Query 031586
Match_columns 157
No_of_seqs 140 out of 1068
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 02:34:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031586.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031586hhsearch_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 6.2E-56 1.4E-60 340.5 17.7 152 4-157 2-153 (153)
2 TIGR00158 L9 ribosomal protein 100.0 2.8E-54 6E-59 330.0 17.3 146 10-157 1-148 (148)
3 PRK00137 rplI 50S ribosomal pr 100.0 5.1E-53 1.1E-57 322.7 18.3 146 10-157 1-147 (147)
4 COG0359 RplI Ribosomal protein 100.0 2.3E-51 5E-56 312.6 16.3 145 10-156 1-146 (148)
5 PRK14538 putative bifunctional 100.0 4.1E-43 9E-48 325.9 13.8 146 9-156 688-834 (838)
6 KOG4607 Mitochondrial ribosoma 99.9 7.3E-28 1.6E-32 191.5 9.3 149 6-156 45-194 (222)
7 PF03948 Ribosomal_L9_C: Ribos 99.9 1E-26 2.3E-31 163.4 10.9 86 71-157 1-87 (87)
8 PF01281 Ribosomal_L9_N: Ribos 99.9 7.8E-27 1.7E-31 147.1 4.2 48 10-57 1-48 (48)
9 PF10045 DUF2280: Uncharacteri 69.0 2.8 6.1E-05 30.4 1.3 24 104-127 21-44 (104)
10 PF07523 Big_3: Bacterial Ig-l 68.5 9.8 0.00021 24.5 3.8 25 129-154 43-67 (67)
11 PF08766 DEK_C: DEK C terminal 65.3 3.5 7.6E-05 25.9 1.1 23 101-123 19-41 (54)
12 PF00571 CBS: CBS domain CBS d 64.4 7.7 0.00017 23.3 2.5 21 93-113 36-56 (57)
13 cd08505 PBP2_NikA_DppA_OppA_li 59.8 15 0.00033 33.0 4.5 56 82-145 63-126 (528)
14 PF13592 HTH_33: Winged helix- 39.6 16 0.00034 23.2 1.0 25 101-125 3-27 (60)
15 PF06560 GPI: Glucose-6-phosph 38.9 23 0.00051 28.0 2.1 25 12-36 95-128 (182)
16 cd08490 PBP2_NikA_DppA_OppA_li 37.3 86 0.0019 27.0 5.5 60 82-145 54-117 (470)
17 PRK07639 acyl carrier protein; 36.0 14 0.00031 25.3 0.4 33 102-134 40-72 (86)
18 TIGR00074 hypC_hupF hydrogenas 34.9 34 0.00074 23.3 2.1 25 9-37 27-51 (76)
19 cd08502 PBP2_NikA_DppA_OppA_li 34.3 99 0.0021 26.9 5.5 57 86-145 59-120 (472)
20 cd08518 PBP2_NikA_DppA_OppA_li 34.2 70 0.0015 27.7 4.5 57 86-145 58-118 (464)
21 cd08496 PBP2_NikA_DppA_OppA_li 33.1 99 0.0021 26.7 5.3 56 86-144 59-119 (454)
22 cd08506 PBP2_clavulanate_OppA2 32.7 64 0.0014 27.9 4.0 45 86-145 65-112 (466)
23 PRK05087 D-alanine--poly(phosp 31.6 20 0.00043 24.2 0.5 34 101-134 35-68 (78)
24 cd03081 TRX_Fd_NuoE_FDH_gamma 31.2 43 0.00093 22.4 2.1 19 96-114 61-79 (80)
25 PF07718 Coatamer_beta_C: Coat 30.1 43 0.00094 25.5 2.2 19 86-104 118-136 (140)
26 smart00116 CBS Domain in cysta 30.1 49 0.0011 17.7 2.0 18 95-112 31-48 (49)
27 PF01282 Ribosomal_S24e: Ribos 29.5 38 0.00082 23.3 1.7 43 101-145 11-56 (84)
28 cd02980 TRX_Fd_family Thioredo 29.1 54 0.0012 21.0 2.3 20 95-114 57-76 (77)
29 PF00496 SBP_bac_5: Bacterial 28.3 1.1E+02 0.0023 25.3 4.5 57 86-145 19-83 (374)
30 cd07694 Ig2_CD4 Second immunog 27.8 1.5E+02 0.0033 20.7 4.5 38 120-157 48-88 (88)
31 PRK07081 acyl carrier protein; 27.7 21 0.00044 24.3 0.1 27 101-127 34-60 (83)
32 PF13565 HTH_32: Homeodomain-l 27.7 46 0.001 21.4 1.8 19 102-120 48-66 (77)
33 cd08514 PBP2_AppA_like The sub 27.5 1.5E+02 0.0033 25.7 5.5 57 86-145 59-123 (483)
34 cd05886 Ig1_Nectin-1_like Firs 26.7 1.4E+02 0.0031 20.7 4.2 31 124-154 64-98 (99)
35 cd04630 CBS_pair_17 The CBS do 26.0 1.1E+02 0.0023 20.4 3.5 19 97-115 35-53 (114)
36 cd04619 CBS_pair_6 The CBS dom 25.6 1.3E+02 0.0028 20.2 3.8 21 94-114 31-51 (114)
37 PF05157 T2SE_Nter: Type II se 25.5 47 0.001 22.4 1.6 19 101-119 5-23 (109)
38 KOG1387 Glycosyltransferase [C 25.4 55 0.0012 29.2 2.3 26 102-127 87-112 (465)
39 cd08503 PBP2_NikA_DppA_OppA_li 25.0 1.7E+02 0.0038 25.2 5.4 56 86-144 66-128 (460)
40 smart00089 PKD Repeats in poly 24.7 1.2E+02 0.0027 19.3 3.5 25 130-154 51-78 (79)
41 cd08501 PBP2_Lpqw The substrat 24.7 2E+02 0.0043 25.0 5.7 57 86-145 64-130 (486)
42 cd08512 PBP2_NikA_DppA_OppA_li 24.4 1.7E+02 0.0036 25.4 5.1 57 86-145 64-130 (476)
43 PF13833 EF-hand_8: EF-hand do 24.4 37 0.00081 20.3 0.8 24 101-125 3-27 (54)
44 PF14221 DUF4330: Domain of un 24.3 60 0.0013 25.1 2.1 19 94-112 5-23 (168)
45 PRK15109 antimicrobial peptide 24.3 1.4E+02 0.0031 26.8 4.8 59 86-144 95-174 (547)
46 PF06570 DUF1129: Protein of u 24.2 38 0.00082 26.8 1.0 17 98-116 50-66 (206)
47 PF13344 Hydrolase_6: Haloacid 24.1 1.4E+02 0.003 20.7 3.8 26 102-128 41-66 (101)
48 cd08494 PBP2_NikA_DppA_OppA_li 24.0 1.8E+02 0.0038 24.9 5.2 57 86-145 60-123 (448)
49 cd04590 CBS_pair_CorC_HlyC_ass 24.0 1.5E+02 0.0033 19.4 3.9 19 97-115 35-53 (111)
50 PF01455 HupF_HypC: HupF/HypC 24.0 45 0.00096 22.1 1.1 18 22-39 38-55 (68)
51 cd08489 PBP2_NikA The substrat 23.9 1.9E+02 0.0041 25.2 5.4 58 86-146 57-121 (488)
52 COG1438 ArgR Arginine represso 23.8 41 0.00089 25.9 1.1 34 104-139 22-55 (150)
53 cd00995 PBP2_NikA_DppA_OppA_li 23.8 1.9E+02 0.0042 24.5 5.4 56 86-144 59-121 (466)
54 cd08517 PBP2_NikA_DppA_OppA_li 23.6 2.2E+02 0.0048 24.5 5.8 56 86-144 61-121 (480)
55 PRK10413 hydrogenase 2 accesso 23.5 79 0.0017 21.8 2.4 30 8-38 29-59 (82)
56 PF09078 CheY-binding: CheY bi 23.4 1.5E+02 0.0033 19.6 3.6 51 73-127 12-64 (65)
57 PF14048 MBD_C: C-terminal dom 23.3 1.5E+02 0.0032 21.0 3.8 39 19-57 44-82 (96)
58 PF07726 AAA_3: ATPase family 23.3 25 0.00053 26.5 -0.2 11 13-23 2-12 (131)
59 cd04604 CBS_pair_KpsF_GutQ_ass 23.1 1.8E+02 0.0038 19.1 4.1 21 95-115 33-53 (114)
60 TIGR02294 nickel_nikA nickel A 22.8 2E+02 0.0044 25.2 5.4 57 86-145 64-127 (500)
61 COG0236 AcpP Acyl carrier prot 22.8 26 0.00056 23.3 -0.2 24 102-125 39-62 (80)
62 cd04607 CBS_pair_NTP_transfera 22.2 1.5E+02 0.0032 19.6 3.6 21 94-114 32-52 (113)
63 cd08499 PBP2_Ylib_like The sub 22.2 2.2E+02 0.0047 24.7 5.4 56 86-144 59-121 (474)
64 cd08492 PBP2_NikA_DppA_OppA_li 22.2 2.5E+02 0.0055 24.2 5.9 56 86-144 61-124 (484)
65 cd04606 CBS_pair_Mg_transporte 22.1 98 0.0021 20.5 2.7 19 94-112 91-109 (109)
66 cd08497 PBP2_NikA_DppA_OppA_li 21.9 1.9E+02 0.0041 25.4 5.0 55 86-144 77-138 (491)
67 cd03063 TRX_Fd_FDH_beta TRX-li 21.7 1E+02 0.0022 21.6 2.7 21 95-115 56-77 (92)
68 cd04632 CBS_pair_19 The CBS do 21.7 1.5E+02 0.0033 20.1 3.7 20 94-113 31-50 (128)
69 PF13954 PapC_N: PapC N-termin 21.5 2E+02 0.0043 21.3 4.4 25 132-156 28-52 (146)
70 cd04592 CBS_pair_EriC_assoc_eu 21.5 1.6E+02 0.0035 21.1 3.8 22 94-115 31-52 (133)
71 KOG3279 Uncharacterized conser 21.4 68 0.0015 26.5 1.9 28 77-105 250-277 (283)
72 PF05402 PqqD: Coenzyme PQQ sy 21.3 78 0.0017 19.9 1.9 22 101-124 28-49 (68)
73 cd08520 PBP2_NikA_DppA_OppA_li 21.1 2.4E+02 0.0051 24.4 5.4 57 86-145 60-122 (468)
74 cd04624 CBS_pair_11 The CBS do 20.9 1.8E+02 0.0038 19.1 3.7 22 94-115 31-52 (112)
75 cd04593 CBS_pair_EriC_assoc_ba 20.8 1.8E+02 0.004 19.2 3.8 21 94-114 31-51 (115)
76 cd03082 TRX_Fd_NuoE_W_FDH_beta 20.7 83 0.0018 20.7 2.0 18 96-113 53-70 (72)
77 cd03064 TRX_Fd_NuoE TRX-like [ 20.7 95 0.0021 20.4 2.3 19 96-114 61-79 (80)
78 TIGR01201 HU_rel DNA-binding p 20.6 82 0.0018 23.7 2.2 42 100-143 28-87 (145)
79 PF01516 Orbi_VP6: Orbivirus h 20.3 84 0.0018 27.2 2.4 37 96-134 123-168 (322)
80 COG0806 RimM RimM protein, req 20.2 58 0.0013 25.6 1.3 24 23-46 129-153 (174)
No 1
>CHL00160 rpl9 ribosomal protein L9; Provisional
Probab=100.00 E-value=6.2e-56 Score=340.54 Aligned_cols=152 Identities=39% Similarity=0.646 Sum_probs=145.2
Q ss_pred CCcCCceEEEEecccccccCCCcEEEecCccccccccCCCceEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 031586 4 MNKKTQIQIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFET 83 (157)
Q Consensus 4 ~~kkk~mkVIL~~dV~~lGk~Gdvv~Vk~GyaRN~LiP~glA~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~ 83 (157)
|+|+ |+|||++||++||++||+|+|+||||||||||+|+|++||++|+++++..++..++++++.+++|+++++.|++
T Consensus 2 ~~kk--mkVIL~~dV~~LGk~Gdiv~Vk~GYaRNyLiP~glA~~AT~~n~~~~e~~~~~~~~~~~~~~~~a~~la~~l~~ 79 (153)
T CHL00160 2 SKKK--IQVILKENIQKLGKSGTVIKVKSGYARNYLIPNKMAKVATQGSLKQQKMYQKILDLKLKEAKEKCLKVKQLLEE 79 (153)
T ss_pred CCce--EEEEEcccccccCCCCCEEEEcCchHhhhhcccCchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 6764 99999999999999999999999999999999999999999999999999999888888999999999999999
Q ss_pred CCeEEEEEecCCCCceeeccCHHHHHHHHHHhcCCCccCccccccCccceeeEEEEEEeCCCcEEEEEEEEeeC
Q 031586 84 VGAFKVKRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPEVTARIRLNVFAN 157 (157)
Q Consensus 84 ~~~l~i~~k~~~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I~l~~Ik~~G~~~v~v~l~~~v~~~l~v~V~~~ 157 (157)
++.++|++++|++|+||||||+.||+++|++++|++||+++|+||+|+++|+|.|+|+||++|+|+++|+|++.
