Query psy13112
Match_columns 302
No_of_seqs 201 out of 437
Neff 3.0
Searched_HMMs 46136
Date Fri Aug 16 19:54:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13112hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3447|consensus 100.0 8.2E-32 1.8E-36 230.5 1.3 141 140-288 7-150 (150)
2 KOG3447|consensus 99.9 5.6E-23 1.2E-27 176.4 0.5 77 94-170 28-104 (150)
3 PRK05610 rpsQ 30S ribosomal pr 99.8 5E-21 1.1E-25 151.4 8.2 60 94-154 24-83 (84)
4 CHL00142 rps17 ribosomal prote 99.8 6.2E-21 1.3E-25 151.2 8.4 62 94-156 21-82 (84)
5 COG0186 RpsQ Ribosomal protein 99.8 4.8E-21 1E-25 153.3 7.7 61 94-155 26-86 (87)
6 PRK08572 rps17p 30S ribosomal 99.8 6E-20 1.3E-24 151.7 8.3 60 94-154 47-107 (108)
7 TIGR03630 arch_S17P archaeal r 99.8 1.5E-19 3.3E-24 148.1 7.7 57 94-151 45-102 (102)
8 PF00366 Ribosomal_S17: Riboso 99.8 1.5E-19 3.3E-24 137.7 7.0 55 95-150 15-69 (69)
9 TIGR03635 S17_bact 30S ribosom 99.8 2.1E-19 4.5E-24 138.2 6.5 52 95-147 20-71 (71)
10 COG0186 RpsQ Ribosomal protein 99.8 5E-19 1.1E-23 141.7 6.5 53 170-223 34-86 (87)
11 PRK05610 rpsQ 30S ribosomal pr 99.8 8.5E-19 1.8E-23 138.7 6.9 74 145-222 7-83 (84)
12 CHL00142 rps17 ribosomal prote 99.8 1E-18 2.2E-23 138.5 7.0 54 170-224 29-82 (84)
13 PRK08572 rps17p 30S ribosomal 99.7 1.4E-17 3.1E-22 137.6 7.0 51 171-222 56-107 (108)
14 PF00366 Ribosomal_S17: Riboso 99.7 1.5E-17 3.3E-22 126.8 5.6 49 169-218 21-69 (69)
15 TIGR03630 arch_S17P archaeal r 99.7 3.6E-17 7.7E-22 134.2 6.5 49 170-219 53-102 (102)
16 PTZ00241 40S ribosomal protein 99.7 6.1E-17 1.3E-21 141.4 8.1 59 95-154 87-146 (158)
17 TIGR03635 S17_bact 30S ribosom 99.7 2.8E-17 6.1E-22 126.5 5.2 66 146-215 3-71 (71)
18 KOG1740|consensus 99.6 1.2E-17 2.6E-22 137.6 -1.2 63 94-157 20-82 (107)
19 PTZ00241 40S ribosomal protein 99.6 3.2E-15 6.9E-20 130.7 6.8 51 171-222 95-146 (158)
20 KOG1740|consensus 99.5 1.7E-15 3.6E-20 125.1 -1.5 63 160-223 15-80 (107)
21 KOG1728|consensus 97.5 6.1E-05 1.3E-09 66.2 2.3 64 92-156 82-149 (156)
22 KOG1728|consensus 97.3 0.00015 3.2E-09 63.9 2.8 46 178-224 102-149 (156)
23 PF02080 TrkA_C: TrkA-C domain 81.8 3.6 7.9E-05 29.5 4.8 53 148-203 2-59 (71)
24 TIGR02063 RNase_R ribonuclease 77.0 32 0.00069 36.3 11.6 121 114-239 92-217 (709)
25 TIGR00358 3_prime_RNase VacB a 70.1 40 0.00086 35.4 10.3 120 114-239 40-165 (654)
26 TIGR02062 RNase_B exoribonucle 67.2 25 0.00053 37.0 8.2 142 92-239 16-165 (639)
27 cd00320 cpn10 Chaperonin 10 Kd 65.4 17 0.00038 29.2 5.3 67 124-203 3-69 (93)
28 PRK14533 groES co-chaperonin G 61.8 21 0.00045 29.0 5.2 61 125-203 5-65 (91)
29 PRK11642 exoribonuclease R; Pr 59.0 1.2E+02 0.0025 33.3 11.5 140 95-239 85-231 (813)
30 COG0234 GroS Co-chaperonin Gro 58.9 27 0.00059 29.3 5.4 81 125-247 5-90 (96)
31 PRK03818 putative transporter; 58.2 60 0.0013 33.6 9.0 105 111-258 239-363 (552)
32 PTZ00414 10 kDa heat shock pro 54.6 30 0.00066 28.8 5.1 67 119-203 8-74 (100)
33 PRK05054 exoribonuclease II; P 51.5 3.2E+02 0.007 29.0 15.3 142 91-239 18-168 (644)
34 PF10377 ATG11: Autophagy-rela 50.9 54 0.0012 28.0 6.2 27 122-148 41-67 (129)
35 PF11302 DUF3104: Protein of u 50.5 28 0.0006 28.1 4.1 40 123-162 5-45 (75)
36 PRK04972 putative transporter; 48.1 34 0.00074 35.4 5.4 88 112-203 252-360 (558)
37 TIGR02854 spore_II_GA sigma-E 43.2 29 0.00064 32.8 3.8 30 211-240 168-197 (288)
38 PRK00364 groES co-chaperonin G 42.5 87 0.0019 25.3 5.9 68 123-203 3-70 (95)
39 PF11302 DUF3104: Protein of u 42.0 43 0.00092 27.0 3.9 39 191-229 5-44 (75)
40 PF08793 2C_adapt: 2-cysteine 41.7 5.4 0.00012 27.8 -1.0 21 158-178 12-32 (37)
41 PF06819 Arc_PepC: Archaeal Pe 37.9 37 0.0008 29.1 3.2 32 226-257 71-102 (110)
42 COG0511 AccB Biotin carboxyl c 36.6 87 0.0019 26.7 5.3 42 187-228 87-131 (140)
43 PF00681 Plectin: Plectin repe 35.8 17 0.00037 25.4 0.8 16 222-237 10-25 (45)
44 COG0511 AccB Biotin carboxyl c 34.9 1.5E+02 0.0033 25.3 6.5 63 98-167 71-136 (140)
45 smart00250 PLEC Plectin repeat 34.9 15 0.00032 24.8 0.3 15 221-235 9-23 (38)
46 PF03419 Peptidase_U4: Sporula 34.5 56 0.0012 30.5 4.1 30 211-240 167-196 (293)
47 PF06107 DUF951: Bacterial pro 32.7 59 0.0013 25.0 3.2 49 192-250 2-51 (57)
48 COG5036 SPX domain-containing 32.2 19 0.00042 37.3 0.8 29 159-189 168-196 (509)
49 COG1273 Ku-homolog [Replicatio 31.8 21 0.00047 34.7 0.9 29 225-253 48-87 (278)
50 COG1499 NMD3 NMD protein affec 31.0 97 0.0021 30.9 5.3 42 121-170 244-285 (355)
51 PTZ00329 eukaryotic translatio 30.9 1.1E+02 0.0023 27.7 5.0 46 193-266 72-117 (155)
52 PF00166 Cpn10: Chaperonin 10 27.2 54 0.0012 26.0 2.4 65 126-203 5-69 (93)
53 TIGR00523 eIF-1A eukaryotic/ar 26.9 1.1E+02 0.0025 25.2 4.2 35 193-253 59-94 (99)
54 PF08145 BOP1NT: BOP1NT (NUC16 25.6 56 0.0012 31.6 2.5 26 224-255 40-65 (260)
55 PLN00208 translation initiatio 25.3 1.5E+02 0.0033 26.4 5.0 48 193-268 72-119 (145)
56 cd01614 EutN_CcmL Ethanolamine 25.0 2.4E+02 0.0052 22.8 5.7 53 127-203 8-60 (83)
57 PF04189 Gcd10p: Gcd10p family 23.8 2.8E+02 0.006 27.1 6.8 47 122-178 2-49 (299)
58 cd05793 S1_IF1A S1_IF1A: Trans 23.6 1.8E+02 0.004 22.8 4.7 11 193-203 40-50 (77)
59 COG0681 LepB Signal peptidase 23.0 2E+02 0.0044 23.4 5.1 24 121-144 42-65 (166)
60 PF03419 Peptidase_U4: Sporula 22.9 85 0.0018 29.4 3.2 30 142-171 166-195 (293)
61 PF10165 Ric8: Guanine nucleot 22.5 67 0.0015 32.2 2.6 55 221-276 383-445 (446)
62 PF13550 Phage-tail_3: Putativ 21.9 1.9E+02 0.0041 23.5 4.7 50 98-151 113-163 (164)
63 PF14085 DUF4265: Domain of un 20.1 1.8E+02 0.0038 24.1 4.2 29 123-157 25-53 (117)
No 1
>KOG3447|consensus
Probab=99.97 E-value=8.2e-32 Score=230.49 Aligned_cols=141 Identities=28% Similarity=0.374 Sum_probs=124.7
Q ss_pred ccceeEEEeeEEeecCCccCCcccee--eecceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEE
Q psy13112 140 TTLITHKVNKVVYPLGDITDPITGKK--VVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNK 217 (302)
Q Consensus 140 SK~KtW~V~eIV~kaG~i~DPiTGK~--VVGLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~e 217 (302)
|..--|.+-+|| |++..|-..-+ ..+|++||.|||+|++.|||||+..+|++||+|+|+++|.|+.++.+|.|.+
T Consensus 7 s~~~~~lmGk~i---g~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD~~~~c~vGDtVLir~lp~r~t~~V~H~v~~ 83 (150)
T KOG3447|consen 7 SVHAQWLMGKVI---GTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHDALQQCTVGDTVLIRALPVRRTKHVKHEVAE 83 (150)
T ss_pred ecccEEEEeeee---eccccccceeeeehhhcCHHHHHHhccccceeecchhhccccCCEEEEecCCcchhhhhhhhhHh
Confidence 555667777774 44444332222 3579999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCccCCCCCceeeccccccccHHH-HHHHHHHhcCCCCCCcccCCCCCCCcccccccCCCccceEee
Q psy13112 218 VVYPLGDITDPITGKKVVGLRTAVLTADF-YKELYELYGKNPQRKFDYKKAPRRGWQEDKKDFTHRESYIRY 288 (302)
Q Consensus 218 IV~k~G~iiDPVTgK~vv~~~Y~~~~~D~-i~~~~~l~g~~~~~~f~y~ka~~rg~~e~~~dfth~~~y~ky 288 (302)
||++.|+||||||||+|++++| +|+ +++...++|++. ..|+|.+|+.||+.++..||+|.+.|++|
T Consensus 84 VVfk~G~IidPvTGkk~~~~ty----~e~~~~~~~~~~~k~~-k~l~~esa~~r~r~~~~irrleqEkeanv 150 (150)
T KOG3447|consen 84 VVFKVGKIIDPVTGKKCAGDTY----LESPLSKETTQLSKNL-KELNIESAQFRERRALQIRRLEQEKEANV 150 (150)
T ss_pred heeecccccCCCcCccccCcch----hcchHHHHHHHhhhcc-cccchhhcChhhhhhhhhhhhhcccccCC
Confidence 9999999999999999999999 999 666677889988 99999999999999999999999999986
No 2
>KOG3447|consensus
Probab=99.85 E-value=5.6e-23 Score=176.37 Aligned_cols=77 Identities=38% Similarity=0.622 Sum_probs=75.0
Q ss_pred ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecce
Q psy13112 94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLR 170 (302)
Q Consensus 94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLr 170 (302)
-.|.|++++|+++|||+|++.|||||+..+|++||+|+|+++|.+++++.+|.|.+||++.|+|+||+|||+|++..
