Query 029201
Match_columns 197
No_of_seqs 136 out of 1131
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 09:07:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029201.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029201hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0092 RpsC Ribosomal protein 100.0 4.4E-65 9.6E-70 431.8 20.1 187 5-196 5-199 (233)
2 PTZ00084 40S ribosomal protein 100.0 2.4E-64 5.3E-69 426.9 18.3 189 4-192 4-192 (220)
3 TIGR01008 rpsC_E_A ribosomal p 100.0 6.3E-63 1.4E-67 412.0 21.2 186 8-195 2-187 (195)
4 PRK04191 rps3p 30S ribosomal p 100.0 1.1E-61 2.3E-66 408.3 20.2 189 5-195 1-189 (207)
5 CHL00048 rps3 ribosomal protei 100.0 3.6E-58 7.7E-63 388.6 23.1 185 6-192 17-213 (214)
6 TIGR01009 rpsC_bact ribosomal 100.0 1.6E-57 3.4E-62 384.0 21.1 184 6-194 17-208 (211)
7 PRK00310 rpsC 30S ribosomal pr 100.0 6.8E-57 1.5E-61 384.8 22.1 183 6-193 17-207 (232)
8 KOG3181 40S ribosomal protein 100.0 1.8E-45 3.8E-50 304.2 10.9 191 1-191 1-191 (244)
9 PF00189 Ribosomal_S3_C: Ribos 100.0 4E-28 8.7E-33 178.1 9.8 83 104-188 1-85 (85)
10 cd02413 40S_S3_KH K homology R 99.9 4.9E-21 1.1E-25 139.7 10.8 80 15-94 1-80 (81)
11 cd02412 30S_S3_KH K homology R 99.8 6.5E-20 1.4E-24 140.3 9.8 87 6-94 16-109 (109)
12 cd02411 archeal_30S_S3_KH K ho 99.8 2.5E-18 5.4E-23 126.0 8.6 84 8-93 2-85 (85)
13 PF07650 KH_2: KH domain syndr 99.5 2.9E-14 6.3E-19 102.1 6.9 77 20-96 1-78 (78)
14 cd02409 KH-II KH-II (K homolo 98.8 3.2E-08 6.9E-13 67.2 7.8 65 22-88 1-67 (68)
15 smart00322 KH K homology RNA-b 97.5 0.00013 2.9E-09 48.4 3.6 68 43-110 2-69 (69)
16 cd02414 jag_KH jag_K homology 96.8 0.0072 1.6E-07 43.1 7.1 56 23-78 2-58 (77)
17 PF13083 KH_4: KH domain; PDB: 96.1 0.0076 1.6E-07 42.3 3.6 67 20-86 3-71 (73)
18 COG1847 Jag Predicted RNA-bind 95.3 0.096 2.1E-06 44.6 7.9 106 19-124 65-185 (208)
19 PRK01064 hypothetical protein; 94.7 0.71 1.5E-05 33.5 10.0 68 22-90 5-76 (78)
20 cd02410 archeal_CPSF_KH The ar 94.0 0.85 1.8E-05 36.9 10.0 85 21-119 54-139 (145)
21 cd02134 NusA_KH NusA_K homolog 93.9 0.21 4.7E-06 34.0 5.6 53 22-74 2-55 (61)
22 PRK08406 transcription elongat 93.3 0.23 5E-06 39.6 5.6 60 20-79 73-134 (140)
23 PRK02821 hypothetical protein; 93.0 1.6 3.4E-05 31.6 9.1 68 20-90 4-74 (77)
24 PRK00468 hypothetical protein; 91.5 3.5 7.7E-05 29.5 9.4 67 21-87 4-73 (75)
25 TIGR00436 era GTP-binding prot 91.1 0.92 2E-05 39.1 7.2 65 21-88 188-267 (270)
26 COG1837 Predicted RNA-binding 89.7 4 8.8E-05 29.5 8.4 67 21-87 4-73 (76)
27 PRK15494 era GTPase Era; Provi 89.6 1.9 4.1E-05 38.8 8.1 67 21-88 240-321 (339)
28 PRK00089 era GTPase Era; Revie 89.1 3.5 7.5E-05 35.6 9.2 67 21-88 195-274 (292)
29 COG1159 Era GTPase [General fu 84.9 11 0.00023 34.0 9.9 59 35-95 212-283 (298)
30 COG1782 Predicted metal-depend 82.3 10 0.00022 36.9 9.1 91 22-126 78-170 (637)
31 TIGR01952 nusA_arch NusA famil 81.9 2 4.4E-05 34.4 3.8 59 21-79 75-135 (141)
32 cd02393 PNPase_KH Polynucleoti 77.0 2.5 5.4E-05 28.7 2.5 30 45-74 3-32 (61)
33 TIGR03675 arCOG00543 arCOG0054 74.2 35 0.00077 33.6 10.6 84 21-118 71-155 (630)
34 PF13014 KH_3: KH domain 70.4 3.6 7.8E-05 25.6 1.9 18 56-73 3-20 (43)
35 TIGR01953 NusA transcription t 68.8 30 0.00064 31.6 8.2 62 19-86 200-270 (341)
36 PF05316 VAR1: Mitochondrial r 66.6 61 0.0013 29.8 9.6 121 65-188 156-347 (350)
37 cd00105 KH-I K homology RNA-bi 65.3 7.5 0.00016 25.4 2.8 27 47-73 3-29 (64)
38 PRK12327 nusA transcription el 64.0 39 0.00084 31.1 8.0 55 20-74 203-266 (362)
39 PF13184 KH_5: NusA-like KH do 63.1 11 0.00023 26.5 3.4 37 44-86 3-44 (69)
40 cd02396 PCBP_like_KH K homolog 60.5 8 0.00017 26.1 2.3 27 47-73 3-29 (65)
41 PF08731 AFT: Transcription fa 60.3 18 0.00039 28.0 4.4 35 17-53 3-37 (111)
42 cd05213 NAD_bind_Glutamyl_tRNA 59.8 80 0.0017 27.9 9.1 53 20-79 25-77 (311)
43 PRK12328 nusA transcription el 59.8 39 0.00084 31.4 7.2 57 18-74 207-272 (374)
44 PF00013 KH_1: KH domain syndr 56.5 4 8.6E-05 26.9 0.2 28 47-74 3-30 (60)
45 cd02394 vigilin_like_KH K homo 55.4 9.4 0.0002 25.2 1.9 27 48-74 4-30 (62)
46 PRK09202 nusA transcription el 53.9 64 0.0014 30.8 7.8 56 19-74 202-266 (470)
47 PRK06418 transcription elongat 50.3 65 0.0014 26.6 6.4 31 43-74 60-90 (166)
48 PRK09202 nusA transcription el 45.2 34 0.00075 32.6 4.6 53 21-73 279-331 (470)
49 COG4604 CeuD ABC-type enteroch 43.9 1.1E+02 0.0024 26.8 7.0 61 44-106 18-78 (252)
50 PF05201 GlutR_N: Glutamyl-tRN 41.1 52 0.0011 26.2 4.5 101 21-132 23-129 (152)
51 PRK12329 nusA transcription el 39.1 1.2E+02 0.0027 28.8 7.2 55 20-74 228-298 (449)
52 COG0195 NusA Transcription elo 37.3 1.1E+02 0.0024 25.6 6.0 35 39-74 69-106 (190)
53 TIGR03665 arCOG04150 arCOG0415 37.3 25 0.00055 28.6 2.1 59 53-114 7-67 (172)
54 PRK08406 transcription elongat 37.2 1E+02 0.0022 24.4 5.5 53 19-73 7-61 (140)
55 PRK06418 transcription elongat 36.7 1.3E+02 0.0029 24.7 6.3 60 21-86 102-163 (166)
56 PRK12328 nusA transcription el 36.1 85 0.0018 29.2 5.5 64 21-91 285-348 (374)
57 PF14480 DNA_pol3_a_NI: DNA po 35.5 1.4E+02 0.0031 20.3 6.9 56 26-87 18-73 (76)
58 COG1942 Uncharacterized protei 33.1 71 0.0015 22.4 3.6 46 48-93 4-49 (69)
59 COG0195 NusA Transcription elo 32.9 81 0.0017 26.5 4.5 52 21-72 118-170 (190)
60 PLN00203 glutamyl-tRNA reducta 32.4 3.1E+02 0.0068 26.4 8.9 53 21-80 110-162 (519)
61 COG1855 ATPase (PilT family) [ 31.9 60 0.0013 31.5 3.9 54 17-74 462-516 (604)
62 PF03780 Asp23: Asp23 family; 31.3 90 0.0019 22.6 4.1 58 34-91 47-107 (108)
63 KOG2192 PolyC-binding hnRNP-K 31.3 18 0.0004 32.5 0.4 38 41-78 120-157 (390)
64 PRK12327 nusA transcription el 31.1 78 0.0017 29.2 4.5 50 21-71 279-330 (362)
65 TIGR01952 nusA_arch NusA famil 30.5 92 0.002 24.9 4.2 43 28-71 18-60 (141)
66 TIGR01035 hemA glutamyl-tRNA r 29.9 1.8E+02 0.0039 26.9 6.7 35 21-55 26-60 (417)
67 TIGR01953 NusA transcription t 29.7 83 0.0018 28.7 4.4 49 21-69 277-326 (341)
68 cd00554 MECDP_synthase MECDP_s 29.4 2.3E+02 0.005 23.1 6.4 49 28-88 82-130 (153)
69 PF12685 SpoIIIAH: SpoIIIAH-li 29.0 2.1E+02 0.0045 23.6 6.3 57 24-86 139-195 (196)
70 PRK13763 putative RNA-processi 28.3 72 0.0016 26.2 3.4 66 47-114 6-73 (180)
71 PRK13764 ATPase; Provisional 28.0 97 0.0021 30.5 4.7 52 20-74 460-511 (602)
72 KOG2192 PolyC-binding hnRNP-K 27.4 78 0.0017 28.5 3.6 79 41-119 45-123 (390)
73 PRK00045 hemA glutamyl-tRNA re 26.0 3E+02 0.0064 25.4 7.4 34 21-54 28-61 (423)
74 COG4509 Uncharacterized protei 26.0 1.1E+02 0.0024 26.5 4.1 46 8-54 129-174 (244)
75 TIGR00013 taut 4-oxalocrotonat 25.9 1.1E+02 0.0025 19.8 3.5 31 63-93 18-48 (63)
76 TIGR01634 tail_P2_I phage tail 25.5 37 0.0008 27.1 1.1 78 88-169 26-114 (139)
77 PRK13763 putative RNA-processi 24.8 1.7E+02 0.0036 24.0 5.0 60 54-119 105-164 (180)
78 TIGR00151 ispF 2C-methyl-D-ery 24.5 2.7E+02 0.006 22.7 6.1 49 28-88 82-130 (155)
79 PF14698 ASL_C2: Argininosucci 24.4 61 0.0013 22.5 2.0 22 96-120 2-23 (70)
80 PF13684 Dak1_2: Dihydroxyacet 22.9 1E+02 0.0022 27.6 3.6 39 17-60 19-57 (313)
81 PRK13940 glutamyl-tRNA reducta 22.8 3.2E+02 0.0069 25.4 7.0 33 21-53 28-60 (414)
82 TIGR03675 arCOG00543 arCOG0054 22.0 1.1E+02 0.0025 30.1 4.0 53 20-77 3-56 (630)
83 KOG1423 Ras-like GTPase ERA [C 21.8 2.4E+02 0.0053 26.1 5.7 41 45-88 327-374 (379)
84 PF11324 DUF3126: Protein of u 21.6 1.3E+02 0.0028 21.0 3.1 20 65-86 1-20 (63)
85 cd00491 4Oxalocrotonate_Tautom 21.5 1.6E+02 0.0035 18.6 3.5 31 63-93 17-47 (58)
86 PRK12329 nusA transcription el 21.3 1.3E+02 0.0027 28.8 3.9 52 21-72 311-363 (449)
No 1
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.4e-65 Score=431.81 Aligned_cols=187 Identities=29% Similarity=0.373 Sum_probs=176.6
Q ss_pred ccccceEeecCcch-------HHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHh
Q 029201 5 ISKKRKFVADGVFF-------AELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRF 77 (197)
Q Consensus 5 ~~~~~~~~~~~~~~-------~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~ 77 (197)
+.|.|+||++...| .+||+||+++|.+||||+|+|+|+|++++|+||+++||+|||++|++|++|+..|+++|
T Consensus 5 ~~w~srwfa~~~~~~~~l~ed~kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~ 84 (233)
T COG0092 5 KDWKSRWFANKKEYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLF 84 (233)
T ss_pred ccchhhhccccccchHHHHHHHHHHHHHHHHHHhCCcceEEEEecCCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHh
Confidence 46899999976655 55999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeEEEEEEecCCCcCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHhcCCceeEEEEecccCccc-cceeecccCe
Q 029201 78 KFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQR-AKSMKFKDGY 156 (197)
Q Consensus 78 ~~~~~~i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~k~~i~~~~~~gakGikI~isGRL~G~r-AR~e~~~~G~ 156 (197)
+.+ +++|++.||++|++||+++|++||+|||+|++||||++++|+++|++||+||||+|||||+|+| ||+|||.+|+
T Consensus 85 g~~--~v~I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGAkGiki~vSGRL~GaeiAR~E~y~eG~ 162 (233)
T COG0092 85 GKE--NVQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGAEIARTEKYREGR 162 (233)
T ss_pred CCC--CceEEEEEcCCCCcCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcCCceeEEEEecccchHHHHhHHHHhcce
Confidence 964 6888899999999999999999999999999999999999999999999999999999999998 9999999999
Q ss_pred eccCCccccceeeEEEEEEecCCeeEEEEEEEECCCccCC
Q 029201 157 MISSGQPVNEYIDSAVRHVLLRQVSLIFVMLISVPVIVLE 196 (197)
Q Consensus 157 v~~tgq~~~~~Idy~~~~a~Tk~GviGIKVwI~~~~~~l~ 196 (197)
|| ++|++++|||++++|.|+||+||||||||+|+ +|+
T Consensus 163 vp--lhtlrAdIDyg~a~A~ttyGiiGVKVwI~~ge-~l~ 199 (233)
T COG0092 163 VP--LHTLRADIDYGTAEAHTTYGVIGVKVWIYKGE-VLP 199 (233)
T ss_pred eE--ccccceeeeeeeEEEEecCceEEEEEEEecCC-cCC
Confidence 95 44499999999999999999999999999998 454
No 2
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=100.00 E-value=2.4e-64 Score=426.93 Aligned_cols=189 Identities=79% Similarity=1.188 Sum_probs=185.8
Q ss_pred cccccceEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCe
Q 029201 4 QISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENS 83 (197)