T Consensus 80 ~~~~~i~~k~ge~gklfGSVt~~dIa~~l~~~~g~~idk~~I~l~~Ik~~G~~~v~v~L~~~V~a~i~v~V~~~ 153 (153)
T CHL00160 80 IQKFSVKKKVGENNQIFGSVTEKEISQIIKNKTNIDLEKQNIELPEIKTIGIYNIEIKLTSDVKANINLQILPE 153 (153)
T ss_pred CceEEEEEEeCCCCeEEcccCHHHHHHHHHHhhCCccccceeehhhccccEeEEEEEEecCCcEEEEEEEEEEC
Confidence 74599999999999999999999999999988899999999999889999999999999999999999999874
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=2.8e-54 Score=329.99 Aligned_cols=146 Identities=36% Similarity=0.570 Sum_probs=140.8
Q ss_pred eEEEEecccccccCCCcEEEecCccccccccCCCceEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCeEEE
Q 031586 10 IQIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKV 89 (157)
Q Consensus 10 mkVIL~~dV~~lGk~Gdvv~Vk~GyaRN~LiP~glA~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~~l~i 89 (157)
|+|||++||++||++||+|+|+||||||||||+|+|++||++|+++++.+++..++++++.+++|+++++.|++. .++|
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 899999999999999999999999999999999999999999999999999998888889999999999999997 7999
Q ss_pred EEecCCCCceeeccCHHHHHHHHHHhcCCCccCcccccc-C-ccceeeEEEEEEeCCCcEEEEEEEEeeC
Q 031586 90 KRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLP-E-IRETGEYIAQLKLHPEVTARIRLNVFAN 157 (157)
Q Consensus 90 ~~k~~~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I~l~-~-Ik~~G~~~v~v~l~~~v~~~l~v~V~~~ 157 (157)
++++|++|+||||||++||+++|+++ |++||+++|.+| + |+++|+|+|+|+||++|+|+++|+|++.
T Consensus 80 ~~k~ge~gklfGSVt~~~I~~~l~~~-g~~idk~~I~l~~~~Ik~~G~y~v~i~L~~~V~a~i~v~V~~e 148 (148)
T TIGR00158 80 SKKVGDEGKLFGSITTKQIADALKAA-GLDLDKKKIELPDGVIRTTGEHEVTIKLHEEVFAVLKVIVVPE 148 (148)
T ss_pred EEEeCCCCeEEEeECHHHHHHHHHHc-CCcccHhhEECCCCceeceEEEEEEEEEcCCcEEEEEEEEEEC
Confidence 99999999999999999999999887 999999999997 4 9999999999999999999999999874
No 3
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=100.00 E-value=5.1e-53 Score=322.73 Aligned_cols=146 Identities=42% Similarity=0.676 Sum_probs=141.2
Q ss_pred eEEEEecccccccCCCcEEEecCccccccccCCCceEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCeEEE
Q 031586 10 IQIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKV 89 (157)
Q Consensus 10 mkVIL~~dV~~lGk~Gdvv~Vk~GyaRN~LiP~glA~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~~l~i 89 (157)
|+|||++||+|||++||+|+|+||||||||||+|+|+|||++|+++++.+++..++++++.+++|+++++.|++. .|+|
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 899999999999999999999999999999999999999999999999999988888889999999999999987 7999
Q ss_pred EEecCCCCceeeccCHHHHHHHHHHhcCCCccCcccccc-CccceeeEEEEEEeCCCcEEEEEEEEeeC
Q 031586 90 KRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLP-EIRETGEYIAQLKLHPEVTARIRLNVFAN 157 (157)
Q Consensus 90 ~~k~~~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I~l~-~Ik~~G~~~v~v~l~~~v~~~l~v~V~~~ 157 (157)
.+++|++|+||||||++||+++|+++ |++||+++|+++ +|+++|+|+|+|+||++|+|+++|+|++.
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 99999999999999999999999998 999999999998 69999999999999999999999999874
No 4
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-51 Score=312.61 Aligned_cols=145 Identities=37% Similarity=0.577 Sum_probs=140.8
Q ss_pred eEEEEecccccccCCCcEEEecCccccccccCCCceEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCeEEE
Q 031586 10 IQIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKV 89 (157)
Q Consensus 10 mkVIL~~dV~~lGk~Gdvv~Vk~GyaRN~LiP~glA~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~~l~i 89 (157)
|+|||++||++||+.||+|+|++|||||||||+|+|+.||++|++.++.++++.+++.++.+++|+++++.|++. .++|
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 899999999999999999999999999999999999999999999999988888888888999999999999995 8999
Q ss_pred EEecCCCCceeeccCHHHHHHHHHHhcCCCccCccccccC-ccceeeEEEEEEeCCCcEEEEEEEEee
Q 031586 90 KRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTARIRLNVFA 156 (157)
Q Consensus 90 ~~k~~~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I~l~~-Ik~~G~~~v~v~l~~~v~~~l~v~V~~ 156 (157)
.+++|++|+||||||++||+++|.++ |++||+++|.+|+ |+++|+|+|+|+||++|+++++|.|.+
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 9999999999996 999999999999999999999999986
No 5
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=100.00 E-value=4.1e-43 Score=325.88 Aligned_cols=146 Identities=23% Similarity=0.345 Sum_probs=141.1
Q ss_pred ceEEEEecccccccCCCcEEEecCccccccccCCCceEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCeEE
Q 031586 9 QIQIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFK 88 (157)
Q Consensus 9 ~mkVIL~~dV~~lGk~Gdvv~Vk~GyaRN~LiP~glA~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~~l~ 88 (157)
.|+|||++||++||++||+|+|+|||| |||||+|+|++||++|+++++.+++..++++++.+++|++++++|+++ .++
T Consensus 688 ~MkVIL~~dv~~lGk~Gdvv~Vk~GYa-NfLiP~~~A~~aT~~nlk~~e~~~~~~~~~~~~~~~~a~~l~~~l~~~-~~~ 765 (838)
T PRK14538 688 NMEIILLTDIKNKGKKHEIIKVNNGYG-NFLIQNKKALLADKENLAKIKKKKILEQEKKRNHELLMKKLKSEIDNK-KIT 765 (838)
T ss_pred hhhHHHHHHHHhcCCCCCEEEECCCch-hhhccCCchhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc-EEE
Confidence 599999999999999999999999999 999999999999999999999999998888889999999999999997 799
Q ss_pred EEEecCCCCceeeccCHHHHHHHHHHhcCCCccCcccccc-CccceeeEEEEEEeCCCcEEEEEEEEee
Q 031586 89 VKRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLP-EIRETGEYIAQLKLHPEVTARIRLNVFA 156 (157)
Q Consensus 89 i~~k~~~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I~l~-~Ik~~G~~~v~v~l~~~v~~~l~v~V~~ 156 (157)
|++++|++|+||||||++||+++|++++|++||++.|.|+ |||++|+|.|+|+||++|+|+++|+|+.
T Consensus 766 i~~k~ge~gklfGSVt~~~I~~~l~~~~g~~idk~~I~l~~~Ik~~G~~~v~i~L~~~V~a~i~v~V~~ 834 (838)
T PRK14538 766 LDIQLGPKGKIYGKITLKQIVEEFHKIHNITIDRKKISLENEIISVGIYPVDVFLTDQIKATFFLNVIE 834 (838)
T ss_pred EEEEeCCCCeeeeccCHHHHHHHHHHhhCCccccceeeCCCcccccEEEEEEEEEcCCeEEEEEEEEEE
Confidence 9999999999999999999999999989999999999997 5999999999999999999999999974
No 6
>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=7.3e-28 Score=191.50 Aligned_cols=149 Identities=40% Similarity=0.611 Sum_probs=125.8
Q ss_pred cCCceEEEEecccccccCCCcEEEecCccccccccCCCceEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 031586 6 KKTQIQIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVG 85 (157)
Q Consensus 6 kkk~mkVIL~~dV~~lGk~Gdvv~Vk~GyaRN~LiP~glA~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~ 85 (157)
.++.++|||++||+|||++||+|+|++||+||+|+|+|+|+|+||.+.+.+....++......+..++++.++ .|.+.
T Consensus 45 ~k~~levIL~~~Ve~lG~qGdvVsVk~g~~RN~Llp~glAvy~tp~~~~~~k~~~~e~~~~k~~vk~e~k~V~-~lqt~- 122 (222)
T KOG4607|consen 45 PKPNLEVILKTDVEKLGKQGDVVSVKRGYFRNFLLPKGLAVYNTPLNLKKYKLREQEEEAEKIRVKEEAKVVA-VLQTV- 122 (222)
T ss_pred CCcceeeeeehhhhhhcccCcEEEeecchhhhhcccccccccCChhhHHHHHHHHHHHHhhhhccHHHHHHHH-HHHhh-
Confidence 4568999999999999999999999999999999999999999999988877655555544445555565555 88876
Q ss_pred eEEEEEecCCCCce-eeccCHHHHHHHHHHhcCCCccCccccccCccceeeEEEEEEeCCCcEEEEEEEEee
Q 031586 86 AFKVKRKGGKGKQI-FGSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPEVTARIRLNVFA 156 (157)
Q Consensus 86 ~l~i~~k~~~~gkl-fGsVt~~dI~~~l~~~~gi~i~k~~I~l~~Ik~~G~~~v~v~l~~~v~~~l~v~V~~ 156 (157)
.+.+.++-+..|.| +++|++++.-..+.+++-+.+|++.|..|.++.-|+|.+.|+++++.++.+...|..
