Query psy6779
Match_columns 144
No_of_seqs 173 out of 1134
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 18:11:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6779.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6779hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0566 SpoU rRNA methylases [ 100.0 1.4E-36 3.1E-41 235.7 13.6 135 10-144 16-157 (260)
2 PRK11181 23S rRNA (guanosine-2 100.0 1.6E-32 3.6E-37 211.3 11.4 129 16-144 3-143 (244)
3 PRK10864 putative methyltransf 100.0 6.2E-31 1.3E-35 210.3 11.2 132 12-144 105-245 (346)
4 TIGR00186 rRNA_methyl_3 rRNA m 100.0 1E-30 2.2E-35 200.6 11.5 126 16-144 2-138 (237)
5 KOG2506|consensus 100.0 4E-30 8.7E-35 200.2 8.9 141 4-144 115-265 (371)
6 PRK10358 putative rRNA methyla 99.7 3.6E-17 7.9E-22 118.5 4.4 46 97-143 2-47 (157)
7 KOG0838|consensus 99.6 4.3E-16 9.3E-21 119.1 7.8 116 14-144 41-159 (271)
8 TIGR00185 rRNA_methyl_2 rRNA m 99.6 3.4E-16 7.3E-21 113.0 4.2 47 98-144 3-49 (153)
9 PF00588 SpoU_methylase: SpoU 99.6 2.4E-16 5.2E-21 111.9 2.6 49 96-144 1-50 (142)
10 PF08032 SpoU_sub_bind: RNA 2' 99.6 3.1E-15 6.6E-20 95.4 5.1 69 17-85 1-75 (76)
11 PRK11081 tRNA guanosine-2'-O-m 99.4 8.7E-13 1.9E-17 100.8 5.3 49 94-144 17-65 (229)
12 PRK15114 tRNA (cytidine/uridin 99.3 1.6E-12 3.5E-17 100.3 4.5 47 97-144 5-51 (245)
13 TIGR00050 rRNA_methyl_1 RNA me 99.2 7.1E-12 1.5E-16 96.1 4.4 47 97-144 4-50 (233)
14 PRK10433 putative RNA methyltr 98.6 7.3E-08 1.6E-12 73.8 4.3 42 97-139 3-44 (228)
15 COG0219 CspR Predicted rRNA me 97.7 4.7E-05 1E-09 54.7 4.4 47 97-143 3-49 (155)
16 PF04705 TSNR_N: Thiostrepton- 97.3 0.0008 1.7E-08 45.1 5.4 79 7-85 23-105 (115)
17 COG0565 LasT rRNA methylase [T 94.5 0.051 1.1E-06 42.0 3.7 43 97-140 5-47 (242)
18 PRK01018 50S ribosomal protein 94.4 0.17 3.7E-06 33.7 5.8 67 16-83 16-90 (99)
19 PF01248 Ribosomal_L7Ae: Ribos 94.1 0.18 4E-06 32.8 5.4 65 17-82 16-88 (95)
20 PTZ00106 60S ribosomal protein 91.5 1.1 2.4E-05 30.4 6.4 67 16-83 25-99 (108)
21 PRK07283 hypothetical protein; 91.4 0.66 1.4E-05 30.8 5.2 64 16-82 18-88 (98)
22 PRK07714 hypothetical protein; 91.2 0.85 1.9E-05 30.3 5.6 65 16-82 18-89 (100)
23 PRK13600 putative ribosomal pr 90.7 1 2.2E-05 29.2 5.4 64 15-79 12-82 (84)
24 KOG0839|consensus 90.4 0.28 6.1E-06 45.4 3.4 36 94-129 1324-1359(1477)
25 TIGR03677 rpl7ae 50S ribosomal 89.6 1.4 3E-05 30.2 5.7 66 16-82 26-99 (117)
26 PRK05583 ribosomal protein L7A 89.6 1.3 2.9E-05 29.7 5.5 65 16-82 17-88 (104)
27 PRK13601 putative L7Ae-like ri 89.2 2 4.3E-05 27.7 5.8 63 16-79 8-77 (82)
28 PRK04175 rpl7ae 50S ribosomal 89.1 1.6 3.5E-05 30.2 5.7 66 16-82 30-103 (122)
29 PRK13602 putative ribosomal pr 88.7 1.8 3.9E-05 27.8 5.4 63 16-79 11-80 (82)
30 PRK06683 hypothetical protein; 88.0 2.4 5.3E-05 27.2 5.7 63 16-79 11-80 (82)
31 TIGR00111 pelota probable tran 76.3 6.8 0.00015 31.9 5.3 65 15-83 276-350 (351)
32 PTZ00222 60S ribosomal protein 70.5 18 0.0004 28.3 6.1 70 13-84 129-206 (263)
33 COG1303 Uncharacterized protei 68.8 3.7 8E-05 30.0 1.9 17 115-131 25-41 (179)
34 COG1358 RPL8A Ribosomal protei 67.5 18 0.0004 24.8 5.0 56 16-72 27-90 (116)
35 COG2106 Uncharacterized conser 65.4 6.8 0.00015 30.9 2.9 25 108-132 26-50 (272)
36 COG3426 Butyrate kinase [Energ 61.8 7.6 0.00017 31.2 2.6 34 104-137 103-138 (358)
37 PF03465 eRF1_3: eRF1 domain 3 55.9 18 0.00038 24.5 3.3 27 15-42 20-46 (113)
38 COG4080 SpoU rRNA Methylase fa 53.7 18 0.00039 25.8 3.1 34 96-129 2-35 (147)
39 PLN03033 2-dehydro-3-deoxyphos 52.6 19 0.00041 28.7 3.4 21 110-130 222-242 (290)
40 PF07071 DUF1341: Protein of u 52.6 11 0.00023 28.7 1.9 22 105-126 186-207 (218)
41 TIGR03676 aRF1/eRF1 peptide ch 52.6 19 0.00041 30.0 3.6 27 15-42 287-313 (403)
42 KOG3361|consensus 52.3 3.2 7E-05 29.3 -0.8 22 100-121 33-54 (157)
43 PRK09190 hypothetical protein; 49.3 55 0.0012 25.0 5.4 65 16-82 111-188 (220)
44 PF13653 GDPD_2: Glycerophosph 49.0 23 0.00051 18.3 2.3 17 111-127 10-26 (30)
45 COG1537 PelA Predicted RNA-bin 46.2 50 0.0011 27.1 4.9 64 13-83 269-350 (352)
46 PRK03958 tRNA 2'-O-methylase; 45.7 19 0.0004 26.7 2.3 18 112-129 21-38 (176)
47 PRK12457 2-dehydro-3-deoxyphos 43.4 26 0.00055 27.9 2.8 34 97-130 192-239 (281)
48 TIGR01362 KDO8P_synth 3-deoxy- 42.6 26 0.00057 27.5 2.8 32 99-130 178-223 (258)
49 TIGR03581 EF_0839 conserved hy 42.0 19 0.00042 27.7 1.9 21 106-126 187-207 (236)
50 KOG2869|consensus 42.0 34 0.00073 28.0 3.3 66 16-88 291-374 (379)
51 cd00884 beta_CA_cladeB Carboni 41.7 1.1E+02 0.0025 22.6 6.0 23 109-131 73-95 (190)
52 PF02598 Methyltrn_RNA_3: Puta 40.9 26 0.00057 27.8 2.6 21 110-130 24-44 (291)
53 COG2877 KdsA 3-deoxy-D-manno-o 40.8 24 0.00052 27.6 2.3 37 101-138 198-245 (279)
54 PRK12703 tRNA 2'-O-methylase; 39.8 21 0.00045 29.1 1.9 18 113-130 21-38 (339)
55 KOG0053|consensus 37.7 41 0.00088 28.2 3.3 56 48-103 136-199 (409)
56 TIGR00259 thylakoid_BtpA membr 37.0 43 0.00092 26.3 3.2 35 106-140 155-191 (257)
57 PRK05198 2-dehydro-3-deoxyphos 36.6 32 0.0007 27.1 2.4 21 110-130 211-231 (264)
58 COG1087 GalE UDP-glucose 4-epi 35.8 1.4E+02 0.003 24.3 5.9 95 20-132 13-120 (329)
59 COG5016 Pyruvate/oxaloacetate 35.7 38 0.00081 28.6 2.8 41 95-135 112-152 (472)
60 PF07577 DUF1547: Domain of Un 35.2 28 0.00061 21.0 1.5 24 107-130 25-49 (58)
61 PRK06852 aldolase; Validated 34.2 60 0.0013 26.1 3.7 28 104-131 55-82 (304)
62 PF04665 Pox_A32: Poxvirus A32 32.6 47 0.001 25.7 2.8 49 94-144 97-149 (241)
63 cd02120 PA_subtilisin_like PA_ 32.3 1.2E+02 0.0027 20.0 4.6 35 95-130 51-85 (126)
64 PTZ00365 60S ribosomal protein 32.2 80 0.0017 24.9 4.0 68 14-83 130-205 (266)
65 COG4075 Uncharacterized conser 31.9 43 0.00093 22.5 2.1 26 104-129 10-35 (110)
66 COG1373 Predicted ATPase (AAA+ 31.4 78 0.0017 26.2 4.0 43 96-138 95-137 (398)
67 COG2086 FixA Electron transfer 31.3 40 0.00087 26.5 2.2 22 109-130 67-88 (260)
68 TIGR02845 spore_V_AD stage V s 31.1 30 0.00064 28.1 1.5 18 102-119 188-205 (327)
69 PRK12404 stage V sporulation p 30.0 32 0.00069 28.0 1.5 18 102-119 192-209 (334)
70 PF07451 SpoVAD: Stage V sporu 28.6 42 0.00091 27.2 1.9 18 102-119 189-206 (329)
71 cd04819 PA_2 PA_2: Protease-as 27.9 1.3E+02 0.0029 20.4 4.2 34 96-129 45-78 (127)
72 PF02225 PA: PA domain; Inter 27.3 1.5E+02 0.0032 18.6 4.2 32 96-129 34-65 (101)
73 KOG3925|consensus 27.1 32 0.0007 28.3 1.1 35 108-142 90-124 (371)
74 PRK12595 bifunctional 3-deoxy- 26.9 1.4E+02 0.0029 24.6 4.7 35 99-134 290-327 (360)
75 PF13380 CoA_binding_2: CoA bi 26.5 54 0.0012 22.0 2.0 27 104-130 62-88 (116)
76 PF13173 AAA_14: AAA domain 26.5 1.3E+02 0.0028 20.1 3.9 36 95-130 61-97 (128)
77 PRK13397 3-deoxy-7-phosphohept 26.0 72 0.0016 24.9 2.8 19 112-130 203-221 (250)
78 PRK08304 stage V sporulation p 26.0 41 0.0009 27.4 1.5 18 102-119 194-211 (337)
79 PF13605 DUF4141: Domain of un 25.6 45 0.00097 19.9 1.2 13 104-116 24-37 (55)
80 PF12696 TraG-D_C: TraM recogn 25.6 1.1E+02 0.0025 20.5 3.5 35 96-130 1-38 (128)
81 cd02133 PA_C5a_like PA_C5a_lik 25.1 2.1E+02 0.0045 19.7 4.8 34 96-131 48-81 (143)
82 PF13242 Hydrolase_like: HAD-h 25.0 84 0.0018 19.0 2.5 30 97-133 24-54 (75)
83 PF14572 Pribosyl_synth: Phosp 24.9 1.1E+02 0.0024 22.8 3.5 31 96-128 84-117 (184)
84 cd01988 Na_H_Antiporter_C The 24.4 1.1E+02 0.0023 19.9 3.2 27 111-137 84-110 (132)
85 cd01294 DHOase Dihydroorotase 24.1 1E+02 0.0022 24.4 3.5 28 103-131 12-39 (335)
86 PRK12723 flagellar biosynthesi 24.0 77 0.0017 26.3 2.8 34 96-129 288-321 (388)
87 TIGR01361 DAHP_synth_Bsub phos 24.0 71 0.0015 24.9 2.4 20 111-130 212-231 (260)
88 PF03184 DDE_1: DDE superfamil 23.5 51 0.0011 23.8 1.5 43 94-137 115-157 (217)
89 PRK06731 flhF flagellar biosyn 23.1 82 0.0018 24.7 2.7 38 96-133 187-225 (270)
90 PF14443 DBC1: DBC1 22.8 58 0.0013 22.8 1.5 22 101-123 30-57 (126)
91 cd04816 PA_SaNapH_like PA_SaNa 22.7 2.3E+02 0.0049 18.9 4.6 35 95-131 43-77 (122)
92 PRK08673 3-deoxy-7-phosphohept 22.5 78 0.0017 25.8 2.5 20 111-130 280-299 (335)
93 PRK13398 3-deoxy-7-phosphohept 22.4 83 0.0018 24.6 2.5 21 110-130 213-233 (266)
94 COG1083 NeuA CMP-N-acetylneura 21.9 48 0.001 25.5 1.1 34 22-56 33-67 (228)
95 PRK12724 flagellar biosynthesi 21.6 92 0.002 26.4 2.8 34 96-129 335-368 (432)
96 cd05016 SIS_PGI_2 Phosphogluco 21.1 67 0.0015 23.2 1.7 21 94-115 111-131 (164)
97 cd00564 TMP_TenI Thiamine mono 21.0 1.9E+02 0.0042 20.3 4.2 29 100-128 4-32 (196)
98 cd02124 PA_PoS1_like PA_PoS1_l 20.8 2.9E+02 0.0063 18.9 5.0 34 96-131 56-89 (129)
99 cd06308 PBP1_sensor_kinase_lik 20.7 1E+02 0.0022 22.9 2.7 18 111-128 71-88 (270)
100 PF13407 Peripla_BP_4: Peripla 20.6 98 0.0021 22.8 2.6 33 98-130 31-64 (257)
No 1
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-36 Score=235.72 Aligned_cols=135 Identities=26% Similarity=0.443 Sum_probs=118.3
Q ss_pred hhhcCCEEEEeHHHHHHHHHcCCceeEEEEecccc--ccc---CCCCCCCCEEEeCHHHHHhhcCCCCCCceEEEEeCCC
Q psy6779 10 REKKGWLMLEGKRILIDALKANLKLKMVFFSQWDI--LKE---LPLPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFELPA 84 (144)
Q Consensus 10 R~~~~~~~v~G~~~v~eal~~~~~i~~l~~~~~~~--~~~---l~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~ 84 (144)
|+++++|++||.|+|+++++++..+.++|+++... +.+ .+...+++++.++++.+++++++.+|||++|+++++.
