Query 025545
Match_columns 251
No_of_seqs 129 out of 1112
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 06:56:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025545.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025545hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00075 rpl21 ribosomal prote 100.0 1.5E-41 3.2E-46 273.6 14.9 104 136-240 2-105 (108)
2 PRK05573 rplU 50S ribosomal pr 100.0 2.7E-41 5.9E-46 269.5 14.5 103 137-240 1-103 (103)
3 COG0261 RplU Ribosomal protein 100.0 1.7E-40 3.7E-45 265.7 13.3 103 137-240 1-103 (103)
4 TIGR00061 L21 ribosomal protei 100.0 2.7E-40 5.8E-45 263.4 13.8 101 138-239 1-101 (101)
5 PRK12278 50S ribosomal protein 100.0 9.3E-39 2E-43 284.2 14.5 104 137-241 1-104 (221)
6 PF00829 Ribosomal_L21p: Ribos 100.0 4.3E-39 9.4E-44 253.5 9.4 96 137-233 1-96 (96)
7 KOG1686 Mitochondrial/chloropl 100.0 4.4E-31 9.6E-36 222.2 10.5 138 112-249 1-138 (151)
8 PF09026 CENP-B_dimeris: Centr 93.3 0.024 5.2E-07 46.1 0.0 9 117-125 56-64 (101)
9 KOG1686 Mitochondrial/chloropl 83.3 0.58 1.3E-05 40.5 1.3 62 129-191 87-151 (151)
10 KOG3130 Uncharacterized conser 81.3 0.91 2E-05 45.3 1.9 15 110-124 337-351 (514)
11 KOG3130 Uncharacterized conser 71.5 2.3 5E-05 42.5 1.7 7 109-115 333-339 (514)
12 COG3168 PilP Tfp pilus assembl 70.6 6.9 0.00015 34.6 4.3 35 118-159 98-132 (170)
13 PF11702 DUF3295: Protein of u 68.4 6.2 0.00014 40.1 4.0 9 80-88 307-315 (507)
14 PF02311 AraC_binding: AraC-li 68.4 7.9 0.00017 29.0 3.7 21 139-159 34-54 (136)
15 COG0662 {ManC} Mannose-6-phosp 66.6 8.7 0.00019 31.0 3.9 26 134-159 57-88 (127)
16 KOG1824 TATA-binding protein-i 65.8 4.9 0.00011 44.1 2.9 32 62-93 310-343 (1233)
17 PF05764 YL1: YL1 nuclear prot 64.2 6.3 0.00014 35.8 2.9 17 53-69 27-43 (240)
18 PF03153 TFIIA: Transcription 63.9 3.8 8.2E-05 38.7 1.5 13 139-151 355-367 (375)
19 PF11356 Pilus_PilP: Type IV p 63.6 8.3 0.00018 28.8 3.0 40 112-157 22-62 (87)
20 PF04351 PilP: Pilus assembly 61.5 9.8 0.00021 32.0 3.4 30 130-159 84-114 (149)
21 KOG2023 Nuclear transport rece 61.1 4.3 9.2E-05 43.1 1.4 8 81-88 362-369 (885)
22 KOG0772 Uncharacterized conser 60.0 4.4 9.6E-05 41.7 1.2 13 144-156 218-230 (641)
23 PF12791 RsgI_N: Anti-sigma fa 59.3 18 0.00039 25.3 3.9 36 136-178 5-40 (56)
24 KOG0127 Nucleolar protein fibr 57.1 6.9 0.00015 40.6 2.0 17 146-162 285-301 (678)
25 PF05285 SDA1: SDA1; InterPro 56.5 9.2 0.0002 36.2 2.7 20 4-23 24-43 (324)
26 PHA03209 serine/threonine kina 55.4 16 0.00035 33.3 4.0 37 110-151 60-97 (357)
27 PF07883 Cupin_2: Cupin domain 52.7 23 0.00049 24.4 3.6 20 141-160 32-51 (71)
28 KOG4264 Nucleo-cytoplasmic pro 51.3 18 0.0004 37.5 3.9 17 56-72 57-73 (694)
29 PF05086 Dicty_REP: Dictyostel 50.8 6.5 0.00014 42.1 0.7 12 60-71 884-895 (911)
30 PF05285 SDA1: SDA1; InterPro 49.4 9.1 0.0002 36.2 1.4 7 12-18 25-31 (324)
31 PF13324 GCIP: Grap2 and cycli 48.3 10 0.00022 34.6 1.5 7 104-110 179-185 (275)
32 PF06249 EutQ: Ethanolamine ut 47.3 34 0.00073 29.7 4.5 27 141-173 108-134 (152)
33 PF14851 FAM176: FAM176 family 46.6 33 0.00071 29.9 4.3 18 107-126 126-143 (153)
34 KOG0699 Serine/threonine prote 45.7 16 0.00035 36.6 2.5 43 136-180 331-385 (542)
35 PF11421 Synthase_beta: ATP sy 44.3 20 0.00044 25.9 2.2 16 1-16 1-16 (49)
36 PRK09943 DNA-binding transcrip 44.0 32 0.00069 29.2 3.8 20 140-159 140-159 (185)
37 KOG1819 FYVE finger-containing 42.9 31 0.00067 36.0 4.1 12 188-199 542-553 (990)
38 KOG4264 Nucleo-cytoplasmic pro 42.8 11 0.00024 39.0 1.0 6 1-6 1-6 (694)
39 KOG2652 RNA polymerase II tran 42.8 18 0.00039 35.4 2.3 28 119-151 313-340 (348)
40 PF04050 Upf2: Up-frameshift s 40.8 9.1 0.0002 32.9 0.0 6 167-172 118-123 (170)
41 PF04889 Cwf_Cwc_15: Cwf15/Cwc 39.3 15 0.00033 33.8 1.2 8 145-152 195-202 (244)
42 PRK15457 ethanolamine utilizat 37.9 42 0.00092 31.1 3.8 21 140-160 187-207 (233)
43 PHA03211 serine/threonine kina 36.3 83 0.0018 30.8 5.8 11 99-109 131-141 (461)
44 TIGR00993 3a0901s04IAP86 chlor 36.1 17 0.00037 38.7 1.1 17 104-120 424-440 (763)
45 cd04867 TGS_YchF_C TGS_YchF_C: 34.4 19 0.00041 28.6 0.9 19 140-158 63-81 (83)
46 PF01050 MannoseP_isomer: Mann 34.0 61 0.0013 27.6 4.0 21 139-159 95-115 (151)
47 TIGR03689 pup_AAA proteasome A 33.6 1.4E+02 0.0031 30.4 7.1 38 138-178 60-97 (512)
48 PF02563 Poly_export: Polysacc 32.9 24 0.00051 26.5 1.2 44 145-196 8-51 (82)
49 PF11699 CENP-C_C: Mif2/CENP-C 32.3 64 0.0014 25.2 3.5 22 141-162 46-67 (85)
50 PF11521 TFIIE-A_C-term: C-ter 31.9 5.9 0.00013 31.4 -2.3 10 104-113 65-74 (86)
51 PF08553 VID27: VID27 cytoplas 31.7 75 0.0016 34.2 5.0 24 167-190 478-501 (794)
52 PHA02664 hypothetical protein; 31.4 50 0.0011 32.8 3.4 10 106-115 515-524 (534)
53 PF12720 DUF3807: Protein of u 30.7 41 0.00089 29.7 2.4 10 56-65 5-14 (172)
54 PF13079 DUF3916: Protein of u 30.3 41 0.00088 29.4 2.3 21 3-23 43-63 (153)
55 TIGR03021 pilP_fam type IV pil 28.7 73 0.0016 26.3 3.5 33 124-156 68-101 (119)
56 KOG1819 FYVE finger-containing 28.3 85 0.0018 33.0 4.5 6 115-120 466-471 (990)
57 TIGR03214 ura-cupin putative a 27.5 78 0.0017 28.9 3.8 21 139-159 211-231 (260)
58 KOG3064 RNA-binding nuclear pr 27.4 21 0.00045 34.1 0.0 11 4-14 106-116 (303)
59 PRK13501 transcriptional activ 26.2 75 0.0016 28.3 3.4 21 139-159 49-69 (290)
60 PRK10296 DNA-binding transcrip 26.2 88 0.0019 27.6 3.8 21 139-159 54-74 (278)
61 PF04050 Upf2: Up-frameshift s 26.0 36 0.00077 29.2 1.2 12 224-235 129-140 (170)
62 KOG3540 Beta amyloid precursor 26.0 54 0.0012 33.9 2.6 6 82-87 214-219 (615)
63 KOG1824 TATA-binding protein-i 25.6 31 0.00068 38.2 1.0 14 57-70 309-322 (1233)
64 KOG0126 Predicted RNA-binding 25.1 82 0.0018 28.9 3.4 38 128-173 29-66 (219)
65 KOG1991 Nuclear transport rece 25.0 32 0.0007 37.8 0.9 26 67-92 897-942 (1010)
66 PF05899 Cupin_3: Protein of u 23.8 1.2E+02 0.0027 22.3 3.6 17 144-160 42-58 (74)
67 COG3264 Small-conductance mech 23.8 1E+02 0.0022 33.6 4.2 70 153-236 652-721 (835)
68 cd05792 S1_eIF1AD_like S1_eIF1 23.5 3.4E+02 0.0073 21.1 6.1 31 174-205 35-65 (78)
69 PRK12784 hypothetical protein; 23.4 1.7E+02 0.0037 23.4 4.4 48 135-183 31-78 (84)
70 PF05896 NQRA: Na(+)-transloca 23.2 80 0.0017 29.6 3.1 57 145-208 26-84 (257)
71 PRK11171 hypothetical protein; 23.1 1E+02 0.0022 28.1 3.7 20 140-159 217-236 (266)
72 PRK10371 DNA-binding transcrip 23.1 1E+02 0.0022 28.2 3.7 21 139-159 57-77 (302)
73 PF06071 YchF-GTPase_C: Protei 23.0 16 0.00035 28.9 -1.3 19 140-158 63-81 (84)
74 KOG0699 Serine/threonine prote 22.3 36 0.00079 34.2 0.7 49 123-173 338-390 (542)
75 PHA03346 US22 family homolog; 22.0 49 0.0011 33.9 1.5 52 52-103 377-458 (520)
76 KOG2925 Predicted translation 21.9 1E+02 0.0022 27.3 3.2 39 133-171 32-82 (167)
77 cd04092 mtEFG2_II_like mtEFG2_ 21.8 97 0.0021 22.8 2.7 21 150-170 61-81 (83)
78 PF03153 TFIIA: Transcription 21.8 35 0.00077 32.2 0.4 9 175-183 356-364 (375)
79 KOG2229 Protein required for a 21.5 62 0.0013 33.7 2.1 27 1-27 370-396 (616)
80 PF05432 BSP_II: Bone sialopro 21.3 65 0.0014 30.8 2.0 16 57-72 39-57 (292)
81 cd04456 S1_IF1A_like S1_IF1A_l 20.6 1.8E+02 0.004 22.3 4.1 12 148-159 37-48 (78)
82 PF03896 TRAP_alpha: Transloco 20.5 1.1E+02 0.0024 29.0 3.4 14 164-177 146-159 (285)
83 PRK13500 transcriptional activ 20.4 1.2E+02 0.0025 27.8 3.5 22 139-160 79-100 (312)
84 PLN03078 Putative tRNA pseudou 20.2 87 0.0019 32.2 2.8 19 131-149 349-367 (513)
85 KOG4364 Chromatin assembly fac 20.1 50 0.0011 35.3 1.1 20 71-90 538-557 (811)
86 KOG2076 RNA polymerase III tra 20.1 52 0.0011 35.9 1.3 8 67-74 40-47 (895)
No 1
>CHL00075 rpl21 ribosomal protein L21
Probab=100.00 E-value=1.5e-41 Score=273.62 Aligned_cols=104 Identities=29% Similarity=0.505 Sum_probs=101.7
Q ss_pred CeEEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEEecCCceEecCCccCCcEEEEEEEeecCCceEEEEEec
Q 025545 136 PAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLLGSQHQTIIGRPMVPDAAVHAVVEEHALDAKVIIFKKK 215 (251)
Q Consensus 136 ~mYAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L~~a~V~AtVleh~rg~KViVfK~K 215 (251)
.|||||++|||||||++||+|.|++|+ +++|+.|+|++|||+++++.+.+|+|||++|+|+|+|++|+|++||++||||
T Consensus 2 ~myAIi~~gGkQykV~~Gd~i~vekl~-~~~G~~i~l~~VL~~~~~~~~~iG~P~v~~a~V~a~V~~h~r~~Ki~vfK~k 80 (108)
T CHL00075 2 MTYAIIEAGGKQLWVEPGRFYDINHFP-LEPGTKILLNRVLLIRNESEILIGKPWLENATVKGRILHHFRGKKITVYKMR 80 (108)
T ss_pred cEEEEEEECCEEEEEeCCCEEEEEEcC-CCCCCEEEEEEEEEEecCCCeEECCcEecCcEEEEEEEeecCCCCEEEEEeC
Confidence 699999999999999999999999997 7999999999999999888999999999999999999999999999999999
Q ss_pred CCCCceeccCccCcceEEEEceEec
Q 025545 216 RRKNYRRTKGHRQELTKLRIVDIQG 240 (251)
Q Consensus 216 RRK~yrRk~GHRQ~yTrLRI~eI~~ 240 (251)
|||+|||++||||+||+|+|++|..
