Query 029153
Match_columns 198
No_of_seqs 159 out of 1177
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 08:20:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029153.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029153hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00160 rpl9 ribosomal protei 100.0 5.7E-53 1.2E-57 341.4 17.7 150 48-197 3-152 (153)
2 TIGR00158 L9 ribosomal protein 100.0 2.1E-51 4.6E-56 330.7 17.4 145 51-197 1-147 (148)
3 PRK00137 rplI 50S ribosomal pr 100.0 1.6E-50 3.4E-55 325.2 18.0 146 51-198 1-147 (147)
4 COG0359 RplI Ribosomal protein 100.0 2.8E-49 6.1E-54 317.4 16.3 145 51-197 1-146 (148)
5 PRK14538 putative bifunctional 100.0 2.2E-41 4.8E-46 331.6 14.0 147 49-197 687-834 (838)
6 KOG4607 Mitochondrial ribosoma 100.0 7.9E-34 1.7E-38 237.9 7.1 192 5-198 3-195 (222)
7 PF03948 Ribosomal_L9_C: Ribos 99.9 6.2E-25 1.3E-29 162.5 10.8 85 112-197 1-86 (87)
8 PF01281 Ribosomal_L9_N: Ribos 99.9 1.4E-25 3E-30 149.1 3.7 48 51-98 1-48 (48)
9 PF10045 DUF2280: Uncharacteri 58.1 5.2 0.00011 30.8 1.0 24 145-168 21-44 (104)
10 PF07523 Big_3: Bacterial Ig-l 55.1 30 0.00065 23.4 4.5 25 170-195 43-67 (67)
11 PF08766 DEK_C: DEK C terminal 54.2 7.2 0.00016 25.8 1.1 24 142-165 19-42 (54)
12 cd08505 PBP2_NikA_DppA_OppA_li 50.8 23 0.00051 33.4 4.4 53 127-186 66-126 (528)
13 PF00571 CBS: CBS domain CBS d 49.3 18 0.00039 22.8 2.5 21 134-154 36-56 (57)
14 cd05886 Ig1_Nectin-1_like Firs 36.0 79 0.0017 23.3 4.5 31 165-195 64-98 (99)
15 cd07694 Ig2_CD4 Second immunog 34.3 96 0.0021 23.0 4.6 38 161-198 48-88 (88)
16 PF02315 MDH: Methanol dehydro 32.4 1.3E+02 0.0028 22.6 5.0 50 64-119 30-81 (93)
17 PF13592 HTH_33: Winged helix- 31.9 27 0.00058 23.4 1.2 25 142-166 3-27 (60)
18 PF14048 MBD_C: C-terminal dom 31.4 76 0.0017 23.8 3.7 45 59-103 43-87 (96)
19 PF06570 DUF1129: Protein of u 31.3 24 0.00052 29.5 1.0 61 89-157 2-66 (206)
20 COG1438 ArgR Arginine represso 28.9 31 0.00066 28.2 1.3 34 145-180 22-55 (150)
21 PF10147 CR6_interact: Growth 26.6 2.2E+02 0.0049 24.5 6.2 21 147-167 159-179 (217)
22 cd05714 Ig_CSPGs_LP Immunoglob 26.0 1.5E+02 0.0032 21.2 4.5 33 165-197 69-104 (106)
23 PF13670 PepSY_2: Peptidase pr 26.0 2.4E+02 0.0051 19.8 5.6 46 143-194 28-73 (83)
24 cd08490 PBP2_NikA_DppA_OppA_li 25.5 1.4E+02 0.0031 27.0 5.1 60 123-186 54-117 (470)
25 TIGR00074 hypC_hupF hydrogenas 23.8 58 0.0013 23.4 1.8 29 48-80 25-53 (76)
26 cd08496 PBP2_NikA_DppA_OppA_li 23.6 1.5E+02 0.0033 26.9 5.0 57 127-186 59-120 (454)
27 PF06560 GPI: Glucose-6-phosph 23.4 56 0.0012 27.4 1.9 26 53-78 95-129 (182)
28 smart00116 CBS Domain in cysta 23.3 71 0.0015 17.9 1.9 18 136-153 31-48 (49)
29 cd08502 PBP2_NikA_DppA_OppA_li 23.2 1.6E+02 0.0036 26.9 5.2 57 127-186 59-120 (472)
30 cd08506 PBP2_clavulanate_OppA2 22.7 1.1E+02 0.0024 27.8 4.0 45 127-186 65-112 (466)
31 cd08518 PBP2_NikA_DppA_OppA_li 22.0 1.3E+02 0.0029 27.4 4.3 57 127-186 58-118 (464)
32 cd03081 TRX_Fd_NuoE_FDH_gamma 21.8 78 0.0017 22.3 2.2 19 137-155 61-79 (80)
33 PF01282 Ribosomal_S24e: Ribos 21.8 61 0.0013 23.6 1.6 43 142-186 11-56 (84)
34 PRK07639 acyl carrier protein; 21.5 32 0.00069 24.9 0.1 33 143-175 40-72 (86)
35 PRK07668 hypothetical protein; 21.4 37 0.0008 29.9 0.5 61 89-157 2-67 (254)
36 cd05713 Ig_MOG_like Immunoglob 21.2 1.6E+02 0.0035 20.7 3.8 30 166-195 67-99 (100)
37 cd02980 TRX_Fd_family Thioredo 21.0 90 0.002 21.1 2.3 20 136-155 57-76 (77)
38 PRK15364 pathogenicity island 20.3 1.1E+02 0.0025 25.8 3.1 86 70-166 28-119 (196)
39 cd05887 Ig1_Nectin-3_like Firs 20.3 2.2E+02 0.0047 20.9 4.4 32 164-195 60-95 (96)
No 1
>CHL00160 rpl9 ribosomal protein L9; Provisional
Probab=100.00 E-value=5.7e-53 Score=341.37 Aligned_cols=150 Identities=38% Similarity=0.637 Sum_probs=144.7
Q ss_pred CCceEEEEccccccccCCCcEEEeCCcccccccccCCceeccCHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhccCCe
Q 029153 48 KKTRKIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGA 127 (198)
Q Consensus 48 kk~mkVIL~edV~~LGk~GdiV~Vk~GyARNfLiP~glA~~aT~~nlk~~~~~~~~~e~~~~~~~~~a~~~~~~L~~~~~ 127 (198)
+|+|+|||++||++||++||+|+|+||||||||||+|+|++||++|+++++.+++.+++++++.+++|+++++.|++++.
T Consensus 3 ~kkmkVIL~~dV~~LGk~Gdiv~Vk~GYaRNyLiP~glA~~AT~~n~~~~e~~~~~~~~~~~~~~~~a~~la~~l~~~~~ 82 (153)
T CHL00160 3 KKKIQVILKENIQKLGKSGTVIKVKSGYARNYLIPNKMAKVATQGSLKQQKMYQKILDLKLKEAKEKCLKVKQLLEEIQK 82 (153)
T ss_pred CceEEEEEcccccccCCCCCEEEEcCchHhhhhcccCchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCce
Confidence 46799999999999999999999999999999999999999999999999999999999999999999999999999745
Q ss_pred EEEEEecCCCCceeeccCHHHHHHHHHHhcCCceecceecccCccceeeEEEEEEeCCCcEEEEEEEEee
Q 029153 128 FKVKRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPEVTARIRLNVFA 197 (198)
Q Consensus 128 l~i~~k~g~~gklfGSVt~~dI~~~l~~~~gi~Idk~~I~l~~Ik~~G~y~V~V~L~~~v~a~i~v~V~~ 197 (198)
++|.+++|++|+||||||++||+++|++++|++||+++|.||+|+++|+|.|+|+||++|+|+++|+|++
T Consensus 83 ~~i~~k~ge~gklfGSVt~~dIa~~l~~~~g~~idk~~I~l~~Ik~~G~~~v~v~L~~~V~a~i~v~V~~ 152 (153)
T CHL00160 83 FSVKKKVGENNQIFGSVTEKEISQIIKNKTNIDLEKQNIELPEIKTIGIYNIEIKLTSDVKANINLQILP 152 (153)
T ss_pred EEEEEEeCCCCeEEcccCHHHHHHHHHHhhCCccccceeehhhccccEeEEEEEEecCCcEEEEEEEEEE
Confidence 9999999999999999999999999998899999999999988999999999999999999999999986
No 2
>TIGR00158 L9 ribosomal protein L9. Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast.
