Query 044581
Match_columns 203
No_of_seqs 115 out of 260
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 04:43:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044581.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044581hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4315 G-patch nucleic acid b 99.9 1.3E-28 2.7E-33 226.9 5.3 122 82-203 331-455 (455)
2 KOG2837 Protein containing a U 99.0 1.5E-11 3.2E-16 109.5 -5.3 62 90-160 247-308 (309)
3 KOG1999 RNA polymerase II tran 98.8 6.6E-09 1.4E-13 104.6 5.1 110 81-196 914-1023(1024)
4 PF00467 KOW: KOW motif; Inte 97.3 0.00044 9.6E-09 42.7 4.2 31 145-175 1-31 (32)
5 smart00739 KOW KOW (Kyprides, 96.7 0.0031 6.6E-08 36.7 3.8 26 143-168 2-27 (28)
6 PRK12281 rplX 50S ribosomal pr 96.5 0.0055 1.2E-07 45.2 4.8 33 144-176 8-40 (76)
7 CHL00141 rpl24 ribosomal prote 96.4 0.0059 1.3E-07 45.8 4.8 33 144-176 10-42 (83)
8 PRK00004 rplX 50S ribosomal pr 96.0 0.013 2.8E-07 45.6 4.8 33 144-176 6-38 (105)
9 TIGR00405 L26e_arch ribosomal 95.9 0.022 4.8E-07 45.6 5.8 52 143-194 87-140 (145)
10 PRK01191 rpl24p 50S ribosomal 95.7 0.019 4.2E-07 46.0 5.0 33 144-176 47-79 (120)
11 TIGR01079 rplX_bact ribosomal 95.6 0.021 4.5E-07 44.5 4.7 33 144-176 5-37 (104)
12 TIGR01080 rplX_A_E ribosomal p 95.6 0.022 4.7E-07 45.2 4.6 39 138-176 37-75 (114)
13 PRK08559 nusG transcription an 95.2 0.061 1.3E-06 43.9 6.2 50 143-192 95-146 (153)
14 PTZ00194 60S ribosomal protein 95.2 0.034 7.3E-07 45.9 4.6 33 144-176 48-80 (143)
15 TIGR00922 nusG transcription t 95.0 0.063 1.4E-06 43.8 5.8 49 143-191 120-170 (172)
16 PRK04313 30S ribosomal protein 94.4 0.56 1.2E-05 41.6 10.7 52 132-184 160-216 (237)
17 PRK05609 nusG transcription an 94.1 0.14 2.9E-06 42.0 5.9 51 143-193 127-179 (181)
18 COG0250 NusG Transcription ant 94.0 0.13 2.9E-06 43.4 5.6 54 141-194 122-177 (178)
19 TIGR01955 RfaH transcriptional 92.5 0.34 7.3E-06 38.9 5.7 48 143-191 109-158 (159)
20 COG0198 RplX Ribosomal protein 92.5 0.22 4.7E-06 39.1 4.3 31 144-176 6-36 (104)
21 PLN00036 40S ribosomal protein 92.4 1.7 3.7E-05 39.1 10.4 37 132-168 163-200 (261)
22 COG5164 SPT5 Transcription elo 92.3 0.49 1.1E-05 46.0 7.3 55 143-199 352-406 (607)
23 PRK09014 rfaH transcriptional 92.3 0.34 7.3E-06 39.3 5.5 50 143-193 110-161 (162)
24 PTZ00118 40S ribosomal protein 91.8 1.6 3.4E-05 39.4 9.5 39 130-168 161-200 (262)
25 KOG1999 RNA polymerase II tran 90.8 1.7 3.7E-05 45.3 9.7 81 85-175 408-490 (1024)
26 TIGR01956 NusG_myco NusG famil 90.6 0.7 1.5E-05 41.5 6.1 49 143-191 206-256 (258)
27 PTZ00223 40S ribosomal protein 89.9 2.6 5.6E-05 38.2 9.1 37 132-168 160-197 (273)
28 PF11623 DUF3252: Protein of u 89.1 1.2 2.5E-05 31.1 4.9 52 85-139 2-53 (53)
29 PF15591 Imm17: Immunity prote 86.3 1.4 3.1E-05 32.6 4.3 50 90-140 10-63 (74)
30 COG1471 RPS4A Ribosomal protei 78.7 5 0.00011 35.8 5.5 38 132-169 162-200 (241)
31 PRK08559 nusG transcription an 78.0 8.3 0.00018 31.4 6.3 54 85-144 95-151 (153)
32 TIGR00405 L26e_arch ribosomal 76.0 8.8 0.00019 30.5 5.9 55 83-143 85-142 (145)
33 PF12656 G-patch_2: DExH-box s 74.3 1.7 3.6E-05 32.1 1.1 21 1-21 45-65 (77)
34 smart00743 Agenet Tudor-like d 74.2 14 0.00031 24.8 5.8 53 87-144 5-59 (61)
35 smart00333 TUDOR Tudor domain. 70.5 21 0.00046 23.3 5.8 53 86-144 4-56 (57)
36 PRK14639 hypothetical protein; 70.4 14 0.00031 29.9 5.9 52 141-194 83-134 (140)
37 PTZ00065 60S ribosomal protein 66.0 19 0.00041 29.4 5.6 52 84-140 7-59 (130)
38 COG2163 RPL14A Ribosomal prote 65.6 16 0.00034 29.6 5.1 35 85-124 5-39 (125)
39 smart00333 TUDOR Tudor domain. 64.3 37 0.00081 22.1 6.2 53 142-195 2-54 (57)
40 PLN00045 photosystem I reactio 63.2 12 0.00025 29.3 3.7 44 136-179 33-81 (101)
41 TIGR01955 RfaH transcriptional 63.1 15 0.00032 29.3 4.6 53 82-139 106-159 (159)
42 COG5164 SPT5 Transcription elo 63.1 11 0.00024 37.0 4.4 44 88-138 355-398 (607)
43 PRK04333 50S ribosomal protein 58.7 29 0.00062 26.0 5.2 31 86-121 5-35 (84)
44 PF02736 Myosin_N: Myosin N-te 58.1 39 0.00084 21.8 5.1 30 158-190 13-42 (42)
45 PF01176 eIF-1a: Translation i 55.6 41 0.0009 23.5 5.3 58 107-164 6-63 (65)
46 cd01734 YlxS_C YxlS is a Bacil 55.2 39 0.00085 24.6 5.4 50 143-194 22-77 (83)
47 KOG1708 Mitochondrial/chloropl 52.5 20 0.00044 31.6 3.9 32 145-176 75-106 (236)
48 cd04508 TUDOR Tudor domains ar 51.4 25 0.00054 22.2 3.4 36 100-138 11-46 (48)
49 TIGR00922 nusG transcription t 50.9 36 0.00079 27.5 5.0 53 82-139 117-171 (172)
50 PRK05609 nusG transcription an 50.8 41 0.00088 27.3 5.3 54 82-140 124-179 (181)
51 PF02427 PSI_PsaE: Photosystem 45.6 50 0.0011 23.7 4.3 49 143-191 1-57 (61)
52 PTZ00471 60S ribosomal protein 45.0 29 0.00063 28.5 3.5 77 84-167 4-90 (134)
53 PRK05585 yajC preprotein trans 44.5 94 0.002 24.1 6.2 46 144-196 54-99 (106)
54 PRK14630 hypothetical protein; 44.0 81 0.0018 25.6 6.0 47 143-194 94-140 (143)
55 PRK14637 hypothetical protein; 43.2 86 0.0019 25.8 6.1 46 145-194 97-143 (151)
56 PRK09014 rfaH transcriptional 42.8 58 0.0012 26.2 5.0 52 84-140 109-161 (162)
57 PRK14631 hypothetical protein; 40.7 86 0.0019 26.4 5.9 53 141-194 112-168 (174)
58 TIGR02760 TraI_TIGR conjugativ 39.1 2.5E+02 0.0055 32.1 10.6 98 84-190 681-796 (1960)
59 PRK14638 hypothetical protein; 37.0 1E+02 0.0022 25.2 5.6 48 143-194 97-144 (150)
60 PRK00092 ribosome maturation p 36.6 95 0.0021 25.2 5.4 51 142-194 94-148 (154)
61 CHL00010 infA translation init 36.5 1.7E+02 0.0036 21.3 8.5 64 106-169 9-73 (78)
62 PRK14633 hypothetical protein; 36.3 1.1E+02 0.0025 24.9 5.8 48 144-194 92-143 (150)
63 PF08863 YolD: YolD-like prote 35.3 75 0.0016 22.7 4.2 40 153-193 52-91 (92)
64 COG1588 POP4 RNase P/RNase MRP 35.0 2.2E+02 0.0047 22.2 7.0 35 87-124 16-50 (95)
65 TIGR00739 yajC preprotein tran 34.7 1.4E+02 0.0031 22.1 5.6 42 145-193 40-81 (84)
66 PRK04333 50S ribosomal protein 34.5 73 0.0016 23.9 4.0 30 145-175 6-35 (84)
67 PRK13889 conjugal transfer rel 34.4 79 0.0017 33.6 5.6 46 143-191 601-651 (988)
68 PF02576 DUF150: Uncharacteris 32.4 1.2E+02 0.0026 24.1 5.2 47 146-194 87-139 (141)
69 PF06003 SMN: Survival motor n 32.2 1.7E+02 0.0037 26.1 6.6 53 144-196 70-123 (264)
70 PF15057 DUF4537: Domain of un 32.0 2.5E+02 0.0055 22.1 9.2 96 93-193 4-111 (124)
71 PRK14712 conjugal transfer nic 31.8 4.5E+02 0.0098 29.8 10.8 98 86-190 518-629 (1623)
72 PRK14645 hypothetical protein; 31.7 1.2E+02 0.0026 25.0 5.3 47 143-194 99-145 (154)
73 PRK13709 conjugal transfer nic 31.5 5.8E+02 0.012 29.2 11.7 99 84-190 648-761 (1747)
74 PRK02001 hypothetical protein; 31.0 1.6E+02 0.0035 24.2 5.9 50 143-194 87-148 (152)
75 PRK04950 ProP expression regul 30.8 1.2E+02 0.0027 26.6 5.4 44 144-191 168-211 (213)
76 PRK14635 hypothetical protein; 30.7 1.2E+02 0.0027 25.0 5.2 47 146-194 99-156 (162)
77 PRK04012 translation initiatio 30.1 2.6E+02 0.0056 21.6 7.6 28 100-130 20-47 (100)
78 PRK14640 hypothetical protein; 30.0 1.6E+02 0.0035 24.0 5.7 48 143-194 94-145 (152)
79 PTZ00471 60S ribosomal protein 29.5 91 0.002 25.6 4.1 25 145-169 7-31 (134)
80 cd04456 S1_IF1A_like S1_IF1A_l 28.8 2.4E+02 0.0051 20.7 7.4 44 108-151 4-47 (78)
81 cd05793 S1_IF1A S1_IF1A: Trans 27.9 2.4E+02 0.0052 20.5 7.4 21 107-127 3-23 (77)
82 TIGR00523 eIF-1A eukaryotic/ar 27.9 2.8E+02 0.0061 21.3 6.6 36 88-128 8-43 (99)
83 PRK14646 hypothetical protein; 27.8 1.8E+02 0.0039 23.9 5.6 48 143-194 97-148 (155)
84 COG0779 Uncharacterized protei 27.7 2E+02 0.0043 23.9 5.9 46 145-194 98-147 (153)
85 PF03947 Ribosomal_L2_C: Ribos 26.9 1.3E+02 0.0029 24.1 4.6 35 156-193 34-68 (130)
86 PRK02749 photosystem I reactio 26.6 1.1E+02 0.0023 22.6 3.6 35 144-178 4-42 (71)
87 TIGR02768 TraA_Ti Ti-type conj 26.4 1.5E+02 0.0032 30.2 5.8 45 144-191 609-658 (744)
88 PRK05886 yajC preprotein trans 26.2 2.5E+02 0.0055 22.1 5.9 46 144-196 40-85 (109)
89 PF12073 DUF3553: Protein of u 26.1 2.1E+02 0.0046 19.9 4.8 50 85-141 1-50 (52)
90 CHL00125 psaE photosystem I su 26.1 1.2E+02 0.0026 22.0 3.7 36 144-179 3-42 (64)
91 PRK00004 rplX 50S ribosomal pr 25.7 2.2E+02 0.0048 21.9 5.5 26 85-115 5-30 (105)
92 PF07076 DUF1344: Protein of u 25.4 1.2E+02 0.0026 21.8 3.6 28 159-189 5-32 (61)
93 PF04319 NifZ: NifZ domain; I 25.2 1.6E+02 0.0034 21.9 4.3 53 88-141 8-75 (75)
94 PRK14643 hypothetical protein; 24.4 2E+02 0.0043 23.9 5.4 49 144-194 102-158 (164)
95 PRK04306 50S ribosomal protein 24.1 1.1E+02 0.0023 23.8 3.4 38 156-193 58-95 (98)
96 PRK14636 hypothetical protein; 24.0 2.4E+02 0.0052 23.7 5.8 49 143-194 95-147 (176)
97 PRK14647 hypothetical protein; 24.0 2.4E+02 0.0052 23.1 5.8 49 143-194 96-153 (159)
98 COG2139 RPL21A Ribosomal prote 24.0 1.2E+02 0.0026 23.7 3.6 40 156-195 56-95 (98)
99 PRK14634 hypothetical protein; 23.8 2.1E+02 0.0046 23.5 5.4 47 144-194 98-148 (155)
100 PRK06531 yajC preprotein trans 23.8 3.3E+02 0.0071 21.6 6.2 46 145-196 39-84 (113)
101 PLN00208 translation initiatio 23.4 4.3E+02 0.0094 21.9 8.1 64 100-166 31-94 (145)
102 PF14509 GH97_C: Glycosyl-hydr 23.0 3.1E+02 0.0068 21.0 5.9 45 148-193 5-51 (103)
103 PF01455 HupF_HypC: HupF/HypC 22.8 2.1E+02 0.0045 20.4 4.5 43 107-154 6-49 (68)
104 PTZ00329 eukaryotic translatio 22.6 4.6E+02 0.01 22.0 7.9 64 100-166 31-94 (155)
105 PF14563 DUF4444: Domain of un 22.3 2.1E+02 0.0045 19.1 4.0 34 156-192 7-40 (42)
106 PTZ00065 60S ribosomal protein 22.2 1.6E+02 0.0036 24.0 4.3 31 146-177 11-41 (130)
107 COG1862 YajC Preprotein transl 21.9 3.2E+02 0.007 21.0 5.7 45 144-195 45-89 (97)
108 PRK00276 infA translation init 21.3 3.1E+02 0.0067 19.4 7.9 24 141-164 45-68 (72)
109 COG2163 RPL14A Ribosomal prote 21.0 1.7E+02 0.0037 23.6 4.2 27 144-170 6-32 (125)
110 smart00443 G_patch glycine ric 20.9 70 0.0015 20.7 1.6 20 1-20 19-38 (47)
111 PRK14632 hypothetical protein; 20.7 3.1E+02 0.0067 22.9 5.9 49 144-194 96-157 (172)
112 PF00567 TUDOR: Tudor domain; 20.5 2E+02 0.0044 20.4 4.3 57 82-145 51-107 (121)
No 1
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=99.95 E-value=1.3e-28 Score=226.94 Aligned_cols=122 Identities=60% Similarity=1.027 Sum_probs=116.4
Q ss_pred CCcccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCceEec-cccCceeeecCCCCC-cEEEEeccccCc
Q 044581 82 VPWLRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQG-VDQDLLETALPRRGG-PVLVLYGRHKGV 159 (203)
Q Consensus 82 ~~Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~-V~q~~LETVIPk~g~-~V~VV~G~~rG~ 159 (203)
..|++++|.|||+|+.|++|+||.+|++|.+|.++.+|+|.++++++.++. |.|++|||++|+.++ +|||+.|+|.|+
T Consensus 331 k~wlR~dl~VR~is~d~Kgg~ly~~K~~i~dv~gp~scd~r~Dedq~~~qg~irq~~lET~~pr~~Ge~vmvv~gkhkg~ 410 (455)
T KOG4315|consen 331 KSWLRSDLKVRFISKDVKGGRLYEKKVRIVDVVGPTSCDIRMDEDQELVQGNIRQELLETALPRRGGEKVMVVSGKHKGV 410 (455)
T ss_pred chhhhcceeEEeeccccccchhhhcccceecccCCCccceeccccccccccchHHHHHhhhcccccCceeEEEecccccc
Confidence 489999999999999999999999999999999999999999998988988 999999999999876 599999999999
Q ss_pred EEEEEEeeCCCceEEEEECCCCcEEEeeccchhcccC-CCCCCCC
Q 044581 160 YGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYIG-DPSYLGY 203 (203)
Q Consensus 160 ~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~g-~~~~~~~ 203 (203)
+|.|+++|.++.+++|++..+++++.+.||+||+|.| +.+|.+|
T Consensus 411 ~g~llskd~~Ke~~~v~~~a~ndvv~~~~D~v~ey~grh~~d~~~ 455 (455)
T KOG4315|consen 411 YGSLLSKDLDKETGVVRLVATNDVVTVYLDQVCEYMGRHEEDIEY 455 (455)
T ss_pred hhhhhhhhhhhhhcceecccccchhhhhHHHHHHhhCCChhhcCC
Confidence 9999999999999999999999999999999999999 7788776
No 2
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=98.96 E-value=1.5e-11 Score=109.50 Aligned_cols=62 Identities=35% Similarity=0.576 Sum_probs=57.3
Q ss_pred EEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCceEeccccCceeeecCCCCCcEEEEeccccCcE
Q 044581 90 RVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLLETALPRRGGPVLVLYGRHKGVY 160 (203)
Q Consensus 90 ~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETVIPk~g~~V~VV~G~~rG~~ 160 (203)
+|+|+++++ +-+ |++||||.+|++.|+..|. +|+|++| .++|.+||||||+ |||+|.|||.-
T Consensus 247 ~vk~~sk~l-~~k-~K~K~vv~~vid~y~~~~K-ld~g~~l-k~dq~~lEtvip~-----~~vng~yRg~~ 308 (309)
T KOG2837|consen 247 VVKVISKSL-GEK-YKQKGVVKKVIDDYTGQIK-LDSGTVL-KVDQEHLETVIPQ-----MIVNGAYRGSE 308 (309)
T ss_pred EEEeehhhh-hHH-hccccHHHHHHHhhhhhee-ccCCcee-cccHHHHHHHhHH-----HHhhhhhccCC
Confidence 899999999 555 9999999999999999999 5688888 8999999999999 99999999964
No 3
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=98.77 E-value=6.6e-09 Score=104.58 Aligned_cols=110 Identities=22% Similarity=0.293 Sum_probs=97.8
Q ss_pred CCCcccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCceEeccccCceeeecCCCCCcEEEEeccccCcE