T Consensus 16 r~~~~~~~~~G~~~v~~al~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~~~hqGi~a~~~~~~ 95 (260)
T COG0566 16 RGRAGEFLIEGEHAVLEALASGPKIVRILVTEGRLPRFEELLALAAAKGIPVYVVSEAILDKLSGTENHQGIVAVVKKRR 95 (260)
T ss_pred hcccCcEEEeeHHHHHHHHhcCCCceEEEEecccchhHHHHHHHHHhcCCeEEEECHHHHHHHhCCCCCCeEEEEEeccc
Confidence 78889999999999999999998999999998743 222 2345689999999999999999999999999999988
Q ss_pred CCCCC-CCC-CCCCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 85 HPIAS-IDP-ASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 85 ~~~~~-~~~-~~~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
+...+ ... ..++++|+||+||||||+|||||||+|||+++||++++|+|+|||+++|+||
T Consensus 96 ~~~~~~~~~~~~~~l~lvLd~V~DP~NlGaIiRtA~a~Gv~~Vi~~~~~~~~~~~~v~r~s~ 157 (260)
T COG0566 96 YPLLDDLLDAEAQPLLLVLDGVTDPHNLGAIIRTADAFGVDGVILPKRRADPLNPKVIRASA 157 (260)
T ss_pred ccchhhhhhcccCCEEEEEecCcCCcchhhHHhhHHHhCCCEEEECCCccCCccceeEEecC
Confidence 65322 111 2468999999999999999999999999999999999999999999999997
No 2
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=99.98 E-value=1.6e-32 Score=211.33 Aligned_cols=129 Identities=16% Similarity=0.210 Sum_probs=107.0
Q ss_pred EEEEeHHHHHHHHHcC-CceeEEEEeccc---cccc---CCCCCCCCEEEeCHHHHHhhcCCCCCCceEEEEeCCCC---
Q psy6779 16 LMLEGKRILIDALKAN-LKLKMVFFSQWD---ILKE---LPLPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFELPAH--- 85 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~-~~i~~l~~~~~~---~~~~---l~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~--- 85 (144)
.++||.|+|+|+|+++ ..++++|++++. .+.+ .+.+.+++++.++++.|++++++.+|||++|+++++.+
T Consensus 3 ~~i~G~~~v~eal~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~v~~~~l~~ls~~~~~qGv~a~~~~~~~~~~ 82 (244)
T PRK11181 3 EIIYGIHAVQALLERAPERFIEVFVLKGREDKRLLPLINELEAQGIVIQLANRQTLDEKAEGAVHQGIIARVKPGRQLQE 82 (244)
T ss_pred cEEEehHHHHHHHhCCCCceeEEEEECCCcchHHHHHHHHHHHcCCcEEEeCHHHHhhhhcCCCCceEEEEEecccccch
Confidence 4789999999999864 688999997652 1222 23345899999999999999999999999999987543
Q ss_pred -CCCCCC-CCCCCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 86 -PIASID-PASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 86 -~~~~~~-~~~~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
++.+.. ....+++++||+||||||+|||+|||+|||+++||++++++++|+|+++|+||
T Consensus 83 ~~~~~~~~~~~~~~~lvLd~v~dp~NlGai~Rta~a~G~~~vi~~~~~~~~~~~~~~r~s~ 143 (244)
T PRK11181 83 NDLPDLLASLEQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVAC 143 (244)
T ss_pred hhHHHHHhcCCCCEEEEEcCCCCcchHHHHHHHHHHcCCCEEEECCCCCCCCCCceEEecC
Confidence 111211 12457899999999999999999999999999999999999999999999997
No 3
>PRK10864 putative methyltransferase; Provisional
Probab=99.97 E-value=6.2e-31 Score=210.33 Aligned_cols=132 Identities=17% Similarity=0.195 Sum_probs=107.6
Q ss_pred hcCCEEEEeHHHHHHHHHcC-CceeEEEEeccc--ccc---cCCCCCCCCEEEeCHHHHHhhcCCCCCCceEEEEeCCCC
Q psy6779 12 KKGWLMLEGKRILIDALKAN-LKLKMVFFSQWD--ILK---ELPLPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFELPAH 85 (144)
Q Consensus 12 ~~~~~~v~G~~~v~eal~~~-~~i~~l~~~~~~--~~~---~l~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~ 85 (144)
....++|||.|+|.|+|+++ ..+.++|+.++. .+. .++...+++++.+++++|++++++.+||||+|+++.+.+
T Consensus 105 ~~~~~~I~G~~aV~ealk~~~~~i~~l~~~~~~~~~~~~il~~~~~~~~~v~~V~~~~l~kls~~~~hqGV~A~v~~~~~ 184 (346)
T PRK10864 105 RAEETRVYGENACQALFQSRPEAIVRAWFIQSVTPRFKEALRWMAANRKAYHVVDEAELTKASGTEHHGGVCFLIKKRNG 184 (346)
T ss_pred cCCCcEEEEHHHHHHHHhCCCCceeEEEEecCccHHHHHHHHHHHHcCCcEEEeCHHHHHHHhCCCCCCeEEEEEeCCCC
Confidence 34468999999999999985 578999998652 122 223345789999999999999999999999999998754
Q ss_pred -CCCCCCC--CCCCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 86 -PIASIDP--ASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 86 -~~~~~~~--~~~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
++.+++. ...+++|+||+||||+|+|||+|||+|||+++||+++. +++++++++|+||
T Consensus 185 ~~l~~~l~~~~~~~~vlvLd~I~DP~NlGaIiRTA~afGv~~Vil~~~-~~~~~~kvvRaS~ 245 (346)
T PRK10864 185 TDVQQWLAQAGAQDCVLALEDVGNPHNLGGIMRSCAHFGVKGVVVQDA-ALLESGAAIRTAE 245 (346)
T ss_pred CCHHHHhhccccCCeEEEEeCCCCCCcHHHHHHHHHHhCCCEEEECCC-CCCCchhHHHHhc
Confidence 3222211 23468999999999999999999999999999999875 5889999999986
No 4
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=99.97 E-value=1e-30 Score=200.64 Aligned_cols=126 Identities=21% Similarity=0.309 Sum_probs=102.5
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEecc---c---ccccCCCCCCCCEEEeCHHHHHhhcCCCCCCceEEEEeCCCC-CCC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQW---D---ILKELPLPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFELPAH-PIA 88 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~---~---~~~~l~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~-~~~ 88 (144)
++|||.|+|+||++++. ++|+... . .+.+++.+.+++++.++++.|++++++.+|||++|+++.+.+ ++.
T Consensus 2 ~~i~G~~~v~eal~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~~~~~ 78 (237)
T TIGR00186 2 EYLYGKNAVLEALLNQQ---RVFILKGLESKRLKKLIQLAKKQGINIQLVDRQKLDQLTKGGNHQGIAAKVKPILYKDLN 78 (237)
T ss_pred cEEEehHHHHHHHhCCC---EEEEEecCcchHHHHHHHHHHHcCCcEEEeCHHHHHHHhCCCCCCeEEEEEecCCCCCHH
Confidence 57899999999999883 3444321 1 122233455799999999999999999999999999988764 322
Q ss_pred CCC----CCCCCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 89 SID----PASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 89 ~~~----~~~~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
++. ....+++++||+|+||+|+|||+|||+|||+++||+++++++||+|+++|+||
T Consensus 79 ~~~~~~~~~~~~~~lvLd~v~dp~NlGaI~Rta~afG~~~vil~~~~~~~~~~~~~r~s~ 138 (237)
T TIGR00186 79 DLYKTAKSKKQPFLLILDEITDPHNLGAILRTAEAFGVDGVILPKRRSAPLNSTVVKTSS 138 (237)
T ss_pred HHHHhhhccCCCEEEEEcCCCCCccHHHHHHHHHHcCCCEEEECCCCcCCCCCceeeeec
Confidence 221 12347899999999999999999999999999999999999999999999997
No 5
>KOG2506|consensus
Probab=99.96 E-value=4e-30 Score=200.18 Aligned_cols=141 Identities=37% Similarity=0.644 Sum_probs=120.6
Q ss_pred cccchhhhhcCCEEEEeHHHHHHHHHcCCceeEEEEecccccccCC--CCCCCCEEEeCHHHHHhhcCCCCCCceEEEEe
Q psy6779 4 MKSRKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQWDILKELP--LPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFE 81 (144)
Q Consensus 4 L~~~k~R~~~~~~~v~G~~~v~eal~~~~~i~~l~~~~~~~~~~l~--~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~ 81 (144)
-++++||.++...+.+|+.++.++|+.+...+.++++....+..++ .+.++.++.++...++++++.++++|+.|+..
T Consensus 115 v~srsf~~kqv~ii~egRrliqdaLk~g~~~ev~~Fs~~~qla~~p~e~e~g~~i~kVks~d~K~wSsLvSP~svmaIf~ 194 (371)
T KOG2506|consen 115 VKSRSFREKQVRIISEGRRLIQDALKGGVHREVCMFSTNKQLATTPIECEAGIRIVKVKSLDMKKWSSLVSPESVMAIFL 194 (371)
T ss_pred eecccchhhcccccccchhhHHHHhhccccceEEEeeccccccccChhhhcCeeEEeccHHHHHHHhcccCCcchhhhcc
Confidence 5688999999999999999999999999777878887665444432 24589999999999999999999999999999
Q ss_pred CCCC--CCCCCC------CCCCCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 82 LPAH--PIASID------PASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 82 ~~~~--~~~~~~------~~~~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
+|-. ...++. ...-|.+|+||+|+||||+|||+|||+|||+++|+++++|||||++|++||++
T Consensus 195 ~P~d~hl~k~~a~~q~~~s~~lp~~lvcdnirdpgnlgti~rsaaa~~cs~v~lt~gccdpwe~kalrag~ 265 (371)
T KOG2506|consen 195 MPIDLHLDKDIATDQNKWSPSLPRVLVCDNIRDPGNLGTIVRSAAAFNCSGVFLTPGCCDPWEDKALRAGR 265 (371)
T ss_pred CcchhchhhhHHHHHhccCCCCCeEEEeccCCCCcchHHHHHHHhhCCCcceeecCCcCCccchhhhhccC
Confidence 8842 111111 23457899999999999999999999999999999999999999999999986
No 6
>PRK10358 putative rRNA methylase; Provisional
Probab=99.67 E-value=3.6e-17 Score=118.47 Aligned_cols=46 Identities=37% Similarity=0.482 Sum_probs=42.1
Q ss_pred eEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeecc
Q psy6779 97 LNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAA 143 (144)
Q Consensus 97 ~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS 143 (144)
+-++||++|||||+|||+|||+|||++.+|+.+ ++|+||||++|++
T Consensus 2 ~~ivL~~~~dPgNlGti~Rta~a~G~~~viv~~-~~d~~~~k~~raa 47 (157)
T PRK10358 2 LNIVLFEPEIPPNTGNIIRLCANTGFRLHIIEP-MGFAWDDKRLRRA 47 (157)
T ss_pred eEEEEeCCCCcChHHHHHHHHHHhCCEEEEECC-CCCCCChHHHHhc
Confidence 458999999999999999999999999999976 5699999999975
No 7
>KOG0838|consensus
Probab=99.65 E-value=4.3e-16 Score=119.12 Aligned_cols=116 Identities=21% Similarity=0.265 Sum_probs=96.6
Q ss_pred CCEEEEeHHHHHHHHHcC-CceeEEEEecccccc--cCCCCCCCCEEEeCHHHHHhhcCCCCCCceEEEEeCCCCCCCCC
Q psy6779 14 GWLMLEGKRILIDALKAN-LKLKMVFFSQWDILK--ELPLPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFELPAHPIASI 90 (144)
Q Consensus 14 ~~~~v~G~~~v~eal~~~-~~i~~l~~~~~~~~~--~l~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~~~~~~ 90 (144)
+--.++|.+++.+++..+ ..++..|+....++. ++..-....+..++++.|+.++++..|||++....
T Consensus 41 ~~e~~~G~~sv~~al~~~kR~~~~~~~~~~~~~~~~e~~~v~~~~~~~~s~h~L~~~t~~r~h~g~~leas--------- 111 (271)
T KOG0838|consen 41 GGESVFGTHSVLAALSNGKRDCRGLLLQSATDFRSTEFELVLRRDIEAVSKHDLNSLTDFRPHNGILLEAS--------- 111 (271)
T ss_pred ccceeechhhhHHHHhcccccceeeeeccccccCcceeeehhhhhhhccChhhHHHHHhhccccceEEeeE---------
Confidence 445799999999999998 468888887632221 22111123677899999999999999999998875
Q ss_pred CCCCCCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 91 DPASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 91 ~~~~~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
+++.||+++||+|+|+|+|+|++||++++.+.++...+.+|.+.++||
T Consensus 112 ------l~vylde~tDp~n~gaI~rsA~~lg~~~v~lv~~n~s~lS~~vskss~ 159 (271)
T KOG0838|consen 112 ------LCVYLDEVTDPQNIGAIIRSAYFLGADGVLLVKGNSSPLSPVVSKSSA 159 (271)
T ss_pred ------EEeeccCccCCcchHHHHHhHHHhcCCceEEEeccCCCCchhHHHhhh
Confidence 689999999999999999999999999999999888999999999886
No 8
>TIGR00185 rRNA_methyl_2 rRNA methylase, putative, group 2. this is part of the trmH (spoU) family of rRNA methylases
Probab=99.62 E-value=3.4e-16 Score=112.96 Aligned_cols=47 Identities=34% Similarity=0.385 Sum_probs=43.1
Q ss_pred EEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 98 NIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 98 ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
-++||++|||+|+|||+|||+|||++++|+.+++.++.++++.|+||
T Consensus 3 ~vvL~~v~dP~NlG~iiRta~afGv~~vi~~~~~~~~~~~~~~ra~~ 49 (153)
T TIGR00185 3 NIVLYEPEIPPNTGNIARTCAATGTRLHLIEPLGFFLDDKRLKRAGL 49 (153)
T ss_pred EEEEcCCCCCChHHHHHHHHHHhCCEEEEECCCCCCCccHHHHhhcc
Confidence 58999999999999999999999999999988888888888889875
No 9
>PF00588 SpoU_methylase: SpoU rRNA Methylase family; InterPro: IPR001537 The spoU gene of Escherichia coli codes for a protein that shows strong similarities to previously characterised 2'-O-methyltransferases [, ]. The Pet56 protein of Saccharomyces cerevisiae has been shown to be required for ribose methylation at a universally conserved nucleotide in the peptidyl transferase centre of the mitochondrial large ribosomal RNA (21S rRNA). Cells reduced in this activity were deficient in formation of functional large subunits of the mitochondrial ribosome. The Pet56 protein catalyzes the site-specific formation of 2'-O-methylguanosine on in vitro transcripts of both mitochondrial 21S rRNA and E. coli 23S rRNA providing evidence for an essential modified nucleotide in rRNA [].; GO: 0003723 RNA binding, 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 3N4J_A 3N4K_A 1IPA_A 3ONP_A 3NK6_A 3NK7_A 3IC6_A 1GZ0_D 1MXI_A 1J85_A ....