Q Consensus 4 ~~~~~~~~~~~~~~~~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~ 83 (197)
|++.+++|++|+.++++||+||+++|.++|||+|+|+|+++.++|+||+++||.+||++|.++++|++.|++.|++++++
T Consensus 4 ~~~~~k~fi~~~~~~~~~re~l~k~~~~agis~ieI~Rt~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~~~~~~ 83 (220)
T PTZ00084 4 QISKKRKFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEGK 83 (220)
T ss_pred ccchhhHHHHcchhhHHHHHHHHHHHHHCCcceEEEEEcCCcEEEEEEECCCccEEcCCchHHHHHHHHHHHHhCCCCce
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999988899
Q ss_pred eEEEEEEecCCCcCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHhcCCceeEEEEecccCccccceeecccCeeccCCcc
Q 029201 84 VELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQP 163 (197)
Q Consensus 84 i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~k~~i~~~~~~gakGikI~isGRL~G~rAR~e~~~~G~v~~tgq~ 163 (197)
++|++.++++|++||+++|++||+|||+|++|||+++++|+++|++||+||||+|||||+|.+||+|||++|++||||++
T Consensus 84 i~i~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGakGikI~iSGRL~~EiARtE~~~eGrVl~Tg~~ 163 (220)
T PTZ00084 84 VELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKLRAQRAKSMKFRDGYMISTGQP 163 (220)
T ss_pred EEEEEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCCceEEEEEccchhhHHHHhhHhhccEEEecCch
Confidence 99999999999999999999999999999999999999999999999999999999999977899999999999999999
Q ss_pred ccceeeEEEEEEecCCeeEEEEEEEECCC
Q 029201 164 VNEYIDSAVRHVLLRQVSLIFVMLISVPV 192 (197)
Q Consensus 164 ~~~~Idy~~~~a~Tk~GviGIKVwI~~~~ 192 (197)
++++|||++.+|+|+||+||||||||+|+
T Consensus 164 ~~~~idy~~~~a~t~yGviGVKVwI~~~~ 192 (220)
T PTZ00084 164 KKDFVDSAVRHVLMRQGVIGVKVKIMLPY 192 (220)
T ss_pred HHHheehheEEEcccCceeeEEEEEECCC
Confidence 99999999999999999999999999998
No 3
>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=6.3e-63 Score=412.04 Aligned_cols=186 Identities=46% Similarity=0.667 Sum_probs=180.3
Q ss_pred cceEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEE
Q 029201 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (197)
Q Consensus 8 ~~~~~~~~~~~~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~ 87 (197)
.++|++|+.++.+||+||+++|.++|||+|+|+|+|+.++|+||+++||.+||++|+++++|++.|+++|+. .++.|+
T Consensus 2 ~kkfi~~~~~~~~ire~l~k~~~~agis~ieI~r~~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~--~~~~I~ 79 (195)
T TIGR01008 2 ERKFVAEGLKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGL--ENPQID 79 (195)
T ss_pred cEehHhcchHHHHHHHHHHHHHHhCCeeEEEEEEcCCcEEEEEEECCCceEECCCchHHHHHHHHHHHHhCC--CceEEE
Confidence 578999999999999999999999999999999999999999999999999999999999999999999975 357888
Q ss_pred EEEecCCCcCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHhcCCceeEEEEecccCccccceeecccCeeccCCccccce
Q 029201 88 AEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEY 167 (197)
Q Consensus 88 i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~k~~i~~~~~~gakGikI~isGRL~G~rAR~e~~~~G~v~~tgq~~~~~ 167 (197)
+.++++|++||.++|++||+|||+|++|||+++++++++|++||+||||+|||||+|.+||+|||++|+|+|||||+...
T Consensus 80 v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGakGikI~iSGRL~GeiARtE~~~eG~v~~sG~Pl~t~ 159 (195)
T TIGR01008 80 VEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVTISGKLTGERARTEKFAAGYLKHSGEPAEEL 159 (195)
T ss_pred EEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCceEEEEEcccccchhhhhhheeccEEecCCCcchhe
Confidence 99999999999999999999999999999999999999999999999999999999977999999999999999999999
Q ss_pred eeEEEEEEecCCeeEEEEEEEECCCccC
Q 029201 168 IDSAVRHVLLRQVSLIFVMLISVPVIVL 195 (197)
Q Consensus 168 Idy~~~~a~Tk~GviGIKVwI~~~~~~l 195 (197)
||||+.+|+|+||+||||||||+|+.+|
T Consensus 160 IDya~~~a~t~yGviGIKVwI~~~~~~~ 187 (195)
T TIGR01008 160 VDKGFAIALLKLGVLGVKVKIMPPDVKL 187 (195)
T ss_pred eeeEEEEEecCCceEEEEEEEECCCCCC
Confidence 9999999999999999999999998866
No 4
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=100.00 E-value=1.1e-61 Score=408.32 Aligned_cols=189 Identities=36% Similarity=0.550 Sum_probs=182.4
Q ss_pred ccccceEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCee
Q 029201 5 ISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSV 84 (197)
Q Consensus 5 ~~~~~~~~~~~~~~~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i 84 (197)
|+..++|++|+.++.+||+||.+.|.+||||+|+|+|+++.+.|+||+++||.+||++|+++++++..|++.|+.. ++
T Consensus 1 ~~~~~~fi~~~~~~~~irefi~~~~~~AgIs~IeI~Rt~~~i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~~~~--~v 78 (207)
T PRK04191 1 MAIEKKFVEEGLKKVMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGLE--NP 78 (207)
T ss_pred CchhhHHHHcchHHHHHHHHHHhhhhhcceeEEEEEEcCCcEEEEEEECCCCeEECCCchhHHHHHHHHHHHhCCC--ce
Confidence 5678999999999999999999999999999999999999999999999999999999999999999999999753 47
Q ss_pred EEEEEEecCCCcCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHhcCCceeEEEEecccCccccceeecccCeeccCCccc
Q 029201 85 ELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPV 164 (197)
Q Consensus 85 ~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~k~~i~~~~~~gakGikI~isGRL~G~rAR~e~~~~G~v~~tgq~~ 164 (197)
.|++.++++|++||.++|++||+|||+|++|||+++++|+++|++||+||||+|||||||.+||+|||++|+|+|||||+
T Consensus 79 ~I~v~ev~~p~~~a~~vA~~ia~qLe~r~~fRra~k~~i~~~~~agakGiki~iSGrL~Ge~AR~e~~~eG~v~~~G~pl 158 (207)
T PRK04191 79 QIDVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTGERARTEKFTEGYIKKSGEPA 158 (207)
T ss_pred eEEEEEEeCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCeeEEEEEccccchHHHHhhhhhcceEeccCCcc
Confidence 77899999999999999999999999999999999999999999999999999999999977999999999999999999
Q ss_pred cceeeEEEEEEecCCeeEEEEEEEECCCccC
Q 029201 165 NEYIDSAVRHVLLRQVSLIFVMLISVPVIVL 195 (197)
Q Consensus 165 ~~~Idy~~~~a~Tk~GviGIKVwI~~~~~~l 195 (197)
...||||+.+|+|+||+||||||||+|+.+|
T Consensus 159 ~tlIdya~~~a~t~~GviGIKVwI~~~~~~~ 189 (207)
T PRK04191 159 EELVDRGFAIAKLKLGIIGVEVRIMPPDAKL 189 (207)
T ss_pred hheeeeEEEEEecCCeeEEEEEEEECCCCCC
Confidence 9999999999999999999999999998766
No 5
>CHL00048 rps3 ribosomal protein S3
Probab=100.00 E-value=3.6e-58 Score=388.60 Aligned_cols=185 Identities=17% Similarity=0.179 Sum_probs=175.9
Q ss_pred cccceEeecCcchHH-------HHHHHHhh----hccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 029201 6 SKKRKFVADGVFFAE-------LNEVLTRE----LAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 6 ~~~~~~~~~~~~~~~-------Ir~~l~~~----~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~ 74 (197)
.++|.||+++++|+. ||+||.+. +.+|||++|+|+|+|+.++|+||+++|+.+||++|+++++|++.|+
T Consensus 17 ~~~S~W~a~~~~y~~~l~eD~~ir~~i~~~l~~~~~~agis~i~I~r~~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 17 KHHSLWFAQPKNYSEGLQEDKKIRDCIKNYVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CCceEEecChhhhHHHHHHHHHHHHHHHHHHHhhhhhCCeeEEEEEEcCCeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 488999999999986 66666665 6899999999999999999999999999999999999999999999
Q ss_pred HHhCCCCCeeEEEEEEecCCCcCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHhcCCceeEEEEecccCcc-ccceeecc
Q 029201 75 KRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFK 153 (197)
Q Consensus 75 ~~~~~~~~~i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~k~~i~~~~~~gakGikI~isGRL~G~-rAR~e~~~ 153 (197)
+.|+++++++.|++.++++|++||.++|++||++||+|++|||+++++++++|++||+||||+|||||+|+ +||+|||+
T Consensus 97 k~~~~~~~~i~I~v~ev~~p~~~A~~iA~~ia~~Le~r~~fRra~~~~i~~~~~~ga~GikI~iSGRL~Gae~AR~e~~~ 176 (214)
T CHL00048 97 KELNSVNRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQISGRLNGAEIARVEWIR 176 (214)
T ss_pred HHhCCCCceEEEEEEEecCCCcCHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHhCCcEEEEEEecccCccchheEEEEe
Confidence 99998778899999999999999999999999999999999999999999999999999999999999998 59999999
Q ss_pred cCeeccCCccccceeeEEEEEEecCCeeEEEEEEEECCC
Q 029201 154 DGYMISSGQPVNEYIDSAVRHVLLRQVSLIFVMLISVPV 192 (197)
Q Consensus 154 ~G~v~~tgq~~~~~Idy~~~~a~Tk~GviGIKVwI~~~~ 192 (197)
+|++| +||++++||||+.+|+|+||++|||||||+++
T Consensus 177 ~G~vp--l~tl~a~Idy~~~~a~t~~G~~GVKVwI~~~~ 213 (214)
T CHL00048 177 EGRVP--LQTLRAKIDYCSYPARTIYGVLGIKIWIFKDE 213 (214)
T ss_pred cceeE--CCcchhheEEEEEEEecCCceEEEEEEEEcCC
Confidence 99997 77799999999999999999999999999986
No 6
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=100.00 E-value=1.6e-57 Score=383.98 Aligned_cols=184 Identities=24% Similarity=0.309 Sum_probs=176.3
Q ss_pred cccceEeecCcchHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 029201 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (197)
Q Consensus 6 ~~~~~~~~~~~~~~~-------Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~ 78 (197)
.|+|.||+++++|+. ||+||+++|.++||++|+|+||++.++|+||+++|+.+||++|+++++|++.|++.|+
T Consensus 17 ~w~S~Wfa~~k~Y~~~l~eD~~IR~~i~k~~~~agis~IeI~rt~~~i~I~I~~~~pg~vIG~~g~~i~~l~~~l~~~~~ 96 (211)
T TIGR01009 17 DWKSRWYANPKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKKGSEIEKLRKDLQKLTG 96 (211)
T ss_pred CCceEEccCcchhHHHHHHHHHHHHHHHHHhhhCCcceEEEEEcCCceEEEEEeCCCcceeCCCchHHHHHHHHHHHHhC
Confidence 488999999999986 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCCCcCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHhcCCceeEEEEecccCcc-ccceeecccCee
Q 029201 79 FPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFKDGYM 157 (197)
Q Consensus 79 ~~~~~i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~k~~i~~~~~~gakGikI~isGRL~G~-rAR~e~~~~G~v 157 (197)
.++.|++.++++|++||.++|++|+++||++++|||+++++++.+|++||+||||+|||||+|+ +||+|||++|++
T Consensus 97 ---~~~~i~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRr~~~~~i~~~~~~g~~GikI~isGRl~g~e~Ar~e~~~~G~v 173 (211)
T TIGR01009 97 ---KEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGAEIARTEWYKEGRV 173 (211)
T ss_pred ---CceEEEEEEecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCCcEEEEEEecccCchhhhheeeeeeCcc
Confidence 4688889999999999999999999999999999999999999999999999999999999998 599999999999
Q ss_pred ccCCccccceeeEEEEEEecCCeeEEEEEEEECCCcc
Q 029201 158 ISSGQPVNEYIDSAVRHVLLRQVSLIFVMLISVPVIV 194 (197)
Q Consensus 158 ~~tgq~~~~~Idy~~~~a~Tk~GviGIKVwI~~~~~~ 194 (197)
| +||++++||||+++|+|+||++|||||||+++..
