Query psy5454
Match_columns 129
No_of_seqs 107 out of 580
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 17:57:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5454.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5454hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0245|consensus 99.9 4.4E-24 9.5E-29 190.9 9.8 96 4-106 451-548 (1221)
2 PF00498 FHA: FHA domain; Int 99.6 1.6E-15 3.5E-20 96.5 8.8 65 35-105 1-68 (68)
3 KOG1892|consensus 99.6 1.5E-15 3.3E-20 136.1 7.2 94 6-107 355-448 (1629)
4 KOG0241|consensus 99.6 3E-15 6.5E-20 134.3 6.3 109 1-120 439-548 (1714)
5 cd00060 FHA Forkhead associate 99.4 2.4E-12 5.3E-17 86.0 11.6 87 8-106 2-93 (102)
6 TIGR03354 VI_FHA type VI secre 99.4 7.2E-12 1.6E-16 104.9 10.9 88 10-106 3-96 (396)
7 COG1716 FOG: FHA domain [Signa 99.2 1.3E-10 2.9E-15 86.4 10.9 70 34-109 90-159 (191)
8 PLN02927 antheraxanthin epoxid 99.2 1.7E-10 3.6E-15 102.1 9.5 97 8-110 534-640 (668)
9 COG3456 Predicted component of 99.1 1.7E-10 3.7E-15 96.7 7.3 88 10-106 5-97 (430)
10 smart00240 FHA Forkhead associ 99.1 3.3E-10 7.2E-15 68.0 6.0 51 35-90 1-52 (52)
11 KOG1882|consensus 97.6 0.00012 2.6E-09 58.3 5.6 71 34-109 195-280 (293)
12 TIGR02500 type_III_yscD type I 97.4 0.0013 2.8E-08 55.4 9.0 73 26-105 13-87 (410)
13 KOG0615|consensus 96.5 0.0039 8.4E-08 53.2 4.7 73 29-108 60-149 (475)
14 KOG2293|consensus 96.3 0.011 2.4E-07 51.5 6.2 76 26-105 441-523 (547)
15 KOG1881|consensus 95.5 0.007 1.5E-07 54.5 1.7 64 35-104 179-255 (793)
16 KOG1880|consensus 94.6 0.039 8.5E-07 45.3 3.5 91 6-106 16-110 (337)
17 PRK01777 hypothetical protein; 94.2 0.047 1E-06 37.4 2.7 27 80-106 49-75 (95)
18 TIGR01663 PNK-3'Pase polynucle 94.0 0.17 3.6E-06 44.4 6.4 71 27-106 26-100 (526)
19 TIGR02988 YaaA_near_RecF S4 do 93.6 0.083 1.8E-06 32.5 2.8 25 80-104 33-58 (59)
20 cd00165 S4 S4/Hsp/ tRNA synthe 92.9 0.25 5.4E-06 29.5 4.2 28 80-107 25-53 (70)
21 smart00363 S4 S4 RNA-binding d 92.6 0.21 4.5E-06 29.0 3.5 27 80-106 25-52 (60)
22 PF14451 Ub-Mut7C: Mut7-C ubiq 92.2 0.19 4.1E-06 33.5 3.2 31 79-109 48-78 (81)
23 PRK06437 hypothetical protein; 92.1 0.23 5E-06 31.6 3.4 27 80-106 36-62 (67)
24 cd00754 MoaD Ubiquitin domain 91.8 0.18 4E-06 32.1 2.8 27 80-106 49-75 (80)
25 COG2501 S4-like RNA binding pr 91.3 0.21 4.6E-06 32.8 2.6 27 80-106 36-63 (73)
26 cd00565 ThiS ThiaminS ubiquiti 90.8 0.31 6.8E-06 30.4 3.0 27 80-106 30-60 (65)
27 PF01479 S4: S4 domain; Inter 90.4 0.17 3.7E-06 29.5 1.5 23 80-102 25-48 (48)
28 PRK11507 ribosome-associated p 88.8 0.5 1.1E-05 30.8 2.8 27 80-106 36-63 (70)
29 PRK08364 sulfur carrier protei 88.8 0.47 1E-05 30.2 2.7 27 80-106 39-65 (70)
30 PF02597 ThiS: ThiS family; I 86.9 0.34 7.3E-06 30.6 1.2 28 79-106 42-72 (77)
31 COG2104 ThiS Sulfur transfer p 86.0 0.93 2E-05 29.2 2.8 27 80-106 33-63 (68)
32 PRK06488 sulfur carrier protei 85.6 1 2.2E-05 28.0 2.9 25 82-106 32-60 (65)
33 TIGR01683 thiS thiamine biosyn 85.2 1.3 2.8E-05 27.5 3.2 27 80-106 29-59 (64)
34 TIGR01682 moaD molybdopterin c 85.0 0.98 2.1E-05 29.2 2.6 27 80-106 49-75 (80)
35 PRK06944 sulfur carrier protei 84.9 1.2 2.6E-05 27.5 3.0 25 82-106 32-60 (65)
36 PRK05659 sulfur carrier protei 84.7 1.3 2.7E-05 27.5 3.0 25 82-106 33-61 (66)
37 PLN02799 Molybdopterin synthas 84.5 1.1 2.5E-05 28.9 2.8 26 81-106 52-77 (82)
38 TIGR01687 moaD_arch MoaD famil 84.5 1 2.2E-05 29.5 2.6 26 81-106 56-83 (88)
39 PF13275 S4_2: S4 domain; PDB: 83.6 0.56 1.2E-05 30.1 1.0 25 81-105 33-58 (65)
40 COG0564 RluA Pseudouridylate s 83.3 2.5 5.4E-05 34.2 4.9 32 80-111 36-67 (289)
41 COG1188 Ribosome-associated he 82.8 1.5 3.2E-05 30.5 2.9 28 79-106 32-59 (100)
42 PRK07440 hypothetical protein; 81.3 2.4 5.2E-05 27.1 3.3 27 80-106 35-65 (70)
43 PRK07696 sulfur carrier protei 81.2 2.1 4.7E-05 27.0 3.0 27 80-106 32-62 (67)
44 PRK15367 type III secretion sy 81.1 7 0.00015 33.3 6.9 67 26-103 17-83 (395)
45 cd01666 TGS_DRG_C TGS_DRG_C: 81.0 1.4 3.1E-05 28.8 2.2 21 85-105 54-74 (75)
46 cd01764 Urm1 Urm1-like ubuitin 80.9 1.6 3.4E-05 29.6 2.4 27 80-106 59-89 (94)
47 PF14478 DUF4430: Domain of un 80.2 1.6 3.5E-05 27.5 2.2 25 80-104 40-67 (68)
48 PRK10626 hypothetical protein; 79.1 2.4 5.2E-05 33.8 3.3 41 48-91 23-64 (239)
49 PRK11130 moaD molybdopterin sy 78.7 2.2 4.8E-05 27.7 2.6 25 82-106 52-76 (81)
50 PF02824 TGS: TGS domain; Int 78.1 1.3 2.8E-05 27.4 1.3 25 82-106 36-60 (60)
51 PRK06083 sulfur carrier protei 77.5 3.1 6.8E-05 27.7 3.1 26 81-106 50-79 (84)
52 PF14453 ThiS-like: ThiS-like 77.0 2.5 5.5E-05 26.4 2.3 25 82-106 31-55 (57)
53 cd01668 TGS_RelA_SpoT TGS_RelA 74.4 4.1 9E-05 24.0 2.8 24 82-105 36-59 (60)
54 PRK08053 sulfur carrier protei 73.6 4.7 0.0001 25.1 3.0 26 81-106 32-61 (66)
55 smart00797 AHS2 Allophanate hy 73.5 13 0.00028 30.1 6.2 44 64-108 39-84 (280)
56 PF11101 DUF2884: Protein of u 70.3 5.7 0.00012 31.1 3.4 34 55-91 8-42 (229)
57 PRK11025 23S rRNA pseudouridyl 70.0 7.5 0.00016 31.5 4.1 27 80-106 44-70 (317)
58 TIGR00691 spoT_relA (p)ppGpp s 68.4 4.8 0.0001 36.4 3.0 53 58-110 357-425 (683)
59 TIGR01017 rpsD_bact ribosomal 67.2 6 0.00013 30.3 2.9 28 80-107 114-142 (200)
60 cd01669 TGS_Ygr210_C TGS_Ygr21 65.7 6.8 0.00015 25.6 2.5 22 85-106 55-76 (76)
61 PF02626 AHS2: Allophanate hyd 65.1 13 0.00028 29.9 4.6 30 78-107 52-83 (271)
62 CHL00113 rps4 ribosomal protei 64.5 7.9 0.00017 29.9 3.1 27 80-106 113-140 (201)
63 PRK05863 sulfur carrier protei 64.2 6.5 0.00014 24.5 2.2 26 80-106 31-60 (65)
64 PRK11092 bifunctional (p)ppGpp 63.7 7 0.00015 35.6 3.1 30 81-110 422-451 (702)
65 COG1984 DUR1 Allophanate hydro 63.6 31 0.00067 28.6 6.5 51 50-109 53-106 (314)
66 PRK05327 rpsD 30S ribosomal pr 63.5 7.6 0.00017 29.8 2.9 27 80-106 117-144 (203)
67 PF03658 Ub-RnfH: RnfH family 61.8 4.3 9.2E-05 27.3 1.0 28 79-106 45-72 (84)
68 TIGR03069 PS_II_S4 photosystem 61.6 9 0.0002 30.5 3.0 28 80-107 207-235 (257)
69 PRK11180 rluD 23S rRNA pseudou 61.4 14 0.0003 30.1 4.1 28 80-107 42-70 (325)
70 PRK10872 relA (p)ppGpp synthet 61.0 7.9 0.00017 35.5 2.9 54 57-110 400-469 (743)
71 PRK10839 16S rRNA pseudouridyl 59.7 9.7 0.00021 29.3 2.9 27 80-106 24-51 (232)
72 cd01616 TGS The TGS domain, na 58.6 14 0.00031 20.8 2.9 23 83-105 37-59 (60)
73 PF12733 Cadherin-like: Cadher 58.5 33 0.00071 22.0 4.9 33 72-104 29-68 (88)
74 PLN00051 RNA-binding S4 domain 58.3 11 0.00024 30.3 3.0 27 80-106 215-242 (267)
75 COG0317 SpoT Guanosine polypho 57.8 12 0.00025 34.3 3.4 29 81-109 423-451 (701)
76 TIGR00005 rluA_subfam pseudour 57.8 17 0.00037 28.9 4.0 26 80-105 30-56 (299)
77 PRK10475 23S rRNA pseudouridin 56.7 11 0.00024 30.6 2.8 26 80-105 30-55 (290)
78 TIGR00724 urea_amlyse_rel biot 56.5 33 0.00071 28.3 5.5 45 63-108 60-107 (314)
79 PRK10348 ribosome-associated h 54.8 15 0.00033 26.6 3.0 26 80-105 33-58 (133)
80 PF08308 PEGA: PEGA domain; I 52.5 17 0.00038 22.4 2.7 22 70-91 2-23 (71)
81 COG0522 RpsD Ribosomal protein 50.6 20 0.00043 27.8 3.2 26 80-105 118-144 (205)
82 cd02558 PSRA_1 PSRA_1: Pseudou 46.5 20 0.00043 28.0 2.7 23 84-106 5-27 (246)
83 KOG3517|consensus 45.8 7.6 0.00016 31.5 0.3 17 81-97 12-28 (334)
84 COG2914 Uncharacterized protei 45.5 18 0.0004 25.0 2.1 26 81-106 50-75 (99)
85 cd00050 MH2 MH2 domain; C term 44.4 37 0.00081 25.8 3.8 41 63-104 69-117 (176)
86 PRK11840 bifunctional sulfur c 42.6 27 0.0006 29.0 3.1 27 80-106 31-61 (326)
87 cd06919 Asp_decarbox Aspartate 41.1 31 0.00068 24.4 2.8 63 54-119 33-106 (111)
88 PF05726 Pirin_C: Pirin C-term 39.7 31 0.00067 23.3 2.5 44 58-102 40-84 (104)
89 TIGR02227 sigpep_I_bact signal 37.8 1.2E+02 0.0026 22.0 5.6 22 68-93 78-99 (163)
90 PF02080 TrkA_C: TrkA-C domain 35.4 15 0.00034 22.3 0.4 22 92-113 44-65 (71)
91 PF02563 Poly_export: Polysacc 31.3 60 0.0013 20.8 2.8 35 92-126 9-43 (82)
92 TIGR02712 urea_carbox urea car 31.1 1.5E+02 0.0033 28.8 6.4 31 78-108 523-555 (1201)
93 COG3450 Predicted enzyme of th 30.8 1.1E+02 0.0025 21.6 4.3 26 69-106 71-96 (116)
94 TIGR00478 tly hemolysin TlyA f 30.6 51 0.0011 25.8 2.7 27 80-106 24-51 (228)
95 KOG3862|consensus 30.3 24 0.00053 29.0 0.9 12 81-92 17-28 (327)
96 cd00248 Mth938-like Mth938-lik 29.4 71 0.0015 21.9 3.0 20 80-99 7-26 (109)
97 PRK05449 aspartate alpha-decar 29.4 59 0.0013 23.5 2.6 69 54-125 34-115 (126)
98 smart00357 CSP Cold shock prot 28.7 1.2E+02 0.0027 17.4 3.9 40 69-108 9-49 (64)
99 PF07908 D-aminoacyl_C: D-amin 28.6 37 0.00081 20.0 1.3 11 81-91 21-31 (48)
100 PF07497 Rho_RNA_bind: Rho ter 28.5 55 0.0012 21.6 2.2 31 79-110 27-59 (78)
101 TIGR00223 panD L-aspartate-alp 28.4 63 0.0014 23.4 2.6 69 54-125 34-115 (126)
102 COG5131 URM1 Ubiquitin-like pr 28.0 53 0.0011 22.5 2.1 27 80-106 61-91 (96)
103 cd01716 Hfq Hfq, an abundant, 27.3 67 0.0014 20.2 2.3 29 83-111 17-45 (61)
104 cd05560 Xcc1710_like Xcc1710_l 26.6 89 0.0019 21.5 3.1 24 80-103 7-30 (109)
105 TIGR02771 TraF_Ti conjugative 26.5 2.2E+02 0.0048 21.1 5.5 22 68-93 92-113 (171)
106 COG2302 Uncharacterized conser 26.4 64 0.0014 26.0 2.6 25 80-104 204-229 (257)
107 PF08531 Bac_rhamnosid_N: Alph 25.9 59 0.0013 23.9 2.2 28 70-99 6-33 (172)
108 cd04458 CSP_CDS Cold-Shock Pro 25.5 73 0.0016 19.2 2.3 41 69-109 12-54 (65)
109 PRK10354 RNA chaperone/anti-te 24.8 1.1E+02 0.0023 19.3 3.1 41 69-109 16-58 (70)
110 PRK13884 conjugal transfer pep 24.7 2.5E+02 0.0053 21.0 5.5 20 68-91 96-115 (178)
111 PF03166 MH2: MH2 domain; Int 24.0 59 0.0013 24.3 2.0 26 63-89 68-94 (181)
112 PRK06788 flagellar motor switc 23.3 1.2E+02 0.0027 21.5 3.4 48 69-116 58-110 (119)
113 TIGR02383 Hfq RNA chaperone Hf 23.0 79 0.0017 19.9 2.1 28 84-111 22-49 (61)
114 PF00292 PAX: 'Paired box' dom 22.7 33 0.00072 24.7 0.3 12 81-92 9-20 (125)
115 PRK00395 hfq RNA-binding prote 22.6 79 0.0017 21.0 2.1 28 84-111 26-53 (79)
116 smart00524 DWB Domain B in dwa 21.9 3.3E+02 0.0071 20.5 5.6 41 63-104 64-112 (171)
117 COG0355 AtpC F0F1-type ATP syn 21.7 1.2E+02 0.0026 21.9 3.1 34 57-90 33-70 (135)
118 PF09014 Sushi_2: Beta-2-glyco 21.6 63 0.0014 21.8 1.5 26 80-105 10-39 (85)
119 COG1977 MoaD Molybdopterin con 21.5 96 0.0021 20.2 2.4 19 88-106 61-79 (84)
120 TIGR02480 fliN flagellar motor 21.3 1.6E+02 0.0034 18.8 3.4 36 69-104 32-68 (77)
121 PF15057 DUF4537: Domain of un 21.0 1.7E+02 0.0038 20.5 3.8 43 59-106 24-66 (124)
122 PF09138 Urm1: Urm1 (Ubiquitin 20.6 55 0.0012 22.4 1.1 26 81-106 62-91 (96)
123 PF06241 DUF1012: Protein of u 20.2 1E+02 0.0022 24.0 2.5 28 81-108 120-150 (206)
124 PRK09890 cold shock protein Cs 20.2 2.2E+02 0.0048 17.8 3.8 42 69-110 16-59 (70)
125 cd05126 Mth938 Mth938 domain. 20.0 1.2E+02 0.0026 21.2 2.7 20 80-99 7-26 (117)
No 1
>KOG0245|consensus
Probab=99.90 E-value=4.4e-24 Score=190.86 Aligned_cols=96 Identities=28% Similarity=0.316 Sum_probs=90.4
Q ss_pred CCceeEEEEecCCCCCCCCCCcEEEEcCCCceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEcCCE--EEEEeCCCCC
Q psy5454 4 ELIKSSLLLKNYNGSEITSGSPKRHRLHPNVTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHTEGI--VTVTPCSREA 81 (129)
