Query psy1178
Match_columns 144
No_of_seqs 188 out of 1262
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 18:45:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1178.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1178hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00425 CBF5 rRNA pseudourid 99.9 3.4E-27 7.3E-32 182.3 11.7 138 1-139 185-322 (322)
2 PRK04270 H/ACA RNA-protein com 99.9 5.7E-24 1.2E-28 163.4 10.8 128 1-129 173-300 (300)
3 PRK14124 tRNA pseudouridine sy 99.8 1.7E-18 3.6E-23 132.8 8.3 115 1-129 188-306 (308)
4 PRK05033 truB tRNA pseudouridi 99.8 6.5E-18 1.4E-22 129.7 10.0 112 1-130 195-309 (312)
5 PRK01851 truB tRNA pseudouridi 99.7 5.4E-18 1.2E-22 129.6 8.4 102 1-129 201-302 (303)
6 PRK01550 truB tRNA pseudouridi 99.7 9.1E-18 2E-22 128.7 8.9 109 1-130 195-303 (304)
7 PRK04642 truB tRNA pseudouridi 99.7 1.1E-17 2.4E-22 127.7 9.1 104 1-129 196-299 (300)
8 PRK00130 truB tRNA pseudouridi 99.7 1.2E-17 2.7E-22 127.3 8.6 103 1-129 188-290 (290)
9 PRK02755 truB tRNA pseudouridi 99.7 2.4E-17 5.2E-22 125.9 9.3 104 1-131 191-294 (295)
10 PRK14123 tRNA pseudouridine sy 99.7 4.9E-17 1.1E-21 124.8 8.8 109 1-129 196-305 (305)
11 PRK05389 truB tRNA pseudouridi 99.7 4.6E-17 9.9E-22 124.9 8.4 105 1-129 199-303 (305)
12 PRK01528 truB tRNA pseudouridi 99.7 5.5E-17 1.2E-21 123.7 8.2 101 1-129 190-290 (292)
13 PRK03287 truB tRNA pseudouridi 99.7 2.4E-16 5.3E-21 120.5 8.9 95 1-129 199-294 (298)
14 PRK02484 truB tRNA pseudouridi 99.7 2.7E-16 5.8E-21 120.2 8.6 98 1-128 196-293 (294)
15 COG0130 TruB Pseudouridine syn 99.6 2.6E-16 5.6E-21 118.9 6.4 102 1-129 169-270 (271)
16 PRK14122 tRNA pseudouridine sy 99.6 1.6E-15 3.4E-20 116.5 8.4 91 1-129 221-311 (312)
17 cd02573 PseudoU_synth_EcTruB P 99.6 2.3E-15 5E-20 114.4 6.6 89 1-105 188-276 (277)
18 PF01472 PUA: PUA domain; Int 99.6 1.7E-14 3.7E-19 89.4 7.6 74 55-128 1-74 (74)
19 COG2016 Predicted RNA-binding 99.5 1.9E-14 4.2E-19 100.1 7.6 94 42-140 60-158 (161)
20 TIGR03684 arCOG00985 arCOG0415 99.5 1.1E-13 2.4E-18 96.7 9.4 93 42-139 53-150 (150)
21 PRK14560 putative RNA-binding 99.5 1.6E-13 3.5E-18 96.9 9.0 94 42-140 60-158 (160)
22 TIGR00451 unchar_dom_2 unchara 99.5 4.1E-13 9E-18 88.8 9.4 78 53-130 29-107 (107)
23 KOG2529|consensus 99.4 1.7E-13 3.6E-18 107.2 3.8 144 1-144 222-365 (395)
24 PRK14846 truB tRNA pseudouridi 99.3 9.4E-13 2E-17 101.8 3.4 66 1-75 190-255 (345)
25 PF09157 TruB-C_2: Pseudouridi 99.2 7.8E-11 1.7E-15 69.5 7.0 58 55-128 1-58 (58)
26 PRK02193 truB tRNA pseudouridi 99.1 2.4E-10 5.1E-15 87.0 7.6 84 1-130 188-271 (279)
27 KOG2523|consensus 99.0 3.2E-10 7E-15 78.7 3.5 94 43-141 77-179 (181)
28 PRK13794 hypothetical protein; 99.0 2.1E-09 4.5E-14 87.8 8.3 73 56-128 126-199 (479)
29 smart00359 PUA Putative RNA-bi 99.0 8.2E-09 1.8E-13 63.8 8.7 73 56-128 2-76 (77)
30 PRK13534 7-cyano-7-deazaguanin 98.9 4.7E-09 1E-13 88.1 8.7 75 55-129 564-638 (639)
31 PRK13795 hypothetical protein; 98.9 5.2E-09 1.1E-13 88.1 9.0 76 54-129 126-201 (636)
32 COG1370 Prefoldin, molecular c 98.8 3.4E-08 7.3E-13 67.9 7.4 71 56-126 82-152 (155)
33 PRK04099 truB tRNA pseudouridi 98.7 3.5E-08 7.6E-13 74.9 5.7 73 1-107 187-259 (273)
34 PRK05429 gamma-glutamyl kinase 98.5 2.3E-07 4.9E-12 73.7 6.9 64 53-116 279-343 (372)
35 PF09142 TruB_C: tRNA Pseudour 98.5 4.9E-07 1.1E-11 52.8 5.9 55 54-128 1-55 (56)
36 TIGR00432 arcsn_tRNA_tgt tRNA- 98.5 3.3E-07 7.2E-12 75.7 7.0 71 56-126 468-538 (540)
37 COG5270 PUA domain (predicted 98.4 6.3E-07 1.4E-11 63.7 5.2 71 55-125 129-199 (202)
38 TIGR01027 proB glutamate 5-kin 98.4 1.3E-06 2.7E-11 69.3 7.1 62 54-115 272-334 (363)
39 KOG2522|consensus 98.2 4.2E-06 9.1E-11 66.9 6.5 97 43-144 75-179 (560)
40 PRK13402 gamma-glutamyl kinase 98.1 1.2E-05 2.7E-10 63.8 6.8 62 54-115 276-338 (368)
41 COG0263 ProB Glutamate 5-kinas 97.7 8.7E-05 1.9E-09 58.1 6.1 62 54-116 279-341 (369)
42 COG1549 Queuine tRNA-ribosyltr 97.3 0.00067 1.4E-08 55.3 6.5 56 72-128 463-518 (519)
43 PRK15128 23S rRNA m(5)C1962 me 94.7 0.2 4.3E-06 40.4 7.7 52 56-107 4-56 (396)
44 PF03657 UPF0113: Uncharacteri 93.5 0.19 4E-06 35.7 4.7 49 56-106 93-141 (162)
45 PF13636 Nol1_Nop2_Fmu_2: pre- 92.9 0.42 9E-06 31.1 5.5 46 53-107 45-90 (102)
46 KOG3492|consensus 88.1 1.5 3.2E-05 30.8 4.9 63 55-117 95-157 (180)
47 PRK08557 hypothetical protein; 86.0 1.1 2.3E-05 36.5 3.8 52 54-109 77-130 (417)
48 cd02867 PseudoU_synth_TruB_4 P 83.5 0.45 9.8E-06 37.2 0.6 15 1-15 219-233 (312)
49 COG3270 Uncharacterized conser 80.1 4.6 0.0001 27.3 4.4 48 52-107 65-112 (127)
50 PRK08035 type III secretion sy 70.9 20 0.00042 28.4 6.4 63 54-132 259-321 (323)
51 smart00841 Elong-fact-P_C Elon 68.1 9.2 0.0002 22.1 3.1 29 67-101 26-54 (56)
52 PRK11933 yebU rRNA (cytosine-C 67.7 16 0.00035 30.3 5.6 62 54-142 407-468 (470)
53 PRK08158 type III secretion sy 65.7 33 0.00071 26.9 6.6 64 54-133 238-301 (303)
54 COG1374 NIP7 Protein involved 63.4 10 0.00022 27.2 3.2 57 56-113 101-157 (176)
55 PF09285 Elong-fact-P_C: Elong 62.9 7.6 0.00016 22.5 2.1 30 67-102 26-55 (56)
56 cd05794 S1_EF-P_repeat_2 S1_EF 60.0 18 0.0004 20.9 3.3 29 67-101 26-54 (56)
57 PF01568 Molydop_binding: Moly 60.0 41 0.0009 21.2 5.7 37 55-107 30-66 (110)
58 cd02783 MopB_CT_2 The MopB_CT_ 54.9 68 0.0015 22.1 6.9 39 52-106 29-67 (156)
59 cd02787 MopB_CT_ydeP The MopB_ 49.7 57 0.0012 20.9 4.9 35 54-104 30-64 (112)
60 cd02776 MopB_CT_Nitrate-R-NarG 49.2 58 0.0013 22.2 5.1 37 53-105 29-65 (141)
61 cd02779 MopB_CT_Arsenite-Ox Th 47.3 76 0.0016 20.5 6.7 36 54-105 32-67 (115)
62 KOG2559|consensus 45.5 6.9 0.00015 29.8 -0.0 15 2-16 240-254 (318)
63 cd02793 MopB_CT_DMSOR-BSOR-TMA 45.3 76 0.0017 20.9 5.1 37 53-105 31-67 (129)
64 cd02784 MopB_CT_PHLH The MopB_ 43.9 98 0.0021 21.1 5.5 14 54-67 37-50 (137)
65 PF13101 DUF3945: Protein of u 43.1 18 0.00039 21.0 1.5 27 52-78 28-54 (59)
66 PRK12784 hypothetical protein; 42.1 21 0.00045 22.2 1.7 17 123-139 15-31 (84)
67 cd02785 MopB_CT_4 The MopB_CT_ 41.0 1E+02 0.0022 20.1 6.8 36 54-105 31-66 (124)
68 cd02792 MopB_CT_Formate-Dh-Na- 40.7 98 0.0021 19.9 6.9 36 53-104 33-68 (122)
69 PRK06933 type III secretion sy 40.3 95 0.0021 24.4 5.5 61 54-130 245-305 (308)
70 PRK02268 hypothetical protein; 38.6 64 0.0014 22.3 3.9 24 84-107 35-67 (141)
71 cd02778 MopB_CT_Thiosulfate-R- 38.4 1.1E+02 0.0024 19.7 7.1 38 53-106 28-65 (123)
72 cd02794 MopB_CT_DmsA-EC The Mo 37.5 1.1E+02 0.0025 19.7 5.4 35 56-106 31-65 (121)
73 PRK06789 flagellar motor switc 36.0 96 0.0021 19.0 4.0 46 54-108 15-60 (74)
74 cd02786 MopB_CT_3 The MopB_CT_ 34.2 1.3E+02 0.0027 19.2 6.7 36 54-105 30-65 (116)
75 cd02781 MopB_CT_Acetylene-hydr 33.4 1.4E+02 0.003 19.5 6.9 35 54-104 32-66 (130)
76 TIGR02551 SpaO_YscQ type III s 33.3 1.2E+02 0.0025 23.4 5.1 46 54-108 241-286 (298)
77 PRK04980 hypothetical protein; 33.1 1.4E+02 0.003 19.4 7.1 50 55-106 3-54 (102)
78 cd02788 MopB_CT_NDH-1_NuoG2-N7 32.5 1.3E+02 0.0028 18.8 6.6 37 54-106 28-64 (96)
79 cd02790 MopB_CT_Formate-Dh_H F 31.6 1.4E+02 0.003 18.9 6.6 14 54-67 34-47 (116)
80 PRK00529 elongation factor P; 31.4 78 0.0017 22.8 3.6 31 67-103 154-184 (186)
81 cd00508 MopB_CT_Fdh-Nap-like T 31.2 1.4E+02 0.0031 18.9 6.7 34 54-103 34-67 (120)
82 TIGR00038 efp translation elon 31.1 69 0.0015 23.0 3.3 30 67-102 153-182 (184)
83 PRK07963 fliN flagellar motor 30.2 1.4E+02 0.003 20.6 4.4 60 55-130 69-128 (137)
84 PF14306 PUA_2: PUA-like domai 30.1 85 0.0018 22.1 3.5 23 84-106 92-114 (160)
85 COG1886 FliN Flagellar motor s 29.9 1.8E+02 0.0039 19.7 5.6 46 54-108 79-124 (136)
86 PF01052 SpoA: Surface present 29.5 1.3E+02 0.0028 17.8 5.5 61 53-129 15-75 (77)
87 PRK15488 thiosulfate reductase 28.8 1.7E+02 0.0038 25.6 5.9 23 84-106 679-701 (759)
88 cd02789 MopB_CT_FmdC-FwdD The 28.5 1.6E+02 0.0035 18.7 6.7 36 53-104 29-64 (106)
89 TIGR03479 DMSO_red_II_alp DMSO 27.9 1.2E+02 0.0026 27.4 4.8 23 84-106 823-845 (912)
90 PF01878 EVE: EVE domain; Int 26.6 91 0.002 21.0 3.1 23 85-107 40-65 (143)
91 TIGR02480 fliN flagellar motor 25.1 1.6E+02 0.0036 17.6 6.3 59 54-128 16-74 (77)
92 PRK04542 elongation factor P; 24.7 1.1E+02 0.0023 22.3 3.3 30 67-102 157-186 (189)
93 COG2411 Uncharacterized conser 24.6 2.8E+02 0.006 20.1 5.6 48 54-106 6-55 (188)
94 PRK08916 flagellar motor switc 24.3 2.2E+02 0.0049 18.9 5.6 60 54-129 53-112 (116)
95 PRK13992 minC septum formation 24.2 2.2E+02 0.0047 20.8 4.9 29 64-92 102-130 (205)
96 TIGR01222 minC septum site-det 23.9 2.2E+02 0.0049 20.8 5.0 29 64-92 116-145 (217)
97 cd02791 MopB_CT_Nitrate-R-NapA 23.2 2.1E+02 0.0046 18.2 6.6 15 53-67 33-47 (122)
98 PRK14990 anaerobic dimethyl su 23.1 1.8E+02 0.0039 25.7 5.0 24 83-106 734-757 (814)
99 TIGR02178 yeiP elongation fact 22.5 1.2E+02 0.0026 22.0 3.2 29 68-102 156-184 (186)
100 cd02782 MopB_CT_1 The MopB_CT_ 22.3 2.3E+02 0.005 18.4 6.7 14 54-67 32-45 (129)
101 cd02777 MopB_CT_DMSOR-like The 22.2 2.3E+02 0.0051 18.4 6.3 36 54-105 33-68 (127)
102 PRK05698 fliN flagellar motor 22.2 2.7E+02 0.0059 19.6 4.8 60 55-130 88-147 (155)
103 COG1092 Predicted SAM-dependen 21.9 1.1E+02 0.0023 25.0 3.1 49 59-107 3-52 (393)
104 TIGR01580 narG respiratory nit 21.6 2.9E+02 0.0064 26.2 6.0 24 84-107 1129-1152(1235)
105 cd02780 MopB_CT_Tetrathionate_ 21.5 2.6E+02 0.0056 18.7 6.9 14 54-67 29-42 (143)
106 PRK15102 trimethylamine N-oxid 21.1 2.2E+02 0.0047 25.4 5.1 23 84-106 723-745 (825)
107 PRK00809 hypothetical protein; 20.9 1.7E+02 0.0038 20.1 3.6 24 84-107 34-65 (144)
108 PRK01973 septum formation inhi 20.7 2.7E+02 0.0059 21.5 4.9 28 64-91 167-194 (271)
109 PF03785 Peptidase_C25_C: Pept 20.4 2E+02 0.0044 17.9 3.4 20 87-107 26-45 (81)
110 PF03775 MinC_C: Septum format 20.2 2.6E+02 0.0057 18.2 4.5 28 65-92 6-33 (105)
No 1
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=99.95 E-value=3.4e-27 Score=182.27 Aligned_cols=138 Identities=51% Similarity=0.851 Sum_probs=116.3
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|+||++|+++...+...+++..+++.|+|++.+|.++|.+.++++++.+++||+.++.+++..
T Consensus 185 ~~~L~R~~~g~f~~~-~a~~l~~l~~~~~~~~~~~~~~~l~~~l~p~~~~l~~lP~V~Vd~~~a~~I~NG~~I~~pgv~~ 263 (322)
T TIGR00425 185 MQELRRTRSGCFGED-DMVTLHDLLDAYVFWKEDGDESYLRRVIKPMEYALRHLKRVVVKDSAVDAICHGADLMVRGIAR 263 (322)
T ss_pred EEEeEeEEECCcccc-ccccHHHHHHhhhhhhcccchhhHhhhcCCHHHHHhhCCceEeCHHHHHHHHCCCccccccccc
Confidence 789999999999999 5799999987532111211122467789999999999999999999999999999999887654
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeecCCccccCcC
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWG 139 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~~~~~~~~w~ 139 (144)
.+..+..++.|++++.+|+++|||++.++++++....+|.++++.|+|.+.|+||+.|+
T Consensus 264 ~d~~i~~gd~V~V~~~~G~~LAIGea~~s~~ei~~~~kG~vV~~~~~~~~~~~~~~~~~ 322 (322)
T TIGR00425 264 LEKGIEKGDTVAVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGTYPRMWK 322 (322)
T ss_pred cccccCCCCEEEEEECCCEEEEEEEEecCHHHHhhcCCcEEEEEEEEeeCCCCCCCCcC
Confidence 43334567788898888899999999999999999899999999999999999999997
No 2
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=99.91 E-value=5.7e-24 Score=163.37 Aligned_cols=128 Identities=43% Similarity=0.683 Sum_probs=107.0
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +++||++|+++...+...++...+++.|+|++.+|.++|.+.++++++++++||+++..+++..