T Consensus 174 p--l~t~~~~Idy~~~~a~T~~G~~GvKVwI~~~~~~ 208 (211)
T TIGR01009 174 P--LHTLRADIDYATAEAHTTYGIIGVKVWIFKGEVL 208 (211)
T ss_pred C--cccchhhcEEEEEEEEcCCceEEEEEEEEcCCcC
Confidence 6 6669999999999999999999999999999753
No 7
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=100.00 E-value=6.8e-57 Score=384.81 Aligned_cols=183 Identities=24% Similarity=0.305 Sum_probs=175.9
Q ss_pred cccceEeecCcchHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 029201 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (197)
Q Consensus 6 ~~~~~~~~~~~~~~~-------Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~ 78 (197)
.|+|.||++..+|++ ||+||+++|.++||++|+|+|+++.++|+||+++|+.+||++|+++++|++.|++.|+
T Consensus 17 ~w~S~Wya~~k~Y~~~L~eD~~IRe~i~k~~~~agis~IeI~R~~~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~~~~~ 96 (232)
T PRK00310 17 DWDSRWYADKKDYADLLHEDLKIRKFLKKKLKKAGVSRIEIERPAKRVRVTIHTARPGIVIGKKGAEIEKLRKELEKLTG 96 (232)
T ss_pred CCCCeEeCCcchhHHHHHHHHHHHHHHHHhHhhCceeEEEEEEcCCeEEEEEEECCCccccCCCcHHHHHHHHHHHHHhC
Confidence 489999999999986 9999999999999999999999999999999999999999999999999999999996
Q ss_pred CCCCeeEEEEEEecCCCcCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHhcCCceeEEEEecccCcc-ccceeecccCee
Q 029201 79 FPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFKDGYM 157 (197)
Q Consensus 79 ~~~~~i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~k~~i~~~~~~gakGikI~isGRL~G~-rAR~e~~~~G~v 157 (197)
+++.|++.++++|++||.++|++||++||++++|||+++++|+++|++||+||||+|||||+|+ +||+|||++|++
T Consensus 97 ---~~~~i~v~ev~~p~~~a~~iA~~ia~~Le~r~~fRr~~~~~i~~~~~~g~~GikI~isGRl~g~e~Ar~e~~~~G~v 173 (232)
T PRK00310 97 ---KPVQINIVEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKVQVSGRLGGAEIARTEWYREGRV 173 (232)
T ss_pred ---CceEEEEEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCcEEEEEEcCCCCcceeeeEEEeeeccc
Confidence 5788889999999999999999999999999999999999999999999999999999999998 599999999999
Q ss_pred ccCCccccceeeEEEEEEecCCeeEEEEEEEECCCc
Q 029201 158 ISSGQPVNEYIDSAVRHVLLRQVSLIFVMLISVPVI 193 (197)
Q Consensus 158 ~~tgq~~~~~Idy~~~~a~Tk~GviGIKVwI~~~~~ 193 (197)
| +||++++||||+.+|+|+||++|||||||+|+.
T Consensus 174 p--l~t~~~~Idy~~~~a~T~~Gv~GVKVwI~~~~~ 207 (232)
T PRK00310 174 P--LHTLRADIDYGTAEAHTTYGIIGVKVWIYKGEV 207 (232)
T ss_pred c--cceeeeeeEEEEEEEecCCceEEEEEEEECCCc
Confidence 6 555999999999999999999999999999985
No 8
>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-45 Score=304.16 Aligned_cols=191 Identities=87% Similarity=1.252 Sum_probs=188.7
Q ss_pred CcccccccceEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC
Q 029201 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP 80 (197)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~ 80 (197)
|+-+|+...+|++||.+|+|++|||.++|.+.|||++|.+-||.+++|+|.+++|..++|.+|.+|++|+...+++|+++
T Consensus 1 ~a~~iSkkrkfv~dGvf~AELnef~treLaedGySgvEvRvtptr~eiIi~atrtq~vlGEkgrRirelt~lvqkRf~f~ 80 (244)
T KOG3181|consen 1 MALQISKKRKFVADGVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKFP 80 (244)
T ss_pred CccccchhhhhhhcchhHHHHHHHHHHHHHhcCcCceEEEeeccceeEEEEecchhhhhhhcchhHHHHHHHHHHhcCCC
Confidence 67788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeEEEEEEecCCCcCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHhcCCceeEEEEecccCccccceeecccCeeccC
Q 029201 81 ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISS 160 (197)
Q Consensus 81 ~~~i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~k~~i~~~~~~gakGikI~isGRL~G~rAR~e~~~~G~v~~t 160 (197)
...|+++.+++.+..+||..+|+++.++|-.+..+||+++.+++.+|++||+||+|.+||+|.|+||++.+|.+|.|.||
T Consensus 81 ~~svelyaEkV~~rGLcAiaQaeslryKllgGlavRRA~ygvlr~vmesgAkGceviVSGKLrgqRAKsmKF~DG~mIhS 160 (244)
T KOG3181|consen 81 EGSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVIVSGKLRGQRAKSMKFVDGLMIHS 160 (244)
T ss_pred CCcEEEehhhhhccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHccCCccEEEEeccchhhhhhccccccceEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccceeeEEEEEEecCCeeEEEEEEEECC
Q 029201 161 GQPVNEYIDSAVRHVLLRQVSLIFVMLISVP 191 (197)
Q Consensus 161 gq~~~~~Idy~~~~a~Tk~GviGIKVwI~~~ 191 (197)
||+.+++||-|+.|+.|++|+|||||.||.|
T Consensus 161 G~pv~dyi~ta~rhVllrQGVlGIkVkIMlp 191 (244)
T KOG3181|consen 161 GQPVKDYIDTAVRHVLLRQGVLGIKVKIMLP 191 (244)
T ss_pred CCcHHHHHHHHHHhhhhhcceeeeEEEEecc
Confidence 9999999999999999999999999999987
No 9
>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=99.95 E-value=4e-28 Score=178.06 Aligned_cols=83 Identities=30% Similarity=0.393 Sum_probs=79.6
Q ss_pred HHHHHHhcCchhHHHHHHHHHHH-HhcCCceeEEEEecccCcc-ccceeecccCeeccCCccccceeeEEEEEEecCCee
Q 029201 104 SLRYKLLGGLAVRRACYGVLRFI-MESGAKGCEVIVSGKLRAQ-RAKSMKFKDGYMISSGQPVNEYIDSAVRHVLLRQVS 181 (197)
Q Consensus 104 ~ia~~Le~r~~fRr~~k~~i~~~-~~~gakGikI~isGRL~G~-rAR~e~~~~G~v~~tgq~~~~~Idy~~~~a~Tk~Gv 181 (197)
+|+++||++.+||++++++++.+ |++|++||||+|||||+|. |||+++|++|.++ +|+++++|||++.++.|++|+
T Consensus 1 ~i~~~l~k~~~~r~~i~~~~~~i~~~~~~~GikI~isGRl~g~~rar~~~~~~G~i~--~~~~~~~Idy~~~~~~tk~G~ 78 (85)
T PF00189_consen 1 FIAQKLEKRISFRRIIKKIIRRIMMNKGIKGIKIQISGRLNGAERARTEKFKKGKIS--LQTFKSNIDYASSHAKTKYGV 78 (85)
T ss_dssp HHHHHHHTTSTHHHHHHHHHHHHHHCTTSSEEEEEEESSGGGTSSSEEEEEEEESSS--SSSSTTEEEEEEEEEEESSSE
T ss_pred ChHHHHhcCcHHHHHHHHHHHHHHhhcccceEEEEEeecCCCCccceEEEEECCCCc--cccceeeeeEEEEEEEcCCee
Confidence 58999999999999999999999 7789999999999999995 7999999999996 888999999999999999999
Q ss_pred EEEEEEE
Q 029201 182 LIFVMLI 188 (197)
Q Consensus 182 iGIKVwI 188 (197)
+||||||
T Consensus 79 ~GIKVwI 85 (85)
T PF00189_consen 79 IGIKVWI 85 (85)
T ss_dssp EEEEEEE
T ss_pred EEEEEEC
Confidence 9999998
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=99.85 E-value=4.9e-21 Score=139.69 Aligned_cols=80 Identities=91% Similarity=1.285 Sum_probs=76.4
Q ss_pred CcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCC
Q 029201 15 GVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNR 94 (197)
Q Consensus 15 ~~~~~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~p 94 (197)
+..+++||+||++.+.+||||+|+|+||++.++|+||+++||.+||++|+++++|++.|++.|+++|++++++++++.+.
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 46789999999999999999999999999999999999999999999999999999999999999999999988888763
No 11
>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=99.82 E-value=6.5e-20 Score=140.29 Aligned_cols=87 Identities=24% Similarity=0.388 Sum_probs=81.5
Q ss_pred cccceEeecCcchHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 029201 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (197)
Q Consensus 6 ~~~~~~~~~~~~~~~-------Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~ 78 (197)
.+.|.||++..+|+. ||+||.+.|.+||||+|+|+|+++.++|+||+++||.+||++|+.+++|++.|++.++
T Consensus 16 ~~~s~W~~~~~~y~~~l~ed~~IR~yL~k~~~~agis~I~I~R~~~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~~~ 95 (109)
T cd02412 16 DWDSRWYADKKDYAELLHEDLKIRKFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIEKLRKELQKLLG 95 (109)
T ss_pred CCcceEcCCchhhHHHHHhHHHHHHHHHHHHhhCCccEEEEEEcCCCEEEEEEeCCCCcccCCchHHHHHHHHHHHHHhC
Confidence 488999999888876 9999999999999999999999999999999999999999999999999999999996
Q ss_pred CCCCeeEEEEEEecCC
Q 029201 79 FPENSVELYAEKVNNR 94 (197)
Q Consensus 79 ~~~~~i~i~i~~i~~p 94 (197)
+ .++.|++.|+++|
T Consensus 96 ~--~~~~I~V~ev~~P 109 (109)
T cd02412 96 N--KKVRINIVEVKKP 109 (109)
T ss_pred C--CceEEEEEEecCC
Confidence 4 4688889999987
No 12
>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=99.76 E-value=2.5e-18 Score=126.03 Aligned_cols=84 Identities=38% Similarity=0.662 Sum_probs=78.2
Q ss_pred cceEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEE
Q 029201 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (197)
Q Consensus 8 ~~~~~~~~~~~~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~ 87 (197)
.++|++++..+..||+||.+.|.+||+|+|+|+|+++.+.|+||+++||.+||++|+++++|+..|++.|+. +++.|+
T Consensus 2 ~~~~~~~~~~~~~Ir~fl~~~~~~agIs~IeI~r~~~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l~k~~~~--~~v~I~ 79 (85)
T cd02411 2 ERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGL--ENPQID 79 (85)
T ss_pred eEeHHhcchHHHHHHHHHHhhhhhCcccEEEEEEcCCcEEEEEEECCCCceECCCchhHHHHHHHHHHHhCC--CCceEE
Confidence 578999999999999999999999999999999999999999999999999999999999999999999974 367777
Q ss_pred EEEecC
Q 029201 88 AEKVNN 93 (197)
Q Consensus 88 i~~i~~ 93 (197)
+.|+++
T Consensus 80 v~ev~~ 85 (85)
T cd02411 80 VQEVEN 85 (85)
T ss_pred EEEecC
Confidence 888864
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=99.52 E-value=2.9e-14 Score=102.08 Aligned_cols=77 Identities=27% Similarity=0.427 Sum_probs=72.1
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC-CCCCeeEEEEEEecCCCc
Q 029201 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK-FPENSVELYAEKVNNRGL 96 (197)
Q Consensus 20 ~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~-~~~~~i~i~i~~i~~p~~ 96 (197)
||++||.+++..+++++++|+|+++.+.|++|+++|+.+||++|+.++++...+++.+. +.+++|.|++.+|++|++
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 68999999999999999999999999999999999999999999999999999999984 456889999999999974
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=98.80 E-value=3.2e-08 Score=67.19 Aligned_cols=65 Identities=42% Similarity=0.598 Sum_probs=57.7
Q ss_pred HHHHHhhhccCCeeeeEEEEcCCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 029201 22 NEVLTRELAEDGYSGVEVRVTPVRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (197)
Q Consensus 22 r~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~--p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i 88 (197)
|+||.+.+..+++++|+|+++++...+.+++.. |+.+||++|+.++.++..++..+ .++++.+++
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 579999999999999999999888999999998 99999999999999999999988 345566543
No 15
>smart00322 KH K homology RNA-binding domain.
Probab=97.48 E-value=0.00013 Score=48.35 Aligned_cols=68 Identities=21% Similarity=0.295 Sum_probs=51.9
Q ss_pred CCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcCHHHHHHHHHHHHh
Q 029201 43 PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLL 110 (197)
Q Consensus 43 ~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~p~~~a~~iA~~ia~~Le 110 (197)
+..++|.|+...|+.+||++|..+++|++.....+..++..-......+..|..++...++.|..+++
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 34678889999999999999999999998887766544332123356778888888888888887763
No 16
>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=96.79 E-value=0.0072 Score=43.12 Aligned_cols=56 Identities=20% Similarity=0.287 Sum_probs=47.2
Q ss_pred HHHHhhhccCCe-eeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 029201 23 EVLTRELAEDGY-SGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (197)
Q Consensus 23 ~~l~~~~~~agi-s~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~ 78 (197)
+||++.+...|+ +.+++......+.+.|....+|.+||++|+.++.|+..+...++
T Consensus 2 ~~L~~il~~mg~~~~v~~~~~~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 2 EFLEEVLELMGIEADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred hHHHHHHHHcCCCcEEEEEecCCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 577777777765 35666677888999999999999999999999999999988776
No 17
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=96.09 E-value=0.0076 Score=42.33 Aligned_cols=67 Identities=13% Similarity=0.165 Sum_probs=44.7
Q ss_pred HHHHHHHhhhccCCeeeeEEE--EcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEE
Q 029201 20 ELNEVLTRELAEDGYSGVEVR--VTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (197)
Q Consensus 20 ~Ir~~l~~~~~~agis~i~I~--r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i 86 (197)
.+++|+...+...+=-.+++. .....+.+.+....+|.+||++|+.++.|+..+....+-.+.++.|
T Consensus 3 ~l~~~l~~l~~~~~~v~v~~~~~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~~v 71 (73)
T PF13083_consen 3 FLEDFLKNLVDKPMDVEVTIEIEEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAANKHGKRVRV 71 (73)
T ss_dssp --HHHHHHHHHHTT--EEEEEEETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHHHT-SS-EE
T ss_pred hHHHHHHHHhCCcCeEEEEEEEcCCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHHHhCCCEEEE
Confidence 367777777653332224444 4467888888888889999999999999999998877533344443
No 18
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=95.31 E-value=0.096 Score=44.62 Aligned_cols=106 Identities=18% Similarity=0.193 Sum_probs=77.3
Q ss_pred HHHHHHHHhhhccCCe-eeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC---CCeeEEEEEEecCC
Q 029201 19 AELNEVLTRELAEDGY-SGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP---ENSVELYAEKVNNR 94 (197)
Q Consensus 19 ~~Ir~~l~~~~~~agi-s~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~---~~~i~i~i~~i~~p 94 (197)
.++.+||...+..-|+ +.|.+...++.+.+.|....++.+||++|+.++.|+...+-.++-. ..+|.+++......