Probab=99.61 E-value=2.4e-16 Score=111.91 Aligned_cols=49 Identities=47% Similarity=0.797 Sum_probs=45.1
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcC-CccCCCCcceeeccC
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSR-GCVDIYDNKVIRAAA 144 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~-~~~d~~~pkviRaS~ 144 (144)
+++++||+++||+|+|+|+|||++||+++|++.+ ++.|+++++++|+|+
T Consensus 1 ~l~vvl~~~~~p~NlG~i~Rta~afG~~~v~l~~~~~~~~~~~~~~r~s~ 50 (142)
T PF00588_consen 1 MLIVVLDNVQDPGNLGAIIRTAAAFGVDGVILVGPRCADPYNPKVLRASA 50 (142)
T ss_dssp SEEEEEES-SSHHHHHHHHHHHHHTTESEEEEESSSSSTTTSHHHHHHTT
T ss_pred CEEEEEeCCCCcCcHHHHHHHHHHhCCchhheeccccccccccccccccC
Confidence 4789999999999999999999999999999966 888999999999986
No 10
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=99.57 E-value=3.1e-15 Score=95.39 Aligned_cols=69 Identities=22% Similarity=0.395 Sum_probs=53.4
Q ss_pred EEEeHHHHHHHHHcCCceeEEEEeccc---c---cccCCCCCCCCEEEeCHHHHHhhcCCCCCCceEEEEeCCCC
Q psy6779 17 MLEGKRILIDALKANLKLKMVFFSQWD---I---LKELPLPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFELPAH 85 (144)
Q Consensus 17 ~v~G~~~v~eal~~~~~i~~l~~~~~~---~---~~~l~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~ 85 (144)
+|||.|+|.|||+++..++++|++++. . +.+.+.+.+++++.+|++.|++++++.+||||+|+++++++
T Consensus 1 lieG~~~V~eaL~~~~~i~~l~~~~~~~~~~~~~i~~~~~~~~i~v~~v~~~~l~~ls~~~~hQGv~a~v~~~~~ 75 (76)
T PF08032_consen 1 LIEGRHAVEEALKSGPRIKKLFVTEEKADKRIKEILKLAKKKGIPVYEVSKKVLDKLSDTENHQGVVAVVKPPQY 75 (76)
T ss_dssp EEESHHHHHHHHHCTGGEEEEEEETT---CCTHHHHHHHHHCT-EEEEE-HHHHHHCTTTSS-TTEEEEEE----
T ss_pred CEEEHHHHHHHHcCCCCccEEEEEcCccchhHHHHHHHHHHcCCeEEEeCHHHHHHHcCCCCCCeEEEEEeCCCC
Confidence 699999999999999779999999872 1 22334556899999999999999999999999999998875
No 11
>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional
Probab=99.36 E-value=8.7e-13 Score=100.85 Aligned_cols=49 Identities=22% Similarity=0.299 Sum_probs=37.7
Q ss_pred CCCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 94 SLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 94 ~~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
.++++|+||+|+||+|+|||+|||+|||++.|++..... -.+++.|+||
T Consensus 17 ~~~l~vvLd~V~~p~NlGAIiRta~AfGv~~V~~v~~~~--~~~~~~~~s~ 65 (229)
T PRK11081 17 QPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGS--RMRTMGSTAA 65 (229)
T ss_pred CCCeEEEEeCCCCcchHHHHHHHHHHhCCCeEEEecCCC--ccchhhhhcC
Confidence 456899999999999999999999999999996643211 1245556654
No 12
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional
Probab=99.31 E-value=1.6e-12 Score=100.34 Aligned_cols=47 Identities=28% Similarity=0.316 Sum_probs=43.2
Q ss_pred eEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 97 LNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 97 ~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
..+||+++|||||+|||+|+|++||++++++.+.+++++++ ++|+||
T Consensus 5 i~vVLv~~~~pgNiGaiaRa~~~fG~~~l~lv~p~~~~~~~-a~~~a~ 51 (245)
T PRK15114 5 IRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQ-AIALAA 51 (245)
T ss_pred eEEEEeCCCCCCcHHHHHHHHHhcCCCEEEEeCCCCCCcCH-HHHHcC
Confidence 67999999999999999999999999999999999999877 777764
No 13
>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1. This is part of the trmH (spoU) family of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and is now characterized, in E. coli, as a tRNA:Cm32/Um32 methyltransferase. It may be named TrMet(Xm32), or TrmJ, according to the nomenclature style chosen
Probab=99.24 E-value=7.1e-12 Score=96.13 Aligned_cols=47 Identities=23% Similarity=0.306 Sum_probs=43.8
Q ss_pred eEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 97 LNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 97 ~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
..++|++++||+|+|+|+|+|++||++.+++.+.+++ +++++.|+|+
T Consensus 4 i~vvL~~~~~p~NiGaiaR~~~~fG~~~l~lv~p~~~-~~~~a~~~a~ 50 (233)
T TIGR00050 4 IRIVLVEPSHSGNIGSIARAMKNMGLTELCLVNPKSH-LEEEAYALAA 50 (233)
T ss_pred eEEEEECCCCCCCHHHHHHHHHhCCCCEEEEeCCCcC-CCHHHHHHhC
Confidence 5799999999999999999999999999999988877 8999999875
No 14
>PRK10433 putative RNA methyltransferase; Provisional
Probab=98.56 E-value=7.3e-08 Score=73.76 Aligned_cols=42 Identities=14% Similarity=0.206 Sum_probs=35.3
Q ss_pred eEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcce
Q psy6779 97 LNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKV 139 (144)
Q Consensus 97 ~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkv 139 (144)
+.+||++++||+|+|++.|++..||++.+++.+.+..+ ++.+
T Consensus 3 i~vVLv~p~~p~NiGaiaRam~nfG~~~L~lV~p~~~~-~~~a 44 (228)
T PRK10433 3 LTIILVAPARAENVGAAARAMKTMGFSELRIVDSQAHL-EPAA 44 (228)
T ss_pred eEEEEEcCCCCccHHHHHHHHHHCCCCEEEEeCCCCCC-cHHH
Confidence 57899999999999999999999999999998655432 4443
No 15
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=97.74 E-value=4.7e-05 Score=54.69 Aligned_cols=47 Identities=38% Similarity=0.496 Sum_probs=37.3
Q ss_pred eEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeecc
Q psy6779 97 LNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAA 143 (144)
Q Consensus 97 ~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS 143 (144)
+-++|-+-+-|.|.|+|+|+|+++|+.-.++-+-.-+.-..+.-||.
T Consensus 3 ~~IvL~~PeIP~NTGNI~R~ca~tga~LhlI~PlGF~l~dk~lkRAG 49 (155)
T COG0219 3 LNIVLYQPEIPPNTGNIIRTCAATGAELHLIEPLGFDLDDKRLKRAG 49 (155)
T ss_pred cEEEEECCCCCCchhHHHHHHHhcCCeEEEEccCCCccchhhhhhcc
Confidence 46889999999999999999999999998887655444444455544
No 16
>PF04705 TSNR_N: Thiostrepton-resistance methylase, N terminus; InterPro: IPR006795 This region is found in some members of the SpoU-type rRNA methylase family (IPR001537 from INTERPRO).; GO: 0008649 rRNA methyltransferase activity, 0046677 response to antibiotic; PDB: 3GYQ_B 3NK6_A 3NK7_A.
Probab=97.29 E-value=0.0008 Score=45.05 Aligned_cols=79 Identities=18% Similarity=0.204 Sum_probs=59.0
Q ss_pred chhhhhcCCEEEEeHHHHHHHHHcCCceeEEEEeccc----ccccCCCCCCCCEEEeCHHHHHhhcCCCCCCceEEEEeC
Q psy6779 7 RKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQWD----ILKELPLPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFEL 82 (144)
Q Consensus 7 ~k~R~~~~~~~v~G~~~v~eal~~~~~i~~l~~~~~~----~~~~l~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~ 82 (144)
|+.|..-...+||...++.+.+.+|..+-.+|.++.. ++..+|.++++++..++..+++++..++....++++..-
T Consensus 23 k~sRs~ikT~LIED~EPL~~~i~AGvefieVYg~~~~p~~~~ll~~c~~r~Ipvrlv~~~v~N~lFk~erK~k~fGiArv 102 (115)
T PF04705_consen 23 KHSRSNIKTTLIEDPEPLTHSIRAGVEFIEVYGSDGSPVPPELLAACRQRGIPVRLVDSAVVNQLFKGERKPKVFGIARV 102 (115)
T ss_dssp CTSTTTTTEEEEESHHHHHHHHCTT-EEEEEEEETTS---CCCCHHHHCTT--EEEE-HHHHCCCS-SSS--SEEEEEE-
T ss_pred ccchhhheeeeecCchHHHHHHhcCcEEEEEeeecCCCCChHHHHHHHhcCCceEEecHHHHHHHHhcccccceeeeecC
Confidence 5667777889999999999999999888889988763 344557788999999999999999999999999999887
Q ss_pred CCC
Q psy6779 83 PAH 85 (144)
Q Consensus 83 ~~~ 85 (144)
|..
T Consensus 103 Prp 105 (115)
T PF04705_consen 103 PRP 105 (115)
T ss_dssp ---
T ss_pred CCC
Confidence 764
No 17
>COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=94.46 E-value=0.051 Score=42.02 Aligned_cols=43 Identities=23% Similarity=0.346 Sum_probs=34.9
Q ss_pred eEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCccee
Q psy6779 97 LNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVI 140 (144)
Q Consensus 97 ~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkvi 140 (144)
.-+||-+-+-|||+|++-|...=||.+.+++-..++. .++.+.
T Consensus 5 i~iVLVep~~~gNIG~vARaMKNfGl~eL~LV~Pr~~-~~eeA~ 47 (242)
T COG0565 5 IRIVLVEPSHPGNIGSVARAMKNFGLSELRLVNPRAG-LDEEAR 47 (242)
T ss_pred cEEEEEcCCCCccHHHHHHHHHhCCcceEEEECCCCC-CCHHHH
Confidence 4688999999999999999999999999999765554 344433
No 18
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=94.39 E-value=0.17 Score=33.71 Aligned_cols=67 Identities=12% Similarity=0.065 Sum_probs=50.3
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCCCCCCEEE--eCHHHHHhhcCCCCCCceEEEEeCC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLPEDVPQHR--VDYKNIQLWSDLVTPPGIIGIFELP 83 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~~~~~~~~--v~~~~l~~l~~~~~~qGv~a~~~~~ 83 (144)
-++.|.+.+..+++++. .+-+++.++. .+..+|...++|++. -+.+.|...++....-.++++.+.-
T Consensus 16 kl~~G~~~v~kai~~gk-aklViiA~D~~~~~~~~i~~~c~~~~Ip~~~~~~tk~eLG~a~Gk~~~~~~vaI~D~G 90 (99)
T PRK01018 16 KVILGSKRTIKAIKLGK-AKLVIVASNCPKDIKEDIEYYAKLSGIPVYEYEGSSVELGTLCGKPFTVSALAIVDPG 90 (99)
T ss_pred CEEEcHHHHHHHHHcCC-ceEEEEeCCCCHHHHHHHHHHHHHcCCCEEEECCCHHHHHHHhCCCCCEEEEEEecCC
Confidence 46999999999999864 5778887652 244456677899755 3999999999876556788887643
No 19
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [].; PDB: 2CZW_A 3V7E_B 2QEX_F 1YJ9_F 1VQ8_F 1YJN_F 3I56_F 1VQ6_F 2OTJ_F 1YIJ_F ....
Probab=94.11 E-value=0.18 Score=32.83 Aligned_cols=65 Identities=20% Similarity=0.237 Sum_probs=51.0
Q ss_pred EEEeHHHHHHHHHcCCceeEEEEeccc------c-cccCCCCCCCCEEEeCH-HHHHhhcCCCCCCceEEEEeC
Q psy6779 17 MLEGKRILIDALKANLKLKMVFFSQWD------I-LKELPLPEDVPQHRVDY-KNIQLWSDLVTPPGIIGIFEL 82 (144)
Q Consensus 17 ~v~G~~~v~eal~~~~~i~~l~~~~~~------~-~~~l~~~~~~~~~~v~~-~~l~~l~~~~~~qGv~a~~~~ 82 (144)
++.|.+-+.++++.+ ..+-+++.++. . +..++.++++|++.++. +.|.++.+......++++.+.
T Consensus 16 lv~G~~~v~k~l~~~-~~~lvilA~d~~~~~~~~~l~~~c~~~~Ip~~~~~s~~eLG~~~g~~~~~~~~~i~d~ 88 (95)
T PF01248_consen 16 LVKGIKEVLKALKKG-KAKLVILAEDCSPDSIKKHLPALCEEKNIPYVFVPSKEELGRACGKKRPVSALAIKDA 88 (95)
T ss_dssp EEESHHHHHHHHHTT-CESEEEEETTSSSGHHHHHHHHHHHHTTEEEEEESHHHHHHHHTTSSSTSSEEEEEES
T ss_pred EEEchHHHHHHHHcC-CCcEEEEcCCCChhhhcccchhheeccceeEEEECCHHHHHHHHCCCCcEEEEEEECc
Confidence 899999999999987 56777777652 1 33456677899998877 799999998877788877654
No 20
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=91.48 E-value=1.1 Score=30.37 Aligned_cols=67 Identities=13% Similarity=0.100 Sum_probs=48.5
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCCCCCCEE-E-eCHHHHHhhcCCCCCCceEEEEeCC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLPEDVPQH-R-VDYKNIQLWSDLVTPPGIIGIFELP 83 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~~~~~~~-~-v~~~~l~~l~~~~~~qGv~a~~~~~ 83 (144)
-++.|.+.+..+++.+ ..+.|++.++. ++..++...++|++ + -+.++|....+....-.++++.+.-
T Consensus 25 Klv~G~~~vlkalk~g-kaklViiA~D~~~~~kkki~~~~~~~~Vpv~~~~~t~~eLG~A~Gk~~r~svvaI~D~G 99 (108)
T PTZ00106 25 KYTLGTKSTLKALRNG-KAKLVIISNNCPPIRRSEIEYYAMLSKTGVHHYAGNNNDLGTACGRHFRVSVMSITDAG 99 (108)
T ss_pred CeeecHHHHHHHHHcC-CeeEEEEeCCCCHHHHHHHHHHHhhcCCCEEEeCCCHHHHHHHhCCccCeEEEEEeCcc
Confidence 3699999999999986 46778887652 24455667789986 3 7899999999854434467776543
No 21
>PRK07283 hypothetical protein; Provisional
Probab=91.40 E-value=0.66 Score=30.79 Aligned_cols=64 Identities=11% Similarity=0.205 Sum_probs=45.6
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCCCCCCEE-EeCHHHHHhhcCCCCCCceEEEEeC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLPEDVPQH-RVDYKNIQLWSDLVTPPGIIGIFEL 82 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~~~~~~~-~v~~~~l~~l~~~~~~qGv~a~~~~ 82 (144)
-++.|...|.++++++. .+-+++.++. .+.+.+...++|++ ..+.++|....+. +..++|+.+.
T Consensus 18 klv~G~~~v~~aik~gk-~~lVi~A~Das~~~~kk~~~~~~~~~Vp~~~~~t~~eLG~a~Gk--~~~vvai~d~ 88 (98)
T PRK07283 18 RIISGEELVVKAIQSGQ-AKLVFLANDAGPNLTKKVTDKSNYYQVEVSTVFSTLELSAAVGK--PRKVLAVTDA 88 (98)
T ss_pred CeeEcHHHHHHHHHcCC-ccEEEEeCCCCHHHHHHHHHHHHHcCCCEEEeCCHHHHHHHhCC--CceEEEEeCh
Confidence 36899999999999875 4667777652 23344555688875 5588899998886 3577777543
No 22
>PRK07714 hypothetical protein; Provisional
Probab=91.19 E-value=0.85 Score=30.29 Aligned_cols=65 Identities=9% Similarity=0.170 Sum_probs=45.6
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCCCCCCEE-EeCHHHHHhhcCCCCCCceEEEEeC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLPEDVPQH-RVDYKNIQLWSDLVTPPGIIGIFEL 82 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~~~~~~~-~v~~~~l~~l~~~~~~qGv~a~~~~ 82 (144)
-++.|.+.+.++++++. ++-+++.++. ++..+|...++|++ ..+.++|....+... ..++|+.+.
T Consensus 18 k~v~G~~~v~~al~~g~-~~lViiA~D~s~~~~~ki~~~~~~~~vp~~~~~sk~eLG~a~Gk~~-~~~vai~d~ 89 (100)
T PRK07714 18 KVISGEELVLKEVRSGK-AKLVLLSEDASVNTTKKITDKCTYYNVPMRKVENRQQLGHAIGKDE-RVVVAVLDE 89 (100)
T ss_pred CeeecHHHHHHHHHhCC-ceEEEEeCCCCHHHHHHHHHHHHhcCCCEEEeCCHHHHHHHhCCCc-ceEEEEeCc
Confidence 36899999999999874 5667776552 34445556678865 568889999988653 336666543
No 23
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=90.73 E-value=1 Score=29.25 Aligned_cols=64 Identities=9% Similarity=0.094 Sum_probs=47.3
Q ss_pred CEEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCCCCCCEEEeC-HHHHHhhcCCCCCCceEEE
Q psy6779 15 WLMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLPEDVPQHRVD-YKNIQLWSDLVTPPGIIGI 79 (144)
Q Consensus 15 ~~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~~~~~~~~v~-~~~l~~l~~~~~~qGv~a~ 79 (144)
..++.|.+-+..+++.+. .+.+|+..+. .+..+|.++++|+.+++ .+.|.+.++...+--.+|+
T Consensus 12 ~~~vvG~kqt~Kai~kg~-~~~v~iA~Da~~~vv~~l~~lceek~Ip~v~V~s~~~LGkAcgi~V~aa~aai 82 (84)
T PRK13600 12 QHFVVGLKETLKALKKDQ-VTSLIIAEDVEVYLMTRVLSQINQKNIPVSFFKSKHALGKHVGINVNATIVAL 82 (84)
T ss_pred cCceeeHHHHHHHHhcCC-ceEEEEeCCCCHHHHHHHHHHHHHcCCCEEEECCHHHHHHHhCCCcCeEEEEE
Confidence 467999999999999874 4668887653 24456778899998875 5689999987655444444
No 24
>KOG0839|consensus
Probab=90.45 E-value=0.28 Score=45.38 Aligned_cols=36 Identities=28% Similarity=0.524 Sum_probs=31.6
Q ss_pred CCCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcC
Q psy6779 94 SLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSR 129 (144)
Q Consensus 94 ~~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~ 129 (144)
...+|||--=|--|-|+|.|.|||+.||++-+++..
