Query 018594
Match_columns 353
No_of_seqs 219 out of 346
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 02:24:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018594.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018594hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2837 Protein containing a U 100.0 7.6E-77 1.7E-81 559.7 5.3 256 1-315 54-309 (309)
2 PF10357 Kin17_mid: Domain of 100.0 3.4E-66 7.4E-71 444.4 7.6 125 1-125 3-127 (127)
3 KOG4315 G-patch nucleic acid b 99.7 2.8E-18 6.2E-23 170.8 2.3 112 237-352 331-445 (455)
4 KOG1999 RNA polymerase II tran 98.2 1.1E-06 2.4E-11 96.0 4.3 108 237-353 915-1022(1024)
5 PF00467 KOW: KOW motif; Inte 97.3 0.00042 9E-09 46.3 4.5 31 299-329 1-31 (32)
6 smart00739 KOW KOW (Kyprides, 96.8 0.0022 4.8E-08 40.5 4.0 26 297-322 2-27 (28)
7 PRK12281 rplX 50S ribosomal pr 96.2 0.0087 1.9E-07 47.9 5.0 33 298-330 8-40 (76)
8 CHL00141 rpl24 ribosomal prote 96.2 0.0091 2E-07 48.5 5.0 32 298-329 10-41 (83)
9 TIGR00405 L26e_arch ribosomal 95.9 0.02 4.2E-07 50.0 6.2 51 297-351 87-139 (145)
10 PRK00004 rplX 50S ribosomal pr 95.6 0.022 4.7E-07 48.1 5.0 33 298-330 6-38 (105)
11 PRK01191 rpl24p 50S ribosomal 95.0 0.043 9.4E-07 47.6 5.2 32 298-329 47-78 (120)
12 TIGR01079 rplX_bact ribosomal 95.0 0.043 9.2E-07 46.4 4.9 33 298-330 5-37 (104)
13 PTZ00194 60S ribosomal protein 95.0 0.039 8.5E-07 49.2 4.9 33 298-330 48-80 (143)
14 PRK05609 nusG transcription an 94.9 0.069 1.5E-06 47.8 6.4 53 297-352 127-180 (181)
15 TIGR01080 rplX_A_E ribosomal p 94.9 0.044 9.4E-07 47.2 4.8 32 298-329 43-74 (114)
16 TIGR00922 nusG transcription t 94.9 0.072 1.6E-06 47.5 6.4 50 297-350 120-171 (172)
17 PRK08559 nusG transcription an 94.5 0.1 2.2E-06 46.5 6.4 50 297-350 95-146 (153)
18 COG0250 NusG Transcription ant 93.4 0.19 4.2E-06 46.1 6.1 56 295-352 122-177 (178)
19 PRK04313 30S ribosomal protein 92.5 1 2.2E-05 43.4 9.9 73 245-324 119-199 (237)
20 TIGR01955 RfaH transcriptional 92.2 0.29 6.3E-06 42.9 5.4 49 297-349 109-158 (159)
21 PLN00036 40S ribosomal protein 91.9 1.2 2.7E-05 43.4 9.7 71 245-322 123-200 (261)
22 PRK09014 rfaH transcriptional 91.8 0.35 7.6E-06 42.8 5.5 50 297-351 110-161 (162)
23 PTZ00118 40S ribosomal protein 91.6 1.5 3.2E-05 42.9 9.9 80 245-332 123-211 (262)
24 PF11623 DUF3252: Protein of u 91.6 0.72 1.6E-05 34.6 6.0 51 240-293 2-53 (53)
25 COG0198 RplX Ribosomal protein 90.7 0.43 9.3E-06 40.6 4.6 30 298-329 6-35 (104)
26 TIGR01956 NusG_myco NusG famil 89.9 0.81 1.8E-05 44.6 6.4 51 297-349 206-256 (258)
27 COG5164 SPT5 Transcription elo 89.9 0.79 1.7E-05 48.1 6.6 70 262-334 298-387 (607)
28 PTZ00223 40S ribosomal protein 89.5 2.4 5.1E-05 41.7 9.3 72 245-323 120-198 (273)
29 COG1471 RPS4A Ribosomal protei 89.4 2.5 5.3E-05 40.8 9.1 53 282-334 156-213 (241)
30 KOG1999 RNA polymerase II tran 85.0 3.5 7.7E-05 46.6 8.4 78 240-324 408-487 (1024)
31 PF15591 Imm17: Immunity prote 84.5 1.9 4.1E-05 34.6 4.5 50 245-294 10-63 (74)
32 PF15057 DUF4537: Domain of un 83.7 13 0.00028 32.2 9.7 97 247-351 3-111 (124)
33 smart00743 Agenet Tudor-like d 78.0 7.4 0.00016 28.7 5.6 54 241-298 4-59 (61)
34 smart00333 TUDOR Tudor domain. 73.7 13 0.00027 26.8 5.7 53 240-297 3-55 (57)
35 PLN00045 photosystem I reactio 71.8 6.5 0.00014 33.1 4.2 58 292-349 35-97 (101)
36 PRK08559 nusG transcription an 71.2 15 0.00032 32.7 6.7 53 240-297 95-150 (153)
37 TIGR00405 L26e_arch ribosomal 70.5 12 0.00026 32.5 5.9 55 238-297 85-142 (145)
38 TIGR02760 TraI_TIGR conjugativ 65.8 43 0.00093 41.3 11.0 89 238-333 680-786 (1960)
39 PTZ00065 60S ribosomal protein 62.3 20 0.00044 31.7 5.6 36 299-338 10-46 (130)
40 PRK04333 50S ribosomal protein 59.1 17 0.00037 29.7 4.3 28 298-325 5-32 (84)
41 cd04508 TUDOR Tudor domains ar 59.0 18 0.00038 25.1 3.9 37 254-292 10-46 (48)
42 PF02427 PSI_PsaE: Photosystem 57.7 37 0.0008 26.4 5.6 53 297-349 1-57 (61)
43 PF10615 DUF2470: Protein of u 56.9 4.8 0.0001 32.0 0.7 36 53-88 16-55 (83)
44 PTZ00471 60S ribosomal protein 56.5 18 0.00038 32.2 4.3 26 298-323 6-31 (134)
45 PF10771 DUF2582: Protein of u 55.6 12 0.00026 29.3 2.7 23 66-88 43-65 (65)
46 smart00333 TUDOR Tudor domain. 55.3 49 0.0011 23.6 5.8 52 296-352 2-53 (57)
47 PF01455 HupF_HypC: HupF/HypC 53.9 43 0.00094 26.1 5.6 42 263-308 7-49 (68)
48 PF01176 eIF-1a: Translation i 51.5 59 0.0013 24.8 6.0 57 262-318 6-63 (65)
49 PF00567 TUDOR: Tudor domain; 51.2 82 0.0018 24.8 7.1 57 236-298 50-106 (121)
50 CHL00010 infA translation init 50.9 1.3E+02 0.0027 24.0 8.8 62 261-323 9-73 (78)
51 cd01734 YlxS_C YxlS is a Bacil 48.5 41 0.00088 26.8 4.9 51 297-351 22-76 (83)
52 PRK14639 hypothetical protein; 47.4 39 0.00084 29.9 5.0 72 271-352 63-134 (140)
53 COG2163 RPL14A Ribosomal prote 44.4 35 0.00075 30.0 4.1 28 297-324 5-32 (125)
54 KOG1708 Mitochondrial/chloropl 40.7 40 0.00086 32.3 4.2 33 298-330 74-106 (236)
55 TIGR01955 RfaH transcriptional 40.6 57 0.0012 28.4 5.0 52 237-293 106-159 (159)
56 PF12872 OST-HTH: OST-HTH/LOTU 39.6 27 0.0006 26.3 2.5 68 17-86 4-74 (74)
57 TIGR00922 nusG transcription t 39.3 78 0.0017 28.0 5.7 53 236-293 116-171 (172)
58 PRK14630 hypothetical protein; 38.1 73 0.0016 28.3 5.3 69 271-352 72-140 (143)
59 PRK14633 hypothetical protein; 38.1 66 0.0014 28.7 5.0 70 272-352 70-143 (150)
60 CHL00125 psaE photosystem I su 38.1 56 0.0012 25.6 3.9 52 298-349 3-58 (64)
61 PRK14638 hypothetical protein; 37.6 60 0.0013 29.0 4.7 69 271-351 75-143 (150)
62 PRK13709 conjugal transfer nic 37.3 2.4E+02 0.0053 34.8 10.8 88 238-332 647-749 (1747)
63 PRK14637 hypothetical protein; 37.1 78 0.0017 28.4 5.4 47 298-352 96-143 (151)
64 COG2163 RPL14A Ribosomal prote 35.8 68 0.0015 28.2 4.6 33 240-277 5-37 (125)
65 PRK14636 hypothetical protein; 35.6 87 0.0019 28.8 5.5 71 271-352 73-147 (176)
66 PRK04914 ATP-dependent helicas 35.0 2.8E+02 0.006 32.1 10.4 63 262-329 18-82 (956)
67 cd08768 Cdc6_C Winged-helix do 34.6 26 0.00057 27.2 1.8 65 18-83 6-70 (87)
68 PRK09014 rfaH transcriptional 34.4 1E+02 0.0022 27.1 5.6 52 238-294 108-161 (162)
69 COG1096 Predicted RNA-binding 33.9 4.1E+02 0.0089 25.1 9.9 91 239-332 7-105 (188)
70 PRK05609 nusG transcription an 33.8 1.4E+02 0.003 26.5 6.5 53 237-294 124-179 (181)
71 KOG3421 60S ribosomal protein 33.4 43 0.00092 29.9 3.0 36 299-338 9-44 (136)
72 PRK04012 translation initiatio 32.5 3.1E+02 0.0066 23.1 8.1 60 261-320 23-83 (100)
73 PF02736 Myosin_N: Myosin N-te 31.6 1.1E+02 0.0024 21.4 4.4 28 261-290 14-41 (42)
74 cd05793 S1_IF1A S1_IF1A: Trans 31.4 2.7E+02 0.0058 22.2 7.9 56 263-318 4-60 (77)
75 TIGR00523 eIF-1A eukaryotic/ar 30.9 2.6E+02 0.0056 23.5 7.2 58 243-305 8-66 (99)
76 PF14505 DUF4438: Domain of un 30.7 51 0.0011 32.2 3.3 35 299-333 60-94 (258)
77 PF07076 DUF1344: Protein of u 30.1 2.3E+02 0.005 22.1 6.1 43 261-308 5-49 (61)
78 PRK04950 ProP expression regul 30.0 1E+02 0.0022 29.5 5.1 35 298-335 168-202 (213)
79 TIGR00739 yajC preprotein tran 29.7 1E+02 0.0022 25.0 4.4 30 298-333 39-68 (84)
80 PRK14631 hypothetical protein; 29.5 1.2E+02 0.0026 27.8 5.4 73 271-352 92-168 (174)
81 PF04717 Phage_base_V: Phage-r 29.3 1.2E+02 0.0027 23.4 4.7 45 263-307 1-54 (79)
82 PF06003 SMN: Survival motor n 29.1 1.4E+02 0.0029 29.2 6.0 57 237-298 67-124 (264)
83 PRK14640 hypothetical protein; 28.7 1.1E+02 0.0025 27.2 5.0 69 272-352 73-145 (152)
84 PF08863 YolD: YolD-like prote 28.6 1.3E+02 0.0028 23.5 4.9 41 307-352 52-92 (92)
85 COG5164 SPT5 Transcription elo 27.7 98 0.0021 33.1 4.9 44 243-292 355-398 (607)
86 cd04456 S1_IF1A_like S1_IF1A_l 27.5 3.2E+02 0.007 21.8 8.0 48 263-310 4-52 (78)
87 PRK14647 hypothetical protein; 27.4 96 0.0021 27.9 4.3 71 271-352 74-153 (159)
88 PRK05585 yajC preprotein trans 27.0 1.1E+02 0.0025 25.8 4.4 30 298-333 54-83 (106)
89 PRK02749 photosystem I reactio 26.9 1.1E+02 0.0024 24.5 4.0 39 298-336 4-46 (71)
90 cd04451 S1_IF1 S1_IF1: Transla 26.9 2.7E+02 0.0059 20.7 7.9 24 294-317 38-61 (64)
91 PRK00276 infA translation init 26.9 3E+02 0.0065 21.3 8.4 56 262-318 10-68 (72)
92 PLN00208 translation initiatio 26.8 4.8E+02 0.01 23.6 8.5 60 263-322 36-96 (145)
93 COG0779 Uncharacterized protei 25.9 1.5E+02 0.0032 26.9 5.2 45 299-351 98-146 (153)
94 PRK00092 ribosome maturation p 25.8 1.1E+02 0.0024 27.1 4.4 71 271-351 73-147 (154)
95 cd05696 S1_Rrp5_repeat_hs4 S1_ 25.6 2.3E+02 0.0051 21.4 5.6 57 262-329 6-69 (71)
96 KOG4235 Mitochondrial thymidin 25.4 1E+02 0.0022 29.8 4.2 44 51-100 128-171 (244)
97 PRK14645 hypothetical protein; 25.2 1.3E+02 0.0027 27.2 4.6 68 271-351 77-144 (154)
98 PRK14712 conjugal transfer nic 24.8 5.2E+02 0.011 31.9 10.7 86 241-332 518-617 (1623)
99 COG3041 Uncharacterized protei 24.4 41 0.00089 28.1 1.3 18 14-31 5-22 (91)
100 PTZ00065 60S ribosomal protein 23.9 2.1E+02 0.0046 25.4 5.7 35 240-279 8-42 (130)
101 PTZ00329 eukaryotic translatio 23.8 5.5E+02 0.012 23.5 8.4 60 263-322 36-96 (155)
102 PF01421 Reprolysin: Reprolysi 23.5 97 0.0021 27.9 3.6 53 18-70 26-78 (199)
103 PF02576 DUF150: Uncharacteris 23.4 2E+02 0.0044 24.9 5.5 74 271-352 62-139 (141)
104 PHA02104 hypothetical protein 23.3 54 0.0012 26.5 1.7 30 235-269 34-64 (89)
105 PF12122 DUF3582: Protein of u 23.3 1.4E+02 0.0031 25.0 4.3 27 64-90 15-42 (101)
106 PRK13316 heme-degrading monoox 22.8 58 0.0013 28.5 1.9 59 4-70 3-76 (121)
107 TIGR02059 swm_rep_I cyanobacte 22.6 4.3E+02 0.0094 22.6 7.0 61 285-348 35-97 (101)
108 PRK04333 50S ribosomal protein 22.1 1.6E+02 0.0034 24.1 4.2 31 241-276 5-35 (84)
109 PRK14634 hypothetical protein; 21.7 1.6E+02 0.0034 26.5 4.6 70 271-352 75-148 (155)
110 PRK14646 hypothetical protein; 21.5 1.7E+02 0.0037 26.2 4.8 70 271-352 75-148 (155)
111 PF02214 BTB_2: BTB/POZ domain 21.2 24 0.00053 27.9 -0.7 20 75-96 34-53 (94)
112 PRK00411 cdc6 cell division co 21.2 1.1E+02 0.0024 30.1 3.9 66 32-97 312-381 (394)
113 PTZ00471 60S ribosomal protein 21.1 1.8E+02 0.004 26.0 4.7 29 239-272 4-32 (134)
114 PF08141 SspH: Small acid-solu 21.0 1.7E+02 0.0036 22.5 3.9 37 310-349 20-56 (58)
115 PF04986 Y2_Tnp: Putative tran 20.6 89 0.0019 28.5 2.8 57 14-71 47-112 (183)
116 PRK14635 hypothetical protein; 20.2 1.4E+02 0.0031 26.9 4.0 74 272-352 75-156 (162)
117 PRK10413 hydrogenase 2 accesso 20.1 3.2E+02 0.0069 22.2 5.6 44 263-308 7-54 (82)
No 1
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=100.00 E-value=7.6e-77 Score=559.68 Aligned_cols=256 Identities=50% Similarity=0.759 Sum_probs=213.0
Q ss_pred CcccccCchhhHhhhHHHHHHHHHHHHHhccCCcccccceeeeeecccccceeecccccccHHHHHHHhcccccEEEeec
Q 018594 1 MQIFGQNPDRIVEGYSEEFEAGFLELMRRSHRFSRIAATVVYNEYIHDRHHVHMNSTRWATLTEFVKYLGRTGKCKVEET 80 (353)
Q Consensus 1 m~lf~enp~~~i~~fS~eF~~~Fl~lLr~~~g~krV~aN~vYneyI~dr~HiHMNaT~W~tLt~Fvk~Lgr~G~c~vdet 80 (353)
|++|++||+++++.||.+|+.+||+|||++||+|||+||+||||||+||+|||||||+|.|||+||+||||+|+|+||+|
T Consensus 54 l~~~~~Np~~~~~~fs~eF~~dFl~LLr~~~g~KrI~aN~VYnEYI~dR~HvHMNaT~w~SLtefvk~LGR~Gkc~vdet 133 (309)
T KOG2837|consen 54 LLLFALNPGRSLERFSNEFEKDFLSLLRQRHGTKRIGANKVYNEYIADRNHVHMNATRWRSLTEFVKYLGRTGKCKVDET 133 (309)
T ss_pred HHHHHhCcchhHHHhHHHHHHHHHHHHHHHhccceechhHHHHHHHccccceeecchhhhhHHHHHHHhccCceeeeecC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeEEEeecCChHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhcCcCCCCCCCCCCCcchhhhhhhhhccccee
Q 018594 81 PKGWFITYIDRDSETLFKEKMKNKRIKLDMVDEERQEREIQKQIEIAASSSVSSTNPLSNSEDNTTRELNLEAAAAVGKV 160 (353)
Q Consensus 81 ekGw~I~yId~~pe~~~r~~~~~k~~~~~~~dee~~~~~i~~qi~r~~~~~~~~~~~~~~~~~~~~~el~r~~~~~~~ki 160 (353)
|+||||+|||++|+++.|+.+..++++++++|||+.+++|+.||.||++. ++.+.+.+..+||.|++......+
T Consensus 134 ekgw~i~yIdk~petl~r~~~d~~r~rqe~~dEe~~~~~id~Qi~Rake~------g~~e~e~e~~~El~~d~~~~~~~v 207 (309)
T KOG2837|consen 134 EKGWFITYIDKFPETLKRIEEDLKRERQEKDDEERGADLIDGQIKRAKEQ------GEKEYEPEMNTELSRDGDDERKSV 207 (309)
T ss_pred CCceEEEEeccChhhhcchhhHHHHHhhhhhHHHHHHHHHHHHHHHHHhc------cccccccccccccccCCccccccc
Confidence 99999999999999999999999999999999999999999999999974 111223444688988765111001
Q ss_pred eeecCCCCCCCCCCCCCCCCCCCCcchhhhhcccccCCCCCCCcccCCCCCCCCCCChHHHHHHHHHHHHhhcCCCCCcc
Q 018594 161 GFALGSSYKDNVTSNGSGNNGSSSTRLVFEELDKDNNNNNNNNRKIDKNGSKVSGNSALEELMREEEKVKEKMNRKDYWL 240 (353)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~saLdeime~ee~kk~~~~r~~~WL 240 (353)
.-+...+.. ..|+... ..+.+.+ .+++ ||||++||.+| |
T Consensus 208 ~~~~~~sk~-------------~~p~~kk--------------~~~~~~~--~~~r---dEi~~~ee~kk--------w- 246 (309)
T KOG2837|consen 208 VVSSALSKR-------------VNPKAKK--------------LPPDKDG--GKKR---DEIMKMEERKK--------W- 246 (309)
T ss_pred eeeeeccCc-------------CChhhhc--------------CCCCccc--ccch---HHHHHhhhcCc--------e-
Confidence 111100000 1111100 0011111 1122 99999999775 8
Q ss_pred cCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEeCCCCCceE
Q 018594 241 CEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVNGAYRGSNA 315 (353)
Q Consensus 241 ~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~G~~RG~~g 315 (353)
+|+||+++++. + |++||||.+|+|.|++.|+ +|+|++|+|||+|||||||+ |||||+|||..|
T Consensus 247 ----~vk~~sk~l~~-k-~K~K~vv~~vid~y~~~~K-ld~g~~lk~dq~~lEtvip~-----~~vng~yRg~~~ 309 (309)
T KOG2837|consen 247 ----VVKVISKSLGE-K-YKQKGVVKKVIDDYTGQIK-LDSGTVLKVDQEHLETVIPQ-----MIVNGAYRGSEA 309 (309)
T ss_pred ----EEEeehhhhhH-H-hccccHHHHHHHhhhhhee-ccCCceecccHHHHHHHhHH-----HHhhhhhccCCC
Confidence 99999999999 6 9999999999999999999 78999999999999999999 899999999754
No 2
>PF10357 Kin17_mid: Domain of Kin17 curved DNA-binding protein; InterPro: IPR019447 This entry represents the conserved central 169 residue region of the Kin17 DNA/RNA-binding proteins. The N-terminal region of Kin17 contains a zinc-finger domain, while in the human and mouse proteins there is a RecA-like domain found in the C-terminal region. In humans, Kin17 protein forms intra-nuclear foci during cell proliferation and is re-distributed in the nucleoplasm during the cell cycle []. ; PDB: 2V1N_A.