T Consensus 65 ~~~~~~L~ell~~m~~~~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~yRer 144 (208)
T COG1847 65 QEAKDYLEELLELMDFEVTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGDYRER 144 (208)
T ss_pred HHHHHHHHHHHHHhCCceEEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhhHHHH
Confidence 5689999998887665 4577888899999999999999999999999999998888877532 13466655444332
Q ss_pred Cc-CHHHHHHHHHHHHhc-Cc--------h-hHHHHHHHHH
Q 029201 95 GL-CAIAQAESLRYKLLG-GL--------A-VRRACYGVLR 124 (197)
Q Consensus 95 ~~-~a~~iA~~ia~~Le~-r~--------~-fRr~~k~~i~ 124 (197)
-. .=..+|+.+|.+..+ +. | =||+++.+++
T Consensus 145 R~e~L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~ 185 (208)
T COG1847 145 RKETLIKLAERAAERVLETGRSVELEPMPPFERKIVHTALS 185 (208)
T ss_pred HHHHHHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHH
Confidence 22 224478888887743 21 2 4788888775
No 19
>PRK01064 hypothetical protein; Provisional
Probab=94.72 E-value=0.71 Score=33.46 Aligned_cols=68 Identities=10% Similarity=0.185 Sum_probs=47.0
Q ss_pred HHHHHhhhcc--CCeeeeEEEEcCCeEEEEEEeccc--ceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEE
Q 029201 22 NEVLTRELAE--DGYSGVEVRVTPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (197)
Q Consensus 22 r~~l~~~~~~--agis~i~I~r~~~~i~I~I~~~~p--~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~ 90 (197)
=+|+-+.|-+ ..++ |+-......+.+.+++... |.+||++|..++.++..+...-.-.+.++.+.+.+
T Consensus 5 v~~iv~~LVd~Pe~V~-V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~~~~~~~~rv~leI~~ 76 (78)
T PRK01064 5 LAYIVKNLVDRPEEVH-IKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIME 76 (78)
T ss_pred HHHHHHHhcCCCCeEE-EEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhhCCCEEEEEEec
Confidence 3455554432 2232 4444446778888888776 67999999999999999998776556777766544
No 20
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=94.00 E-value=0.85 Score=36.88 Aligned_cols=85 Identities=20% Similarity=0.246 Sum_probs=55.0
Q ss_pred HHHHHHhhhc-cCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcCHH
Q 029201 21 LNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI 99 (197)
Q Consensus 21 Ir~~l~~~~~-~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~p~~~a~ 99 (197)
-++.|.+... +||+.++ .-.++.=+|+|++.+||.+||++|..++++.. .+| +.+.-+..|-+.+.
T Consensus 54 A~~~I~~ivP~ea~i~di--~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~----~tg-------W~p~vvRtpPi~S~ 120 (145)
T cd02410 54 AIKIILEIVPEEAGITDI--YFDDDTGEVIIEAEKPGLVIGKGGSTLREITR----ETG-------WAPKVVRTPPIQSR 120 (145)
T ss_pred HHHHHHHhCCCccCceee--EecCCCcEEEEEEcCCeEEEecCchhHHHHHH----HhC-------CeeEEEecCCCCcH
Confidence 5566666554 5788654 44677778999999999999999987766543 333 22344566666666
Q ss_pred HHHHHHHHHHhcCchhHHHH
Q 029201 100 AQAESLRYKLLGGLAVRRAC 119 (197)
Q Consensus 100 ~iA~~ia~~Le~r~~fRr~~ 119 (197)
.+ +.|.+.|......|+-+
T Consensus 121 ti-~~ir~~l~~~~~eR~~~ 139 (145)
T cd02410 121 TV-KSIRRFLRREREERKEI 139 (145)
T ss_pred HH-HHHHHHHHHhHHHHHHH
Confidence 54 34555555555555443
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=93.89 E-value=0.21 Score=34.02 Aligned_cols=53 Identities=15% Similarity=0.289 Sum_probs=42.7
Q ss_pred HHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 029201 22 NEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 22 r~~l~~~~~~agis~i~I~r~-~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~ 74 (197)
.+|+.+.+.-+.+.++.+... .+...+.+....-+..||++|..++.+++.+.
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 478888888888888877654 46777777777788899999999998887776
No 22
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=93.26 E-value=0.23 Score=39.62 Aligned_cols=60 Identities=12% Similarity=0.272 Sum_probs=47.1
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeE--EEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q 029201 20 ELNEVLTRELAEDGYSGVEVRVTPVRT--EIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (197)
Q Consensus 20 ~Ir~~l~~~~~~agis~i~I~r~~~~i--~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~ 79 (197)
...+|+.+.|..+...++.|......- .+.+.-..-+..||++|+.++.++..+...|+.
T Consensus 73 d~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 73 DPEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred CHHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 388999999999999999885544333 344444555679999999999999999988874
No 23
>PRK02821 hypothetical protein; Provisional
Probab=92.99 E-value=1.6 Score=31.61 Aligned_cols=68 Identities=19% Similarity=0.241 Sum_probs=46.7
Q ss_pred HHHHHHHhhhcc-CCeeeeEEEEcCCeEEEEEEeccc--ceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEE
Q 029201 20 ELNEVLTRELAE-DGYSGVEVRVTPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (197)
Q Consensus 20 ~Ir~~l~~~~~~-agis~i~I~r~~~~i~I~I~~~~p--~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~ 90 (197)
++=+||-+.|-+ -.=-.++.+.....+.+.|+++.- |.+||++|..++.++..+.-. .++++.+.+.+
T Consensus 4 ~lv~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~leI~~ 74 (77)
T PRK02821 4 DAVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI---GGRGVRVDVVD 74 (77)
T ss_pred HHHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh---cCCeEEEEEEe
Confidence 344555555543 222235555566778888888654 459999999999999999987 35778876654
No 24
>PRK00468 hypothetical protein; Provisional
Probab=91.53 E-value=3.5 Score=29.53 Aligned_cols=67 Identities=16% Similarity=0.227 Sum_probs=43.3
Q ss_pred HHHHHHhhhccC-CeeeeEEEEcCCeEEEEEEeccc--ceeeccCcccHHHHHHHHHHHhCCCCCeeEEE
Q 029201 21 LNEVLTRELAED-GYSGVEVRVTPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (197)
Q Consensus 21 Ir~~l~~~~~~a-gis~i~I~r~~~~i~I~I~~~~p--~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~ 87 (197)
+=+|+-+.|-+. -=-.++.+.....+.+.++++.- |.+||++|..++.++..+.-.-.-.+.++.+.
T Consensus 4 Lv~~iv~~LVd~Pe~v~V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~le 73 (75)
T PRK00468 4 LVETIAKALVDNPDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVE 73 (75)
T ss_pred HHHHHHHHhcCCCCeEEEEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHHHHHhcCCCEEEEE
Confidence 334555555331 12224445556778888888754 45999999999999999987644344666653
No 25
>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=91.12 E-value=0.92 Score=39.06 Aligned_cols=65 Identities=22% Similarity=0.336 Sum_probs=43.4
Q ss_pred HHHHHHhhhccC-Cee-eeEE---EEcC---CeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeeE
Q 029201 21 LNEVLTRELAED-GYS-GVEV---RVTP---VRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (197)
Q Consensus 21 Ir~~l~~~~~~a-gis-~i~I---~r~~---~~i~I~I~~~~p~---~vig~~g~~i~~l----~~~l~~~~~~~~~~i~ 85 (197)
|||.+-..+.+. -|+ .++| +..+ ..+...|++.+++ ++||++|+.|+++ +..|+++|+ .+|+
T Consensus 188 ire~~~~~~~~e~p~~~~~~~~~~~~~~~~~~~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~~~~~---~~v~ 264 (270)
T TIGR00436 188 IREKIIRYTKEEIPHSVRVEIERKSFNEKGLLKIHALISVERESQKKIIIGKNGSMIKAIGIAARKDILELFD---CDVF 264 (270)
T ss_pred HHHHHHHhcccccCceEEEEEEEEEECCCCeEEEEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHHHHhC---CCEE
Confidence 677776555442 111 1223 2222 2478889999886 6999999999887 788899997 5566
Q ss_pred EEE
Q 029201 86 LYA 88 (197)
Q Consensus 86 i~i 88 (197)
+.+
T Consensus 265 l~l 267 (270)
T TIGR00436 265 LEL 267 (270)
T ss_pred EEE
Confidence 543
No 26
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=89.73 E-value=4 Score=29.49 Aligned_cols=67 Identities=18% Similarity=0.270 Sum_probs=42.1
Q ss_pred HHHHHHhhhccC-CeeeeEEEEcCCeEEEEEEecccc--eeeccCcccHHHHHHHHHHHhCCCCCeeEEE
Q 029201 21 LNEVLTRELAED-GYSGVEVRVTPVRTEIIIRATRTQ--NVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (197)
Q Consensus 21 Ir~~l~~~~~~a-gis~i~I~r~~~~i~I~I~~~~p~--~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~ 87 (197)
+=+|+-+.|-+. .=-+++.+-.+..+.+.++++... -+||++|..++.|+..|.-.=.-.++.+.+.
T Consensus 4 lv~~ivk~lVd~Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~~~~~~v~i~ 73 (76)
T COG1837 4 LVEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGSKDSKRVVVE 73 (76)
T ss_pred HHHHHHHHhcCCccceEEEEEecCCeEEEEEEECcccccceecCCChhHHHHHHHHHHhcccCceEEEEE
Confidence 345555555332 122233334466777777776654 5999999999999999987654334455543
No 27
>PRK15494 era GTPase Era; Provisional
Probab=89.59 E-value=1.9 Score=38.77 Aligned_cols=67 Identities=24% Similarity=0.399 Sum_probs=44.0
Q ss_pred HHHHHHhhhccC-Ce-eeeEEEEc---C---CeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeeE
Q 029201 21 LNEVLTRELAED-GY-SGVEVRVT---P---VRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (197)
Q Consensus 21 Ir~~l~~~~~~a-gi-s~i~I~r~---~---~~i~I~I~~~~p~---~vig~~g~~i~~l----~~~l~~~~~~~~~~i~ 85 (197)
|||-+...+.+. -| ..++|+.- + ..|...||+.+++ +|||++|+.|+++ +..|+++|+. +-.++
T Consensus 240 iRe~~~~~~~~EiP~~~~v~i~~~~~~~~~~~~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~-~v~l~ 318 (339)
T PRK15494 240 TREQLFLNLQKELPYKLTVQTEKWEDLKDKSVKINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGF-PVHLF 318 (339)
T ss_pred HHHHHHhhCCcccCceEEEEEEEEEEcCCCeEEEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCC-CeEEE
Confidence 777776666542 11 12333321 2 2477889999988 5999999999877 7889999973 23345
Q ss_pred EEE
Q 029201 86 LYA 88 (197)
Q Consensus 86 i~i 88 (197)
++|
T Consensus 319 l~V 321 (339)
T PRK15494 319 LFV 321 (339)
T ss_pred EEE
Confidence 544
No 28
>PRK00089 era GTPase Era; Reviewed
Probab=89.12 E-value=3.5 Score=35.59 Aligned_cols=67 Identities=27% Similarity=0.420 Sum_probs=42.7
Q ss_pred HHHHHHhhhccC-Cee-eeEEE---E-cCCeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeeEEE
Q 029201 21 LNEVLTRELAED-GYS-GVEVR---V-TPVRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVELY 87 (197)
Q Consensus 21 Ir~~l~~~~~~a-gis-~i~I~---r-~~~~i~I~I~~~~p~---~vig~~g~~i~~l----~~~l~~~~~~~~~~i~i~ 87 (197)
|||-+...|.+. -|+ .++|+ . ....+.-.|++.+++ +|||++|+.|+++ +..|++.|+. +-.+++.
