Query 035824
Match_columns 121
No_of_seqs 120 out of 632
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:45:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035824hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10343 RNA-binding protein Y 100.0 4.4E-36 9.5E-41 209.6 12.4 87 31-118 2-88 (97)
2 TIGR00253 RNA_bind_YhbY putati 100.0 1.8E-35 4E-40 205.7 12.4 86 32-118 1-86 (95)
3 PF01985 CRS1_YhbY: CRS1 / Yhb 100.0 6.7E-34 1.4E-38 192.9 10.8 84 32-116 1-84 (84)
4 COG1534 Predicted RNA-binding 100.0 1.2E-33 2.6E-38 197.0 11.5 86 31-117 1-86 (97)
5 KOG1990 Poly(A)-specific exori 99.4 1.5E-13 3.4E-18 119.8 5.0 120 2-121 352-476 (564)
6 KOG1990 Poly(A)-specific exori 98.1 3.4E-06 7.4E-11 74.1 4.5 116 5-121 148-266 (564)
7 PF04472 DUF552: Protein of un 75.4 19 0.00041 23.1 6.6 55 63-119 12-69 (73)
8 PF13604 AAA_30: AAA domain; P 70.0 39 0.00084 25.4 7.8 69 31-104 1-71 (196)
9 PF11272 DUF3072: Protein of u 68.9 3.9 8.5E-05 26.1 1.8 19 30-48 14-32 (57)
10 PF03641 Lysine_decarbox: Poss 68.8 8.2 0.00018 27.5 3.7 34 40-73 76-110 (133)
11 TIGR03471 HpnJ hopanoid biosyn 60.4 86 0.0019 26.7 9.0 58 4-67 260-317 (472)
12 PF15337 Vasculin: Vascular pr 58.6 13 0.00027 26.2 3.0 62 5-70 10-71 (97)
13 COG1576 Uncharacterized conser 53.1 34 0.00075 25.9 4.8 65 5-72 55-123 (155)
14 COG0274 DeoC Deoxyribose-phosp 50.1 53 0.0012 26.3 5.7 67 40-106 87-159 (228)
15 PF10369 ALS_ss_C: Small subun 48.4 56 0.0012 21.2 4.7 35 75-114 6-40 (75)
16 cd05795 Ribosomal_P0_L10e Ribo 47.8 46 0.00099 24.9 4.8 34 39-72 9-42 (175)
17 PRK05904 coproporphyrinogen II 47.7 1.3E+02 0.0029 24.8 7.9 57 7-67 75-133 (353)
18 PRK05799 coproporphyrinogen II 46.7 1.2E+02 0.0026 24.8 7.5 57 8-67 71-129 (374)
19 TIGR00730 conserved hypothetic 46.7 32 0.0007 26.0 3.8 33 40-72 119-151 (178)
20 PRK13347 coproporphyrinogen II 46.6 1.4E+02 0.003 25.5 8.1 37 28-67 146-182 (453)
21 PRK08599 coproporphyrinogen II 46.5 1.3E+02 0.0028 24.7 7.7 57 5-66 68-129 (377)
22 cd00379 Ribosomal_L10_P0 Ribos 46.5 1E+02 0.0022 21.8 6.7 30 31-60 27-56 (155)
23 TIGR01305 GMP_reduct_1 guanosi 46.3 1.8E+02 0.0039 24.7 8.5 77 32-111 78-158 (343)
24 TIGR01211 ELP3 histone acetylt 45.1 1.3E+02 0.0029 26.7 7.8 36 28-66 200-235 (522)
25 PRK04019 rplP0 acidic ribosoma 45.0 69 0.0015 26.5 5.8 47 36-84 11-57 (330)
26 PF00466 Ribosomal_L10: Riboso 43.7 57 0.0012 21.6 4.3 75 38-117 11-85 (100)
27 PF11072 DUF2859: Protein of u 43.5 82 0.0018 23.4 5.5 54 37-92 54-107 (142)
28 TIGR03015 pepcterm_ATPase puta 43.4 1.4E+02 0.0031 22.6 7.0 82 19-101 11-97 (269)
29 PF04391 DUF533: Protein of un 43.0 33 0.00072 26.5 3.4 31 30-69 156-186 (188)
30 smart00084 NMU Neuromedin U. N 42.6 18 0.0004 19.5 1.4 12 109-120 15-26 (26)
31 PF06816 NOD: NOTCH protein; 42.5 4.8 0.0001 25.5 -1.1 28 29-56 17-44 (57)
32 PRK05580 primosome assembly pr 42.5 2.6E+02 0.0057 25.3 10.0 78 28-107 141-222 (679)
33 PRK08207 coproporphyrinogen II 42.3 1.8E+02 0.0038 25.5 8.1 37 28-67 263-299 (488)
34 PRK06582 coproporphyrinogen II 42.3 1.7E+02 0.0036 24.6 7.8 36 28-66 105-140 (390)
35 TIGR01125 MiaB-like tRNA modif 42.1 1.6E+02 0.0034 24.8 7.6 60 6-66 203-263 (430)
36 PRK05660 HemN family oxidoredu 41.6 1.9E+02 0.0042 24.0 8.0 57 6-66 76-136 (378)
37 cd05797 Ribosomal_L10 Ribosoma 41.6 1.3E+02 0.0029 21.6 6.7 55 6-64 8-62 (157)
38 COG1799 Uncharacterized protei 41.4 76 0.0017 24.3 5.1 55 63-119 87-144 (167)
39 COG3453 Uncharacterized protei 40.9 1.2E+02 0.0027 22.3 5.9 54 30-84 44-98 (130)
40 PRK14327 (dimethylallyl)adenos 40.7 2E+02 0.0044 25.3 8.3 57 7-67 282-341 (509)
41 COG1098 VacB Predicted RNA bin 40.6 27 0.00059 25.7 2.5 27 58-84 38-64 (129)
42 PF04019 DUF359: Protein of un 40.6 1.1E+02 0.0024 22.0 5.6 48 55-104 43-90 (121)
43 PRK08208 coproporphyrinogen II 40.4 1.9E+02 0.0041 24.5 7.9 36 28-66 135-170 (430)
44 PRK09249 coproporphyrinogen II 40.3 2.2E+02 0.0047 24.2 8.3 57 6-66 120-180 (453)
45 TIGR00539 hemN_rel putative ox 40.2 1.7E+02 0.0037 24.0 7.4 36 28-66 94-129 (360)
46 PRK00099 rplJ 50S ribosomal pr 40.2 1.5E+02 0.0032 21.8 6.8 35 30-64 29-63 (172)
47 PRK07379 coproporphyrinogen II 39.5 2.3E+02 0.005 23.8 9.7 57 7-66 85-144 (400)
48 PF02070 NMU: Neuromedin U; I 38.7 25 0.00055 18.8 1.5 17 100-119 9-25 (25)
49 PRK08898 coproporphyrinogen II 38.7 2.3E+02 0.0051 23.6 8.2 36 28-66 116-151 (394)
50 cd05796 Ribosomal_P0_like Ribo 37.8 94 0.002 22.9 5.1 31 42-72 12-42 (163)
51 PRK05628 coproporphyrinogen II 37.6 2.3E+02 0.005 23.3 7.9 58 6-66 77-137 (375)
52 TIGR01754 flav_RNR ribonucleot 36.2 1.5E+02 0.0032 20.7 7.4 67 31-97 65-138 (140)
53 PF01918 Alba: Alba; InterPro 36.2 1.1E+02 0.0023 19.0 6.1 57 50-106 2-63 (70)
54 PF08572 PRP3: pre-mRNA proces 35.7 40 0.00087 26.7 2.9 18 28-45 137-154 (223)
55 TIGR02026 BchE magnesium-proto 35.5 2.9E+02 0.0063 23.8 8.8 59 5-66 255-316 (497)
56 TIGR00538 hemN oxygen-independ 35.4 2.6E+02 0.0057 23.7 8.1 57 6-66 120-180 (455)
57 PRK11608 pspF phage shock prot 35.3 2E+02 0.0043 23.3 7.1 52 34-85 16-70 (326)
58 PRK14334 (dimethylallyl)adenos 35.2 2.8E+02 0.0061 23.5 8.5 57 7-67 207-266 (440)
59 PLN02759 Formate--tetrahydrofo 35.1 26 0.00057 32.0 2.0 100 10-114 194-335 (637)
60 PRK09057 coproporphyrinogen II 35.1 2.4E+02 0.0053 23.3 7.7 56 7-66 74-133 (380)
61 TIGR00696 wecB_tagA_cpsF bacte 35.0 1.8E+02 0.0038 21.9 6.2 62 39-104 40-104 (177)
62 PLN02561 triosephosphate isome 34.4 2E+02 0.0043 23.1 6.8 64 36-99 111-193 (253)
63 PF11623 DUF3252: Protein of u 34.1 34 0.00074 21.5 1.8 18 103-120 23-41 (53)
64 PRK08446 coproporphyrinogen II 33.6 2.6E+02 0.0056 22.9 7.5 57 7-67 70-128 (350)
65 PRK09423 gldA glycerol dehydro 33.6 1.8E+02 0.0039 23.9 6.6 68 36-107 21-91 (366)
66 cd08170 GlyDH Glycerol dehydro 33.4 2.1E+02 0.0045 23.3 6.9 67 39-109 17-86 (351)
67 TIGR03765 ICE_PFL_4695 integra 32.7 1.7E+02 0.0037 20.8 5.4 47 45-91 22-68 (105)
68 PRK14566 triosephosphate isome 32.5 2.6E+02 0.0056 22.7 7.1 76 38-117 120-219 (260)
69 TIGR01212 radical SAM protein, 31.8 2.7E+02 0.0059 22.4 8.2 85 28-117 117-220 (302)
70 TIGR03820 lys_2_3_AblA lysine- 31.1 3.5E+02 0.0076 23.4 8.1 85 26-119 163-259 (417)
71 PRK10674 deoxyribodipyrimidine 30.7 2.6E+02 0.0055 24.1 7.2 68 39-112 65-134 (472)
72 PRK07315 fructose-bisphosphate 30.2 66 0.0014 26.2 3.4 50 31-85 187-236 (293)
73 PF11608 Limkain-b1: Limkain b 29.9 1.1E+02 0.0023 21.3 3.9 29 85-114 16-44 (90)
74 PF09837 DUF2064: Uncharacteri 29.6 1.3E+02 0.0028 21.2 4.5 47 30-76 43-91 (122)
75 KOG2335 tRNA-dihydrouridine sy 29.5 1.2E+02 0.0027 25.9 5.0 52 58-112 128-179 (358)
76 PRK14862 rimO ribosomal protei 28.9 2.6E+02 0.0055 23.8 6.9 60 5-67 216-275 (440)
77 PTZ00135 60S acidic ribosomal 28.8 1.4E+02 0.0031 24.6 5.2 33 40-72 17-49 (310)
78 PF14532 Sigma54_activ_2: Sigm 28.5 1.1E+02 0.0024 21.1 4.0 63 35-104 9-74 (138)
79 PRK05283 deoxyribose-phosphate 28.4 1.7E+02 0.0036 23.8 5.4 75 35-109 88-169 (257)
80 PF03808 Glyco_tran_WecB: Glyc 28.3 2.3E+02 0.0051 20.7 5.9 63 38-104 39-105 (172)
81 cd08616 PI-PLCXD1c Catalytic d 28.0 3E+02 0.0066 22.2 6.9 47 58-104 98-149 (290)
82 cd02639 R3H_RRM R3H domain of 27.8 52 0.0011 20.9 1.9 20 29-48 23-42 (60)
83 PTZ00333 triosephosphate isome 27.6 3.2E+02 0.007 21.9 7.0 65 36-100 112-197 (255)
84 PF07299 FBP: Fibronectin-bind 27.1 70 0.0015 25.2 2.9 38 3-48 64-101 (208)
85 PF04829 PT-VENN: Pre-toxin do 27.0 44 0.00096 20.9 1.5 18 28-45 1-18 (55)
86 PF12207 DUF3600: Domain of un 26.8 3 6.4E-05 31.7 -4.6 75 10-84 51-132 (162)
87 CHL00100 ilvH acetohydroxyacid 26.7 2.1E+02 0.0046 21.7 5.4 35 75-114 88-122 (174)
88 PRK11895 ilvH acetolactate syn 26.7 2.8E+02 0.006 20.8 7.8 68 33-114 53-122 (161)
89 COG4809 Archaeal ADP-dependent 26.7 1.3E+02 0.0028 26.5 4.7 65 55-119 295-360 (466)
90 PF12682 Flavodoxin_4: Flavodo 26.5 68 0.0015 23.5 2.7 22 86-107 11-32 (156)
91 PF14816 FAM178: Family of unk 26.4 1.4E+02 0.0029 25.7 4.7 44 4-47 32-78 (377)
92 PRK06934 flavodoxin; Provision 26.4 87 0.0019 24.7 3.4 30 84-116 69-98 (221)
93 COG2390 DeoR Transcriptional r 26.4 2.6E+02 0.0056 23.3 6.3 49 55-104 35-83 (321)
94 TIGR00126 deoC deoxyribose-pho 26.4 3.1E+02 0.0067 21.3 6.6 73 37-109 77-154 (211)
95 cd07766 DHQ_Fe-ADH Dehydroquin 26.2 3.2E+02 0.007 21.7 6.8 59 48-109 24-87 (332)
96 TIGR00376 DNA helicase, putati 26.0 5E+02 0.011 23.5 11.0 75 31-110 157-233 (637)
97 COG0092 RpsC Ribosomal protein 25.7 1.9E+02 0.004 23.3 5.2 54 45-98 58-113 (233)
98 PRK14713 multifunctional hydro 25.7 2.7E+02 0.0059 24.3 6.6 63 47-110 130-204 (530)
99 TIGR02768 TraA_Ti Ti-type conj 25.5 4.1E+02 0.0089 24.5 7.9 69 29-102 350-419 (744)
100 cd08557 PI-PLCc_bacteria_like 25.4 3E+02 0.0065 20.9 6.2 63 57-119 79-160 (271)
101 TIGR02974 phageshock_pspF psp 25.3 3.8E+02 0.0082 21.9 7.8 51 35-85 10-63 (329)
102 PF04908 SH3BGR: SH3-binding, 25.2 60 0.0013 22.5 2.0 66 4-75 17-92 (99)
103 PF00158 Sigma54_activat: Sigm 25.1 2.8E+02 0.0061 20.3 6.5 54 35-88 10-66 (168)
104 TIGR02766 crypt_chrom_pln cryp 25.0 3.5E+02 0.0076 23.1 7.1 52 57-112 73-127 (475)
105 PTZ00386 formyl tetrahydrofola 25.0 49 0.0011 30.2 1.9 99 11-114 190-330 (625)
106 PRK06294 coproporphyrinogen II 24.9 4E+02 0.0086 22.0 7.7 36 28-66 97-132 (370)
107 TIGR01574 miaB-methiolase tRNA 24.8 4E+02 0.0087 22.5 7.4 59 7-66 216-275 (438)
108 PF07985 SRR1: SRR1; InterPro 24.7 87 0.0019 19.2 2.5 36 8-44 21-56 (56)
109 TIGR00290 MJ0570_dom MJ0570-re 24.5 3.5E+02 0.0076 21.3 7.8 68 38-105 48-116 (223)
110 COG0673 MviM Predicted dehydro 24.0 1.7E+02 0.0037 22.9 4.7 54 29-82 99-152 (342)
111 cd05312 NAD_bind_1_malic_enz N 24.0 1.3E+02 0.0027 24.8 4.0 71 31-104 77-163 (279)
112 PF02457 DisA_N: DisA bacteria 23.9 93 0.002 22.2 2.9 35 86-120 86-122 (122)
113 TIGR00089 RNA modification enz 23.6 4.4E+02 0.0095 22.1 7.7 60 7-67 208-268 (429)
114 KOG4060 Uncharacterized conser 23.6 1.3E+02 0.0027 23.1 3.6 67 40-106 2-88 (176)
115 PRK05022 anaerobic nitric oxid 23.3 4.1E+02 0.0089 22.9 7.2 51 35-85 198-251 (509)
116 COG1126 GlnQ ABC-type polar am 23.2 4.1E+02 0.0089 21.6 6.7 100 3-104 110-215 (240)
117 PRK00907 hypothetical protein; 23.2 1.1E+02 0.0023 21.0 2.9 49 31-79 29-91 (92)
118 PRK13889 conjugal transfer rel 23.1 4.6E+02 0.0099 25.4 8.0 52 30-82 345-397 (988)
119 PRK03031 rnpA ribonuclease P; 22.8 1.8E+02 0.0039 20.4 4.2 40 38-77 73-119 (122)
120 PRK14567 triosephosphate isome 22.7 3.9E+02 0.0084 21.5 6.5 80 37-117 109-209 (253)
121 PRK00103 rRNA large subunit me 22.7 1.4E+02 0.003 22.2 3.7 40 28-67 76-119 (157)
122 COG0324 MiaA tRNA delta(2)-iso 22.3 86 0.0019 26.1 2.8 35 82-119 10-44 (308)
123 PF06299 DUF1045: Protein of u 22.1 1.1E+02 0.0024 23.2 3.1 39 8-46 61-101 (160)
124 TIGR03822 AblA_like_2 lysine-2 22.1 4.4E+02 0.0094 21.4 8.8 11 110-120 232-242 (321)
125 TIGR02408 ectoine_ThpD ectoine 21.8 2.8E+02 0.0061 21.9 5.6 39 28-72 13-51 (277)
126 PRK06806 fructose-bisphosphate 21.8 2.4E+02 0.0053 22.8 5.3 57 31-93 186-242 (281)
127 COG4089 Predicted membrane pro 21.5 50 0.0011 26.5 1.2 31 32-62 194-224 (235)
128 TIGR03556 photolyase_8HDF deox 21.4 5.3E+02 0.011 22.2 7.5 68 39-112 63-130 (471)
129 COG2921 Uncharacterized conser 21.1 95 0.0021 21.5 2.3 23 57-79 67-89 (90)
130 PRK09058 coproporphyrinogen II 20.8 5.3E+02 0.012 22.0 8.1 37 28-67 157-193 (449)
131 cd02810 DHOD_DHPD_FMN Dihydroo 20.6 4.2E+02 0.009 20.7 6.5 19 79-97 104-122 (289)
132 cd00959 DeoC 2-deoxyribose-5-p 20.5 3.2E+02 0.0069 20.5 5.4 75 36-110 75-154 (203)
No 1
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=100.00 E-value=4.4e-36 Score=209.60 Aligned_cols=87 Identities=20% Similarity=0.283 Sum_probs=85.5
Q ss_pred CCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCC
Q 035824 31 ILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSN 110 (121)
Q Consensus 31 ~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~ 110 (121)
+||++||+|||++||+|+|+|+|||+||||+|+.+|++||++||||||++++++.+++++++++||+.|||++||+| |+
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~I-G~ 80 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVI-GK 80 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeee-Cc
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999998 99
Q ss_pred EEEEEeCC
Q 035824 111 TIIFYRGK 118 (121)
Q Consensus 111 ~~iLYR~~ 118 (121)
++||||+.
T Consensus 81 ~~vlYR~~ 88 (97)
T PRK10343 81 TLVLYRPT 88 (97)
T ss_pred EEEEEecC
Confidence 99999975
No 2
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=100.00 E-value=1.8e-35 Score=205.74 Aligned_cols=86 Identities=23% Similarity=0.328 Sum_probs=84.7
Q ss_pred CCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCCE
Q 035824 32 LTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSNT 111 (121)
Q Consensus 32 LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~~ 111 (121)
||++||+|||++||+|+|+|+|||+||||+|+++|++||++||||||++++++.++++++|++|++.|||++||+| |++
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~i-G~~ 79 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVI-GKT 79 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEE-ccE
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999999998 999
Q ss_pred EEEEeCC
Q 035824 112 IIFYRGK 118 (121)
Q Consensus 112 ~iLYR~~ 118 (121)
+||||+.
T Consensus 80 ~vlYR~~ 86 (95)
T TIGR00253 80 IVLYRPT 86 (95)
T ss_pred EEEEecC
Confidence 9999975
No 3
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=100.00 E-value=6.7e-34 Score=192.93 Aligned_cols=84 Identities=33% Similarity=0.453 Sum_probs=75.5
Q ss_pred CCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCCE
Q 035824 32 LTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSNT 111 (121)
Q Consensus 32 LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~~ 111 (121)
||++|+++||++||+|+|+|+|||+|+||+|+++|+++|++||||||+|++++.+++++++++|++.|||++||+| |++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~i-G~~ 79 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVI-GRT 79 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEE-TTE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEE-CCE
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999999998 999
Q ss_pred EEEEe
Q 035824 112 IIFYR 116 (121)
Q Consensus 112 ~iLYR 116 (121)
+||||
T Consensus 80 ~vlyR 84 (84)
T PF01985_consen 80 IVLYR 84 (84)
T ss_dssp EEEEE
T ss_pred EEEEC
Confidence 99998
No 4
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-33 Score=197.02 Aligned_cols=86 Identities=24% Similarity=0.411 Sum_probs=84.6
Q ss_pred CCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCC
Q 035824 31 ILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSN 110 (121)
Q Consensus 31 ~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~ 110 (121)
+||++|++|||+.||+++|+|+|||+|+|++|+.+|+++|++||||||++.+++.++++++|+.|++.+||++||+| |+
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqvi-G~ 79 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVI-GK 79 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeee-ee
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999998 99
Q ss_pred EEEEEeC
Q 035824 111 TIIFYRG 117 (121)
Q Consensus 111 ~~iLYR~ 117 (121)
++||||.