Q 044581 81 NVPWLRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLLETALPRRGGPVLVLYGRHKGVY 160 (203)
Q Consensus 81 ~~~Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETVIPk~g~~V~VV~G~~rG~~ 160 (203)
..+| ..++.+.+.+.++ +.+..++.++|++|. .+.|++++.+.++.+ .+..++|+++.|..++.++|+.|.++|.+
T Consensus 914 ~~~~-~~~~~~~~~d~~~-~~~~~G~~~~ir~v~-~G~~sv~~~de~~~~-~~s~~~~a~~~p~~~d~~k~~~g~~~g~~ 989 (1024)
T KOG1999|consen 914 SGNG-GDGNSSWGPDTSL-DTQLVGQTGIIRSVA-DGGCSVWLGDEGETI-SNSKPHLAPAPPCKGDDVKSIWGDDRGST 989 (1024)
T ss_pred CCCC-CccceEecccccc-cceecccccceeecc-CCceeeecCCCCccc-ccccccCccCCCCCCCCcccccccccccc
Confidence 3456 6688888888666 899999999999997 689999999888888 89999999999999999999999999999
Q ss_pred EEEEEeeCCCceEEEEECCCCcEEEeeccchhcccC
Q 044581 161 GNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYIG 196 (203)
Q Consensus 161 G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~g 196 (203)
|+|++.|.. .++|+++.+.++.+|++-.+|+++.
T Consensus 990 ~~~~~~dg~--~g~~~~d~~~~~k~l~~~~~~k~~~ 1023 (1024)
T KOG1999|consen 990 GKLVGNDGW--DGIVRIDETSDIKILNLGLLCKMVS 1023 (1024)
T ss_pred ccccCCCcc--cceecccccccchhhhhhhhhhccC
Confidence 999999988 5778887777788999999999975
No 4
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=97.31 E-value=0.00044 Score=42.66 Aligned_cols=31 Identities=32% Similarity=0.442 Sum_probs=27.5
Q ss_pred CCCcEEEEeccccCcEEEEEEeeCCCceEEE
Q 044581 145 RGGPVLVLYGRHKGVYGNLVDRDLDRETGVV 175 (203)
Q Consensus 145 ~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V 175 (203)
+|+.|+|+.|.|+|..|++++++.++..+.|
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEE
Confidence 4789999999999999999999999866554
No 5
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.71 E-value=0.0031 Score=36.68 Aligned_cols=26 Identities=31% Similarity=0.401 Sum_probs=24.0
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeC
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDL 168 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~ 168 (203)
|..|+.|+|+.|.|+|..|.+++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 56799999999999999999999975
No 6
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=96.48 E-value=0.0055 Score=45.23 Aligned_cols=33 Identities=24% Similarity=0.383 Sum_probs=29.9
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEE
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVR 176 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~ 176 (203)
+.|+.|.|+.|.++|..|+++.++.+++.++|+
T Consensus 8 ~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 40 (76)
T PRK12281 8 KKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVE 40 (76)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 468999999999999999999999998877765
No 7
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=96.44 E-value=0.0059 Score=45.77 Aligned_cols=33 Identities=21% Similarity=0.376 Sum_probs=29.9
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEE
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVR 176 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~ 176 (203)
+.|+.|+||.|.++|..|+++.++.+++.++|+
T Consensus 10 ~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 42 (83)
T CHL00141 10 KIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVK 42 (83)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 468999999999999999999999998877764
No 8
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=96.00 E-value=0.013 Score=45.61 Aligned_cols=33 Identities=24% Similarity=0.500 Sum_probs=30.1
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEE
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVR 176 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~ 176 (203)
+.|+.|+||.|.++|..|++++++.+++.+.|+
T Consensus 6 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 38 (105)
T PRK00004 6 KKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVE 38 (105)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 468999999999999999999999998887775
No 9
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=95.87 E-value=0.022 Score=45.57 Aligned_cols=52 Identities=21% Similarity=0.250 Sum_probs=44.5
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcE--EEeeccchhcc
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHEL--VNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i--~~l~~ddvck~ 194 (203)
...|+.|.|+.|.+.|..|.+..+|..+..+.|.+...+.. +++++++|-+.
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~ 140 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRII 140 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEe
Confidence 66899999999999999999999999888999988765544 67888888654
No 10
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=95.75 E-value=0.019 Score=45.97 Aligned_cols=33 Identities=39% Similarity=0.563 Sum_probs=30.3
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEE
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVR 176 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~ 176 (203)
+.|+.|+|+.|.++|..|+++.++..++.++|.
T Consensus 47 kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~Ve 79 (120)
T PRK01191 47 RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVE 79 (120)
T ss_pred eCCCEEEEeecCCCCceEEEEEEEcCCCEEEEe
Confidence 569999999999999999999999998887775
No 11
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=95.65 E-value=0.021 Score=44.49 Aligned_cols=33 Identities=24% Similarity=0.424 Sum_probs=29.9
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEE
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVR 176 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~ 176 (203)
+.|+.|.||.|.++|..|+++.++..++.++|+
T Consensus 5 kkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 37 (104)
T TIGR01079 5 KKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVE 37 (104)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEC
Confidence 468999999999999999999999998887764
No 12
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=95.56 E-value=0.022 Score=45.22 Aligned_cols=39 Identities=28% Similarity=0.340 Sum_probs=32.0
Q ss_pred eeeecCCCCCcEEEEeccccCcEEEEEEeeCCCceEEEE
Q 044581 138 LETALPRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVR 176 (203)
Q Consensus 138 LETVIPk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~ 176 (203)
..++.=+.|+.|+|+.|.++|..|+++.++..++.++|+
T Consensus 37 ~r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Ve 75 (114)
T TIGR01080 37 KRALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVE 75 (114)
T ss_pred cccceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEc
Confidence 333433679999999999999999999999988776665
No 13
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=95.17 E-value=0.061 Score=43.90 Aligned_cols=50 Identities=24% Similarity=0.258 Sum_probs=42.7
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcE--EEeeccchh
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHEL--VNVKLEQIA 192 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i--~~l~~ddvc 192 (203)
...|+.|.|+.|.++|..|.+.++|.++..+.|.+....-- +++++++|.
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~ 146 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVR 146 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEE
Confidence 56799999999999999999999999988899888764434 678888873
No 14
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=95.16 E-value=0.034 Score=45.86 Aligned_cols=33 Identities=24% Similarity=0.333 Sum_probs=30.3
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEE
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVR 176 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~ 176 (203)
+.|+.|+|+.|.++|..|++++++..++.++|.
T Consensus 48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVE 80 (143)
T PTZ00194 48 RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIE 80 (143)
T ss_pred ecCCEEEEecCCCCCCceEEEEEEcCCCEEEEe
Confidence 569999999999999999999999998887775
No 15
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=95.00 E-value=0.063 Score=43.81 Aligned_cols=49 Identities=18% Similarity=0.150 Sum_probs=39.3
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCC--cEEEeeccch
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTH--ELVNVKLEQI 191 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~--~i~~l~~ddv 191 (203)
+..|+.|.|+.|.+.|..|.+..+|..+..+.|.++--+ ..+.+++++|
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~v~~~~l 170 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQV 170 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEEEcHHHe
Confidence 456999999999999999999999987778888776433 3456777765
No 16
>PRK04313 30S ribosomal protein S4e; Validated
Probab=94.42 E-value=0.56 Score=41.61 Aligned_cols=52 Identities=13% Similarity=0.330 Sum_probs=34.7
Q ss_pred ccccCceeeecC-CCCCcEEEEeccccCcEEEEEEeeCCC----ceEEEEECCCCcEE
Q 044581 132 GVDQDLLETALP-RRGGPVLVLYGRHKGVYGNLVDRDLDR----ETGVVRDADTHELV 184 (203)
Q Consensus 132 ~V~q~~LETVIP-k~g~~V~VV~G~~rG~~G~Li~iD~~k----~~a~V~L~~~~~i~ 184 (203)
+++...+.-.+| ..|..+||..|.|.|.+|++.++.... ..+.|+ +.++..+
T Consensus 160 ~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~-d~~G~~F 216 (237)
T PRK04313 160 SLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLE-DKDGEKF 216 (237)
T ss_pred ECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEE-cCCCCEE
Confidence 443443444444 668899999999999999999996432 455555 3345444
No 17
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=94.14 E-value=0.14 Score=42.02 Aligned_cols=51 Identities=18% Similarity=0.163 Sum_probs=40.2
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCC--cEEEeeccchhc
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTH--ELVNVKLEQIAE 193 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~--~i~~l~~ddvck 193 (203)
...|+.|.|+.|.+.|..|.+..+|..+..+.|.+.--+ ..+.++++++-+
T Consensus 127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l~~ 179 (181)
T PRK05609 127 FEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEK 179 (181)
T ss_pred CCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHEEE
Confidence 456999999999999999999999977777877765433 345677777644
No 18
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=93.98 E-value=0.13 Score=43.41 Aligned_cols=54 Identities=15% Similarity=0.153 Sum_probs=43.1
Q ss_pred ecCCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCC--cEEEeeccchhcc
Q 044581 141 ALPRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTH--ELVNVKLEQIAEY 194 (203)
Q Consensus 141 VIPk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~--~i~~l~~ddvck~ 194 (203)
+-+..|+.|+|+.|.++|..|++.++|.++..+.|.+..-+ .-+.|.|++|-++
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVel~~~qVek~ 177 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEKL 177 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEEEehhhEEEe
Confidence 44566899999999999999999999999888888776422 2357888887654
No 19
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=92.54 E-value=0.34 Score=38.87 Aligned_cols=48 Identities=17% Similarity=0.212 Sum_probs=36.1
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCc--EEEeeccch
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHE--LVNVKLEQI 191 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~--i~~l~~ddv 191 (203)
...|+.|.|+.|.+.|..|.+..++.. ..+.|.++--+. .+.+++++|
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~~~~-~r~~v~l~~~gr~~~v~~~~~~~ 158 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEPDGE-KRSMLLLNMIGKQIKVSVPNTSV 158 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEECCC-ceEEEEEhhhCCceEEEecHHHc
Confidence 356999999999999999999999844 477777654332 345666654
No 20
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=92.45 E-value=0.22 Score=39.10 Aligned_cols=31 Identities=29% Similarity=0.462 Sum_probs=27.3
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEE
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVR 176 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~ 176 (203)
++|+.|.||.|.++|..|.+++++..+ ++|+
T Consensus 6 rkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VE 36 (104)
T COG0198 6 KKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVE 36 (104)
T ss_pred ecCCEEEEEecCCCCcceEEEEEecCe--EEEE
Confidence 468999999999999999999999996 5554
No 21
>PLN00036 40S ribosomal protein S4; Provisional
Probab=92.35 E-value=1.7 Score=39.12 Aligned_cols=37 Identities=22% Similarity=0.397 Sum_probs=28.5
Q ss_pred ccccCceeeecC-CCCCcEEEEeccccCcEEEEEEeeC
Q 044581 132 GVDQDLLETALP-RRGGPVLVLYGRHKGVYGNLVDRDL 168 (203)
Q Consensus 132 ~V~q~~LETVIP-k~g~~V~VV~G~~rG~~G~Li~iD~ 168 (203)
+++...+.-.+| ..|..+||..|.|.|.+|+++++..