Probab=100.00 E-value=2.1e-51 Score=330.66 Aligned_cols=145 Identities=37% Similarity=0.574 Sum_probs=140.8
Q ss_pred eEEEEccccccccCCCcEEEeCCcccccccccCCceeccCHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhccCCeEEE
Q 029153 51 RKIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKV 130 (198)
Q Consensus 51 mkVIL~edV~~LGk~GdiV~Vk~GyARNfLiP~glA~~aT~~nlk~~~~~~~~~e~~~~~~~~~a~~~~~~L~~~~~l~i 130 (198)
|+|||++||++||++||+|+|++|||||||||+|+|++||++|+++++.+++.+++++++.+++|++++++|++. .++|
T Consensus 1 MkVIL~~dV~~lGk~GdiV~Vk~GYaRNyLiP~g~A~~aT~~nl~~~e~~~~~~~~~~~~~~~~a~~l~~~l~~~-~~~i 79 (148)
T TIGR00158 1 MKVILLEDVANLGKRGDVVEVKDGYARNFLIPKGLAVPATKKNIEFFEARRKKLEEKLAANKAAAARLKEVLELG-TLTI 79 (148)
T ss_pred CeEEEcccccccCCCCCEEEEcccchhhhhcccCchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc-EEEE
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999997 7999
Q ss_pred EEecCCCCceeeccCHHHHHHHHHHhcCCceecceecccC--ccceeeEEEEEEeCCCcEEEEEEEEee
Q 029153 131 KRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE--IRETGEYIAQLKLHPEVTARIRLNVFA 197 (198)
Q Consensus 131 ~~k~g~~gklfGSVt~~dI~~~l~~~~gi~Idk~~I~l~~--Ik~~G~y~V~V~L~~~v~a~i~v~V~~ 197 (198)
.+++|++|+||||||++||+++|+++ |++||+++|.||+ |+++|+|+|+|+||++|+++|+|+|.+
T Consensus 80 ~~k~ge~gklfGSVt~~~I~~~l~~~-g~~idk~~I~l~~~~Ik~~G~y~v~i~L~~~V~a~i~v~V~~ 147 (148)
T TIGR00158 80 SKKVGDEGKLFGSITTKQIADALKAA-GLDLDKKKIELPDGVIRTTGEHEVTIKLHEEVFAVLKVIVVP 147 (148)
T ss_pred EEEeCCCCeEEEeECHHHHHHHHHHc-CCcccHhhEECCCCceeceEEEEEEEEEcCCcEEEEEEEEEE
Confidence 99999999999999999999999887 9999999999975 999999999999999999999999986
No 3
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=100.00 E-value=1.6e-50 Score=325.24 Aligned_cols=146 Identities=42% Similarity=0.669 Sum_probs=141.6
Q ss_pred eEEEEccccccccCCCcEEEeCCcccccccccCCceeccCHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhccCCeEEE
Q 029153 51 RKIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKV 130 (198)
Q Consensus 51 mkVIL~edV~~LGk~GdiV~Vk~GyARNfLiP~glA~~aT~~nlk~~~~~~~~~e~~~~~~~~~a~~~~~~L~~~~~l~i 130 (198)
|+|||++||+|||++||+|+|++|||||||||+|+|+|||++|+++++.+++..++++++.+++|+++++.|++. .|+|
T Consensus 1 mkVIL~~dv~~lGk~Gdiv~Vk~GYaRNyLiP~~lA~~aT~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~-~l~i 79 (147)
T PRK00137 1 MKVILLEDVKNLGKKGDVVEVKDGYARNFLIPQGKAVRATKGNLKQLEARRAELEAKAAEELAEAEALAEKLEGL-TVTI 79 (147)
T ss_pred CeEEEcccccccCCCCCEEEEcCcchhhhhccCCceeeCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC-EEEE
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999987 8999
Q ss_pred EEecCCCCceeeccCHHHHHHHHHHhcCCceecceecccC-ccceeeEEEEEEeCCCcEEEEEEEEeeC
Q 029153 131 KRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTARIRLNVFAN 198 (198)
Q Consensus 131 ~~k~g~~gklfGSVt~~dI~~~l~~~~gi~Idk~~I~l~~-Ik~~G~y~V~V~L~~~v~a~i~v~V~~~ 198 (198)
.+++|++|++|||||++||+++|.++ |++||++.|.|++ |+++|+|+|+|+||++|+|+++|+|.+.
T Consensus 80 ~~k~g~~gklfGsVt~~~I~~~l~~~-g~~idk~~I~l~~~Ik~~G~y~v~i~L~~~v~a~l~v~V~~~ 147 (147)
T PRK00137 80 KAKAGEDGKLFGSVTTKDIAEALKKQ-GIEIDKRKIELPGPIKTLGEYEVPVKLHPEVTATIKVNVVAE 147 (147)
T ss_pred EEEcCCCCeEEeeeCHHHHHHHHHHc-CCccCHHHeECCCcccccEEEEEEEEECCCcEEEEEEEEEEC
Confidence 99999999999999999999999988 9999999999985 9999999999999999999999999863
No 4
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-49 Score=317.40 Aligned_cols=145 Identities=38% Similarity=0.571 Sum_probs=141.6
Q ss_pred eEEEEccccccccCCCcEEEeCCcccccccccCCceeccCHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhccCCeEEE
Q 029153 51 RKIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKV 130 (198)
Q Consensus 51 mkVIL~edV~~LGk~GdiV~Vk~GyARNfLiP~glA~~aT~~nlk~~~~~~~~~e~~~~~~~~~a~~~~~~L~~~~~l~i 130 (198)
|+|||++||.+||+.||+|+|++|||||||||+|+|+.||+.|++.++.++++++++.++++++|+.+++.|++. +++|
T Consensus 1 MkVILl~dV~~lGk~Gdiv~VkdGYarNfLiPkglAv~At~~n~~~~e~~r~~~e~~~~~~~~~a~~lk~~Le~~-~~~i 79 (148)
T COG0359 1 MKVILLEDVKGLGKKGDIVEVKDGYARNFLIPKGLAVPATKGNLKLLEARRAKLEKKAAEELAEAEALKEKLEGK-TVEI 79 (148)
T ss_pred CeEEEecchhhcCCCCCEEEecchhhhhhhccccchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc-eEEE
Confidence 999999999999999999999999999999999999999999999999999999999889999999999999995 8999
Q ss_pred EEecCCCCceeeccCHHHHHHHHHHhcCCceecceecccC-ccceeeEEEEEEeCCCcEEEEEEEEee
Q 029153 131 KRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTARIRLNVFA 197 (198)
Q Consensus 131 ~~k~g~~gklfGSVt~~dI~~~l~~~~gi~Idk~~I~l~~-Ik~~G~y~V~V~L~~~v~a~i~v~V~~ 197 (198)
.+++|++|++|||||++||+++|.++ |++||+++|.+|+ |+++|+|+|+|+||++|+++++|+|.+
T Consensus 80 ~~kag~~GklfGSVt~~dIa~~l~~~-g~~idk~~i~l~~~ik~~G~~~V~vkLh~eV~a~v~v~V~~ 146 (148)
T COG0359 80 AVKAGEDGKLFGSVTSKDIAEALKAA-GFKLDKRKIRLPNGIKTLGEHEVEVKLHEEVTATVKVNVVA 146 (148)
T ss_pred EEEcCCCCceeccccHHHHHHHHHHc-CCCcchheeEcCchhhhcceeEEEEEecCceEEEEEEEEEe
Confidence 99999999999999999999999999 9999999999998 999999999999999999999999975
No 5
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=100.00 E-value=2.2e-41 Score=331.64 Aligned_cols=147 Identities=23% Similarity=0.332 Sum_probs=142.3
