Query 022692
Match_columns 293
No_of_seqs 91 out of 108
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 05:27:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022692.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022692hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06555 ASCH_PF0470_like ASC-1 100.0 7.6E-40 1.6E-44 268.2 12.0 104 131-235 1-109 (109)
2 COG4043 Preprotein translocase 100.0 1.8E-38 3.8E-43 260.0 10.6 107 130-237 2-109 (111)
3 cd06541 ASCH ASC-1 homology or 99.8 9.2E-21 2E-25 151.5 8.2 100 133-234 2-105 (105)
4 PF04266 ASCH: ASCH domain; I 99.7 1.5E-16 3.3E-21 123.4 7.7 98 133-236 1-104 (105)
5 cd06552 ASCH_yqfb_like ASC-1 h 99.0 1.9E-09 4E-14 84.1 7.6 94 133-234 2-99 (100)
6 PF12961 DUF3850: Domain of Un 98.4 5.3E-07 1.1E-11 70.4 6.3 53 131-186 1-62 (72)
7 PRK04980 hypothetical protein; 96.9 0.0055 1.2E-07 50.8 8.3 92 132-235 4-101 (102)
8 COG2411 Uncharacterized conser 92.6 1.1 2.3E-05 41.1 9.4 116 133-257 9-128 (188)
9 COG3097 Uncharacterized protei 91.6 1.2 2.6E-05 37.4 7.9 91 134-236 7-103 (106)
10 PRK12279 50S ribosomal protein 88.1 3.5 7.6E-05 40.3 9.3 113 114-245 175-295 (311)
11 cd06553 ASCH_Ef3133_like ASC-1 86.1 3.6 7.8E-05 35.1 7.2 87 136-227 13-110 (127)
12 COG4933 Uncharacterized conser 84.8 4.7 0.0001 35.0 7.3 96 133-245 1-105 (124)
13 COG1935 Uncharacterized conser 81.1 3.2 6.9E-05 35.9 4.9 43 141-183 16-71 (122)
14 PRK11507 ribosome-associated p 80.6 2.9 6.3E-05 32.9 4.1 32 142-173 33-64 (70)
15 PF13275 S4_2: S4 domain; PDB: 70.3 1.7 3.6E-05 33.5 0.4 31 142-172 29-59 (65)
16 cd06554 ASCH_ASC-1_like ASC-1 68.8 3.5 7.6E-05 34.6 2.0 28 133-160 4-31 (113)
17 COG1868 FliM Flagellar motor s 66.8 2.6 5.6E-05 41.3 1.0 37 149-185 261-301 (332)
18 TIGR02988 YaaA_near_RecF S4 do 66.4 7.3 0.00016 28.1 3.1 31 141-171 29-59 (59)
19 PF13550 Phage-tail_3: Putativ 63.8 15 0.00032 30.0 4.8 43 139-182 118-163 (164)
20 COG0809 QueA S-adenosylmethion 63.7 10 0.00022 37.8 4.4 73 149-221 78-175 (348)
21 PRK10348 ribosome-associated h 61.2 17 0.00036 31.6 4.8 52 141-193 29-87 (133)
22 COG1188 Ribosome-associated he 57.5 18 0.00039 30.3 4.2 42 141-183 29-73 (100)
23 PF04322 DUF473: Protein of un 56.7 33 0.00072 29.4 5.8 43 141-183 16-71 (119)
24 PF01336 tRNA_anti-codon: OB-f 56.6 15 0.00033 25.9 3.2 30 142-171 21-54 (75)
25 smart00363 S4 S4 RNA-binding d 54.7 14 0.0003 24.3 2.6 33 140-172 20-52 (60)
26 cd04478 RPA2_DBD_D RPA2_DBD_D: 53.6 35 0.00075 26.0 5.0 51 143-193 22-86 (95)
27 smart00350 MCM minichromosome 53.5 17 0.00038 36.6 4.2 45 131-176 86-132 (509)
28 COG1430 Uncharacterized conser 52.1 13 0.00028 32.0 2.6 25 147-171 96-120 (126)
29 PRK06461 single-stranded DNA-b 51.1 35 0.00076 28.5 5.0 44 143-186 46-100 (129)
30 KOG4476 Gluconate transport-in 50.5 13 0.00027 35.6 2.5 32 140-171 21-53 (248)
31 COG5037 TOS9 Gluconate transpo 50.5 13 0.00027 35.6 2.5 32 140-171 21-53 (248)
32 PF11184 DUF2969: Protein of u 49.7 14 0.00031 28.8 2.3 63 147-216 5-67 (71)
33 PF11604 CusF_Ec: Copper bindi 49.2 15 0.00032 28.0 2.3 56 127-182 7-67 (70)
34 PF09953 DUF2187: Uncharacteri 47.8 22 0.00048 27.2 3.0 30 161-190 3-41 (57)
35 PF07527 Hairy_orange: Hairy O 43.3 21 0.00045 24.7 2.1 28 4-40 7-34 (43)
36 PRK00147 queA S-adenosylmethio 42.1 70 0.0015 31.8 6.3 59 160-219 100-171 (342)
37 PF01479 S4: S4 domain; Inter 41.7 13 0.00027 25.4 0.8 29 140-168 20-48 (48)
38 cd03695 CysN_NodQ_II CysN_NodQ 39.5 58 0.0012 24.9 4.2 34 149-185 17-51 (81)
39 COG2501 S4-like RNA binding pr 39.4 45 0.00098 26.5 3.7 32 142-173 33-64 (73)
40 cd00165 S4 S4/Hsp/ tRNA synthe 37.7 43 0.00093 22.5 3.0 31 141-171 21-51 (70)
41 TIGR03069 PS_II_S4 photosystem 35.7 54 0.0012 30.8 4.2 36 138-173 200-235 (257)
42 PRK01424 S-adenosylmethionine: 34.4 1.1E+02 0.0023 31.0 6.2 51 147-198 68-140 (366)
43 cd06863 PX_Atg24p The phosphoi 33.9 53 0.0011 26.7 3.4 51 150-202 1-60 (118)
44 cd04498 hPOT1_OB2 hPOT1_OB2: A 33.3 39 0.00084 29.0 2.6 27 146-172 58-87 (123)
45 KOG3416 Predicted nucleic acid 30.7 75 0.0016 28.1 4.0 25 147-171 47-71 (134)
46 TIGR00113 queA S-adenosylmethi 30.7 1.2E+02 0.0027 30.1 6.0 60 160-220 98-173 (344)
47 COG3264 Small-conductance mech 30.2 63 0.0014 35.7 4.2 27 160-186 659-691 (835)
48 PRK09838 periplasmic copper-bi 30.2 37 0.00081 28.6 2.0 49 123-171 49-98 (115)
49 TIGR00739 yajC preprotein tran 29.5 61 0.0013 25.8 3.0 25 159-183 35-59 (84)
50 COG3127 Predicted ABC-type tra 29.0 46 0.001 36.6 2.9 28 157-184 606-636 (829)
51 COG5569 Uncharacterized conser 29.0 88 0.0019 26.7 4.0 45 127-171 48-93 (108)
52 PRK06033 hypothetical protein; 26.8 67 0.0015 25.4 2.8 28 157-184 23-54 (83)
53 PLN00051 RNA-binding S4 domain 26.8 1E+02 0.0022 29.3 4.5 61 109-172 181-242 (267)
54 PRK03760 hypothetical protein; 26.5 51 0.0011 27.6 2.2 24 148-171 92-115 (117)
55 PF01052 SpoA: Surface present 25.3 45 0.00097 24.9 1.5 26 155-180 22-51 (77)
56 PF02643 DUF192: Uncharacteriz 24.4 33 0.00071 27.9 0.7 27 145-171 81-107 (108)
57 PF13437 HlyD_3: HlyD family s 24.2 1.4E+02 0.0031 22.8 4.2 38 146-183 34-78 (105)
58 cd04491 SoSSB_OBF SoSSB_OBF: A 23.4 81 0.0018 23.6 2.6 29 144-172 30-59 (82)
59 TIGR02480 fliN flagellar motor 23.2 67 0.0014 24.6 2.1 28 157-184 24-55 (77)
60 PRK05585 yajC preprotein trans 23.0 87 0.0019 26.0 2.9 28 156-183 47-74 (106)
61 PF05899 Cupin_3: Protein of u 22.6 1.4E+02 0.0031 22.5 3.8 28 142-171 30-57 (74)
62 COG2820 Udp Uridine phosphoryl 22.6 96 0.0021 29.9 3.4 35 141-176 78-114 (248)
63 PRK05886 yajC preprotein trans 22.5 91 0.002 26.3 2.9 24 159-182 36-59 (109)
64 PF08605 Rad9_Rad53_bind: Fung 20.2 1.2E+02 0.0026 26.3 3.3 39 143-183 43-82 (131)
65 PF12195 End_beta_barrel: Beta 20.1 1.6E+02 0.0034 24.2 3.7 25 144-171 13-37 (83)
No 1
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=100.00 E-value=7.6e-40 Score=268.21 Aligned_cols=104 Identities=35% Similarity=0.487 Sum_probs=101.8
Q ss_pred eeeeccccchHHHhcCCceEEEeecCccccCCCCCCEEEEce-----eEEEEEEEEeecCCHHHHHhccCccccCCCCCC
Q 022692 131 FELHVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILLNK-----CMMLKVQSVCHYDSFSEMLEAESLVKVLPGVKT 205 (293)
Q Consensus 131 heM~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~k-----~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~S 205 (293)
|+|+|+++||++|++|+||||||+||+||++|++||+|+|++ ++.|+|++|++|+||++||++|++++++|+++|
T Consensus 1 h~m~l~~~~F~~I~~G~KtiEiRlnD~kr~~ikvGD~I~f~~~~~~~~l~v~V~~i~~Y~sF~~ll~~e~~~~~~~~~~s 80 (109)
T cd06555 1 HEMGLEEEPFELIKSGKKTIEIRLNDEKRQQIKVGDKILFNDLDTGQQLLVKVVDIRKYDSFRELLEEEGLEKVGPGVDS 80 (109)
T ss_pred CccccChHHHHHHHcCCCEEEEEecccchhcCCCCCEEEEEEcCCCcEEEEEEEEEEecCCHHHHHHhcCHhhcCCCCCc
Confidence 789999999999999999999999999999999999999985 899999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCChHHHhhcCCeEEEEEee
Q 022692 206 IEEVLQVYKFIENSTQRRRKGPMVSLQYAF 235 (293)
