Query psy16497
Match_columns 143
No_of_seqs 116 out of 225
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 22:47:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16497.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16497hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01079 Hint: Hint module; I 100.0 1.3E-50 2.8E-55 324.6 8.3 134 1-136 79-217 (217)
2 KOG3638|consensus 100.0 1.1E-35 2.5E-40 256.8 7.9 134 1-138 275-414 (414)
3 cd00081 Hint Hedgehog/Intein d 98.8 1.3E-08 2.9E-13 73.5 6.2 67 1-79 68-136 (136)
4 smart00305 HintC Hint (Hedgeho 98.2 6.6E-06 1.4E-10 50.7 5.6 43 42-84 2-45 (46)
5 PRK14714 DNA polymerase II lar 91.0 0.77 1.7E-05 45.6 7.1 84 1-93 1009-1099(1337)
6 PF07591 PT-HINT: Pretoxin HIN 90.3 0.45 9.7E-06 35.2 3.9 40 2-54 59-98 (130)
7 PRK12281 rplX 50S ribosomal pr 68.2 15 0.00033 24.9 4.8 38 29-77 6-44 (76)
8 PRK14898 DNA-directed RNA poly 66.7 4.7 0.0001 38.7 2.7 33 1-40 165-197 (858)
9 PF11717 Tudor-knot: RNA bindi 64.6 16 0.00034 22.8 4.0 25 30-54 1-26 (55)
10 smart00439 BAH Bromo adjacent 64.5 12 0.00026 25.8 3.9 28 30-57 2-32 (120)
11 CHL00141 rpl24 ribosomal prote 64.0 17 0.00038 25.0 4.5 38 29-77 8-46 (83)
12 TIGR03784 marine_sortase sorta 63.3 29 0.00062 27.0 6.1 50 27-81 106-158 (174)
13 PF13403 Hint_2: Hint domain 63.2 14 0.00031 27.7 4.3 20 23-42 14-33 (147)
14 COG1935 Uncharacterized conser 62.0 18 0.00039 26.9 4.4 34 23-56 32-73 (122)
15 PF14623 Vint: Hint-domain 60.6 12 0.00025 29.2 3.4 46 23-72 15-61 (162)
16 PF00122 E1-E2_ATPase: E1-E2 A 60.3 6.7 0.00015 30.4 2.1 52 23-74 45-114 (230)
17 PF01426 BAH: BAH domain; Int 59.5 16 0.00036 25.2 3.8 27 29-55 2-31 (119)
18 PF04322 DUF473: Protein of un 56.7 46 0.001 24.6 5.9 40 23-62 32-79 (119)
19 cd06166 Sortase_D_5 Sortase D 56.7 22 0.00048 25.6 4.2 32 28-59 63-94 (126)
20 PF01878 EVE: EVE domain; Int 55.4 22 0.00049 25.9 4.1 38 26-64 36-73 (143)
21 PTZ00328 eukaryotic initiation 55.2 16 0.00034 28.7 3.3 29 23-55 21-49 (166)
22 cd05829 Sortase_E Sortase E (S 53.7 29 0.00063 25.8 4.5 52 28-84 71-128 (144)
23 COG1372 Intein/homing endonucl 51.2 11 0.00024 30.7 2.1 33 1-41 78-110 (420)
24 cd04717 BAH_polybromo BAH, or 51.0 18 0.00038 25.9 2.9 27 29-55 3-32 (121)
25 PF01079 Hint: Hint module; I 50.9 53 0.0011 26.5 5.9 34 19-52 21-55 (217)
26 PF11736 DUF3299: Protein of u 50.8 12 0.00027 28.4 2.1 38 46-83 94-138 (146)
27 PRK02268 hypothetical protein; 50.1 34 0.00074 26.0 4.4 47 22-68 28-79 (141)
28 cd00004 Sortase Sortases are c 49.1 76 0.0017 22.5 6.0 32 28-59 63-94 (128)
29 cd05828 Sortase_D_4 Sortase D 48.9 38 0.00082 24.4 4.4 32 28-59 60-91 (127)
30 PF05203 Hom_end_hint: Hom_end 48.4 24 0.00052 28.4 3.5 34 21-57 12-45 (215)
31 TIGR01080 rplX_A_E ribosomal p 48.2 41 0.00089 24.6 4.4 39 27-76 39-78 (114)
32 cd04482 RPA2_OBF_like RPA2_OBF 47.5 44 0.00095 22.9 4.3 40 2-41 15-59 (91)
33 PF13550 Phage-tail_3: Putativ 46.7 33 0.00072 24.8 3.9 27 27-53 137-163 (164)
34 cd04721 BAH_plant_1 BAH, or Br 46.3 26 0.00057 25.8 3.2 25 30-54 8-33 (130)
35 smart00306 HintN Hint (Hedgeho 46.0 53 0.0012 21.5 4.5 29 22-50 14-44 (100)
36 PTZ00194 60S ribosomal protein 45.8 34 0.00075 26.1 3.8 38 29-77 46-84 (143)
37 PRK04132 replication factor C 45.8 19 0.00042 34.7 3.0 34 1-40 130-163 (846)
38 cd01287 FabA FabA, beta-hydrox 45.2 76 0.0016 23.8 5.7 48 22-78 91-138 (150)
39 cd05830 Sortase_D_5 Sortase D 44.8 45 0.00098 24.4 4.3 41 24-64 58-102 (137)
40 cd04714 BAH_BAHCC1 BAH, or Bro 44.7 27 0.00058 25.2 3.0 25 29-53 3-30 (121)
41 COG3764 SrtA Sortase (surface 43.5 45 0.00098 26.9 4.4 30 28-57 133-162 (210)
42 PRK14701 reverse gyrase; Provi 43.4 20 0.00044 36.9 2.9 33 1-40 956-988 (1638)
43 PF14890 Intein_splicing: Inte 43.1 17 0.00038 30.1 2.0 28 1-39 65-92 (323)
44 TIGR01076 sortase_fam LPXTG-si 43.1 51 0.0011 24.0 4.3 30 28-57 62-91 (136)
45 TIGR01079 rplX_bact ribosomal 42.6 61 0.0013 23.2 4.5 36 29-75 3-39 (104)
46 COG0198 RplX Ribosomal protein 41.8 46 0.001 24.1 3.8 15 27-41 2-16 (104)
47 cd04370 BAH BAH, or Bromo Adja 41.4 39 0.00084 23.1 3.3 26 29-54 3-33 (123)
48 cd06541 ASCH ASC-1 homology or 41.1 58 0.0013 22.8 4.2 32 27-60 28-59 (105)
49 PRK01191 rpl24p 50S ribosomal 39.3 46 0.00099 24.7 3.5 27 27-53 43-70 (120)
50 smart00743 Agenet Tudor-like d 39.0 74 0.0016 19.6 4.1 26 29-54 2-29 (61)
51 PF08194 DIM: DIM protein; In 38.1 26 0.00057 20.7 1.7 16 63-79 20-35 (36)
52 TIGR00074 hypC_hupF hydrogenas 36.9 26 0.00056 23.8 1.8 16 26-41 32-47 (76)
53 PRK10671 copA copper exporting 36.5 39 0.00084 32.0 3.4 54 23-76 334-399 (834)
54 PRK05174 3-hydroxydecanoyl-(ac 35.6 1.3E+02 0.0028 23.2 5.7 46 22-77 110-155 (172)
55 COG1188 Ribosome-associated he 35.6 63 0.0014 23.3 3.6 34 22-55 41-74 (100)
56 PF11302 DUF3104: Protein of u 35.0 71 0.0015 21.9 3.7 24 29-52 5-36 (75)
57 PF01455 HupF_HypC: HupF/HypC 34.9 25 0.00055 23.2 1.4 16 26-41 34-49 (68)
58 COG0469 PykF Pyruvate kinase [ 34.9 58 0.0013 29.5 4.1 25 26-50 116-141 (477)
59 PRK14524 rpsP 30S ribosomal pr 34.7 33 0.00071 24.4 2.1 20 54-73 32-51 (94)
60 cd00081 Hint Hedgehog/Intein d 34.5 1.6E+02 0.0034 20.4 6.2 46 23-68 14-63 (136)
61 PRK00004 rplX 50S ribosomal pr 33.7 81 0.0018 22.5 4.0 26 29-54 4-30 (105)
62 TIGR00002 S16 ribosomal protei 33.2 37 0.00081 23.2 2.1 20 54-73 31-50 (78)
63 cd06552 ASCH_yqfb_like ASC-1 h 33.1 1.4E+02 0.0029 20.2 5.0 15 28-42 27-41 (100)
64 cd04712 BAH_DCM_I BAH, or Brom 33.0 53 0.0012 24.2 3.1 14 28-41 4-17 (130)
65 TIGR01497 kdpB K+-transporting 32.5 57 0.0012 30.7 3.8 54 23-77 117-186 (675)
66 cd03694 GTPBP_II Domain II of 32.5 1.5E+02 0.0033 19.8 5.1 32 24-55 21-54 (87)
67 PRK14525 rpsP 30S ribosomal pr 32.0 38 0.00082 23.8 2.0 20 54-73 33-52 (88)
68 PRK11033 zntA zinc/cadmium/mer 31.4 50 0.0011 31.0 3.3 53 23-76 254-319 (741)
69 PRK00809 hypothetical protein; 31.1 59 0.0013 24.5 3.1 38 22-59 27-68 (144)
70 cd03698 eRF3_II_like eRF3_II_l 30.5 96 0.0021 20.4 3.8 29 24-54 21-49 (83)
71 PRK13922 rod shape-determining 30.1 1.7E+02 0.0037 23.7 5.9 27 28-54 213-244 (276)
72 PRK10413 hydrogenase 2 accesso 30.1 37 0.0008 23.4 1.6 13 29-41 42-54 (82)
73 PRK10409 hydrogenase assembly 29.9 38 0.00083 23.8 1.7 13 29-41 41-53 (90)
74 cd04719 BAH_Orc1p_animal BAH, 29.5 27 0.0006 25.9 1.0 25 29-53 3-29 (128)
75 TIGR00739 yajC preprotein tran 29.2 74 0.0016 21.8 3.1 17 25-41 33-49 (84)
76 PRK14872 rod shape-determining 29.2 67 0.0015 27.8 3.4 30 26-55 257-291 (337)
77 TIGR01511 ATPase-IB1_Cu copper 28.5 52 0.0011 29.8 2.8 19 23-41 103-121 (562)
78 PRK01122 potassium-transportin 28.1 77 0.0017 29.8 3.9 20 23-42 116-135 (679)
79 cd06165 Sortase_A_1 Sortase A 28.1 1.2E+02 0.0025 21.7 4.1 51 28-82 62-114 (127)
80 COG3746 OprP Phosphate-selecti 28.0 34 0.00074 30.3 1.4 26 51-76 205-230 (426)
81 TIGR01512 ATPase-IB2_Cd heavy 27.9 61 0.0013 29.1 3.1 19 23-41 66-84 (536)
82 COG0298 HypC Hydrogenase matur 27.7 44 0.00096 23.3 1.7 15 27-41 36-50 (82)
83 PRK14010 potassium-transportin 27.7 75 0.0016 29.9 3.7 53 23-76 116-184 (673)
84 PF14451 Ub-Mut7C: Mut7-C ubiq 27.6 32 0.00068 23.6 1.0 22 55-78 39-60 (81)
85 cd03691 BipA_TypA_II BipA_TypA 27.1 1.6E+02 0.0035 19.2 4.4 31 23-53 20-51 (86)
86 PF09378 HAS-barrel: HAS barre 26.8 62 0.0013 21.3 2.3 26 29-54 22-48 (91)
87 cd03699 lepA_II lepA_II: This 26.7 1.7E+02 0.0036 19.3 4.5 29 23-53 20-48 (86)
88 cd06555 ASCH_PF0470_like ASC-1 26.6 1.5E+02 0.0032 21.5 4.4 27 28-54 30-58 (109)
89 smart00739 KOW KOW (Kyprides, 26.4 1E+02 0.0022 15.7 3.5 24 30-53 2-26 (28)
90 TIGR01494 ATPase_P-type ATPase 26.3 74 0.0016 28.0 3.3 55 23-77 45-111 (499)
91 PF04203 Sortase: Sortase fami 26.1 1.6E+02 0.0034 20.6 4.5 36 28-63 59-97 (128)
92 PRK06739 pyruvate kinase; Vali 25.9 1.1E+02 0.0024 26.5 4.2 17 25-41 105-121 (352)
93 PF01959 DHQS: 3-dehydroquinat 25.8 1.5E+02 0.0032 26.0 4.9 37 19-55 248-285 (354)
94 PF08844 DUF1815: Domain of un 25.8 25 0.00055 25.3 0.2 15 74-88 30-44 (105)
95 PRK04980 hypothetical protein; 25.7 1.9E+02 0.0041 20.8 4.7 30 27-56 29-61 (102)
96 PF08854 DUF1824: Domain of un 25.7 58 0.0012 24.3 2.1 20 65-84 84-110 (125)
97 PF07977 FabA: FabA-like domai 25.7 2.5E+02 0.0054 20.0 5.7 44 23-77 90-134 (138)
98 PF01272 GreA_GreB: Transcript 24.7 2E+02 0.0043 18.8 4.5 24 30-53 53-76 (77)
99 PF15057 DUF4537: Domain of un 24.3 1.2E+02 0.0026 22.1 3.6 26 27-52 53-81 (124)
100 cd03697 EFTU_II EFTU_II: Elong 23.7 2.2E+02 0.0048 18.8 4.6 31 24-54 21-51 (87)
101 cd05827 Sortase_C_3 Sortase C 23.6 1.7E+02 0.0037 20.9 4.3 29 28-56 65-93 (131)
102 TIGR01525 ATPase-IB_hvy heavy 23.5 94 0.002 27.9 3.5 53 23-76 67-132 (556)
103 PRK09519 recA DNA recombinatio 23.3 54 0.0012 31.5 2.0 28 1-39 320-347 (790)
104 cd04710 BAH_fungalPHD BAH, or 23.3 1E+02 0.0022 23.0 3.1 27 28-54 10-39 (135)
105 PF03120 DNA_ligase_OB: NAD-de 23.1 64 0.0014 22.2 1.8 31 19-49 39-69 (82)
106 PRK14715 DNA polymerase II lar 22.9 65 0.0014 33.1 2.4 18 23-40 999-1016(1627)
107 PRK08332 ribonucleotide-diphos 22.8 68 0.0015 33.6 2.7 34 1-40 396-429 (1740)
108 PF04085 MreC: rod shape-deter 22.5 1.4E+02 0.003 22.3 3.7 29 26-54 90-123 (152)
109 cd04089 eRF3_II eRF3_II: domai 22.4 1.7E+02 0.0037 19.2 3.8 28 24-53 20-47 (82)
110 TIGR00219 mreC rod shape-deter 22.2 1.1E+02 0.0025 25.3 3.5 29 27-55 213-246 (283)
111 COG1862 YajC Preprotein transl 22.0 1.2E+02 0.0026 21.6 3.1 25 26-53 40-64 (97)
112 TIGR03627 arch_S9P archaeal ri 22.0 69 0.0015 23.9 1.9 31 67-100 21-51 (130)
113 cd04498 hPOT1_OB2 hPOT1_OB2: A 22.0 53 0.0011 24.4 1.3 17 24-40 71-87 (123)
114 PF14001 YdfZ: YdfZ protein 21.8 51 0.0011 21.9 1.1 8 57-64 51-58 (64)
115 PRK00132 rpsI 30S ribosomal pr 21.5 68 0.0015 24.0 1.8 33 67-101 25-57 (130)
116 COG1465 Predicted alternative 21.1 2.1E+02 0.0045 25.0 4.8 35 19-53 270-305 (376)
117 PF03144 GTP_EFTU_D2: Elongati 21.0 1.7E+02 0.0038 18.2 3.6 31 24-54 7-40 (74)
118 PRK05886 yajC preprotein trans 20.9 1.2E+02 0.0027 22.0 3.0 16 26-41 35-50 (109)
119 TIGR01116 ATPase-IIA1_Ca sarco 20.5 1.5E+02 0.0032 28.7 4.3 19 23-41 84-102 (917)
120 PF04452 Methyltrans_RNA: RNA 20.4 1.5E+02 0.0033 23.3 3.8 28 27-54 14-42 (225)
121 cd04090 eEF2_II_snRNP Loc2 eEF 20.2 2.6E+02 0.0055 18.8 4.5 34 23-56 21-61 (94)
122 COG1792 MreC Cell shape-determ 20.1 1.4E+02 0.0031 24.8 3.7 31 26-56 209-244 (284)
123 TIGR00037 eIF_5A translation i 20.1 1.2E+02 0.0027 22.3 3.0 29 23-55 5-33 (130)