Q ss_pred CceEEEEccccccccCCCcEEEeCCcccccccccCCceeccCHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhccCCeE
Q 029153 49 KTRKIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAF 128 (198)
Q Consensus 49 k~mkVIL~edV~~LGk~GdiV~Vk~GyARNfLiP~glA~~aT~~nlk~~~~~~~~~e~~~~~~~~~a~~~~~~L~~~~~l 128 (198)
..|||||++||++||++||+|+|+|||| |||||+|+|++||++|+++++.+++++++++++.+++|++++++|+++ .+
T Consensus 687 ~~MkVIL~~dv~~lGk~Gdvv~Vk~GYa-NfLiP~~~A~~aT~~nlk~~e~~~~~~~~~~~~~~~~a~~l~~~l~~~-~~ 764 (838)
T PRK14538 687 KNMEIILLTDIKNKGKKHEIIKVNNGYG-NFLIQNKKALLADKENLAKIKKKKILEQEKKRNHELLMKKLKSEIDNK-KI 764 (838)
T ss_pred hhhhHHHHHHHHhcCCCCCEEEECCCch-hhhccCCchhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc-EE
Confidence 3699999999999999999999999999 999999999999999999999999999999999999999999999997 79
Q ss_pred EEEEecCCCCceeeccCHHHHHHHHHHhcCCceecceecccC-ccceeeEEEEEEeCCCcEEEEEEEEee
Q 029153 129 KVKRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTARIRLNVFA 197 (198)
Q Consensus 129 ~i~~k~g~~gklfGSVt~~dI~~~l~~~~gi~Idk~~I~l~~-Ik~~G~y~V~V~L~~~v~a~i~v~V~~ 197 (198)
+|.+++|++|+||||||++||+++|++++|++||++.|.|++ ||++|+|.|+|+||++|+|+++|+|+.
T Consensus 765 ~i~~k~ge~gklfGSVt~~~I~~~l~~~~g~~idk~~I~l~~~Ik~~G~~~v~i~L~~~V~a~i~v~V~~ 834 (838)
T PRK14538 765 TLDIQLGPKGKIYGKITLKQIVEEFHKIHNITIDRKKISLENEIISVGIYPVDVFLTDQIKATFFLNVIE 834 (838)
T ss_pred EEEEEeCCCCeeeeccCHHHHHHHHHHhhCCccccceeeCCCcccccEEEEEEEEEcCCeEEEEEEEEEE
Confidence 999999999999999999999999999999999999999986 999999999999999999999999974
No 6
>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.9e-34 Score=237.90 Aligned_cols=192 Identities=40% Similarity=0.570 Sum_probs=163.3
Q ss_pred cccccccccccCcc-ccccCCCcccccccCCCceEEEEeeecccCCceEEEEccccccccCCCcEEEeCCcccccccccC
Q 029153 5 SSTAATLSWSSSSF-FQTFGNTVNESVKLPDKRSALLVLAQKKAKKTRKIILKEDVAELGKKGQLLDVKAGFYRNYLHPM 83 (198)
Q Consensus 5 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~a~kk~kk~mkVIL~edV~~LGk~GdiV~Vk~GyARNfLiP~ 83 (198)
+++++...|+.+.| ++.|.+. ..|++++++++-++.+++++.++.++|||++||+|||++||+|+|++||+||+|+|+
T Consensus 3 ~~~q~r~T~~~~r~~~~~l~~~-~np~~~~~~~y~lv~~~~~k~k~~levIL~~~Ve~lG~qGdvVsVk~g~~RN~Llp~ 81 (222)
T KOG4607|consen 3 SSSQSRNTWRLSRCWSPELHKG-ANPNLKHERRYELVEFTQKKPKPNLEVILKTDVEKLGKQGDVVSVKRGYFRNFLLPK 81 (222)
T ss_pred ccccccCeEEEEEeeccccCCC-CChhhHHHhhhhHhHhhhccCCcceeeeeehhhhhhcccCcEEEeecchhhhhcccc
Confidence 46788889998854 8888877 677776677789999999999999999999999999999999999999999999999
Q ss_pred CceeccCHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEEEecCCCCceeeccCHHHHHHHHHHhcCCceec
Q 029153 84 GKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDK 163 (198)
Q Consensus 84 glA~~aT~~nlk~~~~~~~~~e~~~~~~~~~a~~~~~~L~~~~~l~i~~k~g~~gklfGSVt~~dI~~~l~~~~gi~Idk 163 (198)
|+|+|+||.|.+.+...+++....+.+..++++.++ .|.+........+.+.---.+|+|++++....+.+++.+.+|+
T Consensus 82 glAvy~tp~~~~~~k~~~~e~~~~k~~vk~e~k~V~-~lqt~v~~~~~~k~~kw~l~~~~V~~~l~~gv~~~~~t~~l~k 160 (222)
T KOG4607|consen 82 GLAVYNTPLNLKKYKLREQEEEAEKIRVKEEAKVVA-VLQTVVLFKVMNKGGKWKLNPNLVKASLRKGVIVAELTIKLDK 160 (222)
T ss_pred cccccCChhhHHHHHHHHHHHHhhhhccHHHHHHHH-HHHhhhhhheeccCCceeecHHHHHHHHhcceEeccccccCcc
Confidence 999999999999998888888887788888888888 7877632333344443333568888888877777777889999
Q ss_pred ceecccCccceeeEEEEEEeCCCcEEEEEEEEeeC
Q 029153 164 KIVDLPEIRETGEYIAQLKLHPEVTARIRLNVFAN 198 (198)
Q Consensus 164 ~~I~l~~Ik~~G~y~V~V~L~~~v~a~i~v~V~~~ 198 (198)
+.|+.|.++.-|+|.++|++|++.++.+...|..|
T Consensus 161 ~~vs~P~~k~e~~~~~~V~in~~~~vr~~~~v~~~ 195 (222)
T KOG4607|consen 161 ELVSGPITKEEGEYICEVKINPDVTVRVKIRVTHN 195 (222)
T ss_pred cccCCCcccccceEEEEEEECCcceEEeeeeeecc
Confidence 99999999999999999999999999999988754
No 7
>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=99.92 E-value=6.2e-25 Score=162.52 Aligned_cols=85 Identities=47% Similarity=0.777 Sum_probs=81.9
Q ss_pred HHHHHHHHHHhccCCeEEEEEecCCCCceeeccCHHHHHHHHHHhcCCceecceecccC-ccceeeEEEEEEeCCCcEEE
Q 029153 112 KEEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTAR 190 (198)
Q Consensus 112 ~~~a~~~~~~L~~~~~l~i~~k~g~~gklfGSVt~~dI~~~l~~~~gi~Idk~~I~l~~-Ik~~G~y~V~V~L~~~v~a~ 190 (198)
+++|++++++|++. .|+|.+++|++|+||||||++||+++|++++|++||+++|.|++ ||++|+|.|+|+||++|+|+
T Consensus 1 k~~A~~l~~~l~~~-~l~i~~k~g~~gklfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~IK~~G~~~v~v~L~~~V~a~ 79 (87)
T PF03948_consen 1 KAEAQALAEKLEGI-TLTIKRKAGENGKLFGSVTSKDIAKALKEQTGIEIDKKKIELPEPIKSLGEYEVKVKLHPEVSAK 79 (87)
T ss_dssp HHHHHHHHHHHCSS-EEEEEECBSSCSSBSSEBSHHHHHHHHHHCCSSSSSSSSBCSSSTBESSEEEEEEEEEETTEEEE
T ss_pred CHHHHHHHHHhcCC-EEEEEEEecCCcceecCcCHHHHHHHHHHhhCCeEeccEEECCCchhccEEEEEEEEeCCCeEEE
Confidence 47899999999998 79999999999999999999999999999999999999999998 99999999999999999999
Q ss_pred EEEEEee
Q 029153 191 IRLNVFA 197 (198)
Q Consensus 191 i~v~V~~ 197 (198)
|+|+|.+
T Consensus 80 i~v~V~~ 86 (87)
T PF03948_consen 80 IKVNVVA 86 (87)
T ss_dssp EEEEEEE
T ss_pred EEEEEEe
Confidence 9999975
No 8
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 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 L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=99.91 E-value=1.4e-25 Score=149.08 Aligned_cols=48 Identities=48% Similarity=0.774 Sum_probs=45.0