T Consensus 28 VR~~r~eld~yL~kYf~k~~~yfAhD~~~~c~vGDtVLir~lp~r~t~~V~H~v~~VVfk~G~IidPvTGkk~~~~t 104 (150)
T KOG3447|consen 28 VRVTRLELDPYLLKYFNKRKTYFAHDALQQCTVGDTVLIRALPVRRTKHVKHEVAEVVFKVGKIIDPVTGKKCAGDT 104 (150)
T ss_pred eeeehhhcCHHHHHHhccccceeecchhhccccCCEEEEecCCcchhhhhhhhhHhheeecccccCCCcCccccCcc
Confidence 35889999999999999999999999999999999999999999999999999999999999999999999999988
No 3
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=99.84 E-value=5e-21 Score=151.36 Aligned_cols=60 Identities=20% Similarity=0.191 Sum_probs=57.7
Q ss_pred ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeec
Q psy13112 94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL 154 (302)
Q Consensus 94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~ka 154 (302)
..|+|+++||.|+||++++++|+||||+|+|++||+|+|.|| +||||+|+|.|.+|++++
T Consensus 24 V~v~r~~~h~kY~K~~~r~kk~~aHD~~n~~k~GD~V~I~e~-rPlSK~K~~~v~~i~~~~ 83 (84)
T PRK05610 24 VLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIMET-RPLSKTKRWRLVEIVEKA 83 (84)
T ss_pred EEEEEEEEeccccEEEEcceEEEEECCCCCCCCCCEEEEEEc-ccCCCCEEEEEEEEEecc
Confidence 468999999999999999999999999999999999999999 999999999999999865
No 4
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=99.84 E-value=6.2e-21 Score=151.18 Aligned_cols=62 Identities=19% Similarity=0.192 Sum_probs=59.1
Q ss_pred ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCC
Q psy13112 94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD 156 (302)
Q Consensus 94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~ 156 (302)
..|+|+++||.|+||++++++|+||||+|+|++||+|+|.|| +||||+|+|.|.+|++++-.
T Consensus 21 V~v~r~~~h~kY~K~~~r~kk~~aHDe~n~~~~GD~V~I~e~-RPlSKtK~~~v~~i~~~~~~ 82 (84)
T CHL00142 21 VAVENRYKHPIYGKIITKTKKYLVHDEENECNIGDQVLIEET-RPLSKTKRWILKEILSKSSL 82 (84)
T ss_pred EEEEEEEEcCcccEEEEeeEEEEEeCCCCCCCCCCEEEEEEc-CCCCCcEEEEEEEEEEeeec
Confidence 468999999999999999999999999999999999999999 99999999999999998754
No 5
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=4.8e-21 Score=153.30 Aligned_cols=61 Identities=25% Similarity=0.177 Sum_probs=58.6
Q ss_pred ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecC
Q psy13112 94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG 155 (302)
Q Consensus 94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG 155 (302)
-.|+++.+||.|+||++++++|+||||+|+|++||+|.|.|| |||||+|+|.|.+|++.++
T Consensus 26 V~ve~~~~hp~Y~K~v~r~kK~~aHde~~~~k~GD~V~I~Et-RPLSKtK~~~vv~i~~~a~ 86 (87)
T COG0186 26 VEVERKVYHPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAET-RPLSKTKRFVVVEIVEKAV 86 (87)
T ss_pred EEEEEEEecccceEEEEEEeeeEeecccccCCCCCEEEEEEc-cccCCcceEEEEEEeeecc
Confidence 358999999999999999999999999999999999999999 9999999999999999875
No 6
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=99.81 E-value=6e-20 Score=151.67 Aligned_cols=60 Identities=22% Similarity=0.153 Sum_probs=57.8
Q ss_pred ceeeeeeeccccceEEeeeceEEeeCCC-CCCCCCCEEEEeecCcccccceeEEEeeEEeec
Q psy13112 94 YMQPRVANTRNEVRYFPKFTVMYAHDPD-KICKTGDIVLIEELPQKLTTLITHKVNKVVYPL 154 (302)
Q Consensus 94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~-N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~ka 154 (302)
..|+|+++||.|+||++++++|+||||+ |+|++||+|+|.|| |||||+|+|.|.+|++++
T Consensus 47 V~v~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~-RPiSKtK~w~v~~i~~~~ 107 (108)
T PRK08572 47 VEREYLHYVPKYERYEKRRSRIHAHNPPCIDAKVGDKVKIAEC-RPLSKTKSFVVVEKKERA 107 (108)
T ss_pred EEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEc-CCCCCceEEEEEEEEEcC
Confidence 5689999999999999999999999999 99999999999999 999999999999999875
No 7
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=99.79 E-value=1.5e-19 Score=148.09 Aligned_cols=57 Identities=28% Similarity=0.282 Sum_probs=54.9
Q ss_pred ceeeeeeeccccceEEeeeceEEeeCCC-CCCCCCCEEEEeecCcccccceeEEEeeEE
Q psy13112 94 YMQPRVANTRNEVRYFPKFTVMYAHDPD-KICKTGDIVLIEELPQKLTTLITHKVNKVV 151 (302)
Q Consensus 94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~-N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV 151 (302)
..|+|+++||.|+||++++++|+||||+ |+|++||+|+|.|| |||||+|+|.|.+|+
T Consensus 45 V~V~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~-RPlSKtK~w~vv~i~ 102 (102)
T TIGR03630 45 VEREYLYYDRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGET-RPLSKTKSFVVLGKV 102 (102)
T ss_pred EEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEc-CCCCCceEEEEEEeC
Confidence 4689999999999999999999999999 99999999999999 999999999999985
No 8
>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 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 ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....
Probab=99.79 E-value=1.5e-19 Score=137.75 Aligned_cols=55 Identities=27% Similarity=0.383 Sum_probs=52.5
Q ss_pred eeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeE
Q psy13112 95 MQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKV 150 (302)
Q Consensus 95 ~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eI 150 (302)
.|+|+++||.|+|+++++++|+||||+|+|++||+|+|.|| +||||+|+|.|.+|
T Consensus 15 ~v~~~~~~~ky~K~~~~~kk~~aHD~~~~~~vGD~V~I~e~-rPiSk~K~~~v~~v 69 (69)
T PF00366_consen 15 RVERLVYHPKYKKYIKRTKKYMAHDENNICKVGDKVRIREC-RPISKTKRFVVVEV 69 (69)
T ss_dssp EEEEEEEETTTEEEEEEEEEEEEE-TTSSSTTTSEEEEEEE-EEEETTEEEEEEEE
T ss_pred EEEEEEEcceEeeccCccccEEEeCCccCCCCCCEEEEEee-eccCCcEeEEEEEC
Confidence 58899999999999999999999999999999999999999 99999999999986
No 9
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=99.78 E-value=2.1e-19 Score=138.22 Aligned_cols=52 Identities=23% Similarity=0.294 Sum_probs=50.5
Q ss_pred eeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEE
Q psy13112 95 MQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKV 147 (302)
Q Consensus 95 ~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V 147 (302)
.|+|++.||.|+||++++++|+||||+|.|++||+|+|.|| +||||+|+|.|
T Consensus 20 ~v~~~~~h~ky~k~~~r~kk~~aHD~~~~~k~GD~V~I~ec-rPlSK~K~~~~ 71 (71)
T TIGR03635 20 LVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIET-RPLSKTKRWRL 71 (71)
T ss_pred EEEEEEEeccccEEEEccEEEEEECCCCCCCCCCEEEEEEc-CCcCCceEeEC
Confidence 58899999999999999999999999999999999999999 99999999986
No 10
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=99.77 E-value=5e-19 Score=141.73 Aligned_cols=53 Identities=30% Similarity=0.305 Sum_probs=50.5
Q ss_pred eeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112 170 RVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG 223 (302)
Q Consensus 170 rp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G 223 (302)
-|.|+||+++++||+||||+|+|++||+|.|.|| |||||+|+|.|++|++.++
T Consensus 34 hp~Y~K~v~r~kK~~aHde~~~~k~GD~V~I~Et-RPLSKtK~~~vv~i~~~a~ 86 (87)
T COG0186 34 HPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAET-RPLSKTKRFVVVEIVEKAV 86 (87)
T ss_pred cccceEEEEEEeeeEeecccccCCCCCEEEEEEc-cccCCcceEEEEEEeeecc
Confidence 4689999999999999999999999999999999 7999999999999999865
No 11
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=99.76 E-value=8.5e-19 Score=138.72 Aligned_cols=74 Identities=23% Similarity=0.200 Sum_probs=59.0
Q ss_pred EEEeeEEeecCCccCCccceeeec---ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeec
Q psy13112 145 HKVNKVVYPLGDITDPITGKKVVG---LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYP 221 (302)
Q Consensus 145 W~V~eIV~kaG~i~DPiTGK~VVG---Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k 221 (302)
..+..+|-.. .+ | .|....|. ..+.|+||++++++|+||||+|+|++||+|+|.|| |||||+|+|.|.+|+.+
T Consensus 7 ~~l~G~Vvs~-km-~-KTvvV~v~r~~~h~kY~K~~~r~kk~~aHD~~n~~k~GD~V~I~e~-rPlSK~K~~~v~~i~~~ 82 (84)
T PRK05610 7 KTLQGRVVSD-KM-D-KTIVVLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIMET-RPLSKTKRWRLVEIVEK 82 (84)
T ss_pred CEEEEEEEcc-cC-C-ceEEEEEEEEEEeccccEEEEcceEEEEECCCCCCCCCCEEEEEEc-ccCCCCEEEEEEEEEec
Confidence 3455555544 22 2 45443332 45699999999999999999999999999999999 79999999999999986
Q ss_pred C
Q psy13112 222 L 222 (302)
Q Consensus 222 ~ 222 (302)
+
T Consensus 83 ~ 83 (84)
T PRK05610 83 A 83 (84)
T ss_pred c
Confidence 4
No 12
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=99.76 E-value=1e-18 Score=138.55 Aligned_cols=54 Identities=26% Similarity=0.337 Sum_probs=50.7
Q ss_pred eeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCCC
Q psy13112 170 RVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD 224 (302)
Q Consensus 170 rp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~ 224 (302)
.+.|+||++++++|+||||+|+|++||+|+|.|| |||||+|+|.|++|+.++-.