T Consensus 173 ~~~L~R~~~g~f~~~-~a~~l~~l~~~~~~~~~~~d~~~l~~~LlPle~aL~~LP~V~Lde~aa~~I~nG~~L~~~gi~~ 251 (300)
T PRK04270 173 MQELRRTRTGPFTEE-DLVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLPKIIIKDSAVDAIAHGAPLYAPGIAK 251 (300)
T ss_pred EEEEEeEEECCCCcc-hhcCHHHHHHhhhhhhcccchhhHHhhcCCHHHHhhhCCceEECHHHHHHHHcCCccccCCcee
Confidence 689999999999999 5799999987532111111222466789999999999999999999999999999999887654
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
....+..++.|++++.+|+++|+|++.++++++....+|.++++.|||+
T Consensus 252 ~~~~~~~gd~V~I~~~~G~~LAIG~~~~ss~el~~~~kG~~vk~~~~~~ 300 (300)
T PRK04270 252 LEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGIVVDLERVFM 300 (300)
T ss_pred cccccCCCCEEEEEeCCCcEEEEEEEccCHHHHHhcCCceEEEEEEeeC
Confidence 4445567788999988889999999999999999989999999999984
No 3
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=99.76 E-value=1.7e-18 Score=132.84 Aligned_cols=115 Identities=23% Similarity=0.361 Sum_probs=92.6
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|++|+++... .+.+.++|++.+|. +|.+.++++++++++||+.+..+++..
T Consensus 188 m~~LrRt~~G~f~l~-~a~~l~~l~~~-----------~~~~~llp~~~~l~-lp~v~l~~~~~~~i~~G~~i~~~~~~~ 254 (308)
T PRK14124 188 AVELVRLSVGKFSIE-DSINVFEVSPE-----------EIENRIIPMEEILD-LPKVVIHQESTEKILNGSQIYLEMVKE 254 (308)
T ss_pred EEEEEeEEECCCcHH-HccCHHHhhhh-----------hhhhhcCCHHHHhC-CceEEeCHHHHHHHHCCCccccccccc
Confidence 789999999999999 57999999642 23467999999999 999999999999999999997654321
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhc----CCCceEEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMAT----CDHGVVAKIKRVIM 129 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~----~~~g~~v~~~rv~~ 129 (144)
. ..+..++.+++++.+|+|+|||+...++..+.. ..+|.+++|.+||.
T Consensus 255 ~-~~~~~~~~v~v~~~~g~~lai~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~ 306 (308)
T PRK14124 255 W-DNFKKDDVVRVFDEEGRLLAIARAERNSSFLETLKKHERNERVLKLKKVFR 306 (308)
T ss_pred c-cccCCCCEEEEEcCCCeEEEEEEEecCCceeeeeecccccceEEeeeeeec
Confidence 1 123456678999888999999998877765553 34688999999984
No 4
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=99.75 E-value=6.5e-18 Score=129.67 Aligned_cols=112 Identities=17% Similarity=0.304 Sum_probs=86.7
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHH--hhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCe
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLY--DQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGV 78 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~--~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~ 78 (144)
|++||||++|+|+++ +|+||++|+++.... .+.+++..++..|+|++.+|.++|.|.+++++++.++||+.+...+.
T Consensus 195 ~~~LrRt~~G~f~~~-~a~~l~~l~~~~~~~~~~~~~~~~~l~~~llp~~~~l~~lp~v~l~~~~~~~i~~G~~i~~~~~ 273 (312)
T PRK05033 195 VIYLRRTQVAPYPLE-RMVTLEQLEALVEQAEQQEIPPAELLDPLLLPMDSAVSDLPEVNLPEESAYYFKQGQPVRVSGA 273 (312)
T ss_pred EEEEEeEEECCcccc-cccCHHHHHHhhhhhccccccchhhHhhhhCCHHHHHhhCCeEEECHHHHHHHHCcCccccCcC
Confidence 789999999999999 579999998753210 01122234677899999999999999999999999999999864321
Q ss_pred ecccCCCCCCCEEEEE-cCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeec
Q psy1178 79 LRYEDGIEMDEEIVIV-STKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMD 130 (144)
Q Consensus 79 ~~~~~~~~~~~~v~i~-~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~ 130 (144)
..++.|+++ +.+|+|+|||+.. ..| .++|.|+|+.
T Consensus 274 -------~~~~~v~~~~~~~g~~lai~~~~---------~~~-~l~p~rvf~~ 309 (312)
T PRK05033 274 -------PLEGLVRVTEGENGKFIGIGEID---------DDG-RVAPKRLVVE 309 (312)
T ss_pred -------CCCCEEEEEECCCCEEEEEEEEC---------CCC-EEEEEEEEec
Confidence 224468888 7788999999862 135 6999999954
No 5
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=99.74 E-value=5.4e-18 Score=129.64 Aligned_cols=102 Identities=23% Similarity=0.315 Sum_probs=82.7
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|++|++|+++.. ..+.+.|+|++.+|.++|.|.++++++++++||+.+....
T Consensus 201 ~~~LrRt~~G~f~~~-~a~~l~~l~~~~~--------~~~~~~l~p~~~~l~~lp~v~l~~~~~~~i~~G~~i~~~~--- 268 (303)
T PRK01851 201 LTALRRTGVGGLTLE-QAVTLEALEAADE--------AERDALLAPVDALLSTFPRVTLDADAAGRFLHGQRLRLSD--- 268 (303)
T ss_pred EEEEEeEEECCCchH-HcCCHHHHHhchh--------hhhhhhcCCHHHHHhhCCEEEeCHHHHHHHHCcCcccccc---
Confidence 789999999999999 5799999986421 1233479999999999999999999999999999985422
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
...++.+++++.+|+|+|||+.. .+ .++|.|+|+
T Consensus 269 ----~~~~~~v~i~~~~g~~lai~~~~----------~~-~l~p~rvf~ 302 (303)
T PRK01851 269 ----LPDAPRVRVYDDPGRLLGVARWQ----------EG-VLAPERLVV 302 (303)
T ss_pred ----CCCCCEEEEEcCCCeEEEEEEEc----------CC-EEEEEEEeC
Confidence 12344688888888999999863 34 699999996
No 6
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=99.74 E-value=9.1e-18 Score=128.75 Aligned_cols=109 Identities=19% Similarity=0.313 Sum_probs=86.1
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|++|++|+++.. ...+++.|+|++.+|.++|.|.++++++++++||+.+..++...
T Consensus 195 ~~~L~Rt~~G~f~~~-~a~~le~l~~~~~-------~~~l~~~l~p~~~~l~~lp~v~l~~~~~~~i~~G~~i~~~~~~~ 266 (304)
T PRK01550 195 MSHLVRTASGGFTLE-DCLTFEEIEENVQ-------AGTVESILYPIDRALSHLPKLVIDEKQAEKVKNGAFLKNPLFIT 266 (304)
T ss_pred EEEEEeEEECCCCHH-HcCCHHHHHhhhh-------ccchhhhcCCHHHHHhhCCEEEECHHHHHHHHCcCccccCcccc
Confidence 789999999999999 5799999986531 23466789999999999999999999999999999996543210
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeec
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMD 130 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~ 130 (144)
..++.+++++.+|+|+|||+.... ..+ .++|.|+|+.
T Consensus 267 -----~~~~~v~~~~~~g~~lai~~~~~~-------~~~-~l~p~rvf~~ 303 (304)
T PRK01550 267 -----VEAEPIVVLDYNDRCLAIYEHHPK-------KPG-LLKPEKVLVN 303 (304)
T ss_pred -----cCCCcEEEEcCCCeEEEEEEEecC-------CCC-EEEEEEeecC
Confidence 123468888888999999986310 124 6999999963
No 7
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=99.74 E-value=1.1e-17 Score=127.71 Aligned_cols=104 Identities=17% Similarity=0.259 Sum_probs=83.1
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|+||++|+++.. ....+++.|+|++.+|.++|.|.+++.++++++||+.+....
T Consensus 196 m~~L~Rt~~G~f~~~-~a~~l~~l~~~~~------~~~~~~~~l~p~~~~l~~lp~v~l~~~~~~~i~~G~~i~~~~--- 265 (300)
T PRK04642 196 IAALRRLWVEPFRAP-QMITLEALEAALE------AGAEADTLLLPLAAGLADFPRIELDATLAARFRMGQRLRDAS--- 265 (300)
T ss_pred EEEeEeeEECCcchH-HCccHHHHHHhHh------cccchhhcccCHHHHHhhCCEEEeCHHHHHHHHCcCccCCCc---
Confidence 789999999999999 5799999987532 112256789999999999999999999999999999985322
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
.. .+.+++++.+++|+|||+.. ..+ .++|.|+|.
T Consensus 266 ----~~-~~~v~i~~~~~~~lai~~~~---------~~~-~l~p~rvf~ 299 (300)
T PRK04642 266 ----FP-TGQVAVFGPDGSPAGLGLVD---------ADG-LLSPQRLFN 299 (300)
T ss_pred ----CC-CCeEEEEcCCCeEEEEEEEC---------CCC-EEEEEEEEC
Confidence 12 23578888788999999862 134 699999983
No 8
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=99.73 E-value=1.2e-17 Score=127.35 Aligned_cols=103 Identities=19% Similarity=0.302 Sum_probs=83.8
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|++|++|++. .+.+.|+|++.+|.++|.+.++++++++++||+.+..+...
T Consensus 188 ~~~LrRt~~G~f~~~-~a~~l~~l~~~-----------~~~~~l~p~~~~l~~lp~v~l~~~~~~~i~~G~~i~~~~~~- 254 (290)
T PRK00130 188 MWNLIRTETGPFNIE-NSITLEDLNEE-----------NIEDYIIPIDKALKHYPKVSLDEKFEKLLLNGVKIKDRRLL- 254 (290)
T ss_pred EEEEEeEEECCCCHH-HcCCHHHHhhh-----------hhhhhccCHHHHHhhCCEEEECHHHHHHHHCcCccccCccc-
Confidence 789999999999999 57999999752 14567999999999999999999999999999999654321
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
..+..++.+++++.+|+++|||+.. .+ .++|.|+|.
T Consensus 255 --~~~~~~~~v~~~~~~g~~lai~~~~----------~~-~~~p~~vf~ 290 (290)
T PRK00130 255 --DNIEENKLYRVYDEENKFIGIGMKN----------DK-GFKIEKLLV 290 (290)
T ss_pred --ccCCCCCEEEEEcCCCeEEEEEEEc----------CC-EEEEEEEEC
Confidence 1223455788888888999999852 34 699999984
No 9
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=99.72 E-value=2.4e-17 Score=125.90 Aligned_cols=104 Identities=19% Similarity=0.259 Sum_probs=82.9
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|+||++|++... ... ..|+|++.+|.++|.|.++++++++++||+.+..+.
T Consensus 191 m~~LrRt~~G~f~~~-~a~~l~~l~~~~~-------~~~--~~llp~~~~l~~lp~v~l~~~~~~~l~~G~~i~~~~--- 257 (295)
T PRK02755 191 LAALRRTQSLGFHLA-QSLPLPELENQLQ-------AGT--FPLLPPDLALQHLPRVQLSAEEAQRWCCGQRIPLEN--- 257 (295)
T ss_pred EEEEEeEEECCCcHH-HcCCHHHHHhhhh-------ccc--ceecCHHHHHccCCEEEECHHHHHHHHCcCccccCc---
Confidence 789999999999999 5799999976421 011 268999999999999999999999999999986432
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeecC
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDR 131 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~~ 131 (144)
...++.+++++.+|+|+|||+.. ..+ .++|+|+|+.-
T Consensus 258 ----~~~~~~~~~~~~~g~~lai~~~~---------~~~-~~~p~rv~~~~ 294 (295)
T PRK02755 258 ----LPAGGAVVVYDADGRFLGIGLIE---------QDG-LLKPKVVFEAI 294 (295)
T ss_pred ----CCCCCeEEEEcCCCeEEEEEEEC---------CCC-eEEEEEEEeeC
Confidence 12345688888888999999862 124 69999999753
No 10
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=99.71 E-value=4.9e-17 Score=124.77 Aligned_cols=109 Identities=25% Similarity=0.214 Sum_probs=82.0
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhh-HHhhhCCceecCCCee
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSA-VNAVCYGAQIMLPGVL 79 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~-~~~l~~G~~l~~~~~~ 79 (144)
|++||||++|+|+++ +|++|++|+++.. .+.+++.|+|++.+|.++|.|.+++++ .++++||+.+......
T Consensus 196 ~~~LrRt~~G~f~l~-~a~~l~~l~~~~~-------~~~l~~~l~p~~~~l~~lp~v~l~~~~~~~~i~~G~~i~~~~~~ 267 (305)
T PRK14123 196 MSKLTRIESGGFVLK-DSLTLEQIKELHE-------QDSLQNKLFPLEYGLKGLPSIKIKDSHIKKRILNGQKFNKNEFD 267 (305)
T ss_pred EEEEEeEEECCCchH-HcCCHHHHHhhhc-------ccchhhccCCHHHHHhhCCEEEECHHHHHHHHHCcCcccccccc
Confidence 789999999999999 5799999986431 234677899999999999999999995 7899999999643321
Q ss_pred cccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 80 RYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 80 ~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
....+..+++++.+|+|+|||+.... ..+ .++|.|+|+
T Consensus 268 ----~~~~~~~~~~~~~~g~~lai~~~~~~-------~~~-~l~p~rv~~ 305 (305)
T PRK14123 268 ----NKIKDQIVFIDDDSEKVLAIYMVHPT-------KES-EIKPKKVFN 305 (305)
T ss_pred ----cCCCCcEEEEECCCCeEEEEEEeecC-------CCC-EEEEEEeEC
Confidence 00123345666557899999986310 123 699999984
No 11
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=99.70 E-value=4.6e-17 Score=124.86 Aligned_cols=105 Identities=26% Similarity=0.309 Sum_probs=81.3
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|++|++|+++. +...+++.|+|++.+|.++|.+.++++++++++||+.+......
T Consensus 199 ~~~LrRt~~G~f~~~-~a~~l~~l~~~~-------~~~~~~~~l~p~~~~l~~lp~v~l~~~~~~~l~~G~~i~~~~~~- 269 (305)
T PRK05389 199 IAALRRTRVGPFTEE-DAITLEKLEALA-------RFAALDALLLPVETALDDLPALALTDEQAARLRQGNPVLLRGRD- 269 (305)
T ss_pred EEEEEeEEECCCcHH-HccCHHHHHhcc-------cccchhhhcCCHHHHHccCCEEEeCHHHHHHHHCcCccccCccc-
Confidence 789999999999999 579999998642 12346678999999999999999999999999999999654310
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
....+..++++ .+|+|+|||+.. .+ .++|.++|.
T Consensus 270 ---~~~~~~~~~~~-~~g~~lai~~~~----------~~-~l~p~~v~~ 303 (305)
T PRK05389 270 ---APLPEAEAYAT-AGGRLVALGEIR----------AG-ELRPKRVFN 303 (305)
T ss_pred ---cCCCCcEEEEe-cCCEEEEEEEEc----------CC-EEEEEEEEe
Confidence 01112234444 588999999862 24 699999995
No 12
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=99.70 E-value=5.5e-17 Score=123.68 Aligned_cols=101 Identities=23% Similarity=0.272 Sum_probs=79.3
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|+||++|+++.. ..+++.|+|++.+|.++|.+.++++.+++++||+.+....
T Consensus 190 ~~~LrRt~~G~f~~~-~a~~l~~l~~~~~--------~~l~~~llp~~~~l~~lp~i~l~~~~~~~~~~G~~i~~~~--- 257 (292)
T PRK01528 190 VIELRRTQVGIFKEE-NAIRIKSSDAITK--------NSLEEKSIKIEAILDDILVLDATDEQAQKIKYGQKCLFDY--- 257 (292)
T ss_pred EeEEEeEEECCccHH-HcCCHHHHHhhhh--------hhhhhccCCHHHHHhhCCeEEeCHHHHHHHHCcCccccCc---
Confidence 789999999999999 5799999986421 2466789999999999999999999999999999985321
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
.....+.++..+|+|+|||+.. .+ .++|+|+|.
