Query 032727
Match_columns 135
No_of_seqs 104 out of 324
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:10:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032727.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032727hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00071 40S ribosomal protein 100.0 4.5E-55 9.8E-60 328.8 13.7 127 6-132 5-131 (132)
2 KOG3424 40S ribosomal protein 100.0 3.3E-55 7.1E-60 325.2 9.1 131 1-134 1-131 (132)
3 PRK01178 rps24e 30S ribosomal 100.0 4.3E-42 9.4E-47 247.7 11.2 95 8-103 2-96 (99)
4 COG2004 RPS24A Ribosomal prote 100.0 1.8E-41 3.9E-46 247.2 10.5 104 7-116 2-105 (107)
5 PF01282 Ribosomal_S24e: Ribos 100.0 7.1E-35 1.5E-39 204.2 9.8 83 25-108 1-84 (84)
6 PF00076 RRM_1: RNA recognitio 69.3 18 0.0004 21.9 5.0 47 35-88 8-55 (70)
7 smart00360 RRM RNA recognition 67.2 22 0.00048 20.6 5.3 48 35-88 6-54 (71)
8 COG2003 RadC DNA repair protei 63.0 11 0.00024 31.1 3.8 36 28-65 172-210 (224)
9 TIGR03636 L23_arch archaeal ri 56.6 43 0.00093 23.0 5.4 57 18-83 9-66 (77)
10 PF12327 FtsZ_C: FtsZ family, 55.9 13 0.00029 26.0 2.8 51 13-64 22-76 (95)
11 PTZ00191 60S ribosomal protein 53.6 91 0.002 24.1 7.3 56 23-87 83-141 (145)
12 PF00276 Ribosomal_L23: Riboso 52.3 33 0.00071 23.9 4.3 56 16-78 13-76 (91)
13 PF08496 Peptidase_S49_N: Pept 51.9 33 0.00071 26.5 4.6 54 22-77 96-150 (155)
14 PRK14548 50S ribosomal protein 50.3 60 0.0013 22.7 5.4 63 13-84 11-74 (84)
15 PF04432 FrhB_FdhB_C: Coenzyme 48.7 33 0.00071 25.7 4.1 45 20-65 28-72 (161)
16 CHL00030 rpl23 ribosomal prote 47.4 49 0.0011 23.5 4.6 45 14-65 11-55 (93)
17 PF12436 USP7_ICP0_bdg: ICP0-b 44.5 26 0.00057 28.5 3.2 55 17-72 171-234 (249)
18 COG0245 IspF 2C-methyl-D-eryth 41.6 62 0.0014 25.5 4.7 40 25-66 96-135 (159)
19 KOG3439 Protein conjugation fa 39.8 1.5E+02 0.0032 22.3 6.2 34 34-68 83-116 (116)
20 PRK05738 rplW 50S ribosomal pr 38.6 66 0.0014 22.6 4.1 34 15-52 12-46 (92)
21 PLN03134 glycine-rich RNA-bind 36.4 67 0.0015 23.9 4.1 47 35-87 44-91 (144)
22 PRK00084 ispF 2-C-methyl-D-ery 35.3 68 0.0015 25.1 4.1 38 25-64 98-135 (159)
23 COG0710 AroD 3-dehydroquinate 34.9 65 0.0014 26.5 4.1 33 26-59 119-151 (231)
24 PTZ00397 macrophage migration 34.7 84 0.0018 22.1 4.3 35 26-61 60-99 (116)
25 PRK06425 histidinol-phosphate 34.1 52 0.0011 26.9 3.5 43 13-62 22-64 (332)
26 PF14560 Ubiquitin_2: Ubiquiti 33.3 1.4E+02 0.0029 20.0 4.9 27 35-62 22-48 (87)
27 cd08059 MPN_prok_mb Mpr1p, Pad 32.9 95 0.0021 21.1 4.2 31 25-60 59-90 (101)
28 KOG3969 Uncharacterized conser 31.9 52 0.0011 28.4 3.1 58 39-97 218-290 (310)
29 KOG2116 Protein involved in pl 31.5 76 0.0016 30.4 4.4 34 44-79 491-524 (738)
30 PRK10513 sugar phosphate phosp 31.4 69 0.0015 25.1 3.7 33 26-62 187-219 (270)
31 PRK12280 rplW 50S ribosomal pr 31.4 82 0.0018 24.7 4.0 36 13-52 13-48 (158)
32 TIGR00608 radc DNA repair prot 31.3 1E+02 0.0022 24.9 4.7 28 25-52 163-193 (218)
33 PRK15126 thiamin pyrimidine py 30.7 68 0.0015 25.4 3.5 33 26-62 179-211 (272)
34 PF01996 F420_ligase: F420-0:G 30.0 39 0.00084 27.4 2.0 52 28-81 125-176 (228)
35 TIGR01482 SPP-subfamily Sucros 30.0 88 0.0019 23.6 3.9 33 26-62 140-172 (225)
36 cd00554 MECDP_synthase MECDP_s 29.9 1E+02 0.0023 23.9 4.3 36 25-62 95-130 (153)
37 PRK10976 putative hydrolase; P 29.9 69 0.0015 25.1 3.4 33 26-62 181-213 (266)
38 PRK01688 histidinol-phosphate 29.6 49 0.0011 27.4 2.6 27 35-62 55-81 (351)
39 PF04110 APG12: Ubiquitin-like 29.6 19 0.00042 25.4 0.2 34 34-68 54-87 (87)
40 TIGR01661 ELAV_HUD_SF ELAV/HuD 29.5 1.8E+02 0.0038 23.7 5.9 53 27-86 272-325 (352)
41 cd00590 RRM RRM (RNA recogniti 29.5 1.2E+02 0.0026 17.5 5.2 47 35-88 9-56 (74)
42 TIGR00151 ispF 2C-methyl-D-ery 29.4 1E+02 0.0022 24.0 4.2 36 25-62 95-130 (155)
43 PRK13815 ribosome-binding fact 29.4 2.3E+02 0.005 20.8 6.1 44 40-83 10-57 (122)
44 PF02542 YgbB: YgbB family; I 29.1 59 0.0013 25.4 2.8 31 29-61 100-130 (157)
45 TIGR01485 SPP_plant-cyano sucr 28.9 1.1E+02 0.0025 23.9 4.5 32 27-62 159-190 (249)
46 PRK06959 putative threonine-ph 27.1 70 0.0015 26.5 3.1 25 37-62 54-78 (339)
47 PRK14864 putative biofilm stre 26.4 2.6E+02 0.0056 20.3 6.3 51 26-80 53-103 (104)
48 PRK02220 4-oxalocrotonate taut 26.3 76 0.0016 19.5 2.5 20 41-61 23-42 (61)
49 cd01804 midnolin_N Ubiquitin-l 26.2 2E+02 0.0043 18.9 4.9 23 35-58 20-42 (78)
50 PF09581 Spore_III_AF: Stage I 26.2 43 0.00093 25.5 1.6 23 38-61 165-187 (188)
51 PHA01976 helix-turn-helix prot 26.1 33 0.00072 21.4 0.8 24 33-58 38-61 (67)
52 TIGR03576 pyridox_MJ0158 pyrid 25.6 63 0.0014 27.2 2.6 29 33-62 50-78 (346)
53 PF10503 Esterase_phd: Esteras 25.5 8.2 0.00018 31.1 -2.6 36 38-76 80-115 (220)
54 PF07338 DUF1471: Protein of u 25.1 1.9E+02 0.0041 18.4 5.0 50 26-80 7-56 (56)
55 PLN03026 histidinol-phosphate 24.6 83 0.0018 26.4 3.2 26 36-62 85-110 (380)
56 COG2006 Uncharacterized conser 24.6 83 0.0018 27.0 3.1 43 30-74 171-213 (293)
57 PRK01158 phosphoglycolate phos 24.6 1E+02 0.0022 23.4 3.5 33 26-62 148-180 (230)
58 cd02777 MopB_CT_DMSOR-like The 24.6 1.9E+02 0.0042 20.3 4.7 38 40-82 36-73 (127)
59 TIGR00013 taut 4-oxalocrotonat 24.5 1E+02 0.0023 18.9 2.9 19 41-60 23-41 (63)
60 PRK01964 4-oxalocrotonate taut 24.4 87 0.0019 19.6 2.6 20 41-61 23-42 (64)
61 COG3561 Phage anti-repressor p 24.3 1.5E+02 0.0032 22.0 4.0 59 33-91 23-81 (110)
62 cd06397 PB1_UP1 Uncharacterize 24.3 1.5E+02 0.0032 21.0 3.8 30 35-65 18-47 (82)
63 COG1888 Uncharacterized protei 24.2 1.7E+02 0.0037 21.3 4.2 47 23-71 6-52 (97)
64 PF08766 DEK_C: DEK C terminal 24.2 65 0.0014 20.1 1.9 21 33-54 17-37 (54)
65 PRK05387 histidinol-phosphate 24.2 69 0.0015 26.0 2.5 25 37-62 60-84 (353)
66 PRK04781 histidinol-phosphate 24.2 72 0.0016 26.5 2.7 26 36-62 58-83 (364)
67 KOG0113 U1 small nuclear ribon 24.1 2E+02 0.0043 25.2 5.3 53 24-86 104-157 (335)
68 PF03090 Replicase: Replicase 24.1 1.4E+02 0.003 22.5 4.0 40 14-60 17-56 (137)
69 TIGR01642 U2AF_lg U2 snRNP aux 24.0 1.5E+02 0.0032 25.7 4.7 46 35-86 305-351 (509)
70 PF02594 DUF167: Uncharacteris 23.1 1.2E+02 0.0027 20.6 3.2 43 23-65 26-68 (77)
71 PRK07392 threonine-phosphate d 22.8 88 0.0019 25.7 3.0 25 37-62 57-81 (360)
72 cd01796 DDI1_N DNA damage indu 22.5 1E+02 0.0022 19.9 2.7 27 35-61 18-44 (71)
73 PRK00024 hypothetical protein; 22.5 1.6E+02 0.0036 23.6 4.4 36 25-60 169-210 (224)
74 cd00491 4Oxalocrotonate_Tautom 22.4 1.2E+02 0.0025 18.3 2.8 19 41-60 22-40 (58)
75 TIGR01484 HAD-SF-IIB HAD-super 22.4 1.4E+02 0.0031 22.2 3.8 33 26-62 154-186 (204)
76 PLN02862 2-C-methyl-D-erythrit 22.2 1.4E+02 0.0031 24.5 4.0 36 25-62 155-190 (216)
77 PF04002 RadC: RadC-like JAB d 22.2 1.1E+02 0.0025 22.0 3.1 29 24-52 67-101 (123)
78 cd01806 Nedd8 Nebb8-like ubiq 22.0 1.5E+02 0.0032 18.6 3.3 22 35-57 19-40 (76)
79 PRK14807 histidinol-phosphate 22.0 1.1E+02 0.0025 25.1 3.4 26 36-62 58-83 (351)
80 COG0561 Cof Predicted hydrolas 22.0 1.1E+02 0.0025 23.9 3.3 31 27-61 181-211 (264)
81 PF00388 PI-PLC-X: Phosphatidy 21.7 2.3E+02 0.0049 20.6 4.7 42 27-69 55-98 (146)
82 PRK10259 hypothetical protein; 21.2 2.8E+02 0.006 19.5 4.8 40 38-80 47-86 (86)
83 PRK14809 histidinol-phosphate 21.1 1.2E+02 0.0026 24.9 3.4 25 37-62 65-89 (357)
84 PF10264 Stork_head: Winged he 21.1 1.1E+02 0.0023 21.5 2.6 23 30-52 42-64 (80)
85 cd00508 MopB_CT_Fdh-Nap-like T 20.8 2.1E+02 0.0045 19.4 4.1 37 41-82 38-74 (120)
86 PRK04635 histidinol-phosphate 20.6 93 0.002 25.6 2.7 25 37-62 60-84 (354)
87 TIGR01141 hisC histidinol-phos 20.3 1E+02 0.0022 24.9 2.8 27 35-62 52-78 (346)
88 PRK06358 threonine-phosphate d 20.2 1.1E+02 0.0024 25.3 3.0 25 37-62 54-78 (354)
89 COG4900 Predicted metallopepti 20.2 1.8E+02 0.0039 22.1 3.8 56 37-95 7-66 (133)
90 PRK08056 threonine-phosphate d 20.1 99 0.0021 25.5 2.7 25 37-62 55-79 (356)
91 COG0299 PurN Folate-dependent 20.1 1.7E+02 0.0037 23.8 4.0 31 34-64 59-89 (200)
No 1
>PTZ00071 40S ribosomal protein S24; Provisional
Probab=100.00 E-value=4.5e-55 Score=328.80 Aligned_cols=127 Identities=60% Similarity=0.947 Sum_probs=122.1
Q ss_pred cEEEEeeeeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCCHHHH
Q 032727 6 AVTLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSVENA 85 (135)