T Consensus 1324 rssLIVVASLVDKppNLgGicRTcEVFgvs~LvVad 1359 (1477)
T KOG0839|consen 1324 RSSLIVVASLVDKPPNLGGICRTCEVFGVSLLVVAD 1359 (1477)
T ss_pred ceeEEEEeecccCCCccchhhhhhhhhCcceEEEee
Confidence 456888888889999999999999999999988754
No 25
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=89.58 E-value=1.4 Score=30.24 Aligned_cols=66 Identities=15% Similarity=0.151 Sum_probs=49.0
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc-------ccccCCCCCCCCEEEe-CHHHHHhhcCCCCCCceEEEEeC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD-------ILKELPLPEDVPQHRV-DYKNIQLWSDLVTPPGIIGIFEL 82 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~-------~~~~l~~~~~~~~~~v-~~~~l~~l~~~~~~qGv~a~~~~ 82 (144)
-++.|.+.+..+++.+. .+-+++..+. ++..+|...++|+..+ +.+.|....+...+-.++|+.+.
T Consensus 26 kl~~G~~~v~kaikkgk-a~LVilA~D~s~~~~~~~i~~lc~~~~Ip~~~~~sk~eLG~a~Gk~~~~svvaI~d~ 99 (117)
T TIGR03677 26 KIKKGTNEVTKAVERGI-AKLVVIAEDVEPPEIVAHLPALCEEKGIPYVYVKKKEDLGAAAGLEVGAASAAIVDE 99 (117)
T ss_pred CEeEcHHHHHHHHHcCC-ccEEEEeCCCCcHHHHHHHHHHHHHcCCCEEEeCCHHHHHHHhCCCCCeEEEEEEch
Confidence 48999999999999874 4557776542 2334466678887654 77799999987777888888764
No 26
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=89.56 E-value=1.3 Score=29.74 Aligned_cols=65 Identities=15% Similarity=0.095 Sum_probs=45.8
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCCCCCCEE-EeCHHHHHhhcCCCCCCceEEEEeC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLPEDVPQH-RVDYKNIQLWSDLVTPPGIIGIFEL 82 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~~~~~~~-~v~~~~l~~l~~~~~~qGv~a~~~~ 82 (144)
-++.|...|+++++++. ++-|++.++. ++..++...++|++ ..+.++|....+... -.++|+.+.
T Consensus 17 klv~G~~~v~~aik~gk-~~lVI~A~D~s~~~kkki~~~~~~~~vp~~~~~t~~eLg~a~Gk~~-~~~iai~d~ 88 (104)
T PRK05583 17 KLLEGYNKCEEAIKKKK-VYLIIISNDISENSKNKFKNYCNKYNIPYIEGYSKEELGNAIGRDE-IKILGVKDK 88 (104)
T ss_pred CeeecHHHHHHHHHcCC-ceEEEEeCCCCHhHHHHHHHHHHHcCCCEEEecCHHHHHHHhCCCC-eEEEEEeCh
Confidence 36999999999999875 5656666542 34444555678864 578889999887543 667776654
No 27
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=89.15 E-value=2 Score=27.68 Aligned_cols=63 Identities=11% Similarity=0.084 Sum_probs=46.1
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCCCCCCEE-EeCHHHHHhhcCCCCCCceEEE
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLPEDVPQH-RVDYKNIQLWSDLVTPPGIIGI 79 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~~~~~~~-~v~~~~l~~l~~~~~~qGv~a~ 79 (144)
-++.|.+.+..+++++ ..+.+|+..+. .+..++...++|++ .-+.+.|.+..+...+--++|+
T Consensus 8 Klv~G~~~vlkaIk~g-kakLViiA~Da~~~~~k~i~~~c~~~~Vpv~~~~t~~eLG~A~G~~v~aa~~~~ 77 (82)
T PRK13601 8 KRVVGAKQTLKAITNC-NVLQVYIAKDAEEHVTKKIKELCEEKSIKIVYIDTMKELGVMCGIDVGAAAAAD 77 (82)
T ss_pred cEEEchHHHHHHHHcC-CeeEEEEeCCCCHHHHHHHHHHHHhCCCCEEEeCCHHHHHHHHCCccCeeeEEE
Confidence 4689999999999986 46778887652 34455677788884 4577899999887766555554
No 28
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=89.09 E-value=1.6 Score=30.20 Aligned_cols=66 Identities=17% Similarity=0.141 Sum_probs=49.2
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc-------ccccCCCCCCCCEEEe-CHHHHHhhcCCCCCCceEEEEeC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD-------ILKELPLPEDVPQHRV-DYKNIQLWSDLVTPPGIIGIFEL 82 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~-------~~~~l~~~~~~~~~~v-~~~~l~~l~~~~~~qGv~a~~~~ 82 (144)
-++.|.+.+..+++.+. .+-+++.++. .+..+|...++|+..+ +.+.|.+.++...+-.++++.+.
T Consensus 30 klv~G~~~v~kaikkgk-akLVilA~D~s~~~i~~~~~~lc~~~~Vp~~~~~tk~eLG~a~Gk~~~~svvaI~d~ 103 (122)
T PRK04175 30 KIKKGTNETTKAVERGI-AKLVVIAEDVDPEEIVAHLPLLCEEKKIPYVYVPSKKDLGKAAGLEVGAAAAAIVDA 103 (122)
T ss_pred CEeEcHHHHHHHHHcCC-ccEEEEeCCCChHHHHHHHHHHHHHcCCCEEEECCHHHHHHHhCCCCCeEEEEEech
Confidence 47999999999999874 4667776552 2334567778987765 66789999987767788888764
No 29
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=88.73 E-value=1.8 Score=27.77 Aligned_cols=63 Identities=19% Similarity=0.247 Sum_probs=44.5
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCCCCCCEEEe-CHHHHHhhcCCCCCCceEEE
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLPEDVPQHRV-DYKNIQLWSDLVTPPGIIGI 79 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~~~~~~~~v-~~~~l~~l~~~~~~qGv~a~ 79 (144)
-++.|.+.+..+++++. .+-+++.++. .+..+|...++|++.+ +.+.|.+.++....--++|+
T Consensus 11 kl~~G~~~v~kai~~gk-aklViiA~D~~~~~~~~i~~~c~~~~Vp~~~~~s~~eLG~a~G~~~~~a~~ai 80 (82)
T PRK13602 11 SIVIGTKQTVKALKRGS-VKEVVVAEDADPRLTEKVEALANEKGVPVSKVDSMKKLGKACGIEVGAAAVAI 80 (82)
T ss_pred CEEEcHHHHHHHHHcCC-eeEEEEECCCCHHHHHHHHHHHHHcCCCEEEECCHHHHHHHHCCCcCEEEEEE
Confidence 46899999999999864 5677887652 2445567778998765 55788888876554444444
No 30
>PRK06683 hypothetical protein; Provisional
Probab=88.00 E-value=2.4 Score=27.21 Aligned_cols=63 Identities=17% Similarity=0.324 Sum_probs=44.5
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCCCCCCEEEe-CHHHHHhhcCCCCCCceEEE
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLPEDVPQHRV-DYKNIQLWSDLVTPPGIIGI 79 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~~~~~~~~v-~~~~l~~l~~~~~~qGv~a~ 79 (144)
-++.|.+.+..++++| ..+.+|+.++. .+..++...++|++.+ +.++|.+.++....--++|+
T Consensus 11 k~v~G~~~v~kaik~g-kaklViiA~Da~~~~~~~i~~~~~~~~Vpv~~~~t~~eLG~A~G~~~~~a~~ai 80 (82)
T PRK06683 11 NVVVGHKRTLEAIKNG-IVKEVVIAEDADMRLTHVIIRTALQHNIPITKVESVRKLGKVAGIQVGASAIGI 80 (82)
T ss_pred CEEEcHHHHHHHHHcC-CeeEEEEECCCCHHHHHHHHHHHHhcCCCEEEECCHHHHHHHhCCcccEEEEEE
Confidence 4689999999999986 46778887652 2445567778998654 66688888876544444443
No 31
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=76.27 E-value=6.8 Score=31.92 Aligned_cols=65 Identities=12% Similarity=0.081 Sum_probs=43.2
Q ss_pred CEEEEeHHHHHHHHHcCCceeEEEEeccc-----ccccC---CCCCCCCEEEeCHH--HHHhhcCCCCCCceEEEEeCC
Q psy6779 15 WLMLEGKRILIDALKANLKLKMVFFSQWD-----ILKEL---PLPEDVPQHRVDYK--NIQLWSDLVTPPGIIGIFELP 83 (144)
Q Consensus 15 ~~~v~G~~~v~eal~~~~~i~~l~~~~~~-----~~~~l---~~~~~~~~~~v~~~--~l~~l~~~~~~qGv~a~~~~~ 83 (144)
-..+||..-|..|++.|. +++++++++- ++.++ +.+.|..++.+|.. .=++| ..=.||+|+...|
T Consensus 276 ~~~~YG~~eV~~Ale~GA-VetLLIsD~l~~~r~~~~~l~~~v~~~gg~V~i~Ss~~e~G~qL---~~lgGiaAiLRy~ 350 (351)
T TIGR00111 276 DKAVYGEDEVVKAAEYGA-IEYLLVTDKVLVQREEIEKLLDSVESMGGKVVILSTEHELGKQL---DSLGGIAGILRFP 350 (351)
T ss_pred CeEEECHHHHHHHHHcCC-ceEEEEecchhhhHHHHHHHHHHHHHcCCEEEEEcCCCccHHHH---hhCCCEEEEEecc
Confidence 478999999999999874 7889998753 12222 45567888887653 11122 1235888887654
No 32
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=70.47 E-value=18 Score=28.34 Aligned_cols=70 Identities=14% Similarity=0.135 Sum_probs=49.6
Q ss_pred cCCEEEEeHHHHHHHHHcCCceeEEEEeccc-------ccccCCCCCCCCEEEe-CHHHHHhhcCCCCCCceEEEEeCCC
Q psy6779 13 KGWLMLEGKRILIDALKANLKLKMVFFSQWD-------ILKELPLPEDVPQHRV-DYKNIQLWSDLVTPPGIIGIFELPA 84 (144)
Q Consensus 13 ~~~~~v~G~~~v~eal~~~~~i~~l~~~~~~-------~~~~l~~~~~~~~~~v-~~~~l~~l~~~~~~qGv~a~~~~~~ 84 (144)
.-.+++.|.+.|..+++++. .+-+++..+. .+..+|...++|+..+ +++.|..+.+.. ...++|+.+...
T Consensus 129 kp~~LvsG~n~VtkaIekkK-AkLVIIA~DVsPie~vk~LpaLCrk~~VPY~iVktKaeLG~AIGkK-travVAItD~g~ 206 (263)
T PTZ00222 129 APLAVVTGLQEVTRAIEKKQ-ARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIGRK-TATCVAITDVNA 206 (263)
T ss_pred CCCeeccCHHHHHHHHHcCC-ceEEEEeCCCCHHHHHHHHHHHHHhcCCCEEEECCHHHHHHHHCCC-CCeEEEEeeCCc
Confidence 34589999999999999874 4556666542 2445677889998655 667888888754 355777776543
No 33
>COG1303 Uncharacterized protein conserved in archaea [Function unknown]
Probab=68.83 E-value=3.7 Score=29.96 Aligned_cols=17 Identities=18% Similarity=0.139 Sum_probs=14.6
Q ss_pred HHHhHhCCCEEEEcCCc
Q psy6779 115 RVCAAVGARQVVCSRGC 131 (144)
Q Consensus 115 RtA~a~Gv~~vil~~~~ 131 (144)
-||-|||+++|+++..+
T Consensus 25 LtARAfGA~gil~~~e~ 41 (179)
T COG1303 25 LTARAFGADGILLDGEE 41 (179)
T ss_pred hhhHhhCCceEEEcCcc
Confidence 39999999999998654
No 34
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=67.53 E-value=18 Score=24.81 Aligned_cols=56 Identities=18% Similarity=0.113 Sum_probs=42.0
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc-------ccccCCCCCCCCEEEe-CHHHHHhhcCCCC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD-------ILKELPLPEDVPQHRV-DYKNIQLWSDLVT 72 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~-------~~~~l~~~~~~~~~~v-~~~~l~~l~~~~~ 72 (144)
-++.|.+-+..+++++. .+-+++.++- .+..+|..+++|+..+ |.+.|.+.++...
T Consensus 27 ki~~G~~e~~Kai~~g~-a~LVviA~Dv~P~~~~~~l~~lc~~~~vpyv~V~sk~~LG~a~g~~~ 90 (116)
T COG1358 27 KLKKGTNEVTKAIERGK-AKLVVIAEDVSPEELVKHLPALCEEKNVPYVYVGSKKELGKAVGKEV 90 (116)
T ss_pred CchhhHHHHHHHHHcCC-CcEEEEecCCCHHHHHHHHHHHHHhcCCCEEEeCCHHHHHHHhCCCc
Confidence 47999999999999874 3557777653 2345577789998765 6779999988664
No 35
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=65.39 E-value=6.8 Score=30.90 Aligned_cols=25 Identities=16% Similarity=0.193 Sum_probs=21.8
Q ss_pred CcHHHHHHHHhHhCCCEEEEcCCcc
Q psy6779 108 GNMGSILRVCAAVGARQVVCSRGCV 132 (144)
Q Consensus 108 ~NlGaIiRtA~a~Gv~~vil~~~~~ 132 (144)
.=+|.|.|.|+-|||+-||+-++..
T Consensus 26 ~Kvg~IARaaaiF~V~eIii~~D~~ 50 (272)
T COG2106 26 YKVGQIARAAAIFRVDEIIIYEDGD 50 (272)
T ss_pred HHHHHHHHHHHhhcccEEEEEeCCC
Confidence 4589999999999999999987654
No 36
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=61.76 E-value=7.6 Score=31.19 Aligned_cols=34 Identities=24% Similarity=0.434 Sum_probs=27.8
Q ss_pred CCCCCcHHHHH--HHHhHhCCCEEEEcCCccCCCCc
Q psy6779 104 IRDPGNMGSIL--RVCAAVGARQVVCSRGCVDIYDN 137 (144)
Q Consensus 104 i~DP~NlGaIi--RtA~a~Gv~~vil~~~~~d~~~p 137 (144)
-+-|.|||+|| |.|.++|+.+-|+.+-.+|-..|
T Consensus 103 G~haSnLGaiiA~~ia~~~gvPayIVDPvvVDEm~~ 138 (358)
T COG3426 103 GEHASNLGAIIANRIAKALGVPAYIVDPVVVDEMED 138 (358)
T ss_pred CcchhhhhHHHHHHHhhhcCCCeeeeCceehhhcch
Confidence 35788999998 88999999999998877665443
No 37
>PF03465 eRF1_3: eRF1 domain 3; InterPro: IPR005142 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination but this awaits experimental verification.; PDB: 3OBY_A 3E1Y_D 1DT9_A 2KTU_A 2KTV_A 3IR9_A 3E20_H 3OBW_A 3AGJ_F 3MCA_B ....
