Query 025905
Match_columns 246
No_of_seqs 93 out of 108
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 10:53:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025905.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025905hhsearch_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 1.2E-40 2.5E-45 267.8 12.5 104 127-230 1-109 (109)
2 COG4043 Preprotein translocase 100.0 7.2E-40 1.6E-44 262.4 11.0 106 126-231 2-108 (111)
3 cd06541 ASCH ASC-1 homology or 99.8 5.3E-21 1.2E-25 150.1 9.4 100 129-229 2-105 (105)
4 PF04266 ASCH: ASCH domain; I 99.7 1.4E-16 3.1E-21 121.6 9.3 98 129-231 1-104 (105)
5 cd06552 ASCH_yqfb_like ASC-1 h 99.0 1.7E-09 3.7E-14 82.8 8.4 94 129-229 2-99 (100)
6 PF12961 DUF3850: Domain of Un 98.5 3.7E-07 8E-12 69.7 6.6 53 127-182 1-62 (72)
7 PRK04980 hypothetical protein; 96.6 0.026 5.6E-07 45.8 9.4 81 128-215 4-90 (102)
8 COG2411 Uncharacterized conser 91.3 1.7 3.6E-05 39.0 9.0 92 129-230 9-106 (188)
9 COG3097 Uncharacterized protei 89.3 1.8 4E-05 35.4 6.9 91 130-229 7-103 (106)
10 cd06553 ASCH_Ef3133_like ASC-1 84.6 6.2 0.00013 32.9 7.8 84 131-219 12-107 (127)
11 PRK11507 ribosome-associated p 82.8 2.3 4.9E-05 32.6 4.2 55 97-169 10-64 (70)
12 COG1935 Uncharacterized conser 82.3 2.9 6.4E-05 35.2 5.0 43 137-179 16-71 (122)
13 PF07527 Hairy_orange: Hairy O 78.9 1.9 4.2E-05 29.1 2.4 29 14-51 7-35 (43)
14 cd06554 ASCH_ASC-1_like ASC-1 69.6 3.6 7.8E-05 33.7 2.2 28 129-156 4-31 (113)
15 PF13275 S4_2: S4 domain; PDB: 69.0 2 4.4E-05 32.2 0.6 54 97-168 6-59 (65)
16 PF11604 CusF_Ec: Copper bindi 66.9 4.5 9.8E-05 30.0 2.1 58 121-178 5-67 (70)
17 TIGR02988 YaaA_near_RecF S4 do 66.8 7.1 0.00015 27.5 3.0 31 137-167 29-59 (59)
18 PRK12279 50S ribosomal protein 65.8 25 0.00055 33.7 7.3 115 99-231 164-286 (311)
19 COG4933 Uncharacterized conser 64.7 28 0.00062 29.5 6.6 89 129-233 1-98 (124)
20 PF13550 Phage-tail_3: Putativ 61.4 20 0.00044 28.6 5.1 45 133-178 116-163 (164)
21 PRK10348 ribosome-associated h 59.5 18 0.00039 30.6 4.6 52 137-189 29-87 (133)
22 PF04322 DUF473: Protein of un 57.4 35 0.00075 28.6 5.9 43 137-179 16-71 (119)
23 COG0809 QueA S-adenosylmethion 56.4 17 0.00037 35.4 4.5 71 145-216 78-174 (348)
24 COG1188 Ribosome-associated he 55.9 20 0.00044 29.3 4.2 42 137-179 29-73 (100)
25 KOG4476 Gluconate transport-in 54.9 9.8 0.00021 35.5 2.5 32 136-167 21-53 (248)
26 COG5037 TOS9 Gluconate transpo 54.9 9.8 0.00021 35.5 2.5 32 136-167 21-53 (248)
27 COG1430 Uncharacterized conser 54.5 11 0.00024 31.6 2.6 25 143-167 96-120 (126)
28 smart00363 S4 S4 RNA-binding d 53.8 15 0.00032 23.6 2.6 35 134-168 18-52 (60)
29 PF01336 tRNA_anti-codon: OB-f 53.5 20 0.00043 24.8 3.4 29 139-167 22-54 (75)
30 PRK09838 periplasmic copper-bi 50.2 7.5 0.00016 32.0 0.9 53 115-167 45-98 (115)
31 smart00350 MCM minichromosome 50.1 19 0.00042 35.5 3.9 44 128-172 87-132 (509)
32 COG2501 S4-like RNA binding pr 47.6 31 0.00066 26.8 3.8 56 97-170 10-65 (73)
33 PRK06461 single-stranded DNA-b 46.9 43 0.00094 27.4 4.8 44 139-182 46-100 (129)
34 cd04478 RPA2_DBD_D RPA2_DBD_D: 46.4 55 0.0012 24.4 5.0 51 139-189 22-86 (95)
35 PF09953 DUF2187: Uncharacteri 46.3 26 0.00056 26.1 3.1 30 157-186 3-41 (57)
36 COG5569 Uncharacterized conser 45.8 24 0.00052 29.2 3.1 50 118-167 43-93 (108)
37 PRK00147 queA S-adenosylmethio 45.6 60 0.0013 31.5 6.3 60 156-216 100-172 (342)
38 PRK01424 S-adenosylmethionine: 42.9 71 0.0015 31.5 6.3 38 156-194 92-140 (366)
39 PF01479 S4: S4 domain; Inter 39.9 14 0.00031 24.5 0.8 30 135-164 19-48 (48)
40 COG2028 Uncharacterized conser 39.3 1.2E+02 0.0025 26.2 6.4 60 130-192 10-76 (145)
41 smart00511 ORANGE Orange domai 37.7 45 0.00098 22.4 3.1 29 14-51 7-35 (45)
42 cd03695 CysN_NodQ_II CysN_NodQ 37.1 59 0.0013 24.2 3.9 34 145-181 17-51 (81)
43 PF11184 DUF2969: Protein of u 37.0 31 0.00068 26.2 2.4 64 143-213 5-68 (71)
44 cd00165 S4 S4/Hsp/ tRNA synthe 34.7 49 0.0011 21.7 2.9 31 137-167 21-51 (70)
45 TIGR03069 PS_II_S4 photosystem 33.8 61 0.0013 29.7 4.2 36 134-169 200-235 (257)
46 TIGR00113 queA S-adenosylmethi 33.2 1.1E+02 0.0024 29.8 5.9 60 156-216 98-173 (344)
47 PRK06033 hypothetical protein; 32.8 49 0.0011 25.5 2.9 28 153-180 23-54 (83)
48 KOG0432 Valyl-tRNA synthetase 32.5 68 0.0015 35.2 4.8 69 14-82 645-732 (995)
49 COG3127 Predicted ABC-type tra 32.3 39 0.00084 36.4 2.9 28 153-180 606-636 (829)
50 TIGR00739 yajC preprotein tran 32.0 54 0.0012 25.4 3.1 26 154-179 34-59 (84)
51 COG3264 Small-conductance mech 31.6 57 0.0012 35.3 4.0 27 156-182 659-691 (835)
52 KOG3416 Predicted nucleic acid 30.0 81 0.0017 27.2 4.0 25 143-167 47-71 (134)
53 cd02025 PanK Pantothenate kina 29.0 1.2E+02 0.0026 26.6 5.0 43 125-167 60-110 (220)
54 PF01052 SpoA: Surface present 27.4 44 0.00094 24.3 1.7 26 152-177 23-52 (77)
55 COG1868 FliM Flagellar motor s 27.2 84 0.0018 30.3 4.0 34 148-181 264-301 (332)
56 TIGR02480 fliN flagellar motor 26.0 59 0.0013 24.3 2.3 28 153-180 24-55 (77)
57 PRK03760 hypothetical protein; 25.9 53 0.0011 26.8 2.1 24 144-167 92-115 (117)
58 PRK05585 yajC preprotein trans 25.5 76 0.0016 25.7 3.0 43 135-179 32-74 (106)
59 PRK05886 yajC preprotein trans 25.2 78 0.0017 26.0 3.0 42 135-178 18-59 (109)
60 cd04498 hPOT1_OB2 hPOT1_OB2: A 24.6 64 0.0014 27.0 2.4 26 142-167 58-86 (123)
61 PF12195 End_beta_barrel: Beta 24.2 1.2E+02 0.0026 24.1 3.7 38 140-180 13-59 (83)
62 cd06863 PX_Atg24p The phosphoi 23.9 1E+02 0.0023 24.3 3.5 45 146-190 1-54 (118)
63 PF02643 DUF192: Uncharacteriz 23.5 44 0.00096 26.5 1.2 26 142-167 82-107 (108)
64 PF05899 Cupin_3: Protein of u 23.4 1.3E+02 0.0028 22.1 3.7 28 138-167 30-57 (74)
65 PF13437 HlyD_3: HlyD family s 22.8 1.6E+02 0.0034 22.0 4.1 36 144-179 36-78 (105)
66 COG5471 Uncharacterized conser 22.7 1.4E+02 0.003 24.9 3.9 36 143-182 9-44 (107)
67 cd04491 SoSSB_OBF SoSSB_OBF: A 22.2 89 0.0019 22.8 2.6 27 141-167 31-58 (82)
68 PLN00051 RNA-binding S4 domain 21.8 1.4E+02 0.003 27.8 4.3 34 134-167 208-241 (267)
69 COG2820 Udp Uridine phosphoryl 21.3 1.1E+02 0.0023 28.8 3.4 33 137-170 78-112 (248)
70 PF06415 iPGM_N: BPG-independe 21.2 58 0.0013 29.8 1.7 63 96-167 109-175 (223)
71 PRK08433 flagellar motor switc 20.2 1.1E+02 0.0024 25.2 2.9 28 153-180 48-79 (111)
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=1.2e-40 Score=267.79 Aligned_cols=104 Identities=39% Similarity=0.579 Sum_probs=101.5
Q ss_pred eeeeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEcc-----eEEEEEEEEeecCCHHHHHhhcCccccCCCCCC
Q 025905 127 FELHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNK-----CLVLKVQDVHGYLSFSEMLQAESLAKVLPGIKT 201 (246)
Q Consensus 127 heM~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e-----~l~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~S 201 (246)
|+|+|+++||++|++|+|||||||||+||++|++||+|+|++ ++.|+|++|++|+||++||+++++++|+|+++|
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 789999999999999999999999999999999999999974 899999999999999999999999999999999
Q ss_pred HHHHHHHHHhhCCHhHHhhccEEEEEEec
Q 025905 202 IDEGVQVYRRFYTEEKEKTNGVIAICVTK 230 (246)
Q Consensus 202 iEEgv~~yr~iYskEkE~~yGVvAI~I~~ 230 (246)
+|+|+++||+|||+|||++||||||+|++
T Consensus 81 ~ee~~~~~~~~Y~~e~e~~~GvlaI~i~~ 109 (109)
T cd06555 81 IEEGVKDTYKIYSKEQEKKYGVLAIEIRV 109 (109)
T ss_pred HHHHHHHHHHhCCHHHHHhcCEEEEEEEC
Confidence 99999999999999999999999999974
No 2
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=7.2e-40 Score=262.37 Aligned_cols=106 Identities=37% Similarity=0.580 Sum_probs=103.7
Q ss_pred ceeeeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEc-ceEEEEEEEEeecCCHHHHHhhcCccccCCCCCCHHH
Q 025905 126 NFELHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCN-KCLVLKVQDVHGYLSFSEMLQAESLAKVLPGIKTIDE 204 (246)
Q Consensus 126 ~heM~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~-e~l~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~SiEE 204 (246)
.|+|+|+++||++|++|+|||||||||+||++||+||+|.|| +.+.|+|++||.|+||++||+.||+++++|+.+|+|+
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 HHHHHHhhCCHhHHhhccEEEEEEecC
Q 025905 205 GVQVYRRFYTEEKEKTNGVIAICVTKP 231 (246)
Q Consensus 205 gv~~yr~iYskEkE~~yGVvAI~I~~~ 231 (246)
||..||+||++|+|+.|||+||+|+..
