Query psy17590
Match_columns 98
No_of_seqs 102 out of 216
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 17:59:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17590.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17590hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0334|consensus 99.8 6.3E-20 1.4E-24 159.9 4.0 91 2-93 907-997 (997)
2 KOG1960|consensus 99.1 5.1E-11 1.1E-15 97.5 2.0 70 3-72 103-173 (531)
3 cd02395 SF1_like-KH Splicing f 98.3 2.9E-06 6.3E-11 58.9 6.4 61 12-72 24-95 (120)
4 KOG0119|consensus 98.1 7E-06 1.5E-10 68.8 6.5 63 12-74 162-232 (554)
5 PF00013 KH_1: KH domain syndr 96.9 0.0048 1.1E-07 36.6 5.7 44 11-66 17-60 (60)
6 cd02396 PCBP_like_KH K homolog 96.5 0.014 2.9E-07 35.6 6.0 48 11-66 17-64 (65)
7 cd02393 PNPase_KH Polynucleoti 96.5 0.0084 1.8E-07 36.5 4.9 42 12-67 20-61 (61)
8 KOG1588|consensus 95.7 0.018 3.9E-07 45.0 4.5 60 12-71 116-190 (259)
9 COG5176 MSL5 Splicing factor ( 94.7 0.037 8E-07 42.8 3.4 63 12-74 172-242 (269)
10 cd00105 KH-I K homology RNA-bi 94.5 0.26 5.6E-06 28.8 6.2 47 11-66 17-63 (64)
11 cd02394 vigilin_like_KH K homo 94.4 0.11 2.4E-06 30.9 4.3 44 12-66 18-61 (62)
12 TIGR03665 arCOG04150 arCOG0415 93.4 0.26 5.7E-06 35.7 5.5 46 11-72 106-151 (172)
13 smart00322 KH K homology RNA-b 93.4 0.45 9.9E-06 27.1 5.7 49 11-70 20-68 (69)
14 PRK13763 putative RNA-processi 92.6 0.44 9.6E-06 34.7 5.9 46 11-72 112-157 (180)
15 KOG1676|consensus 89.8 1.2 2.5E-05 38.7 6.4 56 12-75 248-303 (600)
16 KOG2814|consensus 89.2 1.4 3E-05 35.9 6.1 54 11-74 74-127 (345)
17 PRK13763 putative RNA-processi 87.9 2.2 4.7E-05 31.1 6.0 47 12-71 21-70 (180)
18 TIGR03665 arCOG04150 arCOG0415 87.2 2.5 5.4E-05 30.5 6.0 48 11-71 15-64 (172)
19 PF13014 KH_3: KH domain 84.1 2.9 6.2E-05 23.2 4.0 18 12-29 9-26 (43)
20 PRK01381 Trp operon repressor; 80.8 0.73 1.6E-05 31.3 0.8 27 6-32 43-76 (99)
21 PF03439 Spt5-NGN: Early trans 80.4 1.4 3E-05 28.3 2.0 35 27-68 32-66 (84)
22 PF00408 PGM_PMM_IV: Phosphogl 79.1 5.1 0.00011 24.6 4.2 32 40-71 42-73 (73)
23 TIGR03591 polynuc_phos polyrib 77.2 6.5 0.00014 34.3 5.7 47 11-71 568-614 (684)
24 PF01371 Trp_repressor: Trp re 77.1 0.6 1.3E-05 30.9 -0.5 24 6-29 37-65 (87)
25 TIGR02696 pppGpp_PNP guanosine 76.8 6.8 0.00015 34.7 5.7 47 12-72 596-642 (719)
26 PRK14321 glmM phosphoglucosami 74.3 7.9 0.00017 31.5 5.2 36 40-75 412-447 (449)
27 PRK14316 glmM phosphoglucosami 71.2 12 0.00025 30.4 5.5 35 40-74 411-445 (448)
28 PRK14318 glmM phosphoglucosami 69.2 12 0.00025 30.5 5.1 35 40-74 413-447 (448)
29 KOG2190|consensus 68.5 14 0.0003 31.2 5.5 55 12-74 156-210 (485)
30 PRK14317 glmM phosphoglucosami 68.3 14 0.00031 30.2 5.5 35 40-74 430-464 (465)
31 PRK14314 glmM phosphoglucosami 66.3 16 0.00034 29.8 5.3 35 40-74 415-449 (450)
32 PRK14320 glmM phosphoglucosami 66.2 14 0.00029 30.1 4.9 35 40-74 408-442 (443)
33 PRK11824 polynucleotide phosph 66.2 11 0.00025 32.8 4.7 48 11-72 571-618 (693)
34 PRK10887 glmM phosphoglucosami 63.9 17 0.00036 29.6 5.0 34 40-73 409-442 (443)
35 COG3140 Uncharacterized protei 63.1 8.5 0.00018 23.9 2.4 23 53-75 7-29 (60)
36 PF09840 DUF2067: Uncharacteri 61.4 35 0.00077 25.3 6.0 32 45-77 34-65 (190)
37 PF00936 BMC: BMC domain; Int 61.4 26 0.00056 21.9 4.6 27 46-73 39-65 (75)
38 PF13065 DUF3928: Protein of u 61.1 30 0.00065 22.9 4.9 62 10-71 7-69 (95)
39 PLN00207 polyribonucleotide nu 60.9 18 0.0004 32.9 5.1 46 12-71 703-749 (891)
40 PRK14323 glmM phosphoglucosami 60.4 22 0.00048 28.8 5.1 33 40-72 405-437 (440)
41 KOG1960|consensus 58.7 20 0.00044 30.4 4.7 62 14-76 235-299 (531)
42 COG1094 Predicted RNA-binding 57.2 9.7 0.00021 28.7 2.4 25 11-35 119-143 (194)
43 COG3286 Uncharacterized protei 56.2 42 0.00092 25.6 5.6 44 44-93 36-79 (204)
44 PRK14319 glmM phosphoglucosami 55.8 29 0.00064 28.0 5.1 33 40-72 392-424 (430)
45 PF14026 DUF4242: Protein of u 55.5 23 0.00049 22.4 3.6 24 42-65 43-66 (77)
46 PF04406 TP6A_N: Type IIB DNA 53.8 20 0.00043 21.9 3.0 44 15-71 14-59 (68)
47 PRK14322 glmM phosphoglucosami 52.4 33 0.00072 27.7 4.9 32 40-71 397-428 (429)
48 cd02978 KaiB_like KaiB-like fa 51.2 24 0.00051 22.5 3.1 28 46-74 3-30 (72)
49 COG3870 Uncharacterized protei 50.5 29 0.00063 24.0 3.6 42 50-91 44-85 (109)
50 PRK14324 glmM phosphoglucosami 50.5 45 0.00097 27.2 5.4 35 40-74 410-444 (446)
51 PRK09542 manB phosphomannomuta 50.0 34 0.00074 27.8 4.7 57 15-71 377-443 (445)
52 PRK05114 hypothetical protein; 49.2 18 0.0004 22.4 2.3 23 53-75 7-29 (59)
53 PF02741 FTR_C: FTR, proximal 48.4 27 0.00058 25.5 3.4 21 45-65 97-117 (150)
54 TIGR02654 circ_KaiB circadian 48.1 34 0.00075 22.6 3.6 28 46-74 5-32 (87)
55 COG1185 Pnp Polyribonucleotide 48.0 45 0.00098 29.7 5.3 48 12-73 570-617 (692)
56 cd03084 phosphohexomutase The 47.8 32 0.0007 26.8 4.1 30 40-69 325-354 (355)
57 PF03701 UPF0181: Uncharacteri 47.6 21 0.00047 21.5 2.4 23 54-76 8-30 (51)
58 PF00352 TBP: Transcription fa 47.5 47 0.001 21.0 4.2 43 30-72 29-84 (86)
59 cd03089 PMM_PGM The phosphoman 47.1 32 0.00069 27.8 4.0 58 12-69 376-442 (443)
60 PRK14315 glmM phosphoglucosami 46.2 54 0.0012 26.7 5.2 33 40-72 413-445 (448)
61 PRK15414 phosphomannomutase Cp 45.8 32 0.00069 28.1 3.9 33 40-72 423-456 (456)
62 TIGR01455 glmM phosphoglucosam 45.6 50 0.0011 26.7 5.0 32 40-71 411-442 (443)
63 TIGR01321 TrpR trp operon repr 45.5 7.7 0.00017 26.1 0.2 28 5-32 42-76 (94)
64 PF07288 DUF1447: Protein of u 43.9 72 0.0016 20.4 4.5 35 32-66 4-39 (69)
65 PF00381 PTS-HPr: PTS HPr comp 43.0 54 0.0012 20.4 3.9 55 15-72 21-83 (84)
66 COG1109 {ManB} Phosphomannomut 43.0 57 0.0012 26.8 5.0 35 40-74 427-461 (464)
67 PRK09301 circadian clock prote 41.8 46 0.00099 22.7 3.6 29 45-74 7-35 (103)
68 COG3265 GntK Gluconate kinase 41.7 23 0.00051 26.0 2.3 40 29-68 111-159 (161)
69 smart00877 BMC Bacterial micro 41.7 69 0.0015 20.0 4.2 26 46-72 38-63 (75)
70 KOG1676|consensus 41.4 30 0.00066 30.2 3.2 56 13-75 337-392 (600)
71 cd07046 BMC_PduU-EutS 1,2-prop 41.1 50 0.0011 22.6 3.7 28 46-74 73-100 (110)
72 TIGR01132 pgm phosphoglucomuta 40.2 71 0.0015 26.9 5.2 33 40-72 507-540 (543)
73 cd06200 SiR_like1 Cytochrome p 39.4 1E+02 0.0022 22.8 5.5 39 48-92 204-242 (245)
74 PLN02371 phosphoglucosamine mu 39.3 67 0.0015 27.4 5.0 34 40-73 536-569 (583)
75 PRK07564 phosphoglucomutase; V 39.0 83 0.0018 26.4 5.4 33 40-72 506-539 (543)
76 PF12513 SUV3_C: Mitochondrial 39.0 69 0.0015 18.3 3.6 23 54-76 26-48 (49)
77 COG2101 SPT15 TATA-box binding 38.7 97 0.0021 23.3 5.1 41 32-72 128-181 (185)
78 COG1761 RPB11 DNA-directed RNA 38.7 1.1E+02 0.0023 20.7 4.9 37 40-76 52-90 (99)
79 cd04904 ACT_AAAH ACT domain of 38.6 56 0.0012 19.9 3.4 26 43-69 41-66 (74)
80 KOG2191|consensus 38.2 1E+02 0.0023 25.6 5.6 53 13-74 151-206 (402)
81 cd04931 ACT_PAH ACT domain of 37.8 52 0.0011 21.4 3.3 28 43-70 55-82 (90)
82 PRK04163 exosome complex RNA-b 37.2 65 0.0014 24.3 4.1 49 11-73 162-210 (235)
83 PF04175 DUF406: Protein of un 37.1 1.3E+02 0.0028 20.1 5.2 45 30-74 12-56 (94)
84 PF02829 3H: 3H domain; Inter 36.8 71 0.0015 21.3 3.9 20 49-68 74-93 (98)
85 PF14893 PNMA: PNMA 36.2 21 0.00045 28.8 1.4 34 49-95 21-54 (331)
86 cd05800 PGM_like2 This PGM-lik 35.4 60 0.0013 26.3 4.0 30 40-69 431-460 (461)
87 TIGR00318 cyaB adenylyl cyclas 34.8 53 0.0012 23.4 3.2 63 9-72 83-156 (174)
88 smart00361 RRM_1 RNA recogniti 33.9 1E+02 0.0023 18.2 6.5 44 22-67 15-58 (70)
89 cd06169 BMC Bacterial Micro-Co 33.2 59 0.0013 19.4 2.8 25 44-69 37-61 (62)
90 cd01026 TOPRIM_OLD TOPRIM_OLD: 32.5 40 0.00086 21.5 2.0 18 49-66 7-24 (97)
91 cd07049 BMC_EutL_repeat1 ethan 32.4 88 0.0019 21.4 3.8 27 47-73 74-100 (103)
92 PHA01632 hypothetical protein 32.4 55 0.0012 20.4 2.5 22 45-66 15-40 (64)
93 cd05805 MPG1_transferase GTP-m 31.4 76 0.0017 25.6 3.9 29 40-68 411-439 (441)
94 cd04880 ACT_AAAH-PDT-like ACT 31.1 81 0.0018 18.7 3.2 44 23-69 23-67 (75)
95 PF02796 HTH_7: Helix-turn-hel 31.1 25 0.00055 19.6 0.8 26 4-29 12-37 (45)
96 PF03506 Flu_C_NS1: Influenza 30.3 28 0.00061 24.8 1.1 36 17-52 12-51 (162)
97 PF08915 tRNA-Thr_ED: Archaea- 29.6 49 0.0011 23.7 2.3 27 46-72 39-69 (138)
98 COG4401 AroH Chorismate mutase 29.4 79 0.0017 22.3 3.2 25 50-74 11-35 (125)
99 PF13388 DUF4106: Protein of u 29.1 31 0.00068 28.3 1.3 26 24-49 162-190 (422)
100 cd04929 ACT_TPH ACT domain of 28.7 82 0.0018 19.6 3.0 26 43-69 41-66 (74)
101 PF11869 DUF3389: Protein of u 26.8 40 0.00087 21.9 1.3 23 6-28 51-75 (75)
102 PRK14622 hypothetical protein; 26.2 1.6E+02 0.0035 19.6 4.3 23 57-79 72-94 (103)
103 KOG3101|consensus 26.1 66 0.0014 25.4 2.6 33 20-54 21-53 (283)
104 PRK00394 transcription factor; 25.8 2.4E+02 0.0053 20.5 5.5 43 30-72 119-174 (179)
105 PRK13667 hypothetical protein; 25.6 1.9E+02 0.0041 18.5 4.3 33 32-64 5-38 (70)
106 PRK00596 rpsJ 30S ribosomal pr 25.3 1.4E+02 0.003 19.8 3.7 28 45-72 4-31 (102)
107 PRK02114 formylmethanofuran--t 25.1 1E+02 0.0022 24.8 3.5 21 45-65 242-262 (297)
108 KOG0071|consensus 24.7 1E+02 0.0022 22.9 3.2 32 43-74 84-115 (180)
109 COG2877 KdsA 3-deoxy-D-manno-o 24.6 44 0.00095 26.5 1.4 36 20-55 127-170 (279)
110 TIGR01049 rpsJ_bact ribosomal 24.6 1.6E+02 0.0034 19.3 3.9 27 46-72 2-28 (99)
111 PF14259 RRM_6: RNA recognitio 24.5 1.5E+02 0.0032 16.9 4.5 36 29-67 25-60 (70)
112 PRK12271 rps10p 30S ribosomal 24.5 1.7E+02 0.0038 19.5 4.1 27 46-72 3-29 (102)
113 cd05801 PGM_like3 This bacteri 24.4 1.5E+02 0.0032 24.8 4.5 29 40-68 491-520 (522)
114 PHA03323 nuclear egress membra 24.2 1E+02 0.0023 24.4 3.4 51 21-71 83-136 (272)
115 PF03445 DUF294: Putative nucl 24.1 2.4E+02 0.0053 19.2 5.5 45 52-97 13-57 (138)
116 PRK08363 alanine aminotransfer 23.9 2.4E+02 0.0051 22.0 5.4 27 48-74 369-396 (398)
117 PF12714 TILa: TILa domain 23.6 46 0.00099 19.7 1.0 11 29-39 5-15 (56)
118 PRK15405 ethanolamine utilizat 23.2 1.7E+02 0.0037 22.5 4.3 33 44-76 80-112 (217)
119 cd07890 CYTH-like_AC_IV-like A 23.1 85 0.0018 21.9 2.5 60 11-72 85-153 (169)
120 cd07758 ThTPase Thiamine Triph 22.8 1.2E+02 0.0026 22.1 3.4 27 48-74 147-176 (196)
121 cd01181 IPT_plexin_repeat3 Thi 22.8 57 0.0012 21.3 1.5 26 23-53 15-40 (99)
122 PF13730 HTH_36: Helix-turn-he 22.8 93 0.002 17.4 2.3 16 53-68 36-51 (55)
123 PF01476 LysM: LysM domain; I 22.5 23 0.00049 19.0 -0.4 19 9-27 2-20 (44)
124 PF00356 LacI: Bacterial regul 22.1 24 0.00052 20.3 -0.4 23 15-37 1-23 (46)
125 TIGR01046 S10_Arc_S20_Euk ribo 22.0 2E+02 0.0042 19.1 4.0 27 46-72 2-28 (99)
126 PLN02607 1-aminocyclopropane-1 21.3 4.4E+02 0.0096 21.4 6.7 46 30-76 394-441 (447)
127 smart00215 VWC_out von Willebr 21.3 67 0.0014 20.0 1.5 15 28-42 2-16 (67)
128 PRK06225 aspartate aminotransf 21.3 3.4E+02 0.0074 20.9 5.8 25 48-72 351-376 (380)
129 COG3360 Uncharacterized conser 21.1 78 0.0017 20.3 1.8 18 49-66 9-26 (71)
130 CHL00135 rps10 ribosomal prote 20.9 1.8E+02 0.0039 19.4 3.7 28 45-72 7-34 (101)
131 PF10728 DUF2520: Domain of un 20.9 1.4E+02 0.0029 20.6 3.1 21 47-68 2-22 (132)
132 PLN00062 TATA-box-binding prot 20.9 2.9E+02 0.0064 20.2 5.1 42 32-73 120-174 (179)
133 COG0360 RpsF Ribosomal protein 20.8 2.9E+02 0.0062 18.9 4.9 41 54-95 13-64 (112)
134 PF09435 DUF2015: Fungal prote 20.5 89 0.0019 22.2 2.1 20 54-73 77-97 (128)
135 cd03087 PGM_like1 This archaea 20.5 1.6E+02 0.0035 23.7 3.9 28 40-67 409-436 (439)
136 PF01913 FTR: Formylmethanofur 20.5 3.4E+02 0.0074 19.6 5.2 45 17-62 35-87 (144)
137 cd04518 TBP_archaea archaeal T 20.3 2.6E+02 0.0056 20.3 4.7 43 30-72 118-173 (174)
No 1
>KOG0334|consensus
Probab=99.78 E-value=6.3e-20 Score=159.93 Aligned_cols=91 Identities=45% Similarity=0.645 Sum_probs=85.0
Q ss_pred CchhHHHHhccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy17590 2 LKSPIHLLALLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKEELIKLSSSA 81 (98)
Q Consensus 2 lpq~~R~~vT~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~~~~~~~~ 81 (98)
+||.+||++|+++++..|.|.++++||+||.|||+++.|.+||++|||+|||.++.+|++|+.++++.+++++.++....