Q Consensus 206 iEEgv~~yr~iYSkEkE~qyGV~VAIeI~l 235 (293)
+|||+++||+|||+|||++||| |||+|++
T Consensus 81 ~ee~~~~~~~~Y~~e~e~~~Gv-laI~i~~ 109 (109)
T cd06555 81 IEEGVKDTYKIYSKEQEKKYGV-LAIEIRV 109 (109)
T ss_pred HHHHHHHHHHhCCHHHHHhcCE-EEEEEEC
Confidence 9999999999999999999999 9999985
No 2
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.8e-38 Score=260.01 Aligned_cols=107 Identities=29% Similarity=0.462 Sum_probs=104.3
Q ss_pred ceeeeccccchHHHhcCCceEEEeecCccccCCCCCCEEEEc-eeEEEEEEEEeecCCHHHHHhccCccccCCCCCCHHH
Q 022692 130 EFELHVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILLN-KCMMLKVQSVCHYDSFSEMLEAESLVKVLPGVKTIEE 208 (293)
Q Consensus 130 ~heM~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~-k~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~SiEE 208 (293)
.|+|+|++.||++|++|+|||||||||+||++||+||+|.|| ..+.|+|++||.|+||++||+.||++|++|+.+|+||
T Consensus 2 ~~~mgL~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~~~l~v~V~~vr~Y~tF~~mlreepiE~v~p~~~S~ee 81 (111)
T COG4043 2 VHRMGLREEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNGDKLKVEVIDVRVYDTFEEMLREEPIENVLPDVPSFEE 81 (111)
T ss_pred ceeechHHHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcCCeeEEEEEEEeehhHHHHHHHhcChhhhCCCCccHHH
Confidence 489999999999999999999999999999999999999999 8999999999999999999999999999999999999
Q ss_pred HHHHHHhcCChHHHhhcCCeEEEEEeecc
Q 022692 209 VLQVYKFIENSTQRRRKGPMVSLQYAFPK 237 (293)
Q Consensus 209 gv~~yr~iYSkEkE~qyGV~VAIeI~lp~ 237 (293)
||..||+||++|+|++||| +||+|+..-
T Consensus 82 ~l~~~~~~Y~~~kE~~yGv-laI~ie~i~ 109 (111)
T COG4043 82 GLRRYRNFYPSEKEKRYGV-LAIEIEPIG 109 (111)
T ss_pred HHHHHHHhCcHhHhhccce-EEEEEEEcC
Confidence 9999999999999999999 999999653
No 3
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=99.83 E-value=9.2e-21 Score=151.47 Aligned_cols=100 Identities=13% Similarity=0.015 Sum_probs=94.1
Q ss_pred eeccccchHHHhcCCceEEEeecCccccCCCCCCEEEEce----eEEEEEEEEeecCCHHHHHhccCccccCCCCCCHHH
Q 022692 133 LHVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILLNK----CMMLKVQSVCHYDSFSEMLEAESLVKVLPGVKTIEE 208 (293)
Q Consensus 133 M~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~k----~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~SiEE 208 (293)
|++.+++|++|.+|+||+|+|+++++++.+++||.|+|.+ .+.++|++|+.|++| +++.++...+.++|..|+++
T Consensus 2 l~~~~~~~~lI~~G~Ktat~r~~~~~~~~~k~Gd~~i~~~~~~~~~~i~v~~V~~~~~f-~~~~~e~a~~eGegd~sl~~ 80 (105)
T cd06541 2 LMFGDRYGQLVVSGRKTIEIRSLDIYEQLPKAGDYLIILDGQQPLAIAEVVKVEIMPMV-NELSEEQEQAEGEGDLTLLY 80 (105)
T ss_pred ceechHHHHHHHCCCCEEEEEcchhcccCCCCCCEEEEecCCCcEEEEEEEEEEEEECH-HHccHHHHHHcCCCchhHHH
Confidence 6789999999999999999999999999999999999997 899999999999999 77777777788888889999
Q ss_pred HHHHHHhcCChHHHhhcCCeEEEEEe
Q 022692 209 VLQVYKFIENSTQRRRKGPMVSLQYA 234 (293)
Q Consensus 209 gv~~yr~iYSkEkE~qyGV~VAIeI~ 234 (293)
.++.+++||+++++.++|| ++|+++
T Consensus 81 ~~~~~~~~~~~~~~~~~~v-v~i~F~ 105 (105)
T cd06541 81 ELKEHAAFFKEELAPDMLL-YAISFE 105 (105)
T ss_pred HHHHHHHHhhHHhCCCCce-EEEEeC
Confidence 9999999999999999999 999985
No 4
>PF04266 ASCH: ASCH domain; InterPro: IPR007374 The ASCH domain adopts a beta-barrel fold similar to that of the PUA domain (IPR002478 from INTERPRO). It is thought to function as an RNA-binding domain during coactivation, RNA-processing and possibly during prokaryotic translation regulation [].; PDB: 1TE7_A 2Z0T_C 1WK2_A 2DP9_A 1T62_A 3S9X_A 2E5O_A 1XNE_A 3IUW_B 1S04_A.
Probab=99.67 E-value=1.5e-16 Score=123.44 Aligned_cols=98 Identities=23% Similarity=0.296 Sum_probs=87.0
Q ss_pred eeccccchHHHhcCCceEEEeecCccccCCCCCCEEEEc------eeEEEEEEEEeecCCHHHHHhccCccccCCCCCCH
Q 022692 133 LHVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILLN------KCMMLKVQSVCHYDSFSEMLEAESLVKVLPGVKTI 206 (293)
Q Consensus 133 M~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~------k~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~Si 206 (293)
|.+.++||++|.+|+||+|+|+.++++..++.++.|+|+ -...++|++|+.+ +|++|.++..... |. |+
T Consensus 1 Lsi~~~~~~~Il~G~Kt~e~R~~~~~~~~~~g~~~iv~~~~~~~~~~~~v~v~~V~~~-~~~e~~~~~a~~e---g~-s~ 75 (105)
T PF04266_consen 1 LSIKPEYAELILSGKKTAEIRLWDEKLPKIRGDLVIVFNTDPDGKPVGIVEVTEVEVY-PFSELTEEHARLE---GE-SL 75 (105)
T ss_dssp EEECHHHHHHHHTTSSCEEEECSTTTCCTTTTCEEEEETETTTTEEEEEEEEEEEEEE-EHHHHHHHHHHHH---CC--H
T ss_pred CEechHHHHHHHCCCcEEEEEcccceeccCCCCEEEEEEEecCCcEEEEEEEEEEEEe-hhhhCCHHHHhHh---cc-CH
Confidence 678999999999999999999999999998888888876 2588999999999 9999999865543 33 99
Q ss_pred HHHHHHHHhcCChHHHhhcCCeEEEEEeec
Q 022692 207 EEVLQVYKFIENSTQRRRKGPMVSLQYAFP 236 (293)
Q Consensus 207 EEgv~~yr~iYSkEkE~qyGV~VAIeI~lp 236 (293)
++..+.+++||+++.+...|| ++|++++|
T Consensus 76 e~~~~~~~~~y~~~~~~~~~v-~~i~f~~v 104 (105)
T PF04266_consen 76 EEWREEHRDIYPREIEPDDGV-VAIEFEVV 104 (105)
T ss_dssp HHHHHHHHHHCHHHHHCCCEE-EEEEEEEE
T ss_pred HHHHHHHHHHccccccccceE-EEEEEEec
Confidence 999999999999999988999 99999986
No 5
>cd06552 ASCH_yqfb_like ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=98.98 E-value=1.9e-09 Score=84.11 Aligned_cols=94 Identities=18% Similarity=0.183 Sum_probs=73.9
Q ss_pred eeccccchHHHhcCCceEEEeecCccccCCCCCCEEEEc----eeEEEEEEEEeecCCHHHHHhccCccccCCCCCCHHH
Q 022692 133 LHVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILLN----KCMMLKVQSVCHYDSFSEMLEAESLVKVLPGVKTIEE 208 (293)
Q Consensus 133 M~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~----k~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~SiEE 208 (293)
|.+.++++++|.+|+||+++|..+ ++.+++||.+.+. ....++|++|+. .+|.+| .++ .+-.-|..|.++
T Consensus 2 ~~f~~~~~~~I~sG~Kt~t~R~~~--~~~~~~Gd~~~~~~~~~~~~~~~v~~V~~-~~~~~l-~~~--~A~~eG~~s~~~ 75 (100)
T cd06552 2 ILFFERYEEAILSGKKTATIRDGG--ESHLKPGDVVEVHTGERIFGEAEITSVEE-KTLGEL-TDE--DARQEGFPSLEE 75 (100)
T ss_pred eechHHHHHHHHcCCCEEEEeCCC--ccCCCCCCEEEEEECCEEEEEEEEEEEEE-EEhhhC-CHH--HHHhcCCccHHH
Confidence 567789999999999999999975 4569999999987 368889999977 889884 443 334457779999
Q ss_pred HHHHHHhcCChHHHhhcCCeEEEEEe
Q 022692 209 VLQVYKFIENSTQRRRKGPMVSLQYA 234 (293)
Q Consensus 209 gv~~yr~iYSkEkE~qyGV~VAIeI~ 234 (293)
..+.++++|+.++.. -=| .-|+++
T Consensus 76 ~~~~l~~~Y~~~~~~-~~v-~vi~F~ 99 (100)
T cd06552 76 LKEALKEIYPGLKDD-DEV-YVIEFR 99 (100)
T ss_pred HHHHHHHHcCCCCCC-CEE-EEEEEE
Confidence 999999999987622 224 566665
No 6
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=98.43 E-value=5.3e-07 Score=70.41 Aligned_cols=53 Identities=21% Similarity=0.422 Sum_probs=46.9
Q ss_pred eeeeccccchHHHhcCCceEEEeecCccccCCCCCCEEEEc---------eeEEEEEEEEeecCC
Q 022692 131 FELHVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILLN---------KCMMLKVQSVCHYDS 186 (293)
Q Consensus 131 heM~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~---------k~L~v~V~~Vr~Y~S 186 (293)
|++.+.+.||+.+.+|+||.|+|.||-.+ ++||.+.++ +.+.++|+-|-.|..