T Consensus 123 v~~~~~~k~~kw~l~~~~V~~~l~~gv~~~~~t~~l~k~~vs~P~~k~e~~~~~~V~in~~~~vr~~~~v~~ 194 (222)
T KOG4607|consen 123 VLFKVMNKGGKWKLNPNLVKASLRKGVIVAELTIKLDKELVSGPITKEEGEYICEVKINPDVTVRVKIRVTH 194 (222)
T ss_pred hhhheeccCCceeecHHHHHHHHhcceEeccccccCcccccCCCcccccceEEEEEEECCcceEEeeeeeec
Confidence 57777777777776 788888888877777778899999999998999999999999999999999998864
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=99.94 E-value=1e-26 Score=163.42 Aligned_cols=86 Identities=47% Similarity=0.772 Sum_probs=82.0
Q ss_pred HHHHHHHHHHhccCCeEEEEEecCCCCceeeccCHHHHHHHHHHhcCCCccCccccccC-ccceeeEEEEEEeCCCcEEE
Q 031586 71 KEEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTAR 149 (157)
Q Consensus 71 ~~~a~~~~~~L~~~~~l~i~~k~~~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I~l~~-Ik~~G~~~v~v~l~~~v~~~ 149 (157)
+++|++++++|++. .|+|.+++|++|+||||||++||+++|++++|++||+++|.++. ||++|+|.|+|+||++|+|+
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 36799999999998 79999999999999999999999999999999999999999995 99999999999999999999
Q ss_pred EEEEEeeC
Q 031586 150 IRLNVFAN 157 (157)
Q Consensus 150 l~v~V~~~ 157 (157)
|+|+|.++
T Consensus 80 i~v~V~~E 87 (87)
T PF03948_consen 80 IKVNVVAE 87 (87)
T ss_dssp EEEEEEEE
T ss_pred EEEEEEeC
Confidence 99999863
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=99.93 E-value=7.8e-27 Score=147.09 Aligned_cols=48 Identities=46% Similarity=0.792 Sum_probs=44.9
Q ss_pred eEEEEecccccccCCCcEEEecCccccccccCCCceEecCHHHHHHHH
Q 031586 10 IQIILKEDVAELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMK 57 (157)
Q Consensus 10 mkVIL~~dV~~lGk~Gdvv~Vk~GyaRN~LiP~glA~~at~~nl~~~~ 57 (157)
|+|||++||+|||++||+|+|++|||||||+|+|+|+|||++|+++++
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 799999999999999999999999999999999999999999999874
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=68.98 E-value=2.8 Score=30.39 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=22.0
Q ss_pred CHHHHHHHHHHhcCCCccCccccc
Q 031586 104 TAQDVVDIIKAQLQRDVDKKIVDL 127 (157)
Q Consensus 104 t~~dI~~~l~~~~gi~i~k~~I~l 127 (157)
||.++++++++.||++|++.+++.
T Consensus 21 TPs~v~~aVk~eFgi~vsrQqve~ 44 (104)
T PF10045_consen 21 TPSEVAEAVKEEFGIDVSRQQVES 44 (104)
T ss_pred CHHHHHHHHHHHhCCccCHHHHHH
Confidence 899999999999999999988764
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=68.46 E-value=9.8 Score=24.52 Aligned_cols=25 Identities=24% Similarity=0.417 Sum_probs=20.4
Q ss_pred CccceeeEEEEEEeCCCcEEEEEEEE
Q 031586 129 EIRETGEYIAQLKLHPEVTARIRLNV 154 (157)
Q Consensus 129 ~Ik~~G~~~v~v~l~~~v~~~l~v~V 154 (157)
+-...|+|.|+++... .+++++|.|
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 3678899999999988 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=65.27 E-value=3.5 Score=25.87 Aligned_cols=23 Identities=17% Similarity=0.378 Sum_probs=15.7
Q ss_pred eccCHHHHHHHHHHhcCCCccCc
Q 031586 101 GSVTAQDVVDIIKAQLQRDVDKK 123 (157)
Q Consensus 101 GsVt~~dI~~~l~~~~gi~i~k~ 123 (157)
.+||.++|..+|.+.||+++..+
T Consensus 19 ~~vT~k~vr~~Le~~~~~dL~~~ 41 (54)
T PF08766_consen 19 DTVTKKQVREQLEERFGVDLSSR 41 (54)
T ss_dssp GG--HHHHHHHHHHH-SS--SHH
T ss_pred hHhhHHHHHHHHHHHHCCCcHHH
Confidence 48999999999999999988754
No 12
>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=64.45 E-value=7.7 Score=23.33 Aligned_cols=21 Identities=10% Similarity=0.305 Sum_probs=18.1
Q ss_pred cCCCCceeeccCHHHHHHHHH
Q 031586 93 GGKGKQIFGSVTAQDVVDIIK 113 (157)
Q Consensus 93 ~~~~gklfGsVt~~dI~~~l~ 113 (157)
.+++|++-|.||..||...+.
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 456799999999999999875
No 13
>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=59.84 E-value=15 Score=32.96 Aligned_cols=56 Identities=21% Similarity=0.350 Sum_probs=41.6
Q ss_pred ccCCeEEEEEecC---CCCcee----e-ccCHHHHHHHHHHhcCCCccCccccccCccceeeEEEEEEeCCC
Q 031586 82 ETVGAFKVKRKGG---KGKQIF----G-SVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 82 ~~~~~l~i~~k~~---~~gklf----G-sVt~~dI~~~l~~~~gi~i~k~~I~l~~Ik~~G~~~v~v~l~~~ 145 (157)
++. +++|+.+.+ .+|..| | +||++|++-.+..-.. + .+..|+.++.|+|+|+|..-
T Consensus 63 D~~-t~tf~LR~~v~fsDG~~~~~~~G~p~TA~Dv~~s~~~~~~----~---~i~~v~~~d~~tv~~~l~~p 126 (528)
T cd08505 63 DGS-VYTIRIKPGIYFQPDPAFPKGKTRELTAEDYVYSIKRLAD----P---PLEGVEAVDRYTLRIRLTGP 126 (528)
T ss_pred Cce-EEEEEEcCCCEeeCCcccccCCCcccchHHhhhhHhhhhc----C---cccceEeccCcEEEEEecCC
Confidence 344 688887766 577777 4 8999999999875422 1 23458899999999999863
No 14
>PF13592 HTH_33: Winged helix-turn helix
Probab=39.63 E-value=16 Score=23.22 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=19.3
Q ss_pred eccCHHHHHHHHHHhcCCCccCccc
Q 031586 101 GSVTAQDVVDIIKAQLQRDVDKKIV 125 (157)
Q Consensus 101 GsVt~~dI~~~l~~~~gi~i~k~~I 125 (157)
+--|..+|++.|.++||+.+..+.|
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v 27 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGV 27 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHH
Confidence 3568888889988888888766654
No 15
>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=38.93 E-value=23 Score=28.01 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=15.3
Q ss_pred EEEeccccc---------ccCCCcEEEecCcccc
Q 031586 12 IILKEDVAE---------LGKKGQLLDVKAGFYR 36 (157)
Q Consensus 12 VIL~~dV~~---------lGk~Gdvv~Vk~GyaR 36 (157)
++|+|+..+ -.++||+|-|.||||-
T Consensus 95 ~~lLq~~~~~~~~~~~~v~~~~G~~v~IPp~yaH 128 (182)
T PF06560_consen 95 LILLQKEEGDDVGDVIAVEAKPGDVVYIPPGYAH 128 (182)
T ss_dssp EEEEE-TTS-----EEEEEE-TTEEEEE-TT-EE
T ss_pred EEEEEecCCCcceeEEEEEeCCCCEEEECCCceE
Confidence 577887766 1567888888888874
No 16
>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=37.33 E-value=86 Score=27.02 Aligned_cols=60 Identities=12% Similarity=0.214 Sum_probs=39.8
Q ss_pred ccCCeEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCc-cccccCccceeeEEEEEEeCCC
Q 031586 82 ETVGAFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK-IVDLPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 82 ~~~~~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~-~I~l~~Ik~~G~~~v~v~l~~~ 145 (157)
++. +++|+.+.| .||. .||++|+.-.+.....-..... .-.+..++.++.|+|.|+|..-
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 554 788888765 4565 7999999998876432211111 1112248889999999999864
No 17
>PRK07639 acyl carrier protein; Provisional
Probab=36.04 E-value=14 Score=25.34 Aligned_cols=33 Identities=21% Similarity=0.208 Sum_probs=25.5
Q ss_pred ccCHHHHHHHHHHhcCCCccCccccccCcccee
Q 031586 102 SVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETG 134 (157)
Q Consensus 102 sVt~~dI~~~l~~~~gi~i~k~~I~l~~Ik~~G 134 (157)
|+..-+++-+|...||++|+...+....+.++|
T Consensus 40 Sld~velv~~lE~~fgi~i~d~~~~~~~~~Tv~ 72 (86)
T PRK07639 40 SVMMLQLIVYIEMDVKLCVPEDEVDPKAFLTVG 72 (86)
T ss_pred hHHHHHHHHHHHHHHCCccCHHHccHHHhCCHH
Confidence 888888999999999999998766433455544
No 18
>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=34.92 E-value=34 Score=23.28 Aligned_cols=25 Identities=24% Similarity=0.375 Sum_probs=19.8
Q ss_pred ceEEEEecccccccCCCcEEEecCccccc
Q 031586 9 QIQIILKEDVAELGKKGQLLDVKAGFYRN 37 (157)
Q Consensus 9 ~mkVIL~~dV~~lGk~Gdvv~Vk~GyaRN 37 (157)
.+.+-|+.+++ .||.|-|..|||+.
T Consensus 27 ~v~l~lv~~~~----vGD~VLVH~G~Ai~ 51 (76)
T TIGR00074 27 DVSLDLVGEVK----VGDYVLVHVGFAIS 51 (76)
T ss_pred EEEEEeeCCCC----CCCEEEEecChhhh
Confidence 46667776654 89999999999984
No 19
>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=34.33 E-value=99 Score=26.94 Aligned_cols=57 Identities=19% Similarity=0.322 Sum_probs=38.2
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCc-ccc-ccCccceeeEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK-IVD-LPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~-~I~-l~~Ik~~G~~~v~v~l~~~ 145 (157)
+++|+.+.+ .+|. .||++|+.-.+..-.+...... ... +..|+..|.|+|.|+|...
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 7999999988876433221111 111 2348889999999999753
No 20
>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=34.24 E-value=70 Score=27.75 Aligned_cols=57 Identities=14% Similarity=0.297 Sum_probs=38.5
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCccc-cccCccceeeEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKIV-DLPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I-~l~~Ik~~G~~~v~v~l~~~ 145 (157)
+++|+.+.| .||. .||++|+.-.+....+-......+ .+..|+.++.|+|+|+|..-
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 688887765 5665 799999999887653322111111 12348889999999998753
No 21
>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=33.11 E-value=99 Score=26.68 Aligned_cols=56 Identities=9% Similarity=0.141 Sum_probs=37.6
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCc-cc-cccCccceeeEEEEEEeCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK-IV-DLPEIRETGEYIAQLKLHP 144 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~-~I-~l~~Ik~~G~~~v~v~l~~ 144 (157)
+++|+.+.| .+|. .||++|+.-.+........... .+ .+..++..|.|+|+|+|..