T Consensus 907 ~Pq~~r~~vt~~~~L~~i~e~~~~~it~rg~f~~~gk~p~~gErklyl~ve~~~e~~vqra~~e~~r~l~e~~~~~~~~~ 986 (997)
T KOG0334|consen 907 FPQNARWRVTYKEALLRISEPTAAGITTRGKFNPPGKEPKPGERKLYLLVEGPDELSVQRAIEELERLLEEEVVNLFSSL 986 (997)
T ss_pred cchhcceeeechhhhhhccCccccceeeccccCCCCCCCCCcchhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999985444
Q ss_pred cCCCCCCceEEe
Q psy17590 82 HQSINKSRYKGV 93 (98)
Q Consensus 82 ~~~~~~GRY~V~ 93 (98)
+...+|||.|+
T Consensus 987 -~~~~~~~y~~~ 997 (997)
T KOG0334|consen 987 -QPSCKGRYLVV 997 (997)
T ss_pred -CCCccceeecC
Confidence 44449999986
No 2
>KOG1960|consensus
Probab=99.06 E-value=5.1e-11 Score=97.50 Aligned_cols=70 Identities=19% Similarity=0.155 Sum_probs=64.2
Q ss_pred chhHHHHhccHHHHHHhHhhhcceeeeeceeeCCCCCC-CCCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 3 KSPIHLLALLGEALAQISEYSEAGITVRGIYIPPGKNP-PEGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 3 pq~~R~~vT~~~tl~~I~e~Tga~It~KG~y~ppg~~p-~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
|+.+|+.+|.+.++++|.++||+.|.+||+|.++..++ .+++++||+||.|.|.+.|++|++.|+-+...
T Consensus 103 ~~~~~~~~TRg~~~d~Ie~~~G~~~~~RGs~~~~El~~vg~~~~pLv~hI~~~T~Ei~~~Ai~RIkgv~~~ 173 (531)
T KOG1960|consen 103 LQSTKATSTRGTSYDHIEGITGTTSASRGSAPAPELPPVGSSEGPLVDHIPPSTAEITSKAIERIKGVFMQ 173 (531)
T ss_pred cccccceeccchhHHhhhhhccceeeccCCCCCccCCCCCCCCCcceeecCCccHHHHHHHHhhCccceee
Confidence 78899999999999999999999999999999999875 46889999999999999999999999954443
No 3
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.28 E-value=2.9e-06 Score=58.89 Aligned_cols=61 Identities=30% Similarity=0.351 Sum_probs=47.9
Q ss_pred cHHHHHHhHhhhcceeeeeceee--CCCCC-----CC--CCCCceEEEEEeCC--HHHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYI--PPGKN-----PP--EGERKLFLAIESTN--ELAVSKAKVEITRLIKE 72 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~--ppg~~-----p~--~ge~kLYL~Ieg~t--e~~V~~A~~eIk~ii~e 72 (98)
.+.|+.+|+++|||.|.++|.-- ..++. |. ..+-+||++|+|++ .+++++|+..|+.++.+
T Consensus 24 gG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~~ 95 (120)
T cd02395 24 RGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLKP 95 (120)
T ss_pred CChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhcc
Confidence 57899999999999999998521 11111 11 13467999999999 99999999999999984
No 4
>KOG0119|consensus
Probab=98.12 E-value=7e-06 Score=68.79 Aligned_cols=63 Identities=24% Similarity=0.347 Sum_probs=50.1
Q ss_pred cHHHHHHhHhhhcceeeeecee-eCCCC------CC-CCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIY-IPPGK------NP-PEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y-~ppg~------~p-~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
.++||+++.++|||.|.+||.= +-.|+ .. ..-+-+||.+|++.|++.|++|++.|+.+|.+++
T Consensus 162 RG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av 232 (554)
T KOG0119|consen 162 RGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAV 232 (554)
T ss_pred CccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhc
Confidence 5789999999999999999932 22222 01 1134889999999999999999999999999743
No 5
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=96.87 E-value=0.0048 Score=36.62 Aligned_cols=44 Identities=23% Similarity=0.237 Sum_probs=36.5
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEI 66 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eI 66 (98)
-++.++.+|.+.|||.|.+... + ..-.+.|.| +.+.|++|.++|
T Consensus 17 ~~G~~i~~I~~~t~~~I~i~~~----------~-~~~~v~I~G-~~~~v~~A~~~I 60 (60)
T PF00013_consen 17 KKGSNIKEIEEETGVKIQIPDD----------D-ERDIVTISG-SPEQVEKAKKMI 60 (60)
T ss_dssp GGGHHHHHHHHHHTSEEEEEST----------T-EEEEEEEEE-SHHHHHHHHHHH
T ss_pred CCCCcHHHhhhhcCeEEEEcCC----------C-CcEEEEEEe-CHHHHHHHHhhC
Confidence 3678999999999999998332 2 445889999 999999999876
No 6
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=96.53 E-value=0.014 Score=35.60 Aligned_cols=48 Identities=31% Similarity=0.309 Sum_probs=35.8
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEI 66 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eI 66 (98)
.+++++.+|.+.|||.|++- +...+.+.++ -+.|+|. .+.|++|+.+|
T Consensus 17 ~~G~~i~~i~~~tga~I~i~-----~~~~~~~~~r--~v~I~G~-~~~v~~A~~~I 64 (65)
T cd02396 17 KGGSTIKEIREETGAKIRVS-----KSVLPGSTER--VVTISGK-PSAVQKALLLI 64 (65)
T ss_pred CCcHHHHHHHHHHCCEEEEc-----CCCCCCCCce--EEEEEeC-HHHHHHHHHhh
Confidence 36789999999999999983 3332334444 3788887 78889998876
No 7
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=96.48 E-value=0.0084 Score=36.52 Aligned_cols=42 Identities=26% Similarity=0.336 Sum_probs=35.1
Q ss_pred cHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEIT 67 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk 67 (98)
.++++.+|++.|||.|.+ +. .+ .+.|.|++.++|+.|+.+|+
T Consensus 20 gG~~ik~I~~~tg~~I~i-----~~-----~g----~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 20 GGKTIKKIIEETGVKIDI-----ED-----DG----TVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred CchHHHHHHHHHCCEEEe-----CC-----CC----EEEEEeCCHHHHHHHHHHhC
Confidence 678999999999999975 22 12 49999999999999999873
No 8
>KOG1588|consensus
Probab=95.70 E-value=0.018 Score=45.01 Aligned_cols=60 Identities=23% Similarity=0.239 Sum_probs=45.4
Q ss_pred cHHHHHHhHhhhcceeeeeceeeCCCCCC------CC----CCCceEEEEEeCC-----HHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYIPPGKNP------PE----GERKLFLAIESTN-----ELAVSKAKVEITRLIK 71 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~ppg~~p------~~----ge~kLYL~Ieg~t-----e~~V~~A~~eIk~ii~ 71 (98)
++.|+.++.++|||.|.+||+--=..+.- .+ =+.+||++||... ...+..|+++|+.+|.
T Consensus 116 rGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~ 190 (259)
T KOG1588|consen 116 RGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLV 190 (259)
T ss_pred CcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcC
Confidence 57799999999999999999865444321 11 1478999999644 3567789999999874
No 9
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.69 E-value=0.037 Score=42.78 Aligned_cols=63 Identities=24% Similarity=0.218 Sum_probs=52.1
Q ss_pred cHHHHHHhHhhhcceeeeeceeeCCCCCCCC--------CCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYIPPGKNPPE--------GERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~--------ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
.+.||.++.+-|+|.|-+||.|--..-+..+ -+-.|+-+|++.++..+.+++..+..+|.++.
T Consensus 172 RG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~~~ik~~~n~I~~a~ 242 (269)
T COG5176 172 RGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREAR 242 (269)
T ss_pred CcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhHHHHHHHHHHHHHHHh
Confidence 4689999999999999999998655433211 35789999999999999999999988888754
No 10
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=94.52 E-value=0.26 Score=28.83 Aligned_cols=47 Identities=30% Similarity=0.319 Sum_probs=34.6
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEI 66 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eI 66 (98)
.++.++.+|.+.|||.|.+. +... ++..--+.|.|+ .+.|..|..+|
T Consensus 17 ~~G~~i~~I~~~s~~~I~i~-----~~~~---~~~~~~v~i~G~-~~~v~~a~~~i 63 (64)
T cd00105 17 KGGSTIKEIREETGAKIKIP-----DSGS---GSEERIVTITGT-PEAVEKAKELI 63 (64)
T ss_pred CCCHHHHHHHHHHCCEEEEc-----CCCC---CCCceEEEEEcC-HHHHHHHHHHh
Confidence 47889999999999999854 3221 233344778888 78888888876
No 11
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=94.35 E-value=0.11 Score=30.85 Aligned_cols=44 Identities=25% Similarity=0.242 Sum_probs=33.5
Q ss_pred cHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEI 66 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eI 66 (98)
++.++.+|.+.|||.|.+- +.. +..=.+.|.|+ ++.|..|+.+|
T Consensus 18 ~G~~i~~i~~~~g~~I~i~-----~~~-----~~~~~v~I~G~-~~~v~~A~~~i 61 (62)
T cd02394 18 KGSNIRKIMEETGVKIRFP-----DPG-----SKSDTITITGP-KENVEKAKEEI 61 (62)
T ss_pred CCCcHHHHHHHhCCEEEcC-----CCC-----CCCCEEEEEcC-HHHHHHHHHHh
Confidence 4689999999999998653 322 22334789999 77999999887
No 12
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=93.36 E-value=0.26 Score=35.66 Aligned_cols=46 Identities=26% Similarity=0.275 Sum_probs=39.5
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
.+++|+..|++.|||.|.+.| . .+.|.| +.+.++.|...|.++++.
T Consensus 106 ~~G~t~~~ie~~t~~~i~i~~-------------~--~v~i~G-~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 106 EGGKTRRIIEELTGVSISVYG-------------K--TVGIIG-DPEQVQIAREAIEMLIEG 151 (172)
T ss_pred CCcHHHHHHHHHHCCeEEEcC-------------C--EEEEEC-CHHHHHHHHHHHHHHHcC
Confidence 467899999999999998864 1 488999 999999999999998843
No 13
>smart00322 KH K homology RNA-binding domain.
Probab=93.35 E-value=0.45 Score=27.12 Aligned_cols=49 Identities=18% Similarity=0.140 Sum_probs=37.6
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLI 70 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii 70 (98)
.++.++.+|.+.|||.|.+.+.-. ..--+.|.|+ ...+..|...|.+.+
T Consensus 20 ~~G~~i~~i~~~~~~~i~~~~~~~----------~~~~v~i~g~-~~~v~~a~~~i~~~~ 68 (69)
T smart00322 20 KGGSTIKKIEEETGVKIDIPEDGS----------EERVVEITGP-PENVEKAAELILEIL 68 (69)
T ss_pred CCchHHHHHHHHHCCEEEECCCCC----------CccEEEEEcC-HHHHHHHHHHHHHHh
Confidence 478899999999999998842111 3344888898 899999999888765
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=92.64 E-value=0.44 Score=34.74 Aligned_cols=46 Identities=28% Similarity=0.268 Sum_probs=38.6
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
.+++++..|++.|||.|.+.|. . +.|.| +.+.++.|...|++++..
T Consensus 112 ~~G~~~k~ie~~t~~~i~i~~~-------------~--v~i~G-~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 112 EGGKTRRIIEELTGVDISVYGK-------------T--VAIIG-DPEQVEIAREAIEMLIEG 157 (180)
T ss_pred CCcHHHHHHHHHHCcEEEEcCC-------------E--EEEEe-CHHHHHHHHHHHHHHHcC
Confidence 4678999999999999998642 1 67778 899999999999998853
No 15
>KOG1676|consensus
Probab=89.84 E-value=1.2 Score=38.66 Aligned_cols=56 Identities=25% Similarity=0.271 Sum_probs=42.7
Q ss_pred cHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKEELI 75 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~~ 75 (98)
.+|++++|+.+|||.|+. .|+.. |..-||.| .|-|+ ...+.+|.+.|++||.+...
T Consensus 248 gGE~IKklq~etG~KIQf----kpDd~-p~speR~~--~IiG~-~d~ie~Aa~lI~eii~~~~~ 303 (600)
T KOG1676|consen 248 GGEMIKKLQNETGAKIQF----KPDDD-PSSPERPA--QIIGT-VDQIEHAAELINEIIAEAEA 303 (600)
T ss_pred CchHHHHHhhccCceeEe----ecCCC-CCCcccee--eeecC-HHHHHHHHHHHHHHHHHHhc
Confidence 579999999999999964 45554 34446664 56674 67899999999999997553
No 16
>KOG2814|consensus
Probab=89.20 E-value=1.4 Score=35.87 Aligned_cols=54 Identities=20% Similarity=0.244 Sum_probs=48.2
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
+++.|+.+|.++|+|.|.+ |.+++.+=.+-|+|.+..+|.+|...|.-+|.+.-
T Consensus 74 ~~g~trkkle~Etq~~i~l----------p~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 74 KQGKTRKKLEEETQTNIFL----------PRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred ccchHHHHHHHhhccceEc----------cCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 5789999999999999865 66778888999999999999999999999988754
No 17
>PRK13763 putative RNA-processing protein; Provisional
Probab=87.90 E-value=2.2 Score=31.09 Aligned_cols=47 Identities=23% Similarity=0.260 Sum_probs=39.2
Q ss_pred cHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEE---eCCHHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIE---STNELAVSKAKVEITRLIK 71 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ie---g~te~~V~~A~~eIk~ii~ 71 (98)
.++++..|++.|||.|.+--. +. .+.|. +.+..++++|+..|+.+..
T Consensus 21 gGk~Ik~I~e~tg~~I~i~~~-----------~g--~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 21 KGETKKEIEERTGVKLEIDSE-----------TG--EVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred chhHHHHHHHHHCcEEEEECC-----------CC--eEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 468999999999999998631 12 45677 8999999999999999887
No 18
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=87.19 E-value=2.5 Score=30.51 Aligned_cols=48 Identities=23% Similarity=0.259 Sum_probs=39.7
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEE--EeCCHHHHHHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAI--ESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~I--eg~te~~V~~A~~eIk~ii~ 71 (98)
..++++..|++.|||.|.+-- ++. .+.| .+.+..++++|+..|+.+..
T Consensus 15 ~gG~~Ik~I~~~tgv~I~Id~-----------~~g--~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 15 KGGETKKEIEERTGVKLDIDS-----------ETG--EVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred CchhHHHHHHHHhCcEEEEEc-----------CCc--eEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 468999999999999999862 112 4666 78999999999999999776
No 19
>PF13014 KH_3: KH domain
Probab=84.15 E-value=2.9 Score=23.17 Aligned_cols=18 Identities=28% Similarity=0.388 Sum_probs=16.2
Q ss_pred cHHHHHHhHhhhcceeee
Q psy17590 12 LGEALAQISEYSEAGITV 29 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~ 29 (98)
++.++.+|+++|||.|.+
T Consensus 9 ~G~~I~~I~~~tg~~I~i 26 (43)
T PF13014_consen 9 GGSTIKEIREETGAKIQI 26 (43)
T ss_pred CChHHHHHHHHhCcEEEE
Confidence 578999999999999976
No 20
>PRK01381 Trp operon repressor; Provisional
Probab=80.75 E-value=0.73 Score=31.32 Aligned_cols=27 Identities=19% Similarity=0.197 Sum_probs=22.8
Q ss_pred HHHHhcc-----HHHHHHhHhhhcceeee--ece
Q psy17590 6 IHLLALL-----GEALAQISEYSEAGITV--RGI 32 (98)
Q Consensus 6 ~R~~vT~-----~~tl~~I~e~Tga~It~--KG~ 32 (98)
.||.|.+ .-++.+|.+.+|+||++ ||.
T Consensus 43 ~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgs 76 (99)
T PRK01381 43 TRVRIVEELLRGELSQREIKQELGVGIATITRGS 76 (99)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhH
Confidence 5888887 35999999999999987 775
No 21
>PF03439 Spt5-NGN: Early transcription elongation factor of RNA pol II, NGN section; InterPro: IPR005100 Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4 []. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit []. ; PDB: 3H7H_B 3QQC_D 3P8B_B 2EXU_A.