Q Consensus 6 ~~~i~~~k~~~N~LL~RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds~e~~ 85 (135)
+|||+|++|++||||+|+||+|+|+|||.||||+.||+++||+||+++|+|+|||++|+|+||+|+|+|||+||||+|+|
T Consensus 5 ~~~ir~rk~~~NpLL~RkE~~~~v~Hpg~~TpSr~eirekLA~~~~v~d~~~Vvv~~~~T~fG~g~StG~a~IYds~e~~ 84 (132)
T PTZ00071 5 EFTVRTRKFLVNPLLNRKQFVVEVLHPGKGTVSKKDIKEKLAKQYKVADARTIVLFGFKTKFGGGKTTGFGLIYDNLAAL 84 (132)
T ss_pred cEEEEEeeeeeccCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHhCCCCCCEEEEEccEecCCCceEEEEEEEECCHHHH
Confidence 59999999999999999999999999999999999999999999994499999999999999999999999999999999
Q ss_pred HhcCCcchhhhcCCccccccchhhHHHHhhhccccccccccccchhh
Q 032727 86 KKFEPKYRLIRNGLDTKVEKSRKQLKERKNRAKKIRGVKKTKASDAA 132 (135)
Q Consensus 86 kk~Epk~~l~Rn~~~e~~k~~Rk~~ke~kn~~kk~rGt~k~~~~~~~ 132 (135)
++|||+|+|.|||+.+..+.+|+||||+||++||+|||+++++..++
T Consensus 85 kk~Epk~~l~Rngl~~~~~~~rk~rke~knr~kk~rg~~k~k~~~~~ 131 (132)
T PTZ00071 85 KKFEPKYRLIRLGLIKKKKAGRKARKELKNRRKKVRGKEKTKVSGKK 131 (132)
T ss_pred HhhCchheeeecCccccCccchHHHHHHHhhhhhhccchhhhhhhcc
Confidence 99999999999999998888999999999999999999999986544
No 2
>KOG3424 consensus 40S ribosomal protein S24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-55 Score=325.16 Aligned_cols=131 Identities=75% Similarity=1.113 Sum_probs=127.4
Q ss_pred CCCCccEEEEeeeeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeC
Q 032727 1 MADTKAVTLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYD 80 (135)
Q Consensus 1 m~~~~~~~i~~~k~~~N~LL~RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYd 80 (135)
|+| +|||+|++||+|+||+|+||+++|+|||.|+||++||+|+||+||.+ ++|.||||+|+|+||+|+|+|||+|||
T Consensus 1 ~~~--~vtirtrk~~tNrLL~RKqmvvdvlHPG~a~vsK~EirEKla~mYkt-~~d~V~vfgfrt~~GggkstgfalIYd 77 (132)
T KOG3424|consen 1 MSD--AVTIRTRKFMTNRLLSRKQMVVDVLHPGKANVSKTEIREKLAKMYKT-TPDAVFVFGFRTHFGGGKSTGFALIYD 77 (132)
T ss_pred CCc--cEEEehhhhhhhhhhhhhheeEEEecCCCCCCCHHHHHHHHHHHhcC-CcceEEEEEeeeccCCcccceeeeeee
Confidence 556 69999999999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred CHHHHHhcCCcchhhhcCCccccccchhhHHHHhhhccccccccccccchhhhc
Q 032727 81 SVENAKKFEPKYRLIRNGLDTKVEKSRKQLKERKNRAKKIRGVKKTKASDAAKK 134 (135)
Q Consensus 81 s~e~~kk~Epk~~l~Rn~~~e~~k~~Rk~~ke~kn~~kk~rGt~k~~~~~~~k~ 134 (135)
|+|+|++|||+|+|+|+|+.|..+.+|+||||++|+++|+|||.|++++.++++
T Consensus 78 sve~akkfEpkyrl~r~gl~e~~kt~RkqrKerknr~kKi~Gt~K~~~~~~~k~ 131 (132)
T KOG3424|consen 78 SVEYAKKFEPKYRLVRLGLAEKIKTSRKQRKERKNRMKKIFGTGKRKAKKAKKK 131 (132)
T ss_pred hHHHHHhcCcceeeeecccccccccHHHHHHHHhhccchheeHHHHHhhhhhcc
Confidence 999999999999999999999998899999999999999999999999988775
No 3
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=100.00 E-value=4.3e-42 Score=247.69 Aligned_cols=95 Identities=36% Similarity=0.603 Sum_probs=91.8
Q ss_pred EEEeeeeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCCHHHHHh
Q 032727 8 TLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSVENAKK 87 (135)
Q Consensus 8 ~i~~~k~~~N~LL~RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds~e~~kk 87 (135)
.|.|.++.+||||+|+||+|+|+|||.|||||.||+++||+||++ |+++|||++|+|+||+|+|+|||+||||.|+|++
T Consensus 2 ei~I~~~~~N~LL~Rke~~~~v~h~g~~tpsr~eirekLa~~~~~-~~~~vvv~~~~t~fG~g~s~G~a~IYds~e~~kk 80 (99)
T PRK01178 2 EIKIISDKENPLLGRREIKFEVYHEGSATPSRKDVRKKLAAMLNA-DKELVVVRKIKTEYGMGKSKGYAKVYDDKERARK 80 (99)
T ss_pred cEEEEEeeecCCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHHCc-CCCEEEEEccCccCCCceEEEEEEEECCHHHHHh
Confidence 367899999999999999999999999999999999999999998 9999999999999999999999999999999999
Q ss_pred cCCcchhhhcCCcccc
Q 032727 88 FEPKYRLIRNGLDTKV 103 (135)
Q Consensus 88 ~Epk~~l~Rn~~~e~~ 103 (135)
|||+|+|.||++.+++
T Consensus 81 ~Epk~~l~Rn~~~~~~ 96 (99)
T PRK01178 81 IEPKYILERNKIEEEE 96 (99)
T ss_pred hCchheeeecCccccc
Confidence 9999999999998764
No 4
>COG2004 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-41 Score=247.23 Aligned_cols=104 Identities=42% Similarity=0.632 Sum_probs=99.7
Q ss_pred EEEEeeeeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCCHHHHH
Q 032727 7 VTLRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSVENAK 86 (135)
Q Consensus 7 ~~i~~~k~~~N~LL~RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds~e~~k 86 (135)
++|.|.++++||||+|+||+|+|+|||.+||||.||+++||++|++ |+++|||++|+|+||+|+|+|||+||||.+.|+
T Consensus 2 ~ei~I~~~r~NpLL~RkEi~~~v~h~g~~TPSr~evrekla~~l~~-d~e~VvV~~ikt~fG~~~s~g~akIY~s~e~~~ 80 (107)
T COG2004 2 MEIKILEKRDNPLLKRKEIVFVVYHEGSPTPSRKEVREKLAAMLGA-DKELVVVDYIKTEFGKGRSKGYAKIYDSVERAK 80 (107)
T ss_pred ceEEeehcccCccccceEEEEEEEeCCCCCCCHHHHHHHHHHHHCC-CcceEEEEehhhhcCCcceeEEEEEECCHHHHH
Confidence 6899999999999999999999999999999999999999999999 999999999999999999999999999999999
Q ss_pred hcCCcchhhhcCCccccccchhhHHHHhhh
Q 032727 87 KFEPKYRLIRNGLDTKVEKSRKQLKERKNR 116 (135)
Q Consensus 87 k~Epk~~l~Rn~~~e~~k~~Rk~~ke~kn~ 116 (135)
+|||+|+|.||+. ..+.+++|.+++
T Consensus 81 ~iEp~yiL~Rn~~-----~~~~~~eE~e~r 105 (107)
T COG2004 81 KIEPEYILERNGG-----AERQEAEEAENR 105 (107)
T ss_pred hcCcceEEEeccc-----hhhhhhHhhhcc
Confidence 9999999999998 456777888877
No 5
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=100.00 E-value=7.1e-35 Score=204.19 Aligned_cols=83 Identities=61% Similarity=1.012 Sum_probs=74.5
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCCHHHHHhcCCcchhhhcCCccccc
Q 032727 25 FVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSVENAKKFEPKYRLIRNGLDTKVE 104 (135)
Q Consensus 25 i~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds~e~~kk~Epk~~l~Rn~~~e~~k 104 (135)
|+|+|+|||.|||||+||+++||+|||+ |+++|||++|+|+||++.|+|||+||||+|+|++|||+|+|.||++.++..
T Consensus 1 ~~~~v~h~g~~Tpsr~ei~~klA~~~~~-~~~~ivv~~~~t~fG~~~s~g~a~IYd~~e~~kk~Ep~~~l~R~~~~e~~~ 79 (84)
T PF01282_consen 1 MVFEVLHPGKPTPSRKEIREKLAAMLNV-DPDLIVVFGIKTEFGGGKSTGFAKIYDSAEALKKFEPKYRLKRNGLEEKKE 79 (84)
T ss_dssp EEEEEE-SSSSS--HHHHHHHHHHHHTS-TGCCEEEEEEEESSSSSEEEEEEEEESSHHHHHHHSTHHHHHHTTSSSS-S
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHhCC-CCCeEEEeccEecCCCceEEEEEEEeCCHHHHHHhCcHHHhHhcCcccccc
Confidence 6899999999999999999999999999 999999999999999999999999999999999999999999999988754
Q ss_pred -cchh
Q 032727 105 -KSRK 108 (135)
Q Consensus 105 -~~Rk 108 (135)
.+|+
T Consensus 80 ~~~r~ 84 (84)
T PF01282_consen 80 KEGRK 84 (84)
T ss_dssp -S-HH
T ss_pred ccccC
Confidence 4553
No 6
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=69.35 E-value=18 Score=21.85 Aligned_cols=47 Identities=26% Similarity=0.515 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEe-eCCHHHHHhc
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLI-YDSVENAKKF 88 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~I-Yds~e~~kk~ 88 (135)
+..+..||++.+.. +|. -... .+.+. +.+...|||.| |+|.+.+++.
T Consensus 8 ~~~t~~~l~~~f~~-~g~-i~~~----~~~~~-~~~~~~~~a~V~F~~~~~a~~a 55 (70)
T PF00076_consen 8 PDVTEEELRDFFSQ-FGK-IESI----KVMRN-SSGKSKGYAFVEFESEEDAEKA 55 (70)
T ss_dssp TTSSHHHHHHHHHT-TST-EEEE----EEEEE-TTSSEEEEEEEEESSHHHHHHH
T ss_pred CcCCHHHHHHHHHH-hhh-cccc----ccccc-ccccccceEEEEEcCHHHHHHH
Confidence 45678899998866 666 2122 22332 77778888876 7777777653
No 7
>smart00360 RRM RNA recognition motif.
Probab=67.15 E-value=22 Score=20.58 Aligned_cols=48 Identities=27% Similarity=0.485 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEe-eCCHHHHHhc
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLI-YDSVENAKKF 88 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~I-Yds~e~~kk~ 88 (135)
...+..+|++.+. .+|. -.++ .+......+.+.|||.| |++.+.+...
T Consensus 6 ~~~~~~~l~~~f~-~~g~-v~~~----~i~~~~~~~~~~~~a~v~f~~~~~a~~a 54 (71)
T smart00360 6 PDVTEEELRELFS-KFGK-IESV----RLVRDKDTGKSKGFAFVEFESEEDAEKA 54 (71)
T ss_pred cccCHHHHHHHHH-hhCC-EeEE----EEEeCCCCCCCCceEEEEeCCHHHHHHH
Confidence 3467789998884 5563 1222 22334446778888888 7888877654
No 8
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=63.01 E-value=11 Score=31.08 Aligned_cols=36 Identities=19% Similarity=0.260 Sum_probs=28.1
Q ss_pred EEEcC-CCCCCCHHHH--HHHHHhHhCCCCCCeEEEeceee
Q 032727 28 DVLHP-GRANVSKAEL--KEKLARMYEVKDPNAIFVFKFRT 65 (135)
Q Consensus 28 ~v~H~-g~~Tpsr~eI--k~kLA~~~~~~~~~~IvV~~~~T 65 (135)
-=.|| |.+|||++|+ -++|++..+. -+..+++.+-.