T Consensus 163 ~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~ 200 (261)
T PLN00036 163 DLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREK 200 (261)
T ss_pred eCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEe
Confidence 444444555555 6678999999999999999999873
No 22
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=92.33 E-value=0.49 Score=46.01 Aligned_cols=55 Identities=22% Similarity=0.273 Sum_probs=44.7
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcccCCCC
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYIGDPS 199 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~g~~~ 199 (203)
|..|..|.|=+|+|+|+.|.+.++|.. .|.|+|-+.+++++++-.-|.-|.-.-|
T Consensus 352 ~aigktVrIr~g~yKG~lGVVKdv~~~--~arVeLhs~nK~VTI~K~~l~y~~reGe 406 (607)
T COG5164 352 PAIGKTVRIRCGEYKGHLGVVKDVDRN--IARVELHSNNKFVTIEKSRLAYLGREGE 406 (607)
T ss_pred cccCceEEEeecccccccceeeeccCc--eEEEEEecCCceEEeehhheEEeccccc
Confidence 666788999999999999999999988 7899998877888777776665543333
No 23
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=92.32 E-value=0.34 Score=39.29 Aligned_cols=50 Identities=16% Similarity=0.213 Sum_probs=37.8
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCC--cEEEeeccchhc
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTH--ELVNVKLEQIAE 193 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~--~i~~l~~ddvck 193 (203)
...|++|.|+.|.+.|..|.+..+|.+ ..+.|.++--+ ..+.+++++|-+
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~~~-~r~~v~v~~~gr~~~v~v~~~~~~~ 161 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPDGE-ARSILLLNLLNKQVKHSVDNTQFRK 161 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeCCC-eEEEEeehhhCCcEEEEECHHHeec
Confidence 457999999999999999999999954 46667665422 335688777743
No 24
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=91.81 E-value=1.6 Score=39.38 Aligned_cols=39 Identities=18% Similarity=0.284 Sum_probs=28.8
Q ss_pred EeccccCceeeecC-CCCCcEEEEeccccCcEEEEEEeeC
Q 044581 130 IQGVDQDLLETALP-RRGGPVLVLYGRHKGVYGNLVDRDL 168 (203)
Q Consensus 130 v~~V~q~~LETVIP-k~g~~V~VV~G~~rG~~G~Li~iD~ 168 (203)
+.+++...+.-.+| ..|..+||..|.|.|.+|+++++..
T Consensus 161 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~ 200 (262)
T PTZ00118 161 RLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEK 200 (262)
T ss_pred EEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEe
Confidence 33444444554555 6678999999999999999999764
No 25
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=90.76 E-value=1.7 Score=45.33 Aligned_cols=81 Identities=25% Similarity=0.233 Sum_probs=58.6
Q ss_pred ccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEec--CCCceEeccccCceeeecCCCCCcEEEEeccccCcEEE
Q 044581 85 LRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMD--ESGELIQGVDQDLLETALPRRGGPVLVLYGRHKGVYGN 162 (203)
Q Consensus 85 l~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~--d~g~~v~~V~q~~LETVIPk~g~~V~VV~G~~rG~~G~ 162 (203)
+.|+=.|.|+ .|.+-|-||+|..|. ...++|... +-...+ .++.+.|--. =+.|+.|+|+.|.|-|.+|.
T Consensus 408 F~~GD~VeV~-----~Gel~glkG~ve~vd-g~~vti~~~~e~l~~pl-~~~~~eLrKy-F~~GDhVKVi~G~~eG~tGl 479 (1024)
T KOG1999|consen 408 FSPGDAVEVI-----VGELKGLKGKVESVD-GTIVTIMSKHEDLKGPL-EVPASELRKY-FEPGDHVKVIAGRYEGDTGL 479 (1024)
T ss_pred cCCCCeEEEe-----eeeeccceeEEEecc-CceEEEeeccccCCCcc-ccchHhhhhh-ccCCCeEEEEeccccCCcce
Confidence 5677777777 688899999999996 344444433 234455 5777777211 23489999999999999999
Q ss_pred EEEeeCCCceEEE
Q 044581 163 LVDRDLDRETGVV 175 (203)
Q Consensus 163 Li~iD~~k~~a~V 175 (203)
++-++.. .+++
T Consensus 480 VvrVe~~--~vi~ 490 (1024)
T KOG1999|consen 480 VVRVEQG--DVIL 490 (1024)
T ss_pred EEEEeCC--eEEE
Confidence 9999977 5555
No 26
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=90.61 E-value=0.7 Score=41.52 Aligned_cols=49 Identities=20% Similarity=0.337 Sum_probs=39.0
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECC--CCcEEEeeccch
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDAD--THELVNVKLEQI 191 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~--~~~i~~l~~ddv 191 (203)
+..|+.|.|+.|.+.|..|.+.++|.++..+.|.++- ....+.|+|++|
T Consensus 206 f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpVeL~~~qV 256 (258)
T TIGR01956 206 FRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDVDLNFKHL 256 (258)
T ss_pred CCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEEEEchHHE
Confidence 5679999999999999999999999776677777654 223456887776
No 27
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=89.94 E-value=2.6 Score=38.24 Aligned_cols=37 Identities=24% Similarity=0.401 Sum_probs=27.9
Q ss_pred ccccCceeeecC-CCCCcEEEEeccccCcEEEEEEeeC
Q 044581 132 GVDQDLLETALP-RRGGPVLVLYGRHKGVYGNLVDRDL 168 (203)
Q Consensus 132 ~V~q~~LETVIP-k~g~~V~VV~G~~rG~~G~Li~iD~ 168 (203)
+++...+.-.+| ..|..+||..|.|.|.+|++.++..
T Consensus 160 ~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~ 197 (273)
T PTZ00223 160 NVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIER 197 (273)
T ss_pred ECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEe
Confidence 445443444444 6688999999999999999999954
No 28
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=89.13 E-value=1.2 Score=31.09 Aligned_cols=52 Identities=15% Similarity=0.059 Sum_probs=30.7
Q ss_pred ccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCceEeccccCcee
Q 044581 85 LRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLLE 139 (203)
Q Consensus 85 l~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LE 139 (203)
+.||..|+|++- +.-||+-.|.|..|.+...+.+.=..+=+.+..+.-+.||
T Consensus 2 ilPG~~V~V~n~---~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eLe 53 (53)
T PF11623_consen 2 ILPGSTVRVKNP---NDIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSELE 53 (53)
T ss_dssp --TT-EEEE--T---TSTTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGEE
T ss_pred ccCCCEEEEeCC---CCccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhCC
Confidence 568999999986 5689999999999986554443322221333366666665
No 29
>PF15591 Imm17: Immunity protein 17
Probab=86.31 E-value=1.4 Score=32.64 Aligned_cols=50 Identities=14% Similarity=0.176 Sum_probs=37.0
Q ss_pred EEEEeecccCCCceecceEEEEEecCCC----eEEEEecCCCceEeccccCceee
Q 044581 90 RVRIISKELKSGRLYLKKGEVVDVVGPT----MCDISMDESGELIQGVDQDLLET 140 (203)
Q Consensus 90 ~VRIidk~~~~Gk~y~kKGvV~dV~~~~----~c~V~l~d~g~~v~~V~q~~LET 140 (203)
+|+|.+..-++.+++|++|+|+.....+ -.+|.+-+..... .++.+.|+|
T Consensus 10 ~V~v~~s~p~~~ei~Gk~GVVlG~SeeD~~~~gY~Vli~d~e~~~-~~ee~~l~~ 63 (74)
T PF15591_consen 10 EVEVVRSCPCDAEIWGKRGVVLGISEEDGGNFGYSVLIFDMECCW-YIEEDELEA 63 (74)
T ss_pred EEEEeccCcchhhhcCceeEEEEEecCCCcEEEEEEEEeeeeeEE-EechHHeee
Confidence 6888875555789999999999986532 3556666665555 788888875
No 30
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=78.66 E-value=5 Score=35.79 Aligned_cols=38 Identities=24% Similarity=0.415 Sum_probs=29.4
Q ss_pred ccccCceeeec-CCCCCcEEEEeccccCcEEEEEEeeCC
Q 044581 132 GVDQDLLETAL-PRRGGPVLVLYGRHKGVYGNLVDRDLD 169 (203)
Q Consensus 132 ~V~q~~LETVI-Pk~g~~V~VV~G~~rG~~G~Li~iD~~ 169 (203)
+++...+.-.| +..|..++|+.|.|.|.+|++.+|...
T Consensus 162 ~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~ 200 (241)
T COG1471 162 SLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQ 200 (241)
T ss_pred eCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEe
Confidence 55555544444 566789999999999999999999765
No 31
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=78.03 E-value=8.3 Score=31.36 Aligned_cols=54 Identities=19% Similarity=0.188 Sum_probs=42.8
Q ss_pred ccCceEEEEeecccCCCceecceEEEEEecC-CCeEEEEecCCCce--EeccccCceeeecCC
Q 044581 85 LRSHIRVRIISKELKSGRLYLKKGEVVDVVG-PTMCDISMDESGEL--IQGVDQDLLETALPR 144 (203)
Q Consensus 85 l~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~-~~~c~V~l~d~g~~--v~~V~q~~LETVIPk 144 (203)
+.+|=.|+|+ +|.|-+..|.|..+.. ...+.|.+.+.... + +|+.++|.+|-+.
T Consensus 95 ~~~G~~V~I~-----~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv-~v~~~~~~~~~~~ 151 (153)
T PRK08559 95 IKEGDIVELI-----AGPFKGEKARVVRVDESKEEVTVELLEAAVPIPV-TVRGDQVRVVKKE 151 (153)
T ss_pred CCCCCEEEEe-----ccCCCCceEEEEEEcCCCCEEEEEEECCcceeeE-EEeccEEEEeccc
Confidence 6789999999 6888889999999964 45678888766544 6 7999999887643
No 32
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=76.00 E-value=8.8 Score=30.50 Aligned_cols=55 Identities=18% Similarity=0.170 Sum_probs=45.1
Q ss_pred CcccCceEEEEeecccCCCceecceEEEEEecC-CCeEEEEecCCCce--EeccccCceeeecC
Q 044581 83 PWLRSHIRVRIISKELKSGRLYLKKGEVVDVVG-PTMCDISMDESGEL--IQGVDQDLLETALP 143 (203)
Q Consensus 83 ~Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~-~~~c~V~l~d~g~~--v~~V~q~~LETVIP 143 (203)
..+.+|=.|+|+ +|.|-|..|.|..+.. +..+.|.+...+.. + .++.++|+.+-+
T Consensus 85 ~~~~~Gd~V~I~-----~GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v-~v~~~~l~~~~~ 142 (145)
T TIGR00405 85 ESIKKGDIVEII-----SGPFKGERAKVIRVDESKEEVTLELIEAAVPIPV-TVKGDQVRIIQK 142 (145)
T ss_pred cccCCCCEEEEe-----ecCCCCCeEEEEEEcCCCCEEEEEEEEcCccceE-EEeeeEEEEecc
Confidence 358899999999 6888899999999964 45788888877766 7 799999988764
No 33
>PF12656 G-patch_2: DExH-box splicing factor binding site
Probab=74.27 E-value=1.7 Score=32.13 Aligned_cols=21 Identities=48% Similarity=0.648 Sum_probs=19.9
Q ss_pred CCCcCCCCCCCeeeEEecccc
Q 044581 1 GRGIGKNSKGNVKIREFGKKS 21 (203)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~ 21 (203)
|.|||+|+++.++.+++.+|+
T Consensus 45 ~~~~g~~~~~~~~~~~~~~Rp 65 (77)
T PF12656_consen 45 GEGIGKNKKKSVKPVEPKRRP 65 (77)
T ss_pred CCCCCCCcccccCcccccccc
Confidence 578999999999999999999
No 34
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=74.15 E-value=14 Score=24.84 Aligned_cols=53 Identities=23% Similarity=0.163 Sum_probs=38.0
Q ss_pred CceEEEEeecccCCCceecceEEEEEecCCCeEEEEecC--CCceEeccccCceeeecCC
Q 044581 87 SHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDE--SGELIQGVDQDLLETALPR 144 (203)
Q Consensus 87 ~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d--~g~~v~~V~q~~LETVIPk 144 (203)
.|-.|-+-.+. ++.+| .|+|+.+.+...|.|.+.+ .+... .++.+.|-+..|-
T Consensus 5 ~G~~Ve~~~~~--~~~W~--~a~V~~~~~~~~~~V~~~~~~~~~~e-~v~~~~LRp~~~w 59 (61)
T smart00743 5 KGDRVEVFSKE--EDSWW--EAVVTKVLGDGKYLVRYLTESEPLKE-TVDWSDLRPHPPW 59 (61)
T ss_pred CCCEEEEEECC--CCEEE--EEEEEEECCCCEEEEEECCCCcccEE-EEeHHHcccCCCC
Confidence 34455555432 45564 6899999876789999988 66655 7899998887764
No 35
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=70.53 E-value=21 Score=23.34 Aligned_cols=53 Identities=15% Similarity=0.195 Sum_probs=37.1
Q ss_pred cCceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCceEeccccCceeeecCC
Q 044581 86 RSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLLETALPR 144 (203)
Q Consensus 86 ~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETVIPk 144 (203)
.+|-.|...- .+|.+| .|.|.++.+...|.|.+.|-|... .|+.++|-+..|.
T Consensus 4 ~~G~~~~a~~---~d~~wy--ra~I~~~~~~~~~~V~f~D~G~~~-~v~~~~l~~l~~~ 56 (57)
T smart00333 4 KVGDKVAARW---EDGEWY--RARIIKVDGEQLYEVFFIDYGNEE-VVPPSDLRPLPEE 56 (57)
T ss_pred CCCCEEEEEe---CCCCEE--EEEEEEECCCCEEEEEEECCCccE-EEeHHHeecCCCC
Confidence 3444444442 267776 589999986688999998867655 6888888776653
No 36
>PRK14639 hypothetical protein; Provisional
Probab=70.37 E-value=14 Score=29.88 Aligned_cols=52 Identities=13% Similarity=0.180 Sum_probs=37.5
Q ss_pred ecCCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 141 ALPRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 141 VIPk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
.....|..|.|-....+-..|+|.+++.+ ..++....++..+.++|++|.+.
T Consensus 83 f~r~~G~~v~v~l~~~~~~~G~L~~~~~~--~i~l~~~~~~~~~~i~~~~I~ka 134 (140)
T PRK14639 83 FAKSIGELVKITTNEKEKFEGKIVSVDDE--NITLENLENKEKTTINFNDIKKA 134 (140)
T ss_pred HHHhCCCEEEEEECCCcEEEEEEEEEeCC--EEEEEEccCCcEEEEEhHHeeeE
Confidence 34556888988654467888999999987 55554423455678999999874
No 37
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=65.97 E-value=19 Score=29.39 Aligned_cols=52 Identities=21% Similarity=0.095 Sum_probs=36.3
Q ss_pred cccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEec-CCCceEeccccCceee
Q 044581 84 WLRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMD-ESGELIQGVDQDLLET 140 (203)
Q Consensus 84 Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~-d~g~~v~~V~q~~LET 140 (203)
.+.+|=+|.|. .|.++|+.++|+||+|...|-|.-+ .+|-.-+.++-.+|+.