Probab=100.00 E-value=3.4e-66 Score=444.43 Aligned_cols=125 Identities=58% Similarity=1.015 Sum_probs=89.9
Q ss_pred CcccccCchhhHhhhHHHHHHHHHHHHHhccCCcccccceeeeeecccccceeecccccccHHHHHHHhcccccEEEeec
Q 018594 1 MQIFGQNPDRIVEGYSEEFEAGFLELMRRSHRFSRIAATVVYNEYIHDRHHVHMNSTRWATLTEFVKYLGRTGKCKVEET 80 (353)
Q Consensus 1 m~lf~enp~~~i~~fS~eF~~~Fl~lLr~~~g~krV~aN~vYneyI~dr~HiHMNaT~W~tLt~Fvk~Lgr~G~c~vdet 80 (353)
|++||+||++||++||++|+++||+|||++||+|||+||+||||||+||+|||||||+|+|||+||+||||+|+|+||+|
T Consensus 3 m~~~~~n~~k~i~~yS~eFe~~Fl~lLr~~hg~krV~AN~vYnEyI~Dk~HvHMNaT~W~sLT~FvkyLgr~G~~~Vdet 82 (127)
T PF10357_consen 3 MLLFAENPGKFIDEYSEEFEKDFLRLLRRRHGTKRVNANKVYNEYIQDKDHVHMNATRWTSLTEFVKYLGREGKCKVDET 82 (127)
T ss_dssp -------GGG-HHHHHHHHHHHHHHHHHHHTSS-EEEHHHHHHHHTTSS----GGGSS-SSHHHHHHHHTTTTSEEEEEE
T ss_pred hHHHhhChhhHHHHHHHHHHHHHHHHHHHhcCCCeechhHHHHHHhcCccceeecccccchHHHHHHHHhhCCeeEeecC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeEEEeecCChHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHH
Q 018594 81 PKGWFITYIDRDSETLFKEKMKNKRIKLDMVDEERQEREIQKQIE 125 (353)
Q Consensus 81 ekGw~I~yId~~pe~~~r~~~~~k~~~~~~~dee~~~~~i~~qi~ 125 (353)
|+||||+|||+||++++|+++..++++++++||||++++|++||+
T Consensus 83 ekg~~I~yID~~pe~l~r~~~~~k~~~~~~~dee~~~~~i~~Qi~ 127 (127)
T PF10357_consen 83 EKGWFISYIDRSPETLARQEELAKKEKAEKDDEERERKLIEKQIE 127 (127)
T ss_dssp TTEEEEEE--SSHHHHHHHHHTGGGT-------------------
T ss_pred CCceEEEeeCCCHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999999999999999995
No 3
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=99.70 E-value=2.8e-18 Score=170.85 Aligned_cols=112 Identities=25% Similarity=0.414 Sum_probs=103.0
Q ss_pred CCcccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCeEE--EEcCCceeeecCC-CCCeEEEEeCCCCCc
Q 018594 237 DYWLCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVL--RVDQDELETVIPQ-IGGLVRIVNGAYRGS 313 (353)
Q Consensus 237 ~~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l--~vdq~~LETVIP~-~G~~V~IV~G~~RG~ 313 (353)
..||+.+|.|||+++.+..|+||.+|++|.+|.+..+|.|.|++++..+ .|+|++|||++|. .|.+||||.|.|.|.
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 3899999999999999999999999999999999999999999877777 3999999999995 677899999999999
Q ss_pred eEEEEeeeCCccEEEEEEeccccCCceeeeccccccccc
Q 018594 314 NARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDICKL 352 (353)
Q Consensus 314 ~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedicKl 352 (353)
+|.|++.|.++.+++|++... ..++ .+.||+||.|
T Consensus 411 ~g~llskd~~Ke~~~v~~~a~---ndvv-~~~~D~v~ey 445 (455)
T KOG4315|consen 411 YGSLLSKDLDKETGVVRLVAT---NDVV-TVYLDQVCEY 445 (455)
T ss_pred hhhhhhhhhhhhhcceecccc---cchh-hhhHHHHHHh
Confidence 999999999999999998863 4555 4999999987
No 4
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=98.20 E-value=1.1e-06 Score=95.95 Aligned_cols=108 Identities=19% Similarity=0.227 Sum_probs=92.2
Q ss_pred CCcccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEeCCCCCceEE
Q 018594 237 DYWLCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVNGAYRGSNAR 316 (353)
Q Consensus 237 ~~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~ 316 (353)
..| ..++.+.+.+-+ .++...++.++|++|.++ .|+|.+-+.|+.+.+...+|+++.|..|+.++|+.|.++|.+|+
T Consensus 915 ~~~-~~~~~~~~~d~~-~~~~~~G~~~~ir~v~~G-~~sv~~~de~~~~~~s~~~~a~~~p~~~d~~k~~~g~~~g~~~~ 991 (1024)
T KOG1999|consen 915 GNG-GDGNSSWGPDTS-LDTQLVGQTGIIRSVADG-GCSVWLGDEGETISNSKPHLAPAPPCKGDDVKSIWGDDRGSTGK 991 (1024)
T ss_pred CCC-CccceEeccccc-ccceecccccceeeccCC-ceeeecCCCCcccccccccCccCCCCCCCCcccccccccccccc
Confidence 356 678888888754 455889999999999887 99999999999999999999999999999999999999999999
Q ss_pred EEeeeCCccEEEEEEeccccCCceeeecccccccccC
Q 018594 317 LLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDICKLA 353 (353)
Q Consensus 317 L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedicKl~ 353 (353)
|++.|..++.+.+...+ + ++.+.+--+||+.
T Consensus 992 ~~~~dg~~g~~~~d~~~----~--~k~l~~~~~~k~~ 1022 (1024)
T KOG1999|consen 992 LVGNDGWDGIVRIDETS----D--IKILNLGLLCKMV 1022 (1024)
T ss_pred ccCCCcccceecccccc----c--chhhhhhhhhhcc
Confidence 99999999766655433 2 4558888899873
No 5
>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=97.33 E-value=0.00042 Score=46.32 Aligned_cols=31 Identities=23% Similarity=0.646 Sum_probs=28.3
Q ss_pred CCCeEEEEeCCCCCceEEEEeeeCCccEEEE
Q 018594 299 IGGLVRIVNGAYRGSNARLLGVDTDKFCAQV 329 (353)
Q Consensus 299 ~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V 329 (353)
+|+.|+|+.|+|+|..|+++++|.++..+.|
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 5899999999999999999999999976654
No 6
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.81 E-value=0.0022 Score=40.50 Aligned_cols=26 Identities=31% Similarity=0.703 Sum_probs=24.3
Q ss_pred CCCCCeEEEEeCCCCCceEEEEeeeC
Q 018594 297 PQIGGLVRIVNGAYRGSNARLLGVDT 322 (353)
Q Consensus 297 P~~G~~V~IV~G~~RG~~g~L~siD~ 322 (353)
|.+|+.|+|+.|.|+|..|++++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57899999999999999999999975
No 7
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=96.22 E-value=0.0087 Score=47.89 Aligned_cols=33 Identities=24% Similarity=0.451 Sum_probs=30.5
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEEE
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVK 330 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~ 330 (353)
..|++|.|+.|.++|..|+++.++.++..+.|+
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 679999999999999999999999999887773
No 8
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=96.19 E-value=0.0091 Score=48.52 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=30.1
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEE
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQV 329 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V 329 (353)
..|++|.|+.|.++|..|++++++.++..+.|
T Consensus 10 ~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~V 41 (83)
T CHL00141 10 KIGDTVKIISGSDKGKIGEVLKIIKKSNKVIV 41 (83)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 57999999999999999999999999988877
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=95.91 E-value=0.02 Score=50.02 Aligned_cols=51 Identities=18% Similarity=0.384 Sum_probs=42.9
Q ss_pred CCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCce--eeecccccccc
Q 018594 297 PQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRV--LNAIDYEDICK 351 (353)
Q Consensus 297 P~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~--v~~l~yedicK 351 (353)
+.+|+.|.|+.|++.|..|.+..+|..+..|.|.|.. .+.. ++ +++++|-+
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~---~~~~~~v~-v~~~~l~~ 139 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIE---AAVPIPVT-VKGDQVRI 139 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEE---cCccceEE-EeeeEEEE
Confidence 5789999999999999999999999998899998885 3444 53 78877754
No 10
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=95.60 E-value=0.022 Score=48.13 Aligned_cols=33 Identities=24% Similarity=0.333 Sum_probs=30.6
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEEE
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVK 330 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~ 330 (353)
..|+.|+|+.|.++|..|++++++.++..+.|+
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 679999999999999999999999999888773
No 11
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=95.04 E-value=0.043 Score=47.64 Aligned_cols=32 Identities=22% Similarity=0.493 Sum_probs=29.7
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEE
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQV 329 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V 329 (353)
..|+.|.|+.|.++|..|++++++.++..+.|
T Consensus 47 kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~V 78 (120)
T PRK01191 47 RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYV 78 (120)
T ss_pred eCCCEEEEeecCCCCceEEEEEEEcCCCEEEE
Confidence 45999999999999999999999999988877
No 12
>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=94.98 E-value=0.043 Score=46.40 Aligned_cols=33 Identities=21% Similarity=0.365 Sum_probs=30.4
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEEE
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVK 330 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~ 330 (353)
..|++|.|+.|.++|..|++++++.++..+.|+
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 579999999999999999999999999888773
No 13
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=94.98 E-value=0.039 Score=49.22 Aligned_cols=33 Identities=18% Similarity=0.360 Sum_probs=30.1
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEEE
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVK 330 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~ 330 (353)
..|+.|+|+.|.++|..|++++++..++.+.|.
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 459999999999999999999999999888773
No 14
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=94.93 E-value=0.069 Score=47.83 Aligned_cols=53 Identities=23% Similarity=0.407 Sum_probs=41.4
Q ss_pred CCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCce-eeeccccccccc
Q 018594 297 PQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRV-LNAIDYEDICKL 352 (353)
Q Consensus 297 P~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~-v~~l~yedicKl 352 (353)
+.+|+.|.|+.|++.|..|++..+|..+..|.|.|.- -|+. .-.++++++-++
T Consensus 127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~---~G~~~~v~l~~~~l~~~ 180 (181)
T PRK05609 127 FEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSI---FGRETPVELEFSQVEKI 180 (181)
T ss_pred CCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEE---CCCceEEEEchHHEEEc
Confidence 4689999999999999999999999888788887763 2432 224777777654
No 15
>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=94.92 E-value=0.044 Score=47.19 Aligned_cols=32 Identities=28% Similarity=0.574 Sum_probs=29.5
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEE
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQV 329 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V 329 (353)
..|+.|+|+.|.++|..|+++.|+..+..|.|
T Consensus 43 kkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~V 74 (114)
T TIGR01080 43 RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYV 74 (114)
T ss_pred ecCCEEEEecCCCCCCEEEEEEEEcCCCEEEE
Confidence 56999999999999999999999999987766
No 16
>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=94.87 E-value=0.072 Score=47.48 Aligned_cols=50 Identities=20% Similarity=0.365 Sum_probs=39.8
Q ss_pred CCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCc--eeeeccccccc
Q 018594 297 PQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGR--VLNAIDYEDIC 350 (353)
Q Consensus 297 P~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~--~v~~l~yedic 350 (353)
+.+|++|.|+.|++.|..|.+..+|.++..|.|.|+- .|+ .+ .+++++|-
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~---~g~~~~v-~v~~~~l~ 171 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSI---FGRETPV-ELEFSQVE 171 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEE---CCCceEE-EEcHHHee
Confidence 4689999999999999999999999888888888774 243 23 36766653
No 17
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=94.55 E-value=0.1 Score=46.47 Aligned_cols=50 Identities=20% Similarity=0.406 Sum_probs=41.1
Q ss_pred CCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCce--eeeccccccc
Q 018594 297 PQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRV--LNAIDYEDIC 350 (353)
Q Consensus 297 P~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~--v~~l~yedic 350 (353)
..+|+.|.|+.|.++|..|++.++|.++..|+|.+..- ... + .++.++|+
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~---~~~~pv-~v~~~~~~ 146 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEA---AVPIPV-TVRGDQVR 146 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECC---cceeeE-EEeccEEE
Confidence 57899999999999999999999999999999988752 222 3 47777764
No 18
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=93.40 E-value=0.19 Score=46.11 Aligned_cols=56 Identities=25% Similarity=0.372 Sum_probs=43.7
Q ss_pred ecCCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccccccccc
Q 018594 295 VIPQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDICKL 352 (353)
Q Consensus 295 VIP~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedicKl 352 (353)
+-+.+|+.|+|+.|++.|..|++.++|.++..++|.+..= ..-..+ .++|++|-++
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~if-gr~tPV-el~~~qVek~ 177 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIF-GRPTPV-ELEFDQVEKL 177 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEe-CCceEE-EEehhhEEEe
Confidence 4456899999999999999999999999998888887741 112234 3888887665
No 19
>PRK04313 30S ribosomal protein S4e; Validated
Probab=92.54 E-value=1 Score=43.39 Aligned_cols=73 Identities=18% Similarity=0.255 Sum_probs=49.0
Q ss_pred EEEEeecccCCcccccceeEEEEecCCceEEEEecC-----CCeEEEEc--CCceeeecC-CCCCeEEEEeCCCCCceEE
Q 018594 245 IVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLE-----KKHVLRVD--QDELETVIP-QIGGLVRIVNGAYRGSNAR 316 (353)
Q Consensus 245 vVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d-----~g~~l~vd--q~~LETVIP-~~G~~V~IV~G~~RG~~g~ 316 (353)
.+||.+|.. .++|++.=+...++..+. ++ .++.|.|+ ...+.-.+| ..|..++|+.|.+.|.+|+
T Consensus 119 L~KV~~k~~------~~gG~~ql~~hDGrni~~-~~~~~~k~~Dtv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~ 191 (237)
T PRK04313 119 LCKIENKTT------VKGGKIQLNLHDGRNILV-DVEDDYKTGDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGK 191 (237)
T ss_pred EEEEEeEEE------ecCCEEEEEecCCceEEc-cCccccccCCEEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEE
Confidence 367776543 445666555443343332 32 57776544 444666666 8999999999999999999
Q ss_pred EEeeeCCc
Q 018594 317 LLGVDTDK 324 (353)
Q Consensus 317 L~siD~~~ 324 (353)
+.++....
