Query 033453
Match_columns 119
No_of_seqs 168 out of 1027
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 02:26:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033453.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033453hhsearch_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 9.8E-42 2.1E-46 249.9 13.8 117 2-118 27-152 (153)
2 TIGR00158 L9 ribosomal protein 100.0 5.5E-40 1.2E-44 239.5 13.9 115 2-118 22-147 (148)
3 COG0359 RplI Ribosomal protein 100.0 1.9E-39 4.1E-44 236.3 13.2 114 3-118 23-146 (148)
4 PRK00137 rplI 50S ribosomal pr 100.0 5.5E-38 1.2E-42 228.6 13.7 115 2-118 22-146 (147)
5 PRK14538 putative bifunctional 100.0 7.2E-33 1.6E-37 244.4 14.2 115 2-118 710-834 (838)
6 PF03948 Ribosomal_L9_C: Ribos 100.0 6.3E-32 1.4E-36 181.5 11.0 85 33-118 1-86 (87)
7 KOG4607 Mitochondrial ribosoma 99.1 2.5E-10 5.5E-15 87.6 6.0 116 1-118 69-194 (222)
8 PF01281 Ribosomal_L9_N: Ribos 97.7 1.7E-06 3.7E-11 52.3 -3.0 16 2-17 22-37 (48)
9 PF10045 DUF2280: Uncharacteri 80.9 0.7 1.5E-05 32.1 0.7 25 66-90 21-45 (104)
10 PF07523 Big_3: Bacterial Ig-l 75.8 7.5 0.00016 23.9 4.3 24 92-116 44-67 (67)
11 PF00571 CBS: CBS domain CBS d 74.8 5.1 0.00011 23.0 3.2 21 55-75 36-56 (57)
12 PF08766 DEK_C: DEK C terminal 72.5 2.3 4.9E-05 25.5 1.3 26 62-87 18-43 (54)
13 PF13592 HTH_33: Winged helix- 56.6 7.5 0.00016 23.6 1.4 33 63-96 3-35 (60)
14 PRK01885 greB transcription el 55.1 31 0.00068 25.1 4.8 19 7-25 4-22 (157)
15 PF07718 Coatamer_beta_C: Coat 54.9 11 0.00023 27.6 2.2 19 48-66 118-136 (140)
16 PRK06342 transcription elongat 50.8 36 0.00079 25.0 4.5 20 7-26 28-47 (160)
17 PF14221 DUF4330: Domain of un 50.2 13 0.00027 27.5 2.0 19 56-74 5-23 (168)
18 smart00116 CBS Domain in cysta 48.2 14 0.00031 19.0 1.6 18 57-74 31-48 (49)
19 cd03081 TRX_Fd_NuoE_FDH_gamma 44.7 21 0.00045 22.8 2.2 19 58-76 61-79 (80)
20 PRK00226 greA transcription el 44.4 37 0.00079 24.4 3.7 21 7-27 4-24 (157)
21 COG2524 Predicted transcriptio 44.2 19 0.00041 29.2 2.2 23 54-76 207-229 (294)
22 TIGR01461 greB transcription e 42.0 51 0.0011 24.0 4.1 20 7-26 2-21 (156)
23 PF12774 AAA_6: Hydrolytic ATP 40.9 5.9 0.00013 30.6 -1.0 17 1-17 141-157 (231)
24 KOG3279 Uncharacterized conser 40.9 32 0.00069 27.2 3.0 28 39-67 250-277 (283)
25 cd02980 TRX_Fd_family Thioredo 39.5 30 0.00065 21.2 2.3 19 58-76 58-76 (77)
26 KOG4196 bZIP transcription fac 38.7 89 0.0019 22.7 4.8 45 2-46 61-114 (135)
27 COG1438 ArgR Arginine represso 37.2 21 0.00045 26.3 1.4 34 66-101 22-55 (150)
28 cd07694 Ig2_CD4 Second immunog 37.2 91 0.002 20.9 4.4 38 82-119 48-88 (88)
29 cd04623 CBS_pair_10 The CBS do 37.1 64 0.0014 20.0 3.7 21 57-77 32-52 (113)
30 PRK07668 hypothetical protein; 36.1 84 0.0018 25.0 4.8 22 60-84 50-71 (254)
31 cd04590 CBS_pair_CorC_HlyC_ass 36.1 79 0.0017 19.7 4.0 18 59-76 35-52 (111)
32 cd08505 PBP2_NikA_DppA_OppA_li 35.9 68 0.0015 27.2 4.5 56 44-107 63-126 (528)
33 cd04630 CBS_pair_17 The CBS do 35.4 80 0.0017 20.0 4.0 19 59-77 35-53 (114)
34 PF13565 HTH_32: Homeodomain-l 35.1 29 0.00063 21.3 1.7 19 64-82 48-66 (77)
35 cd04632 CBS_pair_19 The CBS do 34.8 35 0.00076 22.2 2.2 21 55-75 30-50 (128)
36 cd03082 TRX_Fd_NuoE_W_FDH_beta 34.5 35 0.00076 21.5 2.0 18 58-75 53-70 (72)
37 PRK15365 type III secretion sy 34.5 99 0.0022 21.4 4.3 38 8-45 57-94 (107)
38 PF05157 T2SE_Nter: Type II se 33.8 30 0.00065 22.2 1.7 20 63-82 5-24 (109)
39 COG2047 Uncharacterized protei 33.6 34 0.00074 27.2 2.2 27 57-84 133-159 (258)
40 cd04608 CBS_pair_PALP_assoc Th 33.4 20 0.00044 23.8 0.8 19 56-74 106-124 (124)
41 cd04639 CBS_pair_26 The CBS do 33.4 44 0.00096 21.0 2.4 20 57-76 32-51 (111)
42 PF04282 DUF438: Family of unk 32.7 22 0.00048 22.9 0.9 16 60-75 24-39 (71)
43 cd04619 CBS_pair_6 The CBS dom 32.7 93 0.002 19.8 3.9 22 55-76 30-51 (114)
44 PRK07639 acyl carrier protein; 32.4 18 0.00039 23.6 0.4 34 63-96 39-72 (86)
45 cd04624 CBS_pair_11 The CBS do 32.2 45 0.00097 21.0 2.3 21 56-76 31-51 (112)
46 PHA02119 hypothetical protein 31.7 35 0.00076 22.4 1.6 25 59-84 48-72 (87)
47 cd03064 TRX_Fd_NuoE TRX-like [ 31.5 48 0.001 20.8 2.3 19 58-76 61-79 (80)
48 KOG2639 Sodium sulfate symport 31.4 41 0.0009 30.1 2.5 32 53-85 623-654 (685)
49 cd04629 CBS_pair_16 The CBS do 31.2 47 0.001 20.9 2.3 21 56-76 31-51 (114)
50 PF01316 Arg_repressor: Argini 31.2 23 0.0005 22.6 0.7 34 66-101 21-54 (70)
51 cd04607 CBS_pair_NTP_transfera 31.1 95 0.0021 19.5 3.8 20 56-75 32-51 (113)
52 cd04606 CBS_pair_Mg_transporte 31.0 63 0.0014 20.3 2.9 20 55-74 90-109 (109)
53 cd04593 CBS_pair_EriC_assoc_ba 30.7 1E+02 0.0022 19.5 3.8 20 57-76 32-51 (115)
54 PF10668 Phage_terminase: Phag 30.5 35 0.00075 21.3 1.4 13 63-75 21-33 (60)
55 cd04643 CBS_pair_30 The CBS do 30.2 49 0.0011 20.9 2.2 21 56-76 31-51 (116)
56 cd04582 CBS_pair_ABC_OpuCA_ass 29.7 44 0.00096 20.8 1.9 19 56-74 31-49 (106)
57 cd04592 CBS_pair_EriC_assoc_eu 29.6 50 0.0011 22.6 2.3 22 56-77 31-52 (133)
58 cd04620 CBS_pair_7 The CBS dom 29.5 50 0.0011 20.9 2.2 20 57-76 32-51 (115)
59 PF10826 DUF2551: Protein of u 29.4 36 0.00079 22.7 1.5 23 63-87 24-46 (83)
60 cd04603 CBS_pair_KefB_assoc Th 28.5 72 0.0016 20.3 2.8 18 55-72 93-110 (111)
61 cd04604 CBS_pair_KpsF_GutQ_ass 28.3 1.3E+02 0.0028 18.7 4.0 21 56-76 32-52 (114)
62 PRK05892 nucleoside diphosphat 27.9 1.7E+02 0.0036 21.3 4.9 20 7-26 5-24 (158)
63 cd04801 CBS_pair_M50_like This 27.9 50 0.0011 20.9 1.9 20 56-75 32-51 (114)
64 PF11221 Med21: Subunit 21 of 27.9 1.8E+02 0.004 20.6 5.1 32 14-45 105-136 (144)
65 cd04583 CBS_pair_ABC_OpuCA_ass 27.8 77 0.0017 19.6 2.8 17 55-71 91-107 (109)
66 COG3620 Predicted transcriptio 27.7 43 0.00093 25.4 1.8 36 37-76 150-185 (187)
67 cd04601 CBS_pair_IMPDH This cd 27.0 71 0.0015 19.8 2.6 18 55-72 92-109 (110)
68 cd04641 CBS_pair_28 The CBS do 27.0 1.2E+02 0.0025 19.5 3.7 22 55-76 30-51 (120)
69 cd04587 CBS_pair_CAP-ED_DUF294 27.0 28 0.0006 21.9 0.6 18 55-72 95-112 (113)
70 TIGR02657 amicyanin amicyanin. 26.6 71 0.0015 20.2 2.5 24 92-115 60-83 (83)
71 cd04614 CBS_pair_1 The CBS dom 26.5 93 0.002 19.5 3.1 19 56-74 31-49 (96)
72 smart00089 PKD Repeats in poly 26.5 1.2E+02 0.0026 18.3 3.5 25 92-116 51-78 (79)
73 cd05886 Ig1_Nectin-1_like Firs 26.4 1.6E+02 0.0036 19.4 4.3 31 86-116 64-98 (99)
74 cd04611 CBS_pair_PAS_GGDEF_DUF 26.4 48 0.001 20.6 1.7 17 59-75 33-49 (111)
75 PF01257 2Fe-2S_thioredx: Thio 25.8 45 0.00098 23.7 1.6 19 58-76 125-143 (145)
76 cd04625 CBS_pair_12 The CBS do 25.8 61 0.0013 20.3 2.1 20 57-76 31-50 (112)
77 PF04552 Sigma54_DBD: Sigma-54 25.6 29 0.00064 25.5 0.6 24 64-88 121-144 (160)
78 PRK00441 argR arginine repress 25.4 42 0.00092 24.3 1.4 36 63-100 17-52 (149)
79 cd03083 TRX_Fd_NuoE_hoxF TRX-l 25.3 66 0.0014 20.4 2.2 18 58-75 61-78 (80)
80 cd04605 CBS_pair_MET2_assoc Th 25.1 1E+02 0.0022 19.2 3.0 18 55-72 92-109 (110)
81 COG0757 AroQ 3-dehydroquinate 24.9 66 0.0014 23.6 2.3 27 60-86 20-49 (146)
82 PF13954 PapC_N: PapC N-termin 24.9 1.7E+02 0.0037 20.5 4.4 24 95-118 29-52 (146)
83 cd03063 TRX_Fd_FDH_beta TRX-li 24.7 82 0.0018 21.1 2.6 21 57-77 56-77 (92)
84 COG3620 Predicted transcriptio 24.7 58 0.0013 24.7 2.0 23 55-77 101-123 (187)
85 cd04627 CBS_pair_14 The CBS do 24.6 1.8E+02 0.0039 18.6 4.3 18 59-76 35-52 (123)
86 cd04597 CBS_pair_DRTGG_assoc2 24.4 96 0.0021 20.2 2.9 18 55-72 95-112 (113)
87 cd04636 CBS_pair_23 The CBS do 24.4 67 0.0015 21.1 2.1 21 56-76 31-51 (132)
88 COG5556 Uncharacterized conser 24.2 37 0.00081 23.5 0.8 24 66-89 21-44 (110)
89 PF13833 EF-hand_8: EF-hand do 23.8 47 0.001 18.9 1.1 24 63-87 3-27 (54)
90 KOG3841 TEF-1 and related tran 23.5 1.3E+02 0.0029 25.7 4.0 15 2-16 106-122 (455)
91 smart00874 B5 tRNA synthetase 23.4 66 0.0014 19.5 1.8 23 61-84 14-37 (71)
92 COG2239 MgtE Mg/Co/Ni transpor 23.4 1.1E+02 0.0024 26.3 3.6 43 34-77 213-255 (451)
93 cd04622 CBS_pair_9 The CBS dom 23.0 87 0.0019 19.5 2.4 17 56-72 96-112 (113)
94 PF05402 PqqD: Coenzyme PQQ sy 22.9 60 0.0013 19.4 1.5 22 63-86 28-49 (68)
95 cd04617 CBS_pair_4 The CBS dom 22.7 73 0.0016 20.4 2.0 19 57-75 32-50 (118)
96 cd02205 CBS_pair The CBS domai 22.7 1.8E+02 0.004 17.3 4.3 21 57-77 32-52 (113)
97 cd04609 CBS_pair_PALP_assoc2 T 22.5 1.4E+02 0.0031 18.3 3.4 18 59-76 33-50 (110)
98 PF13344 Hydrolase_6: Haloacid 22.4 86 0.0019 20.7 2.3 27 63-90 40-66 (101)