T Consensus 1 H~LKi~p~yF~~V~~G~KtfEiRkNDRdf---~VGD~L~L~E~~~~~YTGr~~~~~Ityi~~~~~ 62 (72)
T PF12961_consen 1 HELKILPEYFEAVLSGRKTFEIRKNDRDF---QVGDILVLREWDNGEYTGREIEAEITYITDYEQ 62 (72)
T ss_pred CceeecHHHHHHHHCCCceEEEEecCCCC---CCCCEEEEEEecCCCccccEEEEEEEEEeecCC
Confidence 78999999999999999999999999765 699999987 378899999877543
No 7
>PRK04980 hypothetical protein; Provisional
Probab=96.93 E-value=0.0055 Score=50.77 Aligned_cols=92 Identities=22% Similarity=0.242 Sum_probs=62.9
Q ss_pred eeeccccchHHHhcCCceEEEeecCccccCCCCCCEEEE-c---e--eEEEEEEEEeecCCHHHHHhccCccccCCCCCC
Q 022692 132 ELHVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILL-N---K--CMMLKVQSVCHYDSFSEMLEAESLVKVLPGVKT 205 (293)
Q Consensus 132 eM~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F-~---k--~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~S 205 (293)
+|...++|-.+|-+|+||+-+|- +.-...++||.+.- . + -..++|++|. +-+|.+|=++ .+..=|. |
T Consensus 4 ~itF~~r~~~~ILsGkKTiTiRd--~se~~~~~G~~~~V~~~e~g~~~c~ieI~sV~-~i~f~eLte~---hA~qEg~-s 76 (102)
T PRK04980 4 KITFFERFEADILAGRKTITIRD--ESESHFKPGDVLRVGTFEDDRYFCTIEVLSVS-PVTFDELNEK---HAEQENM-T 76 (102)
T ss_pred eeeEHHHHHHHHHcCCceEEeeC--CcccCCCCCCEEEEEECCCCcEEEEEEEEEEE-EEehhhCCHH---HHHHhCC-C
Confidence 46678899999999999999998 44678899999886 3 1 2445555553 3456555443 1112233 7
Q ss_pred HHHHHHHHHhcCChHHHhhcCCeEEEEEee
Q 022692 206 IEEVLQVYKFIENSTQRRRKGPMVSLQYAF 235 (293)
Q Consensus 206 iEEgv~~yr~iYSkEkE~qyGV~VAIeI~l 235 (293)
+++-.+.++++|+.+.+- --|++++
T Consensus 77 L~elk~~i~~iYp~~~~l-----yvI~f~~ 101 (102)
T PRK04980 77 LPELKQVIAEIYPNLDQL-----YVIEFKL 101 (102)
T ss_pred HHHHHHHHHHHCCCCceE-----EEEEEEE
Confidence 999999999999963322 4455554
No 8
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=92.57 E-value=1.1 Score=41.11 Aligned_cols=116 Identities=21% Similarity=0.224 Sum_probs=84.0
Q ss_pred eeccccchHHHhcCCceEEEeecCccccCCCCCCEEEEce----eEEEEEEEEeecCCHHHHHhccCccccCCCCCCHHH
Q 022692 133 LHVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILLNK----CMMLKVQSVCHYDSFSEMLEAESLVKVLPGVKTIEE 208 (293)
Q Consensus 133 M~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~k----~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~SiEE 208 (293)
+.+..+|-+.|-+|+|+.-||+. --..++|+.+.... --.++|++|+ |.--+++=+. ++.+-|..|.||
T Consensus 9 l~f~gkY~~~ii~GkKr~TIR~G---~~~~k~g~eVyIh~~g~i~gkAkIk~V~-~KrV~ELTdE---DAr~DGF~sreE 81 (188)
T COG2411 9 LEFDGKYKDKIIDGKKRTTIRLG---KIVLKPGSEVYIHSGGYIIGKAKIKKVK-TKRVSELTDE---DARLDGFRSREE 81 (188)
T ss_pred eeechHHHHHHhcCceeEEEecC---cccCCCCCEEEEEECCEEEEEEEEEEEE-EeeHhhhhHH---HHHhcccccHHH
Confidence 56788999999999999999998 34568999998872 2345555553 4455666554 555678899999
Q ss_pred HHHHHHhcCChHHHhhcCCeEEEEEeeccCCCCCCCCcchhhhhHHHHH
Q 022692 209 VLQVYKFIENSTQRRRKGPMVSLQYAFPKWLLSPMLHWPAYCLDSVMWA 257 (293)
Q Consensus 209 gv~~yr~iYSkEkE~qyGV~VAIeI~lp~~~~~~m~~~~~~~~~~~~~~ 257 (293)
.++.++++|+.=.-. -=| --|+++++...-.|..+-|.--.|-+--|
T Consensus 82 Li~~LkriYg~lr~e-d~V-TIi~Fe~v~~~d~~i~~~~y~g~dp~eIA 128 (188)
T COG2411 82 LIEELKRIYGELRDE-DIV-TIIEFEVVEKLDKPILDLPYEGRDPIEIA 128 (188)
T ss_pred HHHHHHHHcCcCCCC-ceE-EEEEEEEehhccchhhhccCCCCCHHHHH
Confidence 999999999731111 124 67899999999998766666656655444
No 9
>COG3097 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.63 E-value=1.2 Score=37.44 Aligned_cols=91 Identities=18% Similarity=0.200 Sum_probs=57.1
Q ss_pred eccccchHHHhcCCceEEEeecCccccCCCCCCEEEEc----e--eEEEEEEEEeecCCHHHHHhccCccccCCCCCCHH
Q 022692 134 HVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILLN----K--CMMLKVQSVCHYDSFSEMLEAESLVKVLPGVKTIE 207 (293)
Q Consensus 134 ~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~----k--~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~SiE 207 (293)
....++=..|.+|+|||-|| |.--+..++||.+.-. + -...+|++|..- +|.+|=+. -+. --.-++.
T Consensus 7 TFf~rfe~dilagrKTITIR--D~SEShf~~g~vlrV~r~Ed~~~fc~I~vl~vspv-tld~l~e~--HAe--QEnm~L~ 79 (106)
T COG3097 7 TFFQRFEADILAGRKTITIR--DKSESHFKPGDVLRVGRFEDDRYFCTIEVLAVSPV-TLDELTEK--HAE--QENMTLP 79 (106)
T ss_pred eehhhccHHHhCCCceEEEe--ccchhcCCCCCEEEEEEecCCcEEEEEEEEEeccE-ehhhhhhh--hhh--hhcCCcH
Confidence 34556667899999999999 5556789999999733 1 234455555432 34444332 010 0122678
Q ss_pred HHHHHHHhcCChHHHhhcCCeEEEEEeec
Q 022692 208 EVLQVYKFIENSTQRRRKGPMVSLQYAFP 236 (293)
Q Consensus 208 Egv~~yr~iYSkEkE~qyGV~VAIeI~lp 236 (293)
|.-+++..||+.+.+- =| |++.+.
T Consensus 80 eLk~vI~eIYP~~d~f--yV---I~f~L~ 103 (106)
T COG3097 80 ELKKVIAEIYPNQDQF--YV---IEFQLA 103 (106)
T ss_pred HHHHHHHHHCCCCcEE--EE---EEEEec
Confidence 8889999999976643 34 555443
No 10
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=88.14 E-value=3.5 Score=40.30 Aligned_cols=113 Identities=12% Similarity=-0.004 Sum_probs=76.6
Q ss_pred HhhcChhhHHhhhhccceeeeccccchHHHhcC-CceEEEeecCccccCCCCCCEEEEc-----eeEE--EEEEEEeecC
Q 022692 114 ILNKGSSDLVDILKAVEFELHVQEPFFSFIKDG-LETVEGRCTISDYNSIGPGSVILLN-----KCMM--LKVQSVCHYD 185 (293)
Q Consensus 114 ~~~kG~~el~~~l~~v~heM~L~e~yF~lIksG-kKTIE~RLnDeKRq~IkvGD~I~F~-----k~L~--v~V~~Vr~Y~ 185 (293)
++|+|+ .....=.....=|-|.++|-+.|-+| +|++|.|-.-.+ ..+|+|+++ +.+. .+|.+|.. +
T Consensus 175 ~~~~~~-~~~~~~~~~~vLLSIKPeyaekIl~G~~K~~EfRK~~~~----~~~~~VvIYaTsPvkkIVGef~i~~Ii~-~ 248 (311)
T PRK12279 175 VVEKTA-SQKEEETTETIMISTSPKNAQVLFDDLEKNVIFYKTTPV----NKVLRVLVYVTSPTKKVVGEFDLESVEI-G 248 (311)
T ss_pred HHHHhh-hhhcccCCcEEEEEeCHHHHHHHhCCCceEEEEEeccCC----CCCCEEEEEecCCCcEEEEEEEEEEEEe-C
Confidence 567888 33333344445588999999999999 699999986443 467899998 3332 35555555 7
Q ss_pred CHHHHHhccCccccCCCCCCHHHHHHHHHhcCChHHHhhcCCeEEEEEeeccCCCCCCCC
Q 022692 186 SFSEMLEAESLVKVLPGVKTIEEVLQVYKFIENSTQRRRKGPMVSLQYAFPKWLLSPMLH 245 (293)
Q Consensus 186 SF~eLLe~EgL~kvlPG~~SiEEgv~~yr~iYSkEkE~qyGV~VAIeI~lp~~~~~~m~~ 245 (293)
+-+.+-+.. .. ..|.+ -+.|..||.--+.+ +||+|.-|....+|+.+
T Consensus 249 ~P~~lW~k~--~~-~sGIs-----k~~F~~Yf~g~~~a-----~Ai~I~~~~~y~~Pi~L 295 (311)
T PRK12279 249 AISSIWRKY--GK-QSVIS-----KKEYDAYYEGKDKA-----HALVSKKAYKYRNPKDL 295 (311)
T ss_pred CHHHHHHHH--hh-ccCCC-----HHHHHHHhCCCceE-----EEEEeCCceeCCCCCCH
Confidence 888888862 22 12443 13477888755544 79999988888887754
No 11
>cd06553 ASCH_Ef3133_like ASC-1 homology domain, subfamily similar to Enterococcus faecalis Ef3133. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=86.07 E-value=3.6 Score=35.09 Aligned_cols=87 Identities=9% Similarity=0.055 Sum_probs=58.6
Q ss_pred cccchHHHhcCCceEEEeec----CccccCCCCCCEEEEc-------eeEEEEEEEEeecCCHHHHHhccCccccCCCCC
Q 022692 136 QEPFFSFIKDGLETVEGRCT----ISDYNSIGPGSVILLN-------KCMMLKVQSVCHYDSFSEMLEAESLVKVLPGVK 204 (293)
Q Consensus 136 ~e~yF~lIksGkKTIE~RLn----DeKRq~IkvGD~I~F~-------k~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~ 204 (293)
.++.-++|.+|+||.-.|+. ++.-.--++||.=+.. ..+.+.-+++.+|..-.+-.-. +-+-|..
T Consensus 13 ad~l~~LVl~G~KtAT~s~~~~y~~e~e~~p~vG~~~Ivld~~g~p~cvi~~~~V~~~~f~~vt~~~A~----~EGegd~ 88 (127)
T cd06553 13 ADELAALVLAGKKTATCSALALYEAEEEPLPKVGDYSIILDGQGKPVCIIETTEVEVVPFNDVTEEFAY----AEGEGDR 88 (127)
T ss_pred HHHHHHHHHcCCcEEEEechhhcccCCccCCCCCcEEEEECCCCCEEEEEEEEEEEEEEcccCCHHHHH----HhCCCcc
Confidence 45678899999999999974 3444457899965544 2455566666777765443322 1234556
Q ss_pred CHHHHHHHHHhcCChHHHhhcCC
Q 022692 205 TIEEVLQVYKFIENSTQRRRKGP 227 (293)
Q Consensus 205 SiEEgv~~yr~iYSkEkE~qyGV 227 (293)
|+++=-+..+.||+++-.. .|.