Q Consensus 4 ~~~~PhLvnln~dp~ls~~~~~~~~~L~~~~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~~g~--v~L~p~ss~~ 81 (129)
.++.|||||||+||++| + |++|+|+.|.|.|||.++ ++.+||+|+|..|..+||.|.+.+|. |+|.|+ +++
T Consensus 451 ~kk~phLVNLneDPllS--e-~LlY~ikeG~TrVG~~~a---~~~~DI~LsG~~I~~qHC~i~~~~g~~~vtl~p~-e~a 523 (1221)
T KOG0245|consen 451 GKKTPHLVNLNEDPLLS--E-CLLYYIKEGETRVGREDA---SSRQDIVLSGQLIREQHCSIRNEGGNDVVTLEPC-EDA 523 (1221)
T ss_pred CccCcceeccCCCchhh--c-cEEEEeccCceecCCCCc---ccCCceEecchhhhhhceEEEecCCCceEEeccC-Ccc
Confidence 35899999999999999 9 999999999999999986 46799999999999999999998776 999998 799
Q ss_pred ceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 82 ETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 82 ~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
.|||||++|.+++.|+|||||.+|-
T Consensus 524 etyVNGk~v~ep~qL~~GdRiilG~ 548 (1221)
T KOG0245|consen 524 ETYVNGKLVTEPTQLRSGDRIILGG 548 (1221)
T ss_pred ceeEccEEcCCcceeccCCEEEEcC
Confidence 9999999999999999999999987
No 2
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=99.64 E-value=1.6e-15 Score=96.46 Aligned_cols=65 Identities=23% Similarity=0.250 Sum_probs=58.1
Q ss_pred eEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEcCC-EEEEEeCCCCCceEEcCEEcce--eEEcCCCCEEEEe
Q psy5454 35 TEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHTEG-IVTVTPCSREAETFVNGQRIFE--TTILQVVVAASAV 105 (129)
Q Consensus 35 t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~~g-~v~L~p~ss~~~t~VNG~~I~~--~~~L~~GDrI~~~ 105 (129)
.+|||.+ .+||+|.++.|++.||.|...++ .++|+++++.++|||||+++.. +..|++||+|.||
T Consensus 1 ~~iGR~~------~~di~l~~~~iSr~Ha~i~~~~~~~~~i~d~~s~ngt~vng~~l~~~~~~~L~~gd~i~~G 68 (68)
T PF00498_consen 1 VTIGRSP------DCDIVLPDPSISRRHARISFDDDGQFYIEDLGSTNGTFVNGQRLGPGEPVPLKDGDIIRFG 68 (68)
T ss_dssp EEEESST------TSSEEETSTTSSTTSEEEEEETTEEEEEEESSSSS-EEETTEEESSTSEEEE-TTEEEEET
T ss_pred CEEcCCC------CCCEEECCHheeeeeeEEEEeceeeEEEEeCCCCCcEEECCEEcCCCCEEECCCCCEEEcC
Confidence 3689984 69999999999999999999988 9999999889999999999985 8999999999986
No 3
>KOG1892|consensus
Probab=99.60 E-value=1.5e-15 Score=136.15 Aligned_cols=94 Identities=51% Similarity=0.706 Sum_probs=87.9
Q ss_pred ceeEEEEecCCCCCCCCCCcEEEEcCCCceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEcCCEEEEEeCCCCCceEE
Q psy5454 6 IKSSLLLKNYNGSEITSGSPKRHRLHPNVTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHTEGIVTVTPCSREAETFV 85 (129)
Q Consensus 6 ~~PhLvnln~dp~ls~~~~~~~~~L~~~~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~~g~v~L~p~ss~~~t~V 85 (129)
+.|+|+.++.|+..+ ...|.|..++|.||.... .++.|+|.||+|.++||.|.+.+|+|+++|.+.++.|||
T Consensus 355 ~lPvLve~s~dG~~s----~~ri~L~~~vtEVGs~~~----~~~~iqLfGP~IqprHc~it~meGVvTvTP~~~DA~t~V 426 (1629)
T KOG1892|consen 355 KLPVLVELSPDGSDS----RKRIRLQLSVTEVGSEKL----DDNSIQLFGPGIQPRHCDITNMEGVVTVTPRSMDAETYV 426 (1629)
T ss_pred cCcEEEEEcCCCCCc----ceeEEeccCceecccccc----CCcceeeeCCCCCccccchhhccceEEecccccchhhhc
Confidence 579999999999998 478999999999999863 467999999999999999999999999999988999999
Q ss_pred cCEEcceeEEcCCCCEEEEecC
Q psy5454 86 NGQRIFETTILQVVVAASAVAE 107 (129)
Q Consensus 86 NG~~I~~~~~L~~GDrI~~~~~ 107 (129)
||+.|.+++.|++|+.|.||+-
T Consensus 427 nGh~isqttiL~~G~~v~fGa~ 448 (1629)
T KOG1892|consen 427 NGHRISQTTILQSGMKVQFGAS 448 (1629)
T ss_pred cceecchhhhhccCCEEEeccc
Confidence 9999999999999999999984
No 4
>KOG0241|consensus
Probab=99.57 E-value=3e-15 Score=134.31 Aligned_cols=109 Identities=28% Similarity=0.206 Sum_probs=94.0
Q ss_pred CCcCCceeEEEEecCCCCCCCCCCcEEEEcCCCceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEc-CCEEEEEeCCC
Q psy5454 1 MKSELIKSSLLLKNYNGSEITSGSPKRHRLHPNVTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHT-EGIVTVTPCSR 79 (129)
Q Consensus 1 ~~~~~~~PhLvnln~dp~ls~~~~~~~~~L~~~~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~-~g~v~L~p~ss 79 (129)
+|++..+.||+|+|.||.+. . .++|+++ +.++||... ..+|+++|.+|.|+||.+..+ +|.+++.|+ .
T Consensus 439 ikv~dDK~ylvnlnadP~ln--e-llvyyl~-~~tlig~~~------~~~i~l~glgi~p~h~vidI~~dg~l~~~p~-~ 507 (1714)
T KOG0241|consen 439 IKVGDDKCYLVNLNADPALN--E-LLVYYLK-DHTLIGLFK------SQDIQLSGLGIQPKHCVIDIESDGELRLTPL-L 507 (1714)
T ss_pred ccccccceEEEeccCCccHH--H-HHHHhhc-Cceeecccc------CcceeeecCcccCccceeeeccCCcEEeccc-c
Confidence 58899999999999999999 7 8999995 778899763 689999999999999999985 677999999 6
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEecCchhhhccccccCC
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAVAEKQQQSDNLKEIDN 120 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~~~~~~~~~~~~~~~~ 120 (129)
++.++|||..|.+++.|+|||||.+|..+-=.-+.||.-+.
T Consensus 508 ~~R~~VNGs~v~~~t~L~~GdRiLwGnnHFFrvN~PK~~~~ 548 (1714)
T KOG0241|consen 508 NARSCVNGSLVCSTTQLWHGDRILWGNNHFFRVNLPKRKRR 548 (1714)
T ss_pred cceeeecCceeccccccccCceEEecccceEEecCcccccc
Confidence 88999999999999999999999998866554455544433
No 5
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=99.45 E-value=2.4e-12 Score=86.02 Aligned_cols=87 Identities=26% Similarity=0.332 Sum_probs=74.8
Q ss_pred eEEEEecCCCCCCCCCCcEEEEcCC-CceEEcCCCCCCCCCcc-cEEEcCCCCCCCcEEEEEcC-CEEEEEeCCCCCceE
Q psy5454 8 SSLLLKNYNGSEITSGSPKRHRLHP-NVTEVGSDRASPYGQSQ-SLQLFGPNIQPRHCVIAHTE-GIVTVTPCSREAETF 84 (129)
Q Consensus 8 PhLvnln~dp~ls~~~~~~~~~L~~-~~t~IGr~~~~~~~~~~-dI~L~g~~I~~~Hc~I~~~~-g~v~L~p~ss~~~t~ 84 (129)
.+|..++.+ . . ...|.|.+ ....|||.. .+ +|.|.+..|++.||.|.... +.+++.+..+.+++|
T Consensus 2 ~~L~~~~~~--~---~-~~~~~l~~~~~~~iGr~~------~~~~i~l~~~~iS~~H~~i~~~~~~~~~~~~~~s~~g~~ 69 (102)
T cd00060 2 PRLVVLSGD--A---S-GRRYYLDPGGTYTIGRDS------DNCDIVLDDPSVSRRHAVIRYDGDGGVVLIDLGSTNGTF 69 (102)
T ss_pred eEEEEecCC--C---c-eeEEEECCCCeEEECcCC------CcCCEEcCCCCeeCcceEEEEcCCCCEEEEECCCCCCeE
Confidence 467777755 2 3 47888988 889999985 45 99999999999999999987 777777777889999
Q ss_pred EcCEEcc--eeEEcCCCCEEEEec
Q psy5454 85 VNGQRIF--ETTILQVVVAASAVA 106 (129)
Q Consensus 85 VNG~~I~--~~~~L~~GDrI~~~~ 106 (129)
|||+++. ++..|++||+|.++.
T Consensus 70 vn~~~~~~~~~~~l~~gd~i~ig~ 93 (102)
T cd00060 70 VNGQRVSPGEPVRLRDGDVIRLGN 93 (102)
T ss_pred ECCEECCCCCcEECCCCCEEEECC
Confidence 9999998 789999999999986
No 6
>TIGR03354 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc.
Probab=99.35 E-value=7.2e-12 Score=104.88 Aligned_cols=88 Identities=18% Similarity=0.175 Sum_probs=77.3
Q ss_pred EEEecCCCCCCCCCCcEEEEcCCCceEEcCCCCCCCCCcccEEEcCCC--CCCCcEEEEEcCCEEEEEeCCCCCceEEc-
Q psy5454 10 LLLKNYNGSEITSGSPKRHRLHPNVTEVGSDRASPYGQSQSLQLFGPN--IQPRHCVIAHTEGIVTVTPCSREAETFVN- 86 (129)
Q Consensus 10 Lvnln~dp~ls~~~~~~~~~L~~~~t~IGr~~~~~~~~~~dI~L~g~~--I~~~Hc~I~~~~g~v~L~p~ss~~~t~VN- 86 (129)
|..+|...+.+ |....|.+..+...|||.. .|+++|.++. |++.||.|...++.++|+|. |.++||||
T Consensus 3 L~v~n~~~l~~--g~~~~~~f~~~~~~IGR~~------~~d~~l~d~~~~VS~~Ha~I~~~~g~~~l~Dl-StNGT~VN~ 73 (396)
T TIGR03354 3 LTVLNAHQLTP--GIAAQKTFGTNGGTIGRSE------DCDWVLPDPERHVSGRHARIRYRDGAYLLTDL-STNGVFLNG 73 (396)
T ss_pred EEEeccccCCC--CcceEEEECCCCEEEecCC------CCCEEeCCCCCCcchhhcEEEEECCEEEEEEC-CCCCeEECC
Confidence 56677777776 5346899999999999985 6999999998 99999999999999999999 67899999
Q ss_pred -CEEcce--eEEcCCCCEEEEec
Q psy5454 87 -GQRIFE--TTILQVVVAASAVA 106 (129)
Q Consensus 87 -G~~I~~--~~~L~~GDrI~~~~ 106 (129)
|.+|.. +..|++||+|.||.
T Consensus 74 sg~~l~~~~~~~L~~GD~I~iG~ 96 (396)
T TIGR03354 74 SGSPLGRGNPVRLEQGDRLRLGD 96 (396)
T ss_pred CCCCCCCCCceEcCCCCEEEECC
Confidence 899974 78999999999987
No 7
>COG1716 FOG: FHA domain [Signal transduction mechanisms]
Probab=99.23 E-value=1.3e-10 Score=86.39 Aligned_cols=70 Identities=20% Similarity=0.240 Sum_probs=65.5
Q ss_pred ceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEcCCEEEEEeCCCCCceEEcCEEcceeEEcCCCCEEEEecCch
Q psy5454 34 VTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHTEGIVTVTPCSREAETFVNGQRIFETTILQVVVAASAVAEKQ 109 (129)
Q Consensus 34 ~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~~g~v~L~p~ss~~~t~VNG~~I~~~~~L~~GDrI~~~~~~~ 109 (129)
.+.+||.+ +++|++....|+++||.|...++.+++++++|.++|||||.++.....|++||.|.++....
T Consensus 90 ~~tigr~~------~~~i~~~~~~vSR~Ha~l~~~~~~~~~~d~~S~nGt~vn~~~v~~~~~l~~gd~i~i~~~~~ 159 (191)
T COG1716 90 VTTIGRDP------DNDIVLDDDVVSRRHAELRREGNEVFLEDLGSTNGTYVNGEKVRQRVLLQDGDVIRLGGTLA 159 (191)
T ss_pred eEEeccCC------CCCEEcCCCccccceEEEEEeCCceEEEECCCCcceEECCeEccCcEEcCCCCEEEECccce
Confidence 78999953 69999999999999999999999999999999999999999998889999999999988666
No 8
>PLN02927 antheraxanthin epoxidase/zeaxanthin epoxidase
Probab=99.15 E-value=1.7e-10 Score=102.14 Aligned_cols=97 Identities=11% Similarity=0.089 Sum_probs=75.1
Q ss_pred eEEEEecCCCCCCCCCCcEEEEc---CCCceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEcCCEEEEEeCCCCCceE
Q psy5454 8 SSLLLKNYNGSEITSGSPKRHRL---HPNVTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHTEGIVTVTPCSREAETF 84 (129)
Q Consensus 8 PhLvnln~dp~ls~~~~~~~~~L---~~~~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~~g~v~L~p~ss~~~t~ 84 (129)
.||+....+-..+ ..+.| .....+|||.+.... ....|+|..+.||..||.|..+++.++|+|++|++|||
T Consensus 534 w~l~~~~~~~~~~-----~~~~l~~~~~~p~~iG~~~~~~~-~~~~i~i~~~~vS~~Ha~i~~~~~~~~~~Dl~S~nGT~ 607 (668)
T PLN02927 534 WYLIPHGDDCCVS-----ETLCLTKDEDQPCIVGSEPDQDF-PGMRIVIPSSQVSKMHARVIYKDGAFFLMDLRSEHGTY 607 (668)
T ss_pred eEEEecCCCCccc-----ceeeeecCCCCCeEecCCCCcCC-CCceEEecCCccChhHeEEEEECCEEEEEECCCCCccE
Confidence 5666665444333 34555 445579999863211 12357999999999999999999999999999999999
Q ss_pred EcCEE---cc----eeEEcCCCCEEEEecCchh
Q psy5454 85 VNGQR---IF----ETTILQVVVAASAVAEKQQ 110 (129)
Q Consensus 85 VNG~~---I~----~~~~L~~GDrI~~~~~~~~ 110 (129)
|||.. +. .++.|++||.|.||..|+.
T Consensus 608 v~~~~~~r~~~~p~~~~~l~~~d~I~~g~~~~~ 640 (668)
T PLN02927 608 VTDNEGRRYRATPNFPARFRSSDIIEFGSDKKA 640 (668)
T ss_pred EeCCCCceEecCCCCceEeCCCCEEEeCCCcce
Confidence 97766 76 5899999999999997765
No 9
>COG3456 Predicted component of the type VI protein secretion system, contains a FHA domain [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]
Probab=99.11 E-value=1.7e-10 Score=96.66 Aligned_cols=88 Identities=22% Similarity=0.229 Sum_probs=76.6
Q ss_pred EEEecCCCCCCCCCCcEEEEcCCCceEEcCCCCCCCCCcccEEEcCC--CCCCCcEEEEEcCCEEEEEeCCCCCceEEcC
Q psy5454 10 LLLKNYNGSEITSGSPKRHRLHPNVTEVGSDRASPYGQSQSLQLFGP--NIQPRHCVIAHTEGIVTVTPCSREAETFVNG 87 (129)
Q Consensus 10 Lvnln~dp~ls~~~~~~~~~L~~~~t~IGr~~~~~~~~~~dI~L~g~--~I~~~Hc~I~~~~g~v~L~p~ss~~~t~VNG 87 (129)
|...|.+-+.+ |-+-.+.+..+.-.|||++ +||.+|.++ .|+++||.|.+.+|.++|+|.| +++++|||
T Consensus 5 L~vtn~~~l~s--G~~aq~~f~~~~g~IGrs~------dcdW~i~D~~~~VS~~Hc~I~~~dg~f~L~DtS-~g~l~VNg 75 (430)
T COG3456 5 LQVTNAQKLES--GKAAQKLFDRGGGVIGRSP------DCDWQIDDPERFVSKQHCTISYRDGGFCLTDTS-NGGLLVNG 75 (430)
T ss_pred EEEeccccCCC--chhhhhhhhcCCcccccCC------CCCccccCcccccchhheEEEecCCeEEEEecC-CCceeecc
Confidence 66778888888 7355688889999999985 699999776 8999999999999999999994 89999999
Q ss_pred EEcc--ee-EEcCCCCEEEEec
Q psy5454 88 QRIF--ET-TILQVVVAASAVA 106 (129)
Q Consensus 88 ~~I~--~~-~~L~~GDrI~~~~ 106 (129)
..+. +. .+|++||+|.||.