T Consensus 258 -----~~~~~~~~~~~~~~~lai~~~~----------~~-~l~p~rvf~ 290 (292)
T PRK01528 258 -----EKDVNFLWVRYKGVLLAIGSLN----------KN-CFNSLRVFN 290 (292)
T ss_pred -----CCCCceEEEEECCEEEEEEEEc----------CC-EEEEEEEEe
Confidence 0111134444578999999752 34 699999994
No 13
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=99.67 E-value=2.4e-16 Score=120.45 Aligned_cols=95 Identities=22% Similarity=0.269 Sum_probs=79.1
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCccccccccccccc-ccCcCCEEEEChhhHHhhhCCceecCCCee
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEG-LLVGHKRIILKDSAVNAVCYGAQIMLPGVL 79 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~-aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~ 79 (144)
|++||||++|+|+++ +++||++|.+.. ..++|++. +|.++|.|.++++++++++||+++..+.
T Consensus 199 ~~~LrRt~~G~f~l~-~a~~l~~l~~~~-------------~~l~p~~~~~l~~lp~v~l~~~~~~~i~~G~~i~~~~-- 262 (298)
T PRK03287 199 LTALRRTRVGPFTLD-QARTLDELAEEP-------------ALSLSLDEAAARSFPRRDLTAAEAEALSHGRRLEPAG-- 262 (298)
T ss_pred EEEEEeEEECCCcHH-HccCHHHHHhhh-------------hhcCCHHHHHHccCCeEEeCHHHHHHHHCcCccccCC--
Confidence 789999999999999 579999997531 26889988 7899999999999999999999986432
Q ss_pred cccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 80 RYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 80 ~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
.++.+++++.+|+|+|||+.. .+ .++|.|+|+
T Consensus 263 -------~~~~~~~~~~~~~~lai~~~~----------~~-~l~p~~v~~ 294 (298)
T PRK03287 263 -------IDGVYAAVDPDGRVIALLEER----------GG-RARSVVVFR 294 (298)
T ss_pred -------CCCeEEEEcCCCeEEEEEEEc----------CC-EEEEEEEEc
Confidence 133578888788999999862 34 699999997
No 14
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=99.67 E-value=2.7e-16 Score=120.20 Aligned_cols=98 Identities=20% Similarity=0.241 Sum_probs=78.5
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|+||++|++... ...+ +.|+|++.+|.++|.|.++++++++++||+.+..+.
T Consensus 196 ~~~L~Rt~~G~f~l~-~a~~l~~l~~~~~-------~~~l-~~l~p~~~~l~~lp~v~l~~~~~~~i~~G~~i~~~~--- 263 (294)
T PRK02484 196 MSFLTRTASAGLTLE-QAVTLEEIAEKVE-------AGEL-SFLQPIEYGVADLPKVDLTPEQFTEVSFGRFISLDS--- 263 (294)
T ss_pred EEEEEeEEECCCcHH-HcCCHHHHHhhhh-------ccch-heecCHHHHHccCCeEEeCHHHHHHHHCcCccccCC---
Confidence 789999999999999 5799999986431 1224 489999999999999999999999999999986432
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEe
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVI 128 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~ 128 (144)
.++.+++++ +++|+|||+.. .+ .++|.|+|
T Consensus 264 ------~~~~~~~~~-~~~~lai~~~~----------~~-~~~p~rvf 293 (294)
T PRK02484 264 ------QEPKLAAFY-NDKLKAILEKR----------GQ-LYKPRKVL 293 (294)
T ss_pred ------CCCeEEEEe-CCeEEEEEEEc----------CC-EEEEEEEE
Confidence 123566665 56899999862 23 69999998
No 15
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=99.65 E-value=2.6e-16 Score=118.88 Aligned_cols=102 Identities=43% Similarity=0.565 Sum_probs=83.7
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ ++++|++++++.. +.+.+.++|++.++.++|++.+++.++.+++||++ +++.
T Consensus 169 m~~LrRt~~g~f~~~-~~~~l~~l~~~~~--------~~~~~~~~p~e~~l~~lpk~~i~~~~~~~i~~G~~---~~~~- 235 (271)
T COG0130 169 MSELRRTRVGPFSEE-DAVTLELLDELDA--------ESLLRLLLPLESALSDLPRLVLKDSAANAIKYGAK---PGLL- 235 (271)
T ss_pred hhhhccccccccccc-cccchhhHHHHHh--------hhhhccccchhHHhccCCcEecCHHHHHHHHcCCc---hhcc-
Confidence 789999999999999 4799999987642 33556779999999999999999999999999998 3321
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
.+..+..|++++.+|.++|+|... +. .++|.|||+
T Consensus 236 ---~~~~~~~v~v~~~~~~~~al~~~~----------~~-~~~~~rv~~ 270 (271)
T COG0130 236 ---DIELGGLVRVYTAKGLGIALGEID----------EE-GLKPKRVFM 270 (271)
T ss_pred ---ccccCCcEEEEccCCeEEEEeehh----------hc-CcceeEeec
Confidence 145677899999888888888763 22 289999986
No 16
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=99.62 E-value=1.6e-15 Score=116.51 Aligned_cols=91 Identities=29% Similarity=0.314 Sum_probs=76.0
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ ++++|++|.+. .++|++.++ ++|.+.++++++++++||+.+..+.
T Consensus 221 m~~LrRt~~G~f~l~-~a~~l~~l~~~---------------~~~p~~~~l-~lp~v~l~~~~~~~i~~G~~i~~~~--- 280 (312)
T PRK14122 221 LSGLVRTRVGRYGLE-DAVSLEDLAEA---------------PGIPELDAL-DFPRVELSHAEARRVRQGKPPAIPA--- 280 (312)
T ss_pred EEEEEeEEECCCcHH-HcCCHHHHhhh---------------hcCCHHHHc-CCCeEEcCHHHHHHHHCcCcccCCC---
Confidence 789999999999999 57999999642 367999988 7999999999999999999985321
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
.+.+++++.+|.|+|||+.. .+ .++|.|+|+
T Consensus 281 -------~~~~~~~~~~g~~~ai~~~~----------~~-~l~~~r~~~ 311 (312)
T PRK14122 281 -------QGRVALVDPKGQLVAVAEGD----------GF-KLKIVRVWA 311 (312)
T ss_pred -------CceEEEEcCCCeEEEEEEec----------CC-EEEEEEEec
Confidence 23578888889999999862 24 699999996
No 17
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=99.59 E-value=2.3e-15 Score=114.35 Aligned_cols=89 Identities=24% Similarity=0.340 Sum_probs=74.4
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ +|++|++|.++.. ..++..++|++.+|.++|.+.+++.++++++||+.+.....
T Consensus 188 ~~~L~Rt~~G~f~~~-~a~~l~~l~~~~~--------~~l~~~l~p~~~~l~~~p~v~l~~~~~~~i~~G~~i~~~~~-- 256 (277)
T cd02573 188 LSALRRTRSGPFTLE-DAITLEELEALPE--------EGLDELLLPIDAALSHLPKVELDEEEAKRLRNGQKISLPEE-- 256 (277)
T ss_pred EEEEEEEEECCccHH-HccCHHHHHhhhh--------cccccccCCHHHHHhhCCEEEeCHHHHHHHHCcCccccCCC--
Confidence 789999999999999 5799999986531 12667899999999999999999999999999999965432
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEE
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALAL 105 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~ 105 (144)
..++.+++++.+++|+|||+
T Consensus 257 -----~~~~~~~~~~~~~~~l~i~~ 276 (277)
T cd02573 257 -----PEDGLVRVYDPNGRFLALGE 276 (277)
T ss_pred -----CCCCEEEEEeCCCeEEEEEE
Confidence 23456888887889999986
No 18
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=99.56 E-value=1.7e-14 Score=89.44 Aligned_cols=74 Identities=30% Similarity=0.582 Sum_probs=67.5
Q ss_pred CEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEe
Q psy1178 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVI 128 (144)
Q Consensus 55 p~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~ 128 (144)
|+|.|+++++++|.+|++|+++++....++|..||.|.|++.+|+++|+|++.++++++....+|..++++|++
T Consensus 1 g~vvVd~~a~~~i~~Ga~L~~~GV~~~~~~f~~gd~V~i~~~~g~~ia~G~a~~ss~ei~~~~~g~~~~~~~~l 74 (74)
T PF01472_consen 1 GRVVVDDGAVEAILNGASLFAPGVVEVDGDFRKGDEVAIVDEDGEVIAVGRANMSSEEIKKMKKGKAVKIRHVL 74 (74)
T ss_dssp EEEEE-HHHHHHHHTTSEEEGGGEEEEETT--TTSEEEEEETTSSEEEEEEESSTHHHHHHHSSSEEEEEEEEC
T ss_pred CEEEECccHHHHHHcCCCcchHHhEECCCCcCCCCEEEEEcCCCeEEEEEEEecCHHHHHHHcCCcEehhhhhC
Confidence 68999999999999999999999999999999999999999999999999999999999998899999999874
No 19
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=99.55 E-value=1.9e-14 Score=100.10 Aligned_cols=94 Identities=27% Similarity=0.443 Sum_probs=84.7
Q ss_pred cccccccccc----CcCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCC-CCEEEEEEeecChhhHhcC
Q psy1178 42 RVIRPLEGLL----VGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTK-GEAVALALAQMTTSTMATC 116 (144)
Q Consensus 42 ~~LlP~~~aL----~~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~-g~~laig~~~~~~~~~~~~ 116 (144)
..++|.-+++ ..++.|.||.++.+++.||+.|++||++...+++..||.|.|.+.+ +.++|||.+.+++.+|...
T Consensus 60 ~~~iPTl~~l~~~~~~~~~V~VD~GAvk~v~nGADvM~PGIv~~~~~ik~Gd~VvV~~e~~~~plAVG~alm~~~em~~~ 139 (161)
T COG2016 60 DRLIPTLRLLLKLPPGKYVVVVDEGAVKFVLNGADVMAPGIVSADGEIKEGDIVVVVDEKKGRPLAVGIALMSGKEMEEK 139 (161)
T ss_pred CeechhhHHHHhCCCCccEEEEcCccHhhhcCCCceeccceeecCCCccCCCEEEEEEcCCCCeeEEEeeccCHHHHhhh
Confidence 3578887766 3467899999999999999999999999999999999999887776 8999999999999999999
Q ss_pred CCceEEEEEEEeecCCccccCcCC
Q psy1178 117 DHGVVAKIKRVIMDRDTYPRKWGL 140 (144)
Q Consensus 117 ~~g~~v~~~rv~~~~~~~~~~w~~ 140 (144)
++|.+++..|...| ..|++
T Consensus 140 ~kGkav~~iHhvGD-----~lw~~ 158 (161)
T COG2016 140 KKGKAVKNIHHVGD-----KLWEA 158 (161)
T ss_pred cCCeEEEEEeccCh-----HHHhh
Confidence 99999999999988 78876
No 20
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=99.52 E-value=1.1e-13 Score=96.74 Aligned_cols=93 Identities=24% Similarity=0.421 Sum_probs=82.0
Q ss_pred ccccccccccC----cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCC-CCEEEEEEeecChhhHhcC
Q psy1178 42 RVIRPLEGLLV----GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTK-GEAVALALAQMTTSTMATC 116 (144)
Q Consensus 42 ~~LlP~~~aL~----~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~-g~~laig~~~~~~~~~~~~ 116 (144)
..++|.-+++. .+|.|.++++++++|.+|++|++|++...++++..|+.|.|++.+ +.++|+|++.++++++...
T Consensus 53 ~~~~Ptl~~~~~~~~~~~~v~Vd~~a~~~l~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~vavG~a~~ss~ei~~~ 132 (150)
T TIGR03684 53 GRLIPTLYLLLELNPDKNRVVVDEGAVKFIINGADIMAPGIVSADPSIKEGDIVFVVDETHRKPLAVGIALMDAEEMEEE 132 (150)
T ss_pred CcccccHHHHHhCCccCCEEEECccHHHHHhcCcccccCceecCCCCCCCCCEEEEEECCCCeEEEEEEEeeCHHHHhhc
Confidence 34666655442 369999999999999999999999998888889999999999877 8999999999999999988
Q ss_pred CCceEEEEEEEeecCCccccCcC
Q psy1178 117 DHGVVAKIKRVIMDRDTYPRKWG 139 (144)
Q Consensus 117 ~~g~~v~~~rv~~~~~~~~~~w~ 139 (144)
.+|.+++..|.++| ..|+
T Consensus 133 ~kG~av~~~h~~~D-----~lw~ 150 (150)
T TIGR03684 133 KKGKAVKNIHHVGD-----KIWE 150 (150)
T ss_pred CCCeEEEEEEEcCc-----cccC
Confidence 89999999999999 7885
No 21
>PRK14560 putative RNA-binding protein; Provisional
Probab=99.50 E-value=1.6e-13 Score=96.88 Aligned_cols=94 Identities=22% Similarity=0.390 Sum_probs=83.1
Q ss_pred ccccccccccC----cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCC-CCEEEEEEeecChhhHhcC
Q psy1178 42 RVIRPLEGLLV----GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTK-GEAVALALAQMTTSTMATC 116 (144)
Q Consensus 42 ~~LlP~~~aL~----~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~-g~~laig~~~~~~~~~~~~ 116 (144)
..++|.-+++. ..|.|.+++++++++.+|++|++||+...++++..|+.|.|++.+ +.++|+|.+.++++++...
T Consensus 60 ~~~~Ptl~~~~~~~~~~~~v~Vd~~a~~~i~~Ga~lm~pGV~~~~~~~~~Gd~V~I~~~~~~~~vavG~~~~s~~ei~~~ 139 (160)
T PRK14560 60 DELFPTLRGALKLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEETHGKPLAVGRALMDGDEMVEE 139 (160)
T ss_pred CcccccHHHHHhCCccCCEEEEeccHHHHHHCCCceecCeeeeCCCCCCCCCEEEEEECCCCeEEEEEEEeeCHHHHhhc
Confidence 45667665543 358899999999999999999999998888889999999999876 8999999999999999988
Q ss_pred CCceEEEEEEEeecCCccccCcCC
Q psy1178 117 DHGVVAKIKRVIMDRDTYPRKWGL 140 (144)
Q Consensus 117 ~~g~~v~~~rv~~~~~~~~~~w~~ 140 (144)
.+|.+++..|.+.| ..|++
T Consensus 140 ~kG~~v~~~h~~~D-----~lw~~ 158 (160)
T PRK14560 140 KKGKAVKNIHHVGD-----EIWEF 158 (160)
T ss_pred CCceEEEEEEEcCc-----hhhcc
Confidence 89999999999999 89975
No 22
>TIGR00451 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.
Probab=99.48 E-value=4.1e-13 Score=88.84 Aligned_cols=78 Identities=26% Similarity=0.453 Sum_probs=72.4
Q ss_pred cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCC-CCEEEEEEeecChhhHhcCCCceEEEEEEEeec
Q psy1178 53 GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTK-GEAVALALAQMTTSTMATCDHGVVAKIKRVIMD 130 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~-g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~ 130 (144)
..|.|.+++.+.+++.+|++|+++++....++++.|+.|.|++.+ +.++|+|++.++++++....+|.+++++|.+.|
T Consensus 29 ~~~~v~vd~~a~~~l~~Ga~L~~pGV~~~~~~~~~gd~V~I~~~~~~~~iavG~a~~~s~e~~~~~~G~~v~~~h~~~D 107 (107)
T TIGR00451 29 DKKIVVVDNGAVKFLKNGADVMRPGIVDADEDIKEGDDVVVVDENKDRPLAVGIALMSGEEMKEMDKGKAVKNIHHIGD 107 (107)
T ss_pred hCCEEEEChhHHHHHHCCccccCCeeEeCCCCcCCCCEEEEEECCCCeEEEEEEEecCHHHHHhcCCCeEEEEEEecCC
Confidence 469999999999999999999999999888889999999999876 899999999999999998899999999998864
No 23
>KOG2529|consensus
Probab=99.40 E-value=1.7e-13 Score=107.21 Aligned_cols=144 Identities=59% Similarity=0.959 Sum_probs=126.7
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++|||+++|.-++++.++|+.+..++...++...|+.++.....|++..|..+..+...+..+..++.|..+..++...