T Consensus 82 ~l~~~~~~Y~~~kE~~yGvlaI~ie~i 108 (111)
T COG4043 82 GLRRYRNFYPSEKEKRYGVLAIEIEPI 108 (111)
T ss_pred HHHHHHHhCcHhHhhccceEEEEEEEc
Confidence 999999999999999999999999864
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=99.84 E-value=5.3e-21 Score=150.15 Aligned_cols=100 Identities=19% Similarity=0.077 Sum_probs=93.8
Q ss_pred eeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEcc----eEEEEEEEEeecCCHHHHHhhcCccccCCCCCCHHH
Q 025905 129 LHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNK----CLVLKVQDVHGYLSFSEMLQAESLAKVLPGIKTIDE 204 (246)
Q Consensus 129 M~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e----~l~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~SiEE 204 (246)
|++.+++|++|.+|+||+|+|+++++++.+++||.|+|.+ .+.++|++|+.|++| +++.++...+.++|..|+++
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 6789999999999999999999999999999999999987 899999999999999 77777777788888779999
Q ss_pred HHHHHHhhCCHhHHhhccEEEEEEe
Q 025905 205 GVQVYRRFYTEEKEKTNGVIAICVT 229 (246)
Q Consensus 205 gv~~yr~iYskEkE~~yGVvAI~I~ 229 (246)
.++.+++||+++++.++||++|+++
T Consensus 81 ~~~~~~~~~~~~~~~~~~vv~i~F~ 105 (105)
T cd06541 81 ELKEHAAFFKEELAPDMLLYAISFE 105 (105)
T ss_pred HHHHHHHHhhHHhCCCCceEEEEeC
Confidence 9999999999999999999999984
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=99.69 E-value=1.4e-16 Score=121.59 Aligned_cols=98 Identities=26% Similarity=0.317 Sum_probs=86.5
Q ss_pred eeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEc------ceEEEEEEEEeecCCHHHHHhhcCccccCCCCCCH
Q 025905 129 LHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCN------KCLVLKVQDVHGYLSFSEMLQAESLAKVLPGIKTI 202 (246)
Q Consensus 129 M~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~------e~l~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~Si 202 (246)
|.+.++||++|.+|+||+|+|+.++++..++.++.|+|+ -...++|++|+.+ +|++|.++.....- . |+
T Consensus 1 Lsi~~~~~~~Il~G~Kt~e~R~~~~~~~~~~g~~~iv~~~~~~~~~~~~v~v~~V~~~-~~~e~~~~~a~~eg---~-s~ 75 (105)
T PF04266_consen 1 LSIKPEYAELILSGKKTAEIRLWDEKLPKIRGDLVIVFNTDPDGKPVGIVEVTEVEVY-PFSELTEEHARLEG---E-SL 75 (105)
T ss_dssp EEECHHHHHHHHTTSSCEEEECSTTTCCTTTTCEEEEETETTTTEEEEEEEEEEEEEE-EHHHHHHHHHHHHC---C--H
T ss_pred CEechHHHHHHHCCCcEEEEEcccceeccCCCCEEEEEEEecCCcEEEEEEEEEEEEe-hhhhCCHHHHhHhc---c-CH
Confidence 678999999999999999999999999998888888875 3588899999999 99999998655333 2 99
Q ss_pred HHHHHHHHhhCCHhHHhhccEEEEEEecC
Q 025905 203 DEGVQVYRRFYTEEKEKTNGVIAICVTKP 231 (246)
Q Consensus 203 EEgv~~yr~iYskEkE~~yGVvAI~I~~~ 231 (246)
++..+.+++||+++.+...||++|+++++
T Consensus 76 e~~~~~~~~~y~~~~~~~~~v~~i~f~~v 104 (105)
T PF04266_consen 76 EEWREEHRDIYPREIEPDDGVVAIEFEVV 104 (105)
T ss_dssp HHHHHHHHHHCHHHHHCCCEEEEEEEEEE
T ss_pred HHHHHHHHHHccccccccceEEEEEEEec
Confidence 99999999999999998899999999874
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=99.01 E-value=1.7e-09 Score=82.85 Aligned_cols=94 Identities=18% Similarity=0.226 Sum_probs=74.2
Q ss_pred eeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEc----ceEEEEEEEEeecCCHHHHHhhcCccccCCCCCCHHH
Q 025905 129 LHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCN----KCLVLKVQDVHGYLSFSEMLQAESLAKVLPGIKTIDE 204 (246)
Q Consensus 129 M~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~----e~l~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~SiEE 204 (246)
|.+.++++++|.+|+||+++|..+ ++.+++||.+.+. ....++|++|+. .+|.+ +.++..... |..|.++
T Consensus 2 ~~f~~~~~~~I~sG~Kt~t~R~~~--~~~~~~Gd~~~~~~~~~~~~~~~v~~V~~-~~~~~-l~~~~A~~e--G~~s~~~ 75 (100)
T cd06552 2 ILFFERYEEAILSGKKTATIRDGG--ESHLKPGDVVEVHTGERIFGEAEITSVEE-KTLGE-LTDEDARQE--GFPSLEE 75 (100)
T ss_pred eechHHHHHHHHcCCCEEEEeCCC--ccCCCCCCEEEEEECCEEEEEEEEEEEEE-EEhhh-CCHHHHHhc--CCccHHH
Confidence 566789999999999999999975 4569999999986 368889999977 88988 455443333 5569999
Q ss_pred HHHHHHhhCCHhHHhhccEEEEEEe
Q 025905 205 GVQVYRRFYTEEKEKTNGVIAICVT 229 (246)
Q Consensus 205 gv~~yr~iYskEkE~~yGVvAI~I~ 229 (246)
..+.++++|+.++.. -=|..|+++
T Consensus 76 ~~~~l~~~Y~~~~~~-~~v~vi~F~ 99 (100)
T cd06552 76 LKEALKEIYPGLKDD-DEVYVIEFR 99 (100)
T ss_pred HHHHHHHHcCCCCCC-CEEEEEEEE
Confidence 999999999987632 227777765
No 6
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=98.49 E-value=3.7e-07 Score=69.66 Aligned_cols=53 Identities=23% Similarity=0.381 Sum_probs=46.4
Q ss_pred eeeeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEc---------ceEEEEEEEEeecCC
Q 025905 127 FELHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCN---------KCLVLKVQDVHGYLS 182 (246)
Q Consensus 127 heM~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~---------e~l~v~V~~Vr~Y~S 182 (246)
|++.+.+.||+.+.+|+||.|+|.||..+ ++||.+.+. ..+.++|+-|-.|..
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 78999999999999999999999999655 699999985 578899999877543
No 7
>PRK04980 hypothetical protein; Provisional
Probab=96.56 E-value=0.026 Score=45.80 Aligned_cols=81 Identities=19% Similarity=0.252 Sum_probs=58.3
Q ss_pred eeeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEE-c---c--eEEEEEEEEeecCCHHHHHhhcCccccCCCCCC
Q 025905 128 ELHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILC-N---K--CLVLKVQDVHGYLSFSEMLQAESLAKVLPGIKT 201 (246)
Q Consensus 128 eM~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F-~---e--~l~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~S 201 (246)
+|...++|-.+|-+|+||+-+|- +.-...++||.+.- + + -..++|++|. +-+|.+|=+. .+-.-|. |
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 46778999999999999999998 44678999999876 2 2 2444565553 3456555433 1112244 8
Q ss_pred HHHHHHHHHhhCCH
Q 025905 202 IDEGVQVYRRFYTE 215 (246)
Q Consensus 202 iEEgv~~yr~iYsk 215 (246)
+++-.+.++++|+.
T Consensus 77 L~elk~~i~~iYp~ 90 (102)
T PRK04980 77 LPELKQVIAEIYPN 90 (102)
T ss_pred HHHHHHHHHHHCCC
Confidence 99999999999996
No 8
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=91.33 E-value=1.7 Score=38.95 Aligned_cols=92 Identities=22% Similarity=0.267 Sum_probs=64.5
Q ss_pred eeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEc--ce--EEEEEEEEeecCCHHHHHhhcCccccCCCCCCHHH
Q 025905 129 LHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCN--KC--LVLKVQDVHGYLSFSEMLQAESLAKVLPGIKTIDE 204 (246)
Q Consensus 129 M~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~--e~--l~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~SiEE 204 (246)
+.+..+|-+.|-+|+|+.-||+. --..++|+.+... .. -.++|++|+ |.--+++=+. +..+-|-.|.||
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 67889999999999999999998 3456899998885 22 344555554 3444554443 334556679999
Q ss_pred HHHHHHhhCCH--hHHhhccEEEEEEec
Q 025905 205 GVQVYRRFYTE--EKEKTNGVIAICVTK 230 (246)
Q Consensus 205 gv~~yr~iYsk--EkE~~yGVvAI~I~~ 230 (246)
.+..+.++|+. .... |--|+++.
T Consensus 82 Li~~LkriYg~lr~ed~---VTIi~Fe~ 106 (188)
T COG2411 82 LIEELKRIYGELRDEDI---VTIIEFEV 106 (188)
T ss_pred HHHHHHHHcCcCCCCce---EEEEEEEE
Confidence 99999999973 2222 55666665
No 9
>COG3097 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.28 E-value=1.8 Score=35.42 Aligned_cols=91 Identities=15% Similarity=0.214 Sum_probs=58.2
Q ss_pred eccchhhHHHhcCCceEEEEccCccccCCCCCCEEEE---c-c--eEEEEEEEEeecCCHHHHHhhcCccccCCCCCCHH
Q 025905 130 HVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILC---N-K--CLVLKVQDVHGYLSFSEMLQAESLAKVLPGIKTID 203 (246)
Q Consensus 130 ~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F---~-e--~l~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~SiE 203 (246)
....++=..|.+|.|||-|| |.--+..++||.+.- . + -...+|++|..- +|.+|=+.. .+.- .. ++.