124 PRK14350 ligA NAD-dependent DN 20.0 1.2E+02 0.0027 28.5 3.6 47 18-65 353-399 (669)
No 1
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=100.00 E-value=1.3e-50 Score=324.57 Aligned_cols=134 Identities=44% Similarity=0.783 Sum_probs=61.3
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEee--CCceEEEEEEEEEEEEeeeeeecCCcceeEEEccEEEe
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHK--NGKAYVERVTRLENVIQTGVYAPLTTSGTIVVNNVFAS 78 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~~--~~~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~V~aS 78 (143)
|||+||||+++|+..+. .+.+++||++|++||||++.. ++.++++||++|++++++|+|||||.+||||||||+||
T Consensus 79 LTp~HLI~v~~~~~~~~--~~~~~vfA~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~~~~G~yAPLT~~GtivVdgVlaS 156 (217)
T PF01079_consen 79 LTPNHLIFVADCNGSES--SNFRAVFASDVRVGDCVLVSDEGGGKLRPSRVVRVSTVEKRGVYAPLTSHGTIVVDGVLAS 156 (217)
T ss_dssp E-TT-EEEEEETTTTEE-----EEEEGGG--TT-EEEEE-TTT--EEEEEEEEEEEEEEEEEEEEEESSSEEEETTEEEE
T ss_pred ecCCcEEEEecCCCCcc--cccceeehhhCCCCCEEEEEEcCCCcEEEEEEEEEEEEEEeeEEcCccCcceEEECCEEEE
Confidence 79999999999986321 112899999999999999943 35799999999999999999999999999999999999
Q ss_pred eeeeeccchhhHHHHHHHHHHHHHhhhhcc---CCCCCCCCCceeechHHHHHHhhhhhcC
Q psy16497 79 CYAVIDNQFLAHLSFIPVRLYHSLVNLFSS---NHIENSSHVTGIHWYPKLLYSMSDYFIP 136 (143)
Q Consensus 79 Cya~i~~h~Lah~af~PlR~~~~~~~~~~~---~~~~~~~~~~GiHWY~~~Ly~i~~~~lp 136 (143)
|||++++|.||||+|+|+|+++++.++++. .......+++|||||+++||+|++++||
T Consensus 157 Cya~v~~h~lah~~f~PlR~~~~~~~~~~~~~~~~~~~~~~~~GiHWYa~~Ly~l~~~~L~ 217 (217)
T PF01079_consen 157 CYAVVESHTLAHWAFAPLRLLYSLSSWFGGRSASSSNSSPQQEGIHWYAQLLYRLGQYVLP 217 (217)
T ss_dssp S------------------------------------------------------------
T ss_pred EEEEecchHHHHHHHHHHHHHHHHHHHhccccccccCCCCCCCceehHHHHHHHHhhccCC
Confidence 999999999999999999999999988763 1123467899999999999999999997
No 2
>KOG3638|consensus
Probab=100.00 E-value=1.1e-35 Score=256.77 Aligned_cols=134 Identities=33% Similarity=0.566 Sum_probs=120.0
Q ss_pred CCCCceEEeeeCCCCCC----ccCCcceeeecccccCCEEEEee--CCceEEEEEEEEEEEEeeeeeecCCcceeEEEcc
Q psy16497 1 MTPSHLILRWHRPNAKS----ILSDIEYTYAERVRVNDSIIVHK--NGKAYVERVTRLENVIQTGVYAPLTTSGTIVVNN 74 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~----~~~~~~~vfA~~v~~Gd~v~v~~--~~~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~ 74 (143)
||++||||+++|+.... .+.+.++|||+++++||||++.+ ++++++.||.+|++.+++|+|||||.+|+|+||+
T Consensus 275 lT~~Hl~~~~~c~~~~~~~~~~~~~~~~v~A~~l~~gdcv~~~~~~~~~~~~~~I~~i~~~~~tGiyaPlT~~G~liVn~ 354 (414)
T KOG3638|consen 275 LTPQHLVFVAQCQQQPQQFQYGPAGLEAVFASRLRIGDCVLVAPGAGNKLRQQKIGAISRPVATGIYAPLTSNGDLIVND 354 (414)
T ss_pred cchhheeecCCCCCCccccccccCCcccccHhhCCcccEEEEecCCCCccceeeccccccccccccccCcccCCcEEecc
Confidence 79999999999987421 24577999999999999999999 6689999999999999999999999999999999
Q ss_pred EEEeeeeeeccchhhHHHHHHHHHHHHHhhhhccCCCCCCCCCceeechHHHHHHhhhhhcCCC
Q psy16497 75 VFASCYAVIDNQFLAHLSFIPVRLYHSLVNLFSSNHIENSSHVTGIHWYPKLLYSMSDYFIPSA 138 (143)
Q Consensus 75 V~aSCya~i~~h~Lah~af~PlR~~~~~~~~~~~~~~~~~~~~~GiHWY~~~Ly~i~~~~lp~~ 138 (143)
|+|||||++++|+|||++|+|+|.++++...+. .......+||||+++|+.|.+++||.+
T Consensus 355 vlaSC~s~~~~~~lq~~~f~~~~~~~~~~~~~~----~~~~~~~~ip~~~~~~~~l~~~vlp~~ 414 (414)
T KOG3638|consen 355 VLASCYSEIEEQSLQPTFFAPLRLLHSLFANLF----DSLGAEGGIPTGSALLYELLDLVLPSG 414 (414)
T ss_pred eeeccchhhhhhhchhhhhhhhhhHHHHhhhcc----cccccccCCChHHHHHHHHHHhhcCCC
Confidence 999999999999999999999999987765554 334457799999999999999999974
No 3
>cd00081 Hint Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Probab=98.80 E-value=1.3e-08 Score=73.55 Aligned_cols=67 Identities=24% Similarity=0.474 Sum_probs=57.7
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEeeCCceEEEEEEEEEEEEee-eeeecCCc-ceeEEEccEEEe
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHKNGKAYVERVTRLENVIQT-GVYAPLTT-SGTIVVNNVFAS 78 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~-G~yAPlT~-~GtivVd~V~aS 78 (143)
+||+|.+|+.++. .. ..+.|+++++||+|.+. ...+|.+|+..... ++|+|.+. .++++|||++++
T Consensus 68 ~T~~H~~~~~~~~--~~-----~~~~a~~l~~gd~l~~~-----~~~~v~~i~~~~~~~~vY~~~v~~~~~~~~~g~lvH 135 (136)
T cd00081 68 LTPDHLLFVLEDG--EL-----KWVFASDLKPGDYVLVP-----VLEKVKEIEEIEYTGGVYDLTVEDNHNFIANGVLVH 135 (136)
T ss_pred EcCCCEEEEEeCC--eE-----EEEEHHHCCCCCEEEEc-----cceEEEEEEEEccCCeEEccEEcCCceEEECcEEEc
Confidence 5999999998764 23 67899999999999886 34678888888877 99999999 999999999998
Q ss_pred e
Q psy16497 79 C 79 (143)
Q Consensus 79 C 79 (143)
|
T Consensus 136 N 136 (136)
T cd00081 136 N 136 (136)
T ss_pred C
Confidence 6
No 4
>smart00305 HintC Hint (Hedgehog/Intein) domain C-terminal region. Hedgehog/Intein domain, C-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=98.16 E-value=6.6e-06 Score=50.67 Aligned_cols=43 Identities=30% Similarity=0.483 Sum_probs=38.8
Q ss_pred CceEEEEEEEEEEEEeeeeeec-CCcceeEEEccEEEeeeeeec
Q psy16497 42 GKAYVERVTRLENVIQTGVYAP-LTTSGTIVVNNVFASCYAVID 84 (143)
Q Consensus 42 ~~l~~~rV~~V~~~~~~G~yAP-lT~~GtivVd~V~aSCya~i~ 84 (143)
+.++..||.+|+.....++|.| +|..++.++||++++|.+..+
T Consensus 2 ~~~~~~~V~~i~~~~~~~vYd~~v~~~~~fv~ngi~~hN~~~~~ 45 (46)
T smart00305 2 GDFRFVRVKSIEETEYTGVYDPTVTENHNFIANGILVHNCAEIE 45 (46)
T ss_pred CCEEEEEEEEEEEeCCccEEeeEeCCCCeEEECCEEEEeeeccc
Confidence 3578899999999999999999 999999999999999987653
No 5
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=91.00 E-value=0.77 Score=45.62 Aligned_cols=84 Identities=25% Similarity=0.334 Sum_probs=61.6
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEeeC----CceEEEEEEEEEEEEee-eeeecCCcce--eEEEc
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHKN----GKAYVERVTRLENVIQT-GVYAPLTTSG--TIVVN 73 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~~~----~~l~~~rV~~V~~~~~~-G~yAPlT~~G--tivVd 73 (143)
+|++|=+++.++ +.+ ..+-|+++++||.|.+... +.+...+|.+|..+... +..-=||... ++++|
T Consensus 1009 VT~DHpvLv~~g--ggl-----~wkkA~ELk~GD~I~ip~~~~s~s~V~~d~V~~Ieyv~~e~d~VYDLtV~~tHnfIAN 1081 (1337)
T PRK14714 1009 VTPDHAMLVWDG--GYL-----EKKRAFEVKEGDAVPVPEGVEETGVVLADEVVSIEYVESDDDFVYCLTVAEYHTVVAN 1081 (1337)
T ss_pred ecCCceEEEecC--Cce-----EEEeHHHcCCCCEEeeccccccCCceeeEEEEEEeeecCCCceEEEecccccceEEEc
Confidence 588888888765 334 6789999999999999754 46899999999987754 3334466666 89999
Q ss_pred cEEEeeeeeeccchhhHHHH
Q psy16497 74 NVFASCYAVIDNQFLAHLSF 93 (143)
Q Consensus 74 ~V~aSCya~i~~h~Lah~af 93 (143)
|++.. ++=++.++--+.+
T Consensus 1082 gIiVH--sCDGDED~VMLLl 1099 (1337)
T PRK14714 1082 GIFTG--QCDGDEDCVMLLL 1099 (1337)
T ss_pred ceEEe--ccCchHHHHHHHH
Confidence 99985 5555555444333
No 6
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=90.31 E-value=0.45 Score=35.17 Aligned_cols=40 Identities=23% Similarity=0.292 Sum_probs=15.6
Q ss_pred CCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEeeCCceEEEEEEEEEE
Q psy16497 2 TPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHKNGKAYVERVTRLEN 54 (143)
Q Consensus 2 Tp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~ 54 (143)
||.|-.|+.+ +.-+-|+++++||.|+..++. ...|.++..
T Consensus 59 T~~HPF~~~~----------~gWv~A~~L~~GD~L~~~~G~---~~~v~~i~~ 98 (130)
T PF07591_consen 59 TPNHPFWVEG----------KGWVEAEDLKVGDRLLTADGS---WVTVTSIRR 98 (130)
T ss_dssp -----------------------EEGGG--TTSEEEEE-SS---EEEEE----
T ss_pred ccccccccch----------HhhhhHhhCCCCCEEEcCCCC---EEEEEEEEe
Confidence 7777777653 156899999999999888765 344555543
No 7
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=68.21 E-value=15 Score=24.90 Aligned_cols=38 Identities=18% Similarity=0.237 Sum_probs=26.4
Q ss_pred ccccCCEEEEeeCC-ceEEEEEEEEEEEEeeeeeecCCcceeEEEccEEE
Q psy16497 29 RVRVNDSIIVHKNG-KAYVERVTRLENVIQTGVYAPLTTSGTIVVNNVFA 77 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~-~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~V~a 77 (143)
.++.||.|.+..+. .-+.-+|..|.. ..++++|+|+-.
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~-----------~~~~V~Vegvn~ 44 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLP-----------KKNRVIVEGVKI 44 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEc-----------CCCEEEEcCcEE
Confidence 78999999997762 345566776654 445677777643
No 8
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=66.69 E-value=4.7 Score=38.68 Aligned_cols=33 Identities=15% Similarity=0.193 Sum_probs=27.3
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEee
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHK 40 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~~ 40 (143)
+||.|-+|+-++ +++ ..+-|+++++||+|.+.-
T Consensus 165 vT~~H~~~v~~~--g~~-----~~~~a~~l~~GD~i~~~~ 197 (858)
T PRK14898 165 ATPYHSFVTRKD--NEV-----IPVEGSELKIGDWLPVVR 197 (858)
T ss_pred ECCCCeEEEeeC--CeE-----EEeeHHhCCCCCEEeeee
Confidence 599999998654 455 778999999999998754
No 9
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=64.56 E-value=16 Score=22.85 Aligned_cols=25 Identities=12% Similarity=0.433 Sum_probs=20.8
Q ss_pred cccCCEEEEee-CCceEEEEEEEEEE
Q psy16497 30 VRVNDSIIVHK-NGKAYVERVTRLEN 54 (143)
Q Consensus 30 v~~Gd~v~v~~-~~~l~~~rV~~V~~ 54 (143)
+++|+.|++.. ++...+++|.++..
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~ 26 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIRE 26 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEE
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEe
Confidence 46899999998 67899999999987
No 10
>smart00439 BAH Bromo adjacent homology domain.
Probab=64.46 E-value=12 Score=25.84 Aligned_cols=28 Identities=21% Similarity=0.471 Sum_probs=20.8
Q ss_pred cccCCEEEEeeCC---ceEEEEEEEEEEEEe
Q psy16497 30 VRVNDSIIVHKNG---KAYVERVTRLENVIQ 57 (143)
Q Consensus 30 v~~Gd~v~v~~~~---~l~~~rV~~V~~~~~ 57 (143)
+++||+|++..++ .....+|.++....+
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~ 32 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEIFETKK 32 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEEEECCC
Confidence 6899999998653 467777777766554
No 11
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=64.03 E-value=17 Score=25.00 Aligned_cols=38 Identities=16% Similarity=0.354 Sum_probs=26.4
Q ss_pred ccccCCEEEEeeCC-ceEEEEEEEEEEEEeeeeeecCCcceeEEEccEEE
Q psy16497 29 RVRVNDSIIVHKNG-KAYVERVTRLENVIQTGVYAPLTTSGTIVVNNVFA 77 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~-~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~V~a 77 (143)
.+++||.|.+..+. .-+.-+|.+|... .++++|+|+-.