T Consensus 29 h~kY~K~~~r~kk~~aHDe~n~~~~GD~V~I~e~-RPlSKtK~~~v~~i~~~~~~ 82 (84)
T CHL00142 29 HPIYGKIITKTKKYLVHDEENECNIGDQVLIEET-RPLSKTKRWILKEILSKSSL 82 (84)
T ss_pred cCcccEEEEeeEEEEEeCCCCCCCCCCEEEEEEc-CCCCCcEEEEEEEEEEeeec
Confidence 4689999999999999999999999999999999 79999999999999988643
No 13
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=99.71 E-value=1.4e-17 Score=137.63 Aligned_cols=51 Identities=24% Similarity=0.212 Sum_probs=49.0
Q ss_pred eecceeeeeeeeEEeeCCC-CCCCCCCEEEEeecCCCcCcceeEEEEEeeecC
Q psy13112 171 VDLGKYFPKFTVMYAHDPD-KICKTGDIVLIEELPQKLTTLITHKVNKVVYPL 222 (302)
Q Consensus 171 p~y~K~ikRskKY~AHDen-N~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~ 222 (302)
+.|+||++++++|+||||+ |+|++||+|+|.|| |||||+|+|.|++|+.++
T Consensus 56 pkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~-RPiSKtK~w~v~~i~~~~ 107 (108)
T PRK08572 56 PKYERYEKRRSRIHAHNPPCIDAKVGDKVKIAEC-RPLSKTKSFVVVEKKERA 107 (108)
T ss_pred CCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEc-CCCCCceEEEEEEEEEcC
Confidence 6899999999999999999 99999999999999 799999999999999874
No 14
>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 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 ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....
Probab=99.70 E-value=1.5e-17 Score=126.78 Aligned_cols=49 Identities=31% Similarity=0.443 Sum_probs=45.8
Q ss_pred ceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEe
Q psy13112 169 LRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKV 218 (302)
Q Consensus 169 Lrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eI 218 (302)
..+.|+|+++++++|+||||+|+|++||+|+|+|| +||||+|+|.|.+|
T Consensus 21 ~~~ky~K~~~~~kk~~aHD~~~~~~vGD~V~I~e~-rPiSk~K~~~v~~v 69 (69)
T PF00366_consen 21 YHPKYKKYIKRTKKYMAHDENNICKVGDKVRIREC-RPISKTKRFVVVEV 69 (69)
T ss_dssp EETTTEEEEEEEEEEEEE-TTSSSTTTSEEEEEEE-EEEETTEEEEEEEE
T ss_pred EcceEeeccCccccEEEeCCccCCCCCCEEEEEee-eccCCcEeEEEEEC
Confidence 46789999999999999999999999999999999 79999999999986
No 15
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=99.69 E-value=3.6e-17 Score=134.20 Aligned_cols=49 Identities=29% Similarity=0.329 Sum_probs=46.6
Q ss_pred eeecceeeeeeeeEEeeCCC-CCCCCCCEEEEeecCCCcCcceeEEEEEee
Q psy13112 170 RVDLGKYFPKFTVMYAHDPD-KICKTGDIVLIEELPQKLTTLITHKVNKVV 219 (302)
Q Consensus 170 rp~y~K~ikRskKY~AHDen-N~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV 219 (302)
.+.|+|+++++++|+||||+ |.|++||+|+|.|| |||||+|+|.|++|+
T Consensus 53 hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~-RPlSKtK~w~vv~i~ 102 (102)
T TIGR03630 53 DRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGET-RPLSKTKSFVVLGKV 102 (102)
T ss_pred cCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEc-CCCCCceEEEEEEeC
Confidence 45899999999999999999 99999999999999 799999999999985
No 16
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=99.69 E-value=6.1e-17 Score=141.40 Aligned_cols=59 Identities=22% Similarity=0.215 Sum_probs=56.0
Q ss_pred eeeeeeeccccceEEeeeceEEeeC-CCCCCCCCCEEEEeecCcccccceeEEEeeEEeec
Q psy13112 95 MQPRVANTRNEVRYFPKFTVMYAHD-PDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL 154 (302)
Q Consensus 95 ~VeR~vkHp~YkKy~kKskKY~AHD-e~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~ka 154 (302)
.|+++.+||.|+||++++++|+||| |.|.|++||+|.|.|| |||||+|+|.|.+|+.++
T Consensus 87 ~ve~~~~h~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~Ec-RPLSKTKrf~Vv~V~~~~ 146 (158)
T PTZ00241 87 RRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVGQC-RPLSKTVRFNVLKVEKNE 146 (158)
T ss_pred EEEEEEecCccceEEEeeecEEEeCCccCCCCCCCEEEEEEc-CCCCCceeEEEEEEEecc
Confidence 5678999999999999999999998 5899999999999999 999999999999999875
No 17
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=99.68 E-value=2.8e-17 Score=126.46 Aligned_cols=66 Identities=27% Similarity=0.281 Sum_probs=52.1
Q ss_pred EEeeEEeecCCccCCccceeee---cceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEE
Q psy13112 146 KVNKVVYPLGDITDPITGKKVV---GLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKV 215 (302)
Q Consensus 146 ~V~eIV~kaG~i~DPiTGK~VV---GLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V 215 (302)
.+..+|-... + | .|....| ...+.|+|+++++++|+||||+|.|++||+|+|.|| |||||+|+|.|
T Consensus 3 ~l~G~Vvs~k-m-~-KTvvV~v~~~~~h~ky~k~~~r~kk~~aHD~~~~~k~GD~V~I~ec-rPlSK~K~~~~ 71 (71)
T TIGR03635 3 TLQGVVVSDK-M-D-KTIVVLVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIET-RPLSKTKRWRL 71 (71)
T ss_pred EEEEEEEccc-C-C-ceEEEEEEEEEEeccccEEEEccEEEEEECCCCCCCCCCEEEEEEc-CCcCCceEeEC
Confidence 4555555442 2 2 4554333 245689999999999999999999999999999999 79999999986
No 18
>KOG1740|consensus
Probab=99.64 E-value=1.2e-17 Score=137.62 Aligned_cols=63 Identities=19% Similarity=0.247 Sum_probs=60.6
Q ss_pred ceeeeeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCCc
Q psy13112 94 YMQPRVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDI 157 (302)
Q Consensus 94 ~~VeR~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i 157 (302)
..|+|+++||.|++|++++.+|+|||+.|+|++||.|.|+.| |||||+|.|.+.+||.+++.+
T Consensus 20 V~V~rl~~n~~ynryv~~~~kymahD~~n~cnvGD~Vrleps-RPlSk~K~f~i~eII~~a~r~ 82 (107)
T KOG1740|consen 20 VRVDRLFFNPKYNRYVKRTSKYMAHDDKNQCNVGDRVRLEPS-RPLSKTKHFIIAEIIKKARRY 82 (107)
T ss_pred EEeeeccccHHHHHHHHHhhheeecCccccccccceEEeccC-CcccccceeehHHHHHHHhhh
Confidence 368999999999999999999999999999999999999999 999999999999999998875
No 19
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=99.57 E-value=3.2e-15 Score=130.70 Aligned_cols=51 Identities=24% Similarity=0.260 Sum_probs=48.3
Q ss_pred eecceeeeeeeeEEeeC-CCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecC
Q psy13112 171 VDLGKYFPKFTVMYAHD-PDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPL 222 (302)
Q Consensus 171 p~y~K~ikRskKY~AHD-enN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~ 222 (302)
+.|+||++|+++|+||| |.|.|++||+|.|.|| |||||+|+|.|++|+.++
T Consensus 95 ~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~Ec-RPLSKTKrf~Vv~V~~~~ 146 (158)
T PTZ00241 95 KKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVGQC-RPLSKTVRFNVLKVEKNE 146 (158)
T ss_pred CccceEEEeeecEEEeCCccCCCCCCCEEEEEEc-CCCCCceeEEEEEEEecc
Confidence 48999999999999998 5899999999999999 799999999999999875
No 20
>KOG1740|consensus
Probab=99.49 E-value=1.7e-15 Score=125.06 Aligned_cols=63 Identities=21% Similarity=0.265 Sum_probs=56.1
Q ss_pred Cccceeee---cceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCC
Q psy13112 160 PITGKKVV---GLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLG 223 (302)
Q Consensus 160 PiTGK~VV---GLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G 223 (302)
+.|.+.-| .+++.|++|++++.+|+|||+.|+|++||.|.|+.| |||||+|+|++.+||.+++
T Consensus 15 qKTv~V~V~rl~~n~~ynryv~~~~kymahD~~n~cnvGD~Vrleps-RPlSk~K~f~i~eII~~a~ 80 (107)
T KOG1740|consen 15 QKTVKVRVDRLFFNPKYNRYVKRTSKYMAHDDKNQCNVGDRVRLEPS-RPLSKTKHFIIAEIIKKAR 80 (107)
T ss_pred CceeEEEeeeccccHHHHHHHHHhhheeecCccccccccceEEeccC-CcccccceeehHHHHHHHh
Confidence 45655544 367899999999999999999999999999999999 7999999999999999854
No 21
>KOG1728|consensus
Probab=97.47 E-value=6.1e-05 Score=66.20 Aligned_cols=64 Identities=27% Similarity=0.294 Sum_probs=52.4
Q ss_pred CCceeeeeeec--cccceEEeeeceEEeeC-CCCC-CCCCCEEEEeecCcccccceeEEEeeEEeecCC
Q psy13112 92 RPYMQPRVANT--RNEVRYFPKFTVMYAHD-PDKI-CKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD 156 (302)
Q Consensus 92 ~~~~VeR~vkH--p~YkKy~kKskKY~AHD-e~N~-cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~ 156 (302)
|--+|.|-++| +.|+.|=++.+.+-||= |-.. .++||+|.|-|| +||||++++.|.+++..+|.
T Consensus 82 rTIvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiVtvGec-rPLSKtvrfnVLkv~k~~g~ 149 (156)
T KOG1728|consen 82 RTIVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIVTVGEC-RPLSKTVRFNVLKVIKAAGS 149 (156)
T ss_pred EEEEEEhhhhhHhHHhhHHHHhccCCccccchhhhccccCCEEEEeec-ccccceEEEEEEEEeecCCC
Confidence 45566677777 56777888888888884 3333 789999999999 99999999999999998876
No 22
>KOG1728|consensus
Probab=97.32 E-value=0.00015 Score=63.87 Aligned_cols=46 Identities=28% Similarity=0.358 Sum_probs=36.5
Q ss_pred eeeeeEEeeC-CCCC-CCCCCEEEEeecCCCcCcceeEEEEEeeecCCC
Q psy13112 178 PKFTVMYAHD-PDKI-CKTGDIVLIEELPQKLTTLITHKVNKVVYPLGD 224 (302)
Q Consensus 178 kRskKY~AHD-enN~-ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~ 224 (302)
+|.+.+-||= |-.. .++||+|.|-|| |||||++++.|.+++..+|.
T Consensus 102 krHkN~svh~SPcFrdi~~gDiVtvGec-rPLSKtvrfnVLkv~k~~g~ 149 (156)
T KOG1728|consen 102 KRHKNMSVHVSPCFRDIQEGDIVTVGEC-RPLSKTVRFNVLKVIKAAGS 149 (156)
T ss_pred HhccCCccccchhhhccccCCEEEEeec-ccccceEEEEEEEEeecCCC
Confidence 4555555663 2233 789999999999 79999999999999998763
No 23
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=81.82 E-value=3.6 Score=29.45 Aligned_cols=53 Identities=23% Similarity=0.322 Sum_probs=31.7
Q ss_pred eeEEeecCCccCCccceeeec--ceeecce---eeeeeeeEEeeCCCCCCCCCCEEEEeec
Q psy13112 148 NKVVYPLGDITDPITGKKVVG--LRVDLGK---YFPKFTVMYAHDPDKICKTGDIVLIEEL 203 (302)
Q Consensus 148 ~eIV~kaG~i~DPiTGK~VVG--Lrp~y~K---~ikRskKY~AHDenN~ckvGDiV~I~Ec 203 (302)
.++.-..+. |.-|+.+.. ++..++- -+.|...+..=+++-..+.||+|.|.-.
