123333 34455665 6776533 346666655532
Q ss_pred CCCCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChhhhhhhhcCCceeE
Q psy17938 73 FADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYPAIDAQYCS 121 (307)
Q Consensus 73 ~~~~kI~I~I~eVknP~l~A~lLAe~IA~QLE~Rv~FRRAMkaGAkGIK 121 (307)
.|++-+ +.=|.-.|+-+|+.+ .+||+|||-
T Consensus 146 ----dv~iai--LtVPa~~AQ~vad~L-------------v~aGVkGIl 175 (211)
T COG2344 146 ----DVEIAI--LTVPAEHAQEVADRL-------------VKAGVKGIL 175 (211)
T ss_pred ----CccEEE--EEccHHHHHHHHHHH-------------HHcCCceEE
Confidence 344433 444555666555543 468999984
No 78
>PRK05090 hypothetical protein; Validated
Probab=24.63 E-value=3.9e+02 Score=21.89 Aligned_cols=40 Identities=13% Similarity=0.199 Sum_probs=28.3
Q ss_pred CcccHHHHHHHHHHHhCCCCCeEEE--------EEEEecCCCcCHHHH
Q psy17938 56 KGRRIRELTSVVQKRFKFADGAIEL--------YAEKVATRGLCAIAQ 95 (307)
Q Consensus 56 ~G~~IkkL~~~LqK~~~~~~~kI~I--------~I~eVknP~l~A~lL 95 (307)
+|+-=++|.+.|.+.|+....+|+| ...+|..|+-.+..+
T Consensus 44 eGkAN~ali~~LAk~l~v~ks~I~i~~G~tsr~K~v~I~~~~~~~~~~ 91 (95)
T PRK05090 44 DGQANAHLLKFLAKQFRVAKSQVVIEKGELGRHKQVRIINPQQIPPEI 91 (95)
T ss_pred CChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEEEEcCcccChHhH
Confidence 4555689999999999987666754 566777775544433
No 79
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=24.23 E-value=1.9e+02 Score=23.84 Aligned_cols=52 Identities=12% Similarity=0.148 Sum_probs=33.9
Q ss_pred EecccceeeccCccc---HHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHH
Q psy17938 45 MATRTQNVLGDKGRR---IRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKL 103 (307)
Q Consensus 45 ~tarPg~IIGr~G~~---IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~A~lLAe~IA~QL 103 (307)
|.-+|-+.||++|-. ++++.+.|+.+= =|.|.+ ..+-..+..-+|+.|+++.
T Consensus 16 h~l~Pvv~IGk~Glt~~vi~ei~~aL~~hE-----LIKvkv--~~~~~~~~~e~~~~i~~~~ 70 (97)
T PRK10343 16 HPLKPVVLLGSNGLTEGVLAEIEQALEHHE-----LIKVKI--ATEDRETKTLIVEAIVRET 70 (97)
T ss_pred CCCCCeEEECCCCCCHHHHHHHHHHHHHCC-----cEEEEe--cCCChhHHHHHHHHHHHHH
Confidence 667888999999864 577777777532 234433 3444456677777777665
No 80
>KOG1423|consensus
Probab=24.06 E-value=2.9e+02 Score=28.04 Aligned_cols=42 Identities=12% Similarity=0.322 Sum_probs=29.4
Q ss_pred CeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeEEEEE
Q psy17938 38 ARTEIIIMATRTQ---NVLGDKGRRIREL----TSVVQKRFKFADGAIELYA 82 (307)
Q Consensus 38 ~~I~I~I~tarPg---~IIGr~G~~IkkL----~~~LqK~~~~~~~kI~I~I 82 (307)
..|++.+.+.++. ++||++|..|.+| .++|...|+ ++|.+-+
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~dL~~if~---r~V~l~l 374 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANEDLEDIFQ---RKVFLRL 374 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHHHHHHhh---ceeeEEE
Confidence 4677777777765 6999999998665 456676774 4555543
No 81
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=23.98 E-value=1.2e+02 Score=23.45 Aligned_cols=47 Identities=19% Similarity=0.118 Sum_probs=31.7
Q ss_pred EEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCC
Q psy17938 42 IIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATR 88 (307)
Q Consensus 42 I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP 88 (307)
|+|...+++.--+.+.+-++++++.+.+.+|..+..|.|-++||..-
T Consensus 4 v~Ik~~~g~~~~~~K~~la~~vT~~~~~~lg~~~~~i~Viieev~~~ 50 (69)
T COG1942 4 VNIKLFEGRLDEEQKAELAAEVTEVTVETLGKDPSAIHVIIEEVPPE 50 (69)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHHhCCCcccEEEEEEecChh
Confidence 44555553222222333468899999999998777889988988753
No 82
>PRK10605 N-ethylmaleimide reductase; Provisional
Probab=23.74 E-value=48 Score=32.77 Aligned_cols=57 Identities=12% Similarity=0.152 Sum_probs=43.5
Q ss_pred hhhhhhhhcCCceeEEeeeccceeeEEEeeeeee-ecCCCc-----ccceEeeehhHHHHhhcCC
Q psy17938 107 LAVRRYPAIDAQYCSLLAQFGWSILILVVAVGTL-HQCPGC-----RELRIILTFLDSIVSLKEV 165 (307)
Q Consensus 107 v~FRRAMkaGAkGIKI~~~~~~~~~~~~~~sgrl-ar~e~~-----~e~~i~l~~l~~i~~~w~~ 165 (307)
.+-|||.+||..||.|.|+.|| |..-..|-.. .|+--| ...|..+-.++-|-..+.+
T Consensus 163 ~AA~rA~~AGfDGVEIh~ahGy--Ll~qFLSp~~N~RtDeYGGslENR~Rf~~Eiv~aVr~~vg~ 225 (362)
T PRK10605 163 QAIANAREAGFDLVELHSAHGY--LLHQFLSPSSNQRTDQYGGSVENRARLVLEVVDAGIAEWGA 225 (362)
T ss_pred HHHHHHHHcCCCEEEEcccccc--hHHHhcCCcCCCCCCcCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 3668999999999999999888 4444455555 555544 5678888889999988877
No 83
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=23.39 E-value=1.2e+02 Score=28.19 Aligned_cols=58 Identities=12% Similarity=0.173 Sum_probs=37.9
Q ss_pred cceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChhhhhh
Q psy17938 49 TQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRY 112 (307)
Q Consensus 49 Pg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVknP~l~A~lLAe~IA~QLE~Rv~FRRA 112 (307)
-|.+||++|+..+.+.+.-.-........|. -+-.| ...-+|+...+.|-+..+...+
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~I~V~g~tVa----iiG~~--~~v~iAr~AVemli~G~~h~~V 170 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVYISVYGKTVA----IIGGF--EQVEIAREAVEMLINGAPHGKV 170 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCeEEEeCcEEE----EecCh--hhhHHHHHHHHHHHcCCCchhH
Confidence 4689999998776555433322222223333 36666 7788999999999888876664
No 84
>PF01545 Cation_efflux: Cation efflux family; InterPro: IPR002524 Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [, ], however others are implicated in ion uptake []. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3BYP_B 3BYR_A 3H90_B 2QFI_B 2ZZT_A.
Probab=22.22 E-value=2.5e+02 Score=25.69 Aligned_cols=64 Identities=3% Similarity=0.044 Sum_probs=40.3
Q ss_pred hhHHHHHHHHHHHhhccCCeeeeEEEEcCC-eEEEEEEeccccee-eccCcccHHHHHHHHHHHhC
Q psy17938 9 GVFRAELDEFLTRELAEDGYSGVEIRFTPA-RTEIIIMATRTQNV-LGDKGRRIRELTSVVQKRFK 72 (307)
Q Consensus 9 ~~i~~kIRefl~k~l~~AGIs~IeI~Rt~~-~I~I~I~tarPg~I-IGr~G~~IkkL~~~LqK~~~ 72 (307)
.....++++.+++.=.-.++.++.+.+... ...+.+|...|+.. +++.-+..+++++.+++.++
T Consensus 204 ~~~~~~i~~~i~~~~~v~~v~~~~~~~~g~~~~~v~i~v~v~~~~~v~~~~~i~~~i~~~l~~~~~ 269 (284)
T PF01545_consen 204 PELVEKIRRIIESVPGVIEVHDLRVWQVGRNKYVVEIHVQVDPDMSVEEAHEIRERIEKRLREKFP 269 (284)