T Consensus 89 sl~~Wr~~h~~ff~~~~~~-~~~ 110 (127)
T cd06553 89 SLEYWRKAHEAFFTRELEE-AGK 110 (127)
T ss_pred CHHHHHHHHHHHHHHHHhh-cCC
Confidence 8998889999999877544 443
No 12
>COG4933 Uncharacterized conserved protein [Function unknown]
Probab=84.77 E-value=4.7 Score=35.00 Aligned_cols=96 Identities=16% Similarity=0.124 Sum_probs=65.4
Q ss_pred eeccccchHHHhcCCceEEEeecCccccCCCCCCEEEEc---------eeEEEEEEEEeecCCHHHHHhccCccccCCCC
Q 022692 133 LHVQEPFFSFIKDGLETVEGRCTISDYNSIGPGSVILLN---------KCMMLKVQSVCHYDSFSEMLEAESLVKVLPGV 203 (293)
Q Consensus 133 M~L~e~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~---------k~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~ 203 (293)
|-+.++|-+.|-+|.|+||+|=-.+.. +-.||++.-+ ..++.+-+++..=.|-..++.. +|.
T Consensus 1 mSIkPk~a~~Ifdg~K~velrR~~p~~--~~~~~~~~VY~TsP~~aVvGef~~e~V~~~~~~siw~~~~~-------~~~ 71 (124)
T COG4933 1 MSIKPKFAEAIFDGVKKVELRRITPVP--IVEESTVIVYATSPVKAVVGEFTAERVEQVAIESIWRKAGK-------SGS 71 (124)
T ss_pred CccchhhHHHHhcCcceEEEEEecCCC--cccCcEEEEEecCchhheEEEEEeeeEEEcchHHHHHHhcc-------ccc
Confidence 567889999999999999999777654 4557877755 2344444444444555555554 222
Q ss_pred CCHHHHHHHHHhcCChHHHhhcCCeEEEEEeeccCCCCCCCC
Q 022692 204 KTIEEVLQVYKFIENSTQRRRKGPMVSLQYAFPKWLLSPMLH 245 (293)
Q Consensus 204 ~SiEEgv~~yr~iYSkEkE~qyGV~VAIeI~lp~~~~~~m~~ 245 (293)
-++ -++|.+|+.--+++ .||++.-|-+--.|.++
T Consensus 72 i~~---~~e~~~Y~~G~k~A-----~ai~~~~p~~y~~P~~L 105 (124)
T COG4933 72 IKI---GAEYLEYFEGAKEA-----HAIEVSKPRRYTRPVTL 105 (124)
T ss_pred ccc---hHHHHHHHhcccee-----EEEEeCCceecCCCcCH
Confidence 121 35688888877776 89999988887777764
No 13
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=81.10 E-value=3.2 Score=35.89 Aligned_cols=43 Identities=21% Similarity=0.369 Sum_probs=35.2
Q ss_pred HHHhcCCceEEEee--cCccccCCCCCCEEEEc-----------eeEEEEEEEEee
Q 022692 141 SFIKDGLETVEGRC--TISDYNSIGPGSVILLN-----------KCMMLKVQSVCH 183 (293)
Q Consensus 141 ~lIksGkKTIE~RL--nDeKRq~IkvGD~I~F~-----------k~L~v~V~~Vr~ 183 (293)
++++++.+|||||= |..---++++||.+-.+ .-+.++|..+..
T Consensus 16 ~l~~~~~rTieiRsa~N~~tv~rl~~GDlVFlT~~~~~Dl~~GtsGiiAkV~~vev 71 (122)
T COG1935 16 SLLRNPIRTIEIRSARNLLTVLRLHEGDLVFLTSTSLEDLTKGTSGIIAKVRRVEV 71 (122)
T ss_pred HHHhCCceEEEEEcccchHHhhcCCCCCEEEEehhHhhHhhcCcceeEEEEEEEEE
Confidence 57899999999994 55777889999999887 257888887765
No 14
>PRK11507 ribosome-associated protein; Provisional
Probab=80.57 E-value=2.9 Score=32.86 Aligned_cols=32 Identities=19% Similarity=0.247 Sum_probs=28.2
Q ss_pred HHhcCCceEEEeecCccccCCCCCCEEEEcee
Q 022692 142 FIKDGLETVEGRCTISDYNSIGPGSVILLNKC 173 (293)
Q Consensus 142 lIksGkKTIE~RLnDeKRq~IkvGD~I~F~k~ 173 (293)
+|++|.=.|-+-+.+.++++|.+||+|.|.+.
T Consensus 33 ~I~eg~V~VNGeve~rRgkKl~~GD~V~~~g~ 64 (70)
T PRK11507 33 AIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH 64 (70)
T ss_pred HHHcCceEECCEEecccCCCCCCCCEEEECCE
Confidence 58889888888888899999999999999963
No 15
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=70.32 E-value=1.7 Score=33.52 Aligned_cols=31 Identities=23% Similarity=0.467 Sum_probs=18.7
Q ss_pred HHhcCCceEEEeecCccccCCCCCCEEEEce
Q 022692 142 FIKDGLETVEGRCTISDYNSIGPGSVILLNK 172 (293)
Q Consensus 142 lIksGkKTIE~RLnDeKRq~IkvGD~I~F~k 172 (293)
+|++|.=.|-+-+...++.+|.+||.|.|+.
T Consensus 29 ~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~~ 59 (65)
T PF13275_consen 29 LIQEGEVKVNGEVETRRGKKLRPGDVVEIDG 59 (65)
T ss_dssp HHHHHHHEETTB----SS----SSEEEEETT
T ss_pred HHHcCceEECCEEccccCCcCCCCCEEEECC
Confidence 5778876777777778999999999999974
No 16
>cd06554 ASCH_ASC-1_like ASC-1 homology domain, ASC-1-like subfamily. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=68.79 E-value=3.5 Score=34.57 Aligned_cols=28 Identities=32% Similarity=0.725 Sum_probs=23.9
Q ss_pred eeccccchHHHhcCCceEEEeecCcccc
Q 022692 133 LHVQEPFFSFIKDGLETVEGRCTISDYN 160 (293)
Q Consensus 133 M~L~e~yF~lIksGkKTIE~RLnDeKRq 160 (293)
+-+.++|-.+|..|.|+||+|--..+++
T Consensus 4 lsi~qPwa~li~~g~K~~E~R~w~t~~r 31 (113)
T cd06554 4 LSIHQPWASLIVRGIKRIEGRSWATNYR 31 (113)
T ss_pred eEEeCcHHHHHHcCCCceecccCCCCcc
Confidence 5678899999999999999998776654
No 17
>COG1868 FliM Flagellar motor switch protein [Cell motility and secretion]
Probab=66.80 E-value=2.6 Score=41.32 Aligned_cols=37 Identities=19% Similarity=0.136 Sum_probs=29.2
Q ss_pred eEEEeecCccccCCCCCCEEEEc----eeEEEEEEEEeecC
Q 022692 149 TVEGRCTISDYNSIGPGSVILLN----KCMMLKVQSVCHYD 185 (293)
Q Consensus 149 TIE~RLnDeKRq~IkvGD~I~F~----k~L~v~V~~Vr~Y~ 185 (293)
-.++++.-.+.-++++||+|.|. +.+.+.|.+.-+|.
T Consensus 261 l~~~~ltl~~il~L~vGDVI~l~~~~~d~v~v~v~g~~~f~ 301 (332)
T COG1868 261 LGEISLTLREILRLEVGDVIPLEKPADDRVTVSVGGKPKFL 301 (332)
T ss_pred eecceeeHHHHhCCCCCcEEECCCCCCceEEEEECCEEEEE
Confidence 34455566788899999999998 47888888888773
No 18
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=66.41 E-value=7.3 Score=28.05 Aligned_cols=31 Identities=23% Similarity=0.307 Sum_probs=24.8
Q ss_pred HHHhcCCceEEEeecCccccCCCCCCEEEEc
Q 022692 141 SFIKDGLETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 141 ~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
.+|+.|.=+|-++.-..+..+++.||.|.+.
T Consensus 29 ~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i~ 59 (59)
T TIGR02988 29 WFLQENEVLVNGELENRRGKKLYPGDVIEIP 59 (59)
T ss_pred HHHHcCCEEECCEEccCCCCCCCCCCEEEeC
Confidence 4578888888777766667899999999873
No 19
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=63.78 E-value=15 Score=29.96 Aligned_cols=43 Identities=19% Similarity=0.230 Sum_probs=34.2
Q ss_pred chHHHhcCCceEEEeecCccccCCCCCCEEEEc---eeEEEEEEEEe
Q 022692 139 FFSFIKDGLETVEGRCTISDYNSIGPGSVILLN---KCMMLKVQSVC 182 (293)
Q Consensus 139 yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~---k~L~v~V~~Vr 182 (293)
.......+.+|+..++.-+- -.+.|||.|.+. +...++|++|.
T Consensus 118 ~l~~~~~~r~t~~f~~~~~~-~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 118 LLRRSRYERRTVSFTLPPDG-LALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred HHHHhhccceEEEEEEChhh-ccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 34455678889999988766 679999999998 57888888875
No 20
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]
Probab=63.69 E-value=10 Score=37.77 Aligned_cols=73 Identities=19% Similarity=0.195 Sum_probs=45.5
Q ss_pred eEEEeecCc-----------cccCCCCCCEEEEceeEEEEEEEEe-------ecC---CHH--HHHhccCccccCCCCCC
Q 022692 149 TVEGRCTIS-----------DYNSIGPGSVILLNKCMMLKVQSVC-------HYD---SFS--EMLEAESLVKVLPGVKT 205 (293)
Q Consensus 149 TIE~RLnDe-----------KRq~IkvGD~I~F~k~L~v~V~~Vr-------~Y~---SF~--eLLe~EgL~kvlPG~~S 205 (293)
+||+.|... .-+++|+||.|.|-..+.++|++.. +|+ .|+ ++|++.|--..-|=.++
T Consensus 78 ~vEvll~~~~~~~~w~al~~~~kr~k~G~~i~f~~~l~a~v~e~~~~g~~~l~F~~~~~~~l~e~L~~~G~~PLPPYI~~ 157 (348)
T COG0809 78 KVEVLLERRLDDNRWLALIKPSKRLKAGDEIYFGDGLKATVLERLEHGLRLLEFDYEGIFSLLELLEKYGEMPLPPYIKR 157 (348)
T ss_pred eEEEEEEeecCCCcEEEEeccccCCCCCCEEEeCCCceEEEEEecCCceEEEEEecCCchhHHHHHHHcCCCCCCcccCC
Confidence 478777652 2467999999999966777776543 332 454 78888554333222333
Q ss_pred HHHH--HHHHHhcCChHH
Q 022692 206 IEEV--LQVYKFIENSTQ 221 (293)
Q Consensus 206 iEEg--v~~yr~iYSkEk 221 (293)
-.+. .+.|...|+++.
T Consensus 158 ~~~~~d~~~YQTVYak~~ 175 (348)
T COG0809 158 KLDELDRDRYQTVYAKEP 175 (348)
T ss_pred cccccchhhceeeeecCC
Confidence 2222 356899999764
No 21
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=61.17 E-value=17 Score=31.60 Aligned_cols=52 Identities=12% Similarity=0.142 Sum_probs=39.3
Q ss_pred HHHhcCCceEEEeecCccccCCCCCCEEEEc---eeEEEEEEEEee----cCCHHHHHhc
Q 022692 141 SFIKDGLETVEGRCTISDYNSIGPGSVILLN---KCMMLKVQSVCH----YDSFSEMLEA 193 (293)
Q Consensus 141 ~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~---k~L~v~V~~Vr~----Y~SF~eLLe~ 193 (293)
++|.+|+=.|-++. +..=..+++||.|.+. ....++|.++-. .+-=+.||+.