T Consensus 80 ~~vlyr~ 86 (97)
T COG1534 80 TLVLYRE 86 (97)
T ss_pred EEEEEec
Confidence 9999993
No 5
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.42 E-value=1.5e-13 Score=119.81 Aligned_cols=120 Identities=45% Similarity=0.674 Sum_probs=109.9
Q ss_pred hhHhHHHHHHHHhccCCCCCC-CCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEe
Q 035824 2 KEKRKEAWLIENLTKFELPKA-PTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVS 80 (121)
Q Consensus 2 ~~~~~~~~~~~~l~~~~~~~~-~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~ 80 (121)
+++++++.....|.+++.|+. .+++++++.+|.+++.+++++|..+++.+..|..|+.++++.+++.+|..||++|+.|
T Consensus 352 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~ 431 (564)
T KOG1990|consen 352 KAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVIC 431 (564)
T ss_pred hhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeee
Confidence 457788899999999999955 6677999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCh-HHHHHHHHHHHhHcCCEEEEEee---CCEEEEEeCCCCC
Q 035824 81 KPCEP-WKIHEYAEVLAQLSKGIVIDINP---SNTIIFYRGKNYV 121 (121)
Q Consensus 81 ~~~~~-~~~~~~a~~L~~~tga~vVq~i~---G~~~iLYR~~ny~ 121 (121)
..... ...+..+..++..+|+.+|++.. |..++.||++||.
T Consensus 432 ~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~ 476 (564)
T KOG1990|consen 432 KEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYD 476 (564)
T ss_pred ccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhcc
Confidence 99776 89999999999999999998873 3448999999995
No 6
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=98.09 E-value=3.4e-06 Score=74.08 Aligned_cols=116 Identities=23% Similarity=0.288 Sum_probs=102.4
Q ss_pred hHHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCC
Q 035824 5 RKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCE 84 (121)
Q Consensus 5 ~~~~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~ 84 (121)
.....++++++.+.-|..+-+...+.+||..+..++|.+|-.+.|.+.+|.++.-.++...+.+.|..|+..|+.+...-
T Consensus 148 ~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~ 227 (564)
T KOG1990|consen 148 VDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGV 227 (564)
T ss_pred chhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcc
Confidence 45667899999999999988999999999999999999999999999999999999999999999999999998877754
Q ss_pred hHH-HHHHHHHH--HhHcCCEEEEEeeCCEEEEEeCCCCC
Q 035824 85 PWK-IHEYAEVL--AQLSKGIVIDINPSNTIIFYRGKNYV 121 (121)
Q Consensus 85 ~~~-~~~~a~~L--~~~tga~vVq~i~G~~~iLYR~~ny~ 121 (121)
... ...++..+ -..+|+.+|.. .|...++||++||.
T Consensus 228 ~~~~~~~~a~~l~~~~~tg~~lv~h-N~~~dv~y~~~~Fl 266 (564)
T KOG1990|consen 228 LETRKERMADELQELLLTGKVLVLH-NKLLDVMYRYKNFL 266 (564)
T ss_pred hhhhccchHHHHHHHHhcCCeEEee-ccceeeeeehhhcc
Confidence 433 35667777 78999999976 48999999999984
No 7
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=75.41 E-value=19 Score=23.14 Aligned_cols=55 Identities=11% Similarity=0.068 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHh---HcCCEEEEEeeCCEEEEEeCCC
Q 035824 63 VLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQ---LSKGIVIDINPSNTIIFYRGKN 119 (121)
Q Consensus 63 i~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~---~tga~vVq~i~G~~~iLYR~~n 119 (121)
+.++-++|.....|=+.+..-+.++.+.+.+.++. ..+|.+.+ + |..+++|=++|
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~-i-~~~~~l~~P~~ 69 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQK-I-SEKVFLLTPKG 69 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEE-E-ETTEEEEE---
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEE-E-cCCEEEEECCC
Confidence 45688899999999999999998889999988876 67999996 4 66677776655
No 8
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=70.05 E-value=39 Score=25.37 Aligned_cols=69 Identities=12% Similarity=0.065 Sum_probs=46.0
Q ss_pred CCCHHHHHHHHHhhcCCCceEEe-cCCCCcHH-HHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEE
Q 035824 31 ILTDEERHYLKRTDEKKKNYVQV-GRRGIFGG-VVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVI 104 (121)
Q Consensus 31 ~LT~kqr~~LR~~a~~lkpvv~I-Gk~Glt~~-vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vV 104 (121)
.||++|+..++.+...-+.++.| |..|---+ ++..+..+|+.+. .+|.+.... ..++..|.+.+|....
T Consensus 1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g-~~v~~~apT----~~Aa~~L~~~~~~~a~ 71 (196)
T PF13604_consen 1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAAG-KRVIGLAPT----NKAAKELREKTGIEAQ 71 (196)
T ss_dssp -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHTT---EEEEESS----HHHHHHHHHHHTS-EE
T ss_pred CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhCC-CeEEEECCc----HHHHHHHHHhhCcchh
Confidence 48999999999997666555544 98886544 4777999999987 677766655 3455567777665443
No 9
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=68.92 E-value=3.9 Score=26.14 Aligned_cols=19 Identities=32% Similarity=0.433 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHHHhhcCCC
Q 035824 30 EILTDEERHYLKRTDEKKK 48 (121)
Q Consensus 30 e~LT~kqr~~LR~~a~~lk 48 (121)
+++|+.|+.||+.++..-.
T Consensus 14 ePmT~aQ~syL~tL~e~Ag 32 (57)
T PF11272_consen 14 EPMTGAQASYLKTLSEEAG 32 (57)
T ss_pred CCCcHHHHHHHHHHHHHhC
Confidence 5799999999999987643
No 10
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=68.85 E-value=8.2 Score=27.54 Aligned_cols=34 Identities=9% Similarity=0.135 Sum_probs=28.5
Q ss_pred HHHhhcCCC-ceEEecCCCCcHHHHHHHHHHHHhC
Q 035824 40 LKRTDEKKK-NYVQVGRRGIFGGVVLNMHLHWKKH 73 (121)
Q Consensus 40 LR~~a~~lk-pvv~IGk~Glt~~vi~~i~~al~~h 73 (121)
+.+++.+-+ |++.++.+|.++.+++.++...+..
T Consensus 76 ~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~g 110 (133)
T PF03641_consen 76 LMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEEG 110 (133)
T ss_dssp HHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHTT
T ss_pred HHhhccccCCCEEEeCCcchHHHHHHHHHHHHHCC
Confidence 467777788 9999999999999999998666554
No 11
>TIGR03471 HpnJ hopanoid biosynthesis associated radical SAM protein HpnJ. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift.
Probab=60.42 E-value=86 Score=26.66 Aligned_cols=58 Identities=12% Similarity=0.091 Sum_probs=41.4
Q ss_pred HhHHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 4 KRKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 4 ~~~~~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
++....|.+.|.+..++|....+ ..++.+..+.|++.|.. .+.+|-...++.++..+.
T Consensus 260 ~~~~~~l~~~l~~~~i~~~~~~~---~~~~~e~l~~l~~aG~~---~v~iGiES~s~~~L~~~~ 317 (472)
T TIGR03471 260 KPRAEEIARKLGPLGVTWSCNAR---ANVDYETLKVMKENGLR---LLLVGYESGDQQILKNIK 317 (472)
T ss_pred HHHHHHHHHHHhhcCceEEEEec---CCCCHHHHHHHHHcCCC---EEEEcCCCCCHHHHHHhc
Confidence 34566778888888888874332 24788889999988754 688997777777665543
No 12
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=58.59 E-value=13 Score=26.15 Aligned_cols=62 Identities=19% Similarity=0.300 Sum_probs=44.6
Q ss_pred hHHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHH
Q 035824 5 RKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHW 70 (121)
Q Consensus 5 ~~~~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al 70 (121)
+-|++|++...--+- |+++.+..+||..+.+.+-.....|+ ---+||+|+-.+..-.+-.-|
T Consensus 10 EaEhRLLk~MGWqEy---~eNde~~~PlTEDElkEF~~kseQlr-rNGf~kngfl~~rs~slf~pW 71 (97)
T PF15337_consen 10 EAEHRLLKAMGWQEY---PENDENCLPLTEDELKEFQVKSEQLR-RNGFGKNGFLQSRSLSLFSPW 71 (97)
T ss_pred HHHHHHHHHhccccc---CcCCcccCcCcHHHHHHHHHHHHHHH-Hccccccchhhhhhhhccccc
Confidence 457888888775554 45666788999999999888888877 556788887777444333333
No 13
>COG1576 Uncharacterized conserved protein [Function unknown]
Probab=53.08 E-value=34 Score=25.87 Aligned_cols=65 Identities=11% Similarity=0.090 Sum_probs=42.8
Q ss_pred hHHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHH----HHhhcCCCceEEecCCCCcHHHHHHHHHHHHh
Q 035824 5 RKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYL----KRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKK 72 (121)
Q Consensus 5 ~~~~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~L----R~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~ 72 (121)
+-.++++..+++-..-... +..++++|+++-+.+ +-.| +-=.++.=|.+|+++++.+..+..|.-
T Consensus 55 ~E~~~il~~i~~~~~vi~L--d~~Gk~~sSe~fA~~l~~~~~~G-~~i~f~IGG~~Gl~~~~~~~a~~~~sl 123 (155)
T COG1576 55 KEGEAILAAIPKGSYVVLL--DIRGKALSSEEFADFLERLRDDG-RDISFLIGGADGLSEAVKARADQVLSL 123 (155)
T ss_pred HHHHHHHHhcCCCCeEEEE--ecCCCcCChHHHHHHHHHHHhcC-CeEEEEEeCcccCCHHHHHHHhhheec
Confidence 3456777777764333331 224788999876543 4455 223444556899999999999999975
No 14
>COG0274 DeoC Deoxyribose-phosphate aldolase [Nucleotide transport and metabolism]
Probab=50.13 E-value=53 Score=26.34 Aligned_cols=67 Identities=10% Similarity=0.082 Sum_probs=52.5
Q ss_pred HHHhhcCCCceEEec--CCCCcHHHHHHHHHHHHhC---CeeEEEecCCC-hHHHHHHHHHHHhHcCCEEEEE
Q 035824 40 LKRTDEKKKNYVQVG--RRGIFGGVVLNMHLHWKKH---ETVKVVSKPCE-PWKIHEYAEVLAQLSKGIVIDI 106 (121)
Q Consensus 40 LR~~a~~lkpvv~IG--k~Glt~~vi~~i~~al~~h---ELIKVk~~~~~-~~~~~~~a~~L~~~tga~vVq~ 106 (121)
...=|..++-++.|| |.|-.+.|.++|...-+.. -++||.+.... .++-...+-.++...|+.+|-.
T Consensus 87 i~~GAdEiDmVinig~~k~g~~~~V~~eI~~v~~a~~~~~~lKVIlEt~~Lt~ee~~~A~~i~~~aGAdFVKT 159 (228)
T COG0274 87 IENGADEIDMVINIGALKSGNWEAVEREIRAVVEACADAVVLKVILETGLLTDEEKRKACEIAIEAGADFVKT 159 (228)
T ss_pred HHcCCCeeeeeeeHHHHhcCCHHHHHHHHHHHHHHhCCCceEEEEEeccccCHHHHHHHHHHHHHhCCCEEEc
Confidence 344466789999999 7999999988888777764 38999987653 3444578889999999999954
No 15
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=48.38 E-value=56 Score=21.17 Aligned_cols=35 Identities=23% Similarity=0.366 Sum_probs=21.8
Q ss_pred eeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCCEEEE
Q 035824 75 TVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSNTIIF 114 (121)
Q Consensus 75 LIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~~~iL 114 (121)
||||++. .. .+.-...|++..+|.+|.+- .+++++
T Consensus 6 LiKV~~~---~~-~r~ei~~l~~~f~a~ivd~~-~~~~ii 40 (75)
T PF10369_consen 6 LIKVKAT---PE-NRSEILQLAEIFRARIVDVS-PDSIII 40 (75)
T ss_dssp EEEEE-S---CH-HHHHHHHHHHHTT-EEEEEE-TTEEEE
T ss_pred EEEEECC---cc-CHHHHHHHHHHhCCEEEEEC-CCEEEE
Confidence 5666652 23 34556778899999999875 555554
No 16
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=47.79 E-value=46 Score=24.92 Aligned_cols=34 Identities=6% Similarity=-0.031 Sum_probs=18.1
Q ss_pred HHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHh
Q 035824 39 YLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKK 72 (121)
Q Consensus 39 ~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~ 72 (121)
.|+..-..-+-++.+.-+|++-+-+.+|+..|..
T Consensus 9 el~e~l~~~~~v~v~~~~gl~~~ql~~lR~~lr~ 42 (175)
T cd05795 9 KLTELLKSYPKVLIVDADNVGSKQLQKIRRSLRG 42 (175)
T ss_pred HHHHHHHhCCEEEEEEecCCChHHHHHHHHHhhC
Confidence 3444444445555555555555555555555554
No 17
>PRK05904 coproporphyrinogen III oxidase; Provisional
Probab=47.65 E-value=1.3e+02 Score=24.83 Aligned_cols=57 Identities=16% Similarity=0.355 Sum_probs=38.2
Q ss_pred HHHHHHHhccCCCCCC--CCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 7 EAWLIENLTKFELPKA--PTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 7 ~~~~~~~l~~~~~~~~--~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
.+.+++.+.++ ++.. -.-..+|+.+|.+..+.|+..|- ..|+||-...++.++..+.
T Consensus 75 l~~ll~~i~~~-~~~~~eitiE~nP~~lt~e~l~~lk~~G~---nrisiGvQS~~d~vL~~l~ 133 (353)
T PRK05904 75 LDILLSTIKPY-VDNNCEFTIECNPELITQSQINLLKKNKV---NRISLGVQSMNNNILKQLN 133 (353)
T ss_pred HHHHHHHHHHh-cCCCCeEEEEeccCcCCHHHHHHHHHcCC---CEEEEecccCCHHHHHHcC
Confidence 34566666655 2211 11123588999999999999873 3689998888888875543
No 18
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=46.74 E-value=1.2e+02 Score=24.83 Aligned_cols=57 Identities=16% Similarity=0.202 Sum_probs=38.4
Q ss_pred HHHHHHhccCCCCCCCC--CCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 8 AWLIENLTKFELPKAPT--EAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 8 ~~~~~~l~~~~~~~~~~--~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
+.|.+.+.++..++..+ --.+|..+|.+..+.|+..|-. .|+||-..+.+.++..+.
T Consensus 71 ~~L~~~i~~~~~~~~~eitie~~p~~~t~e~l~~l~~~G~~---rvsiGvqS~~d~~L~~l~ 129 (374)
T PRK05799 71 EILKETIKKLNKKEDLEFTVEGNPGTFTEEKLKILKSMGVN---RLSIGLQAWQNSLLKYLG 129 (374)
T ss_pred HHHHHHHHhCCCCCCCEEEEEeCCCcCCHHHHHHHHHcCCC---EEEEECccCCHHHHHHcC
Confidence 45666665554432110 1124778999999999999843 799998888888876554
No 19
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=46.68 E-value=32 Score=25.96 Aligned_cols=33 Identities=15% Similarity=0.219 Sum_probs=27.7
Q ss_pred HHHhhcCCCceEEecCCCCcHHHHHHHHHHHHh
Q 035824 40 LKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKK 72 (121)
Q Consensus 40 LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~ 72 (121)
+.+++.+-||++.++-+|.++.+++.++...+.
T Consensus 119 ~~qlg~~~kPiil~n~~g~~~~l~~~l~~~~~~ 151 (178)
T TIGR00730 119 WAQLGIHQKPIILFNVNGHFDGLVEWLKYSIQE 151 (178)
T ss_pred HHHcCCCCCCEEEECCcchHHHHHHHHHHHHHC
Confidence 556677889999999999999999988866554
No 20
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=46.62 E-value=1.4e+02 Score=25.46 Aligned_cols=37 Identities=19% Similarity=0.138 Sum_probs=30.5
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
+|..+|.+..+.|++.|-. .|+||-.+.++.+...+.
T Consensus 146 ~p~~lt~e~l~~L~~~G~~---rvsiGvQS~~~~vl~~l~ 182 (453)
T PRK13347 146 DPRTVTAEMLQALAALGFN---RASFGVQDFDPQVQKAIN 182 (453)
T ss_pred ccccCCHHHHHHHHHcCCC---EEEECCCCCCHHHHHHhC
Confidence 5788999999999999843 899998888888765553
No 21
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=46.46 E-value=1.3e+02 Score=24.69 Aligned_cols=57 Identities=18% Similarity=0.216 Sum_probs=38.1
Q ss_pred hHHHHHHHHhccC-CCC----CCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 5 RKEAWLIENLTKF-ELP----KAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 5 ~~~~~~~~~l~~~-~~~----~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
...+.+++.+.+. .++ ++-+ .+|..+|.+..+.|+..|- ..+.||-...++.+++.+
T Consensus 68 ~~l~~ll~~i~~~~~~~~~~eit~e--~~p~~l~~e~l~~l~~~G~---~rvsiGvqS~~~~~l~~l 129 (377)
T PRK08599 68 EQLERLLTAIHRNLPLSGLEEFTFE--ANPGDLTKEKLQVLKDSGV---NRISLGVQTFNDELLKKI 129 (377)
T ss_pred HHHHHHHHHHHHhCCCCCCCEEEEE--eCCCCCCHHHHHHHHHcCC---CEEEEecccCCHHHHHHc
Confidence 3456666666653 221 1111 2577899999999999984 488999888887776543
No 22
>cd00379 Ribosomal_L10_P0 Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in bacteria, P0 in eukaryotes, and L10e in archaea, as well as uncharacterized P0-like eukaryotic proteins. In all three kingdoms, L10 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been sho
Probab=46.45 E-value=1e+02 Score=21.78 Aligned_cols=30 Identities=17% Similarity=0.199 Sum_probs=17.3
Q ss_pred CCCHHHHHHHHHhhcCCCceEEecCCCCcH
Q 035824 31 ILTDEERHYLKRTDEKKKNYVQVGRRGIFG 60 (121)
Q Consensus 31 ~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~ 60 (121)
.+|..|...||+.-..-..-+.+|||-+-.
T Consensus 27 ~l~~~~~~~lR~~l~~~~~~~~v~KNtl~~ 56 (155)
T cd00379 27 GLTVAQLTELRKELRESGAKLKVGKNTLMR 56 (155)
T ss_pred CCcHHHHHHHHHHHHHcCCEEEEEehHHHH
Confidence 466666666666555555566666664443
No 23
>TIGR01305 GMP_reduct_1 guanosine monophosphate reductase, eukaryotic. A deep split separates two families of GMP reductase. This family includes both eukaryotic and some proteobacterial sequences, while the other family contains other bacterial sequences.
Probab=46.34 E-value=1.8e+02 Score=24.72 Aligned_cols=77 Identities=9% Similarity=0.017 Sum_probs=44.2
Q ss_pred CCHH-HHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhC---CeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEe
Q 035824 32 LTDE-ERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKH---ETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDIN 107 (121)
Q Consensus 32 LT~k-qr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~h---ELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i 107 (121)
++.+ |..|.++.-......+.| .-|++++-.+.+...++.. ..|=|.+........-++...|........| |
T Consensus 78 ~~~e~~~~~v~~~~~~~~~~~~v-svG~~~~d~er~~~L~~a~~~~d~iviD~AhGhs~~~i~~ik~ir~~~p~~~v--i 154 (343)
T TIGR01305 78 YSVDEWKAFATNSSPDCLQNVAV-SSGSSDNDLEKMTSILEAVPQLKFICLDVANGYSEHFVEFVKLVREAFPEHTI--M 154 (343)
T ss_pred CCHHHHHHHHHhhcccccceEEE-EeccCHHHHHHHHHHHhcCCCCCEEEEECCCCcHHHHHHHHHHHHhhCCCCeE--E
Confidence 3444 455555544444555555 5666666666666666653 5566666666666666666666666654333 3
Q ss_pred eCCE
Q 035824 108 PSNT 111 (121)
Q Consensus 108 ~G~~ 111 (121)
.||+
T Consensus 155 aGNV 158 (343)
T TIGR01305 155 AGNV 158 (343)
T ss_pred Eecc
Confidence 3544
No 24
>TIGR01211 ELP3 histone acetyltransferase, ELP3 family. The Saccharomyces cerevisiae member YPL086C has been characterized in vitro as an N-terminal acetyltransferase for all four core histones. It is a component of the RNA polymerase II holoenzyme, designated Elp3p for Elongator Protein 3. Members of this family are found in eukaryotes and archaea. These proteins are part of the larger set of GNAT acetyltransferases.
Probab=45.14 E-value=1.3e+02 Score=26.66 Aligned_cols=36 Identities=14% Similarity=0.323 Sum_probs=30.8
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
+|..+|.+..+.|++.|. ..|.+|-.-.++.++..+
T Consensus 200 RPD~i~~e~L~~L~~~G~---~rVslGVQS~~d~VL~~i 235 (522)
T TIGR01211 200 RPDYCREEHIDRMLKLGA---TRVELGVQTIYNDILERT 235 (522)
T ss_pred cCCcCCHHHHHHHHHcCC---CEEEEECccCCHHHHHHh
Confidence 477899999999999997 599999888888887555
No 25
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=44.97 E-value=69 Score=26.48 Aligned_cols=47 Identities=13% Similarity=0.006 Sum_probs=29.7
Q ss_pred HHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCC
Q 035824 36 ERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCE 84 (121)
Q Consensus 36 qr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~ 84 (121)
....|+..-..-+-++.+.-.|++-+-+.+|+..|... .++++-.|.
T Consensus 11 ~v~el~~~l~~~~~v~iv~~~gl~~~ql~~lR~~lr~~--~~~~v~KNt 57 (330)
T PRK04019 11 EVEELKELIKSYPVVGIVDLEGIPARQLQEIRRKLRGK--AELKVSKNT 57 (330)
T ss_pred HHHHHHHHHHhCCEEEEEEcCCCCHHHHHHHHHHHHcC--CEEEEEehH
Confidence 33455555556666777777777777777777777764 555554443
No 26
>PF00466 Ribosomal_L10: Ribosomal protein L10; InterPro: IPR001790 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 [, ]. On the basis of sequence similarities the following prokaryotic and eukaryotic ribosomal proteins can be grouped: Bacterial 50S ribosomal protein L10; Archaebacterial acidic ribosomal protein P0 homologue (L10E); Eukaryotic 60S ribosomal protein P0 (L10E). This entry represents the ribosomal protein L10P family, with includes the above mentioned ribosomal proteins.; GO: 0042254 ribosome biogenesis, 0005622 intracellular; PDB: 3A1Y_G 3D5D_J 3PYT_I 3PYV_I 3D5B_J 3PYO_I 3PYR_I 3MS1_I 3MRZ_I 1VQ9_G ....