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~-----------~~~V~Vegvn~ 46 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKK-----------SNKVIVKGINI 46 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC-----------CCEEEEcCcEE
Confidence 89999999997762 3355666666543 45677877744
No 12
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=63.27 E-value=29 Score=26.96 Aligned_cols=50 Identities=24% Similarity=0.357 Sum_probs=31.9
Q ss_pred ecccccCCEEEEeeCC-ceEEEEEEEEEEEEe--eeeeecCCcceeEEEccEEEeeee
Q psy16497 27 AERVRVNDSIIVHKNG-KAYVERVTRLENVIQ--TGVYAPLTTSGTIVVNNVFASCYA 81 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~~-~l~~~rV~~V~~~~~--~G~yAPlT~~GtivVd~V~aSCya 81 (143)
=.++++||.|.+.+.+ ....=||+++..+.. ..+..| |. +..+ .+..||-
T Consensus 106 L~~L~~GD~I~v~~~~g~~~~Y~V~~~~iV~~~d~~v~~~-~~-~~~L---tLiTC~P 158 (174)
T TIGR03784 106 LQELRPGDVIRLQTPDGQWQSYQVTATRVVDESETGLDLP-AD-DSQL---VLITCYP 158 (174)
T ss_pred hhhCCCCCEEEEEECCCeEEEEEEeEEEEECCccceeccC-CC-CCEE---EEEeCCC
Confidence 3689999999998764 455677888776654 344433 22 1222 5678884
No 13
>PF13403 Hint_2: Hint domain
Probab=63.20 E-value=14 Score=27.67 Aligned_cols=20 Identities=20% Similarity=0.331 Sum_probs=17.1
Q ss_pred ceeeecccccCCEEEEeeCC
Q psy16497 23 EYTYAERVRVNDSIIVHKNG 42 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~ 42 (143)
-.+-.+++++||.|++.+++
T Consensus 14 G~~~Ve~L~~GD~V~T~dgg 33 (147)
T PF13403_consen 14 GPRPVEDLRPGDRVLTRDGG 33 (147)
T ss_pred cCeEeeccCCCCEEEecCCC
Confidence 35678999999999999876
No 14
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=61.97 E-value=18 Score=26.88 Aligned_cols=34 Identities=21% Similarity=0.335 Sum_probs=24.1
Q ss_pred ceeeecccccCCEEEEeeC-------C-ceEEEEEEEEEEEE
Q psy16497 23 EYTYAERVRVNDSIIVHKN-------G-KAYVERVTRLENVI 56 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~-------~-~l~~~rV~~V~~~~ 56 (143)
..--+.++++||+||+... | .-..++|.+++.+-
T Consensus 32 N~~tv~rl~~GDlVFlT~~~~~Dl~~GtsGiiAkV~~vevvh 73 (122)
T COG1935 32 NLLTVLRLHEGDLVFLTSTSLEDLTKGTSGIIAKVRRVEVVH 73 (122)
T ss_pred chHHhhcCCCCCEEEEehhHhhHhhcCcceeEEEEEEEEEEe
Confidence 3345688999999999763 1 24667888887743
No 15
>PF14623 Vint: Hint-domain
Probab=60.62 E-value=12 Score=29.21 Aligned_cols=46 Identities=13% Similarity=0.175 Sum_probs=27.8
Q ss_pred ce-eeecccccCCEEEEeeCCceEEEEEEEEEEEEeeeeeecCCcceeEEE
Q psy16497 23 EY-TYAERVRVNDSIIVHKNGKAYVERVTRLENVIQTGVYAPLTTSGTIVV 72 (143)
Q Consensus 23 ~~-vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~G~yAPlT~~GtivV 72 (143)
+. +-.+++|+||.|.+..+. .+|..|-+..-.+--.+|=.-|.+.|
T Consensus 15 ~~~v~i~~lR~G~~V~tp~G~----r~V~~Vlkt~v~~~~~~lc~vg~Llv 61 (162)
T PF14623_consen 15 RAPVRIDDLRAGDKVWTPRGP----RKVAAVLKTPVESGSEDLCRVGGLLV 61 (162)
T ss_pred ceeEEHHHccCCCEEECCCCC----eEEEEEEEEeecCCceEEEEECCEEE
Confidence 45 899999999999998764 44544443333332244444444443
No 16
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=60.26 E-value=6.7 Score=30.38 Aligned_cols=52 Identities=21% Similarity=0.311 Sum_probs=31.2
Q ss_pred ceeeecccccCCEEEEeeCC-----ceEEE-EEEEEEEEEeeeeeecCCcc------------eeEEEcc
Q psy16497 23 EYTYAERVRVNDSIIVHKNG-----KAYVE-RVTRLENVIQTGVYAPLTTS------------GTIVVNN 74 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~-----~l~~~-rV~~V~~~~~~G~yAPlT~~------------GtivVd~ 74 (143)
+.+.++++++||.|.+..++ .+..+ .-..|+...-+|=-.|.+.. |+.+++|
T Consensus 45 ~~i~~~~L~~GDiI~l~~g~~vPaD~~ll~~g~~~vd~s~ltGes~pv~k~~~~~~~~~~i~~Gs~v~~g 114 (230)
T PF00122_consen 45 QKIPSSELVPGDIIILKAGDIVPADGILLESGSAYVDESALTGESEPVKKTPLPLNPGNIIFAGSIVVSG 114 (230)
T ss_dssp EEEEGGGT-TTSEEEEETTEBESSEEEEEESSEEEEECHHHHSBSSEEEESSSCCCTTTEE-TTEEEEEE
T ss_pred ccchHhhccceeeeecccccccccCccceeccccccccccccccccccccccccccccchhhcccccccc
Confidence 77899999999999997763 12222 22233333334555555554 7777766
No 17
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=59.50 E-value=16 Score=25.17 Aligned_cols=27 Identities=22% Similarity=0.380 Sum_probs=19.7
Q ss_pred ccccCCEEEEeeCC---ceEEEEEEEEEEE
Q psy16497 29 RVRVNDSIIVHKNG---KAYVERVTRLENV 55 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~---~l~~~rV~~V~~~ 55 (143)
.+++||+|++..++ ....++|.+|...
T Consensus 2 ~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~ 31 (119)
T PF01426_consen 2 TYKVGDFVYVKPDDPPEPPYVARIEEIWED 31 (119)
T ss_dssp EEETTSEEEEECTSTTSEEEEEEEEEEEEE
T ss_pred EEeCCCEEEEeCCCCCCCCEEEEEEEEEcC
Confidence 46899999998764 3667777777543
No 18
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=56.70 E-value=46 Score=24.64 Aligned_cols=40 Identities=18% Similarity=0.295 Sum_probs=28.3
Q ss_pred ceeeecccccCCEEEEeeC-------C-ceEEEEEEEEEEEEeeeeee
Q psy16497 23 EYTYAERVRVNDSIIVHKN-------G-KAYVERVTRLENVIQTGVYA 62 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~-------~-~l~~~rV~~V~~~~~~G~yA 62 (143)
...-+.++++||+||+.+. | .---++|.+++...++=.|+
T Consensus 32 N~~~~~~~~~Gd~VFlT~~~~~Dl~~Gt~GiIa~V~~~~i~~qri~~~ 79 (119)
T PF04322_consen 32 NVIALESLDPGDRVFLTSVSLEDLTPGTEGIIAEVKKIEISMQRIVWE 79 (119)
T ss_pred heeeeecCCCCCEEEEecCCHHHCCCCCCeEEEEEEEEEEEEEEEeec
Confidence 4556789999999999873 1 34567788877766664443
No 19
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=56.69 E-value=22 Score=25.62 Aligned_cols=32 Identities=25% Similarity=0.289 Sum_probs=25.4
Q ss_pred cccccCCEEEEeeCCceEEEEEEEEEEEEeee
Q psy16497 28 ERVRVNDSIIVHKNGKAYVERVTRLENVIQTG 59 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~G 59 (143)
.++++||.|++.+.+....=+|+++..+...-
T Consensus 63 ~~l~~Gd~v~v~~~~~~~~Y~V~~~~~v~~~~ 94 (126)
T cd06166 63 DEVEKGDEIKVTTKNGTYKYKITSIFVVEPTD 94 (126)
T ss_pred HHCCCCCEEEEEECCEEEEEEEEEEEEECCCc
Confidence 47899999999988777777888887776543
No 20
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=55.44 E-value=22 Score=25.92 Aligned_cols=38 Identities=16% Similarity=0.255 Sum_probs=23.8
Q ss_pred eecccccCCEEEEeeCCceEEEEEEEEEEEEeeeeeecC
Q psy16497 26 YAERVRVNDSIIVHKNGKAYVERVTRLENVIQTGVYAPL 64 (143)
Q Consensus 26 fA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~G~yAPl 64 (143)
+.+++++||.++....++ ....|+++-++.+...+-|=
T Consensus 36 ~l~~mk~GD~vifY~s~~-~~~~ivai~~V~~~~~~d~~ 73 (143)
T PF01878_consen 36 NLKRMKPGDKVIFYHSGC-KERGIVAIGEVVSEPYPDPT 73 (143)
T ss_dssp HHHC--TT-EEEEEETSS-SS-EEEEEEEEEEEEEE-GG
T ss_pred hhhcCCCCCEEEEEEcCC-CCCEEEEEEEEeccccCCCc
Confidence 456999999999988651 12678888888777766553
No 21
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=55.23 E-value=16 Score=28.68 Aligned_cols=29 Identities=10% Similarity=-0.032 Sum_probs=23.4
Q ss_pred ceeeecccccCCEEEEeeCCceEEEEEEEEEEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNGKAYVERVTRLENV 55 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~ 55 (143)
-++-++.+|.|++|++.+ +|.||+++++-
T Consensus 21 ~p~q~~~LkkG~yvvIkG----rPCKIveistS 49 (166)
T PTZ00328 21 YPLPAGALKKGGYVCING----RPCKVIDLSVS 49 (166)
T ss_pred ecccccceeECCEEEECC----eeeEEEEEecC
Confidence 577899999999999965 67888887543
No 22
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=53.67 E-value=29 Score=25.76 Aligned_cols=52 Identities=23% Similarity=0.369 Sum_probs=33.0
Q ss_pred cccccCCEEEEee-CCceEEEEEEEEEEEEeeee-----eecCCcceeEEEccEEEeeeeeec
Q psy16497 28 ERVRVNDSIIVHK-NGKAYVERVTRLENVIQTGV-----YAPLTTSGTIVVNNVFASCYAVID 84 (143)
Q Consensus 28 ~~v~~Gd~v~v~~-~~~l~~~rV~~V~~~~~~G~-----yAPlT~~GtivVd~V~aSCya~i~ 84 (143)
.++++||.|.+.+ ++....=+|+++..+.+..+ +.+ +...+| ++..|+--..
T Consensus 71 ~~l~~GD~I~v~~~~g~~~~Y~V~~~~~v~~~~~~~~~~~~~-~~~~~L----tLiTC~~~~~ 128 (144)
T cd05829 71 GDLRKGDKVEVTRADGQTATFRVDRVEVYPKDAFPTDAVYGD-TGPPRL----RLITCGGPFD 128 (144)
T ss_pred hcCCCCCEEEEEECCCCEEEEEEeEEEEECcccCChhheecC-CCCCEE----EEEEeCCCCC
Confidence 6899999999998 55566777777766554332 222 222233 4678985443
No 23
>COG1372 Intein/homing endonuclease [DNA replication, recombination, and repair]
Probab=51.16 E-value=11 Score=30.71 Aligned_cols=33 Identities=27% Similarity=0.421 Sum_probs=26.3
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEeeC
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHKN 41 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~~~ 41 (143)
.||.|=+|+ . .+.. ..+-|+++++||.|.+...
T Consensus 78 ~T~~H~~l~-~--~~~~-----~~~~a~~lk~GD~i~~~~~ 110 (420)
T COG1372 78 ATPDHPFLT-R--NGEL-----GWVKAGELKEGDRIAVPRR 110 (420)
T ss_pred ecCCCceEe-c--CCeE-----EEEEhhhcccCCEeecccc
Confidence 489999998 2 3334 7789999999999998764
No 24
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=50.99 E-value=18 Score=25.90 Aligned_cols=27 Identities=30% Similarity=0.369 Sum_probs=18.0
Q ss_pred ccccCCEEEEeeCC---ceEEEEEEEEEEE
Q psy16497 29 RVRVNDSIIVHKNG---KAYVERVTRLENV 55 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~---~l~~~rV~~V~~~ 55 (143)
.+++||||++...+ .....||.++-..
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 32 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKD 32 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEEC
Confidence 47899999997653 3455566655443
No 25
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=50.90 E-value=53 Score=26.46 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=21.2
Q ss_pred cCCcceeeecccccCCEEEEeeC-CceEEEEEEEE
Q psy16497 19 LSDIEYTYAERVRVNDSIIVHKN-GKAYVERVTRL 52 (143)
Q Consensus 19 ~~~~~~vfA~~v~~Gd~v~v~~~-~~l~~~rV~~V 52 (143)
+.+++.+--+++++||.|+..+. +.+.-+.|...
T Consensus 21 ~~~G~~k~m~~L~iGD~Vla~d~~G~~~yS~V~~f 55 (217)
T PF01079_consen 21 LEDGGRKRMSDLKIGDRVLAVDSDGKLVYSPVIMF 55 (217)
T ss_dssp BTTS-EEEGGG--TT-EEEEE-TTS-EEEEEEEEE
T ss_pred eCCCCEeEHHHCCCCCEEEEecCCCcEEEEeEEEE
Confidence 45678889999999999999984 55666666653
No 26
>PF11736 DUF3299: Protein of unknown function (DUF3299); InterPro: IPR021727 This is a family of bacterial proteins of unknown function.
Probab=50.80 E-value=12 Score=28.40 Aligned_cols=38 Identities=18% Similarity=0.358 Sum_probs=28.1
Q ss_pred EEEEEEEEE---EEeeeeeecCCcceeEEEc----cEEEeeeeee
Q psy16497 46 VERVTRLEN---VIQTGVYAPLTTSGTIVVN----NVFASCYAVI 83 (143)
Q Consensus 46 ~~rV~~V~~---~~~~G~yAPlT~~GtivVd----~V~aSCya~i 83 (143)
+-.++.|.. ....+.|.|++-+|++-++ ++..|.|++-
T Consensus 94 pNqiV~V~~~~~~~~~~~~~pv~V~G~l~~~~~~~~~~~~~Y~m~ 138 (146)
T PF11736_consen 94 PNQIVHVKMPKPIPVDSLYDPVWVEGTLKVERSSSDLGTSGYSMD 138 (146)
T ss_pred CccEEEEEeCCCccccccceeEEEEEEEEeccccchheeEEEEEE
Confidence 345555554 4455689999999999998 6777888764
No 27
>PRK02268 hypothetical protein; Provisional
Probab=50.10 E-value=34 Score=25.97 Aligned_cols=47 Identities=21% Similarity=0.215 Sum_probs=34.7
Q ss_pred cceeeecccccCCEEEEee-----CCceEEEEEEEEEEEEeeeeeecCCcce
Q psy16497 22 IEYTYAERVRVNDSIIVHK-----NGKAYVERVTRLENVIQTGVYAPLTTSG 68 (143)
Q Consensus 22 ~~~vfA~~v~~Gd~v~v~~-----~~~l~~~rV~~V~~~~~~G~yAPlT~~G 68 (143)
+..-.=+++++||.|+... +++..+..+++|-++.+.-.|-+-...|
T Consensus 28 gK~apl~RmkpGD~ivyYsp~~~~~~~~~~qaftAig~V~~~~~Yq~~m~~~ 79 (141)
T PRK02268 28 GKAAPLRRMKPGDWIIYYSPKTTFGGKDKLQAFTAIGKVKDDEPYQVEMAPG 79 (141)
T ss_pred CccchhhcCCCCCEEEEEeceEecCCCcccceEEEEEEEcCCceEecccCCC
Confidence 3444458999999998755 2456788999999998888888644433
No 28
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=49.11 E-value=76 Score=22.54 Aligned_cols=32 Identities=31% Similarity=0.519 Sum_probs=25.6
Q ss_pred cccccCCEEEEeeCCceEEEEEEEEEEEEeee
Q psy16497 28 ERVRVNDSIIVHKNGKAYVERVTRLENVIQTG 59 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~G 59 (143)
.++++||.|++.+.+....=+|.++..+....
T Consensus 63 ~~l~~Gd~v~v~~~~~~~~Y~V~~~~~v~~~~ 94 (128)
T cd00004 63 DNLKKGDKIYLTDGGKTYVYKVTSILTVTPTD 94 (128)
T ss_pred HHCCCCCEEEEEECCEEEEEEEEEEEEECCCc
Confidence 47899999999998777777888887766554
No 29
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=48.88 E-value=38 Score=24.41 Aligned_cols=32 Identities=25% Similarity=0.254 Sum_probs=24.4
Q ss_pred cccccCCEEEEeeCCceEEEEEEEEEEEEeee
Q psy16497 28 ERVRVNDSIIVHKNGKAYVERVTRLENVIQTG 59 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~G 59 (143)
.++++||.|++.+.+....=+|+++..+....
T Consensus 60 ~~l~~Gd~i~v~~~~~~~~Y~V~~~~~v~~~~ 91 (127)
T cd05828 60 GELEPGDIITLQTLGGTYTYRVTSTRIVDADD 91 (127)
T ss_pred hcCCCCCEEEEEECCEEEEEEEeeEEEECccc
Confidence 46799999999988766777777777665443
No 30
>PF05203 Hom_end_hint: Hom_end-associated Hint; InterPro: IPR007868 Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce [] revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain containing the protein-splicing active site. This domain corresponds to the protein-splicing domain.; GO: 0030908 protein splicing; PDB: 1LWT_A 1UM2_B 1JVA_B 1GPP_A 1VDE_A 1EF0_B 1DFA_A 1LWS_A.