T Consensus 192 I~~i~~~~ 199 (237)
T PRK04313 192 IKEIEVTK 199 (237)
T ss_pred EEEEEEcc
Confidence 99997544
No 20
>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=92.23 E-value=0.29 Score=42.90 Aligned_cols=49 Identities=24% Similarity=0.381 Sum_probs=35.9
Q ss_pred CCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCcee-eecccccc
Q 018594 297 PQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVL-NAIDYEDI 349 (353)
Q Consensus 297 P~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v-~~l~yedi 349 (353)
+.+|++|.|+.|++.|..|.+..+|. +..+.|.|+- -|+.+ -.+++++|
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~l~~---~gr~~~v~~~~~~~ 158 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLLLNM---IGKQIKVSVPNTSV 158 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEECC-CceEEEEEhh---hCCceEEEecHHHc
Confidence 46899999999999999999999984 4577777763 24432 12555554
No 21
>PLN00036 40S ribosomal protein S4; Provisional
Probab=91.88 E-value=1.2 Score=43.40 Aligned_cols=71 Identities=18% Similarity=0.287 Sum_probs=48.7
Q ss_pred EEEEeecccCCcccccceeEEEEecCCceEEEEecC----CCeEEEE--cCCceeeecC-CCCCeEEEEeCCCCCceEEE
Q 018594 245 IVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLE----KKHVLRV--DQDELETVIP-QIGGLVRIVNGAYRGSNARL 317 (353)
Q Consensus 245 vVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d----~g~~l~v--dq~~LETVIP-~~G~~V~IV~G~~RG~~g~L 317 (353)
.+||.++. ..++|++.=+....+. +...| .++.|.| +...+.-.+| ..|..++|+.|.+.|.+|++
T Consensus 123 LcKV~~k~------~~~gG~~ql~~hDGrn-i~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I 195 (261)
T PLN00036 123 LCKVRKIQ------FGQKGIPYLNTHDGRT-IRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVI 195 (261)
T ss_pred EEEEEEEE------EecCCeEEEEecCCce-eccCCCccccCCEEEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEE
Confidence 35777553 4456666665443333 43222 4777654 4555666777 89999999999999999999
Q ss_pred EeeeC
Q 018594 318 LGVDT 322 (353)
Q Consensus 318 ~siD~ 322 (353)
.++..
T Consensus 196 ~~i~~ 200 (261)
T PLN00036 196 KNREK 200 (261)
T ss_pred EEEEe
Confidence 99984
No 22
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=91.83 E-value=0.35 Score=42.81 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=37.4
Q ss_pred CCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCc--eeeecccccccc
Q 018594 297 PQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGR--VLNAIDYEDICK 351 (353)
Q Consensus 297 P~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~--~v~~l~yedicK 351 (353)
+.+|++|.|+.|++.|..|.+..+|. +..+.|.++- .|+ .+ .+++++|-+
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~~-~~r~~v~v~~---~gr~~~v-~v~~~~~~~ 161 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPDG-EARSILLLNL---LNKQVKH-SVDNTQFRK 161 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeCC-CeEEEEeehh---hCCcEEE-EECHHHeec
Confidence 46899999999999999999999994 4456676663 233 33 377777654
No 23
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=91.65 E-value=1.5 Score=42.90 Aligned_cols=80 Identities=18% Similarity=0.289 Sum_probs=51.6
Q ss_pred EEEEeecccCCcccccceeEEEEec-CCceEEEEec----CCCeEEEE--cCCceeeecC-CCCCeEEEEeCCCCCceEE
Q 018594 245 IVKVMSKALADKGYNKQKGVVRKVI-DKYVGEIEML----EKKHVLRV--DQDELETVIP-QIGGLVRIVNGAYRGSNAR 316 (353)
Q Consensus 245 vVKIi~K~l~dGkyYk~KgvV~~V~-d~~~c~V~l~----d~g~~l~v--dq~~LETVIP-~~G~~V~IV~G~~RG~~g~ 316 (353)
.+||..+ +..++|++.=+. |+ .. +... ..++.|.| +...+.-.+| ..|..++|..|.+.|.+|+
T Consensus 123 LcKV~~k------~~~~gg~~~l~~hDG-rn-i~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~ 194 (262)
T PTZ00118 123 LCRVKKT------FLGPKEVSIAVTHDG-RT-IRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGT 194 (262)
T ss_pred EEEEeEE------EECCCCeEEEEecCc-ce-eccCCCcccCCCEEEEECCCCceeeEEecCCCCEEEEECCeeceeEEE
Confidence 3577654 344566666543 44 33 4322 25777654 4555666677 8999999999999999999
Q ss_pred EEeeeCCccE-EEEEEe
Q 018594 317 LLGVDTDKFC-AQVKIE 332 (353)
Q Consensus 317 L~siD~~~~~-a~V~l~ 332 (353)
+.++.....+ -.|.|.
T Consensus 195 I~~~~~~~~~~~~V~i~ 211 (262)
T PTZ00118 195 IVSKEKHPGSFDLIHVK 211 (262)
T ss_pred EEEEEecCCCCcEEEEE
Confidence 9997654333 234444
No 24
>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=91.64 E-value=0.72 Score=34.64 Aligned_cols=51 Identities=24% Similarity=0.270 Sum_probs=34.0
Q ss_pred ccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCC-CeEEEEcCCcee
Q 018594 240 LCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEK-KHVLRVDQDELE 293 (353)
Q Consensus 240 L~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~-g~~l~vdq~~LE 293 (353)
+.||-.|+|++- .+ -||.=.|.|..|.|+..+++.=-.+ ++.+.+.-++||
T Consensus 2 ilPG~~V~V~n~--~~-~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eLe 53 (53)
T PF11623_consen 2 ILPGSTVRVKNP--ND-IYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSELE 53 (53)
T ss_dssp --TT-EEEE--T--TS-TTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGEE
T ss_pred ccCCCEEEEeCC--CC-ccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhCC
Confidence 568999999865 34 7999999999999997776654333 345677777776
No 25
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=90.71 E-value=0.43 Score=40.58 Aligned_cols=30 Identities=27% Similarity=0.485 Sum_probs=27.3
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEE
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQV 329 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V 329 (353)
..|+.|.|+.|.++|..|.+++++... +.|
T Consensus 6 rkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~V 35 (104)
T COG0198 6 KKGDTVKVIAGKDKGKEGKVLKVLPKK--VVV 35 (104)
T ss_pred ecCCEEEEEecCCCCcceEEEEEecCe--EEE
Confidence 469999999999999999999999998 554
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=89.94 E-value=0.81 Score=44.58 Aligned_cols=51 Identities=22% Similarity=0.436 Sum_probs=39.0
Q ss_pred CCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCceeeecccccc
Q 018594 297 PQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDI 349 (353)
Q Consensus 297 P~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedi 349 (353)
+.+|+.|.|+.|++.|..|.+.++|.++..+.|.|.-- .....+ .|+|++|
T Consensus 206 f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~If-GR~TpV-eL~~~qV 256 (258)
T TIGR01956 206 FRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEIL-GKSVDV-DLNFKHL 256 (258)
T ss_pred CCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEec-CCcEEE-EEchHHE
Confidence 47899999999999999999999998777787777641 122234 3777765
No 27
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=89.93 E-value=0.79 Score=48.07 Aligned_cols=70 Identities=36% Similarity=0.505 Sum_probs=50.4
Q ss_pred eeEEEEecCCceEEEEecCCCeEEEEcC----------------Cceeeec----CCCCCeEEEEeCCCCCceEEEEeee
Q 018594 262 KGVVRKVIDKYVGEIEMLEKKHVLRVDQ----------------DELETVI----PQIGGLVRIVNGAYRGSNARLLGVD 321 (353)
Q Consensus 262 KgvV~~V~d~~~c~V~l~d~g~~l~vdq----------------~~LETVI----P~~G~~V~IV~G~~RG~~g~L~siD 321 (353)
-||++. +.+..|.|..-|--.-+++|- ..||--| |++|..|.|-.|+|+|..|.+..+|
T Consensus 298 nGVfv~-~~~nv~~VAtkd~~~s~k~dl~kmnp~v~~~~~~p~~~~l~r~i~gRd~aigktVrIr~g~yKG~lGVVKdv~ 376 (607)
T COG5164 298 NGVFVK-IEGNVCIVATKDFTESLKVDLDKMNPPVTVNLQNPKTNELERKIVGRDPAIGKTVRIRCGEYKGHLGVVKDVD 376 (607)
T ss_pred CceEEE-ecCceeEEEeccchhhhcccHhhcCchhhcCCCCCcchhhhccccccccccCceEEEeecccccccceeeecc
Confidence 455544 345588888765322333433 3455555 7899999999999999999999998
Q ss_pred CCccEEEEEEecc
Q 018594 322 TDKFCAQVKIEKG 334 (353)
Q Consensus 322 ~~~~~a~V~l~~g 334 (353)
.+. |.|+|.++
T Consensus 377 ~~~--arVeLhs~ 387 (607)
T COG5164 377 RNI--ARVELHSN 387 (607)
T ss_pred Cce--EEEEEecC
Confidence 887 88888875
No 28
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=89.54 E-value=2.4 Score=41.75 Aligned_cols=72 Identities=17% Similarity=0.254 Sum_probs=47.8
Q ss_pred EEEEeecccCCcccccceeEEEEecCCceEEEEec----CCCeEEEE--cCCceeeecC-CCCCeEEEEeCCCCCceEEE
Q 018594 245 IVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEML----EKKHVLRV--DQDELETVIP-QIGGLVRIVNGAYRGSNARL 317 (353)
Q Consensus 245 vVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~----d~g~~l~v--dq~~LETVIP-~~G~~V~IV~G~~RG~~g~L 317 (353)
.+||.++.. .++|++.=+...++. +... ..++.|.| +...+.-.+| ..|..|+|..|.+.|.+|++
T Consensus 120 LcKV~~k~~------~~gG~~ql~~hDGrn-I~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I 192 (273)
T PTZ00223 120 LMKVVNVYT------ATGRIPVAVTHDGHR-IRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEI 192 (273)
T ss_pred EEEEEEEEE------ecCCeeEEEecCCce-eccCCccccCCCEEEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEE
Confidence 367776543 445665555433233 3322 25777754 4444555666 89999999999999999999
Q ss_pred EeeeCC
Q 018594 318 LGVDTD 323 (353)
Q Consensus 318 ~siD~~ 323 (353)
.++...
T Consensus 193 ~~i~~~ 198 (273)
T PTZ00223 193 VSIERH 198 (273)
T ss_pred EEEEec
Confidence 999544
No 29
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=89.42 E-value=2.5 Score=40.80 Aligned_cols=53 Identities=15% Similarity=0.267 Sum_probs=39.3
Q ss_pred CeEE--EEcCCceeeecC-CCCCeEEEEeCCCCCceEEEEeeeCCc--cEEEEEEecc
Q 018594 282 KHVL--RVDQDELETVIP-QIGGLVRIVNGAYRGSNARLLGVDTDK--FCAQVKIEKG 334 (353)
Q Consensus 282 g~~l--~vdq~~LETVIP-~~G~~V~IV~G~~RG~~g~L~siD~~~--~~a~V~l~~g 334 (353)
|+++ .++...+.-.|| .+|..|+|+.|.|.|.+|++.+|.... ..=+|.+++.
T Consensus 156 ~Dtv~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~ 213 (241)
T COG1471 156 GDTVKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDE 213 (241)
T ss_pred ccEEEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecC
Confidence 6655 566666666666 899999999999999999999998763 2223555543
No 30
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=84.98 E-value=3.5 Score=46.61 Aligned_cols=78 Identities=24% Similarity=0.311 Sum_probs=58.0
Q ss_pred ccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEec--CCCeEEEEcCCceeeecCCCCCeEEEEeCCCCCceEEE
Q 018594 240 LCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEML--EKKHVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARL 317 (353)
Q Consensus 240 L~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~--d~g~~l~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L 317 (353)
++|+=.|.|+ .|.+-+-||+|..|.+. .++|... +-..-|.+..+.|- =.-.+|+.|+|+.|.|.|.+|.+
T Consensus 408 F~~GD~VeV~-----~Gel~glkG~ve~vdg~-~vti~~~~e~l~~pl~~~~~eLr-KyF~~GDhVKVi~G~~eG~tGlV 480 (1024)
T KOG1999|consen 408 FSPGDAVEVI-----VGELKGLKGKVESVDGT-IVTIMSKHEDLKGPLEVPASELR-KYFEPGDHVKVIAGRYEGDTGLV 480 (1024)
T ss_pred cCCCCeEEEe-----eeeeccceeEEEeccCc-eEEEeeccccCCCccccchHhhh-hhccCCCeEEEEeccccCCcceE
Confidence 5677777776 33566789999998554 5555543 23556778888872 22368999999999999999999
Q ss_pred EeeeCCc
Q 018594 318 LGVDTDK 324 (353)
Q Consensus 318 ~siD~~~ 324 (353)
+.|+...
T Consensus 481 vrVe~~~ 487 (1024)
T KOG1999|consen 481 VRVEQGD 487 (1024)
T ss_pred EEEeCCe
Confidence 9998766
No 31
>PF15591 Imm17: Immunity protein 17
Probab=84.54 E-value=1.9 Score=34.56 Aligned_cols=50 Identities=20% Similarity=0.325 Sum_probs=37.9
Q ss_pred EEEEeecccCCcccccceeEEEEecCC----ceEEEEecCCCeEEEEcCCceee
Q 018594 245 IVKVMSKALADKGYNKQKGVVRKVIDK----YVGEIEMLEKKHVLRVDQDELET 294 (353)
Q Consensus 245 vVKIi~K~l~dGkyYk~KgvV~~V~d~----~~c~V~l~d~g~~l~vdq~~LET 294 (353)
+|+|.+....+.++++++|||...... +.-.|.+-+......++.+.|++
T Consensus 10 ~V~v~~s~p~~~ei~Gk~GVVlG~SeeD~~~~gY~Vli~d~e~~~~~ee~~l~~ 63 (74)
T PF15591_consen 10 EVEVVRSCPCDAEIWGKRGVVLGISEEDGGNFGYSVLIFDMECCWYIEEDELEA 63 (74)
T ss_pred EEEEeccCcchhhhcCceeEEEEEecCCCcEEEEEEEEeeeeeEEEechHHeee
Confidence 688887666667899999999999642 33556666667777888888875
No 32
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=83.68 E-value=13 Score=32.17 Aligned_cols=97 Identities=15% Similarity=0.153 Sum_probs=61.2
Q ss_pred EEeecccCCcccccceeEEEEecCCceEEEEecCCCeEEEEcCCceeeecC------CCCCeEEEEe--CCCCCceEEEE
Q 018594 247 KVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVLRVDQDELETVIP------QIGGLVRIVN--GAYRGSNARLL 318 (353)
Q Consensus 247 KIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~LETVIP------~~G~~V~IV~--G~~RG~~g~L~ 318 (353)
+|+.++..||-||- |+|++..+.....|+.. .++...++..++=.+-+ ++|++|+... +.++=.-|+++
T Consensus 3 ~VlAR~~~DG~YY~--GtV~~~~~~~~~lV~f~-~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~~~~~~~~Y~Pg~V~ 79 (124)
T PF15057_consen 3 KVLARREEDGFYYP--GTVKKCVSSGQFLVEFD-DGDTQEVPISDIIALSDAMRHSLQVGDKVLAPWEPDDCRYGPGTVI 79 (124)
T ss_pred eEEEeeCCCCcEEe--EEEEEccCCCEEEEEEC-CCCEEEeChHHeEEccCcccCcCCCCCEEEEecCcCCCEEeCEEEE
Confidence 46777888987776 89999888778888873 45555555544433222 4799999984 34555558888
Q ss_pred ee----eCCccEEEEEEeccccCCceeeecccccccc
Q 018594 319 GV----DTDKFCAQVKIEKGVYDGRVLNAIDYEDICK 351 (353)
Q Consensus 319 si----D~~~~~a~V~l~~g~~~g~~v~~l~yedicK 351 (353)
+. -..+...+|.+-+| +.. .++...+.+
T Consensus 80 ~~~~~~~~~~~~~~V~f~ng----~~~-~vp~~~~~~ 111 (124)
T PF15057_consen 80 AGPERRASEDKEYTVRFYNG----KTA-KVPRGEVIW 111 (124)
T ss_pred ECccccccCCceEEEEEECC----CCC-ccchhhEEE
Confidence 62 22333466777764 333 356555544
No 33
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=78.01 E-value=7.4 Score=28.72 Aligned_cols=54 Identities=26% Similarity=0.238 Sum_probs=41.3
Q ss_pred cCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecC--CCeEEEEcCCceeeecCC
Q 018594 241 CEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLE--KKHVLRVDQDELETVIPQ 298 (353)
Q Consensus 241 ~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d--~g~~l~vdq~~LETVIP~ 298 (353)
..|=.|-+-... +|.+|. |+|..|.+...+.|...+ .+....++.+.|-+..|-
T Consensus 4 ~~G~~Ve~~~~~--~~~W~~--a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~~w 59 (61)
T smart00743 4 KKGDRVEVFSKE--EDSWWE--AVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHPPW 59 (61)
T ss_pred CCCCEEEEEECC--CCEEEE--EEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCCCC
Confidence 345566665443 556765 899999986689999999 888999999999887663
No 34
>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=73.71 E-value=13 Score=26.76 Aligned_cols=53 Identities=15% Similarity=0.089 Sum_probs=39.8
Q ss_pred ccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCeEEEEcCCceeeecC
Q 018594 240 LCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVLRVDQDELETVIP 297 (353)
Q Consensus 240 L~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~LETVIP 297 (353)
+.+|-.|.+.- .+|.||. |.|.++.+...+.|...|-|....|+.++|-+..|
T Consensus 3 ~~~G~~~~a~~---~d~~wyr--a~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~~l~~ 55 (57)
T smart00333 3 FKVGDKVAARW---EDGEWYR--ARIIKVDGEQLYEVFFIDYGNEEVVPPSDLRPLPE 55 (57)
T ss_pred CCCCCEEEEEe---CCCCEEE--EEEEEECCCCEEEEEEECCCccEEEeHHHeecCCC
Confidence 34555554442 4778886 79999987568999999989998998888876655
No 35
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=71.78 E-value=6.5 Score=33.10 Aligned_cols=58 Identities=24% Similarity=0.410 Sum_probs=42.7
Q ss_pred eeeecCCCCCeEEEEeCC--CCCceEEEEeeeCC---ccEEEEEEeccccCCceeeecccccc
Q 018594 292 LETVIPQIGGLVRIVNGA--YRGSNARLLGVDTD---KFCAQVKIEKGVYDGRVLNAIDYEDI 349 (353)
Q Consensus 292 LETVIP~~G~~V~IV~G~--~RG~~g~L~siD~~---~~~a~V~l~~g~~~g~~v~~l~yedi 349 (353)
-.++-|+.|.+|+|+.-+ +-..+|++.++|.+ +|-++|+++.-.+.|-.-.++..+.|
T Consensus 35 pp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~kvNY~gvnTNnfa~~El 97 (101)
T PLN00045 35 PPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFEKVNYAGVSTNNYALDEI 97 (101)
T ss_pred CCCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEeeeeeccccccccccHhhh
Confidence 345667889999999765 46788999999988 78899999876666633333455444
No 36
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=71.20 E-value=15 Score=32.68 Aligned_cols=53 Identities=26% Similarity=0.312 Sum_probs=43.9
Q ss_pred ccCCcEEEEeecccCCcccccceeEEEEec-CCceEEEEecCCCeE--EEEcCCceeeecC
Q 018594 240 LCEGIIVKVMSKALADKGYNKQKGVVRKVI-DKYVGEIEMLEKKHV--LRVDQDELETVIP 297 (353)
Q Consensus 240 L~~~IvVKIi~K~l~dGkyYk~KgvV~~V~-d~~~c~V~l~d~g~~--l~vdq~~LETVIP 297 (353)
+.+|=.|+|+ +|-|-+..|.|.++. .+..+.|.+++.... ++|+.+.|.+|=+
T Consensus 95 ~~~G~~V~I~-----~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~~ 150 (153)
T PRK08559 95 IKEGDIVELI-----AGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVKK 150 (153)
T ss_pred CCCCCEEEEe-----ccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEecc
Confidence 6789999998 567778899999996 366789999988777 8899999977754
No 37
>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=70.50 E-value=12 Score=32.51 Aligned_cols=55 Identities=18% Similarity=0.251 Sum_probs=46.3
Q ss_pred CcccCCcEEEEeecccCCcccccceeEEEEec-CCceEEEEecCCCeE--EEEcCCceeeecC
Q 018594 238 YWLCEGIIVKVMSKALADKGYNKQKGVVRKVI-DKYVGEIEMLEKKHV--LRVDQDELETVIP 297 (353)
Q Consensus 238 ~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~-d~~~c~V~l~d~g~~--l~vdq~~LETVIP 297 (353)
..+.+|=.|+|+ +|-|-+-.|.|.++. .+..+.|.+++.+.. +.++.++|+.+=+
T Consensus 85 ~~~~~Gd~V~I~-----~GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~~ 142 (145)
T TIGR00405 85 ESIKKGDIVEII-----SGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQK 142 (145)
T ss_pred cccCCCCEEEEe-----ecCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEecc
Confidence 458999999998 567888899999996 355899999988888 8999999988654
No 38
>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=65.85 E-value=43 Score=41.29 Aligned_cols=89 Identities=9% Similarity=0.148 Sum_probs=62.1
Q ss_pred CcccCCcEEEEeecccCCcccccceeEEEEecC-CceEEEEecCCCeEEEEcCCce-----------eeecC-CCCCeEE
Q 018594 238 YWLCEGIIVKVMSKALADKGYNKQKGVVRKVID-KYVGEIEMLEKKHVLRVDQDEL-----------ETVIP-QIGGLVR 304 (353)
Q Consensus 238 ~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d-~~~c~V~l~d~g~~l~vdq~~L-----------ETVIP-~~G~~V~ 304 (353)
....+|-+|.. +.++.+.+.-++|..|.. ..+.+|.. +.|+.+.++.+.| ..+|| +.|++++
T Consensus 680 ~~Yr~Gdvv~~----y~~~~~~~~~y~V~~V~~~~n~L~l~~-~dG~~~~~~p~~l~~~~~~~svy~~~~l~ia~Gdrl~ 754 (1960)
T TIGR02760 680 AHYKQGMVIRF----WQKGKIPHDDYVVTNVNKHNNTLTLKD-AQGKTQKFKPSSLKDLERPFSVYRPEQLEVAAGERLQ 754 (1960)
T ss_pred hhcCCCCEEEe----ecccCccCCcEEEEEEeCCCCEEEEEc-CCCCEEEECHHHhcccccceeeeccccccccCCCEEE
Confidence 34578888887 333455566678999875 33555544 3588888888887 34467 7899999
Q ss_pred EEe-----CCCCCceEEEEeeeCCccEEEEEEec
Q 018594 305 IVN-----GAYRGSNARLLGVDTDKFCAQVKIEK 333 (353)
Q Consensus 305 IV~-----G~~RG~~g~L~siD~~~~~a~V~l~~ 333 (353)
+.. |--+|..+++.+++... ++|+...