T Consensus 172 aHNHPSGd~~PS~aD~~iT~rl~~a~~l--l~I~vLDHiIi 210 (224)
T COG2003 172 AHNHPSGDPTPSRADILITERLKEAGKL--LGIRLLDHIII 210 (224)
T ss_pred eccCCCCCCCcCHHHHHHHHHHHHHHHh--cCceeeeeEEe
Confidence 34688 6799999964 6888888877 57788888877
No 9
>TIGR03636 L23_arch archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
Probab=56.60 E-value=43 Score=23.01 Aligned_cols=57 Identities=14% Similarity=0.290 Sum_probs=38.1
Q ss_pred cCccc-eEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCCHH
Q 032727 18 RLLSR-KQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSVE 83 (135)
Q Consensus 18 ~LL~R-kEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds~e 83 (135)
.|+.. .++.|.|.-. .++.||+..+-.+|++ ..+-|..+... ++.-.+|..+.+..+
T Consensus 9 ~~~e~~n~y~F~V~~~----anK~eIK~avE~lf~V---kV~~Vnt~~~~--~~~KKA~VtL~~g~~ 66 (77)
T TIGR03636 9 NLIEKENKLTFIVDRK----ATKGDIKRAVEKLFDV---KVEKVNTLITP--RGEKKAYVKLAEEYA 66 (77)
T ss_pred HHHHhCCEEEEEECCC----CCHHHHHHHHHHHhCC---ceEEEEeEEcC--CCceEEEEEECCCCc
Confidence 35554 6888888654 7799999999999999 44445555543 344555665555433
No 10
>PF12327 FtsZ_C: FtsZ family, C-terminal domain; InterPro: IPR024757 The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin []. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea []. This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain TIGR03483 from TIGRFAMs.; PDB: 2RHO_B 2RHJ_A 2VXY_A 2RHL_B 2RHH_A 2VAM_A 1W5F_B 2R75_1 2R6R_1 1RQ7_A ....
Probab=55.90 E-value=13 Score=25.97 Aligned_cols=51 Identities=22% Similarity=0.306 Sum_probs=29.9
Q ss_pred eeeeccCccceEE----EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEecee
Q 032727 13 KFMTNRLLSRKQF----VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFR 64 (135)
Q Consensus 13 k~~~N~LL~RkEi----~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~ 64 (135)
+-+.||||+ ..+ .+-|...+++.++-.|+.+.+-......+++.-+++|..
T Consensus 22 ~Al~spLl~-~~i~~A~~vLvni~~~~d~~l~ev~~~~~~i~~~~~~~a~ii~G~~ 76 (95)
T PF12327_consen 22 QALNSPLLD-VDIKGAKGVLVNITGGPDLSLSEVNEAMEIIREKADPDANIIWGAS 76 (95)
T ss_dssp HHHTSTTST-S-GGG-SEEEEEEEE-TTS-HHHHHHHHHHHHHHSSTTSEEEEEEE
T ss_pred HHHhCcccc-CChHHhceEEEEEEcCCCCCHHHHHHHHHHHHHHhhcCceEEEEEE
Confidence 346789998 444 233444456889999888777555443356666666654
No 11
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=53.56 E-value=91 Score=24.10 Aligned_cols=56 Identities=21% Similarity=0.329 Sum_probs=40.4
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEe---eCCHHHHHh
Q 032727 23 KQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLI---YDSVENAKK 87 (135)
Q Consensus 23 kEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~I---Yds~e~~kk 87 (135)
.+++|.|.-. .++.||++.+-.+|++ +++-|..+.+.- |.=.+|+.. ||.+|.+.+
T Consensus 83 N~yvF~Vd~k----AnK~qIK~AVEklf~V---kV~kVNTli~p~--g~KKA~V~L~~~~~aidva~k 141 (145)
T PTZ00191 83 NTLVFIVDQR----ANKTQIKKAVEKLYDV---KVVKVNTLITPD--GLKKAYIRLSPDVDALDVANK 141 (145)
T ss_pred CEEEEEEcCC----CCHHHHHHHHHHHhCC---eeEEEEeEEcCC--CceEEEEEECCCCcHHHHHHh
Confidence 6788888654 7799999999999999 666666666644 455567777 444555544
No 12
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
Probab=52.32 E-value=33 Score=23.92 Aligned_cols=56 Identities=25% Similarity=0.410 Sum_probs=35.6
Q ss_pred eccCccc-eEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeec-----CCC--CEEEEEEEe
Q 032727 16 TNRLLSR-KQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTH-----FGG--GKSTGFGLI 78 (135)
Q Consensus 16 ~N~LL~R-kEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~-----fG~--~~s~g~a~I 78 (135)
..-|+.. .++.|.|. +..++.||++.|-+.||+ . .+-|..+... +|. |...+|=+.
T Consensus 13 s~~~~~~~n~~tF~V~----~~atK~~Ik~aie~iy~V-~--V~~Vnt~~~~gk~kR~g~~~g~~~~~KKa 76 (91)
T PF00276_consen 13 SMKLLENPNQYTFEVD----PRATKTEIKEAIEKIYGV-K--VKKVNTMNYPGKKKRKGKFVGKTKDYKKA 76 (91)
T ss_dssp HHHHHHHSSEEEEEET----TTSTHHHHHHHHHHHHTS-E--EEEEEEEEETSEEEESSSCEEEE-EEEEE
T ss_pred HHHhhhcCCEEEEEEe----CCCCHHHHHHHHHhhcCC-C--eeEEEEeEeCCCceEeCCccccCCCcEEE
Confidence 3344555 67888774 347899999999999999 3 4445444444 665 344444333
No 13
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=51.91 E-value=33 Score=26.52 Aligned_cols=54 Identities=22% Similarity=0.444 Sum_probs=40.0
Q ss_pred ceEEEEEEEcCCCCCCCH-HHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEE
Q 032727 22 RKQFVIDVLHPGRANVSK-AELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGL 77 (135)
Q Consensus 22 RkEi~~~v~H~g~~Tpsr-~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~ 77 (135)
.+.-.|.+.|.|.---|- +.+++++.+.+.++.|+==||-.+.+ |||...||++
T Consensus 96 ~~~r~~VldF~Gdi~A~~v~~LReeisail~~a~~~DeV~~rLES--~GG~Vh~YGL 150 (155)
T PF08496_consen 96 PKPRLFVLDFKGDIKASEVESLREEISAILSVATPEDEVLVRLES--PGGMVHGYGL 150 (155)
T ss_pred CCCeEEEEecCCCccHHHHHHHHHHHHHHHHhCCCCCeEEEEEec--CCceeeccch
Confidence 455677888887543333 37899999999987777666666766 9999999875
No 14
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=50.31 E-value=60 Score=22.67 Aligned_cols=63 Identities=13% Similarity=0.230 Sum_probs=43.1
Q ss_pred eeeeccCccc-eEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCCHHH
Q 032727 13 KFMTNRLLSR-KQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSVEN 84 (135)
Q Consensus 13 k~~~N~LL~R-kEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds~e~ 84 (135)
.++.+.|+.. .++.|.|.- ..++.||++.+-.+|++ ...-|..+.+. .+.-.+|....+..++
T Consensus 11 TEK~~~~~e~~n~y~F~V~~----~anK~eIK~AvE~lf~V---kV~~VnT~~~~--~~~KKA~V~L~~g~~A 74 (84)
T PRK14548 11 TEKAMNLIEKENKLTFIVDR----RATKPDIKRAVEELFDV---KVEKVNTLITP--KGEKKAYVKLAEEYDA 74 (84)
T ss_pred CHHHHHHHHhCCEEEEEECC----CCCHHHHHHHHHHHhCC---ceEEEEeEEcC--CCcEEEEEEeCCCCcH
Confidence 3444556664 688888754 48899999999999999 55666666664 4555666666555443
No 15
>PF04432 FrhB_FdhB_C: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; InterPro: IPR007525 Coenzyme F420 hydrogenase (1.12.99.1 from EC) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C-termini of F420 hydrogenase and dehydrogenase beta subunits [, ]. The C terminus of Methanobacterium formicicum formate dehydrogenase beta chain (1.2.1.2 from EC, P06130 from SWISSPROT) is also represented in this entry []. This region is often found in association with the 4Fe-4S binding domain, fer4 (IPR001450 from INTERPRO), and the N terminus IPR007516 from INTERPRO.
Probab=48.74 E-value=33 Score=25.72 Aligned_cols=45 Identities=20% Similarity=0.283 Sum_probs=34.0
Q ss_pred ccceEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceee
Q 032727 20 LSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRT 65 (135)
Q Consensus 20 L~RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T 65 (135)
.++.++.+.|--.-.++||..-+++-|+..++. +++.|.=+.|+.
T Consensus 28 ~~~~~~~~~igl~C~g~~s~~~~~~~l~~~~~~-~~~~v~~~~~r~ 72 (161)
T PF04432_consen 28 ENRDEIVYTIGLFCHGVPSPKKLRKYLEEQLGI-KPDDVKKFDFRD 72 (161)
T ss_pred ccCcceEEEEeEECCCCCCHHHHHHHHHHHhCC-ChhheeEEEEeC
Confidence 334335555666667899999999999999999 777777777776
No 16
>CHL00030 rpl23 ribosomal protein L23
Probab=47.37 E-value=49 Score=23.54 Aligned_cols=45 Identities=29% Similarity=0.366 Sum_probs=32.3
Q ss_pred eeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceee
Q 032727 14 FMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRT 65 (135)
Q Consensus 14 ~~~N~LL~RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T 65 (135)
+...-|+...++.|.|.- ..++.||++.+-.+|++ ..+-|..+.+
T Consensus 11 EKs~~l~e~n~y~F~V~~----~anK~eIK~avE~lf~V---kV~~VNt~~~ 55 (93)
T CHL00030 11 DKSIRLLEKNQYTFDVDS----GSTKTEIKHWIELFFGV---KVIAVNSHRL 55 (93)
T ss_pred HHHHHhhHCCEEEEEECC----CCCHHHHHHHHHHHhCC---eEEEEEEEEc
Confidence 344456666788888754 47899999999999999 4444444444
No 17
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=44.46 E-value=26 Score=28.50 Aligned_cols=55 Identities=24% Similarity=0.289 Sum_probs=32.4
Q ss_pred ccCccceEEEEEEEcCCC---------CCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEE
Q 032727 17 NRLLSRKQFVIDVLHPGR---------ANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKS 72 (135)
Q Consensus 17 N~LL~RkEi~~~v~H~g~---------~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s 72 (135)
+-|++|.+|.|.-.+... ..-+=.||.+++|+.+++ ||+.|=++......|...+
T Consensus 171 ~~l~nrv~V~f~~~~~~~~~~F~l~ls~~~tY~~la~~Va~~l~~-dP~~lr~~~~~~~~~~P~~ 234 (249)
T PF12436_consen 171 DFLYNRVEVEFKPKDNPNDPEFTLWLSKKMTYDQLAEKVAEHLNV-DPEHLRFFTVNPYSGKPKS 234 (249)
T ss_dssp HHHHHEEEEEEEETTSTT---EEEEEETT--HHHHHHHHHHHHTS--GGGEEEE---TTS-S---
T ss_pred HHHhCeEEEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHCC-ChHHEEEEEeccCCCCCCC
Confidence 445666666655433211 234668999999999999 9999999988876666553
No 18
>COG0245 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism]
Probab=41.57 E-value=62 Score=25.45 Aligned_cols=40 Identities=15% Similarity=0.218 Sum_probs=31.3
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeec
Q 032727 25 FVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTH 66 (135)
Q Consensus 25 i~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~ 66 (135)
+.+...-| +-.|-+.++++.||++|++ +++.|-|.-=.|+
T Consensus 96 ~tii~~~P-K~~P~~~amr~~ia~~L~i-~~~~invKatT~E 135 (159)
T COG0245 96 ITIIAQRP-KLGPYREAMRANIAELLGI-PVDRINVKATTTE 135 (159)
T ss_pred EEEEEecC-cccchHHHHHHHHHHHhCC-CchheEEEEeccC
Confidence 34445555 5689999999999999999 9999988654443
No 19
>KOG3439 consensus Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones]
Probab=39.81 E-value=1.5e+02 Score=22.28 Aligned_cols=34 Identities=12% Similarity=0.229 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCC
Q 032727 34 RANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFG 68 (135)
Q Consensus 34 ~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG 68 (135)
.-.||-.++-+.|-..|++ |..+|+=+.+...||
T Consensus 83 sFAPsPDq~v~~Ly~cf~~-d~~Lvl~Yc~s~A~G 116 (116)
T KOG3439|consen 83 SFAPSPDQIVGNLYECFGT-DGKLVLNYCISVAWG 116 (116)
T ss_pred ccCCCchhHHHHHHHhcCC-CCEEEEEEeeecccC
Confidence 5679999999999999999 888888777777776
No 20
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=38.58 E-value=66 Score=22.58 Aligned_cols=34 Identities=21% Similarity=0.544 Sum_probs=25.8
Q ss_pred eeccCcc-ceEEEEEEEcCCCCCCCHHHHHHHHHhHhCC
Q 032727 15 MTNRLLS-RKQFVIDVLHPGRANVSKAELKEKLARMYEV 52 (135)
Q Consensus 15 ~~N~LL~-RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~ 52 (135)
..+.|+. -.++.|.|. +..++.||++.|-.+|++
T Consensus 12 Ks~~~~e~~n~~~F~V~----~~a~K~eIK~aie~lf~V 46 (92)
T PRK05738 12 KSTLLMEKQNKYVFEVA----PDATKPEIKAAVEKLFGV 46 (92)
T ss_pred HHHHhHHhCCEEEEEEC----CCCCHHHHHHHHHHHcCC
Confidence 3444555 467787764 458899999999999999
No 21
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=36.44 E-value=67 Score=23.90 Aligned_cols=47 Identities=23% Similarity=0.431 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEe-eCCHHHHHh
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLI-YDSVENAKK 87 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~I-Yds~e~~kk 87 (135)
.+.+-++|++.+.. |+. =.++.++.+-.| +.+.|||.| |.|.++|..