T Consensus 29 ~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~~v~Vl~l~~~R~~a~~A~~lYe~ 87 (133)
T PRK10348 29 EMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERTVIVKAITEQRRPASEAALLYEE 87 (133)
T ss_pred HHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEEEEEEEeECccccCChHHHHHHHHh
Confidence 68999999999988 7777889999999998 356667766543 3444567765
No 22
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=57.53 E-value=18 Score=30.33 Aligned_cols=42 Identities=19% Similarity=0.345 Sum_probs=31.8
Q ss_pred HHHhcCCceEEEeecCccccCCCCCCEEEEc---eeEEEEEEEEee
Q 022692 141 SFIKDGLETVEGRCTISDYNSIGPGSVILLN---KCMMLKVQSVCH 183 (293)
Q Consensus 141 ~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~---k~L~v~V~~Vr~ 183 (293)
+++..|+=.|-+... .-=..+|+||.|.+. +.+.++|.++..
T Consensus 29 ~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~~~~v~Vl~~~~ 73 (100)
T COG1188 29 EMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNKEFTVKVLALGE 73 (100)
T ss_pred HHHHCCeEEECCEEc-ccccccCCCCEEEEEeCCcEEEEEEEeccc
Confidence 468888877777776 445678999999976 578888887643
No 23
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=56.73 E-value=33 Score=29.44 Aligned_cols=43 Identities=21% Similarity=0.417 Sum_probs=33.2
Q ss_pred HHHhcCCceEEEee--cCccccCCCCCCEEEEc-----------eeEEEEEEEEee
Q 022692 141 SFIKDGLETVEGRC--TISDYNSIGPGSVILLN-----------KCMMLKVQSVCH 183 (293)
Q Consensus 141 ~lIksGkKTIE~RL--nDeKRq~IkvGD~I~F~-----------k~L~v~V~~Vr~ 183 (293)
++++..-||+|+|= |----.++++||.|-.+ .=+.++|+++..
T Consensus 16 eL~~~~~RTiEirSa~N~~~~~~~~~Gd~VFlT~~~~~Dl~~Gt~GiIa~V~~~~i 71 (119)
T PF04322_consen 16 ELKKNHIRTIEIRSAHNVIALESLDPGDRVFLTSVSLEDLTPGTEGIIAEVKKIEI 71 (119)
T ss_pred HHHhCCceEEEEEcchheeeeecCCCCCEEEEecCCHHHCCCCCCeEEEEEEEEEE
Confidence 57788999999995 44677788999999887 247777776643
No 24
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=56.59 E-value=15 Score=25.93 Aligned_cols=30 Identities=10% Similarity=0.170 Sum_probs=25.0
Q ss_pred HHhcCCceEEEeecC----ccccCCCCCCEEEEc
Q 022692 142 FIKDGLETVEGRCTI----SDYNSIGPGSVILLN 171 (293)
Q Consensus 142 lIksGkKTIE~RLnD----eKRq~IkvGD~I~F~ 171 (293)
-|.+|+.+|++++.. ..+..|++||.|.+.
T Consensus 21 ~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~ 54 (75)
T PF01336_consen 21 TLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVR 54 (75)
T ss_dssp EEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEE
T ss_pred EEEECCccEEEEEccHHhhHHhhcCCCCeEEEEE
Confidence 367888999999988 677889999999987
No 25
>smart00363 S4 S4 RNA-binding domain.
Probab=54.71 E-value=14 Score=24.28 Aligned_cols=33 Identities=24% Similarity=0.356 Sum_probs=22.8
Q ss_pred hHHHhcCCceEEEeecCccccCCCCCCEEEEce
Q 022692 140 FSFIKDGLETVEGRCTISDYNSIGPGSVILLNK 172 (293)
Q Consensus 140 F~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~k 172 (293)
-.+|++|.-.|-++..+..-..++.||.|.+..
T Consensus 20 ~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 20 RKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred HHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 456777766666666534566789999998863
No 26
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=53.63 E-value=35 Score=26.02 Aligned_cols=51 Identities=22% Similarity=0.236 Sum_probs=40.2
Q ss_pred HhcCCceEEEeecCc-------cccCCCCCCEEEEc-------eeEEEEEEEEeecCCHHHHHhc
Q 022692 143 IKDGLETVEGRCTIS-------DYNSIGPGSVILLN-------KCMMLKVQSVCHYDSFSEMLEA 193 (293)
Q Consensus 143 IksGkKTIE~RLnDe-------KRq~IkvGD~I~F~-------k~L~v~V~~Vr~Y~SF~eLLe~ 193 (293)
+.+|+.+|++|.-+. ..+.+++|+.|... +...+.+..++.=+++.++.-+
T Consensus 22 L~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~i~~i~~v~d~ne~~~h 86 (95)
T cd04478 22 IDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTDFNEVTYH 86 (95)
T ss_pred EECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEEEEEEEEeCCccHHHHh
Confidence 467788999998752 46778999998866 4778888899988888887654
No 27
>smart00350 MCM minichromosome maintenance proteins.
Probab=53.50 E-value=17 Score=36.60 Aligned_cols=45 Identities=13% Similarity=0.080 Sum_probs=37.9
Q ss_pred eeeeccccchHHHhcCC--ceEEEeecCccccCCCCCCEEEEceeEEE
Q 022692 131 FELHVQEPFFSFIKDGL--ETVEGRCTISDYNSIGPGSVILLNKCMML 176 (293)
Q Consensus 131 heM~L~e~yF~lIksGk--KTIE~RLnDeKRq~IkvGD~I~F~k~L~v 176 (293)
-++.||+.+ +.+-.|. ++|++-|.++-=..++|||.|.++..+.+
T Consensus 86 Q~I~iQE~~-e~~p~G~~Prsi~v~l~~dLvd~~~PGD~V~i~Gi~~~ 132 (509)
T smart00350 86 QKIKLQESP-EEVPAGQLPRSVDVILDGDLVDKAKPGDRVEVTGIYRN 132 (509)
T ss_pred EEEEEEcCc-ccCCCCCCCcEEEEEEcccccCcccCCCEEEEEEEEEe
Confidence 458899965 7777888 89999999999999999999999855443
No 28
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=52.07 E-value=13 Score=32.05 Aligned_cols=25 Identities=12% Similarity=-0.024 Sum_probs=23.2
Q ss_pred CceEEEeecCccccCCCCCCEEEEc
Q 022692 147 LETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 147 kKTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
+..+|++.+.-++-+|++||.+.|.
T Consensus 96 ~yvLEl~~G~~~~~~i~vGd~v~~~ 120 (126)
T COG1430 96 RYVLELPAGWAARLGIKVGDRVEFR 120 (126)
T ss_pred cEEEEecCCchhhcCCccCCEEEec
Confidence 5789999999999999999999985
No 29
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=51.10 E-value=35 Score=28.55 Aligned_cols=44 Identities=20% Similarity=0.184 Sum_probs=34.5
Q ss_pred HhcCCceEEEeecCccccCCCCCCEEEEc--------eeEEEEEE---EEeecCC
Q 022692 143 IKDGLETVEGRCTISDYNSIGPGSVILLN--------KCMMLKVQ---SVCHYDS 186 (293)
Q Consensus 143 IksGkKTIE~RLnDeKRq~IkvGD~I~F~--------k~L~v~V~---~Vr~Y~S 186 (293)
|.+.+-+|.+++=+++...+++||.|.+. ..+...|. .|+.-+.
T Consensus 46 l~D~TG~I~~tlW~~~a~~l~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 46 VGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD 100 (129)
T ss_pred EECCCCEEEEEEeCCccccCCCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence 46667789999999999999999999987 35666666 4666664
No 30
>KOG4476 consensus Gluconate transport-inducing protein [Signal transduction mechanisms; Carbohydrate transport and metabolism]
Probab=50.53 E-value=13 Score=35.63 Aligned_cols=32 Identities=25% Similarity=0.455 Sum_probs=28.6
Q ss_pred hHHHhcCC-ceEEEeecCccccCCCCCCEEEEc
Q 022692 140 FSFIKDGL-ETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 140 F~lIksGk-KTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
|++.+.|. +-||.|+.+++|..|..|++.+|.
T Consensus 21 f~a~r~G~l~~I~RR~~~ee~~lIrsGsIFVf~ 53 (248)
T KOG4476|consen 21 FQAVRLGYLPRIERRLTPEERELIRSGSIFVFD 53 (248)
T ss_pred HHHHHcccccccccccCcccceeeecCCEEEEe
Confidence 66777774 789999999999999999999998
No 31
>COG5037 TOS9 Gluconate transport-inducing protein [Signal transduction mechanisms / Carbohydrate transport and metabolism]
Probab=50.53 E-value=13 Score=35.63 Aligned_cols=32 Identities=25% Similarity=0.455 Sum_probs=28.6
Q ss_pred hHHHhcCC-ceEEEeecCccccCCCCCCEEEEc
Q 022692 140 FSFIKDGL-ETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 140 F~lIksGk-KTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
|++.+.|. +-||.|+.+++|..|..|++.+|.
T Consensus 21 f~a~r~G~l~~I~RR~~~ee~~lIrsGsIFVf~ 53 (248)
T COG5037 21 FQAVRLGYLPRIERRLTPEERELIRSGSIFVFD 53 (248)
T ss_pred HHHHHcccccccccccCcccceeeecCCEEEEe
Confidence 66777774 789999999999999999999998
No 32
>PF11184 DUF2969: Protein of unknown function (DUF2969); InterPro: IPR021351 This family of proteins with unknown function appears to be restricted to Lactobacillales.