Probab=48.45 E-value=24 Score=28.37 Aligned_cols=34 Identities=18% Similarity=0.214 Sum_probs=19.9
Q ss_pred CcceeeecccccCCEEEEeeCCceEEEEEEEEEEEEe
Q psy16497 21 DIEYTYAERVRVNDSIIVHKNGKAYVERVTRLENVIQ 57 (143)
Q Consensus 21 ~~~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~ 57 (143)
++..+-.++|++||.|+-.++. |.+|++|.+-.+
T Consensus 12 DG~~k~ie~i~~Gd~vmg~dg~---~r~V~~~~~g~~ 45 (215)
T PF05203_consen 12 DGSIKPIEDIKIGDQVMGPDGR---PRRVTNVPRGRE 45 (215)
T ss_dssp TS-EEEGGG--TT-EEEBTTSS---EEEEEE--EEEE
T ss_pred CCCeeEEeecccCCEEECCCCC---cEEEEEecccce
Confidence 4467788999999999776653 667887755433
No 31
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=48.21 E-value=41 Score=24.65 Aligned_cols=39 Identities=23% Similarity=0.282 Sum_probs=25.7
Q ss_pred ecccccCCEEEEeeCC-ceEEEEEEEEEEEEeeeeeecCCcceeEEEccEE
Q psy16497 27 AERVRVNDSIIVHKNG-KAYVERVTRLENVIQTGVYAPLTTSGTIVVNNVF 76 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~~-~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~V~ 76 (143)
+-.++.||.|.|..|. .-..-+|.+|. +..+.++|+||-
T Consensus 39 ~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~-----------~~~~~V~Vegvn 78 (114)
T TIGR01080 39 ALPVRKGDKVRIMRGDFKGHEGKVSKVD-----------LKRYRIYVEGVT 78 (114)
T ss_pred cceeecCCEEEEecCCCCCCEEEEEEEE-----------cCCCEEEEcCeE
Confidence 3389999999998763 23445666654 445566777665
No 32
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=47.54 E-value=44 Score=22.95 Aligned_cols=40 Identities=8% Similarity=0.014 Sum_probs=23.9
Q ss_pred CCCceEEeeeCCCCCC----ccCCc-ceeeecccccCCEEEEeeC
Q psy16497 2 TPSHLILRWHRPNAKS----ILSDI-EYTYAERVRVNDSIIVHKN 41 (143)
Q Consensus 2 Tp~HLifv~~~~~~~~----~~~~~-~~vfA~~v~~Gd~v~v~~~ 41 (143)
+..|+.|.-+...+.. .-+.+ -.-.+.++++||.|.+.+.
T Consensus 15 ~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~ 59 (91)
T cd04482 15 EGGHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS 59 (91)
T ss_pred CCCCEEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEEEE
Confidence 5679999765433221 11110 1124677899999999875
No 33
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=46.68 E-value=33 Score=24.81 Aligned_cols=27 Identities=22% Similarity=0.361 Sum_probs=19.6
Q ss_pred ecccccCCEEEEeeCCceEEEEEEEEE
Q psy16497 27 AERVRVNDSIIVHKNGKAYVERVTRLE 53 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~~~l~~~rV~~V~ 53 (143)
+-.++|||+|.+.+.+.-..-||++|+
T Consensus 137 ~~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 137 GLALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred hccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 467999999999887544555666553
No 34
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=46.35 E-value=26 Score=25.83 Aligned_cols=25 Identities=24% Similarity=0.371 Sum_probs=18.0
Q ss_pred cccCCEEEEeeC-CceEEEEEEEEEE
Q psy16497 30 VRVNDSIIVHKN-GKAYVERVTRLEN 54 (143)
Q Consensus 30 v~~Gd~v~v~~~-~~l~~~rV~~V~~ 54 (143)
+++||||++... +....++|.++-.
T Consensus 8 i~vGD~V~v~~~~~~~~va~Ie~i~e 33 (130)
T cd04721 8 ISVHDFVYVLSEEEDRYVAYIEDLYE 33 (130)
T ss_pred EECCCEEEEeCCCCCcEEEEEEEEEE
Confidence 899999999764 3455666666544
No 35
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=46.01 E-value=53 Score=21.52 Aligned_cols=29 Identities=17% Similarity=0.141 Sum_probs=20.4
Q ss_pred cceeeecccccCCEEEEeeCC--ceEEEEEE
Q psy16497 22 IEYTYAERVRVNDSIIVHKNG--KAYVERVT 50 (143)
Q Consensus 22 ~~~vfA~~v~~Gd~v~v~~~~--~l~~~rV~ 50 (143)
+..+--+++++||+|+..+.+ .....+++
T Consensus 14 gg~~~i~~l~~g~~V~~~~~~~~~~~~~~~~ 44 (100)
T smart00306 14 GGIKKIEELEEGDKVLALDEGTLKYSPVKVF 44 (100)
T ss_pred CCEEEHHHcCCCCEEEEecCCCcEEEEEEEE
Confidence 356778899999999998863 34444433
No 36
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=45.82 E-value=34 Score=26.13 Aligned_cols=38 Identities=21% Similarity=0.271 Sum_probs=24.2
Q ss_pred ccccCCEEEEeeCC-ceEEEEEEEEEEEEeeeeeecCCcceeEEEccEEE
Q psy16497 29 RVRVNDSIIVHKNG-KAYVERVTRLENVIQTGVYAPLTTSGTIVVNNVFA 77 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~-~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~V~a 77 (143)
.|+.||.|.|..|. .-..-+|.+|. ...|.++|+||-.
T Consensus 46 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~-----------~k~~~ViVEgvn~ 84 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKGREGKVTAVY-----------RKKWVIHIEKITR 84 (143)
T ss_pred eeecCCEEEEecCCCCCCceEEEEEE-----------cCCCEEEEeCeEE
Confidence 79999999997762 22345555553 3445666666544
No 37
>PRK04132 replication factor C small subunit; Provisional
Probab=45.79 E-value=19 Score=34.69 Aligned_cols=34 Identities=21% Similarity=0.405 Sum_probs=26.5
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEee
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHK 40 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~~ 40 (143)
+||+|-+++.+.+ ++. .-+-|+++++||.|.+..
T Consensus 130 ~T~~Hp~lv~~~~-g~~-----~W~~a~eL~~GD~vavpr 163 (846)
T PRK04132 130 VTPYHPLLVNRKN-GEI-----KWVKAEELKPGDKLAIPR 163 (846)
T ss_pred ecCCceEEEeccC-Cce-----eeEEHhHcCCCCEEEecc
Confidence 5999999986432 344 678999999999998753
No 38
>cd01287 FabA FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA structure is a homodimer with two independent active sites located at the dimer interface. Each active site is tunnel-shaped and completely inaccessible to solvent. No metal ions or cofactors are required for ligand binding or catalysis.
Probab=45.17 E-value=76 Score=23.85 Aligned_cols=48 Identities=6% Similarity=0.091 Sum_probs=29.2
Q ss_pred cceeeecccccCCEEEEeeCCceEEEEEEEEEEEEeeeeeecCCcceeEEEccEEEe
Q psy16497 22 IEYTYAERVRVNDSIIVHKNGKAYVERVTRLENVIQTGVYAPLTTSGTIVVNNVFAS 78 (143)
Q Consensus 22 ~~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~V~aS 78 (143)
.+..|=..|.|||..++.+ .+|+++......++. ...|++.|||..+.
T Consensus 91 ~~~kfr~~v~Pgd~~l~~e------~~i~~~~~~~~~~~~---~~~~~~~vdg~~v~ 138 (150)
T cd01287 91 GEWKYRGQITPHNKKVTYE------VHIKEVGRDGPRPYI---IADASLWVDGLRIY 138 (150)
T ss_pred eEEEECccCcCCCEEEEEE------EEEEEEEccCCccEE---EEEEEEEECCEEEE
Confidence 3567888899998543332 455555432222222 67888999988763
No 39
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=44.80 E-value=45 Score=24.36 Aligned_cols=41 Identities=27% Similarity=0.405 Sum_probs=29.0
Q ss_pred eeee--cccccCCEEEEeeCCceEEEEEEEEEEEE--eeeeeecC
Q psy16497 24 YTYA--ERVRVNDSIIVHKNGKAYVERVTRLENVI--QTGVYAPL 64 (143)
Q Consensus 24 ~vfA--~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~--~~G~yAPl 64 (143)
..|+ +++++||.|++.+.+....=+|+++..+. +.-+..|.
T Consensus 58 ~~F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~~v~~~~~~~~~~~ 102 (137)
T cd05830 58 APFNDLDKLRPGDKIVVETADGWYTYVVRSSEIVLPTDVEVIAPV 102 (137)
T ss_pred cccccHhhCCCCCEEEEEECCeEEEEEEeEEEEECCCcceEeeec
Confidence 4677 88999999999987666677788876554 23344443
No 40
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=44.65 E-value=27 Score=25.24 Aligned_cols=25 Identities=32% Similarity=0.574 Sum_probs=16.8
Q ss_pred ccccCCEEEEeeCC---ceEEEEEEEEE
Q psy16497 29 RVRVNDSIIVHKNG---KAYVERVTRLE 53 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~---~l~~~rV~~V~ 53 (143)
-+++||||++...+ ....+||.++-
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~ 30 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLW 30 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEE
Confidence 46899999998753 24455665543
No 41
>COG3764 SrtA Sortase (surface protein transpeptidase) [Cell envelope biogenesis, outer membrane]
Probab=43.54 E-value=45 Score=26.89 Aligned_cols=30 Identities=30% Similarity=0.455 Sum_probs=23.1
Q ss_pred cccccCCEEEEeeCCceEEEEEEEEEEEEe
Q psy16497 28 ERVRVNDSIIVHKNGKAYVERVTRLENVIQ 57 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~ 57 (143)
.++++||.|++...+....-+|+.++.+..
T Consensus 133 ~~lk~GD~iyv~~~~~~~~Y~v~~~~~V~p 162 (210)
T COG3764 133 GKLKVGDKIYVTTKNETYVYKVTDISIVDP 162 (210)
T ss_pred hhhcCCCEEEEEeCCcEEEEEEEEEEEeCc
Confidence 578999999999987666677777665543
No 42
>PRK14701 reverse gyrase; Provisional
Probab=43.40 E-value=20 Score=36.93 Aligned_cols=33 Identities=24% Similarity=0.304 Sum_probs=27.0
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEee
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHK 40 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~~ 40 (143)
+||.|-+|+-+. ++. ..+-|+++++||.|.+.-
T Consensus 956 ~T~dH~~lv~~~--g~~-----~~~~a~~lk~gD~vav~~ 988 (1638)
T PRK14701 956 ATPDHGLLVMRD--GKL-----GWVSAKNIREGDYVAFAF 988 (1638)
T ss_pred eCCCceEEeecC--Cce-----eeEEHHHCCcCCEEEecc
Confidence 489999998753 345 678999999999998864
No 43
>PF14890 Intein_splicing: Intein splicing domain; PDB: 1MI8_A 2CW7_A 2CW8_A.
Probab=43.07 E-value=17 Score=30.05 Aligned_cols=28 Identities=29% Similarity=0.277 Sum_probs=18.0
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEe
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVH 39 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~ 39 (143)
+||.|-+|+.++. + -++++++||.|.+.
T Consensus 65 ~T~~H~~lt~~~w---------k--~~~~Lk~GD~I~v~ 92 (323)
T PF14890_consen 65 ATPDHPFLTPDGW---------K--RLEELKPGDRIAVP 92 (323)
T ss_dssp EETT-EEEECCCC---------C--ECCC--TT-EEEEE
T ss_pred EcCCCcEEEccCC---------E--EhHHhhcccccccc
Confidence 4899999987642 2 35779999999987
No 44
>TIGR01076 sortase_fam LPXTG-site transpeptidase (sortase) family protein. of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known.
Probab=43.07 E-value=51 Score=24.05 Aligned_cols=30 Identities=17% Similarity=0.272 Sum_probs=23.6
Q ss_pred cccccCCEEEEeeCCceEEEEEEEEEEEEe
Q psy16497 28 ERVRVNDSIIVHKNGKAYVERVTRLENVIQ 57 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~ 57 (143)
.++++||.|++...+....=+|+++..+..
T Consensus 62 ~~l~~GD~i~v~~~~~~~~Y~V~~~~~v~~ 91 (136)
T TIGR01076 62 DKLKKGDMLYLHVGNEVLTYQVTSTKIVEP 91 (136)
T ss_pred HHCCCCCEEEEEECCcEEEEEEEEEEEECc
Confidence 578999999998876667777887776653
No 45
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=42.64 E-value=61 Score=23.21 Aligned_cols=36 Identities=17% Similarity=0.333 Sum_probs=23.4
Q ss_pred ccccCCEEEEeeCC-ceEEEEEEEEEEEEeeeeeecCCcceeEEEccE
Q psy16497 29 RVRVNDSIIVHKNG-KAYVERVTRLENVIQTGVYAPLTTSGTIVVNNV 75 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~-~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~V 75 (143)
.++.||.|.+..+. .-..-+|.+|.. ..+.++|+|+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~-----------~~~~V~Vegv 39 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLP-----------KTNKVIVEGV 39 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEc-----------CCCEEEECCc
Confidence 68999999997762 334556666543 2446666665
No 46
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=41.80 E-value=46 Score=24.09 Aligned_cols=15 Identities=20% Similarity=0.302 Sum_probs=12.2
Q ss_pred ecccccCCEEEEeeC
Q psy16497 27 AERVRVNDSIIVHKN 41 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~ 41 (143)
+-.|+.||.|.+..+
T Consensus 2 ~~~IrkGD~V~Vi~G 16 (104)
T COG0198 2 KMKVKKGDTVKVIAG 16 (104)
T ss_pred CcceecCCEEEEEec
Confidence 346899999999775
No 47
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=41.37 E-value=39 Score=23.09 Aligned_cols=26 Identities=27% Similarity=0.475 Sum_probs=17.9
Q ss_pred ccccCCEEEEeeCC-----ceEEEEEEEEEE
Q psy16497 29 RVRVNDSIIVHKNG-----KAYVERVTRLEN 54 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~-----~l~~~rV~~V~~ 54 (143)
..++||+|++..++ .....+|.++..
T Consensus 3 ~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~ 33 (123)
T cd04370 3 TYEVGDSVYVEPDDSIKSDPPYIARIEELWE 33 (123)
T ss_pred EEecCCEEEEecCCcCCCCCCEEEEEeeeeE
Confidence 46889999997653 255666666644
No 48
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=41.09 E-value=58 Score=22.79 Aligned_cols=32 Identities=9% Similarity=0.082 Sum_probs=22.0
Q ss_pred ecccccCCEEEEeeCCceEEEEEEEEEEEEeeee
Q psy16497 27 AERVRVNDSIIVHKNGKAYVERVTRLENVIQTGV 60 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~G~ 60 (143)
-...++||.+.+.+++ ++.-+++|..++..=.
T Consensus 28 ~~~~k~Gd~~i~~~~~--~~~~~i~v~~V~~~~~ 59 (105)
T cd06541 28 EQLPKAGDYLIILDGQ--QPLAIAEVVKVEIMPM 59 (105)
T ss_pred ccCCCCCCEEEEecCC--CcEEEEEEEEEEEEEC
Confidence 4679999999998765 6655566555554433
No 49
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=39.28 E-value=46 Score=24.70 Aligned_cols=27 Identities=22% Similarity=0.322 Sum_probs=18.6
Q ss_pred ecccccCCEEEEeeCC-ceEEEEEEEEE
Q psy16497 27 AERVRVNDSIIVHKNG-KAYVERVTRLE 53 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~~-~l~~~rV~~V~ 53 (143)
+-.++.||.|.|..|. .-...+|.+|.
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~ 70 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVD 70 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEE
Confidence 3379999999997762 23446666664
No 50
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=39.01 E-value=74 Score=19.61 Aligned_cols=26 Identities=15% Similarity=0.197 Sum_probs=22.3
Q ss_pred ccccCCEEEEee--CCceEEEEEEEEEE
Q psy16497 29 RVRVNDSIIVHK--NGKAYVERVTRLEN 54 (143)
Q Consensus 29 ~v~~Gd~v~v~~--~~~l~~~rV~~V~~ 54 (143)
+.++||.|-+.. ++...+++|+++..
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC
Confidence 568999999987 67899999998876
No 51
>PF08194 DIM: DIM protein; InterPro: IPR013172 Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila []. This entry includes DIMs 1 to 4 and DIM23.