T Consensus 76 s~~~~g~~~~RLqqGd~i~iG~ 97 (430)
T COG3456 76 SDLPLGEGSARLQQGDEILIGR 97 (430)
T ss_pred cccCCCCCccccccCCEEeecc
Confidence 8776 44 8999999999876
No 10
>smart00240 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
Probab=99.09 E-value=3.3e-10 Score=68.01 Aligned_cols=51 Identities=33% Similarity=0.513 Sum_probs=44.9
Q ss_pred eEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEcCC-EEEEEeCCCCCceEEcCEEc
Q psy5454 35 TEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHTEG-IVTVTPCSREAETFVNGQRI 90 (129)
Q Consensus 35 t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~~g-~v~L~p~ss~~~t~VNG~~I 90 (129)
+.|||.. ..++|++.++.|++.||.|....+ .++|+|+++.++|||||++|
T Consensus 1 ~~iGr~~-----~~~~i~~~~~~vs~~H~~i~~~~~~~~~i~d~~s~~gt~vng~~v 52 (52)
T smart00240 1 VTIGRSS-----EDCDIQLPGPSISRRHAEIVYDGGGRFYLIDLGSTNGTFVNGKRI 52 (52)
T ss_pred CEeCCCC-----CCCCEEeCCCCcchhHcEEEECCCCeEEEEECCCCCCeeECCEEC
Confidence 4689984 268999999999999999999865 59999998899999999985
No 11
>KOG1882|consensus
Probab=97.63 E-value=0.00012 Score=58.31 Aligned_cols=71 Identities=17% Similarity=0.141 Sum_probs=57.0
Q ss_pred ceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEc-------CC------EEEEEeCCCCCceEEcCEEccee--EEcCC
Q psy5454 34 VTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHT-------EG------IVTVTPCSREAETFVNGQRIFET--TILQV 98 (129)
Q Consensus 34 ~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~-------~g------~v~L~p~ss~~~t~VNG~~I~~~--~~L~~ 98 (129)
.-++||.- --+||.+.-|.-+.+||+|.+. +| ..+|.+++|+++||+|.++|... ..|+.
T Consensus 195 ~yL~gRer-----kIaDi~idhpScSKQHaviQyR~v~~~r~dGt~grrvkpYiiDLgS~NgTfLNnk~IepqRYyEL~e 269 (293)
T KOG1882|consen 195 CYLDGRER-----KIADIPIDHPSCSKQHAVIQYRLVEFTRADGTVGRRVKPYIIDLGSGNGTFLNNKVIEPQRYYELRE 269 (293)
T ss_pred eeecCcee-----eeeccCCCCccccccceeeeeeecccccCCCccceeeeeEEEecCCCCcceecCcccCchheeeeec
Confidence 34677753 3578889999999999999872 22 57889999999999999999733 58999
Q ss_pred CCEEEEecCch
Q psy5454 99 VVAASAVAEKQ 109 (129)
Q Consensus 99 GDrI~~~~~~~ 109 (129)
+|.|.||-+-+
T Consensus 270 kDvlkfgfs~r 280 (293)
T KOG1882|consen 270 KDVLKFGFSSR 280 (293)
T ss_pred CceeeeccchH
Confidence 99999995443
No 12
>TIGR02500 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family. This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein.
Probab=97.37 E-value=0.0013 Score=55.38 Aligned_cols=73 Identities=16% Similarity=0.051 Sum_probs=58.2
Q ss_pred EEEEcCCCceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEcCCEEEEEeCCCCCceEEcC--EEcceeEEcCCCCEEE
Q psy5454 26 KRHRLHPNVTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHTEGIVTVTPCSREAETFVNG--QRIFETTILQVVVAAS 103 (129)
Q Consensus 26 ~~~~L~~~~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~~g~v~L~p~ss~~~t~VNG--~~I~~~~~L~~GDrI~ 103 (129)
..+.|..|..+||..+ ..+||+|.+++++++|+.|......+++.+. ..++.+|| .+..+...|..+-+|.
T Consensus 13 ~~~~L~~g~~~iG~~~-----~~~di~L~d~~~~~~h~~l~v~~~~~~l~~~--~~~~~~~g~~~~~~~g~~l~~~~~l~ 85 (410)
T TIGR02500 13 AELPLPEGNLVLGTDA-----ADCDIVLSDGGIAAVHVSLHVRLEGVTLAGA--VEPAWEEGGVLPDEEGTPLPSGTPLL 85 (410)
T ss_pred cEEECCCCceEeccCC-----CCcEEEeCCCCccchheEEEEcCceEEEecC--CcceeECCcccccCCCCccCCCCcee
Confidence 6789999999999432 3799999999999999999999888888865 34588999 6555666777776665
Q ss_pred Ee
Q psy5454 104 AV 105 (129)
Q Consensus 104 ~~ 105 (129)
++
T Consensus 86 ~g 87 (410)
T TIGR02500 86 VA 87 (410)
T ss_pred cc
Confidence 44
No 13
>KOG0615|consensus
Probab=96.53 E-value=0.0039 Score=53.22 Aligned_cols=73 Identities=22% Similarity=0.119 Sum_probs=56.9
Q ss_pred EcCCCceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEE-------------c--CCEEEEEeCCCCCceEEcCEEcc--
Q psy5454 29 RLHPNVTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAH-------------T--EGIVTVTPCSREAETFVNGQRIF-- 91 (129)
Q Consensus 29 ~L~~~~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~-------------~--~g~v~L~p~ss~~~t~VNG~~I~-- 91 (129)
.+..+..++||.+ .+|.++.+..++..|..+.. . ...+++++. +.++||||-..+.
T Consensus 60 d~~nd~f~fGR~~------~~d~~ln~~~~s~~~~~i~~~~~~~~~~f~~dr~~~sn~~y~~Dh-S~nGT~VN~e~i~k~ 132 (475)
T KOG0615|consen 60 DLANDEFTFGRGD------SCDAPLNLNNVSNKHFKILLYNKISKIHFRIDRDKNSNRVYLHDH-SRNGTFVNDEMIGKG 132 (475)
T ss_pred eeccceEEecCCC------cccccccCccccccchheeeeeeeeeeeecccCCCccceEEEEec-ccCcccccHhHhhcc
Confidence 3456778999986 47888888777777766543 1 358999999 5789999999886
Q ss_pred eeEEcCCCCEEEEecCc
Q psy5454 92 ETTILQVVVAASAVAEK 108 (129)
Q Consensus 92 ~~~~L~~GDrI~~~~~~ 108 (129)
..+.|..||.|.|+..+
T Consensus 133 ~~r~lkN~dei~is~p~ 149 (475)
T KOG0615|consen 133 LSRILKNGDEISISIPA 149 (475)
T ss_pred ccccccCCCEEEeccch
Confidence 66899999999987754
No 14
>KOG2293|consensus
Probab=96.28 E-value=0.011 Score=51.46 Aligned_cols=76 Identities=17% Similarity=0.277 Sum_probs=62.2
Q ss_pred EEEEcCCCceEEcCCCCCCCCCcccEEE--cC--CCCCCCcEEEEEc-CCEEEEEeCCCCCceEEcCEEcc--eeEEcCC
Q psy5454 26 KRHRLHPNVTEVGSDRASPYGQSQSLQL--FG--PNIQPRHCVIAHT-EGIVTVTPCSREAETFVNGQRIF--ETTILQV 98 (129)
Q Consensus 26 ~~~~L~~~~t~IGr~~~~~~~~~~dI~L--~g--~~I~~~Hc~I~~~-~g~v~L~p~ss~~~t~VNG~~I~--~~~~L~~ 98 (129)
..|++.....++||+..+ ...||-| .| ..|+++-+.|... +|..+|.-++ ...++|||.+|. +.+.|.+
T Consensus 441 skh~mrk~EVtlGRat~d---~~VDIDLgkegpatKISRRQa~IkL~n~GsF~IkNlG-K~~I~vng~~l~~gq~~~L~~ 516 (547)
T KOG2293|consen 441 SKHYMRKKEVTLGRATGD---LKVDIDLGKEGPATKISRRQALIKLKNDGSFFIKNLG-KRSILVNGGELDRGQKVILKN 516 (547)
T ss_pred hHhhhcCcceEeeccCCC---cceeeeccccCccceeeccceeEEeccCCcEEeccCc-ceeEEeCCccccCCceEEecc
Confidence 568899999999999642 2346665 44 4899999999986 6899999995 679999999997 7789999
Q ss_pred CCEEEEe
Q psy5454 99 VVAASAV 105 (129)
Q Consensus 99 GDrI~~~ 105 (129)
...|.|.
T Consensus 517 nclveIr 523 (547)
T KOG2293|consen 517 NCLVEIR 523 (547)
T ss_pred CcEEEEc
Confidence 9999874
No 15
>KOG1881|consensus
Probab=95.50 E-value=0.007 Score=54.46 Aligned_cols=64 Identities=19% Similarity=0.074 Sum_probs=51.1
Q ss_pred eEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEc--CC---------EEEEEeCCCCCceEEcCEEcceeE--EcCCCCE
Q psy5454 35 TEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHT--EG---------IVTVTPCSREAETFVNGQRIFETT--ILQVVVA 101 (129)
Q Consensus 35 t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~--~g---------~v~L~p~ss~~~t~VNG~~I~~~~--~L~~GDr 101 (129)
.+|||-. .||+.+.=|.|++.||.+.+. +- .|+|++++++.++|+|-.+|..++ .++-|+.
T Consensus 179 ~~fgr~~------~cD~~~eHpsISr~h~vlQy~~~~~~~p~~s~~~g~~i~dlgsThgt~~NK~rvppk~yir~~Vg~v 252 (793)
T KOG1881|consen 179 CLFGRLG------GCDVALEHPSISRFHAVLQYKASGPDDPCASNGEGWYIYDLGSTHGTFLNKDRVPPKVYIRDRVGHV 252 (793)
T ss_pred EEecccC------CCccccccCcccccceeeeccCCCCCccccCCCCceEEeeccccccceeccccCCCcchhhhhHHHH
Confidence 4889974 799999999999999999984 11 499999999999999999997553 4555554
Q ss_pred EEE
Q psy5454 102 ASA 104 (129)
Q Consensus 102 I~~ 104 (129)
+.+
T Consensus 253 ~~f 255 (793)
T KOG1881|consen 253 ARF 255 (793)
T ss_pred HHh
Confidence 443
No 16
>KOG1880|consensus
Probab=94.58 E-value=0.039 Score=45.30 Aligned_cols=91 Identities=10% Similarity=-0.027 Sum_probs=71.6
Q ss_pred ceeEEEEecCCCCCCCCCCcEEEEcCCCceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEc--CCEEEEEeCCCCCce
Q psy5454 6 IKSSLLLKNYNGSEITSGSPKRHRLHPNVTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHT--EGIVTVTPCSREAET 83 (129)
Q Consensus 6 ~~PhLvnln~dp~ls~~~~~~~~~L~~~~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~--~g~v~L~p~ss~~~t 83 (129)
..+||-.+-.|.+.- . +..+.+..-.+||.. ..||.+|.=...|+.|+.+..+ ...++|-+++++.+|
T Consensus 16 ~g~hldv~k~d~li~--k---l~iddkr~y~Fgrn~-----q~~df~idh~scSrvhaa~vyhkhl~~~~lidl~s~hgt 85 (337)
T KOG1880|consen 16 AGLHLDVVKGDKLIQ--K---LIIDDKRRYLFGRNH-----QTCDFVIDHASCSRVHAALVYHKHLSRIFLIDLGSTHGT 85 (337)
T ss_pred CCCceeeeecchhHH--H---HHhhhhhhhhhccCC-----CccceEeecchhhhhHhhhhhhhccceEEEEEccCCcce
Confidence 457888888777765 2 333445667899996 3689999999999999999886 346999999999999
Q ss_pred EEcCEEcc--eeEEcCCCCEEEEec
Q psy5454 84 FVNGQRIF--ETTILQVVVAASAVA 106 (129)
Q Consensus 84 ~VNG~~I~--~~~~L~~GDrI~~~~ 106 (129)
|+--.+++ +++.|+-|--..++|
T Consensus 86 f~g~~rL~~~~p~~l~i~~~~~fga 110 (337)
T KOG1880|consen 86 FLGNERLEPHKPVQLEIGSTFHFGA 110 (337)
T ss_pred eeeeeeeccCCCccccCCceEEEec
Confidence 99888886 677888887766655
No 17
>PRK01777 hypothetical protein; Validated
Probab=94.16 E-value=0.047 Score=37.44 Aligned_cols=27 Identities=7% Similarity=-0.097 Sum_probs=23.7
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
.+.+.|||+.+.-...|++||||.|-.
T Consensus 49 ~~~vgI~Gk~v~~d~~L~dGDRVeIyr 75 (95)
T PRK01777 49 KNKVGIYSRPAKLTDVLRDGDRVEIYR 75 (95)
T ss_pred cceEEEeCeECCCCCcCCCCCEEEEec
Confidence 468999999999889999999999844
No 18
>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase. Note that the EC number for the kinase function is: 2.7.1.78
Probab=93.98 E-value=0.17 Score=44.38 Aligned_cols=71 Identities=10% Similarity=-0.017 Sum_probs=53.6
Q ss_pred EEEcCCCceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEE--cCCEEEEEeCCCCCceEEcCEEcc--eeEEcCCCCEE
Q psy5454 27 RHRLHPNVTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAH--TEGIVTVTPCSREAETFVNGQRIF--ETTILQVVVAA 102 (129)
Q Consensus 27 ~~~L~~~~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~--~~g~v~L~p~ss~~~t~VNG~~I~--~~~~L~~GDrI 102 (129)
.+.|..+..++||++. -.|.+..=|++-..+.. ..+.|.+..++ .+.+-|||+.+. ....|+|||.+
T Consensus 26 ~~~~~~~~~~~gr~pe--------t~i~d~~cs~~qv~l~a~~~~~~v~~k~lg-~np~~~~~~~~~~~~~~~l~~g~~l 96 (526)
T TIGR01663 26 FIHLDAGALFLGRGPE--------TGIRDRKCSKRQIELQADLEKATVALKQLG-VNPCGTGGLELKPGGEGELGHGDLL 96 (526)
T ss_pred eeccCCCceEEccCcc--------cccchhhhchhhheeeecccCceEEEEEcc-CCCcccCceEecCCCeeeecCCCEE
Confidence 3456677889999863 34555555665555554 36899999996 579999999997 66899999999
Q ss_pred EEec
Q psy5454 103 SAVA 106 (129)
Q Consensus 103 ~~~~ 106 (129)
.+..
T Consensus 97 ~~v~ 100 (526)
T TIGR01663 97 EIVN 100 (526)
T ss_pred EEec
Confidence 8865
No 19
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=93.55 E-value=0.083 Score=32.52 Aligned_cols=25 Identities=24% Similarity=0.092 Sum_probs=21.6
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEE
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASA 104 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~ 104 (129)
.+.++|||+++. ....|+.||+|.+
T Consensus 33 ~G~V~VNg~~~~~~~~~l~~Gd~v~i 58 (59)
T TIGR02988 33 ENEVLVNGELENRRGKKLYPGDVIEI 58 (59)
T ss_pred cCCEEECCEEccCCCCCCCCCCEEEe
Confidence 579999999995 5689999999975
No 20
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=92.86 E-value=0.25 Score=29.49 Aligned_cols=28 Identities=11% Similarity=0.087 Sum_probs=23.4
Q ss_pred CCceEEcCEEc-ceeEEcCCCCEEEEecC
Q psy5454 80 EAETFVNGQRI-FETTILQVVVAASAVAE 107 (129)
Q Consensus 80 ~~~t~VNG~~I-~~~~~L~~GDrI~~~~~ 107 (129)
.+.++|||+.+ .....+..||.|.+..+
T Consensus 25 ~g~V~vn~~~~~~~~~~v~~~d~i~i~~~ 53 (70)
T cd00165 25 HGHVLVNGKVVTKPSYKVKPGDVIEVDGK 53 (70)
T ss_pred cCCEEECCEEccCCccCcCCCCEEEEcCC
Confidence 46899999999 56678999999988753
No 21
>smart00363 S4 S4 RNA-binding domain.