Probab=49.71 E-value=14 Score=28.80 Aligned_cols=63 Identities=16% Similarity=0.146 Sum_probs=39.4
Q ss_pred CceEEEeecCccccCCCCCCEEEEceeEEEEEEEEeecCCHHHHHhccCccccCCCCCCHHHHHHHHHhc
Q 022692 147 LETVEGRCTISDYNSIGPGSVILLNKCMMLKVQSVCHYDSFSEMLEAESLVKVLPGVKTIEEVLQVYKFI 216 (293)
Q Consensus 147 kKTIE~RLnDeKRq~IkvGD~I~F~k~L~v~V~~Vr~Y~SF~eLLe~EgL~kvlPG~~SiEEgv~~yr~i 216 (293)
-|.|||++.|.++. =.+|-.+...+.+.-+|.++ =.-| +.... ++...-.+|+|+|++..-+-
T Consensus 5 ~K~IeI~i~d~~~~-~~~~~~l~Igkk~IG~I~e~--d~~f-av~~~---~~~~~~~Ks~deAve~iI~~ 67 (71)
T PF11184_consen 5 NKKIEIEIKDTKVN-GQPGYELFIGKKVIGEIEED--DGRF-AVVKN---DNVEFFVKSLDEAVEAIIRE 67 (71)
T ss_pred ccceEEEEEecccC-CeEEEEEEECCEEEEEEEEc--CCcE-EEEeC---CCceEEEcCHHHHHHHHHHH
Confidence 48999999999983 33344555567788888776 3344 32222 22222356999999754433
No 33
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=49.20 E-value=15 Score=27.96 Aligned_cols=56 Identities=7% Similarity=-0.003 Sum_probs=33.6
Q ss_pred hccceeeeccccchHHHhcCCceEEEeecC-ccccCCCCCCEEEEc----eeEEEEEEEEe
Q 022692 127 KAVEFELHVQEPFFSFIKDGLETVEGRCTI-SDYNSIGPGSVILLN----KCMMLKVQSVC 182 (293)
Q Consensus 127 ~~v~heM~L~e~yF~lIksGkKTIE~RLnD-eKRq~IkvGD~I~F~----k~L~v~V~~Vr 182 (293)
++..-.+.|.+.+...+.=..=|-..++.+ .....+++||.|.|. +.-...|++|+
T Consensus 7 d~~~~~iti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~~~~~~~~I~~i~ 67 (70)
T PF11604_consen 7 DPEAGTITISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFTFERTDDGSYVITAIE 67 (70)
T ss_dssp ETTTTEEEEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEEEEEETTCEEEEEEEE
T ss_pred ecCCCEEEEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEEEEECCCCcEEEEEEE
Confidence 334455677777777777777788888884 667999999999998 12234555554
No 34
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=47.78 E-value=22 Score=27.15 Aligned_cols=30 Identities=17% Similarity=0.300 Sum_probs=20.3
Q ss_pred CCCCCCEEEEceeEEEEEE---------EEeecCCHHHH
Q 022692 161 SIGPGSVILLNKCMMLKVQ---------SVCHYDSFSEM 190 (293)
Q Consensus 161 ~IkvGD~I~F~k~L~v~V~---------~Vr~Y~SF~eL 190 (293)
+-++||+|.|.+.+..+|. ++..+++|.++
T Consensus 3 ~a~vGdiIefk~g~~G~V~kv~eNSVIVdIT~m~~~~e~ 41 (57)
T PF09953_consen 3 KAKVGDIIEFKDGFTGIVEKVYENSVIVDITIMENFDEL 41 (57)
T ss_pred ccccCcEEEEcCCcEEEEEEEecCcEEEEEEecCCcccc
Confidence 4578999999855555544 44556777664
No 35
>PF07527 Hairy_orange: Hairy Orange; InterPro: IPR003650 This domain confers specificity among members of the Hairy/E(SPL) family. HES-2 (hairy and enhancer of split 2) is a transcription factor, and the hairy protein is a pair-rule protein that regulates embryonic segmentation and adult bristle patterning. These proteins are transcriptional repressors of genes that require the BHLH protein for their transcription.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DB7_A.
Probab=43.27 E-value=21 Score=24.69 Aligned_cols=28 Identities=21% Similarity=0.592 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHHhhcccccccCcCCCCCHHHHhhhhc
Q 022692 4 LKDCMEELLKFTLSSHIDETLDFDLGISSKFCTNLLQ 40 (293)
Q Consensus 4 l~~~~~el~~ftl~sh~~~~~~~~l~ls~~fc~~ll~ 40 (293)
.++|+.|..||.. ++. +++++++.+|+.
T Consensus 7 y~~C~~Ev~~fL~--~~~-------~~~~~~~~rLl~ 34 (43)
T PF07527_consen 7 YSECLNEVSRFLS--SVE-------GVDPGVRARLLS 34 (43)
T ss_dssp HHHHHHHHHHHHH--HTS----------THHHHHHHH
T ss_pred HHHHHHHHHHHHh--cCC-------CCChHHHHHHHH
Confidence 4789999999983 333 124577877773
No 36
>PRK00147 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional
Probab=42.10 E-value=70 Score=31.78 Aligned_cols=59 Identities=17% Similarity=0.237 Sum_probs=37.1
Q ss_pred cCCCCCCEEEEceeEEEEEEEE-------eecC---CHHHHHhccCccccCCCC-CC--HHHHHHHHHhcCCh
Q 022692 160 NSIGPGSVILLNKCMMLKVQSV-------CHYD---SFSEMLEAESLVKVLPGV-KT--IEEVLQVYKFIENS 219 (293)
Q Consensus 160 q~IkvGD~I~F~k~L~v~V~~V-------r~Y~---SF~eLLe~EgL~kvlPG~-~S--iEEgv~~yr~iYSk 219 (293)
+++++|++|.|.+.+.++|.+. -+|+ ++.++|+..|--.. |-+ +. -++-.+.|...|.+
T Consensus 100 k~~k~G~~l~~~~~~~~~v~~~~~~~~~~~~f~~~~~~~~~l~~~G~~Pl-PPYI~r~~~~~D~~~YQTVyA~ 171 (342)
T PRK00147 100 KRPKPGTKLYFGDGLKAEVLERLEDGGRILRFLYEGIFLELLEELGHMPL-PPYIKRPDEDADRERYQTVYAK 171 (342)
T ss_pred CCCCCCCEEEECCCeEEEEEEecCCceEEEEEeCCCCHHHHHHhcCCCCC-CcccCCCCcccchhhccccccC
Confidence 6789999999975466666654 1342 47788888665443 432 22 12234568888875
No 37
>PF01479 S4: S4 domain; InterPro: IPR002942 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 [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=41.66 E-value=13 Score=25.38 Aligned_cols=29 Identities=31% Similarity=0.456 Sum_probs=25.2
Q ss_pred hHHHhcCCceEEEeecCccccCCCCCCEE
Q 022692 140 FSFIKDGLETVEGRCTISDYNSIGPGSVI 168 (293)
Q Consensus 140 F~lIksGkKTIE~RLnDeKRq~IkvGD~I 168 (293)
-.+|++|.=+|-++.-...-..+++||.|
T Consensus 20 ~~~I~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 20 RRLIKQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp HHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred HHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence 46899999888888888888899999987
No 38
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=39.51 E-value=58 Score=24.90 Aligned_cols=34 Identities=21% Similarity=0.276 Sum_probs=27.2
Q ss_pred eEEEeecCccccCCCCCCEEEEc-eeEEEEEEEEeecC
Q 022692 149 TVEGRCTISDYNSIGPGSVILLN-KCMMLKVQSVCHYD 185 (293)
Q Consensus 149 TIE~RLnDeKRq~IkvGD~I~F~-k~L~v~V~~Vr~Y~ 185 (293)
.|-+|+... .|++||.+.+. ....++|.+|..+.
T Consensus 17 ~v~Gkv~~G---~v~~Gd~v~~~P~~~~~~V~si~~~~ 51 (81)
T cd03695 17 GYAGTIASG---SIRVGDEVVVLPSGKTSRVKSIETFD 51 (81)
T ss_pred EEEEEEccc---eEECCCEEEEcCCCCeEEEEEEEECC
Confidence 577888766 67899999998 45678999998774
No 39
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=39.43 E-value=45 Score=26.55 Aligned_cols=32 Identities=22% Similarity=0.341 Sum_probs=26.1
Q ss_pred HHhcCCceEEEeecCccccCCCCCCEEEEcee
Q 022692 142 FIKDGLETVEGRCTISDYNSIGPGSVILLNKC 173 (293)
Q Consensus 142 lIksGkKTIE~RLnDeKRq~IkvGD~I~F~k~ 173 (293)
.|.+|.=+|-+-+-+.++.+|..||.|.|.+.
T Consensus 33 ~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~ 64 (73)
T COG2501 33 FIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQ 64 (73)
T ss_pred HHHCCeEEECCeeeeccCCEeecCCEEEECCE
Confidence 47788667777777789999999999999854
No 40
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=37.67 E-value=43 Score=22.49 Aligned_cols=31 Identities=29% Similarity=0.493 Sum_probs=21.3
Q ss_pred HHHhcCCceEEEeecCccccCCCCCCEEEEc
Q 022692 141 SFIKDGLETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 141 ~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
.+|++|.=.|-++.....-..+++||.|.+.
T Consensus 21 ~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~ 51 (70)
T cd00165 21 QLIKHGHVLVNGKVVTKPSYKVKPGDVIEVD 51 (70)
T ss_pred HHHHcCCEEECCEEccCCccCcCCCCEEEEc
Confidence 4567776556666554455678899998876
No 41
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=35.65 E-value=54 Score=30.76 Aligned_cols=36 Identities=14% Similarity=0.111 Sum_probs=29.6
Q ss_pred cchHHHhcCCceEEEeecCccccCCCCCCEEEEcee
Q 022692 138 PFFSFIKDGLETVEGRCTISDYNSIGPGSVILLNKC 173 (293)
Q Consensus 138 ~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~k~ 173 (293)
.--++|++|+=+|-++..+..-.++++||.|.+.+.
T Consensus 200 ~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~IsvrG~ 235 (257)
T TIGR03069 200 KIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGK 235 (257)
T ss_pred HHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEcCC
Confidence 345678999988888887777789999999999843
No 42
>PRK01424 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional
Probab=34.42 E-value=1.1e+02 Score=31.04 Aligned_cols=51 Identities=8% Similarity=0.100 Sum_probs=34.0
Q ss_pred CceEEEeecCc-----------cccCCCCCCEEEEceeEEEEEEEE-------eec--C--CHHHHHhccCccc
Q 022692 147 LETVEGRCTIS-----------DYNSIGPGSVILLNKCMMLKVQSV-------CHY--D--SFSEMLEAESLVK 198 (293)
Q Consensus 147 kKTIE~RLnDe-----------KRq~IkvGD~I~F~k~L~v~V~~V-------r~Y--~--SF~eLLe~EgL~k 198 (293)
.+.||+.|..+ ..+++++|+.|.|.+ +.++|++. -+| + ++.++|+..|--.
T Consensus 68 g~~iEill~~~l~~~~w~~lv~~~k~~~~G~~l~~~~-~~~~v~~~~~~g~~~~~f~~~~~~~~~~L~~~G~~P 140 (366)
T PRK01424 68 GKNITINLNQKLSDDSWSAFAKPARKLHVGDEFYFDN-HKVIITEKLAMGEIKVKFELNNISVFEFLDKYGEMP 140 (366)
T ss_pred CceEEEEEEEEcCCCeEEEEEecCCCCCCCCEEEECC-eEEEEEEecCCCcEEEEEeCCCCCHHHHHHHcCCCC
Confidence 34688887431 127788999999965 66777664 134 2 5888888866443
No 43
>cd06863 PX_Atg24p The phosphoinositide binding Phox Homology domain of yeast Atg24p, an autophagic degradation protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The yeast Atg24p is a sorting nexin (SNX) which is involved in membrane fusion events at the vacuolar surface during pexophagy. This is facilitated via binding of Atg24p to phosphatidylinositol 3-phosphate (PI3P) through its PX domain. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway.