T Consensus 59 t~tf~Lr~~~~f~DG~---pvTA~Dv~~s~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~ 119 (454)
T cd08496 59 TLTLHLREGLTFSDGT---PLDAAAVKANLDRGKSTGGSQVKQLASISSVEVVDDTTVTLTLSQ 119 (454)
T ss_pred EEEEEeCCCCCccCCC---CcCHHHHHHHHHHHhCCCcchhhhccccceEEecCCCEEEEEeCC
Confidence 678877765 4565 7999999999876533222111 11 1224888999999999975
No 22
>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=32.71 E-value=64 Score=27.93 Aligned_cols=45 Identities=18% Similarity=0.260 Sum_probs=33.4
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCccccccCccceeeEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I~l~~Ik~~G~~~v~v~l~~~ 145 (157)
+++|+.+.| .||. .||++|++-.+....+ ++..+.|+|+|+|...
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 688887765 4555 6999999999976533 6677788888887753
No 23
>PRK05087 D-alanine--poly(phosphoribitol) ligase subunit 2; Validated
Probab=31.59 E-value=20 Score=24.24 Aligned_cols=34 Identities=9% Similarity=0.129 Sum_probs=26.0
Q ss_pred eccCHHHHHHHHHHhcCCCccCccccccCcccee
Q 031586 101 GSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETG 134 (157)
Q Consensus 101 GsVt~~dI~~~l~~~~gi~i~k~~I~l~~Ik~~G 134 (157)
=|+..-+++-+|.+.||+.|+...+....+.++|
T Consensus 35 DSl~~veli~~lE~~fgi~i~~~e~~~~~f~Tv~ 68 (78)
T PRK05087 35 DSMGTVELLVELENRFDIEVPVSEFDRDDWNTPN 68 (78)
T ss_pred chHHHHHHHHHHHHHhCCccChHhcCHHhhcCHH
Confidence 3778888888999999999988877654455544
No 24
>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=31.23 E-value=43 Score=22.38 Aligned_cols=19 Identities=11% Similarity=0.319 Sum_probs=16.5
Q ss_pred CCceeeccCHHHHHHHHHH
Q 031586 96 GKQIFGSVTAQDVVDIIKA 114 (157)
Q Consensus 96 ~gklfGsVt~~dI~~~l~~ 114 (157)
+|.+|+.+|+++|.+.+.+
T Consensus 61 ~~~~~~~~~~e~i~~il~~ 79 (80)
T cd03081 61 DGEVHGRVDPEKFDALLAE 79 (80)
T ss_pred CCEEECCCCHHHHHHHHHc
Confidence 7789999999999988754
No 25
>PF07718 Coatamer_beta_C: Coatomer beta C-terminal region; InterPro: IPR011710 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal IPR002553 from INTERPRO domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat
Probab=30.10 E-value=43 Score=25.51 Aligned_cols=19 Identities=21% Similarity=0.356 Sum_probs=15.7
Q ss_pred eEEEEEecCCCCceeeccC
Q 031586 86 AFKVKRKGGKGKQIFGSVT 104 (157)
Q Consensus 86 ~l~i~~k~~~~gklfGsVt 104 (157)
..+|+..+.++|-+||.|+
T Consensus 118 ~~~iKVsStetGvIfG~I~ 136 (140)
T PF07718_consen 118 KATIKVSSTETGVIFGNIV 136 (140)
T ss_pred EEEEEEEeccCCEEEEEEE
Confidence 5667778889999999885
No 26
>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=30.06 E-value=49 Score=17.65 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=14.5
Q ss_pred CCCceeeccCHHHHHHHH
Q 031586 95 KGKQIFGSVTAQDVVDII 112 (157)
Q Consensus 95 ~~gklfGsVt~~dI~~~l 112 (157)
+++++.|.++..++...+
T Consensus 31 ~~~~~~g~i~~~~l~~~~ 48 (49)
T smart00116 31 EEGRLVGIVTRRDIIKAL 48 (49)
T ss_pred CCCeEEEEEEHHHHHHhh
Confidence 457899999999987765
No 27
>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=29.54 E-value=38 Score=23.31 Aligned_cols=43 Identities=19% Similarity=0.232 Sum_probs=29.4
Q ss_pred eccCHHHHHHHHHHhcCCCccCccccccCc-cceeeEEEE--EEeCCC
Q 031586 101 GSVTAQDVVDIIKAQLQRDVDKKIVDLPEI-RETGEYIAQ--LKLHPE 145 (157)
Q Consensus 101 GsVt~~dI~~~l~~~~gi~i~k~~I~l~~I-k~~G~~~v~--v~l~~~ 145 (157)
++.+..||.+.|+++++ +|++.|.+..| ..+|....+ .++|++
T Consensus 11 ~Tpsr~ei~~klA~~~~--~~~~~ivv~~~~t~fG~~~s~g~a~IYd~ 56 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLN--VDPDLIVVFGIKTEFGGGKSTGFAKIYDS 56 (84)
T ss_dssp SS--HHHHHHHHHHHHT--STGCCEEEEEEEESSSSSEEEEEEEEESS
T ss_pred CCCCHHHHHHHHHHHhC--CCCCeEEEeccEecCCCceEEEEEEEeCC
Confidence 47899999999999977 48888887764 477766443 344444
No 28
>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=29.06 E-value=54 Score=21.04 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=16.7
Q ss_pred CCCceeeccCHHHHHHHHHH
Q 031586 95 KGKQIFGSVTAQDVVDIIKA 114 (157)
Q Consensus 95 ~~gklfGsVt~~dI~~~l~~ 114 (157)
+++.+||-+|+.++.+.|.+
T Consensus 57 ~~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 57 PDGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred CCCeEEccCCHHHHHHHHHh
Confidence 35789999999999888754
No 29
>PF00496 SBP_bac_5: Bacterial extracellular solute-binding proteins, family 5 Middle; InterPro: IPR000914 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into Gram-positive bacteria which are surrounded by a single membrane and therefore have no periplasmic region the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families of clusters, which generally correlate with the nature of the solute bound. Family 5 currently includes periplasmic oligopeptide-binding proteins (oppA) of Gram-negative bacteria and homologous lipoproteins in Gram-positive bacteria (oppA, amiA or appA); periplasmic dipeptide-binding proteins of Escherichia coli (dppA) and Bacillus subtilis (dppE); periplasmic murein peptide-binding protein of E. coli (mppA); periplasmic peptide-binding proteins sapA of E. coli, Salmonella typhimurium and Haemophilus influenzae; periplasmic nickel-binding protein (nikA) of E. coli; haem-binding lipoprotein (hbpA or dppA) from H. influenzae; lipoprotein xP55 from Streptomyces lividans; and hypothetical proteins from H. influenzae (HI0213) and Rhizobium sp. (strain NGR234) symbiotic plasmid (y4tO and y4wM).; GO: 0005215 transporter activity, 0006810 transport; PDB: 1B51_A 1B0H_A 1QKA_A 1B9J_A 1B6H_A 1OLA_A 1B3L_C 1JEV_A 1B5H_A 1JET_A ....
Probab=28.28 E-value=1.1e+02 Score=25.33 Aligned_cols=57 Identities=18% Similarity=0.306 Sum_probs=37.6
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCcc---c--cccCccceeeEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKI---V--DLPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~~---I--~l~~Ik~~G~~~v~v~l~~~ 145 (157)
.++|+.+.| .||. .||++|+.-.+.......-.... . .+..|...+.|+|.|+|...
T Consensus 19 ~~tf~Lr~g~~wsDG~---~lTA~Dv~~s~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~tv~~~l~~p 83 (374)
T PF00496_consen 19 TYTFTLRDGLKWSDGE---PLTAEDVVFSFERLADPDYNSPWAYDFFDSIDSIEAPDDYTVVFTLKEP 83 (374)
T ss_dssp EEEEEE-TT-B-TTST---B-SHHHHHHHHHHHHHCCGSTTTCHHHHHHEEEEEEEETTEEEEEESST
T ss_pred EEEEEEeeeeeecCCC---cceeeEEeeeehhcccCCcccccccccccccccccccCCEEEEEEeecc
Confidence 678887766 4665 79999999988765332222211 1 13359999999999998753
No 30
>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=27.77 E-value=1.5e+02 Score=20.75 Aligned_cols=38 Identities=24% Similarity=0.406 Sum_probs=27.7
Q ss_pred ccCccccccC--ccceeeEEEEEEeCC-CcEEEEEEEEeeC
Q 031586 120 VDKKIVDLPE--IRETGEYIAQLKLHP-EVTARIRLNVFAN 157 (157)
Q Consensus 120 i~k~~I~l~~--Ik~~G~~~v~v~l~~-~v~~~l~v~V~~~ 157 (157)
-+++.+.++. ...=|++.+.|..+. ...+.++|.|.+|
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 3455666663 778999999999774 4457888888765
No 31
>PRK07081 acyl carrier protein; Provisional
Probab=27.71 E-value=21 Score=24.27 Aligned_cols=27 Identities=7% Similarity=0.247 Sum_probs=23.2
Q ss_pred eccCHHHHHHHHHHhcCCCccCccccc
Q 031586 101 GSVTAQDVVDIIKAQLQRDVDKKIVDL 127 (157)
Q Consensus 101 GsVt~~dI~~~l~~~~gi~i~k~~I~l 127 (157)
=|+..-+++-+|.+.||++|+...+..
T Consensus 34 DSl~~v~li~~lE~~f~I~i~~~~~~~ 60 (83)
T PRK07081 34 SSLATVQLMLAIEDAFDIEIPDEMLNR 60 (83)
T ss_pred CHHHHHHHHHHHHHHhCCcCCHHHcCH
Confidence 388999999999999999998887653
No 32
>PF13565 HTH_32: Homeodomain-like domain
Probab=27.68 E-value=46 Score=21.41 Aligned_cols=19 Identities=11% Similarity=0.310 Sum_probs=16.3
Q ss_pred ccCHHHHHHHHHHhcCCCc
Q 031586 102 SVTAQDVVDIIKAQLQRDV 120 (157)
Q Consensus 102 sVt~~dI~~~l~~~~gi~i 120 (157)
--|+.+|++.|.+++|+.+
T Consensus 48 ~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 48 RWTPREIAEYLEEEFGISV 66 (77)
T ss_pred CCCHHHHHHHHHHHhCCCC
Confidence 4689999999999998766
No 33
>cd08514 PBP2_AppA_like The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold. This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also 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 correspondin
Probab=27.46 E-value=1.5e+02 Score=25.69 Aligned_cols=57 Identities=16% Similarity=0.191 Sum_probs=38.0
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccC--c--ccc-ccCccceeeEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDK--K--IVD-LPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k--~--~I~-l~~Ik~~G~~~v~v~l~~~ 145 (157)
+++|+.+-| .||. .||++|+.-.+.....-.... . ... +..+..++.|+|+|+|..-
T Consensus 59 ~~tf~Lr~gv~f~dG~---pvtA~Dv~~s~~r~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~p 123 (483)
T cd08514 59 TYTFKLRKDVKWHDGE---PLTADDVKFTYKAIADPKYAGPRASGDYDEIKGVEVPDDYTVVFHYKEP 123 (483)
T ss_pred EEEEEeCCCCCccCCc---CcCHHHHHhHHHHHhCCCCCCccccccccceeEEEEccCceEEEEECCC
Confidence 688887765 4555 799999999987653322111 1 111 2248889999999999753
No 34
>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=26.66 E-value=1.4e+02 Score=20.72 Aligned_cols=31 Identities=23% Similarity=0.554 Sum_probs=23.3
Q ss_pred cccccC--ccceeeEEEEEEeCCC--cEEEEEEEE
Q 031586 124 IVDLPE--IRETGEYIAQLKLHPE--VTARIRLNV 154 (157)
Q Consensus 124 ~I~l~~--Ik~~G~~~v~v~l~~~--v~~~l~v~V 154 (157)
.|.+.+ +..-|.|.+.|+-+++ -++++.+.|
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 456664 7799999999998655 567777665
No 35
>cd04630 CBS_pair_17 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=25.95 E-value=1.1e+02 Score=20.44 Aligned_cols=19 Identities=26% Similarity=0.532 Sum_probs=16.1
Q ss_pred CceeeccCHHHHHHHHHHh
Q 031586 97 KQIFGSVTAQDVVDIIKAQ 115 (157)
Q Consensus 97 gklfGsVt~~dI~~~l~~~ 115 (157)
|++.|.||..|+...+..+
T Consensus 35 ~~~~G~v~~~dl~~~~~~~ 53 (114)
T cd04630 35 SDAYGIVTMRDILKKVVAE 53 (114)
T ss_pred CcEEEEEehHHHHHHHHhC
Confidence 7999999999999876543
No 36
>cd04619 CBS_pair_6 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=25.64 E-value=1.3e+02 Score=20.19 Aligned_cols=21 Identities=24% Similarity=0.297 Sum_probs=17.5
Q ss_pred CCCCceeeccCHHHHHHHHHH
Q 031586 94 GKGKQIFGSVTAQDVVDIIKA 114 (157)
Q Consensus 94 ~~~gklfGsVt~~dI~~~l~~ 114 (157)
+++|++.|.||..|+...+..