Probab=92.56 E-value=0.21 Score=28.96 Aligned_cols=27 Identities=19% Similarity=0.194 Sum_probs=22.8
Q ss_pred CCceEEcCEEc-ceeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRI-FETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I-~~~~~L~~GDrI~~~~ 106 (129)
.+.++|||+++ .....|..||.|.+..
T Consensus 25 ~g~i~vng~~~~~~~~~l~~gd~i~~~~ 52 (60)
T smart00363 25 QGRVKVNGKKVTKPSYIVKPGDVISVRG 52 (60)
T ss_pred cCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence 46899999999 6678999999998754
No 22
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=92.16 E-value=0.19 Score=33.47 Aligned_cols=31 Identities=13% Similarity=-0.051 Sum_probs=25.9
Q ss_pred CCCceEEcCEEcceeEEcCCCCEEEEecCch
Q psy5454 79 REAETFVNGQRIFETTILQVVVAASAVAEKQ 109 (129)
Q Consensus 79 s~~~t~VNG~~I~~~~~L~~GDrI~~~~~~~ 109 (129)
+=+.++|||+++.=...|++||+|.+-...+
T Consensus 48 EV~~i~vNG~~v~~~~~~~~Gd~v~V~P~~~ 78 (81)
T PF14451_consen 48 EVGLILVNGRPVDFDYRLKDGDRVAVYPVFR 78 (81)
T ss_pred HeEEEEECCEECCCcccCCCCCEEEEEeccc
Confidence 3468999999999778999999999876544
No 23
>PRK06437 hypothetical protein; Provisional
Probab=92.14 E-value=0.23 Score=31.63 Aligned_cols=27 Identities=19% Similarity=0.183 Sum_probs=23.6
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
...+.+||+.+...+.|+.||+|.+..
T Consensus 36 ~vaV~vNg~iv~~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 36 EYVVIVNGSPVLEDHNVKKEDDVLILE 62 (67)
T ss_pred cEEEEECCEECCCceEcCCCCEEEEEe
Confidence 457889999999889999999998754
No 24
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=91.79 E-value=0.18 Score=32.14 Aligned_cols=27 Identities=19% Similarity=0.112 Sum_probs=23.7
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
...++|||+.+...+.|++||+|.|-.
T Consensus 49 ~~~v~vNg~~v~~~~~l~~gD~v~i~p 75 (80)
T cd00754 49 RVRIAVNGEYVRLDTPLKDGDEVAIIP 75 (80)
T ss_pred cEEEEECCeEcCCCcccCCCCEEEEeC
Confidence 468999999999889999999998854
No 25
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=91.29 E-value=0.21 Score=32.85 Aligned_cols=27 Identities=22% Similarity=0.064 Sum_probs=22.7
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~ 106 (129)
.+.++|||+.-+ ....|++||+|.+.-
T Consensus 36 eg~V~vNGe~EtRRgkKlr~gd~V~i~~ 63 (73)
T COG2501 36 EGEVKVNGEVETRRGKKLRDGDVVEIPG 63 (73)
T ss_pred CCeEEECCeeeeccCCEeecCCEEEECC
Confidence 468999999987 457999999999854
No 26
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=90.83 E-value=0.31 Score=30.43 Aligned_cols=27 Identities=22% Similarity=0.116 Sum_probs=22.7
Q ss_pred CCceEEcCEEccee----EEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIFET----TILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~~~----~~L~~GDrI~~~~ 106 (129)
...+.|||+.|... +.|+.||+|.+-+
T Consensus 30 ~i~V~vNg~~v~~~~~~~~~L~~gD~V~ii~ 60 (65)
T cd00565 30 GVAVALNGEIVPRSEWASTPLQDGDRIEIVT 60 (65)
T ss_pred cEEEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 35688999999866 8999999998754
No 27
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=90.44 E-value=0.17 Score=29.54 Aligned_cols=23 Identities=17% Similarity=0.148 Sum_probs=19.9
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEE
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAA 102 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI 102 (129)
.+.++|||+.+. ....+..||+|
T Consensus 25 ~g~V~VNg~~v~~~~~~v~~~d~I 48 (48)
T PF01479_consen 25 QGRVKVNGKVVKDPSYIVKPGDVI 48 (48)
T ss_dssp TTTEEETTEEESSTTSBESTTEEE
T ss_pred CCEEEECCEEEcCCCCCCCCcCCC
Confidence 468999999998 55789999986
No 28
>PRK11507 ribosome-associated protein; Provisional
Probab=88.79 E-value=0.5 Score=30.80 Aligned_cols=27 Identities=15% Similarity=0.049 Sum_probs=22.5
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~ 106 (129)
.+.+.|||+.-. ....|++||.|.+.-
T Consensus 36 eg~V~VNGeve~rRgkKl~~GD~V~~~g 63 (70)
T PRK11507 36 EGQVKVDGAVETRKRCKIVAGQTVSFAG 63 (70)
T ss_pred cCceEECCEEecccCCCCCCCCEEEECC
Confidence 368999999876 557899999999864
No 29
>PRK08364 sulfur carrier protein ThiS; Provisional
Probab=88.75 E-value=0.47 Score=30.25 Aligned_cols=27 Identities=19% Similarity=0.107 Sum_probs=23.0
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
...+.+||+.+...+.|+.||+|.+-.
T Consensus 39 ~v~v~vNg~iv~~~~~l~~gD~Veii~ 65 (70)
T PRK08364 39 SAIAKVNGKVALEDDPVKDGDYVEVIP 65 (70)
T ss_pred cEEEEECCEECCCCcCcCCCCEEEEEc
Confidence 357789999999889999999998753
No 30
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=86.90 E-value=0.34 Score=30.58 Aligned_cols=28 Identities=18% Similarity=0.143 Sum_probs=24.6
Q ss_pred CCCceEEcCEEcce---eEEcCCCCEEEEec
Q psy5454 79 REAETFVNGQRIFE---TTILQVVVAASAVA 106 (129)
Q Consensus 79 s~~~t~VNG~~I~~---~~~L~~GDrI~~~~ 106 (129)
....++|||+.+.. .+.|++||.|.+-.
T Consensus 42 ~~~~v~vN~~~v~~~~~~~~l~~gD~V~i~p 72 (77)
T PF02597_consen 42 DRVAVAVNGEIVPDDGLDTPLKDGDEVAILP 72 (77)
T ss_dssp TTEEEEETTEEEGGGTTTSBEETTEEEEEEE
T ss_pred ccEEEEECCEEcCCccCCcCcCCCCEEEEEC
Confidence 45789999999998 89999999998854
No 31
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=85.98 E-value=0.93 Score=29.20 Aligned_cols=27 Identities=26% Similarity=0.187 Sum_probs=23.3
Q ss_pred CCceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
..-+-+||..|. ....|+.||+|.+.+
T Consensus 33 ~vav~vNg~iVpr~~~~~~~l~~gD~ievv~ 63 (68)
T COG2104 33 GVAVAVNGEIVPRSQWADTILKEGDRIEVVR 63 (68)
T ss_pred eEEEEECCEEccchhhhhccccCCCEEEEEE
Confidence 467889999998 778999999998864
No 32
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=85.62 E-value=1 Score=28.02 Aligned_cols=25 Identities=20% Similarity=0.223 Sum_probs=21.4
Q ss_pred ceEEcCEEcce----eEEcCCCCEEEEec
Q psy5454 82 ETFVNGQRIFE----TTILQVVVAASAVA 106 (129)
Q Consensus 82 ~t~VNG~~I~~----~~~L~~GDrI~~~~ 106 (129)
.+-|||+-|.+ .+.|++||+|.+.+
T Consensus 32 avavN~~iv~~~~~~~~~L~dgD~Ieiv~ 60 (65)
T PRK06488 32 ATAVNGELVHKEARAQFVLHEGDRIEILS 60 (65)
T ss_pred EEEECCEEcCHHHcCccccCCCCEEEEEE
Confidence 58899999984 78999999998854
No 33
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=85.19 E-value=1.3 Score=27.51 Aligned_cols=27 Identities=26% Similarity=0.239 Sum_probs=21.5
Q ss_pred CCceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
...+.|||+.|. ..+.|++||+|.+-+
T Consensus 29 ~v~v~vN~~iv~~~~~~~~~L~~gD~veii~ 59 (64)
T TIGR01683 29 RVAVAVNGEIVPRSEWDDTILKEGDRIEIVT 59 (64)
T ss_pred eEEEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence 456789999995 447899999998754
No 34
>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal. The C-terminal Gly-Gly of this model is critical to function.
Probab=84.98 E-value=0.98 Score=29.16 Aligned_cols=27 Identities=11% Similarity=0.122 Sum_probs=23.3
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
...++|||+.+...+.|++||.|.+-.
T Consensus 49 ~~~v~vn~~~v~~~~~l~dgDevai~P 75 (80)
T TIGR01682 49 QVMVAVNEEYVTDDALLNEGDEVAFIP 75 (80)
T ss_pred ceEEEECCEEcCCCcCcCCCCEEEEeC
Confidence 347999999999889999999998753
No 35
>PRK06944 sulfur carrier protein ThiS; Provisional
Probab=84.92 E-value=1.2 Score=27.46 Aligned_cols=25 Identities=20% Similarity=0.114 Sum_probs=20.5
Q ss_pred ceEEcCEEcce----eEEcCCCCEEEEec
Q psy5454 82 ETFVNGQRIFE----TTILQVVVAASAVA 106 (129)
Q Consensus 82 ~t~VNG~~I~~----~~~L~~GDrI~~~~ 106 (129)
.+.|||+.+.. .+.|+.||+|.+-+
T Consensus 32 ~v~vN~~~v~~~~~~~~~L~~gD~vei~~ 60 (65)
T PRK06944 32 AVAVNGDFVARTQHAARALAAGDRLDLVQ 60 (65)
T ss_pred EEEECCEEcCchhcccccCCCCCEEEEEe
Confidence 57899999863 57899999998854
No 36
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=84.70 E-value=1.3 Score=27.51 Aligned_cols=25 Identities=24% Similarity=0.153 Sum_probs=20.1
Q ss_pred ceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 82 ETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 82 ~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
.+.+||.-+. ..+.|++||+|.+.+
T Consensus 33 av~vNg~iv~r~~~~~~~l~~gD~vei~~ 61 (66)
T PRK05659 33 AVEVNGEIVPRSQHASTALREGDVVEIVH 61 (66)
T ss_pred EEEECCeEeCHHHcCcccCCCCCEEEEEE
Confidence 3678997776 678999999998754
No 37
>PLN02799 Molybdopterin synthase sulfur carrier subunit
Probab=84.53 E-value=1.1 Score=28.94 Aligned_cols=26 Identities=12% Similarity=0.011 Sum_probs=22.4
Q ss_pred CceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 81 AETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 81 ~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
..+.|||+.+...+.|++||.|.+-.
T Consensus 52 ~~vavN~~~v~~~~~l~dgDeVai~P 77 (82)
T PLN02799 52 CVLALNEEYTTESAALKDGDELAIIP 77 (82)
T ss_pred cEEEECCEEcCCCcCcCCCCEEEEeC
Confidence 35889999998889999999998754
No 38
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=84.53 E-value=1 Score=29.45 Aligned_cols=26 Identities=15% Similarity=0.014 Sum_probs=21.3
Q ss_pred CceEEcCEEcceeE--EcCCCCEEEEec
Q psy5454 81 AETFVNGQRIFETT--ILQVVVAASAVA 106 (129)
Q Consensus 81 ~~t~VNG~~I~~~~--~L~~GDrI~~~~ 106 (129)
..++|||+.+.... .|++||.|.|-.
T Consensus 56 ~~v~vN~~~v~~~~~~~l~dgdev~i~P 83 (88)
T TIGR01687 56 VIILVNGRNVDWGLGTELKDGDVVAIFP 83 (88)
T ss_pred EEEEECCEecCccCCCCCCCCCEEEEeC
Confidence 57899999997444 899999998743
No 39
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=83.63 E-value=0.56 Score=30.09 Aligned_cols=25 Identities=20% Similarity=0.015 Sum_probs=15.3
Q ss_pred CceEEcCEEcc-eeEEcCCCCEEEEe
Q psy5454 81 AETFVNGQRIF-ETTILQVVVAASAV 105 (129)
Q Consensus 81 ~~t~VNG~~I~-~~~~L~~GDrI~~~ 105 (129)
+.++|||+... ....|++||.|.+.
T Consensus 33 g~V~VNGe~e~rrg~Kl~~GD~V~~~ 58 (65)
T PF13275_consen 33 GEVKVNGEVETRRGKKLRPGDVVEID 58 (65)
T ss_dssp HHHEETTB----SS----SSEEEEET
T ss_pred CceEECCEEccccCCcCCCCCEEEEC
Confidence 47999999887 55799999999984
No 40
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=83.33 E-value=2.5 Score=34.22 Aligned_cols=32 Identities=13% Similarity=0.120 Sum_probs=27.2
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEecCchhh
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAVAEKQQQ 111 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~~~~~~~ 111 (129)
.+.+.|||+++.....|+.||+|.+......+
T Consensus 36 ~g~v~vNg~~v~~~~~l~~gd~i~~~~~~~~~ 67 (289)
T COG0564 36 KGRVRVNGKKVKPSYKLKPGDVVRIPLPEEPE 67 (289)
T ss_pred CCCEEECCEEccCCeeeCCCCEEEEecccccc
Confidence 45899999999988899999999998865443
No 41
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=82.81 E-value=1.5 Score=30.50 Aligned_cols=28 Identities=21% Similarity=0.093 Sum_probs=24.4
Q ss_pred CCCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 79 REAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 79 s~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
..+.+.|||+.+........||+|.|..
T Consensus 32 ~~GrV~vNG~~aKpS~~VK~GD~l~i~~ 59 (100)
T COG1188 32 EGGRVKVNGQRAKPSKEVKVGDILTIRF 59 (100)
T ss_pred HCCeEEECCEEcccccccCCCCEEEEEe
Confidence 3579999999998888999999998754
No 42
>PRK07440 hypothetical protein; Provisional
Probab=81.33 E-value=2.4 Score=27.12 Aligned_cols=27 Identities=22% Similarity=0.089 Sum_probs=22.3
Q ss_pred CCceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
.-.+-+||+-|. ..+.|+.||+|.+..
T Consensus 35 ~vav~~N~~iv~r~~w~~~~L~~gD~IEIv~ 65 (70)
T PRK07440 35 LVAVEYNGEILHRQFWEQTQVQPGDRLEIVT 65 (70)
T ss_pred eEEEEECCEEeCHHHcCceecCCCCEEEEEE
Confidence 346788999998 778999999998753
No 43
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=81.17 E-value=2.1 Score=27.03 Aligned_cols=27 Identities=11% Similarity=-0.177 Sum_probs=22.0
Q ss_pred CCceEEcCEEccee----EEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIFET----TILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~~~----~~L~~GDrI~~~~ 106 (129)
...+-+||+-|.+. +.|++||+|.+.+
T Consensus 32 ~vav~vN~~iv~r~~w~~~~L~~gD~iEIv~ 62 (67)
T PRK07696 32 IVVVERNKDILQKDDHTDTSVFDGDQIEIVT 62 (67)
T ss_pred eEEEEECCEEeCHHHcCceecCCCCEEEEEE
Confidence 45688999999844 8999999998754
No 44
>PRK15367 type III secretion system protein SsaD; Provisional
Probab=81.07 E-value=7 Score=33.34 Aligned_cols=67 Identities=13% Similarity=0.098 Sum_probs=47.0
Q ss_pred EEEEcCCCceEEcCCCCCCCCCcccEEEcCCCCCCCcEEEEEcCCEEEEEeCCCCCceEEcCEEcceeEEcCCCCEEE
Q psy5454 26 KRHRLHPNVTEVGSDRASPYGQSQSLQLFGPNIQPRHCVIAHTEGIVTVTPCSREAETFVNGQRIFETTILQVVVAAS 103 (129)
Q Consensus 26 ~~~~L~~~~t~IGr~~~~~~~~~~dI~L~g~~I~~~Hc~I~~~~g~v~L~p~ss~~~t~VNG~~I~~~~~L~~GDrI~ 103 (129)
+-..|++|..++|-+ +|||.+.=+. ..-..+...++.+++..- ...+.|||.+-.....|.-+-.|.