99 PF07679 I-set: Immunoglobulin 22.3 1.9E+02 0.0041 17.4 4.0 30 87-116 58-90 (90)
100 cd04640 CBS_pair_27 The CBS do 22.2 1.3E+02 0.0028 19.5 3.2 35 37-72 90-125 (126)
101 PF14848 HU-DNA_bdg: DNA-bindi 22.1 59 0.0013 22.6 1.5 24 63-87 27-50 (124)
102 cd04585 CBS_pair_ACT_assoc2 Th 22.0 1.1E+02 0.0024 19.2 2.8 17 56-72 105-121 (122)
103 cd04803 CBS_pair_15 The CBS do 21.9 79 0.0017 20.1 2.1 20 57-76 32-51 (122)
104 cd04615 CBS_pair_2 The CBS dom 21.5 1.9E+02 0.0042 17.9 3.9 20 56-75 31-50 (113)
105 PRK13690 hypothetical protein; 21.2 1.8E+02 0.0038 22.2 4.0 44 33-77 14-58 (184)
106 PTZ00373 60S Acidic ribosomal 21.1 57 0.0012 22.8 1.3 25 64-89 19-43 (112)
107 cd08496 PBP2_NikA_DppA_OppA_li 21.0 2.2E+02 0.0048 23.2 5.0 57 48-107 59-120 (454)
108 cd08502 PBP2_NikA_DppA_OppA_li 21.0 2.3E+02 0.0049 23.3 5.0 57 48-107 59-120 (472)
109 PF03449 GreA_GreB_N: Transcri 20.9 2.4E+02 0.0051 18.0 4.9 21 7-27 3-23 (74)
110 PF13189 Cytidylate_kin2: Cyti 20.8 94 0.002 22.5 2.4 44 49-100 2-45 (179)
111 cd05833 Ribosomal_P2 Ribosomal 20.7 59 0.0013 22.5 1.3 25 64-89 17-41 (109)
112 PRK05988 formate dehydrogenase 20.4 94 0.002 22.6 2.4 19 58-76 135-153 (156)
113 cd04600 CBS_pair_HPP_assoc Thi 20.0 97 0.0021 19.7 2.2 18 55-72 106-123 (124)
No 1
>CHL00160 rpl9 ribosomal protein L9; Provisional
Probab=100.00 E-value=9.8e-42 Score=249.91 Aligned_cols=117 Identities=31% Similarity=0.508 Sum_probs=110.2
Q ss_pred CccchhcccchH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCeEEEEEecCCCCceeecccHHHHHH
Q 033453 2 NQVFGNLQLFGV---------LCMEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 2 ~~gyarNfL~~~---------~l~~l~~~~~~~~~~~~~~~~~a~~la~kL~~~~~l~i~~k~g~~gkLFGSVt~~dIa~ 72 (119)
.||||||||||+ |+++++.++++.++++++.+++|++++++|+++.+++|.+++|++|+||||||++||++
T Consensus 27 k~GYaRNyLiP~glA~~AT~~n~~~~e~~~~~~~~~~~~~~~~a~~la~~l~~~~~~~i~~k~ge~gklfGSVt~~dIa~ 106 (153)
T CHL00160 27 KSGYARNYLIPNKMAKVATQGSLKQQKMYQKILDLKLKEAKEKCLKVKQLLEEIQKFSVKKKVGENNQIFGSVTEKEISQ 106 (153)
T ss_pred cCchHhhhhcccCchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCceEEEEEEeCCCCeEEcccCHHHHHH
Confidence 489999999999 55778999999999999999999999999999635999999999999999999999999
Q ss_pred HHHHhcCCceecccccccCccceeeEEEEEEeCCCeEEEEEEEEee
Q 033453 73 IIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPEVTARIRLNVFA 118 (119)
Q Consensus 73 ~L~~~~g~~Idkk~I~l~~IK~lG~y~V~I~L~~~V~a~i~V~V~~ 118 (119)
+|++++|++|||++|.||+||++|+|+|+|+||++|+|+++|+|++
T Consensus 107 ~l~~~~g~~idk~~I~l~~Ik~~G~~~v~v~L~~~V~a~i~v~V~~ 152 (153)
T CHL00160 107 IIKNKTNIDLEKQNIELPEIKTIGIYNIEIKLTSDVKANINLQILP 152 (153)
T ss_pred HHHHhhCCccccceeehhhccccEeEEEEEEecCCcEEEEEEEEEE
Confidence 9988889999999999977999999999999999999999999986
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=5.5e-40 Score=239.52 Aligned_cols=115 Identities=29% Similarity=0.427 Sum_probs=108.4
Q ss_pred CccchhcccchH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCeEEEEEecCCCCceeecccHHHHHH
Q 033453 2 NQVFGNLQLFGV---------LCMEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 2 ~~gyarNfL~~~---------~l~~l~~~~~~~~~~~~~~~~~a~~la~kL~~~~~l~i~~k~g~~gkLFGSVt~~dIa~ 72 (119)
.||||||||||+ |+++++.+++..++++++.+++|++++++|+++ +++|.+++|++|+||||||++||++
T Consensus 22 k~GYaRNyLiP~g~A~~aT~~nl~~~e~~~~~~~~~~~~~~~~a~~l~~~l~~~-~~~i~~k~ge~gklfGSVt~~~I~~ 100 (148)
T TIGR00158 22 KDGYARNFLIPKGLAVPATKKNIEFFEARRKKLEEKLAANKAAAARLKEVLELG-TLTISKKVGDEGKLFGSITTKQIAD 100 (148)
T ss_pred cccchhhhhcccCchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc-EEEEEEEeCCCCeEEEeECHHHHHH
Confidence 489999999998 557788888888899999999999999999996 7999999999999999999999999
Q ss_pred HHHHhcCCceecccccccC--ccceeeEEEEEEeCCCeEEEEEEEEee
Q 033453 73 IIKAQLQRDVDKKIVDLPE--IRETGEYIAQLKLHPEVTARIRLNVFA 118 (119)
Q Consensus 73 ~L~~~~g~~Idkk~I~l~~--IK~lG~y~V~I~L~~~V~a~i~V~V~~ 118 (119)
+|+++ |++|||++|.|++ ||++|+|+|+|+||++|+|+|+|+|++
T Consensus 101 ~l~~~-g~~idk~~I~l~~~~Ik~~G~y~v~i~L~~~V~a~i~v~V~~ 147 (148)
T TIGR00158 101 ALKAA-GLDLDKKKIELPDGVIRTTGEHEVTIKLHEEVFAVLKVIVVP 147 (148)
T ss_pred HHHHc-CCcccHhhEECCCCceeceEEEEEEEEEcCCcEEEEEEEEEE
Confidence 99887 9999999999974 999999999999999999999999986
No 3
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-39 Score=236.33 Aligned_cols=114 Identities=29% Similarity=0.433 Sum_probs=108.4
Q ss_pred ccchhcccchH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCeEEEEEecCCCCceeecccHHHHHHH
Q 033453 3 QVFGNLQLFGV---------LCMEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVDI 73 (119)
Q Consensus 3 ~gyarNfL~~~---------~l~~l~~~~~~~~~~~~~~~~~a~~la~kL~~~~~l~i~~k~g~~gkLFGSVt~~dIa~~ 73 (119)
+|||||||+|+ |++.++.++++.+++.+..+++|++++++|++ .+++|..++|++|+||||||++||+++
T Consensus 23 dGYarNfLiPkglAv~At~~n~~~~e~~r~~~e~~~~~~~~~a~~lk~~Le~-~~~~i~~kag~~GklfGSVt~~dIa~~ 101 (148)
T COG0359 23 DGYARNFLIPKGLAVPATKGNLKLLEARRAKLEKKAAEELAEAEALKEKLEG-KTVEIAVKAGEDGKLFGSVTSKDIAEA 101 (148)
T ss_pred chhhhhhhccccchhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC-ceEEEEEEcCCCCceeccccHHHHHHH
Confidence 79999999999 45778998888888899999999999999999 489999999999999999999999999
Q ss_pred HHHhcCCceecccccccC-ccceeeEEEEEEeCCCeEEEEEEEEee
Q 033453 74 IKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTARIRLNVFA 118 (119)
Q Consensus 74 L~~~~g~~Idkk~I~l~~-IK~lG~y~V~I~L~~~V~a~i~V~V~~ 118 (119)
|.++ |++|||++|.||+ ||++|.|+|+|+||++|+++++|.|.+
T Consensus 102 l~~~-g~~idk~~i~l~~~ik~~G~~~V~vkLh~eV~a~v~v~V~~ 146 (148)
T COG0359 102 LKAA-GFKLDKRKIRLPNGIKTLGEHEVEVKLHEEVTATVKVNVVA 146 (148)
T ss_pred HHHc-CCCcchheeEcCchhhhcceeEEEEEecCceEEEEEEEEEe
Confidence 9999 9999999999998 999999999999999999999999985
No 4
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=100.00 E-value=5.5e-38 Score=228.63 Aligned_cols=115 Identities=34% Similarity=0.538 Sum_probs=108.6
Q ss_pred CccchhcccchH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCeEEEEEecCCCCceeecccHHHHHH
Q 033453 2 NQVFGNLQLFGV---------LCMEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 2 ~~gyarNfL~~~---------~l~~l~~~~~~~~~~~~~~~~~a~~la~kL~~~~~l~i~~k~g~~gkLFGSVt~~dIa~ 72 (119)
.||||||||||+ |+++++.+++..++++++.+++|+++++.|++. +++|.+++|++|+||||||++||++
T Consensus 22 k~GYaRNyLiP~~lA~~aT~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~-~l~i~~k~g~~gklfGsVt~~~I~~ 100 (147)
T PRK00137 22 KDGYARNFLIPQGKAVRATKGNLKQLEARRAELEAKAAEELAEAEALAEKLEGL-TVTIKAKAGEDGKLFGSVTTKDIAE 100 (147)
T ss_pred cCcchhhhhccCCceeeCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC-EEEEEEEcCCCCeEEeeeCHHHHHH
Confidence 589999999998 557788888888888999999999999999986 7999999999999999999999999
Q ss_pred HHHHhcCCceecccccccC-ccceeeEEEEEEeCCCeEEEEEEEEee
Q 033453 73 IIKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTARIRLNVFA 118 (119)
Q Consensus 73 ~L~~~~g~~Idkk~I~l~~-IK~lG~y~V~I~L~~~V~a~i~V~V~~ 118 (119)
+|.++ |++|||+.|.|++ ||++|+|+|+|+||++|+|+++|+|++
T Consensus 101 ~l~~~-g~~idk~~I~l~~~Ik~~G~y~v~i~L~~~v~a~l~v~V~~ 146 (147)
T PRK00137 101 ALKKQ-GIEIDKRKIELPGPIKTLGEYEVPVKLHPEVTATIKVNVVA 146 (147)
T ss_pred HHHHc-CCccCHHHeECCCcccccEEEEEEEEECCCcEEEEEEEEEE
Confidence 99988 9999999999986 999999999999999999999999986
No 5
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=100.00 E-value=7.2e-33 Score=244.41 Aligned_cols=115 Identities=19% Similarity=0.258 Sum_probs=108.9
Q ss_pred CccchhcccchH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCeEEEEEecCCCCceeecccHHHHHH
Q 033453 2 NQVFGNLQLFGV---------LCMEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 2 ~~gyarNfL~~~---------~l~~l~~~~~~~~~~~~~~~~~a~~la~kL~~~~~l~i~~k~g~~gkLFGSVt~~dIa~ 72 (119)
-|||| |||+|+ |+++++.+++++++++++.+++|++++++|+++ +++|++++|++|+||||||++||++
T Consensus 710 k~GYa-NfLiP~~~A~~aT~~nlk~~e~~~~~~~~~~~~~~~~a~~l~~~l~~~-~~~i~~k~ge~gklfGSVt~~~I~~ 787 (838)
T PRK14538 710 NNGYG-NFLIQNKKALLADKENLAKIKKKKILEQEKKRNHELLMKKLKSEIDNK-KITLDIQLGPKGKIYGKITLKQIVE 787 (838)
T ss_pred CCCch-hhhccCCchhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc-EEEEEEEeCCCCeeeeccCHHHHHH
Confidence 48999 999998 567789999999999999999999999999996 7999999999999999999999999
Q ss_pred HHHHhcCCceecccccccC-ccceeeEEEEEEeCCCeEEEEEEEEee
Q 033453 73 IIKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTARIRLNVFA 118 (119)
Q Consensus 73 ~L~~~~g~~Idkk~I~l~~-IK~lG~y~V~I~L~~~V~a~i~V~V~~ 118 (119)
+|++++|++||||+|.|++ ||++|+|+|+|+||++|+|+++|+|+.