T Consensus 81 rRK~yrrk~GHRQ~~T~i~I~~I~~ 105 (108)
T CHL00075 81 PKKKTRKKQGHRQKLTRFLIDSISF 105 (108)
T ss_pred CCCCccCCCccCCCcEEEEEEEEEc
Confidence 9999999999999999999999976
No 2
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=100.00 E-value=2.7e-41 Score=269.48 Aligned_cols=103 Identities=46% Similarity=0.738 Sum_probs=100.7
Q ss_pred eEEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEEecCCceEecCCccCCcEEEEEEEeecCCceEEEEEecC
Q 025545 137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLLGSQHQTIIGRPMVPDAAVHAVVEEHALDAKVIIFKKKR 216 (251)
Q Consensus 137 mYAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L~~a~V~AtVleh~rg~KViVfK~KR 216 (251)
|||||++||+||||++||+|.||+|+ +++|++|.|++|||+++++++.+|+|+|++|+|+|+|++|++++|+++|||||
T Consensus 1 MyAIi~~gGkQykV~~Gd~i~v~~l~-~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~A~V~~~~k~~Ki~vfK~kr 79 (103)
T PRK05573 1 MYAIIKTGGKQYKVEEGDVIKVEKLD-AEVGDTVEFDEVLLVGGGEEVKIGAPYVEGAKVTAEVVEHGRGKKVIVFKYKR 79 (103)
T ss_pred CEEEEEECCEEEEEeCCCEEEEcccC-CCCCCEEEEeEEEEEeCCCCEEECCeEcCCCEEEEEEEeccCCCcEEEEEEcC
Confidence 89999999999999999999999997 89999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeccCccCcceEEEEceEec
Q 025545 217 RKNYRRTKGHRQELTKLRIVDIQG 240 (251)
Q Consensus 217 RK~yrRk~GHRQ~yTrLRI~eI~~ 240 (251)
||+|+|++||||+||+|+|++|.+
T Consensus 80 RK~y~r~~GHRQ~~T~i~I~~I~~ 103 (103)
T PRK05573 80 RKNYRKKQGHRQPYTKVKITSINA 103 (103)
T ss_pred CCCccccCCccCCcEEEEEEEEeC
Confidence 999999999999999999999963
No 3
>COG0261 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-40 Score=265.65 Aligned_cols=103 Identities=45% Similarity=0.720 Sum_probs=100.8
Q ss_pred eEEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEEecCCceEecCCccCCcEEEEEEEeecCCceEEEEEecC
Q 025545 137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLLGSQHQTIIGRPMVPDAAVHAVVEEHALDAKVIIFKKKR 216 (251)
Q Consensus 137 mYAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L~~a~V~AtVleh~rg~KViVfK~KR 216 (251)
|||||++|||||+|++||+|.||+|. .++|++|+|++|||+++++.+.||.||+++|+|.|+|++|.|++||++|||||
T Consensus 1 mYAii~tGGKQykV~~G~~i~vEkl~-~e~g~~v~f~~VL~v~~~~~v~iG~P~v~ga~V~aeV~~hgr~kKV~i~K~k~ 79 (103)
T COG0261 1 MYAIIKTGGKQYKVEEGDVIKVEKLD-AEPGDKVEFDEVLMVGGGEEVKIGAPYVEGAKVTAEVVEHGRGKKVIIFKYKR 79 (103)
T ss_pred CeEEEEECCEEEEEecCCEEEEEEcC-CCCCCEEEEEEEEEEcCCCceEECCceecCcEEEEEEhhhCCCceEEEEEecc
Confidence 89999999999999999999999998 79999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeccCccCcceEEEEceEec
Q 025545 217 RKNYRRTKGHRQELTKLRIVDIQG 240 (251)
Q Consensus 217 RK~yrRk~GHRQ~yTrLRI~eI~~ 240 (251)
||+|+|++||||+||+|+|++|..
T Consensus 80 rK~~~rk~GHRQ~yT~vkI~~I~~ 103 (103)
T COG0261 80 RKNYRKKQGHRQPYTRVKITGIVA 103 (103)
T ss_pred CcCcccccCcccceEEEEEEEeeC
Confidence 999999999999999999999963
No 4
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=100.00 E-value=2.7e-40 Score=263.42 Aligned_cols=101 Identities=38% Similarity=0.641 Sum_probs=99.0
Q ss_pred EEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEEecCCceEecCCccCCcEEEEEEEeecCCceEEEEEecCC
Q 025545 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLLGSQHQTIIGRPMVPDAAVHAVVEEHALDAKVIIFKKKRR 217 (251)
Q Consensus 138 YAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L~~a~V~AtVleh~rg~KViVfK~KRR 217 (251)
||||++|||||||++||+|.|++|+ .++|+.|.|++|||+++++++.+|+|+|++|+|+|+|++|++++|+++||||||
T Consensus 1 yAIi~~gGkQykV~~Gd~i~Ve~l~-~~~G~~i~l~~VLlv~~~~~~~iG~P~l~~a~V~a~V~~~~r~~Ki~vfK~krr 79 (101)
T TIGR00061 1 YAIVEIGGKQYKVEEGQTVRIEKLD-AAPGDTVEFDKVLMVNKGGDVKIGKPYVEGAKVVAEVEKHGRGKKVKVYKYRRR 79 (101)
T ss_pred CEEEEECCEEEEEeCCCEEEEcccC-CCCCCEEEEEEEEEEecCCCeEECCeEcCCCEEEEEEEeecCCCCEEEEEeCCC
Confidence 8999999999999999999999997 799999999999999999999999999999999999999999999999999999
Q ss_pred CCceeccCccCcceEEEEceEe
Q 025545 218 KNYRRTKGHRQELTKLRIVDIQ 239 (251)
Q Consensus 218 K~yrRk~GHRQ~yTrLRI~eI~ 239 (251)
|+|+|++||||+||+|+|++|.
T Consensus 80 K~y~r~~GHRQ~~T~i~I~~I~ 101 (101)
T TIGR00061 80 KHSRKKQGHRQPYTKVKVTKIV 101 (101)
T ss_pred CCccCCCccCCCcEEEEEEEeC
Confidence 9999999999999999999984
No 5
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=100.00 E-value=9.3e-39 Score=284.16 Aligned_cols=104 Identities=44% Similarity=0.663 Sum_probs=101.6
Q ss_pred eEEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEEecCCceEecCCccCCcEEEEEEEeecCCceEEEEEecC
Q 025545 137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLLGSQHQTIIGRPMVPDAAVHAVVEEHALDAKVIIFKKKR 216 (251)
Q Consensus 137 mYAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L~~a~V~AtVleh~rg~KViVfK~KR 216 (251)
|||||++|||||||++||+|.|++|. .++|++|.|++|||+++++++.||+|||++++|+|+|++|+|++||++|||||
T Consensus 1 MyAVI~~gGKQykV~~Gd~i~Vekl~-~~~G~~i~~~~VL~v~~~~~~~iG~P~v~~a~V~A~V~~~~kg~Ki~vfK~kr 79 (221)
T PRK12278 1 MFAVIKTGGKQYKVQAGDLLRVEKLA-AEAGETVQFGEVLMLGEGDNVTVGAPFVDGAAVQAEVIEQIKGDKVIHFKKRR 79 (221)
T ss_pred CEEEEEeCCEEEEEeCCCEEEEeccC-CCCCCEEEEeEEEEEecCCCeEECCeEecCCEEEEEEEeecCCCCEEEEEeCC
Confidence 99999999999999999999999998 79999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeccCccCcceEEEEceEecc
Q 025545 217 RKNYRRTKGHRQELTKLRIVDIQGI 241 (251)
Q Consensus 217 RK~yrRk~GHRQ~yTrLRI~eI~~i 241 (251)
||+|||++||||+||+|||++|..-
T Consensus 80 RK~yrrk~GHRQ~~T~i~I~~I~~~ 104 (221)
T PRK12278 80 RQSSRRTKGHRQLLTLVRITEILAS 104 (221)
T ss_pred CCCcccCCCcCCCcEEEEEEEEEcC
Confidence 9999999999999999999999864
No 6
>PF00829 Ribosomal_L21p: Ribosomal prokaryotic L21 protein; InterPro: IPR001787 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L21 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L21 is known to bind to the 23S rRNA in the presence of L20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Bacterial L21. Marchantia polymorpha chloroplast L21. Cyanelle L21. Plant chloroplast L21 (nuclear-encoded). Bacterial L21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XG0_V 2X9S_V 2XG2_V 3UZ1_2 2Y19_V 2WDL_V 3V23_V 2WRO_V 2WRL_V 2Y11_V ....