Probab=55.86 E-value=18 Score=24.49 Aligned_cols=27 Identities=19% Similarity=0.150 Sum_probs=23.0
Q ss_pred CEEEEeHHHHHHHHHcCCceeEEEEecc
Q psy6779 15 WLMLEGKRILIDALKANLKLKMVFFSQW 42 (144)
Q Consensus 15 ~~~v~G~~~v~eal~~~~~i~~l~~~~~ 42 (144)
-..+||.+-|.+|++.|. +++++++++
T Consensus 20 ~~~~yG~~eV~~Al~~Ga-V~~LlI~d~ 46 (113)
T PF03465_consen 20 GLAVYGIEEVKKALEMGA-VETLLISDD 46 (113)
T ss_dssp SSEEESHHHHHHHHHTT--EEEEEEEHH
T ss_pred CcEEECHHHHHHHHHhCC-CcEEEEecc
Confidence 467999999999999974 899999865
No 38
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only]
Probab=53.66 E-value=18 Score=25.77 Aligned_cols=34 Identities=18% Similarity=0.331 Sum_probs=31.6
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcC
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSR 129 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~ 129 (144)
+.++++.++..+.-+=-+-|+|..||++.+++++
T Consensus 2 ev~vvlHN~~S~~rv~e~ariaygfg~k~lV~tk 35 (147)
T COG4080 2 EVIVVLHNVSSVQRVLEFARIAYGFGAKRLVLTK 35 (147)
T ss_pred cEEEEEecCCchHHHHHHHHHHcccCccEEEEEe
Confidence 4688999999999999999999999999999987
No 39
>PLN03033 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=52.60 E-value=19 Score=28.71 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=17.9
Q ss_pred HHHHHHHHhHhCCCEEEEcCC
Q psy6779 110 MGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 110 lGaIiRtA~a~Gv~~vil~~~ 130 (144)
+-.+.|.|.|+|+||+++--+
T Consensus 222 V~~larAAvA~GaDGlfiEvH 242 (290)
T PLN03033 222 IPCIARTAVAVGVDGIFMEVH 242 (290)
T ss_pred HHHHHHHHHHhCCCEEEEEec
Confidence 457999999999999999643
No 40
>PF07071 DUF1341: Protein of unknown function (DUF1341); InterPro: IPR010763 Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.; PDB: 3NZR_D 3LM7_A 3M0Z_B 3M6Y_A 3N73_A 3MUX_A.
Probab=52.60 E-value=11 Score=28.70 Aligned_cols=22 Identities=27% Similarity=0.632 Sum_probs=16.6
Q ss_pred CCCCcHHHHHHHHhHhCCCEEE
Q psy6779 105 RDPGNMGSILRVCAAVGARQVV 126 (144)
Q Consensus 105 ~DP~NlGaIiRtA~a~Gv~~vi 126 (144)
-|..|+..|+|+|.-.|+..||
T Consensus 186 Idl~N~~~I~~i~l~aGv~~vi 207 (218)
T PF07071_consen 186 IDLDNFEEIVKICLDAGVEKVI 207 (218)
T ss_dssp --TTTHHHHHHHHHHTT-S-B-
T ss_pred cCHHHHHHHHHHHHHcCCCeec
Confidence 3999999999999999999876
No 41
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=52.58 E-value=19 Score=30.02 Aligned_cols=27 Identities=19% Similarity=0.151 Sum_probs=22.5
Q ss_pred CEEEEeHHHHHHHHHcCCceeEEEEecc
Q psy6779 15 WLMLEGKRILIDALKANLKLKMVFFSQW 42 (144)
Q Consensus 15 ~~~v~G~~~v~eal~~~~~i~~l~~~~~ 42 (144)
-..+||...|.+|++.|. +++++++++
T Consensus 287 g~avyG~~eV~~ALe~GA-VetLLV~d~ 313 (403)
T TIGR03676 287 GLAAYGEEEVRKALEMGA-VDTLLISED 313 (403)
T ss_pred CcEEEcHHHHHHHHHhCC-CcEEEEEcc
Confidence 467899999999999874 788888764
No 42
>KOG3361|consensus
Probab=52.33 E-value=3.2 Score=29.34 Aligned_cols=22 Identities=36% Similarity=0.561 Sum_probs=17.6
Q ss_pred EEecCCCCCcHHHHHHHHhHhC
Q psy6779 100 VCDNIRDPGNMGSILRVCAAVG 121 (144)
Q Consensus 100 vLD~i~DP~NlGaIiRtA~a~G 121 (144)
++|+-.+|.|+|++=++---.|
T Consensus 33 VidHy~nPRNVGSldK~dpnVG 54 (157)
T KOG3361|consen 33 VIDHYENPRNVGSLDKNDPNVG 54 (157)
T ss_pred hhhcccCccccCccCCCCCCcc
Confidence 5799999999999876655555
No 43
>PRK09190 hypothetical protein; Provisional
Probab=49.29 E-value=55 Score=25.03 Aligned_cols=65 Identities=9% Similarity=0.003 Sum_probs=42.5
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc------ccccCCCC------CCCCEE-EeCHHHHHhhcCCCCCCceEEEEeC
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD------ILKELPLP------EDVPQH-RVDYKNIQLWSDLVTPPGIIGIFEL 82 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~------~~~~l~~~------~~~~~~-~v~~~~l~~l~~~~~~qGv~a~~~~ 82 (144)
-+|.|...|+++++++. +.-|++..+. ++..++.. .++|++ ..+++.|....+. .+-.++++.+.
T Consensus 111 klVsG~~~V~~alk~gk-~~Lvi~A~DaS~~t~kKl~~~~~~~~~~~~~~Vp~v~~~tk~eLg~AlGr-~~~~~vav~d~ 188 (220)
T PRK09190 111 QVVSGFEKVDAALRSGE-AAALIHASDGAADGKRKLDQARRALVHETGREIPVIGLFTAAELGLAFGR-ENVIHAALLAG 188 (220)
T ss_pred CEeecHHHHHHHHHcCC-ceEEEEeccCChhHHHHHHHHHHhhcccccCCccEEEecCHHHHHHHhCC-CceeEEEEcCh
Confidence 47999999999999875 4556665441 24334433 578864 5688888888763 34455555433
No 44
>PF13653 GDPD_2: Glycerophosphoryl diester phosphodiesterase family; PDB: 3RLG_A 2F9R_B 1XX1_A 3RLH_A.
Probab=49.05 E-value=23 Score=18.29 Aligned_cols=17 Identities=12% Similarity=0.163 Sum_probs=13.7
Q ss_pred HHHHHHHhHhCCCEEEE
Q psy6779 111 GSILRVCAAVGARQVVC 127 (144)
Q Consensus 111 GaIiRtA~a~Gv~~vil 127 (144)
-+.+|.+-++|+|+|..
T Consensus 10 ~~~~~~~l~~GVDgI~T 26 (30)
T PF13653_consen 10 PASWRELLDLGVDGIMT 26 (30)
T ss_dssp HHHHHHHHHHT-SEEEE
T ss_pred HHHHHHHHHcCCCEeeC
Confidence 56789999999999975
No 45
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=46.22 E-value=50 Score=27.14 Aligned_cols=64 Identities=14% Similarity=0.076 Sum_probs=43.0
Q ss_pred cCCEEEEeHHHHHHHHHcCCceeEEEEeccc----------ccccC---CCCCCCCEEEeCHH-----HHHhhcCCCCCC
Q psy6779 13 KGWLMLEGKRILIDALKANLKLKMVFFSQWD----------ILKEL---PLPEDVPQHRVDYK-----NIQLWSDLVTPP 74 (144)
Q Consensus 13 ~~~~~v~G~~~v~eal~~~~~i~~l~~~~~~----------~~~~l---~~~~~~~~~~v~~~-----~l~~l~~~~~~q 74 (144)
.+....||..-|++|++.|. ++.++++++. +..++ ....+.+++.+|.+ .|+++ .
T Consensus 269 ~~~~v~YG~~eV~~A~e~GA-ve~LLv~De~lr~~~~~~re~~~~ll~~ve~~ggkV~Ivs~~he~Ge~Lk~l------G 341 (352)
T COG1537 269 DDDKVAYGLEEVEKAAEYGA-VETLLVTDELLRSDDVEEREDVEELLEEVESMGGKVVIVSTEHEPGERLKAL------G 341 (352)
T ss_pred CCCceeEcHHHHHHHHhcCc-ceeEEeehhhhcccchhhHHHHHHHHHHHHHcCCeEEEEecCCcchHHHHhc------c
Confidence 34578999999999999874 7888887652 11112 23457788887653 33333 6
Q ss_pred ceEEEEeCC
Q psy6779 75 GIIGIFELP 83 (144)
Q Consensus 75 Gv~a~~~~~ 83 (144)
||+|+.+.+
T Consensus 342 GiaaILRf~ 350 (352)
T COG1537 342 GIAAILRFP 350 (352)
T ss_pred CeEEEEEec
Confidence 888887654
No 46
>PRK03958 tRNA 2'-O-methylase; Reviewed
Probab=45.69 E-value=19 Score=26.68 Aligned_cols=18 Identities=17% Similarity=0.301 Sum_probs=15.8
Q ss_pred HHHHHHhHhCCCEEEEcC
Q psy6779 112 SILRVCAAVGARQVVCSR 129 (144)
Q Consensus 112 aIiRtA~a~Gv~~vil~~ 129 (144)
-+.|||-+||++++++..
T Consensus 21 hvartARafGa~~~yiv~ 38 (176)
T PRK03958 21 HVGLTARALGADKIILAS 38 (176)
T ss_pred HHHHHHHHcCCceEEEec
Confidence 367999999999999974
No 47
>PRK12457 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=43.36 E-value=26 Score=27.89 Aligned_cols=34 Identities=18% Similarity=0.228 Sum_probs=24.9
Q ss_pred eEEEEe---cCCCCCc-----------HHHHHHHHhHhCCCEEEEcCC
Q psy6779 97 LNIVCD---NIRDPGN-----------MGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 97 ~ilvLD---~i~DP~N-----------lGaIiRtA~a~Gv~~vil~~~ 130 (144)
+=+++| .||-|+- +-.+.|.|.|+|+||+++--+
T Consensus 192 lPVi~DpSHsvq~p~~~g~~s~G~re~v~~larAAvA~GaDGl~iEvH 239 (281)
T PRK12457 192 LPVIFDVTHSLQCRDPLGAASGGRRRQVLDLARAGMAVGLAGLFLEAH 239 (281)
T ss_pred CCEEEeCCccccCCCCCCCCCCCCHHHHHHHHHHHHHhCCCEEEEEec
Confidence 345565 3566654 457899999999999999643
No 48
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase. In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide.
Probab=42.57 E-value=26 Score=27.48 Aligned_cols=32 Identities=22% Similarity=0.529 Sum_probs=24.2
Q ss_pred EEEe---cCCCCCcH-----------HHHHHHHhHhCCCEEEEcCC
Q psy6779 99 IVCD---NIRDPGNM-----------GSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 99 lvLD---~i~DP~Nl-----------GaIiRtA~a~Gv~~vil~~~ 130 (144)
++.| .||-||-. -.+.|.|.|+|+||+++--+
T Consensus 178 Vi~DpSHsvq~pg~~g~~s~G~r~~v~~la~AAvA~GaDGl~iEvH 223 (258)
T TIGR01362 178 VIFDATHSVQQPGGLGGASGGLREFVPTLARAAVAVGIDGLFMETH 223 (258)
T ss_pred EEEeCCccccCCCCCCCCCCCcHHHHHHHHHHHHHhCCCEEEEEeC
Confidence 5555 46667654 47999999999999999643
No 49
>TIGR03581 EF_0839 conserved hypothetical protein EF_0839/AHA_3917. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
Probab=42.00 E-value=19 Score=27.67 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=20.1
Q ss_pred CCCcHHHHHHHHhHhCCCEEE
Q psy6779 106 DPGNMGSILRVCAAVGARQVV 126 (144)
Q Consensus 106 DP~NlGaIiRtA~a~Gv~~vi 126 (144)
|..|+..|++.|.-.|+..||
T Consensus 187 dl~Nf~~I~~i~ldaGv~kvi 207 (236)
T TIGR03581 187 DLDNFEEIVQIALDAGVEKVI 207 (236)
T ss_pred cHHhHHHHHHHHHHcCCCeec
Confidence 999999999999999999886
No 50
>KOG2869|consensus
Probab=41.99 E-value=34 Score=28.04 Aligned_cols=66 Identities=11% Similarity=0.075 Sum_probs=43.8
Q ss_pred EEEEeHHHHHHHHHcCCceeEEEEeccc----c------cccC---CCCCCCCEEEeC-----HHHHHhhcCCCCCCceE
Q psy6779 16 LMLEGKRILIDALKANLKLKMVFFSQWD----I------LKEL---PLPEDVPQHRVD-----YKNIQLWSDLVTPPGII 77 (144)
Q Consensus 16 ~~v~G~~~v~eal~~~~~i~~l~~~~~~----~------~~~l---~~~~~~~~~~v~-----~~~l~~l~~~~~~qGv~ 77 (144)
---||.+-|++|-+.+ .|++++++++- + ...+ .++.+.+++..| -+.|+.+ .||+
T Consensus 291 rA~yG~khV~~A~e~~-AI~tLLitD~lfr~~DV~tRkkyv~lvesVk~~~gkv~Ifss~H~SGEqL~ql------tGia 363 (379)
T KOG2869|consen 291 RACYGPKHVEKANEYG-AIETLLITDELFRSQDVATRKKYVRLVESVKENNGKVFIFSSLHVSGEQLAQL------TGIA 363 (379)
T ss_pred ccccCHHHHHHHHhhc-chhheehhhhhcccccHHHHHHHHHHHHHHHhcCCcEEEEehhhccHHHHHhh------cCee
Confidence 3469999999999976 47888888651 1 1122 234566776654 4455544 6899
Q ss_pred EEEeCCCCCCC
Q psy6779 78 GIFELPAHPIA 88 (144)
Q Consensus 78 a~~~~~~~~~~ 88 (144)
|+.+.|-+.+.
T Consensus 364 AiLrfp~pel~ 374 (379)
T KOG2869|consen 364 AILRFPLPELD 374 (379)
T ss_pred EEEecCCCccc
Confidence 99988866544
No 51
>cd00884 beta_CA_cladeB Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes.
Probab=41.73 E-value=1.1e+02 Score=22.59 Aligned_cols=23 Identities=13% Similarity=0.138 Sum_probs=18.6
Q ss_pred cHHHHHHHHhHhCCCEEEEcCCc
Q psy6779 109 NMGSILRVCAAVGARQVVCSRGC 131 (144)
Q Consensus 109 NlGaIiRtA~a~Gv~~vil~~~~ 131 (144)
=+|+|-=....+|++.|++..++
T Consensus 73 ~~asleyav~~l~v~~ivV~GH~ 95 (190)
T cd00884 73 TSAAIEYAVAVLKVEHIVVCGHS 95 (190)
T ss_pred hhhhHHHHHHHhCCCEEEEeCCC
Confidence 34777778889999999998754
No 52
>PF02598 Methyltrn_RNA_3: Putative RNA methyltransferase; InterPro: IPR003750 This entry describes proteins of unknown function.; PDB: 1K3R_B.
Probab=40.89 E-value=26 Score=27.83 Aligned_cols=21 Identities=24% Similarity=0.332 Sum_probs=16.7
Q ss_pred HHHHHHHHhHhCCCEEEEcCC
Q psy6779 110 MGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 110 lGaIiRtA~a~Gv~~vil~~~ 130 (144)
+|-|.|+|+-|+||-||+-.+
T Consensus 24 ~gqIARaaaiF~VdEIvVydd 44 (291)
T PF02598_consen 24 AGQIARAAAIFRVDEIVVYDD 44 (291)
T ss_dssp HHHHHHHHHHTT--EEEEEE-
T ss_pred HHHHHHHHHeecCcEEEEEcc
Confidence 699999999999999999765
No 53
>COG2877 KdsA 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]
Probab=40.81 E-value=24 Score=27.63 Aligned_cols=37 Identities=24% Similarity=0.424 Sum_probs=29.0
Q ss_pred EecCCCCCcHHH-----------HHHHHhHhCCCEEEEcCCccCCCCcc
Q psy6779 101 CDNIRDPGNMGS-----------ILRVCAAVGARQVVCSRGCVDIYDNK 138 (144)
Q Consensus 101 LD~i~DP~NlGa-----------IiRtA~a~Gv~~vil~~~~~d~~~pk 138 (144)
-..+|-||-.|+ +.|.|.|.|++|+++-. +.||-+.+
T Consensus 198 THSvQ~pgg~g~~SGG~refv~~LaRAa~AvGvaGlF~Et-HpdP~~A~ 245 (279)
T COG2877 198 THSVQQPGGQGGSSGGRREFVPTLARAAVAVGVAGLFIET-HPDPDNAK 245 (279)
T ss_pred ccceeCCCCCCCCCCCcchhHHHHHHHHHHhccceEEEec-cCCcccCC
Confidence 346899998885 89999999999999954 45555544
No 54
>PRK12703 tRNA 2'-O-methylase; Reviewed
Probab=39.79 E-value=21 Score=29.14 Aligned_cols=18 Identities=17% Similarity=0.296 Sum_probs=14.7
Q ss_pred HHHHHhHhCCCEEEEcCC
Q psy6779 113 ILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 113 IiRtA~a~Gv~~vil~~~ 130 (144)
+.=||-|||+++++++..