T Consensus 755 ~trn~~~~gl~ng~~~tV~~i~~~~--i~l~~~~ 786 (1960)
T TIGR02760 755 VTGNHFHSRVRNGELLTVSSINNEG--ITLITED 786 (1960)
T ss_pred EccCCcccCccCCCEEEEEEEcCCe--EEEEeCC
Confidence 983 33578999999998876 5555543
No 39
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=62.32 E-value=20 Score=31.71 Aligned_cols=36 Identities=25% Similarity=0.270 Sum_probs=27.6
Q ss_pred CCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccc-cCC
Q 018594 299 IGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGV-YDG 338 (353)
Q Consensus 299 ~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~-~~g 338 (353)
+|.-|+|..|+|.|..+++++|-..+. |.| .|| ..|
T Consensus 10 iGRVvli~~Gp~~GKL~vIVDIID~nR-vLV---DGP~~tg 46 (130)
T PTZ00065 10 PGRLCLIQYGPDAGKLCFIVDIVTPTR-VLV---DGAFITG 46 (130)
T ss_pred eceEEEEecCCCCCCEEEEEEEEcCCe-EEE---eCCCcCC
Confidence 588888999999999999999966553 333 477 444
No 40
>PRK04333 50S ribosomal protein L14e; Validated
Probab=59.13 E-value=17 Score=29.69 Aligned_cols=28 Identities=14% Similarity=0.341 Sum_probs=24.3
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCcc
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKF 325 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~ 325 (353)
.+|.-|+++.|.|+|..+.++++..+++
T Consensus 5 ~~GrvV~~~~Grd~gk~~vIv~i~d~~~ 32 (84)
T PRK04333 5 EVGRVCVKTAGREAGRKCVIVDIIDKNF 32 (84)
T ss_pred cccEEEEEeccCCCCCEEEEEEEecCCE
Confidence 4799999999999999999999965553
No 41
>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=59.03 E-value=18 Score=25.10 Aligned_cols=37 Identities=11% Similarity=0.162 Sum_probs=28.6
Q ss_pred CCcccccceeEEEEecCCceEEEEecCCCeEEEEcCCce
Q 018594 254 ADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVLRVDQDEL 292 (353)
Q Consensus 254 ~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~L 292 (353)
.+|++|- |.|.++.....+.|...|-|..-.|+.++|
T Consensus 10 ~d~~wyr--a~V~~~~~~~~~~V~f~DyG~~~~v~~~~l 46 (48)
T cd04508 10 DDGKWYR--AKITSILSDGKVEVFFVDYGNTEVVPLSDL 46 (48)
T ss_pred CCCeEEE--EEEEEECCCCcEEEEEEcCCCcEEEeHHHc
Confidence 4578886 899999866689999998888776665554
No 42
>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=57.73 E-value=37 Score=26.41 Aligned_cols=53 Identities=21% Similarity=0.359 Sum_probs=35.7
Q ss_pred CCCCCeEEEEeCC--CCCceEEEEeeeCC--ccEEEEEEeccccCCceeeecccccc
Q 018594 297 PQIGGLVRIVNGA--YRGSNARLLGVDTD--KFCAQVKIEKGVYDGRVLNAIDYEDI 349 (353)
Q Consensus 297 P~~G~~V~IV~G~--~RG~~g~L~siD~~--~~~a~V~l~~g~~~g~~v~~l~yedi 349 (353)
|+.|.+|+|+.-+ +-..+|++.++|.+ ++-++|+++.-.+.|-.-.++..+.+
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 4679999999765 47789999999988 67899999876665533334555544
No 43
>PF10615 DUF2470: Protein of unknown function (DUF2470); InterPro: IPR019595 This entry represents a putative haem-iron utilisation family of proteins, as many members are annotated as being pyridoxamine 5'-phosphate oxidase-related, FMN-binding; however the function of this domain is not known. ; PDB: 3GAS_D 3SWJ_A 2ARZ_B.
Probab=56.91 E-value=4.8 Score=31.99 Aligned_cols=36 Identities=17% Similarity=0.347 Sum_probs=23.3
Q ss_pred eecccccccHHHHHHHhccc---ccEEEee-cCceeEEEe
Q 018594 53 HMNSTRWATLTEFVKYLGRT---GKCKVEE-TPKGWFITY 88 (353)
Q Consensus 53 HMNaT~W~tLt~Fvk~Lgr~---G~c~vde-tekGw~I~y 88 (353)
|||.-...+|..|++++|.- +.|++.. +..|..|.|
T Consensus 16 HMN~DH~d~l~~~~~~~~~~~~~~~a~m~~id~~G~~l~~ 55 (83)
T PF10615_consen 16 HMNDDHADDLLLYARHYGGVPDAASARMTDIDRDGFDLRV 55 (83)
T ss_dssp HHHHH-HHHHHHHHHHHHT-SSSSS-EEEEEETTEEEEEE
T ss_pred HHHHhHHHHHHHHHHhcCCCCCCCCEEEEEEeccccEEEE
Confidence 99999999999999988865 2233322 344555555
No 44
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=56.50 E-value=18 Score=32.24 Aligned_cols=26 Identities=23% Similarity=0.372 Sum_probs=22.7
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCC
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTD 323 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~ 323 (353)
++|.-|+||+|.|.|..|.++....+
T Consensus 6 kpgkVVivL~GR~AGkKaVivk~~dd 31 (134)
T PTZ00471 6 KPGKVVIVTSGRYAGRKAVIVQNFDT 31 (134)
T ss_pred cCCEEEEEEccccCCcEEEEEeecCC
Confidence 57889999999999999999987555
No 45
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=55.57 E-value=12 Score=29.26 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=20.8
Q ss_pred HHHhcccccEEEeecCceeEEEe
Q 018594 66 VKYLGRTGKCKVEETPKGWFITY 88 (353)
Q Consensus 66 vk~Lgr~G~c~vdetekGw~I~y 88 (353)
+=||.|+|++.+++.+.-|||..
T Consensus 43 iGWLarE~KI~~~~~~~~~~v~L 65 (65)
T PF10771_consen 43 IGWLARENKIEFEEKNGELYVSL 65 (65)
T ss_dssp HHHHHCTTSEEEEEETTEEEEEE
T ss_pred HHHHhccCceeEEeeCCEEEEEC
Confidence 67999999999999999999863
No 46
>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=55.26 E-value=49 Score=23.62 Aligned_cols=52 Identities=19% Similarity=0.111 Sum_probs=35.9
Q ss_pred cCCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccccccccc
Q 018594 296 IPQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDICKL 352 (353)
Q Consensus 296 IP~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedicKl 352 (353)
.|++|..|++....-+=..|++++++.+ ..+.|.... .|. ...++.++|..+
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~-~~~~V~f~D---~G~-~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGE-QLYEVFFID---YGN-EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCC-CEEEEEEEC---CCc-cEEEeHHHeecC
Confidence 4688988888863345567899999986 456666664 144 335888888754
No 47
>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=53.92 E-value=43 Score=26.14 Aligned_cols=42 Identities=19% Similarity=0.180 Sum_probs=30.7
Q ss_pred eEEEEe-cCCceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEeC
Q 018594 263 GVVRKV-IDKYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVNG 308 (353)
Q Consensus 263 gvV~~V-~d~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~G 308 (353)
+.|.+| .++..|.|... |..-.|+-..|.. +++|+.|+|=.|
T Consensus 7 ~~Vv~v~~~~~~A~v~~~--G~~~~V~~~lv~~--v~~Gd~VLVHaG 49 (68)
T PF01455_consen 7 GRVVEVDEDGGMAVVDFG--GVRREVSLALVPD--VKVGDYVLVHAG 49 (68)
T ss_dssp EEEEEEETTTTEEEEEET--TEEEEEEGTTCTS--B-TT-EEEEETT
T ss_pred EEEEEEeCCCCEEEEEcC--CcEEEEEEEEeCC--CCCCCEEEEecC
Confidence 467777 34678888764 6777888888877 788999999776
No 48
>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=51.49 E-value=59 Score=24.80 Aligned_cols=57 Identities=18% Similarity=0.273 Sum_probs=39.2
Q ss_pred eeEEEEecCCceEEEEecCCCeEE-EEcCCceeeecCCCCCeEEEEeCCCCCceEEEE
Q 018594 262 KGVVRKVIDKYVGEIEMLEKKHVL-RVDQDELETVIPQIGGLVRIVNGAYRGSNARLL 318 (353)
Q Consensus 262 KgvV~~V~d~~~c~V~l~d~g~~l-~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~ 318 (353)
-|+|..+.+.+...|.+.++...+ .++...--+|-=..|+.|+|-.-.|--..|.++
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 478899999889999988654444 688885555555788888887666666666654
No 49
>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=51.17 E-value=82 Score=24.79 Aligned_cols=57 Identities=18% Similarity=0.256 Sum_probs=37.0
Q ss_pred CCCcccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCeEEEEcCCceeeecCC
Q 018594 236 KDYWLCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVLRVDQDELETVIPQ 298 (353)
Q Consensus 236 ~~~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~LETVIP~ 298 (353)
...++..+..+.+ ..+|.+|- |+|....+...+.|++.|-|.+..|..++|-..-|.
T Consensus 50 ~~~~~~~~~~~~~----~~~~~w~R--a~I~~~~~~~~~~V~~iD~G~~~~v~~~~l~~l~~~ 106 (121)
T PF00567_consen 50 PESNPGEGCLCVV----SEDGRWYR--AVITVDIDENQYKVFLIDYGNTEKVSASDLRPLPPE 106 (121)
T ss_dssp ST--TTEEEEEEE----TTTSEEEE--EEEEEEECTTEEEEEETTTTEEEEEEGGGEEE--HH
T ss_pred cccccCCEEEEEE----ecCCceee--EEEEEecccceeEEEEEecCceEEEcHHHhhhhCHH
Confidence 3444444444433 23557766 677555666799999999999999999998766553
No 50
>CHL00010 infA translation initiation factor 1
Probab=50.91 E-value=1.3e+02 Score=24.01 Aligned_cols=62 Identities=10% Similarity=0.105 Sum_probs=35.8
Q ss_pred ceeEEEEecCCceEEEEecCCCeEE--EEcCCce-eeecCCCCCeEEEEeCCCCCceEEEEeeeCC
Q 018594 261 QKGVVRKVIDKYVGEIEMLEKKHVL--RVDQDEL-ETVIPQIGGLVRIVNGAYRGSNARLLGVDTD 323 (353)
Q Consensus 261 ~KgvV~~V~d~~~c~V~l~d~g~~l--~vdq~~L-ETVIP~~G~~V~IV~G~~RG~~g~L~siD~~ 323 (353)
-+|+|..+.+.....|.+.+ |..+ .+....= ..+-|.+|+.|.|=-=.+-...|.++-+-..
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~-g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDN-GCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCC-CCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 46777777743355555533 4333 3333222 2667899999988744455556666665443
No 51
>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=48.52 E-value=41 Score=26.78 Aligned_cols=51 Identities=24% Similarity=0.429 Sum_probs=33.1
Q ss_pred CCCCCeEEEEe----CCCCCceEEEEeeeCCccEEEEEEeccccCCceeeecccccccc
Q 018594 297 PQIGGLVRIVN----GAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDICK 351 (353)
Q Consensus 297 P~~G~~V~IV~----G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedicK 351 (353)
...|..|.|.. |..+-..|+|.+++.+. +++..+.. ..+..+ .++|++|.+
T Consensus 22 r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~--v~l~~~~~-~~~~~~-~i~~~~I~k 76 (83)
T cd01734 22 RAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDT--VTLEVDIK-TRGKTV-EIPLDKIAK 76 (83)
T ss_pred HhCCCEEEEEEEcccCCeEEEEEEEEeEeCCE--EEEEEecC-CCCeEE-EEEhHHeeE
Confidence 34688888853 33455689999999876 55554421 113445 499999976
No 52
>PRK14639 hypothetical protein; Provisional
Probab=47.39 E-value=39 Score=29.88 Aligned_cols=72 Identities=19% Similarity=0.277 Sum_probs=45.3
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccccccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDIC 350 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedic 350 (353)
.|+-.|..++-++-|+-+.+ .....|..|.|-...-+-..|+|.+++.+. +++....+ +..+ .++|++|.
T Consensus 63 ~Y~LEVSSPGl~RpL~~~~~----f~r~~G~~v~v~l~~~~~~~G~L~~~~~~~--i~l~~~~~---~~~~-~i~~~~I~ 132 (140)
T PRK14639 63 EYFLEVSSPGLERKLSKIEH----FAKSIGELVKITTNEKEKFEGKIVSVDDEN--ITLENLEN---KEKT-TINFNDIK 132 (140)
T ss_pred CeEEEEeCCCCCCcCCCHHH----HHHhCCCEEEEEECCCcEEEEEEEEEeCCE--EEEEEccC---CcEE-EEEhHHee
Confidence 35555555554555543222 335579999997545678889999999876 55533221 3445 49999997
Q ss_pred cc
Q 018594 351 KL 352 (353)
Q Consensus 351 Kl 352 (353)
+.
T Consensus 133 ka 134 (140)
T PRK14639 133 KA 134 (140)
T ss_pred eE
Confidence 63
No 53
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=44.44 E-value=35 Score=30.04 Aligned_cols=28 Identities=18% Similarity=0.459 Sum_probs=25.2
Q ss_pred CCCCCeEEEEeCCCCCceEEEEeeeCCc
Q 018594 297 PQIGGLVRIVNGAYRGSNARLLGVDTDK 324 (353)
Q Consensus 297 P~~G~~V~IV~G~~RG~~g~L~siD~~~ 324 (353)
+.+|.-|.|+.|.++|..+.++++-.++
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~ 32 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN 32 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC
Confidence 4578899999999999999999998887
No 54
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=40.72 E-value=40 Score=32.26 Aligned_cols=33 Identities=21% Similarity=0.285 Sum_probs=29.0
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEEE
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVK 330 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~ 330 (353)
..|+.|.|+-|..+|..|.+..+-..+.-++|.