Probab=38.13 E-value=26 Score=20.73 Aligned_cols=16 Identities=31% Similarity=0.804 Sum_probs=12.6
Q ss_pred cCCcceeEEEccEEEee
Q psy16497 63 PLTTSGTIVVNNVFASC 79 (143)
Q Consensus 63 PlT~~GtivVd~V~aSC 79 (143)
|+| -|++++||.=--|
T Consensus 20 ~~~-pG~ViING~C~dC 35 (36)
T PF08194_consen 20 PAT-PGNVIINGKCIDC 35 (36)
T ss_pred cCC-CCeEEECceeeeC
Confidence 677 8999999976554
No 52
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=36.92 E-value=26 Score=23.84 Aligned_cols=16 Identities=31% Similarity=0.551 Sum_probs=13.5
Q ss_pred eecccccCCEEEEeeC
Q psy16497 26 YAERVRVNDSIIVHKN 41 (143)
Q Consensus 26 fA~~v~~Gd~v~v~~~ 41 (143)
+-.++++||+|++..+
T Consensus 32 lv~~~~vGD~VLVH~G 47 (76)
T TIGR00074 32 LVGEVKVGDYVLVHVG 47 (76)
T ss_pred eeCCCCCCCEEEEecC
Confidence 4478999999999875
No 53
>PRK10671 copA copper exporting ATPase; Provisional
Probab=36.50 E-value=39 Score=32.03 Aligned_cols=54 Identities=15% Similarity=0.185 Sum_probs=36.1
Q ss_pred ceeeecccccCCEEEEeeCCc-----eEEEEEEEEEEEEeeeeeecCCcc-------eeEEEccEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNGK-----AYVERVTRLENVIQTGVYAPLTTS-------GTIVVNNVF 76 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~~-----l~~~rV~~V~~~~~~G~yAPlT~~-------GtivVd~V~ 76 (143)
+.|-++++++||.|.+..++. ....--..|....-+|=--|.... ||++++|-+
T Consensus 334 ~~v~~~~l~~GD~v~v~~G~~iP~Dg~v~~g~~~vdeS~lTGEs~pv~k~~gd~V~aGt~~~~G~~ 399 (834)
T PRK10671 334 KSVPLADVQPGMLLRLTTGDRVPVDGEITQGEAWLDEAMLTGEPIPQQKGEGDSVHAGTVVQDGSV 399 (834)
T ss_pred EEEEHHHcCCCCEEEEcCCCEeeeeEEEEEceEEEeehhhcCCCCCEecCCCCEEEecceecceeE
Confidence 568999999999999987642 111112334444456666666665 899998755
No 54
>PRK05174 3-hydroxydecanoyl-(acyl carrier protein) dehydratase; Validated
Probab=35.61 E-value=1.3e+02 Score=23.21 Aligned_cols=46 Identities=13% Similarity=0.113 Sum_probs=26.2
Q ss_pred cceeeecccccCCEEEEeeCCceEEEEEEEEEEEEeeeeeecCCcceeEEEccEEE
Q psy16497 22 IEYTYAERVRVNDSIIVHKNGKAYVERVTRLENVIQTGVYAPLTTSGTIVVNNVFA 77 (143)
Q Consensus 22 ~~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~V~a 77 (143)
++..|-.+|.+||..++.. .+|+++.. ...|+. +.+|++.|||..+
T Consensus 110 ~~~kfr~~v~Pgd~~l~l~------v~i~~~~~-~~~~~~---~~~~~i~v~g~~v 155 (172)
T PRK05174 110 GEVKFTGQVLPTAKKVTYE------IDIKRVIN-RKLVMG---IADGRVLVDGEEI 155 (172)
T ss_pred cEEEECccCcCCCEEEEEE------EEEEEEec-CCCCEE---EEEEEEEECCEEE
Confidence 3566777777777643321 33333322 223333 5689999999765
No 55
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=35.56 E-value=63 Score=23.28 Aligned_cols=34 Identities=18% Similarity=0.251 Sum_probs=27.7
Q ss_pred cceeeecccccCCEEEEeeCCceEEEEEEEEEEE
Q psy16497 22 IEYTYAERVRVNDSIIVHKNGKAYVERVTRLENV 55 (143)
Q Consensus 22 ~~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~ 55 (143)
..+.-+.+|++||.|-+.-++.....+|..+...
T Consensus 41 ~~aKpS~~VK~GD~l~i~~~~~~~~v~Vl~~~~~ 74 (100)
T COG1188 41 QRAKPSKEVKVGDILTIRFGNKEFTVKVLALGEQ 74 (100)
T ss_pred EEcccccccCCCCEEEEEeCCcEEEEEEEecccc
Confidence 3556889999999999988877888888887653
No 56
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=34.98 E-value=71 Score=21.87 Aligned_cols=24 Identities=21% Similarity=0.390 Sum_probs=16.2
Q ss_pred ccccCCEEEEeeCC--------ceEEEEEEEE
Q psy16497 29 RVRVNDSIIVHKNG--------KAYVERVTRL 52 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~--------~l~~~rV~~V 52 (143)
.||+||+|++.+.+ ......|..+
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~ 36 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHC 36 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEE
Confidence 58999999997653 3555555554
No 57
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=34.88 E-value=25 Score=23.23 Aligned_cols=16 Identities=31% Similarity=0.569 Sum_probs=11.3
Q ss_pred eecccccCCEEEEeeC
Q psy16497 26 YAERVRVNDSIIVHKN 41 (143)
Q Consensus 26 fA~~v~~Gd~v~v~~~ 41 (143)
+=.++++||+|++..+
T Consensus 34 lv~~v~~Gd~VLVHaG 49 (68)
T PF01455_consen 34 LVPDVKVGDYVLVHAG 49 (68)
T ss_dssp TCTSB-TT-EEEEETT
T ss_pred EeCCCCCCCEEEEecC
Confidence 4566999999999875
No 58
>COG0469 PykF Pyruvate kinase [Carbohydrate transport and metabolism]
Probab=34.85 E-value=58 Score=29.50 Aligned_cols=25 Identities=24% Similarity=0.332 Sum_probs=19.3
Q ss_pred eecccccCCEEEEeeCC-ceEEEEEE
Q psy16497 26 YAERVRVNDSIIVHKNG-KAYVERVT 50 (143)
Q Consensus 26 fA~~v~~Gd~v~v~~~~-~l~~~rV~ 50 (143)
++++|++||.|++.++. .++...|.
T Consensus 116 l~~dV~~G~~iLlDDG~i~l~V~~v~ 141 (477)
T COG0469 116 LAKDVKPGDRILLDDGKIELRVVEVD 141 (477)
T ss_pred HHhhcCCCCEEEEeCCeeEEEEEEee
Confidence 89999999999998874 45544444
No 59
>PRK14524 rpsP 30S ribosomal protein S16; Provisional
Probab=34.75 E-value=33 Score=24.37 Aligned_cols=20 Identities=30% Similarity=0.446 Sum_probs=15.1
Q ss_pred EEEeeeeeecCCcceeEEEc
Q psy16497 54 NVIQTGVYAPLTTSGTIVVN 73 (143)
Q Consensus 54 ~~~~~G~yAPlT~~GtivVd 73 (143)
-.|.-|.|.|++...+|-+|
T Consensus 32 ~iE~lG~YnP~~~~~~i~l~ 51 (94)
T PRK14524 32 YIESLGYYNPLKEPYEIKVD 51 (94)
T ss_pred ceeEeeecCCCCCCceEEEc
Confidence 36789999999877655544
No 60
>cd00081 Hint Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.
Probab=34.46 E-value=1.6e+02 Score=20.43 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=30.7
Q ss_pred ceeeeccccc--CCEEEEeeC-CceEEEEEEEEEEE-EeeeeeecCCcce
Q psy16497 23 EYTYAERVRV--NDSIIVHKN-GKAYVERVTRLENV-IQTGVYAPLTTSG 68 (143)
Q Consensus 23 ~~vfA~~v~~--Gd~v~v~~~-~~l~~~rV~~V~~~-~~~G~yAPlT~~G 68 (143)
..+-.+++.. ||.|+..+. +.+...+|..+... ...-+|-=-|..|
T Consensus 14 ~~~~i~~l~~~~g~~V~~~d~~~~~~~~~v~~~~~~~~~~~~~~i~~~~g 63 (136)
T cd00081 14 GRKKIEELVEKKGDKVLALDETGKLVFSKVLKVLRRDYEKKFYKIKTESG 63 (136)
T ss_pred cEEEhHHhhhccCCEEEEECCCCCEEEEEeeEEEEEcCCCcEEEEEECCC
Confidence 5677788999 999999876 45777778777665 3333443334443
No 61
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=33.70 E-value=81 Score=22.51 Aligned_cols=26 Identities=19% Similarity=0.322 Sum_probs=18.1
Q ss_pred ccccCCEEEEeeCC-ceEEEEEEEEEE
Q psy16497 29 RVRVNDSIIVHKNG-KAYVERVTRLEN 54 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~-~l~~~rV~~V~~ 54 (143)
.++.||.|.+..+. .-+.-+|.+|..
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~ 30 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLP 30 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEc
Confidence 68999999998763 334556666643
No 62
>TIGR00002 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles.
Probab=33.18 E-value=37 Score=23.22 Aligned_cols=20 Identities=30% Similarity=0.587 Sum_probs=14.5
Q ss_pred EEEeeeeeecCCcceeEEEc
Q psy16497 54 NVIQTGVYAPLTTSGTIVVN 73 (143)
Q Consensus 54 ~~~~~G~yAPlT~~GtivVd 73 (143)
-.|.-|.|.|++..-+|-+|
T Consensus 31 ~iE~lG~YnP~~~~~~i~l~ 50 (78)
T TIGR00002 31 YIEELGFYNPLTKESRVKLN 50 (78)
T ss_pred ceeEeeeccCCCCCcEEEEc
Confidence 46889999999875444443
No 63
>cd06552 ASCH_yqfb_like ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=33.06 E-value=1.4e+02 Score=20.22 Aligned_cols=15 Identities=20% Similarity=0.381 Sum_probs=11.5
Q ss_pred cccccCCEEEEeeCC
Q psy16497 28 ERVRVNDSIIVHKNG 42 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~ 42 (143)
..+++||++++..++
T Consensus 27 ~~~~~Gd~~~~~~~~ 41 (100)
T cd06552 27 SHLKPGDVVEVHTGE 41 (100)
T ss_pred cCCCCCCEEEEEECC
Confidence 358999999887654
No 64
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=32.98 E-value=53 Score=24.20 Aligned_cols=14 Identities=29% Similarity=0.532 Sum_probs=11.7
Q ss_pred cccccCCEEEEeeC
Q psy16497 28 ERVRVNDSIIVHKN 41 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~ 41 (143)
+++++||+|++..+
T Consensus 4 ~~i~vGD~V~v~~d 17 (130)
T cd04712 4 LTIRVGDVVSVERD 17 (130)
T ss_pred CEEeCCCEEEEcCC
Confidence 56899999999765
No 65
>TIGR01497 kdpB K+-transporting ATPase, B subunit. One sequence is apparently mis-annotated in the primary literature, but properly annotated by TIGR.
Probab=32.49 E-value=57 Score=30.69 Aligned_cols=54 Identities=20% Similarity=0.335 Sum_probs=33.0
Q ss_pred ceeeecccccCCEEEEeeCCc------eEEEEEEEEEEEEeeeeeecCC----------cceeEEEccEEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNGK------AYVERVTRLENVIQTGVYAPLT----------TSGTIVVNNVFA 77 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~~------l~~~rV~~V~~~~~~G~yAPlT----------~~GtivVd~V~a 77 (143)
+.|-++++++||.|.+..++. +... ...|...--+|==.|.. ..||++++|...
T Consensus 117 ~~V~~~~L~~GDiV~V~~Gd~IPaDG~vieG-~~~VDESaLTGES~PV~K~~g~~~~~V~aGT~v~~G~~~ 186 (675)
T TIGR01497 117 DKVPADQLKKGDIVLVEAGDVIPCDGEVIEG-VASVDESAITGESAPVIKESGGDFASVTGGTRILSDWLV 186 (675)
T ss_pred EEEEHHHCCCCCEEEECCCCEEeeeEEEEEc-cEEEEcccccCCCCceeecCCCCcceeecCcEEEeeEEE
Confidence 678999999999999977631 1111 23344333444444443 338888887543
No 66
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=32.47 E-value=1.5e+02 Score=19.76 Aligned_cols=32 Identities=13% Similarity=0.211 Sum_probs=23.6
Q ss_pred eeeecccccCCEEEEeeC--CceEEEEEEEEEEE
Q psy16497 24 YTYAERVRVNDSIIVHKN--GKAYVERVTRLENV 55 (143)
Q Consensus 24 ~vfA~~v~~Gd~v~v~~~--~~l~~~rV~~V~~~ 55 (143)
.+-...+++||.+++... +.....+|.+|...
T Consensus 21 ~v~~G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~ 54 (87)
T cd03694 21 TVSKGVIRLGDTLLLGPDQDGSFRPVTVKSIHRN 54 (87)
T ss_pred EEecCEEeCCCEEEECCCCCCCEeEEEEEEEEEC
Confidence 467889999999998664 33567788887643
No 67
>PRK14525 rpsP 30S ribosomal protein S16; Provisional
Probab=32.04 E-value=38 Score=23.78 Aligned_cols=20 Identities=20% Similarity=0.436 Sum_probs=15.2
Q ss_pred EEEeeeeeecCCcceeEEEc
Q psy16497 54 NVIQTGVYAPLTTSGTIVVN 73 (143)
Q Consensus 54 ~~~~~G~yAPlT~~GtivVd 73 (143)
..|.-|.|.|++...+|.+|
T Consensus 33 ~IE~lG~YnP~~~~~~i~ln 52 (88)
T PRK14525 33 YLEDVGIYDPTKRPERIELK 52 (88)
T ss_pred ceeEEecccCCCCCceEEEc
Confidence 46889999999876655554
No 68
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=31.43 E-value=50 Score=31.04 Aligned_cols=53 Identities=21% Similarity=0.302 Sum_probs=32.4
Q ss_pred ceeeecccccCCEEEEeeCCc------eEEEEEEEEEEEEeeeeeecCCcc-------eeEEEccEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNGK------AYVERVTRLENVIQTGVYAPLTTS-------GTIVVNNVF 76 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~~------l~~~rV~~V~~~~~~G~yAPlT~~-------GtivVd~V~ 76 (143)
+.|-++++++||.|.+..++. +... -..|....-+|=--|.... ||+++||.+
T Consensus 254 ~~v~~~~l~~GDiv~v~~G~~IP~Dg~vi~g-~~~vdes~lTGEs~Pv~k~~Gd~V~aGt~~~~G~~ 319 (741)
T PRK11033 254 EEVAIADLRPGDVIEVAAGGRLPADGKLLSP-FASFDESALTGESIPVERATGEKVPAGATSVDRLV 319 (741)
T ss_pred EEEEHHHCCCCCEEEECCCCEEecceEEEEC-cEEeecccccCCCCCEecCCCCeeccCCEEcCceE
Confidence 678999999999999977631 1111 1223333334433444433 999999854
No 69
>PRK00809 hypothetical protein; Provisional
Probab=31.08 E-value=59 Score=24.47 Aligned_cols=38 Identities=13% Similarity=0.166 Sum_probs=27.7
Q ss_pred cceeeecccccCCEEEEeeCC----ceEEEEEEEEEEEEeee
Q psy16497 22 IEYTYAERVRVNDSIIVHKNG----KAYVERVTRLENVIQTG 59 (143)
Q Consensus 22 ~~~vfA~~v~~Gd~v~v~~~~----~l~~~rV~~V~~~~~~G 59 (143)
+..-+..++++||.++....+ +-.+..|++|-++.+..
T Consensus 27 ~~rn~lr~Mk~GD~v~fYhs~~~~~~~~~~~ivgi~eV~~~~ 68 (144)
T PRK00809 27 RYKNTIEKVKPGDKLIIYVSQEYGAERLPGKIVGIYEVVSEW 68 (144)
T ss_pred hhhhHHhhCCCCCEEEEEECCccCCCCCCceEEEEEEEecCc
Confidence 344466789999999987653 23457788888888776
No 70
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=30.47 E-value=96 Score=20.42 Aligned_cols=29 Identities=10% Similarity=0.091 Sum_probs=21.4
Q ss_pred eeeecccccCCEEEEeeCCceEEEEEEEEEE
Q psy16497 24 YTYAERVRVNDSIIVHKNGKAYVERVTRLEN 54 (143)
Q Consensus 24 ~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~ 54 (143)
.+.+..+++||.|++...+ ...+|.+|..