T Consensus 222 ~~E~~r~r~~~~~E~~~~~t~~d~~~~q~~~d~~~d~~~~r~~~~~les~l~~~~~vv~kd~~v~~~cyg~k~~v~~~~r 301 (395)
T KOG2529|consen 222 MQELRRVRSGICSEEDDMLTEHDEQDAQFEYDTERDESYLRRVKKPLESLLTGYKRVVVKDSTVNAPCYGAKLLVPGLLR 301 (395)
T ss_pred hhhhhhcccccccccccccccccchhhhhhhccccCcceeeeeeeccccccccceeeecccchhcCccccceeeeccccc
Confidence 78999999999999987999999988776666555556788889999999999999999999999999999999998876
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeecCCccccCcCCCCCC
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLGPKS 144 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~~~~~~~~w~~~~~~ 144 (144)
.+..+..+..+.+.+..+++++.+.+.++.+++...+.+...+++++.+..+.|+.+|.+||++
T Consensus 302 ~~~~i~~~~e~v~~t~k~e~~~~~i~~~~~~~~~s~dh~~~a~~k~~~me~d~~~~~~g~~~~~ 365 (395)
T KOG2529|consen 302 YSDDIDGPFEVVDMTTKGEAIASKIAEMSLRQVASCDHGVVAKTKRVIMEADVYERCWGLGPKA 365 (395)
T ss_pred cCccccCceeEEEEeecchhhhhhhhhhhhhhhceeeeeeecccccccccccccceeeccCccc
Confidence 6666665556666677889999999999999999999998999999999999999999999975
No 24
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=99.32 E-value=9.4e-13 Score=101.78 Aligned_cols=66 Identities=24% Similarity=0.352 Sum_probs=58.1
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecC
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIML 75 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~ 75 (144)
|++||||++|+|+++ +|++|++|+++.. ..+++.|+|++.+|.++|.|.++++.+++++||+.+.+
T Consensus 190 l~~LrRtr~G~F~l~-~ai~le~L~~~~~--------~~l~~~llpie~~l~~lp~v~l~~~~~~~i~nG~~i~~ 255 (345)
T PRK14846 190 VIELRRTQVGIFKEE-NAIRIKSPDEITK--------NALEEKSIKIEAILDDILVLDATDSQAQQIKYGQKCLF 255 (345)
T ss_pred EeEEEeEEECCCcHH-HcCCHHHHHhhhh--------cchhhccCCHHHHHhhCCeEEeCHHHHHHHHCcCEEee
Confidence 789999999999999 5799999986531 23667899999999999999999999999999998865
No 25
>PF09157 TruB-C_2: Pseudouridine synthase II TruB, C-terminal; InterPro: IPR015240 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1ZL3_A 1K8W_A 1R3F_A.
Probab=99.21 E-value=7.8e-11 Score=69.54 Aligned_cols=58 Identities=16% Similarity=0.251 Sum_probs=40.4
Q ss_pred CEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEe
Q psy1178 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVI 128 (144)
Q Consensus 55 p~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~ 128 (144)
|.|.|+++++++++|||++..... ....+ .|++|+.+++|+|||++. +.| .++|+|+|
T Consensus 1 P~v~L~~~~~~~~~~Gq~v~~~~~-----~~~~~-~vrvy~~~~~FlGig~~~---------~~g-~L~P~Rl~ 58 (58)
T PF09157_consen 1 PAVVLDEEQAKRFLHGQRVRLRDD-----APPDG-LVRVYDEDGRFLGIGEID---------DDG-RLKPKRLL 58 (58)
T ss_dssp -EEEE-HHHHHHHTTT--B---SS-------SSS-EEEEETTTTEEEEEEEE----------TTS--EEEEEES
T ss_pred CeEEeCHHHHHHHHCcCcccccCC-----CCCCc-eEEEECCCCEEEEEEEEc---------cCC-EEEeeEcC
Confidence 789999999999999999965221 22344 899999899999999984 346 79999986
No 26
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=99.12 E-value=2.4e-10 Score=86.98 Aligned_cols=84 Identities=21% Similarity=0.368 Sum_probs=63.1
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|+++ + ++ ..++|++ +.++|.+.++++.+++++||+.+....
T Consensus 188 ~~~LrRt~~G~f~~~-~------l~----------------~~l~p~~--~~~lp~v~l~~~~~~~i~nG~~i~~~~--- 239 (279)
T PRK02193 188 MSDLERTKIGNLDKN-F------LN----------------QSLNPLD--LIDLEQVKLDKEELELLLQGKKISFFA--- 239 (279)
T ss_pred EEEEEeEEECCcCHH-H------HH----------------hhcChhh--HhhCCeEEeCHHHHHHHHCcCccccCC---
Confidence 789999999999998 4 21 1366775 559999999999999999999985321
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeec
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMD 130 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~ 130 (144)
. ...+++++ +++|+|||+.. .+ .++|.|+|+.
T Consensus 240 -----~-~~~~~~~~-~~~~lai~~~~----------~~-~l~p~rv~~~ 271 (279)
T PRK02193 240 -----N-SEEYALIF-KDEIVGIGKII----------NN-VLKSKKLFGN 271 (279)
T ss_pred -----C-CCeEEEEE-CCEEEEEEEec----------CC-EEEEEEEEch
Confidence 1 22455554 35899999862 34 6999999975
No 27
>KOG2523|consensus
Probab=99.00 E-value=3.2e-10 Score=78.74 Aligned_cols=94 Identities=24% Similarity=0.387 Sum_probs=78.2
Q ss_pred cccccccccCc----CCEEEEChhhHHhhhCCceecCCCeecc----cCCCCCCCEEEEEcCCCC-EEEEEEeecChhhH
Q psy1178 43 VIRPLEGLLVG----HKRIILKDSAVNAVCYGAQIMLPGVLRY----EDGIEMDEEIVIVSTKGE-AVALALAQMTTSTM 113 (144)
Q Consensus 43 ~LlP~~~aL~~----lp~V~l~~~~~~~l~~G~~l~~~~~~~~----~~~~~~~~~v~i~~~~g~-~laig~~~~~~~~~ 113 (144)
-.+|.-..|.. +|.+.||.++++.+.+|+++++||++.. ++.++.++.|+|+..+.+ .+|||...++++||
T Consensus 77 ~~~PTLRllhk~p~~~~~~qvD~GAIkfvlsGAnIMcPGlts~g~~l~~~~ekd~~V~i~aeGK~~alAiG~~~ms~kei 156 (181)
T KOG2523|consen 77 PYIPTLRLLHKYPFIFPHVQVDRGAIKFVLSGANIMCPGLTSPGAKLPPGVEKDTIVAIMAEGKEHALAIGLTKMSAKEI 156 (181)
T ss_pred CccchhHHHhhCCCccceEEecCcceeeeecCCceEcccCCCCcccCCCCccCCCEEEEEecCchhhhhhhhhhhcHHHH
Confidence 45666666643 6889999999999999999999998653 245667778888765444 89999999999999
Q ss_pred hcCCCceEEEEEEEeecCCccccCcCCC
Q psy1178 114 ATCDHGVVAKIKRVIMDRDTYPRKWGLG 141 (144)
Q Consensus 114 ~~~~~g~~v~~~rv~~~~~~~~~~w~~~ 141 (144)
...++|..+...|.++| .+|++-
T Consensus 157 ~s~nKGiGIE~~H~l~D-----gLw~~~ 179 (181)
T KOG2523|consen 157 KSVNKGIGIENYHYLND-----GLWKMK 179 (181)
T ss_pred HhhccCCceEEEEecCC-----chhhee
Confidence 99999999999999999 799864
No 28
>PRK13794 hypothetical protein; Provisional
Probab=98.98 E-value=2.1e-09 Score=87.79 Aligned_cols=73 Identities=25% Similarity=0.508 Sum_probs=68.0
Q ss_pred EEEEChhhHHhhh-CCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEe
Q psy1178 56 RIILKDSAVNAVC-YGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVI 128 (144)
Q Consensus 56 ~V~l~~~~~~~l~-~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~ 128 (144)
.|+|+++++.+++ +|++|+++++....+++..|+.|.|++.+|+++|+|++.+++++|...++|.+|++++.-
T Consensus 126 ~V~Vd~ga~~~v~~~G~~v~~~GV~~~~~~i~~gd~V~Iv~~~g~~iavG~a~~s~~ei~~~~~G~~Vkvr~~~ 199 (479)
T PRK13794 126 FIVVKDDVPKFIRNKGASVLRPGVAEASEDIEEGDDVIILDENGDVVGVGRARMSYEEIVNMEKGMVVKVRKSE 199 (479)
T ss_pred EEEECccHHHHHHhCCCeecCCceEEecCCcCCCCEEEEEcCCCcEEEEEEeecCHHHHHhccCceEEEEEecc
Confidence 4999999999999 999999999998888899999999999899999999999999999999999999998833
No 29
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=98.96 E-value=8.2e-09 Score=63.82 Aligned_cols=73 Identities=36% Similarity=0.721 Sum_probs=64.4
Q ss_pred EEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcC--CCceEEEEEEEe
Q psy1178 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATC--DHGVVAKIKRVI 128 (144)
Q Consensus 56 ~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~--~~g~~v~~~rv~ 128 (144)
++.+++.+.+++++|..|+.+++...++.+..|+.|.+++.+|+++|+|.+.+++..+... .+|..++..+.+
T Consensus 2 ~i~v~~~~~~~i~~g~~v~~~~v~~~~~~~~~g~~V~v~~~~g~~vg~G~~~~~s~~~~~~~~~~g~~v~~~~~~ 76 (77)
T smart00359 2 KVVVDDGAVKAILNGASLLAPGVVRVDGGIKEGDVVVIVDEKGEPLGIGLANMSSEEMARIKGEKGLAVKVRRAV 76 (77)
T ss_pred EEEEchhHHHHHHcCCCcccceeEEEeCCcCCCCEEEEEcCCCCEEEEEEEeCCHHHHHHHhccCceEEEEEEec
Confidence 5889999999999999999999887777888999999999999999999999999987766 488888877765
No 30
>PRK13534 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=98.93 E-value=4.7e-09 Score=88.12 Aligned_cols=75 Identities=15% Similarity=0.268 Sum_probs=70.0
Q ss_pred CEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 55 p~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
..|+|++++...+.+|++|++|++...++++.+||.|.|++++++++|+|++.+++++|....+|.+++++|...
T Consensus 564 ~~V~Vd~~a~~~v~~G~~v~apgVv~~d~~ir~gDeV~Vv~e~~~~lavG~A~~~~~em~~~~~G~avkvR~~~~ 638 (639)
T PRK13534 564 YRVVVDKESEPFARKGKSVFAKFVIDCDEEIRPYDEVLVVNEDDELLAYGKALLNGRELMEFNYGLAVKVRGGVK 638 (639)
T ss_pred cEEEECCcchhhhhCCCcccCCcceecCCCCCCCCEEEEEecCCcEEEEEEEecCHHHHhhcCCceEEEEeecCC
Confidence 589999999999999999999999998889999999999988899999999999999999999999999988753
No 31
>PRK13795 hypothetical protein; Provisional
Probab=98.93 E-value=5.2e-09 Score=88.10 Aligned_cols=76 Identities=25% Similarity=0.434 Sum_probs=71.3
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
.+.|+|+++++.+|.+|++|+.+++...++++..|+.|.|++.+|+++|+|.+.+++++|....+|.+++++|...
T Consensus 126 ~~~VvVd~ga~~~v~~Ga~l~~~GI~~~~~~i~~gd~V~I~~e~g~~vavG~a~~s~~e~~~~~kG~~Vkvr~~~~ 201 (636)
T PRK13795 126 KKWVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVTEDGEVVGVGRAKMDGDDMIKRFRGRAVKVRKSGR 201 (636)
T ss_pred CcEEEEcccHHHHHHcCCcccCCceEEEeCCCCCCCEEEEEeCCCCEEEEEEeccCHHHHhhccCCeEEEEEEccc
Confidence 5889999999999999999999999988888999999999998899999999999999999999999999988875
No 32
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=98.78 E-value=3.4e-08 Score=67.86 Aligned_cols=71 Identities=21% Similarity=0.414 Sum_probs=66.3
Q ss_pred EEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEE
Q psy1178 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKR 126 (144)
Q Consensus 56 ~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~r 126 (144)
+|.|++++...+++|.++.+..++..++++.+++.|.|++++++++|+|++..|..||...+.|.+|++..
T Consensus 82 RVvV~~E~e~f~r~Gk~VFaKfVi~~D~~iR~~dEvlVVne~d~LlAvGra~ls~~E~~~~~~G~AVkVr~ 152 (155)
T COG1370 82 RVVVSDEAEEFVRKGKSVFAKFVIDVDEEIRAGDEVLVVNEDDELLAVGRALLSGAEMREFERGMAVKVRE 152 (155)
T ss_pred EEEeccccHHHHHhccchhhhheeccCcccCCCCeEEEECCCCcEEEeeeEeecHHHHhhccccEEEEEec
Confidence 58899999999999999999988888889999999999999999999999999999999999999998764
No 33
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=98.69 E-value=3.5e-08 Score=74.91 Aligned_cols=73 Identities=15% Similarity=0.120 Sum_probs=56.5
Q ss_pred CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR 80 (144)
Q Consensus 1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~ 80 (144)
|++||||++|+|++++ +.+ |.|++. .++|.+.+.+ .+..|.||+.+..+++..
T Consensus 187 m~~LrRt~~G~f~~~~-~~~-----------------------l~pl~~--l~l~~~~~~~-~~~~i~~G~ki~~~~~~~ 239 (273)
T PRK04099 187 LSSLERLSEGKFVYEN-EKA-----------------------LNPLEY--LNLPQNFYLG-DKNNLELGKKLFVEDLEN 239 (273)
T ss_pred EEEEEeEEECCCcHHH-Cee-----------------------cCChhh--cccceEechh-HHHHHhCCCeeccCcccc
Confidence 7899999999999994 454 335555 2899999998 899999999999876532
Q ss_pred ccCCCCCCCEEEEEcCCCCEEEEEEee
Q psy1178 81 YEDGIEMDEEIVIVSTKGEAVALALAQ 107 (144)
Q Consensus 81 ~~~~~~~~~~v~i~~~~g~~laig~~~ 107 (144)
.+.| .++++ .++|+||++..
T Consensus 240 ----~~~g-~~~~~--~~~f~~I~e~~ 259 (273)
T PRK04099 240 ----KEDG-IYYIE--FEDFFSIIEIK 259 (273)
T ss_pred ----CCCC-EEEEE--cCceEEEEEEc
Confidence 2334 67777 46699999873
No 34
>PRK05429 gamma-glutamyl kinase; Provisional
Probab=98.54 E-value=2.3e-07 Score=73.74 Aligned_cols=64 Identities=20% Similarity=0.329 Sum_probs=59.5
Q ss_pred cCCEEEEChhhHHhh-hCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcC
Q psy1178 53 GHKRIILKDSAVNAV-CYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATC 116 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l-~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~ 116 (144)
.-+.|.|++++.++| .+|++|+++|+..+.+.|..||.|.|++.+|+++|+|.+.++++++...
T Consensus 279 ~~g~i~vd~gA~~al~~~g~sLl~~Gi~~v~g~f~~gd~V~i~~~~g~~va~G~~~~~s~e~~~~ 343 (372)
T PRK05429 279 PAGEIVVDAGAVKALLERGKSLLPAGVTAVEGDFSRGDVVRIVDPDGREIARGLVNYSSDELRRI 343 (372)
T ss_pred CCCeEEECccHHHHHHhcCCccCccchhheECcccCCCEEEEECCCCCEEEEEEecCCHHHHHHH
Confidence 357999999999999 7999999999999999999999999999999999999999999998643
No 35
>PF09142 TruB_C: tRNA Pseudouridine synthase II, C terminal; InterPro: IPR015225 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1SGV_B.
Probab=98.51 E-value=4.9e-07 Score=52.85 Aligned_cols=55 Identities=18% Similarity=0.146 Sum_probs=36.8
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEe
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVI 128 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~ 128 (144)
||.+.|+++++..+.+|+.|...+ .+..+.+++++|++|||++. +|...+|.+||
T Consensus 1 fP~~~ls~~ea~~l~~Gr~l~~~~---------~~g~~aa~~pdG~lvAL~~~-----------~g~~~rp~~Vf 55 (56)
T PF09142_consen 1 FPVRELSAEEARDLRHGRRLPAAG---------PPGPVAAFAPDGRLVALLEE-----------RGGRARPVVVF 55 (56)
T ss_dssp SEEEE--HHHHHHHHTT---B--------------S-EEEE-TTS-EEEEEEE-----------ETTEEEEEEES
T ss_pred CCceECCHHHHHHHhCCCccCCCC---------CCceEEEECCCCcEEEEEEc-----------cCCcEeEEEee
Confidence 689999999999999999998753 23368899999999999965 35579999998
No 36
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=98.50 E-value=3.3e-07 Score=75.68 Aligned_cols=71 Identities=18% Similarity=0.343 Sum_probs=66.2
Q ss_pred EEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEE
Q psy1178 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKR 126 (144)
Q Consensus 56 ~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~r 126 (144)
+|+|+++.+..+..|.++.++++...++++.+|+.|.|++.+++++|+|++.+++.||....+|.+|+++.
T Consensus 468 rV~v~~~~~~f~~~g~~vfak~V~~ad~~IR~~dEV~vv~~~~~llavGra~lsg~em~~~~~G~AVkvR~ 538 (540)
T TIGR00432 468 RVAVNEESEPFARKGKSVFAKFIIDCDNNIRANDEVLIVNADDELLATGKALLCAEEMMDLNHGQAVKTRG 538 (540)
T ss_pred EEEECCcchhhccCCCcccCCccccCCCCCCCCCeEEEEcCCCcEEEEEehhcCHHHHHhhcCceEEEEeC
Confidence 58899999999999999999999988889999999999988999999999999999999999999998764
No 37
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=98.39 E-value=6.3e-07 Score=63.73 Aligned_cols=71 Identities=28% Similarity=0.474 Sum_probs=64.4
Q ss_pred CEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEE
Q psy1178 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIK 125 (144)
Q Consensus 55 p~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~ 125 (144)
..+.++-.+...++||.++.++++.+....++.++.|.|.+.+|+++|+|.+..+++++.+.++|..++|.