T Consensus 7 TFf~rfe~dilagrKTITIR--D~SEShf~~g~vlrV~r~Ed~~~fc~I~vl~vspv-tld~l~e~H-AeQE--nm-~L~ 79 (106)
T COG3097 7 TFFQRFEADILAGRKTITIR--DKSESHFKPGDVLRVGRFEDDRYFCTIEVLAVSPV-TLDELTEKH-AEQE--NM-TLP 79 (106)
T ss_pred eehhhccHHHhCCCceEEEe--ccchhcCCCCCEEEEEEecCCcEEEEEEEEEeccE-ehhhhhhhh-hhhh--cC-CcH
Confidence 34556667899999999999 555688999999974 2 2 234455555432 344443321 0000 12 778
Q ss_pred HHHHHHHhhCCHhHHhhccEEEEEEe
Q 025905 204 EGVQVYRRFYTEEKEKTNGVIAICVT 229 (246)
Q Consensus 204 Egv~~yr~iYskEkE~~yGVvAI~I~ 229 (246)
|.-+.+..||+.+.+ +=|+...+.
T Consensus 80 eLk~vI~eIYP~~d~--fyVI~f~L~ 103 (106)
T COG3097 80 ELKKVIAEIYPNQDQ--FYVIEFQLA 103 (106)
T ss_pred HHHHHHHHHCCCCcE--EEEEEEEec
Confidence 888999999996654 446666554
No 10
>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=84.58 E-value=6.2 Score=32.88 Aligned_cols=84 Identities=15% Similarity=0.137 Sum_probs=55.4
Q ss_pred ccchhhHHHhcCCceEEEEcc----CccccCCCCCCEEEEc-------ceEEEEEEEEeecCCHHHHH-hhcCccccCCC
Q 025905 131 VQEPYFTQLKDGLKTVEGRCA----VGDYNRIGSGSLILCN-------KCLVLKVQDVHGYLSFSEML-QAESLAKVLPG 198 (246)
Q Consensus 131 L~e~yF~lIksGkKTIE~RLn----DeKrq~IkvGD~I~F~-------e~l~v~V~~Vr~Y~SF~eLL-e~E~l~kvlPg 198 (246)
+.++.-++|.+|+||.-.|+. ++.-.--++||.=+.. -.+.+.-+++.+|..-.+-. .+|| .|
T Consensus 12 ~ad~l~~LVl~G~KtAT~s~~~~y~~e~e~~p~vG~~~Ivld~~g~p~cvi~~~~V~~~~f~~vt~~~A~~EG-----eg 86 (127)
T cd06553 12 LADELAALVLAGKKTATCSALALYEAEEEPLPKVGDYSIILDGQGKPVCIIETTEVEVVPFNDVTEEFAYAEG-----EG 86 (127)
T ss_pred HHHHHHHHHHcCCcEEEEechhhcccCCccCCCCCcEEEEECCCCCEEEEEEEEEEEEEEcccCCHHHHHHhC-----CC
Confidence 346778999999999999974 3444467899965543 23555555666666654322 2222 23
Q ss_pred CCCHHHHHHHHHhhCCHhHHh
Q 025905 199 IKTIDEGVQVYRRFYTEEKEK 219 (246)
Q Consensus 199 ~~SiEEgv~~yr~iYskEkE~ 219 (246)
-.|++.=-+..+.||+++-..
T Consensus 87 d~sl~~Wr~~h~~ff~~~~~~ 107 (127)
T cd06553 87 DRSLEYWRKAHEAFFTRELEE 107 (127)
T ss_pred ccCHHHHHHHHHHHHHHHHhh
Confidence 347898888999999876543
No 11
>PRK11507 ribosome-associated protein; Provisional
Probab=82.79 E-value=2.3 Score=32.59 Aligned_cols=55 Identities=13% Similarity=0.122 Sum_probs=43.6
Q ss_pred cCchhhhhhhhhhhhhhhhhHHHHhhcccceeeeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEcce
Q 025905 97 EDDDLKKREDWGKLVLKEGSEMIELLKTVNFELHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNKC 169 (246)
Q Consensus 97 e~~~~~~~~~w~~l~~~~g~el~~~~~~~~heM~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e~ 169 (246)
|-..|.|-=.|.-++.. |-+.. .+|++|.=.|-+-+...++++|.+||.|.|++.
T Consensus 10 e~I~L~QlLK~~~~v~S-GG~AK-----------------~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~g~ 64 (70)
T PRK11507 10 PHVELCDLLKLEGWSES-GAQAK-----------------IAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH 64 (70)
T ss_pred CeEEHHHHHhhhCcccC-hHHHH-----------------HHHHcCceEECCEEecccCCCCCCCCEEEECCE
Confidence 44566666667777766 77776 368899888888888899999999999999853
No 12
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=82.25 E-value=2.9 Score=35.18 Aligned_cols=43 Identities=23% Similarity=0.372 Sum_probs=35.0
Q ss_pred HHHhcCCceEEEEc--cCccccCCCCCCEEEEc-----------ceEEEEEEEEee
Q 025905 137 TQLKDGLKTVEGRC--AVGDYNRIGSGSLILCN-----------KCLVLKVQDVHG 179 (246)
Q Consensus 137 ~lIksGkKTIE~RL--nDeKrq~IkvGD~I~F~-----------e~l~v~V~~Vr~ 179 (246)
++++++.+|||||= |..---++++||.+-.+ .-+.++|..+..
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 55777889999998875 358888887765
No 13
>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=78.88 E-value=1.9 Score=29.09 Aligned_cols=29 Identities=28% Similarity=0.723 Sum_probs=20.4
Q ss_pred hhHHHHHHHHHHHhhccccccccCCCCCHHHHHhhhhc
Q 025905 14 YTKCIEEALKFILESHINQTLELDLGLSKDLCSFLLTH 51 (246)
Q Consensus 14 ~~~~~~e~~~~~l~sh~~~~~~~~l~ls~~~c~~ll~~ 51 (246)
+++|+.|..||.. +.. +++++++.+|+.|
T Consensus 7 y~~C~~Ev~~fL~--~~~-------~~~~~~~~rLl~H 35 (43)
T PF07527_consen 7 YSECLNEVSRFLS--SVE-------GVDPGVRARLLSH 35 (43)
T ss_dssp HHHHHHHHHHHHH--HTS----------THHHHHHHHH
T ss_pred HHHHHHHHHHHHh--cCC-------CCChHHHHHHHHH
Confidence 5799999999993 333 1255888888874
No 14
>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=69.59 E-value=3.6 Score=33.69 Aligned_cols=28 Identities=29% Similarity=0.668 Sum_probs=23.9
Q ss_pred eeccchhhHHHhcCCceEEEEccCcccc
Q 025905 129 LHVQEPYFTQLKDGLKTVEGRCAVGDYN 156 (246)
Q Consensus 129 M~L~e~yF~lIksGkKTIE~RLnDeKrq 156 (246)
+-+..+|-.+|..|.|+||+|--..+++
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 5677899999999999999998776654
No 15
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=69.04 E-value=2 Score=32.23 Aligned_cols=54 Identities=19% Similarity=0.236 Sum_probs=28.1
Q ss_pred cCchhhhhhhhhhhhhhhhhHHHHhhcccceeeeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEcc
Q 025905 97 EDDDLKKREDWGKLVLKEGSEMIELLKTVNFELHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNK 168 (246)
Q Consensus 97 e~~~~~~~~~w~~l~~~~g~el~~~~~~~~heM~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e 168 (246)
|-..|.|-=.|.-++-. |.|.. .+|++|.=.|-+-+...++++|.+||.|.|+.
T Consensus 6 e~I~L~qlLK~~glv~s-GGeAK-----------------~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~~~ 59 (65)
T PF13275_consen 6 EYITLGQLLKLAGLVSS-GGEAK-----------------ALIQEGEVKVNGEVETRRGKKLRPGDVVEIDG 59 (65)
T ss_dssp S---HHHHHHHHTS-SS-SSTTS-----------------HHHHHHHHEETTB----SS----SSEEEEETT
T ss_pred CcEEHHHHHhHcCCccc-HHHHH-----------------HHHHcCceEECCEEccccCCcCCCCCEEEECC
Confidence 34444444445555544 55554 35777866666777778999999999999974
No 16
>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=66.86 E-value=4.5 Score=30.01 Aligned_cols=58 Identities=9% Similarity=-0.019 Sum_probs=35.3
Q ss_pred hhcccceeeeccchhhHHHhcCCceEEEEccC-ccccCCCCCCEEEEc----ceEEEEEEEEe
Q 025905 121 LLKTVNFELHVQEPYFTQLKDGLKTVEGRCAV-GDYNRIGSGSLILCN----KCLVLKVQDVH 178 (246)
Q Consensus 121 ~~~~~~heM~L~e~yF~lIksGkKTIE~RLnD-eKrq~IkvGD~I~F~----e~l~v~V~~Vr 178 (246)
.+++....+.|.+++...+.=..=|-..++.+ .....+++||.|.|. +.-...|++|+
T Consensus 5 ~vd~~~~~iti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~~~~~~~~I~~i~ 67 (70)
T PF11604_consen 5 SVDPEAGTITISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFTFERTDDGSYVITAIE 67 (70)
T ss_dssp EEETTTTEEEEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEEEEEETTCEEEEEEEE
T ss_pred EEecCCCEEEEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEEEEECCCCcEEEEEEE
Confidence 34555566777777777777777888889885 667999999999996 22234455554
No 17
>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=66.76 E-value=7.1 Score=27.47 Aligned_cols=31 Identities=16% Similarity=0.108 Sum_probs=24.9
Q ss_pred HHHhcCCceEEEEccCccccCCCCCCEEEEc
Q 025905 137 TQLKDGLKTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 137 ~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
.+|+.|.=+|-++.-..+..+++.||.|.|.