T Consensus 7 fVEiGRVvli~-----~Gp~~GKL~vIVDIID~nRvLVDGP~~tgV~Rq~i~~k~l~L 59 (130)
T PTZ00065 7 FVEPGRLCLIQ-----YGPDAGKLCFIVDIVTPTRVLVDGAFITGVKRQSIPLKRLKL 59 (130)
T ss_pred ceeeceEEEEe-----cCCCCCCEEEEEEEEcCCeEEEeCCCcCCcceeEEeccceEE
Confidence 35556566555 5889999999999999999888877 4453333455555543
No 38
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=65.64 E-value=16 Score=29.56 Aligned_cols=35 Identities=23% Similarity=0.216 Sum_probs=27.2
Q ss_pred ccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEec
Q 044581 85 LRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMD 124 (203)
Q Consensus 85 l~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~ 124 (203)
+-+|-+|-+. .|+|.|++++|++.++.+...|.-+
T Consensus 5 l~~GrVvvv~-----~GR~aGkk~VIv~~iDd~~v~i~gp 39 (125)
T COG2163 5 LEVGRVVVVT-----AGRFAGKKVVIVKIIDDNFVLITGP 39 (125)
T ss_pred ccCCeEEEEe-----cceeCCceEEEEEEccCCEEEEeCC
Confidence 5677777776 7999999999999998775444433
No 39
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=64.27 E-value=37 Score=22.12 Aligned_cols=53 Identities=11% Similarity=-0.051 Sum_probs=38.1
Q ss_pred cCCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhccc
Q 044581 142 LPRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYI 195 (203)
Q Consensus 142 IPk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~ 195 (203)
.|+.|..|++..-.-.=..|++++++.+ ....|.+.+.+....+++++|..+.
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~-~~~~V~f~D~G~~~~v~~~~l~~l~ 54 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGE-QLYEVFFIDYGNEEVVPPSDLRPLP 54 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCC-CEEEEEEECCCccEEEeHHHeecCC
Confidence 3677877777652233466799999986 4677887765777789998887664
No 40
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=63.19 E-value=12 Score=29.27 Aligned_cols=44 Identities=30% Similarity=0.250 Sum_probs=35.2
Q ss_pred CceeeecCCCCCcEEEEecc--ccCcEEEEEEeeCC---CceEEEEECC
Q 044581 136 DLLETALPRRGGPVLVLYGR--HKGVYGNLVDRDLD---RETGVVRDAD 179 (203)
Q Consensus 136 ~~LETVIPk~g~~V~VV~G~--~rG~~G~Li~iD~~---k~~a~V~L~~ 179 (203)
..-.++-|+.|..|+||+=+ +-..+|++.++|.+ ++-++|+++.
T Consensus 33 ~kpp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~k 81 (101)
T PLN00045 33 PKPPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFEK 81 (101)
T ss_pred CCCCCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEeee
Confidence 34456778889999999755 46789999999987 7888999864
No 41
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=63.12 E-value=15 Score=29.33 Aligned_cols=53 Identities=15% Similarity=0.097 Sum_probs=38.7
Q ss_pred CCcccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCce-EeccccCcee
Q 044581 82 VPWLRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGEL-IQGVDQDLLE 139 (203)
Q Consensus 82 ~~Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~-v~~V~q~~LE 139 (203)
...+.+|=.|+|+ +|.|-+..|.|..+.+...+.|.+.--|+. ...++.++||
T Consensus 106 ~~~~~~G~~V~V~-----~GPf~g~~g~v~~~~~~~r~~v~l~~~gr~~~v~~~~~~~~ 159 (159)
T TIGR01955 106 TTLPYKGDKVRIT-----DGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSVE 159 (159)
T ss_pred ccCCCCCCEEEEe-----ccCCCCcEEEEEEECCCceEEEEEhhhCCceEEEecHHHcC
Confidence 3578899999999 688889999999997666777776544432 2256666654
No 42
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=63.08 E-value=11 Score=37.01 Aligned_cols=44 Identities=20% Similarity=0.318 Sum_probs=36.4
Q ss_pred ceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCceEeccccCce
Q 044581 88 HIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLL 138 (203)
Q Consensus 88 ~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~L 138 (203)
+-.|||. .|.|-++-|+|+||. +..|.|+|-+....| .|+-+.|
T Consensus 355 gktVrIr-----~g~yKG~lGVVKdv~-~~~arVeLhs~nK~V-TI~K~~l 398 (607)
T COG5164 355 GKTVRIR-----CGEYKGHLGVVKDVD-RNIARVELHSNNKFV-TIEKSRL 398 (607)
T ss_pred CceEEEe-----ecccccccceeeecc-CceEEEEEecCCceE-Eeehhhe
Confidence 6689998 678889999999997 678999999777777 6776665
No 43
>PRK04333 50S ribosomal protein L14e; Validated
Probab=58.73 E-value=29 Score=26.05 Aligned_cols=31 Identities=16% Similarity=0.131 Sum_probs=24.2
Q ss_pred cCceEEEEeecccCCCceecceEEEEEecCCCeEEE
Q 044581 86 RSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDI 121 (203)
Q Consensus 86 ~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V 121 (203)
.+|=+|.+. .|++.|+.++|.++++...|-|
T Consensus 5 ~~GrvV~~~-----~Grd~gk~~vIv~i~d~~~vlV 35 (84)
T PRK04333 5 EVGRVCVKT-----AGREAGRKCVIVDIIDKNFVLV 35 (84)
T ss_pred cccEEEEEe-----ccCCCCCEEEEEEEecCCEEEE
Confidence 456566665 6889999999999988777655
No 44
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=58.14 E-value=39 Score=21.76 Aligned_cols=30 Identities=27% Similarity=0.359 Sum_probs=24.3
Q ss_pred CcEEEEEEeeCCCceEEEEECCCCcEEEeeccc
Q 044581 158 GVYGNLVDRDLDRETGVVRDADTHELVNVKLEQ 190 (203)
Q Consensus 158 G~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~dd 190 (203)
=..|.++++..+ .++|++.+ ++.++++.||
T Consensus 13 fv~g~I~~~~g~--~vtV~~~~-G~~~tv~~dd 42 (42)
T PF02736_consen 13 FVKGEIIEEEGD--KVTVKTED-GKEVTVKKDD 42 (42)
T ss_dssp EEEEEEEEEESS--EEEEEETT-TEEEEEEGGG
T ss_pred EEEEEEEEEcCC--EEEEEECC-CCEEEeCCCC
Confidence 356889988888 68899886 8888888875
No 45
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=55.64 E-value=41 Score=23.49 Aligned_cols=58 Identities=19% Similarity=0.348 Sum_probs=35.5
Q ss_pred eEEEEEecCCCeEEEEecCCCceEeccccCceeeecCCCCCcEEEEeccccCcEEEEE
Q 044581 107 KGEVVDVVGPTMCDISMDESGELIQGVDQDLLETALPRRGGPVLVLYGRHKGVYGNLV 164 (203)
Q Consensus 107 KGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETVIPk~g~~V~VV~G~~rG~~G~Li 164 (203)
-|.|....+.+...|.++++...+-.++..+--++-=+.|+.|+|=.-.+--..|.++
T Consensus 6 ~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~d~~kG~Ii 63 (65)
T PF01176_consen 6 IGRVTEMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPYDKVKGRII 63 (65)
T ss_dssp EEEEEEEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTTCTTEEEEE
T ss_pred EEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEecccCCCeEEEE
Confidence 4678899988899999986655555566665555555556666665444444555444
No 46
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=55.25 E-value=39 Score=24.56 Aligned_cols=50 Identities=28% Similarity=0.262 Sum_probs=33.9
Q ss_pred CCCCCcEEEE-e---ccccCcEEEEEEeeCCCceEEEEECC--CCcEEEeeccchhcc
Q 044581 143 PRRGGPVLVL-Y---GRHKGVYGNLVDRDLDRETGVVRDAD--THELVNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~VV-~---G~~rG~~G~Li~iD~~k~~a~V~L~~--~~~i~~l~~ddvck~ 194 (203)
-..|..|.|. . +..+-..|.|.+++.+ .+++..+. .+..+.++|++|.+.
T Consensus 22 r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~--~v~l~~~~~~~~~~~~i~~~~I~ka 77 (83)
T cd01734 22 RAVGKYVHVKLYQPIDGQKEFEGTLLGVDDD--TVTLEVDIKTRGKTVEIPLDKIAKA 77 (83)
T ss_pred HhCCCEEEEEEEcccCCeEEEEEEEEeEeCC--EEEEEEecCCCCeEEEEEhHHeeEE
Confidence 3457777774 3 3345568999999987 55555542 145778999999764
No 47
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=52.49 E-value=20 Score=31.63 Aligned_cols=32 Identities=34% Similarity=0.385 Sum_probs=28.9
Q ss_pred CCCcEEEEeccccCcEEEEEEeeCCCceEEEE
Q 044581 145 RGGPVLVLYGRHKGVYGNLVDRDLDRETGVVR 176 (203)
Q Consensus 145 ~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~ 176 (203)
.|+.|.||.|+.+|..|.+..+......++|.
T Consensus 75 ~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~ 106 (236)
T KOG1708|consen 75 FGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVK 106 (236)
T ss_pred cCCEEEEEecccCCccceEEEEeecCceEEEc
Confidence 48999999999999999999998888788876
No 48
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=51.36 E-value=25 Score=22.20 Aligned_cols=36 Identities=14% Similarity=0.291 Sum_probs=25.7
Q ss_pred CCceecceEEEEEecCCCeEEEEecCCCceEeccccCce
Q 044581 100 SGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLL 138 (203)
Q Consensus 100 ~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~L 138 (203)
+|.+| .|.|.++.....|.|.+.|-|..- .|+.++|
T Consensus 11 d~~wy--ra~V~~~~~~~~~~V~f~DyG~~~-~v~~~~l 46 (48)
T cd04508 11 DGKWY--RAKITSILSDGKVEVFFVDYGNTE-VVPLSDL 46 (48)
T ss_pred CCeEE--EEEEEEECCCCcEEEEEEcCCCcE-EEeHHHc
Confidence 47776 588999987778999998866543 4555444
No 49
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=50.87 E-value=36 Score=27.51 Aligned_cols=53 Identities=17% Similarity=0.098 Sum_probs=39.0
Q ss_pred CCcccCceEEEEeecccCCCceecceEEEEEec-CCCeEEEEecCCCc-eEeccccCcee
Q 044581 82 VPWLRSHIRVRIISKELKSGRLYLKKGEVVDVV-GPTMCDISMDESGE-LIQGVDQDLLE 139 (203)
Q Consensus 82 ~~Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~-~~~~c~V~l~d~g~-~v~~V~q~~LE 139 (203)
...+.+|=.|+|+ +|.|.|..|+|..+. +...+.|.+.--|+ +...++.++|+
T Consensus 117 ~~~~~~G~~V~I~-----~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~v~~~~l~ 171 (172)
T TIGR00922 117 KIDFEVGEQVRVN-----DGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVE 171 (172)
T ss_pred ccCCCCCCEEEEe-----ecCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEEEcHHHee
Confidence 3568899999999 688889999999996 45677777754443 22267766665
No 50
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=50.78 E-value=41 Score=27.33 Aligned_cols=54 Identities=17% Similarity=0.096 Sum_probs=39.7
Q ss_pred CCcccCceEEEEeecccCCCceecceEEEEEec-CCCeEEEEecCCCc-eEeccccCceee
Q 044581 82 VPWLRSHIRVRIISKELKSGRLYLKKGEVVDVV-GPTMCDISMDESGE-LIQGVDQDLLET 140 (203)
Q Consensus 82 ~~Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~-~~~~c~V~l~d~g~-~v~~V~q~~LET 140 (203)
...+.+|=.|+|+ +|.|-|..|.|..+. +...+.|.+.--|+ +...++.+.|+.
T Consensus 124 ~~~~~~Gd~VrI~-----~GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l~~ 179 (181)
T PRK05609 124 KVDFEVGEMVRVI-----DGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEK 179 (181)
T ss_pred ccCCCCCCEEEEe-----ccCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHEEE
Confidence 4678899999999 688999999999996 45566666654343 233677777764
No 51
>PF02427 PSI_PsaE: Photosystem I reaction centre subunit IV / PsaE; InterPro: IPR003375 PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains []. This subunit may form complexes with ferredoxin and ferredoxin-oxidoreductase in the photosystem I reaction centre.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 1PSF_A 1PSE_A 2WSF_E 2WSC_E 2O01_E 2WSE_E 1GXI_E 1JB0_E 3PCQ_E 1QP2_A ....
Probab=45.61 E-value=50 Score=23.68 Aligned_cols=49 Identities=24% Similarity=0.257 Sum_probs=32.5
Q ss_pred CCCCCcEEEEecc--ccCcEEEEEEeeCC--CceEEEEECC----CCcEEEeeccch
Q 044581 143 PRRGGPVLVLYGR--HKGVYGNLVDRDLD--RETGVVRDAD----THELVNVKLEQI 191 (203)
Q Consensus 143 Pk~g~~V~VV~G~--~rG~~G~Li~iD~~--k~~a~V~L~~----~~~i~~l~~ddv 191 (203)
|+.|.+|+|++=+ +--.+|++.++|.+ ++-++|+++. .-.+-.+.++++
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~i~YPV~VRF~kvNY~g~nTnnfa~~El 57 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSGIRYPVVVRFDKVNYAGVNTNNFALDEL 57 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSSSSSSEEEE-SSS-SSSSSEEEE-GGGE
T ss_pred CCCCCEEEEccccceeecccceEEEEccCCccccEEEEEEEecccCccccccchhhh
Confidence 4678999999755 46889999999987 6888999875 112334555554
No 52
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=44.96 E-value=29 Score=28.50 Aligned_cols=77 Identities=16% Similarity=0.075 Sum_probs=43.7
Q ss_pred cccCceEEEEeecccCCCceecceEEEEEecCCC-------eEEEEecCCCceEeccccCceeeecC---CCCCcEEEEe
Q 044581 84 WLRSHIRVRIISKELKSGRLYLKKGEVVDVVGPT-------MCDISMDESGELIQGVDQDLLETALP---RRGGPVLVLY 153 (203)
Q Consensus 84 Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~-------~c~V~l~d~g~~v~~V~q~~LETVIP---k~g~~V~VV~ 153 (203)
.+.||-+|-|. .|+|.|+|++|+...+.+ .|.|.-.+- -.. .|.-.|=..-+- +...-|++++
T Consensus 4 ~~kpgkVVivL-----~GR~AGkKaVivk~~ddgt~drpy~halVaGIdr-yP~-kVtk~M~kkki~KRskiK~FvK~vN 76 (134)
T PTZ00471 4 FLKPGKVVIVT-----SGRYAGRKAVIVQNFDTASKERPYGHALVAGIKK-YPK-KVVRGMSKRTIARRSQVGVFLRVVN 76 (134)
T ss_pred cccCCEEEEEE-----ccccCCcEEEEEeecCCCCccCcCceEEEEeecc-cch-hhhhhccHHHHHHHhccccceEEEe
Confidence 56788888777 799999999999998764 454443210 000 111111111111 1234578888
Q ss_pred ccccCcEEEEEEee
Q 044581 154 GRHKGVYGNLVDRD 167 (203)
Q Consensus 154 G~~rG~~G~Li~iD 167 (203)
=.|-=.|-.-++++
T Consensus 77 ynHlmPTRY~vdi~ 90 (134)
T PTZ00471 77 HKHFLPTRYNMDMS 90 (134)
T ss_pred eceecccceeeecc
Confidence 77765555555555
No 53
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=44.50 E-value=94 Score=24.14 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=33.9
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcccC
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYIG 196 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~g 196 (203)
++|++|+-..| -.|++.+++.+ .+.|++.+ +..+++.-..|.....