T Consensus 74 f~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~ 106 (236)
T KOG1708|consen 74 FFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVK 106 (236)
T ss_pred ecCCEEEEEecccCCccceEEEEeecCceEEEc
Confidence 369999999999999999999998888777763
No 55
>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=40.61 E-value=57 Score=28.37 Aligned_cols=52 Identities=10% Similarity=0.056 Sum_probs=39.7
Q ss_pred CCcccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCe--EEEEcCCcee
Q 018594 237 DYWLCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKH--VLRVDQDELE 293 (353)
Q Consensus 237 ~~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~--~l~vdq~~LE 293 (353)
...+.+|=.|+|+ +|-|-+-.|+|.++.++..+.|.+.--|+ .+.|+.++||
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 4678899999998 56777889999999776677776644444 4678877775
No 56
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=39.59 E-value=27 Score=26.29 Aligned_cols=68 Identities=15% Similarity=0.217 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHhccCC-cccccceeeeeecccccceeecccccccHHHHHHHhcccccEEEeec--CceeEE
Q 018594 17 EEFEAGFLELMRRSHRF-SRIAATVVYNEYIHDRHHVHMNSTRWATLTEFVKYLGRTGKCKVEET--PKGWFI 86 (353)
Q Consensus 17 ~eF~~~Fl~lLr~~~g~-krV~aN~vYneyI~dr~HiHMNaT~W~tLt~Fvk~Lgr~G~c~vdet--ekGw~I 86 (353)
+.|.....++|...++. -+|....+.++|.+--.++.--.=-..+|++|++- -.+.|.|.++ .+.|+|
T Consensus 4 ~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~yG~~~l~~ll~~--~~~~~~i~~~~~g~~~~v 74 (74)
T PF12872_consen 4 EELKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRDYGFSSLSELLES--LPDVVEIEERQHGGQVYV 74 (74)
T ss_dssp HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCCTTSSSHHHHHHT---TTTEEEEEEECCCC---
T ss_pred HHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccccCCCcHHHHHHh--CCCeEEEeeeCCCCcCCC
Confidence 45677788888777763 47999999988886555566555667899999975 4788888555 445654
No 57
>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=39.31 E-value=78 Score=28.01 Aligned_cols=53 Identities=17% Similarity=0.141 Sum_probs=39.6
Q ss_pred CCCcccCCcEEEEeecccCCcccccceeEEEEec-CCceEEEEecCCCe--EEEEcCCcee
Q 018594 236 KDYWLCEGIIVKVMSKALADKGYNKQKGVVRKVI-DKYVGEIEMLEKKH--VLRVDQDELE 293 (353)
Q Consensus 236 ~~~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~-d~~~c~V~l~d~g~--~l~vdq~~LE 293 (353)
....+.+|=.|+|+ +|-|-+..|+|..+. ++..+.|.+.--|+ .+.|+.++|+
T Consensus 116 ~~~~~~~G~~V~I~-----~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~v~~~~l~ 171 (172)
T TIGR00922 116 PKIDFEVGEQVRVN-----DGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVE 171 (172)
T ss_pred cccCCCCCCEEEEe-----ecCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEEEcHHHee
Confidence 34678899999998 567888899999996 45577776644344 5678877775
No 58
>PRK14630 hypothetical protein; Provisional
Probab=38.14 E-value=73 Score=28.29 Aligned_cols=69 Identities=14% Similarity=0.188 Sum_probs=41.5
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccccccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDIC 350 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedic 350 (353)
.|+-.|..++-++.|+-+.+ ..-..|..|.|-...-. ..|+|.+++.+. +++..+ +..+ .+||++|.
T Consensus 72 ~Y~LEVSSPGldRpL~~~~d----f~r~~G~~v~V~l~~~~-~~G~L~~~~d~~--i~l~~~-----~~~~-~i~~~~I~ 138 (143)
T PRK14630 72 NFSLEISTPGINRKIKSDRE----FKIFEGKKIKLMLDNDF-EEGFILEAKADS--FIFKTD-----SKEV-NVLYSDVK 138 (143)
T ss_pred CeEEEEeCCCCCCcCCCHHH----HHHhCCCEEEEEEcCcc-eEEEEEEEeCCE--EEEEEC-----CEEE-EEEhHhcc
Confidence 34555555544555543322 22346888888654332 289999998766 555433 3445 49999998
Q ss_pred cc
Q 018594 351 KL 352 (353)
Q Consensus 351 Kl 352 (353)
|.
T Consensus 139 ka 140 (143)
T PRK14630 139 KA 140 (143)
T ss_pred eE
Confidence 63
No 59
>PRK14633 hypothetical protein; Provisional
Probab=38.11 E-value=66 Score=28.71 Aligned_cols=70 Identities=19% Similarity=0.284 Sum_probs=42.7
Q ss_pred ceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEe----CCCCCceEEEEeeeCCccEEEEEEeccccCCceeeecccc
Q 018594 272 YVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVN----GAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYE 347 (353)
Q Consensus 272 ~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~----G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~ye 347 (353)
|+-.|..++-++.|+-+.++ .-..|..|.|.. +..+-..|+|.+++.+. +++.+.. +..+ .++|+
T Consensus 70 Y~LEVSSPGldRpL~~~~~f----~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~--i~l~~~~----~~~~-~i~~~ 138 (150)
T PRK14633 70 YILEVSSPGMNRQIFNIIQA----QALVGFNVKAVTLAPVGSQTKFKGVLERVEGNN--VILNLED----GKEI-SFDFD 138 (150)
T ss_pred eEEEEeCCCCCCCCCCHHHH----HHhCCCeEEEEEecccCCcEEEEEEEEEEeCCE--EEEEEcC----CcEE-EEEhH
Confidence 44455555445555433332 234688888853 34566789999998776 5554432 3445 49999
Q ss_pred ccccc
Q 018594 348 DICKL 352 (353)
Q Consensus 348 dicKl 352 (353)
+|.+.
T Consensus 139 ~I~ka 143 (150)
T PRK14633 139 ELKKL 143 (150)
T ss_pred HeeeE
Confidence 99863
No 60
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=38.06 E-value=56 Score=25.59 Aligned_cols=52 Identities=23% Similarity=0.396 Sum_probs=36.1
Q ss_pred CCCCeEEEEeCC--CCCceEEEEeeeCC--ccEEEEEEeccccCCceeeecccccc
Q 018594 298 QIGGLVRIVNGA--YRGSNARLLGVDTD--KFCAQVKIEKGVYDGRVLNAIDYEDI 349 (353)
Q Consensus 298 ~~G~~V~IV~G~--~RG~~g~L~siD~~--~~~a~V~l~~g~~~g~~v~~l~yedi 349 (353)
+.|++|+|+.-+ +-..+|++.++|.+ ++-++|+++.-.+.|-.-.++..+.+
T Consensus 3 ~rGskVrIlR~ESYWyn~vGtV~svd~~gi~YPV~VRF~kvNY~g~nTNnfa~~El 58 (64)
T CHL00125 3 KRGSKVRILRKESYWYNEIGTVATVDQSGIRYPVLVRFEKVNYSGTNTNNFSLDEL 58 (64)
T ss_pred ccCCEEEEccccceeecCcceEEEEcCCCCCccEEEEEeeeeccccccccccHHHH
Confidence 468999999665 36778999999987 67788988865555532223444433
No 61
>PRK14638 hypothetical protein; Provisional
Probab=37.62 E-value=60 Score=29.00 Aligned_cols=69 Identities=19% Similarity=0.188 Sum_probs=44.7
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccccccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDIC 350 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedic 350 (353)
.|+-.|..++-++-|+-+.++. -..|..|.|-...-+-.+|+|.+++.+. +++... +..+ .+||++|.
T Consensus 75 ~Y~LEVSSPGldRpL~~~~~f~----r~~G~~v~V~~~~~k~~~G~L~~~~~~~--i~l~~~-----~~~~-~i~~~~I~ 142 (150)
T PRK14638 75 SYTLEVSSPGLDRPLRGPKDYV----RFTGKLAKIVTKDGKTFIGRIESFVDGT--ITISDE-----KEKY-EINIDDVK 142 (150)
T ss_pred ceEEEEeCCCCCCCCCCHHHHH----HhCCCEEEEEECCCcEEEEEEEEEeCCE--EEEEEC-----CcEE-EEEhHHcc
Confidence 4555565555556665444333 3469999996534577899999998765 444422 3445 48999987
Q ss_pred c
Q 018594 351 K 351 (353)
Q Consensus 351 K 351 (353)
+
T Consensus 143 ~ 143 (150)
T PRK14638 143 R 143 (150)
T ss_pred e
Confidence 6
No 62
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=37.32 E-value=2.4e+02 Score=34.79 Aligned_cols=88 Identities=14% Similarity=0.151 Sum_probs=56.3
Q ss_pred CcccCCcEEEEeecccCCcccccceeEEEEecCCce-EEEEecCCCeEEEEcCCce----eeecC-----CCCCeEEEEe
Q 018594 238 YWLCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYV-GEIEMLEKKHVLRVDQDEL----ETVIP-----QIGGLVRIVN 307 (353)
Q Consensus 238 ~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~-c~V~l~d~g~~l~vdq~~L----ETVIP-----~~G~~V~IV~ 307 (353)
.+..+|-+|+.-......+..| +|..|..... .+|. ...|..+.++...+ +-.-| +.|+++++..
T Consensus 647 ~~Y~~G~vi~~~~~~~~~~~~y----~V~~v~~~~n~LtL~-~~~G~~~~~~p~~~~~~~~vy~~~~ieiA~GDrLr~T~ 721 (1747)
T PRK13709 647 DMYRPGMVMEQWNPETRSHDRY----VIDRVTAQSHSLTLR-DAQGETQVVKISSLDSSWSLFRPEKMPVADGERLRVLG 721 (1747)
T ss_pred hcCCCCcEEEeeccccccCccE----EEEEEcCCCCEEEEE-cCCCCEEEeChHHhcccceeccccccccCCCCEEEEcc
Confidence 4558999998754322222333 7888876433 3333 34588888885443 44444 5799999994
Q ss_pred C-----CCCCceEEEEeeeCCccEEEEEEe
Q 018594 308 G-----AYRGSNARLLGVDTDKFCAQVKIE 332 (353)
Q Consensus 308 G-----~~RG~~g~L~siD~~~~~a~V~l~ 332 (353)
. -..|..+++.+++... ++|...
T Consensus 722 nd~~~~l~Ngd~~tV~~i~~~~--i~l~~~ 749 (1747)
T PRK13709 722 KIPGLRLKGGDRLQVTSVSEDG--LTVVVP 749 (1747)
T ss_pred CCcccCccCCCEEEEEEecCCe--EEEEEC
Confidence 3 3578999999998755 666654
No 63
>PRK14637 hypothetical protein; Provisional
Probab=37.09 E-value=78 Score=28.39 Aligned_cols=47 Identities=17% Similarity=0.163 Sum_probs=31.4
Q ss_pred CCCCeEEEEeCCCCCc-eEEEEeeeCCccEEEEEEeccccCCceeeeccccccccc
Q 018594 298 QIGGLVRIVNGAYRGS-NARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDICKL 352 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~-~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedicKl 352 (353)
..|..|.|-....+.. .|+|.+++.+. +++... +..+ .+||++|.+.
T Consensus 96 ~~G~~V~V~l~~~~~~~~G~L~~~~d~~--v~l~~~-----~~~~-~i~~~~I~ka 143 (151)
T PRK14637 96 FVGETVKVWFECTGQWQVGTIAEADETC--LVLTSD-----GVPV-TIPYVQITKA 143 (151)
T ss_pred hCCCEEEEEECCCCcEEEEEEEEEeCCE--EEEEEC-----CEEE-EEEHHHeeeE
Confidence 3688899865223345 59999998876 444432 4445 4999999763
No 64
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=35.81 E-value=68 Score=28.20 Aligned_cols=33 Identities=30% Similarity=0.306 Sum_probs=25.1
Q ss_pred ccCCcEEEEeecccCCcccccceeEEEEecCCceEEEE
Q 018594 240 LCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIE 277 (353)
Q Consensus 240 L~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~ 277 (353)
|-+|-+|-+. .|+|-++++||.+++|.....|.
T Consensus 5 l~~GrVvvv~-----~GR~aGkk~VIv~~iDd~~v~i~ 37 (125)
T COG2163 5 LEVGRVVVVT-----AGRFAGKKVVIVKIIDDNFVLIT 37 (125)
T ss_pred ccCCeEEEEe-----cceeCCceEEEEEEccCCEEEEe
Confidence 4567777555 57999999999999998655444
No 65
>PRK14636 hypothetical protein; Provisional
Probab=35.58 E-value=87 Score=28.81 Aligned_cols=71 Identities=18% Similarity=0.186 Sum_probs=42.9
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEE-eCCC---CCceEEEEeeeCCccEEEEEEeccccCCceeeeccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIV-NGAY---RGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDY 346 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV-~G~~---RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~y 346 (353)
.|+-.|..++-.+.|+-+.++ .-..|..|.|- +.+. +-.+|+|.+++.+. +++.+.. +..+ .+||
T Consensus 73 ~Y~LEVSSPGldRpL~~~~df----~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~~--v~l~~~~----~~~~-~i~~ 141 (176)
T PRK14636 73 AYRLEVSSPGIDRPLTRPKDF----ADWAGHEARIALSEPLDGRKQFRGELKGIDGDT--VTIADNK----AGEV-ILPF 141 (176)
T ss_pred CeEEEEeCCCCCCCCCCHHHH----HHhCCCeEEEEEecccCCeEEEEEEEEEEeCCE--EEEEEcC----CcEE-EEEh
Confidence 455555555545555433222 23469988885 4333 44589999998766 5554432 3345 4899
Q ss_pred cccccc
Q 018594 347 EDICKL 352 (353)
Q Consensus 347 edicKl 352 (353)
++|.+.
T Consensus 142 ~~I~kA 147 (176)
T PRK14636 142 AAIESA 147 (176)
T ss_pred HHcceE
Confidence 999763
No 66
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=35.02 E-value=2.8e+02 Score=32.14 Aligned_cols=63 Identities=13% Similarity=0.083 Sum_probs=48.5
Q ss_pred eeEEEEecCCceEEEEecCCCe--EEEEcCCceeeecCCCCCeEEEEeCCCCCceEEEEeeeCCccEEEE
Q 018594 262 KGVVRKVIDKYVGEIEMLEKKH--VLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQV 329 (353)
Q Consensus 262 KgvV~~V~d~~~c~V~l~d~g~--~l~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V 329 (353)
=|+|++|.++ +++|..+.+|. +..++..-|--|++.+|+.|.+..| ...++..+...++.++-
T Consensus 18 lG~v~~~d~r-~vtv~fpas~e~R~ya~~~apl~Rv~~~~g~~v~~~~~----~~~~v~~v~~~~gl~~y 82 (956)
T PRK04914 18 LGTVVAVDGR-TVTLLFPATGENRLYARNDAPLTRVMFNPGDTITSHEG----WQLTVEEVEEENGLLTY 82 (956)
T ss_pred cEEEEEEeCC-EEEEEecCCCCceeeecCCCCceeeecCCCCEEEecCC----CEEEEEEEeccCCcEEE
Confidence 5899999766 99999988755 4579999999999999999986555 45666666666654443
No 67
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=34.61 E-value=26 Score=27.18 Aligned_cols=65 Identities=17% Similarity=0.201 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHhccCCcccccceeeeeecccccceeecccccccHHHHHHHhcccccEEEeecCce
Q 018594 18 EFEAGFLELMRRSHRFSRIAATVVYNEYIHDRHHVHMNSTRWATLTEFVKYLGRTGKCKVEETPKG 83 (353)
Q Consensus 18 eF~~~Fl~lLr~~~g~krV~aN~vYneyI~dr~HiHMNaT~W~tLt~Fvk~Lgr~G~c~vdetekG 83 (353)
-|.-+-+.++++ -|...+..+.||+.|-.-=.+.+++.-.+....+++.-|.-.|++.++..-+|
T Consensus 6 l~L~Al~~~~~~-~~~~~~~~~~vy~~Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~~~~~~~g 70 (87)
T cd08768 6 LVLLALLLLFKR-GGEEEATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLETEVSSKG 70 (87)
T ss_pred HHHHHHHHHHhc-CCCCCccHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeEEEEecCC
Confidence 344444545533 35677899999999986666678888999999999999999999999876544
No 68
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=34.39 E-value=1e+02 Score=27.14 Aligned_cols=52 Identities=8% Similarity=-0.011 Sum_probs=39.7
Q ss_pred CcccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCe--EEEEcCCceee
Q 018594 238 YWLCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKH--VLRVDQDELET 294 (353)
Q Consensus 238 ~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~--~l~vdq~~LET 294 (353)
..+.+|=.|+|+ +|-|-+-.|+|.++.++..+.|.+.--|+ .+.|+.++|+.
T Consensus 108 ~~~~~G~~V~I~-----~Gp~~g~eg~v~~~~~~~r~~v~v~~~gr~~~v~v~~~~~~~ 161 (162)
T PRK09014 108 ETPKPGDKVIIT-----EGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFRK 161 (162)
T ss_pred cCCCCCCEEEEe-----cCCCCCcEEEEEEeCCCeEEEEeehhhCCcEEEEECHHHeec
Confidence 347889999998 56788899999999877777776643344 55788888864
No 69
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=33.92 E-value=4.1e+02 Score=25.06 Aligned_cols=91 Identities=18% Similarity=0.335 Sum_probs=59.0
Q ss_pred cccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCeEEEEcCCceeeecCCCCCeEE--EEeCCCCCceEE
Q 018594 239 WLCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVR--IVNGAYRGSNAR 316 (353)
Q Consensus 239 WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~--IV~G~~RG~~g~ 316 (353)
...||=+|-..-..+....-|.+.|.|....-+ .+..++...++.|...-.++.+|+.|+.|. |+...-+.....
T Consensus 7 ~v~PGd~~a~~EE~~~G~gt~~~~g~i~Aa~~G---~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~ 83 (188)
T COG1096 7 FVLPGDVLAVIEEFLPGEGTYEEGGEIRAAATG---VVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVR 83 (188)
T ss_pred EEcCcceeeeeeeeecCCCeEeECCEEEEeecc---cEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEE
Confidence 445665665554444433456667777776443 355556677888888888999999999875 445555666667
Q ss_pred EEeeeCCc------cEEEEEEe
Q 018594 317 LLGVDTDK------FCAQVKIE 332 (353)
Q Consensus 317 L~siD~~~------~~a~V~l~ 332 (353)
+.+++... +.+.+.+.