T Consensus 31 d~~g~~~G~vt~~dl~~~~~~ 51 (114)
T cd04619 31 DPHGKLAGVLTKTDVVRQMGR 51 (114)
T ss_pred CCCCCEEEEEehHHHHHHHhh
Confidence 467899999999999987654
No 37
>PF05157 T2SE_Nter: Type II secretion system (T2SS), protein E, N-terminal domain; InterPro: IPR007831 This domain is found at the N terminus of members of the general secretory system II protein E. Proteins in this subfamily are typically involved in Type IV pilus biogenesis (e.g. Q9X4G8 from SWISSPROT), though some are involved in other processes; for instance aggregation in Myxococcus xanthus (e.g. Q9RF11 from SWISSPROT) [].; GO: 0005524 ATP binding, 0006810 transport; PDB: 2D27_A 2D28_C.
Probab=25.54 E-value=47 Score=22.39 Aligned_cols=19 Identities=16% Similarity=0.380 Sum_probs=14.3
Q ss_pred eccCHHHHHHHHHHhcCCC
Q 031586 101 GSVTAQDVVDIIKAQLQRD 119 (157)
Q Consensus 101 GsVt~~dI~~~l~~~~gi~ 119 (157)
|-||..++.++|++++|+.
T Consensus 5 g~ise~~l~~~la~~~~l~ 23 (109)
T PF05157_consen 5 GLISEDQLLEALAEQLGLP 23 (109)
T ss_dssp T-S-HHHHHHHHHHHHT--
T ss_pred CCCCHHHHHHHHHHHhCCC
Confidence 6799999999999999986
No 38
>KOG1387 consensus Glycosyltransferase [Cell wall/membrane/envelope biogenesis]
Probab=25.41 E-value=55 Score=29.18 Aligned_cols=26 Identities=19% Similarity=0.432 Sum_probs=23.6
Q ss_pred ccCHHHHHHHHHHhcCCCccCccccc
Q 031586 102 SVTAQDVVDIIKAQLQRDVDKKIVDL 127 (157)
Q Consensus 102 sVt~~dI~~~l~~~~gi~i~k~~I~l 127 (157)
-+|+.+|....+..|++++|.++|..
T Consensus 87 n~t~~~IL~k~k~~F~idlDs~nI~F 112 (465)
T KOG1387|consen 87 NVTPENILNKVKNKFDIDLDSDNIFF 112 (465)
T ss_pred CCCHHHHHHHHHHhcCceecccceEE
Confidence 49999999999999999999998863
No 39
>cd08503 PBP2_NikA_DppA_OppA_like_17 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=24.99 E-value=1.7e+02 Score=25.22 Aligned_cols=56 Identities=18% Similarity=0.321 Sum_probs=36.8
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCc----cccccCccceeeEEEEEEeCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK----IVDLPEIRETGEYIAQLKLHP 144 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~----~I~l~~Ik~~G~~~v~v~l~~ 144 (157)
.++|..+-+ .+|. .||++|+.-.+..-.+-..... .-.+..|+.++.|+|.|+|..
T Consensus 66 ~~tf~Lr~~~~wsdG~---pvTA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~ 128 (460)
T cd08503 66 TWTFKLRKGVTFHDGK---PLTADDVVASLNRHRDPASGSPAKTGLLDVGAIEAVDDHTVRFTLKR 128 (460)
T ss_pred EEEEEcCCCCCcCCCC---cCCHHHHHHHHHHhhCCcccCccchhhcccceeEecCCCeEEEEeCC
Confidence 577776654 3554 7999999999876433222211 112335888999999999954
No 40
>smart00089 PKD Repeats in polycystic kidney disease 1 (PKD1) and other proteins. Polycystic kidney disease 1 protein contains 14 repeats, present elsewhere such as in microbial collagenases.
Probab=24.71 E-value=1.2e+02 Score=19.26 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=18.8
Q ss_pred ccceeeEEEEEEeCCCc---EEEEEEEE
Q 031586 130 IRETGEYIAQLKLHPEV---TARIRLNV 154 (157)
Q Consensus 130 Ik~~G~~~v~v~l~~~v---~~~l~v~V 154 (157)
..+-|.|.|++.+..+. ++.++|.|
T Consensus 51 y~~~G~y~v~l~v~n~~g~~~~~~~i~v 78 (79)
T smart00089 51 YTKPGTYTVTLTVTNAVGSASATVTVVV 78 (79)
T ss_pred eCCCcEEEEEEEEEcCCCcEEEEEEEEE
Confidence 67889999999988766 45555554
No 41
>cd08501 PBP2_Lpqw The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold. LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature PIMs production into a pathway for LAMs biosynthesis, thus controlling the relative abundance of these two essential components of cell wall. LpqW is thought to have been adapted by the cell-wall biosynthesis machinery of mycobacteria and other closely related pathogens, evolving to play an important role in PIMs/LAMs biosynthesis. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the LpqW protein. The structural topology of these domains is most similar to
Probab=24.71 E-value=2e+02 Score=25.02 Aligned_cols=57 Identities=9% Similarity=-0.021 Sum_probs=37.8
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCc-----cc-cccCcccee-eEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK-----IV-DLPEIRETG-EYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~-----~I-~l~~Ik~~G-~~~v~v~l~~~ 145 (157)
+++|+.+-| .+|. .+|++||.-.+..-.+-.-... .+ .+..|+..+ .|+|+++|..-
T Consensus 64 ~~tf~LR~gv~f~DG~---~~TA~DV~~s~~~~~~~~~~~~~~~~~~~~~i~~i~~~d~~~tv~~~l~~p 130 (486)
T cd08501 64 TVTYTINPEAQWSDGT---PITAADFEYLWKAMSGEPGTYDPASTDGYDLIESVEKGDGGKTVVVTFKQP 130 (486)
T ss_pred EEEEEeCCCCCcCCCC---cCcHHHHHHHHHHhcCCCCccccccCcchheeeeeeccCCCcEEEEEEcCC
Confidence 688887765 4554 7999999999876433221110 11 123488888 99999999853
No 42
>cd08512 PBP2_NikA_DppA_OppA_like_7 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 si
Probab=24.38 E-value=1.7e+02 Score=25.37 Aligned_cols=57 Identities=19% Similarity=0.309 Sum_probs=37.4
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCccc-------cccCccceeeEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKIV-------DLPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I-------~l~~Ik~~G~~~v~v~l~~~ 145 (157)
+++|+.+.+ .||. .||++|+.-.+............. .+..+..++.|+|+|+|..-
T Consensus 64 ~~tf~LR~~~~wsDG~---p~TA~Dv~~s~~~~~~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~p 130 (476)
T cd08512 64 TYTFHLRDGVKFHDGN---PVTAEDVKYSFERALKLNKGPAFILTQTSLNVPETIKAVDDYTVVFKLDKP 130 (476)
T ss_pred EEEEEeCCCCEecCCC---cCCHHHhHhHHHHHhccCCCCcceeeccccccceeEEEcCCCeEEEEECCC
Confidence 678877665 4565 699999999887543222111111 12348889999999998753
No 43
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=24.38 E-value=37 Score=20.27 Aligned_cols=24 Identities=17% Similarity=0.335 Sum_probs=17.9
Q ss_pred eccCHHHHHHHHHHhcCCC-ccCccc
Q 031586 101 GSVTAQDVVDIIKAQLQRD-VDKKIV 125 (157)
Q Consensus 101 GsVt~~dI~~~l~~~~gi~-i~k~~I 125 (157)
|.||+.++..+|. .+|+. +....+
T Consensus 3 G~i~~~~~~~~l~-~~g~~~~s~~e~ 27 (54)
T PF13833_consen 3 GKITREEFRRALS-KLGIKDLSEEEV 27 (54)
T ss_dssp SEEEHHHHHHHHH-HTTSSSSCHHHH
T ss_pred CEECHHHHHHHHH-HhCCCCCCHHHH
Confidence 5789999999994 45877 766554
No 44
>PF14221 DUF4330: Domain of unknown function (DUF4330)
Probab=24.28 E-value=60 Score=25.12 Aligned_cols=19 Identities=21% Similarity=0.557 Sum_probs=15.5
Q ss_pred CCCCceeeccCHHHHHHHH
Q 031586 94 GKGKQIFGSVTAQDVVDII 112 (157)
Q Consensus 94 ~~~gklfGsVt~~dI~~~l 112 (157)
.+.|+|||.|+.-|+.-.|
T Consensus 5 D~kGrlFgkiniiDl~~~l 23 (168)
T PF14221_consen 5 DSKGRLFGKINIIDLLAIL 23 (168)
T ss_pred ccCCcEeeeEeHHHHHHHH
Confidence 5789999999999966544
No 45
>PRK15109 antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional
Probab=24.27 E-value=1.4e+02 Score=26.82 Aligned_cols=59 Identities=15% Similarity=0.336 Sum_probs=37.2
Q ss_pred eEEEEEecC---CCCceee---ccCHHHHHHHHHHhcCCCccCc--------------cc-cccCccceeeEEEEEEeCC
Q 031586 86 AFKVKRKGG---KGKQIFG---SVTAQDVVDIIKAQLQRDVDKK--------------IV-DLPEIRETGEYIAQLKLHP 144 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfG---sVt~~dI~~~l~~~~gi~i~k~--------------~I-~l~~Ik~~G~~~v~v~l~~ 144 (157)
+.+|+.+.| .||..|| .||++|++-.+..-..-..+.. .. .+..+...+.|+|.|+|..
T Consensus 95 t~tf~LR~gvkfsDG~~~~~G~pvTA~DV~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~d~~Tv~~~l~~ 174 (547)
T PRK15109 95 TYRFHLRRDVPFQKTDWFTPTRKMNADDVVFSFQRIFDRNHPWHNVNGGNYPYFDSLQFADNVKSVRKLDNYTVEFRLAQ 174 (547)
T ss_pred EEEEEecCCCeecCCcccCCCccccHHHhhhhHHHHhCcccccccccccccccccccccccceeEEEEeCCCeEEEEecC
Confidence 678877755 3443343 7999999998876533222110 00 1224778899999998875
No 46
>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=24.20 E-value=38 Score=26.75 Aligned_cols=17 Identities=29% Similarity=0.563 Sum_probs=14.8
Q ss_pred ceeeccCHHHHHHHHHHhc
Q 031586 98 QIFGSVTAQDVVDIIKAQL 116 (157)
Q Consensus 98 klfGsVt~~dI~~~l~~~~ 116 (157)
.+|| ||++-|+++.++.