T Consensus 2 ~e~~V~~~s---~~~gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~ 59 (71)
T PF02080_consen 2 VEVRVPENS---PLVGKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGD 59 (71)
T ss_dssp EEEE--TTB---TTTTEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEE
T ss_pred EEEEECCCC---CCCCCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEEC
Confidence 344444555 677888877 3332222 2356677777788999999999999977
No 24
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=77.03 E-value=32 Score=36.25 Aligned_cols=121 Identities=17% Similarity=0.113 Sum_probs=71.7
Q ss_pred eEEee-CCCCCCCCCCEEEEeecCcc-cccceeEEEeeEEeecCCccCCccceeeecceeecceee-ee-eeeEEeeC-C
Q psy13112 114 VMYAH-DPDKICKTGDIVLIEELPQK-LTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYF-PK-FTVMYAHD-P 188 (302)
Q Consensus 114 KY~AH-De~N~cKiGDiVlI~E~PrP-LSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K~i-kR-skKY~AHD-e 188 (302)
.+++. +.-+.+.-||+|+++=.+.+ -.+...=+|++|+.++.+ -+.|.-.....-.+-.-. .+ ...+.+.. .
T Consensus 92 di~I~~~~~~~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~~---~~VG~~~~~~~~~~v~p~d~~~~~~I~i~~~~ 168 (709)
T TIGR02063 92 DIFIPPRQMNGAMHGDRVLVRITGKPDGGDRFEARVIKILERAND---QIVGTFYIENGIGFVIPDDKRIYLDIFIPPEQ 168 (709)
T ss_pred cEEEChHHhCcCCCCCEEEEEEecccCCCCCceEEEEEEEeeCCC---EEEEEEEEcCcEEEEEECCCCCCCCEEECCcc
Confidence 45553 34456888999998855222 123335678889888765 356643322221110000 11 11233332 3
Q ss_pred CCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCCCccCCCCCceeecccc
Q psy13112 189 DKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRT 239 (302)
Q Consensus 189 nN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y 239 (302)
...++.||+|.++=..+|..... -.-+|+...|+.-||-+--..+-.+|
T Consensus 169 ~~~~~~g~~v~v~i~~~p~~~~~--~~g~i~~~lg~~~d~~~~~~~il~~~ 217 (709)
T TIGR02063 169 ILGAEEGDKVLVEITKYPDRNRP--AIGKVVEILGHADDPGIDILIIIRKH 217 (709)
T ss_pred ccCCCCCCEEEEEEccCCCCCCC--ceEEEEEEeCCCCcccchHHHHHHHc
Confidence 35788999999988766665433 46678888888889987776665555
No 25
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=70.06 E-value=40 Score=35.45 Aligned_cols=120 Identities=18% Similarity=0.116 Sum_probs=70.0
Q ss_pred eEEe-eCCCCCCCCCCEEEEeecCcccccc-eeEEEeeEEeecCCccCCccceeeecceeecce-eeeeee-eEEeeC--
Q psy13112 114 VMYA-HDPDKICKTGDIVLIEELPQKLTTL-ITHKVNKVVYPLGDITDPITGKKVVGLRVDLGK-YFPKFT-VMYAHD-- 187 (302)
Q Consensus 114 KY~A-HDe~N~cKiGDiVlI~E~PrPLSK~-KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K-~ikRsk-KY~AHD-- 187 (302)
.+++ -+.-|.|=-||+|+++-.+.. .+. ..=+|++||+++-. -+.|.-+......+-. .-.+-. .+.+=.
T Consensus 40 difI~~~~~~~a~~GD~V~v~i~~~~-~~~~~~g~v~~il~r~~~---~~vG~~~~~~~~~~v~p~~~~~~~~i~i~~~~ 115 (654)
T TIGR00358 40 DYFIPPPQMKKVMHGDLVEACPLSQP-QRGRFEAEVERILEPALT---RFVGKFLGENDFGFVVPDDPRIYLDIIVPKAS 115 (654)
T ss_pred cEEEchHHhCcCCCCCEEEEEEeecC-CCCCceEEEEEEeccCCC---EEEEEEEEeCCeEEEEECCCCCCCcEEEcCCc
Confidence 4555 344577888999988754221 122 36789999998655 3556443322211100 001111 122211
Q ss_pred CCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCCCccCCCCCceeecccc
Q psy13112 188 PDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRT 239 (302)
Q Consensus 188 enN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y 239 (302)
....++.||+|.++=...|+... .-..+|++..|+.-||-+--..+-.+|
T Consensus 116 ~~~~~~~g~~V~v~i~~~p~~~~--~~~g~i~~~lG~~~d~~~~~~~il~~~ 165 (654)
T TIGR00358 116 VKNELAEGDKVVVELTEYPLRRN--LFYGEITQILGNNDDPLIPWWVTLARH 165 (654)
T ss_pred cccCCCCCCEEEEEEccCCCCCC--CceEEEEEEEcCCCCcccHHHHHHHHc
Confidence 12367899999888776676543 357789999999999977665555544
No 26
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=67.24 E-value=25 Score=37.03 Aligned_cols=142 Identities=12% Similarity=0.012 Sum_probs=78.4
Q ss_pred CCceeeeeeeccccceEEe--eeceEEee-CCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeec
Q psy13112 92 RPYMQPRVANTRNEVRYFP--KFTVMYAH-DPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVG 168 (302)
Q Consensus 92 ~~~~VeR~vkHp~YkKy~k--KskKY~AH-De~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVG 168 (302)
.++..=++..|+.=--|+. ..+.+++. +.-|.|--||.|+++-.+. .+.+.=.+++||+++-.- +.|.-...
T Consensus 16 ~~~~~G~i~~~~kGfgFv~~~~~~difI~~~~l~~A~~GD~V~v~i~~~--~~r~~~~v~~iver~~~~---~vG~~~~~ 90 (639)
T TIGR02062 16 TPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDKIIAVIHSE--KERESAEPEELIEPFLTR---FVGKVQGK 90 (639)
T ss_pred CceEEEEEEECCCccEEEEECCCCcEEEChHHHccCCCCCEEEEEEecC--CCCcEEEEEEEEccCCCE---EEEEEEEe
Confidence 3445555556654333442 12356663 3456788899999985522 233334899999876552 55554433
Q ss_pred ceeecce-eeeeeeeEEeeCC----CCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCCCccCCCCCceeecccc
Q psy13112 169 LRVDLGK-YFPKFTVMYAHDP----DKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRT 239 (302)
Q Consensus 169 Lrp~y~K-~ikRskKY~AHDe----nN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y 239 (302)
..-.+-. .-++-.......+ ...++.||.|.++=...|. +....-..+|++..|+.-||-.--..+-.+|
T Consensus 91 ~~~~~v~p~d~~~~~~i~~~~~~~~~~~~~~gd~V~v~I~~~p~-~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~ 165 (639)
T TIGR02062 91 DDKLAIVPDHPLLKDAIPCRAAKGLNHEFQEGDWAVAELRRHPL-KGDRSFYAELTQYITFADDHLAPWWVTLARH 165 (639)
T ss_pred CCeEEEEECCCCCCccEEecCccccccCCCCCCEEEEEEeccCC-CCCCCceEEEEEEeCCCCCCccHHHHHHHHc
Confidence 2211100 0011122223322 2367889999976553343 3323346678888899889877666666555
No 27
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=65.38 E-value=17 Score=29.17 Aligned_cols=67 Identities=21% Similarity=0.186 Sum_probs=38.5
Q ss_pred CCCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeec
Q psy13112 124 CKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEEL 203 (302)
Q Consensus 124 cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec 203 (302)
.-.||.|+|+.. ..-.++..= |+=+...-.-|.+|+.|..+.-.+.. + -......+++||+|++.+.
T Consensus 3 ~Pl~DrVLV~~~-~~e~~T~~G----I~Lp~~~~~k~~~g~VvAVG~g~~~~----~----g~~~~~~vk~GD~Vl~~~~ 69 (93)
T cd00320 3 KPLGDRVLVKRI-EAEEKTKGG----IILPDSAKEKPQEGKVVAVGPGRRNE----N----GERVPLSVKVGDKVLFPKY 69 (93)
T ss_pred eecCCEEEEEEc-cccceecce----EEeCCCcCCCceEEEEEEECCCeECC----C----CCCccccccCCCEEEECCC
Confidence 347999999987 433444332 33333222346777777666521111 0 0112347999999999876
No 28
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=61.76 E-value=21 Score=29.05 Aligned_cols=61 Identities=21% Similarity=0.306 Sum_probs=38.4
Q ss_pred CCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeec
Q psy13112 125 KTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEEL 203 (302)
Q Consensus 125 KiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec 203 (302)
-.||.|+|+.. ..-++++.= |+=+...-.-|.+|+.|..+... -......++||.|++.+.
T Consensus 5 Pl~DRVLVk~~-~~e~~T~gG----I~Lp~~a~ek~~~G~VvavG~g~-------------~~~~~~Vk~GD~Vl~~~y 65 (91)
T PRK14533 5 PLGERLLIKPI-KEEKKTEGG----IVLPDSAKEKPMKAEVVAVGKLD-------------DEEDFDIKVGDKVIFSKY 65 (91)
T ss_pred EcCCEEEEEEc-cccceeccc----EEecccccCCcceEEEEEECCCC-------------ccccccccCCCEEEEccC
Confidence 47999999876 433455443 33333322247788877666411 023567999999999876
No 29
>PRK11642 exoribonuclease R; Provisional
Probab=59.02 E-value=1.2e+02 Score=33.31 Aligned_cols=140 Identities=17% Similarity=0.158 Sum_probs=78.0
Q ss_pred eeeeeeeccccceEEeee---ceEEeeC-CCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecce
Q psy13112 95 MQPRVANTRNEVRYFPKF---TVMYAHD-PDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLR 170 (302)
Q Consensus 95 ~VeR~vkHp~YkKy~kKs---kKY~AHD-e~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLr 170 (302)
++-++..|+.=--|+... ..+++.. .-|.+=-||.|+++-.+.--.+...=+|++||+++-. -+.|.-+....