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 18
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=65.84 E-value=25 Score=33.73 Aligned_cols=115 Identities=17% Similarity=0.100 Sum_probs=75.7
Q ss_pred chhhhhhhhhhhhhhhhhHHHHhhcccceeeeccchhhHHHhcC-CceEEEEccCccccCCCCCCEEEEc-----ceEE-
Q 025905 99 DDLKKREDWGKLVLKEGSEMIELLKTVNFELHVQEPYFTQLKDG-LKTVEGRCAVGDYNRIGSGSLILCN-----KCLV- 171 (246)
Q Consensus 99 ~~~~~~~~w~~l~~~~g~el~~~~~~~~heM~L~e~yF~lIksG-kKTIE~RLnDeKrq~IkvGD~I~F~-----e~l~- 171 (246)
.++|+|.+-=++ +++|+-....-.....-|-|.++|-+.|-+| +|++|.|-.-.+ ..+|+|+++ +.+.
T Consensus 164 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~vLLSIKPeyaekIl~G~~K~~EfRK~~~~----~~~~~VvIYaTsPvkkIVG 238 (311)
T PRK12279 164 ELLKREQQVLKV-VEKTASQKEEETTETIMISTSPKNAQVLFDDLEKNVIFYKTTPV----NKVLRVLVYVTSPTKKVVG 238 (311)
T ss_pred HHHHHHHHHHHH-HHHhhhhhcccCCcEEEEEeCHHHHHHHhCCCceEEEEEeccCC----CCCCEEEEEecCCCcEEEE
Confidence 456665554444 4557766655555666799999999999999 699999976333 467899986 3333
Q ss_pred -EEEEEEeecCCHHHHHhhcCccccCCCCCCHHHHHHHHHhhCCHhHHhhccEEEEEEecC
Q 025905 172 -LKVQDVHGYLSFSEMLQAESLAKVLPGIKTIDEGVQVYRRFYTEEKEKTNGVIAICVTKP 231 (246)
Q Consensus 172 -v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~SiEEgv~~yr~iYskEkE~~yGVvAI~I~~~ 231 (246)
.+|.+|.. .+-+.+-+..+- . -|. |- +.|.+||.--+. .+||+|..+
T Consensus 239 ef~i~~Ii~-~~P~~lW~k~~~--~-sGI-sk----~~F~~Yf~g~~~----a~Ai~I~~~ 286 (311)
T PRK12279 239 EFDLESVEI-GAISSIWRKYGK--Q-SVI-SK----KEYDAYYEGKDK----AHALVSKKA 286 (311)
T ss_pred EEEEEEEEe-CCHHHHHHHHhh--c-cCC-CH----HHHHHHhCCCce----EEEEEeCCc
Confidence 35555555 778888776432 1 133 22 456677774443 468988875
No 19
>COG4933 Uncharacterized conserved protein [Function unknown]
Probab=64.74 E-value=28 Score=29.51 Aligned_cols=89 Identities=21% Similarity=0.212 Sum_probs=55.7
Q ss_pred eeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEc-----ceE----EEEEEEEeecCCHHHHHhhcCccccCCCC
Q 025905 129 LHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCN-----KCL----VLKVQDVHGYLSFSEMLQAESLAKVLPGI 199 (246)
Q Consensus 129 M~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~-----e~l----~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~ 199 (246)
|-+.++|-++|-+|.|+||+|=-.+.. +-.||++.-. +.+ ..+-+++..-.|-..++.+-+
T Consensus 1 mSIkPk~a~~Ifdg~K~velrR~~p~~--~~~~~~~~VY~TsP~~aVvGef~~e~V~~~~~~siw~~~~~~~-------- 70 (124)
T COG4933 1 MSIKPKFAEAIFDGVKKVELRRITPVP--IVEESTVIVYATSPVKAVVGEFTAERVEQVAIESIWRKAGKSG-------- 70 (124)
T ss_pred CccchhhHHHHhcCcceEEEEEecCCC--cccCcEEEEEecCchhheEEEEEeeeEEEcchHHHHHHhcccc--------
Confidence 567889999999999999999766653 4456777653 233 333333333334444443311
Q ss_pred CCHHHHHHHHHhhCCHhHHhhccEEEEEEecCCC
Q 025905 200 KTIDEGVQVYRRFYTEEKEKTNGVIAICVTKPAA 233 (246)
Q Consensus 200 ~SiEEgv~~yr~iYskEkE~~yGVvAI~I~~~~~ 233 (246)
++ ..-++|.+|+.--+++ .||+++.|-.
T Consensus 71 -~i-~~~~e~~~Y~~G~k~A----~ai~~~~p~~ 98 (124)
T COG4933 71 -SI-KIGAEYLEYFEGAKEA----HAIEVSKPRR 98 (124)
T ss_pred -cc-cchHHHHHHHhcccee----EEEEeCCcee
Confidence 11 1136788888877765 7898888643
No 20
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=61.43 E-value=20 Score=28.56 Aligned_cols=45 Identities=11% Similarity=0.191 Sum_probs=35.8
Q ss_pred chhhHHHhcCCceEEEEccCccccCCCCCCEEEEc---ceEEEEEEEEe
Q 025905 133 EPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCN---KCLVLKVQDVH 178 (246)
Q Consensus 133 e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~---e~l~v~V~~Vr 178 (246)
...+.....+.+|+..++.-.- -.+.|||.|.++ ....++|++|.
T Consensus 116 ~~~l~~~~~~r~t~~f~~~~~~-~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 116 ERLLRRSRYERRTVSFTLPPDG-LALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred HHHHHHhhccceEEEEEEChhh-ccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 3455566778899999988766 679999999997 56788888875
No 21
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=59.47 E-value=18 Score=30.63 Aligned_cols=52 Identities=6% Similarity=0.026 Sum_probs=39.7
Q ss_pred HHHhcCCceEEEEccCccccCCCCCCEEEEc---ceEEEEEEEEee----cCCHHHHHhh
Q 025905 137 TQLKDGLKTVEGRCAVGDYNRIGSGSLILCN---KCLVLKVQDVHG----YLSFSEMLQA 189 (246)
Q Consensus 137 ~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~---e~l~v~V~~Vr~----Y~SF~eLLe~ 189 (246)
++|.+|+=.|-++. +..=..+++||.|.+. ....++|.++-. .+-=+.||+.
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 58999999998888 7777889999999996 456667776653 4445567775
No 22
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=57.38 E-value=35 Score=28.57 Aligned_cols=43 Identities=16% Similarity=0.281 Sum_probs=33.4
Q ss_pred HHHhcCCceEEEEc--cCccccCCCCCCEEEEc-----------ceEEEEEEEEee
Q 025905 137 TQLKDGLKTVEGRC--AVGDYNRIGSGSLILCN-----------KCLVLKVQDVHG 179 (246)
Q Consensus 137 ~lIksGkKTIE~RL--nDeKrq~IkvGD~I~F~-----------e~l~v~V~~Vr~ 179 (246)
++++..-||+|+|= |----.++++||.|-.+ +=+.++|+++..
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 44677788999999875 357777777653
No 23
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]
Probab=56.40 E-value=17 Score=35.41 Aligned_cols=71 Identities=24% Similarity=0.261 Sum_probs=44.6
Q ss_pred eEEEEccCc-----------cccCCCCCCEEEEcceEEEEEEEEe-------ecC---CHH--HHHhhcCccccCCCC-C
Q 025905 145 TVEGRCAVG-----------DYNRIGSGSLILCNKCLVLKVQDVH-------GYL---SFS--EMLQAESLAKVLPGI-K 200 (246)
Q Consensus 145 TIE~RLnDe-----------Krq~IkvGD~I~F~e~l~v~V~~Vr-------~Y~---SF~--eLLe~E~l~kvlPg~-~ 200 (246)
+||+.|... .-+++|+||.|.|.+.+.++|++.. +|+ .|+ ++|++.|=-. +|-. +
T Consensus 78 ~vEvll~~~~~~~~w~al~~~~kr~k~G~~i~f~~~l~a~v~e~~~~g~~~l~F~~~~~~~l~e~L~~~G~~P-LPPYI~ 156 (348)
T COG0809 78 KVEVLLERRLDDNRWLALIKPSKRLKAGDEIYFGDGLKATVLERLEHGLRLLEFDYEGIFSLLELLEKYGEMP-LPPYIK 156 (348)
T ss_pred eEEEEEEeecCCCcEEEEeccccCCCCCCEEEeCCCceEEEEEecCCceEEEEEecCCchhHHHHHHHcCCCC-CCcccC
Confidence 477776552 2457999999999866777776543 332 465 8888866322 4433 3
Q ss_pred CHHHHH--HHHHhhCCHh
Q 025905 201 TIDEGV--QVYRRFYTEE 216 (246)
Q Consensus 201 SiEEgv--~~yr~iYskE 216 (246)
+-.+-. +.|...|+++
T Consensus 157 ~~~~~~d~~~YQTVYak~ 174 (348)
T COG0809 157 RKLDELDRDRYQTVYAKE 174 (348)
T ss_pred CcccccchhhceeeeecC
Confidence 222222 5688899875
No 24
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=55.94 E-value=20 Score=29.26 Aligned_cols=42 Identities=19% Similarity=0.286 Sum_probs=31.8
Q ss_pred HHHhcCCceEEEEccCccccCCCCCCEEEEc---ceEEEEEEEEee
Q 025905 137 TQLKDGLKTVEGRCAVGDYNRIGSGSLILCN---KCLVLKVQDVHG 179 (246)
Q Consensus 137 ~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~---e~l~v~V~~Vr~ 179 (246)
+++.+|+=.|-+... .-=..+|+||.|.+. +.+.++|.++..
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 567888877777766 445678999999974 678888887654
No 25
>KOG4476 consensus Gluconate transport-inducing protein [Signal transduction mechanisms; Carbohydrate transport and metabolism]
Probab=54.89 E-value=9.8 Score=35.49 Aligned_cols=32 Identities=25% Similarity=0.424 Sum_probs=28.8
Q ss_pred hHHHhcCC-ceEEEEccCccccCCCCCCEEEEc
Q 025905 136 FTQLKDGL-KTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 136 F~lIksGk-KTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
|++.+.|. +.||.|+-+++|..|..|++.+|.
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 67778884 789999999999999999999996
No 26
>COG5037 TOS9 Gluconate transport-inducing protein [Signal transduction mechanisms / Carbohydrate transport and metabolism]
Probab=54.89 E-value=9.8 Score=35.49 Aligned_cols=32 Identities=25% Similarity=0.424 Sum_probs=28.8
Q ss_pred hHHHhcCC-ceEEEEccCccccCCCCCCEEEEc
Q 025905 136 FTQLKDGL-KTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 136 F~lIksGk-KTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
|++.+.|. +.||.|+-+++|..|..|++.+|.
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 67778884 789999999999999999999996
No 27
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=54.49 E-value=11 Score=31.61 Aligned_cols=25 Identities=12% Similarity=-0.061 Sum_probs=23.0
Q ss_pred CceEEEEccCccccCCCCCCEEEEc
Q 025905 143 LKTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 143 kKTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
+..+|++...-++.+|++||.+.|.