Probab=100.00 E-value=4.3e-39 Score=253.53 Aligned_cols=96 Identities=53% Similarity=0.858 Sum_probs=93.6
Q ss_pred eEEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEEecCCceEecCCccCCcEEEEEEEeecCCceEEEEEecC
Q 025545 137 AFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLLGSQHQTIIGRPMVPDAAVHAVVEEHALDAKVIIFKKKR 216 (251)
Q Consensus 137 mYAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L~~a~V~AtVleh~rg~KViVfK~KR 216 (251)
|||||++|||||||++||+|.||+|. +++|++|+|++||++++++++.+|+|||++|+|+|+|++|++++|+++|||||
T Consensus 1 myAIi~~ggkQykV~~gd~i~v~~l~-~~~G~~i~l~~VL~~~~~~~~~iG~P~l~~a~V~a~V~~~~k~~Ki~v~K~kr 79 (96)
T PF00829_consen 1 MYAIIEIGGKQYKVEEGDVIDVERLD-AEVGDKIELDKVLLIGSEDFTLIGRPYLEGAKVEATVLEHGKGKKIIVFKKKR 79 (96)
T ss_dssp -EEEEESSSEEEEESSSEEEEEESTS-SSTTSEEEETTEEEEETSSSTCSSSSSSSSSEEEEEEEEEEEEEEEEEEEEET
T ss_pred CEEEEEECCEEEEEeCCCEEEECCcC-cCCCCEEEEEEEEEEecCCCeEECCccCCCcEEEEEEEeccCCCcEEEEEECC
Confidence 99999999999999999999999995 89999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeccCccCcceEE
Q 025545 217 RKNYRRTKGHRQELTKL 233 (251)
Q Consensus 217 RK~yrRk~GHRQ~yTrL 233 (251)
||+|+|++||||+||+|
T Consensus 80 RK~y~r~~GhRq~~T~i 96 (96)
T PF00829_consen 80 RKRYRRKQGHRQPYTRI 96 (96)
T ss_dssp TTTEEEEEEEEEEEEEE
T ss_pred ccccccCCccCCCeEEC
Confidence 99999999999999986
No 7
>KOG1686 consensus Mitochondrial/chloroplast ribosomal L21 protein [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=4.4e-31 Score=222.15 Aligned_cols=138 Identities=47% Similarity=0.547 Sum_probs=131.7
Q ss_pred HHHhcceEEcCCCCccccccccCCCeEEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEEecCCceEecCCcc
Q 025545 112 EAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLLGSQHQTIIGRPMV 191 (251)
Q Consensus 112 ea~~ig~kv~g~l~~~~~~~k~~~~mYAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L 191 (251)
||..++|+++|++..+....+.++..||||.+||+||+|..||.|++++++++.+||.|.|++|||+|+-++|++|+|.|
T Consensus 1 ea~~~e~v~vg~l~s~~~~~~kr~~~favv~v~srq~kvs~gd~iy~eg~~p~nv~d~i~l~kVlLvg~~~~T~~grpvv 80 (151)
T KOG1686|consen 1 MAASSETVTVGRLASACSHSIKRPSGFAVVSVGSRQRKVSSGDTIYTEGLKPKNVLDSIPLPKVLLVGPVEETRIGRPVV 80 (151)
T ss_pred CcccceeEEEeccchhhhhccccCCccEEEEEcceeEEecCCCeeeecCccccccccccccceEEEecCcceeEecCccc
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEEEEEEeecCCceEEEEEecCCCCceeccCccCcceEEEEceEecccchhhhhh
Q 025545 192 PDAAVHAVVEEHALDAKVIIFKKKRRKNYRRTKGHRQELTKLRIVDIQGIEKRVEVAT 249 (251)
Q Consensus 192 ~~a~V~AtVleh~rg~KViVfK~KRRK~yrRk~GHRQ~yTrLRI~eI~~i~~~~~~~~ 249 (251)
.+++|.|.|+++.+..|+++||+|++|+|||..||||+.|+|||+.|.+++.+....+
T Consensus 81 ~~vtv~aVv~e~g~~~kvvhfk~k~~k~tr~~~~~~qe~t~LrIt~it~ie~e~~~~v 138 (151)
T KOG1686|consen 81 KKVTVHAVVEEYGLLFKVVHFKSKQWKVTRRDLGHRQEATELRITCITGIELEKVLLV 138 (151)
T ss_pred ccceEEEEeeeccccccEEEEEecchhhhhhhhcccCcccEEEEeeeeeeeeccceec
Confidence 9999999999999999999999999999999999999999999999999877664443
No 8
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=93.29 E-value=0.024 Score=46.08 Aligned_cols=9 Identities=11% Similarity=0.025 Sum_probs=3.7
Q ss_pred ceEEcCCCC
Q 025545 117 GYKVLGPLR 125 (251)
Q Consensus 117 g~kv~g~l~ 125 (251)
-++++++++
T Consensus 56 v~rYltSf~ 64 (101)
T PF09026_consen 56 VKRYLTSFP 64 (101)
T ss_dssp HHHHHCTS-
T ss_pred Hhhhhhccc
Confidence 344454444
No 9
>KOG1686 consensus Mitochondrial/chloroplast ribosomal L21 protein [Translation, ribosomal structure and biogenesis]
Probab=83.33 E-value=0.58 Score=40.54 Aligned_cols=62 Identities=32% Similarity=0.512 Sum_probs=51.0
Q ss_pred cccccCCCeEEEEEECCEEEEEeCCCEEEec---ccCccCCCCeeEeceEEEEecCCceEecCCcc
Q 025545 129 RVFKKYEPAFAVVQIGSHQFKVSNGDSIFTE---RLKFCEVNDKLILNKVLLLGSQHQTIIGRPMV 191 (251)
Q Consensus 129 ~~~k~~~~mYAIVeigGKQYKV~~GD~I~Ve---kL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L 191 (251)
.+--.+...|++++...||+|+..-|..... +|. ...+.-|++.++++++.++|+.+|+|.+
T Consensus 87 aVv~e~g~~~kvvhfk~k~~k~tr~~~~~~qe~t~Lr-It~it~ie~e~~~~v~~~nf~~vgk~~l 151 (151)
T KOG1686|consen 87 AVVEEYGLLFKVVHFKSKQWKVTRRDLGHRQEATELR-ITCITGIELEKVLLVGAPNFTAVGKPLL 151 (151)
T ss_pred EEeeeccccccEEEEEecchhhhhhhhcccCcccEEE-EeeeeeeeeccceeccCccceeeccccC
Confidence 3444667788999999999999988887655 333 4578999999999999999999999964
No 10
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=81.27 E-value=0.91 Score=45.27 Aligned_cols=15 Identities=20% Similarity=0.071 Sum_probs=8.1
Q ss_pred HHHHHhcceEEcCCC
Q 025545 110 EAEAAEIGYKVLGPL 124 (251)
Q Consensus 110 ~~ea~~ig~kv~g~l 124 (251)
..+++.+-.+-.|..
T Consensus 337 ~~~~~r~~~~stG~~ 351 (514)
T KOG3130|consen 337 KEEAKRKRKNSTGSG 351 (514)
T ss_pred hhHHHHHHhcccccc
Confidence 345565555555555
No 11
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.51 E-value=2.3 Score=42.52 Aligned_cols=7 Identities=29% Similarity=0.079 Sum_probs=2.7
Q ss_pred HHHHHHh
Q 025545 109 KEAEAAE 115 (251)
Q Consensus 109 ~~~ea~~ 115 (251)
-++|-++
T Consensus 333 fvee~~~ 339 (514)
T KOG3130|consen 333 FVEEKEE 339 (514)
T ss_pred HHhhhhH
Confidence 3344443
No 12
>COG3168 PilP Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=70.63 E-value=6.9 Score=34.62 Aligned_cols=35 Identities=14% Similarity=0.338 Sum_probs=29.4
Q ss_pred eEEcCCCCccccccccCCCeEEEEEECCEEEEEeCCCEEEec
Q 025545 118 YKVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 118 ~kv~g~l~~~~~~~k~~~~mYAIVeigGKQYKV~~GD~I~Ve 159 (251)
+|.+|-+. .....+|+|+..|+-|+|..|++|-.+
T Consensus 98 ~rlvGtm~-------~g~~~~A~i~~~~~v~~V~vG~YlGqN 132 (170)
T COG3168 98 FRLVGTLK-------SGQGVSALIEAPGGVYRVRVGQYLGQN 132 (170)
T ss_pred eeeEEEec-------CCCceEEEEEcCCceEEEeeccEeecc
Confidence 56666555 668999999999999999999999765
No 13
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=68.43 E-value=6.2 Score=40.14 Aligned_cols=9 Identities=11% Similarity=0.560 Sum_probs=6.3
Q ss_pred cccccccCC
Q 025545 80 DEETADESY 88 (251)
Q Consensus 80 ~~~~~~~~~ 88 (251)
|||||++||
T Consensus 307 dDDDDssDW 315 (507)
T PF11702_consen 307 DDDDDSSDW 315 (507)
T ss_pred cCCccchhh
Confidence 566667778
No 14
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=68.42 E-value=7.9 Score=28.96 Aligned_cols=21 Identities=14% Similarity=0.438 Sum_probs=16.0
Q ss_pred EEEEECCEEEEEeCCCEEEec
Q 025545 139 AVVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 139 AIVeigGKQYKV~~GD~I~Ve 159 (251)
+.+.++|++|.|.+||++.++
T Consensus 34 ~~~~~~~~~~~l~~g~~~li~ 54 (136)
T PF02311_consen 34 GTLHIDGQEYPLKPGDLFLIP 54 (136)
T ss_dssp EEEEETTEEEEE-TT-EEEE-
T ss_pred EEEEECCEEEEEECCEEEEec
Confidence 456899999999999999987
No 15
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=66.62 E-value=8.7 Score=31.04 Aligned_cols=26 Identities=27% Similarity=0.525 Sum_probs=21.9
Q ss_pred CCCeEE------EEEECCEEEEEeCCCEEEec
Q 025545 134 YEPAFA------VVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 134 ~~~mYA------IVeigGKQYKV~~GD~I~Ve 159 (251)
+..+|. +|.++|+++.|.+||.+.||
T Consensus 57 ~dE~~~Vl~G~g~v~~~~~~~~v~~gd~~~iP 88 (127)
T COG0662 57 RDEHWYVLEGTGKVTIGGEEVEVKAGDSVYIP 88 (127)
T ss_pred cceEEEEEeeEEEEEECCEEEEecCCCEEEEC
Confidence 455664 56799999999999999999
No 16
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=65.83 E-value=4.9 Score=44.06 Aligned_cols=32 Identities=38% Similarity=0.408 Sum_probs=14.4
Q ss_pred ecCCCCCCCCCCCCCccccccccc--cCCCCccc
Q 025545 62 SSNKNDDEGEDVDEDEDEDEETAD--ESYEGEEI 93 (251)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~ 93 (251)
-.|.+.|.+||||.+..||+|||+ ++|.+|||
T Consensus 310 DPNy~yd~~eDed~~~~ed~eDde~~deYsDDeD 343 (1233)
T KOG1824|consen 310 DPNYNYDTEEDEDAMFLEDEEDDEQDDEYSDDED 343 (1233)
T ss_pred CCCCCCCCccchhhhhhhccccchhccccccccc
Confidence 344455444443333334444444 55544444
No 17
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=64.19 E-value=6.3 Score=35.78 Aligned_cols=17 Identities=29% Similarity=0.757 Sum_probs=10.6
Q ss_pred CcccccceeecCCCCCC
Q 025545 53 TNWSHYRHFSSNKNDDE 69 (251)
Q Consensus 53 ~~~~~~~~~~~~~~~~~ 69 (251)
.||-|.-.|.-...|++
T Consensus 27 ~~~~~~~~f~Eee~D~e 43 (240)
T PF05764_consen 27 FFWNQYGLFQEEEDDEE 43 (240)
T ss_pred hhhhhcccccccCCCcc
Confidence 46777767776555443
No 18
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=63.90 E-value=3.8 Score=38.68 Aligned_cols=13 Identities=8% Similarity=0.422 Sum_probs=9.3
Q ss_pred EEEEECCEEEEEe
Q 025545 139 AVVQIGSHQFKVS 151 (251)
Q Consensus 139 AIVeigGKQYKV~ 151 (251)
.|+.++||=|...