T Consensus 17 rEl~Lp~G~~tlG~~-------gcDi~lpL~~--~~~~~L~i~e~gi~l~~~--~~~vwVnG~~~~~~~~LPl~q~Ie 83 (395)
T PRK15367 17 REVWLNEGNLSLGEK-------GCDICIPLTI--NEKIILREQADSLFVDAG--KARVRVNGRRFNPNKPLPSSGVLQ 83 (395)
T ss_pred cEEecCCCceeecCC-------CceEEEECCC--CCEEEEEEcCCcEEEecC--CceEEECCEEcCCCCCCCCcchhh
Confidence 567799999999986 4899876533 222334456788888542 369999999987555676665543
No 45
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=81.03 E-value=1.4 Score=28.76 Aligned_cols=21 Identities=19% Similarity=0.059 Sum_probs=19.1
Q ss_pred EcCEEcceeEEcCCCCEEEEe
Q psy5454 85 VNGQRIFETTILQVVVAASAV 105 (129)
Q Consensus 85 VNG~~I~~~~~L~~GDrI~~~ 105 (129)
+||++|.....|++||+|.|.
T Consensus 54 ~~gq~Vgl~~~L~d~DvVeI~ 74 (75)
T cd01666 54 HSPQRVGLDHVLEDEDVVQIV 74 (75)
T ss_pred CCCeECCCCCEecCCCEEEEe
Confidence 599999988999999999885
No 46
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=80.87 E-value=1.6 Score=29.65 Aligned_cols=27 Identities=15% Similarity=0.017 Sum_probs=22.5
Q ss_pred CCceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
.--++|||+.+. ..+.|++||.|.|-.
T Consensus 59 ~i~VlvN~~di~~l~g~~t~L~dgD~v~i~P 89 (94)
T cd01764 59 GIIVLINDTDWELLGEEDYILEDGDHVVFIS 89 (94)
T ss_pred CEEEEECCccccccCCcccCCCCcCEEEEEC
Confidence 368999999985 458999999998854
No 47
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=80.22 E-value=1.6 Score=27.50 Aligned_cols=25 Identities=16% Similarity=-0.049 Sum_probs=17.5
Q ss_pred CCceEEcCEEcc---eeEEcCCCCEEEE
Q psy5454 80 EAETFVNGQRIF---ETTILQVVVAASA 104 (129)
Q Consensus 80 ~~~t~VNG~~I~---~~~~L~~GDrI~~ 104 (129)
....+|||+... ....|++||.|.+
T Consensus 40 ~W~~~vNG~~~~~ga~~~~l~~GD~i~~ 67 (68)
T PF14478_consen 40 YWMYYVNGESANVGAGSYKLKDGDKITW 67 (68)
T ss_dssp EEEEEETTEE-SS-CCC-B--TTEEEEE
T ss_pred eeEEEECCEEhhcCcceeEeCCCCEEEe
Confidence 467899999987 6689999999976
No 48
>PRK10626 hypothetical protein; Provisional
Probab=79.08 E-value=2.4 Score=33.76 Aligned_cols=41 Identities=17% Similarity=0.275 Sum_probs=32.9
Q ss_pred cccEEE-cCCCCCCCcEEEEEcCCEEEEEeCCCCCceEEcCEEcc
Q psy5454 48 SQSLQL-FGPNIQPRHCVIAHTEGIVTVTPCSREAETFVNGQRIF 91 (129)
Q Consensus 48 ~~dI~L-~g~~I~~~Hc~I~~~~g~v~L~p~ss~~~t~VNG~~I~ 91 (129)
.|++-+ .+..|.|.+..|.-..|.+.|.|- +.+||||++|.
T Consensus 23 qC~V~l~~DV~Itpq~v~V~~~sg~l~I~~d---g~L~inGk~v~ 64 (239)
T PRK10626 23 QCSVTPQDDVIISPQTVQVVGASGNLVISPD---GNVMRNGKQLS 64 (239)
T ss_pred CCCCCCCCCeEEcCCeEEEEecCCceEEcCC---CCEEECCEEec
Confidence 466666 555788899999888888888775 79999999985
No 49
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=78.67 E-value=2.2 Score=27.69 Aligned_cols=25 Identities=12% Similarity=-0.168 Sum_probs=21.5
Q ss_pred ceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 82 ETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 82 ~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
.++||++.+...+.|++||.|.|-.
T Consensus 52 ~~aVN~~~~~~~~~l~dgDeVai~P 76 (81)
T PRK11130 52 LAAVNQTLVSFDHPLTDGDEVAFFP 76 (81)
T ss_pred EEEECCEEcCCCCCCCCCCEEEEeC
Confidence 5899999888778999999998743
No 50
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=78.13 E-value=1.3 Score=27.40 Aligned_cols=25 Identities=20% Similarity=0.061 Sum_probs=20.4
Q ss_pred ceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 82 ETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 82 ~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
...|||+++.-...|++||.|.|-+
T Consensus 36 ~A~Vng~~vdl~~~L~~~d~v~iiT 60 (60)
T PF02824_consen 36 AAKVNGQLVDLDHPLEDGDVVEIIT 60 (60)
T ss_dssp EEEETTEEEETTSBB-SSEEEEEEE
T ss_pred EEEEcCEECCCCCCcCCCCEEEEEC
Confidence 5679999998778999999998753
No 51
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=77.47 E-value=3.1 Score=27.73 Aligned_cols=26 Identities=23% Similarity=0.126 Sum_probs=21.4
Q ss_pred CceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 81 AETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 81 ~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
-.+-+||+-|. +.+.|++||+|.+..
T Consensus 50 vAVevNg~iVpr~~w~~t~L~egD~IEIv~ 79 (84)
T PRK06083 50 CVFAINNQVVPRSEWQSTVLSSGDAISLFQ 79 (84)
T ss_pred EEEEECCEEeCHHHcCcccCCCCCEEEEEE
Confidence 46789999997 668899999998754
No 52
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=76.97 E-value=2.5 Score=26.41 Aligned_cols=25 Identities=16% Similarity=-0.003 Sum_probs=21.7
Q ss_pred ceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 82 ETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 82 ~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
-+-+||-++.+-..|+.||.|.+-.
T Consensus 31 I~I~NGF~~~~d~~L~e~D~v~~Ik 55 (57)
T PF14453_consen 31 IVILNGFPTKEDIELKEGDEVFLIK 55 (57)
T ss_pred EEEEcCcccCCccccCCCCEEEEEe
Confidence 5678999999999999999998753
No 53
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=74.40 E-value=4.1 Score=24.02 Aligned_cols=24 Identities=21% Similarity=0.160 Sum_probs=19.7
Q ss_pred ceEEcCEEcceeEEcCCCCEEEEe
Q psy5454 82 ETFVNGQRIFETTILQVVVAASAV 105 (129)
Q Consensus 82 ~t~VNG~~I~~~~~L~~GDrI~~~ 105 (129)
...+||+.+.-.+.|.+||+|.+.
T Consensus 36 a~~vng~~vdl~~~l~~~~~ve~v 59 (60)
T cd01668 36 GAKVNGKLVPLSTVLKDGDIVEII 59 (60)
T ss_pred EEEECCEECCCCCCCCCCCEEEEE
Confidence 456899998866889999998764
No 54
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=73.59 E-value=4.7 Score=25.14 Aligned_cols=26 Identities=23% Similarity=0.001 Sum_probs=21.4
Q ss_pred CceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 81 AETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 81 ~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
-.+-|||+-|. +.+.|+.||.|.+.+
T Consensus 32 vaVavN~~iv~r~~w~~~~L~~gD~Ieii~ 61 (66)
T PRK08053 32 AALAINQQIIPREQWAQHIVQDGDQILLFQ 61 (66)
T ss_pred EEEEECCEEeChHHcCccccCCCCEEEEEE
Confidence 46789999987 567899999998754
No 55
>smart00797 AHS2 Allophanate hydrolase subunit 2. This domain represents subunit 2 of allophanate hydrolase (AHS2).
Probab=73.48 E-value=13 Score=30.08 Aligned_cols=44 Identities=16% Similarity=0.155 Sum_probs=30.8
Q ss_pred EEEEcCCEEEEEeCCCCCceEEcCEEcc--eeEEcCCCCEEEEecCc
Q psy5454 64 VIAHTEGIVTVTPCSREAETFVNGQRIF--ETTILQVVVAASAVAEK 108 (129)
Q Consensus 64 ~I~~~~g~v~L~p~ss~~~t~VNG~~I~--~~~~L~~GDrI~~~~~~ 108 (129)
.+.+....+ |.-.+......+||+++. ....++.||+|.|+..+
T Consensus 39 ~l~f~~~~~-iAitGA~~~~~ln~~~~~~~~~~~v~~Gd~L~~g~~~ 84 (280)
T smart00797 39 TLRFTADAV-IALTGADFPATLDGQPVPPWKPFLVRAGQVLSLGAPK 84 (280)
T ss_pred EEEECCCcE-EEEeCCCCeeeECCEEcCCCeEEEECCCCEEEeCCCC
Confidence 444443322 333334678899999986 67899999999998755
No 56
>PF11101 DUF2884: Protein of unknown function (DUF2884); InterPro: IPR021307 Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=70.27 E-value=5.7 Score=31.05 Aligned_cols=34 Identities=21% Similarity=0.517 Sum_probs=26.2
Q ss_pred CCCCCCCcEEEEEcCC-EEEEEeCCCCCceEEcCEEcc
Q psy5454 55 GPNIQPRHCVIAHTEG-IVTVTPCSREAETFVNGQRIF 91 (129)
Q Consensus 55 g~~I~~~Hc~I~~~~g-~v~L~p~ss~~~t~VNG~~I~ 91 (129)
+..|.+.+..|...++ .+.|.+- +.+||||++|.
T Consensus 8 dv~i~~~~l~v~~~~~~~~~I~~~---g~L~i~G~~v~ 42 (229)
T PF11101_consen 8 DVRINPQSLEVVQASGEKLRIDPD---GNLFINGKKVS 42 (229)
T ss_pred CeEEeCCEEEEEeCCCceEEEcCC---CcEEECCEEcc
Confidence 3356777888888877 7777654 79999999985
No 57
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=69.96 E-value=7.5 Score=31.55 Aligned_cols=27 Identities=22% Similarity=0.097 Sum_probs=23.0
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
.+.++|||+.+.....|+.||.|.+-.
T Consensus 44 ~G~V~VNg~~v~~~~~v~~GD~I~i~~ 70 (317)
T PRK11025 44 KGEVRVNKKRIKPEYKLEAGDEVRIPP 70 (317)
T ss_pred cCCEEECCEEcCcccccCCCCEEEeCC
Confidence 458899999998778999999999853
No 58
>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Probab=68.35 E-value=4.8 Score=36.37 Aligned_cols=53 Identities=15% Similarity=0.117 Sum_probs=37.9
Q ss_pred CCCCcEEEEEcCCEEEEEeCCCC----------------CceEEcCEEcceeEEcCCCCEEEEecCchh
Q psy5454 58 IQPRHCVIAHTEGIVTVTPCSRE----------------AETFVNGQRIFETTILQVVVAASAVAEKQQ 110 (129)
Q Consensus 58 I~~~Hc~I~~~~g~v~L~p~ss~----------------~~t~VNG~~I~~~~~L~~GDrI~~~~~~~~ 110 (129)
+.+...++.-..|.++.-|.+++ -+..|||+.+.-.+.|++||.|.|.+.+.+
T Consensus 357 l~~~~i~vfTPkG~~~~lp~gst~~DfAy~ih~~~g~~~~~a~vng~~v~l~~~l~~gd~vei~t~~~~ 425 (683)
T TIGR00691 357 LFNEEIYVFTPKGDVVELPSGSTPVDFAYAVHTDVGNKCTGAKVNGKIVPLDKELENGDVVEIITGKNS 425 (683)
T ss_pred hccCceEEECCCCeEEEcCCCCCHHHHHHHHhHHhHhceeEEEECCEECCCCccCCCCCEEEEEeCCCC
Confidence 44455554445666666665443 244799999998899999999999887754
No 59
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.
Probab=67.18 E-value=6 Score=30.34 Aligned_cols=28 Identities=14% Similarity=0.134 Sum_probs=23.3
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEecC
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVAE 107 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~~ 107 (129)
.+.++|||+.+. ....+..||.|.+.-.
T Consensus 114 ~G~V~VNgk~v~~ps~~V~~GD~I~V~~~ 142 (200)
T TIGR01017 114 HGHILVNGKKVDIPSYQVRPGDIISIKEK 142 (200)
T ss_pred CCCEEECCEEeCCCCCCCCCCCEEEEeeC
Confidence 578999999996 4579999999998643
No 60
>cd01669 TGS_Ygr210_C TGS_Ygr210_C: The C-terminal TGS domain of Ygr210 GTP-binding protein which is a member of Obg-like family of GTPases, and present in archaea. Several Obg-like family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=65.70 E-value=6.8 Score=25.56 Aligned_cols=22 Identities=23% Similarity=0.152 Sum_probs=19.1
Q ss_pred EcCEEcceeEEcCCCCEEEEec
Q psy5454 85 VNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 85 VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
.||+.+.....|++||.|.|.+
T Consensus 55 k~~~~vg~~~~L~dgDvV~Ii~ 76 (76)
T cd01669 55 RTGRRVGEDYELKHRDVIKIVS 76 (76)
T ss_pred eCCEEeCCCcEecCCCEEEEeC
Confidence 3899999889999999998853
No 61
>PF02626 AHS2: Allophanate hydrolase subunit 2; InterPro: IPR003778 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 2 of allophanate hydrolase (AHS2) which is found in urea carboxylase.; PDB: 3MML_G 3VA7_A 3OEP_A 3OPF_C 3ORE_B.
Probab=65.08 E-value=13 Score=29.92 Aligned_cols=30 Identities=10% Similarity=0.081 Sum_probs=23.0
Q ss_pred CCCCceEEcCEEcc--eeEEcCCCCEEEEecC
Q psy5454 78 SREAETFVNGQRIF--ETTILQVVVAASAVAE 107 (129)
Q Consensus 78 ss~~~t~VNG~~I~--~~~~L~~GDrI~~~~~ 107 (129)
+......+||+++. +...++.||+|.|+..
T Consensus 52 Ga~~~~~lng~~~~~~~~~~v~~Gd~L~~~~~ 83 (271)
T PF02626_consen 52 GADFEATLNGKPVPMWQPFLVKAGDVLKFGPP 83 (271)
T ss_dssp ESCEEEEETTEEE-TTSEEEE-TT-EEEEEEE
T ss_pred CCCCceEECCEEccCCEEEEECCCCEEEecCC
Confidence 34678999999997 8899999999999764
No 62
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=64.46 E-value=7.9 Score=29.90 Aligned_cols=27 Identities=11% Similarity=0.033 Sum_probs=22.8
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~ 106 (129)
.+.++|||+.+. ....+..||.|.+.-
T Consensus 113 ~G~V~VNGk~v~~ps~~Vk~GD~I~V~~ 140 (201)
T CHL00113 113 HGHILVNGRIVDIPSYRCKPKDIITVKD 140 (201)
T ss_pred CCcEEECCEEecCccccCCCCCEEEEcc
Confidence 579999999997 457999999998853
No 63
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=64.23 E-value=6.5 Score=24.51 Aligned_cols=26 Identities=15% Similarity=-0.033 Sum_probs=18.8
Q ss_pred CCceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
.-.+-+||.-|. +. .|++||+|.|.+
T Consensus 31 ~vav~~N~~iv~r~~~~~-~L~~gD~ieIv~ 60 (65)
T PRK05863 31 GIAVAVDWSVLPRSDWAT-KLRDGARLEVVT 60 (65)
T ss_pred cEEEEECCcCcChhHhhh-hcCCCCEEEEEe
Confidence 346777888665 33 599999998754
No 64
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=63.68 E-value=7 Score=35.56 Aligned_cols=30 Identities=10% Similarity=-0.054 Sum_probs=26.3
Q ss_pred CceEEcCEEcceeEEcCCCCEEEEecCchh
Q psy5454 81 AETFVNGQRIFETTILQVVVAASAVAEKQQ 110 (129)
Q Consensus 81 ~~t~VNG~~I~~~~~L~~GDrI~~~~~~~~ 110 (129)
-+-.|||+.+.=.+.|++||.|.|-+.+.+
T Consensus 422 ~gAkVNg~~vpL~~~L~~Gd~VeIiT~~~~ 451 (702)
T PRK11092 422 VGARVDRQPYPLSQPLTSGQTVEIITAPGA 451 (702)
T ss_pred EEEEECCEECCCCccCCCCCEEEEEeCCCC
Confidence 477899999987799999999999987754
No 65
>COG1984 DUR1 Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]
Probab=63.56 E-value=31 Score=28.62 Aligned_cols=51 Identities=20% Similarity=0.304 Sum_probs=36.5
Q ss_pred cEEEcCCCCCCCcEEEEEcCCE-EEEEeCCCCCceEEcCEEcc--eeEEcCCCCEEEEecCch
Q psy5454 50 SLQLFGPNIQPRHCVIAHTEGI-VTVTPCSREAETFVNGQRIF--ETTILQVVVAASAVAEKQ 109 (129)
Q Consensus 50 dI~L~g~~I~~~Hc~I~~~~g~-v~L~p~ss~~~t~VNG~~I~--~~~~L~~GDrI~~~~~~~ 109 (129)
.|.|.|+ .+.+..+. +-|+ +.+...++||+++. .+...+.||+|.++..+.