T Consensus 44 ~~~te~~L~~~F~~-~G~-I~~v~i~~d~~t----g~~kGfaFV~F~~~e~A~~ 91 (144)
T PLN03134 44 WGTDDASLRDAFAH-FGD-VVDAKVIVDRET----GRSRGFGFVNFNDEGAATA 91 (144)
T ss_pred CCCCHHHHHHHHhc-CCC-eEEEEEEecCCC----CCcceEEEEEECCHHHHHH
Confidence 44678889888854 665 345555555544 556666664 555555544
No 22
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=35.30 E-value=68 Score=25.10 Aligned_cols=38 Identities=13% Similarity=0.147 Sum_probs=29.4
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEecee
Q 032727 25 FVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFR 64 (135)
Q Consensus 25 i~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~ 64 (135)
+.+....| +=.|-+.++++.||+.++. +++.|-|.-=.
T Consensus 98 ~tii~e~P-Ki~p~~~~m~~~la~~L~i-~~~~V~iKatT 135 (159)
T PRK00084 98 ITIIAQRP-KMAPHIEEMRANIAEDLGI-PLDDVNVKATT 135 (159)
T ss_pred EEEEcCCC-cchHHHHHHHHHHHHHhCC-CcceEEEEEec
Confidence 34444555 5688999999999999999 88888886543
No 23
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=34.91 E-value=65 Score=26.50 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=27.9
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEE
Q 032727 26 VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIF 59 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~Iv 59 (135)
.+.=+|.=..|||.+++.+.|.+|... ++|.+=
T Consensus 119 vI~SyH~F~~TP~~~~i~~~l~km~~~-~aDivK 151 (231)
T COG0710 119 VIVSYHDFEKTPPLEEIIERLDKMESL-GADIVK 151 (231)
T ss_pred EEEEeccCCCCCcHHHHHHHHHHHHhh-CCCeEE
Confidence 556688888999999999999999999 776653
No 24
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=34.73 E-value=84 Score=22.14 Aligned_cols=35 Identities=20% Similarity=0.301 Sum_probs=23.4
Q ss_pred EEEEEcCCCCCCCH-----HHHHHHHHhHhCCCCCCeEEEe
Q 032727 26 VIDVLHPGRANVSK-----AELKEKLARMYEVKDPNAIFVF 61 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr-----~eIk~kLA~~~~~~~~~~IvV~ 61 (135)
.+.|..-|+.++.. .+|-+.|++.+|+ +++.|+|.
T Consensus 60 ~v~i~~~g~~~~e~k~~l~~~i~~~l~~~lgi-~~~rv~I~ 99 (116)
T PTZ00397 60 FVRVTSIGGISRSNNSSIAAAITKILASHLKV-KSERVYIE 99 (116)
T ss_pred EEEEEEecCCCHHHHHHHHHHHHHHHHHHhCc-CcccEEEE
Confidence 44555445555552 2677888899999 77777763
No 25
>PRK06425 histidinol-phosphate aminotransferase; Validated
Probab=34.09 E-value=52 Score=26.90 Aligned_cols=43 Identities=5% Similarity=0.005 Sum_probs=29.5
Q ss_pred eeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 13 KFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 13 k~~~N~LL~RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
..-+||+.. +.....+ |.|.-.++++.||+.+++ +++.|+|..
T Consensus 22 ~~Nenp~~~---~~~~~~Y---p~~~~~~lr~~ia~~~~~-~~~~I~it~ 64 (332)
T PRK06425 22 SANINDFMD---IGDISIY---PEISYTDIEDQIKIYTQG-LKIKVLIGP 64 (332)
T ss_pred ccccCCCcC---hhhcccC---cCcCHHHHHHHHHHHhCC-CcceEEECC
Confidence 445788841 1111123 457789999999999999 888887743
No 26
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=33.25 E-value=1.4e+02 Score=19.98 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.+-+-.|++.+|...+|+ +++..-+.-
T Consensus 22 ~~~Tv~eLK~kl~~~~Gi-~~~~m~L~l 48 (87)
T PF14560_consen 22 KSITVSELKQKLEKLTGI-PPSDMRLQL 48 (87)
T ss_dssp TTSBHHHHHHHHHHHHTS--TTTEEEEE
T ss_pred CCCCHHHHHHHHHHHhCC-CcccEEEEE
Confidence 456788999999999999 776666643
No 27
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=32.94 E-value=95 Score=21.10 Aligned_cols=31 Identities=26% Similarity=0.382 Sum_probs=20.1
Q ss_pred EEEEEEcC-CCCCCCHHHHHHHHHhHhCCCCCCeEEE
Q 032727 25 FVIDVLHP-GRANVSKAELKEKLARMYEVKDPNAIFV 60 (135)
Q Consensus 25 i~~~v~H~-g~~Tpsr~eIk~kLA~~~~~~~~~~IvV 60 (135)
+.+.=.|| |.+.||.+|+. ++..++. +.++|
T Consensus 59 v~i~HsHP~g~~~PS~~D~~--~~~~~~~---~~iIv 90 (101)
T cd08059 59 VGLVHSHPSGSCRPSEADLS--LFTRFGL---YHVIV 90 (101)
T ss_pred EEEEecCcCCCCCCCHHHHH--HHHhcCC---eEEEE
Confidence 34444677 67899999985 3344444 66666
No 28
>KOG3969 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.86 E-value=52 Score=28.41 Aligned_cols=58 Identities=19% Similarity=0.415 Sum_probs=45.7
Q ss_pred HHHHHHHHHhHhCCCCCCeEEEe---------------ceeecCCCCEEEEEEEeeCCHHHHHhcCCcchhhhc
Q 032727 39 KAELKEKLARMYEVKDPNAIFVF---------------KFRTHFGGGKSTGFGLIYDSVENAKKFEPKYRLIRN 97 (135)
Q Consensus 39 r~eIk~kLA~~~~~~~~~~IvV~---------------~~~T~fG~~~s~g~a~IYds~e~~kk~Epk~~l~Rn 97 (135)
|..+++.+...|++ ++|.+.+| +++-.-|.|.+.|.|+.-|+.=....+-|+|--.+.
T Consensus 218 r~k~~~~i~~~y~v-~~dqlrmf~HYqPSyYHlHVHi~nik~~~~~~~~~~rAilLddVI~nL~~~P~~Y~k~t 290 (310)
T KOG3969|consen 218 RNKSREAIPQRYGV-DPDQLRMFFHYQPSYYHLHVHIVNIKHDHAPGSGCGRAILLDDVIENLELDPEGYKKST 290 (310)
T ss_pred HHHHHHHHHHHhCC-CchhEEEEEEecCceEEEEEEEEeccCCCCCCccccceeeHHHHHHHhccChHhhhhee
Confidence 55678899999999 99988764 344445999999999999998777788888755443
No 29
>KOG2116 consensus Protein involved in plasmid maintenance/nuclear protein involved in lipid metabolism [Cell motility; Lipid transport and metabolism]
Probab=31.51 E-value=76 Score=30.43 Aligned_cols=34 Identities=32% Similarity=0.505 Sum_probs=27.1
Q ss_pred HHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEee
Q 032727 44 EKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIY 79 (135)
Q Consensus 44 ~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IY 79 (135)
+.| +.||.++-.+-|+|+|-|+|+|. +-+-|+||
T Consensus 491 EQL-~sLnLk~G~N~v~FsisT~~~Gt-~~c~~~IY 524 (738)
T KOG2116|consen 491 EQL-KSLNLKDGKNDVVFSISTQYQGT-AQCEGNIY 524 (738)
T ss_pred HHH-hhcCCccCCceeEEEEEecccce-EEEeeEEE
Confidence 445 67898899999999999999864 55667777
No 30
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=31.44 E-value=69 Score=25.12 Aligned_cols=33 Identities=18% Similarity=0.366 Sum_probs=26.6
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 26 VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.++|.++| .|+..--+.|++.||. +++.++++|
T Consensus 187 ~~eI~~~g---vsKg~al~~l~~~~gi-~~~~v~afG 219 (270)
T PRK10513 187 FLEILDKR---VNKGTGVKSLAEHLGI-KPEEVMAIG 219 (270)
T ss_pred eEEEeCCC---CChHHHHHHHHHHhCC-CHHHEEEEC
Confidence 46777765 8899999999999999 777777654
No 31
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=31.41 E-value=82 Score=24.66 Aligned_cols=36 Identities=19% Similarity=0.335 Sum_probs=28.8
Q ss_pred eeeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHhCC
Q 032727 13 KFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEV 52 (135)
Q Consensus 13 k~~~N~LL~RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~ 52 (135)
.+..+-|+...++.|.|... .++.||+..+-.+|++
T Consensus 13 TEKs~~l~e~N~ytF~V~~~----anK~eIK~AVE~iF~V 48 (158)
T PRK12280 13 TEKSYSLMSKNVYTFKVDRR----ANKIEIKKAVEFIFKV 48 (158)
T ss_pred CHHHHhhhhCCEEEEEECCC----CCHHHHHHHHHHHhCC
Confidence 34456667777888888654 7899999999999999
No 32
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.31 E-value=1e+02 Score=24.87 Aligned_cols=28 Identities=25% Similarity=0.532 Sum_probs=17.7
Q ss_pred EEEEEEcC-CCCCCCHHHHH--HHHHhHhCC
Q 032727 25 FVIDVLHP-GRANVSKAELK--EKLARMYEV 52 (135)
Q Consensus 25 i~~~v~H~-g~~Tpsr~eIk--~kLA~~~~~ 52 (135)
|.+.=.|| |.++||.+|+. ..|......
T Consensus 163 vIlaHNHPSG~~~PS~~Di~~T~~l~~a~~~ 193 (218)
T TIGR00608 163 LILAHNHPSGEPSPSQEDILITERLRKAAEL 193 (218)
T ss_pred EEEEeecCCCCCCCCHHHHHHHHHHHHHHHh
Confidence 44445688 67999999764 455444433
No 33
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=30.69 E-value=68 Score=25.37 Aligned_cols=33 Identities=18% Similarity=0.270 Sum_probs=26.0
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 26 VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.++|.++| .|+..--+.|++.||+ +++.++++|
T Consensus 179 ~~eI~~~g---~sKg~al~~l~~~~gi-~~~~v~afG 211 (272)
T PRK15126 179 CLEVLPVG---CNKGAALAVLSQHLGL-SLADCMAFG 211 (272)
T ss_pred EEEeecCC---CChHHHHHHHHHHhCC-CHHHeEEec
Confidence 35677765 7899999999999999 777777654
No 34
>PF01996 F420_ligase: F420-0:Gamma-glutamyl ligase; InterPro: IPR002847 This entry contains F420-0:gamma-glutamyl ligase and related proteins. F420-0:gamma-glutamyl ligase catalyzes the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form polyglutamated F420 derivatives [, , , ].; PDB: 2G9I_A 2PHN_A.