T Consensus 355 g~~~~~~~d~~f~ 367 (375)
T PF03153_consen 355 GIMHINGKDYVFQ 367 (375)
T ss_dssp EEEEETTEEEEEE
T ss_pred eEEEECCeEEEEe
Confidence 4777888877654
No 19
>PF11356 Pilus_PilP: Type IV pilus biogenesis; InterPro: IPR022753 Type IV pili are required for auto-agglutination, twitching motility, biofilm formation, adherence and DNA uptake during transformation []. PilP is an inner membrane protein, required for pilus expression and transformation []. PilP interacts with PilQ which suggests that the two proteins may have coordinated activity in functions such as pilus extrusion/retraction []. ; PDB: 3OSS_C 2LNV_A.
Probab=63.63 E-value=8.3 Score=28.80 Aligned_cols=40 Identities=20% Similarity=0.272 Sum_probs=25.9
Q ss_pred HHHhcceEEcCCCCccccccccCCCeEEEEE-ECCEEEEEeCCCEEE
Q 025545 112 EAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQ-IGSHQFKVSNGDSIF 157 (251)
Q Consensus 112 ea~~ig~kv~g~l~~~~~~~k~~~~mYAIVe-igGKQYKV~~GD~I~ 157 (251)
.+.....+.+|-+ . ......+|||. .+|.|+.+..||.|.
T Consensus 22 ~~~~~~l~L~Gvi-~-----~~~~~~~Aii~~~~~~~~~~~~Gd~i~ 62 (87)
T PF11356_consen 22 PATSLNLTLVGVI-S-----GGGGRSSAIIRPSGGEQRTYRVGDTIP 62 (87)
T ss_dssp --S-SSSEEEEEE-------SCSSS-EEEEE-CTTEEEEE-TTEE-S
T ss_pred CCCCCCcEEEEEE-E-----cCCCceEEEEEeCCCcEEEEECcCEeC
Confidence 3444455666665 1 25578999999 999999999999974
No 20
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=61.52 E-value=9.8 Score=32.02 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=25.6
Q ss_pred ccccCCCeEEEEEE-CCEEEEEeCCCEEEec
Q 025545 130 VFKKYEPAFAVVQI-GSHQFKVSNGDSIFTE 159 (251)
Q Consensus 130 ~~k~~~~mYAIVei-gGKQYKV~~GD~I~Ve 159 (251)
+++....++|+|+. .|+=|+|..||+|-.+
T Consensus 84 ~l~~~~~~~ALv~~pdg~v~~V~~G~yiG~n 114 (149)
T PF04351_consen 84 TLSQGGQPWALVQDPDGKVYRVKVGDYIGQN 114 (149)
T ss_dssp EEEETTEEEEEEEE-TTEEEEEETTEEETTT
T ss_pred EEeeCCEEEEEEEeCCCCEEEecCCCEeccC
Confidence 34467899999999 8999999999998554
No 21
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=61.08 E-value=4.3 Score=43.11 Aligned_cols=8 Identities=13% Similarity=0.339 Sum_probs=3.3
Q ss_pred ccccccCC
Q 025545 81 EETADESY 88 (251)
Q Consensus 81 ~~~~~~~~ 88 (251)
|+|...+|
T Consensus 362 DdD~~~dW 369 (885)
T KOG2023|consen 362 DDDAFSDW 369 (885)
T ss_pred cccccccc
Confidence 33344444
No 22
>KOG0772 consensus Uncharacterized conserved protein, contains WD40 repeat [Function unknown]
Probab=59.98 E-value=4.4 Score=41.71 Aligned_cols=13 Identities=23% Similarity=0.409 Sum_probs=5.5
Q ss_pred CCEEEEEeCCCEE
Q 025545 144 GSHQFKVSNGDSI 156 (251)
Q Consensus 144 gGKQYKV~~GD~I 156 (251)
+.-||-|+.+.+|
T Consensus 218 ~sl~ys~Tg~~iL 230 (641)
T KOG0772|consen 218 NSLQYSVTGDQIL 230 (641)
T ss_pred ceeeecCCCCeEE
Confidence 3344555433333
No 23
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=59.28 E-value=18 Score=25.27 Aligned_cols=36 Identities=19% Similarity=0.279 Sum_probs=27.9
Q ss_pred CeEEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEE
Q 025545 136 PAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLL 178 (251)
Q Consensus 136 ~mYAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlV 178 (251)
+.||||-+. .|+++.|.+-.+.++|+.|.|+..-..
T Consensus 5 ~~~aiVlT~-------dGeF~~ik~~~~~~vG~eI~~~~~~~~ 40 (56)
T PF12791_consen 5 KKYAIVLTP-------DGEFIKIKRKPGMEVGQEIEFDEKDII 40 (56)
T ss_pred CCEEEEEcC-------CCcEEEEeCCCCCcccCEEEEechhhc
Confidence 456777665 588889998888999999999875544
No 24
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=57.14 E-value=6.9 Score=40.62 Aligned_cols=17 Identities=18% Similarity=0.518 Sum_probs=12.9
Q ss_pred EEEEEeCCCEEEecccC
Q 025545 146 HQFKVSNGDSIFTERLK 162 (251)
Q Consensus 146 KQYKV~~GD~I~VekL~ 162 (251)
-|=-+..|++++|-.|.
T Consensus 285 ~~en~~~~~tVFvRNL~ 301 (678)
T KOG0127|consen 285 TRENITEGKTVFVRNLP 301 (678)
T ss_pred ccccccccceEEEecCC
Confidence 35557788999998775
No 25
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=56.51 E-value=9.2 Score=36.19 Aligned_cols=20 Identities=30% Similarity=0.169 Sum_probs=16.0
Q ss_pred hhHHHHHHHhhhhhhccCCC
Q 025545 4 RRCLHVLSRHAAALLSLKTP 23 (251)
Q Consensus 4 ~r~~~~~~~~~~~~~~~~~~ 23 (251)
-|-|..|-|.+.|-|-++..
T Consensus 24 arsli~l~Rev~P~lL~kkd 43 (324)
T PF05285_consen 24 ARSLINLFREVNPELLHKKD 43 (324)
T ss_pred HHHHHHHHHHHCHHhcCchh
Confidence 46688899999998877765
No 26
>PHA03209 serine/threonine kinase US3; Provisional
Probab=55.39 E-value=16 Score=33.30 Aligned_cols=37 Identities=19% Similarity=0.332 Sum_probs=22.5
Q ss_pred HHHHHhcceEEcCCCCccccccccCCCeEEEEEEC-CEEEEEe
Q 025545 110 EAEAAEIGYKVLGPLRKSDRVFKKYEPAFAVVQIG-SHQFKVS 151 (251)
Q Consensus 110 ~~ea~~ig~kv~g~l~~~~~~~k~~~~mYAIVeig-GKQYKV~ 151 (251)
.......+|+++..|... .++..|.....+ ++.+.+.
T Consensus 60 ~~~~~~~~y~~~~~lg~G-----~~g~Vy~~~~~~~~~~valK 97 (357)
T PHA03209 60 REVVASLGYTVIKTLTPG-----SEGRVFVATKPGQPDPVVLK 97 (357)
T ss_pred hhhhhhcCcEEEEEecCC-----CCeEEEEEEECCCCceEEEE
Confidence 344566789999998865 445566555543 2344443
No 27
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=52.67 E-value=23 Score=24.45 Aligned_cols=20 Identities=15% Similarity=0.486 Sum_probs=17.5
Q ss_pred EEECCEEEEEeCCCEEEecc
Q 025545 141 VQIGSHQFKVSNGDSIFTER 160 (251)
Q Consensus 141 VeigGKQYKV~~GD~I~Vek 160 (251)
+.++|..|.+++||.+.++.
T Consensus 32 ~~~~~~~~~l~~Gd~~~i~~ 51 (71)
T PF07883_consen 32 LTVDGERVELKPGDAIYIPP 51 (71)
T ss_dssp EEETTEEEEEETTEEEEEET
T ss_pred EEEccEEeEccCCEEEEECC
Confidence 44899999999999999983
No 28
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=51.30 E-value=18 Score=37.52 Aligned_cols=17 Identities=35% Similarity=0.419 Sum_probs=9.6
Q ss_pred cccceeecCCCCCCCCC
Q 025545 56 SHYRHFSSNKNDDEGED 72 (251)
Q Consensus 56 ~~~~~~~~~~~~~~~~~ 72 (251)
+|.|.+-|-+--..+||
T Consensus 57 lHlrrvesa~~~e~~Ed 73 (694)
T KOG4264|consen 57 LHLRRVESAKPAESVED 73 (694)
T ss_pred cchhcccccCccccccc
Confidence 58887776554333333
No 29
>PF05086 Dicty_REP: Dictyostelium (Slime Mold) REP protein; InterPro: IPR007778 This family consists of REP proteins from a number of Dictyostelium species (Slime molds). REP protein is probably involved in transcription regulation and control of DNA replication, specifically the amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity [].
Probab=50.81 E-value=6.5 Score=42.12 Aligned_cols=12 Identities=42% Similarity=0.736 Sum_probs=4.9
Q ss_pred eeecCCCCCCCC
Q 025545 60 HFSSNKNDDEGE 71 (251)
Q Consensus 60 ~~~~~~~~~~~~ 71 (251)
+|.+...+|.+|
T Consensus 884 ~f~~~~~~d~dE 895 (911)
T PF05086_consen 884 QFQSNGDEDTDE 895 (911)
T ss_pred HHHhcCCccccc
Confidence 344444443333
No 30
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=49.44 E-value=9.1 Score=36.23 Aligned_cols=7 Identities=29% Similarity=0.392 Sum_probs=2.7
Q ss_pred Hhhhhhh
Q 025545 12 RHAAALL 18 (251)
Q Consensus 12 ~~~~~~~ 18 (251)
|-++.|+
T Consensus 25 rsli~l~ 31 (324)
T PF05285_consen 25 RSLINLF 31 (324)
T ss_pred HHHHHHH
Confidence 3334433
No 31
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=48.29 E-value=10 Score=34.60 Aligned_cols=7 Identities=43% Similarity=0.387 Sum_probs=3.0
Q ss_pred cCHHHHH
Q 025545 104 YTLEEKE 110 (251)
Q Consensus 104 ~t~~e~~ 110 (251)
+|++|..
T Consensus 179 ~seee~~ 185 (275)
T PF13324_consen 179 LSEEEME 185 (275)
T ss_dssp --HHHHH
T ss_pred CCHHHHH
Confidence 6676653
No 32
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=47.35 E-value=34 Score=29.68 Aligned_cols=27 Identities=19% Similarity=0.410 Sum_probs=20.4
Q ss_pred EEECCEEEEEeCCCEEEecccCccCCCCeeEec
Q 025545 141 VQIGSHQFKVSNGDSIFTERLKFCEVNDKLILN 173 (251)
Q Consensus 141 VeigGKQYKV~~GD~I~VekL~~~evGd~I~L~ 173 (251)
|.+.|+.|...+||+|++| .|++|.|.