T Consensus 788 ~l~~~~g~~idk~~I~l~~~Ik~~G~~~v~i~L~~~V~a~i~v~V~~ 834 (838)
T PRK14538 788 EFHKIHNITIDRKKISLENEIISVGIYPVDVFLTDQIKATFFLNVIE 834 (838)
T ss_pred HHHHhhCCccccceeeCCCcccccEEEEEEEEEcCCeEEEEEEEEEE
Confidence 9998889999999999986 999999999999999999999999974
No 6
>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=99.98 E-value=6.3e-32 Score=181.46 Aligned_cols=85 Identities=47% Similarity=0.777 Sum_probs=82.2
Q ss_pred HHHHHHHHHhhhccCeEEEEEecCCCCceeecccHHHHHHHHHHhcCCceecccccccC-ccceeeEEEEEEeCCCeEEE
Q 033453 33 KEEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE-IRETGEYIAQLKLHPEVTAR 111 (119)
Q Consensus 33 ~~~a~~la~kL~~~~~l~i~~k~g~~gkLFGSVt~~dIa~~L~~~~g~~Idkk~I~l~~-IK~lG~y~V~I~L~~~V~a~ 111 (119)
+++|++++++|++. +++|.+++|++|+||||||++||+++|++++|++|||++|.|++ ||++|+|+|+|+||++|+|+
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 47899999999997 79999999999999999999999999999999999999999998 99999999999999999999
Q ss_pred EEEEEee
Q 033453 112 IRLNVFA 118 (119)
Q Consensus 112 i~V~V~~ 118 (119)
|+|+|++
T Consensus 80 i~v~V~~ 86 (87)
T PF03948_consen 80 IKVNVVA 86 (87)
T ss_dssp EEEEEEE
T ss_pred EEEEEEe
Confidence 9999985
No 7
>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=99.07 E-value=2.5e-10 Score=87.56 Aligned_cols=116 Identities=32% Similarity=0.380 Sum_probs=87.3
Q ss_pred CCccchhcccchHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHhhhccCeEEEEEecCCCCc-eeecccHHHH
Q 033453 1 MNQVFGNLQLFGVLCME---------MKMEEERIEAEKKRVKEEAQQLALIFETVGAFKVKRKGGKGKQ-IFGSVTAQDV 70 (119)
Q Consensus 1 ~~~gyarNfL~~~~l~~---------l~~~~~~~~~~~~~~~~~a~~la~kL~~~~~l~i~~k~g~~gk-LFGSVt~~dI 70 (119)
|-+||+||+|+|.+++. +...+++......+..++++.++ -|+.. .+.+...-|..+. -+++|++++.
T Consensus 69 Vk~g~~RN~Llp~glAvy~tp~~~~~~k~~~~e~~~~k~~vk~e~k~V~-~lqt~-v~~~~~~k~~kw~l~~~~V~~~l~ 146 (222)
T KOG4607|consen 69 VKRGYFRNFLLPKGLAVYNTPLNLKKYKLREQEEEAEKIRVKEEAKVVA-VLQTV-VLFKVMNKGGKWKLNPNLVKASLR 146 (222)
T ss_pred eecchhhhhcccccccccCChhhHHHHHHHHHHHHhhhhccHHHHHHHH-HHHhh-hhhheeccCCceeecHHHHHHHHh
Confidence 35899999999997754 33344444444444567777777 66654 3444444444444 6899999998
Q ss_pred HHHHHHhcCCceecccccccCccceeeEEEEEEeCCCeEEEEEEEEee
Q 033453 71 VDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPEVTARIRLNVFA 118 (119)
Q Consensus 71 a~~L~~~~g~~Idkk~I~l~~IK~lG~y~V~I~L~~~V~a~i~V~V~~ 118 (119)
-..+.++.-+++|++-|+.|.+|.-|+|.+.|++++++++-+...|..
T Consensus 147 ~gv~~~~~t~~l~k~~vs~P~~k~e~~~~~~V~in~~~~vr~~~~v~~ 194 (222)
T KOG4607|consen 147 KGVIVAELTIKLDKELVSGPITKEEGEYICEVKINPDVTVRVKIRVTH 194 (222)
T ss_pred cceEeccccccCcccccCCCcccccceEEEEEEECCcceEEeeeeeec
Confidence 877777767999999999998999999999999999999999988864
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=97.70 E-value=1.7e-06 Score=52.28 Aligned_cols=16 Identities=6% Similarity=-0.184 Sum_probs=13.7
Q ss_pred CccchhcccchHHHHH
Q 033453 2 NQVFGNLQLFGVLCME 17 (119)
Q Consensus 2 ~~gyarNfL~~~~l~~ 17 (119)
.||||||||+|++++.
T Consensus 22 ~~Gy~RN~L~p~~~A~ 37 (48)
T PF01281_consen 22 KPGYARNFLIPQGLAV 37 (48)
T ss_dssp SHHHHHHTTTTTTSEE
T ss_pred ccceeeehccCCCcee
Confidence 5899999999997754
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=80.92 E-value=0.7 Score=32.10 Aligned_cols=25 Identities=24% Similarity=0.395 Sum_probs=22.8
Q ss_pred cHHHHHHHHHHhcCCceeccccccc
Q 033453 66 TAQDVVDIIKAQLQRDVDKKIVDLP 90 (119)
Q Consensus 66 t~~dIa~~L~~~~g~~Idkk~I~l~ 90 (119)
||+++++++++.+|++|+|.+++.-
T Consensus 21 TPs~v~~aVk~eFgi~vsrQqve~y 45 (104)
T PF10045_consen 21 TPSEVAEAVKEEFGIDVSRQQVESY 45 (104)
T ss_pred CHHHHHHHHHHHhCCccCHHHHHHc
Confidence 7999999999999999999998763
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=75.84 E-value=7.5 Score=23.89 Aligned_cols=24 Identities=25% Similarity=0.397 Sum_probs=20.6
Q ss_pred ccceeeEEEEEEeCCCeEEEEEEEE
Q 033453 92 IRETGEYIAQLKLHPEVTARIRLNV 116 (119)
Q Consensus 92 IK~lG~y~V~I~L~~~V~a~i~V~V 116 (119)
-...|.|+|++.... .+++++|.|
T Consensus 44 ~~~~G~y~Vt~~y~~-~t~t~~VtV 67 (67)
T PF07523_consen 44 TSKAGTYTVTYTYKG-VTATFTVTV 67 (67)
T ss_dssp TTS-CCEEEEEEECT-EEEEEEEEE
T ss_pred cCCCceEEEEEEECC-EEEEEEEEC
Confidence 678899999999988 899998876
No 11
>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=74.85 E-value=5.1 Score=22.97 Aligned_cols=21 Identities=10% Similarity=0.305 Sum_probs=18.5
Q ss_pred cCCCCceeecccHHHHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVDIIK 75 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~~L~ 75 (119)
.+++|++-|.||..||..++.
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 567799999999999999875
No 12
>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=72.49 E-value=2.3 Score=25.54 Aligned_cols=26 Identities=15% Similarity=0.312 Sum_probs=17.8
Q ss_pred eecccHHHHHHHHHHhcCCceecccc
Q 033453 62 FGSVTAQDVVDIIKAQLQRDVDKKIV 87 (119)
Q Consensus 62 FGSVt~~dIa~~L~~~~g~~Idkk~I 87 (119)
+.+||.++|-.+|.+.+|+++.-++=
T Consensus 18 l~~vT~k~vr~~Le~~~~~dL~~~K~ 43 (54)
T PF08766_consen 18 LDTVTKKQVREQLEERFGVDLSSRKK 43 (54)
T ss_dssp GGG--HHHHHHHHHHH-SS--SHHHH
T ss_pred HhHhhHHHHHHHHHHHHCCCcHHHHH
Confidence 67899999999999999998875553
No 13
>PF13592 HTH_33: Winged helix-turn helix
Probab=56.58 E-value=7.5 Score=23.59 Aligned_cols=33 Identities=15% Similarity=0.195 Sum_probs=25.4
Q ss_pred ecccHHHHHHHHHHhcCCceecccccccCcccee
Q 033453 63 GSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETG 96 (119)
Q Consensus 63 GSVt~~dIa~~L~~~~g~~Idkk~I~l~~IK~lG 96 (119)
|--|.++|++.|.+.+|+.+....|.- -++.+|
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~-lL~r~G 35 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYR-LLKRLG 35 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHH-HHHHcC
Confidence 567999999999999999998776631 155555
No 14
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=55.11 E-value=31 Score=25.14 Aligned_cols=19 Identities=11% Similarity=-0.036 Sum_probs=15.2
Q ss_pred hcccchHHHHHHHHHHHHH
Q 033453 7 NLQLFGVLCMEMKMEEERI 25 (119)
Q Consensus 7 rNfL~~~~l~~l~~~~~~~ 25 (119)
+|||+|.+++.|+.+.+..
T Consensus 4 ~~~lT~~g~~~L~~EL~~L 22 (157)
T PRK01885 4 TNYITREGYARLKQELDYL 22 (157)
T ss_pred CcccCHHHHHHHHHHHHHH
Confidence 6999999998877766554
No 15
>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=54.93 E-value=11 Score=27.55 Aligned_cols=19 Identities=21% Similarity=0.356 Sum_probs=16.6
Q ss_pred eEEEEEecCCCCceeeccc
Q 033453 48 AFKVKRKGGKGKQIFGSVT 66 (119)
Q Consensus 48 ~l~i~~k~g~~gkLFGSVt 66 (119)
..+|+..+.++|-+||.|+
T Consensus 118 ~~~iKVsStetGvIfG~I~ 136 (140)
T PF07718_consen 118 KATIKVSSTETGVIFGNIV 136 (140)
T ss_pred EEEEEEEeccCCEEEEEEE
Confidence 4678888999999999985
No 16
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=50.85 E-value=36 Score=24.98 Aligned_cols=20 Identities=0% Similarity=-0.212 Sum_probs=16.0
Q ss_pred hcccchHHHHHHHHHHHHHH
Q 033453 7 NLQLFGVLCMEMKMEEERIE 26 (119)
Q Consensus 7 rNfL~~~~l~~l~~~~~~~~ 26 (119)
.|||+|++++.|+.+.....
T Consensus 28 ~~~lT~~G~~~L~~El~~L~ 47 (160)
T PRK06342 28 PNLVTEAGLKALEDQLAQAR 47 (160)
T ss_pred CceECHHHHHHHHHHHHHHH
Confidence 69999999988877665553
No 17
>PF14221 DUF4330: Domain of unknown function (DUF4330)
Probab=50.19 E-value=13 Score=27.54 Aligned_cols=19 Identities=21% Similarity=0.557 Sum_probs=15.2
Q ss_pred CCCCceeecccHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDII 74 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L 74 (119)
-+.|||||.|+.=|+.-.|
T Consensus 5 D~kGrlFgkiniiDl~~~l 23 (168)
T PF14221_consen 5 DSKGRLFGKINIIDLLAIL 23 (168)
T ss_pred ccCCcEeeeEeHHHHHHHH
Confidence 3689999999999965544
No 18
>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=48.19 E-value=14 Score=18.96 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=14.9
Q ss_pred CCCceeecccHHHHHHHH
Q 033453 57 KGKQIFGSVTAQDVVDII 74 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L 74 (119)
++|++.|.++..++...+
T Consensus 31 ~~~~~~g~i~~~~l~~~~ 48 (49)
T smart00116 31 EEGRLVGIVTRRDIIKAL 48 (49)
T ss_pred CCCeEEEEEEHHHHHHhh
Confidence 457899999999987765
No 19
>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=44.69 E-value=21 Score=22.83 Aligned_cols=19 Identities=11% Similarity=0.319 Sum_probs=16.8
Q ss_pred CCceeecccHHHHHHHHHH
Q 033453 58 GKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 58 ~gkLFGSVt~~dIa~~L~~ 76 (119)
||+.|+-+|+.+|.+.+.+
T Consensus 61 ~~~~~~~~~~e~i~~il~~ 79 (80)
T cd03081 61 DGEVHGRVDPEKFDALLAE 79 (80)
T ss_pred CCEEECCCCHHHHHHHHHc
Confidence 7889999999999988754
No 20
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=44.43 E-value=37 Score=24.45 Aligned_cols=21 Identities=10% Similarity=0.110 Sum_probs=17.3
Q ss_pred hcccchHHHHHHHHHHHHHHH
Q 033453 7 NLQLFGVLCMEMKMEEERIEA 27 (119)
Q Consensus 7 rNfL~~~~l~~l~~~~~~~~~ 27 (119)
.|||+|.+++.|+.+.+....
T Consensus 4 ~~~lt~~g~~~L~~eL~~l~~ 24 (157)
T PRK00226 4 KIPMTQEGYEKLEEELEELKT 24 (157)
T ss_pred ccccCHHHHHHHHHHHHHHHh
Confidence 489999999998887776655
No 21
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=44.23 E-value=19 Score=29.21 Aligned_cols=23 Identities=22% Similarity=0.289 Sum_probs=19.8
Q ss_pred ecCCCCceeecccHHHHHHHHHH
Q 033453 54 KGGKGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 54 k~g~~gkLFGSVt~~dIa~~L~~ 76 (119)
.+=++|++-|-+|..||++++..
T Consensus 207 PVvd~dk~vGiit~~dI~~aia~ 229 (294)
T COG2524 207 PVVDDDKIVGIITLSDIAKAIAN 229 (294)
T ss_pred ceecCCceEEEEEHHHHHHHHHc
Confidence 34478899999999999999976
No 22
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=41.96 E-value=51 Score=23.98 Aligned_cols=20 Identities=10% Similarity=-0.140 Sum_probs=15.4
Q ss_pred hcccchHHHHHHHHHHHHHH
Q 033453 7 NLQLFGVLCMEMKMEEERIE 26 (119)
Q Consensus 7 rNfL~~~~l~~l~~~~~~~~ 26 (119)
.|||+|.+++.|+.+.+...
T Consensus 2 ~~~lT~~G~~~L~~El~~L~ 21 (156)
T TIGR01461 2 TPLITPEGYEKLKQELNYLW 21 (156)
T ss_pred CcccCHHHHHHHHHHHHHHH
Confidence 49999999988777665543
No 23
>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A.