T Consensus 195 iRe~~~~~l~~e~p~~~~v~~~~~~~~~~~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~-~v~l~l~ 273 (292)
T PRK00089 195 IREKLLRLLGDELPYSVAVEIEKFEERGLVRIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGK-KVFLELW 273 (292)
T ss_pred HHHHHHhhCCccCCceEEEEEEEEEECCeEEEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCC-CEEEEEE
Confidence 576666555432 111 12222 1 233477889999887 6999999999877 7888999973 2334554
Q ss_pred E
Q 029201 88 A 88 (197)
Q Consensus 88 i 88 (197)
|
T Consensus 274 v 274 (292)
T PRK00089 274 V 274 (292)
T ss_pred E
Confidence 4
No 29
>COG1159 Era GTPase [General function prediction only]
Probab=84.85 E-value=11 Score=34.01 Aligned_cols=59 Identities=20% Similarity=0.331 Sum_probs=41.0
Q ss_pred eeeEEEEc------CCeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeeEEEEEEecCCC
Q 029201 35 SGVEVRVT------PVRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVELYAEKVNNRG 95 (197)
Q Consensus 35 s~i~I~r~------~~~i~I~I~~~~p~---~vig~~g~~i~~l----~~~l~~~~~~~~~~i~i~i~~i~~p~ 95 (197)
..++|++. ...++-+||++|.+ ++||++|+.|+++ +..|+++|+. +-.++++| +++++.
T Consensus 212 v~VeIe~~~~~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~-kV~L~L~V-KVk~~W 283 (298)
T COG1159 212 VAVEIEEFEEREKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGC-KVYLELWV-KVKKNW 283 (298)
T ss_pred EEEEEEEEEecCCCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCC-ceEEEEEE-EEcccc
Confidence 34666553 23577778887766 6999999999887 8889999973 24455654 555544
No 30
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=82.26 E-value=10 Score=36.90 Aligned_cols=91 Identities=22% Similarity=0.243 Sum_probs=54.0
Q ss_pred HHHHHhhh-ccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcCHHH
Q 029201 22 NEVLTREL-AEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIA 100 (197)
Q Consensus 22 r~~l~~~~-~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~p~~~a~~ 100 (197)
++.|.+.. .+|+++. |.-.++.=+|+|++.+||.+||+.|+.++++... .+ +...-+..|-+....
T Consensus 78 ~~~I~eivP~ea~i~~--i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~----tg-------W~p~ivR~PPi~S~t 144 (637)
T COG1782 78 RKIILEIVPEEAGITD--IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAE----TG-------WAPKIVRTPPIQSRT 144 (637)
T ss_pred HHHHHHhCccccCcee--EEecCCCceEEEEecCCceEEecCchHHHHHHHH----hC-------CcceeeecCCCchhh
Confidence 34444444 3578886 5557788899999999999999999777665433 22 223335556555555
Q ss_pred HHHHHHHHHhcCc-hhHHHHHHHHHHH
Q 029201 101 QAESLRYKLLGGL-AVRRACYGVLRFI 126 (197)
Q Consensus 101 iA~~ia~~Le~r~-~fRr~~k~~i~~~ 126 (197)
+ ++|.+-|.+.. .-|+++++.=+++
T Consensus 145 i-~~ir~~l~~~~~eR~~iL~~vg~rI 170 (637)
T COG1782 145 I-KSIREILRSERKERREILRNVGRRI 170 (637)
T ss_pred H-HHHHHHHHHhHHHHHHHHHHHHHHh
Confidence 4 34555554432 2333444433444
No 31
>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=81.89 E-value=2 Score=34.38 Aligned_cols=59 Identities=15% Similarity=0.255 Sum_probs=44.3
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEe--cccceeeccCcccHHHHHHHHHHHhCC
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRA--TRTQNVLGEKGRRIRELTSVVQKRFKF 79 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~--~~p~~vig~~g~~i~~l~~~l~~~~~~ 79 (197)
+.+|+.+.|.-|.+.+|.+.-.+.....++.+ ..-+..||++|++++.....+...++.
T Consensus 75 ~~~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 75 LEEFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred HHHHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 89999999999999999885533333344444 345679999999999888888777663
No 32
>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=76.99 E-value=2.5 Score=28.65 Aligned_cols=30 Identities=17% Similarity=0.387 Sum_probs=22.5
Q ss_pred eEEEEEEecccceeeccCcccHHHHHHHHH
Q 029201 45 RTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 45 ~i~I~I~~~~p~~vig~~g~~i~~l~~~l~ 74 (197)
-..+.|-..+-+.+||++|+.+++|++.-.
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg 32 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETG 32 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHC
Confidence 345566667778899999999988776544
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=74.24 E-value=35 Score=33.56 Aligned_cols=84 Identities=21% Similarity=0.271 Sum_probs=53.3
Q ss_pred HHHHHHhhhc-cCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcCHH
Q 029201 21 LNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI 99 (197)
Q Consensus 21 Ir~~l~~~~~-~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~p~~~a~ 99 (197)
-++.|.+... +||+.+ |.-.++.=+|+|.+.+||.|||+.|..++++... +| +.+.-+..|-+...
T Consensus 71 ~~~~i~~~~~~~~~~~~--~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~----~~-------w~~~~~~~~~~~~~ 137 (630)
T TIGR03675 71 AIEKIKEIVPEEAGITD--IYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAE----TG-------WTPKVVRTPPIESK 137 (630)
T ss_pred HHHHHHHhCCCcCCcee--EEecCCCceEEEEEcCCeEEEecCcchHHHHHHH----hC-------CeeeEEecCCCCcH
Confidence 4555555543 578865 4456777889999999999999999877665443 33 22344566666666
Q ss_pred HHHHHHHHHHhcCchhHHH
Q 029201 100 AQAESLRYKLLGGLAVRRA 118 (197)
Q Consensus 100 ~iA~~ia~~Le~r~~fRr~ 118 (197)
.+ +.|.+-|......|+-
T Consensus 138 ~~-~~~~~~~~~~~~~r~~ 155 (630)
T TIGR03675 138 TI-KNIREYLRSESEERKE 155 (630)
T ss_pred HH-HHHHHHHHHhHHHHHH
Confidence 54 3455555544444443
No 34
>PF13014 KH_3: KH domain
Probab=70.37 E-value=3.6 Score=25.60 Aligned_cols=18 Identities=22% Similarity=0.543 Sum_probs=14.7
Q ss_pred ceeeccCcccHHHHHHHH
Q 029201 56 QNVLGEKGRRIRELTSVV 73 (197)
Q Consensus 56 ~~vig~~g~~i~~l~~~l 73 (197)
+.|||++|+.|++|++.-
T Consensus 3 g~iIG~~G~~I~~I~~~t 20 (43)
T PF13014_consen 3 GRIIGKGGSTIKEIREET 20 (43)
T ss_pred CeEECCCChHHHHHHHHh
Confidence 679999999998877543
No 35
>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=68.75 E-value=30 Score=31.60 Aligned_cols=62 Identities=23% Similarity=0.454 Sum_probs=46.2
Q ss_pred HHHHHHHHhhhccC--CeeeeE-EEEcC-CeEEEEEEecccc-----eeeccCcccHHHHHHHHHHHhCCCCCeeEE
Q 029201 19 AELNEVLTRELAED--GYSGVE-VRVTP-VRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (197)
Q Consensus 19 ~~Ir~~l~~~~~~a--gis~i~-I~r~~-~~i~I~I~~~~p~-----~vig~~g~~i~~l~~~l~~~~~~~~~~i~i 86 (197)
..+++.|+.+.+.- |.-.|. |-|-| .+++|-+++..|+ ..+|.+|.+++.+.+.|. +.+|+|
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 34788888877764 433333 66765 8999999999887 589999999999988884 356664
No 36
>PF05316 VAR1: Mitochondrial ribosomal protein (VAR1); InterPro: IPR007980 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 [, ]. This family consists of the VAR1 mitochondrial ribosomal proteins found in yeast. Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. VAR1 is the only protein in the yeast mitochondrial ribosome to be encoded in the mitochondria - the remaining approximately 80 ribosomal proteins are encoded in the nucleus []. VAR1 along with 15S rRNA are necessary for the formation of mature 37S subunits [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005761 mitochondrial ribosome
Probab=66.64 E-value=61 Score=29.83 Aligned_cols=121 Identities=8% Similarity=0.076 Sum_probs=79.7
Q ss_pred cHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcCHHHHHHHH-HHHHhc---Cc--hhHHHHHHH-------------HH-
Q 029201 65 RIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESL-RYKLLG---GL--AVRRACYGV-------------LR- 124 (197)
Q Consensus 65 ~i~~l~~~l~~~~~~~~~~i~i~i~~i~~p~~~a~~iA~~i-a~~Le~---r~--~fRr~~k~~-------------i~- 124 (197)
....|...|...+. ++|.|.+..++-|+.+..++.++| .....+ +. .|++.+... +.
T Consensus 156 n~n~LsniLS~yyN---KkV~I~PIkLkY~Y~NsdIlsk~I~~~d~~k~n~~i~~~y~k~L~n~mp~lN~~~I~~nyI~n 232 (350)
T PF05316_consen 156 NYNNLSNILSYYYN---KKVTIEPIKLKYPYNNSDILSKYISINDMNKYNNGISMNYQKNLNNNMPKLNDKNISMNYINN 232 (350)
T ss_pred hHHHHHHHHHHHhc---CceEEEEeEEeeeeccHHHHHHHHHHhhhHhhcchhhHHHHHHHHhhccccchhhHHHHHHHH
Confidence 45577778887774 889999999999999999999999 333332 22 233333211 10
Q ss_pred ----------H---------------------------HHhcCCceeEEEEecccCcc--ccceeecccCeec-------
Q 029201 125 ----------F---------------------------IMESGAKGCEVIVSGKLRAQ--RAKSMKFKDGYMI------- 158 (197)
Q Consensus 125 ----------~---------------------------~~~~gakGikI~isGRL~G~--rAR~e~~~~G~v~------- 158 (197)
. .|..-..|..++++||+.-. |+-+..+..|..-
T Consensus 233 inn~n~~kyNnii~nnnN~~ni~niyn~~nin~i~~n~L~~KyLvG~si~~kGrl~~~~~Rs~~~~l~~Gtf~N~~y~~~ 312 (350)
T PF05316_consen 233 INNINNIKYNNIILNNNNNKNINNIYNSLNINNIPMNLLMYKYLVGWSILFKGRLLNNISRSNKYNLLKGTFNNKLYNWG 312 (350)
T ss_pred HhhhhhhhhhhhhccccchhHHHHHHhhcccccchHHHHHHhhhheeEEEEeeeeccccchhhhhhhhhcchhhHHHHhh
Confidence 0 11234679999999999986 4444455555521
Q ss_pred -----cCCccccceeeEEEEEEecCCeeEEEEEEE
Q 029201 159 -----SSGQPVNEYIDSAVRHVLLRQVSLIFVMLI 188 (197)
Q Consensus 159 -----~tgq~~~~~Idy~~~~a~Tk~GviGIKVwI 188 (197)
..+.-+..+.+...-.-.++.|.+||||..
T Consensus 313 n~~n~ykLNyi~~n~~i~~~s~inknGKynIkvkL 347 (350)
T PF05316_consen 313 NINNNYKLNYIPSNHNIYNNSNINKNGKYNIKVKL 347 (350)
T ss_pred hcccceeecccCCcceeccccccccCceeeeEEEE
Confidence 112224556666666678899999999975
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=65.27 E-value=7.5 Score=25.39 Aligned_cols=27 Identities=15% Similarity=0.473 Sum_probs=20.8
Q ss_pred EEEEEecccceeeccCcccHHHHHHHH
Q 029201 47 EIIIRATRTQNVLGEKGRRIRELTSVV 73 (197)
Q Consensus 47 ~I~I~~~~p~~vig~~g~~i~~l~~~l 73 (197)
++.|-...-+.+||++|+.++++++.-
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s 29 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREET 29 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHH
Confidence 445555666789999999999887765
No 38
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=63.95 E-value=39 Score=31.13 Aligned_cols=55 Identities=22% Similarity=0.424 Sum_probs=42.3
Q ss_pred HHHHHHHhhhccC--CeeeeE-EEEcC-CeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q 029201 20 ELNEVLTRELAED--GYSGVE-VRVTP-VRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 20 ~Ir~~l~~~~~~a--gis~i~-I~r~~-~~i~I~I~~~~p~-----~vig~~g~~i~~l~~~l~ 74 (197)
.+++.|+.+.+.- |+-.|. |-|-| .+++|-+++..|+ ..||.+|.+++.+.+.|.
T Consensus 203 ~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~ 266 (362)
T PRK12327 203 LVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELK 266 (362)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhC
Confidence 4778888777764 333333 56665 8999999999887 589999999999988885
No 39
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=63.12 E-value=11 Score=26.46 Aligned_cols=37 Identities=19% Similarity=0.516 Sum_probs=27.5
Q ss_pred CeEEEEEEecc-----cceeeccCcccHHHHHHHHHHHhCCCCCeeEE
Q 029201 44 VRTEIIIRATR-----TQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (197)
Q Consensus 44 ~~i~I~I~~~~-----p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i 86 (197)
+.+.|.++... -|..+|.+|.+++.+.+.|. +.+|++
T Consensus 3 ~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~------gekIdv 44 (69)
T PF13184_consen 3 NRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELN------GEKIDV 44 (69)
T ss_dssp TEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTT------T-EEEE
T ss_pred ceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhC------CCeEEE
Confidence 56778888877 46799999999999988885 356764
No 40
>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=60.53 E-value=8 Score=26.13 Aligned_cols=27 Identities=15% Similarity=0.529 Sum_probs=20.2
Q ss_pred EEEEEecccceeeccCcccHHHHHHHH
Q 029201 47 EIIIRATRTQNVLGEKGRRIRELTSVV 73 (197)
Q Consensus 47 ~I~I~~~~p~~vig~~g~~i~~l~~~l 73 (197)
++.|-...-+.+||++|..++++++.-
T Consensus 3 r~~ip~~~vg~iIG~~G~~i~~i~~~t 29 (65)
T cd02396 3 RLLVPSSQAGSIIGKGGSTIKEIREET 29 (65)
T ss_pred EEEECHHHcCeeECCCcHHHHHHHHHH
Confidence 445555566789999999998887663
No 41
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=60.30 E-value=18 Score=28.00 Aligned_cols=35 Identities=11% Similarity=0.212 Sum_probs=28.4
Q ss_pred chHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEec
Q 029201 17 FFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRAT 53 (197)
Q Consensus 17 ~~~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~ 53 (197)
+..+|..||.+.+...||. |.|+| ++...|+..+.