T ss_dssp HHHHHHHHHHHHHTSS-SEEEEEEEEEETT-EEEEEEEEEETTTSBHHHHHHHHHHHHHHHHHHST
T ss_pred ccchhHHHHhhccCCceEeccceEEEEecCCcEEEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCC
Confidence 344567777776632234577788888776 88888888776554 22222234677777777773
No 85
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=22.03 E-value=70 Score=24.44 Aligned_cols=22 Identities=27% Similarity=0.225 Sum_probs=16.7
Q ss_pred cCHHHHHHHHHHHHHcChhhhhhhh
Q psy17938 90 LCAIAQAESLRYKLIGGLAVRRYPA 114 (307)
Q Consensus 90 l~A~lLAe~IA~QLE~Rv~FRRAMk 114 (307)
..|.=+|+.++.+ ++|||.|=+
T Consensus 2 ~~ATdlAD~LVr~---GipFR~AH~ 23 (70)
T PF14698_consen 2 STATDLADYLVRK---GIPFREAHH 23 (70)
T ss_dssp GGHHHHHHHHHHT---TS-HHHHHH
T ss_pred ccHHHHHHHHHHc---CCCHHHHHH
Confidence 4577788888876 999999865
No 86
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=21.36 E-value=2.8e+02 Score=28.94 Aligned_cols=61 Identities=18% Similarity=0.275 Sum_probs=42.9
Q ss_pred HHHHHHHHhhccCCeeeeE---EEEc--------CCeEEEEEEecccc-----eeeccCcccHHHHHHHHHHHhCCCCCe
Q psy17938 14 ELDEFLTRELAEDGYSGVE---IRFT--------PARTEIIIMATRTQ-----NVLGDKGRRIRELTSVVQKRFKFADGA 77 (307)
Q Consensus 14 kIRefl~k~l~~AGIs~Ie---I~Rt--------~~~I~I~I~tarPg-----~IIGr~G~~IkkL~~~LqK~~~~~~~k 77 (307)
.+++.|..+.++-.=+-|+ |-|. ..+++|-+++.-|+ ..||.+|.+|+.+.+.|. +.+
T Consensus 228 lv~~Lfe~EVPEI~dG~VeIk~IAREa~~~~ripG~RtKVAV~S~d~~VDPvGacVG~kG~RI~~I~~eL~------gEk 301 (449)
T PRK12329 228 LVVYLFENEVPEIEEGVVRIVAVAREANPPSRYVGPRTKIAVDTLERDVDPVGACIGARGSRIQAVVNELR------GEK 301 (449)
T ss_pred HHHHHHHhhCcccccCeEEEEEEEecCCCCCCCCcceeEEEEEcCCCCCChhhccCCCCcchHHHHHHHhC------CCe
Confidence 4667777777643322244 4454 46899999998875 589999999999888774 356
Q ss_pred EEE
Q psy17938 78 IEL 80 (307)
Q Consensus 78 I~I 80 (307)
|+|
T Consensus 302 IDV 304 (449)
T PRK12329 302 IDV 304 (449)
T ss_pred EEE
Confidence 665
No 87
>cd00554 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits.
Probab=21.07 E-value=2.3e+02 Score=25.24 Aligned_cols=42 Identities=12% Similarity=0.196 Sum_probs=33.0
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q psy17938 38 ARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK 84 (307)
Q Consensus 38 ~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~e 84 (307)
..+.++|-+.+|.+ +.-++++++.|.+.++....+|+|++.-
T Consensus 91 ~niD~tii~e~PKi-----~p~~~~m~~~ls~~L~~~~~~V~iKatT 132 (153)
T cd00554 91 VNIDITIIAERPKI-----SPYREAMRANLAELLGIPPSRVNIKATT 132 (153)
T ss_pred EEEEEEEEecCCcc-----hHHHHHHHHHHHHHhCCCCceEEEEEec
Confidence 35677888999955 5678899999999998876778887654
No 88
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=20.84 E-value=83 Score=24.86 Aligned_cols=54 Identities=11% Similarity=0.045 Sum_probs=31.1
Q ss_pred EEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecC
Q psy17938 33 IRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEKVAT 87 (307)
Q Consensus 33 I~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I~I~eVkn 87 (307)
+.|+.+.+-|.|.+..| .=...|.+=.+.|.+.|+...|..+..|.|.+.|...