Probab=30.00 E-value=39 Score=27.39 Aligned_cols=52 Identities=21% Similarity=0.208 Sum_probs=36.9
Q ss_pred EEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCC
Q 032727 28 DVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDS 81 (135)
Q Consensus 28 ~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds 81 (135)
.++.|..|.-|-.+|+++|.+.++. +..+||++..-+-|=.| ++|+|.=+.-
T Consensus 125 v~LlP~dPd~sA~~i~~~l~~~~g~-~v~ViI~Dt~gr~~r~G-~~~vaig~~G 176 (228)
T PF01996_consen 125 VVLLPEDPDASARRIREELKERTGK-DVGVIITDTNGRPWRLG-QTGVAIGVAG 176 (228)
T ss_dssp EE---S-HHHHHHHHHHHHHHHHS----EEEEEEEEEETTEEC-EEEEEEEEES
T ss_pred EEECCCCHHHHHHHHHHHHHHHHCC-ceEEEEECCCCcEEecC-CccchhhccC
Confidence 4677777777788999999999999 99999999888776666 8888876655
No 35
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=29.95 E-value=88 Score=23.61 Aligned_cols=33 Identities=27% Similarity=0.383 Sum_probs=23.8
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 26 VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.++|.++| .++..--..|++.++. +++.++.+|
T Consensus 140 ~~ei~~~~---~~K~~~i~~l~~~~~i-~~~~~i~~G 172 (225)
T TIGR01482 140 DIHILPQG---VNKGVAVKKLKEKLGI-KPGETLVCG 172 (225)
T ss_pred EEEEeeCC---CCHHHHHHHHHHHhCC-CHHHEEEEC
Confidence 45666654 6888888999999999 666555443
No 36
>cd00554 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits.
Probab=29.87 E-value=1e+02 Score=23.89 Aligned_cols=36 Identities=14% Similarity=0.310 Sum_probs=28.3
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 25 FVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 25 i~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
+.+.+..| +=.|=+.++++.||+.++. +.+.|-|.-
T Consensus 95 ~tii~e~P-Ki~p~~~~m~~~ls~~L~~-~~~~V~iKa 130 (153)
T cd00554 95 ITIIAERP-KISPYREAMRANLAELLGI-PPSRVNIKA 130 (153)
T ss_pred EEEEecCC-cchHHHHHHHHHHHHHhCC-CCceEEEEE
Confidence 44445555 5678899999999999999 888887753
No 37
>PRK10976 putative hydrolase; Provisional
Probab=29.86 E-value=69 Score=25.12 Aligned_cols=33 Identities=24% Similarity=0.342 Sum_probs=24.9
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 26 VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.++|.++| .|+..--+.|++.||. +++.++++|
T Consensus 181 ~~eI~~~g---vsKg~al~~l~~~lgi-~~~~viafG 213 (266)
T PRK10976 181 CLEVMAGG---VSKGHALEAVAKKLGY-SLKDCIAFG 213 (266)
T ss_pred eEEEEcCC---CChHHHHHHHHHHcCC-CHHHeEEEc
Confidence 35666654 7888899999999999 777776654
No 38
>PRK01688 histidinol-phosphate aminotransferase; Provisional
Probab=29.65 E-value=49 Score=27.38 Aligned_cols=27 Identities=19% Similarity=0.294 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
|-|.-.++++.||+.+|+ +++.|+|.+
T Consensus 55 p~~~~~~l~~~~a~~~g~-~~~~I~~~~ 81 (351)
T PRK01688 55 PECQPKAVIENYAAYAGV-KPEQVLVSR 81 (351)
T ss_pred CCCChHHHHHHHHHHhCC-CHHHEEEcC
Confidence 445668999999999999 999998855
No 39
>PF04110 APG12: Ubiquitin-like autophagy protein Apg12 ; InterPro: IPR007242 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents Apg12, which is covalently bound to Apg5 [].; GO: 0000045 autophagic vacuole assembly, 0005737 cytoplasm; PDB: 1WZ3_B.
Probab=29.62 E-value=19 Score=25.44 Aligned_cols=34 Identities=18% Similarity=0.213 Sum_probs=19.3
Q ss_pred CCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCC
Q 032727 34 RANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFG 68 (135)
Q Consensus 34 ~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG 68 (135)
.-.||-.|.-+-|...|++ +.++|+=+..-.-||
T Consensus 54 sFaPspDe~vg~L~~~f~~-~~~Liv~Ys~t~A~G 87 (87)
T PF04110_consen 54 SFAPSPDETVGDLYRCFGT-NGELIVSYSKTPAWG 87 (87)
T ss_dssp EE---TTSBHHHHHHHH-B-TTBEEEEEESSS---
T ss_pred ccCCCchhHHHHHHHHhCC-CCEEEEEEecccccC
Confidence 3567788888888888888 777776555554444
No 40
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=29.54 E-value=1.8e+02 Score=23.70 Aligned_cols=53 Identities=13% Similarity=0.257 Sum_probs=32.9
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEe-eCCHHHHH
Q 032727 27 IDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLI-YDSVENAK 86 (135)
Q Consensus 27 ~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~I-Yds~e~~k 86 (135)
+-|.+- ...-+-++|++.++ .||. =.++-++.+-. .+.+.|||.| |+|.+.|.
T Consensus 272 lfV~NL-~~~~~e~~L~~~F~-~fG~-v~~v~i~~d~~----t~~skG~aFV~F~~~~~A~ 325 (352)
T TIGR01661 272 IFVYNL-SPDTDETVLWQLFG-PFGA-VQNVKIIRDLT----TNQCKGYGFVSMTNYDEAA 325 (352)
T ss_pred EEEeCC-CCCCCHHHHHHHHH-hCCC-eEEEEEeEcCC----CCCccceEEEEECCHHHHH
Confidence 335554 24457778888885 4564 34555554433 4678899887 77777654
No 41
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=29.49 E-value=1.2e+02 Score=17.51 Aligned_cols=47 Identities=26% Similarity=0.449 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEe-eCCHHHHHhc
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLI-YDSVENAKKF 88 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~I-Yds~e~~kk~ 88 (135)
+..+..+|++.++...++ .+..+.. ...+ ...|+|.| |.|.+.+...
T Consensus 9 ~~~~~~~i~~~~~~~g~i--~~~~~~~---~~~~--~~~~~~~v~f~s~~~a~~a 56 (74)
T cd00590 9 PDVTEEDLRELFSKFGKV--ESVRIVR---DKDT--KSKGFAFVEFEDEEDAEKA 56 (74)
T ss_pred CccCHHHHHHHHHhcCCE--EEEEEee---CCCC--CcceEEEEEECCHHHHHHH
Confidence 346778999999775222 2222222 2222 56777777 6888877554
No 42
>TIGR00151 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes.
Probab=29.42 E-value=1e+02 Score=24.04 Aligned_cols=36 Identities=14% Similarity=0.217 Sum_probs=28.0
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 25 FVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 25 i~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
+.+....| +=.|=+.++++.||+.++. +++.|-|.-
T Consensus 95 ~tii~e~P-Ki~p~~~~m~~~la~~L~~-~~~~V~iKa 130 (155)
T TIGR00151 95 ITIIAQRP-KLLPHIPAMRENIAELLGI-PLDSVNVKA 130 (155)
T ss_pred EEEEcCCC-cchHHHHHHHHHHHHHhCC-CcceEEEEE
Confidence 34444455 5678899999999999999 888887754
No 43
>PRK13815 ribosome-binding factor A; Provisional
Probab=29.40 E-value=2.3e+02 Score=20.77 Aligned_cols=44 Identities=14% Similarity=0.134 Sum_probs=34.3
Q ss_pred HHHHHHHHhHh--CCCCCC--eEEEeceeecCCCCEEEEEEEeeCCHH
Q 032727 40 AELKEKLARMY--EVKDPN--AIFVFKFRTHFGGGKSTGFGLIYDSVE 83 (135)
Q Consensus 40 ~eIk~kLA~~~--~~~~~~--~IvV~~~~T~fG~~~s~g~a~IYds~e 83 (135)
++|++.||..+ ++.||. .|.|.++...=....++.|.-++.+.+
T Consensus 10 ~~Ir~eis~il~~~i~dprl~~vtVt~V~vS~Dl~~AkVyvs~~~~~~ 57 (122)
T PRK13815 10 EAIHELISGLLVKGLKDPRIGFVTITGVKVTDDLHLATIYFTVIGDDE 57 (122)
T ss_pred HHHHHHHHHHHHHhCcCCCCCceEEeEEEECCCCCEEEEEEEECCCch
Confidence 46777777775 454665 589999999999999999999997654
No 44
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=29.09 E-value=59 Score=25.36 Aligned_cols=31 Identities=16% Similarity=0.431 Sum_probs=24.9
Q ss_pred EEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEe
Q 032727 29 VLHPGRANVSKAELKEKLARMYEVKDPNAIFVF 61 (135)
Q Consensus 29 v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~ 61 (135)
...| +=.|=+.++++.||+.++. +++.|-|.
T Consensus 100 ~e~P-Ki~p~~~~m~~~la~~L~~-~~~~V~iK 130 (157)
T PF02542_consen 100 AERP-KISPYRPAMRENLAKLLGI-PPDRVNIK 130 (157)
T ss_dssp SSSS-TTGGGHHHHHHHHHHHHTS--GGGEEEE
T ss_pred cCCC-ccHHHHHHHHHHHHHHhCC-CcceEEEE
Confidence 3344 5688999999999999999 98988775
No 45
>TIGR01485 SPP_plant-cyano sucrose-6F-phosphate phosphohydrolase. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Probab=28.94 E-value=1.1e+02 Score=23.89 Aligned_cols=32 Identities=22% Similarity=0.412 Sum_probs=22.6
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 27 IDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 27 ~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
++|.++| .++.+--+.|++.++. +++.++++|
T Consensus 159 ldi~~~~---~~K~~al~~l~~~~~i-~~~~~i~~G 190 (249)
T TIGR01485 159 LDILPQG---SGKGQALQYLLQKLAM-EPSQTLVCG 190 (249)
T ss_pred EEEEeCC---CChHHHHHHHHHHcCC-CccCEEEEE
Confidence 4566654 5777778999999999 666665554
No 46
>PRK06959 putative threonine-phosphate decarboxylase; Provisional
Probab=27.08 E-value=70 Score=26.47 Aligned_cols=25 Identities=20% Similarity=0.220 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 37 VSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 37 psr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
|. .++++.||+.+++.+++.|+|.+
T Consensus 54 ~~-~~L~~~ia~~~~~~~~~~I~i~~ 78 (339)
T PRK06959 54 DD-DGLAACAARYYGAPDAAHVLPVA 78 (339)
T ss_pred ch-HHHHHHHHHHhCCCCcccEEECc
Confidence 55 89999999999994457777654
No 47
>PRK14864 putative biofilm stress and motility protein A; Provisional
Probab=26.38 E-value=2.6e+02 Score=20.33 Aligned_cols=51 Identities=8% Similarity=0.135 Sum_probs=38.6
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeC
Q 032727 26 VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYD 80 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYd 80 (135)
+|.|.|. + |-.|+.+.||+.=+........|-.....=|.+.-.|.|-||.
T Consensus 53 tVSvs~~--g--sp~d~~~~La~KAda~GA~yYrIi~~~e~~~~~~~~atA~iYk 103 (104)
T PRK14864 53 TVSALVR--G--SPDDAEREIQAKANAAGADYYVIVMVDETVVPGQWYSQAILYR 103 (104)
T ss_pred EEEEecC--C--CHHHHHHHHHHHHHHcCCCEEEEEEccccCCCCeEEEEEEEec
Confidence 6667763 3 3568888888776665667777878877677899999999995
No 48
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=26.35 E-value=76 Score=19.50 Aligned_cols=20 Identities=10% Similarity=0.219 Sum_probs=14.0
Q ss_pred HHHHHHHhHhCCCCCCeEEEe
Q 032727 41 ELKEKLARMYEVKDPNAIFVF 61 (135)
Q Consensus 41 eIk~kLA~~~~~~~~~~IvV~ 61 (135)
+|.+.|++.+++ +++.|+|.
T Consensus 23 ~it~~l~~~~~~-p~~~v~V~ 42 (61)
T PRK02220 23 DVTAAVSKNTGA-PAEHIHVI 42 (61)
T ss_pred HHHHHHHHHhCc-ChhhEEEE
Confidence 566778889999 66665553
No 49
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=26.21 E-value=2e+02 Score=18.94 Aligned_cols=23 Identities=13% Similarity=0.303 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeE
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAI 58 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~I 58 (135)
++-+-.|+++.+|+..+. +++..