Probab=43.75 E-value=57 Score=21.55 Aligned_cols=75 Identities=12% Similarity=0.069 Sum_probs=42.5
Q ss_pred HHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCCEEEEEeC
Q 035824 38 HYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSNTIIFYRG 117 (121)
Q Consensus 38 ~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~~~iLYR~ 117 (121)
..++..-..-+-++.+.-+|++-.-+.+++..|..+ =+++++-.|.. ++.+........ .+.+...|.++++|=.
T Consensus 11 ~~~~~~l~~~~~v~v~~~~~l~~~~~~~lR~~l~~~-~~~~~v~KN~l--~~~Al~~~~~~~--~l~~~l~G~~~~if~~ 85 (100)
T PF00466_consen 11 EELKELLKKSKYVIVVDYNGLSANQLQELRKELRKK-GGKFKVVKNTL--MKKALKNTGFEE--ALSPLLKGPTALIFSN 85 (100)
T ss_dssp HHHHHHHHCSSEEEEEECTTSCHHHHHHHHHHHHHH-TEEEEECSHHH--HHHHHHHHHTSS--SSSCCTSSSEEEEEES
T ss_pred HHHHHHHHhCCEEEEEEeCCCCHHHHHHHHHHHHhc-CcEEEEecHHH--HHHHHhcCcccc--CccccccCCEEEEEEC
Confidence 344555555667777778888888888888888665 24455544432 122222221111 1334456888888753
No 27
>PF11072 DUF2859: Protein of unknown function (DUF2859); InterPro: IPR021300 This model describes a protein family exemplified by PFL_4695 of Pseudomonas fluorescens Pf-5. Full-length proteins in this family show some architectural variety, but this model represents a conserved domain. Most or all member proteins belong to laterally transferred chromosomal islands called integrative conjugative elements, or ICE.
Probab=43.55 E-value=82 Score=23.42 Aligned_cols=54 Identities=13% Similarity=0.033 Sum_probs=43.6
Q ss_pred HHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHH
Q 035824 37 RHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYA 92 (121)
Q Consensus 37 r~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a 92 (121)
++-|. .-.+.|+|.||-+.++-.++.+=.+.|...--+-+.++-.+....+++.
T Consensus 54 ~r~l~--~pg~~plFlVGdD~~S~~WL~~~~~~L~~l~AvGlVVNV~t~~~L~~Lr 107 (142)
T PF11072_consen 54 RRPLQ--LPGLQPLFLVGDDPLSRQWLQQNAEELKQLGAVGLVVNVATEAALQRLR 107 (142)
T ss_pred cceec--CCCCCCEEEEcCCHHHHHHHHHHHHHHHHCCCeEEEEecCCHHHHHHHH
Confidence 34444 4556999999999999999999999999998888888877766655544
No 28
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=43.37 E-value=1.4e+02 Score=22.57 Aligned_cols=82 Identities=9% Similarity=-0.061 Sum_probs=46.2
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHhhcCCC----ceEEecCCCCcHHHHH-HHHHHHHhCCeeEEEecCCChHHHHHHHH
Q 035824 19 LPKAPTEAYDPEILTDEERHYLKRTDEKKK----NYVQVGRRGIFGGVVL-NMHLHWKKHETVKVVSKPCEPWKIHEYAE 93 (121)
Q Consensus 19 ~~~~~~~~~~~e~LT~kqr~~LR~~a~~lk----pvv~IGk~Glt~~vi~-~i~~al~~hELIKVk~~~~~~~~~~~~a~ 93 (121)
-|+...++.+--..|...++.+..+.+.++ .++..|.+|.--+.+. .+...+.....+-+.+ .++..+..++..
T Consensus 11 ~pF~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~-~~~~~~~~~~l~ 89 (269)
T TIGR03015 11 KPFQLLPDPDFFYPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKL-VNTRVDAEDLLR 89 (269)
T ss_pred CCCCCCCCHHHhCCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeee-eCCCCCHHHHHH
Confidence 466644433333467777778887766553 4788999999988744 4544545444433222 222223344555
Q ss_pred HHHhHcCC
Q 035824 94 VLAQLSKG 101 (121)
Q Consensus 94 ~L~~~tga 101 (121)
.|+...|.
T Consensus 90 ~i~~~lG~ 97 (269)
T TIGR03015 90 MVAADFGL 97 (269)
T ss_pred HHHHHcCC
Confidence 55555443
No 29
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=43.01 E-value=33 Score=26.46 Aligned_cols=31 Identities=23% Similarity=0.308 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHH
Q 035824 30 EILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLH 69 (121)
Q Consensus 30 e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~a 69 (121)
...|..||.||..+|..| ||.+.++.+|++.
T Consensus 156 d~d~~~Er~YL~~LA~aL---------~L~~~lv~~le~~ 186 (188)
T PF04391_consen 156 DVDTFAERAYLDELAQAL---------GLDPDLVAQLEQQ 186 (188)
T ss_pred CCCCHHHHHHHHHHHHHh---------CcCHHHHHHHHHH
Confidence 457999999999999987 7999999999864
No 30
>smart00084 NMU Neuromedin U. Neuromedin U (NmU) is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C- terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved in mammals, birds and amphibians.
Probab=42.63 E-value=18 Score=19.54 Aligned_cols=12 Identities=25% Similarity=0.515 Sum_probs=10.0
Q ss_pred CCEEEEEeCCCC
Q 035824 109 SNTIIFYRGKNY 120 (121)
Q Consensus 109 G~~~iLYR~~ny 120 (121)
++-..|||++|.
T Consensus 15 srgyFLfRPRN~ 26 (26)
T smart00084 15 SRGYFLFRPRNX 26 (26)
T ss_pred cCceEEeccCCC
Confidence 567899999984
No 31
>PF06816 NOD: NOTCH protein; InterPro: IPR010660 NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals []. NOD (NOTCH protein domain) represents a region present in many NOTCH proteins and NOTCH homologues in multiple species such as 0, NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. Role of NOD domain remains to be elucidated.; GO: 0030154 cell differentiation, 0016021 integral to membrane; PDB: 2OO4_A 3ETO_A 3I08_A 3L95_X.
Probab=42.54 E-value=4.8 Score=25.49 Aligned_cols=28 Identities=14% Similarity=0.375 Sum_probs=21.7
Q ss_pred CCCCCHHHHHHHHHhhcCCCceEEecCC
Q 035824 29 PEILTDEERHYLKRTDEKKKNYVQVGRR 56 (121)
Q Consensus 29 ~e~LT~kqr~~LR~~a~~lkpvv~IGk~ 56 (121)
|+.+-..+..|||.+++.|+..|.|-++
T Consensus 17 P~~f~~~~~~FLr~Ls~~Lrt~V~ikkD 44 (57)
T PF06816_consen 17 PEEFRNNSVQFLRELSRVLRTTVRIKKD 44 (57)
T ss_dssp HHHHHHTHHHHHHHHHHHCTSEEEE-B-
T ss_pred HHHHHHHHHHHHHHHHHHHeeeEEEEEC
Confidence 4445566789999999999999999876
No 32
>PRK05580 primosome assembly protein PriA; Validated
Probab=42.52 E-value=2.6e+02 Score=25.33 Aligned_cols=78 Identities=9% Similarity=-0.012 Sum_probs=53.8
Q ss_pred CCCCCCHHHHHHHHHhhcC--CCceEEecC--CCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEE
Q 035824 28 DPEILTDEERHYLKRTDEK--KKNYVQVGR--RGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIV 103 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~--lkpvv~IGk--~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~v 103 (121)
.+-.||+.|.+.+..+-.. -.+++..|. .|=|...+.-+..++...- ++-+.-...+...++.+.+.+..|..+
T Consensus 141 ~~~~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~--~vLvLvPt~~L~~Q~~~~l~~~fg~~v 218 (679)
T PRK05580 141 EPPTLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGK--QALVLVPEIALTPQMLARFRARFGAPV 218 (679)
T ss_pred CCCCCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcCC--eEEEEeCcHHHHHHHHHHHHHHhCCCE
Confidence 3556999999999998764 355666663 5677777777888887642 344555566677778888887776555
Q ss_pred EEEe
Q 035824 104 IDIN 107 (121)
Q Consensus 104 Vq~i 107 (121)
+.+.
T Consensus 219 ~~~~ 222 (679)
T PRK05580 219 AVLH 222 (679)
T ss_pred EEEE
Confidence 5443
No 33
>PRK08207 coproporphyrinogen III oxidase; Provisional
Probab=42.34 E-value=1.8e+02 Score=25.46 Aligned_cols=37 Identities=14% Similarity=0.269 Sum_probs=30.7
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
.|..+|.+..+.|+..|-. .++||-...++.++..+.
T Consensus 263 rPd~it~e~L~~Lk~~Gv~---RISIGvQS~~d~vLk~ig 299 (488)
T PRK08207 263 RPDTITEEKLEVLKKYGVD---RISINPQTMNDETLKAIG 299 (488)
T ss_pred CCCCCCHHHHHHHHhcCCC---eEEEcCCcCCHHHHHHhC
Confidence 5778999999999999854 799998888888776553
No 34
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=42.27 E-value=1.7e+02 Score=24.63 Aligned_cols=36 Identities=17% Similarity=0.235 Sum_probs=29.4
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
+|+.+|.+..+.||..|- ..++||-....+.++..+
T Consensus 105 nP~~~~~e~l~~l~~~Gv---nRiSiGvQS~~d~~L~~l 140 (390)
T PRK06582 105 NPTSFETEKFKAFKLAGI---NRVSIGVQSLKEDDLKKL 140 (390)
T ss_pred CCCcCCHHHHHHHHHCCC---CEEEEECCcCCHHHHHHc
Confidence 578899999999999985 589999888888776443
No 35
>TIGR01125 MiaB-like tRNA modifying enzyme YliG, TIGR01125. This clade spans alpha and gamma proteobacteria, cyano bacteria, deinococcus, porphyromonas, aquifex, helicobacter, campylobacter, thermotoga, chlamydia, streptococcus coelicolor and clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes.
Probab=42.13 E-value=1.6e+02 Score=24.84 Aligned_cols=60 Identities=18% Similarity=0.146 Sum_probs=39.0
Q ss_pred HHHHHHHHhccCC-CCCCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 6 KEAWLIENLTKFE-LPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 6 ~~~~~~~~l~~~~-~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
.-..|++.+.+.. ++|-.-.-..|..++++-...|+..+. .=+.+.||-...++.++..+
T Consensus 203 ~l~~Ll~~i~~~~~i~~~r~~~~~p~~~~~ell~~~~~~~~-~~~~l~iglES~s~~vLk~m 263 (430)
T TIGR01125 203 KLVDLLEELGKVGGIYWIRMHYLYPDELTDDVIDLMAEGPK-VLPYLDIPLQHASDRILKLM 263 (430)
T ss_pred cHHHHHHHHHhcCCccEEEEccCCcccCCHHHHHHHhhCCc-ccCceEeCCCCCCHHHHhhC
Confidence 4567888888776 666321223456788888888877542 34678888777766665544
No 36
>PRK05660 HemN family oxidoreductase; Provisional
Probab=41.57 E-value=1.9e+02 Score=23.96 Aligned_cols=57 Identities=12% Similarity=0.181 Sum_probs=38.9
Q ss_pred HHHHHHHHhccCCCCCCCCC----CCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 6 KEAWLIENLTKFELPKAPTE----AYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 6 ~~~~~~~~l~~~~~~~~~~~----~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
..+++++.+.+.- |+.+.. -.+|..+|.+..+.||..|-. .++||-.+.++.++..+
T Consensus 76 ~l~~ll~~l~~~~-~~~~~~eit~e~np~~l~~e~l~~Lk~~Gv~---risiGvqS~~~~~L~~l 136 (378)
T PRK05660 76 AIQRLLDGVRARL-PFAPDAEITMEANPGTVEADRFVGYQRAGVN---RISIGVQSFSEEKLKRL 136 (378)
T ss_pred HHHHHHHHHHHhC-CCCCCcEEEEEeCcCcCCHHHHHHHHHcCCC---EEEeccCcCCHHHHHHh
Confidence 4456666665531 221100 124788999999999999853 89999999999887544
No 37
>cd05797 Ribosomal_L10 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-in
Probab=41.55 E-value=1.3e+02 Score=21.60 Aligned_cols=55 Identities=16% Similarity=0.008 Sum_probs=35.2
Q ss_pred HHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHH
Q 035824 6 KEAWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVL 64 (121)
Q Consensus 6 ~~~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~ 64 (121)
-.+.+.+.++++..-.-- +-..||.+|...||+.-..-...+.++||-+..-.++
T Consensus 8 ~v~~l~~~l~~~~~v~v~----~~~gl~~~~~~~lR~~lr~~~~~~~V~KNtL~~~Al~ 62 (157)
T cd05797 8 IVAELKEKLKEAKSVVVA----DYRGLTVAQLTELRKELREAGVKLKVVKNTLAKRALE 62 (157)
T ss_pred HHHHHHHHHHhCCEEEEE----ecCCCcHHHHHHHHHHHHHcCCEEEEehhHHHHHHHh
Confidence 345566666666433221 2346888888888888777777788888866554444
No 38
>COG1799 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.40 E-value=76 Score=24.28 Aligned_cols=55 Identities=15% Similarity=0.190 Sum_probs=45.7
Q ss_pred HHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHh---HcCCEEEEEeeCCEEEEEeCCC
Q 035824 63 VLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQ---LSKGIVIDINPSNTIIFYRGKN 119 (121)
Q Consensus 63 i~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~---~tga~vVq~i~G~~~iLYR~~n 119 (121)
..+|-+.|+.++-|=|.+..-+..+.+.+.+.|+. .++|.+.+ | |..+.|.=+.|
T Consensus 87 a~~ia~~lk~~k~Vvinl~~m~~~qArRivDFlaG~~~al~G~~qk-V-g~~ifL~tP~n 144 (167)
T COG1799 87 AQEIADYLKNRKAVVINLQRMDPAQARRIVDFLAGAVFALRGSIQK-V-GSKIFLLTPSN 144 (167)
T ss_pred HHHHHHHHhcCceEEEEeeeCCHHHHHHHHHHhcchhhhhcccHHh-h-cceeEEecccc
Confidence 56788999999999999999999999999999876 56788775 5 87777765554
No 39
>COG3453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.94 E-value=1.2e+02 Score=22.31 Aligned_cols=54 Identities=11% Similarity=-0.039 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCC-eeEEEecCCC
Q 035824 30 EILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHE-TVKVVSKPCE 84 (121)
Q Consensus 30 e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hE-LIKVk~~~~~ 84 (121)
-+.+...+...+..|.. =-++.++..|+|+.=|+.+.+|+..-| =|=..|....
T Consensus 44 QP~~~~i~~aa~~aGl~-y~~iPV~~~~iT~~dV~~f~~Al~eaegPVlayCrsGt 98 (130)
T COG3453 44 QPGFAAIAAAAEAAGLT-YTHIPVTGGGITEADVEAFQRALDEAEGPVLAYCRSGT 98 (130)
T ss_pred CCChHHHHHHHHhcCCc-eEEeecCCCCCCHHHHHHHHHHHHHhCCCEEeeecCCc
Confidence 35788899999999998 678999999999999999999999866 3444444443
No 40
>PRK14327 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=40.67 E-value=2e+02 Score=25.30 Aligned_cols=57 Identities=14% Similarity=0.141 Sum_probs=39.2
Q ss_pred HHHHHHHhccCCCC---CCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 7 EAWLIENLTKFELP---KAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 7 ~~~~~~~l~~~~~~---~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
-..|++.+.+..++ |.. ..|..+|++-...++..+ .+=+.+.||-.-.++.++..|.
T Consensus 282 l~~Ll~~I~~~~i~~ir~~s---~~P~~i~deli~~m~~~g-~~~~~l~lgvQSgsd~vLk~M~ 341 (509)
T PRK14327 282 LGDLMDEIRKIDIPRVRFTT---SHPRDFDDHLIEVLAKGG-NLVEHIHLPVQSGSTEVLKIMA 341 (509)
T ss_pred HHHHHHHHHhCCCceEEEee---cCcccCCHHHHHHHHhcC-CccceEEeccCCCCHHHHHhcC
Confidence 45678888776665 332 136678998888888754 3447899997777777765554
No 41
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=40.63 E-value=27 Score=25.73 Aligned_cols=27 Identities=33% Similarity=0.367 Sum_probs=24.6
Q ss_pred CcHHHHHHHHHHHHhCCeeEEEecCCC
Q 035824 58 IFGGVVLNMHLHWKKHETVKVVSKPCE 84 (121)
Q Consensus 58 lt~~vi~~i~~al~~hELIKVk~~~~~ 84 (121)
|++++|..|+++|.--+=|+|+|+.-+
T Consensus 38 Ia~~fVkdI~d~L~vG~eV~vKVl~id 64 (129)
T COG1098 38 IADGFVKDIHDHLKVGQEVKVKVLDID 64 (129)
T ss_pred hhhhhHHhHHHHhcCCCEEEEEEEeec
Confidence 689999999999999999999998743
No 42
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=40.61 E-value=1.1e+02 Score=21.96 Aligned_cols=48 Identities=8% Similarity=0.070 Sum_probs=40.0
Q ss_pred CCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEE
Q 035824 55 RRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVI 104 (121)
Q Consensus 55 k~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vV 104 (121)
..-||+++++.|..|+....=+.|.+.+ .+|.-.+...+....|+.|+
T Consensus 43 pG~It~el~~ai~~a~~~~~~~~I~V~G--EEDL~~lPail~aP~gs~V~ 90 (121)
T PF04019_consen 43 PGTITEELIEAIKKALESGKPVVIFVDG--EEDLAVLPAILYAPEGSVVL 90 (121)
T ss_pred CCcccHHHHHHHHHHHhCCCCEEEEEeC--hHHHHHHHHHHhCCCCCEEE
Confidence 4679999999999999888888888877 47777888888888887776
No 43
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=40.35 E-value=1.9e+02 Score=24.51 Aligned_cols=36 Identities=17% Similarity=0.249 Sum_probs=28.8
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
+|..+|.+..+.|+..|. ..|.||-...++.++..+
T Consensus 135 ~P~~lt~e~l~~l~~~G~---~rvslGvQS~~~~~L~~l 170 (430)
T PRK08208 135 SPATTTAEKLALLAARGV---NRLSIGVQSFHDSELHAL 170 (430)
T ss_pred CcCcCCHHHHHHHHHcCC---CEEEEecccCCHHHHHHh
Confidence 477899999999999875 489999888887776443
No 44
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=40.26 E-value=2.2e+02 Score=24.24 Aligned_cols=57 Identities=21% Similarity=0.163 Sum_probs=37.7
Q ss_pred HHHHHHHHhccCCCCCCC----CCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 6 KEAWLIENLTKFELPKAP----TEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 6 ~~~~~~~~l~~~~~~~~~----~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
..+.|++.+.+. +|+.+ .=..+|..+|.+..+.|++.|- ..+.||-.+.++.++..+
T Consensus 120 ~l~~ll~~l~~~-~~~~~~~e~tie~np~~lt~e~l~~l~~aG~---~risiGvqS~~~~~L~~l 180 (453)
T PRK09249 120 QLRRLMALLREH-FNFAPDAEISIEIDPRELDLEMLDALRELGF---NRLSLGVQDFDPEVQKAV 180 (453)
T ss_pred HHHHHHHHHHHh-CCCCCCCEEEEEecCCcCCHHHHHHHHHcCC---CEEEECCCCCCHHHHHHh
Confidence 445666666543 22211 0012477899999999999984 489999888888776544
No 45
>TIGR00539 hemN_rel putative oxygen-independent coproporphyrinogen III oxidase. Experimentally determined examples of oxygen-independent coproporphyrinogen III oxidase, an enzyme that replaces HemF function under anaerobic conditions, belong to a family of proteins described by the model hemN. This model, hemN_rel, models a closely related protein, shorter at the amino end and lacking the region containing the motif PYRT[SC]YP found in members of the hemN family. Several species, including E. coli, Helicobacter pylori, Aquifex aeolicus, and Chlamydia trachomatis, have members of both this family and the E. coli hemN family. The member of this family from Bacillus subtilis was shown to complement an hemF/hemN double mutant of Salmonella typimurium and to prevent accumulation of coproporphyrinogen III under anaerobic conditions, but the exact role of this protein is still uncertain. It is found in a number of species that do not synthesize heme de novo.