T Consensus 54 k~Gd~VvT~gG----i~G~Vv~i~~~--~v~lei~~-g~~i~~~r~aI~~v~~ 99 (106)
T PRK05585 54 AKGDEVVTNGG----IIGKVTKVSED--FVIIELND-DTEIKIQKSAIAAVLP 99 (106)
T ss_pred CCCCEEEECCC----eEEEEEEEeCC--EEEEEECC-CeEEEEEhHHhhhhcC
Confidence 34788887776 89999999875 88888854 5456677667776554
No 54
>PRK14630 hypothetical protein; Provisional
Probab=44.04 E-value=81 Score=25.64 Aligned_cols=47 Identities=13% Similarity=0.171 Sum_probs=32.6
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
-..|..|.|-..... ..|+|.+.+.+ .+++.+ ++..+.++|++|.+.
T Consensus 94 r~~G~~v~V~l~~~~-~~G~L~~~~d~--~i~l~~--~~~~~~i~~~~I~ka 140 (143)
T PRK14630 94 IFEGKKIKLMLDNDF-EEGFILEAKAD--SFIFKT--DSKEVNVLYSDVKKA 140 (143)
T ss_pred HhCCCEEEEEEcCcc-eEEEEEEEeCC--EEEEEE--CCEEEEEEhHhcceE
Confidence 345777888543322 38999999877 555554 456788999999764
No 55
>PRK14637 hypothetical protein; Provisional
Probab=43.20 E-value=86 Score=25.76 Aligned_cols=46 Identities=20% Similarity=0.174 Sum_probs=31.9
Q ss_pred CCCcEEEEeccccCc-EEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 145 RGGPVLVLYGRHKGV-YGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 145 ~g~~V~VV~G~~rG~-~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
.|..|.|-....... +|+|.+++.+ .+++.. ++..+.++|++|.+.
T Consensus 97 ~G~~V~V~l~~~~~~~~G~L~~~~d~--~v~l~~--~~~~~~i~~~~I~ka 143 (151)
T PRK14637 97 VGETVKVWFECTGQWQVGTIAEADET--CLVLTS--DGVPVTIPYVQITKA 143 (151)
T ss_pred CCCEEEEEECCCCcEEEEEEEEEeCC--EEEEEE--CCEEEEEEHHHeeeE
Confidence 467788854223345 5999999887 555543 456788999999764
No 56
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=42.78 E-value=58 Score=26.17 Aligned_cols=52 Identities=12% Similarity=0.064 Sum_probs=38.2
Q ss_pred cccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCC-ceEeccccCceee
Q 044581 84 WLRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESG-ELIQGVDQDLLET 140 (203)
Q Consensus 84 Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g-~~v~~V~q~~LET 140 (203)
.+.+|=.|+|+ +|.|-|..|+|..+.+...+.|.+.--| .+...++.++|+.
T Consensus 109 ~~~~G~~V~I~-----~Gp~~g~eg~v~~~~~~~r~~v~v~~~gr~~~v~v~~~~~~~ 161 (162)
T PRK09014 109 TPKPGDKVIIT-----EGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFRK 161 (162)
T ss_pred CCCCCCEEEEe-----cCCCCCcEEEEEEeCCCeEEEEeehhhCCcEEEEECHHHeec
Confidence 47889999999 6888899999999987777777765433 2223577777654
No 57
>PRK14631 hypothetical protein; Provisional
Probab=40.74 E-value=86 Score=26.41 Aligned_cols=53 Identities=15% Similarity=0.160 Sum_probs=35.8
Q ss_pred ecCCCCCcEEEEe----ccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 141 ALPRRGGPVLVLY----GRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 141 VIPk~g~~V~VV~----G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
.....|..|.|-. +..+-.+|+|.+++.+...+.+.+. ++..+.++|++|.+.
T Consensus 112 f~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~-~~~~~~i~~~~I~ka 168 (174)
T PRK14631 112 LQGYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVE-GKHVLDIDSNNIDKA 168 (174)
T ss_pred HHHhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEc-CCcEEEEEhHHcceE
Confidence 3445577788753 3356788999999933336666554 245678999999874
No 58
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=39.11 E-value=2.5e+02 Score=32.09 Aligned_cols=98 Identities=10% Similarity=0.076 Sum_probs=61.6
Q ss_pred cccCceEEEEeecccCCCceecceEEEEEecCC-CeEEEEecCCCceEeccccCcee-----------eecC-CCCCcEE
Q 044581 84 WLRSHIRVRIISKELKSGRLYLKKGEVVDVVGP-TMCDISMDESGELIQGVDQDLLE-----------TALP-RRGGPVL 150 (203)
Q Consensus 84 Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~-~~c~V~l~d~g~~v~~V~q~~LE-----------TVIP-k~g~~V~ 150 (203)
...+|-+|+.- ..+.+.+..++|..|... .+.+|... +|+.+ .++.+.|. ..+| ..|++++
T Consensus 681 ~Yr~Gdvv~~y----~~~~~~~~~y~V~~V~~~~n~L~l~~~-dG~~~-~~~p~~l~~~~~~~svy~~~~l~ia~Gdrl~ 754 (1960)
T TIGR02760 681 HYKQGMVIRFW----QKGKIPHDDYVVTNVNKHNNTLTLKDA-QGKTQ-KFKPSSLKDLERPFSVYRPEQLEVAAGERLQ 754 (1960)
T ss_pred hcCCCCEEEee----cccCccCCcEEEEEEeCCCCEEEEEcC-CCCEE-EECHHHhcccccceeeeccccccccCCCEEE
Confidence 45788888873 234455556789998753 45555543 56666 57776662 2234 3377888
Q ss_pred EEe-----ccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccc
Q 044581 151 VLY-----GRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQ 190 (203)
Q Consensus 151 VV~-----G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~dd 190 (203)
+.. |-.+|..+++.+++.. ...|+.. ++..+.|+.++
T Consensus 755 ~trn~~~~gl~ng~~~tV~~i~~~--~i~l~~~-~g~~~~L~~~~ 796 (1960)
T TIGR02760 755 VTGNHFHSRVRNGELLTVSSINNE--GITLITE-DGQTLHLPHGA 796 (1960)
T ss_pred EccCCcccCccCCCEEEEEEEcCC--eEEEEeC-CCceEEccCCC
Confidence 874 3347899999999987 4556554 34556666554
No 59
>PRK14638 hypothetical protein; Provisional
Probab=37.02 E-value=1e+02 Score=25.25 Aligned_cols=48 Identities=13% Similarity=0.110 Sum_probs=34.3
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
-..|..|.|-....+-.+|+|.+++.+ .+++.. ++..+.++|++|.+.
T Consensus 97 r~~G~~v~V~~~~~k~~~G~L~~~~~~--~i~l~~--~~~~~~i~~~~I~~a 144 (150)
T PRK14638 97 RFTGKLAKIVTKDGKTFIGRIESFVDG--TITISD--EKEKYEINIDDVKRA 144 (150)
T ss_pred HhCCCEEEEEECCCcEEEEEEEEEeCC--EEEEEE--CCcEEEEEhHHcceE
Confidence 345778888543357789999999876 454443 456788999998764
No 60
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=36.58 E-value=95 Score=25.18 Aligned_cols=51 Identities=24% Similarity=0.176 Sum_probs=33.8
Q ss_pred cCCCCCcEEEEe----ccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 142 LPRRGGPVLVLY----GRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 142 IPk~g~~V~VV~----G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
....|..|.|-. +..+-.+|+|.+++.+ .+++........+.++|++|.+.
T Consensus 94 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~--~i~l~~~~~~~~~~i~~~~I~~a 148 (154)
T PRK00092 94 RRFIGREVKVKLYEPIDGRKKFQGILLAVDGE--TVTLEVEGKEKEVEIPLDNIAKA 148 (154)
T ss_pred HHhCCCeEEEEEEcccCCceEEEEEEEEeeCC--EEEEEECCCeEEEEEEHHHcceE
Confidence 345578888852 3344558999999887 45555432112788999999764
No 61
>CHL00010 infA translation initiation factor 1
Probab=36.46 E-value=1.7e+02 Score=21.29 Aligned_cols=64 Identities=14% Similarity=0.149 Sum_probs=32.8
Q ss_pred ceEEEEEecCCCeEEEEecCCCceEeccccCc-eeeecCCCCCcEEEEeccccCcEEEEEEeeCC
Q 044581 106 KKGEVVDVVGPTMCDISMDESGELIQGVDQDL-LETALPRRGGPVLVLYGRHKGVYGNLVDRDLD 169 (203)
Q Consensus 106 kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~-LETVIPk~g~~V~VV~G~~rG~~G~Li~iD~~ 169 (203)
..|+|..+++.+.+.|.+.++....-.+.-.. ...+.|..|+.|.+=.-.+-...|.++-+-..
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 35666666644445555432212111222211 12566888999888644444555676666443
No 62
>PRK14633 hypothetical protein; Provisional
Probab=36.32 E-value=1.1e+02 Score=24.88 Aligned_cols=48 Identities=10% Similarity=0.120 Sum_probs=33.5
Q ss_pred CCCCcEEEEe----ccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 144 RRGGPVLVLY----GRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 144 k~g~~V~VV~----G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
..|..|.|.. +..+-.+|+|.+++.+ .+.+.+. ++..+.++|++|.+.
T Consensus 92 ~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~--~i~l~~~-~~~~~~i~~~~I~ka 143 (150)
T PRK14633 92 LVGFNVKAVTLAPVGSQTKFKGVLERVEGN--NVILNLE-DGKEISFDFDELKKL 143 (150)
T ss_pred hCCCeEEEEEecccCCcEEEEEEEEEEeCC--EEEEEEc-CCcEEEEEhHHeeeE
Confidence 3477788843 3456678999999877 5555443 345678999999875
No 63
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=35.29 E-value=75 Score=22.70 Aligned_cols=40 Identities=20% Similarity=0.230 Sum_probs=31.1
Q ss_pred eccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhc
Q 044581 153 YGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAE 193 (203)
Q Consensus 153 ~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck 193 (203)
.|.+.-.+|++..+|.......+.-. ++....++|++|+.
T Consensus 52 ~g~~~~~~G~I~~id~~~~~l~~~~~-~~~~~~I~~~~I~~ 91 (92)
T PF08863_consen 52 DGYYQSVTGTIHKIDEINRTLKLKDE-DGETEKIPFDDIID 91 (92)
T ss_pred CCeeEEEEEEEEEEcCCCCEEEEEeC-CCCEEEEEhhhEEE
Confidence 57788899999999998666555432 46678899999975
No 64
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=34.99 E-value=2.2e+02 Score=22.17 Aligned_cols=35 Identities=20% Similarity=0.214 Sum_probs=25.0
Q ss_pred CceEEEEeecccCCCceecceEEEEEecCCCeEEEEec
Q 044581 87 SHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMD 124 (203)
Q Consensus 87 ~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~ 124 (203)
.|+.|+|+... +-.|-|-.|.|++=. ..+..|...
T Consensus 16 iGl~vrVv~s~--~~s~vGI~G~VVdET-kNtLvi~t~ 50 (95)
T COG1588 16 IGLEVRVVRST--NPSYVGIEGRVVDET-KNTLVIDTG 50 (95)
T ss_pred cCcEEEEEecC--CCCccceeEEEEeee-ccEEEEECC
Confidence 48999999765 567889999998854 444444443
No 65
>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=34.73 E-value=1.4e+02 Score=22.08 Aligned_cols=42 Identities=24% Similarity=0.349 Sum_probs=29.5
Q ss_pred CCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhc
Q 044581 145 RGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAE 193 (203)
Q Consensus 145 ~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck 193 (203)
+|++|+-..| -.|++.+++.+ .+.|++.+ +..+.+.-..|++
T Consensus 40 ~Gd~VvT~gG----i~G~V~~i~d~--~v~vei~~-g~~i~~~r~aI~~ 81 (84)
T TIGR00739 40 KGDKVLTIGG----IIGTVTKIAEN--TIVIELND-NTEITFSKNAIVE 81 (84)
T ss_pred CCCEEEECCC----eEEEEEEEeCC--EEEEEECC-CeEEEEEhHHhhh
Confidence 4788877766 88999999976 67777753 4445565555544
No 66
>PRK04333 50S ribosomal protein L14e; Validated
Probab=34.53 E-value=73 Score=23.86 Aligned_cols=30 Identities=23% Similarity=0.104 Sum_probs=23.1
Q ss_pred CCCcEEEEeccccCcEEEEEEeeCCCceEEE
Q 044581 145 RGGPVLVLYGRHKGVYGNLVDRDLDRETGVV 175 (203)
Q Consensus 145 ~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V 175 (203)
.|.-|.++.|.++|..+.++++..++ .+.|
T Consensus 6 ~GrvV~~~~Grd~gk~~vIv~i~d~~-~vlV 35 (84)
T PRK04333 6 VGRVCVKTAGREAGRKCVIVDIIDKN-FVLV 35 (84)
T ss_pred ccEEEEEeccCCCCCEEEEEEEecCC-EEEE
Confidence 35668888999999999999985442 5555
No 67
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=34.40 E-value=79 Score=33.56 Aligned_cols=46 Identities=24% Similarity=0.299 Sum_probs=34.1
Q ss_pred CCCCCcEEEEe-----ccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccch
Q 044581 143 PRRGGPVLVLY-----GRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQI 191 (203)
Q Consensus 143 Pk~g~~V~VV~-----G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddv 191 (203)
-..|++||.+. |-+.|.+|++.+++.+ ..+|++++ +..+.++..++
T Consensus 601 ~~vGDrVm~~rNd~~lgV~NGd~GtV~~I~~~--~i~V~~d~-gr~V~~~~~~~ 651 (988)
T PRK13889 601 FASGDRVMFLQNERGLGVKNGTLGTIEQVSAQ--SMSVRLDD-GRSVAFDLKDY 651 (988)
T ss_pred ccCCCEEEEeecCCcCCEeCCCeEEEEEecCC--eEEEEECC-CeEEEecHHHc
Confidence 36799999985 4468999999999986 67788763 55666665544
No 68
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=32.42 E-value=1.2e+02 Score=24.07 Aligned_cols=47 Identities=21% Similarity=0.222 Sum_probs=28.0
Q ss_pred CCcEEEEe-cc---ccCcEEEEEEeeCCCceEEEEECCCC--cEEEeeccchhcc
Q 044581 146 GGPVLVLY-GR---HKGVYGNLVDRDLDRETGVVRDADTH--ELVNVKLEQIAEY 194 (203)
Q Consensus 146 g~~V~VV~-G~---~rG~~G~Li~iD~~k~~a~V~L~~~~--~i~~l~~ddvck~ 194 (203)
|..|.|-. -+ .+-..|+|.+.+.+ ..++++...+ ..+.++|++|.+.