T Consensus 3 ~k~~ikpwlq~~~~~~Gi~-iVIer-Sd~~ki~FkCk 37 (111)
T PF08731_consen 3 DKDEIKPWLQKIFYPQGIG-IVIER-SDKKKIVFKCK 37 (111)
T ss_pred chHHHHHHHHHHhhhcCce-EEEEe-cCCceEEEEEe
Confidence 4678999999999999988 99999 66777775553
No 42
>cd05213 NAD_bind_Glutamyl_tRNA_reduct NADP-binding domain of glutamyl-tRNA reductase. Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate,
Probab=59.79 E-value=80 Score=27.85 Aligned_cols=53 Identities=25% Similarity=0.272 Sum_probs=37.2
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q 029201 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (197)
Q Consensus 20 ~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~ 79 (197)
++.+++.......++..+.|-.|.|+++|++++..|. ...+.+.+.|...+++
T Consensus 25 ~~~~~l~~l~~~~~~~e~viLsTCNR~EiY~~~~~~~-------~~~~~~~~~l~~~~~~ 77 (311)
T cd05213 25 ELKEALRRLLEKPGISEAVLLSTCNRVELYLVGDNFH-------KLADELEELLAELLNE 77 (311)
T ss_pred HHHHHHHHHhcCCCCceEEEEecCCeEEEEEEeCCcc-------hhHHHHHHHHHHhcCc
Confidence 4566666655567889999999999999999876543 2234556666666553
No 43
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=59.76 E-value=39 Score=31.38 Aligned_cols=57 Identities=21% Similarity=0.260 Sum_probs=43.3
Q ss_pred hHHHHHHHHhhhccC--CeeeeE-EEEcC-CeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q 029201 18 FAELNEVLTRELAED--GYSGVE-VRVTP-VRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 18 ~~~Ir~~l~~~~~~a--gis~i~-I~r~~-~~i~I~I~~~~p~-----~vig~~g~~i~~l~~~l~ 74 (197)
-..+++.|+.+.+.- |.-.|. |-|-| .+++|-+++..|+ ..||.+|.+++.+.+.|.
T Consensus 207 p~~v~~Lfe~EVPEI~dG~VeIk~IARepG~RtKVAV~S~d~~iDPvGacIG~~G~rI~~I~~eL~ 272 (374)
T PRK12328 207 PKFLEALLELEVPEIKDGEVIIIHSARIPGERAKVALFSNNPNIDPIGATVGVKGVRINAVSKELN 272 (374)
T ss_pred HHHHHHHHHHhCccccCCeEEEEEEeccCcceeEEEEEcCCCCCChHHhhcCCCcchHHHHHHHhC
Confidence 344788888887764 333333 56665 8999999999987 488999999999988884
No 44
>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=56.48 E-value=4 Score=26.88 Aligned_cols=28 Identities=21% Similarity=0.447 Sum_probs=20.8
Q ss_pred EEEEEecccceeeccCcccHHHHHHHHH
Q 029201 47 EIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 47 ~I~I~~~~p~~vig~~g~~i~~l~~~l~ 74 (197)
++.+-...-+.+||++|+.+++|++.-.
T Consensus 3 ~i~vp~~~~~~iIG~~G~~i~~I~~~t~ 30 (60)
T PF00013_consen 3 RIEVPSSLVGRIIGKKGSNIKEIEEETG 30 (60)
T ss_dssp EEEEEHHHHHHHHTGGGHHHHHHHHHHT
T ss_pred EEEECHHHcCEEECCCCCcHHHhhhhcC
Confidence 4555556667899999999988776554
No 45
>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=55.38 E-value=9.4 Score=25.20 Aligned_cols=27 Identities=22% Similarity=0.398 Sum_probs=19.8
Q ss_pred EEEEecccceeeccCcccHHHHHHHHH
Q 029201 48 IIIRATRTQNVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 48 I~I~~~~p~~vig~~g~~i~~l~~~l~ 74 (197)
+.|=...-+.+||++|+.+++|++.-.
T Consensus 4 i~Vp~~~~~~iIG~~G~~i~~i~~~~g 30 (62)
T cd02394 4 VEIPKKLHRFIIGKKGSNIRKIMEETG 30 (62)
T ss_pred EEeCHHHhhhccCCCCCcHHHHHHHhC
Confidence 334445567899999999999877553
No 46
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=53.87 E-value=64 Score=30.76 Aligned_cols=56 Identities=20% Similarity=0.454 Sum_probs=43.0
Q ss_pred HHHHHHHHhhhccC--CeeeeE-EEEcC-CeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q 029201 19 AELNEVLTRELAED--GYSGVE-VRVTP-VRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 19 ~~Ir~~l~~~~~~a--gis~i~-I~r~~-~~i~I~I~~~~p~-----~vig~~g~~i~~l~~~l~ 74 (197)
..+++.|+.+.+.- |+-.|. |-|.| .+++|-+++..|. ..+|.+|.+++.+.+.|.
T Consensus 202 ~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ 266 (470)
T PRK09202 202 EFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELG 266 (470)
T ss_pred HHHHHHHHHhCcccccCeEEEEEEeecCcceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhC
Confidence 44778888877764 433333 66766 8999999998887 589999999999988884
No 47
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=50.28 E-value=65 Score=26.55 Aligned_cols=31 Identities=10% Similarity=0.203 Sum_probs=24.1
Q ss_pred CCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 029201 43 PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 43 ~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~ 74 (197)
.+.+-+.+..+. |.-||++|+.+++|++.|.
T Consensus 60 ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lg 90 (166)
T PRK06418 60 DDLVILLVTSGP-RIPIGKGGKIAKALSRKLG 90 (166)
T ss_pred CCEEEEEEeCCC-cccccccchHHHHHHHHhC
Confidence 567766666666 8899999999888777664
No 48
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=45.21 E-value=34 Score=32.56 Aligned_cols=53 Identities=13% Similarity=0.270 Sum_probs=42.1
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHH
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l 73 (197)
..+|+.+.|..|.+.+|.+......+.|++--..-+..||++|++++......
T Consensus 279 ~~~fi~nal~pa~v~~v~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~ 331 (470)
T PRK09202 279 PAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLT 331 (470)
T ss_pred HHHHHHHhCCCCEEEEEEEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHH
Confidence 78899999999999999776666677776666677789999999987654433
No 49
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=43.89 E-value=1.1e+02 Score=26.75 Aligned_cols=61 Identities=13% Similarity=0.159 Sum_probs=47.5
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcCHHHHHHHHH
Q 029201 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR 106 (197)
Q Consensus 44 ~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~p~~~a~~iA~~ia 106 (197)
+.+.+.|..+..-.+||++|++-..|-+....+++.++.+|.+.=.++.. -+..-+|+.++
T Consensus 18 ~~isl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~~d~G~i~i~g~~~~~--~~s~~LAk~lS 78 (252)
T COG4604 18 DDVSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKKDSGEITIDGLELTS--TPSKELAKKLS 78 (252)
T ss_pred ccceeeecCCceeEEECCCCccHHHHHHHHHHhccccCceEEEeeeeccc--CChHHHHHHHH
Confidence 35666667777778999999999999999999999888888877666665 34666666654
No 50
>PF05201 GlutR_N: Glutamyl-tRNAGlu reductase, N-terminal domain; InterPro: IPR015895 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents the N-terminal domain of glutamyl-tRNA reductase (1.2.1.70 from EC), which reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway [, ]. The enzyme requires NADPH as a cofactor.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process, 0055114 oxidation-reduction process; PDB: 1GPJ_A.
Probab=41.09 E-value=52 Score=26.21 Aligned_cols=101 Identities=18% Similarity=0.141 Sum_probs=44.6
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCC--eeEEEEEEecCCCcCH
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPEN--SVELYAEKVNNRGLCA 98 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~--~i~i~i~~i~~p~~~a 98 (197)
+.+.+.......++..+.|-.|.|+++|++++..|. .....+.+.|....+++.. .-.+++ .. +.+|
T Consensus 23 ~~~~l~~l~~~~~i~e~viLsTCNR~Eiy~~~~~~~-------~~~~~~~~~l~~~~~~~~~~~~~~~~~--~~--g~~a 91 (152)
T PF05201_consen 23 LPEALAELKSFPGIEEAVILSTCNRVEIYVVSDDPE-------AGIDDVKEFLADFSGVDPDELSEYLYV--YT--GDEA 91 (152)
T ss_dssp HHH---HHHHHTT-SEEEEEEETTEEEEEEES-TT--------------HHHHH-------HTT-TT-EE--EE--HHHH
T ss_pred HHHHHHHHhccCCCceEEEeecCCeEEEEEEeCcch-------hhHHHHHHHHHhhcccchhhhhcceEE--Ec--ChHH
Confidence 444444344457899999999999999999887662 2234455555543332211 111111 11 2334
Q ss_pred HHHHHHHHHHHhcCc----hhHHHHHHHHHHHHhcCCc
Q 029201 99 IAQAESLRYKLLGGL----AVRRACYGVLRFIMESGAK 132 (197)
Q Consensus 99 ~~iA~~ia~~Le~r~----~fRr~~k~~i~~~~~~gak 132 (197)
..--..++.-|+.-+ ..-..+|.|...+.++|.-
T Consensus 92 ~~HLf~VasGLdS~V~GE~qIlgQvk~A~~~A~~~g~~ 129 (152)
T PF05201_consen 92 VRHLFRVASGLDSMVVGEDQILGQVKRAYEFAREAGTT 129 (152)
T ss_dssp HHHHHHHHTTTTSSSTT-HHHHHHHHHHHHHHHHHT--
T ss_pred HHHHHHHHhcchhhhcChHHHHHHHHHHHHHHHHcCCh
Confidence 444444555554322 2334555666666665544
No 51
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=39.09 E-value=1.2e+02 Score=28.84 Aligned_cols=55 Identities=20% Similarity=0.322 Sum_probs=41.6
Q ss_pred HHHHHHHhhhccC--CeeeeE-EEEc--------CCeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q 029201 20 ELNEVLTRELAED--GYSGVE-VRVT--------PVRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 20 ~Ir~~l~~~~~~a--gis~i~-I~r~--------~~~i~I~I~~~~p~-----~vig~~g~~i~~l~~~l~ 74 (197)
.+.+.|+.+.+.. |+-.|. |-|. ..+++|-+++..|+ ..||.+|.+|+.+.+.|.
T Consensus 228 lv~~Lfe~EVPEI~dG~VeIk~IAREa~~~~ripG~RtKVAV~S~d~~VDPvGacVG~kG~RI~~I~~eL~ 298 (449)
T PRK12329 228 LVVYLFENEVPEIEEGVVRIVAVAREANPPSRYVGPRTKIAVDTLERDVDPVGACIGARGSRIQAVVNELR 298 (449)
T ss_pred HHHHHHHhhCcccccCeEEEEEEEecCCCCCCCCcceeEEEEEcCCCCCChhhccCCCCcchHHHHHHHhC
Confidence 4777777777754 443333 6675 46899999998887 588999999999988884
No 52
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=37.31 E-value=1.1e+02 Score=25.62 Aligned_cols=35 Identities=14% Similarity=0.398 Sum_probs=23.3
Q ss_pred EEEcCCeEEEEEEec--cc-ceeeccCcccHHHHHHHHH
Q 029201 39 VRVTPVRTEIIIRAT--RT-QNVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 39 I~r~~~~i~I~I~~~--~p-~~vig~~g~~i~~l~~~l~ 74 (197)
+.|.+.. .+.++.. -| |..||++|++++.+++.|.