T Consensus 21 ~v~~G~i~~Gd~v~i~P~~--~~~~V~si~~ 49 (83)
T cd03698 21 KVESGSIQKGDTLLVMPSK--ESVEVKSIYV 49 (83)
T ss_pred EEeeeEEeCCCEEEEeCCC--cEEEEEEEEE
Confidence 4678899999999987655 3466666653
No 71
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=30.14 E-value=1.7e+02 Score=23.66 Aligned_cols=27 Identities=26% Similarity=0.393 Sum_probs=21.4
Q ss_pred cccccCCEEEEeeCC-----ceEEEEEEEEEE
Q psy16497 28 ERVRVNDSIIVHKNG-----KAYVERVTRLEN 54 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~-----~l~~~rV~~V~~ 54 (143)
.++++||.|++.+-+ ++...+|++|..
T Consensus 213 ~~i~~GD~VvTSGl~g~fP~Gi~VG~V~~v~~ 244 (276)
T PRK13922 213 ADIKVGDLVVTSGLGGIFPAGLPVGKVTSVER 244 (276)
T ss_pred CCCCCCCEEEECCCCCcCCCCCEEEEEEEEEe
Confidence 569999999998853 477788888844
No 72
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=30.05 E-value=37 Score=23.44 Aligned_cols=13 Identities=15% Similarity=0.209 Sum_probs=11.2
Q ss_pred ccccCCEEEEeeC
Q psy16497 29 RVRVNDSIIVHKN 41 (143)
Q Consensus 29 ~v~~Gd~v~v~~~ 41 (143)
++++||+|++..+
T Consensus 42 ~~~vGDyVLVHaG 54 (82)
T PRK10413 42 ADLLGQWVLVHVG 54 (82)
T ss_pred ccccCCEEEEecc
Confidence 5789999999875
No 73
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=29.89 E-value=38 Score=23.82 Aligned_cols=13 Identities=31% Similarity=0.508 Sum_probs=11.5
Q ss_pred ccccCCEEEEeeC
Q psy16497 29 RVRVNDSIIVHKN 41 (143)
Q Consensus 29 ~v~~Gd~v~v~~~ 41 (143)
++++||+|++..+
T Consensus 41 ~~~vGDyVLVHaG 53 (90)
T PRK10409 41 QPRVGQWVLVHVG 53 (90)
T ss_pred ccCCCCEEEEecC
Confidence 6899999999875
No 74
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=29.54 E-value=27 Score=25.93 Aligned_cols=25 Identities=20% Similarity=0.364 Sum_probs=16.2
Q ss_pred ccccCCEEEEeeCCc--eEEEEEEEEE
Q psy16497 29 RVRVNDSIIVHKNGK--AYVERVTRLE 53 (143)
Q Consensus 29 ~v~~Gd~v~v~~~~~--l~~~rV~~V~ 53 (143)
-+++||||++...+. -..+||.++.
T Consensus 3 ~i~vGd~VlI~~~d~~~~yVAkI~~i~ 29 (128)
T cd04719 3 TIEVGDFVLIEGEDADGPDVARILHLY 29 (128)
T ss_pred EEecCCEEEEECCCCCCCcEeeehhhh
Confidence 478999999987542 3445555443
No 75
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=29.25 E-value=74 Score=21.79 Aligned_cols=17 Identities=12% Similarity=0.270 Sum_probs=14.5
Q ss_pred eeecccccCCEEEEeeC
Q psy16497 25 TYAERVRVNDSIIVHKN 41 (143)
Q Consensus 25 vfA~~v~~Gd~v~v~~~ 41 (143)
-+-+++++||.|.+.+|
T Consensus 33 ~m~~~L~~Gd~VvT~gG 49 (84)
T TIGR00739 33 KLIESLKKGDKVLTIGG 49 (84)
T ss_pred HHHHhCCCCCEEEECCC
Confidence 46789999999998876
No 76
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=29.17 E-value=67 Score=27.78 Aligned_cols=30 Identities=20% Similarity=0.216 Sum_probs=23.8
Q ss_pred eecccccCCEEEEeeCC-----ceEEEEEEEEEEE
Q psy16497 26 YAERVRVNDSIIVHKNG-----KAYVERVTRLENV 55 (143)
Q Consensus 26 fA~~v~~Gd~v~v~~~~-----~l~~~rV~~V~~~ 55 (143)
-.+++++||.|.+.+-+ ++...+|++|...
T Consensus 257 ~~~di~~GD~lVTSGlgGvfP~Gl~Vg~V~~V~~~ 291 (337)
T PRK14872 257 DGKTLRVGDILVTTGLDGVFPPGLLVATVTKVLPP 291 (337)
T ss_pred CCCCcCCCCEEEECCCCCcCCCCCEEEEEEEEEEC
Confidence 36899999999887732 5888888888764
No 77
>TIGR01511 ATPase-IB1_Cu copper-(or silver)-translocating P-type ATPase. One member from Halobacterium is annotated as "molybdenum-binding protein" although no evidence can be found for this classification.
Probab=28.50 E-value=52 Score=29.78 Aligned_cols=19 Identities=16% Similarity=0.051 Sum_probs=16.9
Q ss_pred ceeeecccccCCEEEEeeC
Q psy16497 23 EYTYAERVRVNDSIIVHKN 41 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~ 41 (143)
+.|-++++++||.|.+..+
T Consensus 103 ~~v~~~~l~~GDii~v~~G 121 (562)
T TIGR01511 103 EEVPVALLQPGDIVKVLPG 121 (562)
T ss_pred EEEEHHHCCCCCEEEECCC
Confidence 6789999999999999775
No 78
>PRK01122 potassium-transporting ATPase subunit B; Provisional
Probab=28.14 E-value=77 Score=29.84 Aligned_cols=20 Identities=25% Similarity=0.293 Sum_probs=17.4
Q ss_pred ceeeecccccCCEEEEeeCC
Q psy16497 23 EYTYAERVRVNDSIIVHKNG 42 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~ 42 (143)
+.|-++++++||.|.+..++
T Consensus 116 ~~V~~~eL~~GDiV~v~~Gd 135 (679)
T PRK01122 116 EEVPATELRKGDIVLVEAGE 135 (679)
T ss_pred EEEEHHHcCCCCEEEEcCCC
Confidence 67899999999999997763
No 79
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=28.09 E-value=1.2e+02 Score=21.70 Aligned_cols=51 Identities=22% Similarity=0.304 Sum_probs=32.1
Q ss_pred cccccCCEEEEeeCCceEEEEEEEEEEEE--eeeeeecCCcceeEEEccEEEeeeee
Q psy16497 28 ERVRVNDSIIVHKNGKAYVERVTRLENVI--QTGVYAPLTTSGTIVVNNVFASCYAV 82 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~--~~G~yAPlT~~GtivVd~V~aSCya~ 82 (143)
.++++||.|++...++...=+|+++..+. +..++.|....-.| .+..|+..
T Consensus 62 ~~l~~Gd~I~l~~~~~~~~Y~V~~~~~v~~~~~~~~~~~~~~~~l----tLiTC~p~ 114 (127)
T cd06165 62 YKVKVGDKIYLTDKDNVYEYKVTSKKIVDPTRVDVIDDVPGKKLI----TLITCDDA 114 (127)
T ss_pred HHCcCCCEEEEEECCEEEEEEEeeEEEECcccceeeccCCCCCEE----EEEecCCC
Confidence 57889999999987666666777766554 33455553311111 35578764
No 80
>COG3746 OprP Phosphate-selective porin [Inorganic ion transport and metabolism]
Probab=27.97 E-value=34 Score=30.31 Aligned_cols=26 Identities=23% Similarity=0.406 Sum_probs=20.7
Q ss_pred EEEEEEeeeeeecCCcceeEEEccEE
Q psy16497 51 RLENVIQTGVYAPLTTSGTIVVNNVF 76 (143)
Q Consensus 51 ~V~~~~~~G~yAPlT~~GtivVd~V~ 76 (143)
++...-.+|+|||++.+|+++==|+-
T Consensus 205 ~~~~~~~Rgv~ap~~~~gdvLHLG~s 230 (426)
T COG3746 205 SVKGLNGRGVWAPKHETGDVLHLGVS 230 (426)
T ss_pred ccccccceEEeccCCCCCcEEEeehh
Confidence 34556689999999999999866654
No 81
>TIGR01512 ATPase-IB2_Cd heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase. .
Probab=27.86 E-value=61 Score=29.08 Aligned_cols=19 Identities=26% Similarity=0.436 Sum_probs=16.7
Q ss_pred ceeeecccccCCEEEEeeC
Q psy16497 23 EYTYAERVRVNDSIIVHKN 41 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~ 41 (143)
+.+-++++++||.|.+..+
T Consensus 66 ~~i~~~~l~~GDiv~v~~G 84 (536)
T TIGR01512 66 EEVAVEELKVGDVVVVKPG 84 (536)
T ss_pred EEEEHHHCCCCCEEEEcCC
Confidence 6789999999999999765
No 82
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=27.71 E-value=44 Score=23.25 Aligned_cols=15 Identities=40% Similarity=0.694 Sum_probs=12.6
Q ss_pred ecccccCCEEEEeeC
Q psy16497 27 AERVRVNDSIIVHKN 41 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~ 41 (143)
-+++++||+|++..+
T Consensus 36 ~~~v~~GdyVLVHvG 50 (82)
T COG0298 36 GEEVKVGDYVLVHVG 50 (82)
T ss_pred cCccccCCEEEEEee
Confidence 349999999999875
No 83
>PRK14010 potassium-transporting ATPase subunit B; Provisional
Probab=27.68 E-value=75 Score=29.88 Aligned_cols=53 Identities=21% Similarity=0.262 Sum_probs=33.8
Q ss_pred ceeeecccccCCEEEEeeCC------ceEEEEEEEEEEEEeeeeeecCCc----------ceeEEEccEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNG------KAYVERVTRLENVIQTGVYAPLTT----------SGTIVVNNVF 76 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~------~l~~~rV~~V~~~~~~G~yAPlT~----------~GtivVd~V~ 76 (143)
+.+-++++++||.|++..++ .+... ...|..-.-+|=-.|... .||++++|..
T Consensus 116 ~~I~a~eLv~GDiV~v~~Gd~IPaDG~vieG-~~~VDESaLTGES~PV~K~~g~d~~~V~aGT~v~~G~~ 184 (673)
T PRK14010 116 EMIDASDLKKGHIVRVATGEQIPNDGKVIKG-LATVDESAITGESAPVIKESGGDFDNVIGGTSVASDWL 184 (673)
T ss_pred EEEEHHHcCCCCEEEECCCCcccCCeEEEEc-ceEEecchhcCCCCceeccCCCccCeeecCceeecceE
Confidence 67899999999999997763 12222 224444444555555544 3888888743
No 84
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=27.59 E-value=32 Score=23.55 Aligned_cols=22 Identities=36% Similarity=0.454 Sum_probs=17.8
Q ss_pred EEeeeeeecCCcceeEEEccEEEe
Q psy16497 55 VIQTGVYAPLTTSGTIVVNNVFAS 78 (143)
Q Consensus 55 ~~~~G~yAPlT~~GtivVd~V~aS 78 (143)
++.-|+ |+|.-|-|+|||..+.
T Consensus 39 IEsLGV--P~tEV~~i~vNG~~v~ 60 (81)
T PF14451_consen 39 IESLGV--PHTEVGLILVNGRPVD 60 (81)
T ss_pred HHHcCC--ChHHeEEEEECCEECC
Confidence 455665 9999999999998774
No 85
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=27.12 E-value=1.6e+02 Score=19.20 Aligned_cols=31 Identities=23% Similarity=0.299 Sum_probs=21.0
Q ss_pred ceeeecccccCCEEEEeeCC-ceEEEEEEEEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNG-KAYVERVTRLE 53 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~-~l~~~rV~~V~ 53 (143)
--+|...+++||.|.+.+.+ ..+..+|.++.
T Consensus 20 ~Rv~sG~l~~g~~v~~~~~~~~~~~~~v~~l~ 51 (86)
T cd03691 20 GRIFRGTVKVGQQVAVVKRDGKIEKAKITKLF 51 (86)
T ss_pred EEEEeCEEcCCCEEEEEcCCCCEEEEEEeeEe
Confidence 45799999999999887652 23334454443
No 86
>PF09378 HAS-barrel: HAS barrel domain; InterPro: IPR018538 The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family []. ; PDB: 3OAA_I.
Probab=26.84 E-value=62 Score=21.29 Aligned_cols=26 Identities=23% Similarity=0.473 Sum_probs=18.8
Q ss_pred ccccCCEEEEeeC-CceEEEEEEEEEE
Q psy16497 29 RVRVNDSIIVHKN-GKAYVERVTRLEN 54 (143)
Q Consensus 29 ~v~~Gd~v~v~~~-~~l~~~rV~~V~~ 54 (143)
+++.|++|.+..+ +.-...+|++|++
T Consensus 22 ~v~~GeyV~i~~~~~~~vlG~V~~i~~ 48 (91)
T PF09378_consen 22 DVRVGEYVVIEYDDGEKVLGMVTSISR 48 (91)
T ss_dssp T-BTTEEEEES----TTEEEEEEEEES
T ss_pred CCCcCeEEEEEEechhhhhhhhheeEE
Confidence 7999999999876 5567788888877
No 87
>cd03699 lepA_II lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu and IF2 have all been demonstrated to interact at overlapping sites on the ribosome. Chemical protection studies demonstrate that they all include the universally conserved alpha-sarcin loop as part of their binding site. These data indicate that LepA may bind to this location on the ribosome as well. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=26.68 E-value=1.7e+02 Score=19.35 Aligned_cols=29 Identities=17% Similarity=0.225 Sum_probs=20.7
Q ss_pred ceeeecccccCCEEEEeeCCceEEEEEEEEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNGKAYVERVTRLE 53 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~ 53 (143)
--+|...+++||.|+....+. ..||.+|.
T Consensus 20 ~Rv~sG~l~~~~~v~~~~~~~--~~~i~~l~ 48 (86)
T cd03699 20 VRVFDGTLKKGDKIRFMSTGK--EYEVEEVG 48 (86)
T ss_pred EEEEcCEEcCCCEEEEecCCC--eEEEEEEE
Confidence 457999999999998765442 34555555
No 88
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=26.64 E-value=1.5e+02 Score=21.49 Aligned_cols=27 Identities=19% Similarity=0.505 Sum_probs=17.9
Q ss_pred cccccCCEEEEeeC--CceEEEEEEEEEE
Q psy16497 28 ERVRVNDSIIVHKN--GKAYVERVTRLEN 54 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~--~~l~~~rV~~V~~ 54 (143)
.++++||.+...+- +.-...+|+.|..
T Consensus 30 ~~ikvGD~I~f~~~~~~~~l~v~V~~i~~ 58 (109)
T cd06555 30 QQIKVGDKILFNDLDTGQQLLVKVVDIRK 58 (109)
T ss_pred hcCCCCCEEEEEEcCCCcEEEEEEEEEEe
Confidence 46999999988663 2345555666553
No 89
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=26.43 E-value=1e+02 Score=15.66 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=15.6
Q ss_pred cccCCEEEEeeCC-ceEEEEEEEEE
Q psy16497 30 VRVNDSIIVHKNG-KAYVERVTRLE 53 (143)
Q Consensus 30 v~~Gd~v~v~~~~-~l~~~rV~~V~ 53 (143)
+++||.|.+..+. .=....|.++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~ 26 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVD 26 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEc
Confidence 5789999998863 22445555543
No 90
>TIGR01494 ATPase_P-type ATPase, P-type (transporting), HAD superfamily, subfamily IC. The crystal structure of one calcium-pumping ATPase and an analysis of the fold of the catalytic domain of the P-type ATPases have been published. These reveal that the catalytic core of these enzymes is a haloacid dehalogenase(HAD)-type aspartate-nucleophile hydrolase. The location of the ATP-binding loop in between the first and second HAD conserved catalytic motifs defines these enzymes as members of subfamily I of the HAD superfamily (see also TIGR01493, TIGR01509, TIGR01549, TIGR01544 and TIGR01545). Based on these classifications, the P-type ATPase _superfamily_ corresponds to the IC subfamily of the HAD superfamily.