Probab=33.92 E-value=53 Score=26.65 Aligned_cols=51 Identities=14% Similarity=0.074 Sum_probs=32.8
Q ss_pred EEEeecCccccC-CCCCCEEEEceeEE--------EEEEEEeecCCHHHHHhccCccccCCC
Q 022692 150 VEGRCTISDYNS-IGPGSVILLNKCMM--------LKVQSVCHYDSFSEMLEAESLVKVLPG 202 (293)
Q Consensus 150 IE~RLnDeKRq~-IkvGD~I~F~k~L~--------v~V~~Vr~Y~SF~eLLe~EgL~kvlPG 202 (293)
|+|++.|+.... -..+-.+.|.-.+. ....=-|+|..|..|.++ +.+-.||
T Consensus 1 ~~i~V~dP~~~~~~~~~~y~~Y~I~~~t~~~~~~~~~~~V~RRYsdF~~L~~~--L~~~~p~ 60 (118)
T cd06863 1 LECLVSDPQKELDGSSDTYISYLITTKTNLPSFSRKEFKVRRRYSDFVFLHEC--LSNDFPA 60 (118)
T ss_pred CEEEEeCcccccCCCccCEEEEEEEEeeCCCCcccCceEEEecHHHHHHHHHH--HHHHCcC
Confidence 577888877654 45566677763222 234556899999999987 4444444
No 44
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=33.34 E-value=39 Score=29.01 Aligned_cols=27 Identities=15% Similarity=0.165 Sum_probs=21.9
Q ss_pred CCceEEEeecCccc---cCCCCCCEEEEce
Q 022692 146 GLETVEGRCTISDY---NSIGPGSVILLNK 172 (293)
Q Consensus 146 GkKTIE~RLnDeKR---q~IkvGD~I~F~k 172 (293)
|+.||+|=|+|+.. +.+|+||.|.+.+
T Consensus 58 g~~ti~It~yD~H~~~ar~lK~GdfV~L~N 87 (123)
T cd04498 58 KQLTIDILVYDNHVELAKSLKPGDFVRIYN 87 (123)
T ss_pred CeEEEEEEEEcchHHHHhhCCCCCEEEEEE
Confidence 68899999999643 2389999999864
No 45
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=30.70 E-value=75 Score=28.08 Aligned_cols=25 Identities=20% Similarity=0.182 Sum_probs=22.0
Q ss_pred CceEEEeecCccccCCCCCCEEEEc
Q 022692 147 LETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 147 kKTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
+-+|++-+-|+.=..|+|||+|.|+
T Consensus 47 TgsI~isvW~e~~~~~~PGDIirLt 71 (134)
T KOG3416|consen 47 TGSINISVWDEEGCLIQPGDIIRLT 71 (134)
T ss_pred cceEEEEEecCcCcccCCccEEEec
Confidence 4568888888888999999999998
No 46
>TIGR00113 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase. This model describes the enzyme for S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). QueA synthesizes Queuosine which is usually in the first position of the anticodon of tRNAs specific for asparagine, aspartate, histidine, and tyrosine.
Probab=30.69 E-value=1.2e+02 Score=30.14 Aligned_cols=60 Identities=12% Similarity=0.243 Sum_probs=34.7
Q ss_pred cCCCCCCEEEEcee----EEEEEEE----Eee--cC---CHHHHHhccCccccCCC-CCC--HHHHHHHHHhcCChH
Q 022692 160 NSIGPGSVILLNKC----MMLKVQS----VCH--YD---SFSEMLEAESLVKVLPG-VKT--IEEVLQVYKFIENST 220 (293)
Q Consensus 160 q~IkvGD~I~F~k~----L~v~V~~----Vr~--Y~---SF~eLLe~EgL~kvlPG-~~S--iEEgv~~yr~iYSkE 220 (293)
+++++|+.|.|.+- +.+.+.+ +-+ |+ +|.++|++.|--.. |- .+. -++-.+.|...|.+.
T Consensus 98 k~~~~G~~l~~~~~~~~~lv~~~~~~~~~~~~~~~~~~~~~~~~l~~~G~~Pl-PPYI~r~~~~~D~~rYQTVyA~~ 173 (344)
T TIGR00113 98 KKPKIGAKVKFGEGYGEKIMAEMLAHNGRLFEFEFNDPNVLLDVLESYGHMPL-PPYIKRPDEKADEERYQTVYSKK 173 (344)
T ss_pred CCCCCCCEEEECCCceeEEEEEeecCCceEEEEEcCCCccHHHHHHhcCCCCC-CcccCCCCcccchhhccccccCC
Confidence 67889999999632 2333322 222 44 58999998765444 43 222 111234688888753
No 47
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=30.23 E-value=63 Score=35.73 Aligned_cols=27 Identities=7% Similarity=0.375 Sum_probs=24.0
Q ss_pred cCCCCCCEEEEc------eeEEEEEEEEeecCC
Q 022692 160 NSIGPGSVILLN------KCMMLKVQSVCHYDS 186 (293)
Q Consensus 160 q~IkvGD~I~F~------k~L~v~V~~Vr~Y~S 186 (293)
+.+|+||+|++. +.+.++-|.|+.|+.
T Consensus 659 rpvkvGD~It~g~~~G~V~~I~vRAT~I~~fd~ 691 (835)
T COG3264 659 RPVKVGDTVTIGTVSGTVRKISVRATTIRTFDR 691 (835)
T ss_pred cCcccCCEEEECCceEEEEEEEeeEEEEEeCCC
Confidence 468999999998 589999999999987
No 48
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=30.18 E-value=37 Score=28.61 Aligned_cols=49 Identities=12% Similarity=0.051 Sum_probs=42.6
Q ss_pred HhhhhccceeeeccccchHHHhcCCceEEEeecCcc-ccCCCCCCEEEEc
Q 022692 123 VDILKAVEFELHVQEPFFSFIKDGLETVEGRCTISD-YNSIGPGSVILLN 171 (293)
Q Consensus 123 ~~~l~~v~heM~L~e~yF~lIksGkKTIE~RLnDeK-Rq~IkvGD~I~F~ 171 (293)
++.+++....+.|.+.|...+.=+.=|-..++.++. -..+++||.|.|.
T Consensus 49 V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~~~~~l~~lk~G~~V~F~ 98 (115)
T PRK09838 49 VKGIDLESKKITIHHEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFN 98 (115)
T ss_pred EEEEeCCCCEEEEeecccccCCCCCccccccCCChhhhccCCCCCEEEEE
Confidence 566677777899999999999999999999999876 5789999999997
No 49
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=29.55 E-value=61 Score=25.75 Aligned_cols=25 Identities=16% Similarity=0.228 Sum_probs=21.4
Q ss_pred ccCCCCCCEEEEceeEEEEEEEEee
Q 022692 159 YNSIGPGSVILLNKCMMLKVQSVCH 183 (293)
Q Consensus 159 Rq~IkvGD~I~F~k~L~v~V~~Vr~ 183 (293)
.+.+++||.|+...-+..+|+++..
T Consensus 35 ~~~L~~Gd~VvT~gGi~G~V~~i~d 59 (84)
T TIGR00739 35 IESLKKGDKVLTIGGIIGTVTKIAE 59 (84)
T ss_pred HHhCCCCCEEEECCCeEEEEEEEeC
Confidence 5679999999999888888888873
No 50
>COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=29.04 E-value=46 Score=36.61 Aligned_cols=28 Identities=11% Similarity=0.160 Sum_probs=24.5
Q ss_pred ccccCCCCCCEEEEc---eeEEEEEEEEeec
Q 022692 157 SDYNSIGPGSVILLN---KCMMLKVQSVCHY 184 (293)
Q Consensus 157 eKRq~IkvGD~I~F~---k~L~v~V~~Vr~Y 184 (293)
.|+-.+|.||+++|+ +.+.++|+.+|+-
T Consensus 606 A~~LglKLGDtvTf~v~gq~i~A~I~slR~V 636 (829)
T COG3127 606 AKRLGLKLGDTVTFMVLGQNITAKITSLRKV 636 (829)
T ss_pred HHHhCCccCCEEEEEeccceEEeeeceeeee
Confidence 566789999999999 6899999999874
No 51
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=29.01 E-value=88 Score=26.71 Aligned_cols=45 Identities=7% Similarity=-0.017 Sum_probs=38.8
Q ss_pred hccceeeeccccchHHHhcCCceEEEeecC-ccccCCCCCCEEEEc
Q 022692 127 KAVEFELHVQEPFFSFIKDGLETVEGRCTI-SDYNSIGPGSVILLN 171 (293)
Q Consensus 127 ~~v~heM~L~e~yF~lIksGkKTIE~RLnD-eKRq~IkvGD~I~F~ 171 (293)
++..=+..|-+++...+.=+.=|.-.|+.| .+...||.||.|.|+
T Consensus 48 D~~akKVTl~He~i~~l~mp~MTM~F~Vkd~a~lsglKeGdkV~fv 93 (108)
T COG5569 48 DLEAKKVTLHHEPIKNLNMPAMTMVFRVKDQAKLSGLKEGDKVEFV 93 (108)
T ss_pred ccccceEEEeccchhhCCCcceEEEEEeccHHHhhccccCCcEEEE
Confidence 444456788889999999999999999998 688999999999998
No 52
>PRK06033 hypothetical protein; Validated
Probab=26.79 E-value=67 Score=25.44 Aligned_cols=28 Identities=18% Similarity=0.176 Sum_probs=20.2
Q ss_pred ccccCCCCCCEEEEc----eeEEEEEEEEeec
Q 022692 157 SDYNSIGPGSVILLN----KCMMLKVQSVCHY 184 (293)
Q Consensus 157 eKRq~IkvGD~I~F~----k~L~v~V~~Vr~Y 184 (293)
.+--++++||+|.++ +.+.+.|-+...|
T Consensus 23 ~dlL~L~~GDVI~L~~~~~~~v~v~V~~~~~f 54 (83)
T PRK06033 23 HQVLRMGRGAVIPLDATEADEVWILANNHPIA 54 (83)
T ss_pred HHHhCCCCCCEEEeCCCCCCcEEEEECCEEEE
Confidence 445578999999997 3577777666655
No 53
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=26.76 E-value=1e+02 Score=29.30 Aligned_cols=61 Identities=15% Similarity=0.120 Sum_probs=40.0
Q ss_pred HHHHHHhhcChhhHHhhhhccceeeeccc-cchHHHhcCCceEEEeecCccccCCCCCCEEEEce
Q 022692 109 EWSQLILNKGSSDLVDILKAVEFELHVQE-PFFSFIKDGLETVEGRCTISDYNSIGPGSVILLNK 172 (293)
Q Consensus 109 ~W~~l~~~kG~~el~~~l~~v~heM~L~e-~yF~lIksGkKTIE~RLnDeKRq~IkvGD~I~F~k 172 (293)
+|+.....--+.-|.+++-... ++.. +--++|++|+=+|-.+....+-..+++||.|...+
T Consensus 181 ~~~e~~~~vas~RLD~vla~~~---~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG 242 (267)
T PLN00051 181 RVESFKSVEASLRLDALASAGF---RMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSG 242 (267)
T ss_pred ceEEccCCcCcccHHHHHHHHh---ccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEee
Confidence 3554333223335666555433 3433 34578999998888887777778999999999873
No 54
>PRK03760 hypothetical protein; Provisional
Probab=26.47 E-value=51 Score=27.60 Aligned_cols=24 Identities=17% Similarity=0.047 Sum_probs=21.6
Q ss_pred ceEEEeecCccccCCCCCCEEEEc
Q 022692 148 ETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 148 KTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
-++|+.-..-.+..|++||.|.|.