Probab=40.16 E-value=1.7e+02 Score=23.97 Aligned_cols=36 Identities=25% Similarity=0.309 Sum_probs=29.5
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
+|..+|.+..+.|++.|- ..++||-.+.++.++..+
T Consensus 94 np~~lt~e~l~~l~~~Gv---~risiGvqS~~~~~l~~l 129 (360)
T TIGR00539 94 NPELITAEWCKGLKGAGI---NRLSLGVQSFRDDKLLFL 129 (360)
T ss_pred CCCCCCHHHHHHHHHcCC---CEEEEecccCChHHHHHh
Confidence 478899999999999984 488899888888776555
No 46
>PRK00099 rplJ 50S ribosomal protein L10; Reviewed
Probab=40.16 E-value=1.5e+02 Score=21.80 Aligned_cols=35 Identities=11% Similarity=-0.024 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHH
Q 035824 30 EILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVL 64 (121)
Q Consensus 30 e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~ 64 (121)
..||..|...||+.-..-...+.++||-|..--++
T Consensus 29 ~gl~~~~~~~lR~~lr~~~~~~~V~KNtL~~~Al~ 63 (172)
T PRK00099 29 RGLTVAQMTELRKKLREAGVEYKVVKNTLARRALE 63 (172)
T ss_pred CCCcHHHHHHHHHHHHHcCCEEEEehhHHHHHHHh
Confidence 35777777777777666566677777766554443
No 47
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=39.45 E-value=2.3e+02 Score=23.76 Aligned_cols=57 Identities=12% Similarity=0.124 Sum_probs=37.5
Q ss_pred HHHHHHHhccC-CCCCCCC--CCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 7 EAWLIENLTKF-ELPKAPT--EAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 7 ~~~~~~~l~~~-~~~~~~~--~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
.+.+++.+.+. .+.+..+ -..+|..+|.+..+.|++.|- ..++||-....|.++..+
T Consensus 85 l~~ll~~i~~~~~~~~~~eit~E~~P~~lt~e~l~~l~~~Gv---nrislGvQS~~d~~L~~l 144 (400)
T PRK07379 85 LERILTTLDQRFGIAPDAEISLEIDPGTFDLEQLQGYRSLGV---NRVSLGVQAFQDELLALC 144 (400)
T ss_pred HHHHHHHHHHhCCCCCCCEEEEEeCCCcCCHHHHHHHHHCCC---CEEEEEcccCCHHHHHHh
Confidence 45556666543 3332210 113578899999999999874 489999888887776554
No 48
>PF02070 NMU: Neuromedin U; InterPro: IPR008199 Neuromedin U (NmU) [, ] is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C-terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved.; GO: 0006940 regulation of smooth muscle contraction
Probab=38.68 E-value=25 Score=18.85 Aligned_cols=17 Identities=18% Similarity=0.174 Sum_probs=11.1
Q ss_pred CCEEEEEeeCCEEEEEeCCC
Q 035824 100 KGIVIDINPSNTIIFYRGKN 119 (121)
Q Consensus 100 ga~vVq~i~G~~~iLYR~~n 119 (121)
|.-.+|. +-..|||++|
T Consensus 9 gP~~~qs---rgyFlfRPRN 25 (25)
T PF02070_consen 9 GPGGIQS---RGYFLFRPRN 25 (25)
T ss_pred CCccccc---ccEEEeccCC
Confidence 3334543 4578999987
No 49
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=38.65 E-value=2.3e+02 Score=23.62 Aligned_cols=36 Identities=8% Similarity=0.204 Sum_probs=28.9
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
+|+.+|.+..+.|+..|-. .+.||-.-.++.+++.+
T Consensus 116 ~p~~~~~e~L~~l~~~Gvn---risiGvQS~~~~~L~~l 151 (394)
T PRK08898 116 NPGTFEAEKFAQFRASGVN---RLSIGIQSFNDAHLKAL 151 (394)
T ss_pred CCCCCCHHHHHHHHHcCCC---eEEEecccCCHHHHHHh
Confidence 4788999999999998864 68888888888777543
No 50
>cd05796 Ribosomal_P0_like Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WAS
Probab=37.80 E-value=94 Score=22.95 Aligned_cols=31 Identities=13% Similarity=0.207 Sum_probs=14.0
Q ss_pred HhhcCCCceEEecCCCCcHHHHHHHHHHHHh
Q 035824 42 RTDEKKKNYVQVGRRGIFGGVVLNMHLHWKK 72 (121)
Q Consensus 42 ~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~ 72 (121)
..-..-+-++.+.-.|++-+-+.+|+..|..
T Consensus 12 e~l~~y~~v~iv~~~gl~~~ql~~iR~~lr~ 42 (163)
T cd05796 12 EAVDKYKYIYVFSVDNMRNNKLKDIRQEWKD 42 (163)
T ss_pred HHHHhCCEEEEEEecCCCHHHHHHHHHHhcC
Confidence 3333334444444444444444444444444
No 51
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=37.58 E-value=2.3e+02 Score=23.26 Aligned_cols=58 Identities=19% Similarity=0.181 Sum_probs=37.9
Q ss_pred HHHHHHHHhcc-CCCCC--CCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 6 KEAWLIENLTK-FELPK--APTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 6 ~~~~~~~~l~~-~~~~~--~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
.-++|++.+.+ +.+.. .-.--.+|..+|.+..+.|++.|- ..|+||-...++.+++.+
T Consensus 77 ~l~~ll~~i~~~~~~~~~~e~t~e~~p~~i~~e~l~~l~~~G~---~rvslGvQS~~~~~L~~l 137 (375)
T PRK05628 77 GLARVLDAVRDTFGLAPGAEVTTEANPESTSPEFFAALRAAGF---TRVSLGMQSAAPHVLAVL 137 (375)
T ss_pred HHHHHHHHHHHhCCCCCCCEEEEEeCCCCCCHHHHHHHHHcCC---CEEEEecccCCHHHHHHc
Confidence 44566666665 22211 100112477899999999999874 489999888888887554
No 52
>TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative. This model represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulfate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation.
Probab=36.24 E-value=1.5e+02 Score=20.69 Aligned_cols=67 Identities=15% Similarity=0.119 Sum_probs=49.6
Q ss_pred CCCHHHHHHHHHhhcCCCceEEecCC--CCcH----HHHHHHHHHHHhC-CeeEEEecCCChHHHHHHHHHHHh
Q 035824 31 ILTDEERHYLKRTDEKKKNYVQVGRR--GIFG----GVVLNMHLHWKKH-ETVKVVSKPCEPWKIHEYAEVLAQ 97 (121)
Q Consensus 31 ~LT~kqr~~LR~~a~~lkpvv~IGk~--Glt~----~vi~~i~~al~~h-ELIKVk~~~~~~~~~~~~a~~L~~ 97 (121)
.+.+.-+.+|+.+..+-+.+..+|-. |-.+ ..+..++..+... +.+||........|+..+.+.+++
T Consensus 65 ~~p~~~~~fl~~l~~~~k~~avfgtgd~~~~~~~f~~a~~~~~~~l~~~~~~~~i~~~~~~~~d~~~~~~~~~~ 138 (140)
T TIGR01754 65 RTPDEMKDFIAELGYKPSNVAIFGTGETQWGDDLYCGAVDRLAHFFGSSHPVLKIEQMPHGEQDGRAIYDWLEG 138 (140)
T ss_pred cCCHHHHHHHHHhcccCCEEEEEEcCCCCcCcchHhHHHHHHHHHHcCcCCceeEecCCcccccHHHHHHHHHH
Confidence 46667888899887777888777755 4542 7899999999653 688999877776677776666554
No 53
>PF01918 Alba: Alba; InterPro: IPR002775 Members of this family include the archaeal protein Alba and a number of eukaryotic proteins with no known function. The DNA/RNA-binding protein Alba binds double-stranded DNA tightly but without sequence specificity. It binds rRNA and mRNA in vivo, and may play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes. It is distributed uniformly and abundantly on the chromosome. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner []. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [].; GO: 0003676 nucleic acid binding; PDB: 3TOE_B 3IAB_A 1NFJ_A 1NFH_B 2Q3V_B 1VM0_B 1NH9_A 1Y9X_A 3U6Y_C 2H9U_A ....
Probab=36.23 E-value=1.1e+02 Score=19.02 Aligned_cols=57 Identities=14% Similarity=0.012 Sum_probs=46.5
Q ss_pred eEEecCCCCcHHHHHHHHHHH-----HhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEE
Q 035824 50 YVQVGRRGIFGGVVLNMHLHW-----KKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDI 106 (121)
Q Consensus 50 vv~IGk~Glt~~vi~~i~~al-----~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~ 106 (121)
.+.|+++.-..+.+..+...| ..++-|.+.-.+..-...=.+|+.+.+..+..+.|+
T Consensus 2 ~I~V~~~~~~~~~v~~~~~~L~~~~~~~~~~V~l~g~G~aI~kaI~vaei~K~~~~~~~~qv 63 (70)
T PF01918_consen 2 EIYVSSNSPIKSYVKRALKLLEGRENGKNDEVVLKGRGKAISKAISVAEILKRRFGEGLYQV 63 (70)
T ss_dssp EEEE-STS-HHHHHHHHHHHHT-TTHTTCSEEEEEEECCHHHHHHHHHHHHHHHTSTTTEEE
T ss_pred EEEECCCCCHHHHHHHHHHHHhhhhcCCCCEEEEEEEcHHHHHHHHHHHHHHHhhcCCCEEE
Confidence 578888888889999999999 778999999999888888899999999986555543
No 54
>PF08572 PRP3: pre-mRNA processing factor 3 (PRP3); InterPro: IPR013881 Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa [].
Probab=35.70 E-value=40 Score=26.68 Aligned_cols=18 Identities=39% Similarity=0.571 Sum_probs=14.8
Q ss_pred CCCCCCHHHHHHHHHhhc
Q 035824 28 DPEILTDEERHYLKRTDE 45 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~ 45 (121)
-+..||.+|++.||+.-.
T Consensus 137 ~~~~LTkkErKKlRr~rR 154 (223)
T PF08572_consen 137 PPVYLTKKERKKLRRQRR 154 (223)
T ss_pred cCcccChHHHHHHHHHHH
Confidence 467799999999998653
No 55
>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase. This model respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This model identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologs of this gene are not found in plants which rely solely on the aerobic cyclase.
Probab=35.49 E-value=2.9e+02 Score=23.82 Aligned_cols=59 Identities=8% Similarity=0.071 Sum_probs=37.0
Q ss_pred hHHHHHHHHhcc---CCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 5 RKEAWLIENLTK---FELPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 5 ~~~~~~~~~l~~---~~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
++...|.+.|.+ ..+.|....+.+.-..+.+..+.|++.|. -.|.+|-...++.+++.+
T Consensus 255 ~~~~~l~~~l~~~~~l~i~w~~~~r~~~i~~d~ell~~l~~aG~---~~v~iGiES~~~~~L~~~ 316 (497)
T TIGR02026 255 KKFQEFCEEIIARNPISVTWGINTRVTDIVRDADILHLYRRAGL---VHISLGTEAAAQATLDHF 316 (497)
T ss_pred HHHHHHHHHHHhcCCCCeEEEEecccccccCCHHHHHHHHHhCC---cEEEEccccCCHHHHHHh
Confidence 345566666653 44566644433332337778888888875 378889777777666544
No 56
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=35.45 E-value=2.6e+02 Score=23.70 Aligned_cols=57 Identities=16% Similarity=0.194 Sum_probs=37.7
Q ss_pred HHHHHHHHhccCCCCCCC----CCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 6 KEAWLIENLTKFELPKAP----TEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 6 ~~~~~~~~l~~~~~~~~~----~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
....+++.+.+. +|+.. .-..+|..+|.+..+.|++.|- ..+.||-.+.++.++..+
T Consensus 120 ~l~~ll~~i~~~-~~~~~~~eitie~np~~l~~e~l~~lk~~G~---~risiGvqS~~~~~l~~l 180 (455)
T TIGR00538 120 QISRLMKLIREN-FPFNADAEISIEIDPRYITKDVIDALRDEGF---NRLSFGVQDFNKEVQQAV 180 (455)
T ss_pred HHHHHHHHHHHh-CCCCCCCeEEEEeccCcCCHHHHHHHHHcCC---CEEEEcCCCCCHHHHHHh
Confidence 445566666553 22211 0112477899999999999984 388999888888776555
No 57
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=35.29 E-value=2e+02 Score=23.35 Aligned_cols=52 Identities=13% Similarity=0.122 Sum_probs=40.3
Q ss_pred HHHHHHHHHhhcCCCceEEecCCCCcHHHHH-HHHHHHH--hCCeeEEEecCCCh
Q 035824 34 DEERHYLKRTDEKKKNYVQVGRRGIFGGVVL-NMHLHWK--KHETVKVVSKPCEP 85 (121)
Q Consensus 34 ~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~-~i~~al~--~hELIKVk~~~~~~ 85 (121)
..-+..+++.|..-.||+..|..|.--..+. .||..-. ...+|.|.|...+.
T Consensus 16 ~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~ 70 (326)
T PRK11608 16 LEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNE 70 (326)
T ss_pred HHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCH
Confidence 3456778888989999999999999988875 4564443 24799999998654
No 58
>PRK14334 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=35.21 E-value=2.8e+02 Score=23.52 Aligned_cols=57 Identities=18% Similarity=0.123 Sum_probs=38.2
Q ss_pred HHHHHHHhccCCCC---CCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 7 EAWLIENLTKFELP---KAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 7 ~~~~~~~l~~~~~~---~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
-..|++.+.+..++ |.. ..|..+|++....|+..+. .=+.+.||=...++.++..+.
T Consensus 207 ~~~Ll~~l~~~~i~~ir~~~---~~p~~i~~ell~~l~~~~~-g~~~l~igvQSgs~~vLk~m~ 266 (440)
T PRK14334 207 FAELLRLVGASGIPRVKFTT---SHPMNFTDDVIAAMAETPA-VCEYIHLPVQSGSDRVLRRMA 266 (440)
T ss_pred HHHHHHHHHhcCCcEEEEcc---CCcccCCHHHHHHHHhcCc-CCCeEEeccccCCHHHHHHhC
Confidence 44566666554433 332 2366799998888887542 336899998888888876654
No 59
>PLN02759 Formate--tetrahydrofolate ligase
Probab=35.14 E-value=26 Score=31.99 Aligned_cols=100 Identities=18% Similarity=0.192 Sum_probs=57.3
Q ss_pred HHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCCce---------------EEecCCCCcHH----------HHH
Q 035824 10 LIENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKKNY---------------VQVGRRGIFGG----------VVL 64 (121)
Q Consensus 10 ~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpv---------------v~IGk~Glt~~----------vi~ 64 (121)
.++-|+|+-.-.. ||..||++|++.+..++...+.+ +.||..|-..+ +--
T Consensus 194 ~~~rl~~l~i~~~-----~p~~lt~~e~~~~~~L~IDp~~I~w~RvlD~NDR~LR~I~vGlgg~~~G~~Re~gFdITvAS 268 (637)
T PLN02759 194 MFRRLKKLGISKT-----DPDELTPEERKKFARLDIDPASITWRRVMDVNDRFLRKITVGQGPEEKGMTRETGFDITVAS 268 (637)
T ss_pred HHHHHHhhccCcC-----CccccCHHHhhhhhccCcCcceeEEEeeccccchhhhceeeCcCCCCCCCcccCCceeeHHH
Confidence 3455666665333 67789999999999988665533 66776654332 111
Q ss_pred HHHHH------HHh--CCeeEEEec----CCC--hH---HHHHHHHHHHhHcCCEEEEEeeCCEEEE
Q 035824 65 NMHLH------WKK--HETVKVVSK----PCE--PW---KIHEYAEVLAQLSKGIVIDINPSNTIIF 114 (121)
Q Consensus 65 ~i~~a------l~~--hELIKVk~~----~~~--~~---~~~~~a~~L~~~tga~vVq~i~G~~~iL 114 (121)
||=.- |+. +-|=+|.+- +.+ .. ..-.|+..|.++..-.+||.++|.=+++
T Consensus 269 EiMAILcLa~dl~Dlk~Rlg~ivvg~~~~g~pVta~DL~~~GAmt~LLkDAikPNLvQTlEgtPa~v 335 (637)
T PLN02759 269 EIMAVLALTTSLADMRERLGKMVIGNSKAGEPVTADDLGVGGALTVLMKDAIHPTLMQTLEGTPVLV 335 (637)
T ss_pred HHHHHHHHcCCHHHHHHHHhCEEEEEcCCCCceeHHHcCchHhHHHHHHhhhCccceeecCCCceEE
Confidence 11111 111 123333332 211 11 2246788889999999999885544443
No 60
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=35.12 E-value=2.4e+02 Score=23.34 Aligned_cols=56 Identities=14% Similarity=0.180 Sum_probs=36.0
Q ss_pred HHHHHHHhccCCCCCCC--C--CCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 7 EAWLIENLTKFELPKAP--T--EAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 7 ~~~~~~~l~~~~~~~~~--~--~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
-+++++.+.+. +|+.+ + =-.+|..+|.+..+.|+..|- ..+.||-.-..|.++..+
T Consensus 74 L~~ll~~i~~~-f~~~~~~eit~E~~P~~i~~e~L~~l~~~Gv---nrislGvQS~~d~vL~~l 133 (380)
T PRK09057 74 VAALLDAIARL-WPVADDIEITLEANPTSVEAGRFRGYRAAGV---NRVSLGVQALNDADLRFL 133 (380)
T ss_pred HHHHHHHHHHh-CCCCCCccEEEEECcCcCCHHHHHHHHHcCC---CEEEEecccCCHHHHHHc
Confidence 45566666552 23221 1 112478899999999999885 378888777777775433
No 61
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=35.00 E-value=1.8e+02 Score=21.92 Aligned_cols=62 Identities=18% Similarity=0.139 Sum_probs=35.8
Q ss_pred HHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhC-CeeE-EEecCC-ChHHHHHHHHHHHhHcCCEEE
Q 035824 39 YLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKH-ETVK-VVSKPC-EPWKIHEYAEVLAQLSKGIVI 104 (121)
Q Consensus 39 ~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~h-ELIK-Vk~~~~-~~~~~~~~a~~L~~~tga~vV 104 (121)
.|+..+.+=.+++.+|. ++++++.+.+.|+.+ .-++ +-+.+. +.++.+++++.|.+ +++.+|
T Consensus 40 l~~~~~~~~~~vfllG~---~~~v~~~~~~~l~~~yP~l~i~g~~g~f~~~~~~~i~~~I~~-s~~dil 104 (177)
T TIGR00696 40 LCQRAGKEKLPIFLYGG---KPDVLQQLKVKLIKEYPKLKIVGAFGPLEPEERKAALAKIAR-SGAGIV 104 (177)
T ss_pred HHHHHHHcCCeEEEECC---CHHHHHHHHHHHHHHCCCCEEEEECCCCChHHHHHHHHHHHH-cCCCEE
Confidence 34443333357777754 577777777777663 2222 222332 34455677777776 778777
No 62
>PLN02561 triosephosphate isomerase
Probab=34.41 E-value=2e+02 Score=23.12 Aligned_cols=64 Identities=19% Similarity=0.084 Sum_probs=43.7
Q ss_pred HHHHHHHhhcCCCceEEecCC------CCcHHHH-HHHHHHHHhCCe-eEEEe---------c--CCChHHHHHHHHHHH
Q 035824 36 ERHYLKRTDEKKKNYVQVGRR------GIFGGVV-LNMHLHWKKHET-VKVVS---------K--PCEPWKIHEYAEVLA 96 (121)
Q Consensus 36 qr~~LR~~a~~lkpvv~IGk~------Glt~~vi-~~i~~al~~hEL-IKVk~---------~--~~~~~~~~~~a~~L~ 96 (121)
-++..+.+.+.|.|++=||-. |-|..++ .++...+..-.- -.+-+ - -.+.++.++++..|.
T Consensus 111 ~~Kv~~al~~gl~pIvCvGE~~~er~~~~~~~~v~~Ql~~~l~~v~~~~~iiIAYEPvWAIGtG~~as~~~~~~v~~~Ir 190 (253)
T PLN02561 111 GDKVAYALSQGLKVIACVGETLEQRESGSTMDVVAAQTKAIADKVSDWANVVLAYEPVWAIGTGKVATPAQAQEVHDELR 190 (253)
T ss_pred HHHHHHHHHCcCEEEEEcCCCHHHHhcCCHHHHHHHHHHHHHhccccccceEEEECCHHHhCCCCCCCHHHHHHHHHHHH
Confidence 456678889999999999965 7888876 778877765221 12222 0 125688888888887
Q ss_pred hHc
Q 035824 97 QLS 99 (121)
Q Consensus 97 ~~t 99 (121)
+..
T Consensus 191 ~~l 193 (253)
T PLN02561 191 KWL 193 (253)
T ss_pred HHH
Confidence 643
No 63
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=34.09 E-value=34 Score=21.52 Aligned_cols=18 Identities=11% Similarity=0.442 Sum_probs=14.3
Q ss_pred EEEEe-eCCEEEEEeCCCC
Q 035824 103 VIDIN-PSNTIIFYRGKNY 120 (121)
Q Consensus 103 vVq~i-~G~~~iLYR~~ny 120 (121)
+||.+ -|+.+|||-|.||
T Consensus 23 ~VQRvsdgkaaVLFEGGnW 41 (53)
T PF11623_consen 23 FVQRVSDGKAAVLFEGGNW 41 (53)
T ss_dssp EEEEEETTEEEEEEEETTE
T ss_pred EEEEeeCCeEEEEecCCCc
Confidence 45554 5799999999998
No 64
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=33.60 E-value=2.6e+02 Score=22.91 Aligned_cols=57 Identities=14% Similarity=0.099 Sum_probs=36.6
Q ss_pred HHHHHHHhccCCCCCCC--CCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 7 EAWLIENLTKFELPKAP--TEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 7 ~~~~~~~l~~~~~~~~~--~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
-++|++.+.+. ++... .=..+|..+|.+..+.|++.|-. .++||-.++.+.++..+.