Probab=26.34 E-value=74 Score=28.01 Aligned_cols=55 Identities=18% Similarity=0.210 Sum_probs=32.7
Q ss_pred ceeeecccccCCEEEEeeCCc-----eEEEEEEEEEEEEeeeeeecCCc-------ceeEEEccEEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNGK-----AYVERVTRLENVIQTGVYAPLTT-------SGTIVVNNVFA 77 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~~-----l~~~rV~~V~~~~~~G~yAPlT~-------~GtivVd~V~a 77 (143)
..|-++++++||.|.+..++. ...+--..|+...-+|=-.|... .|+++.+|.+.
T Consensus 45 ~~V~~~~l~~GDiv~v~~G~~iP~Dg~vl~g~~~vdes~LTGEs~pv~k~~g~~v~~gs~~~~G~~~ 111 (499)
T TIGR01494 45 KEIPASDLVPGDIVLVKSGEIVPADGVLLSGSCFVDESNLTGESVPVLKTAGDAVFAGTYVFNGTLI 111 (499)
T ss_pred EEEEHHHCCCCCEEEECCCCEeeeeEEEEEccEEEEcccccCCCCCeeeccCCccccCcEEeccEEE
Confidence 667899999999999987631 11111222333334444444444 46777777654
No 91
>PF04203 Sortase: Sortase family; InterPro: IPR005754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan []. Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported [, ]. Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope. ; PDB: 2W1K_A 2OQZ_A 1RZ2_A 2OQW_A 1T2W_A 1IJA_A 1T2P_A 1T2O_C 2KID_A 3RCC_N ....
Probab=26.05 E-value=1.6e+02 Score=20.60 Aligned_cols=36 Identities=31% Similarity=0.493 Sum_probs=25.3
Q ss_pred cccccCCEEEEee-CCceEEEEEEEEEEEEee--eeeec
Q psy16497 28 ERVRVNDSIIVHK-NGKAYVERVTRLENVIQT--GVYAP 63 (143)
Q Consensus 28 ~~v~~Gd~v~v~~-~~~l~~~rV~~V~~~~~~--G~yAP 63 (143)
.++++||.|++.. ++....=+|.++..+... -++.|
T Consensus 59 ~~~~~gd~i~~~~~~g~~~~Y~V~~~~~v~~~~~~~~~~ 97 (128)
T PF04203_consen 59 NKLKKGDEIYLTTPDGKTYEYRVTSVKIVDPDDVDVLNP 97 (128)
T ss_dssp GGGHTT-EEEEEETSSEEEEEEEEEEEEECTTSGGGGSH
T ss_pred cccCCCCEEEEEEecCEEEEEEEEEEEEEcCCceEEeee
Confidence 4679999999999 566667788888876543 34455
No 92
>PRK06739 pyruvate kinase; Validated
Probab=25.90 E-value=1.1e+02 Score=26.52 Aligned_cols=17 Identities=24% Similarity=0.431 Sum_probs=14.7
Q ss_pred eeecccccCCEEEEeeC
Q psy16497 25 TYAERVRVNDSIIVHKN 41 (143)
Q Consensus 25 vfA~~v~~Gd~v~v~~~ 41 (143)
-|++++++||.|++.++
T Consensus 105 ~l~~~v~~Gd~IlidDG 121 (352)
T PRK06739 105 GIANDVKVGSRILMNDG 121 (352)
T ss_pred HHHhhcCCCCEEEEeCC
Confidence 47889999999998775
No 93
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=25.83 E-value=1.5e+02 Score=25.97 Aligned_cols=37 Identities=19% Similarity=0.311 Sum_probs=29.5
Q ss_pred cCCcceeeecccccCCEEEEeeC-CceEEEEEEEEEEE
Q psy16497 19 LSDIEYTYAERVRVNDSIIVHKN-GKAYVERVTRLENV 55 (143)
Q Consensus 19 ~~~~~~vfA~~v~~Gd~v~v~~~-~~l~~~rV~~V~~~ 55 (143)
.++.+..|=++++.||.|++.+. |.-|.+.|=+|...
T Consensus 248 ~pg~kT~YLSEL~sG~~VlvVd~~G~tR~~~VGRvKIE 285 (354)
T PF01959_consen 248 MPGGKTRYLSELRSGDEVLVVDADGRTRTAIVGRVKIE 285 (354)
T ss_pred cCCCceeehhhhcCCCEEEEEeCCCCEEEEEeeEEEEe
Confidence 36788999999999999999986 45677777776544
No 94
>PF08844 DUF1815: Domain of unknown function (DUF1815); InterPro: IPR014943 This entry is about 100 amino acids in length and is functionally uncharacterised.
Probab=25.75 E-value=25 Score=25.32 Aligned_cols=15 Identities=33% Similarity=0.583 Sum_probs=11.3
Q ss_pred cEEEeeeeeeccchh
Q psy16497 74 NVFASCYAVIDNQFL 88 (143)
Q Consensus 74 ~V~aSCya~i~~h~L 88 (143)
|..||||++-+-...
T Consensus 30 G~~AsCYtC~dG~~~ 44 (105)
T PF08844_consen 30 GYLASCYTCGDGRDM 44 (105)
T ss_pred CceeEEEecCCCCCC
Confidence 889999999654443
No 95
>PRK04980 hypothetical protein; Provisional
Probab=25.68 E-value=1.9e+02 Score=20.80 Aligned_cols=30 Identities=13% Similarity=0.118 Sum_probs=18.6
Q ss_pred ecccccCCEEEEe--eCC-ceEEEEEEEEEEEE
Q psy16497 27 AERVRVNDSIIVH--KNG-KAYVERVTRLENVI 56 (143)
Q Consensus 27 A~~v~~Gd~v~v~--~~~-~l~~~rV~~V~~~~ 56 (143)
-+..++||.+.+. +++ .+-..+|.+|+.+.
T Consensus 29 e~~~~~G~~~~V~~~e~g~~~c~ieI~sV~~i~ 61 (102)
T PRK04980 29 ESHFKPGDVLRVGTFEDDRYFCTIEVLSVSPVT 61 (102)
T ss_pred ccCCCCCCEEEEEECCCCcEEEEEEEEEEEEEe
Confidence 4568899999995 333 23444566665543
No 96
>PF08854 DUF1824: Domain of unknown function (DUF1824); InterPro: IPR014953 This uncharacterised group of proteins are principally found in cyanobacteria. ; PDB: 2Q22_B.
Probab=25.67 E-value=58 Score=24.31 Aligned_cols=20 Identities=30% Similarity=0.456 Sum_probs=13.1
Q ss_pred CcceeEEEc-------cEEEeeeeeec
Q psy16497 65 TTSGTIVVN-------NVFASCYAVID 84 (143)
Q Consensus 65 T~~GtivVd-------~V~aSCya~i~ 84 (143)
+..|++-|+ ||+.||.+.-+
T Consensus 84 ~~tg~~yv~~y~G~~rGVLiScqs~~~ 110 (125)
T PF08854_consen 84 QKTGSCYVRSYTGLGRGVLISCQSDDD 110 (125)
T ss_dssp TTT--EEEEE--S--BEEEEEEE-SST
T ss_pred CCCCcEEEeecCCccceEEEEeccCCc
Confidence 556777777 99999998544
No 97
>PF07977 FabA: FabA-like domain; InterPro: IPR013114 Fatty acids biosynthesis occurs by two distinct pathways: in fungi, mammals and mycobacteria, type I or associative fatty-acid biosynthesis (type I FAS) is accomplished by multifunctional proteins in which distinct domains catalyse specific reactions; in plants and most bacteria, type II or dissociative fatty-acid biosynthesis (type II FAS) is accomplished by distinct enzymes []. Both FabZ and FabA catalyse the dehydration of beta-hydroxyacyl acyl carrier protein (ACP) to trans 2-enoyl ACP. However, FabZ and FabA display subtle differences in substrate specificities, whereby FabA is most effective on acyl ACPs of 9-11 carbon atoms in length, while FabZ is less specific. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains. This enzyme domain has a HotDog fold.; PDB: 3D6X_F 2GLV_J 2GLM_E 2GLP_E 2GLL_C 1U1Z_F 3ESI_A 3AZB_T 3AZA_M 3AZ9_U ....
Probab=25.66 E-value=2.5e+02 Score=19.97 Aligned_cols=44 Identities=14% Similarity=0.266 Sum_probs=23.3
Q ss_pred ceeeecccccCC-EEEEeeCCceEEEEEEEEEEEEeeeeeecCCcceeEEEccEEE
Q psy16497 23 EYTYAERVRVND-SIIVHKNGKAYVERVTRLENVIQTGVYAPLTTSGTIVVNNVFA 77 (143)
Q Consensus 23 ~~vfA~~v~~Gd-~v~v~~~~~l~~~rV~~V~~~~~~G~yAPlT~~GtivVd~V~a 77 (143)
+..|-+.|.||| .+-+. .++.++. ....+. ...+|++.|||..+
T Consensus 90 ~~kF~~~v~Pg~~~l~~~-------v~i~~~~-~~~~~~---~~~~~~~~vdg~~v 134 (138)
T PF07977_consen 90 NVKFRGPVYPGDKTLRIE-------VEIKKIR-RREGGM---AIFDGTAYVDGELV 134 (138)
T ss_dssp EEEE-S-B-TTE-EEEEE-------EEEEEEE-EEETTE---EEEEEEEEETTEEE
T ss_pred EEEECccEeCCCcEEEEE-------EEEEEee-cccCCE---EEEEEEEEECCEEE
Confidence 556888899998 44331 3444442 222222 13578888998765
No 98
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=24.73 E-value=2e+02 Score=18.77 Aligned_cols=24 Identities=21% Similarity=0.268 Sum_probs=17.4
Q ss_pred cccCCEEEEeeCCceEEEEEEEEE
Q psy16497 30 VRVNDSIIVHKNGKAYVERVTRLE 53 (143)
Q Consensus 30 v~~Gd~v~v~~~~~l~~~rV~~V~ 53 (143)
-++||.+-+...++-+.-+|.+|+
T Consensus 53 ~~~Gd~v~~~~~~g~~~~~I~~I~ 76 (77)
T PF01272_consen 53 KKVGDEVEVELPGGERKYEILEIE 76 (77)
T ss_dssp -BTT-EEEEEETTBEEEEEEEEEE
T ss_pred CCCCCEEEEEeCCceEEEEEEEEE
Confidence 478999999887666777887775
No 99
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=24.35 E-value=1.2e+02 Score=22.10 Aligned_cols=26 Identities=12% Similarity=0.045 Sum_probs=18.9
Q ss_pred ecccccCCEEEEeeC---CceEEEEEEEE
Q psy16497 27 AERVRVNDSIIVHKN---GKAYVERVTRL 52 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~---~~l~~~rV~~V 52 (143)
-..+++||+|+.... ...-|.+|...
T Consensus 53 ~~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~ 81 (124)
T PF15057_consen 53 RHSLQVGDKVLAPWEPDDCRYGPGTVIAG 81 (124)
T ss_pred cCcCCCCCEEEEecCcCCCEEeCEEEEEC
Confidence 678999999999764 24666666654
No 100
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=23.73 E-value=2.2e+02 Score=18.85 Aligned_cols=31 Identities=19% Similarity=0.223 Sum_probs=20.9
Q ss_pred eeeecccccCCEEEEeeCCceEEEEEEEEEE
Q psy16497 24 YTYAERVRVNDSIIVHKNGKAYVERVTRLEN 54 (143)
Q Consensus 24 ~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~ 54 (143)
.+.+..+++||.|.+...+.-...+|.+|..
T Consensus 21 ~v~~G~v~~gd~v~~~p~~~~~~~~V~si~~ 51 (87)
T cd03697 21 RIERGTIKVGDEVEIVGFGETLKTTVTGIEM 51 (87)
T ss_pred EECCCCCccCCEEEEeCCCCCceEEEEEEEE
Confidence 4567889999999876532224566777653
No 101
>cd05827 Sortase_C_3 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Sortase C cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall cross bridges. It is a narrow-range enzyme required for anchoring a few substrates. It plays a role in Streptococcus pneumoniae pathogenesis and is required in the assembly of pili on the surface of Corynebacterium diphtheriae. Sortase C is
Probab=23.62 E-value=1.7e+02 Score=20.94 Aligned_cols=29 Identities=21% Similarity=0.469 Sum_probs=21.3
Q ss_pred cccccCCEEEEeeCCceEEEEEEEEEEEE
Q psy16497 28 ERVRVNDSIIVHKNGKAYVERVTRLENVI 56 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~ 56 (143)
.++++||.+++...+....=+|.++..+.
T Consensus 65 ~~l~~gd~i~l~t~~~~~~Y~V~~~~~v~ 93 (131)
T cd05827 65 DKLKKGDKFYIHVLGETLAYQVDQIEVVL 93 (131)
T ss_pred HHCCCCCEEEEEECCeEEEEEEEEEEEEC
Confidence 57889999999887655556677766554
No 102
>TIGR01525 ATPase-IB_hvy heavy metal translocating P-type ATPase. This alignment encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512.
Probab=23.49 E-value=94 Score=27.93 Aligned_cols=53 Identities=23% Similarity=0.328 Sum_probs=32.9
Q ss_pred ceeeecccccCCEEEEeeCCc------eEEEEEEEEEEEEeeeeeecCCcc-------eeEEEccEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNGK------AYVERVTRLENVIQTGVYAPLTTS-------GTIVVNNVF 76 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~~------l~~~rV~~V~~~~~~G~yAPlT~~-------GtivVd~V~ 76 (143)
..+-++++++||.|.+..+.. +.... ..|....-+|=--|.... ||++++|..
T Consensus 67 ~~i~~~~l~~GDiv~v~~G~~iP~Dg~vi~g~-~~vdes~lTGEs~pv~k~~g~~v~aGt~v~~g~~ 132 (556)
T TIGR01525 67 EEVPVEELQVGDIVIVRPGERIPVDGVVISGE-SEVDESALTGESMPVEKKEGDEVFAGTINGDGSL 132 (556)
T ss_pred EEEEHHHCCCCCEEEECCCCEeccceEEEecc-eEEeehhccCCCCCEecCCcCEEeeceEECCceE
Confidence 578999999999999976531 11111 234444444544555443 898888743
No 103
>PRK09519 recA DNA recombination protein RecA; Reviewed
Probab=23.34 E-value=54 Score=31.50 Aligned_cols=28 Identities=25% Similarity=0.317 Sum_probs=21.8
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEe
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVH 39 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~ 39 (143)
+||+|.+++-. .-+-|+++++||.|.+.
T Consensus 320 ~T~~Hp~lt~~-----------gw~~~~~L~~gD~ia~p 347 (790)
T PRK09519 320 ATPDHKVLTEY-----------GWRAAGELRKGDRVAQP 347 (790)
T ss_pred EcCCCeEEecC-----------CcEEHhHcCCCCEEecC
Confidence 58999999632 34579999999999754
No 104
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=23.26 E-value=1e+02 Score=22.96 Aligned_cols=27 Identities=26% Similarity=0.443 Sum_probs=18.9
Q ss_pred cccccCCEEEEeeCC---ceEEEEEEEEEE
Q psy16497 28 ERVRVNDSIIVHKNG---KAYVERVTRLEN 54 (143)
Q Consensus 28 ~~v~~Gd~v~v~~~~---~l~~~rV~~V~~ 54 (143)
..+++||+|++.... .....||..+..
T Consensus 10 ~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~ 39 (135)
T cd04710 10 ELLKVNDHIYMSSEPPGEPYYIGRIMEFVP 39 (135)
T ss_pred eEEeCCCEEEEecCCCCCCCEEEEEEEEEe
Confidence 357899999998642 366667766544
No 105
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=23.12 E-value=64 Score=22.25 Aligned_cols=31 Identities=23% Similarity=0.493 Sum_probs=21.2
Q ss_pred cCCcceeeecccccCCEEEEeeCCceEEEEE
Q psy16497 19 LSDIEYTYAERVRVNDSIIVHKNGKAYVERV 49 (143)
Q Consensus 19 ~~~~~~vfA~~v~~Gd~v~v~~~~~l~~~rV 49 (143)
+++...+...++++||.|.+.-.|++-|.-+
T Consensus 39 LhN~~~i~~~~i~~Gd~V~V~raGdVIP~I~ 69 (82)
T PF03120_consen 39 LHNYDYIKELDIRIGDTVLVTRAGDVIPKIV 69 (82)
T ss_dssp --SHHHHHHTT-BBT-EEEEEEETTTEEEEE
T ss_pred ecCHHHHHHcCCCCCCEEEEEECCCccceEe
Confidence 4566778889999999999988776666543
No 106
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=22.88 E-value=65 Score=33.14 Aligned_cols=18 Identities=22% Similarity=0.211 Sum_probs=15.8
Q ss_pred ceeeecccccCCEEEEee
Q psy16497 23 EYTYAERVRVNDSIIVHK 40 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~ 40 (143)
-.+-|++|++||+|.+..