T Consensus 85 ~~G~v~~~~~GfgFv~~e~~~~difI~~~~l~~A~~GD~V~v~i~~~~~~~r~eg~Vv~IleR~~~---~~vG~~~~~~~ 161 (813)
T PRK11642 85 LKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTS---QIVGRYFTDAG 161 (813)
T ss_pred EEEEEEECCCccEEEEECCCCCCEEEChHHHccCCCCCEEEEEEccCCCCCCcEEEEEEEEecCCC---EEEEEEEEeCC
Confidence 445666665422344322 3566632 3345666999999854110112235689999998755 25554433222
Q ss_pred eecceee-ee-eeeEE-eeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCCCccCCCCCceeecccc
Q psy13112 171 VDLGKYF-PK-FTVMY-AHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRT 239 (302)
Q Consensus 171 p~y~K~i-kR-skKY~-AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y 239 (302)
..+-.=. .+ ...+. ..+..+.++.||+|.++=...|..... -.-+|++..|..-||-+--.++-.+|
T Consensus 162 ~~~v~P~d~r~~~~i~i~~~~~~~~~~gd~V~v~I~~~p~~~~~--~~g~iv~vLG~~~d~~~d~~~il~~~ 231 (813)
T PRK11642 162 VGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTK--AVGKIVEVLGDNMGTGMAVDIALRTH 231 (813)
T ss_pred eEEEEECCCCCCCcEEeccccccCCCCCCEEEEEEecCCCcCCC--CCEEEEEEecCCCCcchHHHHHHHHc
Confidence 1110000 11 11122 234445788999999987766665433 46778888999999976555554444
No 30
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=58.94 E-value=27 Score=29.29 Aligned_cols=81 Identities=26% Similarity=0.314 Sum_probs=51.7
Q ss_pred CCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecceeecceeeeeeeeEEeeCCC-----CCCCCCCEEE
Q psy13112 125 KTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPD-----KICKTGDIVL 199 (302)
Q Consensus 125 KiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K~ikRskKY~AHDen-----N~ckvGDiV~ 199 (302)
-.||.|+|+-. .-=+|++. .||-+.-.-..|-.|+.|..+. +.. +++ -..++||+|+
T Consensus 5 PL~DRVlVk~~-e~EekT~g----GIvlpdsakeK~~~g~VvAVG~---G~~----------~~~g~~~~~~VkvGD~Vl 66 (96)
T COG0234 5 PLGDRVLVKRV-EEEEKTAG----GIVLPDSAKEKPQEGEVVAVGP---GRR----------DENGELVPLDVKVGDRVL 66 (96)
T ss_pred ecCCEEEEEEc-hhhccccC----cEEecCccccCCcceEEEEEcc---cee----------cCCCCEeccccccCCEEE
Confidence 36899998866 32344433 4444444445678888887774 111 222 2589999999
Q ss_pred EeecCCCcCcceeEEEEEeeecCCCccCCCCCceeeccccccccHHHH
Q psy13112 200 IEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFY 247 (302)
Q Consensus 200 I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y~~~~~D~i 247 (302)
+.+-- | |=.++.+.+|..|.++||
T Consensus 67 f~ky~------------------G------~evk~dgeeylil~e~DI 90 (96)
T COG0234 67 FGKYA------------------G------TEVKIDGEEYLILSESDI 90 (96)
T ss_pred ECccC------------------C------cEEEECCEEEEEechHHe
Confidence 99872 2 234556788888888776
No 31
>PRK03818 putative transporter; Validated
Probab=58.21 E-value=60 Score=33.58 Aligned_cols=105 Identities=20% Similarity=0.278 Sum_probs=63.7
Q ss_pred eeceEEeeCCCCCCCCCCEEEEeecCcccccc---------------eeEEEeeEEeecCCccCCccceeeecce--eec
Q psy13112 111 KFTVMYAHDPDKICKTGDIVLIEELPQKLTTL---------------ITHKVNKVVYPLGDITDPITGKKVVGLR--VDL 173 (302)
Q Consensus 111 KskKY~AHDe~N~cKiGDiVlI~E~PrPLSK~---------------KtW~V~eIV~kaG~i~DPiTGK~VVGLr--p~y 173 (302)
|..+.....++...+.||+|.+.-.+.-+.+. ....+.+.+-..+. ..-||.+..++ .-|
T Consensus 239 R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~~~~~~~~~~~~~~E~Vvv~~S---~liGkTL~eL~~r~~~ 315 (552)
T PRK03818 239 RGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEVDTSLSTRGTDLRSERVVVTNE---KVLGKKLRDLHLKNKY 315 (552)
T ss_pred ECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCccCccccccCcceEEEEEEEcCh---hccCCcHHHhcccccC
Confidence 34456666788999999999995442211110 01133344433333 46777776664 222
Q ss_pred cee---eeeeeeEEeeCCCCCCCCCCEEEEeecCCCcCcceeEEEEEeeecCCCccCCCCCceeeccccccccHHHHHHH
Q psy13112 174 GKY---FPKFTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKEL 250 (302)
Q Consensus 174 ~K~---ikRskKY~AHDenN~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y~~~~~D~i~~~ 250 (302)
+=. ++|.-......++-..+.||++++.-. +++++.+
T Consensus 316 Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~----------------------------------------~~~i~~l 355 (552)
T PRK03818 316 GVVISRLNRAGVELVASPDLSLQFGDILNLVGR----------------------------------------PEAIDAV 355 (552)
T ss_pred CeEEEEEeECCeecCCCCCCEEecCCEEEEEEC----------------------------------------HHHHHHH
Confidence 222 233333332355778999999999866 8999999
Q ss_pred HHHhcCCC
Q psy13112 251 YELYGKNP 258 (302)
Q Consensus 251 ~~l~g~~~ 258 (302)
.+.+|...
T Consensus 356 ~~~Lg~~~ 363 (552)
T PRK03818 356 ANVLGNAQ 363 (552)
T ss_pred HHHhCCcc
Confidence 99888654
No 32
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=54.58 E-value=30 Score=28.83 Aligned_cols=67 Identities=22% Similarity=0.197 Sum_probs=40.9
Q ss_pred CCCCCCCCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecceeecceeeeeeeeEEeeCCCCCCCCCCEE
Q psy13112 119 DPDKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIV 198 (302)
Q Consensus 119 De~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K~ikRskKY~AHDenN~ckvGDiV 198 (302)
+=.+.--.||.|+|+.. ..=.+++.= |+=+...---|.+|+.|..+.-. .+..-..++||+|
T Consensus 8 ~~~~ikPL~dRVLVk~~-~~e~kT~gG----IiLP~sakekp~~g~VvAVG~G~-------------~~~~~~Vk~GD~V 69 (100)
T PTZ00414 8 ALKKLQPLGQRVLVKRT-LAAKQTKAG----VLIPEQVAGKVNEGTVVAVAAAT-------------KDWTPTVKVGDTV 69 (100)
T ss_pred ccccceecCCEEEEEEc-ccccccccC----EEcccccccCCceeEEEEECCCC-------------ccccceecCCCEE
Confidence 33455568999999977 433444433 33332222237778887666521 1124568999999
Q ss_pred EEeec
Q psy13112 199 LIEEL 203 (302)
Q Consensus 199 ~I~Ec 203 (302)
++.+-
T Consensus 70 l~~~y 74 (100)
T PTZ00414 70 LLPEF 74 (100)
T ss_pred EEcCC
Confidence 99876
No 33
>PRK05054 exoribonuclease II; Provisional
Probab=51.46 E-value=3.2e+02 Score=28.95 Aligned_cols=142 Identities=13% Similarity=0.036 Sum_probs=77.8
Q ss_pred cCCceeeeeeeccccceEEee--eceEEee-CCCCCCCCCCEEEEeecCcccccceeE-EEeeEEeecCCccCCccceee
Q psy13112 91 ARPYMQPRVANTRNEVRYFPK--FTVMYAH-DPDKICKTGDIVLIEELPQKLTTLITH-KVNKVVYPLGDITDPITGKKV 166 (302)
Q Consensus 91 ~~~~~VeR~vkHp~YkKy~kK--skKY~AH-De~N~cKiGDiVlI~E~PrPLSK~KtW-~V~eIV~kaG~i~DPiTGK~V 166 (302)
..+++.=++..|+.=--|+.. .+.+++. +.-|.|--||+|++.-. +. +.+.. .|++||.++-.- +.|.-.
T Consensus 18 ~~~~~~G~~~~~~~gfgFv~~~~~~difI~~~~l~~a~~GD~V~v~i~-~~--~~r~~g~v~~il~r~~~~---~vG~~~ 91 (644)
T PRK05054 18 QTPRVEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIH-TE--KDREIAEPEELIEPFLTR---FVGRVQ 91 (644)
T ss_pred cCCeEEEEEEECCCccEEEEECCCCcEEEChHHHccCCCCCEEEEEEe-cC--CCCcEEEEEEEEecCCCE---EEEEEE
Confidence 344566667777653334432 1256663 33466777999998844 21 23334 889999986552 444433
Q ss_pred ecceeec-ceeeee-eeeEEeeCCC---CCCCCCCEEEEeecCCCcCcceeEEEEEeeecCCCccCCCCCceeecccc
Q psy13112 167 VGLRVDL-GKYFPK-FTVMYAHDPD---KICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRT 239 (302)
Q Consensus 167 VGLrp~y-~K~ikR-skKY~AHDen---N~ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y 239 (302)
......+ ...-.+ ...+.+..++ ..++.||+|.++=.+.|.-..+.+ ..+|++-.|+.-||-.--..+-.+|
T Consensus 92 ~~~~~~~~~p~d~~~~~~i~i~~~~~~~~~~~~gd~V~v~i~~~p~~~~~~~-~g~i~~~lG~~~d~~~d~~~il~~~ 168 (644)
T PRK05054 92 KKDDRLSIVPDHPLLKDAIPCRAAKGLNHEFKEGDWVVAELRRHPLKGDRGF-YAEITQFITDADDHFAPWWVTLARH 168 (644)
T ss_pred EeCceEEEEECCCCCCccEEeccccccccCCCCCCEEEEEEecCCCCCCCCc-eEEEEEEECCCCCCccHHHHHHHHc
Confidence 2222110 000011 1223443332 368899999988775565322322 5567888888888865544444444
No 34
>PF10377 ATG11: Autophagy-related protein 11; InterPro: IPR019460 This family consists of proteins involved in telomere maintenance. In Schizosaccharomyces pombe (fission yeast) this protein is called Taf1 (taz1 interacting factor) and is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) this protein is called ATG11 and is known to be involved in vacuolar targeting and peroxisome degradation [, ].
Probab=50.88 E-value=54 Score=27.96 Aligned_cols=27 Identities=15% Similarity=0.106 Sum_probs=17.3
Q ss_pred CCCCCCCEEEEeecCcccccceeEEEe
Q psy13112 122 KICKTGDIVLIEELPQKLTTLITHKVN 148 (302)
Q Consensus 122 N~cKiGDiVlI~E~PrPLSK~KtW~V~ 148 (302)
+.|++||+|++.-.+..-+...-|.+.