T Consensus 20 ~~~TV~~LK~~I~~~~~~-~~~~q 42 (78)
T cd01804 20 PDETVEGLKKRISQRLKV-PKERL 42 (78)
T ss_pred CcCHHHHHHHHHHHHhCC-ChHHE
Confidence 456788999999999998 55543
No 50
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=26.15 E-value=43 Score=25.46 Aligned_cols=23 Identities=35% Similarity=0.673 Sum_probs=19.7
Q ss_pred CHHHHHHHHHhHhCCCCCCeEEEe
Q 032727 38 SKAELKEKLARMYEVKDPNAIFVF 61 (135)
Q Consensus 38 sr~eIk~kLA~~~~~~~~~~IvV~ 61 (135)
...+|+..||..||+ +++.|-|.
T Consensus 165 ~~~~i~~~la~~~~i-~~~~I~V~ 187 (188)
T PF09581_consen 165 EEEEIKQYLADFYGI-SPEQIKVY 187 (188)
T ss_pred HHHHHHHHHHHHhCC-CHHHeEEe
Confidence 345899999999999 99998774
No 51
>PHA01976 helix-turn-helix protein
Probab=26.11 E-value=33 Score=21.44 Aligned_cols=24 Identities=13% Similarity=-0.006 Sum_probs=16.9
Q ss_pred CCCCCCHHHHHHHHHhHhCCCCCCeE
Q 032727 33 GRANVSKAELKEKLARMYEVKDPNAI 58 (135)
Q Consensus 33 g~~Tpsr~eIk~kLA~~~~~~~~~~I 58 (135)
|...|+.. ...+||..|++ +++.+
T Consensus 38 g~~~p~~~-~l~~ia~~l~v-~~~~l 61 (67)
T PHA01976 38 DKRLPNLK-TLLRLADALGV-TLDWL 61 (67)
T ss_pred CCCCCCHH-HHHHHHHHHCc-CHHHH
Confidence 44556654 45799999999 77654
No 52
>TIGR03576 pyridox_MJ0158 pyridoxal phosphate enzyme, MJ0158 family. Members of this archaeal protein family are pyridoxal phosphate enzymes of unknown function. Sequence similarity to SelA, a bacterial enzyme of selenocysteine biosynthesis, has led to some members being misannotated as functionally equivalent, but selenocysteine is made on tRNA in Archaea by a two-step process that does not involve a SelA homolog.
Probab=25.59 E-value=63 Score=27.18 Aligned_cols=29 Identities=14% Similarity=0.114 Sum_probs=23.9
Q ss_pred CCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 33 GRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 33 g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
|+.++--.++.+.||+.+|+ +++.++|++
T Consensus 50 ~g~~~~~~~Le~~lA~~~g~-~~e~ilv~~ 78 (346)
T TIGR03576 50 VGPAIFEEKVQELGREHLGG-PEEKILVFN 78 (346)
T ss_pred cCCHHHHHHHHHHHHHHcCC-CcceEEEEC
Confidence 35667788999999999999 778888765
No 53
>PF10503 Esterase_phd: Esterase PHB depolymerase
Probab=25.47 E-value=8.2 Score=31.14 Aligned_cols=36 Identities=25% Similarity=0.431 Sum_probs=27.8
Q ss_pred CHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEE
Q 032727 38 SKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFG 76 (135)
Q Consensus 38 sr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a 76 (135)
.-.+|.+.|+..|++ |++.|+|-||.. |+..+...+
T Consensus 80 ~i~~lv~~v~~~~~i-D~~RVyv~G~S~--Gg~ma~~la 115 (220)
T PF10503_consen 80 FIAALVDYVAARYNI-DPSRVYVTGLSN--GGMMANVLA 115 (220)
T ss_pred hHHHHHHhHhhhccc-CCCceeeEEECH--HHHHHHHHH
Confidence 455778889999999 999999999987 555444333
No 54
>PF07338 DUF1471: Protein of unknown function (DUF1471); InterPro: IPR010854 This entry consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some of the proteins are annotated as ydgH precursors and contain two copies of this region, one at the N terminus and the other at the C terminus. The function of this family is unknown.; PDB: 2NOC_A 2JNA_B 4EVU_B.
Probab=25.11 E-value=1.9e+02 Score=18.37 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=32.5
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeC
Q 032727 26 VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYD 80 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYd 80 (135)
.+.|.+.. +| -.|+.++||+.=.....+...|-.+.+ .++.-.+-|-||.
T Consensus 7 ~Isvs~~~-~s--~~d~~~~la~kAd~~GA~~y~I~~~~~--~~~~~~~tA~lYk 56 (56)
T PF07338_consen 7 TISVSGNF-GS--PDDAEEALAKKADEKGAKYYRITSASE--DGNNWHATAELYK 56 (56)
T ss_dssp EEEEEEEC-SS--HHHHHHHHHHHHHHTT-SEEEEEEEEE--CSSEEEEEEEEEE
T ss_pred EEEEcccc-CC--HHHHHHHHHHHHHHcCCCEEEEEEEEc--CCCeEEEEEEEEC
Confidence 34555542 33 456666666554433447777878877 8999999999993
No 55
>PLN03026 histidinol-phosphate aminotransferase; Provisional
Probab=24.61 E-value=83 Score=26.40 Aligned_cols=26 Identities=19% Similarity=0.192 Sum_probs=21.1
Q ss_pred CCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 36 NVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 36 Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.|.-.++++.||+.+++ +++.|++..
T Consensus 85 ~~~~~~lr~~ia~~~~~-~~~~I~~t~ 110 (380)
T PLN03026 85 DPESRRLRAALAEDSGL-ESENILVGC 110 (380)
T ss_pred CCCHHHHHHHHHHHhCc-ChhhEEEcC
Confidence 35567999999999999 888887643
No 56
>COG2006 Uncharacterized conserved protein [Function unknown]
Probab=24.58 E-value=83 Score=27.05 Aligned_cols=43 Identities=23% Similarity=0.324 Sum_probs=35.6
Q ss_pred EcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEE
Q 032727 30 LHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTG 74 (135)
Q Consensus 30 ~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g 74 (135)
+|.+.+ .+....+.|+..|.+=.|++.+++++.-.=|.|-+.|
T Consensus 171 ~h~~~~--~~~~Fg~mlvei~~~~~P~ltI~Dgi~G~egNGP~~G 213 (293)
T COG2006 171 WHMEEG--DRDRFGEMLVEIYLVVKPDLTIMDGIIGMEGNGPSGG 213 (293)
T ss_pred cchhcC--chHHHHHHHHHHHhhcCCcEEEEeeeEecccCCCCCC
Confidence 454443 6778899999999977999999999999888887766
No 57
>PRK01158 phosphoglycolate phosphatase; Provisional
Probab=24.58 E-value=1e+02 Score=23.38 Aligned_cols=33 Identities=30% Similarity=0.516 Sum_probs=24.3
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 26 VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.+++.++| .|+..--+.|++.|+. +++.++++|
T Consensus 148 ~~ei~~~~---~~Kg~al~~l~~~~~i-~~~~~i~~G 180 (230)
T PRK01158 148 AIHIKSPG---VNKGTGLKKLAELMGI-DPEEVAAIG 180 (230)
T ss_pred EEEEeeCC---CChHHHHHHHHHHhCC-CHHHEEEEC
Confidence 35666654 7888888899999999 766666554
No 58
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=24.58 E-value=1.9e+02 Score=20.30 Aligned_cols=38 Identities=18% Similarity=0.165 Sum_probs=29.8
Q ss_pred HHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCCH
Q 032727 40 AELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSV 82 (135)
Q Consensus 40 ~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds~ 82 (135)
-+|-...|+.+|+.+-|.|.|.+ +.|...+.|.|-++.
T Consensus 36 v~i~p~dA~~lgi~~Gd~V~v~s-----~~g~i~~~v~i~~~v 73 (127)
T cd02777 36 VWINPLDAAARGIKDGDIVRVFN-----DRGAVLAGARVTDRI 73 (127)
T ss_pred EEECHHHHHHcCCCCCCEEEEEc-----CCeEEEEEEEECCCc
Confidence 56666889999998899998874 446788888887764
No 59
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=24.48 E-value=1e+02 Score=18.93 Aligned_cols=19 Identities=21% Similarity=0.317 Sum_probs=13.2
Q ss_pred HHHHHHHhHhCCCCCCeEEE
Q 032727 41 ELKEKLARMYEVKDPNAIFV 60 (135)
Q Consensus 41 eIk~kLA~~~~~~~~~~IvV 60 (135)
+|-+.|+..+|+ +++.++|
T Consensus 23 ~it~~l~~~lg~-~~~~v~V 41 (63)
T TIGR00013 23 GVTEAMAETLGA-NLESIVV 41 (63)
T ss_pred HHHHHHHHHhCC-CcccEEE
Confidence 566777888999 6665544
No 60
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=24.41 E-value=87 Score=19.64 Aligned_cols=20 Identities=20% Similarity=0.348 Sum_probs=14.5
Q ss_pred HHHHHHHhHhCCCCCCeEEEe
Q 032727 41 ELKEKLARMYEVKDPNAIFVF 61 (135)
Q Consensus 41 eIk~kLA~~~~~~~~~~IvV~ 61 (135)
+|-+.|+..+++ +++.|+|.
T Consensus 23 ~it~~l~~~lg~-p~~~v~V~ 42 (64)
T PRK01964 23 EVTEAISATLDV-PKERVRVI 42 (64)
T ss_pred HHHHHHHHHhCc-ChhhEEEE
Confidence 466678888999 77766653
No 61
>COG3561 Phage anti-repressor protein [Transcription]
Probab=24.30 E-value=1.5e+02 Score=22.04 Aligned_cols=59 Identities=14% Similarity=0.159 Sum_probs=46.0
Q ss_pred CCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCCHHHHHhcCCc
Q 032727 33 GRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSVENAKKFEPK 91 (135)
Q Consensus 33 g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds~e~~kk~Epk 91 (135)
|-+||+-..+++.+.+.-=+-+.|.|+|..+...|-+....+|+.--|-...+-.+||.
T Consensus 23 ~~~tr~s~wf~er~~~ygfien~d~i~~~~~~~~~~~~~~~d~~l~id~aKei~M~ern 81 (110)
T COG3561 23 DVKTRYSAWFRERISEYGFIENIDYIGCSDYGEEFSGVIGMDYALTIDMAKEIAMVERN 81 (110)
T ss_pred hccchHHHHHHHHHHhhcceeccceEEEEecccccccccccceeeeechhhhhheeccC
Confidence 56899999999888665546578899999998888877778898887776666555553
No 62
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=24.25 E-value=1.5e+02 Score=21.01 Aligned_cols=30 Identities=17% Similarity=0.130 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEeceee
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVFKFRT 65 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T 65 (135)
..|+-..++++|...|+. +++-+.|.-+..
T Consensus 18 ~~pt~~~L~~kl~~Lf~l-p~~~~~vtYiDe 47 (82)
T cd06397 18 DIPTWEALASKLENLYNL-PEIKVGVTYIDN 47 (82)
T ss_pred CCccHHHHHHHHHHHhCC-ChhHeEEEEEcC
Confidence 379999999999999999 766677766654
No 63
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.25 E-value=1.7e+02 Score=21.26 Aligned_cols=47 Identities=26% Similarity=0.335 Sum_probs=37.3
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCE
Q 032727 23 KQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGK 71 (135)
Q Consensus 23 kEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~ 71 (135)
|-+++|++-| ---|+-.|+...|++.-|+ +.=+|.|..+.-.-=+-.
T Consensus 6 RRlVLDvlKP-~~~p~ive~A~~lskl~gV-egVNItv~eiD~et~~~~ 52 (97)
T COG1888 6 RRLVLDVLKP-HRGPTIVELALELSKLEGV-EGVNITVTEIDVETENLK 52 (97)
T ss_pred eeeeeeecCC-cCCCcHHHHHHHHhhcCCc-ceEEEEEEEeeehhcceE
Confidence 3488899987 3469999999999999999 888898888765543333
No 64
>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=24.20 E-value=65 Score=20.06 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=14.4
Q ss_pred CCCCCCHHHHHHHHHhHhCCCC
Q 032727 33 GRANVSKAELKEKLARMYEVKD 54 (135)
Q Consensus 33 g~~Tpsr~eIk~kLA~~~~~~~ 54 (135)
+-.|.+..+|++.|.+.||+ |
T Consensus 17 dl~~vT~k~vr~~Le~~~~~-d 37 (54)
T PF08766_consen 17 DLDTVTKKQVREQLEERFGV-D 37 (54)
T ss_dssp -GGG--HHHHHHHHHHH-SS--
T ss_pred CHhHhhHHHHHHHHHHHHCC-C
Confidence 44688999999999999998 5
No 65
>PRK05387 histidinol-phosphate aminotransferase; Provisional
Probab=24.19 E-value=69 Score=26.02 Aligned_cols=25 Identities=28% Similarity=0.557 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 37 VSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 37 psr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
|.-.++++.||+.|++ +++.|+|..