Probab=40.87 E-value=5.9 Score=30.63 Aligned_cols=17 Identities=12% Similarity=-0.029 Sum_probs=10.4
Q ss_pred CCccchhcccchHHHHH
Q 033453 1 MNQVFGNLQLFGVLCME 17 (119)
Q Consensus 1 ~~~gyarNfL~~~~l~~ 17 (119)
|||||+.+.-+|.|++.
T Consensus 141 ~np~y~gr~~LP~nLk~ 157 (231)
T PF12774_consen 141 MNPGYAGRSELPENLKA 157 (231)
T ss_dssp E-B-CCCC--S-HHHCT
T ss_pred eccccCCcccCCHhHHH
Confidence 79999999999999964
No 24
>KOG3279 consensus Uncharacterized conserved protein (melanoma antigen P15) [Function unknown]
Probab=40.86 E-value=32 Score=27.21 Aligned_cols=28 Identities=11% Similarity=0.039 Sum_probs=19.0
Q ss_pred HHHhhhccCeEEEEEecCCCCceeecccH
Q 033453 39 LALIFETVGAFKVKRKGGKGKQIFGSVTA 67 (119)
Q Consensus 39 la~kL~~~~~l~i~~k~g~~gkLFGSVt~ 67 (119)
.++.|+.- ....+..+|.+.+.||-+++
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 45567777888888887654
No 25
>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=39.53 E-value=30 Score=21.18 Aligned_cols=19 Identities=32% Similarity=0.567 Sum_probs=16.2
Q ss_pred CCceeecccHHHHHHHHHH
Q 033453 58 GKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 58 ~gkLFGSVt~~dIa~~L~~ 76 (119)
+|.+||-||+.++.+.|.+
T Consensus 58 ~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 58 DGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred CCeEEccCCHHHHHHHHHh
Confidence 5789999999999887754
No 26
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=38.71 E-value=89 Score=22.65 Aligned_cols=45 Identities=11% Similarity=0.232 Sum_probs=24.5
Q ss_pred CccchhcccchHHHH--HHHHHHHHHHHHHHHH-------HHHHHHHHHhhhcc
Q 033453 2 NQVFGNLQLFGVLCM--EMKMEEERIEAEKKRV-------KEEAQQLALIFETV 46 (119)
Q Consensus 2 ~~gyarNfL~~~~l~--~l~~~~~~~~~~~~~~-------~~~a~~la~kL~~~ 46 (119)
|-|||-|-=+++.-. +||.++.....+-+.. ..+.-+++.+.+.+
T Consensus 61 NRGYA~sCR~KRv~Qk~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l 114 (135)
T KOG4196|consen 61 NRGYAQSCRVKRVQQKHELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEAL 114 (135)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 789999988887443 3444443333332222 33444555555554
No 27
>COG1438 ArgR Arginine repressor [Transcription]
Probab=37.23 E-value=21 Score=26.27 Aligned_cols=34 Identities=18% Similarity=0.403 Sum_probs=26.2
Q ss_pred cHHHHHHHHHHhcCCceecccccccCccceeeEEEE
Q 033453 66 TAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQ 101 (119)
Q Consensus 66 t~~dIa~~L~~~~g~~Idkk~I~l~~IK~lG~y~V~ 101 (119)
|-.||++.|++. |+++.--.+.= +||++|-..|+
T Consensus 22 TQ~Elv~~L~~~-Gi~vTQaTvSR-DlkelglvKv~ 55 (150)
T COG1438 22 TQEELVELLQEE-GIEVTQATVSR-DLKELGLVKVR 55 (150)
T ss_pred CHHHHHHHHHHc-CCeEehHHHHH-HHHHcCCEEec
Confidence 456799999987 99887665542 38999988886
No 28
>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=37.16 E-value=91 Score=20.90 Aligned_cols=38 Identities=21% Similarity=0.377 Sum_probs=29.4
Q ss_pred eecccccccC--ccceeeEEEEEEeCCC-eEEEEEEEEeeC
Q 033453 82 VDKKIVDLPE--IRETGEYIAQLKLHPE-VTARIRLNVFAN 119 (119)
Q Consensus 82 Idkk~I~l~~--IK~lG~y~V~I~L~~~-V~a~i~V~V~~~ 119 (119)
-+++.+.++. .-.-|+.++.|..... ..++++|.|.+|
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 4677777765 7789999999997654 458888888775
No 29
>cd04623 CBS_pair_10 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=37.14 E-value=64 Score=20.05 Aligned_cols=21 Identities=19% Similarity=0.479 Sum_probs=17.6
Q ss_pred CCCceeecccHHHHHHHHHHh
Q 033453 57 KGKQIFGSVTAQDVVDIIKAQ 77 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L~~~ 77 (119)
++|++.|.||..|+...+...
T Consensus 32 ~~~~~~Giv~~~~l~~~~~~~ 52 (113)
T cd04623 32 DGGRLVGIFSERDIVRKVALR 52 (113)
T ss_pred CCCCEEEEEehHHHHHHHhhc
Confidence 458999999999999887653
No 30
>PRK07668 hypothetical protein; Validated
Probab=36.07 E-value=84 Score=24.98 Aligned_cols=22 Identities=23% Similarity=0.572 Sum_probs=17.5
Q ss_pred ceeecccHHHHHHHHHHhcCCceec
Q 033453 60 QIFGSVTAQDVVDIIKAQLQRDVDK 84 (119)
Q Consensus 60 kLFGSVt~~dIa~~L~~~~g~~Idk 84 (119)
.+||+ +|+++|+++.+. .+.|+
T Consensus 50 ~IfG~-sPk~yA~EL~~~--~~~~~ 71 (254)
T PRK07668 50 DIFGD-SPKEYANELVKE--MEVDR 71 (254)
T ss_pred HHhCC-CHHHHHHHHhcc--cCCCc
Confidence 39999 999999999875 34454
No 31
>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=36.06 E-value=79 Score=19.73 Aligned_cols=18 Identities=22% Similarity=0.484 Sum_probs=16.0
Q ss_pred CceeecccHHHHHHHHHH
Q 033453 59 KQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 59 gkLFGSVt~~dIa~~L~~ 76 (119)
|++.|.||..|+...+..
T Consensus 35 ~~~~G~v~~~~l~~~~~~ 52 (111)
T cd04590 35 DNIIGVVHVKDLLRALAE 52 (111)
T ss_pred ceEEEEEEHHHHHHHHHc
Confidence 899999999999988754
No 32
>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=35.91 E-value=68 Score=27.24 Aligned_cols=56 Identities=21% Similarity=0.329 Sum_probs=41.9
Q ss_pred hccCeEEEEEecCC---CCcee-----ecccHHHHHHHHHHhcCCceecccccccCccceeeEEEEEEeCCC
Q 033453 44 ETVGAFKVKRKGGK---GKQIF-----GSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQLKLHPE 107 (119)
Q Consensus 44 ~~~~~l~i~~k~g~---~gkLF-----GSVt~~dIa~~L~~~~g~~Idkk~I~l~~IK~lG~y~V~I~L~~~ 107 (119)
++. +++|..+-|- ||.-| ..||+.|++-.+..... . .+..|+.++.|+|.|+|..-
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 7889988875 77666 56899999999865421 1 34459999999999999864
No 33
>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=35.40 E-value=80 Score=19.98 Aligned_cols=19 Identities=26% Similarity=0.532 Sum_probs=16.1
Q ss_pred CceeecccHHHHHHHHHHh
Q 033453 59 KQIFGSVTAQDVVDIIKAQ 77 (119)
Q Consensus 59 gkLFGSVt~~dIa~~L~~~ 77 (119)
|++.|.||..|+...+...
T Consensus 35 ~~~~G~v~~~dl~~~~~~~ 53 (114)
T cd04630 35 SDAYGIVTMRDILKKVVAE 53 (114)
T ss_pred CcEEEEEehHHHHHHHHhC
Confidence 7999999999999876543
No 34
>PF13565 HTH_32: Homeodomain-like domain
Probab=35.07 E-value=29 Score=21.30 Aligned_cols=19 Identities=11% Similarity=0.310 Sum_probs=16.5
Q ss_pred cccHHHHHHHHHHhcCCce
Q 033453 64 SVTAQDVVDIIKAQLQRDV 82 (119)
Q Consensus 64 SVt~~dIa~~L~~~~g~~I 82 (119)
--|+.+|++.|..++|+.+
T Consensus 48 ~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 48 RWTPREIAEYLEEEFGISV 66 (77)
T ss_pred CCCHHHHHHHHHHHhCCCC
Confidence 5689999999999988766
No 35
>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=34.84 E-value=35 Score=22.25 Aligned_cols=21 Identities=29% Similarity=0.450 Sum_probs=17.2
Q ss_pred cCCCCceeecccHHHHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVDIIK 75 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~~L~ 75 (119)
+.++|++.|.||..|+...+.
T Consensus 30 v~~~~~~~G~it~~dl~~~~~ 50 (128)
T cd04632 30 VDDNGKLTGIVTRHDIVDFVV 50 (128)
T ss_pred ECCCCcEEEEEEHHHHHHHHh
Confidence 456689999999999987763
No 36
>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=34.52 E-value=35 Score=21.50 Aligned_cols=18 Identities=17% Similarity=0.311 Sum_probs=15.9
Q ss_pred CCceeecccHHHHHHHHH
Q 033453 58 GKQIFGSVTAQDVVDIIK 75 (119)
Q Consensus 58 ~gkLFGSVt~~dIa~~L~ 75 (119)
+|++|+.+|+.+|-+.+.
T Consensus 53 ~~~~~~~~t~~~i~~~~~ 70 (72)
T cd03082 53 GQRPVDGATPAAVAAAVE 70 (72)
T ss_pred CCEEeCCcCHHHHHHHHh
Confidence 788999999999988765
No 37
>PRK15365 type III secretion system chaperone SseA; Provisional
Probab=34.48 E-value=99 Score=21.42 Aligned_cols=38 Identities=11% Similarity=-0.008 Sum_probs=23.4
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 033453 8 LQLFGVLCMEMKMEEERIEAEKKRVKEEAQQLALIFET 45 (119)
Q Consensus 8 NfL~~~~l~~l~~~~~~~~~~~~~~~~~a~~la~kL~~ 45 (119)
|-|||+++..+++++.+.-..-.-.-...+.--..|+.
T Consensus 57 d~aFP~G~~~~~qE~~k~m~~i~~~FKQLEt~LKnlnt 94 (107)
T PRK15365 57 HNLFPQGVAGVNQEAEKDLKKIVSLFKQLEVRLKQLNA 94 (107)
T ss_pred HHHCcchhhHHhHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 56889999888887776665544333444444444444
No 38
>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=33.84 E-value=30 Score=22.19 Aligned_cols=20 Identities=15% Similarity=0.363 Sum_probs=14.7
Q ss_pred ecccHHHHHHHHHHhcCCce
Q 033453 63 GSVTAQDVVDIIKAQLQRDV 82 (119)
Q Consensus 63 GSVt~~dIa~~L~~~~g~~I 82 (119)
|-||..++.++|++++|++.
T Consensus 5 g~ise~~l~~~la~~~~l~~ 24 (109)
T PF05157_consen 5 GLISEDQLLEALAEQLGLPF 24 (109)
T ss_dssp T-S-HHHHHHHHHHHHT--B
T ss_pred CCCCHHHHHHHHHHHhCCCe
Confidence 78999999999999999873
No 39
>COG2047 Uncharacterized protein (ATP-grasp superfamily) [General function prediction only]
Probab=33.58 E-value=34 Score=27.19 Aligned_cols=27 Identities=15% Similarity=0.458 Sum_probs=22.0
Q ss_pred CCCceeecccHHHHHHHHHHhcCCceec
Q 033453 57 KGKQIFGSVTAQDVVDIIKAQLQRDVDK 84 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L~~~~g~~Idk 84 (119)
++-+.+|++|++++++.|++. |+....
T Consensus 133 eep~VlGA~ts~eLi~~lke~-gV~fr~ 159 (258)
T COG2047 133 EEPRVLGAVTSKELIEELKEH-GVEFRS 159 (258)
T ss_pred CCceeEEecCCHHHHHHHHHc-CeEecc
Confidence 355789999999999999886 876543
No 40
>cd04608 CBS_pair_PALP_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well as the 5'-phosphate esters of pyridoxal (PALP) and pyridoxamine, the last two being the biologically active coenzyme derivatives. The members of the PALP family are principally involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and other amine-containing compounds. 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 poten
Probab=33.38 E-value=20 Score=23.82 Aligned_cols=19 Identities=32% Similarity=0.405 Sum_probs=15.8
Q ss_pred CCCCceeecccHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDII 74 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L 74 (119)
.++|++-|-||..||.+++
T Consensus 106 ~~~~~~~Givt~~Dl~~~~ 124 (124)
T cd04608 106 EKQEKPIGIVTKIDLLSYI 124 (124)
T ss_pred ccccceEEEEehhHhhhhC
Confidence 3568999999999998763
No 41
>cd04639 CBS_pair_26 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=33.36 E-value=44 Score=20.95 Aligned_cols=20 Identities=15% Similarity=0.368 Sum_probs=16.8
Q ss_pred CCCceeecccHHHHHHHHHH
Q 033453 57 KGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L~~ 76 (119)
++|++.|.||..++...+..
T Consensus 32 ~~~~~~G~v~~~~l~~~~~~ 51 (111)
T cd04639 32 GDGHLVGLLTRDDLIRALAE 51 (111)
T ss_pred CCCcEEEEeeHHHHHHHHHh
Confidence 46899999999999887654
No 42
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=32.67 E-value=22 Score=22.91 Aligned_cols=16 Identities=19% Similarity=0.463 Sum_probs=13.3
Q ss_pred ceeecccHHHHHHHHH
Q 033453 60 QIFGSVTAQDVVDIIK 75 (119)
Q Consensus 60 kLFGSVt~~dIa~~L~ 75 (119)
++|++|++.+|+.+=.