T Consensus 108 i~~~G~~~~A~~GDvi~iP------kGs~I~fs 134 (152)
T PF06249_consen 108 ISIDGQTVTAKPGDVIFIP------KGSTITFS 134 (152)
T ss_dssp EEETTEEEEEETT-EEEE-------TT-EEEEE
T ss_pred EEECCEEEEEcCCcEEEEC------CCCEEEEe
Confidence 4589999999999999987 37888874
No 33
>PF14851 FAM176: FAM176 family
Probab=46.59 E-value=33 Score=29.86 Aligned_cols=18 Identities=33% Similarity=0.237 Sum_probs=11.2
Q ss_pred HHHHHHHHhcceEEcCCCCc
Q 025545 107 EEKEAEAAEIGYKVLGPLRK 126 (251)
Q Consensus 107 ~e~~~ea~~ig~kv~g~l~~ 126 (251)
||.+..-++|| .+|+++-
T Consensus 126 EeRe~iirEIW--~n~~~d~ 143 (153)
T PF14851_consen 126 EERERIIREIW--MNGQPDI 143 (153)
T ss_pred HHHHHHHHHHH--HhcCCCC
Confidence 44555667777 6676664
No 34
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=45.72 E-value=16 Score=36.61 Aligned_cols=43 Identities=26% Similarity=0.356 Sum_probs=22.2
Q ss_pred CeEEEE-EECCEEEEEe-CCCE----------EEecccCccCCCCeeEeceEEEEec
Q 025545 136 PAFAVV-QIGSHQFKVS-NGDS----------IFTERLKFCEVNDKLILNKVLLLGS 180 (251)
Q Consensus 136 ~mYAIV-eigGKQYKV~-~GD~----------I~VekL~~~evGd~I~L~kVLlVgs 180 (251)
..-||| -++|+|.-|. .||. |.+-- . -++-|.++++||...|+
T Consensus 331 GtTAvVcLv~g~~liVANAGDSRcV~sr~GkAvdmS~-D-HKPEDevE~~RI~~AGG 385 (542)
T KOG0699|consen 331 GTTAVVCLVGGDKLIVANAGDSRCVLSRNGKAVDMSV-D-HKPEDEVETNRIHAAGG 385 (542)
T ss_pred CceEEEEEecCceEEEecCCCcceEEecCCceeeccc-C-CCcccHHHHHHHHhcCC
Confidence 344444 4667776654 4554 22211 1 24556666666665544
No 35
>PF11421 Synthase_beta: ATP synthase F1 beta subunit; InterPro: IPR020971 F-type ATPases have 2 components, CF1 - the catalytic core - and CF0 - the membrane proton channel. CF1 has five subunits: alpha3, beta3, gamma1, delta1, epsilon1. CF0 has three main subunits: a, b and c. This entry represents the beta subunit of the F1 component. The NMR solution structure of the protein in SDS micelles was found to contain two helices, an N-terminal amphipathic alpha-helix and a C-terminal alpha-helix separated by a large unstructured internal domain. The N-terminal alpha-helix is the Tom20 receptor binding site whereas the C-terminal alpha-helix is located upstream of the mitochondrial processing peptidase cleavage site [].; GO: 0005524 ATP binding, 0016887 ATPase activity, 0006200 ATP catabolic process, 0006754 ATP biosynthetic process, 0000275 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1); PDB: 1PYV_A.
Probab=44.26 E-value=20 Score=25.93 Aligned_cols=16 Identities=44% Similarity=0.526 Sum_probs=11.3
Q ss_pred CchhhHHHHHHHhhhh
Q 025545 1 MAHRRCLHVLSRHAAA 16 (251)
Q Consensus 1 ~~~~r~~~~~~~~~~~ 16 (251)
||+||-|-.|+|.+.-
T Consensus 1 MASRR~lSSlLRSssr 16 (49)
T PF11421_consen 1 MASRRLLSSLLRSSSR 16 (49)
T ss_dssp ---SHHHHHHHHHHHT
T ss_pred CchHHHHHHHHHHHhc
Confidence 9999999999987665
No 36
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=43.97 E-value=32 Score=29.16 Aligned_cols=20 Identities=20% Similarity=0.423 Sum_probs=18.1
Q ss_pred EEEECCEEEEEeCCCEEEec
Q 025545 140 VVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 140 IVeigGKQYKV~~GD~I~Ve 159 (251)
.+.++|+.|.+.+||.+.++
T Consensus 140 ~~~~~~~~~~l~~Gd~~~~~ 159 (185)
T PRK09943 140 VLTINGQDYHLVAGQSYAIN 159 (185)
T ss_pred EEEECCEEEEecCCCEEEEc
Confidence 46799999999999999988
No 37
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=42.91 E-value=31 Score=36.01 Aligned_cols=12 Identities=17% Similarity=0.304 Sum_probs=8.2
Q ss_pred CCccCCcEEEEE
Q 025545 188 RPMVPDAAVHAV 199 (251)
Q Consensus 188 kP~L~~a~V~At 199 (251)
.|+.+.-+++|.
T Consensus 542 eplaep~~~kas 553 (990)
T KOG1819|consen 542 EPLAEPKKCKAS 553 (990)
T ss_pred ccccCcccccch
Confidence 377777777765
No 38
>KOG4264 consensus Nucleo-cytoplasmic protein MLN51 [General function prediction only]
Probab=42.79 E-value=11 Score=38.98 Aligned_cols=6 Identities=67% Similarity=0.866 Sum_probs=3.3
Q ss_pred CchhhH
Q 025545 1 MAHRRC 6 (251)
Q Consensus 1 ~~~~r~ 6 (251)
||.||-
T Consensus 1 MAdrr~ 6 (694)
T KOG4264|consen 1 MADRRM 6 (694)
T ss_pred Ccchhc
Confidence 666553
No 39
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=42.77 E-value=18 Score=35.35 Aligned_cols=28 Identities=21% Similarity=0.195 Sum_probs=19.1
Q ss_pred EEcCCCCccccccccCCCeEEEEEECCEEEEEe
Q 025545 119 KVLGPLRKSDRVFKKYEPAFAVVQIGSHQFKVS 151 (251)
Q Consensus 119 kv~g~l~~~~~~~k~~~~mYAIVeigGKQYKV~ 151 (251)
||+..=-+|.-.||+. |+.|+||-|...
T Consensus 313 KV~RsKnKWKc~LKDG-----IM~ingkDY~F~ 340 (348)
T KOG2652|consen 313 KVNRSKNKWKCYLKDG-----VMHINGKDYVFQ 340 (348)
T ss_pred eeccccceeeEEeecc-----eEEeCCceeEee
Confidence 5555555665556665 888999988654
No 40
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=40.78 E-value=9.1 Score=32.88 Aligned_cols=6 Identities=17% Similarity=0.373 Sum_probs=1.8
Q ss_pred CCeeEe
Q 025545 167 NDKLIL 172 (251)
Q Consensus 167 Gd~I~L 172 (251)
|.+|.|
T Consensus 118 ~~~v~F 123 (170)
T PF04050_consen 118 GGKVAF 123 (170)
T ss_dssp --EEEE
T ss_pred CCeEEE
Confidence 334444
No 41
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=39.32 E-value=15 Score=33.83 Aligned_cols=8 Identities=50% Similarity=0.654 Sum_probs=3.2
Q ss_pred CEEEEEeC
Q 025545 145 SHQFKVSN 152 (251)
Q Consensus 145 GKQYKV~~ 152 (251)
+-.|.|..
T Consensus 195 ~~~~~~kr 202 (244)
T PF04889_consen 195 SGDFKVKR 202 (244)
T ss_pred CCCCcccc
Confidence 33444443
No 42
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=37.93 E-value=42 Score=31.15 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=18.6
Q ss_pred EEEECCEEEEEeCCCEEEecc
Q 025545 140 VVQIGSHQFKVSNGDSIFTER 160 (251)
Q Consensus 140 IVeigGKQYKV~~GD~I~Vek 160 (251)
.+.++|+.|.+.+||++++++
T Consensus 187 ~l~IdG~t~~l~pGDvlfIPk 207 (233)
T PRK15457 187 HVRHEGETMIAKAGDVMFIPK 207 (233)
T ss_pred EEEECCEEEEeCCCcEEEECC
Confidence 367899999999999999984
No 43
>PHA03211 serine/threonine kinase US3; Provisional
Probab=36.28 E-value=83 Score=30.81 Aligned_cols=11 Identities=27% Similarity=-0.019 Sum_probs=5.4
Q ss_pred CCCCccCHHHH
Q 025545 99 DLGREYTLEEK 109 (251)
Q Consensus 99 ~~~~~~t~~e~ 109 (251)
.++..+|.++-
T Consensus 131 ~~~~~~t~~~l 141 (461)
T PHA03211 131 APPGGLTPEEL 141 (461)
T ss_pred CCCCCCChhhh
Confidence 34445555553
No 44
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=36.08 E-value=17 Score=38.73 Aligned_cols=17 Identities=29% Similarity=0.472 Sum_probs=8.7
Q ss_pred cCHHHHHHHHHhcceEE
Q 025545 104 YTLEEKEAEAAEIGYKV 120 (251)
Q Consensus 104 ~t~~e~~~ea~~ig~kv 120 (251)
||.+++.+-..+..|++
T Consensus 424 l~k~q~k~y~de~dyr~ 440 (763)
T TIGR00993 424 LSKEQRKAYLEEYDYRV 440 (763)
T ss_pred HhHHHHHHHHHHHHHHH
Confidence 34455555555555543
No 45
>cd04867 TGS_YchF_C TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the family contain a C-terminal TGS domain. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=34.43 E-value=19 Score=28.58 Aligned_cols=19 Identities=26% Similarity=0.447 Sum_probs=16.8
Q ss_pred EEEECCEEEEEeCCCEEEe
Q 025545 140 VVQIGSHQFKVSNGDSIFT 158 (251)
Q Consensus 140 IVeigGKQYKV~~GD~I~V 158 (251)
.+++-||+|.|..||++.+
T Consensus 63 kir~eGK~Yiv~DGDi~~f 81 (83)
T cd04867 63 KYRQEGKDYVVQDGDIIFF 81 (83)
T ss_pred hhhhhCCceEeeCCeEEEE
Confidence 5778899999999999875
No 46
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=33.97 E-value=61 Score=27.63 Aligned_cols=21 Identities=29% Similarity=0.634 Sum_probs=19.1
Q ss_pred EEEEECCEEEEEeCCCEEEec
Q 025545 139 AVVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 139 AIVeigGKQYKV~~GD~I~Ve 159 (251)
|.|.++|+.+.|.+||.++|+
T Consensus 95 a~v~~~~~~~~~~~g~sv~Ip 115 (151)
T PF01050_consen 95 AEVTLDDEEFTLKEGDSVYIP 115 (151)
T ss_pred EEEEECCEEEEEcCCCEEEEC
Confidence 557899999999999999998
No 47
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=33.57 E-value=1.4e+02 Score=30.38 Aligned_cols=38 Identities=18% Similarity=0.217 Sum_probs=31.4
Q ss_pred EEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEE
Q 025545 138 FAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLL 178 (251)
Q Consensus 138 YAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlV 178 (251)
-|-|.++|+.|+|...-.|.+..| .+|+.|.|+.-+.+
T Consensus 60 ~~~v~~~g~~~~~~~~~~~~~~~l---~~g~~v~l~e~~~~ 97 (512)
T TIGR03689 60 TAEVFTAGRRMRVTVSPNVNAAEL---VPGQTVRLNEALQV 97 (512)
T ss_pred eEEEEeCCceEEEEeCCCCCHHHC---CCCCEEEECCccee
Confidence 488899999999998888777655 58999999877765
No 48
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=32.92 E-value=24 Score=26.50 Aligned_cols=44 Identities=14% Similarity=0.265 Sum_probs=20.1
Q ss_pred CEEEEEeCCCEEEecccCccCCCCeeEeceEEEEecCCceEecCCccCCcEE
Q 025545 145 SHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLLGSQHQTIIGRPMVPDAAV 196 (251)
Q Consensus 145 GKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L~~a~V 196 (251)
...|++.+||.|.|.-....+ |+.-..|+.++.+. -|++....|
T Consensus 8 ~~~y~l~pGD~l~i~v~~~~~------l~~~~~V~~dG~I~--lP~iG~v~v 51 (82)
T PF02563_consen 8 PPEYRLGPGDVLRISVFGWPE------LSGEYTVDPDGTIS--LPLIGPVKV 51 (82)
T ss_dssp T------TT-EEEEEETT-HH------HCCSEE--TTSEEE--ETTTEEEE-
T ss_pred CCCCEECCCCEEEEEEecCCC------cccceEECCCCcEe--ecccceEEE
Confidence 357999999999987443212 55566777666543 366655444
No 49
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=32.32 E-value=64 Score=25.20 Aligned_cols=22 Identities=32% Similarity=0.380 Sum_probs=17.1
Q ss_pred EEECCEEEEEeCCCEEEecccC
Q 025545 141 VQIGSHQFKVSNGDSIFTERLK 162 (251)
Q Consensus 141 VeigGKQYKV~~GD~I~VekL~ 162 (251)
|.+++.+|.|.+|+...||+=+
T Consensus 46 Vti~~~~f~v~~G~~F~VP~gN 67 (85)
T PF11699_consen 46 VTIHETSFVVTKGGSFQVPRGN 67 (85)
T ss_dssp EEETTEEEEEETT-EEEE-TT-
T ss_pred EEEcCcEEEEeCCCEEEECCCC
Confidence 5789999999999999999654
No 50
>PF11521 TFIIE-A_C-term: C-terminal general transcription factor TFIIE alpha; InterPro: IPR021600 TFIIE is compiled of two subunits, alpha and beta. This family of proteins are the C-terminal domain of the alpha subunit of the protein which is the largest subunit and contains several functional domains which are important for basal transcription and cell growth. The C-terminal end of the protein binds directly to the amino-terminal PH domain of p62/Tfb1 (of IIH) which is involved in the recruitment of the general transcription factor IIH to the transcription preinitiation complex. P53 competes for the same binding site as TFIIE alpha which shows their structural similarity. Like p53, TFIIE alpha 336-439 can activate transcription in vivo []. ; PDB: 2RNR_A 2RNQ_A 2JTX_A.