T Consensus 96 ~yvLEl~~G~~~~~~i~vGd~v~~~ 120 (126)
T COG1430 96 RYVLELPAGWAARLGIKVGDRVEFR 120 (126)
T ss_pred cEEEEecCCchhhcCCccCCEEEec
Confidence 4689999999999999999999984
No 28
>smart00363 S4 S4 RNA-binding domain.
Probab=53.75 E-value=15 Score=23.63 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=23.9
Q ss_pred hhhHHHhcCCceEEEEccCccccCCCCCCEEEEcc
Q 025905 134 PYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNK 168 (246)
Q Consensus 134 ~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e 168 (246)
..-.+|++|.-.|-++..+..-..++.||.|.+..
T Consensus 18 ~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 18 QARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred HHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 34456777866666666534566789999998853
No 29
>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=53.47 E-value=20 Score=24.76 Aligned_cols=29 Identities=14% Similarity=0.221 Sum_probs=23.9
Q ss_pred HhcCCceEEEEccC----ccccCCCCCCEEEEc
Q 025905 139 LKDGLKTVEGRCAV----GDYNRIGSGSLILCN 167 (246)
Q Consensus 139 IksGkKTIE~RLnD----eKrq~IkvGD~I~F~ 167 (246)
|.+|+.+|++++.. ..+..+++||.|.+.
T Consensus 22 l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~ 54 (75)
T PF01336_consen 22 LEDGTGSIQVVFFNEEYERFREKLKEGDIVRVR 54 (75)
T ss_dssp EEETTEEEEEEEETHHHHHHHHTS-TTSEEEEE
T ss_pred EEECCccEEEEEccHHhhHHhhcCCCCeEEEEE
Confidence 56788899999888 677889999999986
No 30
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=50.25 E-value=7.5 Score=31.96 Aligned_cols=53 Identities=9% Similarity=0.097 Sum_probs=46.2
Q ss_pred hhHHHHhhcccceeeeccchhhHHHhcCCceEEEEccCcc-ccCCCCCCEEEEc
Q 025905 115 GSEMIELLKTVNFELHVQEPYFTQLKDGLKTVEGRCAVGD-YNRIGSGSLILCN 167 (246)
Q Consensus 115 g~el~~~~~~~~heM~L~e~yF~lIksGkKTIE~RLnDeK-rq~IkvGD~I~F~ 167 (246)
|...++.+++....+.|.+.+...+.=+.=|-..++.++- -..+++||.|.|+
T Consensus 45 ~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~~~~~l~~lk~G~~V~F~ 98 (115)
T PRK09838 45 GTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFN 98 (115)
T ss_pred EEEEEEEEeCCCCEEEEeecccccCCCCCccccccCCChhhhccCCCCCEEEEE
Confidence 3445778888888999999999999999999999999876 5789999999996
No 31
>smart00350 MCM minichromosome maintenance proteins.
Probab=50.14 E-value=19 Score=35.51 Aligned_cols=44 Identities=11% Similarity=0.108 Sum_probs=35.6
Q ss_pred eeeccchhhHHHhcCC--ceEEEEccCccccCCCCCCEEEEcceEEE
Q 025905 128 ELHVQEPYFTQLKDGL--KTVEGRCAVGDYNRIGSGSLILCNKCLVL 172 (246)
Q Consensus 128 eM~L~e~yF~lIksGk--KTIE~RLnDeKrq~IkvGD~I~F~e~l~v 172 (246)
++.||+.+ +.+-.|. ++|++-|.|+-=..++|||.|.++..+.+
T Consensus 87 ~I~iQE~~-e~~p~G~~Prsi~v~l~~dLvd~~~PGD~V~i~Gi~~~ 132 (509)
T smart00350 87 KIKLQESP-EEVPAGQLPRSVDVILDGDLVDKAKPGDRVEVTGIYRN 132 (509)
T ss_pred EEEEEcCc-ccCCCCCCCcEEEEEEcccccCcccCCCEEEEEEEEEe
Confidence 46677754 6666787 89999999999999999999999865544
No 32
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=47.59 E-value=31 Score=26.76 Aligned_cols=56 Identities=14% Similarity=0.134 Sum_probs=39.8
Q ss_pred cCchhhhhhhhhhhhhhhhhHHHHhhcccceeeeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEcceE
Q 025905 97 EDDDLKKREDWGKLVLKEGSEMIELLKTVNFELHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNKCL 170 (246)
Q Consensus 97 e~~~~~~~~~w~~l~~~~g~el~~~~~~~~heM~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e~l 170 (246)
|-..|.|-=.|..++.. |.+... .|.+|.=+|-+-+-+.++.+|..||.|.|.+..
T Consensus 10 e~I~L~qlLK~~g~i~s-GG~AK~-----------------~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~~ 65 (73)
T COG2501 10 EFITLGQLLKLAGLIES-GGQAKA-----------------FIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQR 65 (73)
T ss_pred ceEEHHHHHHHhCcccC-cHHHHH-----------------HHHCCeEEECCeeeeccCCEeecCCEEEECCEE
Confidence 45555555556666666 666652 477886666667777899999999999998543
No 33
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=46.88 E-value=43 Score=27.36 Aligned_cols=44 Identities=11% Similarity=0.026 Sum_probs=34.2
Q ss_pred HhcCCceEEEEccCccccCCCCCCEEEEc--------ceEEEEEE---EEeecCC
Q 025905 139 LKDGLKTVEGRCAVGDYNRIGSGSLILCN--------KCLVLKVQ---DVHGYLS 182 (246)
Q Consensus 139 IksGkKTIE~RLnDeKrq~IkvGD~I~F~--------e~l~v~V~---~Vr~Y~S 182 (246)
|.+.+-+|.+++-|++...+++||.|.+. .++...|. .|+.-+.
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 45667789999999999999999999985 45666666 4666665
No 34
>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=46.37 E-value=55 Score=24.36 Aligned_cols=51 Identities=18% Similarity=0.208 Sum_probs=39.5
Q ss_pred HhcCCceEEEEccCc-------cccCCCCCCEEEEc-------ceEEEEEEEEeecCCHHHHHhh
Q 025905 139 LKDGLKTVEGRCAVG-------DYNRIGSGSLILCN-------KCLVLKVQDVHGYLSFSEMLQA 189 (246)
Q Consensus 139 IksGkKTIE~RLnDe-------Krq~IkvGD~I~F~-------e~l~v~V~~Vr~Y~SF~eLLe~ 189 (246)
+.+|+.+|++|.-+. ..+.+++|+.|... ++..+.+..++.=+++.++.-+
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 456778899998752 46778999998864 5777788899988888887654
No 35
>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=46.30 E-value=26 Score=26.07 Aligned_cols=30 Identities=20% Similarity=0.242 Sum_probs=19.8
Q ss_pred CCCCCCEEEEcceEEEEE---------EEEeecCCHHHH
Q 025905 157 RIGSGSLILCNKCLVLKV---------QDVHGYLSFSEM 186 (246)
Q Consensus 157 ~IkvGD~I~F~e~l~v~V---------~~Vr~Y~SF~eL 186 (246)
+-++||+|.|.+-+..+| +++..+++|.++
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 457899999974444444 355566777764
No 36
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=45.83 E-value=24 Score=29.23 Aligned_cols=50 Identities=8% Similarity=0.034 Sum_probs=41.0
Q ss_pred HHHhhcccceeeeccchhhHHHhcCCceEEEEccC-ccccCCCCCCEEEEc
Q 025905 118 MIELLKTVNFELHVQEPYFTQLKDGLKTVEGRCAV-GDYNRIGSGSLILCN 167 (246)
Q Consensus 118 l~~~~~~~~heM~L~e~yF~lIksGkKTIE~RLnD-eKrq~IkvGD~I~F~ 167 (246)
.++-.|...-+..|-+++...+.=+.=|.-.|+-| .+..+||.||.|.|.
T Consensus 43 ~VkkvD~~akKVTl~He~i~~l~mp~MTM~F~Vkd~a~lsglKeGdkV~fv 93 (108)
T COG5569 43 VVKKVDLEAKKVTLHHEPIKNLNMPAMTMVFRVKDQAKLSGLKEGDKVEFV 93 (108)
T ss_pred ceeeeccccceEEEeccchhhCCCcceEEEEEeccHHHhhccccCCcEEEE
Confidence 33344555567888888888899999999999998 688999999999996
No 37
>PRK00147 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional
Probab=45.57 E-value=60 Score=31.50 Aligned_cols=60 Identities=25% Similarity=0.358 Sum_probs=37.4
Q ss_pred cCCCCCCEEEEcceEEEEEEEE-------eecC---CHHHHHhhcCccccCCCC-CC--HHHHHHHHHhhCCHh
Q 025905 156 NRIGSGSLILCNKCLVLKVQDV-------HGYL---SFSEMLQAESLAKVLPGI-KT--IDEGVQVYRRFYTEE 216 (246)
Q Consensus 156 q~IkvGD~I~F~e~l~v~V~~V-------r~Y~---SF~eLLe~E~l~kvlPg~-~S--iEEgv~~yr~iYskE 216 (246)
+++++||+|.|.+.+.++|.+. -+|+ ++.++|+..|--- +|-. +. -++-.+.|...|.+.
T Consensus 100 k~~k~G~~l~~~~~~~~~v~~~~~~~~~~~~f~~~~~~~~~l~~~G~~P-lPPYI~r~~~~~D~~~YQTVyA~~ 172 (342)
T PRK00147 100 KRPKPGTKLYFGDGLKAEVLERLEDGGRILRFLYEGIFLELLEELGHMP-LPPYIKRPDEDADRERYQTVYAKE 172 (342)
T ss_pred CCCCCCCEEEECCCeEEEEEEecCCceEEEEEeCCCCHHHHHHhcCCCC-CCcccCCCCcccchhhccccccCC
Confidence 6789999999975566666654 1342 4788888877443 3432 11 112335688888753
No 38
>PRK01424 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional
Probab=42.87 E-value=71 Score=31.48 Aligned_cols=38 Identities=11% Similarity=0.115 Sum_probs=27.4
Q ss_pred cCCCCCCEEEEcceEEEEEEEE-------eec--C--CHHHHHhhcCccc
Q 025905 156 NRIGSGSLILCNKCLVLKVQDV-------HGY--L--SFSEMLQAESLAK 194 (246)
Q Consensus 156 q~IkvGD~I~F~e~l~v~V~~V-------r~Y--~--SF~eLLe~E~l~k 194 (246)
+++++||.|.|.+ +.++|++. -+| + +|.++|+..|--.