Probab=80.45 E-value=1.4 Score=28.32 Aligned_cols=35 Identities=23% Similarity=0.370 Sum_probs=24.5
Q ss_pred eeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHH
Q psy17590 27 ITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITR 68 (98)
Q Consensus 27 It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ 68 (98)
+.+.-.|.|++ -|=|++||+.++.+|.+|+..|..
T Consensus 32 l~I~Si~~~~~-------lkGyIyVEA~~~~~V~~ai~gi~~ 66 (84)
T PF03439_consen 32 LNIYSIFAPDS-------LKGYIYVEAERESDVKEAIRGIRH 66 (84)
T ss_dssp ----EEEE-TT-------STSEEEEEESSHHHHHHHHTT-TT
T ss_pred CceEEEEEeCC-------CceEEEEEeCCHHHHHHHHhcccc
Confidence 77788888877 345999999999999999987653
No 22
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=79.06 E-value=5.1 Score=24.56 Aligned_cols=32 Identities=28% Similarity=0.385 Sum_probs=27.9
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~ 71 (98)
|...||.|=+.+||.++..+++...+|...|+
T Consensus 42 ~SgTEP~iRv~~Ea~~~~~~~~~~~~i~~~ik 73 (73)
T PF00408_consen 42 PSGTEPKIRVYVEAPDEEELEEIAEEIAEAIK 73 (73)
T ss_dssp EESSSSEEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred CCCCCceEEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 45568999999999999999999999888774
No 23
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=77.25 E-value=6.5 Score=34.30 Aligned_cols=47 Identities=19% Similarity=0.196 Sum_probs=39.3
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~ 71 (98)
..+.++.+|+|+|||+|.+-- + =.+.|.+.+...+++|+..|+.+..
T Consensus 568 ~gGk~Ik~I~~~tg~~I~i~d------------d--G~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 568 PGGKVIREITEETGAKIDIED------------D--GTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred CCcHHHHHHHHHHCCEEEEec------------C--eEEEEEECcHHHHHHHHHHHHhhhc
Confidence 357899999999999999832 1 3567889999999999999998865
No 24
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=77.08 E-value=0.6 Score=30.85 Aligned_cols=24 Identities=17% Similarity=0.210 Sum_probs=20.1
Q ss_pred HHHHhcc-----HHHHHHhHhhhcceeee
Q psy17590 6 IHLLALL-----GEALAQISEYSEAGITV 29 (98)
Q Consensus 6 ~R~~vT~-----~~tl~~I~e~Tga~It~ 29 (98)
.||.|.+ +-++.+|.+.||+|+.|
T Consensus 37 ~R~~va~~lL~~g~syreIa~~tgvS~aT 65 (87)
T PF01371_consen 37 QRWQVAKELLDEGKSYREIAEETGVSIAT 65 (87)
T ss_dssp HHHHHHHHHHHTTSSHHHHHHHHTSTHHH
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHH
Confidence 4776665 78999999999999976
No 25
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=76.76 E-value=6.8 Score=34.73 Aligned_cols=47 Identities=17% Similarity=0.256 Sum_probs=39.6
Q ss_pred cHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
-+.++..|+|+||+.|.+-- + =.+.|.|++.+++++|+..|+.+...
T Consensus 596 gGk~I~~i~~~tg~~Idi~d------------~--G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 596 KGKMINQIQDETGAEISIED------------D--GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CcHhHHHHHHHHCCEEEEec------------C--cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 46789999999999998743 1 24678899999999999999999884
No 26
>PRK14321 glmM phosphoglucosamine mutase; Provisional
Probab=74.34 E-value=7.9 Score=31.54 Aligned_cols=36 Identities=19% Similarity=0.302 Sum_probs=32.0
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEELI 75 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~~ 75 (98)
|...||.|.+.+|+.|++..++-.+++.+++++.+.
T Consensus 412 pS~TeP~~riy~Ea~s~e~~~~l~~~~~~~i~~~~~ 447 (449)
T PRK14321 412 PSGTEPIMRITLEAHTEEKAEELMEKAEKLVKEAIK 447 (449)
T ss_pred cCCCCceEEEEEecCCHHHHHHHHHHHHHHHHHHhh
Confidence 667899999999999999999999999999987554
No 27
>PRK14316 glmM phosphoglucosamine mutase; Provisional
Probab=71.17 E-value=12 Score=30.40 Aligned_cols=35 Identities=20% Similarity=0.262 Sum_probs=31.2
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
|...||.+.+.+|+.|++.+++-.+++.++|++.+
T Consensus 411 pS~TEP~irvy~Ea~~~e~~~~l~~~~~~~i~~~~ 445 (448)
T PRK14316 411 PSGTEPLVRVMAEAPTQEEVDKYVDRIADVVEAEM 445 (448)
T ss_pred cCCCCcEEEEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence 66789999999999999999999999999988743
No 28
>PRK14318 glmM phosphoglucosamine mutase; Provisional
Probab=69.24 E-value=12 Score=30.51 Aligned_cols=35 Identities=17% Similarity=0.316 Sum_probs=31.6
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
|...||-+.+.+||.|++..++=..++.+++++++
T Consensus 413 pS~teP~irv~~Ea~~~~~a~~l~~~~~~~v~~~~ 447 (448)
T PRK14318 413 PSGTEPLVRVMVEAADEETARRVAGRLADVVAEAL 447 (448)
T ss_pred eCCCCcEEEEEEeECCHHHHHHHHHHHHHHHHHhc
Confidence 66789999999999999999999999999998765
No 29
>KOG2190|consensus
Probab=68.48 E-value=14 Score=31.24 Aligned_cols=55 Identities=31% Similarity=0.341 Sum_probs=41.6
Q ss_pred cHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
+++.+.+|.|.|||.|.+=+...|.. .++- +.|.| +..+|.+|+..|-.+|.+..
T Consensus 156 ~G~~Ik~Ire~TgA~I~v~~~~lP~s-----ter~--V~IsG-~~~av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 156 GGSLIKEIREETGAKIRVSSDMLPNS-----TERA--VTISG-EPDAVKKALVQISSRLLENP 210 (485)
T ss_pred CcHHHHHHHHhcCceEEecCCCCCcc-----ccee--EEEcC-chHHHHHHHHHHHHHHHhcC
Confidence 47889999999999999876633333 3333 44544 68899999999999998854
No 30
>PRK14317 glmM phosphoglucosamine mutase; Provisional
Probab=68.28 E-value=14 Score=30.15 Aligned_cols=35 Identities=11% Similarity=0.195 Sum_probs=31.1
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
|...||.+.+.+||.|++.+++-.+++.+++++.+
T Consensus 430 pS~TEP~irv~~Ea~~~~~~~~l~~~~~~~v~~~~ 464 (465)
T PRK14317 430 ASGTEPLIRVMVEAEDAELVNHWTNHLVAVVQQHL 464 (465)
T ss_pred cCCCCCEEEEEEEeCCHHHHHHHHHHHHHHHHHHh
Confidence 66789999999999999999999999999988743
No 31
>PRK14314 glmM phosphoglucosamine mutase; Provisional
Probab=66.31 E-value=16 Score=29.77 Aligned_cols=35 Identities=20% Similarity=0.244 Sum_probs=31.1
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
|...||-+.+.+||.|++.++.-.+++.+++++.+
T Consensus 415 pS~tEP~iri~~Ea~~~~~a~~l~~~~~~~v~~~~ 449 (450)
T PRK14314 415 YSGTENLCRVMVEGEDKHQVDSLAKEIADVVEKEL 449 (450)
T ss_pred cCCCCcEEEEEEeeCCHHHHHHHHHHHHHHHHHhh
Confidence 66789999999999999999999999999888754
No 32
>PRK14320 glmM phosphoglucosamine mutase; Provisional
Probab=66.25 E-value=14 Score=30.07 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=31.3
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
|...||.+.+.+||.|++.++.-.+++.++|++.+
T Consensus 408 pS~teP~~rv~~Ea~s~e~a~~l~~~~~~~i~~~~ 442 (443)
T PRK14320 408 PSGTEPVLRVMVEADDKSLATNEAEYLVEKVKQKL 442 (443)
T ss_pred cCCCCceEEEEEecCCHHHHHHHHHHHHHHHHhhc
Confidence 66789999999999999999999999999888754
No 33
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=66.16 E-value=11 Score=32.83 Aligned_cols=48 Identities=25% Similarity=0.264 Sum_probs=39.5
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
..+.|+.+|+++||+.|.++- --.+.|.+.+..++++|+..|+.+..+
T Consensus 571 ~gg~~ik~I~~~~~~~idi~d--------------~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 571 PGGKTIREITEETGAKIDIED--------------DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CCchhHHHHHHHHCCccccCC--------------CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 567899999999999887622 234788899999999999999988753
No 34
>PRK10887 glmM phosphoglucosamine mutase; Provisional
Probab=63.92 E-value=17 Score=29.56 Aligned_cols=34 Identities=18% Similarity=0.212 Sum_probs=29.8
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEE 73 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~ 73 (98)
|...||-+.+.+|+.|++.++.=..++.+++++.
T Consensus 409 pS~tEP~iri~~Ea~s~e~a~~l~~~~~~~v~~~ 442 (443)
T PRK10887 409 KSGTEPLIRVMVEGEDEAQVTALAERIADAVKAA 442 (443)
T ss_pred cCCCCeEEEEEEeeCCHHHHHHHHHHHHHHHHhh
Confidence 6678999999999999999998888888888653
No 35
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.05 E-value=8.5 Score=23.86 Aligned_cols=23 Identities=26% Similarity=0.208 Sum_probs=20.7
Q ss_pred eCCHHHHHHHHHHHHHHHHHHHH
Q psy17590 53 STNELAVSKAKVEITRLIKEELI 75 (98)
Q Consensus 53 g~te~~V~~A~~eIk~ii~e~~~ 75 (98)
+.|.+.-++|+..|.++|.|++.
T Consensus 7 ~LtHeqQQ~AVE~Iq~lMaeGmS 29 (60)
T COG3140 7 SLTHEQQQKAVERIQELMAEGMS 29 (60)
T ss_pred cccHHHHHHHHHHHHHHHHcccc
Confidence 67889999999999999999875
No 36
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=61.44 E-value=35 Score=25.33 Aligned_cols=32 Identities=19% Similarity=0.265 Sum_probs=27.4
Q ss_pred CceEEEEEeCCHHHHHHHHHHHHHHHHHHHHHh
Q psy17590 45 RKLFLAIESTNELAVSKAKVEITRLIKEELIKL 77 (98)
Q Consensus 45 ~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~~~~ 77 (98)
-.||+.|.|... .+..|...|++++...-.+.
T Consensus 34 n~l~I~i~G~~~-eike~~~~Ik~~~~~vr~k~ 65 (190)
T PF09840_consen 34 NSLKIEIQGYEK-EIKEAIRRIKELVRRVRSKY 65 (190)
T ss_pred CEEEEEEecChH-HHHHHHHHHHHHHHHHHHHh
Confidence 689999999988 99999999999998744433
No 37
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=61.41 E-value=26 Score=21.91 Aligned_cols=27 Identities=19% Similarity=0.106 Sum_probs=24.3
Q ss_pred ceEEEEEeCCHHHHHHHHHHHHHHHHHH
Q psy17590 46 KLFLAIESTNELAVSKAKVEITRLIKEE 73 (98)
Q Consensus 46 kLYL~Ieg~te~~V~~A~~eIk~ii~e~ 73 (98)
+.++.|.| +..+|+.|++..++...+.
T Consensus 39 ~~~~~i~G-~vs~V~~Av~a~~~~~~~~ 65 (75)
T PF00936_consen 39 KVTVIITG-DVSAVKAAVDAAEEAAGKK 65 (75)
T ss_dssp EEEEEEEE-SHHHHHHHHHHHHHHHHHT
T ss_pred eEEEEEEE-CHHHHHHHHHHHHHHHhhc
Confidence 88999999 9999999999999888764
No 38
>PF13065 DUF3928: Protein of unknown function (DUF3928)
Probab=61.14 E-value=30 Score=22.90 Aligned_cols=62 Identities=26% Similarity=0.299 Sum_probs=44.5
Q ss_pred hccHHHHHHhHhhhcceeeeeceeeCCCCCCCCC-CCceEEEEEeCCHHHHHHHHHHHHHHHH
Q psy17590 10 ALLGEALAQISEYSEAGITVRGIYIPPGKNPPEG-ERKLFLAIESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 10 vT~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~g-e~kLYL~Ieg~te~~V~~A~~eIk~ii~ 71 (98)
+++|+.+-+....-...-.++..|+.-|...-+- --|.|.+|.=..-..-++|..+|-++++
T Consensus 7 vsdreavyqfasyv~vvqgve~vyvevge~lyehplmkfyvhi~i~etye~~kalqeiarlve 69 (95)
T PF13065_consen 7 VSDREAVYQFASYVRVVQGVEDVYVEVGEPLYEHPLMKFYVHITIEETYEQQKALQEIARLVE 69 (95)
T ss_pred eccHHHHHHHHHHHHHHhccceeeeecCchhhhCchheeEEEEEeHHHHHHHHHHHHHHHHHH
Confidence 3456666655555555556788899888753332 3688999988777788899999988875
No 39
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=60.90 E-value=18 Score=32.89 Aligned_cols=46 Identities=20% Similarity=0.192 Sum_probs=38.8
Q ss_pred cHHHHHHhHhhhcce-eeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAG-ITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~-It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~ 71 (98)
.+.++..|+++||+. |.+.- .-.+.|-|++.+++++|+..|+.+..
T Consensus 703 GGktIk~I~eetg~~~Idi~d--------------dg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 703 GGKKVKSIIEETGVEAIDTQD--------------DGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred CchhHHHHHHHHCCCccCcCC--------------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 467999999999998 66543 25688999999999999999999875
No 40
>PRK14323 glmM phosphoglucosamine mutase; Provisional
Probab=60.37 E-value=22 Score=28.76 Aligned_cols=33 Identities=15% Similarity=0.334 Sum_probs=29.3
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
|...||.+.+.+||.|++.+++=.+++.+++++
T Consensus 405 pS~TEP~irv~~Ea~s~~~~~~l~~~~~~~v~~ 437 (440)
T PRK14323 405 PSGTEPLVRVMVEGPDEAEIEEVARELAGVVER 437 (440)
T ss_pred cCCCccEeEEEEeeCCHHHHHHHHHHHHHHHHH
Confidence 667899999999999999999888888888864
No 41
>KOG1960|consensus
Probab=58.69 E-value=20 Score=30.36 Aligned_cols=62 Identities=18% Similarity=0.072 Sum_probs=48.0
Q ss_pred HHHHHhHhhhcceeeeeceeeCCCCCCCCC---CCceEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q psy17590 14 EALAQISEYSEAGITVRGIYIPPGKNPPEG---ERKLFLAIESTNELAVSKAKVEITRLIKEELIK 76 (98)
Q Consensus 14 ~tl~~I~e~Tga~It~KG~y~ppg~~p~~g---e~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~~~ 76 (98)
-+|..+.-+|++.+-.+|++----. |..| .-+.|++|.+.+.+.+..|..+|..+.+.-...
T Consensus 235 ~~La~~~ie~~i~~l~~Gr~SG~iE-P~~G~EsnEPMYI~i~h~~~~g~~~A~r~~~nl~~~v~~~ 299 (531)
T KOG1960|consen 235 LTLALQEIESWINPLIDGRRSGRRE-PNEGNESNEPMYIFSTHGNGNGENGAPRRKWNLEEKVYIN 299 (531)
T ss_pred hhhhhhhhhhhhhhhhccccccccC-cccccccCCceeEEeecCCchhhccchhHHHhHHHHHHHH
Confidence 3677788889999888898854333 4433 389999999999999999999998887654433
No 42
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=57.19 E-value=9.7 Score=28.75 Aligned_cols=25 Identities=24% Similarity=0.243 Sum_probs=22.1
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeC
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIP 35 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~p 35 (98)
+++-|..-|.++|||.|.+-|.++.