T Consensus 21 v~l~ara~ga~~~~~~~~ 38 (339)
T PRK12703 21 VALTARAFGASSILVDER 38 (339)
T ss_pred HHHHHHHhcCCeeEecCC
Confidence 344999999999999854
No 55
>KOG0053|consensus
Probab=37.73 E-value=41 Score=28.22 Aligned_cols=56 Identities=16% Similarity=0.180 Sum_probs=37.9
Q ss_pred CCCCCCCCEEEeCHHHHHhhcCCCCCCceEEEEeCCCCCCC---CCC-----CCCCCeEEEEec
Q psy6779 48 LPLPEDVPQHRVDYKNIQLWSDLVTPPGIIGIFELPAHPIA---SID-----PASLPLNIVCDN 103 (144)
Q Consensus 48 l~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~~~~---~~~-----~~~~~~ilvLD~ 103 (144)
+....++....++...++++......+.-+..++.|..+.. |+. ....++++++|+
T Consensus 136 ~~~~~gie~~~vd~~~~~~~~~~i~~~t~~V~~ESPsNPll~v~DI~~l~~la~~~g~~vvVDn 199 (409)
T KOG0053|consen 136 FLPKFGGEGDFVDVDDLKKILKAIKENTKAVFLESPSNPLLKVPDIEKLARLAHKYGFLVVVDN 199 (409)
T ss_pred HHHHhCceeeeechhhHHHHHHhhccCceEEEEECCCCCccccccHHHHHHHHhhCCCEEEEeC
Confidence 33355888888998888888776666666666777665432 221 235678899987
No 56
>TIGR00259 thylakoid_BtpA membrane complex biogenesis protein, BtpA family. Members of this family are found in C. elegans, Synechocystis sp., E. coli, and several of the Archaea. Members in Cyanobacteria have been shown to play a role in protein complex biogenesis, and designated BtpA (biogenesis of thylakoid protein). Homologs in non-photosynthetic species, where thylakoid intracytoplasmic membranes are lacking, are likely to act elsewhere in membrane protein biogenesis.
Probab=37.03 E-value=43 Score=26.25 Aligned_cols=35 Identities=20% Similarity=0.130 Sum_probs=27.3
Q ss_pred CCCcHHHHHHHHhHhC-CCEEEEcC-CccCCCCccee
Q psy6779 106 DPGNMGSILRVCAAVG-ARQVVCSR-GCVDIYDNKVI 140 (144)
Q Consensus 106 DP~NlGaIiRtA~a~G-v~~vil~~-~~~d~~~pkvi 140 (144)
.+.++..+.|++..+| +|+||++. ++-.++++..+
T Consensus 155 ~~~~~~e~a~~~~~~~~aDavivtG~~TG~~~d~~~l 191 (257)
T TIGR00259 155 GNRDLESIALDTVERGLADAVILSGKTTGTEVDLELL 191 (257)
T ss_pred CCCCHHHHHHHHHHhcCCCEEEECcCCCCCCCCHHHH
Confidence 3578999999999999 99999986 44455665544
No 57
>PRK05198 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=36.63 E-value=32 Score=27.09 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=17.5
Q ss_pred HHHHHHHHhHhCCCEEEEcCC
Q psy6779 110 MGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 110 lGaIiRtA~a~Gv~~vil~~~ 130 (144)
+=.+.|.|.|+|+||+++--+
T Consensus 211 v~~la~AAvA~GadGl~iEvH 231 (264)
T PRK05198 211 VPVLARAAVAVGVAGLFIETH 231 (264)
T ss_pred HHHHHHHHHHcCCCEEEEEeC
Confidence 336999999999999999643
No 58
>COG1087 GalE UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]
Probab=35.80 E-value=1.4e+02 Score=24.33 Aligned_cols=95 Identities=12% Similarity=0.136 Sum_probs=55.3
Q ss_pred eHHHHHHHHHcCCceeEEEEeccc--ccccCCCCCCCCEEE---eCHHHHHhhcCCCCCCceEEEEeCCCCCCCCCCCCC
Q psy6779 20 GKRILIDALKANLKLKMVFFSQWD--ILKELPLPEDVPQHR---VDYKNIQLWSDLVTPPGIIGIFELPAHPIASIDPAS 94 (144)
Q Consensus 20 G~~~v~eal~~~~~i~~l~~~~~~--~~~~l~~~~~~~~~~---v~~~~l~~l~~~~~~qGv~a~~~~~~~~~~~~~~~~ 94 (144)
|.|.|.+++++|..+ +.+..-. ....+... ..+++. .+++.|+++........|+=.+..
T Consensus 13 GSHtv~~Ll~~G~~v--vV~DNL~~g~~~~v~~~-~~~f~~gDi~D~~~L~~vf~~~~idaViHFAa~------------ 77 (329)
T COG1087 13 GSHTVRQLLKTGHEV--VVLDNLSNGHKIALLKL-QFKFYEGDLLDRALLTAVFEENKIDAVVHFAAS------------ 77 (329)
T ss_pred HHHHHHHHHHCCCeE--EEEecCCCCCHHHhhhc-cCceEEeccccHHHHHHHHHhcCCCEEEECccc------------
Confidence 789999999999643 3332211 11111110 034443 577788888876666666543322
Q ss_pred CCeEEEEecCCCC-----CcH---HHHHHHHhHhCCCEEEEcCCcc
Q psy6779 95 LPLNIVCDNIRDP-----GNM---GSILRVCAAVGARQVVCSRGCV 132 (144)
Q Consensus 95 ~~~ilvLD~i~DP-----~Nl---GaIiRtA~a~Gv~~vil~~~~~ 132 (144)
..|=+.+++| .|+ =+++..+..+|++.+|+++.++
T Consensus 78 ---~~VgESv~~Pl~Yy~NNv~gTl~Ll~am~~~gv~~~vFSStAa 120 (329)
T COG1087 78 ---ISVGESVQNPLKYYDNNVVGTLNLIEAMLQTGVKKFIFSSTAA 120 (329)
T ss_pred ---cccchhhhCHHHHHhhchHhHHHHHHHHHHhCCCEEEEecchh
Confidence 2222333333 133 3578999999999999986544
No 59
>COG5016 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]
Probab=35.72 E-value=38 Score=28.61 Aligned_cols=41 Identities=12% Similarity=0.106 Sum_probs=32.3
Q ss_pred CCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCC
Q psy6779 95 LPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIY 135 (144)
Q Consensus 95 ~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~ 135 (144)
-..+=+.|-+.||.|+=+-++.+.-+|.+.--...-+..|.
T Consensus 112 idvfRiFDAlND~RNl~~ai~a~kk~G~h~q~~i~YT~sPv 152 (472)
T COG5016 112 IDVFRIFDALNDVRNLKTAIKAAKKHGAHVQGTISYTTSPV 152 (472)
T ss_pred CcEEEechhccchhHHHHHHHHHHhcCceeEEEEEeccCCc
Confidence 35677899999999999999999999987655544454443
No 60
>PF07577 DUF1547: Domain of Unknown Function (DUF1547); InterPro: IPR011443 This domain appears to be found only in a small family of Chlamydia species. It is usually found repeated. The function of these proteins is not known.
Probab=35.21 E-value=28 Score=20.97 Aligned_cols=24 Identities=17% Similarity=0.275 Sum_probs=15.9
Q ss_pred CCcHHHHHHHHhHhCC-CEEEEcCC
Q psy6779 107 PGNMGSILRVCAAVGA-RQVVCSRG 130 (144)
Q Consensus 107 P~NlGaIiRtA~a~Gv-~~vil~~~ 130 (144)
-.|||+|||...-=-. .+||.+..
T Consensus 25 nq~LG~vI~~~e~gt~~~tiv~~~~ 49 (58)
T PF07577_consen 25 NQNLGDVIRDFENGTGSPTIVAPNP 49 (58)
T ss_pred CCCHHHHHHHHhccCCCCCEeecCC
Confidence 5799999999983222 34555443
No 61
>PRK06852 aldolase; Validated
Probab=34.21 E-value=60 Score=26.08 Aligned_cols=28 Identities=11% Similarity=0.210 Sum_probs=23.4
Q ss_pred CCCCCcHHHHHHHHhHhCCCEEEEcCCc
Q psy6779 104 IRDPGNMGSILRVCAAVGARQVVCSRGC 131 (144)
Q Consensus 104 i~DP~NlGaIiRtA~a~Gv~~vil~~~~ 131 (144)
+.+-.|...++|.+...|+++++++++-
T Consensus 55 ~~gl~dp~~~i~~~~~~g~dav~~~~G~ 82 (304)
T PRK06852 55 AKDDADPEHLFRIASKAKIGVFATQLGL 82 (304)
T ss_pred CcccCCHHHHHHHHHhcCCCEEEeCHHH
Confidence 4566677889999999999999998754
No 62
>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein. This is thought to be an ATPase involved in viral DNA packaging [].
Probab=32.63 E-value=47 Score=25.72 Aligned_cols=49 Identities=12% Similarity=0.179 Sum_probs=34.3
Q ss_pred CCCeEEEEecCCC---CCc-HHHHHHHHhHhCCCEEEEcCCccCCCCcceeeccC
Q psy6779 94 SLPLNIVCDNIRD---PGN-MGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144 (144)
Q Consensus 94 ~~~~ilvLD~i~D---P~N-lGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRaS~ 144 (144)
.+..++|+|++.| =.+ +..++-.+.-++++-+++....-+. |+.+|+++
T Consensus 97 ~~~~LiIlDD~~~~~~k~~~l~~~~~~gRH~~is~i~l~Q~~~~l--p~~iR~n~ 149 (241)
T PF04665_consen 97 NPRFLIILDDLGDKKLKSKILRQFFNNGRHYNISIIFLSQSYFHL--PPNIRSNI 149 (241)
T ss_pred CCCeEEEEeCCCCchhhhHHHHHHHhcccccceEEEEEeeecccC--CHHHhhcc
Confidence 3468999999987 222 6777777888899888887544333 66677763
No 63
>cd02120 PA_subtilisin_like PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from Alnus glutinosa ag12, members of the tomato P69 family, and tomato LeSBT2. These proteins belong to the peptidase S8 family. Cucumisin from the juice of melon fruits is a thermostable serine peptidase, with a broad substrate specificity for oligopeptides and proteins. A. thaliana Ara12 is a thermostable, extracellular serine protease, found chiefly in silique tissue and stem tissue. Ara12 is stimulated by Ca2+ ions. A. glutinosa ag12 is expressed at high levels in the nodules, and at low levels in the shoot tips; it is implicated in both symbiotic and non-symbiotic processes in plant development. The tomato P69 protease family is comprised of various protein isoforms of approximately 69KDa. These isoforms accu
Probab=32.25 E-value=1.2e+02 Score=19.99 Aligned_cols=35 Identities=11% Similarity=0.107 Sum_probs=25.6
Q ss_pred CCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCC
Q psy6779 95 LPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 95 ~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~ 130 (144)
.+.|+++++-.. .-+....+.+.+.|+.++|+...
T Consensus 51 ~GkIVlc~~~~~-~~~~~k~~~~~~~GA~gvI~~~~ 85 (126)
T cd02120 51 KGKIVLCDRGGN-TSRVAKGDAVKAAGGAGMILAND 85 (126)
T ss_pred cccEEEEeCCCC-ccHHHHHHHHHHcCCcEEEEEec
Confidence 356888876432 14567789999999999999543
No 64
>PTZ00365 60S ribosomal protein L7Ae-like; Provisional
Probab=32.21 E-value=80 Score=24.90 Aligned_cols=68 Identities=13% Similarity=0.161 Sum_probs=47.8
Q ss_pred CCEEEEeHHHHHHHHHcCCceeEEEEeccc-------ccccCCCCCCCCEEEe-CHHHHHhhcCCCCCCceEEEEeCC
Q psy6779 14 GWLMLEGKRILIDALKANLKLKMVFFSQWD-------ILKELPLPEDVPQHRV-DYKNIQLWSDLVTPPGIIGIFELP 83 (144)
Q Consensus 14 ~~~~v~G~~~v~eal~~~~~i~~l~~~~~~-------~~~~l~~~~~~~~~~v-~~~~l~~l~~~~~~qGv~a~~~~~ 83 (144)
-.++-+|.+-|..+++.+. ..-|++..+. .+..+|...++|+..+ +.+.|....+. .+..++|+.+-.
T Consensus 130 p~~vk~Gin~VtklIekkK-AkLVIIA~DVsP~t~kk~LP~LC~k~~VPY~iv~sK~eLG~AIGk-ktraVVAItdV~ 205 (266)
T PTZ00365 130 PFMLKYGLNHVTDLVEYKK-AKLVVIAHDVDPIELVCFLPALCRKKEVPYCIIKGKSRLGKLVHQ-KTAAVVAIDNVR 205 (266)
T ss_pred chHHHhhhHHHHHHHHhCC-ccEEEEeCCCCHHHHHHHHHHHHhccCCCEEEECCHHHHHHHhCC-CCceEEEecccC
Confidence 3467899999999999874 4556666542 1346678889998655 66688887764 456777777543
No 65
>COG4075 Uncharacterized conserved protein, homolog of nitrogen regulatory protein PII [Function unknown]
Probab=31.94 E-value=43 Score=22.47 Aligned_cols=26 Identities=15% Similarity=0.293 Sum_probs=23.4
Q ss_pred CCCCCcHHHHHHHHhHhCCCEEEEcC
Q psy6779 104 IRDPGNMGSILRVCAAVGARQVVCSR 129 (144)
Q Consensus 104 i~DP~NlGaIiRtA~a~Gv~~vil~~ 129 (144)
.-+|.|+|-.+..-+-.|+.|.++-+
T Consensus 10 FVe~eNvGkaiN~mad~GiTGFfl~e 35 (110)
T COG4075 10 FVEEENVGKAINIMADAGITGFFLHE 35 (110)
T ss_pred EecHHHHHHHHHHHHhcCcceEEEEE
Confidence 34799999999999999999999876
No 66
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=31.37 E-value=78 Score=26.19 Aligned_cols=43 Identities=14% Similarity=0.175 Sum_probs=34.2
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCcc
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNK 138 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pk 138 (144)
..+++||+||...+.-..++.-.--|-..|+++.+++...+.+
T Consensus 95 ~~yifLDEIq~v~~W~~~lk~l~d~~~~~v~itgsss~ll~~~ 137 (398)
T COG1373 95 KSYIFLDEIQNVPDWERALKYLYDRGNLDVLITGSSSSLLSKE 137 (398)
T ss_pred CceEEEecccCchhHHHHHHHHHccccceEEEECCchhhhccc
Confidence 4689999999999999999998887776677776666555443
No 67
>COG2086 FixA Electron transfer flavoprotein, beta subunit [Energy production and conversion]
Probab=31.32 E-value=40 Score=26.45 Aligned_cols=22 Identities=23% Similarity=0.285 Sum_probs=16.3
Q ss_pred cHHHHHHHHhHhCCCEEEEcCC
Q psy6779 109 NMGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 109 NlGaIiRtA~a~Gv~~vil~~~ 130 (144)
..-..+|.|.|+|+|..|+-.+
T Consensus 67 ~a~~~lr~aLAmGaDraili~d 88 (260)
T COG2086 67 QAEEALREALAMGADRAILITD 88 (260)
T ss_pred hhHHHHHHHHhcCCCeEEEEec
Confidence 3456778899999988877664
No 68
>TIGR02845 spore_V_AD stage V sporulation protein AD. Bacillus and Clostridium species contain about 10 % dipicolinic acid (pyridine-2,6-dicarboxylic acid) by weight. This protein family, SpoVAD, belongs to the spoVA operon that is suggested to act in the transport of dipicolinic acid (DPA) from the mother cell, where DPA is synthesized, to the forespore, a process essential to sporulation. Members of this protein family are found, so far, in exactly those species believed capable of endospore formation.