T Consensus 24 ~~~~~Vs~~EI~~~Eq 39 (71)
T PF04282_consen 24 KLFSDVSASEISAAEQ 39 (71)
T ss_pred HHHCCCCHHHHHHHHH
Confidence 5899999999997633
No 43
>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=32.66 E-value=93 Score=19.80 Aligned_cols=22 Identities=23% Similarity=0.253 Sum_probs=17.9
Q ss_pred cCCCCceeecccHHHHHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~~L~~ 76 (119)
+.++|++.|.||..|+..++..
T Consensus 30 vd~~g~~~G~vt~~dl~~~~~~ 51 (114)
T cd04619 30 CDPHGKLAGVLTKTDVVRQMGR 51 (114)
T ss_pred ECCCCCEEEEEehHHHHHHHhh
Confidence 3567899999999999887654
No 44
>PRK07639 acyl carrier protein; Provisional
Probab=32.42 E-value=18 Score=23.61 Aligned_cols=34 Identities=21% Similarity=0.203 Sum_probs=25.1
Q ss_pred ecccHHHHHHHHHHhcCCceecccccccCcccee
Q 033453 63 GSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETG 96 (119)
Q Consensus 63 GSVt~~dIa~~L~~~~g~~Idkk~I~l~~IK~lG 96 (119)
=|+..-++.-+|...+|++|+-..+....+.++|
T Consensus 39 DSld~velv~~lE~~fgi~i~d~~~~~~~~~Tv~ 72 (86)
T PRK07639 39 DSVMMLQLIVYIEMDVKLCVPEDEVDPKAFLTVG 72 (86)
T ss_pred ChHHHHHHHHHHHHHHCCccCHHHccHHHhCCHH
Confidence 4788888888899999999987765433355554
No 45
>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=32.18 E-value=45 Score=20.97 Aligned_cols=21 Identities=29% Similarity=0.447 Sum_probs=17.1
Q ss_pred CCCCceeecccHHHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L~~ 76 (119)
.++|++.|.||..|+..++..
T Consensus 31 d~~~~~~G~v~~~~l~~~~~~ 51 (112)
T cd04624 31 DPDERPIGIVTERDIVRAVAA 51 (112)
T ss_pred CCCCCEEEEeeHHHHHHHHhc
Confidence 456899999999999877654
No 46
>PHA02119 hypothetical protein
Probab=31.71 E-value=35 Score=22.36 Aligned_cols=25 Identities=20% Similarity=0.396 Sum_probs=20.5
Q ss_pred CceeecccHHHHHHHHHHhcCCceec
Q 033453 59 KQIFGSVTAQDVVDIIKAQLQRDVDK 84 (119)
Q Consensus 59 gkLFGSVt~~dIa~~L~~~~g~~Idk 84 (119)
|--|-.|-++||+|.|... |+++.-
T Consensus 48 ~~kfp~i~~~divdylr~l-gy~~~~ 72 (87)
T PHA02119 48 VAKFPAIMPKDIVDYLRSL-GYDAKS 72 (87)
T ss_pred cccCCccccHHHHHHHHHc-cchhcc
Confidence 3468889999999999987 988743
No 47
>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=31.46 E-value=48 Score=20.78 Aligned_cols=19 Identities=26% Similarity=0.594 Sum_probs=16.2
Q ss_pred CCceeecccHHHHHHHHHH
Q 033453 58 GKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 58 ~gkLFGSVt~~dIa~~L~~ 76 (119)
+|.+|+-||+.+|.+.+.+
T Consensus 61 ~g~~y~~vt~~~i~~i~~~ 79 (80)
T cd03064 61 NDDVYGRLTPEKVDAILEA 79 (80)
T ss_pred CCEEECCCCHHHHHHHHHh
Confidence 5899999999999987753
No 48
>KOG2639 consensus Sodium sulfate symporter and related arsenite permeases [Inorganic ion transport and metabolism]
Probab=31.45 E-value=41 Score=30.08 Aligned_cols=32 Identities=19% Similarity=0.076 Sum_probs=26.0
Q ss_pred EecCCCCceeecccHHHHHHHHHHhcCCceecc
Q 033453 53 RKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKK 85 (119)
Q Consensus 53 ~k~g~~gkLFGSVt~~dIa~~L~~~~g~~Idkk 85 (119)
+-.|.||-|+||- +.-|+..+.+|||+++.=.
T Consensus 623 a~~gGNgTLiGas-ANvv~A~iAeqHGYkltF~ 654 (685)
T KOG2639|consen 623 ACLGGNGTLIGAS-ANVVAAGIAEQHGYKLTFT 654 (685)
T ss_pred hhhcCCceeechh-hHHHHHHHHHHcCceEEeh
Confidence 4468899999994 6789999999999987643
No 49
>cd04629 CBS_pair_16 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=31.22 E-value=47 Score=20.87 Aligned_cols=21 Identities=14% Similarity=0.305 Sum_probs=17.4
Q ss_pred CCCCceeecccHHHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L~~ 76 (119)
.++|++.|.||..++..++.+
T Consensus 31 ~~~~~~~G~v~~~~l~~~~~~ 51 (114)
T cd04629 31 DDNGNLVGFLSEQDCLKQLLE 51 (114)
T ss_pred CCCCeEEEEeehHHHHHHhhh
Confidence 357899999999999887654
No 50
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=31.19 E-value=23 Score=22.62 Aligned_cols=34 Identities=12% Similarity=0.398 Sum_probs=22.7
Q ss_pred cHHHHHHHHHHhcCCceecccccccCccceeeEEEE
Q 033453 66 TAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIAQ 101 (119)
Q Consensus 66 t~~dIa~~L~~~~g~~Idkk~I~l~~IK~lG~y~V~ 101 (119)
|-.|+++.|++. |+++.=-.|.= +|+.+|...|+
T Consensus 21 sQ~eL~~~L~~~-Gi~vTQaTiSR-DLkeL~~vKv~ 54 (70)
T PF01316_consen 21 SQEELVELLEEE-GIEVTQATISR-DLKELGAVKVP 54 (70)
T ss_dssp SHHHHHHHHHHT-T-T--HHHHHH-HHHHHT-EEEE
T ss_pred CHHHHHHHHHHc-CCCcchhHHHH-HHHHcCcEEee
Confidence 567899999987 99887665542 38888888775
No 51
>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=31.12 E-value=95 Score=19.53 Aligned_cols=20 Identities=20% Similarity=0.418 Sum_probs=16.6
Q ss_pred CCCCceeecccHHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDIIK 75 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L~ 75 (119)
.++|++.|.||..|+..++.
T Consensus 32 d~~~~~~G~v~~~dl~~~~~ 51 (113)
T cd04607 32 DENGRLLGTVTDGDIRRALL 51 (113)
T ss_pred CCCCCEEEEEEcHHHHHHHh
Confidence 45789999999999987664
No 52
>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=31.04 E-value=63 Score=20.32 Aligned_cols=20 Identities=30% Similarity=0.582 Sum_probs=15.7
Q ss_pred cCCCCceeecccHHHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVDII 74 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~~L 74 (119)
..++|++.|-||..|+..+|
T Consensus 90 v~~~~~~~Gvit~~dll~~~ 109 (109)
T cd04606 90 VDEEGRLVGIITVDDVIDVI 109 (109)
T ss_pred ECCCCcEEEEEEhHHhhhhC
Confidence 34568899999999988653
No 53
>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=30.72 E-value=1e+02 Score=19.49 Aligned_cols=20 Identities=20% Similarity=0.443 Sum_probs=16.9
Q ss_pred CCCceeecccHHHHHHHHHH
Q 033453 57 KGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L~~ 76 (119)
++|++.|.|+.+|+...+.+
T Consensus 32 ~~~~~~G~v~~~dl~~~~~~ 51 (115)
T cd04593 32 RDGGVVGIITLPDLLRALEA 51 (115)
T ss_pred CCCCEEEEEEHHHHHHHHhc
Confidence 46899999999999987754
No 54
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=30.49 E-value=35 Score=21.32 Aligned_cols=13 Identities=15% Similarity=0.524 Sum_probs=11.4
Q ss_pred ecccHHHHHHHHH
Q 033453 63 GSVTAQDVVDIIK 75 (119)
Q Consensus 63 GSVt~~dIa~~L~ 75 (119)
|.++.+|||+.|.
T Consensus 21 g~i~lkdIA~~Lg 33 (60)
T PF10668_consen 21 GKIKLKDIAEKLG 33 (60)
T ss_pred CCccHHHHHHHHC
Confidence 7899999999883
No 55
>cd04643 CBS_pair_30 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=30.19 E-value=49 Score=20.87 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=17.4
Q ss_pred CCCCceeecccHHHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L~~ 76 (119)
.++|++.|.||.+||...+..
T Consensus 31 d~~~~~~Giv~~~dl~~~~~~ 51 (116)
T cd04643 31 DKEGKYVGTISLTDILWKLKG 51 (116)
T ss_pred CCCCcEEEEEeHHHHHHHhhc
Confidence 357899999999999887753
No 56
>cd04582 CBS_pair_ABC_OpuCA_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzi
Probab=29.67 E-value=44 Score=20.75 Aligned_cols=19 Identities=21% Similarity=0.202 Sum_probs=15.7
Q ss_pred CCCCceeecccHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDII 74 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L 74 (119)
.++|++.|.||..||..+.
T Consensus 31 d~~g~~~Giv~~~dl~~~~ 49 (106)
T cd04582 31 DADGQPLGFVTRREAARAS 49 (106)
T ss_pred CCCCCEEEEEeHHHHHHhc
Confidence 4578999999999998754
No 57
>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=29.56 E-value=50 Score=22.60 Aligned_cols=22 Identities=14% Similarity=0.181 Sum_probs=18.4
Q ss_pred CCCCceeecccHHHHHHHHHHh
Q 033453 56 GKGKQIFGSVTAQDVVDIIKAQ 77 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L~~~ 77 (119)
.++|++.|.||..|+..++...
T Consensus 31 D~~g~l~Givt~~Dl~~~~~~~ 52 (133)
T cd04592 31 DSDDFLEGILTLGDIQRFLFTN 52 (133)
T ss_pred CCCCeEEEEEEHHHHHHHHhhc
Confidence 4578999999999999988643
No 58
>cd04620 CBS_pair_7 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=29.53 E-value=50 Score=20.92 Aligned_cols=20 Identities=20% Similarity=0.436 Sum_probs=16.4
Q ss_pred CCCceeecccHHHHHHHHHH
Q 033453 57 KGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L~~ 76 (119)
++|++.|.||..|+...+..
T Consensus 32 ~~~~~~G~v~~~dl~~~~~~ 51 (115)
T cd04620 32 EKGRLLGIFTERDIVRLTAI 51 (115)
T ss_pred CCCcEEEEEeHHHHHHHHhc
Confidence 35899999999999886653
No 59
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=29.40 E-value=36 Score=22.71 Aligned_cols=23 Identities=26% Similarity=0.328 Sum_probs=20.7
Q ss_pred ecccHHHHHHHHHHhcCCceecccc
Q 033453 63 GSVTAQDVVDIIKAQLQRDVDKKIV 87 (119)
Q Consensus 63 GSVt~~dIa~~L~~~~g~~Idkk~I 87 (119)
|+.|..||-+.|.++ ++|.++.+
T Consensus 24 ~~~T~~di~e~L~~~--f~vs~~~V 46 (83)
T PF10826_consen 24 KKFTTDDIYERLKEK--FDVSYRGV 46 (83)
T ss_pred CCeeHHHHHHHHHHH--cCchHHHH
Confidence 899999999999987 78888876
No 60
>cd04603 CBS_pair_KefB_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain which is involved in inorganic ion transport and metabolism. 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=28.55 E-value=72 Score=20.29 Aligned_cols=18 Identities=11% Similarity=0.359 Sum_probs=13.8
Q ss_pred cCCCCceeecccHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~ 72 (119)
+.++|++-|-||..||..
T Consensus 93 vd~~~~~~Giit~~di~~ 110 (111)
T cd04603 93 VDKEGKLVGTIYERELLR 110 (111)
T ss_pred EcCCCeEEEEEEhHHhhc
Confidence 445588999999998853
No 61
>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=28.30 E-value=1.3e+02 Score=18.69 Aligned_cols=21 Identities=14% Similarity=0.284 Sum_probs=17.4
Q ss_pred CCCCceeecccHHHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L~~ 76 (119)
.++|++.|.|+..+|...+..
T Consensus 32 d~~~~~~G~v~~~~i~~~~~~ 52 (114)
T cd04604 32 DEDGRLVGIFTDGDLRRALEK 52 (114)
T ss_pred cCCCCEEEEechHHHHHHHhc
Confidence 346899999999999988764
No 62
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=27.93 E-value=1.7e+02 Score=21.35 Aligned_cols=20 Identities=15% Similarity=0.069 Sum_probs=15.1
Q ss_pred hcccchHHHHHHHHHHHHHH
Q 033453 7 NLQLFGVLCMEMKMEEERIE 26 (119)
Q Consensus 7 rNfL~~~~l~~l~~~~~~~~ 26 (119)
++||+|++++.|+.+.+...