T Consensus 87 G~~v~v~~~~~~~~~~~~~G~L~~~~~~--~i~l~~~~~~~~~~~~I~~~~I~ka 139 (141)
T PF02576_consen 87 GRKVKVKLKQPVNGRKEFEGKLLEVDED--EITLEVEGKGKKKEVEIPFSDIKKA 139 (141)
T ss_dssp SEEEEEE-SS-SSS-SEEEEEEEEEETT--EEEEEEE-SS-EEEEEE-SS--SS-
T ss_pred CCeEEEEEeccCCCcEEEEEEEEEEeCC--EEEEEECCccceEEEEEEHHHCceE
Confidence 66777754 22 23358999999997 6667665432 3678999998763
No 69
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=32.17 E-value=1.7e+02 Score=26.09 Aligned_cols=53 Identities=17% Similarity=0.149 Sum_probs=35.4
Q ss_pred CCCCcEEEEec-cccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcccC
Q 044581 144 RRGGPVLVLYG-RHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYIG 196 (203)
Q Consensus 144 k~g~~V~VV~G-~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~g 196 (203)
++|++++.+.- .-.=.-|+|.+|+.+..+++|.+..=+..-++.+.||-...+
T Consensus 70 kvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~dL~~~~~ 123 (264)
T PF06003_consen 70 KVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLSDLKPSEG 123 (264)
T ss_dssp -TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGGGEEETT-
T ss_pred CCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehhhhccccc
Confidence 35888888863 334567999999998888999887644455566666655444
No 70
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=32.00 E-value=2.5e+02 Score=22.06 Aligned_cols=96 Identities=15% Similarity=0.165 Sum_probs=53.6
Q ss_pred EeecccCCCceecceEEEEEecCCCeEEEEecCCCceEeccccCceeeecC------CCCCcEEEEe--ccccCcEEEEE
Q 044581 93 IISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLLETALP------RRGGPVLVLY--GRHKGVYGNLV 164 (203)
Q Consensus 93 Iidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETVIP------k~g~~V~VV~--G~~rG~~G~Li 164 (203)
|+-....||-|| -|.|++.++.+...|.+... +.. .++..++=+.-+ +.|+.|+... +.++=.-|+++
T Consensus 4 VlAR~~~DG~YY--~GtV~~~~~~~~~lV~f~~~-~~~-~v~~~~iI~~~~~~~~~L~~GD~VLA~~~~~~~~Y~Pg~V~ 79 (124)
T PF15057_consen 4 VLARREEDGFYY--PGTVKKCVSSGQFLVEFDDG-DTQ-EVPISDIIALSDAMRHSLQVGDKVLAPWEPDDCRYGPGTVI 79 (124)
T ss_pred EEEeeCCCCcEE--eEEEEEccCCCEEEEEECCC-CEE-EeChHHeEEccCcccCcCCCCCEEEEecCcCCCEEeCEEEE
Confidence 444455577665 58999988778888888532 222 344444433322 2388998873 33444447888
Q ss_pred Ee----eCCCceEEEEECCCCcEEEeeccchhc
Q 044581 165 DR----DLDRETGVVRDADTHELVNVKLEQIAE 193 (203)
Q Consensus 165 ~i----D~~k~~a~V~L~~~~~i~~l~~ddvck 193 (203)
+. -.+....+|.+-+ +....++...+.+
T Consensus 80 ~~~~~~~~~~~~~~V~f~n-g~~~~vp~~~~~~ 111 (124)
T PF15057_consen 80 AGPERRASEDKEYTVRFYN-GKTAKVPRGEVIW 111 (124)
T ss_pred ECccccccCCceEEEEEEC-CCCCccchhhEEE
Confidence 62 2223355666654 3344455544443
No 71
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=31.75 E-value=4.5e+02 Score=29.78 Aligned_cols=98 Identities=16% Similarity=0.070 Sum_probs=60.7
Q ss_pred cCceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCceEeccccCce----eeecCCC-----CCcEEEEecc-
Q 044581 86 RSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLL----ETALPRR-----GGPVLVLYGR- 155 (203)
Q Consensus 86 ~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~L----ETVIPk~-----g~~V~VV~G~- 155 (203)
.||.+|+--++.++.+..| +|..|.....+.+-..+.|+.. .++.+.+ +-.-|.. |+++++....
T Consensus 518 ~~GmVl~~~~r~~k~~~~y----~V~~V~~~~n~LtL~~~dG~~~-~~~p~~~~~~~~vy~~e~lelA~GDrlr~t~nd~ 592 (1623)
T PRK14712 518 RPGMVMEQWNPETRSHDRY----VTERVTAQSHSLTLRNAQGETQ-VVRISSLDSSWSLFRPEKMPVADGERLRVTGKIP 592 (1623)
T ss_pred CCCCEEEecccCcCcCceE----EEEEEcCCCceEEEEcCCCcEE-EechHHcccceeeecccccccCCCCEEEEccCCc
Confidence 7888887333444334444 7888876655543344566666 5766664 4555544 7888888543
Q ss_pred ----ccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccc
Q 044581 156 ----HKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQ 190 (203)
Q Consensus 156 ----~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~dd 190 (203)
..|..+++.+++.+ .++|....+..+..+++++
T Consensus 593 ~~~L~ngd~~tV~~i~~~--~itl~~~G~~~~~~l~~~~ 629 (1623)
T PRK14712 593 GLRVSGGDRLQVASVSED--AMTVVVPGRAEPATLPVSD 629 (1623)
T ss_pred ccCccCCCEEEEEEecCC--eEEEEECCcceeecccccc
Confidence 36789999999987 5666665433334455444
No 72
>PRK14645 hypothetical protein; Provisional
Probab=31.69 E-value=1.2e+02 Score=25.01 Aligned_cols=47 Identities=11% Similarity=-0.065 Sum_probs=33.4
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
-..|..|.|-.| .+-..|+|.+++.+ .+++.. ++..+.++|++|.+-
T Consensus 99 r~~G~~v~v~~~-~k~~~G~L~~~~d~--~i~l~~--~~~~~~i~~~~I~~~ 145 (154)
T PRK14645 99 RFAGLKAKVRGP-GENFTGRIKAVSGD--QVTFDV--GGEDRTLRIGTFQAN 145 (154)
T ss_pred HhCCCEEEEEcC-CeEEEEEEEEEeCC--EEEEEE--CCeEEEEEHHHhhhh
Confidence 344777888643 46678999999876 555544 456788999999644
No 73
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=31.53 E-value=5.8e+02 Score=29.18 Aligned_cols=99 Identities=16% Similarity=0.081 Sum_probs=60.2
Q ss_pred cccCceEEEEeecccCCCceecceEEEEEecCCCe-EEEEecCCCceEeccccCc----eeeecCCC-----CCcEEEEe
Q 044581 84 WLRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTM-CDISMDESGELIQGVDQDL----LETALPRR-----GGPVLVLY 153 (203)
Q Consensus 84 Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~-c~V~l~d~g~~v~~V~q~~----LETVIPk~-----g~~V~VV~ 153 (203)
+-.+|.+|++-+.....+.. .+|..|..... .++. .++|+.. .++.+. ++..-|.. |+++++..
T Consensus 648 ~Y~~G~vi~~~~~~~~~~~~----y~V~~v~~~~n~LtL~-~~~G~~~-~~~p~~~~~~~~vy~~~~ieiA~GDrLr~T~ 721 (1747)
T PRK13709 648 MYRPGMVMEQWNPETRSHDR----YVIDRVTAQSHSLTLR-DAQGETQ-VVKISSLDSSWSLFRPEKMPVADGERLRVLG 721 (1747)
T ss_pred cCCCCcEEEeeccccccCcc----EEEEEEcCCCCEEEEE-cCCCCEE-EeChHHhcccceeccccccccCCCCEEEEcc
Confidence 44789888875432112223 37888875433 3333 3456655 566433 44555543 88999884
Q ss_pred c-----cccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccc
Q 044581 154 G-----RHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQ 190 (203)
Q Consensus 154 G-----~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~dd 190 (203)
. -..|..+++.+++.. .++|+....+..+.|+.+.
T Consensus 722 nd~~~~l~Ngd~~tV~~i~~~--~i~l~~~~~gk~~~L~~~~ 761 (1747)
T PRK13709 722 KIPGLRLKGGDRLQVTSVSED--GLTVVVPGRAEPATLPVDD 761 (1747)
T ss_pred CCcccCccCCCEEEEEEecCC--eEEEEECCCceEEEeCCcc
Confidence 3 346899999999886 6777765444556565554
No 74
>PRK02001 hypothetical protein; Validated
Probab=31.03 E-value=1.6e+02 Score=24.24 Aligned_cols=50 Identities=18% Similarity=0.163 Sum_probs=34.5
Q ss_pred CCCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCC------------CcEEEeeccchhcc
Q 044581 143 PRRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADT------------HELVNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~------------~~i~~l~~ddvck~ 194 (203)
-..|..|.|.....+-..|+|.+.+.+ .+++.+... .....++|++|.+.
T Consensus 87 r~~G~~v~V~l~~~~~~~G~L~~~~~~--~i~l~~~~~~~~~~~k~~~~~~~~~~i~~~~I~ka 148 (152)
T PRK02001 87 KNIGRELEVLTKNGKKIEGELKSADEN--DITLEVKAREPKEGGKGKVTVEKEETITYDDIKEA 148 (152)
T ss_pred HhCCCEEEEEECCCCEEEEEEEEEeCC--EEEEEEcccccccccccccccceeEEEEhHheeeE
Confidence 345788888653357789999999977 555555431 23577999998763
No 75
>PRK04950 ProP expression regulator; Provisional
Probab=30.76 E-value=1.2e+02 Score=26.62 Aligned_cols=44 Identities=18% Similarity=0.162 Sum_probs=34.0
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccch
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQI 191 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddv 191 (203)
+.|..|.|-.|. .-.-|++++|..+ .+.|||++ |=++.+..|+|
T Consensus 168 ~~gq~v~vk~g~-~~~~a~i~ei~kd--~v~vql~~-Gl~~~v~ae~l 211 (213)
T PRK04950 168 TVGQAVKVKAGK-SAMDATVLEITKD--DVRVQLDS-GLSMIVRAEHL 211 (213)
T ss_pred ccCCEEEEeccC-CCCceEEEEEecC--cEEEEcCC-CcEEEEeHhhh
Confidence 458899999884 4477899999988 79999986 43566777665
No 76
>PRK14635 hypothetical protein; Provisional
Probab=30.71 E-value=1.2e+02 Score=24.97 Aligned_cols=47 Identities=21% Similarity=0.217 Sum_probs=30.4
Q ss_pred CCcEEEE--e-c--cccCcEEEEEEeeCCCceEEEEECC------CCcEEEeeccchhcc
Q 044581 146 GGPVLVL--Y-G--RHKGVYGNLVDRDLDRETGVVRDAD------THELVNVKLEQIAEY 194 (203)
Q Consensus 146 g~~V~VV--~-G--~~rG~~G~Li~iD~~k~~a~V~L~~------~~~i~~l~~ddvck~ 194 (203)
|..|.|- . | ++.|.+|+|.+++.+ .+++.+.. .+..+.+||++|.+.
T Consensus 99 G~~v~v~~~~~~~~~~~g~~g~L~~~~~~--~v~l~~~~k~~~~~~~~~~~ip~~~I~ka 156 (162)
T PRK14635 99 GIPVRLVFRSEESEKWQEGIFRLVNRDGD--QVELEKFQKGKKSKVKKQTTLNLKDILKG 156 (162)
T ss_pred CCEEEEEEecCCCcEEEecceEEEEEcCC--EEEEEEecccccccCCeEEEEEhHHeeee
Confidence 5556552 1 2 455666799999887 45554421 255678999999874
No 77
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=30.07 E-value=2.6e+02 Score=21.57 Aligned_cols=28 Identities=18% Similarity=0.291 Sum_probs=19.2
Q ss_pred CCceecceEEEEEecCCCeEEEEecCCCceE
Q 044581 100 SGRLYLKKGEVVDVVGPTMCDISMDESGELI 130 (203)
Q Consensus 100 ~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v 130 (203)
.|+. -|+|..+.+++...|.+.+....+
T Consensus 20 e~e~---~g~V~~~lG~~~~~V~~~dG~~~l 47 (100)
T PRK04012 20 EGEV---FGVVEQMLGANRVRVRCMDGVERM 47 (100)
T ss_pred CCEE---EEEEEEEcCCCEEEEEeCCCCEEE
Confidence 4554 457888888888888887544433
No 78
>PRK14640 hypothetical protein; Provisional
Probab=29.99 E-value=1.6e+02 Score=23.98 Aligned_cols=48 Identities=10% Similarity=-0.004 Sum_probs=33.5
Q ss_pred CCCCCcEEEEe----ccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 143 PRRGGPVLVLY----GRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~VV~----G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
-..|..|.|-. +..+-.+|+|.+++.+ .+++.+ +++...++|++|.+.
T Consensus 94 r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~--~v~l~~--~~~~~~i~~~~I~ka 145 (152)
T PRK14640 94 KYVGQEAAVTLRMATNNRRKFKGVIKAVQGD--MITLTV--DGKDEVLAFTNIQKA 145 (152)
T ss_pred HhCCCeEEEEEecccCCceEEEEEEEEEeCC--EEEEEE--CCeEEEEEhHHeeeE
Confidence 34577888853 3346778999999876 555544 355678999998775
No 79
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=29.47 E-value=91 Score=25.61 Aligned_cols=25 Identities=28% Similarity=0.236 Sum_probs=19.6
Q ss_pred CCCcEEEEeccccCcEEEEEEeeCC
Q 044581 145 RGGPVLVLYGRHKGVYGNLVDRDLD 169 (203)
Q Consensus 145 ~g~~V~VV~G~~rG~~G~Li~iD~~ 169 (203)
+|.-|+||.|.|+|..+.++.-..+
T Consensus 7 pgkVVivL~GR~AGkKaVivk~~dd 31 (134)
T PTZ00471 7 PGKVVIVTSGRYAGRKAVIVQNFDT 31 (134)
T ss_pred CCEEEEEEccccCCcEEEEEeecCC
Confidence 4556788899999999998886444
No 80
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=28.81 E-value=2.4e+02 Score=20.69 Aligned_cols=44 Identities=14% Similarity=0.267 Sum_probs=24.1
Q ss_pred EEEEEecCCCeEEEEecCCCceEeccccCceeeecCCCCCcEEE
Q 044581 108 GEVVDVVGPTMCDISMDESGELIQGVDQDLLETALPRRGGPVLV 151 (203)
Q Consensus 108 GvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETVIPk~g~~V~V 151 (203)
|.|....+++...|.+.+....+-.++..+=-++-=+.|+.|+|
T Consensus 4 ~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV 47 (78)
T cd04456 4 VRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIV 47 (78)
T ss_pred EEEEEECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEE
Confidence 67888888888888887554444333333333322333444433
No 81
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=27.95 E-value=2.4e+02 Score=20.54 Aligned_cols=21 Identities=14% Similarity=0.243 Sum_probs=15.4
Q ss_pred eEEEEEecCCCeEEEEecCCC
Q 044581 107 KGEVVDVVGPTMCDISMDESG 127 (203)
Q Consensus 107 KGvV~dV~~~~~c~V~l~d~g 127 (203)
-|.|..+.+.+...|.+.++.
T Consensus 3 ~g~V~~~~g~~~~~V~~~~g~ 23 (77)
T cd05793 3 YGQVEKMLGNGRLEVRCFDGK 23 (77)
T ss_pred EEEEEEEcCCCEEEEEECCCC
Confidence 367888888888888877543
No 82
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=27.86 E-value=2.8e+02 Score=21.29 Aligned_cols=36 Identities=25% Similarity=0.440 Sum_probs=23.2
Q ss_pred ceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCc
Q 044581 88 HIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGE 128 (203)
Q Consensus 88 ~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~ 128 (203)
.+.+++..+. .|+. -|.|+.+.+.+...|.+.+...