T Consensus 70 l~~ll~~i~~~-~~~~~eitiE~nP~~~~~e~l~~l~~~Gvn---RiSiGvQS~~~~~L~~lg 128 (350)
T PRK08446 70 YEPIFEIISPY-LSKDCEITTEANPNSATKAWLKGMKNLGVN---RISFGVQSFNEDKLKFLG 128 (350)
T ss_pred HHHHHHHHHHh-cCCCceEEEEeCCCCCCHHHHHHHHHcCCC---EEEEecccCCHHHHHHcC
Confidence 45566666554 22110 01125788999999999998643 778888887777765443
No 65
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=33.57 E-value=1.8e+02 Score=23.93 Aligned_cols=68 Identities=16% Similarity=0.019 Sum_probs=41.4
Q ss_pred HHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhC--CeeEEEecCCC-hHHHHHHHHHHHhHcCCEEEEEe
Q 035824 36 ERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKH--ETVKVVSKPCE-PWKIHEYAEVLAQLSKGIVIDIN 107 (121)
Q Consensus 36 qr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~h--ELIKVk~~~~~-~~~~~~~a~~L~~~tga~vVq~i 107 (121)
--..|++.+ +.++.|...++...+.+.+...|+.+ +.+-..+.+++ .+..+++++.+.+ .++.+|=-+
T Consensus 21 l~~~l~~~g---~~~livtd~~~~~~~~~~v~~~l~~~~~~~~~~~~~~ep~~~~v~~~~~~~~~-~~~d~IIav 91 (366)
T PRK09423 21 LGEYLKPLG---KRALVIADEFVLGIVGDRVEASLKEAGLTVVFEVFNGECSDNEIDRLVAIAEE-NGCDVVIGI 91 (366)
T ss_pred HHHHHHHcC---CEEEEEEChhHHHHHHHHHHHHHHhCCCeEEEEEeCCCCCHHHHHHHHHHHHh-cCCCEEEEe
Confidence 345566665 55666666778888899999999876 43333454544 3455666655544 455555234
No 66
>cd08170 GlyDH Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway . In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=33.36 E-value=2.1e+02 Score=23.26 Aligned_cols=67 Identities=15% Similarity=-0.010 Sum_probs=40.0
Q ss_pred HHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCe--eEEEecCCCh-HHHHHHHHHHHhHcCCEEEEEeeC
Q 035824 39 YLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHET--VKVVSKPCEP-WKIHEYAEVLAQLSKGIVIDINPS 109 (121)
Q Consensus 39 ~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hEL--IKVk~~~~~~-~~~~~~a~~L~~~tga~vVq~i~G 109 (121)
.+++.+ +.++.|+..++..++.+.+..+|+.+.+ .-..+.+++. ++.+++++...+ .++.+|=-+.|
T Consensus 17 ~~~~~~---~r~livt~~~~~~~~~~~v~~~L~~~~i~~~~~~~~~~p~~~~v~~~~~~~~~-~~~D~IIavGG 86 (351)
T cd08170 17 YLARLG---KRALIIADEFVLDLVGAKIEESLAAAGIDARFEVFGGECTRAEIERLAEIARD-NGADVVIGIGG 86 (351)
T ss_pred HHHHhC---CeEEEEECHHHHHHHHHHHHHHHHhCCCeEEEEEeCCcCCHHHHHHHHHHHhh-cCCCEEEEecC
Confidence 455553 5566677677778899999999998743 2223445544 455565555444 56555523433
No 67
>TIGR03765 ICE_PFL_4695 integrating conjugative element protein, PFL_4695 family. This model describes a protein family exemplified by PFL_4695 of Pseudomonas fluorescens Pf-5. Full-length proteins in this family show some architectural variety, but this model represents a conserved domain. Most or all member proteins belong to laterally transferred chromosomal islands called integrative conjugative elements, or ICE.
Probab=32.68 E-value=1.7e+02 Score=20.78 Aligned_cols=47 Identities=9% Similarity=-0.048 Sum_probs=39.0
Q ss_pred cCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHH
Q 035824 45 EKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEY 91 (121)
Q Consensus 45 ~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~ 91 (121)
-.+.|+|.||-+-.+-.++.+=.+.|..---+-+.++-.+....+++
T Consensus 22 pg~~p~FlIGdD~~S~~WL~~~~~~L~~l~AvGlVVnV~t~~~l~~L 68 (105)
T TIGR03765 22 PGLTPLFLIGDDPASRQWLQQNAAALKSLGAVGLVVNVETAAALQRL 68 (105)
T ss_pred CCCCceEEEeCCHHHHHHHHHHHHHHHHCCCeEEEEecCCHHHHHHH
Confidence 34679999999999999999999999998888888877776655444
No 68
>PRK14566 triosephosphate isomerase; Provisional
Probab=32.49 E-value=2.6e+02 Score=22.65 Aligned_cols=76 Identities=13% Similarity=0.123 Sum_probs=50.9
Q ss_pred HHHHHhhcCCCceEEecC------CCCcHHHH-HHHHHHHHh-C--CeeEEEec---------C--CChHHHHHHHHHHH
Q 035824 38 HYLKRTDEKKKNYVQVGR------RGIFGGVV-LNMHLHWKK-H--ETVKVVSK---------P--CEPWKIHEYAEVLA 96 (121)
Q Consensus 38 ~~LR~~a~~lkpvv~IGk------~Glt~~vi-~~i~~al~~-h--ELIKVk~~---------~--~~~~~~~~~a~~L~ 96 (121)
+..+.+.+.|.|++=||- .|.|..++ .++...|+. . +.-+|.+. + .++++.++++..|.
T Consensus 120 Kv~~al~~gl~pIvCvGEtleere~g~t~~vv~~Ql~~~l~~~~~~~~~~ivIAYEPvWAIGTG~~At~e~a~~v~~~IR 199 (260)
T PRK14566 120 KFAAAQKHGLTPILCVGESGPAREARRTFEVIAEELDIVIEKNGTMAFDNAIIAYEPLWAVGTGKSATPEQAQEVHAFIR 199 (260)
T ss_pred HHHHHHHCCCEEEEEcCCcHHHHhcCCHHHHHHHHHHHHHhccchhhcCcEEEEECcHHhcCCCCCCCHHHHHHHHHHHH
Confidence 667889999999999995 48888886 588888862 1 12333332 1 25688888888888
Q ss_pred hHcC---CEEEEEeeCCEEEEEeC
Q 035824 97 QLSK---GIVIDINPSNTIIFYRG 117 (121)
Q Consensus 97 ~~tg---a~vVq~i~G~~~iLYR~ 117 (121)
+... ..+- .++-|||=|
T Consensus 200 ~~l~~~~~~~a----~~~rIlYGG 219 (260)
T PRK14566 200 KRLSEVSPFIG----ENIRILYGG 219 (260)
T ss_pred HHHHhcCcccc----ccceEEecC
Confidence 7653 2222 246677754
No 69
>TIGR01212 radical SAM protein, TIGR01212 family. This uncharacterized protein family shows significant similarity to TIGR01211, a longer protein that is a histone acetyltransferase at its C-terminus and is a subunit of RNA polymerase II (in yeast). This family lacks the GNAT acetyltransferase domain.
Probab=31.76 E-value=2.7e+02 Score=22.37 Aligned_cols=85 Identities=19% Similarity=0.239 Sum_probs=48.9
Q ss_pred CCCCCCHHHHHHHHHhhcC-CCceEEecCCCCcHHHHHHHHH------------HHHhCCeeEEEec------CCChHHH
Q 035824 28 DPEILTDEERHYLKRTDEK-KKNYVQVGRRGIFGGVVLNMHL------------HWKKHETVKVVSK------PCEPWKI 88 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~-lkpvv~IGk~Glt~~vi~~i~~------------al~~hELIKVk~~------~~~~~~~ 88 (121)
.|..++.+....|+.+... .+..+.+|-.-.++.+++.|.. .+..+- ++|.+. +...+++
T Consensus 117 rpd~l~~e~l~~L~~l~~~G~~~~i~lGlQS~~d~~L~~i~Rg~t~~~~~~ai~~l~~~g-i~v~~~lI~GlPget~e~~ 195 (302)
T TIGR01212 117 RPDCVPDEVLDLLAEYVERGYEVWVELGLQTAHDKTLKKINRGHDFACYVDAVKRARKRG-IKVCSHVILGLPGEDREEM 195 (302)
T ss_pred cCCcCCHHHHHHHHHhhhCCceEEEEEccCcCCHHHHHHHcCcChHHHHHHHHHHHHHcC-CEEEEeEEECCCCCCHHHH
Confidence 4678999988888877543 4467899977777776655432 222222 344432 2344555
Q ss_pred HHHHHHHHhHcCCEEEEEeeCCEEEEEeC
Q 035824 89 HEYAEVLAQLSKGIVIDINPSNTIIFYRG 117 (121)
Q Consensus 89 ~~~a~~L~~~tga~vVq~i~G~~~iLYR~ 117 (121)
.+.+..+.+ ++..-|.+ +.+.++++
T Consensus 196 ~~t~~~l~~-l~~d~i~i---~~l~~~pg 220 (302)
T TIGR01212 196 METAKIVSL-LDVDGIKI---HPLHVVKG 220 (302)
T ss_pred HHHHHHHHh-cCCCEEEE---EEEEecCC
Confidence 555555543 45555543 34555544
No 70
>TIGR03820 lys_2_3_AblA lysine-2,3-aminomutase. This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
Probab=31.09 E-value=3.5e+02 Score=23.42 Aligned_cols=85 Identities=20% Similarity=0.241 Sum_probs=50.5
Q ss_pred CCCCCCCCHHHHHH----HHHhhcCCCceEEecCC-------CCcHHHHHHHHHHHHhCCeeEEEecCC-ChHHHHHHHH
Q 035824 26 AYDPEILTDEERHY----LKRTDEKKKNYVQVGRR-------GIFGGVVLNMHLHWKKHETVKVVSKPC-EPWKIHEYAE 93 (121)
Q Consensus 26 ~~~~e~LT~kqr~~----LR~~a~~lkpvv~IGk~-------Glt~~vi~~i~~al~~hELIKVk~~~~-~~~~~~~~a~ 93 (121)
-.||-+++++.... |+++-| + ..+.||-+ =+|++++..+..+ -.+-|.+.-| +.+...++.+
T Consensus 163 GGDPLll~d~~L~~iL~~L~~Iph-V-~~IRI~TR~pvv~P~RIT~ell~~Lk~~----~~~~v~~h~nhp~Eit~~a~~ 236 (417)
T TIGR03820 163 GGDPLLLSDDYLDWILTELRAIPH-V-EVIRIGTRVPVVLPQRITDELVAILKKH----HPVWLNTHFNHPREITASSKK 236 (417)
T ss_pred CCccccCChHHHHHHHHHHhhcCC-C-ceEEEeeccccccccccCHHHHHHHHhc----CCeEEEEeCCChHhChHHHHH
Confidence 35677787755433 333322 1 34678877 5888887766654 3445544443 3455667777
Q ss_pred HHHhHcCCEEEEEeeCCEEEEEeCCC
Q 035824 94 VLAQLSKGIVIDINPSNTIIFYRGKN 119 (121)
Q Consensus 94 ~L~~~tga~vVq~i~G~~~iLYR~~n 119 (121)
.+.....+-+. + |+..+|-||=|
T Consensus 237 Al~~L~~aGI~--l-~nQsVLLkGVN 259 (417)
T TIGR03820 237 ALAKLADAGIP--L-GNQSVLLAGVN 259 (417)
T ss_pred HHHHHHHcCCE--E-EeeceEECCcC
Confidence 77776555443 2 67778877754
No 71
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=30.70 E-value=2.6e+02 Score=24.08 Aligned_cols=68 Identities=1% Similarity=-0.133 Sum_probs=36.4
Q ss_pred HHHHhhcCCCceEEecC-CCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHc-CCEEEEEeeCCEE
Q 035824 39 YLKRTDEKKKNYVQVGR-RGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLS-KGIVIDINPSNTI 112 (121)
Q Consensus 39 ~LR~~a~~lkpvv~IGk-~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~t-ga~vVq~i~G~~~ 112 (121)
.|+++|..| +|.-|. .|-..+++.++-..+. .-.|-+.....-.-.+.-+.+++.+ |..+.++ .++++
T Consensus 65 ~L~~~g~~L--~v~~g~~~g~~~~vl~~l~~~~~---i~~v~~~~~~~~~~~~rd~~v~~~l~~i~~~~~-~~~~l 134 (472)
T PRK10674 65 ALAEKGIPL--LFHEVDDFAASVEWLKQFCQQHQ---VTHLFYNYQYEVNERQRDAAVERALRNVVCQGF-DDSVL 134 (472)
T ss_pred HHHHcCCce--EEEecCCcCCHHHHHHHHHHHcC---CCEEEEecccCHHHHHHHHHHHHHcCCCEEEEe-cCceE
Confidence 345555444 666676 7889999988876665 4445555543322333333344433 4333333 25544
No 72
>PRK07315 fructose-bisphosphate aldolase; Provisional
Probab=30.20 E-value=66 Score=26.22 Aligned_cols=50 Identities=18% Similarity=0.001 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCCh
Q 035824 31 ILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEP 85 (121)
Q Consensus 31 ~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~ 85 (121)
.|.-+-.+.+++.-.. -|+|.+|-.|++++-+..+ + ..-..||.+...-.
T Consensus 187 ~l~~e~L~~i~~~~~~-iPlVlhGGSGi~~e~~~~~---i-~~Gi~KiNv~T~i~ 236 (293)
T PRK07315 187 GLDLDHLEKLTEAVPG-FPIVLHGGSGIPDDQIQEA---I-KLGVAKVNVNTECQ 236 (293)
T ss_pred cCCHHHHHHHHHhccC-CCEEEECCCCCCHHHHHHH---H-HcCCCEEEEccHHH
Confidence 4666655555544311 5999999999999776544 2 35577777765433
No 73
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=29.87 E-value=1.1e+02 Score=21.32 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=17.4
Q ss_pred hHHHHHHHHHHHhHcCCEEEEEeeCCEEEE
Q 035824 85 PWKIHEYAEVLAQLSKGIVIDINPSNTIIF 114 (121)
Q Consensus 85 ~~~~~~~a~~L~~~tga~vVq~i~G~~~iL 114 (121)
....+.=-.+|++-+||.|+++. |.+++|
T Consensus 16 ~~~I~~RL~qLsdNCGGkVl~v~-~~tAil 44 (90)
T PF11608_consen 16 PSSIKNRLRQLSDNCGGKVLSVS-GGTAIL 44 (90)
T ss_dssp HHHHHHHHHHHHHTTT--EEE---TT-EEE
T ss_pred HHHHHHHHHHHhhccCCEEEEEe-CCEEEE
Confidence 34445556788889999999986 777665
No 74
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=29.63 E-value=1.3e+02 Score=21.19 Aligned_cols=47 Identities=11% Similarity=0.128 Sum_probs=29.0
Q ss_pred CCCCHHHHHHHHHhhcCCCceEEecCC--CCcHHHHHHHHHHHHhCCee
Q 035824 30 EILTDEERHYLKRTDEKKKNYVQVGRR--GIFGGVVLNMHLHWKKHETV 76 (121)
Q Consensus 30 e~LT~kqr~~LR~~a~~lkpvv~IGk~--Glt~~vi~~i~~al~~hELI 76 (121)
..|-..=...++..+....+++.||.+ .|+...+.+.-++|+.+++|
T Consensus 43 ~dLG~Rm~~a~~~~~~g~~~vvliGsD~P~l~~~~l~~A~~~L~~~d~V 91 (122)
T PF09837_consen 43 GDLGERMANAFQQAARGYEPVVLIGSDCPDLTPDDLEQAFEALQRHDVV 91 (122)
T ss_dssp SSHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHHHHHHHHHTTT-SEE
T ss_pred CCHHHHHHHHHHHHHcCCCcEEEEcCCCCCCCHHHHHHHHHHhccCCEE
Confidence 345555555566666666788888865 67778888888888877765
No 75
>KOG2335 consensus tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=29.53 E-value=1.2e+02 Score=25.88 Aligned_cols=52 Identities=15% Similarity=0.127 Sum_probs=35.6
Q ss_pred CcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCCEE
Q 035824 58 IFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSNTI 112 (121)
Q Consensus 58 lt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~~~ 112 (121)
+..++|..++.-+..-=-+||++.... ++.-+.+. ..+.+|+.++-+. |+|-
T Consensus 128 Lv~e~V~~v~~~l~~pVs~KIRI~~d~-~kTvd~ak-~~e~aG~~~ltVH-GRtr 179 (358)
T KOG2335|consen 128 LVGEMVSAVRANLNVPVSVKIRIFVDL-EKTVDYAK-MLEDAGVSLLTVH-GRTR 179 (358)
T ss_pred HHHHHHHHHHhhcCCCeEEEEEecCcH-HHHHHHHH-HHHhCCCcEEEEe-cccH
Confidence 345566667777776778899987654 44444554 5567899999776 8874
No 76
>PRK14862 rimO ribosomal protein S12 methylthiotransferase; Provisional
Probab=28.91 E-value=2.6e+02 Score=23.84 Aligned_cols=60 Identities=17% Similarity=0.059 Sum_probs=38.6
Q ss_pred hHHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 5 RKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 5 ~~~~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
..-..|++.|.+..+ |-.-.--.|..++++-...++. | ..-|.+.||-...++.++..+.
T Consensus 216 ~~~~~Ll~~l~~~~~-~~r~~~~~p~~~~dell~~m~~-g-~~~~~l~IglESgs~~vLk~m~ 275 (440)
T PRK14862 216 TRMTDLCEALGELGA-WVRLHYVYPYPHVDEVIPLMAE-G-KILPYLDIPFQHASPRVLKRMK 275 (440)
T ss_pred hHHHHHHHHHHhcCC-EEEEecCCCCcCCHHHHHHHhc-C-CCccccccccccCCHHHHHhcC
Confidence 456677777876654 3211111233467766777776 5 5778899998888888876664
No 77
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=28.85 E-value=1.4e+02 Score=24.63 Aligned_cols=33 Identities=15% Similarity=0.066 Sum_probs=16.5
Q ss_pred HHHhhcCCCceEEecCCCCcHHHHHHHHHHHHh
Q 035824 40 LKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKK 72 (121)
Q Consensus 40 LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~ 72 (121)
|+..-..-+-++.++-+|++-+-+.+|+..|..
T Consensus 17 l~e~l~~y~~v~vv~~~nv~s~ql~~iR~~LR~ 49 (310)
T PTZ00135 17 LYELLEKYKKILIVSVDNVGSKQMQDIRRSLRG 49 (310)
T ss_pred HHHHHHhCCEEEEEEcCCCCHHHHHHHHHHHhc
Confidence 444444444455555555555555555555543
No 78
>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H.
Probab=28.46 E-value=1.1e+02 Score=21.13 Aligned_cols=63 Identities=17% Similarity=0.184 Sum_probs=39.9
Q ss_pred HHHHHHHHhhcCCCceEEecCCCCcHHHH-HHHHHHHHhC--CeeEEEecCCChHHHHHHHHHHHhHcCCEEE
Q 035824 35 EERHYLKRTDEKKKNYVQVGRRGIFGGVV-LNMHLHWKKH--ETVKVVSKPCEPWKIHEYAEVLAQLSKGIVI 104 (121)
Q Consensus 35 kqr~~LR~~a~~lkpvv~IGk~Glt~~vi-~~i~~al~~h--ELIKVk~~~~~~~~~~~~a~~L~~~tga~vV 104 (121)
+=++.+++++..-.|++..|-.|---..+ ..||...... -.+-+.|...+ .+.+....|+.++
T Consensus 9 ~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~-------~~~l~~a~~gtL~ 74 (138)
T PF14532_consen 9 RLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP-------AELLEQAKGGTLY 74 (138)
T ss_dssp HHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC-------HHHHHHCTTSEEE
T ss_pred HHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc-------HHHHHHcCCCEEE
Confidence 44678889999999999999999988876 4456555542 34444555433 3344444555544
No 79
>PRK05283 deoxyribose-phosphate aldolase; Provisional
Probab=28.42 E-value=1.7e+02 Score=23.77 Aligned_cols=75 Identities=12% Similarity=-0.053 Sum_probs=55.2
Q ss_pred HHHHHHHHhhcCCCceEEec--CCCCcHHHHHHHHHHHHh-C--CeeEEEecCCCh--HHHHHHHHHHHhHcCCEEEEEe
Q 035824 35 EERHYLKRTDEKKKNYVQVG--RRGIFGGVVLNMHLHWKK-H--ETVKVVSKPCEP--WKIHEYAEVLAQLSKGIVIDIN 107 (121)
Q Consensus 35 kqr~~LR~~a~~lkpvv~IG--k~Glt~~vi~~i~~al~~-h--ELIKVk~~~~~~--~~~~~~a~~L~~~tga~vVq~i 107 (121)
+=+..++.=|..++-++.+| +.|-++.|-++|..--+. | =.+||.+..... ++...-+-.++...|+.+|..-
T Consensus 88 Ea~~Ai~~GAdEiD~Vinig~lk~g~~~~v~~ei~~v~~~~~~~~~lKVIlEt~~L~~ee~i~~a~~~a~~aGADFVKTS 167 (257)
T PRK05283 88 ETRAAIAYGADEVDVVFPYRALMAGNEQVGFELVKACKEACAANVLLKVIIETGELKDEALIRKASEIAIKAGADFIKTS 167 (257)
T ss_pred HHHHHHHcCCCEEeeeccHHHHhCCcHHHHHHHHHHHHHHhCCCceEEEEEeccccCCHHHHHHHHHHHHHhCCCEEEcC
Confidence 34456666778899999999 899999998888877665 4 379999876532 2224456678889999999753
Q ss_pred eC
Q 035824 108 PS 109 (121)
Q Consensus 108 ~G 109 (121)
.|
T Consensus 168 TG 169 (257)
T PRK05283 168 TG 169 (257)
T ss_pred CC
Confidence 35
No 80
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=28.31 E-value=2.3e+02 Score=20.74 Aligned_cols=63 Identities=11% Similarity=0.197 Sum_probs=39.2
Q ss_pred HHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhC-CeeEEE-ecC--CChHHHHHHHHHHHhHcCCEEE
Q 035824 38 HYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKH-ETVKVV-SKP--CEPWKIHEYAEVLAQLSKGIVI 104 (121)
Q Consensus 38 ~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~h-ELIKVk-~~~--~~~~~~~~~a~~L~~~tga~vV 104 (121)
..|+.....=.+++.+|.. +++++.+...|..+ .=+.|. ... .+.++.+++++.|.. +++.+|
T Consensus 39 ~l~~~~~~~~~~ifllG~~---~~~~~~~~~~l~~~yP~l~ivg~~~g~f~~~~~~~i~~~I~~-~~pdiv 105 (172)
T PF03808_consen 39 DLLRRAEQRGKRIFLLGGS---EEVLEKAAANLRRRYPGLRIVGYHHGYFDEEEEEAIINRINA-SGPDIV 105 (172)
T ss_pred HHHHHHHHcCCeEEEEeCC---HHHHHHHHHHHHHHCCCeEEEEecCCCCChhhHHHHHHHHHH-cCCCEE
Confidence 3455444454688888765 78888888777775 233333 222 245666777777766 666666
No 81
>cd08616 PI-PLCXD1c Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing 1. This subfamily corresponds to the catalytic domain present in a group of phosphatidylinositol-specific phospholipase C X domain containing 1 (PI-PLCXD1), 2 (PI-PLCXD2) and 3 (PI-PLCXD3), which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs found in vertebrates. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, members in this group contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to
Probab=28.04 E-value=3e+02 Score=22.17 Aligned_cols=47 Identities=6% Similarity=0.042 Sum_probs=35.2
Q ss_pred CcHHHHHHHHHHHHhC--CeeEEEecC---CChHHHHHHHHHHHhHcCCEEE
Q 035824 58 IFGGVVLNMHLHWKKH--ETVKVVSKP---CEPWKIHEYAEVLAQLSKGIVI 104 (121)
Q Consensus 58 lt~~vi~~i~~al~~h--ELIKVk~~~---~~~~~~~~~a~~L~~~tga~vV 104 (121)
--++++.+|.+-|..| |+|-+.+.. .+.++-+.+...|....|..++
T Consensus 98 ~~~~~L~~i~~fl~~~p~Evvil~~~~~~~~~~~~~~~l~~~l~~~fg~~l~ 149 (290)
T cd08616 98 LVKEILEEINDFLTEHPKEVVILDFNHFYGMTEEDHEKLLKMIKSIFGKKLC 149 (290)
T ss_pred hHHHHHHHHHHHHHHCCCcEEEEEEEccCCCCHHHHHHHHHHHHHHhccccc
Confidence 4567899999999986 999999874 3345556777788877776654
No 82
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=27.83 E-value=52 Score=20.86 Aligned_cols=20 Identities=20% Similarity=0.290 Sum_probs=17.3
Q ss_pred CCCCCHHHHHHHHHhhcCCC
Q 035824 29 PEILTDEERHYLKRTDEKKK 48 (121)
Q Consensus 29 ~e~LT~kqr~~LR~~a~~lk 48 (121)
|..||+.||+.+-.+|+.|-
T Consensus 23 p~~ls~~eRriih~la~~lG 42 (60)
T cd02639 23 PSSLSPAERRIVHLLASRLG 42 (60)
T ss_pred CCCCCHHHHHHHHHHHHHcC
Confidence 44799999999999999874
No 83
>PTZ00333 triosephosphate isomerase; Provisional
Probab=27.62 E-value=3.2e+02 Score=21.86 Aligned_cols=65 Identities=14% Similarity=0.111 Sum_probs=43.2
Q ss_pred HHHHHHHhhcCCCceEEecC------CCCcHHHHH-HHHHHHHhC---CeeEEEe---------cC--CChHHHHHHHHH
Q 035824 36 ERHYLKRTDEKKKNYVQVGR------RGIFGGVVL-NMHLHWKKH---ETVKVVS---------KP--CEPWKIHEYAEV 94 (121)
Q Consensus 36 qr~~LR~~a~~lkpvv~IGk------~Glt~~vi~-~i~~al~~h---ELIKVk~---------~~--~~~~~~~~~a~~ 94 (121)
-++..+.+.+.|.|++=||- +|-|.+++. ++...++.- .+-++.+ -+ .++++..+++..