T Consensus 119 ~~GkTr~~IE~lt~~~I~V~g~tVa 143 (194)
T COG1094 119 REGKTRRAIEELTGVYISVYGKTVA 143 (194)
T ss_pred CCchHHHHHHHHhCCeEEEeCcEEE
Confidence 5778899999999999999998763
No 43
>COG3286 Uncharacterized protein conserved in archaea [Function unknown]
Probab=56.20 E-value=42 Score=25.55 Aligned_cols=44 Identities=14% Similarity=0.097 Sum_probs=34.2
Q ss_pred CCceEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCceEEe
Q psy17590 44 ERKLFLAIESTNELAVSKAKVEITRLIKEELIKLSSSAHQSINKSRYKGV 93 (98)
Q Consensus 44 e~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~~~~~~~~~~~~~~GRY~V~ 93 (98)
.-+||.-++|. +.+++.|+..|++++..--.+. .+...|.|+.-
T Consensus 36 ~n~vkV~v~G~-~~eireair~irel~~~vr~r~-----~~~~~~ly~l~ 79 (204)
T COG3286 36 KNRVKVNVFGT-KDEIREAIRAIRELHRRVRRRL-----YPDRQGLYTLY 79 (204)
T ss_pred CceEEEEEecc-hHHHHHHHHHHHHHHHHHHhhh-----ccCccceEeeH
Confidence 35799999999 9999999999999998765554 23455777653
No 44
>PRK14319 glmM phosphoglucosamine mutase; Provisional
Probab=55.76 E-value=29 Score=28.02 Aligned_cols=33 Identities=27% Similarity=0.379 Sum_probs=28.8
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
|...||.+.+.+||.|++..++-.+++.+++++
T Consensus 392 pS~TeP~irv~~Ea~~~~~a~~l~~~~~~~v~~ 424 (430)
T PRK14319 392 PSGTEPVVRVLVEGPDEEYITNIANDIAGLIKE 424 (430)
T ss_pred cCCCccEEEEEEEeCCHHHHHHHHHHHHHHHHH
Confidence 666789999999999999988888888888764
No 45
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=55.54 E-value=23 Score=22.44 Aligned_cols=24 Identities=29% Similarity=0.374 Sum_probs=20.1
Q ss_pred CCCCceEEEEEeCCHHHHHHHHHH
Q psy17590 42 EGERKLFLAIESTNELAVSKAKVE 65 (98)
Q Consensus 42 ~ge~kLYL~Ieg~te~~V~~A~~e 65 (98)
+++.|.|-+.+|+|+++|+++-.+
T Consensus 43 ~d~~k~~Cly~Ap~~eaV~~~~~~ 66 (77)
T PF14026_consen 43 EDDGKIFCLYEAPDEEAVREHARR 66 (77)
T ss_pred cCCCeEEEEEECCCHHHHHHHHHH
Confidence 345699999999999999988654
No 46
>PF04406 TP6A_N: Type IIB DNA topoisomerase; InterPro: IPR013049 This entry represents the N-terminal domain found in Spo11, a meiotic recombination protein found in eukaryotes, and in subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [, ]. These two types of proteins share structural homology. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination []. DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (5.99.1.2 from EC, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC, topoisomerases II, IV and VI) break double-strand DNA []. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003824 catalytic activity, 0005524 ATP binding, 0006259 DNA metabolic process, 0005694 chromosome; PDB: 1D3Y_B 2ZBK_A 2Q2E_A.
Probab=53.82 E-value=20 Score=21.88 Aligned_cols=44 Identities=32% Similarity=0.348 Sum_probs=31.8
Q ss_pred HHHHhHh--hhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHH
Q psy17590 15 ALAQISE--YSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 15 tl~~I~e--~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~ 71 (98)
.++.|.+ .+|..+|.|+.||-... || .++..|+.++..|..++.
T Consensus 14 vl~~i~~~l~~~~~~T~RdiYY~~~~--------lF-----~~Q~~vd~~i~di~~~l~ 59 (68)
T PF04406_consen 14 VLAIIHELLQNNKTSTKRDIYYRNVS--------LF-----KSQREVDRAIDDICCLLG 59 (68)
T ss_dssp HHHHHHHHHHTT--EEHHHHHHHCSC--------S------SSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHcCCccchHHHHHhchh--------hc-----cCHHHHHHHHHHHHHHHC
Confidence 3445555 57889999999997655 22 779999999999988765
No 47
>PRK14322 glmM phosphoglucosamine mutase; Provisional
Probab=52.45 E-value=33 Score=27.69 Aligned_cols=32 Identities=22% Similarity=0.395 Sum_probs=27.1
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~ 71 (98)
|...||.+.+.+||+|++..+.=.+++.++++
T Consensus 397 pS~teP~irv~~Ea~~~~~a~~l~~~~~~~l~ 428 (429)
T PRK14322 397 PSGTEPVVRITVEGKDREEIEKIVEEISRVLE 428 (429)
T ss_pred cCCCCcEEEEEEEECCHHHHHHHHHHHHHHHh
Confidence 55678999999999999998888888777764
No 48
>cd02978 KaiB_like KaiB-like family; composed of the circadian clock proteins, KaiB and the N-terminal KaiB-like sensory domain of SasA. KaiB is an essential protein in maintaining circadian rhythm. It was originally discovered from the cyanobacterium Synechococcus as part of the circadian clock gene cluster, kaiABC. KaiB attenuates KaiA-enhanced KaiC autokinase activity by interacting with KaiA-KaiC complexes in a circadian fashion. KaiB is membrane-associated as well as cytosolic. The amount of membrane-associated protein peaks in the evening (at circadian time (CT) 12-16) while the cytosolic form peaks later (at CT 20). The rhythmic localization of KaiB may function in regulating the formation of Kai complexes. SasA is a sensory histidine kinase which associates with KaiC. Although it is not an essential oscillator component, it is important in enhancing kaiABC expression and is important in metabolic growth control under day/night cycle conditions. SasA contains an N-terminal sensor
Probab=51.17 E-value=24 Score=22.53 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=23.1
Q ss_pred ceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 46 KLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 46 kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
.|-|+|.|.|..+ ++|++.|++++++.+
T Consensus 3 ~L~Lyv~g~tp~S-~~ai~nl~~i~e~~l 30 (72)
T cd02978 3 VLRLYVAGRTPKS-ERALQNLKRILEELL 30 (72)
T ss_pred EEEEEECCCCchH-HHHHHHHHHHHHHhc
Confidence 5789999998877 568899999999854
No 49
>COG3870 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.55 E-value=29 Score=23.95 Aligned_cols=42 Identities=10% Similarity=-0.001 Sum_probs=28.8
Q ss_pred EEEeCCHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCceE
Q psy17590 50 AIESTNELAVSKAKVEITRLIKEELIKLSSSAHQSINKSRYK 91 (98)
Q Consensus 50 ~Ieg~te~~V~~A~~eIk~ii~e~~~~~~~~~~~~~~~GRY~ 91 (98)
++.|..+..|+.+..-|++-++.--+..+..++-+.+.++|.
T Consensus 44 fliGved~~vd~~~s~Ike~C~~req~v~~~~~~~~sa~~yv 85 (109)
T COG3870 44 FLIGVEDDRVDALRSLIKENCKSREQLVTPISPMGGSADSYV 85 (109)
T ss_pred EEEecccchhHHHHHHHHHHhhhHhhccCCCCccCCCCCccc
Confidence 577999999999999999998854333322233344567774
No 50
>PRK14324 glmM phosphoglucosamine mutase; Provisional
Probab=50.54 E-value=45 Score=27.18 Aligned_cols=35 Identities=26% Similarity=0.329 Sum_probs=30.8
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
|...||.|=+.+|+.|++.+++=.+++.+++++.+
T Consensus 410 ~SgTEp~irv~~Ea~~~~~~~~l~~~~~~~~~~~~ 444 (446)
T PRK14324 410 YSGTENKLRILLEGKDEKLLEKKMQELVEFFKKAL 444 (446)
T ss_pred cCCCCceEEEEEEECCHHHHHHHHHHHHHHHHHHh
Confidence 66679999999999999999999999999887754
No 51
>PRK09542 manB phosphomannomutase/phosphoglucomutase; Reviewed
Probab=50.03 E-value=34 Score=27.82 Aligned_cols=57 Identities=18% Similarity=0.262 Sum_probs=37.4
Q ss_pred HHHHhHhhhc-c--eee-eec--eeeCCCC----CCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHH
Q psy17590 15 ALAQISEYSE-A--GIT-VRG--IYIPPGK----NPPEGERKLFLAIESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 15 tl~~I~e~Tg-a--~It-~KG--~y~ppg~----~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~ 71 (98)
.+.+|.+..+ . .+. +=| .+++++. .|...||+|.+.+|++|++.+++=..++.+++.
T Consensus 377 ~~~~l~~~~~~~~~~~~~~DGvki~~~dg~WvliRpSgTEP~lriy~Ea~~~e~~~~l~~~~~~~v~ 443 (445)
T PRK09542 377 RMEAVLKAFADRIVSVDHLDGVTVDLGDGSWFNLRASNTEPLLRLNVEARTEEEVDALVDEVLAIIR 443 (445)
T ss_pred HHHHHHHHhhhccCCceecceEEEEecCCcEEEEEecCCCcEEEEEEEeCCHHHHHHHHHHHHHHhh
Confidence 5566655433 1 122 233 3455553 267789999999999999888877777776663
No 52
>PRK05114 hypothetical protein; Provisional
Probab=49.22 E-value=18 Score=22.45 Aligned_cols=23 Identities=22% Similarity=0.180 Sum_probs=20.1
Q ss_pred eCCHHHHHHHHHHHHHHHHHHHH
Q psy17590 53 STNELAVSKAKVEITRLIKEELI 75 (98)
Q Consensus 53 g~te~~V~~A~~eIk~ii~e~~~ 75 (98)
..|.+.=+.|+.+|.++|.+++.
T Consensus 7 ~LtHeeQQ~AVErIq~LMaqGmS 29 (59)
T PRK05114 7 SLTHEQQQKAVERIQELMAQGMS 29 (59)
T ss_pred cCCHHHHHHHHHHHHHHHHcccc
Confidence 45788889999999999998875
No 53
>PF02741 FTR_C: FTR, proximal lobe; InterPro: IPR002770 Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction: N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin Ftr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr, determined to a reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel beta sheet flanked by alpha helices forming an alpha/beta sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface []. Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure []. In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates [].; GO: 0016740 transferase activity, 0006730 one-carbon metabolic process; PDB: 1M5S_B 1M5H_E 1FTR_C 2FHJ_B 2FHK_D.
Probab=48.37 E-value=27 Score=25.47 Aligned_cols=21 Identities=24% Similarity=0.181 Sum_probs=16.9
Q ss_pred CceEEEEEeCCHHHHHHHHHH
Q psy17590 45 RKLFLAIESTNELAVSKAKVE 65 (98)
Q Consensus 45 ~kLYL~Ieg~te~~V~~A~~e 65 (98)
-=+-+.|.|.|+++|.+|+..
T Consensus 97 ~V~EIVIdGl~~~av~~Amr~ 117 (150)
T PF02741_consen 97 AVYEIVIDGLSEEAVAEAMRA 117 (150)
T ss_dssp EEEEEEEEESSHHHHHHHHHH
T ss_pred eEEEEEEcCCCHHHHHHHHHH
Confidence 445588999999999999753
No 54
>TIGR02654 circ_KaiB circadian clock protein KaiB. Members of this protein family are the circadian clock protein KaiB of Cyanobacteria, encoded in the circadian clock gene cluster kaiABC. KaiB has homologs of unknown function in some Archaea and Proteobacteria, and has paralogs of unknown function in some Cyanobacteria. KaiB forms homodimers, homotetramers, and multimeric complexes with KaiA and/or KaiC.
Probab=48.11 E-value=34 Score=22.59 Aligned_cols=28 Identities=14% Similarity=0.223 Sum_probs=23.2
Q ss_pred ceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 46 KLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 46 kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
.|-|+|.|.+..+ ++|++-|++++++.+
T Consensus 5 ~LrLyvag~~p~S-~~ai~nl~~i~e~~l 32 (87)
T TIGR02654 5 VLKLYVAGNTPNS-VRALKTLKNILETEF 32 (87)
T ss_pred EEEEEEeCCCchH-HHHHHHHHHHHHHhc
Confidence 4779999999877 568999999999754
No 55
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=47.99 E-value=45 Score=29.68 Aligned_cols=48 Identities=23% Similarity=0.350 Sum_probs=38.4
Q ss_pred cHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKEE 73 (98)
Q Consensus 12 ~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~ 73 (98)
.++++..|.|+||+.|.+- +.|. ..|-+.+..++++|+..|..+..|-
T Consensus 570 gGk~I~~I~eetg~~Idie----ddGt----------v~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 570 GGKTIKAITEETGVKIDIE----DDGT----------VKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred cccchhhhhhhhCcEEEec----CCCc----------EEEEecchHHHHHHHHHHHHHHhhc
Confidence 3578899999999999883 2222 4577889999999999999998653
No 56
>cd03084 phosphohexomutase The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=47.84 E-value=32 Score=26.83 Aligned_cols=30 Identities=20% Similarity=0.192 Sum_probs=24.3
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRL 69 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~i 69 (98)
|...||.+.+.+||.|++.++.-.++++++
T Consensus 325 ps~tep~~ri~~Ea~~~e~a~~l~~~~~~~ 354 (355)
T cd03084 325 ASGTEPAIRIYAEADTQEDVEQIKKEAREL 354 (355)
T ss_pred cCCCCcEEEEEEeeCCHHHHHHHHHHHHhh
Confidence 666789999999999998877776666554
No 57
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=47.64 E-value=21 Score=21.54 Aligned_cols=23 Identities=13% Similarity=0.128 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH
Q psy17590 54 TNELAVSKAKVEITRLIKEELIK 76 (98)
Q Consensus 54 ~te~~V~~A~~eIk~ii~e~~~~ 76 (98)
.|.+.=+.|+.+|.++|.+++..
T Consensus 8 LtHeeQQ~AvE~Iq~LMaqGmSs 30 (51)
T PF03701_consen 8 LTHEEQQQAVERIQELMAQGMSS 30 (51)
T ss_pred CCHHHHHHHHHHHHHHHHhcccH
Confidence 47788899999999999998753
No 58
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=47.46 E-value=47 Score=20.98 Aligned_cols=43 Identities=19% Similarity=0.191 Sum_probs=30.0
Q ss_pred eceeeCCCCCCC----CCCCceEEEEE--------e-CCHHHHHHHHHHHHHHHHH
Q psy17590 30 RGIYIPPGKNPP----EGERKLFLAIE--------S-TNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 30 KG~y~ppg~~p~----~ge~kLYL~Ie--------g-~te~~V~~A~~eIk~ii~e 72 (98)
+..-|.|..-|. ..+|+..++|- | .|++.++.|+.+|-++|.+
T Consensus 29 ~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~~~L~~ 84 (86)
T PF00352_consen 29 ENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKILPILQK 84 (86)
T ss_dssp TTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred cCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 344566665443 24566665554 5 5999999999999999875
No 59
>cd03089 PMM_PGM The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a bisphosphorylated sugar intermediate. The reaction involves two phosphoryl transfers, with an intervening 180 degree reorientation of the reaction intermediate during catalysis. Reorientation of the intermediate occurs without dissociation from the active site of the enzyme and is thus, a simple example of processivity, as defined by multiple rounds of catalysis without release of substrate. Glucose-6-phosphate and glucose-1-phosphate are known to be utilized for energy metabolism and cell surface construction, respectively. PMM/PGM belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other membe
Probab=47.06 E-value=32 Score=27.84 Aligned_cols=58 Identities=22% Similarity=0.295 Sum_probs=37.2
Q ss_pred cHHHHHHhHhhhcc---ee-eeec--eeeCCCC---CCCCCCCceEEEEEeCCHHHHHHHHHHHHHH
Q psy17590 12 LGEALAQISEYSEA---GI-TVRG--IYIPPGK---NPPEGERKLFLAIESTNELAVSKAKVEITRL 69 (98)
Q Consensus 12 ~~~tl~~I~e~Tga---~I-t~KG--~y~ppg~---~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~i 69 (98)
++..+..+.+.... .+ ++-| .++..+- .|...||.+.+.+|+.|++.+++-.++++++
T Consensus 376 k~~~~~~l~~~~~~~~~~~~~~DGiki~~~~~WvliRpSgtEP~iriy~Ea~~~~~a~~l~~~~~~~ 442 (443)
T cd03089 376 KFAVIERLKEHFEFPGAEIIDIDGVRVDFEDGWGLVRASNTEPVLVLRFEADTEEGLEEIKAELRKL 442 (443)
T ss_pred HHHHHHHHHHHhccccCCeeeecCEEEEECCeeEEEeecCCCCEEEEEEEeCCHHHHHHHHHHHHhh
Confidence 34555667664431 22 2334 2334332 2667899999999999999988777777654
No 60
>PRK14315 glmM phosphoglucosamine mutase; Provisional
Probab=46.22 E-value=54 Score=26.66 Aligned_cols=33 Identities=18% Similarity=0.208 Sum_probs=28.0
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
|...||-+.+.+||.|++.+++=.+++.+++++
T Consensus 413 pS~teP~iri~~Ea~s~~~~~~l~~~~~~~i~~ 445 (448)
T PRK14315 413 PSGTEPLIRVMAEGDDRALVEEVVDEIVDAVSA 445 (448)
T ss_pred cCCCCcEEEEEEeeCCHHHHHHHHHHHHHHHHH
Confidence 667899999999999999988877777777764
No 61
>PRK15414 phosphomannomutase CpsG; Provisional
Probab=45.78 E-value=32 Score=28.13 Aligned_cols=33 Identities=18% Similarity=0.211 Sum_probs=26.3
Q ss_pred CCCCCCceEEEEEeC-CHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIEST-NELAVSKAKVEITRLIKE 72 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~-te~~V~~A~~eIk~ii~e 72 (98)
|...||.+.+.+|+. ++..+++-.+++.+++.|
T Consensus 423 pSgTEP~iri~~Ea~~~~~~~~~~~~~~~~~~~~ 456 (456)
T PRK15414 423 SSNTEPVVRLNVESRGDVPLMEARTRTLLTLLNE 456 (456)
T ss_pred cCCCceEEEEEEecCCCHHHHHHHHHHHHHHhhC
Confidence 667889999999999 888777777777766653
No 62
>TIGR01455 glmM phosphoglucosamine mutase. This model describes GlmM, phosphoglucosamine mutase, also designated in MrsA and YhbF E. coli, UreC in Helicobacter pylori, and femR315 or FemD in Staphlococcus aureus. It converts glucosamine-6-phosphate to glucosamine-1-phosphate as part of the pathway toward UDP-N-acetylglucosamine for peptidoglycan and lipopolysaccharides.