Q ss_pred eEEEEccccccccCCCcEEEeCCcccccccccCCceeccCHHHHHHhH
Q 029153 51 RKIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMK 98 (198)
Q Consensus 51 mkVIL~edV~~LGk~GdiV~Vk~GyARNfLiP~glA~~aT~~nlk~~~ 98 (198)
|+|||++||+|||++||+|+|++|||||||+|+|+|+|||++|+++++
T Consensus 1 m~ViL~~dv~~lG~~Gdiv~V~~Gy~RN~L~p~~~A~~at~~~~~~~e 48 (48)
T PF01281_consen 1 MKVILLKDVPGLGKKGDIVEVKPGYARNFLIPQGLAVYATPENLKQLE 48 (48)
T ss_dssp -EEEESSCCTTSBSTTEEEE-SHHHHHHTTTTTTSEEECSHHHHHHHH
T ss_pred CEEEEcccccccCCCCCEEEEccceeeehccCCCceeeCCHHHHHhcC
Confidence 899999999999999999999999999999999999999999999875
No 9
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=58.15 E-value=5.2 Score=30.75 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=21.8
Q ss_pred CHHHHHHHHHHhcCCceecceecc
Q 029153 145 TAQDVVDIIKAQLQRDVDKKIVDL 168 (198)
Q Consensus 145 t~~dI~~~l~~~~gi~Idk~~I~l 168 (198)
||.++++++++.||++|++..++-
T Consensus 21 TPs~v~~aVk~eFgi~vsrQqve~ 44 (104)
T PF10045_consen 21 TPSEVAEAVKEEFGIDVSRQQVES 44 (104)
T ss_pred CHHHHHHHHHHHhCCccCHHHHHH
Confidence 789999999999999999988764
No 10
>PF07523 Big_3: Bacterial Ig-like domain (group 3); InterPro: IPR011080 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.; PDB: 2L7Y_A 2KPN_A.
Probab=55.12 E-value=30 Score=23.45 Aligned_cols=25 Identities=24% Similarity=0.417 Sum_probs=20.6
Q ss_pred CccceeeEEEEEEeCCCcEEEEEEEE
Q 029153 170 EIRETGEYIAQLKLHPEVTARIRLNV 195 (198)
Q Consensus 170 ~Ik~~G~y~V~V~L~~~v~a~i~v~V 195 (198)
+-...|.|.|.+.... .+++++|.|
T Consensus 43 d~~~~G~y~Vt~~y~~-~t~t~~VtV 67 (67)
T PF07523_consen 43 DTSKAGTYTVTYTYKG-VTATFTVTV 67 (67)
T ss_dssp -TTS-CCEEEEEEECT-EEEEEEEEE
T ss_pred ecCCCceEEEEEEECC-EEEEEEEEC
Confidence 3678899999999998 888888876
No 11
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=54.18 E-value=7.2 Score=25.84 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=16.4
Q ss_pred eccCHHHHHHHHHHhcCCceecce
Q 029153 142 GSVTAQDVVDIIKAQLQRDVDKKI 165 (198)
Q Consensus 142 GSVt~~dI~~~l~~~~gi~Idk~~ 165 (198)
..||.++|.+.|.+.||+++..++
T Consensus 19 ~~vT~k~vr~~Le~~~~~dL~~~K 42 (54)
T PF08766_consen 19 DTVTKKQVREQLEERFGVDLSSRK 42 (54)
T ss_dssp GG--HHHHHHHHHHH-SS--SHHH
T ss_pred hHhhHHHHHHHHHHHHCCCcHHHH
Confidence 589999999999999999987554
No 12
>cd08505 PBP2_NikA_DppA_OppA_like_18 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=50.80 E-value=23 Score=33.44 Aligned_cols=53 Identities=23% Similarity=0.365 Sum_probs=40.0
Q ss_pred eEEEEEecC---CCCcee----e-ccCHHHHHHHHHHhcCCceecceecccCccceeeEEEEEEeCCC
Q 029153 127 AFKVKRKGG---KGKQIF----G-SVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPE 186 (198)
Q Consensus 127 ~l~i~~k~g---~~gklf----G-SVt~~dI~~~l~~~~gi~Idk~~I~l~~Ik~~G~y~V~V~L~~~ 186 (198)
+++|+.+.+ .||..| | .||++|++-.+..-.+ + .+..|+.++.|+|+|+|..-
T Consensus 66 t~tf~LR~~v~fsDG~~~~~~~G~p~TA~Dv~~s~~~~~~----~---~i~~v~~~d~~tv~~~l~~p 126 (528)
T cd08505 66 VYTIRIKPGIYFQPDPAFPKGKTRELTAEDYVYSIKRLAD----P---PLEGVEAVDRYTLRIRLTGP 126 (528)
T ss_pred EEEEEEcCCCEeeCCcccccCCCcccchHHhhhhHhhhhc----C---cccceEeccCcEEEEEecCC
Confidence 688887765 466776 3 7999999999975422 2 34458999999999999863
No 13
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=49.29 E-value=18 Score=22.84 Aligned_cols=21 Identities=10% Similarity=0.305 Sum_probs=17.7
Q ss_pred cCCCCceeeccCHHHHHHHHH
Q 029153 134 GGKGKQIFGSVTAQDVVDIIK 154 (198)
Q Consensus 134 ~g~~gklfGSVt~~dI~~~l~ 154 (198)
.+++|++-|.||..||.+.+.
T Consensus 36 ~d~~~~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 36 VDEDGKLVGIISRSDLLKALL 56 (57)
T ss_dssp ESTTSBEEEEEEHHHHHHHHH
T ss_pred EecCCEEEEEEEHHHHHhhhh
Confidence 346689999999999998874
No 14
>cd05886 Ig1_Nectin-1_like First immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins. Ig1_Nectin-1_like: domain similar to the first immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111). Nectin-1 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. In addition nectins heterophilically trans-interact with other CAMs such as nectin-like molecules (Necls), nectin-1 for example, has been shown to trans-interact with Necl-1. Nectins also interact with various other proteins, including the actin filament (F-actin)-binding protein, afadin. Mutation in the human nectin-1 gene is
Probab=36.00 E-value=79 Score=23.32 Aligned_cols=31 Identities=23% Similarity=0.554 Sum_probs=23.6
Q ss_pred eecccC--ccceeeEEEEEEeCCC--cEEEEEEEE
Q 029153 165 IVDLPE--IRETGEYIAQLKLHPE--VTARIRLNV 195 (198)
Q Consensus 165 ~I~l~~--Ik~~G~y~V~V~L~~~--v~a~i~v~V 195 (198)
.|.|.+ +...|.|.|+|+-+++ -++++.+.|
T Consensus 64 Si~i~nl~~~D~G~Y~C~v~t~P~g~~~~~~~L~V 98 (99)
T cd05886 64 TISLSRLELEDEGVYICEFATFPTGNRESQLNLTV 98 (99)
T ss_pred eEEEcCCccccCEEEEEEEEeCCCCCeEEEEEEEE
Confidence 466665 7899999999998655 567777766
No 15
>cd07694 Ig2_CD4 Second immunoglobulin (Ig) domain of CD4. Ig2_CD4; second immunoglobulin (Ig) domain of CD4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.