T Consensus 8 ~~~~~~p~~~--e~e~---~g~V~~~lG~~~~~V~~~dG~~ 43 (99)
T TIGR00523 8 QIRVRLPRKE--EGEI---LGVIEQMLGAGRVKVRCLDGKT 43 (99)
T ss_pred cceeeCCCCC--CCEE---EEEEEEEcCCCEEEEEeCCCCE
Confidence 3556666442 4554 4578888888888888875433
No 83
>PRK14646 hypothetical protein; Provisional
Probab=27.79 E-value=1.8e+02 Score=23.90 Aligned_cols=48 Identities=17% Similarity=0.181 Sum_probs=33.7
Q ss_pred CCCCCcEEEE-ecc---ccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 143 PRRGGPVLVL-YGR---HKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~VV-~G~---~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
-..|..|.|- ... .+-..|+|.+.+.+ .+++.+ ++..+.++|++|.+.
T Consensus 97 r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~--~v~l~~--~g~~~~i~~~~I~ka 148 (155)
T PRK14646 97 TFKGFPVNVELNQKNSKIKFLNGLLYEKSKD--YLAINI--KGKIKKIPFNEVLKI 148 (155)
T ss_pred HhCCCEEEEEEecCcCCeEEEEEEEEEEeCC--EEEEEE--CCEEEEEEHHHeeeE
Confidence 3457788884 222 34456999999987 555544 466788999999875
No 84
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.72 E-value=2e+02 Score=23.90 Aligned_cols=46 Identities=24% Similarity=0.208 Sum_probs=32.7
Q ss_pred CCCcEEEEe----ccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 145 RGGPVLVLY----GRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 145 ~g~~V~VV~----G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
.|..|+|.. ..-+-..|+|..++.+ +.++.++ +..+.++|+.+.+-
T Consensus 98 ~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~--~v~~~~~--~k~v~Ip~~~i~kA 147 (153)
T COG0779 98 IGEKVKVKLRLPIEGRKKFEGKIVAVDGE--TVTLEVD--GKEVEIPFSDIAKA 147 (153)
T ss_pred cCcEEEEEEecccCCceEEEEEEEEEcCC--eEEEEEC--CEEEEEEcccchhh
Confidence 366777754 3345578999999998 5555543 45589999999874
No 85
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3MRZ_C 3F1H_D 3PYO_C 3F1F_D 3PYV_C 3PYR_C 1VSA_B 3D5B_D 3PYT_C 3MS1_C ....
Probab=26.87 E-value=1.3e+02 Score=24.11 Aligned_cols=35 Identities=17% Similarity=0.239 Sum_probs=28.2
Q ss_pred ccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhc
Q 044581 156 HKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAE 193 (203)
Q Consensus 156 ~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck 193 (203)
-+|..++|+..+.. .++|+|-+ +++..|+.+..|-
T Consensus 34 aAGt~a~ii~k~~~--~~~ikLPS-G~~k~v~~~c~At 68 (130)
T PF03947_consen 34 AAGTYAQIISKEGN--YVVIKLPS-GEIKLVSSNCRAT 68 (130)
T ss_dssp STTBBEEEEEEESS--EEEEEETT-SEEEEEETTSEEE
T ss_pred eCCCEEEEEEeccc--eeEEEecC-CCeEeecccceEE
Confidence 47899999999985 89999985 6777788777653
No 86
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=26.61 E-value=1.1e+02 Score=22.64 Aligned_cols=35 Identities=23% Similarity=0.232 Sum_probs=27.8
Q ss_pred CCCCcEEEEecc--ccCcEEEEEEeeCC--CceEEEEEC
Q 044581 144 RRGGPVLVLYGR--HKGVYGNLVDRDLD--RETGVVRDA 178 (203)
Q Consensus 144 k~g~~V~VV~G~--~rG~~G~Li~iD~~--k~~a~V~L~ 178 (203)
+.|.+|+|++=+ +-..+|++.++|.+ ++-++|+++
T Consensus 4 ~rGskVrIlR~ESYWyn~vGtV~svD~sgi~YPV~VRF~ 42 (71)
T PRK02749 4 SRGDKVRILRPESYWYNEVGTVASVDKSGIKYPVIVRFD 42 (71)
T ss_pred ccCCEEEEccccceeecCcceEEEEccCCCeeeEEEEee
Confidence 458899999755 46789999999987 577788875
No 87
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=26.37 E-value=1.5e+02 Score=30.24 Aligned_cols=45 Identities=22% Similarity=0.296 Sum_probs=33.7
Q ss_pred CCCCcEEEEe-----ccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccch
Q 044581 144 RRGGPVLVLY-----GRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQI 191 (203)
Q Consensus 144 k~g~~V~VV~-----G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddv 191 (203)
..|++||.+. |-+-|.+|++.+++.. ...|++++ +..+.++.+++
T Consensus 609 ~~GDrV~~~~N~~~~gv~NGd~g~V~~i~~~--~i~v~~~~-G~~v~~~~~~~ 658 (744)
T TIGR02768 609 AAGDRIVFLENNRDLGVKNGMLGTVEEIEDG--RLVVQLDS-GELVIIPQAEY 658 (744)
T ss_pred cCCCEEEEEecccccCCcCCCEEEEEEecCC--eEEEEECC-CCEEEECHHHh
Confidence 5789999983 4567999999999865 67787764 55666776654
No 88
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=26.24 E-value=2.5e+02 Score=22.08 Aligned_cols=46 Identities=17% Similarity=0.048 Sum_probs=31.5
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcccC
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYIG 196 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~g 196 (203)
++|++|+-..| ..|++.+++.+ .+.|++.. +-.+.+.-..|++..-
T Consensus 40 k~GD~VvT~gG----i~G~V~~I~d~--~v~leia~-gv~i~~~r~AI~~v~~ 85 (109)
T PRK05886 40 QPGDRVHTTSG----LQATIVGITDD--TVDLEIAP-GVVTTWMKLAVRDRIL 85 (109)
T ss_pred CCCCEEEECCC----eEEEEEEEeCC--EEEEEECC-CeEEEEEhhheeeecC
Confidence 34778877666 88999999865 78888753 4345566666665443
No 89
>PF12073 DUF3553: Protein of unknown function (DUF3553); InterPro: IPR021938 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=26.13 E-value=2.1e+02 Score=19.88 Aligned_cols=50 Identities=16% Similarity=0.184 Sum_probs=32.0
Q ss_pred ccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCceEeccccCceeee
Q 044581 85 LRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLLETA 141 (203)
Q Consensus 85 l~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETV 141 (203)
|.||..||=.+.. ..=-|-|.+.. .+..+|.+.+-|+.+.+...=.|+.|
T Consensus 1 l~pG~~VrHP~~p------dWG~GqVqS~i-~~rvTVnF~~aGK~vI~~~~v~L~~v 50 (52)
T PF12073_consen 1 LEPGMLVRHPDHP------DWGIGQVQSNI-GGRVTVNFEHAGKKVIDGSRVALEKV 50 (52)
T ss_pred CCCCCEEeCCCCC------CCcceEEEEec-CCeEEEeeccCCeEEEeccEEEEEEc
Confidence 3566666544321 23467888876 56789999988887755555555554
No 90
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=26.10 E-value=1.2e+02 Score=21.98 Aligned_cols=36 Identities=25% Similarity=0.278 Sum_probs=28.4
Q ss_pred CCCCcEEEEecc--ccCcEEEEEEeeCC--CceEEEEECC
Q 044581 144 RRGGPVLVLYGR--HKGVYGNLVDRDLD--RETGVVRDAD 179 (203)
Q Consensus 144 k~g~~V~VV~G~--~rG~~G~Li~iD~~--k~~a~V~L~~ 179 (203)
+.|.+|+|++=+ +-..+|++.++|.+ ++-++|+++.
T Consensus 3 ~rGskVrIlR~ESYWyn~vGtV~svd~~gi~YPV~VRF~k 42 (64)
T CHL00125 3 KRGSKVRILRKESYWYNEIGTVATVDQSGIRYPVLVRFEK 42 (64)
T ss_pred ccCCEEEEccccceeecCcceEEEEcCCCCCccEEEEEee
Confidence 458899999755 45788999999886 5778888864
No 91
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=25.70 E-value=2.2e+02 Score=21.94 Aligned_cols=26 Identities=27% Similarity=0.401 Sum_probs=21.0
Q ss_pred ccCceEEEEeecccCCCceecceEEEEEecC
Q 044581 85 LRSHIRVRIISKELKSGRLYLKKGEVVDVVG 115 (203)
Q Consensus 85 l~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~ 115 (203)
+.+|=.|.|+ .|++.|+.|.|..|..
T Consensus 5 i~kGD~V~Vi-----~G~dKGk~G~V~~V~~ 30 (105)
T PRK00004 5 IKKGDTVIVI-----AGKDKGKRGKVLKVLP 30 (105)
T ss_pred ccCCCEEEEe-----EcCCCCcEEEEEEEEc
Confidence 3456678888 5888999999999964
No 92
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=25.35 E-value=1.2e+02 Score=21.76 Aligned_cols=28 Identities=18% Similarity=0.111 Sum_probs=20.3
Q ss_pred cEEEEEEeeCCCceEEEEECCCCcEEEeecc
Q 044581 159 VYGNLVDRDLDRETGVVRDADTHELVNVKLE 189 (203)
Q Consensus 159 ~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~d 189 (203)
..|++.++|.. ..+|.|+ |++.+.+|.+
T Consensus 5 veG~I~~id~~--~~titLd-DGksy~lp~e 32 (61)
T PF07076_consen 5 VEGTIKSIDPE--TMTITLD-DGKSYKLPEE 32 (61)
T ss_pred ceEEEEEEcCC--ceEEEec-CCCEEECCCc
Confidence 46899999998 5667787 4666665544
No 93
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=25.23 E-value=1.6e+02 Score=21.87 Aligned_cols=53 Identities=21% Similarity=0.222 Sum_probs=33.5
Q ss_pred ceEEEEeecccCCCce-----------ecceEEEEEec----CCCeEEEEecCCCceEeccccCceeee
Q 044581 88 HIRVRIISKELKSGRL-----------YLKKGEVVDVV----GPTMCDISMDESGELIQGVDQDLLETA 141 (203)
Q Consensus 88 ~I~VRIidk~~~~Gk~-----------y~kKGvV~dV~----~~~~c~V~l~d~g~~v~~V~q~~LETV 141 (203)
+-.|+....=.+||.| -|..|.|+++- +.+...|.+.+.+..+ +--++.|++|
T Consensus 8 G~~V~a~~~irNDGt~Pg~~~g~lLv~~G~~G~V~~iG~flq~~~IY~V~F~~~~~vV-Gcre~EL~~~ 75 (75)
T PF04319_consen 8 GDKVRARKDIRNDGTFPGKEIGELLVRKGDVGYVVSIGTFLQDFYIYLVHFLERGRVV-GCREEELEPV 75 (75)
T ss_pred CCEEEEEEEeEcCCCCCCCCCCCEEEcCCCcEEEEEeeEEcceeEEEEEEEcCCCCEE-eEcHHHcccC
Confidence 6666666554556665 34568888872 1334566776777766 7777777765
No 94
>PRK14643 hypothetical protein; Provisional
Probab=24.43 E-value=2e+02 Score=23.94 Aligned_cols=49 Identities=20% Similarity=0.150 Sum_probs=33.1
Q ss_pred CCCCcEEEE-ecc---ccCcEEEEEEeeCCCceEEEEE----CCCCcEEEeeccchhcc
Q 044581 144 RRGGPVLVL-YGR---HKGVYGNLVDRDLDRETGVVRD----ADTHELVNVKLEQIAEY 194 (203)
Q Consensus 144 k~g~~V~VV-~G~---~rG~~G~Li~iD~~k~~a~V~L----~~~~~i~~l~~ddvck~ 194 (203)
..|..|.|- ..+ .+-..|+|.+.+.+. ..+.+ ...+..+.++|++|.+.
T Consensus 102 ~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~--~~l~l~~~~~~~~~~~~ip~~~I~ka 158 (164)
T PRK14643 102 ALNQWVYVQLNNEIKKVKEFEGYVTKYNVNT--NTFRFTFFIKGQKKKLDVKYEQIKFI 158 (164)
T ss_pred hcCCeEEEEEecccCCceEEEEEEEEEeCCc--EEEEEEeeccCcCcEEEEeHHHhhhe
Confidence 347788884 332 345789999999873 44442 23356778999999874
No 95
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=24.05 E-value=1.1e+02 Score=23.84 Aligned_cols=38 Identities=18% Similarity=0.226 Sum_probs=28.5
Q ss_pred ccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhc
Q 044581 156 HKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAE 193 (203)
Q Consensus 156 ~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck 193 (203)
|-|.||++.++...-+-+.|++.+....+.+..++|-.
T Consensus 58 yhGkTG~V~~v~~~A~~V~v~vg~k~Kri~vr~eHlk~ 95 (98)
T PRK04306 58 FHGKTGTVVGKRGRAYIVEVKDGGKEKTLIVRPEHLRP 95 (98)
T ss_pred ccCCCEEEEeecCeEEEEEEEECCceeEEEcCHHHcCc
Confidence 67999999999999777777665544556677777654
No 96
>PRK14636 hypothetical protein; Provisional
Probab=24.04 E-value=2.4e+02 Score=23.75 Aligned_cols=49 Identities=22% Similarity=0.169 Sum_probs=33.4
Q ss_pred CCCCCcEEE-Eecc---ccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 143 PRRGGPVLV-LYGR---HKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~V-V~G~---~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
-..|..|.| +..+ .+-.+|+|.+.+.+ .+++.+.. +..+.++|++|.+.
T Consensus 95 r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~--~v~l~~~~-~~~~~i~~~~I~kA 147 (176)
T PRK14636 95 DWAGHEARIALSEPLDGRKQFRGELKGIDGD--TVTIADNK-AGEVILPFAAIESA 147 (176)
T ss_pred HhCCCeEEEEEecccCCeEEEEEEEEEEeCC--EEEEEEcC-CcEEEEEhHHcceE
Confidence 345778888 4433 34558999999887 55555432 44678999999874
No 97
>PRK14647 hypothetical protein; Provisional
Probab=24.01 E-value=2.4e+02 Score=23.13 Aligned_cols=49 Identities=18% Similarity=0.128 Sum_probs=33.8
Q ss_pred CCCCCcEEEEe-c--------cccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 143 PRRGGPVLVLY-G--------RHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 143 Pk~g~~V~VV~-G--------~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
-..|..|.|-. . ..+-.+|+|.+++.+ .+.+.+. ++..+.++|++|.+.