T Consensus 60 ~~~~~lr~aia~~~~~-~~~~I~it~ 84 (353)
T PRK05387 60 PNADALRQAIAAYYGL-DPEQVFVGN 84 (353)
T ss_pred CcHHHHHHHHHHHhCC-CHHHEEEcC
Confidence 3457999999999999 888888765
No 66
>PRK04781 histidinol-phosphate aminotransferase; Provisional
Probab=24.15 E-value=72 Score=26.54 Aligned_cols=26 Identities=19% Similarity=0.450 Sum_probs=21.3
Q ss_pred CCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 36 NVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 36 Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.|.-.++++.||+.+++ +++.|++..
T Consensus 58 ~~~~~~lr~~ia~~~~~-~~~~I~~t~ 83 (364)
T PRK04781 58 DPQPPGLRSALAALYGC-APEQLLIGR 83 (364)
T ss_pred CCCHHHHHHHHHHHhCc-ChHHEEEeC
Confidence 45568999999999999 888887744
No 67
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=24.14 E-value=2e+02 Score=25.21 Aligned_cols=53 Identities=26% Similarity=0.380 Sum_probs=37.7
Q ss_pred EEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEe-eCCHHHHH
Q 032727 24 QFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLI-YDSVENAK 86 (135)
Q Consensus 24 Ei~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~I-Yds~e~~k 86 (135)
=++..+.|. -+-.+|+..+ ..||- =..+.+|.+..| |++.|||.| |...-.|+
T Consensus 104 LFv~RLnyd----T~EskLrreF-~~YG~-IkrirlV~d~vT----gkskGYAFIeye~erdm~ 157 (335)
T KOG0113|consen 104 LFVARLNYD----TSESKLRREF-EKYGP-IKRIRLVRDKVT----GKSKGYAFIEYEHERDMK 157 (335)
T ss_pred eeeeecccc----ccHHHHHHHH-HhcCc-ceeEEEeeeccc----CCccceEEEEeccHHHHH
Confidence 345556665 3456788888 56675 588999999998 678899987 66665554
No 68
>PF03090 Replicase: Replicase family; InterPro: IPR004322 This is a family of bacterial plasmid DNA replication initiator proteins. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or may be mediated by Hsp70 chaperones. A similar RepA family of proteins found mainly in Escherichia coli is involved in plasmid replication (see IPR000525 from INTERPRO).
Probab=24.08 E-value=1.4e+02 Score=22.49 Aligned_cols=40 Identities=25% Similarity=0.200 Sum_probs=25.3
Q ss_pred eeeccCccceEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEE
Q 032727 14 FMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFV 60 (135)
Q Consensus 14 ~~~N~LL~RkEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV 60 (135)
..-||..-+.-|+|||.|++. .. .-.-...+.+.|..|++
T Consensus 17 Iq~N~~~~~~~lV~DiD~~~~-----~~--~~~w~~~~lp~Pn~i~~ 56 (137)
T PF03090_consen 17 IQLNPPQYVNWLVFDIDHPGA-----AL--ALAWEDEGLPPPNWIVI 56 (137)
T ss_pred eeeCChhhEEEEEEECCCCCc-----hh--hHHHHhcCCCCCeEEEE
Confidence 345887778889999999964 11 11223445645666665
No 69
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=24.03 E-value=1.5e+02 Score=25.67 Aligned_cols=46 Identities=15% Similarity=0.237 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEe-eCCHHHHH
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLI-YDSVENAK 86 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~I-Yds~e~~k 86 (135)
.+.+-++|++.+. .||. =..+.++... ..|.+.|||.| |.+.+.+.
T Consensus 305 ~~~~~~~l~~~f~-~~G~-i~~~~~~~~~----~~g~~~g~afv~f~~~~~a~ 351 (509)
T TIGR01642 305 LYLGEDQIKELLE-SFGD-LKAFNLIKDI----ATGLSKGYAFCEYKDPSVTD 351 (509)
T ss_pred CCCCHHHHHHHHH-hcCC-eeEEEEEecC----CCCCcCeEEEEEECCHHHHH
Confidence 3567788888775 4554 2344444433 34667788887 77766653
No 70
>PF02594 DUF167: Uncharacterised ACR, YggU family COG1872; InterPro: IPR003746 This entry describes proteins of unknown function. Structures for two of these proteins, YggU from Escherichia coli and MTH637 from the archaea Methanobacterium thermoautotrophicum, have been determined; they have a core 2-layer alpha/beta structure consisting of beta(2)-loop-alpha-beta(2)-alpha [, ].; PDB: 1YH5_A 1N91_A 1JRM_A.
Probab=23.11 E-value=1.2e+02 Score=20.56 Aligned_cols=43 Identities=19% Similarity=0.146 Sum_probs=25.4
Q ss_pred eEEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEeceee
Q 032727 23 KQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRT 65 (135)
Q Consensus 23 kEi~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~T 65 (135)
.++.+.|..|-.--=.-+++.+-||+.|+++..+.-++.|-.+
T Consensus 26 ~~l~i~v~app~~GkAN~ali~~La~~l~v~ks~i~i~~G~~S 68 (77)
T PF02594_consen 26 GALKIRVTAPPVDGKANKALIRFLAKALGVPKSDIEIVSGHTS 68 (77)
T ss_dssp T-EEEEBSTTCCCCCHHHHHHHHHHHHCT--TTCEEECC-CCC
T ss_pred eEEEEEEecCCCcChhHHHHHHHHHHHhCCCcccEEEEecCCC
Confidence 3456666655222233569999999999996666666665443
No 71
>PRK07392 threonine-phosphate decarboxylase; Validated
Probab=22.81 E-value=88 Score=25.75 Aligned_cols=25 Identities=24% Similarity=0.202 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 37 VSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 37 psr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
|.-.++++.||+.|++ +++.|+|..
T Consensus 57 ~~~~~Lr~aia~~~~v-~~~~I~it~ 81 (360)
T PRK07392 57 PDYRELRLALAQHHQL-PPEWILPGN 81 (360)
T ss_pred cCHHHHHHHHHHHhCc-ChhhEEECC
Confidence 4456999999999999 889888765
No 72
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=22.49 E-value=1e+02 Score=19.94 Aligned_cols=27 Identities=4% Similarity=0.138 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEe
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVF 61 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~ 61 (135)
++-+-.+|++.|++..|++..++.+++
T Consensus 18 ~~~TV~~lK~~I~~~~gip~~~q~Li~ 44 (71)
T cd01796 18 PDLELENFKALCEAESGIPASQQQLIY 44 (71)
T ss_pred CcCCHHHHHHHHHHHhCCCHHHeEEEE
Confidence 457788999999999999444444444
No 73
>PRK00024 hypothetical protein; Reviewed
Probab=22.45 E-value=1.6e+02 Score=23.63 Aligned_cols=36 Identities=19% Similarity=0.467 Sum_probs=20.6
Q ss_pred EEEEEEcC-CCCCCCHHHHH--HHHH---hHhCCCCCCeEEE
Q 032727 25 FVIDVLHP-GRANVSKAELK--EKLA---RMYEVKDPNAIFV 60 (135)
Q Consensus 25 i~~~v~H~-g~~Tpsr~eIk--~kLA---~~~~~~~~~~IvV 60 (135)
|.+.=.|| |.++||.+|+. ..|+ +++++.=-|-|||
T Consensus 169 iIl~HNHPSG~~~PS~~D~~~T~~l~~a~~~l~I~llDHiIv 210 (224)
T PRK00024 169 LILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIII 210 (224)
T ss_pred eEEEecCCCCCCCCCHHHHHHHHHHHHHHHhCCCEEeeEEEE
Confidence 34445688 57899999764 3444 4555422334444
No 74
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=22.42 E-value=1.2e+02 Score=18.27 Aligned_cols=19 Identities=16% Similarity=0.303 Sum_probs=12.5
Q ss_pred HHHHHHHhHhCCCCCCeEEE
Q 032727 41 ELKEKLARMYEVKDPNAIFV 60 (135)
Q Consensus 41 eIk~kLA~~~~~~~~~~IvV 60 (135)
+|.+.|++.+++ +++.++|
T Consensus 22 ~i~~~l~~~~g~-~~~~v~V 40 (58)
T cd00491 22 RVTEAVSEILGA-PEATIVV 40 (58)
T ss_pred HHHHHHHHHhCc-CcccEEE
Confidence 466667778888 5555544
No 75
>TIGR01484 HAD-SF-IIB HAD-superfamily hydrolase, subfamily IIB. The IIB subfamily consists of Trehalose-6-phosphatase (TIGR00685), plant and cyanobacterial Sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase (pfam03332), a large subfamily ("Cof-like hydrolases", TIGR00099) containing many closely related bacterial sequences, a hypothetical equivalog containing the E. coli YedP protein, as well as two small clusters containing sequences whose relationship to the other groups is unclear.
Probab=22.40 E-value=1.4e+02 Score=22.22 Aligned_cols=33 Identities=24% Similarity=0.370 Sum_probs=23.9
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 26 VIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 26 ~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.++|.++| .++.+.-+.|++.++. +++.++++|
T Consensus 154 ~~ev~p~~---~~K~~~~~~~~~~~~~-~~~~~~~~G 186 (204)
T TIGR01484 154 DLEVLPAG---VDKGSALQALLKELNG-KRDEILAFG 186 (204)
T ss_pred EEEEecCC---CChHHHHHHHHHHhCC-CHHHEEEEc
Confidence 44565543 7888899999999998 766666553
No 76
>PLN02862 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Probab=22.25 E-value=1.4e+02 Score=24.51 Aligned_cols=36 Identities=14% Similarity=0.339 Sum_probs=27.9
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 25 FVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 25 i~~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
+.+....| +=.|=+.++++.||+.+++ +++.|-|.-
T Consensus 155 ~tII~q~P-Ki~p~~~~m~~~La~lL~i-~~~~VnIKA 190 (216)
T PLN02862 155 ATLILQRP-KLSPHKEAIRSNLSKLLGA-DPSVVNLKA 190 (216)
T ss_pred EEEEcCCC-cchHHHHHHHHHHHHHhCC-CcceEEEEE
Confidence 33444455 5678999999999999999 888887754
No 77
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=22.20 E-value=1.1e+02 Score=22.03 Aligned_cols=29 Identities=28% Similarity=0.527 Sum_probs=14.6
Q ss_pred EEEEEEEcC-CCCCCCHHHHH-----HHHHhHhCC
Q 032727 24 QFVIDVLHP-GRANVSKAELK-----EKLARMYEV 52 (135)
Q Consensus 24 Ei~~~v~H~-g~~Tpsr~eIk-----~kLA~~~~~ 52 (135)
-+.+.=.|| |.++||.+|+. ...++.+++
T Consensus 67 ~vIl~HNHPsG~~~PS~~D~~~T~~L~~~~~~l~I 101 (123)
T PF04002_consen 67 SVILAHNHPSGDPEPSDADIALTRRLKKAARLLGI 101 (123)
T ss_dssp EEEEEEE-TTS--S--HHHHHHHHHHHHHHHHHT-
T ss_pred eEEEEEEcCCCCCCCCHhHHHHHHHHHHHHHHcCC
Confidence 355666788 57899999873 344555665
No 78
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=22.01 E-value=1.5e+02 Score=18.63 Aligned_cols=22 Identities=14% Similarity=0.256 Sum_probs=18.1
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCe
Q 032727 35 ANVSKAELKEKLARMYEVKDPNA 57 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~ 57 (135)
++-+-.+|+++|++..++ +++.