Probab=31.09 E-value=30 Score=28.14 Aligned_cols=18 Identities=39% Similarity=0.527 Sum_probs=15.6
Q ss_pred ecCCCCCcHHHHHHHHhH
Q psy6779 102 DNIRDPGNMGSILRVCAA 119 (144)
Q Consensus 102 D~i~DP~NlGaIiRtA~a 119 (144)
=++.||.|+|+.+--|++
T Consensus 188 ~g~~d~~nmgaamapaa~ 205 (327)
T TIGR02845 188 YGITDPLDMGAAMAPAAA 205 (327)
T ss_pred cCCCCcccchhhhhHHHH
Confidence 489999999998888775
No 69
>PRK12404 stage V sporulation protein AD; Provisional
Probab=29.98 E-value=32 Score=28.04 Aligned_cols=18 Identities=33% Similarity=0.460 Sum_probs=15.6
Q ss_pred ecCCCCCcHHHHHHHHhH
Q psy6779 102 DNIRDPGNMGSILRVCAA 119 (144)
Q Consensus 102 D~i~DP~NlGaIiRtA~a 119 (144)
=++.||.|+|+.+--|++
T Consensus 192 ~g~~d~~nMGaaMAPAA~ 209 (334)
T PRK12404 192 MGLTDPFNMGGAMAPAAV 209 (334)
T ss_pred cCCCCcccchhhhhHHHH
Confidence 489999999998888775
No 70
>PF07451 SpoVAD: Stage V sporulation protein AD (SpoVAD); InterPro: IPR010894 This family contains the bacterial stage V sporulation protein AD (SpoVAD), which is approximately 340 residues long. This is one of six proteins encoded by the spoVA operon, which is transcribed exclusively in the forespore at about the time of dipicolinic acid (DPA) synthesis in the mother cell. The functions of the proteins encoded by the spoVA operon are unknown, but it has been suggested they are involved in DPA transport during sporulation [].; PDB: 3LMA_D 3LM6_A.
Probab=28.61 E-value=42 Score=27.20 Aligned_cols=18 Identities=44% Similarity=0.695 Sum_probs=11.8
Q ss_pred ecCCCCCcHHHHHHHHhH
Q psy6779 102 DNIRDPGNMGSILRVCAA 119 (144)
Q Consensus 102 D~i~DP~NlGaIiRtA~a 119 (144)
=++.||.|+|+-+--|++
T Consensus 189 ~G~~D~~nMGaAMAPAA~ 206 (329)
T PF07451_consen 189 MGIKDPNNMGAAMAPAAA 206 (329)
T ss_dssp SS---TT-HHHHHHHHHH
T ss_pred cCCCCcccchhhHhHHHH
Confidence 489999999999888876
No 71
>cd04819 PA_2 PA_2: Protease-associated (PA) domain subgroup 2. A subgroup of PA-domain containing proteins. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabidopsis ReMembR-H2 protein, iv) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), v) various plant vacuola
Probab=27.85 E-value=1.3e+02 Score=20.39 Aligned_cols=34 Identities=15% Similarity=-0.023 Sum_probs=26.1
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcC
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSR 129 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~ 129 (144)
+.|++.+.-..+-.+..-++.|...|+.+||+-.
T Consensus 45 GkIvlv~~g~~~~~~~~k~~~A~~~GA~avi~~~ 78 (127)
T cd04819 45 GKIAVVKRDDPDVDRKEKYAKAVAAGAAAFVVVN 78 (127)
T ss_pred CeEEEEEcCCCchhHHHHHHHHHHCCCEEEEEEe
Confidence 4577777755434567889999999999999964
No 72
>PF02225 PA: PA domain; InterPro: IPR003137 The PA (Protease associated) domain is found as an insert domain in diverse proteases, which include the MEROPS peptidase families A22B, M28, and S8A []. The PA domain is also found in a plant vacuolar sorting receptor O22925 from SWISSPROT and members of the RZF family, e.g. O43567 from SWISSPROT.; PDB: 3EIF_A 1XF1_B 3BXM_A 2C6P_A 1Z8L_C 3SJF_A 3BHX_A 2C6G_A 3D7F_A 2XEG_A ....
Probab=27.34 E-value=1.5e+02 Score=18.55 Aligned_cols=32 Identities=13% Similarity=0.141 Sum_probs=23.7
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcC
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSR 129 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~ 129 (144)
..++++++=.- ++..-++.|...|+.++|+-.
T Consensus 34 gkIvlv~rg~~--~~~~k~~~a~~~GA~gvIi~~ 65 (101)
T PF02225_consen 34 GKIVLVERGSC--SFDDKVRNAQKAGAKGVIIYN 65 (101)
T ss_dssp TSEEEEESTSS--CHHHHHHHHHHTTESEEEEE-
T ss_pred ceEEEEecCCC--CHHHHHHHHHHcCCEEEEEEe
Confidence 44555533322 789999999999999999976
No 73
>KOG3925|consensus
Probab=27.12 E-value=32 Score=28.29 Aligned_cols=35 Identities=11% Similarity=0.137 Sum_probs=29.3
Q ss_pred CcHHHHHHHHhHhCCCEEEEcCCccCCCCcceeec
Q psy6779 108 GNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRA 142 (144)
Q Consensus 108 ~NlGaIiRtA~a~Gv~~vil~~~~~d~~~pkviRa 142 (144)
.=.|-|-|+|--|+++-||+-.+..++-+..+-+.
T Consensus 90 ~~a~QIAR~aslf~V~Eiivldd~~~~~~~~~~~~ 124 (371)
T KOG3925|consen 90 YFAGQIARAASLFRVDEIIVLDDSEYVTNEQVNTS 124 (371)
T ss_pred HHhhhhhhhheeecceeEEEecccchhhhhhhccc
Confidence 44689999999999999999998887777776654
No 74
>PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed
Probab=26.86 E-value=1.4e+02 Score=24.57 Aligned_cols=35 Identities=14% Similarity=0.130 Sum_probs=25.3
Q ss_pred EEE--ecCC-CCCcHHHHHHHHhHhCCCEEEEcCCccCC
Q psy6779 99 IVC--DNIR-DPGNMGSILRVCAAVGARQVVCSRGCVDI 134 (144)
Q Consensus 99 lvL--D~i~-DP~NlGaIiRtA~a~Gv~~vil~~~~~d~ 134 (144)
+++ |+-. +...+=++-|.|.|+|+||+++-.+. ||
T Consensus 290 V~~d~~Hs~G~r~~~~~~a~aAva~GAdg~~iE~H~-dp 327 (360)
T PRK12595 290 VMVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHP-DP 327 (360)
T ss_pred EEEeCCCCCcchhhHHHHHHHHHHcCCCeEEEEecC-CC
Confidence 455 5543 33356678999999999999998765 44
No 75
>PF13380 CoA_binding_2: CoA binding domain; PDB: 3FF4_A 2D5A_A 2D59_A 2E6U_X 1IUL_A 1IUK_A 1Y81_A 2DUW_A.
Probab=26.50 E-value=54 Score=22.05 Aligned_cols=27 Identities=26% Similarity=0.372 Sum_probs=21.5
Q ss_pred CCCCCcHHHHHHHHhHhCCCEEEEcCC
Q psy6779 104 IRDPGNMGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 104 i~DP~NlGaIiRtA~a~Gv~~vil~~~ 130 (144)
...|.....+++.|.+.|+.++|+..+
T Consensus 62 ~~~~~~~~~~v~~~~~~g~~~v~~~~g 88 (116)
T PF13380_consen 62 CVPPDKVPEIVDEAAALGVKAVWLQPG 88 (116)
T ss_dssp -S-HHHHHHHHHHHHHHT-SEEEE-TT
T ss_pred EcCHHHHHHHHHHHHHcCCCEEEEEcc
Confidence 467889999999999999999999876
No 76
>PF13173 AAA_14: AAA domain
Probab=26.46 E-value=1.3e+02 Score=20.12 Aligned_cols=36 Identities=14% Similarity=0.152 Sum_probs=28.2
Q ss_pred CCeEEEEecCCCCCcHHHHHHHHhHhCCC-EEEEcCC
Q psy6779 95 LPLNIVCDNIRDPGNMGSILRVCAAVGAR-QVVCSRG 130 (144)
Q Consensus 95 ~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~-~vil~~~ 130 (144)
...++++|+||--.|+...++...--+-+ .++++..
T Consensus 61 ~~~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS 97 (128)
T PF13173_consen 61 GKKYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGS 97 (128)
T ss_pred CCcEEEEehhhhhccHHHHHHHHHHhccCceEEEEcc
Confidence 35689999999999999999999888733 5555543
No 77
>PRK13397 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=26.00 E-value=72 Score=24.89 Aligned_cols=19 Identities=21% Similarity=0.335 Sum_probs=17.3
Q ss_pred HHHHHHhHhCCCEEEEcCC
Q psy6779 112 SILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 112 aIiRtA~a~Gv~~vil~~~ 130 (144)
++-|.|.|+|++|+++-.+
T Consensus 203 ~~a~AAvA~GAdGl~IE~H 221 (250)
T PRK13397 203 PAAKIAKAVGANGIMMEVH 221 (250)
T ss_pred HHHHHHHHhCCCEEEEEec
Confidence 8999999999999999754
No 78
>PRK08304 stage V sporulation protein AD; Validated
Probab=26.00 E-value=41 Score=27.43 Aligned_cols=18 Identities=39% Similarity=0.647 Sum_probs=15.6
Q ss_pred ecCCCCCcHHHHHHHHhH
Q psy6779 102 DNIRDPGNMGSILRVCAA 119 (144)
Q Consensus 102 D~i~DP~NlGaIiRtA~a 119 (144)
=++.||.|+|+.+--|++
T Consensus 194 ~g~~d~~nmgaaMapAa~ 211 (337)
T PRK08304 194 LGIKDPNDMGAAMAPAAA 211 (337)
T ss_pred cCCCCcccchhhhhHHHH
Confidence 489999999998888776
No 79
>PF13605 DUF4141: Domain of unknown function (DUF4141)
Probab=25.57 E-value=45 Score=19.88 Aligned_cols=13 Identities=38% Similarity=0.930 Sum_probs=8.5
Q ss_pred CCCCCcHHH-HHHH
Q psy6779 104 IRDPGNMGS-ILRV 116 (144)
Q Consensus 104 i~DP~NlGa-IiRt 116 (144)
|.||+|+-- |+-+
T Consensus 24 V~DP~NlAQ~Iina 37 (55)
T PF13605_consen 24 VTDPGNLAQNIINA 37 (55)
T ss_pred EeCchHHHHHHHHH
Confidence 469999864 4433
No 80
>PF12696 TraG-D_C: TraM recognition site of TraD and TraG
Probab=25.56 E-value=1.1e+02 Score=20.50 Aligned_cols=35 Identities=14% Similarity=0.336 Sum_probs=26.9
Q ss_pred CeEEEEecCCCCC---cHHHHHHHHhHhCCCEEEEcCC
Q psy6779 96 PLNIVCDNIRDPG---NMGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 96 ~~ilvLD~i~DP~---NlGaIiRtA~a~Gv~~vil~~~ 130 (144)
|+.++||+..+-+ ++-.++-++..+|+.-+++..+
T Consensus 1 pv~~~lDE~~~~~~~~~l~~~~~~~r~~gi~~~~~~Qs 38 (128)
T PF12696_consen 1 PVLFILDEFGNLGPIPGLEDLLATGRSYGISFILAFQS 38 (128)
T ss_pred CEEEEEEChhhcCCcHhHHHHHHHHhcCCCEEEEEEcc
Confidence 5678899988764 4677788888888888877654
No 81
>cd02133 PA_C5a_like PA_C5a_like: Protease-associated domain containing proteins like Streptococcus pyogenes C5a peptidase. This group contains various PA domain-containing proteins similar to S. pyogenes C5a, including, i) Vpr, a minor extracellular serine protease from Bacillus subtilis, ii) a large molecular mass collagenolytic protease from Geobacillus collagenovorans MO-1, and iii) PrtS, a cell envelope protease from Streptococcus thermophilus CNRZ 385. Proteins in this group belong to the peptidase S8 family. C5a peptidase is a cell surface serine protease which specifically inactivates C5a [a chemotactic peptide, which attracts polymorphonuclear leukocytes (PMNs)], by cleaving it to release a 7-residue carboxy-terminal fragment which contains the PMN binding site. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promotin
Probab=25.12 E-value=2.1e+02 Score=19.73 Aligned_cols=34 Identities=12% Similarity=0.017 Sum_probs=25.1
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCc
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGC 131 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~ 131 (144)
..|+++++ .+ -.+..-++.|...|+.+||+-.+.
T Consensus 48 GkIvL~~r-g~-c~~~~K~~~a~~aGA~gvIi~n~~ 81 (143)
T cd02133 48 GKIALIQR-GE-ITFVEKIANAKAAGAVGVIIYNNV 81 (143)
T ss_pred ceEEEEEC-CC-CCHHHHHHHHHHCCCeEEEEeecC
Confidence 45777764 22 367788999999999999995433
No 82
>PF13242 Hydrolase_like: HAD-hyrolase-like; PDB: 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A 2HX1_D 2X4D_A 3HLT_C 3L1U_B ....
Probab=25.01 E-value=84 Score=18.96 Aligned_cols=30 Identities=20% Similarity=0.308 Sum_probs=23.6
Q ss_pred eEEEEec-CCCCCcHHHHHHHHhHhCCCEEEEcCCccC
Q psy6779 97 LNIVCDN-IRDPGNMGSILRVCAAVGARQVVCSRGCVD 133 (144)
Q Consensus 97 ~ilvLD~-i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d 133 (144)
.++|=|. .+| |+.|.+.|++.|++..+..+
T Consensus 24 ~~~VGD~~~~D-------i~~a~~~G~~~ilV~tG~~~ 54 (75)
T PF13242_consen 24 CVMVGDSLETD-------IEAAKAAGIDTILVLTGVYS 54 (75)
T ss_dssp EEEEESSTTTH-------HHHHHHTTSEEEEESSSSSC
T ss_pred EEEEcCCcHhH-------HHHHHHcCCcEEEECCCCCC
Confidence 4555577 677 89999999999999876544
No 83
>PF14572 Pribosyl_synth: Phosphoribosyl synthetase-associated domain; PDB: 2H07_B 2H06_B 3S5J_B 2HCR_A 3EFH_A 2H08_A 1DKR_B 1DKU_B 1IBS_B 2JI4_A ....
Probab=24.90 E-value=1.1e+02 Score=22.80 Aligned_cols=31 Identities=29% Similarity=0.657 Sum_probs=24.5
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHh---CCCEEEEc
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAV---GARQVVCS 128 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~---Gv~~vil~ 128 (144)
..++++|++-|-| ||++++|..+ |+..|+..