T Consensus 84 i~~ve~~~r~~~~~~~~~ihvs 105 (188)
T COG1096 84 IVGVEGKERELATSGAADIHVS 105 (188)
T ss_pred EEEEecccccCCCCceeeEEEE
Confidence 77777644 55655554
No 70
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=33.80 E-value=1.4e+02 Score=26.52 Aligned_cols=53 Identities=17% Similarity=0.177 Sum_probs=39.8
Q ss_pred CCcccCCcEEEEeecccCCcccccceeEEEEec-CCceEEEEecCCC--eEEEEcCCceee
Q 018594 237 DYWLCEGIIVKVMSKALADKGYNKQKGVVRKVI-DKYVGEIEMLEKK--HVLRVDQDELET 294 (353)
Q Consensus 237 ~~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~-d~~~c~V~l~d~g--~~l~vdq~~LET 294 (353)
...+.+|=.|+|+ +|-|-+..|+|..+. ++..+.|.+.--| ..+.|+.+.||.
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 4778899999998 567888999999997 4546666654334 456788888765
No 71
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=33.43 E-value=43 Score=29.93 Aligned_cols=36 Identities=17% Similarity=0.338 Sum_probs=28.0
Q ss_pred CCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCC
Q 018594 299 IGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDG 338 (353)
Q Consensus 299 ~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g 338 (353)
+|.-++|..|+|.|...-+..++..+ .+.++ ||+++
T Consensus 9 VGrva~v~~G~~~GkL~AIVdviDqn---r~lvD-Gp~t~ 44 (136)
T KOG3421|consen 9 VGRVALVSFGPDAGKLVAIVDVIDQN---RALVD-GPCTG 44 (136)
T ss_pred cceEEEEEecCCCceEEEEEEeecch---hhhcc-Ccccc
Confidence 58889999999999999999998776 23334 67554
No 72
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=32.46 E-value=3.1e+02 Score=23.13 Aligned_cols=60 Identities=12% Similarity=0.175 Sum_probs=35.4
Q ss_pred ceeEEEEecCCceEEEEecCCCeEE-EEcCCceeeecCCCCCeEEEEeCCCCCceEEEEee
Q 018594 261 QKGVVRKVIDKYVGEIEMLEKKHVL-RVDQDELETVIPQIGGLVRIVNGAYRGSNARLLGV 320 (353)
Q Consensus 261 ~KgvV~~V~d~~~c~V~l~d~g~~l-~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~si 320 (353)
.-|+|..+.+.+...|.+.++..++ .++..+=-+|-=..|+.|+|-.=+|--..|.++-+
T Consensus 23 ~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~~~~kg~Iv~r 83 (100)
T PRK04012 23 VFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADIIWR 83 (100)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEecccCCCEEEEEEE
Confidence 3467888888878888887644444 46555544444456666666544444444444433
No 73
>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=31.62 E-value=1.1e+02 Score=21.40 Aligned_cols=28 Identities=14% Similarity=0.146 Sum_probs=21.9
Q ss_pred ceeEEEEecCCceEEEEecCCCeEEEEcCC
Q 018594 261 QKGVVRKVIDKYVGEIEMLEKKHVLRVDQD 290 (353)
Q Consensus 261 ~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~ 290 (353)
-+|.|.+..++ .++|++.+ |..+.|..+
T Consensus 14 v~g~I~~~~g~-~vtV~~~~-G~~~tv~~d 41 (42)
T PF02736_consen 14 VKGEIIEEEGD-KVTVKTED-GKEVTVKKD 41 (42)
T ss_dssp EEEEEEEEESS-EEEEEETT-TEEEEEEGG
T ss_pred EEEEEEEEcCC-EEEEEECC-CCEEEeCCC
Confidence 46888887665 89999987 888877654
No 74
>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=31.39 E-value=2.7e+02 Score=22.18 Aligned_cols=56 Identities=20% Similarity=0.286 Sum_probs=31.2
Q ss_pred eEEEEecCCceEEEEecCCCeEE-EEcCCceeeecCCCCCeEEEEeCCCCCceEEEE
Q 018594 263 GVVRKVIDKYVGEIEMLEKKHVL-RVDQDELETVIPQIGGLVRIVNGAYRGSNARLL 318 (353)
Q Consensus 263 gvV~~V~d~~~c~V~l~d~g~~l-~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~ 318 (353)
|.|..+.+.....|.+.++..++ .++-.+=-.+-=.+|+.|+|-.=+|--..|.++
T Consensus 4 g~V~~~~g~~~~~V~~~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~d~~kg~Iv 60 (77)
T cd05793 4 GQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADII 60 (77)
T ss_pred EEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEeccccCCEEEEE
Confidence 67888888778888887644433 455444433333456666554333433344333
No 75
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=30.90 E-value=2.6e+02 Score=23.49 Aligned_cols=58 Identities=19% Similarity=0.248 Sum_probs=33.2
Q ss_pred CcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCeEE-EEcCCceeeecCCCCCeEEE
Q 018594 243 GIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVL-RVDQDELETVIPQIGGLVRI 305 (353)
Q Consensus 243 ~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l-~vdq~~LETVIP~~G~~V~I 305 (353)
.+.+++..+. +|. .-|.|..+.+.+...|.+.++..++ .|+..+=-.|-=..|+.|+|
T Consensus 8 ~~~~~~p~~~--e~e---~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlV 66 (99)
T TIGR00523 8 QIRVRLPRKE--EGE---ILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIV 66 (99)
T ss_pred cceeeCCCCC--CCE---EEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEE
Confidence 3455666442 333 3467888888878888877644333 45544443333445555555
No 76
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=30.74 E-value=51 Score=32.24 Aligned_cols=35 Identities=20% Similarity=0.317 Sum_probs=27.3
Q ss_pred CCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEec
Q 018594 299 IGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEK 333 (353)
Q Consensus 299 ~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~ 333 (353)
+|...+|+.|+-+|..|.+...+..-.-+.|.++.
T Consensus 60 iGN~A~VvSG~AKG~~G~VtGkHGGieHVlV~F~~ 94 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAKGVVTGKHGGIEHVLVDFPD 94 (258)
T ss_dssp BT-EEEE-SSTTTT-EEEEEEEETTTTEEEEE--H
T ss_pred cCceeEEeecccCCCcCeEecccCCeeeEEEECCH
Confidence 69999999999999999999999988788887764
No 77
>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=30.09 E-value=2.3e+02 Score=22.09 Aligned_cols=43 Identities=9% Similarity=0.110 Sum_probs=30.6
Q ss_pred ceeEEEEecCCceEEEEecCCCeEEEEcCCceeeecC--CCCCeEEEEeC
Q 018594 261 QKGVVRKVIDKYVGEIEMLEKKHVLRVDQDELETVIP--QIGGLVRIVNG 308 (353)
Q Consensus 261 ~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~LETVIP--~~G~~V~IV~G 308 (353)
-.|+|.+|... +.+|.|. +|...+++.+.= ++ ++|.+|+|..-
T Consensus 5 veG~I~~id~~-~~titLd-DGksy~lp~ef~---~~~L~~G~kV~V~yd 49 (61)
T PF07076_consen 5 VEGTIKSIDPE-TMTITLD-DGKSYKLPEEFD---FDGLKPGMKVVVFYD 49 (61)
T ss_pred ceEEEEEEcCC-ceEEEec-CCCEEECCCccc---ccccCCCCEEEEEEE
Confidence 36899998554 8888775 588887765432 55 57899988754
No 78
>PRK04950 ProP expression regulator; Provisional
Probab=29.95 E-value=1e+02 Score=29.52 Aligned_cols=35 Identities=23% Similarity=0.538 Sum_probs=28.4
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccc
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGV 335 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~ 335 (353)
+.|..|.|--| -.-.-|++++|+.++ |.|+|++|.
T Consensus 168 ~~gq~v~vk~g-~~~~~a~i~ei~kd~--v~vql~~Gl 202 (213)
T PRK04950 168 TVGQAVKVKAG-KSAMDATVLEITKDD--VRVQLDSGL 202 (213)
T ss_pred ccCCEEEEecc-CCCCceEEEEEecCc--EEEEcCCCc
Confidence 34888888888 445779999999998 999999863
No 79
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=29.70 E-value=1e+02 Score=25.00 Aligned_cols=30 Identities=10% Similarity=0.235 Sum_probs=23.1
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEec
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEK 333 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~ 333 (353)
++|++|+-..| -.|++.+++.+. +.|++..
T Consensus 39 ~~Gd~VvT~gG----i~G~V~~i~d~~--v~vei~~ 68 (84)
T TIGR00739 39 KKGDKVLTIGG----IIGTVTKIAENT--IVIELND 68 (84)
T ss_pred CCCCEEEECCC----eEEEEEEEeCCE--EEEEECC
Confidence 46899977766 889999999764 6777654
No 80
>PRK14631 hypothetical protein; Provisional
Probab=29.52 E-value=1.2e+02 Score=27.84 Aligned_cols=73 Identities=29% Similarity=0.239 Sum_probs=43.9
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEe----CCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVN----GAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDY 346 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~----G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~y 346 (353)
.|+-.|..++-.+-|+=. .-.....|..|.|-. +..+-.+|+|.+++-++..+++.+.. +..+ .++|
T Consensus 92 ~Y~LEVSSPGldRpL~~~----~df~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~----~~~~-~i~~ 162 (174)
T PRK14631 92 EYALEVSSPGWDRPFFQL----EQLQGYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEG----KHVL-DIDS 162 (174)
T ss_pred CeEEEEeCCCCCCcCCCH----HHHHHhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcC----CcEE-EEEh
Confidence 355555555445555322 223445688888863 33567889999998434446665542 3345 4899
Q ss_pred cccccc
Q 018594 347 EDICKL 352 (353)
Q Consensus 347 edicKl 352 (353)
++|.|.
T Consensus 163 ~~I~ka 168 (174)
T PRK14631 163 NNIDKA 168 (174)
T ss_pred HHcceE
Confidence 999763
No 81
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=29.35 E-value=1.2e+02 Score=23.42 Aligned_cols=45 Identities=22% Similarity=0.177 Sum_probs=21.0
Q ss_pred eEEEEecC-CceEEEEecCCCeEE----EEcCCc---e-eeecCCCCCeEEEEe
Q 018594 263 GVVRKVID-KYVGEIEMLEKKHVL----RVDQDE---L-ETVIPQIGGLVRIVN 307 (353)
Q Consensus 263 gvV~~V~d-~~~c~V~l~d~g~~l----~vdq~~---L-ETVIP~~G~~V~IV~ 307 (353)
|+|.+|.. ..++.|++.+.+..+ .+-+-+ . --..|.+|+.|+|+.
T Consensus 1 G~V~~v~~~~grvrV~~~~~~~~~s~Wl~~~~~~ag~~g~~~~P~iGeqV~v~~ 54 (79)
T PF04717_consen 1 GTVTAVDPDKGRVRVRFPDDGDIVSDWLPVLQPRAGGWGFWFPPEIGEQVLVLF 54 (79)
T ss_dssp EEEEEEETTTTEEEEE-B-CTTEEEEEEEE--S-BSSSB------TT-EEEEEE
T ss_pred CeEEEEECCCCEEEEEEecCCCccceEEEeeehhccCCeeEccCCCCcEEEEEc
Confidence 67777754 467888874444432 222211 2 234578999999984
No 82
>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=29.06 E-value=1.4e+02 Score=29.17 Aligned_cols=57 Identities=11% Similarity=0.066 Sum_probs=37.5
Q ss_pred CCcccCCcEEEEeecccCCcccccceeEEEEecC-CceEEEEecCCCeEEEEcCCceeeecCC
Q 018594 237 DYWLCEGIIVKVMSKALADKGYNKQKGVVRKVID-KYVGEIEMLEKKHVLRVDQDELETVIPQ 298 (353)
Q Consensus 237 ~~WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d-~~~c~V~l~d~g~~l~vdq~~LETVIP~ 298 (353)
..| ..|=.... ..-.||.||. ++|.+|.. +.+|+|...+-|..-.|.-.+|-+.-..
T Consensus 67 ~~W-kvGd~C~A--~~s~Dg~~Y~--A~I~~i~~~~~~~~V~f~gYgn~e~v~l~dL~~~~~~ 124 (264)
T PF06003_consen 67 KKW-KVGDKCMA--VYSEDGQYYP--ATIESIDEEDGTCVVVFTGYGNEEEVNLSDLKPSEGD 124 (264)
T ss_dssp T----TT-EEEE--E-TTTSSEEE--EEEEEEETTTTEEEEEETTTTEEEEEEGGGEEETT--
T ss_pred cCC-CCCCEEEE--EECCCCCEEE--EEEEEEcCCCCEEEEEEcccCCeEeeehhhhcccccc
Confidence 467 44544444 4567999997 89999975 5699999988788777777777655443
No 83
>PRK14640 hypothetical protein; Provisional
Probab=28.65 E-value=1.1e+02 Score=27.22 Aligned_cols=69 Identities=14% Similarity=0.144 Sum_probs=41.8
Q ss_pred ceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEe----CCCCCceEEEEeeeCCccEEEEEEeccccCCceeeecccc
Q 018594 272 YVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVN----GAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYE 347 (353)
Q Consensus 272 ~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~----G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~ye 347 (353)
|.-.|..++-++-|+-+.. ..-..|..|.|-. +..+-..|+|.+++.+. +++.+. |+.+ .+||+
T Consensus 73 Y~LEVSSPGl~RpL~~~~~----f~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~--v~l~~~-----~~~~-~i~~~ 140 (152)
T PRK14640 73 YYLEVSSPGLDRPLFKVAQ----FEKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDM--ITLTVD-----GKDE-VLAFT 140 (152)
T ss_pred eEEEEeCCCCCCcCCCHHH----HHHhCCCeEEEEEecccCCceEEEEEEEEEeCCE--EEEEEC-----CeEE-EEEhH
Confidence 4444544444454443322 2234688888863 33567789999998765 544433 3445 48999
Q ss_pred ccccc
Q 018594 348 DICKL 352 (353)
Q Consensus 348 dicKl 352 (353)
+|.+.
T Consensus 141 ~I~ka 145 (152)
T PRK14640 141 NIQKA 145 (152)
T ss_pred HeeeE
Confidence 98763
No 84
>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=28.62 E-value=1.3e+02 Score=23.53 Aligned_cols=41 Identities=22% Similarity=0.394 Sum_probs=30.2
Q ss_pred eCCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccccccccc
Q 018594 307 NGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDICKL 352 (353)
Q Consensus 307 ~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedicKl 352 (353)
+|.|.-.+|++..+|.......+.-.. +... .++|+||+.+
T Consensus 52 ~g~~~~~~G~I~~id~~~~~l~~~~~~----~~~~-~I~~~~I~~I 92 (92)
T PF08863_consen 52 DGYYQSVTGTIHKIDEINRTLKLKDED----GETE-KIPFDDIIDI 92 (92)
T ss_pred CCeeEEEEEEEEEEcCCCCEEEEEeCC----CCEE-EEEhhhEEEC
Confidence 677888999999999999766654321 3333 5999999853
No 85
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=27.71 E-value=98 Score=33.14 Aligned_cols=44 Identities=20% Similarity=0.437 Sum_probs=35.3
Q ss_pred CcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCeEEEEcCCce
Q 018594 243 GIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVLRVDQDEL 292 (353)
Q Consensus 243 ~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~L 292 (353)
+-.|||. .|.|-++=|||+||.+. .|.|+|-.....+.|+-+.|
T Consensus 355 gktVrIr-----~g~yKG~lGVVKdv~~~-~arVeLhs~nK~VTI~K~~l 398 (607)
T COG5164 355 GKTVRIR-----CGEYKGHLGVVKDVDRN-IARVELHSNNKFVTIEKSRL 398 (607)
T ss_pred CceEEEe-----ecccccccceeeeccCc-eEEEEEecCCceEEeehhhe
Confidence 5578886 34688899999999765 99999987777788887777
No 86
>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=27.50 E-value=3.2e+02 Score=21.83 Aligned_cols=48 Identities=10% Similarity=0.068 Sum_probs=31.3
Q ss_pred eEEEEecCCceEEEEecCCCeEE-EEcCCceeeecCCCCCeEEEEeCCC
Q 018594 263 GVVRKVIDKYVGEIEMLEKKHVL-RVDQDELETVIPQIGGLVRIVNGAY 310 (353)
Q Consensus 263 gvV~~V~d~~~c~V~l~d~g~~l-~vdq~~LETVIP~~G~~V~IV~G~~ 310 (353)
|+|....+.+...|++.|+..++ .++..+=-+|-=..|+.|+|-.-+|
T Consensus 4 ~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 4 VRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIEE 52 (78)
T ss_pred EEEEEECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEEEeccc
Confidence 67788877778888887654444 5766666664446677776644333
No 87
>PRK14647 hypothetical protein; Provisional
Probab=27.36 E-value=96 Score=27.87 Aligned_cols=71 Identities=18% Similarity=0.253 Sum_probs=42.9
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEe-C--------CCCCceEEEEeeeCCccEEEEEEeccccCCcee
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVN-G--------AYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVL 341 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~-G--------~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v 341 (353)
.|+-.|..++-++.|+-+..+ .-..|..|.|-. . ..+-..|+|.+++.+. +++.+.. ++.+
T Consensus 74 ~Y~LEVSSPG~~RpL~~~~~f----~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~--v~l~~~~----~~~~ 143 (159)
T PRK14647 74 RYTLEVSSPGLDRPLKKEADY----ERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGV--VTIALKE----GQQA 143 (159)
T ss_pred CeEEEEcCCCCCCcCCCHHHH----HHhCCcEEEEEEeccccccccCCceEEEEEEEeecCCE--EEEEEcC----CcEE
Confidence 345555555445555433322 245688888863 1 2466789999998655 5554432 3445
Q ss_pred eeccccccccc
Q 018594 342 NAIDYEDICKL 352 (353)
Q Consensus 342 ~~l~yedicKl 352 (353)
.+||++|.+.
T Consensus 144 -~i~~~~I~ka 153 (159)
T PRK14647 144 -RIPLDKIAKA 153 (159)
T ss_pred -EEEHHHCCEE
Confidence 4899999863
No 88
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=26.99 E-value=1.1e+02 Score=25.85 Aligned_cols=30 Identities=17% Similarity=0.220 Sum_probs=22.8
Q ss_pred CCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEec
Q 018594 298 QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEK 333 (353)
Q Consensus 298 ~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~ 333 (353)
++|++|+-..| -.|++.++|.+ .+.|++..