Probab=31.88 E-value=5.9 Score=31.37 Aligned_cols=10 Identities=60% Similarity=0.431 Sum_probs=4.4
Q ss_pred cCHHHHHHHH
Q 025545 104 YTLEEKEAEA 113 (251)
Q Consensus 104 ~t~~e~~~ea 113 (251)
.|++||++=.
T Consensus 65 MT~~EKEaYi 74 (86)
T PF11521_consen 65 MTPEEKEAYI 74 (86)
T ss_dssp S-HHHHHHHH
T ss_pred cCHHHHHHHH
Confidence 4555554433
No 51
>PF08553 VID27: VID27 cytoplasmic protein; InterPro: IPR013863 This entry represents fungal and plant proteins and contains many hypothetical proteins. Vid27p is a cytoplasmic protein of unknown function, possibly regulates import of fructose-1,6-bisphosphatase into Vacuolar Import and Degradation (Vid) vesicles and is not essential for proteasome-dependent degradation of fructose-1,6-bisphosphatase (FBPase) [, ].
Probab=31.71 E-value=75 Score=34.23 Aligned_cols=24 Identities=17% Similarity=0.268 Sum_probs=12.1
Q ss_pred CCeeEeceEEEEecCCceEecCCc
Q 025545 167 NDKLILNKVLLLGSQHQTIIGRPM 190 (251)
Q Consensus 167 Gd~I~L~kVLlVgs~~~t~IGkP~ 190 (251)
|..+.=.++||...+...++=.|-
T Consensus 478 g~~~~P~k~mL~~~d~~mil~~~~ 501 (794)
T PF08553_consen 478 GKNFTPKKAMLHDQDRNMILLDPN 501 (794)
T ss_pred CcccCcchhhhhccccceEeecCC
Confidence 444444566665544444444454
No 52
>PHA02664 hypothetical protein; Provisional
Probab=31.41 E-value=50 Score=32.81 Aligned_cols=10 Identities=50% Similarity=0.425 Sum_probs=4.5
Q ss_pred HHHHHHHHHh
Q 025545 106 LEEKEAEAAE 115 (251)
Q Consensus 106 ~~e~~~ea~~ 115 (251)
+||.++|++-
T Consensus 515 eee~~ee~~v 524 (534)
T PHA02664 515 EEEEEEERAV 524 (534)
T ss_pred hHHHHHHHHH
Confidence 3344445543
No 53
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=30.75 E-value=41 Score=29.67 Aligned_cols=10 Identities=40% Similarity=0.660 Sum_probs=7.3
Q ss_pred cccceeecCC
Q 025545 56 SHYRHFSSNK 65 (251)
Q Consensus 56 ~~~~~~~~~~ 65 (251)
+|.+||+...
T Consensus 5 Fh~~HF~~~~ 14 (172)
T PF12720_consen 5 FHAKHFSGSA 14 (172)
T ss_pred HHHHHCCCcc
Confidence 5778888765
No 54
>PF13079 DUF3916: Protein of unknown function (DUF3916)
Probab=30.29 E-value=41 Score=29.36 Aligned_cols=21 Identities=29% Similarity=0.482 Sum_probs=19.3
Q ss_pred hhhHHHHHHHhhhhhhccCCC
Q 025545 3 HRRCLHVLSRHAAALLSLKTP 23 (251)
Q Consensus 3 ~~r~~~~~~~~~~~~~~~~~~ 23 (251)
+|.|+|+|.++|.-++..+|.
T Consensus 43 kr~c~Q~LIn~a~~Li~~kp~ 63 (153)
T PF13079_consen 43 KRLCIQTLINAAEHLIQAKPD 63 (153)
T ss_pred HHHHHHHHHHHHHHHHhCCcC
Confidence 588999999999999999985
No 55
>TIGR03021 pilP_fam type IV pilus biogenesis protein PilP. Members of this protein family are found in type IV pilus biogenesis loci and include proteins designated PilP.
Probab=28.69 E-value=73 Score=26.34 Aligned_cols=33 Identities=24% Similarity=0.415 Sum_probs=27.3
Q ss_pred CCccccccccCCCeEEEEEE-CCEEEEEeCCCEE
Q 025545 124 LRKSDRVFKKYEPAFAVVQI-GSHQFKVSNGDSI 156 (251)
Q Consensus 124 l~~~~~~~k~~~~mYAIVei-gGKQYKV~~GD~I 156 (251)
++.-..++-....+.|.+.+ +|++.-|..||.|
T Consensus 68 ~P~v~~I~G~~~~l~A~l~l~~G~~~~v~~G~~l 101 (119)
T TIGR03021 68 LPRVVEIFGRGGRLTATLRLPGGREVDVQVGDSL 101 (119)
T ss_pred CCEEEEEEccCCCeEEEEEeCCCcEEEecCCCcc
Confidence 34444677788899999999 8999999999985
No 56
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=28.29 E-value=85 Score=32.96 Aligned_cols=6 Identities=33% Similarity=0.756 Sum_probs=2.6
Q ss_pred hcceEE
Q 025545 115 EIGYKV 120 (251)
Q Consensus 115 ~ig~kv 120 (251)
+.||-+
T Consensus 466 asgyli 471 (990)
T KOG1819|consen 466 ASGYLI 471 (990)
T ss_pred cccccc
Confidence 345543
No 57
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=27.55 E-value=78 Score=28.91 Aligned_cols=21 Identities=24% Similarity=0.385 Sum_probs=18.7
Q ss_pred EEEEECCEEEEEeCCCEEEec
Q 025545 139 AVVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 139 AIVeigGKQYKV~~GD~I~Ve 159 (251)
+++.++|+-+.|++||+|.++
T Consensus 211 G~~~~~g~~~~V~~GD~i~i~ 231 (260)
T TIGR03214 211 GVYNLDNNWVPVEAGDYIWMG 231 (260)
T ss_pred EEEEECCEEEEecCCCEEEEC
Confidence 456799999999999999998
No 58
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=27.39 E-value=21 Score=34.07 Aligned_cols=11 Identities=18% Similarity=0.570 Sum_probs=6.6
Q ss_pred hhHHHHHHHhh
Q 025545 4 RRCLHVLSRHA 14 (251)
Q Consensus 4 ~r~~~~~~~~~ 14 (251)
-+|=|+||+-.