T Consensus 50 ~lfG--~P~~~a~eli~~~ 66 (206)
T PF06570_consen 50 QLFG--DPKEYADELIKPL 66 (206)
T ss_pred HHcC--CHHHHHHHHhccc
Confidence 6999 9999999998763
No 47
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=24.14 E-value=1.4e+02 Score=20.70 Aligned_cols=26 Identities=19% Similarity=0.180 Sum_probs=19.0
Q ss_pred ccCHHHHHHHHHHhcCCCccCcccccc
Q 031586 102 SVTAQDVVDIIKAQLQRDVDKKIVDLP 128 (157)
Q Consensus 102 sVt~~dI~~~l~~~~gi~i~k~~I~l~ 128 (157)
+-|+.++++.|++ +|++++.+.|-.+
T Consensus 41 ~~s~~~~~~~L~~-~Gi~~~~~~i~ts 66 (101)
T PF13344_consen 41 SRSREEYAKKLKK-LGIPVDEDEIITS 66 (101)
T ss_dssp SS-HHHHHHHHHH-TTTT--GGGEEEH
T ss_pred CCCHHHHHHHHHh-cCcCCCcCEEECh
Confidence 6788999999966 5999999888654
No 48
>cd08494 PBP2_NikA_DppA_OppA_like_6 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 si
Probab=24.03 E-value=1.8e+02 Score=24.86 Aligned_cols=57 Identities=11% Similarity=0.190 Sum_probs=37.3
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCc---cc-cccCccceeeEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK---IV-DLPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~---~I-~l~~Ik~~G~~~v~v~l~~~ 145 (157)
.++|+.+-+ .||. +||++|+.-.+.....-..... .. .+..|+.++.|+|+++|...
T Consensus 60 ~~tf~Lr~~~~fsdG~---pvTA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~p 123 (448)
T cd08494 60 TYTFTLRSGVTFHDGT---PFDAADVKFSLQRARAPDSTNADKALLAAIASVEAPDAHTVVVTLKHP 123 (448)
T ss_pred EEEEEeCCCCEecCcC---CCCHHHHHhHHHHHhCCCCCccccchhcceeEEEecCCCEEEEEECCC
Confidence 688887765 3554 7999999999876432221111 11 12348889999999998753
No 49
>cd04590 CBS_pair_CorC_HlyC_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in magnesium and cobalt efflux, and in association with some proteins of unknown function. The function of the CorC_HlyC domain is uncertain but it might be involved in modulating transport of ion substrates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role,
Probab=23.98 E-value=1.5e+02 Score=19.39 Aligned_cols=19 Identities=21% Similarity=0.441 Sum_probs=16.4
Q ss_pred CceeeccCHHHHHHHHHHh
Q 031586 97 KQIFGSVTAQDVVDIIKAQ 115 (157)
Q Consensus 97 gklfGsVt~~dI~~~l~~~ 115 (157)
|++.|.||..++...+...
T Consensus 35 ~~~~G~v~~~~l~~~~~~~ 53 (111)
T cd04590 35 DNIIGVVHVKDLLRALAEG 53 (111)
T ss_pred ceEEEEEEHHHHHHHHHcC
Confidence 8999999999999887643
No 50
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=23.98 E-value=45 Score=22.07 Aligned_cols=18 Identities=33% Similarity=0.381 Sum_probs=13.5
Q ss_pred cCCCcEEEecCccccccc
Q 031586 22 GKKGQLLDVKAGFYRNYL 39 (157)
Q Consensus 22 Gk~Gdvv~Vk~GyaRN~L 39 (157)
=..||.|-|..|||+.-+
T Consensus 38 v~~Gd~VLVHaG~Ai~~i 55 (68)
T PF01455_consen 38 VKVGDYVLVHAGFAIEKI 55 (68)
T ss_dssp B-TT-EEEEETTEEEEEE
T ss_pred CCCCCEEEEecChhheeC
Confidence 468999999999998644
No 51
>cd08489 PBP2_NikA The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. 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,
Probab=23.91 E-value=1.9e+02 Score=25.18 Aligned_cols=58 Identities=16% Similarity=0.252 Sum_probs=38.1
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCccc----cccCccceeeEEEEEEeCCCc
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKIV----DLPEIRETGEYIAQLKLHPEV 146 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I----~l~~Ik~~G~~~v~v~l~~~v 146 (157)
+++|+.+.+ .||. .||++|++-.+.......-..... .+..++.+|.|+|+++|....
T Consensus 57 t~tf~Lr~~~~fsdG~---pvTA~Dv~~s~~r~~~~~~~~~~~~~~~~i~~v~~~d~~tv~~~l~~p~ 121 (488)
T cd08489 57 TYTFHLRKGVKFSDGT---PFNAEAVKKNFDAVLANRDRHSWLELVNKIDSVEVVDEYTVRLHLKEPY 121 (488)
T ss_pred EEEEEeCCCCCccCCC---cCCHHHHHHHHHHHhccCCCCchhhcccceeeEEEccCCEEEEEECCCC
Confidence 678877665 4665 699999999987542211000001 123488999999999998643
No 52
>COG1438 ArgR Arginine repressor [Transcription]
Probab=23.79 E-value=41 Score=25.89 Aligned_cols=34 Identities=18% Similarity=0.416 Sum_probs=22.5
Q ss_pred CHHHHHHHHHHhcCCCccCccccccCccceeeEEEE
Q 031586 104 TAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQ 139 (157)
Q Consensus 104 t~~dI~~~l~~~~gi~i~k~~I~l~~Ik~~G~~~v~ 139 (157)
|..+|++.|++. |+++.-..+. ..||++|-..|+
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 567888888876 8776543332 147777777766
No 53
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=23.77 E-value=1.9e+02 Score=24.52 Aligned_cols=56 Identities=16% Similarity=0.284 Sum_probs=37.4
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCcc---c-cccCccceeeEEEEEEeCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKI---V-DLPEIRETGEYIAQLKLHP 144 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~~---I-~l~~Ik~~G~~~v~v~l~~ 144 (157)
+++|+.+.| .||. .||++|+.-.+.....-...... . .+..|..++.|+|+|+|..
T Consensus 59 ~~tf~Lr~~~~~sDG~---p~TA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~ 121 (466)
T cd00995 59 TYTFKLRDGVKFHDGT---PLTAEDVVFSFERLADPKNASPSAGKADEIEGVEVVDDYTVTITLKE 121 (466)
T ss_pred EEEEEecCCCCcCCCC---CcCHHHHHhHHHHhcCCccCCcccccccceeeEEecCCCeEEEEECC
Confidence 688887765 4565 69999999998765332221111 1 1224888999999999875
No 54
>cd08517 PBP2_NikA_DppA_OppA_like_13 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=23.55 E-value=2.2e+02 Score=24.50 Aligned_cols=56 Identities=16% Similarity=0.256 Sum_probs=37.1
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCcc-c-cccCccceeeEEEEEEeCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKI-V-DLPEIRETGEYIAQLKLHP 144 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~~-I-~l~~Ik~~G~~~v~v~l~~ 144 (157)
+++|+.+.| .||. .||++|++-.+............ . .+..|+.++.|+|+|+|..
T Consensus 61 ~~tf~LR~~v~f~DG~---pltA~Dv~~s~~r~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~ 121 (480)
T cd08517 61 TYTFKLRPGVKWHDGK---PFTSADVKFSIDTLKEEHPRRRRTFANVESIETPDDLTVVFKLKK 121 (480)
T ss_pred EEEEEecCCCEeeCCC---CCCHHHHHhHHHHHhcCCCCccccccccceEEecCCeEEEEEecC
Confidence 677877665 4554 79999999998765332211111 1 1234888999999999874
No 55
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=23.50 E-value=79 Score=21.80 Aligned_cols=30 Identities=23% Similarity=0.253 Sum_probs=21.8
Q ss_pred CceEEEEeccc-ccccCCCcEEEecCcccccc
Q 031586 8 TQIQIILKEDV-AELGKKGQLLDVKAGFYRNY 38 (157)
Q Consensus 8 k~mkVIL~~dV-~~lGk~Gdvv~Vk~GyaRN~ 38 (157)
+.+.+-|..+. |. -..||.|-|..|||++-
T Consensus 29 r~V~l~Lv~~~~~~-~~vGDyVLVHaGfAi~~ 59 (82)
T PRK10413 29 RDVNIALICEGNPA-DLLGQWVLVHVGFAMSI 59 (82)
T ss_pred EEEEeeeeccCCcc-cccCCEEEEecchhhhh
Confidence 34666677654 23 47899999999999853
No 56
>PF09078 CheY-binding: CheY binding; InterPro: IPR015162 The CheY binding domain is found in the response regulator histidine kinase CheA. It adopts a secondary structure consisting of an open-face beta/alpha sandwich, with four antiparallel beta-strands and two alpha-helices. It binds to a corresponding domain on CheY, with subsequent phosphorylation of the CheY Asp57 residue, and activation of CheY, which then affects flagellar rotation []. ; PDB: 1FWP_A 1EAY_C 1A0O_D 1FFG_B 1FFS_B 1FFW_D.
Probab=23.45 E-value=1.5e+02 Score=19.65 Aligned_cols=51 Identities=20% Similarity=0.304 Sum_probs=31.2
Q ss_pred HHHHHHHHhccCCeEEEEEecCCCC--ceeeccCHHHHHHHHHHhcCCCccCccccc
Q 031586 73 EAQQLALIFETVGAFKVKRKGGKGK--QIFGSVTAQDVVDIIKAQLQRDVDKKIVDL 127 (157)
Q Consensus 73 ~a~~~~~~L~~~~~l~i~~k~~~~g--klfGsVt~~dI~~~l~~~~gi~i~k~~I~l 127 (157)
++..+.+.|.+++.+.-..+.++.- .|=+++++.||..-+ -+-||+.+|.+
T Consensus 12 d~~lL~eELgnLG~v~~~~~~~~~l~~~L~T~~s~DDI~AV~----CFVid~dQI~i 64 (65)
T PF09078_consen 12 DVDLLLEELGNLGTVSDQEKGGDSLEVWLETSVSADDIIAVC----CFVIDPDQISI 64 (65)
T ss_dssp HHHHHHHHHHHHS--EEEEEESSEEEEEE-STSSHHHHHHHH----TTTS-GGGEEE
T ss_pred HHHHHHHHHhcCccEEEEecCCCeEEEEECCCCChhhEEEEE----EEEEcHHHeEE
Confidence 3455777777777666655554322 233689999999876 46788877753
No 57
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=23.31 E-value=1.5e+02 Score=21.04 Aligned_cols=39 Identities=18% Similarity=0.162 Sum_probs=7.0
Q ss_pred ccccCCCcEEEecCccccccccCCCceEecCHHHHHHHH
Q 031586 19 AELGKKGQLLDVKAGFYRNYLHPMGKAQIVTPLLLKEMK 57 (157)
Q Consensus 19 ~~lGk~Gdvv~Vk~GyaRN~LiP~glA~~at~~nl~~~~ 57 (157)
+|.-..-+.++..||.+.|-.-|-=.+...|++.++.-+
T Consensus 44 ~gQ~~~~~~~e~~P~~~~~~~QPLc~~~~VT~eDIr~QE 82 (96)
T PF14048_consen 44 TGQTSSKDALEKNPGVGLNPPQPLCKQFVVTEEDIRRQE 82 (96)
T ss_dssp -------------------------T-----HHHHHHHH
T ss_pred cCCccchhhhccCcccccCCCcccccCCccCHHHHHHHH
Confidence 333333448999999999999999999999999887655
No 58
>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model. AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.