T Consensus 112 ~~Kv~~al~~gl~pIlCvGE~~~~~~~~~~~~~v~~Ql~~~l~~v~~~~~~~iiIAYEPvWAIGtg~~a~~e~i~~~~~~ 191 (255)
T PTZ00333 112 AQKVKNALENGLKVILCIGETLEEREAGQTSDVLSKQLEAIVKKVSDEAWDNIVIAYEPVWAIGTGKVATPEQAQEVHAF 191 (255)
T ss_pred HHHHHHHHHCCCEEEEEcCCCHHHHhCCCHHHHHHHHHHHHHhcCCHHHcceEEEEECCHHHhCCCCCCCHHHHHHHHHH
Confidence 34556888899999999995 477777765 777766531 2233333 11 256888888888
Q ss_pred HHhHcC
Q 035824 95 LAQLSK 100 (121)
Q Consensus 95 L~~~tg 100 (121)
|.+...
T Consensus 192 IR~~l~ 197 (255)
T PTZ00333 192 IRKWLA 197 (255)
T ss_pred HHHHHH
Confidence 877543
No 84
>PF07299 FBP: Fibronectin-binding protein (FBP); InterPro: IPR010841 This entry consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species [,].; PDB: 4ADO_B 4ADN_B 2YB5_F.
Probab=27.10 E-value=70 Score=25.17 Aligned_cols=38 Identities=18% Similarity=0.279 Sum_probs=24.2
Q ss_pred hHhHHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCC
Q 035824 3 EKRKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKK 48 (121)
Q Consensus 3 ~~~~~~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lk 48 (121)
-++..+.+++.|+.|-.|++ .+|.+|.+.|=+.+-+|+
T Consensus 64 ~~~~~~~~L~~L~~yV~pF~--------~~t~~qi~kLF~K~KKLk 101 (208)
T PF07299_consen 64 TREEAEKYLEELKPYVIPFP--------PITEKQIKKLFPKAKKLK 101 (208)
T ss_dssp -HHHHHHHHHHHHCCB---------------HHHHHHHTTTSSS--
T ss_pred CHHHHHHHHHHHHHHhcCCC--------CCCHHHHHHHhhhhhccC
Confidence 46788999999999999999 578999988877666654
No 85
>PF04829 PT-VENN: Pre-toxin domain with VENN motif; InterPro: IPR006914 This group of proteins, mainly from Neisseria meningitidis, may have haemagglutinin or haemolysin activity. A number of them have a second conserved domain, IPR006915 from INTERPRO, which is found in possible Pseudomonas aeruginosa haemagglutinins []. Filamentous haemagglutinin (FHA) is a major virulence attachment factor produced by certain bacterial species that functions as both a primary adhesin and an immunomodulator. Haemolysin is pore-forming toxin.
Probab=26.99 E-value=44 Score=20.87 Aligned_cols=18 Identities=33% Similarity=0.560 Sum_probs=14.4
Q ss_pred CCCCCCHHHHHHHHHhhc
Q 035824 28 DPEILTDEERHYLKRTDE 45 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~ 45 (121)
||+.||.+||..+..++.
T Consensus 1 d~~~Lte~eK~~v~~ls~ 18 (55)
T PF04829_consen 1 DPSELTEEEKQKVSALSQ 18 (55)
T ss_pred ChHhcCHHHHHHHHHHHH
Confidence 577899999998887653
No 86
>PF12207 DUF3600: Domain of unknown function (DUF3600); InterPro: IPR022019 This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C-terminal of the putative ecf-type sigma factor negative effector. ; PDB: 3FGG_A 3FH3_A.
Probab=26.82 E-value=3 Score=31.67 Aligned_cols=75 Identities=21% Similarity=0.185 Sum_probs=49.8
Q ss_pred HHHHhccCCCCCC-CCCCCCCCCCCHHHHHHHHHhhcCCCceEE------ecCCCCcHHHHHHHHHHHHhCCeeEEEecC
Q 035824 10 LIENLTKFELPKA-PTEAYDPEILTDEERHYLKRTDEKKKNYVQ------VGRRGIFGGVVLNMHLHWKKHETVKVVSKP 82 (121)
Q Consensus 10 ~~~~l~~~~~~~~-~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~------IGk~Glt~~vi~~i~~al~~hELIKVk~~~ 82 (121)
++.+|.-..+... +--..|.+.||..++..++++...|.|+|- --|.=+|+.=.+.--+||-.+|.|+|+...
T Consensus 51 lLK~lt~~kLkygD~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~vlt~~E~d~y~eALm~~e~v~vk~~~ 130 (162)
T PF12207_consen 51 LLKKLTNAKLKYGDKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEVLTQEEYDQYIEALMTYETVRVKTKS 130 (162)
T ss_dssp HHHHHHHHHHHHB-TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHHS-HHHHHHHHHHHHHHHHHHHHCT-
T ss_pred HHHHHHHhHHhhcccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhhcCHHHHHHHHHHHhhhheeeeeccC
Confidence 4455554444432 334456889999999999999999999873 223445666667777899999999988875
Q ss_pred CC
Q 035824 83 CE 84 (121)
Q Consensus 83 ~~ 84 (121)
..
T Consensus 131 ~~ 132 (162)
T PF12207_consen 131 SG 132 (162)
T ss_dssp SS
T ss_pred CC
Confidence 43
No 87
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=26.71 E-value=2.1e+02 Score=21.71 Aligned_cols=35 Identities=17% Similarity=0.295 Sum_probs=21.8
Q ss_pred eeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCCEEEE
Q 035824 75 TVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSNTIIF 114 (121)
Q Consensus 75 LIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~~~iL 114 (121)
||||++.... +.-..++++..+|.+|.+- -.++++
T Consensus 88 LiKv~~~~~~----r~ei~~~~~~f~a~ivdv~-~~~~~i 122 (174)
T CHL00100 88 LIKINVNSQT----RPEILEIAQIFRAKVVDLS-EESLIL 122 (174)
T ss_pred EEEEecCCcC----HHHHHHHHHHhCCEEEEec-CCEEEE
Confidence 6666664433 3445567778899999875 444443
No 88
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=26.70 E-value=2.8e+02 Score=20.78 Aligned_cols=68 Identities=15% Similarity=0.139 Sum_probs=43.4
Q ss_pred CHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCC--eeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCC
Q 035824 33 TDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHE--TVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSN 110 (121)
Q Consensus 33 T~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hE--LIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~ 110 (121)
++.....+.++=++|-+++.+----=.+.| .+| ||||++.... +.-..+|++..+|.+|.+- -.
T Consensus 53 ~~~~i~qi~kQl~KLidV~~V~~~~~~~~v---------~rEl~LiKv~~~~~~----r~~i~~i~~~f~a~ivdv~-~~ 118 (161)
T PRK11895 53 DEQVIEQITKQLNKLIDVLKVVDLTEEAHV---------ERELALVKVRASGEN----RAEILRLADIFRAKIVDVT-PE 118 (161)
T ss_pred CHHHHHHHHHHHhccccEEEEEecCCcchh---------heEEEEEEEECCccc----HHHHHHHHHHhCCEEEEec-CC
Confidence 566778888888888888887543222222 266 5555553322 4456778888999999874 44
Q ss_pred EEEE
Q 035824 111 TIIF 114 (121)
Q Consensus 111 ~~iL 114 (121)
++++
T Consensus 119 ~~~i 122 (161)
T PRK11895 119 SLTI 122 (161)
T ss_pred EEEE
Confidence 5443
No 89
>COG4809 Archaeal ADP-dependent phosphofructokinase/glucokinase [Carbohydrate transport and metabolism]
Probab=26.67 E-value=1.3e+02 Score=26.50 Aligned_cols=65 Identities=12% Similarity=-0.063 Sum_probs=51.3
Q ss_pred CCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEe-eCCEEEEEeCCC
Q 035824 55 RRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDIN-PSNTIIFYRGKN 119 (121)
Q Consensus 55 k~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i-~G~~~iLYR~~n 119 (121)
.=|+.+.=++++-+.+-.+||-+=.+..+...+.-+-+-+|...+|-+.||+. .|..+-++++.|
T Consensus 295 SvGldE~ElA~vl~vlG~~eLa~~I~~~~~~~avieg~~~L~~e~~~e~i~vHT~~y~l~i~~~~n 360 (466)
T COG4809 295 SVGLDEVELANVLNVLGYRELADRIISKDDIEAVIEGAMILLDELGLERIHVHTYGYYLAITKRGN 360 (466)
T ss_pred hcCCCHHHHHHHHHhhChHHHHHhhhccccHHHHHHHHHHHHHhcCccEEEEEEeeEEEEEecCCC
Confidence 34788888999998999999998888778788888999999999999999875 244444555444
No 90
>PF12682 Flavodoxin_4: Flavodoxin; PDB: 3EDO_B 3KLB_A.
Probab=26.54 E-value=68 Score=23.48 Aligned_cols=22 Identities=18% Similarity=0.226 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHhHcCCEEEEEe
Q 035824 86 WKIHEYAEVLAQLSKGIVIDIN 107 (121)
Q Consensus 86 ~~~~~~a~~L~~~tga~vVq~i 107 (121)
-..+.+|+.|++.+||.++.+.
T Consensus 11 GnT~~vA~~Ia~~~gadi~eI~ 32 (156)
T PF12682_consen 11 GNTKKVAEKIAEKTGADIFEIE 32 (156)
T ss_dssp SHHHHHHHHHHHCCT-EEEE-B
T ss_pred chHHHHHHHHHHHHCCCEEEEE
Confidence 3568899999999999999753
No 91
>PF14816 FAM178: Family of unknown function, FAM178
Probab=26.42 E-value=1.4e+02 Score=25.73 Aligned_cols=44 Identities=18% Similarity=0.193 Sum_probs=28.6
Q ss_pred HhHHHHHHHHhccC---CCCCCCCCCCCCCCCCHHHHHHHHHhhcCC
Q 035824 4 KRKEAWLIENLTKF---ELPKAPTEAYDPEILTDEERHYLKRTDEKK 47 (121)
Q Consensus 4 ~~~~~~~~~~l~~~---~~~~~~~~~~~~e~LT~kqr~~LR~~a~~l 47 (121)
++-|..|.+..++- +.....+..+|.+.||++.|.++++-+-.+
T Consensus 32 ~e~e~~L~~d~~~g~~~~~~e~e~~~~~~~~l~~Ehr~~lekfsv~~ 78 (377)
T PF14816_consen 32 QELEKQLLQDCKQGRSIDSDEEEESTDDGGDLTPEHREFLEKFSVSL 78 (377)
T ss_pred HHHHHHHHHHHhccccccCccccccccCCCcCCHHHHHHHHHhchhh
Confidence 34455566655553 333333344567789999999999987664
No 92
>PRK06934 flavodoxin; Provisional
Probab=26.42 E-value=87 Score=24.70 Aligned_cols=30 Identities=17% Similarity=0.164 Sum_probs=22.6
Q ss_pred ChHHHHHHHHHHHhHcCCEEEEEeeCCEEEEEe
Q 035824 84 EPWKIHEYAEVLAQLSKGIVIDINPSNTIIFYR 116 (121)
Q Consensus 84 ~~~~~~~~a~~L~~~tga~vVq~i~G~~~iLYR 116 (121)
..-..+.+|+.|++.+||.+..+. ..-.|-
T Consensus 69 ~~GnTk~vAe~Ia~~~gaDl~eI~---~~~~Y~ 98 (221)
T PRK06934 69 VLGSTQYVAQIIQEETGGDLFRIE---TVKPYP 98 (221)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEEE---EccccC
Confidence 335779999999999999999754 445554
No 93
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=26.41 E-value=2.6e+02 Score=23.27 Aligned_cols=49 Identities=16% Similarity=0.016 Sum_probs=38.1
Q ss_pred CCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEE
Q 035824 55 RRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVI 104 (121)
Q Consensus 55 k~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vV 104 (121)
+=|||...+..+-...+..-+|||++. .+....-++.+.|.++.|-.=+
T Consensus 35 ~LgiSR~~v~rlL~~Ar~~GiV~I~i~-~~~~~~~~Le~~L~~~fgL~~a 83 (321)
T COG2390 35 RLGISRATVSRLLAKAREEGIVKISIN-SPVEGCLELEQQLKERFGLKEA 83 (321)
T ss_pred HhCCCHHHHHHHHHHHHHCCeEEEEeC-CCCcchHHHHHHHHHhcCCCeE
Confidence 458888888888888888889999998 5555556788888888776533
No 94
>TIGR00126 deoC deoxyribose-phosphate aldolase. Deoxyribose-phosphate aldolase is involved in the catabolism of nucleotides and deoxyriibonucleotides. The catalytic process is as follows: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde. It is found in both gram-postive and gram-negative bacteria.
Probab=26.39 E-value=3.1e+02 Score=21.27 Aligned_cols=73 Identities=10% Similarity=0.006 Sum_probs=52.6
Q ss_pred HHHHHHhhcCCCceEEec--CCCCcHHHHHHHHHHHHhC--CeeEEEecCCC-hHHHHHHHHHHHhHcCCEEEEEeeC
Q 035824 37 RHYLKRTDEKKKNYVQVG--RRGIFGGVVLNMHLHWKKH--ETVKVVSKPCE-PWKIHEYAEVLAQLSKGIVIDINPS 109 (121)
Q Consensus 37 r~~LR~~a~~lkpvv~IG--k~Glt~~vi~~i~~al~~h--ELIKVk~~~~~-~~~~~~~a~~L~~~tga~vVq~i~G 109 (121)
+..++.=|..++-++.+| +.|-.+.+.++|...-+.. =.+||.+.... .++-...+-.++...|+.+|..--|
T Consensus 77 ~~Av~~GAdEiDvv~n~g~l~~g~~~~v~~ei~~i~~~~~g~~lKvIlE~~~L~~~ei~~a~~ia~eaGADfvKTsTG 154 (211)
T TIGR00126 77 KEAIKYGADEVDMVINIGALKDGNEEVVYDDIRAVVEACAGVLLKVIIETGLLTDEEIRKACEICIDAGADFVKTSTG 154 (211)
T ss_pred HHHHHcCCCEEEeecchHhhhCCcHHHHHHHHHHHHHHcCCCeEEEEEecCCCCHHHHHHHHHHHHHhCCCEEEeCCC
Confidence 344555578899999999 5999999999998777753 36888655432 2233446777888999999976434
No 95
>cd07766 DHQ_Fe-ADH Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH). Dehydroquinate synthase-like. This superfamily divides into two subgroups: the dehydroquinate synthase-like, and a large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. Dehydroquinate synthase-like group includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. The alcohol dehydrogenases in this superfamily contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alc
Probab=26.21 E-value=3.2e+02 Score=21.75 Aligned_cols=59 Identities=17% Similarity=0.049 Sum_probs=37.2
Q ss_pred CceEEecCCCCcHHHHHHHHHHHHhCCeeEEEec----C-CChHHHHHHHHHHHhHcCCEEEEEeeC
Q 035824 48 KNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSK----P-CEPWKIHEYAEVLAQLSKGIVIDINPS 109 (121)
Q Consensus 48 kpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~----~-~~~~~~~~~a~~L~~~tga~vVq~i~G 109 (121)
+.++.|.-.++.++..+.+...|+.+ +.+.+. . .+.++.+++++.+.+ .++.+|=-+.|
T Consensus 24 ~~~liv~~~~~~~~~~~~v~~~l~~~--~~~~~~~~~~~~p~~~~v~~~~~~~~~-~~~d~IIaiGG 87 (332)
T cd07766 24 DRALVVSDEGVVKGVGEKVADSLKKL--IAVHIFDGVGPNPTFEEVKEAVERARA-AEVDAVIAVGG 87 (332)
T ss_pred CeEEEEeCCchhhhHHHHHHHHHHhc--CcEEEeCCcCCCcCHHHHHHHHHHHHh-cCcCEEEEeCC
Confidence 56666766777778888889898876 333332 2 245667777777766 34555423433
No 96
>TIGR00376 DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.
Probab=25.97 E-value=5e+02 Score=23.48 Aligned_cols=75 Identities=13% Similarity=0.092 Sum_probs=53.8
Q ss_pred CCCHHHHHHHHHhhcCCCceEEecCCCC--cHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEee
Q 035824 31 ILTDEERHYLKRTDEKKKNYVQVGRRGI--FGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINP 108 (121)
Q Consensus 31 ~LT~kqr~~LR~~a~~lkpvv~IGk~Gl--t~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~ 108 (121)
.|+..|+..++.....-+.++..|.-|- |--+++-+.+++.... +|-+...+..-.+.+.+.|... +..+| .+
T Consensus 157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~g~--~VLv~a~sn~Avd~l~e~l~~~-~~~vv-Rl- 231 (637)
T TIGR00376 157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKRGL--RVLVTAPSNIAVDNLLERLALC-DQKIV-RL- 231 (637)
T ss_pred CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHcCC--CEEEEcCcHHHHHHHHHHHHhC-CCcEE-Ee-
Confidence 6999999999886544467788886654 5556666666666555 7777777777788888888765 66666 34
Q ss_pred CC
Q 035824 109 SN 110 (121)
Q Consensus 109 G~ 110 (121)
|+
T Consensus 232 g~ 233 (637)
T TIGR00376 232 GH 233 (637)
T ss_pred CC
Confidence 64
No 97
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=25.74 E-value=1.9e+02 Score=23.34 Aligned_cols=54 Identities=15% Similarity=0.064 Sum_probs=33.4
Q ss_pred cCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecC--CChHHHHHHHHHHHhH
Q 035824 45 EKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKP--CEPWKIHEYAEVLAQL 98 (121)
Q Consensus 45 ~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~--~~~~~~~~~a~~L~~~ 98 (121)
|.-+|=+-||+.|-.=.-+...-+-+-.-+-|.|.+.. ++..|..-+|+.|+..
T Consensus 58 ~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~i~EV~~peL~A~lvA~~IA~q 113 (233)
T COG0092 58 HAARPGLVIGKKGSNIEKLRKELEKLFGKENVQINIEEVKKPELDAQLVAESIAQQ 113 (233)
T ss_pred EeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEEEEEcCCCCcCHHHHHHHHHHH
Confidence 56789999999997655544444444445556666654 4555555555555543
No 98
>PRK14713 multifunctional hydroxymethylpyrimidine phosphokinase/4-amino-5-aminomethyl-2-methylpyrimidine hydrolase; Provisional
Probab=25.66 E-value=2.7e+02 Score=24.29 Aligned_cols=63 Identities=10% Similarity=-0.041 Sum_probs=40.7
Q ss_pred CCceEE--ecCCCCcHHHHHHHHHHHHhCCeeEEEecC----------CChHHHHHHHHHHHhHcCCEEEEEeeCC
Q 035824 47 KKNYVQ--VGRRGIFGGVVLNMHLHWKKHETVKVVSKP----------CEPWKIHEYAEVLAQLSKGIVIDINPSN 110 (121)
Q Consensus 47 lkpvv~--IGk~Glt~~vi~~i~~al~~hELIKVk~~~----------~~~~~~~~~a~~L~~~tga~vVq~i~G~ 110 (121)
++|++. -|...++++.++.+.+.+..-.+|+....+ .+.++..+++..|....|+.|| +..|+
T Consensus 130 lDPv~~~~~G~~l~~~~~~~~~~~Ll~~advItPN~~Ea~~Ltg~~~~~~~~d~~~aa~~L~~~~g~~Vv-ItgG~ 204 (530)
T PRK14713 130 LDPVMVATSGDRLLEEDAEAALRELVPRADLITPNLPELAVLLGEPPATTWEEALAQARRLAAETGTTVL-VKGGH 204 (530)
T ss_pred ECCcccCCCCCCCCCHHHHHHHHHHhhhhheecCChHHHHHHhCCCCCCCHHHHHHHHHHHHHhcCCEEE-EeCCC
Confidence 456543 255567888888888777767777766543 1345667778888877677666 44343
No 99
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=25.50 E-value=4.1e+02 Score=24.48 Aligned_cols=69 Identities=19% Similarity=0.150 Sum_probs=48.6
Q ss_pred CCCCCHHHHHHHHHhhcCCCceEEecCCCCcHH-HHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCE
Q 035824 29 PEILTDEERHYLKRTDEKKKNYVQVGRRGIFGG-VVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGI 102 (121)
Q Consensus 29 ~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~-vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~ 102 (121)
...||.+|+..++.+...-+-++..|..|---+ ++..+..+|+.... +|.+.... -.++..|.+.+|..