T Consensus 92 k~~~~G~~l~~~~-~~~~v~~~~~~g~~~~~f~~~~~~~~~~L~~~G~~P 140 (366)
T PRK01424 92 RKLHVGDEFYFDN-HKVIITEKLAMGEIKVKFELNNISVFEFLDKYGEMP 140 (366)
T ss_pred CCCCCCCEEEECC-eEEEEEEecCCCcEEEEEeCCCCCHHHHHHHcCCCC
Confidence 7788999999965 66777664 134 2 5888999877433
No 39
>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=39.94 E-value=14 Score=24.50 Aligned_cols=30 Identities=20% Similarity=0.263 Sum_probs=25.6
Q ss_pred hhHHHhcCCceEEEEccCccccCCCCCCEE
Q 025905 135 YFTQLKDGLKTVEGRCAVGDYNRIGSGSLI 164 (246)
Q Consensus 135 yF~lIksGkKTIE~RLnDeKrq~IkvGD~I 164 (246)
--.+|++|.=+|-++.-...-..+++||.|
T Consensus 19 a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 19 ARRLIKQGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp HHHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred HHHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence 346899999888888888888899999987
No 40
>COG2028 Uncharacterized conserved protein [Function unknown]
Probab=39.30 E-value=1.2e+02 Score=26.23 Aligned_cols=60 Identities=12% Similarity=0.036 Sum_probs=46.8
Q ss_pred eccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEcc-------eEEEEEEEEeecCCHHHHHhhcCc
Q 025905 130 HVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNK-------CLVLKVQDVHGYLSFSEMLQAESL 192 (246)
Q Consensus 130 ~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e-------~l~v~V~~Vr~Y~SF~eLLe~E~l 192 (246)
-+..+|++-|=.-.|.|=+.-++-+ +++|..++|.. -=.++|..|..|.+-.+.++.+|-
T Consensus 10 pvp~efldrifkegk~vfvkpatl~---vepgMKviFYaSredqGf~GEAeie~Ve~~en~~ei~ekygd 76 (145)
T COG2028 10 PVPKEFLDRIFKEGKDVFVKPATLW---VEPGMKVIFYASREDQGFYGEAEIERVELFENPMEIIEKYGD 76 (145)
T ss_pred CCcHHHHHHHHhcCCceEeecceEE---ecCCcEEEEEEecccCcccceeEEEEEeeecCHHHHHHHhCC
Confidence 3556777777766677767666555 89999999972 245799999999999999999873
No 41
>smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
Probab=37.74 E-value=45 Score=22.43 Aligned_cols=29 Identities=31% Similarity=0.619 Sum_probs=20.8
Q ss_pred hhHHHHHHHHHHHhhccccccccCCCCCHHHHHhhhhc
Q 025905 14 YTKCIEEALKFILESHINQTLELDLGLSKDLCSFLLTH 51 (246)
Q Consensus 14 ~~~~~~e~~~~~l~sh~~~~~~~~l~ls~~~c~~ll~~ 51 (246)
++.|+.|.++|.-+.. +++++.+.+|+.|
T Consensus 7 y~~C~~Ev~~fLs~~~---------~~~~~~~~~Ll~H 35 (45)
T smart00511 7 YRECANEVSRFLSQLP---------GTDPDVRARLLSH 35 (45)
T ss_pred HHHHHHHHHHHHhcCC---------CCChHHHHHHHHH
Confidence 5799999999976221 2345788888874
No 42
>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=37.07 E-value=59 Score=24.24 Aligned_cols=34 Identities=18% Similarity=0.243 Sum_probs=26.7
Q ss_pred eEEEEccCccccCCCCCCEEEEc-ceEEEEEEEEeecC
Q 025905 145 TVEGRCAVGDYNRIGSGSLILCN-KCLVLKVQDVHGYL 181 (246)
Q Consensus 145 TIE~RLnDeKrq~IkvGD~I~F~-e~l~v~V~~Vr~Y~ 181 (246)
.|-+|+... .|++||.+.|. ....++|.+|..+.
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 577787766 67899999996 34678899998774
No 43
>PF11184 DUF2969: Protein of unknown function (DUF2969); InterPro: IPR021351 This family of proteins with unknown function appears to be restricted to Lactobacillales.
Probab=37.04 E-value=31 Score=26.21 Aligned_cols=64 Identities=20% Similarity=0.216 Sum_probs=38.8
Q ss_pred CceEEEEccCccccCCCCCCEEEEcceEEEEEEEEeecCCHHHHHhhcCccccCCCCCCHHHHHHHHHhhC
Q 025905 143 LKTVEGRCAVGDYNRIGSGSLILCNKCLVLKVQDVHGYLSFSEMLQAESLAKVLPGIKTIDEGVQVYRRFY 213 (246)
Q Consensus 143 kKTIE~RLnDeKrq~IkvGD~I~F~e~l~v~V~~Vr~Y~SF~eLLe~E~l~kvlPg~~SiEEgv~~yr~iY 213 (246)
-|.|||++.|.++.. .+|-.+...+.+.-+|.+. =.-| +..... +...-.+|+|+|++..-+-|
T Consensus 5 ~K~IeI~i~d~~~~~-~~~~~l~Igkk~IG~I~e~--d~~f-av~~~~---~~~~~~Ks~deAve~iI~~y 68 (71)
T PF11184_consen 5 NKKIEIEIKDTKVNG-QPGYELFIGKKVIGEIEED--DGRF-AVVKND---NVEFFVKSLDEAVEAIIREY 68 (71)
T ss_pred ccceEEEEEecccCC-eEEEEEEECCEEEEEEEEc--CCcE-EEEeCC---CceEEEcCHHHHHHHHHHHh
Confidence 489999999999832 3344455567777777776 3344 222221 22223368999996654443
No 44
>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=34.73 E-value=49 Score=21.70 Aligned_cols=31 Identities=19% Similarity=0.351 Sum_probs=21.2
Q ss_pred HHHhcCCceEEEEccCccccCCCCCCEEEEc
Q 025905 137 TQLKDGLKTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 137 ~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
.+|++|.=.|-++.....-..+++||.|.+.
T Consensus 21 ~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~ 51 (70)
T cd00165 21 QLIKHGHVLVNGKVVTKPSYKVKPGDVIEVD 51 (70)
T ss_pred HHHHcCCEEECCEEccCCccCcCCCCEEEEc
Confidence 4677776556555554455678899998875
No 45
>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=33.79 E-value=61 Score=29.72 Aligned_cols=36 Identities=11% Similarity=0.087 Sum_probs=29.3
Q ss_pred hhhHHHhcCCceEEEEccCccccCCCCCCEEEEcce
Q 025905 134 PYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNKC 169 (246)
Q Consensus 134 ~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e~ 169 (246)
.--++|++|+=+|-++..+..-.++++||.|.+...
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 445678999988888887777789999999999743
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=33.21 E-value=1.1e+02 Score=29.80 Aligned_cols=60 Identities=10% Similarity=0.233 Sum_probs=34.8
Q ss_pred cCCCCCCEEEEcce----EEEEEEE----Eee--cC---CHHHHHhhcCccccCCCC-CC--HHHHHHHHHhhCCHh
Q 025905 156 NRIGSGSLILCNKC----LVLKVQD----VHG--YL---SFSEMLQAESLAKVLPGI-KT--IDEGVQVYRRFYTEE 216 (246)
Q Consensus 156 q~IkvGD~I~F~e~----l~v~V~~----Vr~--Y~---SF~eLLe~E~l~kvlPg~-~S--iEEgv~~yr~iYskE 216 (246)
+++++|+.|.|.+- +.+.+.+ +-+ |+ +|.++|+..|---. |-. +. -++--+.|...|.+.
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 223 34 58999999774433 432 11 111235688888754
No 47
>PRK06033 hypothetical protein; Validated
Probab=32.81 E-value=49 Score=25.55 Aligned_cols=28 Identities=14% Similarity=0.139 Sum_probs=19.9
Q ss_pred ccccCCCCCCEEEEc----ceEEEEEEEEeec
Q 025905 153 GDYNRIGSGSLILCN----KCLVLKVQDVHGY 180 (246)
Q Consensus 153 eKrq~IkvGD~I~F~----e~l~v~V~~Vr~Y 180 (246)
...-++++||.|.++ +.+.+.|-+...|
T Consensus 23 ~dlL~L~~GDVI~L~~~~~~~v~v~V~~~~~f 54 (83)
T PRK06033 23 HQVLRMGRGAVIPLDATEADEVWILANNHPIA 54 (83)
T ss_pred HHHhCCCCCCEEEeCCCCCCcEEEEECCEEEE
Confidence 345578999999996 4577777666655
No 48
>KOG0432 consensus Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=32.55 E-value=68 Score=35.23 Aligned_cols=69 Identities=26% Similarity=0.373 Sum_probs=46.1
Q ss_pred hhHHHHHHHHHHHhhccccccccCCCCC-----HHHHHhhhh----------cC-CCCCCCCCCCCCc---hhHHHHHHH
Q 025905 14 YTKCIEEALKFILESHINQTLELDLGLS-----KDLCSFLLT----------HN-VPLTAGSSDTESQ---YPLYKRLAS 74 (246)
Q Consensus 14 ~~~~~~e~~~~~l~sh~~~~~~~~l~ls-----~~~c~~ll~----------~~-~~~~~~~~~g~~~---~~l~~~la~ 74 (246)
+..|=-+.|||+|-||..+.=+++|..+ +-||..|-+ ++ .|.++...+|... -=.+-|||.
T Consensus 645 IpeCGtDALRFaL~s~~~~~~dInLDv~rv~g~r~FcNKlWNa~rF~l~~lg~~~~p~~~~~~~~~~~~~d~WIlsrL~~ 724 (995)
T KOG0432|consen 645 IPECGTDALRFALCSYTTQGRDINLDVLRVEGYRHFCNKLWNATRFALQRLGENFVPSPTEDLSGNESLVDEWILSRLAE 724 (995)
T ss_pred CcccchHHHHHHHHHccccCccccccHHHHhhHHHHHHHHHHHHHHHHHhcccCCCCCcccccCCCcchhHHHHHHHHHH
Confidence 4566678999999999988655555543 679988766 22 3556666666532 123788888
Q ss_pred HHHHhHhc
Q 025905 75 VFHESVTS 82 (246)
Q Consensus 75 ~l~~~~~~ 82 (246)
+...|-.+
T Consensus 725 av~~~~~~ 732 (995)
T KOG0432|consen 725 AVEEVNES 732 (995)
T ss_pred HHHHHHhh
Confidence 88776543
No 49
>COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=32.25 E-value=39 Score=36.35 Aligned_cols=28 Identities=7% Similarity=0.094 Sum_probs=24.5
Q ss_pred ccccCCCCCCEEEEc---ceEEEEEEEEeec
Q 025905 153 GDYNRIGSGSLILCN---KCLVLKVQDVHGY 180 (246)
Q Consensus 153 eKrq~IkvGD~I~F~---e~l~v~V~~Vr~Y 180 (246)
.|+-.+|.||+++|+ +.+.++|+.+|+-
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 467789999999998 7899999999874
No 50
>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=32.05 E-value=54 Score=25.37 Aligned_cols=26 Identities=12% Similarity=0.137 Sum_probs=21.5
Q ss_pred cccCCCCCCEEEEcceEEEEEEEEee
Q 025905 154 DYNRIGSGSLILCNKCLVLKVQDVHG 179 (246)
Q Consensus 154 Krq~IkvGD~I~F~e~l~v~V~~Vr~ 179 (246)
-.+.+++||.|+...-+..+|+++..