Probab=45.56 E-value=50 Score=26.74 Aligned_cols=32 Identities=16% Similarity=0.275 Sum_probs=27.8
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~ 71 (98)
|...||.+.+.+||.|++..++-.+++.++++
T Consensus 411 pS~teP~irv~~Ea~~~e~~~~l~~~~~~~v~ 442 (443)
T TIGR01455 411 PSGTEPLIRVMVEAADEELVQQLADTLADVVS 442 (443)
T ss_pred cCCCCceEEEEEEECCHHHHHHHHHHHHHHHh
Confidence 66789999999999999998888888877764
No 63
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=45.45 E-value=7.7 Score=26.06 Aligned_cols=28 Identities=14% Similarity=0.094 Sum_probs=22.4
Q ss_pred hHHHHhcc-----HHHHHHhHhhhcceeee--ece
Q psy17590 5 PIHLLALL-----GEALAQISEYSEAGITV--RGI 32 (98)
Q Consensus 5 ~~R~~vT~-----~~tl~~I~e~Tga~It~--KG~ 32 (98)
..||.|.. +-+|.+|.+.+|+|+++ ||.
T Consensus 42 ~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 42 GDRIRIVNELLNGNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence 35888876 46999999999999986 553
No 64
>PF07288 DUF1447: Protein of unknown function (DUF1447); InterPro: IPR009907 This family consists of several bacterial proteins of around 70 residues in length. The function of this family is unknown.
Probab=43.91 E-value=72 Score=20.35 Aligned_cols=35 Identities=20% Similarity=0.232 Sum_probs=24.1
Q ss_pred eeeCCCCCCCC-CCCceEEEEEeCCHHHHHHHHHHH
Q psy17590 32 IYIPPGKNPPE-GERKLFLAIESTNELAVSKAKVEI 66 (98)
Q Consensus 32 ~y~ppg~~p~~-ge~kLYL~Ieg~te~~V~~A~~eI 66 (98)
.||-+.+.-.| -|...=|.||+.|+..|++.+++-
T Consensus 4 V~YQe~k~~~P~RE~T~sLYvEa~s~~evR~~ve~~ 39 (69)
T PF07288_consen 4 VFYQETKDEVPVRENTQSLYVEAESEVEVRKLVEDN 39 (69)
T ss_pred EeecCCCCcCCccccceEEEEEcCCHHHHHHHHHhC
Confidence 57777776333 455555556999999988877665
No 65
>PF00381 PTS-HPr: PTS HPr component phosphorylation site; InterPro: IPR005698 The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species [, ]. PTS catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is as follows: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to Enzyme I (EI) of the PTS, which in turn transfers it to the phosphoryl carrier protein (HPr) [, ]. Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease complex (enzymes EII/EIII). HPr [, ] is a small cytoplasmic protein of 70 to 90 amino acid residues. In some bacteria, HPr is a domain in a larger protein that includes a EIII(Fru) (IIA) domain and in some cases also the EI domain. A conserved histidine in the N-terminal section of HPr serves as an acceptor for the phosphoryl group of EI. In the central part of HPr, there is a conserved serine which (in Gram-positive bacteria only) is phosphorylated by an ATP-dependent protein kinase; a process which probably play a regulatory role in sugar transport. The overall architecture of the HPr domain has been described as an open faced beta-sandwich in which a beta-sheet is packed against three alpha-helices. Regulatory phosphorylation at the conserved Ser residue does not appear to induce large structural changes to the HPr domain, in particular in the region of the active site [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TXE_A 1QR5_A 1RZR_S 2NZU_L 2OEN_L 2NZV_L 1Y51_B 1Y4Y_A 1Y50_A 2HPR_A ....
Probab=43.03 E-value=54 Score=20.43 Aligned_cols=55 Identities=20% Similarity=0.237 Sum_probs=34.6
Q ss_pred HHHHhHhhhcceeee-eceeeCCCCCCC-------CCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 15 ALAQISEYSEAGITV-RGIYIPPGKNPP-------EGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 15 tl~~I~e~Tga~It~-KG~y~ppg~~p~-------~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
.+.++....+|.|++ +|.+--+.+... ...-++.|.++|+++. .|..+|.+++++
T Consensus 21 ~lv~~a~~~~~~i~i~~~~~~vdakSil~l~~L~~~~G~~i~i~~~G~de~---~a~~~i~~~~~~ 83 (84)
T PF00381_consen 21 ELVQIASKFDSDITIRKGGKTVDAKSILGLMSLGAKKGDEIEIEAEGEDEE---EALEAIAEFLES 83 (84)
T ss_dssp HHHHHHHTSSSEEEEEETTEEEETTSHHHHHHHTBSTTEEEEEEEESTTHH---HHHHHHHHHHHH
T ss_pred HHHHHHhhCCCEEEEEeCceeEecCCHHHHhhhhcCCCCEEEEEEECcCHH---HHHHHHHHHHhc
Confidence 355666667888887 333333333311 1345799999999885 466677777765
No 66
>COG1109 {ManB} Phosphomannomutase [Carbohydrate transport and metabolism]
Probab=43.03 E-value=57 Score=26.78 Aligned_cols=35 Identities=26% Similarity=0.378 Sum_probs=31.3
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
|...||+|-+.+|+.+++.++...+++.+++.+.+
T Consensus 427 pSGTEP~lrvy~Ea~~~~~~~~~~~~~~~~v~~~~ 461 (464)
T COG1109 427 PSGTEPLIRVYVEAKDEELAEELAEEIAELVREAL 461 (464)
T ss_pred eCCCceEEEEEEEECCHHHHHHHHHHHHHHHHhhh
Confidence 66689999999999999999999999999988754
No 67
>PRK09301 circadian clock protein KaiB; Provisional
Probab=41.79 E-value=46 Score=22.72 Aligned_cols=29 Identities=14% Similarity=0.190 Sum_probs=23.9
Q ss_pred CceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 45 RKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 45 ~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
--|-|+|.|.+..+ ++|++-|++++++.+
T Consensus 7 ~~LrLyVag~tp~S-~~ai~nL~~icE~~l 35 (103)
T PRK09301 7 YILKLYVAGNTPNS-VRALKTLKNILETEF 35 (103)
T ss_pred EEEEEEEeCCCchH-HHHHHHHHHHHHHhc
Confidence 35789999999877 568999999999754
No 68
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=41.70 E-value=23 Score=26.02 Aligned_cols=40 Identities=23% Similarity=0.370 Sum_probs=31.1
Q ss_pred eeceeeCCCC---------CCCCCCCceEEEEEeCCHHHHHHHHHHHHH
Q psy17590 29 VRGIYIPPGK---------NPPEGERKLFLAIESTNELAVSKAKVEITR 68 (98)
Q Consensus 29 ~KG~y~ppg~---------~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ 68 (98)
-+|+|||+.- .|.++|.-+-+-|..+=+..|+.|+.-|++
T Consensus 111 R~gHFM~~~ll~SQfa~LE~P~~de~vi~idi~~~~e~vv~~~~~~l~~ 159 (161)
T COG3265 111 RKGHFMPASLLDSQFATLEEPGADEDVLTIDIDQPPEEVVAQALAWLKE 159 (161)
T ss_pred cccCCCCHHHHHHHHHHhcCCCCCCCEEEeeCCCCHHHHHHHHHHHHhc
Confidence 3899999983 366677777777778888999988887764
No 69
>smart00877 BMC Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.
Probab=41.68 E-value=69 Score=19.96 Aligned_cols=26 Identities=19% Similarity=0.072 Sum_probs=22.0
Q ss_pred ceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 46 KLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 46 kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
+.++.|.| +..+|+.|++..++.+.+
T Consensus 38 ~~~~~v~G-dvs~V~~Av~a~~~~~~~ 63 (75)
T smart00877 38 KVTVIITG-DVAAVRAAVEAGLEAAER 63 (75)
T ss_pred EEEEEEEE-cHHHHHHHHHHHHHHHhh
Confidence 68888888 899999999998887753
No 70
>KOG1676|consensus
Probab=41.43 E-value=30 Score=30.23 Aligned_cols=56 Identities=23% Similarity=0.292 Sum_probs=43.7
Q ss_pred HHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHHH
Q psy17590 13 GEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKEELI 75 (98)
Q Consensus 13 ~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~~ 75 (98)
+||+..|..+|||.|..- ..+..+.++.=+++.--++..|+.|..+|+..+.+-..
T Consensus 337 GEtIK~in~qSGA~~el~-------r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~~~ 392 (600)
T KOG1676|consen 337 GETIKQINQQSGARCELS-------RQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDIAP 392 (600)
T ss_pred ccchhhhcccCCcccccc-------CCCCCCCccceEEEEecCcccchHHHHHHHHHhcccCC
Confidence 588999999999987652 11444566677788888999999999999999987443
No 71
>cd07046 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to
Probab=41.06 E-value=50 Score=22.59 Aligned_cols=28 Identities=21% Similarity=0.215 Sum_probs=24.2
Q ss_pred ceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 46 KLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 46 kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
+-++.|.| +..+|+.|++...+.+++.+
T Consensus 73 ~g~vii~G-dvsaV~aAl~a~~~~~~~~~ 100 (110)
T cd07046 73 SGALVITG-DVSEVESALEAVVDYLRETL 100 (110)
T ss_pred eEEEEEEE-CHHHHHHHHHHHHHHHhhcc
Confidence 44888999 99999999999999988754
No 72
>TIGR01132 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific. This enzyme interconverts alpha-D-glucose-1-P and alpha-D-glucose-6-P.
Probab=40.15 E-value=71 Score=26.85 Aligned_cols=33 Identities=21% Similarity=0.255 Sum_probs=29.1
Q ss_pred CCCCCCceEEEEEe-CCHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIES-TNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 40 p~~ge~kLYL~Ieg-~te~~V~~A~~eIk~ii~e 72 (98)
|...||++.+.+|+ .|++.++.-.+++..++++
T Consensus 507 pSgTEP~irvy~Ea~~~~~~~~~l~~~~~~~v~~ 540 (543)
T TIGR01132 507 PSGTEDVYKIYCESFKGEEHLKQIEKEAVEIVSE 540 (543)
T ss_pred cCCCCceEEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 67789999999999 6999999888888888876
No 73
>cd06200 SiR_like1 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD
Probab=39.41 E-value=1e+02 Score=22.78 Aligned_cols=39 Identities=10% Similarity=0.211 Sum_probs=26.7
Q ss_pred EEEEEeCCHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCceEE
Q psy17590 48 FLAIESTNELAVSKAKVEITRLIKEELIKLSSSAHQSINKSRYKG 92 (98)
Q Consensus 48 YL~Ieg~te~~V~~A~~eIk~ii~e~~~~~~~~~~~~~~~GRY~V 92 (98)
++.++|+...-++.+.+.+.+++.+.-.+ .....|||.+
T Consensus 204 ~vy~CGp~~~m~~~v~~~l~~~~~~~~~~------~~~~~~r~~~ 242 (245)
T cd06200 204 AIYVCGSLQGMAPGVDAVLDEILGEEAVE------ALLAAGRYRR 242 (245)
T ss_pred EEEEECCchhhhHHHHHHHHHHHHHHHHH------HHHHCCCeEE
Confidence 68899999666777777777777764322 2345699975
No 74
>PLN02371 phosphoglucosamine mutase family protein
Probab=39.31 E-value=67 Score=27.36 Aligned_cols=34 Identities=21% Similarity=0.154 Sum_probs=30.5
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRLIKEE 73 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~ 73 (98)
|...||.+.+.+|+.|++.++.-.+++.+++++.
T Consensus 536 pS~TEP~iri~~Ea~s~e~a~~l~~~~~~~v~~~ 569 (583)
T PLN02371 536 QSLHDPVIPLNIESSSPGGAQKMALVVLTWLKEF 569 (583)
T ss_pred eCCCCceEEEEEeECCHHHHHHHHHHHHHHHhhh
Confidence 6678999999999999999999999999988765
No 75
>PRK07564 phosphoglucomutase; Validated
Probab=39.05 E-value=83 Score=26.45 Aligned_cols=33 Identities=15% Similarity=0.252 Sum_probs=27.6
Q ss_pred CCCCCCceEEEEEe-CCHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIES-TNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 40 p~~ge~kLYL~Ieg-~te~~V~~A~~eIk~ii~e 72 (98)
|...||++-+.+|+ .+++.+++-.+++.+++++
T Consensus 506 pSgTEP~iriy~Ea~~~~~~~~~l~~~~~~~~~~ 539 (543)
T PRK07564 506 PSGTETTYKIYAESFEGDEHLHQIQKEAQEIVAD 539 (543)
T ss_pred ccCCCCeEEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 66788999999999 6888888887888877765
No 76
>PF12513 SUV3_C: Mitochondrial degradasome RNA helicase subunit C terminal; InterPro: IPR022192 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00271 from PFAM. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 3RC8_A 3RC3_A.
Probab=39.03 E-value=69 Score=18.33 Aligned_cols=23 Identities=17% Similarity=0.208 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH
Q psy17590 54 TNELAVSKAKVEITRLIKEELIK 76 (98)
Q Consensus 54 ~te~~V~~A~~eIk~ii~e~~~~ 76 (98)
++.+.+...+..+.+.|.+++.+
T Consensus 26 ~d~e~a~~~k~~~~~~I~~~L~~ 48 (49)
T PF12513_consen 26 PDRELAEELKKRVEEKIEEGLER 48 (49)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHHHHHHhc
Confidence 57788999999999999998864
No 77
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=38.71 E-value=97 Score=23.31 Aligned_cols=41 Identities=22% Similarity=0.250 Sum_probs=33.1
Q ss_pred eeeCCCCCCC----CCCCceEEEEEe---------CCHHHHHHHHHHHHHHHHH
Q psy17590 32 IYIPPGKNPP----EGERKLFLAIES---------TNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 32 ~y~ppg~~p~----~ge~kLYL~Ieg---------~te~~V~~A~~eIk~ii~e 72 (98)
.=|.|..=|. .++|+.-++|.| .+++.+..|++.|.+.++|
T Consensus 128 ~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~ed~~~Av~~i~~~L~e 181 (185)
T COG2101 128 IEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKIQSRLEE 181 (185)
T ss_pred cccccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCHHHHHHHHHHHHHHHHH
Confidence 4566766554 378999888874 7899999999999998886
No 78
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=38.67 E-value=1.1e+02 Score=20.68 Aligned_cols=37 Identities=19% Similarity=0.223 Sum_probs=29.6
Q ss_pred CCCCCCceEEEEEeC-C-HHHHHHHHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIEST-N-ELAVSKAKVEITRLIKEELIK 76 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~-t-e~~V~~A~~eIk~ii~e~~~~ 76 (98)
|..+.+++|+-..+. + ..++.+|...|-+.+.+...+
T Consensus 52 P~~~~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~~l~~~ 90 (99)
T COG1761 52 PLIDNPKIRIKTKGGVDPKEALKRAARKILKDLEELLDQ 90 (99)
T ss_pred CCCCCceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 455789999999876 3 588999999999888876653
No 79
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=38.55 E-value=56 Score=19.89 Aligned_cols=26 Identities=15% Similarity=0.285 Sum_probs=18.3
Q ss_pred CCCceEEEEEeCCHHHHHHHHHHHHHH
Q psy17590 43 GERKLFLAIESTNELAVSKAKVEITRL 69 (98)
Q Consensus 43 ge~kLYL~Ieg~te~~V~~A~~eIk~i 69 (98)
++---|+-++| ....+++|+++|++.
T Consensus 41 ~~y~Ffvd~~~-~~~~~~~~l~~L~~~ 66 (74)
T cd04904 41 SEYEFFVDCEV-DRGDLDQLISSLRRV 66 (74)
T ss_pred ceEEEEEEEEc-ChHHHHHHHHHHHHh
Confidence 34455677888 556788888888764
No 80
>KOG2191|consensus
Probab=38.18 E-value=1e+02 Score=25.55 Aligned_cols=53 Identities=30% Similarity=0.320 Sum_probs=37.2
Q ss_pred HHHHHHhHhhhcceeeeeceeeCCCCCCCC---CCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 13 GEALAQISEYSEAGITVRGIYIPPGKNPPE---GERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 13 ~~tl~~I~e~Tga~It~KG~y~ppg~~p~~---ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
+.|+..|+|++||-|++ +| .+|.. .|| +..-.-+.+.+.+|+.+|-+.|.|+-
T Consensus 151 gAtiK~~~Eqsga~iqi----sP--qkpt~~sLqer---vvt~sge~e~~~~A~~~IL~Ki~eDp 206 (402)
T KOG2191|consen 151 GATIKAIQEQSGAWIQI----SP--QKPTGISLQER---VVTVSGEPEQNMKAVSLILQKIQEDP 206 (402)
T ss_pred cchHHHHHHhhCcceEe----cc--cCCCCccceeE---EEEecCCHHHHHHHHHHHHHHhhcCC
Confidence 67899999999999986 33 22222 122 23335677889999999998888754
No 81
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=37.75 E-value=52 Score=21.38 Aligned_cols=28 Identities=14% Similarity=0.258 Sum_probs=20.1
Q ss_pred CCCceEEEEEeCCHHHHHHHHHHHHHHH
Q psy17590 43 GERKLFLAIESTNELAVSKAKVEITRLI 70 (98)
Q Consensus 43 ge~kLYL~Ieg~te~~V~~A~~eIk~ii 70 (98)
++---|+-|+|.....+++|+++|++.|
T Consensus 55 ~~Y~FfVDieg~~~~~~~~~l~~L~~~~ 82 (90)
T cd04931 55 DEYEFFINLDKKSAPALDPIIKSLRNDI 82 (90)
T ss_pred ceEEEEEEEEcCCCHHHHHHHHHHHHHh
Confidence 3445667788875688888888887744
No 82
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=37.15 E-value=65 Score=24.30 Aligned_cols=49 Identities=18% Similarity=0.146 Sum_probs=38.5
Q ss_pred ccHHHHHHhHhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKEE 73 (98)
Q Consensus 11 T~~~tl~~I~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~ 73 (98)
.++.++..|.+.||+.|.+= . . =+++|.|++++.+++|+..|+.+-+|+
T Consensus 162 ~~g~~i~~l~~~~~~~I~ig-~---------N----G~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 162 KKGSMINMLKEETGCDIIVG-Q---------N----GRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred CCChhHhhhhhhhCcEEEEc-C---------C----cEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 35667888888888888761 1 1 378999999999999999999876654
No 83
>PF04175 DUF406: Protein of unknown function (DUF406) ; InterPro: IPR005272 These small proteins are approximately 100 amino acids in length and appear to be found only in gamma proteobacteria. The function of this protein family is unknown. ; PDB: 2JZ5_A 2KHD_A 2K3I_A.