T Consensus 350 ~~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~~i~~~~~~~g~-~V~~~ApT----g~Aa~~L~~~~g~~ 419 (744)
T TIGR02768 350 HYRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLKAAREAWEAAGY-RVIGAALS----GKAAEGLQAESGIE 419 (744)
T ss_pred cCCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHHHHHHHHHhCCC-eEEEEeCc----HHHHHHHHhccCCc
Confidence 346999999999998765466789999998877 68888888887653 44444433 33555555555543
No 100
>cd08557 PI-PLCc_bacteria_like Catalytic domain of bacterial phosphatidylinositol-specific phospholipase C and similar proteins. This subfamily corresponds to the catalytic domain present in bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and their sequence homologs found in eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. Bacterial PI-PLCs contain a single TIM-barrel type catalytic domain. Its catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. Eukaryotic homologs in this family are named as phosphatidylinositol-specific phospholipase C X
Probab=25.40 E-value=3e+02 Score=20.90 Aligned_cols=63 Identities=10% Similarity=0.011 Sum_probs=47.3
Q ss_pred CCcHHHHHHHHHHHHhC--CeeEEEecCCChH----HHHHHHHHHHhHcCCEEEEE------------ee-CCEEEEEeC
Q 035824 57 GIFGGVVLNMHLHWKKH--ETVKVVSKPCEPW----KIHEYAEVLAQLSKGIVIDI------------NP-SNTIIFYRG 117 (121)
Q Consensus 57 Glt~~vi~~i~~al~~h--ELIKVk~~~~~~~----~~~~~a~~L~~~tga~vVq~------------i~-G~~~iLYR~ 117 (121)
...+.++.+|.+-|..| |.|-+.+...... +...+.+.|.+..|..+... .. |+.+|+++.
T Consensus 79 ~~~~~vL~~i~~fl~~~p~E~vil~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ptL~el~~gK~vi~~~~ 158 (271)
T cd08557 79 QTLEDVLNEVKDFLDAHPSEVVILDLEHEYGGDNGEDHDELDALLRDVLGDPLYRPPVRAGGWPTLGELRAGKRVLLFYF 158 (271)
T ss_pred ccHHHHHHHHHHHHHHCCCcEEEEEEEccCCCcchhhHHHHHHHHHHHhCccccCCccccCCCCcHHHHhcCCeEEEEEC
Confidence 45678999999999985 8888888764322 36788899998888776621 14 888888887
Q ss_pred CC
Q 035824 118 KN 119 (121)
Q Consensus 118 ~n 119 (121)
..
T Consensus 159 ~~ 160 (271)
T cd08557 159 GG 160 (271)
T ss_pred CC
Confidence 54
No 101
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=25.31 E-value=3.8e+02 Score=21.89 Aligned_cols=51 Identities=18% Similarity=0.187 Sum_probs=40.3
Q ss_pred HHHHHHHHhhcCCCceEEecCCCCcHHHHHH-HHHHHH--hCCeeEEEecCCCh
Q 035824 35 EERHYLKRTDEKKKNYVQVGRRGIFGGVVLN-MHLHWK--KHETVKVVSKPCEP 85 (121)
Q Consensus 35 kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~-i~~al~--~hELIKVk~~~~~~ 85 (121)
+-++.+++.|..-.||+..|-.|.--..++. ||..-. ...+|.|.|...+.
T Consensus 10 ~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~ 63 (329)
T TIGR02974 10 EVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSE 63 (329)
T ss_pred HHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCCh
Confidence 3467888899999999999999999988765 554443 35799999987654
No 102
>PF04908 SH3BGR: SH3-binding, glutamic acid-rich protein; InterPro: IPR006993 This family of proteins, which contains SH3BGRL3, is functionally uncharacterised. SH3BGRL3 is a highly conserved small protein, which is widely expressed and shows a significant similarity to glutaredoxin 1 (GRX1) of Escherichia coli which is predicted to belong to the thioredoxin superfamily. However, SH3BGRL3 lacks both conserved cysteine residues, which characterise the enzymatic active site of GRX. This structural feature raises the possibility that SH3BGRL3 and its homologues could function as endogenous modulators of GRX activity []. ; PDB: 1SJ6_A 1U6T_A 1WRY_A 1T1V_B 1J0F_A 2CT6_A.
Probab=25.24 E-value=60 Score=22.50 Aligned_cols=66 Identities=14% Similarity=0.217 Sum_probs=39.6
Q ss_pred HhHHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhh----------cCCCceEEecCCCCcHHHHHHHHHHHHhC
Q 035824 4 KRKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTD----------EKKKNYVQVGRRGIFGGVVLNMHLHWKKH 73 (121)
Q Consensus 4 ~~~~~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a----------~~lkpvv~IGk~Glt~~vi~~i~~al~~h 73 (121)
|++.+++..-|....+|... .|..+ +.+.|+++|+.+ ..|.|-+-.| |-+-+-.+++.+|-+..
T Consensus 17 kk~q~~v~~iL~a~kI~fe~---vDIa~-~e~~r~~mr~~~g~~~~~~~~~~~lpPqiF~~--~~Y~Gdye~f~ea~E~~ 90 (99)
T PF04908_consen 17 KKRQQRVLMILEAKKIPFEE---VDIAM-DEEARQWMRENAGPEEKDPGNGKPLPPQIFNG--DEYCGDYEDFEEANENG 90 (99)
T ss_dssp HHHHHHHHHHHHHTT--EEE---EETTT--HHHHHHHHHHT--CCCS-TSTT--S-EEEET--TEEEEEHHHHHHHHCTT
T ss_pred HHHHHHHHHHHHHcCCCcEE---EeCcC-CHHHHHHHHHhccccccCCCCCCCCCCEEEeC--CEEEeeHHHHHHHHhhC
Confidence 66777888888888888652 22323 889999999876 4578877777 44555556666665554
Q ss_pred Ce
Q 035824 74 ET 75 (121)
Q Consensus 74 EL 75 (121)
+|
T Consensus 91 ~L 92 (99)
T PF04908_consen 91 EL 92 (99)
T ss_dssp -H
T ss_pred HH
Confidence 43
No 103
>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....
Probab=25.11 E-value=2.8e+02 Score=20.35 Aligned_cols=54 Identities=13% Similarity=0.069 Sum_probs=39.2
Q ss_pred HHHHHHHHhhcCCCceEEecCCCCcHHHHHH-HHHHHH--hCCeeEEEecCCChHHH
Q 035824 35 EERHYLKRTDEKKKNYVQVGRRGIFGGVVLN-MHLHWK--KHETVKVVSKPCEPWKI 88 (121)
Q Consensus 35 kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~-i~~al~--~hELIKVk~~~~~~~~~ 88 (121)
+-+..+++.|..--|++..|..|---..++. ||..-. ....|.|.|..-+.+..
T Consensus 10 ~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~~~~ 66 (168)
T PF00158_consen 10 RLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPEELL 66 (168)
T ss_dssp HHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-HHHH
T ss_pred HHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhcchh
Confidence 4567888999999999999999999888654 555433 24699999998765543
No 104
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=24.98 E-value=3.5e+02 Score=23.08 Aligned_cols=52 Identities=8% Similarity=-0.088 Sum_probs=32.8
Q ss_pred CCcHHHHHHHHHHHHhCCeeEEEecCC---ChHHHHHHHHHHHhHcCCEEEEEeeCCEE
Q 035824 57 GIFGGVVLNMHLHWKKHETVKVVSKPC---EPWKIHEYAEVLAQLSKGIVIDINPSNTI 112 (121)
Q Consensus 57 Glt~~vi~~i~~al~~hELIKVk~~~~---~~~~~~~~a~~L~~~tga~vVq~i~G~~~ 112 (121)
|-+.+++.++...+... .|-+... ....+++.....+...|.++.... ++++
T Consensus 73 g~~~~~l~~l~~~~~i~---~v~~~~~~~~~~~~rd~~v~~~l~~~gi~~~~~~-~~~l 127 (475)
T TIGR02766 73 TDTVAALLDCVRSTGAT---RLFFNHLYDPVSLVRDHRAKEVLTAQGISVQSFN-ADLL 127 (475)
T ss_pred CCHHHHHHHHHHHcCCC---EEEEecccCHHHHHHHHHHHHHHHHcCCEEEEec-CCEE
Confidence 66778877776555443 4444432 334556666677777788887664 7776
No 105
>PTZ00386 formyl tetrahydrofolate synthetase; Provisional
Probab=24.97 E-value=49 Score=30.20 Aligned_cols=99 Identities=19% Similarity=0.274 Sum_probs=55.9
Q ss_pred HHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhhcCCCce---------------EEecCCCCcHH--------------
Q 035824 11 IENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKKNY---------------VQVGRRGIFGG-------------- 61 (121)
Q Consensus 11 ~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpv---------------v~IGk~Glt~~-------------- 61 (121)
++-|.++-.... ||..||++|++.+..+...-+.+ +.||..|-..+
T Consensus 190 ~~rl~~lgi~~~-----~p~~lt~ee~~~~~~L~IDp~~I~w~Rv~D~NDR~LR~I~vGlG~~~~G~~Re~gFdITvASE 264 (625)
T PTZ00386 190 LKRLEKLGISKT-----DPKQLTEEERVRFARLDIDPDTISWRRVTDVNDRMLREITIGQGKEEKGITRKTGFDISVASE 264 (625)
T ss_pred HHHHHhhccCcC-----CccccCHHHhhhhhhcCcCcceeEEEeeccccchhhhceeeCcCCCCCCCcccCCceeEHHHH
Confidence 344555555433 67789999999999988665533 56765543332
Q ss_pred HHHHHHHH--HHh--CCeeEEEecC---CCh---H---HHHHHHHHHHhHcCCEEEEEeeCCEEEE
Q 035824 62 VVLNMHLH--WKK--HETVKVVSKP---CEP---W---KIHEYAEVLAQLSKGIVIDINPSNTIIF 114 (121)
Q Consensus 62 vi~~i~~a--l~~--hELIKVk~~~---~~~---~---~~~~~a~~L~~~tga~vVq~i~G~~~iL 114 (121)
+++=+.-+ |+. .-|=+|.+-. +.+ . ..-.|+..|.++..-.+||.++|.=+++
T Consensus 265 iMAIl~La~dl~Dlr~Rlg~ivva~~~~g~pVta~DL~~~GAmt~LLkDAikPNLvQTlEgtPa~V 330 (625)
T PTZ00386 265 VMAILALATDLADMRQRLGAIVVAKSKSGEPVTAEDLGCAGAMTVLMKDTIEPTLMQTLEGTPVLV 330 (625)
T ss_pred HHHHHHHhCCHHHHHHHHhceeeeecCCCCceeHHHcCchHHHHHHHHhhcccceeeecCCCceEE
Confidence 22111111 111 1233444322 111 1 2246888899999999999986544443
No 106
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=24.89 E-value=4e+02 Score=22.02 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=29.1
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
+|+.+|.+..+.|+..|- ..+.||-..+.+.++..+
T Consensus 97 ~P~~~~~~~l~~l~~~G~---nrislGvQS~~~~~L~~l 132 (370)
T PRK06294 97 NPENLSESYIRALALTGI---NRISIGVQTFDDPLLKLL 132 (370)
T ss_pred CCCCCCHHHHHHHHHCCC---CEEEEccccCCHHHHHHc
Confidence 477899999999999984 378999888888776544
No 107
>TIGR01574 miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB. Hits to this model span all major groups of bacteria and eukaryotes, but not archaea, which are known to lack this particular tRNA modification. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterized and shown to complement the E. coli MiaB enzyme.
Probab=24.84 E-value=4e+02 Score=22.51 Aligned_cols=59 Identities=10% Similarity=0.054 Sum_probs=36.2
Q ss_pred HHHHHHHhccC-CCCCCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHH
Q 035824 7 EAWLIENLTKF-ELPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNM 66 (121)
Q Consensus 7 ~~~~~~~l~~~-~~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i 66 (121)
-..|++.|.+. .++|-.-....|..+|.+....|+..+ .+=+.+.||-.-.++.++..+
T Consensus 216 l~~Ll~~l~~~~~~~~ir~~~~~p~~l~~ell~~l~~~g-~~~~~l~iglQSgsd~vLk~m 275 (438)
T TIGR01574 216 FSDLLRELSTIDGIERIRFTSSHPLDFDDDLIEVFANNP-KLCKSMHLPVQSGSSEILKLM 275 (438)
T ss_pred HHHHHHHHHhcCCceEEEEecCCcccCCHHHHHHHHhCC-CccCceeeCCCcCCHHHHHhc
Confidence 34566666542 233321111246679999999998754 345788999777666666544
No 108
>PF07985 SRR1: SRR1; InterPro: IPR012942 Sensitivity To Red Light Reduced proteins (SRR1) are signalling proteins thought to be involved in regulating the circadian clock input pathway, which is required for normal oscillator function. In Arabidopsis thaliana it regulates the expression of clock-regulated genes such as CCA1 and TOC1. It is also involved in both the phytochrome B (PHYB) and PHYB-independent signaling pathways [].
Probab=24.69 E-value=87 Score=19.23 Aligned_cols=36 Identities=22% Similarity=0.537 Sum_probs=23.6
Q ss_pred HHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHHHHhh
Q 035824 8 AWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTD 44 (121)
Q Consensus 8 ~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~LR~~a 44 (121)
+.++.-...+..|...-...|| .+|+.++++|.++|
T Consensus 21 A~ll~l~~~l~~~~~~v~~yDP-vft~~d~~~L~~lG 56 (56)
T PF07985_consen 21 ALLLLLKEELSIPRDQVSIYDP-VFTEVDKAFLESLG 56 (56)
T ss_pred HHHHHHHHHhCCCCCcEEEECC-CCCHHHHHHHHHcC
Confidence 3444445555555343455567 79999999999876
No 109
>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.
Probab=24.52 E-value=3.5e+02 Score=21.25 Aligned_cols=68 Identities=10% Similarity=-0.079 Sum_probs=47.0
Q ss_pred HHHHHhhcCCC-ceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEE
Q 035824 38 HYLKRTDEKKK-NYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVID 105 (121)
Q Consensus 38 ~~LR~~a~~lk-pvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq 105 (121)
..++.+|..|. |++.+-..|-.++-++.+.++|..-..--|.+-.-..++.+.-.+.+|+.+|-+.+-
T Consensus 48 ~~~~~qA~algipl~~~~~~~~~e~~~e~l~~~l~~~gv~~vv~GdI~s~~qr~~~e~v~~~lgl~~~~ 116 (223)
T TIGR00290 48 HLTDLQAESIGIPLIKLYTEGTEEDEVEELKGILHTLDVEAVVFGAIYSEYQKTRIERVCRELGLKSFA 116 (223)
T ss_pred HHHHHHHHHcCCCeEEeecCCCccHHHHHHHHHHHHcCCCEEEECCcccHHHHHHHHHHHHhcCCEEec
Confidence 55666666664 777776778888999999999977643333333334556677778888888877764
No 110
>COG0673 MviM Predicted dehydrogenases and related proteins [General function prediction only]
Probab=24.00 E-value=1.7e+02 Score=22.91 Aligned_cols=54 Identities=26% Similarity=0.132 Sum_probs=47.9
Q ss_pred CCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecC
Q 035824 29 PEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKP 82 (121)
Q Consensus 29 ~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~ 82 (121)
|-.+|.+|-+.|-.+|.+-.-.+++|-+--++..+..+.+.+..-+|-+|....
T Consensus 99 Pla~t~~ea~~l~~~a~~~~~~l~v~~~~Rf~p~~~~~k~li~~g~lG~v~~~~ 152 (342)
T COG0673 99 PLALTLEEAEELVELARKAGVKLMVGFNRRFDPAVQALKELIDSGALGEVVSVQ 152 (342)
T ss_pred CCCCCHHHHHHHHHHHHHcCCceeeehhhhcCHHHHHHHHHHhcCCcCceEEEE
Confidence 467999999999999999999999999999999999999999998777666554
No 111
>cd05312 NAD_bind_1_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 1. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists of eukaryotic and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH
Probab=24.00 E-value=1.3e+02 Score=24.76 Aligned_cols=71 Identities=18% Similarity=0.138 Sum_probs=46.0
Q ss_pred CCCHHHHHHHHHhh-----------cCCCceEEecCCC----CcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHH
Q 035824 31 ILTDEERHYLKRTD-----------EKKKNYVQVGRRG----IFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVL 95 (121)
Q Consensus 31 ~LT~kqr~~LR~~a-----------~~lkpvv~IGk~G----lt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L 95 (121)
.|++.|+.|.+... ...+|-+.||-.| +|+++|+.|..+- .+-+|= -+.|+....+-..++.
T Consensus 77 ~l~~~~~~~a~~~~~~~~~~L~e~i~~v~ptvlIG~S~~~g~ft~evv~~Ma~~~-~~PIIF--aLSNPt~~~E~~pe~a 153 (279)
T cd05312 77 DLTPFKKPFARKDEEKEGKSLLEVVKAVKPTVLIGLSGVGGAFTEEVVRAMAKSN-ERPIIF--ALSNPTSKAECTAEDA 153 (279)
T ss_pred cchHHHHHHHhhcCcccCCCHHHHHHhcCCCEEEEeCCCCCCCCHHHHHHHHhcC-CCCEEE--ECCCcCCccccCHHHH
Confidence 48999999998744 1249999999665 7889999888553 233332 2344443334466677
Q ss_pred HhHcCCE-EE
Q 035824 96 AQLSKGI-VI 104 (121)
Q Consensus 96 ~~~tga~-vV 104 (121)
-+.|+|. ++
T Consensus 154 ~~~t~G~ai~ 163 (279)
T cd05312 154 YKWTDGRALF 163 (279)
T ss_pred HHhhcCCEEE
Confidence 7777544 44
No 112
>PF02457 DisA_N: DisA bacterial checkpoint controller nucleotide-binding; InterPro: IPR003390 The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. This domain is the first and is a globular, nucleotide-binding region; the next 146-289 residues constitute the DisA-linker family, IPR018906 from INTERPRO that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), which thus forms a spine like-linker between domains 1 and 3. The C-terminal residues, of domain 3, are represented by family HHH, IPR000445 from INTERPRO the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis.; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 2FB5_A.
Probab=23.93 E-value=93 Score=22.17 Aligned_cols=35 Identities=26% Similarity=0.317 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhHcCCEEEEEee--CCEEEEEeCCCC
Q 035824 86 WKIHEYAEVLAQLSKGIVIDINP--SNTIIFYRGKNY 120 (121)
Q Consensus 86 ~~~~~~a~~L~~~tga~vVq~i~--G~~~iLYR~~ny 120 (121)
-.+..+|.-+.+.|+|.+|-+-+ |.+-+.|.|+=|
T Consensus 86 GtRHraA~gise~tdaivivVSEe~G~Is~~~~G~~y 122 (122)
T PF02457_consen 86 GTRHRAALGISEQTDAIVIVVSEETGTISLAYGGKLY 122 (122)
T ss_dssp SHHHHHHHHHHCCCSSEEEEE-TTTS-EEEEETTEE-
T ss_pred cHHHHHHHHHHHhcCCEEEEEEccCCcEEEEECCEEC
Confidence 46788999999999999985542 677777777654
No 113
>TIGR00089 RNA modification enzyme, MiaB family. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.
Probab=23.63 E-value=4.4e+02 Score=22.06 Aligned_cols=60 Identities=13% Similarity=0.166 Sum_probs=35.6
Q ss_pred HHHHHHHhccCC-CCCCCCCCCCCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 7 EAWLIENLTKFE-LPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 7 ~~~~~~~l~~~~-~~~~~~~~~~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
-..|++.+.+.. ..|-.-.-..|..++++-...|+..+. .=+.+.||-.-.++.++..|.
T Consensus 208 l~~Ll~~l~~~~g~~~i~~~~~~p~~i~~ell~~m~~~~~-~~~~l~igiES~s~~vLk~m~ 268 (429)
T TIGR00089 208 LADLLRELSKIDGIERIRFGSSHPDDVTDDLIELIAENPK-VCKHLHLPVQSGSDRILKRMN 268 (429)
T ss_pred HHHHHHHHhcCCCCCEEEECCCChhhcCHHHHHHHHhCCC-ccCceeeccccCChHHHHhCC
Confidence 455667776652 333211112345678888877776532 345788998877777765544
No 114
>KOG4060 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.58 E-value=1.3e+02 Score=23.14 Aligned_cols=67 Identities=22% Similarity=0.178 Sum_probs=46.7
Q ss_pred HHHhhcCCCceEEecCCCCcH-----HH------HHHHHHHHHh-CCe-----eEEEecCCC---hHHHHHHHHHHHhHc
Q 035824 40 LKRTDEKKKNYVQVGRRGIFG-----GV------VLNMHLHWKK-HET-----VKVVSKPCE---PWKIHEYAEVLAQLS 99 (121)
Q Consensus 40 LR~~a~~lkpvv~IGk~Glt~-----~v------i~~i~~al~~-hEL-----IKVk~~~~~---~~~~~~~a~~L~~~t 99 (121)
||..-..++|++++|+.|++- ++ +....--+.. +|. +-|++.+.+ .+........+|...