T Consensus 5 ~~~lT~eg~~~L~~EL~~L~ 24 (158)
T PRK05892 5 SKGLAPAARDHLEAELARLR 24 (158)
T ss_pred CCccCHHHHHHHHHHHHHHH
Confidence 58999999988777665544
No 63
>cd04801 CBS_pair_M50_like This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50. 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=27.91 E-value=50 Score=20.95 Aligned_cols=20 Identities=15% Similarity=0.229 Sum_probs=16.7
Q ss_pred CCCCceeecccHHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDIIK 75 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L~ 75 (119)
.++|++.|.||..||...+.
T Consensus 32 d~~~~~~G~v~~~dl~~~~~ 51 (114)
T cd04801 32 DNEGRYVGIISLADLRAIPT 51 (114)
T ss_pred cCCCcEEEEEEHHHHHHHHH
Confidence 34688999999999988764
No 64
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=27.88 E-value=1.8e+02 Score=20.60 Aligned_cols=32 Identities=25% Similarity=0.263 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 033453 14 LCMEMKMEEERIEAEKKRVKEEAQQLALIFET 45 (119)
Q Consensus 14 ~l~~l~~~~~~~~~~~~~~~~~a~~la~kL~~ 45 (119)
.|+.|+.+.+..+.+..+...+++++-+++++
T Consensus 105 ~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~ 136 (144)
T PF11221_consen 105 RIKELEEENEEAEEELQEAVKEAEELLKQVQE 136 (144)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56778888888888878888888888888776
No 65
>cd04583 CBS_pair_ABC_OpuCA_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyz
Probab=27.79 E-value=77 Score=19.60 Aligned_cols=17 Identities=18% Similarity=0.331 Sum_probs=13.9
Q ss_pred cCCCCceeecccHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVV 71 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa 71 (119)
..++|++.|-||.+|+.
T Consensus 91 v~~~g~~~Gvit~~~l~ 107 (109)
T cd04583 91 VDEDGKLVGLITRSSLV 107 (109)
T ss_pred ECCCCeEEEEEehHHhh
Confidence 45678999999999875
No 66
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=27.66 E-value=43 Score=25.41 Aligned_cols=36 Identities=11% Similarity=0.305 Sum_probs=24.9
Q ss_pred HHHHHhhhccCeEEEEEecCCCCceeecccHHHHHHHHHH
Q 033453 37 QQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 37 ~~la~kL~~~~~l~i~~k~g~~gkLFGSVt~~dIa~~L~~ 76 (119)
..+..-|+.. .-.+-. ++|++-|.||-.||...+..
T Consensus 150 ~vI~~LL~~~-~AVlV~---e~G~~vGIITk~DI~k~~~~ 185 (187)
T COG3620 150 NVISQLLEEH-PAVLVV---ENGKVVGIITKADIMKLLAG 185 (187)
T ss_pred HHHHHHHhhC-CeEEEE---eCCceEEEEeHHHHHHHHhc
Confidence 4455566654 233222 78899999999999988753
No 67
>cd04601 CBS_pair_IMPDH This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key role in the regulation of cell proliferation and differentiation. 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. Mutations of conserved residues within this domain in IMPDH have been associated with retinitis pigmentosa.
Probab=27.04 E-value=71 Score=19.79 Aligned_cols=18 Identities=17% Similarity=0.270 Sum_probs=13.8
Q ss_pred cCCCCceeecccHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~ 72 (119)
..++|++.|-||..||..
T Consensus 92 v~~~~~~~Gvi~~~dil~ 109 (110)
T cd04601 92 VDDEGKLKGLITVKDIEK 109 (110)
T ss_pred EcCCCCEEEEEEhhhhhc
Confidence 445778999999888753
No 68
>cd04641 CBS_pair_28 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=27.03 E-value=1.2e+02 Score=19.46 Aligned_cols=22 Identities=14% Similarity=0.258 Sum_probs=17.7
Q ss_pred cCCCCceeecccHHHHHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~~L~~ 76 (119)
+.++|++-|.||.+|+..++..
T Consensus 30 v~~~~~~~Giv~~~dl~~~~~~ 51 (120)
T cd04641 30 VDENGKVVDVYSRFDVINLAKE 51 (120)
T ss_pred ECCCCeEEEEEeHHHHHHHHhc
Confidence 3458899999999999987643
No 69
>cd04587 CBS_pair_CAP-ED_DUF294_PBI_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. The PB1 domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pai
Probab=27.01 E-value=28 Score=21.94 Aligned_cols=18 Identities=17% Similarity=0.267 Sum_probs=14.5
Q ss_pred cCCCCceeecccHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~ 72 (119)
..++|++.|.||..||..
T Consensus 95 v~~~~~~~Gvvs~~dl~~ 112 (113)
T cd04587 95 VDKSGQVVGLLDVTKLTH 112 (113)
T ss_pred ECCCCCEEEEEEHHHhcc
Confidence 344689999999999864
No 70
>TIGR02657 amicyanin amicyanin. Members of this family are amicyanin, a type I blue copper protein that accepts electrons from the tryptophan tryptophylquinone (TTQ) cofactor of the methylamine dehydrogenase light chain and then transfers them to the heme group of cytochrome c-551i. Amicyanin, methylamine dehydrogenase, and cytochrome c-551i are periplasmic and form a complex. This system has been studied primarily in Paracoccus denitrificans and Methylobacterium extorquens. Related type I blue copper proteins include plastocyanin, pseudoazurin, halocyanin, etc.
Probab=26.63 E-value=71 Score=20.24 Aligned_cols=24 Identities=21% Similarity=0.403 Sum_probs=21.4
Q ss_pred ccceeeEEEEEEeCCCeEEEEEEE
Q 033453 92 IRETGEYIAQLKLHPEVTARIRLN 115 (119)
Q Consensus 92 IK~lG~y~V~I~L~~~V~a~i~V~ 115 (119)
..+-|.|......|+...+.|.|.
T Consensus 60 f~~~G~y~y~C~~Hp~M~G~v~V~ 83 (83)
T TIGR02657 60 FTEAGTYDYHCTPHPFMRGKVVVE 83 (83)
T ss_pred CCCCEEEEEEcCCCCCCeEEEEEC
Confidence 567899999999999999998873
No 71
>cd04614 CBS_pair_1 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=26.47 E-value=93 Score=19.48 Aligned_cols=19 Identities=16% Similarity=0.324 Sum_probs=15.6
Q ss_pred CCCCceeecccHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDII 74 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L 74 (119)
.++|++.|.||..|+....
T Consensus 31 d~~~~~~Giv~~~dl~~~~ 49 (96)
T cd04614 31 DDDGKLSGIITERDLIAKS 49 (96)
T ss_pred CCCCCEEEEEEHHHHhcCC
Confidence 4678999999999987643
No 72
>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=26.46 E-value=1.2e+02 Score=18.32 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=19.1
Q ss_pred ccceeeEEEEEEeCCCe---EEEEEEEE
Q 033453 92 IRETGEYIAQLKLHPEV---TARIRLNV 116 (119)
Q Consensus 92 IK~lG~y~V~I~L~~~V---~a~i~V~V 116 (119)
...-|.|.|.+.+..+. ++++.|.|
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 67889999999988776 45555555
No 73
>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=26.42 E-value=1.6e+02 Score=19.39 Aligned_cols=31 Identities=23% Similarity=0.554 Sum_probs=23.1
Q ss_pred cccccC--ccceeeEEEEEEeCCC--eEEEEEEEE
Q 033453 86 IVDLPE--IRETGEYIAQLKLHPE--VTARIRLNV 116 (119)
Q Consensus 86 ~I~l~~--IK~lG~y~V~I~L~~~--V~a~i~V~V 116 (119)
.|.|.+ ...-|.|.+.|+-+|+ -++++.+.|
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 355555 7789999999999877 566666655
No 74
>cd04611 CBS_pair_PAS_GGDEF_DUF1_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. 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 CB
Probab=26.37 E-value=48 Score=20.64 Aligned_cols=17 Identities=24% Similarity=0.520 Sum_probs=15.2
Q ss_pred CceeecccHHHHHHHHH
Q 033453 59 KQIFGSVTAQDVVDIIK 75 (119)
Q Consensus 59 gkLFGSVt~~dIa~~L~ 75 (119)
|++.|.+|.+|+...+.
T Consensus 33 ~~~~G~v~~~~l~~~~~ 49 (111)
T cd04611 33 GRPLGIVTERDILRLLA 49 (111)
T ss_pred CEEEEEEeHHHHHHHHh
Confidence 89999999999988764
No 75
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=25.81 E-value=45 Score=23.71 Aligned_cols=19 Identities=26% Similarity=0.546 Sum_probs=16.8
Q ss_pred CCceeecccHHHHHHHHHH
Q 033453 58 GKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 58 ~gkLFGSVt~~dIa~~L~~ 76 (119)
||.+||-+|+.+|.+.|++
T Consensus 125 ~~~~y~~vt~e~v~~il~~ 143 (145)
T PF01257_consen 125 DGEWYGNVTPEKVDEILEE 143 (145)
T ss_dssp CCCEEESSSCCHHHHHHHH
T ss_pred CCEEECCCCHHHHHHHHHh
Confidence 7889999999999888765
No 76
>cd04625 CBS_pair_12 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=25.81 E-value=61 Score=20.31 Aligned_cols=20 Identities=15% Similarity=0.361 Sum_probs=16.7
Q ss_pred CCCceeecccHHHHHHHHHH
Q 033453 57 KGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L~~ 76 (119)
++|++.|.||..|+...+..
T Consensus 31 ~~~~~~G~v~~~dl~~~~~~ 50 (112)
T cd04625 31 ERGELVGLLTFREVLQAMAQ 50 (112)
T ss_pred eCCEEEEEEEHHHHHHHHHh
Confidence 45899999999999987753
No 77
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=25.63 E-value=29 Score=25.51 Aligned_cols=24 Identities=13% Similarity=0.470 Sum_probs=15.3
Q ss_pred cccHHHHHHHHHHhcCCceeccccc
Q 033453 64 SVTAQDVVDIIKAQLQRDVDKKIVD 88 (119)
Q Consensus 64 SVt~~dIa~~L~~~~g~~Idkk~I~ 88 (119)
-.|-.+|++.|.++ |+.|-||.|.
T Consensus 121 PlSD~~i~~~L~~~-gi~isRRTVa 144 (160)
T PF04552_consen 121 PLSDQEIAELLKEE-GIKISRRTVA 144 (160)
T ss_dssp ---HHHHHHHHTTT-TS---HHHHH
T ss_pred CCCHHHHHHHHHHc-CCCccHHHHH
Confidence 34678899999988 8999998774
No 78
>PRK00441 argR arginine repressor; Provisional
Probab=25.37 E-value=42 Score=24.29 Aligned_cols=36 Identities=19% Similarity=0.186 Sum_probs=25.0
Q ss_pred ecccHHHHHHHHHHhcCCceecccccccCccceeeEEE
Q 033453 63 GSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIA 100 (119)
Q Consensus 63 GSVt~~dIa~~L~~~~g~~Idkk~I~l~~IK~lG~y~V 100 (119)
|.+|..|+++.|++. |+.+.--.|.= +|+.+|..+|
T Consensus 17 ~~~~q~eL~~~L~~~-G~~vSqaTisR-Dl~~L~lvKv 52 (149)
T PRK00441 17 EIETQEELAEELKKM-GFDVTQATVSR-DIKELKLIKV 52 (149)
T ss_pred CCCcHHHHHHHHHhc-CCCcCHHHHHH-HHHHcCcEEe
Confidence 677889999999888 99887555432 2555555444
No 79
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like 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. HoxF may be involved
Probab=25.35 E-value=66 Score=20.39 Aligned_cols=18 Identities=17% Similarity=0.377 Sum_probs=15.4
Q ss_pred CCceeecccHHHHHHHHH
Q 033453 58 GKQIFGSVTAQDVVDIIK 75 (119)
Q Consensus 58 ~gkLFGSVt~~dIa~~L~ 75 (119)
+|.+||-||+.++.+.+.
T Consensus 61 ~~~~y~~v~~~~v~~iv~ 78 (80)
T cd03083 61 NNRVFTRLTPGRIDQIAE 78 (80)
T ss_pred CCEEECCCCHHHHHHHHh
Confidence 578999999999887764
No 80
>cd04605 CBS_pair_MET2_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the MET2 domain. Met2 is a key enzyme in the biosynthesis of methionine. It encodes a homoserine transacetylase involved in converting homoserine to O-acetyl homoserine. 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=25.09 E-value=1e+02 Score=19.19 Aligned_cols=18 Identities=17% Similarity=0.418 Sum_probs=14.4
Q ss_pred cCCCCceeecccHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~ 72 (119)
..++|++.|-||..||..
T Consensus 92 v~~~~~~~G~v~~~di~~ 109 (110)
T cd04605 92 VDAENRVIGIITSEDISK 109 (110)
T ss_pred ECCCCcEEEEEEHHHhhh
Confidence 456789999999999853
No 81
>COG0757 AroQ 3-dehydroquinate dehydratase II [Amino acid transport and metabolism]
Probab=24.94 E-value=66 Score=23.63 Aligned_cols=27 Identities=26% Similarity=0.427 Sum_probs=21.5
Q ss_pred ceeecccHHHHHHHHHH---hcCCceeccc
Q 033453 60 QIFGSVTAQDVVDIIKA---QLQRDVDKKI 86 (119)
Q Consensus 60 kLFGSVt~~dIa~~L~~---~~g~~Idkk~ 86 (119)
.+||+.|-.||.+.+++ +.|++++=++
T Consensus 20 ~iYG~~Tl~di~~~~~~~a~~~g~~v~~~Q 49 (146)
T COG0757 20 GIYGSTTLEDIEADLEEEAAKLGVEVEFRQ 49 (146)
T ss_pred CccCcccHHHHHHHHHHHHHHcCceEEEEe
Confidence 39999999999998874 3578887655
No 82
>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=24.88 E-value=1.7e+02 Score=20.52 Aligned_cols=24 Identities=17% Similarity=0.387 Sum_probs=19.9
Q ss_pred eeeEEEEEEeCCCeEEEEEEEEee
Q 033453 95 TGEYIAQLKLHPEVTARIRLNVFA 118 (119)
Q Consensus 95 lG~y~V~I~L~~~V~a~i~V~V~~ 118 (119)
-|+|.|.|.+...-..+..|.+..