T Consensus 129 k~~~i~~~~~E~~~Ng~nV~~~gV~e~~~~i~~~d~viVv~~ng~~vGVg~a~~~~~~~in~~rG~~v~~~ 199 (202)
T COG5270 129 KGRKIDRGAVEPVKNGKNVLPPGVIEAEDSIERGDEVIVVSENGRVVGVGIAKKSYEELINPERGTGVKPR 199 (202)
T ss_pred ccEEEEcccchhhhccCcccCCceeeccCCcccCCeEEEEecCCEEEEEEEEecCHHHhcCcccCcccCCC
Confidence 45778888899999999999999988888888889999999999999999999999999988899888876
No 38
>TIGR01027 proB glutamate 5-kinase. Bacterial ProB proteins hit the full length of this model, but the ProB-like domain of delta 1-pyrroline-5-carboxylate synthetase does not hit the C-terminal 100 residues of this model. The noise cutoff is set low enough to hit delta 1-pyrroline-5-carboxylate synthetase and other partial matches to this family.
Probab=98.37 E-value=1.3e-06 Score=69.32 Aligned_cols=62 Identities=16% Similarity=0.332 Sum_probs=57.7
Q ss_pred CCEEEEChhhHHhhh-CCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhc
Q psy1178 54 HKRIILKDSAVNAVC-YGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMAT 115 (144)
Q Consensus 54 lp~V~l~~~~~~~l~-~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~ 115 (144)
-+.|.||+++.++|. +|++|+++|+..+.+.|..||.|.|++++|+++|.|.+.++++++..
T Consensus 272 ~G~i~vD~gA~~al~~~g~sLl~~Gi~~v~g~F~~gd~v~i~~~~~~~ia~g~~~y~s~~~~~ 334 (363)
T TIGR01027 272 AGEITVDAGAEEALLERGKSLLPAGIVGVEGNFSRGEVVEILNPEGQDIGRGLVNYSSDELEK 334 (363)
T ss_pred CCeEEEChhHHHHHHhcCCccCCccceeeECcccCCCEEEEECCCCCEEEEEEecCCHHHHHH
Confidence 478999999999997 49999999999999999999999999999999999999999999864
No 39
>KOG2522|consensus
Probab=98.20 E-value=4.2e-06 Score=66.87 Aligned_cols=97 Identities=18% Similarity=0.227 Sum_probs=70.8
Q ss_pred cccccccccCcCCE----EEEChhh-HHhhhCCceecCCCe-ecccCCCCCCCEEEEEcCC-CCEEEEEEeecChhhHhc
Q psy1178 43 VIRPLEGLLVGHKR----IILKDSA-VNAVCYGAQIMLPGV-LRYEDGIEMDEEIVIVSTK-GEAVALALAQMTTSTMAT 115 (144)
Q Consensus 43 ~LlP~~~aL~~lp~----V~l~~~~-~~~l~~G~~l~~~~~-~~~~~~~~~~~~v~i~~~~-g~~laig~~~~~~~~~~~ 115 (144)
.|+|.-+.+..+|. +....-. .+.+-||..|+..+. ....+.++.|+...|.-.+ ..++|||.+.||++||..
T Consensus 75 ~lfPTVy~lWeyp~llP~f~t~~~v~e~~~~~~~~l~~~~m~ppg~p~~~~G~lcai~lpgn~ap~AiGc~~Msseem~v 154 (560)
T KOG2522|consen 75 QLFPTVYSLWEYPALLPIFLTHGFVIEEHLFNGANLMISGMIPPGDPRCKIGTLCAIALPGNEAPLAIGCVEMSSEEMKV 154 (560)
T ss_pred cccchhHhhhcChhhcceeeccchhhhhhhcccccccccccCCCCCcccccCceeeEecCCCcCceeeeeeecchHHHHH
Confidence 48899999987655 3322333 345568877654332 1123466888887776554 358999999999999987
Q ss_pred CC-CceEEEEEEEeecCCccccCcCCCCCC
Q psy1178 116 CD-HGVVAKIKRVIMDRDTYPRKWGLGPKS 144 (144)
Q Consensus 116 ~~-~g~~v~~~rv~~~~~~~~~~w~~~~~~ 144 (144)
.. +|.++++.|+|.| .+|+.||.+
T Consensus 155 ~GlkGkav~ilH~frD-----~Lw~sgp~~ 179 (560)
T KOG2522|consen 155 IGLKGKAVKILHHFRD-----GLWKSGPMK 179 (560)
T ss_pred hccccceEEEEeehhh-----hhhhcCCCC
Confidence 76 9999999999999 899999974
No 40
>PRK13402 gamma-glutamyl kinase; Provisional
Probab=98.07 E-value=1.2e-05 Score=63.77 Aligned_cols=62 Identities=11% Similarity=0.208 Sum_probs=57.5
Q ss_pred CCEEEEChhhHHhhh-CCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhc
Q psy1178 54 HKRIILKDSAVNAVC-YGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMAT 115 (144)
Q Consensus 54 lp~V~l~~~~~~~l~-~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~ 115 (144)
-..+.||+++.++|. +|.+|.+.|+..+.+.|..||.|.|++++|+.+|.|.+.++|+|+..
T Consensus 276 ~G~i~vd~ga~~al~~~~~sLl~~gi~~v~g~F~~gd~v~i~~~~g~~~~rg~~~y~s~~~~~ 338 (368)
T PRK13402 276 QGEIVVENDFDRALDNHSEQLTSDDVVEIKGDFSVGDTILVRKGDGTKLAKGKSNYSSCLLNF 338 (368)
T ss_pred CeeEEECccHHHHHHhcCCcccccceEEEeCEecCCCEEEEECCCCCEEEEEEccCCHHHHHH
Confidence 368999999999996 78999999999999999999999999999999999999999999864
No 41
>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism]
Probab=97.73 E-value=8.7e-05 Score=58.15 Aligned_cols=62 Identities=19% Similarity=0.310 Sum_probs=56.3
Q ss_pred CCEEEEChhhHHhhh-CCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcC
Q psy1178 54 HKRIILKDSAVNAVC-YGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATC 116 (144)
Q Consensus 54 lp~V~l~~~~~~~l~-~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~ 116 (144)
-..|.||+++..++. +|++|.+.|+....+.|..|+.|.|. ++|..+|.|.+.++++++...
T Consensus 279 ~G~i~iD~GA~~Al~~~gkSLLpaGV~~V~G~F~rGdvV~i~-~~g~~iarG~v~Y~s~el~~i 341 (369)
T COG0263 279 AGEITVDAGAVEALLEQGKSLLPAGVTSVEGNFSRGDVVRIR-PQGGEIARGLVNYSSDELRKI 341 (369)
T ss_pred CceEEECccHHHHHHhcCCccccccceEeeeeecCCCEEEEe-cCCceeEeeeccCCHHHHHHH
Confidence 367999999999997 89999999999999999999999999 688899999999999998643
No 42
>COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis]
Probab=97.34 E-value=0.00067 Score=55.30 Aligned_cols=56 Identities=25% Similarity=0.520 Sum_probs=47.6
Q ss_pred eecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEe
Q psy1178 72 QIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVI 128 (144)
Q Consensus 72 ~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~ 128 (144)
++.++|+...+.++.++|.|.++ .+|++.|+|++.|++.+|....+|.+|+++|++
T Consensus 463 ~v~a~GV~da~edIrpnDeV~vv-~~~~v~gVGrA~msg~eM~~akkGiaV~VR~~~ 518 (519)
T COG1549 463 SVFAPGVVDADEDIRPNDEVVVV-HGGEVRGVGRAVMSGREMVEAKKGIAVRVRRRK 518 (519)
T ss_pred cccccccccCCCCCCcCCEEEEE-eCCeEEEEeeeecChHHhcccCCceEEEEEecc
Confidence 45667777777788888888665 478999999999999999999999999999875
No 43
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=94.65 E-value=0.2 Score=40.40 Aligned_cols=52 Identities=21% Similarity=0.235 Sum_probs=39.8
Q ss_pred EEEEChhhHHhhhCCcee-cCCCeecccCCCCCCCEEEEEcCCCCEEEEEEee
Q psy1178 56 RIILKDSAVNAVCYGAQI-MLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQ 107 (144)
Q Consensus 56 ~V~l~~~~~~~l~~G~~l-~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~ 107 (144)
.|.+.....+++++|.+- +...+....+....|+.|.+++.+|+|+|.|-+.
T Consensus 4 ~v~l~~~~~~~~~~ghpwv~~~~i~~~~~~~~~G~~v~v~~~~g~~lg~g~~n 56 (396)
T PRK15128 4 RLVLAKGREKSLLRRHPWVFSGAVARMEGKASLGETIDIVDHQGKWLARGAYS 56 (396)
T ss_pred EEEECcchHhHHhcCCCeEEhHHhccccCCCCCCCEEEEEcCCCCEEEEEEEC
Confidence 467888888999999854 3333433333567899999999999999999885
No 44
>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ]. PUA domains are predicted to bind RNA molecules with complex folded structures []. NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These three proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.; PDB: 1T5Y_A 1SQW_A 2P38_A.
Probab=93.47 E-value=0.19 Score=35.65 Aligned_cols=49 Identities=12% Similarity=0.274 Sum_probs=36.3
Q ss_pred EEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 56 ~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~ 106 (144)
.|.|++.+.+.+..|+.|...++....++.+.. |.|++.++.++|+|..
T Consensus 93 kvwvk~~~e~~FLYGndV~ks~i~~i~e~~~~~--VvV~n~~d~~LGfG~~ 141 (162)
T PF03657_consen 93 KVWVKPKAEMLFLYGNDVLKSSIGRITEDTPQN--VVVYNMNDVPLGFGCR 141 (162)
T ss_dssp EEEE-HHHHHHHCTT--EEGGGEEEEETTS-TC--EEEEETTS-EEEEEEC
T ss_pred eEEECCCceEEeeecCCchHhhcEEecCCCCce--EEEEeCCCCeEEEEEe
Confidence 899999999999999999988876665554433 8999989999999943
No 45
>PF13636 Nol1_Nop2_Fmu_2: pre-rRNA processing and ribosome biogenesis; PDB: 3M4X_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A.
Probab=92.90 E-value=0.42 Score=31.08 Aligned_cols=46 Identities=15% Similarity=0.104 Sum_probs=30.5
Q ss_pred cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEee
Q psy1178 53 GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQ 107 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~ 107 (144)
.-+.|.++++++.+..+|..+..... ..| .|.+. .+|..+|.|+..
T Consensus 45 ~~~~iel~~e~a~~yl~Ge~i~~~~~-------~~G-~vlv~-~~g~~LG~gk~~ 90 (102)
T PF13636_consen 45 TKNVIELDDEQALRYLRGEDIELDPP-------DKG-WVLVT-YEGFPLGWGKYV 90 (102)
T ss_dssp CS-EEEETCHHHHHHHCT--EE-SS---------EE-EEEEE-ECCCEEEEEEEE
T ss_pred cceEEECCHHHHHHHHcCCcccCCCC-------CCc-EEEEE-ECCEeeEEEEee
Confidence 34679999999999999999976541 234 44443 368999999874
No 46
>KOG3492|consensus
Probab=88.11 E-value=1.5 Score=30.76 Aligned_cols=63 Identities=22% Similarity=0.382 Sum_probs=49.8
Q ss_pred CEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCC
Q psy1178 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCD 117 (144)
Q Consensus 55 p~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~ 117 (144)
-+|.+.+.+...+..|+.+.-.++-.+.+++...+-|.||+-++.++|.|....|..+-...+
T Consensus 95 ~KvWiKp~~Em~flYGNhvlKs~vgRitd~~p~~~GVvVysm~DvPLGFGv~Akst~d~r~~d 157 (180)
T KOG3492|consen 95 YKVWIKPNAEMQFLYGNHVLKSGVGRITDGIPQHQGVVVYSMNDVPLGFGVTAKSTQDCRKAD 157 (180)
T ss_pred eeEEeccCcccceeecccchhcccceecCCCCCcceEEEEeccCCccccceeecCcccccccC
Confidence 357788888888889999988777666667777778999998899999999887776655443
No 47
>PRK08557 hypothetical protein; Provisional
Probab=85.98 E-value=1.1 Score=36.53 Aligned_cols=52 Identities=15% Similarity=0.123 Sum_probs=33.9
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccC--CCCCCCEEEEEcCCCCEEEEEEeecC
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYED--GIEMDEEIVIVSTKGEAVALALAQMT 109 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~--~~~~~~~v~i~~~~g~~laig~~~~~ 109 (144)
-+.|.++. .++..+|..+....+..... ++..|+.|.+. .|+++|+|.+.++
T Consensus 77 ~~~~~~~~--~~~~~~g~~v~~~~~~~~~~~~~~~~~~~v~~~--~~~~~gvg~~~~~ 130 (417)
T PRK08557 77 EPKIKLKP--TKRRLKGKYIKEELIENPEELNEILENDYVGVE--IGNFLGVGVKKED 130 (417)
T ss_pred Cceeeecc--cccccCCccccccccccccccccCCCCCEEEEe--cCCEEEEEEeecc
Confidence 35677765 33334899988766543332 45667766654 3789999998754
No 48
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=83.54 E-value=0.45 Score=37.19 Aligned_cols=15 Identities=33% Similarity=0.373 Sum_probs=13.9
Q ss_pred CCccEeeeeeccccc
Q psy1178 1 MIELRRNRSGIQSEE 15 (144)
Q Consensus 1 m~~LrRt~~g~F~~~ 15 (144)
|+.||||++|+|+++
T Consensus 219 ~~~L~Rt~~g~f~~~ 233 (312)
T cd02867 219 VTELTATAEGDPVEE 233 (312)
T ss_pred EEEEEeeeecCcccc
Confidence 689999999999987
No 49
>COG3270 Uncharacterized conserved protein [Function unknown]
Probab=80.09 E-value=4.6 Score=27.30 Aligned_cols=48 Identities=13% Similarity=0.111 Sum_probs=35.0
Q ss_pred CcCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEee
Q psy1178 52 VGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQ 107 (144)
Q Consensus 52 ~~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~ 107 (144)
+....|.|+++++.....|..|..+.- ...| .|.+. .++.++|.|+..
T Consensus 65 ~~~nsiELd~e~a~~w~rG~dV~~~~~------~~~g-~viv~-~~~~~lG~aK~v 112 (127)
T COG3270 65 AVRNSIELDEEEAREWMRGRDVEPQES------GPAG-WVIVK-FQGNGLGLAKVV 112 (127)
T ss_pred hhcceEEeCHHHHHhhhcCCccccCCC------CCCc-eEEEE-ECCcccceeeec
Confidence 345789999999999999999976542 1223 45543 368899999874
No 50
>PRK08035 type III secretion system protein SsaQ; Validated
Probab=70.94 E-value=20 Score=28.35 Aligned_cols=63 Identities=17% Similarity=0.331 Sum_probs=45.0
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeecCC
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRD 132 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~~~ 132 (144)
+.+..++=.....+..|.-+..... .++.|.|+- +|+.+|.|+... .+....|+..+.|..++
T Consensus 259 lGr~~l~l~eL~~L~~GsVl~L~~~--------~~~~VdI~v-NG~~ia~GElV~-------v~~~lGVRIt~~~~~~~ 321 (323)
T PRK08035 259 IGRLSLPIGQLRQLAVGDVLPVGGC--------FYPEVTIRL-NGRIIGQGELLA-------CDNELMVRITRWYLQKN 321 (323)
T ss_pred EccEEeeHHHHhcCCCCCEEEcCCC--------CCCceEEEE-CCEEEEEEEEEE-------ECCEEEEEEEEeeccCC
Confidence 4667777778888888988766541 234577764 899999998753 23455789999987764
No 51
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=68.07 E-value=9.2 Score=22.13 Aligned_cols=29 Identities=24% Similarity=0.376 Sum_probs=22.3
Q ss_pred hhCCceecCCCeecccCCCCCCCEEEEEcCCCCEE
Q psy1178 67 VCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAV 101 (144)
Q Consensus 67 l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~l 101 (144)
|-+|..++.|.+. +.|+.+.|-+.+|.++
T Consensus 26 letG~~i~VP~FI------~~Gd~I~V~T~~g~Y~ 54 (56)
T smart00841 26 LETGAVVQVPLFI------NEGDKIKVDTRTGEYV 54 (56)
T ss_pred ECCCCEEEcCCcc------cCCCEEEEECCCCcEE
Confidence 4589999888753 6788999988777765
No 52
>PRK11933 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Probab=67.73 E-value=16 Score=30.32 Aligned_cols=62 Identities=15% Similarity=0.205 Sum_probs=42.9
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeecCCc
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDT 133 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~~~~ 133 (144)
.+.+.++.+++.+..+|..|.... ....| .|.|. .+|..+|.|+.. .| .+ ++.