T Consensus 54 k~Gd~VvT~gG----i~G~Vv~i~~~--~v~lei~~ 83 (106)
T PRK05585 54 AKGDEVVTNGG----IIGKVTKVSED--FVIIELND 83 (106)
T ss_pred CCCCEEEECCC----eEEEEEEEeCC--EEEEEECC
Confidence 46888877766 88999999864 57777754
No 89
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=26.91 E-value=1.1e+02 Score=24.45 Aligned_cols=39 Identities=26% Similarity=0.381 Sum_probs=29.9
Q ss_pred CCCCeEEEEeCC--CCCceEEEEeeeCC--ccEEEEEEecccc
Q 018594 298 QIGGLVRIVNGA--YRGSNARLLGVDTD--KFCAQVKIEKGVY 336 (353)
Q Consensus 298 ~~G~~V~IV~G~--~RG~~g~L~siD~~--~~~a~V~l~~g~~ 336 (353)
+.|++|+|++-+ +-..+|++.++|.+ ++-++|+++.-.+
T Consensus 4 ~rGskVrIlR~ESYWyn~vGtV~svD~sgi~YPV~VRF~kvNY 46 (71)
T PRK02749 4 SRGDKVRILRPESYWYNEVGTVASVDKSGIKYPVIVRFDKVNY 46 (71)
T ss_pred ccCCEEEEccccceeecCcceEEEEccCCCeeeEEEEeeeeec
Confidence 468999999665 46788999999987 6778888875433
No 90
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=26.88 E-value=2.7e+02 Score=20.74 Aligned_cols=24 Identities=17% Similarity=0.209 Sum_probs=14.1
Q ss_pred eecCCCCCeEEEEeCCCCCceEEE
Q 018594 294 TVIPQIGGLVRIVNGAYRGSNARL 317 (353)
Q Consensus 294 TVIP~~G~~V~IV~G~~RG~~g~L 317 (353)
.+-|..|+.|.+-...+-+..|.+
T Consensus 38 ~~~~~vGD~V~~~~~~~~~~~g~I 61 (64)
T cd04451 38 YIRILPGDRVKVELSPYDLTKGRI 61 (64)
T ss_pred CcccCCCCEEEEEEeecCCCEEEE
Confidence 445889999977643333333433
No 91
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=26.88 E-value=3e+02 Score=21.30 Aligned_cols=56 Identities=14% Similarity=0.190 Sum_probs=29.1
Q ss_pred eeEEEEecCCceEEEEecCCCeEE--EEcCCce-eeecCCCCCeEEEEeCCCCCceEEEE
Q 018594 262 KGVVRKVIDKYVGEIEMLEKKHVL--RVDQDEL-ETVIPQIGGLVRIVNGAYRGSNARLL 318 (353)
Q Consensus 262 KgvV~~V~d~~~c~V~l~d~g~~l--~vdq~~L-ETVIP~~G~~V~IV~G~~RG~~g~L~ 318 (353)
+|+|..+..+..+.|.+.+ |..+ .+....= --+-|.+|+.|.|---.+-...|.++
T Consensus 10 ~G~Vi~~~~~~~y~V~~~~-g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv 68 (72)
T PRK00276 10 EGTVVEALPNAMFRVELEN-GHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRIT 68 (72)
T ss_pred EEEEEEEcCCCEEEEEeCC-CCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEE
Confidence 4667766654344455432 3332 2333222 13448889999877444444445444
No 92
>PLN00208 translation initiation factor (eIF); Provisional
Probab=26.82 E-value=4.8e+02 Score=23.60 Aligned_cols=60 Identities=12% Similarity=0.103 Sum_probs=39.9
Q ss_pred eEEEEecCCceEEEEecCCCeEE-EEcCCceeeecCCCCCeEEEEeCCCCCceEEEEeeeC
Q 018594 263 GVVRKVIDKYVGEIEMLEKKHVL-RVDQDELETVIPQIGGLVRIVNGAYRGSNARLLGVDT 322 (353)
Q Consensus 263 gvV~~V~d~~~c~V~l~d~g~~l-~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~siD~ 322 (353)
|+|..+.+...+.|...+...++ .|+-.+=-.|-=.+|+.|+|-.-+|--..|.++-+-.
T Consensus 36 g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~VlVel~~~d~~KgdIv~ry~ 96 (145)
T PLN00208 36 AQVLRMLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLRDYQDDKADVILKYM 96 (145)
T ss_pred EEEEEEcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCEEEEEccCCCCCEEEEEEEcC
Confidence 46777777777777776654444 5666555544456788888876667777777776544
No 93
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.95 E-value=1.5e+02 Score=26.89 Aligned_cols=45 Identities=22% Similarity=0.497 Sum_probs=32.3
Q ss_pred CCCeEEEEe----CCCCCceEEEEeeeCCccEEEEEEeccccCCceeeecccccccc
Q 018594 299 IGGLVRIVN----GAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDICK 351 (353)
Q Consensus 299 ~G~~V~IV~----G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedicK 351 (353)
.|..|+|.. ..-+-..|+|.++|.+. +++.++ ++.+ .+||.+|.|
T Consensus 98 ~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~--v~~~~~-----~k~v-~Ip~~~i~k 146 (153)
T COG0779 98 IGEKVKVKLRLPIEGRKKFEGKIVAVDGET--VTLEVD-----GKEV-EIPFSDIAK 146 (153)
T ss_pred cCcEEEEEEecccCCceEEEEEEEEEcCCe--EEEEEC-----CEEE-EEEcccchh
Confidence 577777775 33566789999999888 555443 4446 499999876
No 94
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=25.83 E-value=1.1e+02 Score=27.07 Aligned_cols=71 Identities=21% Similarity=0.286 Sum_probs=43.0
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEE-e---CCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIV-N---GAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDY 346 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV-~---G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~y 346 (353)
.|+-.|..++-++-|+-+.. .....|..|.|- + +.-+-..|+|.+++.+. +++.+... ++.+ .++|
T Consensus 73 ~Y~LEVSSPGi~RpL~~~~~----f~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~--i~l~~~~~---~~~~-~i~~ 142 (154)
T PRK00092 73 AYTLEVSSPGLDRPLKKARD----FRRFIGREVKVKLYEPIDGRKKFQGILLAVDGET--VTLEVEGK---EKEV-EIPL 142 (154)
T ss_pred CeEEEEeCCCCCCcCCCHHH----HHHhCCCeEEEEEEcccCCceEEEEEEEEeeCCE--EEEEECCC---eEEE-EEEH
Confidence 35555555554555543322 335679999996 2 33345589999998876 44444321 1245 4999
Q ss_pred ccccc
Q 018594 347 EDICK 351 (353)
Q Consensus 347 edicK 351 (353)
++|.+
T Consensus 143 ~~I~~ 147 (154)
T PRK00092 143 DNIAK 147 (154)
T ss_pred HHcce
Confidence 99876
No 95
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.58 E-value=2.3e+02 Score=21.39 Aligned_cols=57 Identities=19% Similarity=0.095 Sum_probs=31.7
Q ss_pred eeEEEEecCCceEEEEecCCCeEEEEcCCce-----eeecC--CCCCeEEEEeCCCCCceEEEEeeeCCccEEEE
Q 018594 262 KGVVRKVIDKYVGEIEMLEKKHVLRVDQDEL-----ETVIP--QIGGLVRIVNGAYRGSNARLLGVDTDKFCAQV 329 (353)
Q Consensus 262 KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~L-----ETVIP--~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V 329 (353)
.|.|++|...+-+.|.+.+ |-.--|..++| +...- ++|+.| .++++++|..+..+.+
T Consensus 6 ~g~V~~v~~~~G~~V~l~~-gv~G~i~~s~l~~~~~~~~~~~~~vG~~v----------~~kV~~id~~~~~i~l 69 (71)
T cd05696 6 SVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDKVPSDTGPFKAGTTH----------KARIIGYSPMDGLLQL 69 (71)
T ss_pred eeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcchhcCcccccCCCCEE----------EEEEEEEeCCCCEEEE
Confidence 4888898655678888865 32223444444 22110 245544 3455677777655544
No 96
>KOG4235 consensus Mitochondrial thymidine kinase 2/deoxyguanosine kinase [Nucleotide transport and metabolism]
Probab=25.37 E-value=1e+02 Score=29.80 Aligned_cols=44 Identities=20% Similarity=0.355 Sum_probs=37.8
Q ss_pred ceeecccccccHHHHHHHhcccccEEEeecCceeEEEeecCChHHHHHHH
Q 018594 51 HVHMNSTRWATLTEFVKYLGRTGKCKVEETPKGWFITYIDRDSETLFKEK 100 (353)
Q Consensus 51 HiHMNaT~W~tLt~Fvk~Lgr~G~c~vdetekGw~I~yId~~pe~~~r~~ 100 (353)
-=-||-+-|+.+.+.-.|+-+++.+.+| -|-|+--+||+....-
T Consensus 128 sg~m~e~e~~iy~eW~d~i~~~~~v~~d------giIYLrasPetc~~Ri 171 (244)
T KOG4235|consen 128 SGSMNEVEYVIYQEWFDWILRSMDVSLD------GIIYLRASPETCYKRI 171 (244)
T ss_pred cCCcccchhhhHHHHHHHHHhccccccc------eEEEeecChHHHHHHH
Confidence 3469999999999999999999888888 4889999999986433
No 97
>PRK14645 hypothetical protein; Provisional
Probab=25.18 E-value=1.3e+02 Score=27.17 Aligned_cols=68 Identities=15% Similarity=0.094 Sum_probs=41.3
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccccccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDIC 350 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedic 350 (353)
.|+-.|..++-.+.|+-+.++ .-..|..|.|..| .+-..|+|.+++.+. +++.+. +..+ .+||++|.
T Consensus 77 ~Y~LEVSSPGldRpL~~~~df----~r~~G~~v~v~~~-~k~~~G~L~~~~d~~--i~l~~~-----~~~~-~i~~~~I~ 143 (154)
T PRK14645 77 EYRLEVESPGPKRPLFTARHF----ERFAGLKAKVRGP-GENFTGRIKAVSGDQ--VTFDVG-----GEDR-TLRIGTFQ 143 (154)
T ss_pred ceEEEEeCCCCCCCCCCHHHH----HHhCCCEEEEEcC-CeEEEEEEEEEeCCE--EEEEEC-----CeEE-EEEHHHhh
Confidence 345555554444555433222 2346888988653 456689999998765 545432 4445 49999985
Q ss_pred c
Q 018594 351 K 351 (353)
Q Consensus 351 K 351 (353)
+
T Consensus 144 ~ 144 (154)
T PRK14645 144 A 144 (154)
T ss_pred h
Confidence 3
No 98
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=24.79 E-value=5.2e+02 Score=31.87 Aligned_cols=86 Identities=14% Similarity=0.137 Sum_probs=58.1
Q ss_pred cCCcEEEEeecccCCcccccceeEEEEecCCceEEEEecCCCeEEEEcCCce----eeecC-----CCCCeEEEEeCC--
Q 018594 241 CEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEMLEKKHVLRVDQDEL----ETVIP-----QIGGLVRIVNGA-- 309 (353)
Q Consensus 241 ~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~d~g~~l~vdq~~L----ETVIP-----~~G~~V~IV~G~-- 309 (353)
.||-+|+--++.+..+..| +|..|.....+.+-....|....++.+.+ +-.-| +.|++|++....
T Consensus 518 ~~GmVl~~~~r~~k~~~~y----~V~~V~~~~n~LtL~~~dG~~~~~~p~~~~~~~~vy~~e~lelA~GDrlr~t~nd~~ 593 (1623)
T PRK14712 518 RPGMVMEQWNPETRSHDRY----VTERVTAQSHSLTLRNAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKIPG 593 (1623)
T ss_pred CCCCEEEecccCcCcCceE----EEEEEcCCCceEEEEcCCCcEEEechHHcccceeeecccccccCCCCEEEEccCCcc
Confidence 7899997333444333444 78888776555443455688888888775 33444 579999999553
Q ss_pred ---CCCceEEEEeeeCCccEEEEEEe
Q 018594 310 ---YRGSNARLLGVDTDKFCAQVKIE 332 (353)
Q Consensus 310 ---~RG~~g~L~siD~~~~~a~V~l~ 332 (353)
-.|..+++.+++.+. ++|...
T Consensus 594 ~~L~ngd~~tV~~i~~~~--itl~~~ 617 (1623)
T PRK14712 594 LRVSGGDRLQVASVSEDA--MTVVVP 617 (1623)
T ss_pred cCccCCCEEEEEEecCCe--EEEEEC
Confidence 366889999998777 555544
No 99
>COG3041 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.40 E-value=41 Score=28.13 Aligned_cols=18 Identities=33% Similarity=0.728 Sum_probs=16.1
Q ss_pred hhHHHHHHHHHHHHHhcc
Q 018594 14 GYSEEFEAGFLELMRRSH 31 (353)
Q Consensus 14 ~fS~eF~~~Fl~lLr~~~ 31 (353)
.||.+|.+||-.+.++.+
T Consensus 5 ~~skqF~kD~k~~~k~~~ 22 (91)
T COG3041 5 EYSKQFKKDFKKLIKRGP 22 (91)
T ss_pred ehhhhhhHHHHHHHhcCc
Confidence 589999999999999875
No 100
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=23.88 E-value=2.1e+02 Score=25.37 Aligned_cols=35 Identities=3% Similarity=-0.079 Sum_probs=27.4
Q ss_pred ccCCcEEEEeecccCCcccccceeEEEEecCCceEEEEec
Q 018594 240 LCEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEIEML 279 (353)
Q Consensus 240 L~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V~l~ 279 (353)
+.+|=+|.|. .|.|+++-++|+||+|...|-|--+
T Consensus 8 VEiGRVvli~-----~Gp~~GKL~vIVDIID~nRvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQ-----YGPDAGKLCFIVDIVTPTRVLVDGA 42 (130)
T ss_pred eeeceEEEEe-----cCCCCCCEEEEEEEEcCCeEEEeCC
Confidence 4456566554 4579999999999999989988766
No 101
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=23.84 E-value=5.5e+02 Score=23.47 Aligned_cols=60 Identities=15% Similarity=0.130 Sum_probs=38.1
Q ss_pred eEEEEecCCceEEEEecCCCeEE-EEcCCceeeecCCCCCeEEEEeCCCCCceEEEEeeeC
Q 018594 263 GVVRKVIDKYVGEIEMLEKKHVL-RVDQDELETVIPQIGGLVRIVNGAYRGSNARLLGVDT 322 (353)
Q Consensus 263 gvV~~V~d~~~c~V~l~d~g~~l-~vdq~~LETVIP~~G~~V~IV~G~~RG~~g~L~siD~ 322 (353)
|+|..+.+...+.|.+.+...++ .|+-.+=--|-=.+|+.|+|-.-+|--..|.++-+-.
T Consensus 36 g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~VlVel~~yd~~KgdIi~Ry~ 96 (155)
T PTZ00329 36 AQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDFQDSKADVILKYT 96 (155)
T ss_pred EEEEEEcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCEEEEeccCCCCCEEEEEEEcC
Confidence 56777777777777776644444 4555554444446678887766667666676665543
No 102
>PF01421 Reprolysin: Reprolysin (M12B) family zinc metalloprotease This Prosite motif covers only the active site.; InterPro: IPR001590 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12B (adamalysin family, clan (MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The adamalysins are zinc dependent endopeptidases found in snake venom. There are some mammalian proteins such as P78325 from SWISSPROT, and fertilin Q28472 from SWISSPROT. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes. CD156 (also called ADAM8 (3.4.24 from EC) or MS2 human) has been implicated in extravasation of leukocytes. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2E3X_A 2W15_A 2W14_A 2W13_A 2W12_A 1ND1_A 3K7L_A 2DW2_A 2DW0_B 2DW1_A ....
Probab=23.48 E-value=97 Score=27.92 Aligned_cols=53 Identities=11% Similarity=0.192 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHhccCCcccccceeeeeecccccceeecccccccHHHHHHHhc
Q 018594 18 EFEAGFLELMRRSHRFSRIAATVVYNEYIHDRHHVHMNSTRWATLTEFVKYLG 70 (353)
Q Consensus 18 eF~~~Fl~lLr~~~g~krV~aN~vYneyI~dr~HiHMNaT~W~tLt~Fvk~Lg 70 (353)
+|.-..+.+.-.-|-.=.|..-.++=|.-.++++|+++.....||..|.+|--
T Consensus 26 ~~~~~i~n~v~~~y~~l~i~v~l~~leiw~~~d~i~~~~~~~~~L~~F~~w~~ 78 (199)
T PF01421_consen 26 QYVLTIVNIVDSIYQQLNIRVVLVGLEIWTEEDKINISNDADSTLENFCNWQK 78 (199)
T ss_dssp HHHHHHHHHHHHHHGGGTEEEEEEEEEEESSSTSS---SSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhhcccCCeEEEEEEEEEcccCCceeeecchHHHHHHHHHHHH
Confidence 34445555555555444455566788888999999999999999999999954
No 103
>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=23.40 E-value=2e+02 Score=24.87 Aligned_cols=74 Identities=23% Similarity=0.276 Sum_probs=34.7
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEe-CCC---CCceEEEEeeeCCccEEEEEEeccccCCceeeeccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVN-GAY---RGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDY 346 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~-G~~---RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~y 346 (353)
.|.-.|..++-.+.|+-+..+. =..|..|.|-. .+. +-..|+|.+++.+. +++++..+. ....+ .++|
T Consensus 62 ~y~LEVSSPG~~r~L~~~~~~~----~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~--i~l~~~~~~-~~~~~-~I~~ 133 (141)
T PF02576_consen 62 DYTLEVSSPGIDRPLKSPRDFE----RFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDE--ITLEVEGKG-KKKEV-EIPF 133 (141)
T ss_dssp -EEEEEE--SSSS--SSHHHHH----HH-SEEEEEE-SS-SSS-SEEEEEEEEEETTE--EEEEEE-SS--EEEE-EE-S
T ss_pred ceEEEEeCCCCCCcCCCHHHHH----HhcCCeEEEEEeccCCCcEEEEEEEEEEeCCE--EEEEECCcc-ceEEE-EEEH
Confidence 3455555554344443222211 12588888874 223 33489999999866 666665421 11245 4999
Q ss_pred cccccc
Q 018594 347 EDICKL 352 (353)
Q Consensus 347 edicKl 352 (353)
++|.|.