T Consensus 29 pG~Y~vdv~vN~~~~~~~~i~f~~ 52 (146)
T PF13954_consen 29 PGEYSVDVYVNGKFIGRYDIEFIN 52 (146)
T ss_dssp SEEEEEEEEETTEEEEEEEEEEEE
T ss_pred CeEEEEEEEECCeeeeeEEEEEEe
Confidence 499999999999988888777653
No 83
>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=24.67 E-value=82 Score=21.05 Aligned_cols=21 Identities=33% Similarity=0.586 Sum_probs=17.2
Q ss_pred CCC-ceeecccHHHHHHHHHHh
Q 033453 57 KGK-QIFGSVTAQDVVDIIKAQ 77 (119)
Q Consensus 57 ~~g-kLFGSVt~~dIa~~L~~~ 77 (119)
.+| -+||-||+.|+.+.+.+.
T Consensus 56 p~g~v~Y~~V~~edv~~Iv~~~ 77 (92)
T cd03063 56 PGGRVAYGPVTPADVASLLDAG 77 (92)
T ss_pred CCCcEEEEeCCHHHHHHHHHHH
Confidence 345 799999999999888764
No 84
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=24.67 E-value=58 Score=24.72 Aligned_cols=23 Identities=22% Similarity=0.330 Sum_probs=19.3
Q ss_pred cCCCCceeecccHHHHHHHHHHh
Q 033453 55 GGKGKQIFGSVTAQDVVDIIKAQ 77 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~~L~~~ 77 (119)
+=++|++-||||-.+|.+++-+.
T Consensus 101 Vi~~~k~VGsItE~~iv~~~le~ 123 (187)
T COG3620 101 VIEEDKVVGSITENDIVRALLEG 123 (187)
T ss_pred eeeCCeeeeeecHHHHHHHHhcc
Confidence 34568999999999999998654
No 85
>cd04627 CBS_pair_14 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=24.62 E-value=1.8e+02 Score=18.60 Aligned_cols=18 Identities=11% Similarity=0.409 Sum_probs=15.3
Q ss_pred CceeecccHHHHHHHHHH
Q 033453 59 KQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 59 gkLFGSVt~~dIa~~L~~ 76 (119)
|++.|.||..|+..++..
T Consensus 35 ~~~~Giv~~~dl~~~~~~ 52 (123)
T cd04627 35 GEVIGILSQRRLVEFLWE 52 (123)
T ss_pred CcEEEEEEHHHHHHHHHH
Confidence 789999999999887643
No 86
>cd04597 CBS_pair_DRTGG_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. 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=24.42 E-value=96 Score=20.22 Aligned_cols=18 Identities=17% Similarity=0.156 Sum_probs=14.2
Q ss_pred cCCCCceeecccHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~ 72 (119)
+.++|++.|-||..||+.
T Consensus 95 vd~~~~l~Givt~~dl~~ 112 (113)
T cd04597 95 VDDDGTPAGIITLLDLAE 112 (113)
T ss_pred ECCCCeEEEEEEHHHhhc
Confidence 446788999999998864
No 87
>cd04636 CBS_pair_23 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=24.37 E-value=67 Score=21.08 Aligned_cols=21 Identities=19% Similarity=0.336 Sum_probs=17.5
Q ss_pred CCCCceeecccHHHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L~~ 76 (119)
.++|++.|.|+..+|...+..
T Consensus 31 d~~~~~~G~i~~~~l~~~~~~ 51 (132)
T cd04636 31 DNEGRVVGIVSEGDLIRKIYK 51 (132)
T ss_pred CCCCCEEEEEeHHHHHHHHhc
Confidence 356899999999999987754
No 88
>COG5556 Uncharacterized conserved protein [Function unknown]
Probab=24.25 E-value=37 Score=23.48 Aligned_cols=24 Identities=21% Similarity=0.380 Sum_probs=20.2
Q ss_pred cHHHHHHHHHHhcCCceecccccc
Q 033453 66 TAQDVVDIIKAQLQRDVDKKIVDL 89 (119)
Q Consensus 66 t~~dIa~~L~~~~g~~Idkk~I~l 89 (119)
|+.-++++.++.+|+++.|..++-
T Consensus 21 s~S~Va~aVkkEfGi~VsrQlves 44 (110)
T COG5556 21 SPSVVAAAVKKEFGIDVSRQLVES 44 (110)
T ss_pred cHHHHHHHHHHHhcchHHHHHHHh
Confidence 467789999999999999887754
No 89
>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=23.78 E-value=47 Score=18.85 Aligned_cols=24 Identities=13% Similarity=0.231 Sum_probs=17.9
Q ss_pred ecccHHHHHHHHHHhcCCc-eecccc
Q 033453 63 GSVTAQDVVDIIKAQLQRD-VDKKIV 87 (119)
Q Consensus 63 GSVt~~dIa~~L~~~~g~~-Idkk~I 87 (119)
|.||..++-.+|... |+. +....+
T Consensus 3 G~i~~~~~~~~l~~~-g~~~~s~~e~ 27 (54)
T PF13833_consen 3 GKITREEFRRALSKL-GIKDLSEEEV 27 (54)
T ss_dssp SEEEHHHHHHHHHHT-TSSSSCHHHH
T ss_pred CEECHHHHHHHHHHh-CCCCCCHHHH
Confidence 788999999999544 877 665543
No 90
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=23.45 E-value=1.3e+02 Score=25.70 Aligned_cols=15 Identities=13% Similarity=0.275 Sum_probs=12.4
Q ss_pred Ccc--chhcccchHHHH
Q 033453 2 NQV--FGNLQLFGVLCM 16 (119)
Q Consensus 2 ~~g--yarNfL~~~~l~ 16 (119)
+.| |+||=||.+-++
T Consensus 106 degkmyGRNELIarYIK 122 (455)
T KOG3841|consen 106 DEGKMYGRNELIARYIK 122 (455)
T ss_pred cCccccchHHHHHHHHH
Confidence 345 999999999775
No 91
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=23.41 E-value=66 Score=19.53 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=18.1
Q ss_pred eee-cccHHHHHHHHHHhcCCceec
Q 033453 61 IFG-SVTAQDVVDIIKAQLQRDVDK 84 (119)
Q Consensus 61 LFG-SVt~~dIa~~L~~~~g~~Idk 84 (119)
+-| ++|..++.+.|... |++++.
T Consensus 14 llG~~i~~~ei~~~L~~l-g~~~~~ 37 (71)
T smart00874 14 LLGLDLSAEEIEEILKRL-GFEVEV 37 (71)
T ss_pred HHCCCCCHHHHHHHHHHC-CCeEEe
Confidence 444 78899999999887 888864
No 92
>COG2239 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]
Probab=23.39 E-value=1.1e+02 Score=26.29 Aligned_cols=43 Identities=19% Similarity=0.456 Sum_probs=33.9
Q ss_pred HHHHHHHHhhhccCeEEEEEecCCCCceeecccHHHHHHHHHHh
Q 033453 34 EEAQQLALIFETVGAFKVKRKGGKGKQIFGSVTAQDVVDIIKAQ 77 (119)
Q Consensus 34 ~~a~~la~kL~~~~~l~i~~k~g~~gkLFGSVt~~dIa~~L~~~ 77 (119)
...++.+..++.- .+..-..+.++++|-|.||-.||.+.+.+.
T Consensus 213 ~dqeevA~~~~~y-dl~a~PVVd~~~~LiG~itiDDiidvi~eE 255 (451)
T COG2239 213 DDQEEVARLFEKY-DLLAVPVVDEDNRLIGIITIDDIIDVIEEE 255 (451)
T ss_pred CCHHHHHHHHHHh-CCeecceECCCCceeeeeeHHHHHHHHHHH
Confidence 3456667777765 466677788999999999999999998765
No 93
>cd04622 CBS_pair_9 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=22.97 E-value=87 Score=19.53 Aligned_cols=17 Identities=18% Similarity=0.350 Sum_probs=13.4
Q ss_pred CCCCceeecccHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~ 72 (119)
.++|++.|-||..||.+
T Consensus 96 ~~~~~~~G~it~~di~~ 112 (113)
T cd04622 96 DDDGRLVGIVSLGDLAR 112 (113)
T ss_pred CCCCcEEEEEEHHHhhc
Confidence 34588999999999854
No 94
>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=22.90 E-value=60 Score=19.44 Aligned_cols=22 Identities=27% Similarity=0.507 Sum_probs=15.0
Q ss_pred ecccHHHHHHHHHHhcCCceeccc
Q 033453 63 GSVTAQDVVDIIKAQLQRDVDKKI 86 (119)
Q Consensus 63 GSVt~~dIa~~L~~~~g~~Idkk~ 86 (119)
|..|..+|++.|.++++ +|+..
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 66889999999999864 55443
No 95
>cd04617 CBS_pair_4 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=22.71 E-value=73 Score=20.44 Aligned_cols=19 Identities=16% Similarity=0.344 Sum_probs=16.4
Q ss_pred CCCceeecccHHHHHHHHH
Q 033453 57 KGKQIFGSVTAQDVVDIIK 75 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L~ 75 (119)
++|++.|.||..||..++.
T Consensus 32 ~~~~~~Givt~~dl~~~~~ 50 (118)
T cd04617 32 EDGDLVGVVSRKDLLKASI 50 (118)
T ss_pred CCCCEEEEEEHHHHHHHHH
Confidence 4688999999999998875
No 96
>cd02205 CBS_pair 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 generali
Probab=22.69 E-value=1.8e+02 Score=17.35 Aligned_cols=21 Identities=19% Similarity=0.393 Sum_probs=17.4
Q ss_pred CCCceeecccHHHHHHHHHHh
Q 033453 57 KGKQIFGSVTAQDVVDIIKAQ 77 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L~~~ 77 (119)
++|++.|.|+..|+...+...
T Consensus 32 ~~~~~~G~v~~~~l~~~~~~~ 52 (113)
T cd02205 32 DDGRLVGIVTERDLLRALAEG 52 (113)
T ss_pred CCCCEEEEEeHHHHHHHHHhc
Confidence 458999999999999887653
No 97
>cd04609 CBS_pair_PALP_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well as the 5'-phosphate esters of pyridoxal (PALP) and pyridoxamine, the last two being the biologically active coenzyme derivatives. The members of the PALP family are principally involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and other amine-containing compounds. 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 pote
Probab=22.53 E-value=1.4e+02 Score=18.27 Aligned_cols=18 Identities=22% Similarity=0.530 Sum_probs=15.8
Q ss_pred CceeecccHHHHHHHHHH
Q 033453 59 KQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 59 gkLFGSVt~~dIa~~L~~ 76 (119)
|++.|.||..|+...+..
T Consensus 33 ~~~~G~v~~~dl~~~~~~ 50 (110)
T cd04609 33 GRVVGSIDESDLLDALIE 50 (110)
T ss_pred CeeEEEEeHHHHHHHHhc
Confidence 789999999999998754
No 98
>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=22.36 E-value=86 Score=20.70 Aligned_cols=27 Identities=15% Similarity=0.110 Sum_probs=19.5
Q ss_pred ecccHHHHHHHHHHhcCCceeccccccc
Q 033453 63 GSVTAQDVVDIIKAQLQRDVDKKIVDLP 90 (119)
Q Consensus 63 GSVt~~dIa~~L~~~~g~~Idkk~I~l~ 90 (119)
++-|+.++++.|... |++++...|-.+
T Consensus 40 s~~s~~~~~~~L~~~-Gi~~~~~~i~ts 66 (101)
T PF13344_consen 40 SSRSREEYAKKLKKL-GIPVDEDEIITS 66 (101)
T ss_dssp SSS-HHHHHHHHHHT-TTT--GGGEEEH
T ss_pred CCCCHHHHHHHHHhc-CcCCCcCEEECh
Confidence 567889999999775 999999887653
No 99
>PF07679 I-set: Immunoglobulin I-set domain; InterPro: IPR013098 The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; IPR013106 from INTERPRO), C1-set (constant-1; IPR003597 from INTERPRO), C2-set (constant-2; IPR008424 from INTERPRO) and I-set (intermediate; IPR013098 from INTERPRO) []. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns [, ]. Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system []. This entry represents I-set domains, which are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM). I-set domains are also present in several other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1 [], and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis [].; PDB: 3MTR_A 2EDK_A 3DMK_B 1KOA_A 3NCM_A 2NCM_A 2V9Q_A 2CR3_A 3QQN_A 3QR2_A ....