T Consensus 92 ~VLEl~aG~~~~~gi~~Gd~v~~~ 115 (117)
T PRK03760 92 YIIEGPVGKIRVLKVEVGDEIEWI 115 (117)
T ss_pred EEEEeCCChHHHcCCCCCCEEEEe
Confidence 478999999999999999999985
No 55
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=25.30 E-value=45 Score=24.86 Aligned_cols=26 Identities=27% Similarity=0.431 Sum_probs=14.6
Q ss_pred cCccccCCCCCCEEEEc----eeEEEEEEE
Q 022692 155 TISDYNSIGPGSVILLN----KCMMLKVQS 180 (293)
Q Consensus 155 nDeKRq~IkvGD~I~F~----k~L~v~V~~ 180 (293)
.-.+-.++++||+|.+. +.+.+.|-+
T Consensus 22 ~l~el~~L~~Gdvi~l~~~~~~~v~l~v~g 51 (77)
T PF01052_consen 22 TLGELLNLKVGDVIPLDKPADEPVELRVNG 51 (77)
T ss_dssp EHHHHHC--TT-EEEECCESSTEEEEEETT
T ss_pred EHHHHhcCCCCCEEEeCCCCCCCEEEEECC
Confidence 33567789999999998 244444433
No 56
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=24.40 E-value=33 Score=27.88 Aligned_cols=27 Identities=11% Similarity=-0.015 Sum_probs=19.1
Q ss_pred cCCceEEEeecCccccCCCCCCEEEEc
Q 022692 145 DGLETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 145 sGkKTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
..+-.+|++-..-++..|++||.|.|+
T Consensus 81 ~a~~vLE~~aG~~~~~~i~~Gd~v~~~ 107 (108)
T PF02643_consen 81 PARYVLELPAGWFEKLGIKVGDRVRIE 107 (108)
T ss_dssp EECEEEEEETTHHHHHT--TT-EEE--
T ss_pred ccCEEEEcCCCchhhcCCCCCCEEEec
Confidence 356789999999999999999999884
No 57
>PF13437 HlyD_3: HlyD family secretion protein
Probab=24.23 E-value=1.4e+02 Score=22.77 Aligned_cols=38 Identities=26% Similarity=0.229 Sum_probs=30.6
Q ss_pred CCceEEEeecCccccCCC-CCCEEEEc------eeEEEEEEEEee
Q 022692 146 GLETVEGRCTISDYNSIG-PGSVILLN------KCMMLKVQSVCH 183 (293)
Q Consensus 146 GkKTIE~RLnDeKRq~Ik-vGD~I~F~------k~L~v~V~~Vr~ 183 (293)
+.=.|++.+.......|+ +|+.+.+. ..+..+|..|..
T Consensus 34 ~~~~v~~~v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 34 DDLWVEAYVPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred ceEEEEEEEChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 344578888889999998 99999987 367888888876
No 58
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=23.39 E-value=81 Score=23.61 Aligned_cols=29 Identities=17% Similarity=0.223 Sum_probs=22.9
Q ss_pred hcCCceEEEeecCcc-ccCCCCCCEEEEce
Q 022692 144 KDGLETVEGRCTISD-YNSIGPGSVILLNK 172 (293)
Q Consensus 144 ksGkKTIE~RLnDeK-Rq~IkvGD~I~F~k 172 (293)
.+++-+|++++=++. ...+++||.|.+.+
T Consensus 30 ~D~TG~i~~~~W~~~~~~~~~~G~vv~i~~ 59 (82)
T cd04491 30 GDETGTIRFTLWDEKAADDLEPGDVVRIEN 59 (82)
T ss_pred ECCCCEEEEEEECchhcccCCCCCEEEEEe
Confidence 344557888888876 88999999999874
No 59
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=23.17 E-value=67 Score=24.58 Aligned_cols=28 Identities=29% Similarity=0.310 Sum_probs=19.7
Q ss_pred ccccCCCCCCEEEEc----eeEEEEEEEEeec
Q 022692 157 SDYNSIGPGSVILLN----KCMMLKVQSVCHY 184 (293)
Q Consensus 157 eKRq~IkvGD~I~F~----k~L~v~V~~Vr~Y 184 (293)
..--++++||+|.+. +.+.+.|-+...|
T Consensus 24 ~ell~L~~Gdvi~L~~~~~~~v~l~v~g~~~~ 55 (77)
T TIGR02480 24 GDLLKLGEGSVIELDKLAGEPLDILVNGRLIA 55 (77)
T ss_pred HHHhcCCCCCEEEcCCCCCCcEEEEECCEEEE
Confidence 556788999999997 3566666555544
No 60
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=23.01 E-value=87 Score=25.98 Aligned_cols=28 Identities=21% Similarity=0.258 Sum_probs=22.8
Q ss_pred CccccCCCCCCEEEEceeEEEEEEEEee
Q 022692 156 ISDYNSIGPGSVILLNKCMMLKVQSVCH 183 (293)
Q Consensus 156 DeKRq~IkvGD~I~F~k~L~v~V~~Vr~ 183 (293)
.+-++.+++||.|+...=+..+|++|..
T Consensus 47 ~~~~~~Lk~Gd~VvT~gGi~G~Vv~i~~ 74 (106)
T PRK05585 47 KKMLSSLAKGDEVVTNGGIIGKVTKVSE 74 (106)
T ss_pred HHHHHhcCCCCEEEECCCeEEEEEEEeC
Confidence 3446789999999999888888888863
No 61
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=22.62 E-value=1.4e+02 Score=22.49 Aligned_cols=28 Identities=14% Similarity=0.185 Sum_probs=19.9
Q ss_pred HHhcCCceEEEeecCccccCCCCCCEEEEc
Q 022692 142 FIKDGLETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 142 lIksGkKTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
.|-+|.=+ +.-.+.....+++||.+.|-
T Consensus 30 ~vleG~v~--it~~~G~~~~~~aGD~~~~p 57 (74)
T PF05899_consen 30 YVLEGEVT--ITDEDGETVTFKAGDAFFLP 57 (74)
T ss_dssp EEEEEEEE--EEETTTEEEEEETTEEEEE-
T ss_pred EEEEeEEE--EEECCCCEEEEcCCcEEEEC
Confidence 45555433 33457889999999999998
No 62
>COG2820 Udp Uridine phosphorylase [Nucleotide transport and metabolism]
Probab=22.57 E-value=96 Score=29.87 Aligned_cols=35 Identities=20% Similarity=0.295 Sum_probs=26.0
Q ss_pred HHHhcCCceEEEeecCc-ccc-CCCCCCEEEEceeEEE
Q 022692 141 SFIKDGLETVEGRCTIS-DYN-SIGPGSVILLNKCMML 176 (293)
Q Consensus 141 ~lIksGkKTIE~RLnDe-KRq-~IkvGD~I~F~k~L~v 176 (293)
++.+-|.||+ ||+.+- -.| .|.+||.|+=+..+..
T Consensus 78 EL~~lGa~tf-iRVGT~Galq~~i~~Gdvvi~tgAvr~ 114 (248)
T COG2820 78 ELARLGAKTF-IRVGTTGALQPDINVGDVVVATGAVRL 114 (248)
T ss_pred HHHhcCCeEE-EEeeccccccCCCCCCCEEEecccccc
Confidence 4556699999 999983 333 6999999987754443
No 63
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=22.52 E-value=91 Score=26.34 Aligned_cols=24 Identities=13% Similarity=0.268 Sum_probs=19.8
Q ss_pred ccCCCCCCEEEEceeEEEEEEEEe
Q 022692 159 YNSIGPGSVILLNKCMMLKVQSVC 182 (293)
Q Consensus 159 Rq~IkvGD~I~F~k~L~v~V~~Vr 182 (293)
++.+++||.|+...=+..+|++|.
T Consensus 36 ~~~Lk~GD~VvT~gGi~G~V~~I~ 59 (109)
T PRK05886 36 HESLQPGDRVHTTSGLQATIVGIT 59 (109)
T ss_pred HHhcCCCCEEEECCCeEEEEEEEe
Confidence 468999999999977777777775
No 64
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=20.24 E-value=1.2e+02 Score=26.26 Aligned_cols=39 Identities=15% Similarity=0.161 Sum_probs=29.8
Q ss_pred HhcCCceEEEeecCccccCCCCCCEEEEc-eeEEEEEEEEee
Q 022692 143 IKDGLETVEGRCTISDYNSIGPGSVILLN-KCMMLKVQSVCH 183 (293)
Q Consensus 143 IksGkKTIE~RLnDeKRq~IkvGD~I~F~-k~L~v~V~~Vr~ 183 (293)
..+|. .|+...|-++=.|++||.+... ++..-.|+++.+
T Consensus 43 Fedg~--~~i~~~dv~~LDlRIGD~Vkv~~~k~~yiV~Gl~~ 82 (131)
T PF08605_consen 43 FEDGT--YEIKNEDVKYLDLRIGDTVKVDGPKVTYIVVGLEC 82 (131)
T ss_pred EecCc--eEeCcccEeeeeeecCCEEEECCCCccEEEEEeee
Confidence 45666 8888888999999999999987 445566666554
No 65
>PF12195 End_beta_barrel: Beta barrel domain of bacteriophage endosialidase; InterPro: IPR024427 This entry represents the beta barrel domain of endosialidases which is nested in a beta propeller domain. This beta barrel domain is approximately 80 amino acids in length and represents one of the two sialic acid binding sites of the enzyme [].; PDB: 1V0E_B 1V0F_E 3JU4_A 3GVL_A 3GVK_B 3GVJ_A.
Probab=20.12 E-value=1.6e+02 Score=24.18 Aligned_cols=25 Identities=12% Similarity=-0.008 Sum_probs=15.3
Q ss_pred hcCCceEEEeecCccccCCCCCCEEEEc
Q 022692 144 KDGLETVEGRCTISDYNSIGPGSVILLN 171 (293)
Q Consensus 144 ksGkKTIE~RLnDeKRq~IkvGD~I~F~ 171 (293)
.++..++-|++-+. .|.+||.|.|.
T Consensus 13 a~n~~~ati~l~~H---Gl~vGD~VnFs 37 (83)
T PF12195_consen 13 AANQTTATITLTDH---GLFVGDFVNFS 37 (83)
T ss_dssp -TTSSEEEEE-TT-------TT-EEEEE
T ss_pred ecCceEEEEEEccC---ceeecceEEEe
Confidence 45667888888774 68999999998
Done!