Probab=23.25 E-value=25 Score=26.53 Aligned_cols=11 Identities=45% Similarity=0.703 Sum_probs=4.9
Q ss_pred EEecccccccC
Q 031586 13 ILKEDVAELGK 23 (157)
Q Consensus 13 IL~~dV~~lGk 23 (157)
+|++|+||+||
T Consensus 2 vLleg~PG~GK 12 (131)
T PF07726_consen 2 VLLEGVPGVGK 12 (131)
T ss_dssp EEEES---HHH
T ss_pred EeeECCCccHH
Confidence 46666666665
No 59
>cd04604 CBS_pair_KpsF_GutQ_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway intermediate D-ribulose 5-phosphate into A5P, a precursor of 3-deoxy-D-manno-octulosonate, which is an integral carbohydrate component of various glycolipids coating the surface of the outer membrane of Gram-negative bacteria, including lipopolysaccharide and many group 2 K-antigen capsules. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other funct
Probab=23.06 E-value=1.8e+02 Score=19.07 Aligned_cols=21 Identities=14% Similarity=0.267 Sum_probs=17.6
Q ss_pred CCCceeeccCHHHHHHHHHHh
Q 031586 95 KGKQIFGSVTAQDVVDIIKAQ 115 (157)
Q Consensus 95 ~~gklfGsVt~~dI~~~l~~~ 115 (157)
++|++.|.|+..+|...+...
T Consensus 33 ~~~~~~G~v~~~~i~~~~~~~ 53 (114)
T cd04604 33 EDGRLVGIFTDGDLRRALEKG 53 (114)
T ss_pred CCCCEEEEechHHHHHHHhcc
Confidence 467999999999999887654
No 60
>TIGR02294 nickel_nikA nickel ABC transporter, periplasmic nickel-binding protein. Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Nickel is bound specifically, albeit weakly, through water molecules positioned in the binding site. The amino acids whose side chains line the binding site include Tyr-44, Met-49, Trp-122, Arg-159, Trp-420, and Tyr-424 (numbering based on the precursor sequence of E. coli NikA) with the Arg contributing a hydrogen bond indirectly through a water molecule. Sequences that exactly (or mostly) have the same binding site residues score above the trusted (or noise) cutoffs to this model. Most appear to be lipoproteins.
Probab=22.85 E-value=2e+02 Score=25.20 Aligned_cols=57 Identities=18% Similarity=0.277 Sum_probs=37.3
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCcccc----ccCccceeeEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVD----LPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~~I~----l~~Ik~~G~~~v~v~l~~~ 145 (157)
+++|+.+-| .+|. .||++|+.-.+.....-.-...... +..|+..+.|+|.|+|..-
T Consensus 64 t~tf~LR~~~kfsDG~---pvTA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~v~~~d~~Tv~i~l~~p 127 (500)
T TIGR02294 64 TYTFKLRDDVKFSDGT---PFDAEAVKKNFDAVLQNSQRHSWLELSNQLDNVKALDKYTFELVLKEA 127 (500)
T ss_pred EEEEEECCCCCcCCCC---CCCHHHHHHHHHHHhcCCcccchhhccccceeEEecCCCEEEEEECCC
Confidence 688887765 4665 6999999998875432111111111 2248889999999998763
No 61
>COG0236 AcpP Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.81 E-value=26 Score=23.32 Aligned_cols=24 Identities=8% Similarity=0.218 Sum_probs=22.1
Q ss_pred ccCHHHHHHHHHHhcCCCccCccc
Q 031586 102 SVTAQDVVDIIKAQLQRDVDKKIV 125 (157)
Q Consensus 102 sVt~~dI~~~l~~~~gi~i~k~~I 125 (157)
|+..-+++-+|.+.||++|+...+
T Consensus 39 Sld~veLi~~lE~~f~i~i~~e~~ 62 (80)
T COG0236 39 SLDLVELVMALEEEFGIEIPDEEL 62 (80)
T ss_pred HHHHHHHHHHHHHHHCCcCCHHHH
Confidence 999999999999999999998765
No 62
>cd04607 CBS_pair_NTP_transferase_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=22.20 E-value=1.5e+02 Score=19.64 Aligned_cols=21 Identities=19% Similarity=0.392 Sum_probs=17.1
Q ss_pred CCCCceeeccCHHHHHHHHHH
Q 031586 94 GKGKQIFGSVTAQDVVDIIKA 114 (157)
Q Consensus 94 ~~~gklfGsVt~~dI~~~l~~ 114 (157)
.++|++.|.||..|+...+.+
T Consensus 32 d~~~~~~G~v~~~dl~~~~~~ 52 (113)
T cd04607 32 DENGRLLGTVTDGDIRRALLK 52 (113)
T ss_pred CCCCCEEEEEEcHHHHHHHhc
Confidence 357899999999999877653
No 63
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. 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 similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling
Probab=22.16 E-value=2.2e+02 Score=24.67 Aligned_cols=56 Identities=14% Similarity=0.307 Sum_probs=37.5
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCc--cCcc-cc-ccCccceeeEEEEEEeCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDV--DKKI-VD-LPEIRETGEYIAQLKLHP 144 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i--~k~~-I~-l~~Ik~~G~~~v~v~l~~ 144 (157)
.++|+.+-| .||. .||++|+.-.+.....-.. .... +. +..|+.++.|+|+|+|..
T Consensus 59 ~~tf~Lr~~v~fsDG~---p~tA~Dv~~s~~~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~ 121 (474)
T cd08499 59 TWTFKLREGVKFHDGT---PFNAEAVKANLDRVLDPETASPRASLFSMIEEVEVVDDYTVKITLKE 121 (474)
T ss_pred EEEEEeCCCCCccCCC---CCCHHHHHHHHHhhcCCccCcccccccceeeeEEEcCCCeEEEEECC
Confidence 688887765 4554 7999999999876533221 1111 11 234788999999999875
No 64
>cd08492 PBP2_NikA_DppA_OppA_like_15 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=22.15 E-value=2.5e+02 Score=24.22 Aligned_cols=56 Identities=9% Similarity=0.187 Sum_probs=36.9
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCc----ccc-ccCccceeeEEEEEEeCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKK----IVD-LPEIRETGEYIAQLKLHP 144 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~----~I~-l~~Ik~~G~~~v~v~l~~ 144 (157)
+++|+.+-+ .+|. .||++|+.-.+.....-..... ... +..|..++.|+|+|+|..
T Consensus 61 ~~tf~Lr~~~~wsdG~---pvTA~Dv~~s~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~tv~i~l~~ 124 (484)
T cd08492 61 TYTFHLRDGVTFSDGT---PLDAEAVKANFDRILDGSTKSGLAASYLGPYKSTEVVDPYTVKVHFSE 124 (484)
T ss_pred EEEEEeCCCCEecCCC---CCCHHHHHHHHHHhcCCCcCCCccccccccceeEEeccCCEEEEEECC
Confidence 688877665 4555 7999999999876532211110 111 124888999999999975
No 65
>cd04606 CBS_pair_Mg_transporter This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other divalent cations into the cell via two highly conserved aspartates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=22.13 E-value=98 Score=20.47 Aligned_cols=19 Identities=32% Similarity=0.671 Sum_probs=15.4
Q ss_pred CCCCceeeccCHHHHHHHH
Q 031586 94 GKGKQIFGSVTAQDVVDII 112 (157)
Q Consensus 94 ~~~gklfGsVt~~dI~~~l 112 (157)
.++|++.|.||..|+.+++
T Consensus 91 ~~~~~~~Gvit~~dll~~~ 109 (109)
T cd04606 91 DEEGRLVGIITVDDVIDVI 109 (109)
T ss_pred CCCCcEEEEEEhHHhhhhC
Confidence 4568999999999998653
No 66
>cd08497 PBP2_NikA_DppA_OppA_like_14 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=21.90 E-value=1.9e+02 Score=25.42 Aligned_cols=55 Identities=13% Similarity=0.165 Sum_probs=37.8
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccC--cc-c-cccCccceeeEEEEEEeCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDK--KI-V-DLPEIRETGEYIAQLKLHP 144 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k--~~-I-~l~~Ik~~G~~~v~v~l~~ 144 (157)
+++|+.+.| .+|. .||++|++-.+....+-. .. .. + .+..+..+|.|+|+|+|..
T Consensus 77 t~tf~Lr~gv~fsDG~---p~tA~DV~~s~~~~~~~~-~~~~~~~~~~i~~v~~~d~~tv~i~l~~ 138 (491)
T cd08497 77 WVTFHLRPEARFSDGT---PVTAEDVVFSFETLKSKG-PPYYRAYYADVEKVEALDDHTVRFTFKE 138 (491)
T ss_pred EEEEEECCCCCcCCCC---cccHhHhhhHHHHHhCCC-CchhhhhhhceeEEEEECCCEEEEEECC
Confidence 688887765 4555 699999999887653322 11 11 1 1234888999999999987
No 67
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta 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 beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=21.73 E-value=1e+02 Score=21.60 Aligned_cols=21 Identities=33% Similarity=0.586 Sum_probs=17.5
Q ss_pred CCC-ceeeccCHHHHHHHHHHh
Q 031586 95 KGK-QIFGSVTAQDVVDIIKAQ 115 (157)
Q Consensus 95 ~~g-klfGsVt~~dI~~~l~~~ 115 (157)
++| .+||.||++|+.+.+.+.
T Consensus 56 p~g~v~Y~~V~~edv~~Iv~~~ 77 (92)
T cd03063 56 PGGRVAYGPVTPADVASLLDAG 77 (92)
T ss_pred CCCcEEEEeCCHHHHHHHHHHH
Confidence 345 789999999999988775
No 68
>cd04632 CBS_pair_19 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=21.70 E-value=1.5e+02 Score=20.14 Aligned_cols=20 Identities=30% Similarity=0.527 Sum_probs=16.6
Q ss_pred CCCCceeeccCHHHHHHHHH
Q 031586 94 GKGKQIFGSVTAQDVVDIIK 113 (157)
Q Consensus 94 ~~~gklfGsVt~~dI~~~l~ 113 (157)
+++|++.|.||..|+...+.
T Consensus 31 ~~~~~~~G~it~~dl~~~~~ 50 (128)
T cd04632 31 DDNGKLTGIVTRHDIVDFVV 50 (128)
T ss_pred CCCCcEEEEEEHHHHHHHHh
Confidence 45689999999999987764
No 69
>PF13954 PapC_N: PapC N-terminal domain; PDB: 2VQI_B 3FIP_A 3RFZ_E 3OHN_A 1ZDV_A 1ZE3_D 3BWU_D 1ZDX_A.
Probab=21.53 E-value=2e+02 Score=21.27 Aligned_cols=25 Identities=16% Similarity=0.365 Sum_probs=20.2
Q ss_pred ceeeEEEEEEeCCCcEEEEEEEEee
Q 031586 132 ETGEYIAQLKLHPEVTARIRLNVFA 156 (157)
Q Consensus 132 ~~G~~~v~v~l~~~v~~~l~v~V~~ 156 (157)
.-|+|.|.|.++..-.....|.+..