T Consensus 407 ~~~~~l~~~~~~~Yl~ge~l~~~~------~~~~G-~~lv~-~~g~~lG~gK~~----------~~-~l--------kN~ 459 (470)
T PRK11933 407 ANAFELTPQEAEEWYMGRDIYPQT------APPAG-EVIVT-YQGQPIGLAKRV----------GN-RL--------KNS 459 (470)
T ss_pred cceEecCHHHHHHHHCCCCccCCC------CCCCC-EEEEE-ECCEeeEEEEee----------CC-Ee--------cCC
Confidence 477899999999999999986542 11235 44443 479999999874 23 33 357
Q ss_pred cccCcCCCC
Q psy1178 134 YPRKWGLGP 142 (144)
Q Consensus 134 ~~~~w~~~~ 142 (144)
||+.|-.|-
T Consensus 460 yPkg~~~~~ 468 (470)
T PRK11933 460 LPRELVRDG 468 (470)
T ss_pred CCHHHhcCC
Confidence 889997764
No 53
>PRK08158 type III secretion system protein SpaO; Validated
Probab=65.71 E-value=33 Score=26.87 Aligned_cols=64 Identities=13% Similarity=0.159 Sum_probs=44.9
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeecCCc
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDT 133 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~~~~ 133 (144)
+.+..++=.....+..|.-+.... ..++.|.||- +|+++|-|+... .+....|+...++..+++
T Consensus 238 lGr~~~tl~eL~~L~~GsVl~L~~--------~~~~~V~I~v-Ng~lva~GELV~-------v~~~lGVrIt~i~~~~~~ 301 (303)
T PRK08158 238 LYRKNVTLAELEELCQQQLLSLPT--------NAELNVEIRA-NGALLGNGELVQ-------MDDTLGVEIHEWLSGSGN 301 (303)
T ss_pred EeceeeeHHHHhhcCCCCEEECCC--------CCCCceEEEE-CCEEEEEEEEEE-------ECCEEEEEEEEEecCCCC
Confidence 355666667778888898876653 2356788875 899999998753 233456888888877653
No 54
>COG1374 NIP7 Protein involved in ribosomal biogenesis, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=63.37 E-value=10 Score=27.19 Aligned_cols=57 Identities=12% Similarity=0.214 Sum_probs=32.3
Q ss_pred EEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhH
Q psy1178 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTM 113 (144)
Q Consensus 56 ~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~ 113 (144)
++.+.......+..|..+. ..+......+.....+.|+..++.++|+|....++++.
T Consensus 101 k~~v~~~~e~~FLYg~~lk-d~~~e~~~~~~~~~~v~V~~~nd~~lgiGvg~~s~~ed 157 (176)
T COG1374 101 KNYVKERGEMLFLYGNDLK-DHVKEIIDEIPENGGVFVFNMNDVPLGIGVGALSPSED 157 (176)
T ss_pred eeeeccCceeEEEeccccc-hhhhhhccccCCcceEEEEEcCCCceEEEecccCchhh
Confidence 4445544444444555421 11112222334445688888888999999887766654
No 55
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=62.89 E-value=7.6 Score=22.48 Aligned_cols=30 Identities=30% Similarity=0.419 Sum_probs=19.8
Q ss_pred hhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEE
Q psy1178 67 VCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVA 102 (144)
Q Consensus 67 l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~la 102 (144)
+-+|..+..|.+ ++.||.+.|-+.+|.++.
T Consensus 26 letG~~i~VP~F------I~~Gd~I~VdT~~g~Yv~ 55 (56)
T PF09285_consen 26 LETGAEIQVPLF------IEEGDKIKVDTRDGSYVE 55 (56)
T ss_dssp ETTS-EEEEETT--------TT-EEEEETTTTEEEE
T ss_pred EcCCCEEEccce------ecCCCEEEEECCCCeEeC
Confidence 358888887764 367999999888887764
No 56
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=60.03 E-value=18 Score=20.87 Aligned_cols=29 Identities=28% Similarity=0.426 Sum_probs=22.0
Q ss_pred hhCCceecCCCeecccCCCCCCCEEEEEcCCCCEE
Q psy1178 67 VCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAV 101 (144)
Q Consensus 67 l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~l 101 (144)
+-+|..++.|.+. +.||.+.|-+.+|.++
T Consensus 26 letG~~i~VP~FI------~~Gd~I~V~T~~g~Y~ 54 (56)
T cd05794 26 LETGAEVQVPLFI------KEGEKIKVDTRTGEYV 54 (56)
T ss_pred ECCCCEEEcCCee------cCCCEEEEECCCCcEe
Confidence 3578888887653 5789999988777765
No 57
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=60.01 E-value=41 Score=21.24 Aligned_cols=37 Identities=11% Similarity=0.156 Sum_probs=27.2
Q ss_pred CEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEee
Q psy1178 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQ 107 (144)
Q Consensus 55 p~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~ 107 (144)
|.|.++++.++++ ++..||.|.|.+..|.+.+..+..
T Consensus 30 ~~v~inp~dA~~~----------------Gi~~Gd~V~v~s~~G~v~~~v~~~ 66 (110)
T PF01568_consen 30 PFVEINPEDAAKL----------------GIKDGDWVRVSSPRGSVEVRVKVT 66 (110)
T ss_dssp EEEEEEHHHHHHC----------------T--TTCEEEEEETTEEEEEEEEEE
T ss_pred CEEEEcHHHHHHh----------------cCcCCCEEEEEeccceEeeeeEEe
Confidence 4899999888776 235688899988888877776654
No 58
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=54.89 E-value=68 Score=22.15 Aligned_cols=39 Identities=13% Similarity=0.164 Sum_probs=25.8
Q ss_pred CcCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 52 VGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 52 ~~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~ 106 (144)
...|.|.++++.++.+ .+..||.|.|.+..|.+.+..+.
T Consensus 29 ~~~~~v~inp~dA~~~----------------GI~dGd~V~v~s~~G~~~~~a~v 67 (156)
T cd02783 29 HTRNYLYMHPKTAKEL----------------GIKDGDWVWVESVNGRVKGQARF 67 (156)
T ss_pred CCCCEEEECHHHHHHc----------------CCCCCCEEEEEcCCeeEEEEEEE
Confidence 3457899998877765 23457777777777765554443
No 59
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=49.66 E-value=57 Score=20.88 Aligned_cols=35 Identities=9% Similarity=0.285 Sum_probs=22.0
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEE
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALA 104 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig 104 (144)
-|.+.++++.++++ ++..||.|.|++..|...+..
T Consensus 30 ~~~v~i~p~dA~~l----------------gI~dGd~V~v~s~~G~i~~~a 64 (112)
T cd02787 30 RDVVFMNPDDIARL----------------GLKAGDRVDLESAFGDGQGRI 64 (112)
T ss_pred ccEEEECHHHHHHh----------------CCCCCCEEEEEecCCCCeEEE
Confidence 36789998887766 123456666666666554433
No 60
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=49.24 E-value=58 Score=22.17 Aligned_cols=37 Identities=19% Similarity=0.294 Sum_probs=22.8
Q ss_pred cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEE
Q psy1178 53 GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALAL 105 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~ 105 (144)
..|.|.++++.++.+ .+..|+.|+|++..|+..+..+
T Consensus 29 ~~~~v~inp~dA~~l----------------gI~dGd~V~v~~~~G~v~~~a~ 65 (141)
T cd02776 29 GGPVVWMNPKDAAEL----------------GIKDNDWVEVFNDNGVVVARAK 65 (141)
T ss_pred CCCEEEECHHHHHHc----------------CCCCCCEEEEEeCCeEEEEEEE
Confidence 357788988877655 2245666666666665554433
No 61
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=47.34 E-value=76 Score=20.46 Aligned_cols=36 Identities=14% Similarity=0.211 Sum_probs=23.2
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEE
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALAL 105 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~ 105 (144)
-|.|.++++.++++ ++..||.|.+++..|.+.+..+
T Consensus 32 ~~~v~in~~dA~~l----------------gi~~Gd~V~v~s~~G~i~~~~~ 67 (115)
T cd02779 32 LPYIEVNPEDAKRE----------------GLKNGDLVEVYNDYGSTTAMAY 67 (115)
T ss_pred CCEEEECHHHHHHc----------------CCCCCCEEEEEeCCEEEEEEEE
Confidence 46799998877766 1245667777766665554443
No 62
>KOG2559|consensus
Probab=45.45 E-value=6.9 Score=29.75 Aligned_cols=15 Identities=40% Similarity=0.636 Sum_probs=13.6
Q ss_pred CccEeeeeecccccC
Q psy1178 2 IELRRNRSGIQSEED 16 (144)
Q Consensus 2 ~~LrRt~~g~F~~~~ 16 (144)
+.|||++-|+|+.++
T Consensus 240 ~qlrr~r~g~F~~d~ 254 (318)
T KOG2559|consen 240 IQLRRQRFGPFGSDN 254 (318)
T ss_pred eeeeeeccCCCCccH
Confidence 579999999999994
No 63
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=45.25 E-value=76 Score=20.94 Aligned_cols=37 Identities=22% Similarity=0.359 Sum_probs=23.3
Q ss_pred cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEE
Q psy1178 53 GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALAL 105 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~ 105 (144)
..|.|.++++.++++ .+..|+.|.|++..|...+...
T Consensus 31 ~~~~v~i~p~dA~~~----------------gi~~Gd~V~v~s~~G~~~~~~~ 67 (129)
T cd02793 31 GREPIRINPADAAAR----------------GIADGDIVRVFNDRGACLAGAV 67 (129)
T ss_pred CCCEEEECHHHHHHc----------------CCCCCCEEEEEcCCEEEEEEEE
Confidence 357788988877655 1245667777766666554443
No 64
>cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=43.94 E-value=98 Score=21.07 Aligned_cols=14 Identities=7% Similarity=0.226 Sum_probs=10.4
Q ss_pred CCEEEEChhhHHhh
Q psy1178 54 HKRIILKDSAVNAV 67 (144)
Q Consensus 54 lp~V~l~~~~~~~l 67 (144)
-|.|.++++.++++
T Consensus 37 ~~~v~InP~dA~~l 50 (137)
T cd02784 37 DNAALVSPRTAEAL 50 (137)
T ss_pred CceEEECHHHHHHc
Confidence 36788988877765
No 65
>PF13101 DUF3945: Protein of unknown function (DUF3945)
Probab=43.08 E-value=18 Score=20.96 Aligned_cols=27 Identities=19% Similarity=0.202 Sum_probs=22.9
Q ss_pred CcCCEEEEChhhHHhhhCCceecCCCe
Q psy1178 52 VGHKRIILKDSAVNAVCYGAQIMLPGV 78 (144)
Q Consensus 52 ~~lp~V~l~~~~~~~l~~G~~l~~~~~ 78 (144)
..+..+.|++++.+.+++|..|...++
T Consensus 28 ~~i~g~~Ls~~q~~~L~~G~~v~le~m 54 (59)
T PF13101_consen 28 DKIKGVELSPEQKEDLREGKPVYLEGM 54 (59)
T ss_pred ceecCccCCHHHHHHHHCCCeEEEeee
Confidence 446679999999999999999987765
No 66
>PRK12784 hypothetical protein; Provisional
Probab=42.12 E-value=21 Score=22.19 Aligned_cols=17 Identities=18% Similarity=0.726 Sum_probs=15.2
Q ss_pred EEEEEeecCCccccCcC
Q psy1178 123 KIKRVIMDRDTYPRKWG 139 (144)
Q Consensus 123 ~~~rv~~~~~~~~~~w~ 139 (144)
++.++|.+.++|-++|.
T Consensus 15 ~Vekifi~esSyVYEWE 31 (84)
T PRK12784 15 KVEEIFVNESSYVYEWE 31 (84)
T ss_pred EEEEEEEcCCceEEeee
Confidence 56699999999999997
No 67
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=40.97 E-value=1e+02 Score=20.09 Aligned_cols=36 Identities=19% Similarity=0.294 Sum_probs=22.1
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEE
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALAL 105 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~ 105 (144)
-|.+.++++.++++ ++..|+.|+|.+..|...+..+
T Consensus 31 ~~~v~i~p~dA~~~----------------gi~~Gd~V~v~s~~G~i~~~a~ 66 (124)
T cd02785 31 EPRVKINPIDAAAR----------------GIAHGDLVEVYNDRGSVVCKAK 66 (124)
T ss_pred CCeEEECHHHHHHc----------------CCCCCCEEEEEeCCCEEEEEEE
Confidence 36788888877765 1234566666666665554444
No 68
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=40.70 E-value=98 Score=19.87 Aligned_cols=36 Identities=14% Similarity=0.162 Sum_probs=21.6
Q ss_pred cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEE
Q psy1178 53 GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALA 104 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig 104 (144)
..|.+.++++.++++ .+..||.|.|++..|++.+..
T Consensus 33 ~~~~v~i~p~dA~~l----------------gi~~Gd~V~v~s~~G~~~~~v 68 (122)
T cd02792 33 PEMFVEISPELAAER----------------GIKNGDMVWVSSPRGKIKVKA 68 (122)
T ss_pred CCcEEEECHHHHHHc----------------CCCCCCEEEEEcCCceEEEEE
Confidence 357789998877766 123455566665555544433
No 69
>PRK06933 type III secretion system protein; Validated
Probab=40.25 E-value=95 Score=24.37 Aligned_cols=61 Identities=15% Similarity=0.168 Sum_probs=41.5
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeec
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMD 130 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~ 130 (144)
+.+..++-.....+.-|.-+.... ...+.|.|+- +|+.+|.|+.... +...+|++.+++..
T Consensus 245 LG~~~ltl~eLl~L~~GdVi~L~~--------~~~~~V~I~v-ng~~i~~Gelv~v-------~~~laVrI~~~~~~ 305 (308)
T PRK06933 245 VGRQTLDLHTLTSLQPGSLIDLTT--------PVDGEVRLLA-NGRLLGHGRLVEI-------QGRLGVRVERLFGV 305 (308)
T ss_pred EecccccHHHHhcCCCCCEEEcCC--------CCCCCEEEEE-CCEEEEEEEEEEE-------CCEEEEEEEEeecC
Confidence 456666777778888888776643 1234677775 7899999987532 33446888888754
No 70
>PRK02268 hypothetical protein; Provisional
Probab=38.55 E-value=64 Score=22.33 Aligned_cols=24 Identities=13% Similarity=0.088 Sum_probs=17.2
Q ss_pred CCCCCCEEEEEcC---------CCCEEEEEEee
Q psy1178 84 GIEMDEEIVIVST---------KGEAVALALAQ 107 (144)
Q Consensus 84 ~~~~~~~v~i~~~---------~g~~laig~~~ 107 (144)
...+||.+.+|.+ -..|.|||++.
T Consensus 35 RmkpGD~ivyYsp~~~~~~~~~~qaftAig~V~ 67 (141)
T PRK02268 35 RMKPGDWIIYYSPKTTFGGKDKLQAFTAIGKVK 67 (141)
T ss_pred cCCCCCEEEEEeceEecCCCcccceEEEEEEEc
Confidence 3478888888763 23589999865
No 71
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=38.38 E-value=1.1e+02 Score=19.72 Aligned_cols=38 Identities=13% Similarity=0.275 Sum_probs=24.5
Q ss_pred cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 53 GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~ 106 (144)
..|.+.++++.++++ .+..|+.|.|++..|.+.+..++
T Consensus 28 ~~~~v~i~p~dA~~~----------------gi~~Gd~V~v~s~~G~i~~~v~v 65 (123)
T cd02778 28 PENTLWINPETAARL----------------GIKDGDRVEVSSARGKVTGKARL 65 (123)
T ss_pred CCCeEEECHHHHHHc----------------CCCCCCEEEEEeCCCcEEEEEEE
Confidence 347888998877765 12456677777766666554443
No 72
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=37.53 E-value=1.1e+02 Score=19.72 Aligned_cols=35 Identities=11% Similarity=0.309 Sum_probs=22.2
Q ss_pred EEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 56 ~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~ 106 (144)
.+.++++.++++ ++..|+.|.|.+..|...+....
T Consensus 31 ~v~i~p~~A~~~----------------gi~~Gd~V~v~s~~g~i~~~a~~ 65 (121)
T cd02794 31 EVWINPLDAAAR----------------GIKDGDRVLVFNDRGKVIRPVKV 65 (121)
T ss_pred CEEECHHHHHHc----------------CCCCCCEEEEEcCCceEEEEEEE
Confidence 477888776655 22456777777767766554443
No 73
>PRK06789 flagellar motor switch protein; Validated
Probab=36.00 E-value=96 Score=18.96 Aligned_cols=46 Identities=9% Similarity=0.034 Sum_probs=30.8
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeec
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQM 108 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~ 108 (144)
+.+..+.=...-.+..|.-+.... ..++.|.++- +|+++|.|+...