T Consensus 53 Eitl~g~-------t~~f~~~~~ialT--Gad~~a~ld~~~i~~~~~~~vk~Gq~L~~g~~~~ 106 (314)
T COG1984 53 EITLGGP-------TLEFTSDALIALT--GADCEATLDGQEVPPWSPYLVKAGQTLKLGRPKQ 106 (314)
T ss_pred EEecCCe-------EEEEecCcEEEEe--CCcccceECCEEcCCCceEEccCCCEEEecCCCC
Confidence 5555665 45554333 3333 34678999999997 889999999999988664
No 66
>PRK05327 rpsD 30S ribosomal protein S4; Validated
Probab=63.47 E-value=7.6 Score=29.84 Aligned_cols=27 Identities=11% Similarity=0.129 Sum_probs=22.9
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~ 106 (129)
.+.++|||+.+. ....+..||.|.+..
T Consensus 117 ~G~V~VNgk~v~~ps~~v~~GD~I~v~~ 144 (203)
T PRK05327 117 HGHILVNGKKVNIPSYRVKPGDVIEVRE 144 (203)
T ss_pred CCcEEECCEEECCCCcCCCCCCEEEECC
Confidence 468999999997 557999999999864
No 67
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=61.76 E-value=4.3 Score=27.30 Aligned_cols=28 Identities=11% Similarity=-0.005 Sum_probs=16.2
Q ss_pred CCCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 79 REAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 79 s~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
+.+.+-|=|+.+.-...|++||||.|=+
T Consensus 45 ~~~~vGIfGk~~~~d~~L~~GDRVEIYR 72 (84)
T PF03658_consen 45 EKNKVGIFGKLVKLDTVLRDGDRVEIYR 72 (84)
T ss_dssp TTSEEEEEE-S--TT-B--TT-EEEEE-
T ss_pred ccceeeeeeeEcCCCCcCCCCCEEEEec
Confidence 3567778899998888999999999855
No 68
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=61.60 E-value=9 Score=30.50 Aligned_cols=28 Identities=11% Similarity=-0.022 Sum_probs=23.2
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEecC
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVAE 107 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~~ 107 (129)
.+.+.|||+.+. ....+..||.|.+.-.
T Consensus 207 ~G~V~VNg~~v~~~s~~v~~gD~IsvrG~ 235 (257)
T TIGR03069 207 AGRLRLNWKTVTQPSRELKVGDRLQLRGK 235 (257)
T ss_pred CCeEEECCEEcCCCCCcCCCCCEEEEcCC
Confidence 579999999995 5579999999988543
No 69
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=61.37 E-value=14 Score=30.09 Aligned_cols=28 Identities=21% Similarity=0.139 Sum_probs=22.8
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEecC
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVAE 107 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~~ 107 (129)
.+.++|||+++. ....++.||+|.+..+
T Consensus 42 ~G~V~VNg~~v~~~~~~v~~gD~I~v~~~ 70 (325)
T PRK11180 42 DQRVLVNGKVINKPKEKVLGGEQVAIDAE 70 (325)
T ss_pred CCCEEECCEEccCCCcCcCCCCEEEEeec
Confidence 468999999985 4568999999998653
No 70
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=61.04 E-value=7.9 Score=35.53 Aligned_cols=54 Identities=17% Similarity=0.140 Sum_probs=38.5
Q ss_pred CCCCCcEEEEEcCCEEEEEeCCCC----------------CceEEcCEEcceeEEcCCCCEEEEecCchh
Q psy5454 57 NIQPRHCVIAHTEGIVTVTPCSRE----------------AETFVNGQRIFETTILQVVVAASAVAEKQQ 110 (129)
Q Consensus 57 ~I~~~Hc~I~~~~g~v~L~p~ss~----------------~~t~VNG~~I~~~~~L~~GDrI~~~~~~~~ 110 (129)
++++...++.-..|.++.-|.+++ -+..|||+.+.-.+.|++||.|.|-+.+.+
T Consensus 400 dl~~d~V~VfTPkG~~~~Lp~gaT~lDfAy~iHt~iG~~~~gAkvng~~v~l~~~L~~GD~VeIits~~~ 469 (743)
T PRK10872 400 QVFDDRVYVFTPKGDVVDLPAGSTPLDFAYHIHSDVGHRCIGAKIGGRIVPFTYQLQMGDQIEIITQKQP 469 (743)
T ss_pred HhcCCeEEEECCCCCeEEcCCCCcHHHHHHHHhHHHHhhceEEEECCEECCCCcCCCCCCEEEEEeCCCC
Confidence 344455444445666666665442 245799999998899999999999987764
No 71
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=59.68 E-value=9.7 Score=29.26 Aligned_cols=27 Identities=11% Similarity=-0.026 Sum_probs=22.2
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~ 106 (129)
.+.++|||+++. ....|+.||.|.+.-
T Consensus 24 ~g~V~VNg~~~~~~~~~l~~gd~I~l~~ 51 (232)
T PRK10839 24 ANRVTVDGEIVKNGAFKLLPEHDVAYDG 51 (232)
T ss_pred cCeEEECCEEeccCCcCcCCCCEEEECC
Confidence 468999999986 567899999998853
No 72
>cd01616 TGS The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=58.64 E-value=14 Score=20.80 Aligned_cols=23 Identities=35% Similarity=0.216 Sum_probs=18.6
Q ss_pred eEEcCEEcceeEEcCCCCEEEEe
Q psy5454 83 TFVNGQRIFETTILQVVVAASAV 105 (129)
Q Consensus 83 t~VNG~~I~~~~~L~~GDrI~~~ 105 (129)
..+||+.+.-...|.+||.|.+.
T Consensus 37 ~~vn~~~~~l~~~l~~~~~i~~i 59 (60)
T cd01616 37 ALVNGQLVDLSYTLQDGDTVSIV 59 (60)
T ss_pred EEECCEECCCCcCcCCCCEEEEe
Confidence 45899888766789999998774
No 73
>PF12733 Cadherin-like: Cadherin-like beta sandwich domain
Probab=58.47 E-value=33 Score=21.98 Aligned_cols=33 Identities=30% Similarity=0.221 Sum_probs=23.1
Q ss_pred EEEEeCCCCCceEEcCEEcce-----eEEcCCCC-E-EEE
Q psy5454 72 VTVTPCSREAETFVNGQRIFE-----TTILQVVV-A-ASA 104 (129)
Q Consensus 72 v~L~p~ss~~~t~VNG~~I~~-----~~~L~~GD-r-I~~ 104 (129)
+...+..+.+.++|||..+.. ...|..|+ . |.|
T Consensus 29 v~a~~~~~~a~v~vng~~~~~~~~~~~i~L~~G~n~~i~i 68 (88)
T PF12733_consen 29 VTATPEDSGATVTVNGVPVNSGGYSATIPLNEGENTVITI 68 (88)
T ss_pred EEEEECCCCEEEEEcCEEccCCCcceeeEccCCCceEEEE
Confidence 334455567899999998853 67899994 4 444
No 74
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=58.33 E-value=11 Score=30.29 Aligned_cols=27 Identities=19% Similarity=0.116 Sum_probs=22.8
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~ 106 (129)
.+.++|||+.+. ....+..||+|.+.-
T Consensus 215 ~g~V~vN~~~v~~~s~~v~~gD~isiRG 242 (267)
T PLN00051 215 SGDVRVNWREVTKNGTTLKTGDVVSVSG 242 (267)
T ss_pred cCcEEECCEEcCCCCCCCCCCCEEEEee
Confidence 478999999996 457999999998854
No 75
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=57.79 E-value=12 Score=34.27 Aligned_cols=29 Identities=28% Similarity=0.187 Sum_probs=25.6
Q ss_pred CceEEcCEEcceeEEcCCCCEEEEecCch
Q psy5454 81 AETFVNGQRIFETTILQVVVAASAVAEKQ 109 (129)
Q Consensus 81 ~~t~VNG~~I~~~~~L~~GDrI~~~~~~~ 109 (129)
-+..|||+.+.=.+.|+.||.|.|.+.|.
T Consensus 423 ~gAkVnG~ivpl~~~Lk~Gd~VEIit~k~ 451 (701)
T COG0317 423 IGAKVNGRIVPLTTKLQTGDQVEIITSKH 451 (701)
T ss_pred eEEEECCEEeccceecCCCCEEEEEeCCC
Confidence 47899999988778999999999988765
No 76
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=57.76 E-value=17 Score=28.87 Aligned_cols=26 Identities=12% Similarity=-0.023 Sum_probs=20.9
Q ss_pred CCceEEcCEEc-ceeEEcCCCCEEEEe
Q psy5454 80 EAETFVNGQRI-FETTILQVVVAASAV 105 (129)
Q Consensus 80 ~~~t~VNG~~I-~~~~~L~~GDrI~~~ 105 (129)
.+.++|||+.+ .....|+.||.|.+.
T Consensus 30 ~G~V~VNg~~~~~~~~~v~~gd~I~i~ 56 (299)
T TIGR00005 30 NGQVKVNGKVTANPKLKVKDGDRITVR 56 (299)
T ss_pred CCcEEECCEeccCcccCCCCCCEEEEe
Confidence 46899999654 466899999999984
No 77
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=56.73 E-value=11 Score=30.55 Aligned_cols=26 Identities=15% Similarity=0.213 Sum_probs=21.0
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEe
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAV 105 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~ 105 (129)
.+.++|||+.+.....+..||.|.+.
T Consensus 30 ~G~V~VNGk~v~~~~~V~~gD~V~v~ 55 (290)
T PRK10475 30 QGNVFINGKRATIGDQVKAGDVVKVN 55 (290)
T ss_pred CCcEEECCEEccCCCCcCCCCEEEEC
Confidence 46899999988655678899998874
No 78
>TIGR00724 urea_amlyse_rel biotin-dependent carboxylase uncharacterized domain. Urea amidolyase of Saccharomyces cerevisiae is a 1835 amino acid protein with an amidase domain, a biotin/lipoyl cofactor attachment domain, a carbamoyl-phosphate synthase L chain-like domain, and uncharacterized regions. It has both urea carboxylase and allophanate hydrolase activities. This alignment models a domain that represents uncharacterized prokaryotic proteins of about 300 amino acids, regions of prokaryotic urea carboxylase and of the urea carboxylase region of yeast urea amidolyase, and regions of other biotin-containing proteins.
Probab=56.45 E-value=33 Score=28.30 Aligned_cols=45 Identities=11% Similarity=0.003 Sum_probs=30.5
Q ss_pred EEEEEcCCEEEEEeCCCCCceEEcCEEcc---eeEEcCCCCEEEEecCc
Q psy5454 63 CVIAHTEGIVTVTPCSREAETFVNGQRIF---ETTILQVVVAASAVAEK 108 (129)
Q Consensus 63 c~I~~~~g~v~L~p~ss~~~t~VNG~~I~---~~~~L~~GDrI~~~~~~ 108 (129)
+.+.+..+ .+|.-++......+||+++. ....++.||+|.|+..+
T Consensus 60 ~~l~f~~~-~~iAltGA~~~~~lng~~~~~~~~~~~v~~Gd~L~~g~~~ 107 (314)
T TIGR00724 60 PTIRFHCD-VIFAVTGADTDLCLNDGQVIPQWRPYEVKRGQILSLGRLK 107 (314)
T ss_pred EEEEEcCC-eEEEEeCCCCcceeCCcccCCCceEEEECCCCEEEeCCCC
Confidence 33444433 23333345678999999983 55899999999998755
No 79
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=54.79 E-value=15 Score=26.65 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=21.4
Q ss_pred CCceEEcCEEcceeEEcCCCCEEEEe
Q psy5454 80 EAETFVNGQRIFETTILQVVVAASAV 105 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~~~ 105 (129)
.+.|.|||++..-...+..||.|.+.
T Consensus 33 ~G~V~vnG~~~Kps~~V~~gd~l~v~ 58 (133)
T PRK10348 33 GGKVHYNGQRSKPSKIVELNATLTLR 58 (133)
T ss_pred CCCEEECCEECCCCCccCCCCEEEEE
Confidence 47899999996556788999999873
No 80
>PF08308 PEGA: PEGA domain; InterPro: IPR013229 This domain is found in both archaea and bacteria and has similarity to S-layer (surface layer) proteins. It is named after the characteristic PEGA sequence motif found in this domain. The secondary structure of this domain is predicted to be beta-strands.
Probab=52.49 E-value=17 Score=22.39 Aligned_cols=22 Identities=36% Similarity=0.505 Sum_probs=16.2
Q ss_pred CEEEEEeCCCCCceEEcCEEcc
Q psy5454 70 GIVTVTPCSREAETFVNGQRIF 91 (129)
Q Consensus 70 g~v~L~p~ss~~~t~VNG~~I~ 91 (129)
|.+.|...-+++.+||||+.+.
T Consensus 2 g~l~V~s~p~gA~V~vdg~~~G 23 (71)
T PF08308_consen 2 GTLRVTSNPSGAEVYVDGKYIG 23 (71)
T ss_pred EEEEEEEECCCCEEEECCEEec
Confidence 4456655445899999999886
No 81
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]
Probab=50.59 E-value=20 Score=27.83 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=22.3
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEe
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAV 105 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~ 105 (129)
.+.+.|||+.|+ -...++.||.|.+.
T Consensus 118 HGHI~VnGk~V~iPSy~V~~gdei~V~ 144 (205)
T COG0522 118 HGHILVNGKRVNIPSYLVSPGDEISVR 144 (205)
T ss_pred cceEEECCEEeccCcEEecCCCEEEee
Confidence 468999999999 44799999999874
No 82
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=46.54 E-value=20 Score=28.04 Aligned_cols=23 Identities=4% Similarity=-0.158 Sum_probs=19.9
Q ss_pred EEcCEEcceeEEcCCCCEEEEec
Q psy5454 84 FVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 84 ~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
..||+++.....|+.||+|.+-.
T Consensus 5 ~~ng~~~~~~~~l~~gd~i~~~~ 27 (246)
T cd02558 5 DADGEPLDPDSPYRPGTFVWYYR 27 (246)
T ss_pred CCCCcCCCCCceecCCCEEEEeC
Confidence 36999998888999999998864
No 83
>KOG3517|consensus
Probab=45.83 E-value=7.6 Score=31.54 Aligned_cols=17 Identities=29% Similarity=0.473 Sum_probs=13.3
Q ss_pred CceEEcCEEcceeEEcC
Q psy5454 81 AETFVNGQRIFETTILQ 97 (129)
Q Consensus 81 ~~t~VNG~~I~~~~~L~ 97 (129)
+++||||+|+....+|+
T Consensus 12 GGVFVNGRPLPna~Rlr 28 (334)
T KOG3517|consen 12 GGVFVNGRPLPNAIRLR 28 (334)
T ss_pred cceeEcCccCcchhhhh
Confidence 69999999997655543
No 84
>COG2914 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.55 E-value=18 Score=25.02 Aligned_cols=26 Identities=4% Similarity=-0.176 Sum_probs=19.6
Q ss_pred CceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 81 AETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 81 ~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
|.+-|=|+++.-...|++||||.|-.
T Consensus 50 n~~GI~~k~~kl~~~l~dgDRVEIyR 75 (99)
T COG2914 50 NKVGIYSKPVKLDDELHDGDRVEIYR 75 (99)
T ss_pred cceeEEccccCccccccCCCEEEEec
Confidence 45555677777667899999998844
No 85
>cd00050 MH2 MH2 domain; C terminal domain of SMAD family proteins, responsible for receptor interaction, transactivation, and homo- and heterooligomerisation; also known as Domain B in dwarfin family proteins
Probab=44.44 E-value=37 Score=25.77 Aligned_cols=41 Identities=10% Similarity=0.011 Sum_probs=28.5
Q ss_pred EEEEEcCCEEEEEeCCCCCceEEcCEEcce--------eEEcCCCCEEEE
Q psy5454 63 CVIAHTEGIVTVTPCSREAETFVNGQRIFE--------TTILQVVVAASA 104 (129)
Q Consensus 63 c~I~~~~g~v~L~p~ss~~~t~VNG~~I~~--------~~~L~~GDrI~~ 104 (129)
..+..++|.|+++-+ ++..+|||.--... -.++.+|--+.+
T Consensus 69 v~L~~~~g~Vw~~~~-S~~~VFVqS~~l~~~~~~~~~~V~Kv~pg~~lKv 117 (176)
T cd00050 69 VQLSYENGEVWAYNL-SDHPIFVQSPTLDYPLGRPLLTVHKVPPGYSLKV 117 (176)
T ss_pred EEEEEeCCeEEEEEc-CCCCEEEcCCCCCcccCCCCcceEEeCCCCEEEE
Confidence 456667899999999 58999999865442 134556655554
No 86
>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional
Probab=42.60 E-value=27 Score=29.04 Aligned_cols=27 Identities=11% Similarity=-0.118 Sum_probs=21.6
Q ss_pred CCceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
.-.+-|||+.|. ..+.|+.||+|.|..