T Consensus 34 m~~~L~~Gd~VvT~gGi~G~V~~i~d 59 (84)
T TIGR00739 34 LIESLKKGDKVLTIGGIIGTVTKIAE 59 (84)
T ss_pred HHHhCCCCCEEEECCCeEEEEEEEeC
Confidence 34679999999999888888888863
No 51
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=31.57 E-value=57 Score=35.29 Aligned_cols=27 Identities=4% Similarity=0.213 Sum_probs=23.4
Q ss_pred cCCCCCCEEEEc------ceEEEEEEEEeecCC
Q 025905 156 NRIGSGSLILCN------KCLVLKVQDVHGYLS 182 (246)
Q Consensus 156 q~IkvGD~I~F~------e~l~v~V~~Vr~Y~S 182 (246)
+.+|+||+|++. ..+.++-|.|+.|+.
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 468999999996 689999999998875
No 52
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=30.04 E-value=81 Score=27.15 Aligned_cols=25 Identities=12% Similarity=0.001 Sum_probs=22.0
Q ss_pred CceEEEEccCccccCCCCCCEEEEc
Q 025905 143 LKTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 143 kKTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
+-+|++-+-|+.=..|++||.|.|+
T Consensus 47 TgsI~isvW~e~~~~~~PGDIirLt 71 (134)
T KOG3416|consen 47 TGSINISVWDEEGCLIQPGDIIRLT 71 (134)
T ss_pred cceEEEEEecCcCcccCCccEEEec
Confidence 4578888888888999999999996
No 53
>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.
Probab=29.00 E-value=1.2e+02 Score=26.65 Aligned_cols=43 Identities=9% Similarity=0.200 Sum_probs=32.0
Q ss_pred cceeeeccchhhHHHhcCCceEEEEccCcccc--------CCCCCCEEEEc
Q 025905 125 VNFELHVQEPYFTQLKDGLKTVEGRCAVGDYN--------RIGSGSLILCN 167 (246)
Q Consensus 125 ~~heM~L~e~yF~lIksGkKTIE~RLnDeKrq--------~IkvGD~I~F~ 167 (246)
..|.+.+....++.+++|.++|.++.+|-... .+.+.|.|+|.
T Consensus 60 ~~~d~~~l~~~L~~l~~g~~~v~~P~yd~~~~~~~~~~~~~~~~~~vvIvE 110 (220)
T cd02025 60 ESYDMEALLKFLKDIKSGKKNVKIPVYSHLTYDVIPGEKQTVDQPDILIIE 110 (220)
T ss_pred ccCCHHHHHHHHHHHHCCCCcEEccccceeccccCCCCceecCCCCEEEEC
Confidence 45666777889999999988999998885543 25566777765
No 54
>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=27.35 E-value=44 Score=24.33 Aligned_cols=26 Identities=19% Similarity=0.358 Sum_probs=14.8
Q ss_pred CccccCCCCCCEEEEc----ceEEEEEEEE
Q 025905 152 VGDYNRIGSGSLILCN----KCLVLKVQDV 177 (246)
Q Consensus 152 DeKrq~IkvGD~I~F~----e~l~v~V~~V 177 (246)
-.+..++++||.|.++ +.+.+.|-+.
T Consensus 23 l~el~~L~~Gdvi~l~~~~~~~v~l~v~g~ 52 (77)
T PF01052_consen 23 LGELLNLKVGDVIPLDKPADEPVELRVNGQ 52 (77)
T ss_dssp HHHHHC--TT-EEEECCESSTEEEEEETTE
T ss_pred HHHHhcCCCCCEEEeCCCCCCCEEEEECCE
Confidence 3566789999999996 3455555433
No 55
>COG1868 FliM Flagellar motor switch protein [Cell motility and secretion]
Probab=27.16 E-value=84 Score=30.32 Aligned_cols=34 Identities=15% Similarity=0.194 Sum_probs=27.1
Q ss_pred EEccCccccCCCCCCEEEEc----ceEEEEEEEEeecC
Q 025905 148 GRCAVGDYNRIGSGSLILCN----KCLVLKVQDVHGYL 181 (246)
Q Consensus 148 ~RLnDeKrq~IkvGD~I~F~----e~l~v~V~~Vr~Y~ 181 (246)
++|.-.+.-++++||.|.|+ +.+.+.|.+..+|.
T Consensus 264 ~~ltl~~il~L~vGDVI~l~~~~~d~v~v~v~g~~~f~ 301 (332)
T COG1868 264 ISLTLREILRLEVGDVIPLEKPADDRVTVSVGGKPKFL 301 (332)
T ss_pred ceeeHHHHhCCCCCcEEECCCCCCceEEEEECCEEEEE
Confidence 34444778899999999997 67888998888873
No 56
>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=26.02 E-value=59 Score=24.26 Aligned_cols=28 Identities=29% Similarity=0.318 Sum_probs=19.7
Q ss_pred ccccCCCCCCEEEEc----ceEEEEEEEEeec
Q 025905 153 GDYNRIGSGSLILCN----KCLVLKVQDVHGY 180 (246)
Q Consensus 153 eKrq~IkvGD~I~F~----e~l~v~V~~Vr~Y 180 (246)
...-++++||.|.++ +.+.+.|-+...|
T Consensus 24 ~ell~L~~Gdvi~L~~~~~~~v~l~v~g~~~~ 55 (77)
T TIGR02480 24 GDLLKLGEGSVIELDKLAGEPLDILVNGRLIA 55 (77)
T ss_pred HHHhcCCCCCEEEcCCCCCCcEEEEECCEEEE
Confidence 456788999999986 4566666555544
No 57
>PRK03760 hypothetical protein; Provisional
Probab=25.89 E-value=53 Score=26.84 Aligned_cols=24 Identities=17% Similarity=0.076 Sum_probs=21.2
Q ss_pred ceEEEEccCccccCCCCCCEEEEc
Q 025905 144 KTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 144 KTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
-.+|+.-..-.+..|++||.|.|.
T Consensus 92 ~VLEl~aG~~~~~gi~~Gd~v~~~ 115 (117)
T PRK03760 92 YIIEGPVGKIRVLKVEVGDEIEWI 115 (117)
T ss_pred EEEEeCCChHHHcCCCCCCEEEEe
Confidence 378988888899999999999985
No 58
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=25.50 E-value=76 Score=25.67 Aligned_cols=43 Identities=19% Similarity=0.245 Sum_probs=29.7
Q ss_pred hhHHHhcCCceEEEEccCccccCCCCCCEEEEcceEEEEEEEEee
Q 025905 135 YFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNKCLVLKVQDVHG 179 (246)
Q Consensus 135 yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e~l~v~V~~Vr~ 179 (246)
||-+|+..+|.-. -..+-++.+++||.|+...=+..+|++|..
T Consensus 32 yf~~~RpqkK~~k--~~~~~~~~Lk~Gd~VvT~gGi~G~Vv~i~~ 74 (106)
T PRK05585 32 YFLIIRPQQKRQK--EHKKMLSSLAKGDEVVTNGGIIGKVTKVSE 74 (106)
T ss_pred HHHhccHHHHHHH--HHHHHHHhcCCCCEEEECCCeEEEEEEEeC
Confidence 4556655554432 224556789999999998888888888753
No 59
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=25.17 E-value=78 Score=26.03 Aligned_cols=42 Identities=7% Similarity=0.143 Sum_probs=26.2
Q ss_pred hhHHHhcCCceEEEEccCccccCCCCCCEEEEcceEEEEEEEEe
Q 025905 135 YFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCNKCLVLKVQDVH 178 (246)
Q Consensus 135 yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~e~l~v~V~~Vr 178 (246)
||-+|+--+|.-. --.+-++.+++||.|+...=+..+|++|.
T Consensus 18 yF~~iRPQkKr~K--~~~~m~~~Lk~GD~VvT~gGi~G~V~~I~ 59 (109)
T PRK05886 18 MYFASRRQRKAMQ--ATIDLHESLQPGDRVHTTSGLQATIVGIT 59 (109)
T ss_pred HHHHccHHHHHHH--HHHHHHHhcCCCCEEEECCCeEEEEEEEe
Confidence 4555555554311 00123468999999999877777777765
No 60
>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=24.61 E-value=64 Score=26.99 Aligned_cols=26 Identities=8% Similarity=0.023 Sum_probs=21.1
Q ss_pred CCceEEEEccCccc---cCCCCCCEEEEc
Q 025905 142 GLKTVEGRCAVGDY---NRIGSGSLILCN 167 (246)
Q Consensus 142 GkKTIE~RLnDeKr---q~IkvGD~I~F~ 167 (246)
|+.||+|=|+|+.. +.+|+||.|.+.
T Consensus 58 g~~ti~It~yD~H~~~ar~lK~GdfV~L~ 86 (123)
T cd04498 58 KQLTIDILVYDNHVELAKSLKPGDFVRIY 86 (123)
T ss_pred CeEEEEEEEEcchHHHHhhCCCCCEEEEE
Confidence 67899999999653 238999999985
No 61
>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=24.16 E-value=1.2e+02 Score=24.15 Aligned_cols=38 Identities=13% Similarity=0.073 Sum_probs=21.1
Q ss_pred hcCCceEEEEccCccccCCCCCCEEEEc---------ceEEEEEEEEeec
Q 025905 140 KDGLKTVEGRCAVGDYNRIGSGSLILCN---------KCLVLKVQDVHGY 180 (246)
Q Consensus 140 ksGkKTIE~RLnDeKrq~IkvGD~I~F~---------e~l~v~V~~Vr~Y 180 (246)
.++..++-|+|-+. .|.+||.|.|. +...+.|.+-..|
T Consensus 13 a~n~~~ati~l~~H---Gl~vGD~VnFsnsa~tGvSG~mTVatVid~ntF 59 (83)
T PF12195_consen 13 AANQTTATITLTDH---GLFVGDFVNFSNSAVTGVSGNMTVATVIDANTF 59 (83)
T ss_dssp -TTSSEEEEE-TT-------TT-EEEEES-SSTT--EEEEEEEEEETTEE
T ss_pred ecCceEEEEEEccC---ceeecceEEEeccccccccccEEEEEEecCCcE
Confidence 35667888888774 78999999995 3444556554443
No 62
>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=23.94 E-value=1e+02 Score=24.32 Aligned_cols=45 Identities=11% Similarity=-0.058 Sum_probs=29.3
Q ss_pred EEEEccCccccC-CCCCCEEEEcceEE--------EEEEEEeecCCHHHHHhhc
Q 025905 146 VEGRCAVGDYNR-IGSGSLILCNKCLV--------LKVQDVHGYLSFSEMLQAE 190 (246)
Q Consensus 146 IE~RLnDeKrq~-IkvGD~I~F~e~l~--------v~V~~Vr~Y~SF~eLLe~E 190 (246)
|+|++.|+.... -..+-.+.|.=.+. ....=-|+|..|..|.++.