Probab=34.25 E-value=96 Score=23.05 Aligned_cols=38 Identities=21% Similarity=0.377 Sum_probs=28.9
Q ss_pred eecceecccC--ccceeeEEEEEEeCCC-cEEEEEEEEeeC
Q 029153 161 VDKKIVDLPE--IRETGEYIAQLKLHPE-VTARIRLNVFAN 198 (198)
Q Consensus 161 Idk~~I~l~~--Ik~~G~y~V~V~L~~~-v~a~i~v~V~~~ 198 (198)
-+++.+.++. ..+=|++.|.|..+.. ..+.++|.|.++
T Consensus 48 ~~~ktL~~~qv~~qdSG~WtC~V~~~~k~~~~~~~V~Vl~f 88 (88)
T cd07694 48 QDKKTLNLVQLGPNDSGTWDCIVSVNSSEKTLKLDIKVLAF 88 (88)
T ss_pred CCccEEEeceeCcccCCEEEEEEEECceEEEEEeeEEEEeC
Confidence 4566777775 7899999999998744 457888888764
No 16
>PF02315 MDH: Methanol dehydrogenase beta subunit; InterPro: IPR003420 Methanol dehydrogenase (MDH) (1.1.99.8 from EC), found in Gram-negative bacteria, is a pyrroloquinoline quinone (PQQ)-containing enzyme which oxidises methanol to formaldehyde. It is located in the periplasmic space and passes electrons derived from the oxidation of methanol to the soluble cytochrome cL []. The enzyme is a tetramer composed of two large alpha subunits and two smaller beta subunits. The alpha subunit binds the PQQ cofactor and contains the active site, while the function of the beta subunit is currently unknown []. The alpha subunit forms an eight-bladed propeller structure, with several novel tryptophan-docking motifs linking the individual blades together. This entry represents the beta subunit of methanol dehydrogenase.; GO: 0004022 alcohol dehydrogenase (NAD) activity, 0015946 methanol oxidation, 0055114 oxidation-reduction process; PDB: 1LRW_B 2D0V_J 2AD6_B 1G72_B 4AAH_D 2AD8_D 2AD7_D 1H4J_D 1H4I_B 1W6S_B ....
Probab=32.44 E-value=1.3e+02 Score=22.57 Aligned_cols=50 Identities=22% Similarity=0.290 Sum_probs=25.9
Q ss_pred CCCcEEEeCCcccccccccCCcee--ccCHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 029153 64 KKGQLLDVKAGFYRNYLHPMGKAQ--IVTPLLLKEMKMEEERIEAEKKRVKEEAQQLA 119 (198)
Q Consensus 64 k~GdiV~Vk~GyARNfLiP~glA~--~aT~~nlk~~~~~~~~~e~~~~~~~~~a~~~~ 119 (198)
..|+.-+-+||| |.+.|- |-...+-+++..+.+.+++.+++.....+.++
T Consensus 30 apG~CWEpkPGy------PekiaGSKYDPkHdp~ELnKQ~~si~~me~RN~kR~~~fk 81 (93)
T PF02315_consen 30 APGNCWEPKPGY------PEKIAGSKYDPKHDPKELNKQQESIKAMEERNAKRVENFK 81 (93)
T ss_dssp BTTB-----TTS-------SS-TTSTT-----HHHHTHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCccccCCCCCC------cccccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 468888999998 877763 55566778888877777776665555544444
No 17
>PF13592 HTH_33: Winged helix-turn helix
Probab=31.92 E-value=27 Score=23.41 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=20.7
Q ss_pred eccCHHHHHHHHHHhcCCceeccee
Q 029153 142 GSVTAQDVVDIIKAQLQRDVDKKIV 166 (198)
Q Consensus 142 GSVt~~dI~~~l~~~~gi~Idk~~I 166 (198)
+--|..+|++.|.+++|+.+....|
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v 27 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGV 27 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHH
Confidence 4578899999999999998876655
No 18
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=31.43 E-value=76 Score=23.84 Aligned_cols=45 Identities=16% Similarity=0.169 Sum_probs=9.2
Q ss_pred cccccCCCcEEEeCCcccccccccCCceeccCHHHHHHhHHHHHH
Q 029153 59 VAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEER 103 (198)
Q Consensus 59 V~~LGk~GdiV~Vk~GyARNfLiP~glA~~aT~~nlk~~~~~~~~ 103 (198)
|.|.-..-+.++..||.+.|-.-|-=.++..|++.|+.-+.+-..
T Consensus 43 i~gQ~~~~~~~e~~P~~~~~~~QPLc~~~~VT~eDIr~QE~rVk~ 87 (96)
T PF14048_consen 43 ITGQTSSKDALEKNPGVGLNPPQPLCKQFVVTEEDIRRQERRVKK 87 (96)
T ss_dssp --------------------------T-----HHHHHHHHHHHHH
T ss_pred CcCCccchhhhccCcccccCCCcccccCCccCHHHHHHHHHHHHH
Confidence 444433444889999999999999999999999988766544433
No 19
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=31.30 E-value=24 Score=29.47 Aligned_cols=61 Identities=18% Similarity=0.282 Sum_probs=32.9
Q ss_pred cCHHHHHHhHHHHHHHHHHHH---HHHHHHHH-HHHHhccCCeEEEEEecCCCCceeeccCHHHHHHHHHHhc
Q 029153 89 VTPLLLKEMKMEEERIEAEKK---RVKEEAQQ-LALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVDIIKAQL 157 (198)
Q Consensus 89 aT~~nlk~~~~~~~~~e~~~~---~~~~~a~~-~~~~L~~~~~l~i~~k~g~~gklfGSVt~~dI~~~l~~~~ 157 (198)
.|++|.+-+..-.....+... +..+-.++ +.+-||+. .++-.--.+|| ||++-|+++.++.
T Consensus 2 LTkkN~~y~~~l~~~L~~~~~~e~~~e~~L~eil~~LleaQ------k~G~tA~~lfG--~P~~~a~eli~~~ 66 (206)
T PF06570_consen 2 LTKKNQEYIFDLRKYLRSSGVSEEEIEELLEEILPHLLEAQ------KKGKTARQLFG--DPKEYADELIKPL 66 (206)
T ss_pred CchHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH------hCCCcHHHHcC--CHHHHHHHHhccc
Confidence 478888877766655522111 11111222 22223432 22212235999 9999999998764
No 20
>COG1438 ArgR Arginine repressor [Transcription]
Probab=28.91 E-value=31 Score=28.15 Aligned_cols=34 Identities=18% Similarity=0.416 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHhcCCceecceecccCccceeeEEEE
Q 029153 145 TAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQ 180 (198)
Q Consensus 145 t~~dI~~~l~~~~gi~Idk~~I~l~~Ik~~G~y~V~ 180 (198)
|..||++.|+++ |++|.-..|. -+||++|..+|+
T Consensus 22 TQ~Elv~~L~~~-Gi~vTQaTvS-RDlkelglvKv~ 55 (150)
T COG1438 22 TQEELVELLQEE-GIEVTQATVS-RDLKELGLVKVR 55 (150)
T ss_pred CHHHHHHHHHHc-CCeEehHHHH-HHHHHcCCEEec
Confidence 667889998876 8887655443 247888877776
No 21
>PF10147 CR6_interact: Growth arrest and DNA-damage-inducible proteins-interacting protein 1; InterPro: IPR018472 Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity []. They may be involved in the hormone-mediated regulation of NR4A1 transcriptional activity.; GO: 0007049 cell cycle, 0005634 nucleus
Probab=26.62 E-value=2.2e+02 Score=24.54 Aligned_cols=21 Identities=10% Similarity=0.276 Sum_probs=16.6
Q ss_pred HHHHHHHHHhcCCceecceec
Q 029153 147 QDVVDIIKAQLQRDVDKKIVD 167 (198)
Q Consensus 147 ~dI~~~l~~~~gi~Idk~~I~ 167 (198)
.-+++++++.||+.||++.=.