T Consensus 2 lrr~~s~~~~i~sv~~~~ls~~R~t~gig~~~~~~~~~ePKf~~~re~~ey~~lNV~i~gyD~~~lEsYq~yvH~la~~l 81 (176)
T KOG4060|consen 2 LRRRTSGEKPIYSVGGILLSISRKTHGIGKYKHLIKAEEPKFKKEREINEYGVLNVHITGYDMTLLESYQQYVHNLANSL 81 (176)
T ss_pred ccccccccceeeeccccceeeeeecccccccchhhhhhCCcccchhcccccceEEEEEEecccchHHHHHHHHHHHHHHc
Confidence 566777889999999888763 22 2222222222 555 888888864 567788889999999
Q ss_pred CCEEEEE
Q 035824 100 KGIVIDI 106 (121)
Q Consensus 100 ga~vVq~ 106 (121)
+-.|+..
T Consensus 82 ~~~V~ds 88 (176)
T KOG4060|consen 82 SIKVEDS 88 (176)
T ss_pred CceeEee
Confidence 9988854
No 115
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=23.28 E-value=4.1e+02 Score=22.95 Aligned_cols=51 Identities=12% Similarity=0.120 Sum_probs=39.2
Q ss_pred HHHHHHHHhhcCCCceEEecCCCCcHHHHHH-HHHHHH--hCCeeEEEecCCCh
Q 035824 35 EERHYLKRTDEKKKNYVQVGRRGIFGGVVLN-MHLHWK--KHETVKVVSKPCEP 85 (121)
Q Consensus 35 kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~-i~~al~--~hELIKVk~~~~~~ 85 (121)
+=+..+++.|..-.|++..|..|.--..+.. ||..-. ...+|.|.|..-+.
T Consensus 198 ~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~ 251 (509)
T PRK05022 198 QLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPE 251 (509)
T ss_pred HHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCCh
Confidence 3456788889999999999999999887654 444432 35799999988653
No 116
>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]
Probab=23.22 E-value=4.1e+02 Score=21.56 Aligned_cols=100 Identities=15% Similarity=0.075 Sum_probs=65.6
Q ss_pred hHhHHHHHHHHhccCCCCCCCCCCCCCCCCCHHHHHHH-HHhhcCCCceEEec---CCCCcHHHHHHHHHHHHh--CCee
Q 035824 3 EKRKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYL-KRTDEKKKNYVQVG---RRGIFGGVVLNMHLHWKK--HETV 76 (121)
Q Consensus 3 ~~~~~~~~~~~l~~~~~~~~~~~~~~~e~LT~kqr~~L-R~~a~~lkpvv~IG---k~Glt~~vi~~i~~al~~--hELI 76 (121)
+.+-+++-.+-|.++-++.- .+.=|..||+-|.+.- =+.|..|+|-+++= -.-|.+.++.++-+.+.. +|=.
T Consensus 110 k~eA~~~A~~lL~~VGL~~k--a~~yP~qLSGGQqQRVAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA~eGm 187 (240)
T COG1126 110 KAEAREKALELLEKVGLADK--ADAYPAQLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLAEEGM 187 (240)
T ss_pred HHHHHHHHHHHHHHcCchhh--hhhCccccCcHHHHHHHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHHHcCC
Confidence 44556666777788888855 2234778999876654 25677789998874 456778888888777765 5545
Q ss_pred EEEecCCChHHHHHHHHHHHhHcCCEEE
Q 035824 77 KVVSKPCEPWKIHEYAEVLAQLSKGIVI 104 (121)
Q Consensus 77 KVk~~~~~~~~~~~~a~~L~~~tga~vV 104 (121)
-.-|-.-...-.+++|+.+.-.-+|.++
T Consensus 188 TMivVTHEM~FAr~VadrviFmd~G~ii 215 (240)
T COG1126 188 TMIIVTHEMGFAREVADRVIFMDQGKII 215 (240)
T ss_pred eEEEEechhHHHHHhhheEEEeeCCEEE
Confidence 5555555555666666665555555444
No 117
>PRK00907 hypothetical protein; Provisional
Probab=23.16 E-value=1.1e+02 Score=21.04 Aligned_cols=49 Identities=18% Similarity=0.039 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHhhcCC---CceEEecCCCC-----------cHHHHHHHHHHHHhCCeeEEE
Q 035824 31 ILTDEERHYLKRTDEKK---KNYVQVGRRGI-----------FGGVVLNMHLHWKKHETVKVV 79 (121)
Q Consensus 31 ~LT~kqr~~LR~~a~~l---kpvv~IGk~Gl-----------t~~vi~~i~~al~~hELIKVk 79 (121)
.|...=..-++..|... .+-+.--++|= +..-+++|.++|.+|+.||+.
T Consensus 29 ~l~~~V~~vv~~h~p~~~~~~i~~r~Ss~GkY~Svtv~i~ats~eQld~iY~~L~~~~~Vkmv 91 (92)
T PRK00907 29 GLETELPRLLAATGVELLQERISWKHSSSGKYVSVRIGFRAESREQYDAAHQALRDHPEVKWT 91 (92)
T ss_pred hHHHHHHHHHHHhCCCCCcCcEEeccCCCCEEEEEEEEEEECCHHHHHHHHHHHhhCCCEEEe
Confidence 34444455555555432 22334445553 355699999999999999875
No 118
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=23.15 E-value=4.6e+02 Score=25.36 Aligned_cols=52 Identities=17% Similarity=0.181 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHHHhhcCCCceEEecCCCCcHH-HHHHHHHHHHhCCeeEEEecC
Q 035824 30 EILTDEERHYLKRTDEKKKNYVQVGRRGIFGG-VVLNMHLHWKKHETVKVVSKP 82 (121)
Q Consensus 30 e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~-vi~~i~~al~~hELIKVk~~~ 82 (121)
..||++|+..++.+...-+-++..|-.|---+ ++..+..+|+.... +|....
T Consensus 345 ~~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~l~~~~~~~e~~G~-~V~~~A 397 (988)
T PRK13889 345 LVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAMLGVAREAWEAAGY-EVRGAA 397 (988)
T ss_pred CCCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHHHHHHHHHHHcCC-eEEEec
Confidence 46999999999988876667899999998887 57778889987543 344433
No 119
>PRK03031 rnpA ribonuclease P; Reviewed
Probab=22.81 E-value=1.8e+02 Score=20.38 Aligned_cols=40 Identities=8% Similarity=0.013 Sum_probs=26.5
Q ss_pred HHHHHhhcCCCc---eEEecCCCCcH----HHHHHHHHHHHhCCeeE
Q 035824 38 HYLKRTDEKKKN---YVQVGRRGIFG----GVVLNMHLHWKKHETVK 77 (121)
Q Consensus 38 ~~LR~~a~~lkp---vv~IGk~Glt~----~vi~~i~~al~~hELIK 77 (121)
..+|...+.++| +|.|.+.|+.+ .+.+++...|+...+..
T Consensus 73 e~~R~~~~~l~~g~diVvi~r~~~~~~~~~~l~~~l~~ll~k~~~~~ 119 (122)
T PRK03031 73 AALRQLLPRIAPGWDLVIIVKPTAAECNYEQFLQELEQLLIQAEIIH 119 (122)
T ss_pred HHHHHhhhccCCCceEEEEECCCcccCCHHHHHHHHHHHHHHccCcc
Confidence 344444455543 67788888654 77888888888876654
No 120
>PRK14567 triosephosphate isomerase; Provisional
Probab=22.74 E-value=3.9e+02 Score=21.52 Aligned_cols=80 Identities=23% Similarity=0.218 Sum_probs=50.5
Q ss_pred HHHHHHhhcCCCceEEecC------CCCcHHH-HHHHHHHHHhC---CeeEEEec-----------CCChHHHHHHHHHH
Q 035824 37 RHYLKRTDEKKKNYVQVGR------RGIFGGV-VLNMHLHWKKH---ETVKVVSK-----------PCEPWKIHEYAEVL 95 (121)
Q Consensus 37 r~~LR~~a~~lkpvv~IGk------~Glt~~v-i~~i~~al~~h---ELIKVk~~-----------~~~~~~~~~~a~~L 95 (121)
++..+.+.+.|.|++=||- +|-|..+ ..++...|..- .+-++.+. -.++++..+++..|
T Consensus 109 ~Kv~~al~~gl~pI~CiGEt~eere~g~~~~vv~~Ql~~~l~~i~~~~~~~ivIAYEPvWAIGTG~~as~e~i~~~~~~I 188 (253)
T PRK14567 109 KKLNKIIDTTITPVVCIGESLDDRQSGKLKQVLATQLSLILENLSVEQLAKVVIAYEPVWAIGTGVVASLEQIQETHQFI 188 (253)
T ss_pred HHHHHHHHCCCEEEEEcCCcHHHHHcCCHHHHHHHHHHHHHccCCHHHhCCEEEEECCHHHhCCCCCCCHHHHHHHHHHH
Confidence 5666888999999999994 4777666 46677777532 12334331 13578889999888
Q ss_pred HhHcCCEEEEEeeCCEEEEEeC
Q 035824 96 AQLSKGIVIDINPSNTIIFYRG 117 (121)
Q Consensus 96 ~~~tga~vVq~i~G~~~iLYR~ 117 (121)
.+.+.. +-+-..-++-|||=|
T Consensus 189 R~~l~~-~~~~~a~~v~IlYGG 209 (253)
T PRK14567 189 RSLLAK-VDERLAKNIKIVYGG 209 (253)
T ss_pred HHHHHh-hcccccccceEEEcC
Confidence 886533 211111256777755
No 121
>PRK00103 rRNA large subunit methyltransferase; Provisional
Probab=22.72 E-value=1.4e+02 Score=22.22 Aligned_cols=40 Identities=18% Similarity=0.098 Sum_probs=27.3
Q ss_pred CCCCCCHHHHHHHHH-h-hcC-CCceEEecC-CCCcHHHHHHHH
Q 035824 28 DPEILTDEERHYLKR-T-DEK-KKNYVQVGR-RGIFGGVVLNMH 67 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~-~-a~~-lkpvv~IGk-~Glt~~vi~~i~ 67 (121)
.+..||+.|-+.+=. . ... -+..|-||. .|++++|...-+
T Consensus 76 ~Gk~~sS~~fA~~l~~~~~~g~~~i~F~IGGa~G~~~~v~~~a~ 119 (157)
T PRK00103 76 RGKQLSSEEFAQELERWRDDGRSDVAFVIGGADGLSPAVKKRAD 119 (157)
T ss_pred CCCcCCHHHHHHHHHHHHhcCCccEEEEEcCccccCHHHHHhcC
Confidence 467899998765433 2 222 267888885 599999987644
No 122
>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=22.33 E-value=86 Score=26.06 Aligned_cols=35 Identities=23% Similarity=0.230 Sum_probs=26.8
Q ss_pred CCChHHHHHHHHHHHhHcCCEEEEEeeCCEEEEEeCCC
Q 035824 82 PCEPWKIHEYAEVLAQLSKGIVIDINPSNTIIFYRGKN 119 (121)
Q Consensus 82 ~~~~~~~~~~a~~L~~~tga~vVq~i~G~~~iLYR~~n 119 (121)
+....=.-+++-.||+.+||+||. +..+-+||+-|
T Consensus 10 GPTAsGKT~lai~LAk~~~~eIIs---~DSmQvYr~md 44 (308)
T COG0324 10 GPTASGKTALAIALAKRLGGEIIS---LDSMQVYRGLD 44 (308)
T ss_pred CCCCcCHHHHHHHHHHHcCCcEEe---cchhhhcCCCc
Confidence 333444567999999999999995 46888899865
No 123
>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=22.07 E-value=1.1e+02 Score=23.16 Aligned_cols=39 Identities=23% Similarity=0.265 Sum_probs=30.1
Q ss_pred HHHHHHhccCCCCCCCCCC--CCCCCCCHHHHHHHHHhhcC
Q 035824 8 AWLIENLTKFELPKAPTEA--YDPEILTDEERHYLKRTDEK 46 (121)
Q Consensus 8 ~~~~~~l~~~~~~~~~~~~--~~~e~LT~kqr~~LR~~a~~ 46 (121)
...++.|..|..|-+.++. -.++.||..|+.+|.+-|..
T Consensus 61 a~cV~~~d~fRAPls~aelaRR~~~~Ls~~Q~~~L~rWGYP 101 (160)
T PF06299_consen 61 AACVRAFDPFRAPLSEAELARRRPAGLSPRQRANLERWGYP 101 (160)
T ss_pred HHHHHhhhhccCCCChHHHhhcCcccCCHHHHHHHHHhCCC
Confidence 4567888889888664333 33588999999999999974
No 124
>TIGR03822 AblA_like_2 lysine-2,3-aminomutase-related protein. Members of this protein form a distinctive clade, homologous to lysine-2,3-aminomutase (of Bacillus, Clostridium, and methanogenic archaea) and likely similar in function. Members of this family are found in Rhodopseudomonas, Caulobacter crescentus, Bradyrhizobium, etc.
Probab=22.06 E-value=4.4e+02 Score=21.44 Aligned_cols=11 Identities=27% Similarity=0.449 Sum_probs=6.3
Q ss_pred CEEEEEeCCCC
Q 035824 110 NTIIFYRGKNY 120 (121)
Q Consensus 110 ~~~iLYR~~ny 120 (121)
...+|.||-|.
T Consensus 232 ~q~vLl~gvNd 242 (321)
T TIGR03822 232 SQSVLLRGVND 242 (321)
T ss_pred EEeeEeCCCCC
Confidence 45566666554
No 125
>TIGR02408 ectoine_ThpD ectoine hydroxylase. Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms.
Probab=21.83 E-value=2.8e+02 Score=21.88 Aligned_cols=39 Identities=8% Similarity=-0.033 Sum_probs=31.3
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHh
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKK 72 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~ 72 (121)
.+.+||.+|+++++.-|. .+-++=++++.|+.+..+++.
T Consensus 13 ~~~~Lt~eqi~~f~~dGy------vvl~~vls~eev~~lr~~i~~ 51 (277)
T TIGR02408 13 AAGPLSAKQLQSYERDGF------LLLENLFSDDEVAALLAEVER 51 (277)
T ss_pred CCCCCCHHHHHHHHHCCE------EECcccCCHHHHHHHHHHHHH
Confidence 467899999999999995 445667888888888887755
No 126
>PRK06806 fructose-bisphosphate aldolase; Provisional
Probab=21.79 E-value=2.4e+02 Score=22.79 Aligned_cols=57 Identities=12% Similarity=-0.015 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHH
Q 035824 31 ILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAE 93 (121)
Q Consensus 31 ~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~ 93 (121)
.|.-+-.+.+++.- --|+|.+|..|++++-+..+ -..-..||.+...-..+..+.+.
T Consensus 186 ~l~~~~L~~i~~~~--~iPlV~hG~SGI~~e~~~~~----i~~G~~kinv~T~i~~a~~~a~~ 242 (281)
T PRK06806 186 NLRFDRLQEINDVV--HIPLVLHGGSGISPEDFKKC----IQHGIRKINVATATFNSVITAVN 242 (281)
T ss_pred ccCHHHHHHHHHhc--CCCEEEECCCCCCHHHHHHH----HHcCCcEEEEhHHHHHHHHHHHH
Confidence 56666666666543 27999999999999766543 33557788876644334433333
No 127
>COG4089 Predicted membrane protein [Function unknown]
Probab=21.51 E-value=50 Score=26.50 Aligned_cols=31 Identities=26% Similarity=0.422 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHhhcCCCceEEecCCCCcHHH
Q 035824 32 LTDEERHYLKRTDEKKKNYVQVGRRGIFGGV 62 (121)
Q Consensus 32 LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~v 62 (121)
|-+.+.=.||+.-+-=.|+++||..|-+|++
T Consensus 194 LiGADlLnLkki~n~g~pvvSIGGaGtFDgI 224 (235)
T COG4089 194 LIGADLLNLKKIINEGPPVVSIGGAGTFDGI 224 (235)
T ss_pred HhhhHhhhHHHHhccCCCeEEecCccceeee
Confidence 4456667788877777999999999999986
No 128
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=21.42 E-value=5.3e+02 Score=22.15 Aligned_cols=68 Identities=4% Similarity=-0.067 Sum_probs=38.4
Q ss_pred HHHHhhcCCCceEEecCCCCcHHHHHHHHHHHHhCCeeEEEecCCChHHHHHHHHHHHhHcCCEEEEEeeCCEE
Q 035824 39 YLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSNTI 112 (121)
Q Consensus 39 ~LR~~a~~lkpvv~IGk~Glt~~vi~~i~~al~~hELIKVk~~~~~~~~~~~~a~~L~~~tga~vVq~i~G~~~ 112 (121)
.|+++|..| +|. .|-..+++.++.+.+....++=-..-......+++...+.+...|..+.... |+++
T Consensus 63 ~L~~~G~~L--~v~---~G~p~~vl~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~~~-~~~l 130 (471)
T TIGR03556 63 RYQQAGSQL--LIL---QGDPVQLIPQLAQQLGAKAVYWNLDVEPYGRKRDRAVAAALKEAGIAVVTLW-DQLL 130 (471)
T ss_pred HHHHCCCCe--EEE---ECCHHHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHCCCEEEEeC-CcEE
Confidence 455555544 444 4667888888777665555543333333334455555555555676666543 6664
No 129
>COG2921 Uncharacterized conserved protein [Function unknown]
Probab=21.09 E-value=95 Score=21.55 Aligned_cols=23 Identities=30% Similarity=0.218 Sum_probs=18.7
Q ss_pred CCcHHHHHHHHHHHHhCCeeEEE
Q 035824 57 GIFGGVVLNMHLHWKKHETVKVV 79 (121)
Q Consensus 57 Glt~~vi~~i~~al~~hELIKVk 79 (121)
-..-.-++.++++|.+|++||+.
T Consensus 67 A~~~EQ~e~ly~eL~~~~~VkmV 89 (90)
T COG2921 67 ATNIEQVEALYRELRKHEIVKMV 89 (90)
T ss_pred ECCHHHHHHHHHHHhhCCceEEe
Confidence 34456689999999999999985
No 130
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=20.80 E-value=5.3e+02 Score=21.97 Aligned_cols=37 Identities=11% Similarity=0.019 Sum_probs=28.3
Q ss_pred CCCCCCHHHHHHHHHhhcCCCceEEecCCCCcHHHHHHHH
Q 035824 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMH 67 (121)
Q Consensus 28 ~~e~LT~kqr~~LR~~a~~lkpvv~IGk~Glt~~vi~~i~ 67 (121)
+|..+|.+..+.|+..|-. .++||-.-..+.++..+.
T Consensus 157 ~p~~~t~e~l~~l~~aGvn---RiSiGVQSf~d~vLk~lg 193 (449)
T PRK09058 157 RINGFDDEKADAALDAGAN---RFSIGVQSFNTQVRRRAG 193 (449)
T ss_pred CcCcCCHHHHHHHHHcCCC---EEEecCCcCCHHHHHHhC
Confidence 4677899999999987743 688888888877776554
No 131
>cd02810 DHOD_DHPD_FMN Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of
Probab=20.64 E-value=4.2e+02 Score=20.66 Aligned_cols=19 Identities=11% Similarity=-0.041 Sum_probs=7.8
Q ss_pred EecCCChHHHHHHHHHHHh
Q 035824 79 VSKPCEPWKIHEYAEVLAQ 97 (121)
Q Consensus 79 k~~~~~~~~~~~~a~~L~~ 97 (121)
.+..++.++..++++.+.+
T Consensus 104 si~g~~~~~~~~~a~~~~~ 122 (289)
T cd02810 104 SVGGSSKEDYVELARKIER 122 (289)
T ss_pred EeccCCHHHHHHHHHHHHH
Confidence 3333344444444444433
No 132
>cd00959 DeoC 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family. DERA belongs to the class I aldolases and catalyzes a reversible aldol reaction between acetaldehyde and glyceraldehyde 3-phosphate to generate 2-deoxyribose 5-phosphate. DERA is unique in catalyzing the aldol reaction between two aldehydes, and its broad substrate specificity confers considerable utility as a biocatalyst, offering an environmentally benign alternative to chiral transition metal catalysis of the asymmetric aldol reaction.
Probab=20.47 E-value=3.2e+02 Score=20.50 Aligned_cols=75 Identities=12% Similarity=0.035 Sum_probs=51.7
Q ss_pred HHHHHHHhhcCCCceEEecC--CCCcHHHHHHHHHHHHhCC--eeEEEecCCC-hHHHHHHHHHHHhHcCCEEEEEeeCC
Q 035824 36 ERHYLKRTDEKKKNYVQVGR--RGIFGGVVLNMHLHWKKHE--TVKVVSKPCE-PWKIHEYAEVLAQLSKGIVIDINPSN 110 (121)
Q Consensus 36 qr~~LR~~a~~lkpvv~IGk--~Glt~~vi~~i~~al~~hE--LIKVk~~~~~-~~~~~~~a~~L~~~tga~vVq~i~G~ 110 (121)
=...+|-=|..++-++.+|. .|-.+.+.++|...-+... .+||.+.... ..+.-..+..++...|+.+|..--|.
T Consensus 75 ve~A~~~GAdevdvv~~~g~~~~~~~~~~~~ei~~v~~~~~g~~lkvI~e~~~l~~~~i~~a~ria~e~GaD~IKTsTG~ 154 (203)
T cd00959 75 AREAIADGADEIDMVINIGALKSGDYEAVYEEIAAVVEACGGAPLKVILETGLLTDEEIIKACEIAIEAGADFIKTSTGF 154 (203)
T ss_pred HHHHHHcCCCEEEEeecHHHHhCCCHHHHHHHHHHHHHhcCCCeEEEEEecCCCCHHHHHHHHHHHHHhCCCEEEcCCCC
Confidence 34566766788899999994 8888889888887777643 4677443332 23445566677888899999753343
Done!