Probab=37.06 E-value=1.3e+02 Score=20.11 Aligned_cols=45 Identities=16% Similarity=0.073 Sum_probs=32.8
Q ss_pred eceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 30 RGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 30 KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
-|.|+.-|....+++.-+-+.+.++|+...+.+...+.+.-++--
T Consensus 12 CGc~vdvGsIIdn~D~~~~~~~~~~~~~~Ae~~l~~l~~kAk~v~ 56 (94)
T PF04175_consen 12 CGCCVDVGSIIDNSDCVAEVSIVFASEAEAEAALAKLTEKAKQVE 56 (94)
T ss_dssp S--S--SS-SS--STSEEEEEEEESSHHHHHHHHHHHHHHHHHHS
T ss_pred CceEEeeeeEEcCCCcEEEEEEEeCCHHHHHHHHHHHHHHHHhhc
Confidence 578888899899999999999999999999999888887766533
No 84
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=36.84 E-value=71 Score=21.32 Aligned_cols=20 Identities=20% Similarity=0.331 Sum_probs=17.4
Q ss_pred EEEEeCCHHHHHHHHHHHHH
Q psy17590 49 LAIESTNELAVSKAKVEITR 68 (98)
Q Consensus 49 L~Ieg~te~~V~~A~~eIk~ 68 (98)
-.|++++++.++++.+++++
T Consensus 74 HtI~a~~~e~l~~I~~~L~~ 93 (98)
T PF02829_consen 74 HTIEAPDEEDLDKIEEALKK 93 (98)
T ss_dssp EEEEESSHHHHHHHHHHHHH
T ss_pred EEEEECCHHHHHHHHHHHHH
Confidence 45999999999999988875
No 85
>PF14893 PNMA: PNMA
Probab=36.17 E-value=21 Score=28.82 Aligned_cols=34 Identities=26% Similarity=0.398 Sum_probs=20.3
Q ss_pred EEEEeCCHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCceEEeec
Q psy17590 49 LAIESTNELAVSKAKVEITRLIKEELIKLSSSAHQSINKSRYKGVGR 95 (98)
Q Consensus 49 L~Ieg~te~~V~~A~~eIk~ii~e~~~~~~~~~~~~~~~GRY~V~~~ 95 (98)
|+|-|.-+..=+ .+|.+.+..++..+ |||.|+++
T Consensus 21 lLv~giP~dc~~---~ei~e~l~~~l~pl----------g~yrvl~~ 54 (331)
T PF14893_consen 21 LLVLGIPEDCEE---AEIEEALQAALSPL----------GRYRVLGK 54 (331)
T ss_pred heeecCCCCCCH---HHHHHHHHHhhccc----------ccceehhh
Confidence 555554332222 46666666655444 99999987
No 86
>cd05800 PGM_like2 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four structural domains (subdomains) with a centrally located active site formed by four loops, one from each subdomain. All four subdomains are included in this alignment model.
Probab=35.43 E-value=60 Score=26.33 Aligned_cols=30 Identities=20% Similarity=0.098 Sum_probs=24.4
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITRL 69 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~i 69 (98)
|...||.+.+.+|+.|++..++-.+++..+
T Consensus 431 pS~tep~iriy~Ea~~~~~a~~l~~~~~~~ 460 (461)
T cd05800 431 PSGTEPLLRIYAEAPSPEKVEALLDAGKKL 460 (461)
T ss_pred cCCCCceEEEEEecCCHHHHHHHHHHHHhh
Confidence 777899999999999998877766666543
No 87
>TIGR00318 cyaB adenylyl cyclase CyaB, putative. The protein CyaB from Aeromonas hydrophila is a second adenylyl cyclase from that species, as demonstrated by complementation in E. coli and by assay of the enzymatic properties of purified recombinant protein. It has no detectable homology to any other protein of known function, and has several unusual properties, including an optimal temperature of 65 degrees and an optimal pH of 9.5. A cluster of uncharaterized archaeal homologs may be orthologous and serve (under certain circumstances) to produce the regulatory metabolite cyclic AMP (cAMP).
Probab=34.82 E-value=53 Score=23.35 Aligned_cols=63 Identities=21% Similarity=0.035 Sum_probs=42.5
Q ss_pred HhccHHHHHHhHhhhcce----eeeeceeeCCCCC-C----CCCCCceEEEEEeCC--HHHHHHHHHHHHHHHHH
Q psy17590 9 LALLGEALAQISEYSEAG----ITVRGIYIPPGKN-P----PEGERKLFLAIESTN--ELAVSKAKVEITRLIKE 72 (98)
Q Consensus 9 ~vT~~~tl~~I~e~Tga~----It~KG~y~ppg~~-p----~~ge~kLYL~Ieg~t--e~~V~~A~~eIk~ii~e 72 (98)
.|.+.+.+..|-...|.. +.-+-..|..+.. . -+| =.-|+.||+.+ +..++.|...|.+++..
T Consensus 83 ~v~d~~~~~~iL~~LG~~~~~~v~K~R~~~~l~~~~i~lD~v~~-lG~FvEIE~~~~~~~~~~~~~~~i~~~~~~ 156 (174)
T TIGR00318 83 KIEDIENALQILKKLGFKKVYEVIKKRRIYQTNELNVSIDDVEG-LGFFLEIEKIINNINDKDLALEEIFEIINQ 156 (174)
T ss_pred EECCHHHHHHHHHHCCCeEEEEEEEEEEEEEECCEEEEEEccCC-CccEEEEEEecCCccchHHHHHHHHHHHHH
Confidence 456778888888888877 3444444444331 1 112 25789999965 57999999999888764
No 88
>smart00361 RRM_1 RNA recognition motif.
Probab=33.85 E-value=1e+02 Score=18.18 Aligned_cols=44 Identities=18% Similarity=0.162 Sum_probs=33.0
Q ss_pred hhcceeeeeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHH
Q psy17590 22 YSEAGITVRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEIT 67 (98)
Q Consensus 22 ~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk 67 (98)
.-|.-..+...++|+... .+..+=|.+|+-.+++..++|+..++
T Consensus 15 ~fG~v~~v~~v~~~~~~~--~~~~rG~~fV~f~~~~dA~~A~~~l~ 58 (70)
T smart00361 15 YFGEVGKINKIYIDNVGY--ENHKRGNVYITFERSEDAARAIVDLN 58 (70)
T ss_pred hcCCeeEEEEEEeCCCCC--CCCCcEEEEEEECCHHHHHHHHHHhC
Confidence 456666666677877542 34566799999999999999998754
No 89
>cd06169 BMC Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypo
Probab=33.24 E-value=59 Score=19.38 Aligned_cols=25 Identities=20% Similarity=0.044 Sum_probs=20.2
Q ss_pred CCceEEEEEeCCHHHHHHHHHHHHHH
Q psy17590 44 ERKLFLAIESTNELAVSKAKVEITRL 69 (98)
Q Consensus 44 e~kLYL~Ieg~te~~V~~A~~eIk~i 69 (98)
..+-++.|.|.. .+|+.|++..++.
T Consensus 37 ~g~~~~~i~G~~-s~V~~A~~a~~~~ 61 (62)
T cd06169 37 GGLVTLIIRGDV-SAVKAAVEAAEQA 61 (62)
T ss_pred CcEEEEEEEECH-HHHHHHHHHHHhh
Confidence 467888889966 9999999887754
No 90
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=32.53 E-value=40 Score=21.49 Aligned_cols=18 Identities=17% Similarity=0.154 Sum_probs=14.3
Q ss_pred EEEEeCCHHHHHHHHHHH
Q psy17590 49 LAIESTNELAVSKAKVEI 66 (98)
Q Consensus 49 L~Ieg~te~~V~~A~~eI 66 (98)
++|||+||..+=.+..+.
T Consensus 7 IlVEG~tE~~~l~~~~~~ 24 (97)
T cd01026 7 ILVEGDSEEILLPALAKK 24 (97)
T ss_pred EEEecHHHHHHHHHHHHH
Confidence 899999998876666554
No 91
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=32.40 E-value=88 Score=21.37 Aligned_cols=27 Identities=11% Similarity=0.121 Sum_probs=23.1
Q ss_pred eEEEEEeCCHHHHHHHHHHHHHHHHHH
Q psy17590 47 LFLAIESTNELAVSKAKVEITRLIKEE 73 (98)
Q Consensus 47 LYL~Ieg~te~~V~~A~~eIk~ii~e~ 73 (98)
+...|-|++...|+.|++.+.+.+++.
T Consensus 74 vi~ii~G~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 74 VIGILAGPSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred EEEEEeCCCHHHHHHHHHHHHHHHhcc
Confidence 566799999999999999998888753
No 92
>PHA01632 hypothetical protein
Probab=32.35 E-value=55 Score=20.40 Aligned_cols=22 Identities=27% Similarity=0.389 Sum_probs=17.4
Q ss_pred CceEEEEE----eCCHHHHHHHHHHH
Q psy17590 45 RKLFLAIE----STNELAVSKAKVEI 66 (98)
Q Consensus 45 ~kLYL~Ie----g~te~~V~~A~~eI 66 (98)
-|.|++|| -||++.++++.-+|
T Consensus 15 ikiyilieqvp~kpteeelrkvlpki 40 (64)
T PHA01632 15 IKIYILIEQVPQKPTEEELRKVLPKI 40 (64)
T ss_pred EEEEEehhhcCCCCCHHHHHHHHHHH
Confidence 57889998 48899888887665
No 93
>cd05805 MPG1_transferase GTP-mannose-1-phosphate guanyltransferase (MPG1 transferase), also known as GDP-mannose pyrophosphorylase, is a bifunctional enzyme with both phosphomannose isomerase (PMI) activity and GDP-mannose phosphorylase (GMP) activity. The protein contains an N-terminal NTP transferase domain, an L-beta-H domain, and a C-terminal PGM-like domain that belongs to the alpha-D-phosphohexomutase superfamily. This subfamily is limited to bacteria and archaea. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this group appear to lack conserved residues necessary for metal binding and catalytic activity. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional
Probab=31.44 E-value=76 Score=25.63 Aligned_cols=29 Identities=10% Similarity=0.072 Sum_probs=22.9
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEITR 68 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk~ 68 (98)
|...||.+-+.+|+.|++..++=.+++.+
T Consensus 411 pS~TeP~iri~~Ea~~~~~~~~l~~~~~~ 439 (441)
T cd05805 411 PDADEPLCHIYAEGSDQERAEELTEFYVE 439 (441)
T ss_pred cCCCCCEEEEEEecCCHHHHHHHHHHHHh
Confidence 66789999999999998886666555544
No 94
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=31.08 E-value=81 Score=18.74 Aligned_cols=44 Identities=23% Similarity=0.238 Sum_probs=29.1
Q ss_pred hcceeeeeceeeCCCCCCCCCCCceEEEEEeC-CHHHHHHHHHHHHHH
Q psy17590 23 SEAGITVRGIYIPPGKNPPEGERKLFLAIEST-NELAVSKAKVEITRL 69 (98)
Q Consensus 23 Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~-te~~V~~A~~eIk~i 69 (98)
-|+.|+.= .-.|... ..++.-.|+.++|. .+..++.++++|+..
T Consensus 23 ~~vni~~I-~Srp~~~--~~~~~~f~id~~~~~~~~~~~~~l~~l~~~ 67 (75)
T cd04880 23 RGINLTKI-ESRPSRK--GLWEYEFFVDFEGHIDDPDVKEALEELKRV 67 (75)
T ss_pred CCCCEEEE-EeeecCC--CCceEEEEEEEECCCCCHHHHHHHHHHHHh
Confidence 45544442 3333222 34678888999997 788999999888764
No 95
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=31.06 E-value=25 Score=19.63 Aligned_cols=26 Identities=19% Similarity=0.162 Sum_probs=17.9
Q ss_pred hhHHHHhccHHHHHHhHhhhcceeee
Q psy17590 4 SPIHLLALLGEALAQISEYSEAGITV 29 (98)
Q Consensus 4 q~~R~~vT~~~tl~~I~e~Tga~It~ 29 (98)
+.++-...++-++.+|.+.+|+|-+|
T Consensus 12 ~~i~~l~~~G~si~~IA~~~gvsr~T 37 (45)
T PF02796_consen 12 EEIKELYAEGMSIAEIAKQFGVSRST 37 (45)
T ss_dssp HHHHHHHHTT--HHHHHHHTTS-HHH
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHH
Confidence 34556677889999999999998665
No 96
>PF03506 Flu_C_NS1: Influenza C non-structural protein (NS1); InterPro: IPR005187 The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment encodes a 286 amino acid non-structural protein NS1 []. This protein contains 6 conserved cysteines that may be functionally important, perhaps binding to a metal ion.
Probab=30.34 E-value=28 Score=24.79 Aligned_cols=36 Identities=22% Similarity=0.342 Sum_probs=27.0
Q ss_pred HHhHhhhcceeeeeceeeCCCCCCC----CCCCceEEEEE
Q psy17590 17 AQISEYSEAGITVRGIYIPPGKNPP----EGERKLFLAIE 52 (98)
Q Consensus 17 ~~I~e~Tga~It~KG~y~ppg~~p~----~ge~kLYL~Ie 52 (98)
++-.-+|-+++.+||.-||-.-.|. -|+-|+||--.
T Consensus 12 aesitmtpasvevkgkkfpidfvpsniapigqnpiylspc 51 (162)
T PF03506_consen 12 AESITMTPASVEVKGKKFPIDFVPSNIAPIGQNPIYLSPC 51 (162)
T ss_pred ccCCccCccceeecCCcCCcccCccccccCCCCCeeeccc
Confidence 3445578999999999888766543 38899998644
No 97
>PF08915 tRNA-Thr_ED: Archaea-specific editing domain of threonyl-tRNA synthetase; InterPro: IPR015011 Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet []. ; GO: 0004829 threonine-tRNA ligase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0005737 cytoplasm; PDB: 3PD4_B 3PD3_A 2HL0_A 2HL1_A 2HKZ_A 3PD5_B 2HL2_A 3PD2_B 1Y2Q_A.
Probab=29.64 E-value=49 Score=23.67 Aligned_cols=27 Identities=37% Similarity=0.468 Sum_probs=19.4
Q ss_pred ceEEEEEeCCHHH----HHHHHHHHHHHHHH
Q psy17590 46 KLFLAIESTNELA----VSKAKVEITRLIKE 72 (98)
Q Consensus 46 kLYL~Ieg~te~~----V~~A~~eIk~ii~e 72 (98)
-+|..||..++.. |++|+++|+.+...
T Consensus 39 VvF~~VE~~De~~~~~vv~~av~eI~~~a~k 69 (138)
T PF08915_consen 39 VVFIAVEKGDEENPEGVVEKAVEEIKWVAKK 69 (138)
T ss_dssp EEEEE-BGGGGG-HHHHHHHHHHHHHHHHHH
T ss_pred EEEEEEcCCCCCCHHHHHHHHHHHHHHHHHh
Confidence 3677888766555 99999999988764
No 98
>COG4401 AroH Chorismate mutase [Amino acid transport and metabolism]
Probab=29.38 E-value=79 Score=22.28 Aligned_cols=25 Identities=32% Similarity=0.344 Sum_probs=20.1
Q ss_pred EEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 50 AIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 50 ~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
-|++.|++.+..|.+++-+-|.+.-
T Consensus 11 TV~~nt~eeI~~at~eLl~~i~~~N 35 (125)
T COG4401 11 TVESNTEEEILDATKELLEEIEEEN 35 (125)
T ss_pred eecCCCHHHHHHHHHHHHHHHHHhc
Confidence 3788999999999998877776643
No 99
>PF13388 DUF4106: Protein of unknown function (DUF4106)
Probab=29.06 E-value=31 Score=28.28 Aligned_cols=26 Identities=38% Similarity=0.626 Sum_probs=16.1
Q ss_pred cceeeeeceeeCCCC---CCCCCCCceEE
Q psy17590 24 EAGITVRGIYIPPGK---NPPEGERKLFL 49 (98)
Q Consensus 24 ga~It~KG~y~ppg~---~p~~ge~kLYL 49 (98)
|+-|-.-|.|+||+- .|.||-||-|+
T Consensus 162 gtYILASGTYIPPNPPrEAPAPGLPKTFT 190 (422)
T PF13388_consen 162 GTYILASGTYIPPNPPREAPAPGLPKTFT 190 (422)
T ss_pred cceecccccccCCCCcccccCCCCcchhh
Confidence 344445566667765 36777777775
No 100
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.68 E-value=82 Score=19.57 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=18.8
Q ss_pred CCCceEEEEEeCCHHHHHHHHHHHHHH
Q psy17590 43 GERKLFLAIESTNELAVSKAKVEITRL 69 (98)
Q Consensus 43 ge~kLYL~Ieg~te~~V~~A~~eIk~i 69 (98)
++---|+-++|... .++.|+++|++.