T Consensus 28 ~pG~Y~vdv~vN~~~~~~~~i~f~~ 52 (146)
T PF13954_consen 28 PPGEYSVDVYVNGKFIGRYDIEFIN 52 (146)
T ss_dssp -SEEEEEEEEETTEEEEEEEEEEEE
T ss_pred CCeEEEEEEEECCeeeeeEEEEEEe
Confidence 3599999999999888888877654
No 70
>cd04592 CBS_pair_EriC_assoc_euk This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually
Probab=21.50 E-value=1.6e+02 Score=21.11 Aligned_cols=22 Identities=14% Similarity=0.181 Sum_probs=18.5
Q ss_pred CCCCceeeccCHHHHHHHHHHh
Q 031586 94 GKGKQIFGSVTAQDVVDIIKAQ 115 (157)
Q Consensus 94 ~~~gklfGsVt~~dI~~~l~~~ 115 (157)
.++|++.|.||..|+..++...
T Consensus 31 D~~g~l~Givt~~Dl~~~~~~~ 52 (133)
T cd04592 31 DSDDFLEGILTLGDIQRFLFTN 52 (133)
T ss_pred CCCCeEEEEEEHHHHHHHHhhc
Confidence 4578999999999999988654
No 71
>KOG3279 consensus Uncharacterized conserved protein (melanoma antigen P15) [Function unknown]
Probab=21.43 E-value=68 Score=26.47 Aligned_cols=28 Identities=11% Similarity=0.039 Sum_probs=16.6
Q ss_pred HHHHhccCCeEEEEEecCCCCceeeccCH
Q 031586 77 LALIFETVGAFKVKRKGGKGKQIFGSVTA 105 (157)
Q Consensus 77 ~~~~L~~~~~l~i~~k~~~~gklfGsVt~ 105 (157)
.++.|++- ....+..++.++++||-+.|
T Consensus 250 ~~Q~Le~P-ea~~K~eS~~~~~~~~k~np 277 (283)
T KOG3279|consen 250 EAQKLEKP-EALTKLESSPSSSWLSKINP 277 (283)
T ss_pred HhhhhcCc-hhhhhcccCcchhhhhhcCC
Confidence 44566653 34445566677778876544
No 72
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=21.29 E-value=78 Score=19.88 Aligned_cols=22 Identities=27% Similarity=0.507 Sum_probs=15.2
Q ss_pred eccCHHHHHHHHHHhcCCCccCcc
Q 031586 101 GSVTAQDVVDIIKAQLQRDVDKKI 124 (157)
Q Consensus 101 GsVt~~dI~~~l~~~~gi~i~k~~ 124 (157)
|.-|..+|++.|.++|+ +++..
T Consensus 28 g~~t~~ei~~~l~~~y~--~~~~~ 49 (68)
T PF05402_consen 28 GPRTVEEIVDALAEEYD--VDPEE 49 (68)
T ss_dssp SSS-HHHHHHHHHHHTT----HHH
T ss_pred CCCCHHHHHHHHHHHcC--CCHHH
Confidence 56899999999999975 55443
No 73
>cd08520 PBP2_NikA_DppA_OppA_like_21 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=21.14 E-value=2.4e+02 Score=24.45 Aligned_cols=57 Identities=12% Similarity=0.209 Sum_probs=36.4
Q ss_pred eEEEEEecC---CCCceeeccCHHHHHHHHHHhcCCCccCcc--cc-ccCccceeeEEEEEEeCCC
Q 031586 86 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVDKKI--VD-LPEIRETGEYIAQLKLHPE 145 (157)
Q Consensus 86 ~l~i~~k~~---~~gklfGsVt~~dI~~~l~~~~gi~i~k~~--I~-l~~Ik~~G~~~v~v~l~~~ 145 (157)
+++|+.+.| .||. .||++|+.-.+.....-.-.-.. .. +..|+.++.|+|.|+|..-
T Consensus 60 t~tf~LR~gv~fsDG~---pvtA~Dv~~s~~r~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~p 122 (468)
T cd08520 60 TYTFHLREGAKWHDGE---PLTAEDVAFTFDYMKKHPYVWVDIELSIIERVEALDDYTVKITLKRP 122 (468)
T ss_pred EEEEEeCCCCEeCCCC---CccHHHHHHHHHHHhhCCCCcccccccceeeEEecCCcEEEEEEccC
Confidence 677877665 4554 79999999888754221100011 11 2248889999999998753
No 74
>cd04624 CBS_pair_11 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=20.87 E-value=1.8e+02 Score=19.11 Aligned_cols=22 Identities=27% Similarity=0.412 Sum_probs=17.6
Q ss_pred CCCCceeeccCHHHHHHHHHHh
Q 031586 94 GKGKQIFGSVTAQDVVDIIKAQ 115 (157)
Q Consensus 94 ~~~gklfGsVt~~dI~~~l~~~ 115 (157)
.++|++.|.||..++...+...
T Consensus 31 d~~~~~~G~v~~~~l~~~~~~~ 52 (112)
T cd04624 31 DPDERPIGIVTERDIVRAVAAG 52 (112)
T ss_pred CCCCCEEEEeeHHHHHHHHhcc
Confidence 3568999999999998876543
No 75
>cd04593 CBS_pair_EriC_assoc_bac_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in bacteria and archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS d
Probab=20.79 E-value=1.8e+02 Score=19.25 Aligned_cols=21 Identities=19% Similarity=0.423 Sum_probs=17.3
Q ss_pred CCCCceeeccCHHHHHHHHHH
Q 031586 94 GKGKQIFGSVTAQDVVDIIKA 114 (157)
Q Consensus 94 ~~~gklfGsVt~~dI~~~l~~ 114 (157)
.++|++.|.|+..|+...+.+
T Consensus 31 d~~~~~~G~v~~~dl~~~~~~ 51 (115)
T cd04593 31 DRDGGVVGIITLPDLLRALEA 51 (115)
T ss_pred cCCCCEEEEEEHHHHHHHHhc
Confidence 346899999999999987754
No 76
>cd03082 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex 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 in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. Similarly, the beta subunit of W-FDH is most likely involved in the electron transport chain during the NAD-dependen
Probab=20.71 E-value=83 Score=20.72 Aligned_cols=18 Identities=17% Similarity=0.311 Sum_probs=15.6
Q ss_pred CCceeeccCHHHHHHHHH
Q 031586 96 GKQIFGSVTAQDVVDIIK 113 (157)
Q Consensus 96 ~gklfGsVt~~dI~~~l~ 113 (157)
++++|+.+|+..|-+.+.
T Consensus 53 ~~~~~~~~t~~~i~~~~~ 70 (72)
T cd03082 53 GQRPVDGATPAAVAAAVE 70 (72)
T ss_pred CCEEeCCcCHHHHHHHHh
Confidence 678999999999988764
No 77
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=20.67 E-value=95 Score=20.36 Aligned_cols=19 Identities=26% Similarity=0.594 Sum_probs=16.1
Q ss_pred CCceeeccCHHHHHHHHHH
Q 031586 96 GKQIFGSVTAQDVVDIIKA 114 (157)
Q Consensus 96 ~gklfGsVt~~dI~~~l~~ 114 (157)
+|.+|+-+|+.+|.+.+.+
T Consensus 61 ~g~~y~~vt~~~i~~i~~~ 79 (80)
T cd03064 61 NDDVYGRLTPEKVDAILEA 79 (80)
T ss_pred CCEEECCCCHHHHHHHHHh
Confidence 4789999999999988754
No 78
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=20.61 E-value=82 Score=23.65 Aligned_cols=42 Identities=14% Similarity=0.247 Sum_probs=30.0
Q ss_pred eeccCHHHHHHHHHHhcCCCccCcccc-------------c--c---CccceeeEEEEEEeC
Q 031586 100 FGSVTAQDVVDIIKAQLQRDVDKKIVD-------------L--P---EIRETGEYIAQLKLH 143 (157)
Q Consensus 100 fGsVt~~dI~~~l~~~~gi~i~k~~I~-------------l--~---~Ik~~G~~~v~v~l~ 143 (157)
.|.+|.+++++.+.+..++ .+..+. | . .|..||+|.+.++-.
T Consensus 28 ~~~mt~~el~~~Ia~~s~~--s~~dv~~vl~~l~~~i~~~L~~G~~V~L~gfGtF~~~~~s~ 87 (145)
T TIGR01201 28 SGVIDFEEIAELIAEESSL--SPGDVKGIIDRLAYVLRRELANGKTVRLGEIGTFRLSATAK 87 (145)
T ss_pred CCCcCHHHHHHHHHHHhCC--CHHHHHHHHHHHHHHHHHHHhCCCeEEeCCCEEEEEEeccC
Confidence 4579999999999888654 333221 1 1 288999999999853
No 79
>PF01516 Orbi_VP6: Orbivirus helicase VP6; InterPro: IPR001399 Bluetongue virus VP6 protein binds ATP and exhibits an RNA-dependent ATPase function and a helicase activity that catalyses the unwinding of double-stranded RNA substrates []. VP6 from five United States prototype bluetongue virus (BTV) serotypes contain unusually high concentrations of glycine, few aromatic amino acids, but a high concentration of charged amino acids, a characteristic of hydrophilic proteins []. VP6 is an inner capsid protein that surrounds the genomic DS-RNA. Its hydrophilic nature coupled with a capability to bind ss- and ds-RNA, suggests that it interacts directly with the BTV genomic RNA.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=20.27 E-value=84 Score=27.19 Aligned_cols=37 Identities=24% Similarity=0.505 Sum_probs=25.8
Q ss_pred CCceeeccCHHHHHHHHHHhcCCCccCc-------ccccc-C-cccee
Q 031586 96 GKQIFGSVTAQDVVDIIKAQLQRDVDKK-------IVDLP-E-IRETG 134 (157)
Q Consensus 96 ~gklfGsVt~~dI~~~l~~~~gi~i~k~-------~I~l~-~-Ik~~G 134 (157)
.|++| |-+.+|+++|+.+||.+|+-- .|.+. . +|++|
T Consensus 123 ~Gr~~--V~T~eIa~ai~~ryg~~I~VY~~e~~~~iI~le~slqKELG 168 (322)
T PF01516_consen 123 GGRWF--VLTEEIARAIRSRYGTDIPVYKDEANGRIIELESSLQKELG 168 (322)
T ss_pred CceEE--EeCHHHHHHHHHhcCCcceeecCCCCceEEEehhhHHHhhC
Confidence 45565 889999999999999776532 34444 2 66666
No 80
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=20.17 E-value=58 Score=25.56 Aligned_cols=24 Identities=29% Similarity=0.267 Sum_probs=19.9
Q ss_pred CCCcEEEec-CccccccccCCCceE
Q 031586 23 KKGQLLDVK-AGFYRNYLHPMGKAQ 46 (157)
Q Consensus 23 k~Gdvv~Vk-~GyaRN~LiP~glA~ 46 (157)
.+||+..|+ ++.++.+|||.--++
T Consensus 129 Ga~Dvl~V~~~~~~k~~LIPf~~~~ 153 (174)
T COG0806 129 GANDVLVVKAKGGKKERLIPFVDAV 153 (174)
T ss_pred CCccEEEEEecCCCcEEEecchHhe
Confidence 478999999 588999999976544
Done!