T Consensus 31 ~VAVeVNgeIVpr~~w~~t~LkeGD~IEII~ 61 (326)
T PRK11840 31 KVAVERNLEIVPRSEYGQVALEEGDELEIVH 61 (326)
T ss_pred eEEEEECCEECCHHHcCccccCCCCEEEEEE
Confidence 346779999998 567999999998844
No 87
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=41.10 E-value=31 Score=24.38 Aligned_cols=63 Identities=14% Similarity=0.134 Sum_probs=38.7
Q ss_pred cCCCCCCC-cEEEEEc-CC----EEEEEeCCCCCceEEcCEEcceeEEcCCCCEEEEec-----CchhhhccccccC
Q psy5454 54 FGPNIQPR-HCVIAHT-EG----IVTVTPCSREAETFVNGQRIFETTILQVVVAASAVA-----EKQQQSDNLKEID 119 (129)
Q Consensus 54 ~g~~I~~~-Hc~I~~~-~g----~v~L~p~ss~~~t~VNG~~I~~~~~L~~GDrI~~~~-----~~~~~~~~~~~~~ 119 (129)
...+|.+- -..|.+- +| .+.|.-..-.+.+.+||... ..-+.||+|.|.+ +.+.+...|+++.
T Consensus 33 ~aagi~~~E~V~I~Nv~NG~Rf~TYvI~g~~gSg~I~lNGAAA---r~~~~GD~vII~sy~~~~~~e~~~~~P~vv~ 106 (111)
T cd06919 33 EAAGILPYEKVLVVNVNNGARFETYVIPGERGSGVICLNGAAA---RLGQPGDRVIIMAYALMDEEEAEGHKPKVVL 106 (111)
T ss_pred HhcCCCCCCEEEEEECCCCcEEEEEEEEcCCCCCEEEeCCHHH---hcCCCCCEEEEEECccCCHHHHhcCCCEEEE
Confidence 34567663 3555553 33 44454331246889999765 4678999999977 4445556666654
No 88
>PF05726 Pirin_C: Pirin C-terminal cupin domain; InterPro: IPR008778 This entry represents C-terminal domain of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures []. Pirin is composed of two structurally similar domains arranged face to face. The N-terminal domain additionally features four beta-strands, and the C-terminal domain also includes four additional -strands and a short alpha-helix. Although the two domains are similar, the C-terminal domain of Pirin differs from the N-terminal domain as it does not contain a metal binding site and its sequence does not contain the conserved metal-coordinating residues []. Pirin is confirmed to be a member of the cupin superfamily on the basis of primary sequence and structural similarity. The presence of a metal binding site in the N-terminal beta-barrel of Pirin, may be significant in its role in regulating NFI DNA replication and NF-kappaB transcription factor activity []. Pirin structure has been found to closely resemble members of the cupin superfamily. Pirin contains the two characteristic sequences of the cupin superfamily, namely PG-(X)5-HXH-(X)4-E-(X)6-G and G-(X)5-PXG-(X)2-H-(X)3-N separated by a variable stretch of 15-50 amino acids. These motifs are best conserved in the N-terminal where the conserved histidine and glutamic acid residues correspond to the metal-coordinating residues. The C-terminal domain motifs lack the metal binding residues normally associated with the cupin fold []. Pirin was identified to be a metal-binding protein [], and was found that the metal-binding residues of Pirins are highly conserved across mammals, plants, fungi, and prokaryotic organisms. Pirin acts as a cofactor for the transcription factor NFI, the regulatory mechanism of which is generally believed to require the assistance of a metal ion []. Structural data supports the hypothesis that the bound iron of Pirin may participate in this transcriptional regulation by enhancing and stabilising the formation of the p50,Bcl3,DNA complex []. Metals have been implicated directly or indirectly in the NF-kappaB family of transcription factors that control expression of a number of early response genes associated with inflammatory responses, cell growth, cell cycle progression, and neoplastic transformation []. However, most metal-dependent transcription factors are DNA-binding proteins that bind to specific sequences when the metal binds to the protein. Pirin, on the other hand, appears to function differently and bind to the transcription factor DNA complex [].; PDB: 1J1L_A 3ACL_A 2P17_A.
Probab=39.67 E-value=31 Score=23.25 Aligned_cols=44 Identities=14% Similarity=0.163 Sum_probs=25.7
Q ss_pred CCCCcEEEEEcCCEEEEEeCCC-CCceEEcCEEcceeEEcCCCCEE
Q psy5454 58 IQPRHCVIAHTEGIVTVTPCSR-EAETFVNGQRIFETTILQVVVAA 102 (129)
Q Consensus 58 I~~~Hc~I~~~~g~v~L~p~ss-~~~t~VNG~~I~~~~~L~~GDrI 102 (129)
+.+.|..+...++.+.++..+. ..-+.+-|+|+.++ ..++|-+|
T Consensus 40 ~~~~~~~~l~~g~~i~~~a~~~~a~~lll~GePl~Ep-i~~~GpFV 84 (104)
T PF05726_consen 40 LEAGQLVVLEDGDEIELTAGEEGARFLLLGGEPLNEP-IVQYGPFV 84 (104)
T ss_dssp EETTEEEEE-SECEEEEEESSSSEEEEEEEE----S---EEETTEE
T ss_pred ECCCcEEEECCCceEEEEECCCCcEEEEEEccCCCCC-EEEECCcc
Confidence 6666777766667888887633 34567789999876 55788876
No 89
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=37.82 E-value=1.2e+02 Score=22.02 Aligned_cols=22 Identities=23% Similarity=0.398 Sum_probs=16.0
Q ss_pred cCCEEEEEeCCCCCceEEcCEEccee
Q psy5454 68 TEGIVTVTPCSREAETFVNGQRIFET 93 (129)
Q Consensus 68 ~~g~v~L~p~ss~~~t~VNG~~I~~~ 93 (129)
.++.+.+.+ ..+||||+++.++
T Consensus 78 pGd~v~i~~----~~l~vNg~~~~~~ 99 (163)
T TIGR02227 78 PGDKVEFRD----GKLYINGKKIDEP 99 (163)
T ss_pred CCCEEEEEC----CEEEECCEECccc
Confidence 456666654 5799999998764
No 90
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=35.39 E-value=15 Score=22.28 Aligned_cols=22 Identities=18% Similarity=0.128 Sum_probs=14.7
Q ss_pred eeEEcCCCCEEEEecCchhhhc
Q psy5454 92 ETTILQVVVAASAVAEKQQQSD 113 (129)
Q Consensus 92 ~~~~L~~GDrI~~~~~~~~~~~ 113 (129)
..+.|+.||.|.+...++.-++
T Consensus 44 ~~~~l~~gD~l~v~g~~~~i~~ 65 (71)
T PF02080_consen 44 GDTVLQAGDILIVVGDPEDIER 65 (71)
T ss_dssp TT-BE-TTEEEEEEEEHHHHHH
T ss_pred CCCEECCCCEEEEEECHHHHHH
Confidence 3478999999998877665443
No 91
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=31.28 E-value=60 Score=20.83 Aligned_cols=35 Identities=14% Similarity=-0.070 Sum_probs=18.6
Q ss_pred eeEEcCCCCEEEEecCchhhhccccccCCCccEEe
Q psy5454 92 ETTILQVVVAASAVAEKQQQSDNLKEIDNDTTILM 126 (129)
Q Consensus 92 ~~~~L~~GDrI~~~~~~~~~~~~~~~~~~~~~~~~ 126 (129)
..-.|..||+|.+.--...+-+..-.+|+|-+|.+
T Consensus 9 ~~y~l~pGD~l~i~v~~~~~l~~~~~V~~dG~I~l 43 (82)
T PF02563_consen 9 PEYRLGPGDVLRISVFGWPELSGEYTVDPDGTISL 43 (82)
T ss_dssp ------TT-EEEEEETT-HHHCCSEE--TTSEEEE
T ss_pred CCCEECCCCEEEEEEecCCCcccceEECCCCcEee
Confidence 44679999999987766655555777888887764
No 92
>TIGR02712 urea_carbox urea carboxylase. Members of this family are ATP-dependent urea carboxylase, including characterized members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae. The allophanate hydrolase domain of the yeast enzyme is not included in this model and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from Oleomonas sagaranensis was shown to be highly active on acetamide and formamide as well as urea.
Probab=31.11 E-value=1.5e+02 Score=28.85 Aligned_cols=31 Identities=13% Similarity=0.051 Sum_probs=26.3
Q ss_pred CCCCceEEcCEEcc--eeEEcCCCCEEEEecCc
Q psy5454 78 SREAETFVNGQRIF--ETTILQVVVAASAVAEK 108 (129)
Q Consensus 78 ss~~~t~VNG~~I~--~~~~L~~GDrI~~~~~~ 108 (129)
+......+||++|. .+..++.||++.++..+
T Consensus 523 Ga~~~~~l~g~~v~~~~~~~v~~G~~L~~g~~~ 555 (1201)
T TIGR02712 523 GAPAPATLDGQPVPQWKPITVKAGSTLSIGKIA 555 (1201)
T ss_pred CCCCcceECCEEcCCCeEEEECCCCEEEecCCC
Confidence 34578899999997 77899999999998765
No 93
>COG3450 Predicted enzyme of the cupin superfamily [General function prediction only]
Probab=30.84 E-value=1.1e+02 Score=21.61 Aligned_cols=26 Identities=31% Similarity=0.256 Sum_probs=18.3
Q ss_pred CCEEEEEeCCCCCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 69 EGIVTVTPCSREAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 69 ~g~v~L~p~ss~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
+|.+.++|- +|++ +.++.||.+.+-+
T Consensus 71 ~G~v~~T~d--------~Ge~----v~~~aGD~~~~~~ 96 (116)
T COG3450 71 EGRVEVTPD--------GGEP----VEVRAGDSFVFPA 96 (116)
T ss_pred eeEEEEECC--------CCeE----EEEcCCCEEEECC
Confidence 377777776 3444 6889999988743
No 94
>TIGR00478 tly hemolysin TlyA family protein. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).
Probab=30.64 E-value=51 Score=25.75 Aligned_cols=27 Identities=11% Similarity=0.251 Sum_probs=21.8
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~~~ 106 (129)
.+.++|||+++. ....+..||.|.+..
T Consensus 24 ~G~V~Vng~~v~k~s~~V~~~d~I~v~~ 51 (228)
T TIGR00478 24 KGFVLVNGKKVDKPSALVDFDAKIELLQ 51 (228)
T ss_pred CCcEEECCEEeCCCCCCCCCCCEEeccC
Confidence 468999999996 447888999988754
No 95
>KOG3862|consensus
Probab=30.33 E-value=24 Score=28.96 Aligned_cols=12 Identities=33% Similarity=0.634 Sum_probs=10.4
Q ss_pred CceEEcCEEcce
Q psy5454 81 AETFVNGQRIFE 92 (129)
Q Consensus 81 ~~t~VNG~~I~~ 92 (129)
+++||||+|+..
T Consensus 17 GGvFVNGRPlpd 28 (327)
T KOG3862|consen 17 GGVFVNGRPLPD 28 (327)
T ss_pred cceeecCccCch
Confidence 699999999863
No 96
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=29.44 E-value=71 Score=21.87 Aligned_cols=20 Identities=10% Similarity=-0.059 Sum_probs=14.9
Q ss_pred CCceEEcCEEcceeEEcCCC
Q psy5454 80 EAETFVNGQRIFETTILQVV 99 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~G 99 (129)
.+++.|||+...++..+.++
T Consensus 7 ~g~~~i~g~~y~~~viv~p~ 26 (109)
T cd00248 7 PGGFRIAGQVYRGPLLVLPD 26 (109)
T ss_pred CCEEEECCEEEeeCEEEeCC
Confidence 56788888888777766666
No 97
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=29.43 E-value=59 Score=23.52 Aligned_cols=69 Identities=19% Similarity=0.211 Sum_probs=41.5
Q ss_pred cCCCCCC-CcEEEEEc-CC----EEEEEeCCCCCceEEcCEEcceeEEcCCCCEEEEec-----Cchhhhcccccc--CC
Q psy5454 54 FGPNIQP-RHCVIAHT-EG----IVTVTPCSREAETFVNGQRIFETTILQVVVAASAVA-----EKQQQSDNLKEI--DN 120 (129)
Q Consensus 54 ~g~~I~~-~Hc~I~~~-~g----~v~L~p~ss~~~t~VNG~~I~~~~~L~~GDrI~~~~-----~~~~~~~~~~~~--~~ 120 (129)
...+|.+ +-..|.+- +| .+.|.-..-.+.+.+||... ..-+.||+|.|.+ +.+.....|+++ |.
T Consensus 34 ~aagi~p~E~V~V~Nv~NG~Rf~TYvI~g~~GSg~I~lNGAAA---r~~~~GD~vII~ay~~~~~~e~~~~~P~vv~vd~ 110 (126)
T PRK05449 34 DAAGILENEKVQIVNVNNGARFETYVIAGERGSGVICLNGAAA---RLVQVGDLVIIAAYAQMDEEEAKTHKPKVVFVDE 110 (126)
T ss_pred HhcCCCCCCEEEEEECCCCcEEEEEEEEcCCCCCEEEeCCHHH---hcCCCCCEEEEEECccCCHHHHhcCCCEEEEECC
Confidence 3457777 34555553 33 34444321235789999865 4678999999977 444455667664 44
Q ss_pred CccEE
Q psy5454 121 DTTIL 125 (129)
Q Consensus 121 ~~~~~ 125 (129)
+-+|.
T Consensus 111 ~N~i~ 115 (126)
T PRK05449 111 DNRIK 115 (126)
T ss_pred CCCEE
Confidence 44443
No 98
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=28.70 E-value=1.2e+02 Score=17.39 Aligned_cols=40 Identities=15% Similarity=0.110 Sum_probs=23.8
Q ss_pred CCEEEEEeCCCCCceEEcCEEcce-eEEcCCCCEEEEecCc
Q psy5454 69 EGIVTVTPCSREAETFVNGQRIFE-TTILQVVVAASAVAEK 108 (129)
Q Consensus 69 ~g~v~L~p~ss~~~t~VNG~~I~~-~~~L~~GDrI~~~~~~ 108 (129)
.|.-++.|.+....+||--..+.. ...+.+||+|.+...+
T Consensus 9 ~g~gfv~~~~~~~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~ 49 (64)
T smart00357 9 KGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVS 49 (64)
T ss_pred CCeeEEecCCCCccEEEEhHHhhcCCCcCCCCCEEEEEEEE
Confidence 355566665332468873222211 4568999999987654
No 99
>PF07908 D-aminoacyl_C: D-aminoacylase, C-terminal region; InterPro: IPR012855 D-aminoacylase (Q9AGH8 from SWISSPROT, 3.5.1.81 from EC) hydrolyses a wide variety of N-acyl derivatives of neutral D-amino acids, in a zinc-dependent manner. The enzyme is composed of a small beta-barrel domain and a larger catalytic alpha/beta-barrel that contains a short alpha/beta insert. The overall structure shares significant similarity to the alpha/beta-barrel amidohydrolase superfamily, in which the beta-strands in both barrels superimpose well []. The C-terminal region featured in this entry forms part of the beta-barrel domain, together with a short N-terminal segment. This domain does not seem to contribute to the substrate-binding site or to be involved in the catalytic process.; GO: 0008270 zinc ion binding, 0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides; PDB: 3GIQ_B 3GIP_B 1V4Y_A 1M7J_A 1RK5_A 1RJP_A 1RJR_A 1RJQ_A 1RK6_A 1V51_A.
Probab=28.63 E-value=37 Score=19.99 Aligned_cols=11 Identities=45% Similarity=0.646 Sum_probs=9.0
Q ss_pred CceEEcCEEcc
Q psy5454 81 AETFVNGQRIF 91 (129)
Q Consensus 81 ~~t~VNG~~I~ 91 (129)
..|+|||+.+-
T Consensus 21 ~~V~VNG~~vv 31 (48)
T PF07908_consen 21 DYVFVNGQIVV 31 (48)
T ss_dssp EEEEETTEEEE
T ss_pred EEEEECCEEEE
Confidence 47999999874
No 100
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=28.53 E-value=55 Score=21.59 Aligned_cols=31 Identities=10% Similarity=0.093 Sum_probs=19.3
Q ss_pred CCCceEEcCEEcceeEEcCCCCEEE--EecCchh
Q psy5454 79 REAETFVNGQRIFETTILQVVVAAS--AVAEKQQ 110 (129)
Q Consensus 79 s~~~t~VNG~~I~~~~~L~~GDrI~--~~~~~~~ 110 (129)
+...+||-...| .+.-|+.||+|. +.+.+..