T Consensus 159 erl~eEvre~fGy~vDprdpr 179 (217)
T PF10147_consen 159 ERLIEEVREHFGYKVDPRDPR 179 (217)
T ss_pred HHHHHHHHHHhCCcCCCCChH
Confidence 446788889999999998643
No 22
>cd05714 Ig_CSPGs_LP Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage link protein (LP) and similar proteins. Ig_CSPGs_LP: immunoglobulin (Ig)-like domain similar to that found in chondroitin sulfate proteoglycans (CSPGs) and human cartilage link protein (LP). Included in this group are the CSPGs aggrecan, versican, and neurocan. In CSPGs this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggrecan and versican have a wide distribution in connective tissue and extracellular matrices. Neurocan is localized almost exclusively in nervous tissue.
Probab=25.99 E-value=1.5e+02 Score=21.19 Aligned_cols=33 Identities=15% Similarity=0.271 Sum_probs=24.6
Q ss_pred eecccC--ccceeeEEEEEEeCCC-cEEEEEEEEee
Q 029153 165 IVDLPE--IRETGEYIAQLKLHPE-VTARIRLNVFA 197 (198)
Q Consensus 165 ~I~l~~--Ik~~G~y~V~V~L~~~-v~a~i~v~V~~ 197 (198)
.|.+.+ ...-|+|.|.|.-..+ .+..+.+.|.+
T Consensus 69 sL~I~~v~~sD~G~Y~C~v~~~~~~~~~~v~L~V~~ 104 (106)
T cd05714 69 SLVITDLRLEDSGRYRCEVIDGIEDEQDTVELEVRG 104 (106)
T ss_pred eEEECCCCHHHCEEEEEEEEcCCCceEEEEEEEEEE
Confidence 344555 6789999999997633 58888888864
No 23
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=25.96 E-value=2.4e+02 Score=19.75 Aligned_cols=46 Identities=15% Similarity=0.257 Sum_probs=32.8
Q ss_pred ccCHHHHHHHHHHhcCCceecceecccCccceeeEEEEEEeCCCcEEEEEEE
Q 029153 143 SVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPEVTARIRLN 194 (198)
Q Consensus 143 SVt~~dI~~~l~~~~gi~Idk~~I~l~~Ik~~G~y~V~V~L~~~v~a~i~v~ 194 (198)
.++..+|...+..+ |.+| +.|++ ..-|-|+|++.-..+-..++.|+
T Consensus 28 ~~~~~~~~~~l~~~-G~~v--~~ve~---~~~g~yev~~~~~dG~~~ev~vD 73 (83)
T PF13670_consen 28 WLSIEQAVAKLEAQ-GYQV--REVEF---DDDGCYEVEARDKDGKKVEVYVD 73 (83)
T ss_pred cCCHHHHHHHHHhc-CCce--EEEEE---cCCCEEEEEEEECCCCEEEEEEc
Confidence 45899999999987 8755 44543 33455999888777777776664
No 24
>cd08490 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=25.50 E-value=1.4e+02 Score=27.04 Aligned_cols=60 Identities=12% Similarity=0.214 Sum_probs=39.1
Q ss_pred ccCCeEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCceecc-eecccCccceeeEEEEEEeCCC
Q 029153 123 ETVGAFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK-IVDLPEIRETGEYIAQLKLHPE 186 (198)
Q Consensus 123 ~~~~~l~i~~k~g---~~gklfGSVt~~dI~~~l~~~~gi~Idk~-~I~l~~Ik~~G~y~V~V~L~~~ 186 (198)
++. +++|+.+.| .||. .||++|+.-.+.....-..... .-.+..|+.++.|+|+|+|...
T Consensus 54 d~~-~~tf~Lr~~~~wsDG~---plTA~Dv~~s~~~~~~~~~~~~~~~~~~~v~~~d~~tv~i~l~~p 117 (470)
T cd08490 54 DDT-TWEFTLRDGVKFHDGT---PLTAEAVKASLERALAKSPRAKGGALIISVIAVDDYTVTITTKEP 117 (470)
T ss_pred CCC-EEEEEECCCCCccCCC---CCCHHHHHHHHHHHhccCccccccccceEEEecCCCEEEEEeCCC
Confidence 454 688887765 4565 6999999998875432111111 1112248889999999999864
No 25
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=23.85 E-value=58 Score=23.43 Aligned_cols=29 Identities=28% Similarity=0.354 Sum_probs=22.2
Q ss_pred CCceEEEEccccccccCCCcEEEeCCccccccc
Q 029153 48 KKTRKIILKEDVAELGKKGQLLDVKAGFYRNYL 80 (198)
Q Consensus 48 kk~mkVIL~edV~~LGk~GdiV~Vk~GyARNfL 80 (198)
.+.+.+.|..+++ .||.|-|..|||+.-+
T Consensus 25 ~~~v~l~lv~~~~----vGD~VLVH~G~Ai~~i 53 (76)
T TIGR00074 25 KRDVSLDLVGEVK----VGDYVLVHVGFAISVL 53 (76)
T ss_pred EEEEEEEeeCCCC----CCCEEEEecChhhhhC
Confidence 4446777776654 8999999999998543
No 26
>cd08496 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=23.55 E-value=1.5e+02 Score=26.90 Aligned_cols=57 Identities=9% Similarity=0.136 Sum_probs=37.6
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCceecc-ee-cccCccceeeEEEEEEeCCC
Q 029153 127 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK-IV-DLPEIRETGEYIAQLKLHPE 186 (198)
Q Consensus 127 ~l~i~~k~g---~~gklfGSVt~~dI~~~l~~~~gi~Idk~-~I-~l~~Ik~~G~y~V~V~L~~~ 186 (198)
+++|+.+.| .||+ .||++|++-.+..-...+.... .+ .+..++..|.|+|+|+|...
T Consensus 59 t~tf~Lr~~~~f~DG~---pvTA~Dv~~s~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~p 120 (454)
T cd08496 59 TLTLHLREGLTFSDGT---PLDAAAVKANLDRGKSTGGSQVKQLASISSVEVVDDTTVTLTLSQP 120 (454)
T ss_pred EEEEEeCCCCCccCCC---CcCHHHHHHHHHHHhCCCcchhhhccccceEEecCCCEEEEEeCCC
Confidence 678877755 4565 6899999999976533221111 11 12248889999999999753
No 27
>PF06560 GPI: Glucose-6-phosphate isomerase (GPI); InterPro: IPR010551 This entry consists of several bacterial and archaeal glucose-6-phosphate isomerase (GPI) proteins (5.3.1.9 from EC), which are involved in glycolysis and in gluconeogenesis and catalyse the conversion of D-glucose 6-phosphate to D-fructose 6-phosphate. The deduced amino acid sequence of the first archaeal PGI isolated from Pyrococcus furiosus revealed that it is not related to its eukaryotic and many of its bacterial counterparts. In contrast, this archaeal PGI shares similarity with the cupin superfamily that consists of a variety of proteins that are generally involved in sugar metabolism in both prokaryotes and eukaryotes [].; GO: 0004347 glucose-6-phosphate isomerase activity, 0006094 gluconeogenesis, 0006096 glycolysis, 0005737 cytoplasm; PDB: 1J3Q_B 1J3R_B 1J3P_A 2GC0_A 1X8E_A 1X82_A 1QY4_B 2GC2_B 1QXJ_A 1QXR_B ....