T Consensus 999 i~K~A~dlK~GD~vvIPK 1016 (1627)
T PRK14715 999 IKKRAMDVKEGDLMLIPK 1016 (1627)
T ss_pred ceeehhhcCcCceeeccc
Confidence 557899999999999975
No 107
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=22.79 E-value=68 Score=33.55 Aligned_cols=34 Identities=18% Similarity=0.122 Sum_probs=26.4
Q ss_pred CCCCceEEeeeCCCCCCccCCcceeeecccccCCEEEEee
Q psy16497 1 MTPSHLILRWHRPNAKSILSDIEYTYAERVRVNDSIIVHK 40 (143)
Q Consensus 1 LTp~HLifv~~~~~~~~~~~~~~~vfA~~v~~Gd~v~v~~ 40 (143)
.||.|-+||.+.+ +.+ ...-|.++++||.|.+..
T Consensus 396 vTp~Hp~~V~~~~-g~~-----~~~~a~~l~~gD~i~~~~ 429 (1740)
T PRK08332 396 TSPWHPFFVLTPD-FKI-----VEKRADELKEGDILIGGM 429 (1740)
T ss_pred ecCCcceEEecCC-CCc-----ccchhhhcccCCEEeecC
Confidence 4999999998443 444 556799999999998864
No 108
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=22.53 E-value=1.4e+02 Score=22.29 Aligned_cols=29 Identities=17% Similarity=0.229 Sum_probs=17.6
Q ss_pred eecccccCCEEEEeeCC-----ceEEEEEEEEEE
Q psy16497 26 YAERVRVNDSIIVHKNG-----KAYVERVTRLEN 54 (143)
Q Consensus 26 fA~~v~~Gd~v~v~~~~-----~l~~~rV~~V~~ 54 (143)
-..++++||.|++.+-+ ++..-+|++|+.
T Consensus 90 ~~~~i~~GD~V~TSG~~~~fP~Gi~VG~V~~v~~ 123 (152)
T PF04085_consen 90 KDADIKKGDIVVTSGLGGIFPPGIPVGTVSSVEP 123 (152)
T ss_dssp TTS---TT-EEEEE-TTSSS-CCEEEEEEEEEEC
T ss_pred CCCCCCCCCEEEECCCCCcCCCCCEEEEEEEEEe
Confidence 56789999999998753 467777777764
No 109
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=22.44 E-value=1.7e+02 Score=19.19 Aligned_cols=28 Identities=14% Similarity=0.139 Sum_probs=20.1
Q ss_pred eeeecccccCCEEEEeeCCceEEEEEEEEE
Q psy16497 24 YTYAERVRVNDSIIVHKNGKAYVERVTRLE 53 (143)
Q Consensus 24 ~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~ 53 (143)
.+.+..+++||.|++...+ ...+|.+|.
T Consensus 20 ~v~~G~i~~G~~v~i~P~~--~~~~V~si~ 47 (82)
T cd04089 20 KVESGTIKKGDKLLVMPNK--TQVEVLSIY 47 (82)
T ss_pred EEeeeEEecCCEEEEeCCC--cEEEEEEEE
Confidence 4678889999999887654 345566654
No 110
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=22.22 E-value=1.1e+02 Score=25.34 Aligned_cols=29 Identities=17% Similarity=0.157 Sum_probs=22.2
Q ss_pred ecccccCCEEEEeeCC-----ceEEEEEEEEEEE
Q psy16497 27 AERVRVNDSIIVHKNG-----KAYVERVTRLENV 55 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~~-----~l~~~rV~~V~~~ 55 (143)
-.++++||.|++.+-+ ++...+|++|...
T Consensus 213 ~~~v~~GD~VvTSGlgg~fP~Gl~VG~V~~v~~~ 246 (283)
T TIGR00219 213 EKDIKKGDLIVTSGLGGRFPEGYPIGVVTSVHID 246 (283)
T ss_pred CCCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeC
Confidence 4689999999998853 4777788887653
No 111
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=22.03 E-value=1.2e+02 Score=21.61 Aligned_cols=25 Identities=16% Similarity=0.298 Sum_probs=17.1
Q ss_pred eecccccCCEEEEeeCCceEEEEEEEEE
Q psy16497 26 YAERVRVNDSIIVHKNGKAYVERVTRLE 53 (143)
Q Consensus 26 fA~~v~~Gd~v~v~~~~~l~~~rV~~V~ 53 (143)
.=+++++||.|.+.++ ...+|++|.
T Consensus 40 ml~sL~kGD~VvT~gG---i~G~V~~v~ 64 (97)
T COG1862 40 LLNSLKKGDEVVTIGG---IVGTVTKVG 64 (97)
T ss_pred HHHhccCCCEEEEcCC---eEEEEEEEe
Confidence 4568999999988875 234455444
No 112
>TIGR03627 arch_S9P archaeal ribosomal protein S9P. This model describes exclusively the archaeal ribosomal protein S9P. Homologous eukaryotic and bacterial ribosomal proteins are excluded from this model.
Probab=21.98 E-value=69 Score=23.93 Aligned_cols=31 Identities=19% Similarity=0.237 Sum_probs=25.2
Q ss_pred ceeEEEccEEEeeeeeeccchhhHHHHHHHHHHH
Q psy16497 67 SGTIVVNNVFASCYAVIDNQFLAHLSFIPVRLYH 100 (143)
Q Consensus 67 ~GtivVd~V~aSCya~i~~h~Lah~af~PlR~~~ 100 (143)
+|.|.|||.-...| .+......++.|+.+..
T Consensus 21 ~G~i~VNg~~~~~y---~~~~~r~~i~~Pl~~~~ 51 (130)
T TIGR03627 21 KGRVRINGVPVELY---PPELARLKIMEPLILAG 51 (130)
T ss_pred ceEEEECCEeHHHh---CCHHHHHHHHHHHHHHh
Confidence 59999999987776 35667778899999885
No 113
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=21.96 E-value=53 Score=24.37 Aligned_cols=17 Identities=12% Similarity=0.190 Sum_probs=14.3
Q ss_pred eeeecccccCCEEEEee
Q psy16497 24 YTYAERVRVNDSIIVHK 40 (143)
Q Consensus 24 ~vfA~~v~~Gd~v~v~~ 40 (143)
+-||.++++||+|.+.+
T Consensus 71 ~~~ar~lK~GdfV~L~N 87 (123)
T cd04498 71 VELAKSLKPGDFVRIYN 87 (123)
T ss_pred HHHHhhCCCCCEEEEEE
Confidence 34899999999998876
No 114
>PF14001 YdfZ: YdfZ protein
Probab=21.75 E-value=51 Score=21.93 Aligned_cols=8 Identities=38% Similarity=0.792 Sum_probs=4.9
Q ss_pred eeeeeecC
Q psy16497 57 QTGVYAPL 64 (143)
Q Consensus 57 ~~G~yAPl 64 (143)
..|.|+|+
T Consensus 51 ~~g~f~P~ 58 (64)
T PF14001_consen 51 CEGRFAPV 58 (64)
T ss_pred CCceEcch
Confidence 45667775
No 115
>PRK00132 rpsI 30S ribosomal protein S9; Reviewed
Probab=21.47 E-value=68 Score=23.96 Aligned_cols=33 Identities=27% Similarity=0.299 Sum_probs=26.5
Q ss_pred ceeEEEccEEEeeeeeeccchhhHHHHHHHHHHHH
Q psy16497 67 SGTIVVNNVFASCYAVIDNQFLAHLSFIPVRLYHS 101 (143)
Q Consensus 67 ~GtivVd~V~aSCya~i~~h~Lah~af~PlR~~~~ 101 (143)
+|.|.|||.-...| +.+..+..-++.|+.+...
T Consensus 25 ~G~i~INg~~~~~y--f~~~~~r~~i~~Pl~~~~~ 57 (130)
T PRK00132 25 SGKITVNGRDLEEY--FPRETLRMVVRQPLELTET 57 (130)
T ss_pred ccEEEECCEeHHHH--cCCHHHHHHHHHHHHHhCc
Confidence 59999999998877 4566677788999988764
No 116
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=21.11 E-value=2.1e+02 Score=24.96 Aligned_cols=35 Identities=14% Similarity=0.318 Sum_probs=27.2
Q ss_pred cCCcceeeecccccCCEEEEeeC-CceEEEEEEEEE
Q psy16497 19 LSDIEYTYAERVRVNDSIIVHKN-GKAYVERVTRLE 53 (143)
Q Consensus 19 ~~~~~~vfA~~v~~Gd~v~v~~~-~~l~~~rV~~V~ 53 (143)
.|+.+..|-++++.||-|++.+. |.-|.+-|=++.
T Consensus 270 vPg~kTkYLaEL~aGDeV~iVD~dGr~R~aiVGRvK 305 (376)
T COG1465 270 VPGGKTKYLAELKAGDEVLIVDFDGRTRSAIVGRVK 305 (376)
T ss_pred cCCCceEEhhhhcCCCeEEEEecCCceeEEEEEEEE
Confidence 46788999999999999999986 455666555554
No 117
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=20.97 E-value=1.7e+02 Score=18.23 Aligned_cols=31 Identities=23% Similarity=0.345 Sum_probs=21.1
Q ss_pred eeeecccccCCEEEEeeC--C-ceEEEEEEEEEE
Q psy16497 24 YTYAERVRVNDSIIVHKN--G-KAYVERVTRLEN 54 (143)
Q Consensus 24 ~vfA~~v~~Gd~v~v~~~--~-~l~~~rV~~V~~ 54 (143)
-++...+++||.|.+... + +....+|.++..
T Consensus 7 rV~sG~l~~gd~v~~~~~~~~~~~~~~~I~~i~~ 40 (74)
T PF03144_consen 7 RVYSGTLKKGDKVRVLPNGTGKKGQVVKIKSIFM 40 (74)
T ss_dssp EEEESEEETTEEEEEESTTTTEECEEEEEEEEEE
T ss_pred EEEEeEEcCCCEEEECccCCcceeeeeecccccc
Confidence 478999999999999442 1 234566666543
No 118
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=20.91 E-value=1.2e+02 Score=21.97 Aligned_cols=16 Identities=13% Similarity=0.212 Sum_probs=13.9
Q ss_pred eecccccCCEEEEeeC
Q psy16497 26 YAERVRVNDSIIVHKN 41 (143)
Q Consensus 26 fA~~v~~Gd~v~v~~~ 41 (143)
+-+++++||.|.+.+|
T Consensus 35 m~~~Lk~GD~VvT~gG 50 (109)
T PRK05886 35 LHESLQPGDRVHTTSG 50 (109)
T ss_pred HHHhcCCCCEEEECCC
Confidence 5688999999999876
No 119
>TIGR01116 ATPase-IIA1_Ca sarco/endoplasmic reticulum calcium-translocating P-type ATPase. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1, the latter of which is modelled by TIGR01522.
Probab=20.50 E-value=1.5e+02 Score=28.70 Aligned_cols=19 Identities=11% Similarity=0.022 Sum_probs=16.9
Q ss_pred ceeeecccccCCEEEEeeC
Q psy16497 23 EYTYAERVRVNDSIIVHKN 41 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~ 41 (143)
..+-++++.+||.|++..+
T Consensus 84 ~~I~~~~Lv~GDiv~l~~G 102 (917)
T TIGR01116 84 SVIKAKDLVPGDIVELAVG 102 (917)
T ss_pred EEEEHHHCCCCCEEEECCC
Confidence 6789999999999999776
No 120
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=20.45 E-value=1.5e+02 Score=23.31 Aligned_cols=28 Identities=29% Similarity=0.464 Sum_probs=19.5
Q ss_pred ecccccCCEEEEeeC-CceEEEEEEEEEE
Q psy16497 27 AERVRVNDSIIVHKN-GKAYVERVTRLEN 54 (143)
Q Consensus 27 A~~v~~Gd~v~v~~~-~~l~~~rV~~V~~ 54 (143)
.-+.++||.|-+.++ +....++|+.+++
T Consensus 14 VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~ 42 (225)
T PF04452_consen 14 VLRLKEGDSIEVFDGDGGEYRAEITEISK 42 (225)
T ss_dssp TST--TT-EEEEEESSSEEEEEEEEEEES
T ss_pred hcCCCCCCEEEEEECCCCEEEEEEEECcC
Confidence 357899999999995 5677888887764
No 121
>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=20.25 E-value=2.6e+02 Score=18.80 Aligned_cols=34 Identities=12% Similarity=0.104 Sum_probs=23.0
Q ss_pred ceeeecccccCCEEEEeeC-------CceEEEEEEEEEEEE
Q psy16497 23 EYTYAERVRVNDSIIVHKN-------GKAYVERVTRLENVI 56 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~-------~~l~~~rV~~V~~~~ 56 (143)
--||...+++||.|++.+. +..+..||.++....
T Consensus 21 ~RV~sGtl~~g~~v~~~~~~~~~~~~~~~~~~~i~~l~~~~ 61 (94)
T cd04090 21 GRIYSGTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWILG 61 (94)
T ss_pred EEEeeCeEcCCCEEEEECCCCCCccCCcEEEEEEeEEEEec
Confidence 4579999999999988542 124556666665443
No 122
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=20.14 E-value=1.4e+02 Score=24.80 Aligned_cols=31 Identities=13% Similarity=0.083 Sum_probs=23.2
Q ss_pred eecccccCCEEEEeeCC-----ceEEEEEEEEEEEE
Q psy16497 26 YAERVRVNDSIIVHKNG-----KAYVERVTRLENVI 56 (143)
Q Consensus 26 fA~~v~~Gd~v~v~~~~-----~l~~~rV~~V~~~~ 56 (143)
-..++++||.|.+.+-+ ++-..+|++|....
T Consensus 209 ~~~~i~~GD~vvTSGlgg~fP~Gl~Vg~V~~v~~~~ 244 (284)
T COG1792 209 PNSDIKEGDLVVTSGLGGVFPAGLPVGEVSSVKLDD 244 (284)
T ss_pred CCCCccCCCEEEecCCCCcCCCCcEEEEEEEEEeCC
Confidence 57899999988776632 47777888887654
No 123
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=20.09 E-value=1.2e+02 Score=22.32 Aligned_cols=29 Identities=7% Similarity=0.186 Sum_probs=21.5
Q ss_pred ceeeecccccCCEEEEeeCCceEEEEEEEEEEE
Q psy16497 23 EYTYAERVRVNDSIIVHKNGKAYVERVTRLENV 55 (143)
Q Consensus 23 ~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~ 55 (143)
.++-|+++|.|.++.+.+ +|-+|++++..
T Consensus 5 ~~~~~~~irkG~~i~~~g----~p~~V~e~~~~ 33 (130)
T TIGR00037 5 KQVQVSALRVGGYVVIDG----RPCKIVDISTS 33 (130)
T ss_pred eeccHHHccCCCEEEECC----EEEEEEEEEec
Confidence 457899999999998754 46677766544
No 124
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=20.04 E-value=1.2e+02 Score=28.49 Aligned_cols=47 Identities=15% Similarity=0.263 Sum_probs=30.8
Q ss_pred ccCCcceeeecccccCCEEEEeeCCceEEEEEEEEEEEEeeeeeecCC
Q psy16497 18 ILSDIEYTYAERVRVNDSIIVHKNGKAYVERVTRLENVIQTGVYAPLT 65 (143)
Q Consensus 18 ~~~~~~~vfA~~v~~Gd~v~v~~~~~l~~~rV~~V~~~~~~G~yAPlT 65 (143)
.+++...+-..++++||.|.|.-.|++.|. |++|-.....|-|.+-+
T Consensus 353 TLhN~~~I~~~di~iGD~V~V~raGdVIP~-I~~v~~~~r~~~~~~P~ 399 (669)
T PRK14350 353 SLHNQDYIDSIGLNVGDVVKISRRGDVIPA-VELVIEKLSVGFFKIPD 399 (669)
T ss_pred ccCCHHHHHHcCCCCCCEEEEEecCCCCCc-eeeecccccCCCCCCCC
Confidence 356668888899999999999888777774 33433322223354433
Done!