T Consensus 41 ~~f~~GDlvLflpt~~~~~~~~~~~af 67 (129)
T PF10377_consen 41 RNFQVGDLVLFLPTRNHNNKKQPWAAF 67 (129)
T ss_pred ecCCCCCEEEEEecCCCCccccceEEe
Confidence 579999999999773333223335443
No 35
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=50.53 E-value=28 Score=28.08 Aligned_cols=40 Identities=20% Similarity=0.242 Sum_probs=32.0
Q ss_pred CCCCCCEEEEeecCcc-cccceeEEEeeEEeecCCccCCcc
Q psy13112 123 ICKTGDIVLIEELPQK-LTTLITHKVNKVVYPLGDITDPIT 162 (302)
Q Consensus 123 ~cKiGDiVlI~E~PrP-LSK~KtW~V~eIV~kaG~i~DPiT 162 (302)
..|.||.|+++..++- .+..+.|-+-+||..-|--.||.-
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~ 45 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKV 45 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCC
Confidence 3689999999988422 467789999999999887778753
No 36
>PRK04972 putative transporter; Provisional
Probab=48.13 E-value=34 Score=35.36 Aligned_cols=88 Identities=16% Similarity=0.267 Sum_probs=50.9
Q ss_pred eceEEeeCCCCCCCCCCEEEEeecCcccccce-----------------eEEEeeEEeecCCccCCccceeeecceee-c
Q psy13112 112 FTVMYAHDPDKICKTGDIVLIEELPQKLTTLI-----------------THKVNKVVYPLGDITDPITGKKVVGLRVD-L 173 (302)
Q Consensus 112 skKY~AHDe~N~cKiGDiVlI~E~PrPLSK~K-----------------tW~V~eIV~kaG~i~DPiTGK~VVGLrp~-y 173 (302)
..+....+++...+.||+|.|.-.+.-+.+.. ...++.|+- .+. +..||.+..++-. |
T Consensus 252 ~g~~~~p~~dt~L~~GDiL~V~G~~e~l~~l~~~~~lg~e~~~~~~~~~~~~~E~vVv-~~s---~liGkTL~eL~~r~~ 327 (558)
T PRK04972 252 NGILANPDGDAVLQMGDEIALVGYPDAHARLDPSFRNGKEVFDRDLLDMRIVTEEIVV-KNH---NAVGKRLSQLKLTDH 327 (558)
T ss_pred CCEEecCCCCCEeCCCCEEEEEECHHHHHHHHHhhcCCCcccCccccCcceEEEEEEE-cCc---ccCCCCHHHhCCccC
Confidence 33444456778899999999954422222111 122333333 333 5778887777521 2
Q ss_pred cee---eeeeeeEEeeCCCCCCCCCCEEEEeec
Q psy13112 174 GKY---FPKFTVMYAHDPDKICKTGDIVLIEEL 203 (302)
Q Consensus 174 ~K~---ikRskKY~AHDenN~ckvGDiV~I~Ec 203 (302)
+=. ++|...-...+++-..+.||++++.-.
T Consensus 328 gv~Vl~I~R~g~~~~~~~~~~L~~GD~LlVvG~ 360 (558)
T PRK04972 328 GCFLNRVIRSQIEMPIDDNVVLNKGDVLQVSGD 360 (558)
T ss_pred CeEEEEEecCCcccCCCCCCEecCCCEEEEEEC
Confidence 222 244334444556777899999999766
No 37
>TIGR02854 spore_II_GA sigma-E processing peptidase SpoIIGA. Members of this protein family are the stage II sporulation protein SpoIIGA. This protein acts as an activating protease for Sigma-E, one of several specialized sigma factors of the sporulation process in Bacillus subtilis and related endospore-forming bacteria.
Probab=43.24 E-value=29 Score=32.81 Aligned_cols=30 Identities=13% Similarity=0.164 Sum_probs=24.7
Q ss_pred eeEEEEEeeecCCCccCCCCCceeeccccc
Q psy13112 211 ITHKVNKVVYPLGDITDPITGKKVVGLRTA 240 (302)
Q Consensus 211 KtW~V~eIV~k~G~iiDPVTgK~vv~~~Y~ 240 (302)
+.-.+...+--.-...||+||++|+--+|.
T Consensus 168 ~~~~~~alvDTGN~L~DPlT~~PV~Ive~~ 197 (288)
T TIGR02854 168 KKVTIKGFLDTGNQLRDPLTKLPVIVVEYD 197 (288)
T ss_pred EEEEEEEEEecCCcccCCCCCCCEEEEEHH
Confidence 455667777777789999999999998886
No 38
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=42.53 E-value=87 Score=25.33 Aligned_cols=68 Identities=22% Similarity=0.146 Sum_probs=37.9
Q ss_pred CCCCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecceeecceeeeeeeeEEeeCCCCCCCCCCEEEEee
Q psy13112 123 ICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEE 202 (302)
Q Consensus 123 ~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~E 202 (302)
..-.||.|+|+.. ..-.+++. .|+=+...-.-|.+|+.|..+.-.+. ..-.+ .-...++||+|++.+
T Consensus 3 i~Pl~drVLV~~~-~~e~~T~g----GI~Lp~~a~~k~~~G~VvaVG~G~~~----~~G~~----~~~~vk~GD~Vlf~~ 69 (95)
T PRK00364 3 LKPLGDRVLVKRL-EEEEKTAG----GIVLPDSAKEKPQEGEVVAVGPGRRL----DNGER----VPLDVKVGDKVLFGK 69 (95)
T ss_pred ceEcCCEEEEEEc-ccCccccc----eEEcCccccCCcceEEEEEECCCeEC----CCCCE----eecccCCCCEEEEcC
Confidence 3457999999977 33345444 23333332234677777755552110 00011 123689999999986
Q ss_pred c
Q psy13112 203 L 203 (302)
Q Consensus 203 c 203 (302)
.
T Consensus 70 ~ 70 (95)
T PRK00364 70 Y 70 (95)
T ss_pred C
Confidence 5
No 39
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=42.00 E-value=43 Score=27.02 Aligned_cols=39 Identities=21% Similarity=0.226 Sum_probs=31.8
Q ss_pred CCCCCCEEEEeecC-CCcCcceeEEEEEeeecCCCccCCC
Q psy13112 191 ICKTGDIVLIEELP-QKLTTLITHKVNKVVYPLGDITDPI 229 (302)
Q Consensus 191 ~ckvGDiV~I~Ec~-rPLSKtKtW~V~eIV~k~G~iiDPV 229 (302)
..|.||.|+++... --.+..+.|-+-+|++..|---||-
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~ 44 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPK 44 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCC
Confidence 36899999999874 1246678999999999999888885
No 40
>PF08793 2C_adapt: 2-cysteine adaptor domain; InterPro: IPR014901 The virus-specific 2-cysteine adaptor is found fused to OTU/A20-like peptidases and S/T protein kinases. The associations to these proteins indicate that they might function as viral adaptors connecting the kinases and OTU/A20 peptidases to specific targets [].
Probab=41.66 E-value=5.4 Score=27.83 Aligned_cols=21 Identities=29% Similarity=0.366 Sum_probs=18.5
Q ss_pred cCCccceeeecceeecceeee
Q psy13112 158 TDPITGKKVVGLRVDLGKYFP 178 (302)
Q Consensus 158 ~DPiTGK~VVGLrp~y~K~ik 178 (302)
+.|+||+++...-|.|.++.+
T Consensus 12 ~NP~Tgr~Ik~~gp~y~~l~~ 32 (37)
T PF08793_consen 12 VNPITGRKIKPGGPTYKKLVK 32 (37)
T ss_pred CCCCCCCcCCCCChHHHHHHH
Confidence 579999999999999988764
No 41
>PF06819 Arc_PepC: Archaeal Peptidase A24 C-terminal Domain; InterPro: IPR009639 This region is of unknown function found at the C terminus of some archael proteins that have multiple transmembrane domains and are predicted to be aspartic peptidases belonging to the MEROPS peptidase subfamily A24A (type 4 prepilin peptidase 1.
Probab=37.86 E-value=37 Score=29.06 Aligned_cols=32 Identities=19% Similarity=0.315 Sum_probs=27.5
Q ss_pred cCCCCCceeeccccccccHHHHHHHHHHhcCC
Q psy13112 226 TDPITGKKVVGLRTAVLTADFYKELYELYGKN 257 (302)
Q Consensus 226 iDPVTgK~vv~~~Y~~~~~D~i~~~~~l~g~~ 257 (302)
...+||+.++.+.=.-||.++||++++|+-+.
T Consensus 71 ~~~l~g~~i~~~~~EGLs~E~IE~Lk~Lv~eG 102 (110)
T PF06819_consen 71 GSALTGEKIISTDAEGLSKEDIEKLKKLVEEG 102 (110)
T ss_pred cccccCCeEEeccccCCCHHHHHHHHHHHHcC
Confidence 45667999999998999999999999999643
No 42
>COG0511 AccB Biotin carboxyl carrier protein [Lipid metabolism]
Probab=36.57 E-value=87 Score=26.73 Aligned_cols=42 Identities=17% Similarity=0.211 Sum_probs=35.0
Q ss_pred CCCCCCCCCCEEEEeecC---CCcCcceeEEEEEeeecCCCccCC
Q psy13112 187 DPDKICKTGDIVLIEELP---QKLTTLITHKVNKVVYPLGDITDP 228 (302)
Q Consensus 187 DenN~ckvGDiV~I~Ec~---rPLSKtKtW~V~eIV~k~G~iiDP 228 (302)
.+....+.||+|.|.|.- -+|..-+.=+|.+|+-+.|..|++
T Consensus 87 ~vGd~V~~Gq~l~IiEAMKmeneI~A~~~G~V~~Ilv~~G~~Ve~ 131 (140)
T COG0511 87 EVGDTVKAGQTLAIIEAMKMENEIEAPADGVVKEILVKNGDPVEY 131 (140)
T ss_pred ccCCEEcCCCEEEEEEeeeccceecCCCCcEEEEEEecCCCccCC
Confidence 357788999999999953 577888888999999999988875
No 43
>PF00681 Plectin: Plectin repeat; InterPro: IPR001101 Plectin may have a role in cross-linking intermediate filaments, in inter-linking intermediate filaments with microtubules and microfilaments and in anchoring intermediate filaments to the plasma and nuclear membranes. Plectin is recruited into hemidesmosomes, multiprotein complexes that facilitate adhesion of epithelia to the basement membrane, thereby providing linkage between the intracellular keratin filaments to the laminins of the extracellular matrix. Plectin binds to hemidesmosomes through association of its actin-binding domain with the first pair of fibronectin type III repeats and a small part of the connecting segment of the integrin-beta4 subunit, the latter (integrin-alpha6,beta4) acting as a receptor for the extracellular matrix component laminin-5. The plectin repeat is also seen in the cell adhesion junction plaque proteins, desmoplakin, envoplakin, and bullous pemphigoid antigen. The domains in plakins show considerable sequence homology. The N terminus consists of a plakin domain containing a number of subdomains with high alpha-helical content, while the central coiled-coil domain is composed of heptad repeats involved in the dimerisation of plakin, and the C terminus contains one or more homologous repeat sequences referred to plectin repeats []. This entry represents the plectin repeats found in the C terminus of plakin proteins.; GO: 0005856 cytoskeleton; PDB: 1LM7_A 1LM5_A.
Probab=35.78 E-value=17 Score=25.41 Aligned_cols=16 Identities=38% Similarity=0.545 Sum_probs=13.2
Q ss_pred CCCccCCCCCceeecc
Q psy13112 222 LGDITDPITGKKVVGL 237 (302)
Q Consensus 222 ~G~iiDPVTgK~vv~~ 237 (302)
-|-||||.||+++--.
T Consensus 10 ~gGiidp~tg~~lsv~ 25 (45)
T PF00681_consen 10 TGGIIDPETGERLSVE 25 (45)
T ss_dssp TTSEEETTTTEEEEHH
T ss_pred eeeEEeCCCCeEEcHH
Confidence 5789999999998543
No 44
>COG0511 AccB Biotin carboxyl carrier protein [Lipid metabolism]
Probab=34.92 E-value=1.5e+02 Score=25.28 Aligned_cols=63 Identities=13% Similarity=0.174 Sum_probs=48.6
Q ss_pred eeeeccccceEEeeeceEEeeCCCCCCCCCCEEEEeec---CcccccceeEEEeeEEeecCCccCCccceeee
Q psy13112 98 RVANTRNEVRYFPKFTVMYAHDPDKICKTGDIVLIEEL---PQKLTTLITHKVNKVVYPLGDITDPITGKKVV 167 (302)
Q Consensus 98 R~vkHp~YkKy~kKskKY~AHDe~N~cKiGDiVlI~E~---PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VV 167 (302)
..+.-|.-+++++ ++|.. -...+.||+|.|.|. -.+|.--+.=.|.+|+-+.|+.++ .|.+..