T Consensus 96 r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~--~v~l~~~-~~~~~~i~~~~I~ka 153 (159)
T PRK14647 96 RYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADG--VVTIALK-EGQQARIPLDKIAKA 153 (159)
T ss_pred HhCCcEEEEEEeccccccccCCceEEEEEEEeecCC--EEEEEEc-CCcEEEEEHHHCCEE
Confidence 34577788843 2 246778999999876 5555543 245678999999874
No 98
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=23.97 E-value=1.2e+02 Score=23.74 Aligned_cols=40 Identities=18% Similarity=0.140 Sum_probs=29.5
Q ss_pred ccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhccc
Q 044581 156 HKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYI 195 (203)
Q Consensus 156 ~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~ 195 (203)
|-|.||+++....+-+.+.|.+.+....+++..++|-.+-
T Consensus 56 f~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv~peHLk~~~ 95 (98)
T COG2139 56 FQGKTGTVVGVRGRAYKVEVYDGNKEKTLIVRPEHLKPQK 95 (98)
T ss_pred ccCcceEEEeccCCEEEEEEecCCceEEEEeCHHHccccc
Confidence 6799999999999977777665444456678777775543
No 99
>PRK14634 hypothetical protein; Provisional
Probab=23.84 E-value=2.1e+02 Score=23.48 Aligned_cols=47 Identities=19% Similarity=0.213 Sum_probs=33.2
Q ss_pred CCCCcEEE-Eec---cccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcc
Q 044581 144 RRGGPVLV-LYG---RHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEY 194 (203)
Q Consensus 144 k~g~~V~V-V~G---~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~ 194 (203)
..|..|.| +.. ..+-..|+|.+.+.+ .+.+.+ ++..+.++|++|.+.
T Consensus 98 ~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~--~v~l~~--~~~~~~i~~~~I~ka 148 (155)
T PRK14634 98 FRGFPVEVSHRDDDGSEQRLEGLLLERNED--HLQINI--RGRIKRIPRDSVISV 148 (155)
T ss_pred hCCCeEEEEEecCCCCeEEEEEEEEEEeCC--EEEEEE--CCEEEEEEHHHeeeE
Confidence 34777888 333 235678999999877 555444 456788999999875
No 100
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=23.81 E-value=3.3e+02 Score=21.56 Aligned_cols=46 Identities=22% Similarity=0.371 Sum_probs=32.1
Q ss_pred CCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhcccC
Q 044581 145 RGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYIG 196 (203)
Q Consensus 145 ~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~g 196 (203)
+|++|+-..| ..|++.+++.+...+.++. ++-.+.+.-..|+....
T Consensus 39 ~GD~VvT~GG----i~G~V~~I~~~~~~v~le~--~gv~i~v~r~AI~~Vv~ 84 (113)
T PRK06531 39 KGDEVVTIGG----LYGTVDEVDTEAKTIVLDV--DGVYLTFELAAIKRVVP 84 (113)
T ss_pred CCCEEEECCC----cEEEEEEEecCCCEEEEEE--CCEEEEEEhhHhhhhcC
Confidence 4777776665 8899999998766777665 34445677667776544
No 101
>PLN00208 translation initiation factor (eIF); Provisional
Probab=23.40 E-value=4.3e+02 Score=21.90 Aligned_cols=64 Identities=13% Similarity=0.226 Sum_probs=38.1
Q ss_pred CCceecceEEEEEecCCCeEEEEecCCCceEeccccCceeeecCCCCCcEEEEeccccCcEEEEEEe
Q 044581 100 SGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLLETALPRRGGPVLVLYGRHKGVYGNLVDR 166 (203)
Q Consensus 100 ~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETVIPk~g~~V~VV~G~~rG~~G~Li~i 166 (203)
.|+-| |.|+.+++.+.+.|.+.+....+-.|+-.+=-.|-=..|+.|+|-.-+|--..|.++-+
T Consensus 31 egq~~---g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~VlVel~~~d~~KgdIv~r 94 (145)
T PLN00208 31 DGQEY---AQVLRMLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
T ss_pred CCcEE---EEEEEEcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCEEEEEccCCCCCEEEEEEE
Confidence 45544 46888888888888887655555444444433333444666666544455555555554
No 102
>PF14509 GH97_C: Glycosyl-hydrolase 97 C-terminal, oligomerisation; PDB: 3A24_A 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A.
Probab=23.02 E-value=3.1e+02 Score=21.00 Aligned_cols=45 Identities=18% Similarity=0.122 Sum_probs=28.7
Q ss_pred cEEEEeccccCcEEEEEEee--CCCceEEEEECCCCcEEEeeccchhc
Q 044581 148 PVLVLYGRHKGVYGNLVDRD--LDRETGVVRDADTHELVNVKLEQIAE 193 (203)
Q Consensus 148 ~V~VV~G~~rG~~G~Li~iD--~~k~~a~V~L~~~~~i~~l~~ddvck 193 (203)
..++|.|. -|....+--+. .+.+-+-.--..+...+.|+|++|.+
T Consensus 5 eT~~L~g~-pGeyvviARr~~~G~~Wyvg~in~~~~r~i~l~L~FL~~ 51 (103)
T PF14509_consen 5 ETRVLDGY-PGEYVVIARRKRDGDDWYVGGINGEDARTITLPLSFLDK 51 (103)
T ss_dssp EEEEEEEE-TTTEEEEEEEETTTTEEEEEEEE-TT-EEEEEEGCCS-T
T ss_pred ceEEeCCc-CceEEEEEEEcCCCCCEEEEEeeCCCceEEEEECcccCC
Confidence 45778885 88888888888 66654433233345567788888764
No 103
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=22.81 E-value=2.1e+02 Score=20.41 Aligned_cols=43 Identities=30% Similarity=0.346 Sum_probs=27.8
Q ss_pred eEEEEEe-cCCCeEEEEecCCCceEeccccCceeeecCCCCCcEEEEec
Q 044581 107 KGEVVDV-VGPTMCDISMDESGELIQGVDQDLLETALPRRGGPVLVLYG 154 (203)
Q Consensus 107 KGvV~dV-~~~~~c~V~l~d~g~~v~~V~q~~LETVIPk~g~~V~VV~G 154 (203)
.+.|+++ .+...+.|... |... .|+-..|.. ++.|+.|+|=.|
T Consensus 6 P~~Vv~v~~~~~~A~v~~~--G~~~-~V~~~lv~~--v~~Gd~VLVHaG 49 (68)
T PF01455_consen 6 PGRVVEVDEDGGMAVVDFG--GVRR-EVSLALVPD--VKVGDYVLVHAG 49 (68)
T ss_dssp EEEEEEEETTTTEEEEEET--TEEE-EEEGTTCTS--B-TT-EEEEETT
T ss_pred cEEEEEEeCCCCEEEEEcC--CcEE-EEEEEEeCC--CCCCCEEEEecC
Confidence 4567777 33677888765 4333 677777776 777999999655
No 104
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=22.64 E-value=4.6e+02 Score=21.98 Aligned_cols=64 Identities=11% Similarity=0.169 Sum_probs=38.6
Q ss_pred CCceecceEEEEEecCCCeEEEEecCCCceEeccccCceeeecCCCCCcEEEEeccccCcEEEEEEe
Q 044581 100 SGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLLETALPRRGGPVLVLYGRHKGVYGNLVDR 166 (203)
Q Consensus 100 ~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETVIPk~g~~V~VV~G~~rG~~G~Li~i 166 (203)
.|+-| |.|+.+++.+.+.|.+.+....+-.|+-.+=--|-=..|+.|+|-.-+|--..|.++-+
T Consensus 31 egq~~---g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~VlVel~~yd~~KgdIi~R 94 (155)
T PTZ00329 31 EGQEY---AQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDFQDSKADVILK 94 (155)
T ss_pred CCcEE---EEEEEEcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCEEEEeccCCCCCEEEEEEE
Confidence 45544 46888888888888887655555444444333333444666666555555566666655
No 105
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=22.31 E-value=2.1e+02 Score=19.12 Aligned_cols=34 Identities=21% Similarity=0.259 Sum_probs=20.3
Q ss_pred ccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchh
Q 044581 156 HKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIA 192 (203)
Q Consensus 156 ~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvc 192 (203)
+.|.+|+.+.+|.+ |--.++. +.....+|+-++-
T Consensus 7 ~~g~tGtFlGvDE~-FGmLLr~--~~~T~LIPLT~lL 40 (42)
T PF14563_consen 7 VAGLTGTFLGVDED-FGMLLRD--DDTTHLIPLTTLL 40 (42)
T ss_dssp ETTEEEEEEEE-TT---EEEE---SS-EEEE-GGGGS
T ss_pred EcCcceeEEeeccc-cceEEEe--CCccEEEEchHhh
Confidence 57899999999987 3333343 3457778877653
No 106
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=22.16 E-value=1.6e+02 Score=23.96 Aligned_cols=31 Identities=26% Similarity=0.292 Sum_probs=23.5
Q ss_pred CCcEEEEeccccCcEEEEEEeeCCCceEEEEE
Q 044581 146 GGPVLVLYGRHKGVYGNLVDRDLDRETGVVRD 177 (203)
Q Consensus 146 g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L 177 (203)
|.-|+|..|++.|..+.+++|-..+ .+.|.=
T Consensus 11 GRVvli~~Gp~~GKL~vIVDIID~n-RvLVDG 41 (130)
T PTZ00065 11 GRLCLIQYGPDAGKLCFIVDIVTPT-RVLVDG 41 (130)
T ss_pred ceEEEEecCCCCCCEEEEEEEEcCC-eEEEeC
Confidence 5567777999999999999985443 566643
No 107
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=21.87 E-value=3.2e+02 Score=21.02 Aligned_cols=45 Identities=18% Similarity=0.282 Sum_probs=33.2
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCCceEEEEECCCCcEEEeeccchhccc
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDRETGVVRDADTHELVNVKLEQIAEYI 195 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k~~a~V~L~~~~~i~~l~~ddvck~~ 195 (203)
++|++|.-..| ..|++.+++.+. ..|.+. ++..+.+.-+.++...
T Consensus 45 ~kGD~VvT~gG----i~G~V~~v~d~~--v~I~l~-~~~~i~~~k~aI~~v~ 89 (97)
T COG1862 45 KKGDEVVTIGG----IVGTVTKVGDDT--VEIELG-DGTKIKFEKEAIATVL 89 (97)
T ss_pred cCCCEEEEcCC----eEEEEEEEecCc--EEEEEC-CCeEEEEEHHHHHhhc
Confidence 35788877766 899999999884 778887 4545667777777643
No 108
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=21.31 E-value=3.1e+02 Score=19.40 Aligned_cols=24 Identities=17% Similarity=0.018 Sum_probs=13.4
Q ss_pred ecCCCCCcEEEEeccccCcEEEEE
Q 044581 141 ALPRRGGPVLVLYGRHKGVYGNLV 164 (203)
Q Consensus 141 VIPk~g~~V~VV~G~~rG~~G~Li 164 (203)
+-|..|+.|.+-.-.+-...|.++
T Consensus 45 i~i~vGD~V~ve~~~~~~~~g~Iv 68 (72)
T PRK00276 45 IRILPGDKVTVELSPYDLTKGRIT 68 (72)
T ss_pred cccCCCCEEEEEEcccCCCeEEEE
Confidence 347788888775433333344444
No 109
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=20.98 E-value=1.7e+02 Score=23.60 Aligned_cols=27 Identities=30% Similarity=0.211 Sum_probs=22.1
Q ss_pred CCCCcEEEEeccccCcEEEEEEeeCCC
Q 044581 144 RRGGPVLVLYGRHKGVYGNLVDRDLDR 170 (203)
Q Consensus 144 k~g~~V~VV~G~~rG~~G~Li~iD~~k 170 (203)
..|.=|.|+.|.++|..+.++++-.++
T Consensus 6 ~~GrVvvv~~GR~aGkk~VIv~~iDd~ 32 (125)
T COG2163 6 EVGRVVVVTAGRFAGKKVVIVKIIDDN 32 (125)
T ss_pred cCCeEEEEecceeCCceEEEEEEccCC
Confidence 345567778999999999999987775
No 110
>smart00443 G_patch glycine rich nucleic binding domain. A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.
Probab=20.90 E-value=70 Score=20.67 Aligned_cols=20 Identities=40% Similarity=0.574 Sum_probs=16.4
Q ss_pred CCCcCCCCCCCeeeEEeccc
Q 044581 1 GRGIGKNSKGNVKIREFGKK 20 (203)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~ 20 (203)
|.|+|+++.+-+..+++..+
T Consensus 19 G~GLG~~~~g~~~pi~~~~~ 38 (47)
T smart00443 19 GQGLGKNEQGIVEPISAEIK 38 (47)
T ss_pred CCcCCCCCCcCccceeEeec
Confidence 68999999988887777665
No 111
>PRK14632 hypothetical protein; Provisional
Probab=20.75 E-value=3.1e+02 Score=22.91 Aligned_cols=49 Identities=14% Similarity=0.209 Sum_probs=33.0
Q ss_pred CCCCcEEEE-ecc------ccCcEEEEEEeeCCCceEEEEECCC------CcEEEeeccchhcc
Q 044581 144 RRGGPVLVL-YGR------HKGVYGNLVDRDLDRETGVVRDADT------HELVNVKLEQIAEY 194 (203)
Q Consensus 144 k~g~~V~VV-~G~------~rG~~G~Li~iD~~k~~a~V~L~~~------~~i~~l~~ddvck~ 194 (203)
..|..|.|- ... .+-..|+|.+++.+ .+++..... ...+.++|++|.+.
T Consensus 96 ~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~--~i~l~~~~~~~~~~~~~~~~i~~~~I~ka 157 (172)
T PRK14632 96 YVGRQIELTLIDPTPEWPGRRKFRGELLAVEGD--TVVLRPEGAPAPEAEEAVLRTSWQGVRKA 157 (172)
T ss_pred hCCCEEEEEEeccccccCCceEEEEEEEEEeCC--EEEEEEcCcccccCCceeEEEEhHHccEE
Confidence 347788884 332 45678999999876 555555321 23678999999874
No 112
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=20.51 E-value=2e+02 Score=20.38 Aligned_cols=57 Identities=12% Similarity=0.071 Sum_probs=36.2
Q ss_pred CCcccCceEEEEeecccCCCceecceEEEEEecCCCeEEEEecCCCceEeccccCceeeecCCC
Q 044581 82 VPWLRSHIRVRIISKELKSGRLYLKKGEVVDVVGPTMCDISMDESGELIQGVDQDLLETALPRR 145 (203)
Q Consensus 82 ~~Wl~~~I~VRIidk~~~~Gk~y~kKGvV~dV~~~~~c~V~l~d~g~~v~~V~q~~LETVIPk~ 145 (203)
..++..+..+.+. . ++.+| -|+|....+...+.|++.|-|... .++.++|-...|.-
T Consensus 51 ~~~~~~~~~~~~~---~-~~~w~--Ra~I~~~~~~~~~~V~~iD~G~~~-~v~~~~l~~l~~~~ 107 (121)
T PF00567_consen 51 ESNPGEGCLCVVS---E-DGRWY--RAVITVDIDENQYKVFLIDYGNTE-KVSASDLRPLPPEF 107 (121)
T ss_dssp T--TTEEEEEEET---T-TSEEE--EEEEEEEECTTEEEEEETTTTEEE-EEEGGGEEE--HHH
T ss_pred ccccCCEEEEEEe---c-CCcee--eEEEEEecccceeEEEEEecCceE-EEcHHHhhhhCHHH
Confidence 4444444444432 2 56665 567755566889999999999877 68888887766543
Done!