T Consensus 23 ~~Rs~~~v~I~It~~~g-Rs~e~K~~ly~~l~~~L~~~~gi~p~Dv~I~l~e~~~ 76 (82)
T PF14552_consen 23 IDRSDDFVIIQITSGAG-RSTEQKKALYRALAERLAEKLGIRPEDVMIVLVENPR 76 (82)
T ss_dssp -TS-TT-EEEEEEECS----HHHHHHHHHHHHHHHHHHH---GGGEEEEEEEE-G
T ss_pred CCCCCCEEEEEEEECCC-CCHHHHHHHHHHHHHHHHHHcCCCHHHEEEEEEECCc
Confidence 77888888888766543 2122222224778888888899888889998888764
No 89
>KOG1676|consensus
Probab=20.78 E-value=63 Score=34.59 Aligned_cols=27 Identities=30% Similarity=0.546 Sum_probs=24.0
Q ss_pred eEEEEEEecccceeeccCcccHHHHHH
Q psy17938 39 RTEIIIMATRTQNVLGDKGRRIRELTS 65 (307)
Q Consensus 39 ~I~I~I~tarPg~IIGr~G~~IkkL~~ 65 (307)
..+|.|=+.|-|.|||++|+.|++|++
T Consensus 140 tqeI~IPa~k~GlIIGKgGETikqlqe 166 (600)
T KOG1676|consen 140 TQEILIPANKCGLIIGKGGETIKQLQE 166 (600)
T ss_pred eeeeccCccceeeEeccCccHHHHHHh
Confidence 667788889999999999999999886
No 90
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=20.29 E-value=1.2e+02 Score=32.42 Aligned_cols=56 Identities=18% Similarity=0.317 Sum_probs=42.5
Q ss_pred HHHHHHHHHhhc-cCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q psy17938 13 AELDEFLTRELA-EDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF 73 (307)
Q Consensus 13 ~kIRefl~k~l~-~AGIs~IeI~Rt~~~I~I~I~tarPg~IIGr~G~~IkkL~~~LqK~~~~ 73 (307)
.++++-+.+.+. ++.|.+||.+ +-++.||+..|..+.. +|.-+++|.+.|+|+.-.
T Consensus 8 ~ei~~~i~~~~p~~~~It~vefE----GPelvvY~k~P~~~~~-~~dlik~lAk~lrKRI~i 64 (637)
T COG1782 8 EEIRNKINEILPSDVKITDVEFE----GPELVVYTKNPELFAK-DGDLIKDLAKDLRKRIII 64 (637)
T ss_pred HHHHHHHHHhCCCcCceEEEEec----CCeEEEEecCHHHhcc-chhHHHHHHHHHhhceEe
Confidence 457777777776 4777777764 6788999999987754 456788999999887754
No 91
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=20.25 E-value=3e+02 Score=28.63 Aligned_cols=62 Identities=21% Similarity=0.395 Sum_probs=44.9
Q ss_pred HHHHHHHHHhhccCCeeeeEE---EEcC-CeEEEEEEecccc-----eeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q psy17938 13 AELDEFLTRELAEDGYSGVEI---RFTP-ARTEIIIMATRTQ-----NVLGDKGRRIRELTSVVQKRFKFADGAIEL 80 (307)
Q Consensus 13 ~kIRefl~k~l~~AGIs~IeI---~Rt~-~~I~I~I~tarPg-----~IIGr~G~~IkkL~~~LqK~~~~~~~kI~I 80 (307)
..+++.|..+.++-.=+-|+| -|.| .+.+|-+++.-|. ..||.+|.+|+.+.+.|. +.+|+|
T Consensus 202 ~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~------ge~Idi 272 (470)
T PRK09202 202 EFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELG------GEKIDI 272 (470)
T ss_pred HHHHHHHHHhCcccccCeEEEEEEeecCcceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhC------CCeEEE
Confidence 456777777777543333555 4555 7999999988874 589999999999888774 456665
No 92
>KOG1676|consensus
Probab=20.11 E-value=78 Score=33.94 Aligned_cols=27 Identities=19% Similarity=0.429 Sum_probs=21.7
Q ss_pred eEEEEEEecccceeeccCcccHHHHHH
Q psy17938 39 RTEIIIMATRTQNVLGDKGRRIRELTS 65 (307)
Q Consensus 39 ~I~I~I~tarPg~IIGr~G~~IkkL~~ 65 (307)
..+|.|=-.+-|+|||++|+.||+|..
T Consensus 231 ~~~V~VPr~~VG~IIGkgGE~IKklq~ 257 (600)
T KOG1676|consen 231 TREVKVPRSKVGIIIGKGGEMIKKLQN 257 (600)
T ss_pred eeEEeccccceeeEEecCchHHHHHhh
Confidence 566666667778999999999998775
Done!