T Consensus 106 HKcKQRltklT 116 (303)
T KOG3064|consen 106 HKCKQRLTKLT 116 (303)
T ss_pred HHHHHHHHHHH
Confidence 46777776533
No 59
>PRK13501 transcriptional activator RhaR; Provisional
Probab=26.21 E-value=75 Score=28.34 Aligned_cols=21 Identities=14% Similarity=0.578 Sum_probs=18.7
Q ss_pred EEEEECCEEEEEeCCCEEEec
Q 025545 139 AVVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 139 AIVeigGKQYKV~~GD~I~Ve 159 (251)
+.+.++|+.|.+++||.+.|+
T Consensus 49 ~~~~i~~~~~~l~~g~~~~I~ 69 (290)
T PRK13501 49 GLHVLNDHPYRITCGDVFYIQ 69 (290)
T ss_pred eEEEECCeeeeecCCeEEEEc
Confidence 456789999999999999997
No 60
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=26.15 E-value=88 Score=27.55 Aligned_cols=21 Identities=19% Similarity=0.344 Sum_probs=18.7
Q ss_pred EEEEECCEEEEEeCCCEEEec
Q 025545 139 AVVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 139 AIVeigGKQYKV~~GD~I~Ve 159 (251)
+.+.++|+.|.+.+||.+.|+
T Consensus 54 ~~~~i~~~~~~l~~g~l~~i~ 74 (278)
T PRK10296 54 YYQEINGKRVLLERGDFVFIP 74 (278)
T ss_pred EEEEECCEEEEECCCcEEEeC
Confidence 357789999999999999987
No 61
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=25.97 E-value=36 Score=29.25 Aligned_cols=12 Identities=33% Similarity=0.709 Sum_probs=7.0
Q ss_pred cCccCcceEEEE
Q 025545 224 KGHRQELTKLRI 235 (251)
Q Consensus 224 ~GHRQ~yTrLRI 235 (251)
+|+||.+-.|.|
T Consensus 129 kGnK~q~k~l~v 140 (170)
T PF04050_consen 129 KGNKQQTKELNV 140 (170)
T ss_dssp ETTEEEEEEEEE
T ss_pred cCCCCCCeEEec
Confidence 566666555554
No 62
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=25.97 E-value=54 Score=33.93 Aligned_cols=6 Identities=0% Similarity=0.280 Sum_probs=2.3
Q ss_pred cccccC
Q 025545 82 ETADES 87 (251)
Q Consensus 82 ~~~~~~ 87 (251)
|+|+++
T Consensus 214 d~~ede 219 (615)
T KOG3540|consen 214 DGYEDE 219 (615)
T ss_pred cccccc
Confidence 333333
No 63
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=25.65 E-value=31 Score=38.22 Aligned_cols=14 Identities=14% Similarity=0.328 Sum_probs=7.1
Q ss_pred ccceeecCCCCCCC
Q 025545 57 HYRHFSSNKNDDEG 70 (251)
Q Consensus 57 ~~~~~~~~~~~~~~ 70 (251)
+.--|-++..+|++
T Consensus 309 YDPNy~yd~~eDed 322 (1233)
T KOG1824|consen 309 YDPNYNYDTEEDED 322 (1233)
T ss_pred cCCCCCCCCccchh
Confidence 34455555555544
No 64
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=25.11 E-value=82 Score=28.92 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=28.8
Q ss_pred ccccccCCCeEEEEEECCEEEEEeCCCEEEecccCccCCCCeeEec
Q 025545 128 DRVFKKYEPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILN 173 (251)
Q Consensus 128 ~~~~k~~~~mYAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~ 173 (251)
-..+|+. |-|.+||-.|-+++||+|.|- -+-|..|.++
T Consensus 29 H~~Ykds----A~Iyiggl~~~LtEgDil~VF----SqyGe~vdin 66 (219)
T KOG0126|consen 29 HQEYKDS----AYIYIGGLPYELTEGDILCVF----SQYGEIVDIN 66 (219)
T ss_pred hhhcccc----eEEEECCCcccccCCcEEEEe----eccCceEEEE
Confidence 3445555 999999999999999999884 2456666553
No 65
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=24.97 E-value=32 Score=37.79 Aligned_cols=26 Identities=42% Similarity=0.752 Sum_probs=0.0
Q ss_pred CCCCCCCCCCcccccccc--------------------ccCCCCcc
Q 025545 67 DDEGEDVDEDEDEDEETA--------------------DESYEGEE 92 (251)
Q Consensus 67 ~~~~~~~~~~~~~~~~~~--------------------~~~~~~~~ 92 (251)
++++|+-.||++|+|+|+ +||||+++
T Consensus 897 ~~~~e~~~~d~dD~d~~d~d~~~~~~~~~~~~~~~~~~ddd~d~~~ 942 (1010)
T KOG1991|consen 897 DDEEEDFIDDEDDIDEDDQDYLDEYGELALEKEDSLDDDDDFDEDE 942 (1010)
T ss_pred CcchhhccCccccccccchhHHHhhccccccccccccccccccchh
No 66
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=23.83 E-value=1.2e+02 Score=22.29 Aligned_cols=17 Identities=18% Similarity=0.438 Sum_probs=14.2
Q ss_pred CCEEEEEeCCCEEEecc
Q 025545 144 GSHQFKVSNGDSIFTER 160 (251)
Q Consensus 144 gGKQYKV~~GD~I~Vek 160 (251)
+|.++.+.+||.+.+++
T Consensus 42 ~G~~~~~~aGD~~~~p~ 58 (74)
T PF05899_consen 42 DGETVTFKAGDAFFLPK 58 (74)
T ss_dssp TTEEEEEETTEEEEE-T
T ss_pred CCCEEEEcCCcEEEECC
Confidence 88999999999998873
No 67
>COG3264 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=23.82 E-value=1e+02 Score=33.57 Aligned_cols=70 Identities=24% Similarity=0.188 Sum_probs=49.0
Q ss_pred CCEEEecccCccCCCCeeEeceEEEEecCCceEecCCccCCcEEEEEEEeecCCceEEEEEecCCCCceeccCccCcceE
Q 025545 153 GDSIFTERLKFCEVNDKLILNKVLLLGSQHQTIIGRPMVPDAAVHAVVEEHALDAKVIIFKKKRRKNYRRTKGHRQELTK 232 (251)
Q Consensus 153 GD~I~VekL~~~evGd~I~L~kVLlVgs~~~t~IGkP~L~~a~V~AtVleh~rg~KViVfK~KRRK~yrRk~GHRQ~yTr 232 (251)
|=+|.+||- +++||.|++..+- | +|....|.||.++.+.++.|+|=-.-==.+--..+-||..+||
T Consensus 652 GlIiL~Erp--vkvGD~It~g~~~----------G--~V~~I~vRAT~I~~fd~~~vIVPNs~fI~~qV~NWs~~~~~~R 717 (835)
T COG3264 652 GLIILFERP--VKVGDTVTIGTVS----------G--TVRKISVRATTIRTFDRKEVIVPNSAFITEQVINWSLRDTTTR 717 (835)
T ss_pred hhhhheecC--cccCCEEEECCce----------E--EEEEEEeeEEEEEeCCCCeEEeccHHHHhhheeeeeccCceEE
Confidence 445667753 6899999886632 1 4677889999999999998886322111233445689999999
Q ss_pred EEEc
Q 025545 233 LRIV 236 (251)
Q Consensus 233 LRI~ 236 (251)
+.|.
T Consensus 718 ~~i~ 721 (835)
T COG3264 718 LVIP 721 (835)
T ss_pred EEEE
Confidence 9885
No 68
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.
Probab=23.46 E-value=3.4e+02 Score=21.07 Aligned_cols=31 Identities=13% Similarity=0.185 Sum_probs=18.0
Q ss_pred eEEEEecCCceEecCCccCCcEEEEEEEeecC
Q 025545 174 KVLLLGSQHQTIIGRPMVPDAAVHAVVEEHAL 205 (251)
Q Consensus 174 kVLlVgs~~~t~IGkP~L~~a~V~AtVleh~r 205 (251)
+-+-+.-+++.++ .|+-.+.+|+|+|+--..
T Consensus 35 k~iWIkrGd~VlV-~p~~~~~kvkgeIv~i~~ 65 (78)
T cd05792 35 KNIWIKRGDFVLV-EPIEEGDKVKAEIVKILT 65 (78)
T ss_pred ccEEEEeCCEEEE-EecccCCceEEEEEEEEC
Confidence 4555555555555 355555678888765443
No 69
>PRK12784 hypothetical protein; Provisional
Probab=23.43 E-value=1.7e+02 Score=23.37 Aligned_cols=48 Identities=15% Similarity=0.059 Sum_probs=38.9
Q ss_pred CCeEEEEEECCEEEEEeCCCEEEecccCccCCCCeeEeceEEEEecCCc
Q 025545 135 EPAFAVVQIGSHQFKVSNGDSIFTERLKFCEVNDKLILNKVLLLGSQHQ 183 (251)
Q Consensus 135 ~~mYAIVeigGKQYKV~~GD~I~VekL~~~evGd~I~L~kVLlVgs~~~ 183 (251)
+++|.|=..+|+--+|..|=.=.+..++ +++|+.|.-+.+|..=.++-
T Consensus 31 EkL~~I~~~dg~le~v~vGiSG~I~~v~-Ve~Gq~i~~dtlL~~~edDl 78 (84)
T PRK12784 31 EKLMMIRKNNGELEKVAVGISGNIRLVN-VVVGQQIHTDTLLVRLEDDL 78 (84)
T ss_pred eeeeEEeecCCcEEEEEEeeeeeEEEEE-eecCceecCCcEEEEEeece
Confidence 4677888888999999999887787777 89999999988887644443
No 70
>PF05896 NQRA: Na(+)-translocating NADH-quinone reductase subunit A (NQRA); InterPro: IPR008703 This family consists of several bacterial Na+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na+-translocating NADH: ubiquinone oxidoreductase (Na+-NQR) generates an electrochemical Na+ potential driven by aerobic respiration [].; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0006814 sodium ion transport, 0055114 oxidation-reduction process
Probab=23.21 E-value=80 Score=29.62 Aligned_cols=57 Identities=11% Similarity=0.085 Sum_probs=39.9
Q ss_pred CEEEEEeCCCEEEe-cccCccCCCCeeEeceEEEEecCC-ceEecCCccCCcEEEEEEEeecCCce
Q 025545 145 SHQFKVSNGDSIFT-ERLKFCEVNDKLILNKVLLLGSQH-QTIIGRPMVPDAAVHAVVEEHALDAK 208 (251)
Q Consensus 145 GKQYKV~~GD~I~V-ekL~~~evGd~I~L~kVLlVgs~~-~t~IGkP~L~~a~V~AtVleh~rg~K 208 (251)
-+.|-|.+.|++-+ ++|. +++||+|.....|+.+..+ .+.+= +-|.++|.+-.||.|
T Consensus 26 ~~~~al~~~Df~g~~Pkm~-VkeGD~Vk~Gq~LF~dK~~p~v~ft------sPvsG~V~~I~RG~r 84 (257)
T PF05896_consen 26 SRTVALLPDDFPGMKPKML-VKEGDRVKAGQPLFEDKKNPGVKFT------SPVSGTVKAINRGER 84 (257)
T ss_pred CcEEEEcCcccCCCCccEE-eccCCEEeCCCeeEeeCCCCCcEEe------cCCCeEEEEEecCCC
Confidence 36677778888764 5887 8999999999999997553 23222 335677777666654
No 71
>PRK11171 hypothetical protein; Provisional
Probab=23.13 E-value=1e+02 Score=28.15 Aligned_cols=20 Identities=25% Similarity=0.436 Sum_probs=15.8
Q ss_pred EEEECCEEEEEeCCCEEEec
Q 025545 140 VVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 140 IVeigGKQYKV~~GD~I~Ve 159 (251)
++.++|+-|.|++||.|.++
T Consensus 217 ~~~~~~~~~~l~~GD~i~~~ 236 (266)
T PRK11171 217 VYRLNNDWVEVEAGDFIWMR 236 (266)
T ss_pred EEEECCEEEEeCCCCEEEEC
Confidence 45678888888888888876
No 72
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=23.11 E-value=1e+02 Score=28.24 Aligned_cols=21 Identities=10% Similarity=0.147 Sum_probs=19.2
Q ss_pred EEEEECCEEEEEeCCCEEEec
Q 025545 139 AVVQIGSHQFKVSNGDSIFTE 159 (251)
Q Consensus 139 AIVeigGKQYKV~~GD~I~Ve 159 (251)
+.+.++|++|.+.+||.+.++
T Consensus 57 ~~~~i~g~~~~l~~Gd~ili~ 77 (302)
T PRK10371 57 VEYLINNEKVQINQGHITLFW 77 (302)
T ss_pred EEEEECCEEEEEcCCcEEEEe
Confidence 468899999999999999997
No 73
>PF06071 YchF-GTPase_C: Protein of unknown function (DUF933); InterPro: IPR013029 This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of P44681 from SWISSPROT from Haemophilus influenzae has been determined []. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.; PDB: 1NI3_A 1JAL_A 2DWQ_B 2DBY_A 2OHF_A.