T Consensus 19 ~~~tv~~lK~~i~~~~g~-~~~~ 40 (76)
T cd01806 19 PTDKVERIKERVEEKEGI-PPQQ 40 (76)
T ss_pred CCCCHHHHHHHHhHhhCC-Chhh
Confidence 556789999999999999 5553
No 79
>PRK14807 histidinol-phosphate aminotransferase; Provisional
Probab=21.98 E-value=1.1e+02 Score=25.07 Aligned_cols=26 Identities=38% Similarity=0.553 Sum_probs=21.0
Q ss_pred CCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 36 NVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 36 Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
.|.-.++++.||+.+++ +++.|+|.+
T Consensus 58 ~~~~~~lr~~ia~~~~~-~~~~i~it~ 83 (351)
T PRK14807 58 DPTAEKLREELARYCSV-VPTNIFVGN 83 (351)
T ss_pred CccHHHHHHHHHHHhCC-CcccEEEec
Confidence 35567999999999999 888777654
No 80
>COG0561 Cof Predicted hydrolases of the HAD superfamily [General function prediction only]
Probab=21.96 E-value=1.1e+02 Score=23.89 Aligned_cols=31 Identities=26% Similarity=0.500 Sum_probs=24.4
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHhCCCCCCeEEEe
Q 032727 27 IDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVF 61 (135)
Q Consensus 27 ~~v~H~g~~Tpsr~eIk~kLA~~~~~~~~~~IvV~ 61 (135)
++|.+.| .|+..--..|++.|+. +++.|+.|
T Consensus 181 lei~~~g---~~K~~al~~l~~~lgi-~~~~v~af 211 (264)
T COG0561 181 LDITPKG---VSKGYALQRLAKLLGI-KLEEVIAF 211 (264)
T ss_pred EEEecCC---CchHHHHHHHHHHhCC-CHHHeEEe
Confidence 5666665 7899999999999999 66666655
No 81
>PF00388 PI-PLC-X: Phosphatidylinositol-specific phospholipase C, X domain This entry is for the whole phospholipase C protein; InterPro: IPR000909 Phosphatidylinositol-specific phospholipase C (3.1.4.11 from EC), a eukaryotic intracellular enzyme, plays an important role in signal transduction processes []. It catalyzes the hydrolysis of 1-phosphatidyl-D-myo-inositol-3,4,5-triphosphate into the second messenger molecules diacylglycerol and inositol-1,4,5-triphosphate. This catalytic process is tightly regulated by reversible phosphorylation and binding of regulatory proteins [, , ]. In mammals, there are at least 6 different isoforms of PI-PLC, they differ in their domain structure, their regulation, and their tissue distribution. Lower eukaryotes also possess multiple isoforms of PI-PLC. All eukaryotic PI-PLCs contain two regions of homology, sometimes referred to as the 'X-box' and 'Y-box'. The order of these two regions is always the same (NH2-X-Y-COOH), but the spacing is variable. In most isoforms, the distance between these two regions is only 50-100 residues but in the gamma isoforms one PH domain, two SH2 domains, and one SH3 domain are inserted between the two PLC-specific domains. The two conserved regions have been shown to be important for the catalytic activity. By profile analysis, we could show that sequences with significant similarity to the X-box domain occur also in prokaryotic and trypanosome PI-specific phospholipases C. Apart from this region, the prokaryotic enzymes show no similarity to their eukaryotic counterparts.; GO: 0004629 phospholipase C activity, 0006629 lipid metabolic process, 0035556 intracellular signal transduction; PDB: 2FJU_B 2ZKM_X 3V18_A 3V1H_A 3V16_A 3QR1_D 3EA3_A 3EA1_A 2OR2_A 1T6M_B ....
Probab=21.72 E-value=2.3e+02 Score=20.56 Aligned_cols=42 Identities=7% Similarity=0.222 Sum_probs=32.8
Q ss_pred EEEEcCCCCC--CCHHHHHHHHHhHhCCCCCCeEEEeceeecCCC
Q 032727 27 IDVLHPGRAN--VSKAELKEKLARMYEVKDPNAIFVFKFRTHFGG 69 (135)
Q Consensus 27 ~~v~H~g~~T--psr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~ 69 (135)
+.|.|-.-.+ .+-.+|.+.+..-+.. .|+.+||-.|+.+++.
T Consensus 55 ~~v~Hg~~~~~~~~~~dvL~~i~~fl~~-~p~E~VIl~~~~~~~~ 98 (146)
T PF00388_consen 55 LVVYHGITSTSGITFEDVLNDIRDFLFE-HPSEPVILSLKHEYSP 98 (146)
T ss_dssp EEEEETTSEE-EEEHHHHHHHHHHHTTH-STTS-EEEEEEEESTH
T ss_pred eEEEeCCEeeeeEeHHHHHHHHHHHHhc-CCCeEEEEEeecccch
Confidence 6789943332 5788999999999998 8899999999988754
No 82
>PRK10259 hypothetical protein; Provisional
Probab=21.23 E-value=2.8e+02 Score=19.49 Aligned_cols=40 Identities=20% Similarity=0.235 Sum_probs=29.3
Q ss_pred CHHHHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeC
Q 032727 38 SKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYD 80 (135)
Q Consensus 38 sr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYd 80 (135)
+-.|+.++||+.=.....+...|-.. .|.+.-.|-|-||.
T Consensus 47 s~~d~~~~La~KAd~~GA~~YrIi~a---~~~n~~~~tA~iYk 86 (86)
T PRK10259 47 TLDALEAKLAEKAAAAGASGYSITSA---TNNNKLSGTAVIYK 86 (86)
T ss_pred CHHHHHHHHHHHHHHcCCCEEEEEEe---cCCCcEEEEEEEeC
Confidence 44899999988766545565555554 56688999999994
No 83
>PRK14809 histidinol-phosphate aminotransferase; Provisional
Probab=21.06 E-value=1.2e+02 Score=24.87 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 37 VSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 37 psr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
+.-.++++.||+.+++ +++.|+|..
T Consensus 65 ~~~~~lr~~ia~~~~~-~~~~I~it~ 89 (357)
T PRK14809 65 ASHADLTAALADRWDV-SPEQVWLAN 89 (357)
T ss_pred CCHHHHHHHHHHHhCC-CcceEEECC
Confidence 4567999999999999 888887653
No 84
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=21.05 E-value=1.1e+02 Score=21.46 Aligned_cols=23 Identities=26% Similarity=0.232 Sum_probs=20.6
Q ss_pred EcCCCCCCCHHHHHHHHHhHhCC
Q 032727 30 LHPGRANVSKAELKEKLARMYEV 52 (135)
Q Consensus 30 ~H~g~~Tpsr~eIk~kLA~~~~~ 52 (135)
.|||-++||.+-|...|+..+..
T Consensus 42 ~yp~i~~Ps~e~l~~~L~~Li~e 64 (80)
T PF10264_consen 42 HYPGIAIPSQEVLYNTLGTLIKE 64 (80)
T ss_pred hCCCCCCCCHHHHHHHHHHHHHc
Confidence 47899999999999999998776
No 85
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.84 E-value=2.1e+02 Score=19.42 Aligned_cols=37 Identities=22% Similarity=0.170 Sum_probs=27.4
Q ss_pred HHHHHHHhHhCCCCCCeEEEeceeecCCCCEEEEEEEeeCCH
Q 032727 41 ELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSTGFGLIYDSV 82 (135)
Q Consensus 41 eIk~kLA~~~~~~~~~~IvV~~~~T~fG~~~s~g~a~IYds~ 82 (135)
.|-..-|+.+|+.+-|.|.|++ +.|...+.|.|-++.
T Consensus 38 ~inp~dA~~lgi~~Gd~V~v~~-----~~G~~~~~v~~~~~i 74 (120)
T cd00508 38 EIHPEDAARLGIKDGDLVRVSS-----RRGSVVVRARVTDRV 74 (120)
T ss_pred EECHHHHHHcCCCCCCEEEEEe-----CCEEEEEEEEECCCc
Confidence 3444578999998999998885 445777777776654
No 86
>PRK04635 histidinol-phosphate aminotransferase; Provisional
Probab=20.64 E-value=93 Score=25.63 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=21.1
Q ss_pred CCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 37 VSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 37 psr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
|.-.++++.||+.+++ +++.|+|..
T Consensus 60 ~~~~~Lr~aia~~~~~-~~~~I~it~ 84 (354)
T PRK04635 60 CQPPELINAYSAYAGV-APEQILTSR 84 (354)
T ss_pred CCHHHHHHHHHHHhCc-CHHHEEEeC
Confidence 3457999999999999 999888754
No 87
>TIGR01141 hisC histidinol-phosphate aminotransferase. Histidinol-phosphate aminotransferase is a pyridoxal-phosphate dependent enzyme.
Probab=20.33 E-value=1e+02 Score=24.91 Aligned_cols=27 Identities=41% Similarity=0.591 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 35 ANVSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 35 ~Tpsr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
+.|.-.++++.||+.+++ +++.|++..
T Consensus 52 ~~~~~~~lr~~ia~~~~~-~~~~i~~~~ 78 (346)
T TIGR01141 52 PDPDPAELKQALADYYGV-DPEQILLGN 78 (346)
T ss_pred CCCCHHHHHHHHHHHhCc-ChHHEEEcC
Confidence 345568999999999998 777776643
No 88
>PRK06358 threonine-phosphate decarboxylase; Provisional
Probab=20.23 E-value=1.1e+02 Score=25.29 Aligned_cols=25 Identities=16% Similarity=0.288 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 37 VSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 37 psr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
|.-.++++.||+.+++ +++.|++..
T Consensus 54 ~~~~~lr~~ia~~~~~-~~~~i~it~ 78 (354)
T PRK06358 54 PDYLELRKRIASFEQL-DLENVILGN 78 (354)
T ss_pred ccHHHHHHHHHHHhCC-ChhhEEECC
Confidence 4557999999999999 888887754
No 89
>COG4900 Predicted metallopeptidase [General function prediction only]
Probab=20.21 E-value=1.8e+02 Score=22.09 Aligned_cols=56 Identities=13% Similarity=0.170 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHhHhCCCCCCeEEEeceeecCC-CCEEEEEEEeeCCHHH---HHhcCCcchhh
Q 032727 37 VSKAELKEKLARMYEVKDPNAIFVFKFRTHFG-GGKSTGFGLIYDSVEN---AKKFEPKYRLI 95 (135)
Q Consensus 37 psr~eIk~kLA~~~~~~~~~~IvV~~~~T~fG-~~~s~g~a~IYds~e~---~kk~Epk~~l~ 95 (135)
|+-++.-+-+.-.+|. |.|++..+..-|- +..|.++|.||..+.. +--++|-|++.
T Consensus 7 ~dve~~~~~~V~~lgL---dyi~~~rv~vVys~gS~~~A~ARIwg~pki~~e~lglnP~YviE 66 (133)
T COG4900 7 ADVEADIKNAVVRLGL---DYIFQVRVVVVYSPGSHSKAVARIWGIPKIFQEVLGLNPVYVIE 66 (133)
T ss_pred ccHHHHHHHHHHHhCc---ceeeeeeEEEEECCCCcceehhhhhcccHHHHHHhCCCCeeeee
Confidence 4445444445566777 6777777766554 3478999999998654 44678988764
No 90
>PRK08056 threonine-phosphate decarboxylase; Provisional
Probab=20.10 E-value=99 Score=25.48 Aligned_cols=25 Identities=28% Similarity=0.248 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHhHhCCCCCCeEEEec
Q 032727 37 VSKAELKEKLARMYEVKDPNAIFVFK 62 (135)
Q Consensus 37 psr~eIk~kLA~~~~~~~~~~IvV~~ 62 (135)
+.-.++++.||+.|++ +++.|++..
T Consensus 55 ~~~~~lr~~ia~~~~~-~~~~i~it~ 79 (356)
T PRK08056 55 VEYRHLHQALARHHQV-PASWILAGN 79 (356)
T ss_pred ccHHHHHHHHHHHhCc-ChhhEEECC
Confidence 4568999999999999 888887643
No 91
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=20.09 E-value=1.7e+02 Score=23.83 Aligned_cols=31 Identities=10% Similarity=0.232 Sum_probs=27.4
Q ss_pred CCCCCHHHHHHHHHhHhCCCCCCeEEEecee
Q 032727 34 RANVSKAELKEKLARMYEVKDPNAIFVFKFR 64 (135)
Q Consensus 34 ~~Tpsr~eIk~kLA~~~~~~~~~~IvV~~~~ 64 (135)
+.-|||.+.-..|++.+....+|+|++-|+-
T Consensus 59 k~~~~r~~~d~~l~~~l~~~~~dlvvLAGyM 89 (200)
T COG0299 59 KEFPSREAFDRALVEALDEYGPDLVVLAGYM 89 (200)
T ss_pred ccCCCHHHHHHHHHHHHHhcCCCEEEEcchH
Confidence 5789999999999999998899999997753
Done!