T Consensus 15 lGr~~~~i~dll~L~~Gsvi~Ldk--------~~~epvdI~v-Ng~lia~GEvVv 60 (74)
T PRK06789 15 IGNTKKKIEDLLHITKGTLYRLEN--------STKNTVRLML-ENEEIGTGKILT 60 (74)
T ss_pred EeeeEeEHHHHhcCCCCCEEEeCC--------cCCCCEEEEE-CCEEEeEEeEEE
Confidence 445555555566677787766543 3456788875 799999998753
No 74
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=34.21 E-value=1.3e+02 Score=19.21 Aligned_cols=36 Identities=17% Similarity=0.313 Sum_probs=22.4
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEE
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALAL 105 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~ 105 (144)
-|.|.++++.++.+ ++..||.|.|.+..|+..+..+
T Consensus 30 ~~~v~i~p~dA~~l----------------gi~~Gd~V~v~s~~G~~~~~v~ 65 (116)
T cd02786 30 EPTLLIHPADAAAR----------------GIADGDLVVVFNDRGSVTLRAK 65 (116)
T ss_pred CCEEEECHHHHHHc----------------CCCCCCEEEEEcCCeEEEEEEE
Confidence 36788888877765 1244666777666666554443
No 75
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=33.38 E-value=1.4e+02 Score=19.45 Aligned_cols=35 Identities=14% Similarity=0.181 Sum_probs=21.7
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEE
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALA 104 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig 104 (144)
.|.+.++++.++++ .+..|+.|.|++..|...+..
T Consensus 32 ~~~v~inp~dA~~~----------------gi~~Gd~V~v~s~~G~~~~~v 66 (130)
T cd02781 32 DPVAEINPETAAKL----------------GIADGDWVWVETPRGRARQKA 66 (130)
T ss_pred CCEEEECHHHHHHc----------------CCCCCCEEEEECCCCEEEEEE
Confidence 46788888877665 123466667666666554443
No 76
>TIGR02551 SpaO_YscQ type III secretion system apparatus protein YscQ/HrcQ. Genes in this family are found in type III secretion operons. The gene (YscQ) in Yersinia is essential for YOPs secretion, while SpaO in Shigella is involved in the Surface Presentation of Antigens apparatus found on the virulence plasmid, and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae.
Probab=33.25 E-value=1.2e+02 Score=23.45 Aligned_cols=46 Identities=15% Similarity=0.135 Sum_probs=33.6
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeec
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQM 108 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~ 108 (144)
+.+..++-.....++-|.-+.... ...+.|.++- +|+.+|.|+...
T Consensus 241 lg~~~l~l~el~~L~~G~vl~L~~--------~~~~~v~l~~-~g~~~~~Gel~~ 286 (298)
T TIGR02551 241 LGRLTLTLAELAALQPGSVLELNV--------PVDGPVRLRA-NGRLLGRGELVD 286 (298)
T ss_pred EecceeeHHHHhCCCCCCEEEcCC--------CCCCcEEEEE-CCEEEEEEEEEE
Confidence 567777778888888998887643 1234677764 789999998753
No 77
>PRK04980 hypothetical protein; Provisional
Probab=33.13 E-value=1.4e+02 Score=19.45 Aligned_cols=50 Identities=6% Similarity=0.080 Sum_probs=31.5
Q ss_pred CEEEEChhhHHhhhCCceec-CCCeecccCCCCCCCEEEE-EcCCCCEEEEEEe
Q psy1178 55 KRIILKDSAVNAVCYGAQIM-LPGVLRYEDGIEMDEEIVI-VSTKGEAVALALA 106 (144)
Q Consensus 55 p~V~l~~~~~~~l~~G~~l~-~~~~~~~~~~~~~~~~v~i-~~~~g~~laig~~ 106 (144)
+.++........|..|..-- ... ...+.+.+|+.+.| .+.+|+++|.-+.
T Consensus 3 ~~itF~~r~~~~ILsGkKTiTiRd--~se~~~~~G~~~~V~~~e~g~~~c~ieI 54 (102)
T PRK04980 3 NKITFFERFEADILAGRKTITIRD--ESESHFKPGDVLRVGTFEDDRYFCTIEV 54 (102)
T ss_pred ceeeEHHHHHHHHHcCCceEEeeC--CcccCCCCCCEEEEEECCCCcEEEEEEE
Confidence 34666666667777776431 211 11235678998888 5668888887765
No 78
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=32.49 E-value=1.3e+02 Score=18.76 Aligned_cols=37 Identities=8% Similarity=0.031 Sum_probs=24.5
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~ 106 (144)
.|.+.++++.++++ ++..|+.|.+.+..|...+..+.
T Consensus 28 ~~~v~inp~dA~~l----------------Gi~~Gd~V~v~s~~G~i~~~v~v 64 (96)
T cd02788 28 APYARLSPADAARL----------------GLADGDLVEFSLGDGTLTLPVQI 64 (96)
T ss_pred CCEEEECHHHHHHc----------------CCCCCCEEEEEECCeEEEEEEEE
Confidence 46788888877766 22457778887767665554443
No 79
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.58 E-value=1.4e+02 Score=18.89 Aligned_cols=14 Identities=0% Similarity=0.124 Sum_probs=10.4
Q ss_pred CCEEEEChhhHHhh
Q psy1178 54 HKRIILKDSAVNAV 67 (144)
Q Consensus 54 lp~V~l~~~~~~~l 67 (144)
.|.+.++++.++++
T Consensus 34 ~~~v~in~~dA~~l 47 (116)
T cd02790 34 EEYVEINPEDAKRL 47 (116)
T ss_pred CcEEEECHHHHHHc
Confidence 46788888877655
No 80
>PRK00529 elongation factor P; Validated
Probab=31.40 E-value=78 Score=22.78 Aligned_cols=31 Identities=29% Similarity=0.351 Sum_probs=22.7
Q ss_pred hhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEE
Q psy1178 67 VCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVAL 103 (144)
Q Consensus 67 l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~lai 103 (144)
+-+|..+..|.+ +..|+.++|-+.+|.++..
T Consensus 154 letG~~v~VP~f------I~~Gd~I~v~T~~g~y~~R 184 (186)
T PRK00529 154 LETGAVVQVPLF------INEGEKIKVDTRTGEYVER 184 (186)
T ss_pred EcCCCEEEeCCe------ecCCCEEEEECCCCcEEee
Confidence 346777777664 3678999998888887754
No 81
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.21 E-value=1.4e+02 Score=18.90 Aligned_cols=34 Identities=15% Similarity=0.252 Sum_probs=20.6
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEE
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVAL 103 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~lai 103 (144)
.|.+.++++.++++ ++..|+.|.|++..|++.+.
T Consensus 34 ~~~v~inp~dA~~l----------------gi~~Gd~V~v~~~~G~~~~~ 67 (120)
T cd00508 34 EPFVEIHPEDAARL----------------GIKDGDLVRVSSRRGSVVVR 67 (120)
T ss_pred CCEEEECHHHHHHc----------------CCCCCCEEEEEeCCEEEEEE
Confidence 47788988877765 12345566666555554433
No 82
>TIGR00038 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria.
Probab=31.15 E-value=69 Score=23.01 Aligned_cols=30 Identities=33% Similarity=0.417 Sum_probs=22.0
Q ss_pred hhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEE
Q psy1178 67 VCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVA 102 (144)
Q Consensus 67 l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~la 102 (144)
|-+|..+..|.+ +..|+.++|-+.+|.++.
T Consensus 153 letG~~v~VP~f------i~~Gd~I~v~T~~g~y~~ 182 (184)
T TIGR00038 153 LETGAVVQVPLF------IEEGEKIKVDTRTGEYVE 182 (184)
T ss_pred EcCCCEEEeCCc------ccCCCEEEEECCCCcEEe
Confidence 347777777654 367889999888888764
No 83
>PRK07963 fliN flagellar motor switch protein FliN; Validated
Probab=30.21 E-value=1.4e+02 Score=20.58 Aligned_cols=60 Identities=17% Similarity=0.180 Sum_probs=35.7
Q ss_pred CEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeec
Q psy1178 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMD 130 (144)
Q Consensus 55 p~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~ 130 (144)
.+..++-...-.+..|.-|.... ..++.+.|+- +|.+++.|++... +...+|+...++..
T Consensus 69 G~t~itlrdLL~L~~GDVI~Ld~--------~~~epv~V~V-ng~~if~GevGvv-------~~k~AVrIteii~~ 128 (137)
T PRK07963 69 GRTRMTIKELLRLTQGSVVALDG--------LAGEPLDILI-NGYLIAQGEVVVV-------ADKYGVRITDIITP 128 (137)
T ss_pred ecccccHHHHhCCCCCCEEEeCC--------CCCCCEEEEE-CCEEEEEEEEEEE-------CCEEEEEEEEecCc
Confidence 34444444455556676665432 2345677764 7899999987542 33446777777653
No 84
>PF14306 PUA_2: PUA-like domain; PDB: 1M8P_C 1I2D_B 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2QJF_A 2OFX_B 1J70_B 1G8F_A ....
Probab=30.07 E-value=85 Score=22.08 Aligned_cols=23 Identities=13% Similarity=0.364 Sum_probs=17.4
Q ss_pred CCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 84 GIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 84 ~~~~~~~v~i~~~~g~~laig~~ 106 (144)
.+..|+.|.+.+.+|+.+|+=.+
T Consensus 92 ~l~~G~~v~L~~~~G~~~a~l~V 114 (160)
T PF14306_consen 92 SLKEGDKVALRDPEGKPVAILEV 114 (160)
T ss_dssp TCTTTSEEEEEETTTEEEEEEEE
T ss_pred hccCCCEEEEECCCCCEEEEEEe
Confidence 35678888888877888887654
No 85
>COG1886 FliN Flagellar motor switch/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=29.89 E-value=1.8e+02 Score=19.75 Aligned_cols=46 Identities=17% Similarity=0.129 Sum_probs=31.0
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeec
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQM 108 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~ 108 (144)
+.+..++=....++..|.-+.... ..++.|.|+- +|+.+|.|+...
T Consensus 79 lGr~~~~l~ell~l~~Gsvi~Ld~--------~~~~~VdI~v-Ng~~Ig~GEvVv 124 (136)
T COG1886 79 LGRTKMPLGELLALGKGSVIELDK--------LAGEPVDILV-NGRLIGRGEVVV 124 (136)
T ss_pred EeeeeeeHHHHHhcCCCCEEEcCC--------cCCCceEEEE-CCEEEEEEeEEE
Confidence 345555556667777888776543 2456677764 799999998753
No 86
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells [, ].They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins []. The C-terminal region of flagellar motor switch proteins FliN and FliM is also included in this entry. ; PDB: 3UEP_A 1O9Y_B 1YAB_A.
Probab=29.48 E-value=1.3e+02 Score=17.84 Aligned_cols=61 Identities=15% Similarity=0.114 Sum_probs=38.1
Q ss_pred cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 53 GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
.+....++-.....++-|.-+....- ..+.+.++- +|..++.|+.... +...+++..+.+.
T Consensus 15 ~l~~~~l~l~el~~L~~Gdvi~l~~~--------~~~~v~l~v-~g~~~~~g~lg~~-------~~~~av~I~~~~~ 75 (77)
T PF01052_consen 15 ELGEASLTLGELLNLKVGDVIPLDKP--------ADEPVELRV-NGQPIFRGELGRV-------NGRLAVRITELIE 75 (77)
T ss_dssp EEEEEEEEHHHHHC--TT-EEEECCE--------SSTEEEEEE-TTEEEEEEEEEEE-------TTEEEEEEEEE--
T ss_pred EEEeeEeEHHHHhcCCCCCEEEeCCC--------CCCCEEEEE-CCEEEEEEEEEEE-------CCEEEEEEEEEcc
Confidence 35678888888899999998876531 234677764 7899999987532 3344677666553
No 87
>PRK15488 thiosulfate reductase PhsA; Provisional
Probab=28.81 E-value=1.7e+02 Score=25.58 Aligned_cols=23 Identities=30% Similarity=0.445 Sum_probs=18.6
Q ss_pred CCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 84 GIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 84 ~~~~~~~v~i~~~~g~~laig~~ 106 (144)
++..||.|+|++..|.+.+..++
T Consensus 679 GI~dGD~V~v~n~~G~i~~~a~v 701 (759)
T PRK15488 679 GIKNGDEIRLENSVGKEKGKALV 701 (759)
T ss_pred CCCCCCEEEEEcCCCcEEEEEEE
Confidence 56779999999988988776655
No 88
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=28.52 E-value=1.6e+02 Score=18.74 Aligned_cols=36 Identities=17% Similarity=0.222 Sum_probs=22.7
Q ss_pred cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEE
Q psy1178 53 GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALA 104 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig 104 (144)
.-|.|.++++.++++ ++..|+.|.+.+..|.+.+..
T Consensus 29 ~~~~v~i~p~dA~~l----------------gi~~Gd~V~v~~~~G~v~~~v 64 (106)
T cd02789 29 ACAYCEINPEDYKLL----------------GKPEGDKVKVTSEFGEVVVFA 64 (106)
T ss_pred CCcEEEECHHHHHHc----------------CCCCCCEEEEEcCCEEEEEEE
Confidence 457899999887766 123456666666555544433
No 89
>TIGR03479 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane.
Probab=27.86 E-value=1.2e+02 Score=27.36 Aligned_cols=23 Identities=26% Similarity=0.319 Sum_probs=19.0
Q ss_pred CCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 84 GIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 84 ~~~~~~~v~i~~~~g~~laig~~ 106 (144)
+++.||.|+|++..|.+.+..++
T Consensus 823 GI~dGD~V~V~n~~G~~~~~a~v 845 (912)
T TIGR03479 823 GIKDGDQVRIFNDLAEFEAMAKI 845 (912)
T ss_pred CCCcCCEEEEEeCCcEEEEEEEE
Confidence 56789999999988988876665
No 90
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=26.56 E-value=91 Score=20.98 Aligned_cols=23 Identities=9% Similarity=0.203 Sum_probs=14.9
Q ss_pred CCCCCEEEEEcCC---CCEEEEEEee
Q psy1178 85 IEMDEEIVIVSTK---GEAVALALAQ 107 (144)
Q Consensus 85 ~~~~~~v~i~~~~---g~~laig~~~ 107 (144)
+..||.+.+|..+ ..++|+|++.
T Consensus 40 mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 40 MKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp --TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred CCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 4678998888654 3689999873
No 91
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=25.06 E-value=1.6e+02 Score=17.64 Aligned_cols=59 Identities=15% Similarity=0.156 Sum_probs=39.6
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEe
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVI 128 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~ 128 (144)
+.+..++-.....+.-|.-+.... ...+.+.++- +|.+++.|+.... +...+++..++.
T Consensus 16 Lg~~~itl~ell~L~~Gdvi~L~~--------~~~~~v~l~v-~g~~~~~g~lg~~-------~~~~avrI~~~~ 74 (77)
T TIGR02480 16 LGRTRITLGDLLKLGEGSVIELDK--------LAGEPLDILV-NGRLIARGEVVVV-------EDKFGIRITEIV 74 (77)
T ss_pred EeceEeEHHHHhcCCCCCEEEcCC--------CCCCcEEEEE-CCEEEEEEEEEEE-------CCEEEEEEEEEe
Confidence 467777777888888898877642 1234577764 7899999987532 334467766665
No 92
>PRK04542 elongation factor P; Provisional
Probab=24.70 E-value=1.1e+02 Score=22.33 Aligned_cols=30 Identities=23% Similarity=0.327 Sum_probs=21.5
Q ss_pred hhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEE
Q psy1178 67 VCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVA 102 (144)
Q Consensus 67 l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~la 102 (144)
+-+|..|..|.+ +..|+.++|-+..|.++.
T Consensus 157 LetG~~v~VP~F------I~~Gd~I~VdT~tgeYv~ 186 (189)
T PRK04542 157 LSTGLVIQVPEY------ISTGEKIRINTEERKFMG 186 (189)
T ss_pred EcCCCEEEeCCc------ccCCCEEEEECCCCcEEe
Confidence 346777776654 367888999888887764
No 93
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=24.59 E-value=2.8e+02 Score=20.08 Aligned_cols=48 Identities=17% Similarity=0.113 Sum_probs=34.2
Q ss_pred CCEEEEChhhHHhhhCCceecC--CCeecccCCCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 54 HKRIILKDSAVNAVCYGAQIML--PGVLRYEDGIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~--~~~~~~~~~~~~~~~v~i~~~~g~~laig~~ 106 (144)
++.+.++......|.+|..... .|. ....+|+.|.|.. .|..+|.++.