Probab=22.96 E-value=16 Score=28.92 Aligned_cols=19 Identities=21% Similarity=0.448 Sum_probs=12.9
Q ss_pred EEEECCEEEEEeCCCEEEe
Q 025545 140 VVQIGSHQFKVSNGDSIFT 158 (251)
Q Consensus 140 IVeigGKQYKV~~GD~I~V 158 (251)
.+++.||.|.|+.||+|.+
T Consensus 63 k~r~eGK~YivqDGDIi~f 81 (84)
T PF06071_consen 63 KLRLEGKDYIVQDGDIIHF 81 (84)
T ss_dssp -SEEEETT-B--TTEEEEE
T ss_pred CccccCCceeEeCCCEEEE
Confidence 3567899999999999875
No 74
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=22.32 E-value=36 Score=34.23 Aligned_cols=49 Identities=12% Similarity=0.182 Sum_probs=32.3
Q ss_pred CCCccccccccCCCeEEEEEECCEEEEEe----CCCEEEecccCccCCCCeeEec
Q 025545 123 PLRKSDRVFKKYEPAFAVVQIGSHQFKVS----NGDSIFTERLKFCEVNDKLILN 173 (251)
Q Consensus 123 ~l~~~~~~~k~~~~mYAIVeigGKQYKV~----~GD~I~VekL~~~evGd~I~L~ 173 (251)
.+.+..++...-..--|||.-+||-.-.+ |-|-+.+.||+ ..|.+|+|+
T Consensus 338 Lv~g~~liVANAGDSRcV~sr~GkAvdmS~DHKPEDevE~~RI~--~AGG~vtlD 390 (542)
T KOG0699|consen 338 LVGGDKLIVANAGDSRCVLSRNGKAVDMSVDHKPEDEVETNRIH--AAGGQVTLD 390 (542)
T ss_pred EecCceEEEecCCCcceEEecCCceeecccCCCcccHHHHHHHH--hcCCeEeec
Confidence 33333444455556778888888876554 55667777887 578888764
No 75
>PHA03346 US22 family homolog; Provisional
Probab=21.99 E-value=49 Score=33.90 Aligned_cols=52 Identities=23% Similarity=0.302 Sum_probs=0.0
Q ss_pred CCccc---ccceeecCCCCC------CCCCC--------------------CCCc-cccccccccCCCCcccccCCCCCC
Q 025545 52 PTNWS---HYRHFSSNKNDD------EGEDV--------------------DEDE-DEDEETADESYEGEEIGDTVPDLG 101 (251)
Q Consensus 52 ~~~~~---~~~~~~~~~~~~------~~~~~--------------------~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 101 (251)
..+|+ +++-|..+-+.. ++++. |+++ |++|+|+.|++..+.++..+.+.+
T Consensus 377 ~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~ 456 (520)
T PHA03346 377 FALWHARVLRGEFAERRRPRGPPENEDEADGGGGLAPPPEPPRPPPPPFPDDDDEGDDEDDDDWEDLGFDLDEDDVYDLK 456 (520)
T ss_pred HHHHHHHHHhcchhhhccCCCCCCcccccccccCcCCCCCCCCCCCCCCCCcccccccccccccccCCccccccccccch
Q ss_pred Cc
Q 025545 102 RE 103 (251)
Q Consensus 102 ~~ 103 (251)
..
T Consensus 457 ~~ 458 (520)
T PHA03346 457 DV 458 (520)
T ss_pred hh
No 76
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=21.90 E-value=1e+02 Score=27.32 Aligned_cols=39 Identities=8% Similarity=0.103 Sum_probs=23.7
Q ss_pred cCCCeEEEEEECCEEE------------EEeCCCEEEecccCccCCCCeeE
Q 025545 133 KYEPAFAVVQIGSHQF------------KVSNGDSIFTERLKFCEVNDKLI 171 (251)
Q Consensus 133 ~~~~mYAIVeigGKQY------------KV~~GD~I~VekL~~~evGd~I~ 171 (251)
..++++-|+..+|.-| ||.-|+++.|+.+...+.|++|.
T Consensus 32 rGsnlheV~danGq~~lvsmP~KfRksiWiRRg~FvvVdpiee~~~g~KVk 82 (167)
T KOG2925|consen 32 RGSNLHEVMDANGQNSLVSMPAKFRKSIWIRRGSFVVVDPIEEEKSGSKVK 82 (167)
T ss_pred CCcchhhhhhcCCceeeeeCCHhhhhceEEeeCCEEEEccccccccCCccc
Confidence 3455666666666555 55667777777666545566553
No 77
>cd04092 mtEFG2_II_like mtEFG2_C: C-terminus of mitochondrial Elongation factor G2 (mtEFG2)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG1s are n
Probab=21.82 E-value=97 Score=22.77 Aligned_cols=21 Identities=29% Similarity=0.292 Sum_probs=11.9
Q ss_pred EeCCCEEEecccCccCCCCee
Q 025545 150 VSNGDSIFTERLKFCEVNDKL 170 (251)
Q Consensus 150 V~~GD~I~VekL~~~evGd~I 170 (251)
+..||++.+..++.+.+||+|
T Consensus 61 ~~aGdI~~i~gl~~~~~Gdtl 81 (83)
T cd04092 61 LSAGNIGVITGLKQTRTGDTL 81 (83)
T ss_pred eCCCCEEEEECCCCcccCCEE
Confidence 455666655555555555554
No 78
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=21.78 E-value=35 Score=32.20 Aligned_cols=9 Identities=0% Similarity=0.290 Sum_probs=5.2
Q ss_pred EEEEecCCc
Q 025545 175 VLLLGSQHQ 183 (251)
Q Consensus 175 VLlVgs~~~ 183 (251)
||.|++.++
T Consensus 356 ~~~~~~~d~ 364 (375)
T PF03153_consen 356 IMHINGKDY 364 (375)
T ss_dssp EEEETTEEE
T ss_pred EEEECCeEE
Confidence 566655554
No 79
>KOG2229 consensus Protein required for actin cytoskeleton organization and cell cycle progression [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=21.52 E-value=62 Score=33.72 Aligned_cols=27 Identities=26% Similarity=0.260 Sum_probs=20.1
Q ss_pred CchhhHHHHHHHhhhhhhccCCCCCCC
Q 025545 1 MAHRRCLHVLSRHAAALLSLKTPPTLP 27 (251)
Q Consensus 1 ~~~~r~~~~~~~~~~~~~~~~~~~~~~ 27 (251)
|+.-|-|-+|-|-..|-+-.+.+-+-|
T Consensus 370 ~maarSLI~L~Rev~P~mL~kKDRGk~ 396 (616)
T KOG2229|consen 370 MMAARSLIALYREVLPDMLIKKDRGKP 396 (616)
T ss_pred HHHHHHHHHHHHHHCHHHHhHHhcCCC
Confidence 455678889999999988877764443
No 80
>PF05432 BSP_II: Bone sialoprotein II (BSP-II); InterPro: IPR008412 The major non-collagenous matrix proteins (chondroitin-sulphate glycoproteins decorin and biglycan, sialoproteins osteopontin and bone sialoprotein, osteocalcin and osteonectin) have important roles in formation and organisation of the collagen matrix and nucleation and growth of hydroxyapatite crystals. Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully differentiated osteoblasts [], [] and is highly specific for mineralising tissues. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth; it is thought to be responsible for nucleation of hydroxyapatite crystals. BSP also displays a high affinity for calcium ions. The mature protein has a molecular weight of around 33 kDa and consists predominantly of Glu and Gly residues. It is subject to extensive posttranslational modification, and is predominantly phosphorylated at Ser residues. Posttranslational modifications can also cause BSP to act as an inhibitor of hydroxyapatite crystal formation. Ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone []. This entry represents the bone sialoprotein II group of proteins.; GO: 0001503 ossification, 0007155 cell adhesion, 0005576 extracellular region
Probab=21.29 E-value=65 Score=30.85 Aligned_cols=16 Identities=19% Similarity=0.414 Sum_probs=7.8
Q ss_pred ccce---eecCCCCCCCCC
Q 025545 57 HYRH---FSSNKNDDEGED 72 (251)
Q Consensus 57 ~~~~---~~~~~~~~~~~~ 72 (251)
..|+ ++|+|+..++|.
T Consensus 39 lKR~~vq~~sDSSEEngdg 57 (292)
T PF05432_consen 39 LKRFPVQSNSDSSEENGDG 57 (292)
T ss_pred hhhccccCCCCcccccCCC
Confidence 4555 455555444433
No 81
>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=20.58 E-value=1.8e+02 Score=22.25 Aligned_cols=12 Identities=17% Similarity=0.446 Sum_probs=5.7
Q ss_pred EEEeCCCEEEec
Q 025545 148 FKVSNGDSIFTE 159 (251)
Q Consensus 148 YKV~~GD~I~Ve 159 (251)
.||.+||++.|+
T Consensus 37 iwI~~GD~VlV~ 48 (78)
T cd04456 37 IWIKRGDFLIVD 48 (78)
T ss_pred EEEcCCCEEEEE
Confidence 444455554443
No 82
>PF03896 TRAP_alpha: Translocon-associated protein (TRAP), alpha subunit; InterPro: IPR005595 The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane [].; GO: 0005783 endoplasmic reticulum
Probab=20.51 E-value=1.1e+02 Score=28.99 Aligned_cols=14 Identities=0% Similarity=-0.024 Sum_probs=8.9
Q ss_pred cCCCCeeEeceEEE
Q 025545 164 CEVNDKLILNKVLL 177 (251)
Q Consensus 164 ~evGd~I~L~kVLl 177 (251)
+.+|.+..|.=...
T Consensus 146 V~pg~~aT~~YsF~ 159 (285)
T PF03896_consen 146 VPPGEEATFPYSFT 159 (285)
T ss_pred cCCCCeEEEEEEEe
Confidence 56777777765544
No 83
>PRK13500 transcriptional activator RhaR; Provisional
Probab=20.38 E-value=1.2e+02 Score=27.80 Aligned_cols=22 Identities=9% Similarity=0.457 Sum_probs=19.3
Q ss_pred EEEEECCEEEEEeCCCEEEecc
Q 025545 139 AVVQIGSHQFKVSNGDSIFTER 160 (251)
Q Consensus 139 AIVeigGKQYKV~~GD~I~Vek 160 (251)
+.+.++|+.|.+.+||++.|+.
T Consensus 79 g~~~v~~~~~~l~~Gdl~~I~~ 100 (312)
T PRK13500 79 GLHVLNDRPYRITRGDLFYIHA 100 (312)
T ss_pred EEEEECCEEEeecCCeEEEECC
Confidence 4578899999999999999983
No 84
>PLN03078 Putative tRNA pseudouridine synthase; Provisional
Probab=20.18 E-value=87 Score=32.19 Aligned_cols=19 Identities=21% Similarity=0.147 Sum_probs=10.8
Q ss_pred cccCCCeEEEEEECCEEEE
Q 025545 131 FKKYEPAFAVVQIGSHQFK 149 (251)
Q Consensus 131 ~k~~~~mYAIVeigGKQYK 149 (251)
++..+.-|+.|.|-|.-|.
T Consensus 349 ~~~~g~~fv~i~I~GqSFm 367 (513)
T PLN03078 349 EKSLGFDFVELSIWGESFM 367 (513)
T ss_pred cccCCceEEEEEEEehhHH
Confidence 3344456666666666553
No 85
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=20.14 E-value=50 Score=35.27 Aligned_cols=20 Identities=25% Similarity=0.581 Sum_probs=0.0
Q ss_pred CCCCCCccccccccccCCCC
Q 025545 71 EDVDEDEDEDEETADESYEG 90 (251)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~ 90 (251)
++|||++++.+||.++++||
T Consensus 538 ~sEddedd~~eEd~edEdDg 557 (811)
T KOG4364|consen 538 DSEDDEDDSLEEDCEDEDDG 557 (811)
T ss_pred ccccccccccccccccccCC
No 86
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=20.12 E-value=52 Score=35.87 Aligned_cols=8 Identities=63% Similarity=0.779 Sum_probs=3.2
Q ss_pred CCCCCCCC
Q 025545 67 DDEGEDVD 74 (251)
Q Consensus 67 ~~~~~~~~ 74 (251)
+|+++++|
T Consensus 40 ~de~~~~~ 47 (895)
T KOG2076|consen 40 DDEIDDED 47 (895)
T ss_pred cccccchh
Confidence 34444433
Done!