T Consensus 71 ~~V~SPm~Gtv~~----~~V~v-Gd~V~~Gq~l~IiEAMKmeneI~A~~~G~V~~Ilv~~G~~Ve--~G~~L~ 136 (140)
T COG0511 71 TQVTSPMVGTVYK----PFVEV-GDTVKAGQTLAIIEAMKMENEIEAPADGVVKEILVKNGDPVE--YGDPLA 136 (140)
T ss_pred ceEecCcceEEEE----Eeecc-CCEEcCCCEEEEEEeeeccceecCCCCcEEEEEEecCCCccC--CCCEEE
Confidence 3466677888887 66665 578999999999997 667788888899999998998755 455444
No 45
>smart00250 PLEC Plectin repeat.
Probab=34.86 E-value=15 Score=24.82 Aligned_cols=15 Identities=47% Similarity=0.831 Sum_probs=12.2
Q ss_pred cCCCccCCCCCceee
Q psy13112 221 PLGDITDPITGKKVV 235 (302)
Q Consensus 221 k~G~iiDPVTgK~vv 235 (302)
..|-|+||.||+++-
T Consensus 9 ~~~Giidp~t~~~ls 23 (38)
T smart00250 9 AIGGIIDPETGQKLS 23 (38)
T ss_pred heeEEEcCCCCCCcC
Confidence 457899999999864
No 46
>PF03419 Peptidase_U4: Sporulation factor SpoIIGA This family belongs to family U4 of the peptidase classification.; InterPro: IPR005081 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 asexual sporulation
Probab=34.50 E-value=56 Score=30.55 Aligned_cols=30 Identities=20% Similarity=0.341 Sum_probs=23.9
Q ss_pred eeEEEEEeeecCCCccCCCCCceeeccccc
Q psy13112 211 ITHKVNKVVYPLGDITDPITGKKVVGLRTA 240 (302)
Q Consensus 211 KtW~V~eIV~k~G~iiDPVTgK~vv~~~Y~ 240 (302)
+.-.+.-.+--.-...||+||++|+--+|.
T Consensus 167 ~~~~~~allDTGN~L~DPitg~PV~Vve~~ 196 (293)
T PF03419_consen 167 KKIELKALLDTGNQLRDPITGRPVIVVEYE 196 (293)
T ss_pred EEEEEEEEEECCCcccCCCCCCcEEEEEHH
Confidence 455566667766679999999999999985
No 47
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=32.66 E-value=59 Score=25.05 Aligned_cols=49 Identities=14% Similarity=0.152 Sum_probs=32.5
Q ss_pred CCCCCEEEEeecCCCcCcceeEEEEEeeecCCCccCCCCCceeeccccc-cccHHHHHHH
Q psy13112 192 CKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTA-VLTADFYKEL 250 (302)
Q Consensus 192 ckvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y~-~~~~D~i~~~ 250 (302)
+.+||+|....-. ..-+..|.|.++=.- -+-+|.+..-. -|+|-+.|+.
T Consensus 2 ~~vgDiV~mKK~H--PCG~~~Wei~R~GaD--------ikikC~gCg~~imlpR~~feK~ 51 (57)
T PF06107_consen 2 YEVGDIVEMKKPH--PCGSNEWEIIRIGAD--------IKIKCLGCGRQIMLPRSKFEKR 51 (57)
T ss_pred ccCCCEEEEcCCC--CCCCCEEEEEEccCc--------EEEEECCCCCEEEEeHHHHHHH
Confidence 5799999999863 456799999886432 23455554433 5666666654
No 48
>COG5036 SPX domain-containing protein involved in vacuolar polyphosphate accumulation [Inorganic ion transport and metabolism]
Probab=32.18 E-value=19 Score=37.32 Aligned_cols=29 Identities=14% Similarity=0.238 Sum_probs=23.9
Q ss_pred CCccceeeecceeecceeeeeeeeEEeeCCC
Q psy13112 159 DPITGKKVVGLRVDLGKYFPKFTVMYAHDPD 189 (302)
Q Consensus 159 DPiTGK~VVGLrp~y~K~ikRskKY~AHDen 189 (302)
+|+.|+.-.+.+ .-+|+++|.|||||+.|
T Consensus 168 ~~ik~~sk~~~n--~~~f~r~t~KyWVH~dN 196 (509)
T COG5036 168 SPIKSKSKASSN--QQMFVRRTFKYWVHPDN 196 (509)
T ss_pred CccccccccCcc--hhhhhhhhceeEecCCC
Confidence 388888877754 56799999999999976
No 49
>COG1273 Ku-homolog [Replication, recombination, and repair]
Probab=31.81 E-value=21 Score=34.75 Aligned_cols=29 Identities=21% Similarity=0.173 Sum_probs=22.4
Q ss_pred ccCCCCCceee-----------ccccccccHHHHHHHHHH
Q psy13112 225 ITDPITGKKVV-----------GLRTAVLTADFYKELYEL 253 (302)
Q Consensus 225 iiDPVTgK~vv-----------~~~Y~~~~~D~i~~~~~l 253 (302)
.||++|||.|. .++|.+|+.||++.+...
T Consensus 48 ~Vd~~tGk~Ve~~d~VKGYE~~~~~yViledeel~s~~~e 87 (278)
T COG1273 48 YVDSVTGKEVERDDIVKGYEYGKGDYVILEDEELESVPLE 87 (278)
T ss_pred EeccccCCccCccceeeeeEecCCcEEEecHHHHhhcccc
Confidence 47888888775 457889999999887543
No 50
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=30.99 E-value=97 Score=30.95 Aligned_cols=42 Identities=19% Similarity=0.014 Sum_probs=34.2
Q ss_pred CCCCCCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecce
Q psy13112 121 DKICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLR 170 (302)
Q Consensus 121 ~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLr 170 (302)
.-....||+|.+.- ....+..++.+...++|+.||+++.-.-
T Consensus 244 ip~~~~gDiV~~~~--------~~~~~v~~~~~~~~~~dl~t~e~~~~~~ 285 (355)
T COG1499 244 IPEFRPGDIVSVRG--------RQLVLVRSIGKGIVVLDLETGEPVEITW 285 (355)
T ss_pred CCCCCCCCEEEECC--------CeEEEEEEecCceEEEecccCCccccCh
Confidence 45688999999875 5789999999999999999996654433
No 51
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=30.91 E-value=1.1e+02 Score=27.70 Aligned_cols=46 Identities=22% Similarity=0.343 Sum_probs=31.3
Q ss_pred CCCCEEEEeecCCCcCcceeEEEEEeeecCCCccCCCCCceeeccccccccHHHHHHHHHHhcCCCCCCcccCC
Q psy13112 193 KTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDYKK 266 (302)
Q Consensus 193 kvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y~~~~~D~i~~~~~l~g~~~~~~f~y~k 266 (302)
+.||+|+|+- +|..++| -+|+++ |+.|++..|.+. |.-+ ..|.-+.
T Consensus 72 ~~GD~VlVel--~~yd~~K----gdIi~R--------------------y~~devr~Lk~~-g~~P-~~~~~~~ 117 (155)
T PTZ00329 72 NIGDIILVSL--RDFQDSK----ADVILK--------------------YTPDEARALKQH-GELP-ETAKINE 117 (155)
T ss_pred cCCCEEEEec--cCCCCCE----EEEEEE--------------------cCHHHHHHHHHc-CCCC-cceeecc
Confidence 6899999963 4555444 234443 579999999886 8888 5664443
No 52
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=27.21 E-value=54 Score=26.05 Aligned_cols=65 Identities=23% Similarity=0.230 Sum_probs=33.3
Q ss_pred CCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeec
Q psy13112 126 TGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEEL 203 (302)
Q Consensus 126 iGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec 203 (302)
.||.|+|+.. ..-.++..=.+.- ..++. -|.+|+.|..+. ++.. .+-.. ....+++||+|++.+.
T Consensus 5 l~drVLV~~~-~~e~~T~~GiiLp--~~~~~--~~~~G~VvaVG~---G~~~-~~g~~----~~~~vk~GD~Vl~~~~ 69 (93)
T PF00166_consen 5 LGDRVLVKKI-EAEEKTASGIILP--ESAKE--KPNQGKVVAVGP---GRYN-ENGEE----VPMDVKVGDKVLFPKY 69 (93)
T ss_dssp STTEEEEEEC-SCTCTCTTSCCE---CCSSS--SEEEEEEEEE-S---EEET-TTSSE----EETSS-TTSEEEEETT
T ss_pred cCCEEEEEEc-cccceecceEEec--ccccc--ccceeEEEEcCC---cccc-CCCcE----eeeeeeeccEEecccc
Confidence 6899999987 4334443322222 22222 356666655554 1111 11111 1236889999999876
No 53
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=26.88 E-value=1.1e+02 Score=25.24 Aligned_cols=35 Identities=20% Similarity=0.320 Sum_probs=22.5
Q ss_pred CCCCEEEEeecCCCcC-cceeEEEEEeeecCCCccCCCCCceeeccccccccHHHHHHHHHH
Q psy13112 193 KTGDIVLIEELPQKLT-TLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYEL 253 (302)
Q Consensus 193 kvGDiV~I~Ec~rPLS-KtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y~~~~~D~i~~~~~l 253 (302)
+.||.|++. ++.++ +.| -+|+++ |+.|++..|.+.
T Consensus 59 ~~GD~VlVs--p~d~~~~~k----g~Iv~r--------------------~~~~qv~~L~~~ 94 (99)
T TIGR00523 59 REGDVVIVK--PWEFQGDDK----CDIVWR--------------------YTKTQVEWLKRK 94 (99)
T ss_pred cCCCEEEEE--EccCCCCcc----EEEEEE--------------------cCHHHHHHHHHc
Confidence 679999993 34555 322 344443 578999888764
No 54
>PF08145 BOP1NT: BOP1NT (NUC169) domain; InterPro: IPR012953 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This N-terminal domain is found in BOP1-like WD40 proteins. Bop1 is a nucleolar protein involved in rRNA processing, thereby controlling the cell cycle []. It is required for the maturation of the 25S and 5.8S ribosomal RNAs. It may serve as an essential factor in ribosome formation that coordinates processing of the spacer regions in pre-rRNA. The Pes1-Bop1 complex has several components: BOP1, GRWD1, PES1, ORC6L, and RPL3 and is involved in ribosome biogenesis and altered chromosome segregation. The overexpression of BOP1 increases the percentage of multipolar spindles in human cells. Deregulation of the BOP1 pathway may contribute to colorectal tumourigenesis in humans []. Elevated levels of Bop1 induces Bop1/WDR12 and Bop1/Pes1 subcomplexes and the assembly and integrity of the PeBoW complex is highly sensitive to changes in Bop1 protein levels []. Nop7p-Erb1p-Ytm1p, found in yeast, is potentially the homologous complex of Pes1-Bop1-WDR12 as it is involved in the control of ribosome biogenesis and S phase entry. The integrity of the PeBoW complex is required for ribosome biogenesis and cell proliferation in mammalian cells []. In Giardia, the species specific cytoskeleton protein, beta-giardin, interacts with Bop1 []. ; GO: 0006364 rRNA processing, 0005634 nucleus
Probab=25.56 E-value=56 Score=31.56 Aligned_cols=26 Identities=23% Similarity=0.332 Sum_probs=22.5
Q ss_pred CccCCCCCceeeccccccccHHHHHHHHHHhc
Q psy13112 224 DITDPITGKKVVGLRTAVLTADFYKELYELYG 255 (302)
Q Consensus 224 ~iiDPVTgK~vv~~~Y~~~~~D~i~~~~~l~g 255 (302)
.|.|+.||+.| +||.+|++++..+-.