T Consensus 69 i~rd~r~-av~~~~~~~d~vG~~iG~~G~rvk~i~~eLg 106 (190)
T COG0195 69 VARDPRA-AVVSNVVKIDPVGACIGKRGSRVKAVSEELG 106 (190)
T ss_pred EEecccc-ceEEeecCcCchhhhccCCChHHHHHHHHhC
Confidence 4555522 2333443 23 6799999999999888876
No 53
>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=37.26 E-value=25 Score=28.63 Aligned_cols=59 Identities=15% Similarity=0.286 Sum_probs=37.0
Q ss_pred cccceeeccCcccHHHHHHHHHHHhCCCC--CeeEEEEEEecCCCcCHHHHHHHHHHHHhcCch
Q 029201 53 TRTQNVLGEKGRRIRELTSVVQKRFKFPE--NSVELYAEKVNNRGLCAIAQAESLRYKLLGGLA 114 (197)
Q Consensus 53 ~~p~~vig~~g~~i~~l~~~l~~~~~~~~--~~i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~ 114 (197)
.+-+.+||++|+.+++|++...-...++. ..|.| . -..++.++..-|..+-..|-.+.+
T Consensus 7 ~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I--~-~~t~d~~~i~kA~~~I~~i~~gf~ 67 (172)
T TIGR03665 7 DRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKI--E-EEDEDPLAVMKAREVVKAIGRGFS 67 (172)
T ss_pred HHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEE--e-cCCCCHHHHHHHHHHHHHHHcCCC
Confidence 45567999999999887766554333221 22222 1 145666677788888877776544
No 54
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=37.16 E-value=1e+02 Score=24.45 Aligned_cols=53 Identities=9% Similarity=0.201 Sum_probs=34.9
Q ss_pred HHHHHHHH--hhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHH
Q 029201 19 AELNEVLT--RELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (197)
Q Consensus 19 ~~Ir~~l~--~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l 73 (197)
.+-..|+. ..+.++..-.|.+ ..+.+-+.+.....|..+|++|++++.+++.+
T Consensus 7 ~~~~~~i~~fe~~t~~~~~dc~~--d~~~vi~vV~~~~vG~~IG~~G~rI~~i~e~l 61 (140)
T PRK08406 7 TEEIRYIALFESITGATVKDCII--DDDRIIFVVKEGDMGLAIGKGGENVKRLEEKL 61 (140)
T ss_pred HHHHHHHHHHHHHhCCCceEEEE--eCCEEEEEEeCCCccccCCcCchHHHHHHHHh
Confidence 34444543 2333444444443 34888888888889999999999999986544
No 55
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=36.71 E-value=1.3e+02 Score=24.71 Aligned_cols=60 Identities=22% Similarity=0.231 Sum_probs=43.7
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEE-EEecccce-eeccCcccHHHHHHHHHHHhCCCCCeeEE
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEII-IRATRTQN-VLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~-I~~~~p~~-vig~~g~~i~~l~~~l~~~~~~~~~~i~i 86 (197)
+.+|+.+.|.-|.+.++.+.-.+++...+ +++..... -+ ...++.+...+++++| +.+.+
T Consensus 102 ~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~~Dk~~l---~~k~e~~~~v~~kltg---k~v~~ 163 (166)
T PRK06418 102 IKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSRRDRRRL---PAKPELLESILSKITG---TEVKI 163 (166)
T ss_pred HHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECHHHhhcc---cccHHHHHHHHHHHHC---CcEEE
Confidence 89999999999999999997777765444 66643221 22 4467889999999997 44554
No 56
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=36.09 E-value=85 Score=29.20 Aligned_cols=64 Identities=17% Similarity=0.195 Sum_probs=42.9
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEe
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKV 91 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i 91 (197)
..+|+.+.|.-|.+.+|.+........+++--..-+..||++|++++.-. +++| .+|+|...+-
T Consensus 285 ~~~fI~Nal~Pa~V~~V~i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~----~LtG---wkIDI~s~~~ 348 (374)
T PRK12328 285 PEIFIARALAPAIISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRLAS----MLTG---YEIELNEIGS 348 (374)
T ss_pred HHHHHHHhCCCceeeEEEEcCCCcEEEEEEChHHhhhhhcCCChhHHHHH----HHhC---CEEEEEECCC
Confidence 78999999999999888776333444444444455679999999986433 3444 5677654333
No 57
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=35.51 E-value=1.4e+02 Score=20.27 Aligned_cols=56 Identities=13% Similarity=0.138 Sum_probs=41.8
Q ss_pred HhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEE
Q 029201 26 TRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (197)
Q Consensus 26 ~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~ 87 (197)
...|.++-+.++.+.+..+..++++.. |..+ .-+.+..+.+.|++.|+.. .+|++.
T Consensus 18 ~~~f~~~~I~kv~v~k~~~~w~f~l~~--~~~l---~~~~~~~~~~~l~~~F~~i-a~v~~~ 73 (76)
T PF14480_consen 18 NPLFEDAEIEKVTVHKKSRKWRFHLSS--PHIL---PFEVYQKFEEKLKKQFSHI-AKVELI 73 (76)
T ss_pred hhhhcccEEEEEEEEccCCEEEEEEEe--CCcC---CHHHHHHHHHHHHHHhCCc-CeEEEE
Confidence 456788899999999999998887766 4443 3457789999999998632 366654
No 58
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=33.12 E-value=71 Score=22.45 Aligned_cols=46 Identities=15% Similarity=0.123 Sum_probs=30.7
Q ss_pred EEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 029201 48 IIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (197)
Q Consensus 48 I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~ 93 (197)
|+|.+.++..-=..|.+-++++.+.+.+.+|.++..+.|-+.+++.
T Consensus 4 v~Ik~~~g~~~~~~K~~la~~vT~~~~~~lg~~~~~i~Viieev~~ 49 (69)
T COG1942 4 VNIKLFEGRLDEEQKAELAAEVTEVTVETLGKDPSAIHVIIEEVPP 49 (69)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHHhCCCcccEEEEEEecCh
Confidence 3445544222222244457889999999999877788888877765
No 59
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=32.89 E-value=81 Score=26.48 Aligned_cols=52 Identities=13% Similarity=0.244 Sum_probs=38.5
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCC-eEEEEEEecccceeeccCcccHHHHHHH
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPV-RTEIIIRATRTQNVLGEKGRRIRELTSV 72 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~-~i~I~I~~~~p~~vig~~g~~i~~l~~~ 72 (197)
..+|+.+.|..|...+|.+.-..+ ...+.+.-..-+.+||++|..++..++.
T Consensus 118 ~~~fI~nal~Pa~v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~L 170 (190)
T COG0195 118 PAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQL 170 (190)
T ss_pred HHHHHHHhcCcceEeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHH
Confidence 789999999999999998877433 4555555566668999999777654443
No 60
>PLN00203 glutamyl-tRNA reductase
Probab=32.37 E-value=3.1e+02 Score=26.43 Aligned_cols=53 Identities=21% Similarity=0.184 Sum_probs=35.0
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP 80 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~ 80 (197)
+.+++.......++..+.|-.|.|+++|++++..+. ...+.+.+.|.+..+++
T Consensus 110 ~~~~l~~l~~~~~i~e~viLSTCNR~EiY~~~~~~~-------~~~~~v~~~l~~~~~~~ 162 (519)
T PLN00203 110 WPRAIAELCSLNHIEEAAVLSTCNRMEIYVVALSWH-------RGVKEVTEWMSKTSGIP 162 (519)
T ss_pred HHHHHHHHHhcCCcceEEEEeccCeEEEEEEecCcc-------hhHHHHHHHHHHhcCCC
Confidence 444455444557899999999999999998765431 12345556666655543
No 61
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=31.94 E-value=60 Score=31.51 Aligned_cols=54 Identities=26% Similarity=0.386 Sum_probs=34.7
Q ss_pred chHHHHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 029201 17 FFAELNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 17 ~~~~Ir~~l~~~~~~agis~i~I~r~-~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~ 74 (197)
-+.+|.+++.+.+.. .++++-. +...-|.+.-...+.+||++|.++++|++.|.
T Consensus 462 a~~~i~~~i~r~~p~----~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klg 516 (604)
T COG1855 462 AEEEIEREIKRYLPG----DVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLG 516 (604)
T ss_pred HHHHHHHHHHHhCCC----CceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhC
Confidence 344577888877765 3444444 44555544444556799999999988765543
No 62
>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=31.29 E-value=90 Score=22.65 Aligned_cols=58 Identities=16% Similarity=0.131 Sum_probs=34.0
Q ss_pred eeeeEEEEc-CCeEEEEEEec--ccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEe
Q 029201 34 YSGVEVRVT-PVRTEIIIRAT--RTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKV 91 (197)
Q Consensus 34 is~i~I~r~-~~~i~I~I~~~--~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i 91 (197)
-.++.++.. ...+.|.+++. .+..+-.--.+--+++++.|+++++++-..|++.+..+
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 455677766 66677666663 22222111111225677788888888766788776554
No 63
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=31.26 E-value=18 Score=32.46 Aligned_cols=38 Identities=24% Similarity=0.538 Sum_probs=31.7
Q ss_pred EcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 029201 41 VTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (197)
Q Consensus 41 r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~ 78 (197)
+.|-.++.-||-.-.|-+|||+|+.|++|++...-+++
T Consensus 120 ~~pce~rllihqs~ag~iigrngskikelrekcsarlk 157 (390)
T KOG2192|consen 120 PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLK 157 (390)
T ss_pred CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhh
Confidence 44556777788888999999999999999998887664
No 64
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=31.13 E-value=78 Score=29.15 Aligned_cols=50 Identities=16% Similarity=0.167 Sum_probs=35.8
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEe--cccceeeccCcccHHHHHH
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRA--TRTQNVLGEKGRRIRELTS 71 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~--~~p~~vig~~g~~i~~l~~ 71 (197)
..+|+.+.|.-|.+.++.+.. ++.-.+++++ ..-+..||++|++++.-..
T Consensus 279 ~~~fi~nal~Pa~v~~v~i~~-~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~ 330 (362)
T PRK12327 279 PAEFVANALSPAKVVSVEVDD-EEEKAARVVVPDYQLSLAIGKEGQNARLAAR 330 (362)
T ss_pred HHHHHHHhCCCceEEEEEEEc-CCCcEEEEEEChhhcchhhcCCChhHHHHHH
Confidence 789999999999999998743 3333344444 4455799999999865443
No 65
>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=30.46 E-value=92 Score=24.88 Aligned_cols=43 Identities=9% Similarity=0.275 Sum_probs=27.8
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHH
Q 029201 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTS 71 (197)
Q Consensus 28 ~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~ 71 (197)
.+.++..-.|.+.-.. .+-..+.....|..+|++|++++.+++
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 3445555555553322 555555556678899999999999853
No 66
>TIGR01035 hemA glutamyl-tRNA reductase. This enzyme, together with glutamate-1-semialdehyde-2,1-aminomutase (TIGR00713), leads to the production of delta-amino-levulinic acid from Glu-tRNA.
Probab=29.88 E-value=1.8e+02 Score=26.87 Aligned_cols=35 Identities=26% Similarity=0.124 Sum_probs=27.2
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEeccc
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRT 55 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p 55 (197)
+.+++.......++..+.|-.|.|+++|++++..|
T Consensus 26 ~~~~l~~l~~~~~~~e~viLsTCNR~EiY~~~~~~ 60 (417)
T TIGR01035 26 LKKALDTLKAEPSIEEAMVLSTCNRVEIYAVVDNL 60 (417)
T ss_pred HHHHHHHHHhcCCCceEEEEecCCeEEEEEEeCCc
Confidence 45555555555789999999999999999887654
No 67
>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=29.71 E-value=83 Score=28.69 Aligned_cols=49 Identities=18% Similarity=0.270 Sum_probs=35.2
Q ss_pred HHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHH
Q 029201 21 LNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIREL 69 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~-~~~i~I~I~~~~p~~vig~~g~~i~~l 69 (197)
..+|+.+.|.-|.+.+|.+... .....|++--..-+..||++|++++.-
T Consensus 277 ~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la 326 (341)
T TIGR01953 277 PAEFIANALSPAKVISVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLA 326 (341)
T ss_pred HHHHHHHhcCCceEEEEEEEcCCCcEEEEEEChHHcchhhcCCChhHHHH
Confidence 7899999999999999987443 234444444445557999999998643
No 68
>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=29.39 E-value=2.3e+02 Score=23.06 Aligned_cols=49 Identities=22% Similarity=0.321 Sum_probs=36.5
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 029201 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (197)
Q Consensus 28 ~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i 88 (197)
.+.+.||. ..++.++|-+.+|.+ +....++++.|.+.++.+..+|+|..
T Consensus 82 ~~~~~g~~-------i~niD~tii~e~PKi-----~p~~~~m~~~ls~~L~~~~~~V~iKa 130 (153)
T cd00554 82 LIREKGYE-------IVNIDITIIAERPKI-----SPYREAMRANLAELLGIPPSRVNIKA 130 (153)
T ss_pred HHHHcCCE-------EEEEEEEEEecCCcc-----hHHHHHHHHHHHHHhCCCCceEEEEE
Confidence 34556654 456778888988854 45678999999999998777787654
No 69
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=29.03 E-value=2.1e+02 Score=23.61 Aligned_cols=57 Identities=12% Similarity=0.345 Sum_probs=40.1
Q ss_pred HHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEE
Q 029201 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (197)
Q Consensus 24 ~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i 86 (197)
-+++.+...||..+...-..+.+.|++.+.. + ..+...++.+.+.+.+|++..+|.|
T Consensus 139 ~iE~llkakGf~davv~~~~~~v~VvV~~~~----L--~~~~~~~I~diV~~~~~v~~~~I~V 195 (196)
T PF12685_consen 139 EIENLLKAKGFEDAVVFIEDDSVDVVVKADK----L--SDAEAAQIIDIVMRETGVPAENISV 195 (196)
T ss_dssp HHHHHHHTTS-SEEEEE-SSSEEEEEEE-S---------HHHHHHHHHHHHHHHC-STSEEEE
T ss_pred HHHHHHHhCCCCceEEEeeCCEEEEEEeCCC----C--CHHHHHHHHHHHHHHhCCCcCeEEe
Confidence 3455666789999999999999999888754 1 2457788999999999987677764
No 70
>PRK13763 putative RNA-processing protein; Provisional
Probab=28.31 E-value=72 Score=26.17 Aligned_cols=66 Identities=15% Similarity=0.245 Sum_probs=40.2
Q ss_pred EEEEEecccceeeccCcccHHHHHHHHHHHhCCC--CCeeEEEEEEecCCCcCHHHHHHHHHHHHhcCch
Q 029201 47 EIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP--ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLA 114 (197)
Q Consensus 47 ~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~--~~~i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~ 114 (197)
.+.|-..+.+.+||++|+.++.|++...-...++ +..|.|... ..++..+..-|..+...|-.+..
T Consensus 6 ~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~--~~~d~~~i~kA~~~I~ai~~gf~ 73 (180)
T PRK13763 6 YVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPT--DGEDPLAVLKARDIVKAIGRGFS 73 (180)
T ss_pred EEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeC--CCCCHHHHHHHHHHHHHHhcCCC
Confidence 3444456667899999998888776654333222 133433221 14566777778888877776544
No 71
>PRK13764 ATPase; Provisional
Probab=28.01 E-value=97 Score=30.53 Aligned_cols=52 Identities=23% Similarity=0.419 Sum_probs=32.7
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 029201 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (197)
Q Consensus 20 ~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~ 74 (197)
+|.+-+.+.+ .|...+++. .++...|++--.--+.+||++|.+|+++++.|.