T Consensus 6 ~k~l~f~gkY~~~ii~GkKr~TIR~G~----~~~k~g~eVyIh~-~g~i~gkAkI 55 (188)
T COG2411 6 MKHLEFDGKYKDKIIDGKKRTTIRLGK----IVLKPGSEVYIHS-GGYIIGKAKI 55 (188)
T ss_pred hhheeechHHHHHHhcCceeEEEecCc----ccCCCCCEEEEEE-CCEEEEEEEE
Confidence 5678889999999999987642 231 1456788888864 6777777655
No 94
>PRK08916 flagellar motor switch protein; Reviewed
Probab=24.27 E-value=2.2e+02 Score=18.93 Aligned_cols=60 Identities=15% Similarity=0.140 Sum_probs=39.6
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEee
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIM 129 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~ 129 (144)
+.+..++-...-.+.-|.-|.... ..++.|.+|- +|++++.|+.... +...+++..+++.
T Consensus 53 LG~~~ltl~ELL~L~~GDVI~Ld~--------~~~e~V~I~V-ng~~~~~Gelg~~-------~~rlAVrIteii~ 112 (116)
T PRK08916 53 LGRSKMDVGQLLKLGPGSVLELDR--------KVGEAIDIYV-NNRLVARGEVVLV-------EDRLGVTMTEIIK 112 (116)
T ss_pred EecccccHHHHhcCCCCCEEEcCC--------CCCCCEEEEE-CCEEEEEEEEEEE-------CCEEEEEEEEeec
Confidence 456666667777778888776543 2345677764 7899999987542 3344677777664
No 95
>PRK13992 minC septum formation inhibitor; Provisional
Probab=24.23 E-value=2.2e+02 Score=20.79 Aligned_cols=29 Identities=14% Similarity=0.189 Sum_probs=18.8
Q ss_pred HHhhhCCceecCCCeecccCCCCCCCEEE
Q psy1178 64 VNAVCYGAQIMLPGVLRYEDGIEMDEEIV 92 (144)
Q Consensus 64 ~~~l~~G~~l~~~~~~~~~~~~~~~~~v~ 92 (144)
.+.++.||.++.++-+-+-+++.+|..|.
T Consensus 102 ~~~vRSGQ~I~~~gdlvIlGdVn~GAeVi 130 (205)
T PRK13992 102 KKNLRSGQTVVHSGDVIVFGNVHKGAEIL 130 (205)
T ss_pred eCCccCCCEEEeCCCEEEEccCCCCCEEE
Confidence 34678899998877444446666665443
No 96
>TIGR01222 minC septum site-determining protein MinC. The minC protein assists in correct placement of the septum for cell division by inhibiting septum formation at other sites. Homologs from Deinocoocus, Synechocystis PCC 6803, and Helicobacter pylori do not hit the full length of the model and score between the trusted and noise cutoffs.
Probab=23.91 E-value=2.2e+02 Score=20.82 Aligned_cols=29 Identities=24% Similarity=0.269 Sum_probs=18.3
Q ss_pred HHhhhCCceecCC-CeecccCCCCCCCEEE
Q psy1178 64 VNAVCYGAQIMLP-GVLRYEDGIEMDEEIV 92 (144)
Q Consensus 64 ~~~l~~G~~l~~~-~~~~~~~~~~~~~~v~ 92 (144)
.+.|+.||.++.+ +-+-+-+++.+|..|.
T Consensus 116 ~~~vRSGQ~i~~~~gDliilG~Vn~GAeVi 145 (217)
T TIGR01222 116 KTPVRSGQQIYAKHGDLIVLGNVNAGAEVL 145 (217)
T ss_pred eCcccCCCEEEecCCCEEEECCCCCCCEEE
Confidence 3457889999887 4333445666775543
No 97
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=23.24 E-value=2.1e+02 Score=18.24 Aligned_cols=15 Identities=0% Similarity=0.011 Sum_probs=11.1
Q ss_pred cCCEEEEChhhHHhh
Q psy1178 53 GHKRIILKDSAVNAV 67 (144)
Q Consensus 53 ~lp~V~l~~~~~~~l 67 (144)
..|.+.++++.++++
T Consensus 33 ~~~~v~in~~dA~~l 47 (122)
T cd02791 33 PEPYVEIHPEDAARL 47 (122)
T ss_pred CCCEEEECHHHHHHc
Confidence 457788888877765
No 98
>PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional
Probab=23.12 E-value=1.8e+02 Score=25.74 Aligned_cols=24 Identities=25% Similarity=0.375 Sum_probs=19.5
Q ss_pred CCCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 83 DGIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 83 ~~~~~~~~v~i~~~~g~~laig~~ 106 (144)
-++..||.|+|++..|++.+..++
T Consensus 734 ~GI~dGD~V~V~n~~G~v~~~a~v 757 (814)
T PRK14990 734 RGINNGDKVRIFNDRGEVHIEAKV 757 (814)
T ss_pred cCCCCCCEEEEEcCCceEEEEEEE
Confidence 356789999999988988876665
No 99
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=22.46 E-value=1.2e+02 Score=21.96 Aligned_cols=29 Identities=24% Similarity=0.340 Sum_probs=20.1
Q ss_pred hCCceecCCCeecccCCCCCCCEEEEEcCCCCEEE
Q psy1178 68 CYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVA 102 (144)
Q Consensus 68 ~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~la 102 (144)
-+|..|..|.+ +..||.|+|-+..|.+++
T Consensus 156 eTG~~v~VP~F------I~~Gd~IkVdTrtg~Y~~ 184 (186)
T TIGR02178 156 ITGLVVQVPEY------ITTGERILINTTERAFMG 184 (186)
T ss_pred cCCCEEEeCCe------ecCCCEEEEECCCCcEEc
Confidence 46777666654 357888888887777654
No 100
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.34 E-value=2.3e+02 Score=18.39 Aligned_cols=14 Identities=7% Similarity=0.119 Sum_probs=10.4
Q ss_pred CCEEEEChhhHHhh
Q psy1178 54 HKRIILKDSAVNAV 67 (144)
Q Consensus 54 lp~V~l~~~~~~~l 67 (144)
-|.|.++++.++++
T Consensus 32 ~~~v~i~p~dA~~~ 45 (129)
T cd02782 32 RCTLRIHPDDAAAL 45 (129)
T ss_pred CceEEECHHHHHHc
Confidence 47788888877755
No 101
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=22.19 E-value=2.3e+02 Score=18.38 Aligned_cols=36 Identities=17% Similarity=0.246 Sum_probs=22.6
Q ss_pred CCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEE
Q psy1178 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALAL 105 (144)
Q Consensus 54 lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~ 105 (144)
.+.+.++++.++.+ ++..|+.|+|.+..|...+...
T Consensus 33 ~~~v~i~p~dA~~l----------------gi~~Gd~V~v~s~~g~i~~~v~ 68 (127)
T cd02777 33 REPVWINPLDAAAR----------------GIKDGDIVRVFNDRGAVLAGAR 68 (127)
T ss_pred CCeEEECHHHHHHc----------------CCCCCCEEEEEcCCeEEEEEEE
Confidence 35688888877755 2245677777766666554433
No 102
>PRK05698 fliN flagellar motor switch protein; Validated
Probab=22.17 E-value=2.7e+02 Score=19.57 Aligned_cols=60 Identities=13% Similarity=0.114 Sum_probs=34.0
Q ss_pred CEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeec
Q psy1178 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMD 130 (144)
Q Consensus 55 p~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~ 130 (144)
.+..++-...-.+..|.-|.... ..++.+.||- +|++++.|++... +...+|+...++..
T Consensus 88 G~t~itlrdLL~L~~GDVI~Ldk--------~~~epv~V~V-nG~~~f~Ge~Gvv-------n~k~AVrIteii~~ 147 (155)
T PRK05698 88 GSTDINIRNLLQLNQGSVIELDR--------LAGEPLDVLV-NGTLIAHGEVVVV-------NEKFGIRLTDVISP 147 (155)
T ss_pred ecCcccHHHHhCCCCCCEEEeCC--------CCCCCEEEEE-CCEEEEEEEEEEE-------CCEEEEEEEEecCc
Confidence 33344444444555565554322 2345566664 7889999987542 33446777777643
No 103
>COG1092 Predicted SAM-dependent methyltransferases [General function prediction only]
Probab=21.85 E-value=1.1e+02 Score=24.96 Aligned_cols=49 Identities=16% Similarity=0.211 Sum_probs=30.9
Q ss_pred EChhhHHhhhCCceecCC-CeecccCCCCCCCEEEEEcCCCCEEEEEEee
Q psy1178 59 LKDSAVNAVCYGAQIMLP-GVLRYEDGIEMDEEIVIVSTKGEAVALALAQ 107 (144)
Q Consensus 59 l~~~~~~~l~~G~~l~~~-~~~~~~~~~~~~~~v~i~~~~g~~laig~~~ 107 (144)
+.....+++.+|.+.-.. .+....+....|+.+.+++.+|.++|.|.+.
T Consensus 3 ~~k~~~~~~~~~~~~~~~~~i~~~~~~~~~g~~~~v~~~~g~~l~~g~~~ 52 (393)
T COG1092 3 LKKGAEKKIRRGYPWVFRKEIARVEGRLKPGDVVDVYDKGGKFLARGYYS 52 (393)
T ss_pred ccchhhhhhccCceeeehhhhhhcccccCCCceeeeecCCCCEeeeeccC
Confidence 344556677777665332 2222223345677888888889999999764
No 104
>TIGR01580 narG respiratory nitrate reductase, alpha subunit. The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the alpha subunit for nitrate reductase I (narG) and nitrate reductase II (narZ) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model The seed members used to make the model include Nitrate reductases from Pseudomonas fluorescens, E.coli and B.subtilis. All seed members are experimentally characterized. Some unpublished nitrate reductases, that are shorter sequences, and probably fragments fall in between the noise and trusted cutoffs. P
Probab=21.60 E-value=2.9e+02 Score=26.16 Aligned_cols=24 Identities=25% Similarity=0.316 Sum_probs=19.0
Q ss_pred CCCCCCEEEEEcCCCCEEEEEEee
Q psy1178 84 GIEMDEEIVIVSTKGEAVALALAQ 107 (144)
Q Consensus 84 ~~~~~~~v~i~~~~g~~laig~~~ 107 (144)
.+..+|.|.+|+.+|.++|...+.
T Consensus 1129 Gi~DnDwVEv~N~nG~v~arAvvs 1152 (1235)
T TIGR01580 1129 GIADNDWIECFNSNGALTARAVVS 1152 (1235)
T ss_pred CCCCCCEEEEEecCCeEEEEEEEc
Confidence 456788999999999888877654
No 105
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=21.55 E-value=2.6e+02 Score=18.66 Aligned_cols=14 Identities=0% Similarity=0.136 Sum_probs=10.6
Q ss_pred CCEEEEChhhHHhh
Q psy1178 54 HKRIILKDSAVNAV 67 (144)
Q Consensus 54 lp~V~l~~~~~~~l 67 (144)
-|.|.++++.++++
T Consensus 29 ~~~v~inp~dA~~l 42 (143)
T cd02780 29 ENPVWINPEDAAKL 42 (143)
T ss_pred CCEEEECHHHHHHc
Confidence 46788888877755
No 106
>PRK15102 trimethylamine N-oxide reductase I catalytic subunit; Provisional
Probab=21.06 E-value=2.2e+02 Score=25.38 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=18.9
Q ss_pred CCCCCCEEEEEcCCCCEEEEEEe
Q psy1178 84 GIEMDEEIVIVSTKGEAVALALA 106 (144)
Q Consensus 84 ~~~~~~~v~i~~~~g~~laig~~ 106 (144)
++..||.|+|++..|.+.+..++
T Consensus 723 GI~dGD~V~V~n~rG~~~~~a~v 745 (825)
T PRK15102 723 GIKDGDVVRVFNDRGQVLAGAVV 745 (825)
T ss_pred CCCCCCEEEEECCCeEEEEeEEE
Confidence 56789999999988988776665
No 107
>PRK00809 hypothetical protein; Provisional
Probab=20.90 E-value=1.7e+02 Score=20.10 Aligned_cols=24 Identities=13% Similarity=0.320 Sum_probs=18.1
Q ss_pred CCCCCCEEEEEcCC--------CCEEEEEEee
Q psy1178 84 GIEMDEEIVIVSTK--------GEAVALALAQ 107 (144)
Q Consensus 84 ~~~~~~~v~i~~~~--------g~~laig~~~ 107 (144)
..+.||.+.+|..+ ..++|||++.
T Consensus 34 ~Mk~GD~v~fYhs~~~~~~~~~~~ivgi~eV~ 65 (144)
T PRK00809 34 KVKPGDKLIIYVSQEYGAERLPGKIVGIYEVV 65 (144)
T ss_pred hCCCCCEEEEEECCccCCCCCCceEEEEEEEe
Confidence 35789988888765 3589999875
No 108
>PRK01973 septum formation inhibitor; Reviewed
Probab=20.71 E-value=2.7e+02 Score=21.47 Aligned_cols=28 Identities=21% Similarity=0.201 Sum_probs=18.4
Q ss_pred HHhhhCCceecCCCeecccCCCCCCCEE
Q psy1178 64 VNAVCYGAQIMLPGVLRYEDGIEMDEEI 91 (144)
Q Consensus 64 ~~~l~~G~~l~~~~~~~~~~~~~~~~~v 91 (144)
.+-|+.||.|+.++-+-+.+++..|..|
T Consensus 167 ~~~vRSGQ~i~a~gdliilg~V~~GAEv 194 (271)
T PRK01973 167 DRPLRSGQQIYAKGDLVVLGPVSYGAEV 194 (271)
T ss_pred eCcccCCCEEEeCCCEEEEccCCCCCEE
Confidence 3467899999887744444566666543
No 109
>PF03785 Peptidase_C25_C: Peptidase family C25, C terminal ig-like domain; InterPro: IPR005536 This domain is found in almost all members of MEROPS peptidase family C25, (clan CD). Peptidase family C25 is a protein family found in the bacteria Porphyromonas gingivalis (Bacteroides gingivalis) a Gram-negative anaerobic bacterial species strongly associated with adult periodontitis. One of its distinguishing characteristics and putative virulence properties is the ability to agglutinate erythrocytes []. It is a highly proteolytic organism which metabolises small peptides and amino acids. Indirect evidence suggests that the proteases produced by this microorganism constitute an important virulence factor []. Protease-encoding genes have been shown to contain multiple copies of repeated nucleotide sequences. These conserved sequences have also been found in haemagglutinin genes [].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 1CVR_A.
Probab=20.38 E-value=2e+02 Score=17.92 Aligned_cols=20 Identities=10% Similarity=0.207 Sum_probs=14.1
Q ss_pred CCCEEEEEcCCCCEEEEEEee
Q psy1178 87 MDEEIVIVSTKGEAVALALAQ 107 (144)
Q Consensus 87 ~~~~v~i~~~~g~~laig~~~ 107 (144)
+|..|.+.. +|.+.|.+.+.
T Consensus 26 ~gs~ValS~-dg~l~G~ai~~ 45 (81)
T PF03785_consen 26 PGSYVALSQ-DGDLYGKAIVN 45 (81)
T ss_dssp TT-EEEEEE-TTEEEEEEE-B
T ss_pred CCcEEEEec-CCEEEEEEEec
Confidence 566777764 88999999885
No 110
>PF03775 MinC_C: Septum formation inhibitor MinC, C-terminal domain; InterPro: IPR005526 In Escherichia coli, three Min proteins (MinC, MinD and MinE) negatively regulate FtsZ assembly at the cell poles in order to ensure the Z-ring only assembles at cell midpoint. MinC inhibits formation of the Z-ring by preventing FtsZ assembly. MinD binds to MinC near the cell poles, sequestering MinC away from the cell midpoint so the Z-ring can form there. MinC is an oligomer, probably a dimer, that consists of two domains: the N-terminal domain is responsible for FtsZ inhibition, while the C-terminal domain is responsible for binding to MinD and to a component of the division septum [, ].; GO: 0000902 cell morphogenesis; PDB: 1HF2_C.
Probab=20.17 E-value=2.6e+02 Score=18.16 Aligned_cols=28 Identities=18% Similarity=0.241 Sum_probs=15.0
Q ss_pred HhhhCCceecCCCeecccCCCCCCCEEE
Q psy1178 65 NAVCYGAQIMLPGVLRYEDGIEMDEEIV 92 (144)
Q Consensus 65 ~~l~~G~~l~~~~~~~~~~~~~~~~~v~ 92 (144)
+.|+.||.+..++-+-.-++..+|..|.
T Consensus 6 ~~vRSGq~i~~~gdvvilGdVn~GA~V~ 33 (105)
T PF03775_consen 6 RTVRSGQEIEADGDVVILGDVNPGAEVI 33 (105)
T ss_dssp S-B-TTEEEEESSEEEESS-B-TT-EEE
T ss_pred CCccCCCEEEECCCEEEEccCCCCCEEE
Confidence 4577888888776544456667775443
Done!