T Consensus 134 ~~I~ka 139 (141)
T PF02576_consen 134 SDIKKA 139 (141)
T ss_dssp S--SS-
T ss_pred HHCceE
Confidence 999763
No 104
>PHA02104 hypothetical protein
Probab=23.28 E-value=54 Score=26.52 Aligned_cols=30 Identities=23% Similarity=0.492 Sum_probs=23.2
Q ss_pred CCCCcccCCc-EEEEeecccCCcccccceeEEEEec
Q 018594 235 RKDYWLCEGI-IVKVMSKALADKGYNKQKGVVRKVI 269 (353)
Q Consensus 235 r~~~WL~~~I-vVKIi~K~l~dGkyYk~KgvV~~V~ 269 (353)
..-+|-.||| .|+| ++.+||-+.|.|-...
T Consensus 34 ~ti~w~fp~i~ev~i-----g~s~yfa~~gkiynat 64 (89)
T PHA02104 34 STIFWTFPGITEVRI-----GSSTYFAQNGKIYNAT 64 (89)
T ss_pred eEEEEecCCcEEEEe-----cceeeehhCCeEEeeE
Confidence 4579999999 5665 4568999999886653
No 105
>PF12122 DUF3582: Protein of unknown function (DUF3582); InterPro: IPR022732 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents the N-terminal domain of membrane-bound serine endopeptidases belonging to MEROPS peptidase family S54 (rhomboid-1, clan ST). This domain contains a conserved ASW sequence motif and a single completely conserved residue F that may be functionally important. The tertiary structure of the GlpG protein from Escherichia coli has been determined []. The GlpG protein has six transmembrane domains (other members of the family are predicted to have seven), with the N- and C-terminal ends anchored in the cytoplasm. One transmembrane domain is shorter than the rest, creating an internal, aqueous cavity just below the membrane surface and it is here were proteolysis occurs. There is also a membrane-embedded loop between the first and second transmembrane domains which is postulated to act as a gate controlling substrate access to the active site. No other family of serine peptidases is known to have active site residues within transmembrane domains (although transmembrane active sites are known for aspartic peptidase and metallopeptidases), and the GlpG protein has the type structure for clan ST.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=23.27 E-value=1.4e+02 Score=25.02 Aligned_cols=27 Identities=26% Similarity=0.650 Sum_probs=17.4
Q ss_pred HHHHHhcccc-cEEEeecCceeEEEeec
Q 018594 64 EFVKYLGRTG-KCKVEETPKGWFITYID 90 (353)
Q Consensus 64 ~Fvk~Lgr~G-~c~vdetekGw~I~yId 90 (353)
.|+.||-..| .|.|+..+.|=|--||.
T Consensus 15 aF~DYl~sqgI~~~i~~~~~~~~~lwl~ 42 (101)
T PF12122_consen 15 AFIDYLASQGIELQIEPEGQGQFALWLH 42 (101)
T ss_dssp HHHHHHHHTT--EEEE-SSSE--EEEES
T ss_pred HHHHHHHHCCCeEEEEECCCCceEEEEe
Confidence 5899998888 57888778884444444
No 106
>PRK13316 heme-degrading monooxygenase IsdG; Provisional
Probab=22.76 E-value=58 Score=28.48 Aligned_cols=59 Identities=14% Similarity=0.232 Sum_probs=42.4
Q ss_pred cccCchhhHhhhHHHHHHHHHH---------HHHhccCCccccc------ceeeeeecccccceeecccccccHHHHHHH
Q 018594 4 FGQNPDRIVEGYSEEFEAGFLE---------LMRRSHRFSRIAA------TVVYNEYIHDRHHVHMNSTRWATLTEFVKY 68 (353)
Q Consensus 4 f~enp~~~i~~fS~eF~~~Fl~---------lLr~~~g~krV~a------N~vYneyI~dr~HiHMNaT~W~tLt~Fvk~ 68 (353)
+..|-=++-.++.++|+.-|.. +|.+.=|.-+.+. +.-|-||+. -|+|.|-..|-.|
T Consensus 3 Iv~Nri~V~~g~a~~~~~rF~~r~~~g~~~~~ie~~pGFv~f~lL~~~~~~~~~~e~~V--------~T~WeSeeaF~aW 74 (121)
T PRK13316 3 IVTNTIKVEKGAAEHVIRQFTGANGDGHPTKDIAEVEGFLGFELWHSKPEDKDYEEVVV--------TSKWESEEAQRNW 74 (121)
T ss_pred EEEEEEEeCCCcHHHHHHHHhccCcccccccchhcCCCceEEEEeeccCCCCCceEEEE--------EEEECCHHHHHHH
Confidence 4456666778899999999976 7777777665442 234444443 2899999999999
Q ss_pred hc
Q 018594 69 LG 70 (353)
Q Consensus 69 Lg 70 (353)
.-
T Consensus 75 ~~ 76 (121)
T PRK13316 75 VK 76 (121)
T ss_pred hc
Confidence 75
No 107
>TIGR02059 swm_rep_I cyanobacterial long protein repeat. This domain appears in 29 copies in a large (10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (<3500) proteins of Synechocystis PCC6803.
Probab=22.59 E-value=4.3e+02 Score=22.58 Aligned_cols=61 Identities=16% Similarity=0.246 Sum_probs=44.3
Q ss_pred EEEcCCce--eeecCCCCCeEEEEeCCCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccccc
Q 018594 285 LRVDQDEL--ETVIPQIGGLVRIVNGAYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYED 348 (353)
Q Consensus 285 l~vdq~~L--ETVIP~~G~~V~IV~G~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yed 348 (353)
|..++.-- ..-.|..+.-..-|+|..+-..| ++++...-.+++.|...-..|+.|. +.|-+
T Consensus 35 LtY~e~L~~~t~~~p~~~~FtVtVnG~~n~Vt~--VsV~~s~ktVTLTL~~~V~~Gq~VT-VsYt~ 97 (101)
T TIGR02059 35 LTFNEPLADITNHAPTRDQFAVTVNGAPNTVTS--VSLGGSNTTITLTLAQVVEDGDEVT-LSYTK 97 (101)
T ss_pred EEechhcCccccCCCCCCcEEEEeCCcEeeEEE--EEEcCcccEEEEEecccccCCCEEE-EEeeC
Confidence 45555533 34457777777677998888888 6777777779999987777788775 88754
No 108
>PRK04333 50S ribosomal protein L14e; Validated
Probab=22.06 E-value=1.6e+02 Score=24.06 Aligned_cols=31 Identities=19% Similarity=0.113 Sum_probs=23.3
Q ss_pred cCCcEEEEeecccCCcccccceeEEEEecCCceEEE
Q 018594 241 CEGIIVKVMSKALADKGYNKQKGVVRKVIDKYVGEI 276 (353)
Q Consensus 241 ~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~~c~V 276 (353)
.+|=+|.+. .|++.++.++|.+++|...|-|
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 456667654 4588899999999988766666
No 109
>PRK14634 hypothetical protein; Provisional
Probab=21.66 E-value=1.6e+02 Score=26.48 Aligned_cols=70 Identities=24% Similarity=0.252 Sum_probs=42.4
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEE-eC---CCCCceEEEEeeeCCccEEEEEEeccccCCceeeeccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIV-NG---AYRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDY 346 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV-~G---~~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~y 346 (353)
.|+-.|..++-.+.|+-+.++ .-..|..|.|- .+ ..+-..|+|.+++.+. +++.+. +..+ .+||
T Consensus 75 ~Y~LEVSSPGldRpL~~~~~f----~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~--v~l~~~-----~~~~-~i~~ 142 (155)
T PRK14634 75 AYVLEISSPGIGDQLSSDRDF----QTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDH--LQINIR-----GRIK-RIPR 142 (155)
T ss_pred CeEEEEeCCCCCCcCCCHHHH----HHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCE--EEEEEC-----CEEE-EEEH
Confidence 355555555445555432222 23469989884 32 2366789999998766 545432 4445 4999
Q ss_pred cccccc
Q 018594 347 EDICKL 352 (353)
Q Consensus 347 edicKl 352 (353)
++|.+.
T Consensus 143 ~~I~ka 148 (155)
T PRK14634 143 DSVISV 148 (155)
T ss_pred HHeeeE
Confidence 999864
No 110
>PRK14646 hypothetical protein; Provisional
Probab=21.52 E-value=1.7e+02 Score=26.25 Aligned_cols=70 Identities=20% Similarity=0.223 Sum_probs=40.9
Q ss_pred CceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEEe-CC---CCCceEEEEeeeCCccEEEEEEeccccCCceeeeccc
Q 018594 271 KYVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIVN-GA---YRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDY 346 (353)
Q Consensus 271 ~~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV~-G~---~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~y 346 (353)
.|+-.|..++-++.|+=+. -..-..|..|.|-. .. .+-..|+|.+++.+. +++.+. |+.+ .+||
T Consensus 75 ~Y~LEVSSPGldRpL~~~~----df~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~--v~l~~~-----g~~~-~i~~ 142 (155)
T PRK14646 75 SYVLEISSQGVSDELTSER----DFKTFKGFPVNVELNQKNSKIKFLNGLLYEKSKDY--LAINIK-----GKIK-KIPF 142 (155)
T ss_pred CeEEEEcCCCCCCcCCCHH----HHHHhCCCEEEEEEecCcCCeEEEEEEEEEEeCCE--EEEEEC-----CEEE-EEEH
Confidence 3455555544444443222 12334688888862 22 233469999998775 555432 4556 4999
Q ss_pred cccccc
Q 018594 347 EDICKL 352 (353)
Q Consensus 347 edicKl 352 (353)
++|.|.
T Consensus 143 ~~I~ka 148 (155)
T PRK14646 143 NEVLKI 148 (155)
T ss_pred HHeeeE
Confidence 999864
No 111
>PF02214 BTB_2: BTB/POZ domain; InterPro: IPR003131 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated potassium channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels []. This domain is found in a subset of a larger group of proteins that contain the BTB/POZ domain.; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0008076 voltage-gated potassium channel complex, 0016020 membrane; PDB: 1NN7_A 3KVT_A 1EXB_E 1QDV_A 1DSX_E 1QDW_F 3LUT_B 3LNM_B 2A79_B 3DRY_C ....
Probab=21.21 E-value=24 Score=27.92 Aligned_cols=20 Identities=30% Similarity=0.548 Sum_probs=14.7
Q ss_pred EEEeecCceeEEEeecCChHHH
Q 018594 75 CKVEETPKGWFITYIDRDSETL 96 (353)
Q Consensus 75 c~vdetekGw~I~yId~~pe~~ 96 (353)
+.....+.|.| ||||||+..
T Consensus 34 ~~~~~~~~~~~--fiDRdp~~F 53 (94)
T PF02214_consen 34 SDDYDDDDGEY--FIDRDPELF 53 (94)
T ss_dssp GGGEETTTTEE--EESS-HHHH
T ss_pred ccccCCccceE--EeccChhhh
Confidence 55566778887 899999876
No 112
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=21.17 E-value=1.1e+02 Score=30.13 Aligned_cols=66 Identities=17% Similarity=0.224 Sum_probs=45.8
Q ss_pred CCcccccceeeeeecccccceeecccccccHHHHHHHhcccccEEEeecCce----eEEEeecCChHHHH
Q 018594 32 RFSRIAATVVYNEYIHDRHHVHMNSTRWATLTEFVKYLGRTGKCKVEETPKG----WFITYIDRDSETLF 97 (353)
Q Consensus 32 g~krV~aN~vYneyI~dr~HiHMNaT~W~tLt~Fvk~Lgr~G~c~vdetekG----w~I~yId~~pe~~~ 97 (353)
+...|....+|++|-.=-.-+.+..-.+.++.+++..|...|++......+| +-+--+.-+|+.+.
T Consensus 312 ~~~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~~~~~~~g~~g~~~~~~~~~~~~~~~ 381 (394)
T PRK00411 312 GGDEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINTRYSGKGGRGRTRLISLSYDPEDVL 381 (394)
T ss_pred CCCcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeEEEEecCCCCCCeEEEEecCCHHHHH
Confidence 4456888999988863323334555578899999999999999998765444 33334456776553
No 113
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=21.06 E-value=1.8e+02 Score=25.96 Aligned_cols=29 Identities=28% Similarity=0.385 Sum_probs=23.4
Q ss_pred cccCCcEEEEeecccCCcccccceeEEEEecCCc
Q 018594 239 WLCEGIIVKVMSKALADKGYNKQKGVVRKVIDKY 272 (353)
Q Consensus 239 WL~~~IvVKIi~K~l~dGkyYk~KgvV~~V~d~~ 272 (353)
.|.||-+|=|. .|+|.++|+||....|.+
T Consensus 4 ~~kpgkVVivL-----~GR~AGkKaVivk~~ddg 32 (134)
T PTZ00471 4 FLKPGKVVIVT-----SGRYAGRKAVIVQNFDTA 32 (134)
T ss_pred cccCCEEEEEE-----ccccCCcEEEEEeecCCC
Confidence 46788888554 569999999999998863
No 114
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=20.96 E-value=1.7e+02 Score=22.47 Aligned_cols=37 Identities=19% Similarity=0.210 Sum_probs=29.0
Q ss_pred CCCceEEEEeeeCCccEEEEEEeccccCCceeeecccccc
Q 018594 310 YRGSNARLLGVDTDKFCAQVKIEKGVYDGRVLNAIDYEDI 349 (353)
Q Consensus 310 ~RG~~g~L~siD~~~~~a~V~l~~g~~~g~~v~~l~yedi 349 (353)
|.|.---+.++|.++..|+|.....| +... .+|..+|
T Consensus 20 y~G~pV~Ie~vde~~~tA~V~~l~~p--~~~~-~Vpv~~L 56 (58)
T PF08141_consen 20 YNGVPVWIEHVDEENGTARVHPLDNP--EEEQ-EVPVNDL 56 (58)
T ss_pred ECCEEEEEEEEcCCCCeEEEEECCCC--CcEE-EEEHHHc
Confidence 78888999999999999999988655 3333 3777665
No 115
>PF04986 Y2_Tnp: Putative transposase; InterPro: IPR007069 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases IS1294 and IS801 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=20.58 E-value=89 Score=28.47 Aligned_cols=57 Identities=19% Similarity=0.247 Sum_probs=36.5
Q ss_pred hhHHHHHHHHHHHHHhccCCcccc---------cceeeeeecccccceeecccccccHHHHHHHhcc
Q 018594 14 GYSEEFEAGFLELMRRSHRFSRIA---------ATVVYNEYIHDRHHVHMNSTRWATLTEFVKYLGR 71 (353)
Q Consensus 14 ~fS~eF~~~Fl~lLr~~~g~krV~---------aN~vYneyI~dr~HiHMNaT~W~tLt~Fvk~Lgr 71 (353)
.=++.|...||++|+.++..-.+. .+.++++--++.=+||+...-. .-..=++||||
T Consensus 47 ~l~~~fr~k~l~~L~~~~~~~~l~~~~~~~~~~~~~~~~~~~~k~w~V~~~~~~~-~~~~~~~YL~R 112 (183)
T PF04986_consen 47 ALSKVFRGKFLQALRQRYDKGLLRRGPIENFQEWSNLLNKLYRKGWVVYCKKPVG-NGEQVLEYLGR 112 (183)
T ss_pred hhhHHHHHHHHHHHHHHHHhcccccccccchhhhhhhccccccCccccccCcccc-cchHHHHHHHH
Confidence 347899999999999996544333 3444444445566777764433 44455777775
No 116
>PRK14635 hypothetical protein; Provisional
Probab=20.17 E-value=1.4e+02 Score=26.88 Aligned_cols=74 Identities=19% Similarity=0.199 Sum_probs=41.8
Q ss_pred ceEEEEecCCCeEEEEcCCceeeecCCCCCeEEEE--e-C--CCCCceEEEEeeeCCccEEEEEEecc---ccCCceeee
Q 018594 272 YVGEIEMLEKKHVLRVDQDELETVIPQIGGLVRIV--N-G--AYRGSNARLLGVDTDKFCAQVKIEKG---VYDGRVLNA 343 (353)
Q Consensus 272 ~~c~V~l~d~g~~l~vdq~~LETVIP~~G~~V~IV--~-G--~~RG~~g~L~siD~~~~~a~V~l~~g---~~~g~~v~~ 343 (353)
|+-.|..++-++.|+-+.++.- ..|..|.|- . | .+.|-+|+|.++|.+. +++.+... +..+..+ .
T Consensus 75 Y~LEVSSPGldRpL~~~~~~~r----~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~--v~l~~~~k~~~~~~~~~~-~ 147 (162)
T PRK14635 75 FTLKVSSAGAERKLRLPEDLDR----FRGIPVRLVFRSEESEKWQEGIFRLVNRDGDQ--VELEKFQKGKKSKVKKQT-T 147 (162)
T ss_pred eEEEEcCCCCCCcCCCHHHHHH----hCCCEEEEEEecCCCcEEEecceEEEEEcCCE--EEEEEecccccccCCeEE-E
Confidence 4555555554556655444332 247766553 1 2 4567777999998776 55544211 0113445 4
Q ss_pred ccccccccc
Q 018594 344 IDYEDICKL 352 (353)
Q Consensus 344 l~yedicKl 352 (353)
+||++|.+.
T Consensus 148 ip~~~I~ka 156 (162)
T PRK14635 148 LNLKDILKG 156 (162)
T ss_pred EEhHHeeee
Confidence 999998763
No 117
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=20.10 E-value=3.2e+02 Score=22.24 Aligned_cols=44 Identities=20% Similarity=0.185 Sum_probs=27.3
Q ss_pred eEEEEecCC--ceEEEEecCCCeEEEEcCCceeeecC--CCCCeEEEEeC
Q 018594 263 GVVRKVIDK--YVGEIEMLEKKHVLRVDQDELETVIP--QIGGLVRIVNG 308 (353)
Q Consensus 263 gvV~~V~d~--~~c~V~l~d~g~~l~vdq~~LETVIP--~~G~~V~IV~G 308 (353)
|.|.++.+. ..|.|... |-.-.|+-..+..+-| ++|++|+|=.|
T Consensus 7 ~kVi~i~~~~~~~A~vd~~--Gv~r~V~l~Lv~~~~~~~~vGDyVLVHaG 54 (82)
T PRK10413 7 GQVLAVGEDIHQLAQVEVC--GIKRDVNIALICEGNPADLLGQWVLVHVG 54 (82)
T ss_pred eEEEEECCCCCcEEEEEcC--CeEEEEEeeeeccCCcccccCCEEEEecc
Confidence 345555543 35767654 4444566666654433 78999999776
Done!