Probab=23.43 E-value=56 Score=27.35 Aligned_cols=26 Identities=19% Similarity=0.386 Sum_probs=15.5
Q ss_pred EEEcccccc---------ccCCCcEEEeCCccccc
Q 029153 53 IILKEDVAE---------LGKKGQLLDVKAGFYRN 78 (198)
Q Consensus 53 VIL~edV~~---------LGk~GdiV~Vk~GyARN 78 (198)
++|+|+..+ -.++||+|-|.+|||-.
T Consensus 95 ~~lLq~~~~~~~~~~~~v~~~~G~~v~IPp~yaH~ 129 (182)
T PF06560_consen 95 LILLQKEEGDDVGDVIAVEAKPGDVVYIPPGYAHR 129 (182)
T ss_dssp EEEEE-TTS-----EEEEEE-TTEEEEE-TT-EEE
T ss_pred EEEEEecCCCcceeEEEEEeCCCCEEEECCCceEE
Confidence 567777665 15778888888888753
No 28
>smart00116 CBS Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease.
Probab=23.32 E-value=71 Score=17.89 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=14.4
Q ss_pred CCCceeeccCHHHHHHHH
Q 029153 136 KGKQIFGSVTAQDVVDII 153 (198)
Q Consensus 136 ~~gklfGSVt~~dI~~~l 153 (198)
+++++.|.++..++...+
T Consensus 31 ~~~~~~g~i~~~~l~~~~ 48 (49)
T smart00116 31 EEGRLVGIVTRRDIIKAL 48 (49)
T ss_pred CCCeEEEEEEHHHHHHhh
Confidence 346899999999987765
No 29
>cd08502 PBP2_NikA_DppA_OppA_like_16 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=23.22 E-value=1.6e+02 Score=26.92 Aligned_cols=57 Identities=19% Similarity=0.322 Sum_probs=37.9
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCceecc-eec-ccCccceeeEEEEEEeCCC
Q 029153 127 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK-IVD-LPEIRETGEYIAQLKLHPE 186 (198)
Q Consensus 127 ~l~i~~k~g---~~gklfGSVt~~dI~~~l~~~~gi~Idk~-~I~-l~~Ik~~G~y~V~V~L~~~ 186 (198)
+++|+.+.+ .||. .||++||.-.+..-.+...... ... +..|+..|.|+|.|+|...
T Consensus 59 ~~tf~LR~~v~wsdG~---~lTA~Dv~~s~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~~~l~~p 120 (472)
T cd08502 59 TYTFTLRDGLKFHDGS---PVTAADVVASLKRWAKRDAMGQALMAAVESLEAVDDKTVVITLKEP 120 (472)
T ss_pred EEEEEEcCCCEecCCc---cCcHHHHHHHHHHHhccCcccccccccceeEEecCCCEEEEEeCCC
Confidence 688887765 4554 6999999988875433221111 111 2348889999999999754
No 30
>cd08506 PBP2_clavulanate_OppA2 The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold. Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. Most of other periplasmic binding proteins are comprised of only two globular subdomains cor
Probab=22.75 E-value=1.1e+02 Score=27.80 Aligned_cols=45 Identities=18% Similarity=0.260 Sum_probs=33.2
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCceecceecccCccceeeEEEEEEeCCC
Q 029153 127 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPE 186 (198)
Q Consensus 127 ~l~i~~k~g---~~gklfGSVt~~dI~~~l~~~~gi~Idk~~I~l~~Ik~~G~y~V~V~L~~~ 186 (198)
+++|+.+.| .||. .||++|++..+....+ |+.++.|+|+|+|...
T Consensus 65 ~~tf~Lr~~vkf~dG~---p~TA~Dv~~s~~~~~~------------v~~~d~~tv~i~l~~p 112 (466)
T cd08506 65 TWTYTLRDGLKFEDGT---PITAKDVKYGIERSFA------------IETPDDKTIVFHLNRP 112 (466)
T ss_pred EEEEEECCCCEeCCCC---eeeHHHHHHhhhheEE------------EEecCCCeEEEEecCC
Confidence 688887755 3565 5999999999976432 6677788888888753
No 31
>cd08518 PBP2_NikA_DppA_OppA_like_19 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=22.04 E-value=1.3e+02 Score=27.39 Aligned_cols=57 Identities=14% Similarity=0.297 Sum_probs=38.1
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCceeccee-cccCccceeeEEEEEEeCCC
Q 029153 127 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKIV-DLPEIRETGEYIAQLKLHPE 186 (198)
Q Consensus 127 ~l~i~~k~g---~~gklfGSVt~~dI~~~l~~~~gi~Idk~~I-~l~~Ik~~G~y~V~V~L~~~ 186 (198)
+++|+.+.| .||. .||++|++-.+....+-......+ .+..|+.++.|+|+|+|..-
T Consensus 58 t~tf~LR~gv~fsDG~---p~TA~Dv~~s~~r~~~~~~~~~~~~~i~~v~~~d~~Tv~i~l~~p 118 (464)
T cd08518 58 TWTFTLRDDVKFSDGE---PLTAEDVAFTYNTAKDPGSASDILSNLEDVEAVDDYTVKFTLKKP 118 (464)
T ss_pred EEEEEECCCCEecCCc---CCchHHhhehHHHhhCCCCCcccccceeEEEecCCCEEEEEEcCC
Confidence 688887755 4664 699999999887653322111111 12348889999999999753
No 32
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=21.84 E-value=78 Score=22.31 Aligned_cols=19 Identities=11% Similarity=0.319 Sum_probs=16.5
Q ss_pred CCceeeccCHHHHHHHHHH
Q 029153 137 GKQIFGSVTAQDVVDIIKA 155 (198)
Q Consensus 137 ~gklfGSVt~~dI~~~l~~ 155 (198)
|+.+|+-+|+++|.+.|.+
T Consensus 61 ~~~~~~~~~~e~i~~il~~ 79 (80)
T cd03081 61 DGEVHGRVDPEKFDALLAE 79 (80)
T ss_pred CCEEECCCCHHHHHHHHHc
Confidence 6789999999999988853
No 33
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 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 [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=21.82 E-value=61 Score=23.58 Aligned_cols=43 Identities=16% Similarity=0.166 Sum_probs=29.6
Q ss_pred eccCHHHHHHHHHHhcCCceecceecccCc-cceeeEE--EEEEeCCC
Q 029153 142 GSVTAQDVVDIIKAQLQRDVDKKIVDLPEI-RETGEYI--AQLKLHPE 186 (198)
Q Consensus 142 GSVt~~dI~~~l~~~~gi~Idk~~I~l~~I-k~~G~y~--V~V~L~~~ 186 (198)
++.+-.||.+.|.+++|. |++.|.+..| ..+|... ...++|++
T Consensus 11 ~Tpsr~ei~~klA~~~~~--~~~~ivv~~~~t~fG~~~s~g~a~IYd~ 56 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNV--DPDLIVVFGIKTEFGGGKSTGFAKIYDS 56 (84)
T ss_dssp SS--HHHHHHHHHHHHTS--TGCCEEEEEEEESSSSSEEEEEEEEESS
T ss_pred CCCCHHHHHHHHHHHhCC--CCCeEEEeccEecCCCceEEEEEEEeCC
Confidence 578999999999999775 8888887764 4676653 33445444
No 34
>PRK07639 acyl carrier protein; Provisional
Probab=21.50 E-value=32 Score=24.89 Aligned_cols=33 Identities=21% Similarity=0.208 Sum_probs=25.2
Q ss_pred ccCHHHHHHHHHHhcCCceecceecccCcccee
Q 029153 143 SVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETG 175 (198)
Q Consensus 143 SVt~~dI~~~l~~~~gi~Idk~~I~l~~Ik~~G 175 (198)
|+..-+++-+|...||++|+...+....+.++|
T Consensus 40 Sld~velv~~lE~~fgi~i~d~~~~~~~~~Tv~ 72 (86)
T PRK07639 40 SVMMLQLIVYIEMDVKLCVPEDEVDPKAFLTVG 72 (86)
T ss_pred hHHHHHHHHHHHHHHCCccCHHHccHHHhCCHH
Confidence 888888899999999999988776433344443
No 35
>PRK07668 hypothetical protein; Validated
Probab=21.40 E-value=37 Score=29.91 Aligned_cols=61 Identities=16% Similarity=0.229 Sum_probs=33.9
Q ss_pred cCHHHHHHhHHHHHHHHHH---HHHHHHHHHHHHHH-hccCCeEEEEEecCC-CCceeeccCHHHHHHHHHHhc
Q 029153 89 VTPLLLKEMKMEEERIEAE---KKRVKEEAQQLALI-FETVGAFKVKRKGGK-GKQIFGSVTAQDVVDIIKAQL 157 (198)
Q Consensus 89 aT~~nlk~~~~~~~~~e~~---~~~~~~~a~~~~~~-L~~~~~l~i~~k~g~-~gklfGSVt~~dI~~~l~~~~ 157 (198)
.|++|.+-+.+-......+ +++..+-.+++... +++ .+.|+ ...+||+ +|+++++++.+..