Probab=22.31 E-value=1.9e+02 Score=17.41 Aligned_cols=30 Identities=20% Similarity=0.338 Sum_probs=21.6
Q ss_pred ccccC--ccceeeEEEEEEeCCC-eEEEEEEEE
Q 033453 87 VDLPE--IRETGEYIAQLKLHPE-VTARIRLNV 116 (119)
Q Consensus 87 I~l~~--IK~lG~y~V~I~L~~~-V~a~i~V~V 116 (119)
+.+.+ -..-|.|.+.+.-..+ .+++++|.|
T Consensus 58 L~I~~v~~~D~G~Y~C~~~n~~g~~~~~~~l~V 90 (90)
T PF07679_consen 58 LTIKNVTREDAGTYTCVASNSSGEATASVNLTV 90 (90)
T ss_dssp EEESSESGGGSEEEEEEEEETTEEEEEEEEEEE
T ss_pred EccCCCChhhCEEEEEEEEECCCEEEEEEEEEC
Confidence 44444 6688999999987655 567777765
No 100
>cd04640 CBS_pair_27 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=22.17 E-value=1.3e+02 Score=19.52 Aligned_cols=35 Identities=11% Similarity=0.138 Sum_probs=20.2
Q ss_pred HHHHHhhhccCeEEEEEecCCC-CceeecccHHHHHH
Q 033453 37 QQLALIFETVGAFKVKRKGGKG-KQIFGSVTAQDVVD 72 (119)
Q Consensus 37 ~~la~kL~~~~~l~i~~k~g~~-gkLFGSVt~~dIa~ 72 (119)
.++.+.+... .+..-.=+.++ |++.|-||..||..
T Consensus 90 ~~~l~~m~~~-~~~~lpVvd~~~~~~~G~it~~di~~ 125 (126)
T cd04640 90 GDVVETLKAS-GRQHALVVDREHHQIRGIISTSDIAR 125 (126)
T ss_pred HHHHHHHHHC-CCceEEEEECCCCEEEEEEeHHHHhh
Confidence 3444455442 24322223333 78999999999864
No 101
>PF14848 HU-DNA_bdg: DNA-binding domain
Probab=22.15 E-value=59 Score=22.55 Aligned_cols=24 Identities=17% Similarity=0.389 Sum_probs=19.6
Q ss_pred ecccHHHHHHHHHHhcCCceecccc
Q 033453 63 GSVTAQDVVDIIKAQLQRDVDKKIV 87 (119)
Q Consensus 63 GSVt~~dIa~~L~~~~g~~Idkk~I 87 (119)
|++|-.||++.+.+. |-.+.+-.|
T Consensus 27 ~~~tl~~Ia~~i~~~-~s~~t~~di 50 (124)
T PF14848_consen 27 GTLTLEDIAEEIAKE-GSTLTRADI 50 (124)
T ss_pred CccCHHHHHHHHHHh-CCCCCHHHH
Confidence 889999999999876 777776554
No 102
>cd04585 CBS_pair_ACT_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are associated with a downstream ACT domain, which is linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. 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 i
Probab=22.00 E-value=1.1e+02 Score=19.15 Aligned_cols=17 Identities=18% Similarity=0.390 Sum_probs=13.5
Q ss_pred CCCCceeecccHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~ 72 (119)
.++|++.|-||..||.+
T Consensus 105 ~~~~~~~Gvvt~~di~~ 121 (122)
T cd04585 105 DDQGRLVGIITESDLFR 121 (122)
T ss_pred CCCCcEEEEEEHHHhhh
Confidence 34678999999998864
No 103
>cd04803 CBS_pair_15 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=21.93 E-value=79 Score=20.11 Aligned_cols=20 Identities=15% Similarity=0.336 Sum_probs=16.7
Q ss_pred CCCceeecccHHHHHHHHHH
Q 033453 57 KGKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 57 ~~gkLFGSVt~~dIa~~L~~ 76 (119)
++|++.|.||..||...+..
T Consensus 32 ~~~~~~G~v~~~~l~~~~~~ 51 (122)
T cd04803 32 EDGKLVGLLTQRDLLRAALS 51 (122)
T ss_pred CCCCEEEEEEHHHHHHHhcc
Confidence 45899999999999887653
No 104
>cd04615 CBS_pair_2 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=21.48 E-value=1.9e+02 Score=17.90 Aligned_cols=20 Identities=25% Similarity=0.368 Sum_probs=16.1
Q ss_pred CCCCceeecccHHHHHHHHH
Q 033453 56 GKGKQIFGSVTAQDVVDIIK 75 (119)
Q Consensus 56 g~~gkLFGSVt~~dIa~~L~ 75 (119)
.++|++.|.||.+|+...+.
T Consensus 31 d~~~~~~G~v~~~dl~~~~~ 50 (113)
T cd04615 31 DDKKRLVGIITRYDVLSYAL 50 (113)
T ss_pred cCCCCEEEEEEHHHHHHhhh
Confidence 35688999999999987543
No 105
>PRK13690 hypothetical protein; Provisional
Probab=21.18 E-value=1.8e+02 Score=22.22 Aligned_cols=44 Identities=16% Similarity=0.108 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhhccCeEEEEEecCC-CCceeecccHHHHHHHHHHh
Q 033453 33 KEEAQQLALIFETVGAFKVKRKGGK-GKQIFGSVTAQDVVDIIKAQ 77 (119)
Q Consensus 33 ~~~a~~la~kL~~~~~l~i~~k~g~-~gkLFGSVt~~dIa~~L~~~ 77 (119)
..+..+.+.--.+ .-+.+-+.++| -|.--|+-++.||++++-+.
T Consensus 14 ~~El~~~a~l~~g-~i~VvGcSTSEV~G~~IGt~ss~eva~~i~~~ 58 (184)
T PRK13690 14 LEELLEQANLKPG-QIFVLGCSTSEVLGERIGTAGSLEVAEAIVEA 58 (184)
T ss_pred HHHHHHhhCCCCC-CEEEEecchHhhCCcccCCcChHHHHHHHHHH
Confidence 3344444433344 36888898888 67777999999999888653
No 106
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=21.14 E-value=57 Score=22.81 Aligned_cols=25 Identities=24% Similarity=0.464 Sum_probs=21.5
Q ss_pred cccHHHHHHHHHHhcCCceecccccc
Q 033453 64 SVTAQDVVDIIKAQLQRDVDKKIVDL 89 (119)
Q Consensus 64 SVt~~dIa~~L~~~~g~~Idkk~I~l 89 (119)
++|..||-..|+.. |+++|.-++.+
T Consensus 19 ~pTaddI~kIL~Aa-GveVd~~~~~l 43 (112)
T PTZ00373 19 NPTKKEVKNVLSAV-NADVEDDVLDN 43 (112)
T ss_pred CCCHHHHHHHHHHc-CCCccHHHHHH
Confidence 59999999999887 99999877654
No 107
>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=21.04 E-value=2.2e+02 Score=23.17 Aligned_cols=57 Identities=9% Similarity=0.123 Sum_probs=37.9
Q ss_pred eEEEEEecCC---CCceeecccHHHHHHHHHHhcCCceecc-cc-cccCccceeeEEEEEEeCCC
Q 033453 48 AFKVKRKGGK---GKQIFGSVTAQDVVDIIKAQLQRDVDKK-IV-DLPEIRETGEYIAQLKLHPE 107 (119)
Q Consensus 48 ~l~i~~k~g~---~gkLFGSVt~~dIa~~L~~~~g~~Idkk-~I-~l~~IK~lG~y~V~I~L~~~ 107 (119)
+++|..+-|- ||. -||+.|++-.+......+.... .+ .+..++.+|.|+|.|+|...
T Consensus 59 t~tf~Lr~~~~f~DG~---pvTA~Dv~~s~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~i~l~~p 120 (454)
T cd08496 59 TLTLHLREGLTFSDGT---PLDAAAVKANLDRGKSTGGSQVKQLASISSVEVVDDTTVTLTLSQP 120 (454)
T ss_pred EEEEEeCCCCCccCCC---CcCHHHHHHHHHHHhCCCcchhhhccccceEEecCCCEEEEEeCCC
Confidence 6888888764 776 5799999999875322211110 11 12238889999999999753
No 108
>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=20.98 E-value=2.3e+02 Score=23.34 Aligned_cols=57 Identities=19% Similarity=0.327 Sum_probs=38.5
Q ss_pred eEEEEEecC---CCCceeecccHHHHHHHHHHhcCCcee-ccccc-ccCccceeeEEEEEEeCCC
Q 033453 48 AFKVKRKGG---KGKQIFGSVTAQDVVDIIKAQLQRDVD-KKIVD-LPEIRETGEYIAQLKLHPE 107 (119)
Q Consensus 48 ~l~i~~k~g---~~gkLFGSVt~~dIa~~L~~~~g~~Id-kk~I~-l~~IK~lG~y~V~I~L~~~ 107 (119)
+++|..+-| .|| -.||+.|++-.+..-.+.... +.... +..|+.+|.|+|.|+|...
T Consensus 59 ~~tf~LR~~v~wsdG---~~lTA~Dv~~s~~~~~~~~~~~~~~~~~i~~v~~~d~~tv~~~l~~p 120 (472)
T cd08502 59 TYTFTLRDGLKFHDG---SPVTAADVVASLKRWAKRDAMGQALMAAVESLEAVDDKTVVITLKEP 120 (472)
T ss_pred EEEEEEcCCCEecCC---ccCcHHHHHHHHHHHhccCcccccccccceeEEecCCCEEEEEeCCC
Confidence 688888887 477 469999999888643222111 11121 2348899999999999754
No 109
>PF03449 GreA_GreB_N: Transcription elongation factor, N-terminal; InterPro: IPR022691 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A 2ETN_C 2P4V_B.
Probab=20.93 E-value=2.4e+02 Score=17.96 Aligned_cols=21 Identities=14% Similarity=0.033 Sum_probs=15.1
Q ss_pred hcccchHHHHHHHHHHHHHHH
Q 033453 7 NLQLFGVLCMEMKMEEERIEA 27 (119)
Q Consensus 7 rNfL~~~~l~~l~~~~~~~~~ 27 (119)
++|++|.++..++.+......
T Consensus 3 ~~~lT~~g~~~L~~EL~~L~~ 23 (74)
T PF03449_consen 3 KKYLTPEGYEKLQAELEHLKN 23 (74)
T ss_dssp --EEEHHHHHHHHHHHHHHHH
T ss_pred ccccCHHHHHHHHHHHHHHHH
Confidence 457999999888877766554
No 110
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=20.77 E-value=94 Score=22.50 Aligned_cols=44 Identities=14% Similarity=0.227 Sum_probs=22.3
Q ss_pred EEEEEecCCCCceeecccHHHHHHHHHHhcCCceecccccccCccceeeEEE
Q 033453 49 FKVKRKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPEIRETGEYIA 100 (119)
Q Consensus 49 l~i~~k~g~~gkLFGSVt~~dIa~~L~~~~g~~Idkk~I~l~~IK~lG~y~V 100 (119)
+||.+..|.+| .+|+..|++.+|++.=-+.|...-.+..|.-+-
T Consensus 2 ITIsr~~Gsgg--------~~Ia~~LA~~Lg~~~~d~~ii~~~a~~~~~~~~ 45 (179)
T PF13189_consen 2 ITISRQYGSGG--------REIAERLAEKLGYPYYDREIIEEAAKESGISEE 45 (179)
T ss_dssp EEEEE-TTSSH--------HHHHHHHHHHCT--EE-HHHHHHCT--------
T ss_pred EEECCCCCCCh--------HHHHHHHHHHcCCccCCHHHHHHHHHHccCCHH
Confidence 67888877776 789999999989876333443222555554443
No 111
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=20.68 E-value=59 Score=22.49 Aligned_cols=25 Identities=28% Similarity=0.343 Sum_probs=21.6
Q ss_pred cccHHHHHHHHHHhcCCceecccccc
Q 033453 64 SVTAQDVVDIIKAQLQRDVDKKIVDL 89 (119)
Q Consensus 64 SVt~~dIa~~L~~~~g~~Idkk~I~l 89 (119)
++|..||-..|+.. |+++|.-++.+
T Consensus 17 ~pTa~dI~~IL~Aa-GveVe~~~~~l 41 (109)
T cd05833 17 SPSAADVKKILGSV-GVEVDDEKLNK 41 (109)
T ss_pred CCCHHHHHHHHHHc-CCCccHHHHHH
Confidence 79999999999887 99999877654
No 112
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=20.36 E-value=94 Score=22.61 Aligned_cols=19 Identities=11% Similarity=0.324 Sum_probs=16.6
Q ss_pred CCceeecccHHHHHHHHHH
Q 033453 58 GKQIFGSVTAQDVVDIIKA 76 (119)
Q Consensus 58 ~gkLFGSVt~~dIa~~L~~ 76 (119)
||++||.+|+.++.+.|.+
T Consensus 135 n~~~~~~lt~~~~~~il~~ 153 (156)
T PRK05988 135 DGEVHGRLDPQRLDALLAE 153 (156)
T ss_pred CCEEeCCCCHHHHHHHHHH
Confidence 7889999999999888764
No 113
>cd04600 CBS_pair_HPP_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is uncertain, but they are thought to be transporters. 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=20.02 E-value=97 Score=19.74 Aligned_cols=18 Identities=22% Similarity=0.464 Sum_probs=13.7
Q ss_pred cCCCCceeecccHHHHHH
Q 033453 55 GGKGKQIFGSVTAQDVVD 72 (119)
Q Consensus 55 ~g~~gkLFGSVt~~dIa~ 72 (119)
+.++|++.|-||..||..
T Consensus 106 v~~~g~~~Gvit~~di~~ 123 (124)
T cd04600 106 VDEDRRLVGIVTQTDLIA 123 (124)
T ss_pred EcCCCCEEEEEEhHHhhc
Confidence 345778999999988764
Done!