T Consensus 40 tv~D~~~g~~v------~Lt~eel~lI~ri~~ 65 (260)
T PF08145_consen 40 TVYDKKNGREV------VLTDEELELIRRIQK 65 (260)
T ss_pred eeEcCCCCcee------eeCHHHHHHHHHHHc
Confidence 68899999877 589999999999863
No 55
>PLN00208 translation initiation factor (eIF); Provisional
Probab=25.31 E-value=1.5e+02 Score=26.45 Aligned_cols=48 Identities=21% Similarity=0.292 Sum_probs=32.7
Q ss_pred CCCCEEEEeecCCCcCcceeEEEEEeeecCCCccCCCCCceeeccccccccHHHHHHHHHHhcCCCCCCcccCCCC
Q psy13112 193 KTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRTAVLTADFYKELYELYGKNPQRKFDYKKAP 268 (302)
Q Consensus 193 kvGDiV~I~Ec~rPLSKtKtW~V~eIV~k~G~iiDPVTgK~vv~~~Y~~~~~D~i~~~~~l~g~~~~~~f~y~ka~ 268 (302)
+.||+|+++ . +|..+.|. +|++ .|+.|++..|.+. |.-+ ..|.-+..-
T Consensus 72 ~~GD~VlVe-l-~~~d~~Kg----dIv~--------------------ry~~dqvr~Lkk~-G~~P-~~f~~~~~~ 119 (145)
T PLN00208 72 AAGDIILVG-L-RDYQDDKA----DVIL--------------------KYMPDEARLLKAY-GELP-ENTRLNEGI 119 (145)
T ss_pred cCCCEEEEE-c-cCCCCCEE----EEEE--------------------EcCHHHHHHHHHc-CCCC-cceeecccc
Confidence 689999998 2 34444332 2333 2579999999887 8888 778665544
No 56
>cd01614 EutN_CcmL Ethanolamine utilisation protein and carboxysome structural protein domain family. Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation,
Probab=24.95 E-value=2.4e+02 Score=22.77 Aligned_cols=53 Identities=19% Similarity=0.165 Sum_probs=34.9
Q ss_pred CCEEEEeecCcccccceeEEEeeEEeecCCccCCccceeeecceeecceeeeeeeeEEeeCCCCCCCCCCEEEEeec
Q psy13112 127 GDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKVVGLRVDLGKYFPKFTVMYAHDPDKICKTGDIVLIEEL 203 (302)
Q Consensus 127 GDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp~y~K~ikRskKY~AHDenN~ckvGDiV~I~Ec 203 (302)
|.+|.=+..| -=.-.+|.|++.+...|. .+|...|..+ .--|.+||+|++.+-
T Consensus 8 G~vvaT~K~~--~L~G~kLliVq~~~~~~~----~~g~~~VA~D------------------~vGAG~Ge~Vlv~~G 60 (83)
T cd01614 8 GTVVATRKHP--SLAGKKLLVVQPLDGEGK----PKGEPLVAVD------------------PVGAGVGEWVLVATG 60 (83)
T ss_pred eEEEEeeEcC--CCCCcEEEEEEECccCCC----cCCCEEEEEE------------------CCCCCCCCEEEEeCC
Confidence 4445444441 134456777777766665 4677777777 357899999999863
No 57
>PF04189 Gcd10p: Gcd10p family; InterPro: IPR007316 eIF-3 is a multisubunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit of eIF3 [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation
Probab=23.76 E-value=2.8e+02 Score=27.05 Aligned_cols=47 Identities=30% Similarity=0.386 Sum_probs=27.5
Q ss_pred CCCCCCCEEEEeecCcccccceeEEEeeEEeecCCccCCccceee-ecceeecceeee
Q psy13112 122 KICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDITDPITGKKV-VGLRVDLGKYFP 178 (302)
Q Consensus 122 N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i~DPiTGK~V-VGLrp~y~K~ik 178 (302)
+..+.||.|+|+ +|. -.+++++|. +.+.| .=||-- +.++.++|+-|-
T Consensus 2 ~~I~~gd~Vil~-~~~-----~~~k~v~l~-~~~~i---~lGK~~sf~~~~lIG~pyg 49 (299)
T PF04189_consen 2 SIIQEGDYVILR-LPS-----GNMKIVKLK-PNKTI---SLGKFGSFPLNDLIGRPYG 49 (299)
T ss_pred CCcCCCCEEEEE-cCC-----CcEEEEEEC-CCCEE---EecCCCcccHHHhcCCCCC
Confidence 567899999997 422 345566543 33343 235544 666666666554
No 58
>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=23.58 E-value=1.8e+02 Score=22.82 Aligned_cols=11 Identities=45% Similarity=0.767 Sum_probs=9.4
Q ss_pred CCCCEEEEeec
Q psy13112 193 KTGDIVLIEEL 203 (302)
Q Consensus 193 kvGDiV~I~Ec 203 (302)
+.||.|+++..
T Consensus 40 ~~GD~V~Ve~~ 50 (77)
T cd05793 40 NEGDIVLVAPW 50 (77)
T ss_pred cCCCEEEEEec
Confidence 68999999965
No 59
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=22.98 E-value=2e+02 Score=23.43 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=15.4
Q ss_pred CCCCCCCCEEEEeecCccccccee
Q psy13112 121 DKICKTGDIVLIEELPQKLTTLIT 144 (302)
Q Consensus 121 ~N~cKiGDiVlI~E~PrPLSK~Kt 144 (302)
+-....||.|++..........+.
T Consensus 42 ~Ptl~~GD~v~v~k~~~~~~~~~~ 65 (166)
T COG0681 42 EPTLNVGDRVLVKKFSYGFGKLKV 65 (166)
T ss_pred ccccccCCEEEEEeccccccCCcc
Confidence 345569999999988443333333
No 60
>PF03419 Peptidase_U4: Sporulation factor SpoIIGA This family belongs to family U4 of the peptidase classification.; InterPro: IPR005081 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 asexual sporulation
Probab=22.92 E-value=85 Score=29.35 Aligned_cols=30 Identities=20% Similarity=0.301 Sum_probs=24.0
Q ss_pred ceeEEEeeEEeecCCccCCccceeeeccee
Q psy13112 142 LITHKVNKVVYPLGDITDPITGKKVVGLRV 171 (302)
Q Consensus 142 ~KtW~V~eIV~kaG~i~DPiTGK~VVGLrp 171 (302)
.+.-.+...+-......||+||+||+....
T Consensus 166 ~~~~~~~allDTGN~L~DPitg~PV~Vve~ 195 (293)
T PF03419_consen 166 GKKIELKALLDTGNQLRDPITGRPVIVVEY 195 (293)
T ss_pred CEEEEEEEEEECCCcccCCCCCCcEEEEEH
Confidence 356677778887778999999999987663
No 61
>PF10165 Ric8: Guanine nucleotide exchange factor synembryn; InterPro: IPR019318 Ric8 is involved in the EGL-30 neurotransmitter signalling pathway []. It is a guanine nucleotide exchange factor [] that regulates neurotransmitter secretion.
Probab=22.53 E-value=67 Score=32.20 Aligned_cols=55 Identities=18% Similarity=0.270 Sum_probs=34.7
Q ss_pred cCCCccCCCCCceeeccc---cccccHHHHH----HHHHHhcCCCC-CCcccCCCCCCCccccc
Q psy13112 221 PLGDITDPITGKKVVGLR---TAVLTADFYK----ELYELYGKNPQ-RKFDYKKAPRRGWQEDK 276 (302)
Q Consensus 221 k~G~iiDPVTgK~vv~~~---Y~~~~~D~i~----~~~~l~g~~~~-~~f~y~ka~~rg~~e~~ 276 (302)
.++..||||||....... ...+|++|-| .+-.||-+-.. +.++- ..|-+.|+++-
T Consensus 383 ~~~~~~npitg~~~~~~~~~~~~~mt~eeke~ea~~l~~lf~rl~~~g~i~~-~npv~~~~~~G 445 (446)
T PF10165_consen 383 EAKRPINPITGQREDAEKPNPMPEMTEEEKEREAERLFVLFDRLEKTGVIQV-QNPVRQAGQDG 445 (446)
T ss_pred ccccCcCCCcCCCCCCCCCCCccccchhHHHHHHHHHHHHHHHHHhCCCcCc-chhhhhhhccC
Confidence 457789999999988444 3378888755 44456654333 45554 45556665543
No 62
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=21.88 E-value=1.9e+02 Score=23.49 Aligned_cols=50 Identities=8% Similarity=0.145 Sum_probs=33.0
Q ss_pred eeeeccccceEEee-eceEEeeCCCCCCCCCCEEEEeecCcccccceeEEEeeEE
Q psy13112 98 RVANTRNEVRYFPK-FTVMYAHDPDKICKTGDIVLIEELPQKLTTLITHKVNKVV 151 (302)
Q Consensus 98 R~vkHp~YkKy~kK-skKY~AHDe~N~cKiGDiVlI~E~PrPLSK~KtW~V~eIV 151 (302)
|+...-+......+ +-.|-+--+.-.+.+||+|.|.-- .+...|+|.+|-
T Consensus 113 r~a~~~l~~~~~~r~t~~f~~~~~~~~l~pGDvi~l~~~----~~~~~~RI~~i~ 163 (164)
T PF13550_consen 113 RLAERLLRRSRYERRTVSFTLPPDGLALEPGDVIALSDD----GRDMRFRITEIE 163 (164)
T ss_pred HHHHHHHHHhhccceEEEEEEChhhccCCCCCEEEEEeC----CCceEEEEEEEe
Confidence 33333334443333 666666666777999999998743 567889988873
No 63
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=20.12 E-value=1.8e+02 Score=24.15 Aligned_cols=29 Identities=28% Similarity=0.113 Sum_probs=24.3
Q ss_pred CCCCCCEEEEeecCcccccceeEEEeeEEeecCCc
Q psy13112 123 ICKTGDIVLIEELPQKLTTLITHKVNKVVYPLGDI 157 (302)
Q Consensus 123 ~cKiGDiVlI~E~PrPLSK~KtW~V~eIV~kaG~i 157 (302)
....||+|.+..= . ..+.+.+++.+.|+-
T Consensus 25 glA~gDvV~~~~~----~--g~~~~~~~v~~sGns 53 (117)
T PF14085_consen 25 GLALGDVVRAEPD----D--GELWFQKVVESSGNS 53 (117)
T ss_pred CCCCCCEEEEEeC----C--CeEEEEEEEecCCCE
Confidence 3568999999966 2 788999999999994
Done!