T Consensus 41 ~~y~F~id~e~~~~-~i~~~l~~l~~~ 66 (74)
T cd04929 41 SEFEIFVDCECDQR-RLDELVQLLKRE 66 (74)
T ss_pred ceEEEEEEEEcCHH-HHHHHHHHHHHh
Confidence 34456677888765 888888888764
No 101
>PF11869 DUF3389: Protein of unknown function (DUF3389); InterPro: IPR021811 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=26.79 E-value=40 Score=21.86 Aligned_cols=23 Identities=22% Similarity=0.079 Sum_probs=19.4
Q ss_pred HHH--HhccHHHHHHhHhhhcceee
Q psy17590 6 IHL--LALLGEALAQISEYSEAGIT 28 (98)
Q Consensus 6 ~R~--~vT~~~tl~~I~e~Tga~It 28 (98)
+|| ++-+.+.+..|.+++|+.|+
T Consensus 51 vkWSikLD~eeQL~~ia~~lGi~iq 75 (75)
T PF11869_consen 51 VKWSIKLDNEEQLQAIAEELGIDIQ 75 (75)
T ss_pred eEEEEEcCCHHHHHHHHHHhCcccC
Confidence 566 56799999999999999874
No 102
>PRK14622 hypothetical protein; Provisional
Probab=26.20 E-value=1.6e+02 Score=19.64 Aligned_cols=23 Identities=22% Similarity=0.163 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Q psy17590 57 LAVSKAKVEITRLIKEELIKLSS 79 (98)
Q Consensus 57 ~~V~~A~~eIk~ii~e~~~~~~~ 79 (98)
.+++.|+.++++...+.+.++..
T Consensus 72 aA~N~A~~k~~~~~~~~m~~~tg 94 (103)
T PRK14622 72 AAVNAAVEKARTAADESMSKATG 94 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhC
Confidence 57888899999999999888743
No 103
>KOG3101|consensus
Probab=26.13 E-value=66 Score=25.43 Aligned_cols=33 Identities=24% Similarity=0.423 Sum_probs=22.2
Q ss_pred HhhhcceeeeeceeeCCCCCCCCCCCceEEEEEeC
Q psy17590 20 SEYSEAGITVRGIYIPPGKNPPEGERKLFLAIEST 54 (98)
Q Consensus 20 ~e~Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg~ 54 (98)
++.++|+.|. |.|+||...-....|-||.+ .|.
T Consensus 21 S~tl~c~Mtf-~vylPp~a~~~k~~P~lf~L-SGL 53 (283)
T KOG3101|consen 21 SNTLKCSMTF-GVYLPPDAPRGKRCPVLFYL-SGL 53 (283)
T ss_pred ccccccceEE-EEecCCCcccCCcCceEEEe-cCC
Confidence 4567788765 99999887544456777743 443
No 104
>PRK00394 transcription factor; Reviewed
Probab=25.83 E-value=2.4e+02 Score=20.49 Aligned_cols=43 Identities=21% Similarity=0.238 Sum_probs=33.0
Q ss_pred eceeeCCCCCCCC----CCCceEEEEE---------eCCHHHHHHHHHHHHHHHHH
Q psy17590 30 RGIYIPPGKNPPE----GERKLFLAIE---------STNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 30 KG~y~ppg~~p~~----ge~kLYL~Ie---------g~te~~V~~A~~eIk~ii~e 72 (98)
+..-|.|..-|.- .+|+.-++|. +.|++.+++|++.|-.+|.+
T Consensus 119 ~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~~~l~~ 174 (179)
T PRK00394 119 ENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDAEKAVEKILEKLEE 174 (179)
T ss_pred CCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 5677888876542 5677776665 46899999999999988875
No 105
>PRK13667 hypothetical protein; Provisional
Probab=25.60 E-value=1.9e+02 Score=18.51 Aligned_cols=33 Identities=18% Similarity=0.207 Sum_probs=18.9
Q ss_pred eeeCCCCCCCC-CCCceEEEEEeCCHHHHHHHHH
Q psy17590 32 IYIPPGKNPPE-GERKLFLAIESTNELAVSKAKV 64 (98)
Q Consensus 32 ~y~ppg~~p~~-ge~kLYL~Ieg~te~~V~~A~~ 64 (98)
.||-+.+.-.| -|..--|.||+.|+..|++-++
T Consensus 5 VfYQ~~k~~~P~RE~T~sLYlEa~s~~e~R~~v~ 38 (70)
T PRK13667 5 VFYQETKDEVPVRETTQTLYLEADSEVEVRGRLK 38 (70)
T ss_pred EEecCCCCcCCcccccceEEEEcCCHHHHHHHHh
Confidence 57877776433 3444445567777755554433
No 106
>PRK00596 rpsJ 30S ribosomal protein S10; Reviewed
Probab=25.29 E-value=1.4e+02 Score=19.81 Aligned_cols=28 Identities=11% Similarity=0.222 Sum_probs=25.6
Q ss_pred CceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 45 RKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 45 ~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
.++.+-+.|-+...++.+...|.+..+.
T Consensus 4 ~~irI~l~S~d~~~L~~~~~~i~~~a~~ 31 (102)
T PRK00596 4 QKIRIRLKAFDHRLLDQSAKKIVETAKR 31 (102)
T ss_pred cEEEEEEEECCHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999998875
No 107
>PRK02114 formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional
Probab=25.07 E-value=1e+02 Score=24.80 Aligned_cols=21 Identities=24% Similarity=0.202 Sum_probs=17.3
Q ss_pred CceEEEEEeCCHHHHHHHHHH
Q psy17590 45 RKLFLAIESTNELAVSKAKVE 65 (98)
Q Consensus 45 ~kLYL~Ieg~te~~V~~A~~e 65 (98)
-=+-+.|.|.|+++|.+|+..
T Consensus 242 ~V~EIVIdGl~~~aV~~Amr~ 262 (297)
T PRK02114 242 AVYEIVIDGLDEEAVAEAMRA 262 (297)
T ss_pred eEEEEEEcCCCHHHHHHHHHH
Confidence 445588899999999999865
No 108
>KOG0071|consensus
Probab=24.66 E-value=1e+02 Score=22.88 Aligned_cols=32 Identities=22% Similarity=0.487 Sum_probs=26.3
Q ss_pred CCCceEEEEEeCCHHHHHHHHHHHHHHHHHHH
Q psy17590 43 GERKLFLAIESTNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 43 ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~ 74 (98)
|..-|-+.+.+.+...++.|.+|+.++|.+--
T Consensus 84 gtqglIFV~Dsa~~dr~eeAr~ELh~ii~~~e 115 (180)
T KOG0071|consen 84 GTQGLIFVVDSADRDRIEEARNELHRIINDRE 115 (180)
T ss_pred CCceEEEEEeccchhhHHHHHHHHHHHhCCHh
Confidence 44556688888889999999999999997643
No 109
>COG2877 KdsA 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]
Probab=24.62 E-value=44 Score=26.51 Aligned_cols=36 Identities=19% Similarity=0.372 Sum_probs=29.3
Q ss_pred Hhhhcceeee-eceeeCCCCCC-------CCCCCceEEEEEeCC
Q psy17590 20 SEYSEAGITV-RGIYIPPGKNP-------PEGERKLFLAIESTN 55 (98)
Q Consensus 20 ~e~Tga~It~-KG~y~ppg~~p-------~~ge~kLYL~Ieg~t 55 (98)
...||+.|.+ ||||+.|...- ..|.++++|+=-|.|
T Consensus 127 ~AkTg~~vNiKKgQFLaPwdMknvv~K~~~~gn~~v~lcERG~s 170 (279)
T COG2877 127 AAKTGAVVNVKKGQFLAPWDMKNIVEKFLETGNNKVILCERGAS 170 (279)
T ss_pred HHHhCCeEeeccccccChhHhhhHHHHHHhcCCCcEEEEeccCc
Confidence 4469999999 99999998753 248899999888766
No 110
>TIGR01049 rpsJ_bact ribosomal protein S10, bacterial/organelle. This model describes bacterial 30S ribosomal protein S10. In species that have a transcription antitermination complex, or N utilization substance, with NusA, NusB, NusG, and NusE, this ribosomal protein is responsible for NusE activity. Included in the family are one member each from Saccharomyces cerevisiae and Schizosaccharomyces pombe. These proteins lack an N-terminal mitochondrial transit peptide but contain additional sequence C-terminal to the ribosomal S10 protein region.
Probab=24.60 E-value=1.6e+02 Score=19.31 Aligned_cols=27 Identities=15% Similarity=0.238 Sum_probs=24.4
Q ss_pred ceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 46 KLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 46 kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
++.|.+.|-+...++.+...|.+..+.
T Consensus 2 ~irI~l~s~d~~~L~~~~~~i~~~a~~ 28 (99)
T TIGR01049 2 KIRIKLKSYDHRLLDQSTKKIVETAKR 28 (99)
T ss_pred eEEEEEEECCHHHHHHHHHHHHHHHHH
Confidence 578899999999999999999998765
No 111
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=24.52 E-value=1.5e+02 Score=16.88 Aligned_cols=36 Identities=19% Similarity=0.260 Sum_probs=27.5
Q ss_pred eeceeeCCCCCCCCCCCceEEEEEeCCHHHHHHHHHHHH
Q psy17590 29 VRGIYIPPGKNPPEGERKLFLAIESTNELAVSKAKVEIT 67 (98)
Q Consensus 29 ~KG~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A~~eIk 67 (98)
+....+...+. +.++-+-+|+-.|++..++|+....
T Consensus 25 v~~v~~~~~~~---~~~~~~a~v~f~~~~~a~~al~~~~ 60 (70)
T PF14259_consen 25 VEKVRLIKNKD---GQSRGFAFVEFSSEEDAKRALELLN 60 (70)
T ss_dssp EEEEEEEESTT---SSEEEEEEEEESSHHHHHHHHHHHT
T ss_pred cceEEEEeeec---cccCCEEEEEeCCHHHHHHHHHHCC
Confidence 45555655432 5889999999999999999987753
No 112
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=24.48 E-value=1.7e+02 Score=19.54 Aligned_cols=27 Identities=19% Similarity=0.217 Sum_probs=24.5
Q ss_pred ceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 46 KLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 46 kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
++.+-+.+-+...++.+.++|.+..+.
T Consensus 3 ~irI~L~S~d~~~Ld~~~~~I~~~~k~ 29 (102)
T PRK12271 3 KARIRLSSTNPEDLDEVCDQIKEIAEK 29 (102)
T ss_pred eEEEEEEeCCHHHHHHHHHHHHHHHHH
Confidence 678889999999999999999998875
No 113
>cd05801 PGM_like3 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=24.39 E-value=1.5e+02 Score=24.80 Aligned_cols=29 Identities=24% Similarity=0.196 Sum_probs=23.1
Q ss_pred CCCCCCceEEEEEe-CCHHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIES-TNELAVSKAKVEITR 68 (98)
Q Consensus 40 p~~ge~kLYL~Ieg-~te~~V~~A~~eIk~ 68 (98)
|...||++-+.+|+ .|++.+++-.+++.+
T Consensus 491 pSgTEP~iriy~Ea~~~~~~~~~l~~~~~~ 520 (522)
T cd05801 491 PSGTEDVYKIYAESFLSEEHLKKIQKEAQE 520 (522)
T ss_pred ccCCCceEEEEEEecCCHHHHHHHHHHHHH
Confidence 66789999999999 698877766666554
No 114
>PHA03323 nuclear egress membrane protein UL34; Provisional
Probab=24.17 E-value=1e+02 Score=24.41 Aligned_cols=51 Identities=12% Similarity=0.160 Sum_probs=31.7
Q ss_pred hhhcceeeeeceeeCCCCCCCC---CCCceEEEEEeCCHHHHHHHHHHHHHHHH
Q psy17590 21 EYSEAGITVRGIYIPPGKNPPE---GERKLFLAIESTNELAVSKAKVEITRLIK 71 (98)
Q Consensus 21 e~Tga~It~KG~y~ppg~~p~~---ge~kLYL~Ieg~te~~V~~A~~eIk~ii~ 71 (98)
..||.||-+.|-|.+|-..+.. -|..=-++-...|--..-.|+++||+...
T Consensus 83 QNTGvsVl~qG~f~~p~na~~~~it~~~~nv~L~st~stg~sls~l~~iK~~~g 136 (272)
T PHA03323 83 QNTGVSVLFQGFFFRPPNAPGAAITAEQNNVILKSTESTGLSLSDLERIKRRGG 136 (272)
T ss_pred ecCCeEEEEeecccCCCCCCCCccccccceeEEeeccccceehhHHHHHHHhcC
Confidence 3599999999999988765443 33333344333444444456677776543
No 115
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=24.07 E-value=2.4e+02 Score=19.24 Aligned_cols=45 Identities=11% Similarity=0.180 Sum_probs=31.9
Q ss_pred EeCCHHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCceEEeeccC
Q psy17590 52 ESTNELAVSKAKVEITRLIKEELIKLSSSAHQSINKSRYKGVGRGK 97 (98)
Q Consensus 52 eg~te~~V~~A~~eIk~ii~e~~~~~~~~~~~~~~~GRY~V~~~~~ 97 (98)
.|.+-..+.+.+..+.+.|..-+..++...- ..+..+|.+++.|.
T Consensus 13 ~g~~~~~i~~~~s~~~d~l~~r~~~la~~~~-~~pp~~~a~lalGS 57 (138)
T PF03445_consen 13 RGASVRQIARILSELNDALIRRLIELAEAEM-GPPPVPFAWLALGS 57 (138)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCCEEEEEECc
Confidence 4667777888888887776666666654432 23689999999885
No 116
>PRK08363 alanine aminotransferase; Validated
Probab=23.92 E-value=2.4e+02 Score=21.97 Aligned_cols=27 Identities=11% Similarity=0.150 Sum_probs=22.2
Q ss_pred EEEEE-eCCHHHHHHHHHHHHHHHHHHH
Q psy17590 48 FLAIE-STNELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 48 YL~Ie-g~te~~V~~A~~eIk~ii~e~~ 74 (98)
|+-|. +.+++.++.|++.|++.+.+.+
T Consensus 369 ~iRis~~~~~~~l~~~l~~l~~~~~~~~ 396 (398)
T PRK08363 369 HFRLVFLPPVEILEEAMDRFEEFMRERL 396 (398)
T ss_pred eEEEEecCCHHHHHHHHHHHHHHHHHhc
Confidence 67666 7788999999999999887643
No 117
>PF12714 TILa: TILa domain
Probab=23.64 E-value=46 Score=19.73 Aligned_cols=11 Identities=45% Similarity=1.041 Sum_probs=9.3
Q ss_pred eeceeeCCCCC
Q psy17590 29 VRGIYIPPGKN 39 (98)
Q Consensus 29 ~KG~y~ppg~~ 39 (98)
..|+|||+|..
T Consensus 5 ~~G~yy~~Ge~ 15 (56)
T PF12714_consen 5 YNGRYYPPGES 15 (56)
T ss_pred cCCEEECCCCE
Confidence 47999999985
No 118
>PRK15405 ethanolamine utilization protein EutL; Provisional
Probab=23.24 E-value=1.7e+02 Score=22.47 Aligned_cols=33 Identities=9% Similarity=0.057 Sum_probs=27.2
Q ss_pred CCceEEEEEeCCHHHHHHHHHHHHHHHHHHHHH
Q psy17590 44 ERKLFLAIESTNELAVSKAKVEITRLIKEELIK 76 (98)
Q Consensus 44 e~kLYL~Ieg~te~~V~~A~~eIk~ii~e~~~~ 76 (98)
.-++.+.|.|++...|+.|++...+.+++.+.-
T Consensus 80 ~G~viiIi~G~dvsdVrsAveaa~~~i~~~~~f 112 (217)
T PRK15405 80 AGEVIGILAGPNPAEVRAGLDAMVAFIENGAAF 112 (217)
T ss_pred CccEEEEEeCCCHHHHHHHHHHHHHHHHhhhce
Confidence 356677888889999999999999999886643
No 119
>cd07890 CYTH-like_AC_IV-like Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily. This subgroup contains class IV ACs and similar proteins. AC catalyzes the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. cAMP is a key signaling molecule which conveys a variety of signals in different cell types. In prokaryotes, cAMP is a catabolite derepression signal which triggers the expression of metabolic pathways including the lactose operon. Six non-homologous classes of ACs have been identified (I-VI). Class IV ACs are found in this group. In bacteria, the gene encoding Class IV AC has been designated cyaB and the protein as AC2. AC-IV occurs in addition to AC-I in bacterial pathogens such as Yersinia pestis (plague disease). The role of AC-IV is unknown but it has been speculated that it may be a factor in pathogenesis, perhaps providing cAMP for a secondary internal signaling function, or for secretion and uptake into host cells, where it may disrupt normal cel
Probab=23.11 E-value=85 Score=21.86 Aligned_cols=60 Identities=23% Similarity=0.144 Sum_probs=38.3
Q ss_pred ccHHHHHHhHhhhc-----ceeeeeceeeCCCCCC----CCCCCceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 11 LLGEALAQISEYSE-----AGITVRGIYIPPGKNP----PEGERKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 11 T~~~tl~~I~e~Tg-----a~It~KG~y~ppg~~p----~~ge~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
.+.+.+..|-+..| ..-+.|-.|.-.+... .++ ..-|+.||+.++. ++.|..+|..++..