T Consensus 460 ~~~~~~~~~~--~~~~~~~~~-~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~ 511 (602)
T PRK13764 460 EIEREIKRYL--PGPVEVEVV-SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLG 511 (602)
T ss_pred HHHHHHHHhc--CCceEEEEe-cCCeEEEEEChhhhhHHhccCcchHHHHHHHhC
Confidence 4666666666 455566666 455554444333345699999999988765543
No 72
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=27.37 E-value=78 Score=28.55 Aligned_cols=79 Identities=15% Similarity=0.225 Sum_probs=43.5
Q ss_pred EcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcCHHHHHHHHHHHHhcCchhHHHH
Q 029201 41 VTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRAC 119 (197)
Q Consensus 41 r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~ 119 (197)
|....+.|-+.+...|.|||++|++|+.|+.+..-...+++.+--=.+..|.-..-..--+-..|--.||.+.+.+.-|
T Consensus 45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f~~~~pc 123 (390)
T KOG2192|consen 45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGFQLPSPC 123 (390)
T ss_pred hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCCCCCCch
Confidence 3344567777788889999999999999887665444333211000011222222222234445556677666544444
No 73
>PRK00045 hemA glutamyl-tRNA reductase; Reviewed
Probab=26.04 E-value=3e+02 Score=25.41 Aligned_cols=34 Identities=29% Similarity=0.198 Sum_probs=26.7
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecc
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATR 54 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~ 54 (197)
+.+++.......++..+.|-.|.|+++|++++..
T Consensus 28 ~~~~~~~l~~~~~~~e~viLsTCNR~EiY~~~~~ 61 (423)
T PRK00045 28 LEEALESLLASPSVLEAVILSTCNRTEIYAVVDQ 61 (423)
T ss_pred HHHHHHHHhcCCCCceEEEEecCCeEEEEEEeCC
Confidence 4555555555578999999999999999988654
No 74
>COG4509 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.00 E-value=1.1e+02 Score=26.50 Aligned_cols=46 Identities=20% Similarity=0.201 Sum_probs=32.3
Q ss_pred cceEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecc
Q 029201 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATR 54 (197)
Q Consensus 8 ~~~~~~~~~~~~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~ 54 (197)
+.+-.+++.+++++++|+++.|.++ -...+++-.-...+|.|+++.
T Consensus 129 YgHhm~dnsMF~~L~~flkksF~~k-Hk~fsyetk~~~y~veiFaay 174 (244)
T COG4509 129 YGHHMADNSMFAELPNFLKKSFFNK-HKEFSYETKYKQYKVEIFAAY 174 (244)
T ss_pred EeeecCCCcHHHHHHHHHHHHHHhh-CCceEeecccceEEEEEEEEE
Confidence 4566789999999999999988654 222445555556777777643
No 75
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=25.85 E-value=1.1e+02 Score=19.80 Aligned_cols=31 Identities=10% Similarity=0.150 Sum_probs=23.3
Q ss_pred cccHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 029201 63 GRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (197)
Q Consensus 63 g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~ 93 (197)
.+-++.+.+.|...+|.+...+.+.+.++..
T Consensus 18 ~~l~~~it~~l~~~lg~~~~~v~V~i~e~~~ 48 (63)
T TIGR00013 18 RQLIEGVTEAMAETLGANLESIVVIIDEMPK 48 (63)
T ss_pred HHHHHHHHHHHHHHhCCCcccEEEEEEEcCH
Confidence 3345777888888999887788887777654
No 76
>TIGR01634 tail_P2_I phage tail protein, P2 protein I family. This model represents the family of phage P2 protein I and related tail proteins from a number of temperate phage of Gram-negative bacteria. This alignment is built as a fragment model and identifies some phage tail proteins with strong but local similarity to members of the seed alignment.
Probab=25.51 E-value=37 Score=27.11 Aligned_cols=78 Identities=9% Similarity=0.030 Sum_probs=55.8
Q ss_pred EEEecCCCcCHHHHHHHHHHHHhc-----Cc---hhHHHHHHHHHHHHhcCC-ceeEEEEecccCccccceeecccC--e
Q 029201 88 AEKVNNRGLCAIAQAESLRYKLLG-----GL---AVRRACYGVLRFIMESGA-KGCEVIVSGKLRAQRAKSMKFKDG--Y 156 (197)
Q Consensus 88 i~~i~~p~~~a~~iA~~ia~~Le~-----r~---~fRr~~k~~i~~~~~~ga-kGikI~isGRL~G~rAR~e~~~~G--~ 156 (197)
+..+-+|+.|+.-+-.++|-++-= .. ..|..++.++..-...|- .|++-.+.. |+|.-.=+|||++| -
T Consensus 26 ~~~l~dp~~~p~~~Lp~LAw~~~Vd~W~~~w~~~~KR~~Ik~A~~~hr~kGT~~avr~~l~~-lg~~~~i~EW~e~~p~g 104 (139)
T TIGR01634 26 LRQLWNPDTCPANLLPWLAWAFSVDRWDSTWPEKVKRDVIRSAYFIHRHKGTIGAVRRVVEP-FGGIVNITEWWQTGPPG 104 (139)
T ss_pred hhhhCChhhCCHHHHHHHHHHcCcCccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH-cCCCeEEeehhccCCCC
Confidence 456789999999999999976642 11 478888988887777774 466655544 77654458999997 3
Q ss_pred eccCCccccceee
Q 029201 157 MISSGQPVNEYID 169 (197)
Q Consensus 157 v~~tgq~~~~~Id 169 (197)
-||| ++-.++
T Consensus 105 ~P~t---F~i~~~ 114 (139)
T TIGR01634 105 PPGT---FELTLT 114 (139)
T ss_pred CCeE---EEEEEE
Confidence 4777 665544
No 77
>PRK13763 putative RNA-processing protein; Provisional
Probab=24.77 E-value=1.7e+02 Score=24.01 Aligned_cols=60 Identities=13% Similarity=0.185 Sum_probs=33.1
Q ss_pred ccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcCHHHHHHHHHHHHhcCchhHHHH
Q 029201 54 RTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRAC 119 (197)
Q Consensus 54 ~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~p~~~a~~iA~~ia~~Le~r~~fRr~~ 119 (197)
..|.+||++|+.++.|++.-.-.+.+.+..+.| +-+ ....-.|...-..|-.+.+.-.+.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~i----~G~--~~~~~~A~~~I~~li~g~~~~~~~ 164 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVAI----IGD--PEQVEIAREAIEMLIEGAPHGTVY 164 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCCEEEE----EeC--HHHHHHHHHHHHHHHcCCCcHHHH
Confidence 466799999988777665544433333333332 222 234445555556666555444443
No 78
>TIGR00151 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes.
Probab=24.54 E-value=2.7e+02 Score=22.67 Aligned_cols=49 Identities=24% Similarity=0.302 Sum_probs=35.9
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 029201 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (197)
Q Consensus 28 ~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~~~~~~~i~i~i 88 (197)
.+.+.|+. ..++.++|-+.+|.+ +....++++.|.+.++++..+|+|..
T Consensus 82 ~~~~~g~~-------i~niD~tii~e~PKi-----~p~~~~m~~~la~~L~~~~~~V~iKa 130 (155)
T TIGR00151 82 LIKEKGYR-------IGNVDITIIAQRPKL-----LPHIPAMRENIAELLGIPLDSVNVKA 130 (155)
T ss_pred HHHHcCCE-------EEEEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEE
Confidence 34455653 346777888988854 45678999999999998777777654
No 79
>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=24.43 E-value=61 Score=22.54 Aligned_cols=22 Identities=32% Similarity=0.270 Sum_probs=14.7
Q ss_pred cCHHHHHHHHHHHHhcCchhHHHHH
Q 029201 96 LCAIAQAESLRYKLLGGLAVRRACY 120 (197)
Q Consensus 96 ~~a~~iA~~ia~~Le~r~~fRr~~k 120 (197)
..|.=+|+++..+ ++|||.+=.
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 3466677777765 999997654
No 80
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=22.85 E-value=1e+02 Score=27.59 Aligned_cols=39 Identities=21% Similarity=0.095 Sum_probs=29.5
Q ss_pred chHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeec
Q 029201 17 FFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60 (197)
Q Consensus 17 ~~~~Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~~p~~vig 60 (197)
+..++|++|... |=| +.+--+...++|.||+..||.++.
T Consensus 19 ~~~~lr~~L~~~----GdS-lvVv~~~~~~kVHvHT~~Pg~vle 57 (313)
T PF13684_consen 19 DAEELRARLEEL----GDS-LVVVGDDDLVKVHVHTNDPGAVLE 57 (313)
T ss_pred CHHHHHHHHHhc----CCE-EEEEecCCeEEEEEeeCCHHHHHH
Confidence 556688877644 333 555577889999999999998875
No 81
>PRK13940 glutamyl-tRNA reductase; Provisional
Probab=22.79 E-value=3.2e+02 Score=25.45 Aligned_cols=33 Identities=21% Similarity=0.175 Sum_probs=26.5
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEec
Q 029201 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRAT 53 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~~~~i~I~I~~~ 53 (197)
+.+++.......+++.+.|-.|.|+++|+.++.
T Consensus 28 ~~~~l~~l~~~~~i~e~viLsTCNR~EiY~~~~ 60 (414)
T PRK13940 28 VSMLYRSILAIDNVVHAVILSTCNRTEVYLEIS 60 (414)
T ss_pred HHHHHHHHhcCCCCceEEEEecCCeEEEEEEeC
Confidence 555666555568899999999999999998764
No 82
>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=22.03 E-value=1.1e+02 Score=30.09 Aligned_cols=53 Identities=21% Similarity=0.370 Sum_probs=38.7
Q ss_pred HHHHHHHhhhc-cCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHh
Q 029201 20 ELNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRF 77 (197)
Q Consensus 20 ~Ir~~l~~~~~-~agis~i~I~r~~~~i~I~I~~~~p~~vig~~g~~i~~l~~~l~~~~ 77 (197)
+|++-+.+.+. ++.+++|+.+ +-+|.||+..|..+... +.-+++|.+.|+|+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~e----gp~~~~~~~~~~~~~~~-~~~~~~~~~~~~~r~ 56 (630)
T TIGR03675 3 EIKEIINELLPKDIKITDVEFE----GPELVIYTKNPELFAKD-DDLVKELAKKLRKRI 56 (630)
T ss_pred HHHHHHHHhCCCCCeEEEEEEe----CCeEEEEeCCHHHhccc-hHHHHHHHHHhhceE
Confidence 56666666775 6789988876 46889999999987653 356677777776654
No 83
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=21.76 E-value=2.4e+02 Score=26.10 Aligned_cols=41 Identities=15% Similarity=0.333 Sum_probs=30.2
Q ss_pred eEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeeEEEE
Q 029201 45 RTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVELYA 88 (197)
Q Consensus 45 ~i~I~I~~~~p~---~vig~~g~~i~~l----~~~l~~~~~~~~~~i~i~i 88 (197)
.|.+.+-+.++. ++||++|..|.++ .+.|..+|+ .++.+.+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~dL~~if~---r~V~l~l 374 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANEDLEDIFQ---RKVFLRL 374 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHHHHHHHhh---ceeeEEE
Confidence 566666676666 5999999999876 677888886 5666543
No 84
>PF11324 DUF3126: Protein of unknown function (DUF3126); InterPro: IPR021473 This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=21.62 E-value=1.3e+02 Score=20.99 Aligned_cols=20 Identities=15% Similarity=0.488 Sum_probs=16.3
Q ss_pred cHHHHHHHHHHHhCCCCCeeEE
Q 029201 65 RIRELTSVVQKRFKFPENSVEL 86 (197)
Q Consensus 65 ~i~~l~~~l~~~~~~~~~~i~i 86 (197)
++++|+..|++.|+ |+.+.|
T Consensus 1 Ei~klq~yLr~~f~--n~~i~v 20 (63)
T PF11324_consen 1 EIKKLQAYLRRTFG--NPGITV 20 (63)
T ss_pred ChHHHHHHHHHHhC--CCceEE
Confidence 47899999999997 567765
No 85
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=21.51 E-value=1.6e+02 Score=18.59 Aligned_cols=31 Identities=16% Similarity=0.291 Sum_probs=23.4
Q ss_pred cccHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 029201 63 GRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (197)
Q Consensus 63 g~~i~~l~~~l~~~~~~~~~~i~i~i~~i~~ 93 (197)
.+-.+.+.+.+.+.++.+...+.+.+.++..
T Consensus 17 ~~l~~~i~~~l~~~~g~~~~~v~V~i~e~~~ 47 (58)
T cd00491 17 RELIERVTEAVSEILGAPEATIVVIIDEMPK 47 (58)
T ss_pred HHHHHHHHHHHHHHhCcCcccEEEEEEEeCc
Confidence 3445677888888898887788888877654
No 86
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=21.32 E-value=1.3e+02 Score=28.80 Aligned_cols=52 Identities=10% Similarity=0.211 Sum_probs=36.5
Q ss_pred HHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHH
Q 029201 21 LNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSV 72 (197)
Q Consensus 21 Ir~~l~~~~~~agis~i~I~r~-~~~i~I~I~~~~p~~vig~~g~~i~~l~~~ 72 (197)
..+|+.+.|.-|.+.+|.+... .....|++--..-+..||++|++++.-...
T Consensus 311 p~~fI~NaLsPA~V~~V~i~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~L 363 (449)
T PRK12329 311 PATYIANALSPARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARL 363 (449)
T ss_pred HHHHHHHhcCCceeeEEEEEcCCCcEEEEEEChHhcchhhcCCChhHHHHHHH
Confidence 7889999999999999987442 223444444455567999999998654433
Done!