T Consensus 2 LTkeNeefl~~L~~yL~~~glseeeieeiL~Ei~~hLlEg-------Qk~GkTA~~IfG~-sPk~yA~EL~~~~ 67 (254)
T PRK07668 2 LSKEGRKFLDDTRVYLIAKGIKEEDIESFLEDAELHLIEG-------EKDGKTVEDIFGD-SPKEYANELVKEM 67 (254)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-------HHcCCcHHHHhCC-CHHHHHHHHhccc
Confidence 5788877777655444211 11111222233333 233 23333 2469999 9999999998763
No 36
>cd05713 Ig_MOG_like Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG). Ig_MOG_like: immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG). MOG, a minor component of the myelin sheath, is an important CNS-specific autoantigen, linked to the pathogenesis of multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE). It is a transmembrane protein having an extracellular Ig domain. MOG is expressed in the CNS on the outermost lamellae of the myelin sheath, and on the surface of oligodendrocytes, and may participate in the completion, compaction, and/or maintenance of myelin. This group also includes butyrophilin (BTN). BTN is the most abundant protein in bovine milk-fat globule membrane (MFGM).
Probab=21.20 E-value=1.6e+02 Score=20.68 Aligned_cols=30 Identities=17% Similarity=0.255 Sum_probs=20.9
Q ss_pred ecccC--ccceeeEEEEEEeCCC-cEEEEEEEE
Q 029153 166 VDLPE--IRETGEYIAQLKLHPE-VTARIRLNV 195 (198)
Q Consensus 166 I~l~~--Ik~~G~y~V~V~L~~~-v~a~i~v~V 195 (198)
+.|.+ ...-|+|.|.|.-.++ .++.|.++|
T Consensus 67 L~I~~v~~~D~G~Y~C~v~~~~~~~~~~i~l~v 99 (100)
T cd05713 67 LRIHNVRASDEGLYTCFFQSDGFYEEATVELKV 99 (100)
T ss_pred EEEEcCChhhCEEEEEEEecCCcEEEEEEEEEE
Confidence 44554 6789999999985555 446666665
No 37
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=21.00 E-value=90 Score=21.07 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=16.9
Q ss_pred CCCceeeccCHHHHHHHHHH
Q 029153 136 KGKQIFGSVTAQDVVDIIKA 155 (198)
Q Consensus 136 ~~gklfGSVt~~dI~~~l~~ 155 (198)
+++.+||-||+++|.+.|.+
T Consensus 57 ~~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 57 PDGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred CCCeEEccCCHHHHHHHHHh
Confidence 35789999999999988864
No 38
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=20.31 E-value=1.1e+02 Score=25.84 Aligned_cols=86 Identities=13% Similarity=0.128 Sum_probs=45.7
Q ss_pred EeCCcccccccccCCceeccCHH------HHHHhHHHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEEEecCCCCceeec
Q 029153 70 DVKAGFYRNYLHPMGKAQIVTPL------LLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKVKRKGGKGKQIFGS 143 (198)
Q Consensus 70 ~Vk~GyARNfLiP~glA~~aT~~------nlk~~~~~~~~~e~~~~~~~~~a~~~~~~L~~~~~l~i~~k~g~~gklfGS 143 (198)
+--+|...|-.+-.|+.+...-- ....|...+++ .+....+|+++...+.+. -.+ .+. +++.-+.
T Consensus 28 ~~~~~~~~~n~~s~g~svL~~~~~ll~~La~akf~~Mq~~-----s~~ar~aQ~mAN~VDevI-A~v-~k~--ddK~k~~ 98 (196)
T PRK15364 28 GSQDDLSQQNPFAEGYGVLLILLMVIQAIANNKFIEVQKN-----AERARNTQEKSNEMDEVI-AKA-AKG--DAKTKEE 98 (196)
T ss_pred ccccchhhhhhhhhhHHHHHHHHHHHHHHHHhHHHHHHHH-----HHHHHHHHHHHHHHHHHH-HHH-hcC--CCccccc
Confidence 33455555556666666544222 12222222222 223345677776666541 112 222 2233344
Q ss_pred cCHHHHHHHHHHhcCCceeccee
Q 029153 144 VTAQDVVDIIKAQLQRDVDKKIV 166 (198)
Q Consensus 144 Vt~~dI~~~l~~~~gi~Idk~~I 166 (198)
+ |+||++.+++. ||.||-..|
T Consensus 99 L-PddVI~YmrdN-gI~VdG~si 119 (196)
T PRK15364 99 V-PEDVIKYMRDN-GILIDGMTI 119 (196)
T ss_pred C-CHHHHHHHHHc-Cceecccch
Confidence 4 78999999996 999987776
No 39
>cd05887 Ig1_Nectin-3_like First immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3) and similar proteins. Ig1_Nectin-3_like: domain similar to the first immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3). Nectin-3 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which participate in adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. For example, during spermatid development, the nectin-3,-2 trans-interaction is required for the formation of Sertoli cell-spermatid junctions in testis, and during morphogenesis of the ciliary body, the nectin-3,-1 trans-interaction is important for apex-apex adhesion between the pigment and non-pigment layers of the ciliary epithelia. Nectins also
Probab=20.26 E-value=2.2e+02 Score=20.93 Aligned_cols=32 Identities=19% Similarity=0.326 Sum_probs=22.8
Q ss_pred ceecccC--ccceeeEEEEEEeCCC--cEEEEEEEE
Q 029153 164 KIVDLPE--IRETGEYIAQLKLHPE--VTARIRLNV 195 (198)
Q Consensus 164 ~~I~l~~--Ik~~G~y~V~V~L~~~--v~a~i~v~V 195 (198)
-.|.|.+ ....|.|.|+++-+|. .++.+.+.|
T Consensus 60 ~sl~i~nv~~~D~G~Y~C~v~tfP~G~~~~~~~l~~ 95 (96)
T cd05887 60 ATIMLENVGFSDIGVYICKAVTFPLGNTQSSTTVTV 95 (96)
T ss_pred cEEEEeCCCccccEEEEEEEEeCCCCCeeEEEEEEE
Confidence 3455555 5678999999987765 457766665
Done!