T Consensus 1 ~~i~V~dP~~~~~~~~~~y~~Y~I~~~t~~~~~~~~~~~V~RRYsdF~~L~~~L 54 (118)
T cd06863 1 LECLVSDPQKELDGSSDTYISYLITTKTNLPSFSRKEFKVRRRYSDFVFLHECL 54 (118)
T ss_pred CEEEEeCcccccCCCccCEEEEEEEEeeCCCCcccCceEEEecHHHHHHHHHHH
Confidence 467777876654 44566677752221 2345568999999998873
No 63
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=23.47 E-value=44 Score=26.49 Aligned_cols=26 Identities=12% Similarity=-0.079 Sum_probs=17.9
Q ss_pred CCceEEEEccCccccCCCCCCEEEEc
Q 025905 142 GLKTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 142 GkKTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
.+-.+|++-..-++-.|++||.|.|.
T Consensus 82 a~~vLE~~aG~~~~~~i~~Gd~v~~~ 107 (108)
T PF02643_consen 82 ARYVLELPAGWFEKLGIKVGDRVRIE 107 (108)
T ss_dssp ECEEEEEETTHHHHHT--TT-EEE--
T ss_pred cCEEEEcCCCchhhcCCCCCCEEEec
Confidence 45688988888889999999999874
No 64
>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=23.43 E-value=1.3e+02 Score=22.12 Aligned_cols=28 Identities=14% Similarity=0.115 Sum_probs=19.5
Q ss_pred HHhcCCceEEEEccCccccCCCCCCEEEEc
Q 025905 138 QLKDGLKTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 138 lIksGkKTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
.|-+|. +++.-.+.....+++||.+.|-
T Consensus 30 ~vleG~--v~it~~~G~~~~~~aGD~~~~p 57 (74)
T PF05899_consen 30 YVLEGE--VTITDEDGETVTFKAGDAFFLP 57 (74)
T ss_dssp EEEEEE--EEEEETTTEEEEEETTEEEEE-
T ss_pred EEEEeE--EEEEECCCCEEEEcCCcEEEEC
Confidence 344453 3344458889999999999996
No 65
>PF13437 HlyD_3: HlyD family secretion protein
Probab=22.80 E-value=1.6e+02 Score=22.01 Aligned_cols=36 Identities=25% Similarity=0.221 Sum_probs=29.5
Q ss_pred ceEEEEccCccccCCC-CCCEEEEc------ceEEEEEEEEee
Q 025905 144 KTVEGRCAVGDYNRIG-SGSLILCN------KCLVLKVQDVHG 179 (246)
Q Consensus 144 KTIE~RLnDeKrq~Ik-vGD~I~F~------e~l~v~V~~Vr~ 179 (246)
=.+++.+......+|+ +|+.+.+. ..+..+|..|..
T Consensus 36 ~~v~~~v~~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 36 LWVEAYVPEKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred EEEEEEEChHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 3578888889999998 99999985 468888888877
No 66
>COG5471 Uncharacterized conserved protein [Function unknown]
Probab=22.74 E-value=1.4e+02 Score=24.87 Aligned_cols=36 Identities=28% Similarity=0.296 Sum_probs=29.2
Q ss_pred CceEEEEccCccccCCCCCCEEEEcceEEEEEEEEeecCC
Q 025905 143 LKTVEGRCAVGDYNRIGSGSLILCNKCLVLKVQDVHGYLS 182 (246)
Q Consensus 143 kKTIE~RLnDeKrq~IkvGD~I~F~e~l~v~V~~Vr~Y~S 182 (246)
-||||+--. +.|+.||.+.|-+.+-|-++++..=++
T Consensus 9 gktveiva~----~~i~SGd~VlvG~~f~VA~td~~AG~~ 44 (107)
T COG5471 9 GKTVEIVAP----AAIKSGDLVLVGDMFAVALTDIPAGEA 44 (107)
T ss_pred CCEEEEecc----cccccCCEEEEeeeEEEEEecccCccc
Confidence 378888654 899999999999999888888765443
No 67
>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=22.17 E-value=89 Score=22.83 Aligned_cols=27 Identities=11% Similarity=0.070 Sum_probs=21.8
Q ss_pred cCCceEEEEccCcc-ccCCCCCCEEEEc
Q 025905 141 DGLKTVEGRCAVGD-YNRIGSGSLILCN 167 (246)
Q Consensus 141 sGkKTIE~RLnDeK-rq~IkvGD~I~F~ 167 (246)
+.+-+|.+++=++. ...+++||.|.+.
T Consensus 31 D~TG~i~~~~W~~~~~~~~~~G~vv~i~ 58 (82)
T cd04491 31 DETGTIRFTLWDEKAADDLEPGDVVRIE 58 (82)
T ss_pred CCCCEEEEEEECchhcccCCCCCEEEEE
Confidence 34457888888877 8899999999986
No 68
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=21.84 E-value=1.4e+02 Score=27.82 Aligned_cols=34 Identities=12% Similarity=0.154 Sum_probs=28.1
Q ss_pred hhhHHHhcCCceEEEEccCccccCCCCCCEEEEc
Q 025905 134 PYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 134 ~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
+--++|++|+=+|-.+....+-..+++||.|...
T Consensus 208 k~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiR 241 (267)
T PLN00051 208 KLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVS 241 (267)
T ss_pred HHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEe
Confidence 4457899999888888777777899999999985
No 69
>COG2820 Udp Uridine phosphorylase [Nucleotide transport and metabolism]
Probab=21.26 E-value=1.1e+02 Score=28.83 Aligned_cols=33 Identities=21% Similarity=0.343 Sum_probs=25.3
Q ss_pred HHHhcCCceEEEEccC-cccc-CCCCCCEEEEcceE
Q 025905 137 TQLKDGLKTVEGRCAV-GDYN-RIGSGSLILCNKCL 170 (246)
Q Consensus 137 ~lIksGkKTIE~RLnD-eKrq-~IkvGD~I~F~e~l 170 (246)
++.+.|.||+ ||+-. .-.| .|.+||.|+=+..+
T Consensus 78 EL~~lGa~tf-iRVGT~Galq~~i~~Gdvvi~tgAv 112 (248)
T COG2820 78 ELARLGAKTF-IRVGTTGALQPDINVGDVVVATGAV 112 (248)
T ss_pred HHHhcCCeEE-EEeeccccccCCCCCCCEEEecccc
Confidence 4566799999 99998 3333 69999999976444
No 70
>PF06415 iPGM_N: BPG-independent PGAM N-terminus (iPGM_N); InterPro: IPR011258 This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (5.4.2.1 from EC). The family is found in conjunction with Metalloenzyme (located in the C-terminal region of the protein). ; GO: 0004619 phosphoglycerate mutase activity, 0030145 manganese ion binding, 0006007 glucose catabolic process, 0005737 cytoplasm; PDB: 1EQJ_A 1EJJ_A 1O99_A 1O98_A 3IGZ_B 3IGY_B 3NVL_A 2IFY_A.
Probab=21.23 E-value=58 Score=29.76 Aligned_cols=63 Identities=14% Similarity=0.336 Sum_probs=27.0
Q ss_pred ccCchhhh-hhhhhhhhhhhhh-HHHHhhcccc--eeeeccchhhHHHhcCCceEEEEccCccccCCCCCCEEEEc
Q 025905 96 NEDDDLKK-REDWGKLVLKEGS-EMIELLKTVN--FELHVQEPYFTQLKDGLKTVEGRCAVGDYNRIGSGSLILCN 167 (246)
Q Consensus 96 ~e~~~~~~-~~~w~~l~~~~g~-el~~~~~~~~--heM~L~e~yF~lIksGkKTIE~RLnDeKrq~IkvGD~I~F~ 167 (246)
+-|.+|.+ +..|+.++.+.|. .-.++...++ |.=++.+++.. =..+.+..+..|+.||.|+|.
T Consensus 109 DRD~rWeRv~~Ay~alv~g~g~~~~~~~~~ai~~~Y~~g~tDEFi~---------P~vi~~~~~~~i~dgD~vif~ 175 (223)
T PF06415_consen 109 DRDKRWERVEKAYDALVNGEGPNKFDDALEAIEASYARGITDEFIP---------PTVISDKPYGGIKDGDAVIFF 175 (223)
T ss_dssp --TS-HHHHHHHHHHHCT--SE-EESSHHHHHHHHHHTT--GGG------------EEEB-SBS----TT-EEEE-
T ss_pred ccccCHHHHHHHHHHHhcCccccccCCHHHHHHHHHcCCCCCcCCC---------CEEecCCCCCCccCCCEEEEE
Confidence 67888999 9999999999887 1111111110 11122222221 223333678999999999984
No 71
>PRK08433 flagellar motor switch protein; Validated
Probab=20.20 E-value=1.1e+02 Score=25.21 Aligned_cols=28 Identities=14% Similarity=0.025 Sum_probs=20.5
Q ss_pred ccccCCCCCCEEEEc----ceEEEEEEEEeec
Q 025905 153 GDYNRIGSGSLILCN----KCLVLKVQDVHGY 180 (246)
Q Consensus 153 eKrq~IkvGD~I~F~----e~l~v~V~~Vr~Y 180 (246)
...-++++||.|.++ +.+.+.|-++..|
T Consensus 48 ~dlL~Lq~GDVI~Ld~~~~e~v~v~V~g~~~f 79 (111)
T PRK08433 48 LEILKFEKGSVIDLEKPAGESVELYINGRIIG 79 (111)
T ss_pred HHHhCCCCCCEEEeCCCCCCCEEEEECCEEEE
Confidence 345578999999997 3577777666655
Done!