T Consensus 84 k~~IIvDDiIdtg--~Tl~~aA~~Lk~~GA~~V~~~ 117 (184)
T PF14572_consen 84 KICIIVDDIIDTG--GTLIKAAELLKERGAKKVYAC 117 (184)
T ss_dssp SEEEEEEEEESST--HHHHHHHHHHHHTTESEEEEE
T ss_pred CeEeeecccccch--HHHHHHHHHHHHcCCCEEEEE
Confidence 4688999999876 7888888665 88888764
No 84
>cd01988 Na_H_Antiporter_C The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the regio
Probab=24.41 E-value=1.1e+02 Score=19.89 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=22.5
Q ss_pred HHHHHHHhHhCCCEEEEcCCccCCCCc
Q psy6779 111 GSILRVCAAVGARQVVCSRGCVDIYDN 137 (144)
Q Consensus 111 GaIiRtA~a~Gv~~vil~~~~~d~~~p 137 (144)
++|++.|...++|-|++.......+..
T Consensus 84 ~~I~~~a~~~~~dlIV~G~~~~~~~~~ 110 (132)
T cd01988 84 SGILRTAKERQADLIIMGWHGSTSLRD 110 (132)
T ss_pred HHHHHHHHhcCCCEEEEecCCCCCccc
Confidence 789999999999999998876665533
No 85
>cd01294 DHOase Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is monofunctional and mainly dimeric.
Probab=24.13 E-value=1e+02 Score=24.44 Aligned_cols=28 Identities=14% Similarity=0.106 Sum_probs=23.3
Q ss_pred cCCCCCcHHHHHHHHhHhCCCEEEEcCCc
Q psy6779 103 NIRDPGNMGSILRVCAAVGARQVVCSRGC 131 (144)
Q Consensus 103 ~i~DP~NlGaIiRtA~a~Gv~~vil~~~~ 131 (144)
++.||.++-+..|+|++.| +.++..+.+
T Consensus 12 h~~~~~~~~~~~~aa~~gG-Ttvv~mpnt 39 (335)
T cd01294 12 HLRDGAMLKLVLPYTARGF-SRAIVMPNL 39 (335)
T ss_pred cCCCchHHHHHHHHHHhCC-CEEEECCCC
Confidence 4566789999999999999 999987654
No 86
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=24.02 E-value=77 Score=26.30 Aligned_cols=34 Identities=6% Similarity=0.263 Sum_probs=31.6
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcC
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSR 129 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~ 129 (144)
..+|+||.-..+..+=.+++....+|++++|+++
T Consensus 288 e~~LVlsat~~~~~~~~~~~~~~~~~~~~~I~TK 321 (388)
T PRK12723 288 EFHLAVSSTTKTSDVKEIFHQFSPFSYKTVIFTK 321 (388)
T ss_pred eEEEEEcCCCCHHHHHHHHHHhcCCCCCEEEEEe
Confidence 5789999999999999999999999999999998
No 87
>TIGR01361 DAHP_synth_Bsub phospho-2-dehydro-3-deoxyheptonate aldolase. The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis.
Probab=23.97 E-value=71 Score=24.86 Aligned_cols=20 Identities=15% Similarity=0.157 Sum_probs=17.2
Q ss_pred HHHHHHHhHhCCCEEEEcCC
Q psy6779 111 GSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 111 GaIiRtA~a~Gv~~vil~~~ 130 (144)
=++.|.|.|+|++|+++-++
T Consensus 212 ~~~~~aAva~Ga~gl~iE~H 231 (260)
T TIGR01361 212 IPLAKAAIAAGADGLMIEVH 231 (260)
T ss_pred HHHHHHHHHcCCCEEEEEeC
Confidence 37889999999999999764
No 88
>PF03184 DDE_1: DDE superfamily endonuclease; InterPro: IPR004875 These proteins are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere []. ; GO: 0003676 nucleic acid binding
Probab=23.46 E-value=51 Score=23.85 Aligned_cols=43 Identities=9% Similarity=0.133 Sum_probs=33.4
Q ss_pred CCCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCccCCCCc
Q psy6779 94 SLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDN 137 (144)
Q Consensus 94 ~~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~~d~~~p 137 (144)
..+.+|+||+-.-..+. .+...|...++.-+++|+++.+.+.|
T Consensus 115 ~~~~lLllD~~~~h~~~-~~~~~~~~~~i~l~~lP~~~t~~lQP 157 (217)
T PF03184_consen 115 GRPVLLLLDSHSSHISP-EFKQLCKSNNIILVFLPPNTTHLLQP 157 (217)
T ss_pred ccccccccccccccccc-cchhhhhccccccceecccccccccc
Confidence 45788999986554433 34888999999999999998887666
No 89
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=23.10 E-value=82 Score=24.71 Aligned_cols=38 Identities=8% Similarity=0.065 Sum_probs=32.4
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcC-CccC
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSR-GCVD 133 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~-~~~d 133 (144)
..+|+||.-..+..+-.+++.=..++++++|+++ +.+.
T Consensus 187 ~~~LVl~a~~~~~d~~~~~~~f~~~~~~~~I~TKlDet~ 225 (270)
T PRK06731 187 YICLTLSASMKSKDMIEIITNFKDIHIDGIVFTKFDETA 225 (270)
T ss_pred eEEEEEcCccCHHHHHHHHHHhCCCCCCEEEEEeecCCC
Confidence 4688999999999999999998889999999998 4433
No 90
>PF14443 DBC1: DBC1
Probab=22.81 E-value=58 Score=22.78 Aligned_cols=22 Identities=32% Similarity=0.708 Sum_probs=13.1
Q ss_pred EecCCCCCc-----HHHHHHHHhHh-CCC
Q psy6779 101 CDNIRDPGN-----MGSILRVCAAV-GAR 123 (144)
Q Consensus 101 LD~i~DP~N-----lGaIiRtA~a~-Gv~ 123 (144)
||| .||.+ +=|.||++.+. |+|
T Consensus 30 LDG-~DP~~dp~~LI~TAiR~~K~~tgiD 57 (126)
T PF14443_consen 30 LDG-GDPSSDPSVLIRTAIRTCKALTGID 57 (126)
T ss_pred cCC-CCCCCCcHHHHHHHHHHHHHHhccc
Confidence 566 67776 55666666543 444
No 91
>cd04816 PA_SaNapH_like PA_SaNapH_like: Protease-associated domain containing proteins like Streptomyces anulatus N-acetylpuromycin N-acetylhydrolase (SaNapH).This group contains various PA domain-containing proteins similar SaNapH. Proteins in this group belong to the peptidase M28 family. NapH is a terminal enzyme in the puromycin biosynthetic pathway; NapH hydrolyzes N-acetylpuromycin to the active antibiotic. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
Probab=22.73 E-value=2.3e+02 Score=18.93 Aligned_cols=35 Identities=20% Similarity=0.147 Sum_probs=26.5
Q ss_pred CCeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCc
Q psy6779 95 LPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGC 131 (144)
Q Consensus 95 ~~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~ 131 (144)
.+.++++++=. -.+..-.+-|.+.|+.++|+-.+.
T Consensus 43 ~GkIvLv~rg~--c~f~~K~~~A~~aGA~avIi~n~~ 77 (122)
T cd04816 43 KGAIVLVDRGG--CPFADKQKVAAARGAVAVIVVNNS 77 (122)
T ss_pred CCeEEEEECCC--CCHHHHHHHHHHCCCcEEEEEeCC
Confidence 35677777533 348889999999999999996543
No 92
>PRK08673 3-deoxy-7-phosphoheptulonate synthase; Reviewed
Probab=22.47 E-value=78 Score=25.75 Aligned_cols=20 Identities=15% Similarity=0.195 Sum_probs=17.5
Q ss_pred HHHHHHHhHhCCCEEEEcCC
Q psy6779 111 GSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 111 GaIiRtA~a~Gv~~vil~~~ 130 (144)
-.+-|.|.|+|++|+++-.+
T Consensus 280 ~~~a~AAvA~GAdGliIE~H 299 (335)
T PRK08673 280 EPLALAAVAAGADGLIVEVH 299 (335)
T ss_pred HHHHHHHHHhCCCEEEEEec
Confidence 37899999999999999754
No 93
>PRK13398 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=22.35 E-value=83 Score=24.64 Aligned_cols=21 Identities=14% Similarity=0.170 Sum_probs=18.2
Q ss_pred HHHHHHHHhHhCCCEEEEcCC
Q psy6779 110 MGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 110 lGaIiRtA~a~Gv~~vil~~~ 130 (144)
+-++.+.|.|+|++|+++-++
T Consensus 213 v~~~~~aAva~Ga~Gl~iE~H 233 (266)
T PRK13398 213 VIPMAKAAIAAGADGLMIEVH 233 (266)
T ss_pred HHHHHHHHHHcCCCEEEEecc
Confidence 458899999999999999764
No 94
>COG1083 NeuA CMP-N-acetylneuraminic acid synthetase [Cell envelope biogenesis, outer membrane]
Probab=21.95 E-value=48 Score=25.49 Aligned_cols=34 Identities=18% Similarity=0.057 Sum_probs=21.4
Q ss_pred HHHHHHHHcCCceeEEEEeccc-ccccCCCCCCCCE
Q psy6779 22 RILIDALKANLKLKMVFFSQWD-ILKELPLPEDVPQ 56 (144)
Q Consensus 22 ~~v~eal~~~~~i~~l~~~~~~-~~~~l~~~~~~~~ 56 (144)
++|+.|++++. +++|+++.+. ++.+.++..|..+
T Consensus 33 ~~I~aA~ns~~-fd~VviSsDs~~Il~~A~~ygak~ 67 (228)
T COG1083 33 YTIEAALNSKL-FDKVVISSDSEEILEEAKKYGAKV 67 (228)
T ss_pred HHHHHHhcCCc-cceEEEcCCcHHHHHHHHHhCccc
Confidence 67788888764 7889887653 4444444444444
No 95
>PRK12724 flagellar biosynthesis regulator FlhF; Provisional
Probab=21.61 E-value=92 Score=26.35 Aligned_cols=34 Identities=9% Similarity=0.167 Sum_probs=32.2
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcC
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSR 129 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~ 129 (144)
..+|+||.-..+.++=.+++.-..+|++++|+++
T Consensus 335 e~~LVLsAt~~~~~~~~~~~~f~~~~~~glIlTK 368 (432)
T PRK12724 335 ENLLVLSSTSSYHHTLTVLKAYESLNYRRILLTK 368 (432)
T ss_pred eEEEEEeCCCCHHHHHHHHHHhcCCCCCEEEEEc
Confidence 5789999999999999999999999999999998
No 96
>cd05016 SIS_PGI_2 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. As an extracellular protein, PGI also has functions equivalent to neuroleukin (NLK), autocrine motility factor (AMF), and maturation factor (MF). Evidence suggests that PGI, NLK, AMF, and MF are closely related or identical. NLK is a neurotrophic growth factor that promotes regeneration and survival of neurons. The dimeric form of NLK has isomerase function, whereas its monomeric form carries out neurotrophic activity. AMF is a cytokine that stimulates cell migration and metastasis. MF mediates the differentiation of human myeloid leukemic HL-60 cells to terminal monocytic cells.
Probab=21.06 E-value=67 Score=23.25 Aligned_cols=21 Identities=24% Similarity=0.320 Sum_probs=15.8
Q ss_pred CCCeEEEEecCCCCCcHHHHHH
Q psy6779 94 SLPLNIVCDNIRDPGNMGSILR 115 (144)
Q Consensus 94 ~~~~ilvLD~i~DP~NlGaIiR 115 (144)
.+...+.+|. .||.++|+++=
T Consensus 111 ~P~~~i~l~~-l~~~~lG~L~~ 131 (164)
T cd05016 111 RPSNTIVLPE-LTPYTLGALLA 131 (164)
T ss_pred CceEEEEeCC-CCHHHHHHHHH
Confidence 4445677787 59999999874
No 97
>cd00564 TMP_TenI Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl) thiazole phosphate to yield thiamine phosphate. TenI is a enzymatically inactive regulatory protein involved in the regulation of several extracellular enzymes. This superfamily also contains other enzymatically inactive proteins with unknown functions.
Probab=21.04 E-value=1.9e+02 Score=20.26 Aligned_cols=29 Identities=14% Similarity=0.142 Sum_probs=13.6
Q ss_pred EEecCCCCCcHHHHHHHHhHhCCCEEEEc
Q psy6779 100 VCDNIRDPGNMGSILRVCAAVGARQVVCS 128 (144)
Q Consensus 100 vLD~i~DP~NlGaIiRtA~a~Gv~~vil~ 128 (144)
+.|...++.++...++.+...|++.|.+.
T Consensus 4 it~~~~~~~~~~~~l~~l~~~g~~~i~lr 32 (196)
T cd00564 4 ITDRRLDGEDLLEVVEAALKGGVTLVQLR 32 (196)
T ss_pred EeCCccccchHHHHHHHHHhcCCCEEEEe
Confidence 33333334445555555555555555443
No 98
>cd02124 PA_PoS1_like PA_PoS1_like: Protease-associated (PA) domain PoS1-like. This group includes various PA domain-containing proteins similar to Pleurotus ostreatus (Po)S1. PoSl, the main extracellular protease in P. ostreatus is a subtilisin-like serine protease belonging to the peptidase S8 family. Ca2+ and Mn2+ both stimulate the protease activity of (Po)S1. Ca2+ protects PoS1 from autolysis. PoS1 is a monomeric glycoprotein, which may play a role in the regulation of laccases in lignin formation. (Po)S1 participates in the degradation of POXA1b, and in the activation of POXA3, (POXA1b and POXA3 are laccase isoenzymes), but its effect may be indirect. The significance of the PA domain to PoS1 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.
Probab=20.80 E-value=2.9e+02 Score=18.94 Aligned_cols=34 Identities=15% Similarity=0.064 Sum_probs=26.7
Q ss_pred CeEEEEecCCCCCcHHHHHHHHhHhCCCEEEEcCCc
Q psy6779 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGC 131 (144)
Q Consensus 96 ~~ilvLD~i~DP~NlGaIiRtA~a~Gv~~vil~~~~ 131 (144)
..|+++++=. =++..=.+.|.+.|+.+||+-...
T Consensus 56 g~IaLv~rg~--c~f~~K~~nA~~aGA~aviiyn~~ 89 (129)
T cd02124 56 GYIVLVRRGT--CTFATKAANAAAKGAKYVLIYNNG 89 (129)
T ss_pred CeEEEEECCC--CCHHHHHHHHHHcCCcEEEEEECC
Confidence 4677777633 468889999999999999996443
No 99
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=20.70 E-value=1e+02 Score=22.88 Aligned_cols=18 Identities=6% Similarity=0.146 Sum_probs=9.8
Q ss_pred HHHHHHHhHhCCCEEEEc
Q psy6779 111 GSILRVCAAVGARQVVCS 128 (144)
Q Consensus 111 GaIiRtA~a~Gv~~vil~ 128 (144)
-..++.+...|+.-|++.
T Consensus 71 ~~~~~~~~~~~ipvV~~~ 88 (270)
T cd06308 71 TPVVEEAYRAGIPVILLD 88 (270)
T ss_pred hHHHHHHHHCCCCEEEeC
Confidence 344555555566655553
No 100
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=20.57 E-value=98 Score=22.79 Aligned_cols=33 Identities=15% Similarity=0.164 Sum_probs=26.6
Q ss_pred EEE-EecCCCCCcHHHHHHHHhHhCCCEEEEcCC
Q psy6779 98 NIV-CDNIRDPGNMGSILRVCAAVGARQVVCSRG 130 (144)
Q Consensus 98 ilv-LD~i~DP~NlGaIiRtA~a~Gv~~vil~~~ 130 (144)
+.+ .|.-.|+...-+.++.+..-|+|+||+..-
T Consensus 31 ~~~~~~~~~d~~~q~~~i~~~i~~~~d~Iiv~~~ 64 (257)
T PF13407_consen 31 VEIVFDAQNDPEEQIEQIEQAISQGVDGIIVSPV 64 (257)
T ss_dssp EEEEEESTTTHHHHHHHHHHHHHTTESEEEEESS
T ss_pred EEEeCCCCCCHHHHHHHHHHHHHhcCCEEEecCC
Confidence 344 588888888889999999999999888653
Done!