T Consensus 85 ~~~~~~~~iL~~lg~~~~~~~~K~R~~~~~~~~~v~lD~~~~-lG~f~EiE~~~~~-~~~~~~~l~~~~~~ 153 (169)
T cd07890 85 ADPEAMKEILERLGFGPVGRVKKEREIYLLGQTRVHLDRVEG-LGDFVEIEVVLED-IEEAEEGLGEAAEL 153 (169)
T ss_pred CCHHHHHHHHHHcCCceeEEEEEEEEEEEECCEEEEEEccCC-CCceEEEEEEeCC-cHHHHHHHHHHHHH
Confidence 35556666665544 3334477776655321 112 3449999998887 88888888887764
No 120
>cd07758 ThTPase Thiamine Triphosphatase. ThTPase is a soluble cytosolic enzyme which converts thiamine triphosphate (ThTP) to thiamine diphosphate. This catalytic activity depends on a divalent metal cofactor, for example Mg++. ThTPase regulates the intracellular concentration of ThTP, maintaining it at a low concentration in vivo. ThTP acts as a messenger in cell signaling in response to cellular stress, and in addition, can phosphorylate proteins in certain tissues. There is another class of membrane-associated enzymes in animal tissues which also convert ThTP to thiamine diphosphate, however they do not belong to this subgroup. This subgroup belongs to the CYTH/triphosphate tunnel metalloenzyme (TTM)-like superfamily, whose enzymes have a unique active site located within an eight-stranded beta barrel.
Probab=22.85 E-value=1.2e+02 Score=22.11 Aligned_cols=27 Identities=22% Similarity=0.219 Sum_probs=21.4
Q ss_pred EEEEEeCC---HHHHHHHHHHHHHHHHHHH
Q psy17590 48 FLAIESTN---ELAVSKAKVEITRLIKEEL 74 (98)
Q Consensus 48 YL~Ieg~t---e~~V~~A~~eIk~ii~e~~ 74 (98)
-|.++..+ +..++.|+++|.+++....
T Consensus 147 EiE~~v~~~~~~~~~~~a~~~i~~~~~~lg 176 (196)
T cd07758 147 EVELLVEEEDNEAEVPAALAKIDELISALM 176 (196)
T ss_pred EEEEEEecccchhhHHHHHHHHHHHHHHhC
Confidence 35566677 8899999999999997644
No 121
>cd01181 IPT_plexin_repeat3 Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains.
Probab=22.81 E-value=57 Score=21.31 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=18.3
Q ss_pred hcceeeeeceeeCCCCCCCCCCCceEEEEEe
Q psy17590 23 SEAGITVRGIYIPPGKNPPEGERKLFLAIES 53 (98)
Q Consensus 23 Tga~It~KG~y~ppg~~p~~ge~kLYL~Ieg 53 (98)
-|+.||+.|+++.-+. +|.+++.+.+
T Consensus 15 GGt~itV~G~~Lds~q-----~p~~~V~~~~ 40 (99)
T cd01181 15 GGTPITVTGTNLNTVQ-----EPRIRVKYGG 40 (99)
T ss_pred CCEEEEEEeeccCccc-----ccEEEEEECC
Confidence 5889999999998886 3444544443
No 122
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.78 E-value=93 Score=17.38 Aligned_cols=16 Identities=19% Similarity=0.245 Sum_probs=12.3
Q ss_pred eCCHHHHHHHHHHHHH
Q psy17590 53 STNELAVSKAKVEITR 68 (98)
Q Consensus 53 g~te~~V~~A~~eIk~ 68 (98)
|.++..|++|++++++
T Consensus 36 g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 36 GVSRRTVQRAIKELEE 51 (55)
T ss_pred CcCHHHHHHHHHHHHH
Confidence 6778888888887765
No 123
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=22.47 E-value=23 Score=18.96 Aligned_cols=19 Identities=16% Similarity=0.176 Sum_probs=11.1
Q ss_pred HhccHHHHHHhHhhhccee
Q psy17590 9 LALLGEALAQISEYSEAGI 27 (98)
Q Consensus 9 ~vT~~~tl~~I~e~Tga~I 27 (98)
.|..+||+..|....|.+.
T Consensus 2 ~V~~gDtl~~IA~~~~~~~ 20 (44)
T PF01476_consen 2 TVQPGDTLWSIAKRYGISV 20 (44)
T ss_dssp EE-TT--HHHHHHHTTS-H
T ss_pred EECcCCcHHHHHhhhhhhH
Confidence 4667888888888776654
No 124
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=22.14 E-value=24 Score=20.32 Aligned_cols=23 Identities=4% Similarity=0.010 Sum_probs=16.2
Q ss_pred HHHHhHhhhcceeeeeceeeCCC
Q psy17590 15 ALAQISEYSEAGITVRGIYIPPG 37 (98)
Q Consensus 15 tl~~I~e~Tga~It~KG~y~ppg 37 (98)
|+.+|.+.+|+|++|=-+++-..
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC
Confidence 46788888888888765555443
No 125
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=22.01 E-value=2e+02 Score=19.12 Aligned_cols=27 Identities=26% Similarity=0.334 Sum_probs=24.1
Q ss_pred ceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 46 KLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 46 kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
++.+-+.+-+...++.+.++|.+..+.
T Consensus 2 ~irI~L~S~d~~~Ld~~~~~I~~~ak~ 28 (99)
T TIGR01046 2 KARIKLTSTNVRSLEKVCAQIKRIAEK 28 (99)
T ss_pred cEEEEEEECCHHHHHHHHHHHHHHHHH
Confidence 577888999999999999999998875
No 126
>PLN02607 1-aminocyclopropane-1-carboxylate synthase
Probab=21.31 E-value=4.4e+02 Score=21.42 Aligned_cols=46 Identities=17% Similarity=0.218 Sum_probs=30.8
Q ss_pred eceeeCCCCCCCCCCCceEEEEE-e-CCHHHHHHHHHHHHHHHHHHHHH
Q psy17590 30 RGIYIPPGKNPPEGERKLFLAIE-S-TNELAVSKAKVEITRLIKEELIK 76 (98)
Q Consensus 30 KG~y~ppg~~p~~ge~kLYL~Ie-g-~te~~V~~A~~eIk~ii~e~~~~ 76 (98)
.|.++.||......++. |+-|. + .+++.++.|++.|...+.+...+
T Consensus 394 ~gV~v~pG~~f~~~~~g-~fRi~fa~~~~~~l~~gl~Ri~~~l~~~~~~ 441 (447)
T PLN02607 394 VKLNISPGSSCHCSEPG-WFRVCFANMSEDTLEVALKRIHRFMDRRKTA 441 (447)
T ss_pred CCEEEcCccccCCCCCC-EEEEEeccCCHHHHHHHHHHHHHHHHHHHhh
Confidence 46666666654333333 55555 4 37999999999999999765443
No 127
>smart00215 VWC_out von Willebrand factor (vWF) type C domain.
Probab=21.28 E-value=67 Score=19.99 Aligned_cols=15 Identities=33% Similarity=0.607 Sum_probs=11.7
Q ss_pred eeeceeeCCCCCCCC
Q psy17590 28 TVRGIYIPPGKNPPE 42 (98)
Q Consensus 28 t~KG~y~ppg~~p~~ 42 (98)
+.+|+||+|+..-.+
T Consensus 2 ~~~G~~y~~g~~w~d 16 (67)
T smart00215 2 YNNGSYYPPGAKWDD 16 (67)
T ss_pred eECCEEcCCCCcccc
Confidence 568999999987443
No 128
>PRK06225 aspartate aminotransferase; Provisional
Probab=21.26 E-value=3.4e+02 Score=20.88 Aligned_cols=25 Identities=12% Similarity=0.189 Sum_probs=19.9
Q ss_pred EEEEE-eCCHHHHHHHHHHHHHHHHH
Q psy17590 48 FLAIE-STNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 48 YL~Ie-g~te~~V~~A~~eIk~ii~e 72 (98)
|+.|. +.+++.+++++..|++++.+
T Consensus 351 ~iR~s~~~~~e~l~~~~~~l~~~~~~ 376 (380)
T PRK06225 351 YIRVSFSIPREQVEVFCEEFPDVVET 376 (380)
T ss_pred eEEEEeCCCHHHHHHHHHHHHHHHHH
Confidence 55555 56789999999999998873
No 129
>COG3360 Uncharacterized conserved protein [Function unknown]
Probab=21.13 E-value=78 Score=20.33 Aligned_cols=18 Identities=11% Similarity=0.196 Sum_probs=14.6
Q ss_pred EEEEeCCHHHHHHHHHHH
Q psy17590 49 LAIESTNELAVSKAKVEI 66 (98)
Q Consensus 49 L~Ieg~te~~V~~A~~eI 66 (98)
+.|.|.|+.+++.|++.-
T Consensus 9 IelvGtSp~S~d~Ai~~A 26 (71)
T COG3360 9 IELVGTSPTSIDAAIANA 26 (71)
T ss_pred EEEEecCCccHHHHHHHH
Confidence 567799999999997653
No 130
>CHL00135 rps10 ribosomal protein S10; Validated
Probab=20.89 E-value=1.8e+02 Score=19.40 Aligned_cols=28 Identities=14% Similarity=0.132 Sum_probs=25.8
Q ss_pred CceEEEEEeCCHHHHHHHHHHHHHHHHH
Q psy17590 45 RKLFLAIESTNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 45 ~kLYL~Ieg~te~~V~~A~~eIk~ii~e 72 (98)
.++.+-+.|-+...++.+...|.+..+.
T Consensus 7 ~kirI~LkS~d~~~L~~~~~~I~~~~k~ 34 (101)
T CHL00135 7 AKIRIKLKSFNHELLNSSCKKIIDTASR 34 (101)
T ss_pred CeEEEEEEECCHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999998875
No 131
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=20.87 E-value=1.4e+02 Score=20.65 Aligned_cols=21 Identities=24% Similarity=0.199 Sum_probs=14.0
Q ss_pred eEEEEEeCCHHHHHHHHHHHHH
Q psy17590 47 LFLAIESTNELAVSKAKVEITR 68 (98)
Q Consensus 47 LYL~Ieg~te~~V~~A~~eIk~ 68 (98)
.|+.||| ++..++.+...+++
T Consensus 2 ~~~~iEg-d~~~~~~l~~l~~~ 22 (132)
T PF10728_consen 2 IPFAIEG-DEEALEVLQELAKE 22 (132)
T ss_dssp --EEEEE-SHHHHHHHHHHHHH
T ss_pred eEEEEec-CHHHHHHHHHHHHH
Confidence 4789999 88877766655543
No 132
>PLN00062 TATA-box-binding protein; Provisional
Probab=20.85 E-value=2.9e+02 Score=20.17 Aligned_cols=42 Identities=19% Similarity=0.083 Sum_probs=29.8
Q ss_pred eeeCCCCCCCC----CCCceEEEEE---------eCCHHHHHHHHHHHHHHHHHH
Q psy17590 32 IYIPPGKNPPE----GERKLFLAIE---------STNELAVSKAKVEITRLIKEE 73 (98)
Q Consensus 32 ~y~ppg~~p~~----ge~kLYL~Ie---------g~te~~V~~A~~eIk~ii~e~ 73 (98)
.-|.|..-|.- .+++.=++|. +.+++.+++|++.|..+|.+-
T Consensus 120 ~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~~ai~~i~p~L~~~ 174 (179)
T PLN00062 120 SSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIYTAFENIYPVLTEF 174 (179)
T ss_pred cccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHHHh
Confidence 34666665542 4566665555 467999999999999998863
No 133
>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]
Probab=20.79 E-value=2.9e+02 Score=18.87 Aligned_cols=41 Identities=10% Similarity=0.102 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHHHHHHH-----------HHHHhhhhccCCCCCCceEEeec
Q psy17590 54 TNELAVSKAKVEITRLIKE-----------ELIKLSSSAHQSINKSRYKGVGR 95 (98)
Q Consensus 54 ~te~~V~~A~~eIk~ii~e-----------~~~~~~~~~~~~~~~GRY~V~~~ 95 (98)
.|++.+...+...+.+|.+ |..+++... +....|.|.+++-
T Consensus 13 ~see~~~~~ve~~~~~l~~~gg~i~~~e~wG~R~LAY~I-kK~~~g~Y~l~~f 64 (112)
T COG0360 13 LSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPI-KKLREGHYVLMNF 64 (112)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCEEEEehhhhhhhhccee-cccceEEEEEEEE
Confidence 4578999999999999998 555665533 4567799988763
No 134
>PF09435 DUF2015: Fungal protein of unknown function (DUF2015); InterPro: IPR018559 This entry represents uncharacterised proteins found in fungi.
Probab=20.54 E-value=89 Score=22.16 Aligned_cols=20 Identities=30% Similarity=0.459 Sum_probs=14.0
Q ss_pred CCHHHHH-HHHHHHHHHHHHH
Q psy17590 54 TNELAVS-KAKVEITRLIKEE 73 (98)
Q Consensus 54 ~te~~V~-~A~~eIk~ii~e~ 73 (98)
.+...++ .|+.||++||++.
T Consensus 77 D~R~GLD~~ak~EI~~IM~~~ 97 (128)
T PF09435_consen 77 DSRAGLDDAAKREIRRIMKRR 97 (128)
T ss_pred CcccCcCHHHHHHHHHHHHHc
Confidence 3344454 5799999999864
No 135
>cd03087 PGM_like1 This archaeal PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.
Probab=20.53 E-value=1.6e+02 Score=23.67 Aligned_cols=28 Identities=21% Similarity=0.178 Sum_probs=21.6
Q ss_pred CCCCCCceEEEEEeCCHHHHHHHHHHHH
Q psy17590 40 PPEGERKLFLAIESTNELAVSKAKVEIT 67 (98)
Q Consensus 40 p~~ge~kLYL~Ieg~te~~V~~A~~eIk 67 (98)
|...||++.+.+|+.|++..+.=...+.
T Consensus 409 pS~tep~~rvy~Ea~~~~~a~~l~~~~~ 436 (439)
T cd03087 409 PSGTEPKIRITAEAKTEERAKELLEEGR 436 (439)
T ss_pred ccCCccEEEEEEeeCCHHHHHHHHHHHH
Confidence 6678899999999999887655444443
No 136
>PF01913 FTR: Formylmethanofuran-tetrahydromethanopterin formyltransferase; InterPro: IPR022667 Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction: N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin Ftr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr, determined to a reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel beta sheet flanked by alpha helices forming an alpha/beta sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface []. Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure []. In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates [].; GO: 0016740 transferase activity, 0006730 one-carbon metabolic process; PDB: 1M5H_E 1M5S_C 1FTR_C 2FHJ_B 2FHK_D.
Probab=20.48 E-value=3.4e+02 Score=19.60 Aligned_cols=45 Identities=18% Similarity=0.267 Sum_probs=31.0
Q ss_pred HHhHhhhcceeeeec--------eeeCCCCCCCCCCCceEEEEEeCCHHHHHHH
Q psy17590 17 AQISEYSEAGITVRG--------IYIPPGKNPPEGERKLFLAIESTNELAVSKA 62 (98)
Q Consensus 17 ~~I~e~Tga~It~KG--------~y~ppg~~p~~ge~kLYL~Ieg~te~~V~~A 62 (98)
.--.+.||-.-++=| +|++|.. .++|.|-..++|.+.+...+++.
T Consensus 35 ~AA~~~TGfatSVIgC~~EAGIEr~l~p~e-TPDGRPGv~il~f~~~~~~L~~~ 87 (144)
T PF01913_consen 35 IAATEATGFATSVIGCGCEAGIERELSPEE-TPDGRPGVSILIFAMSKKKLEKQ 87 (144)
T ss_dssp HHHHHHHSS-S-TTTSS-EEEEEEEE-GGG-STTSS-EEEEEEEESSHHHHHHH
T ss_pred HHHHHhhcCccceeccCcceeeccccCccc-CCCCCCcEEEEEEeCCHHHHHHH
Confidence 344567777666666 7888886 44678999999999999888754
No 137
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=20.30 E-value=2.6e+02 Score=20.28 Aligned_cols=43 Identities=21% Similarity=0.211 Sum_probs=31.9
Q ss_pred eceeeCCCCCCCC----CCCceEEEEE---------eCCHHHHHHHHHHHHHHHHH
Q psy17590 30 RGIYIPPGKNPPE----GERKLFLAIE---------STNELAVSKAKVEITRLIKE 72 (98)
Q Consensus 30 KG~y~ppg~~p~~----ge~kLYL~Ie---------g~te~~V~~A~~eIk~ii~e 72 (98)
+..-|.|..-|.- .+|+.-++|. +.|++.+++|++.|-.+|++
T Consensus 118 ~~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~~~l~~ 173 (174)
T cd04518 118 PNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDAKRAVEKLLSRLKE 173 (174)
T ss_pred CCCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 4567777775542 5577766665 48999999999999888864
Done!