T Consensus 27 ~~~DvYVs~~qI-rrf~LR~GD~V~G~vr~p~~~ 59 (78)
T PF07497_consen 27 SPDDVYVSPSQI-RRFGLRTGDLVEGQVRPPREG 59 (78)
T ss_dssp STTSEEE-CCCC-CCTT--TTEEEEEEEE--STT
T ss_pred CCCCEEECHHHH-HHcCCCCCCEEEEEEeCCCCC
Confidence 357899988888 558999999997 4444433
No 101
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=28.39 E-value=63 Score=23.36 Aligned_cols=69 Identities=13% Similarity=0.123 Sum_probs=41.7
Q ss_pred cCCCCCC-CcEEEEEc-CC----EEEEEeCCCCCceEEcCEEcceeEEcCCCCEEEEec-----Cchhhhcccccc--CC
Q psy5454 54 FGPNIQP-RHCVIAHT-EG----IVTVTPCSREAETFVNGQRIFETTILQVVVAASAVA-----EKQQQSDNLKEI--DN 120 (129)
Q Consensus 54 ~g~~I~~-~Hc~I~~~-~g----~v~L~p~ss~~~t~VNG~~I~~~~~L~~GDrI~~~~-----~~~~~~~~~~~~--~~ 120 (129)
...+|.+ +...+.+- +| .+.|.-.--.+-+.+||... ..-+.||+|.|.+ +.+.....|+++ |.
T Consensus 34 ~aagi~p~E~V~V~Nv~NG~Rf~TYvI~G~~GSg~I~lNGAAA---rl~~~GD~VII~sy~~~~~~e~~~~~P~vv~vd~ 110 (126)
T TIGR00223 34 DAAGILENEKVDIVNVNNGKRFSTYAIAGKRGSRIICVNGAAA---RCVSVGDIVIIASYVTMPDEEARTHRPNVAYFEG 110 (126)
T ss_pred HhcCCCCCCEEEEEECCCCcEEEEEEEEcCCCCCEEEeCCHHH---hcCCCCCEEEEEECCcCCHHHHhcCCCEEEEECC
Confidence 3457776 44555553 33 34444321135789999765 4678999999877 444455677765 34
Q ss_pred CccEE
Q psy5454 121 DTTIL 125 (129)
Q Consensus 121 ~~~~~ 125 (129)
+-+|.
T Consensus 111 ~N~i~ 115 (126)
T TIGR00223 111 DNEIK 115 (126)
T ss_pred CCCEE
Confidence 44554
No 102
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=28.01 E-value=53 Score=22.55 Aligned_cols=27 Identities=11% Similarity=-0.096 Sum_probs=19.6
Q ss_pred CCceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 80 EAETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 80 ~~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
+--|.+|++-=. ++..|.+||.|.+.+
T Consensus 61 GiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 61 GIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred cEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 345778886432 557999999999865
No 103
>cd01716 Hfq Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.
Probab=27.29 E-value=67 Score=20.25 Aligned_cols=29 Identities=17% Similarity=0.056 Sum_probs=19.5
Q ss_pred eEEcCEEcceeEEcCCCCEEEEecCchhh
Q psy5454 83 TFVNGQRIFETTILQVVVAASAVAEKQQQ 111 (129)
Q Consensus 83 t~VNG~~I~~~~~L~~GDrI~~~~~~~~~ 111 (129)
..+||.++.+...=.+.-.|.+..+.+||
T Consensus 17 ~L~NG~~l~G~I~~fD~ftVll~~~g~qq 45 (61)
T cd01716 17 YLVNGVQLKGQIESFDNFTVLLESDGKQQ 45 (61)
T ss_pred EEeCCcEEEEEEEEEcceEEEEEECCcEE
Confidence 35688888776666666666666665554
No 104
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=26.57 E-value=89 Score=21.46 Aligned_cols=24 Identities=17% Similarity=0.081 Sum_probs=15.7
Q ss_pred CCceEEcCEEcceeEEcCCCCEEE
Q psy5454 80 EAETFVNGQRIFETTILQVVVAAS 103 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~GDrI~ 103 (129)
.+++.|||+...+...+.+.-.+.
T Consensus 7 ~g~~~i~g~~y~~sviv~p~~~~~ 30 (109)
T cd05560 7 DGYVEINDQRYEHSLIVTPDELIT 30 (109)
T ss_pred CCEEEECCEEEecCEEEECCceee
Confidence 567788888777666665554433
No 105
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=26.49 E-value=2.2e+02 Score=21.09 Aligned_cols=22 Identities=27% Similarity=0.209 Sum_probs=16.2
Q ss_pred cCCEEEEEeCCCCCceEEcCEEccee
Q psy5454 68 TEGIVTVTPCSREAETFVNGQRIFET 93 (129)
Q Consensus 68 ~~g~v~L~p~ss~~~t~VNG~~I~~~ 93 (129)
.++.|.+.+ ..++|||+++.+.
T Consensus 92 pGD~V~i~~----~~v~INg~~~~~~ 113 (171)
T TIGR02771 92 PGDRVTVRA----DVVAINGQLLPYS 113 (171)
T ss_pred CCCEEEEEC----CEEEECCEEcccc
Confidence 467777753 4899999988643
No 106
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=26.39 E-value=64 Score=26.04 Aligned_cols=25 Identities=16% Similarity=-0.083 Sum_probs=22.2
Q ss_pred CCceEEcCEEcc-eeEEcCCCCEEEE
Q psy5454 80 EAETFVNGQRIF-ETTILQVVVAASA 104 (129)
Q Consensus 80 ~~~t~VNG~~I~-~~~~L~~GDrI~~ 104 (129)
.+.+.||++.+. ....++-||.|++
T Consensus 204 ~g~VkVN~k~v~~~s~~v~~GDliSi 229 (257)
T COG2302 204 KGKVKVNWKVVDKASYEVQEGDLISI 229 (257)
T ss_pred cCceEEeeEEeccccceeccCCEEEE
Confidence 478999999998 6679999999986
No 107
>PF08531 Bac_rhamnosid_N: Alpha-L-rhamnosidase N-terminal domain; InterPro: IPR013737 This domain is found in bacterial rhamnosidase A and B enzymes and is probably involved in substrate recognition. ; PDB: 2OKX_B.
Probab=25.88 E-value=59 Score=23.92 Aligned_cols=28 Identities=21% Similarity=0.261 Sum_probs=15.9
Q ss_pred CEEEEEeCCCCCceEEcCEEcceeEEcCCC
Q psy5454 70 GIVTVTPCSREAETFVNGQRIFETTILQVV 99 (129)
Q Consensus 70 g~v~L~p~ss~~~t~VNG~~I~~~~~L~~G 99 (129)
..+++.-. .-...||||++|.. -.|.+|
T Consensus 6 A~l~isa~-g~Y~l~vNG~~V~~-~~l~P~ 33 (172)
T PF08531_consen 6 ARLYISAL-GRYELYVNGERVGD-GPLAPG 33 (172)
T ss_dssp -EEEEEEE-SEEEEEETTEEEEE-E-----
T ss_pred EEEEEEeC-eeEEEEECCEEeeC-Cccccc
Confidence 45666666 35789999999963 334443
No 108
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=25.53 E-value=73 Score=19.22 Aligned_cols=41 Identities=17% Similarity=0.109 Sum_probs=29.9
Q ss_pred CCEEEEEeCCCCCceEEcCEEccee--EEcCCCCEEEEecCch
Q psy5454 69 EGIVTVTPCSREAETFVNGQRIFET--TILQVVVAASAVAEKQ 109 (129)
Q Consensus 69 ~g~v~L~p~ss~~~t~VNG~~I~~~--~~L~~GDrI~~~~~~~ 109 (129)
.|-=+|.+......+|+.-..+... ..|..||+|.+..++.
T Consensus 12 kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 12 KGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG 54 (65)
T ss_pred CCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEEC
Confidence 4555777765567888877777654 7899999999876554
No 109
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=24.79 E-value=1.1e+02 Score=19.26 Aligned_cols=41 Identities=22% Similarity=0.178 Sum_probs=28.2
Q ss_pred CCEEEEEeCCCCCceEEcCEEccee--EEcCCCCEEEEecCch
Q psy5454 69 EGIVTVTPCSREAETFVNGQRIFET--TILQVVVAASAVAEKQ 109 (129)
Q Consensus 69 ~g~v~L~p~ss~~~t~VNG~~I~~~--~~L~~GDrI~~~~~~~ 109 (129)
.|-=||+|.+....+||--.-+... ..|..||+|.+..+..
T Consensus 16 kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~ 58 (70)
T PRK10354 16 KGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESG 58 (70)
T ss_pred CCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEEC
Confidence 4444788775445788866666532 5799999999866443
No 110
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=24.72 E-value=2.5e+02 Score=20.98 Aligned_cols=20 Identities=30% Similarity=0.280 Sum_probs=15.2
Q ss_pred cCCEEEEEeCCCCCceEEcCEEcc
Q psy5454 68 TEGIVTVTPCSREAETFVNGQRIF 91 (129)
Q Consensus 68 ~~g~v~L~p~ss~~~t~VNG~~I~ 91 (129)
.++.|.+.+ ..++|||+.+.
T Consensus 96 pGD~V~~~~----~~l~VNG~~v~ 115 (178)
T PRK13884 96 KGDAVSVTD----DGVRVNGELLP 115 (178)
T ss_pred CCcEEEEEC----CEEEECCEEcc
Confidence 466777764 47999999984
No 111
>PF03166 MH2: MH2 domain; InterPro: IPR001132 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the SMAD (Mothers against decapentaplegic (MAD) homologue) (also called MH2 for MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C terminus of MH2 [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1MK2_A 1U7F_A 1MJS_A 1KHU_A 1DD1_C 1G88_A 1U7V_B 1MR1_B 1YGS_A 3DIT_B ....
Probab=24.04 E-value=59 Score=24.31 Aligned_cols=26 Identities=15% Similarity=0.210 Sum_probs=18.1
Q ss_pred EEEEEc-CCEEEEEeCCCCCceEEcCEE
Q psy5454 63 CVIAHT-EGIVTVTPCSREAETFVNGQR 89 (129)
Q Consensus 63 c~I~~~-~g~v~L~p~ss~~~t~VNG~~ 89 (129)
..|..+ +|.|.|+-. +...+||+.--
T Consensus 68 i~l~~~~~G~V~l~n~-s~~pVFVqS~~ 94 (181)
T PF03166_consen 68 IKLSYEEDGNVWLYNR-SDSPVFVQSPT 94 (181)
T ss_dssp EEEEEETTTEEEEEE--SSS-EEEE-HH
T ss_pred EEEEEecCCeEEEEEC-CCCCEEEccCC
Confidence 566677 789999999 57899998643
No 112
>PRK06788 flagellar motor switch protein; Validated
Probab=23.29 E-value=1.2e+02 Score=21.51 Aligned_cols=48 Identities=6% Similarity=0.149 Sum_probs=31.5
Q ss_pred CCEEEEE-eCCCCCceEEcCEEcceeEEcCCCCEEEEe----cCchhhhcccc
Q psy5454 69 EGIVTVT-PCSREAETFVNGQRIFETTILQVVVAASAV----AEKQQQSDNLK 116 (129)
Q Consensus 69 ~g~v~L~-p~ss~~~t~VNG~~I~~~~~L~~GDrI~~~----~~~~~~~~~~~ 116 (129)
++.+.|. +.++.-.++|||+++..-..-..+++..+. -.+++|++.||
T Consensus 58 GDVI~Ldk~~~dpv~v~Vng~~~f~G~~Gv~~~~~AVrItei~~~~~~~~~~~ 110 (119)
T PRK06788 58 GDVLEVEKNLGHKVDVYLSNMKVGIGEAIVMDEKFGIIISEIEADKKQAALMK 110 (119)
T ss_pred CCEEEeCCcCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEecChHHHHHHHH
Confidence 4566663 344557899999999866677777776542 24556666554
No 113
>TIGR02383 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PubMed:8197116). The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.
Probab=23.03 E-value=79 Score=19.95 Aligned_cols=28 Identities=18% Similarity=0.069 Sum_probs=18.6
Q ss_pred EEcCEEcceeEEcCCCCEEEEecCchhh
Q psy5454 84 FVNGQRIFETTILQVVVAASAVAEKQQQ 111 (129)
Q Consensus 84 ~VNG~~I~~~~~L~~GDrI~~~~~~~~~ 111 (129)
.+||.++.+...=.+.-.|.+..+.+||
T Consensus 22 L~nG~~l~G~I~~fD~ftVll~~~g~qq 49 (61)
T TIGR02383 22 LVNGVQLKGVIESFDNFTVLLESQGKQQ 49 (61)
T ss_pred EeCCcEEEEEEEEEeeeEEEEEECCcEE
Confidence 4688888776666666666666665554
No 114
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=22.71 E-value=33 Score=24.67 Aligned_cols=12 Identities=25% Similarity=0.576 Sum_probs=8.8
Q ss_pred CceEEcCEEcce
Q psy5454 81 AETFVNGQRIFE 92 (129)
Q Consensus 81 ~~t~VNG~~I~~ 92 (129)
+++|+||+|+..
T Consensus 9 Gg~~~nGrPLp~ 20 (125)
T PF00292_consen 9 GGVFINGRPLPN 20 (125)
T ss_dssp S-EEETTSSS-H
T ss_pred CceeeCCccCcH
Confidence 799999999873
No 115
>PRK00395 hfq RNA-binding protein Hfq; Provisional
Probab=22.62 E-value=79 Score=21.01 Aligned_cols=28 Identities=14% Similarity=0.012 Sum_probs=17.8
Q ss_pred EEcCEEcceeEEcCCCCEEEEecCchhh
Q psy5454 84 FVNGQRIFETTILQVVVAASAVAEKQQQ 111 (129)
Q Consensus 84 ~VNG~~I~~~~~L~~GDrI~~~~~~~~~ 111 (129)
.+||.++.+.+.=.+.-.|.+..+.+||
T Consensus 26 L~NG~~l~G~I~~fD~ftVll~~~gkqq 53 (79)
T PRK00395 26 LVNGIKLQGQIESFDNFVVLLRNTGKSQ 53 (79)
T ss_pred EeCCcEEEEEEEEEccEEEEEEECCcEE
Confidence 4577777766666666666666665544
No 116
>smart00524 DWB Domain B in dwarfin family proteins.
Probab=21.93 E-value=3.3e+02 Score=20.54 Aligned_cols=41 Identities=12% Similarity=0.054 Sum_probs=29.3
Q ss_pred EEEEEcCCEEEEEeCCCCCceEEcCEEcc--------eeEEcCCCCEEEE
Q psy5454 63 CVIAHTEGIVTVTPCSREAETFVNGQRIF--------ETTILQVVVAASA 104 (129)
Q Consensus 63 c~I~~~~g~v~L~p~ss~~~t~VNG~~I~--------~~~~L~~GDrI~~ 104 (129)
..+..++|.|+++-+ ++..+||+.--.. ...+|.+|--+.+
T Consensus 64 v~L~~~~g~Vw~~~~-s~~~VFVqS~~~~~~~~~~~~~V~Kv~pg~~lKv 112 (171)
T smart00524 64 VQLSYENGDVWLYNR-SDSPIFVQSPYLDEPGGRTLDTVHKLPPGYSIKV 112 (171)
T ss_pred eEEEEeCCeEEEEEc-CCCCeEEcCCCcccccCCCCcceEEECCCCeEEE
Confidence 355667899999999 5889999875443 3346677766665
No 117
>COG0355 AtpC F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit) [Energy production and conversion]
Probab=21.74 E-value=1.2e+02 Score=21.88 Aligned_cols=34 Identities=21% Similarity=0.365 Sum_probs=26.1
Q ss_pred CCCCCcEEEEE--cCCEEEEEeCCC-C-CceEEcCEEc
Q psy5454 57 NIQPRHCVIAH--TEGIVTVTPCSR-E-AETFVNGQRI 90 (129)
Q Consensus 57 ~I~~~Hc~I~~--~~g~v~L~p~ss-~-~~t~VNG~~I 90 (129)
+|+|.|+-+.- ..|.+.+...+. . ..++|+|--+
T Consensus 33 GILp~H~Plit~Lk~g~v~i~~~~~~~~~~i~VsgGfl 70 (135)
T COG0355 33 GILPGHAPLITALKPGVVRIKTEDGDKEEKIAVSGGFL 70 (135)
T ss_pred ecCCCCccceeeecCcEEEEEEcCCCceEEEEEeccEE
Confidence 89999988865 578888887742 3 3889998655
No 118
>PF09014 Sushi_2: Beta-2-glycoprotein-1 fifth domain; InterPro: IPR015104 The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively charged compounds and subsequent capture for binding of anti-b2GP-1 antibodies []. ; PDB: 1C1Z_A 3OP8_B 2KRI_A 1QUB_A 1G4G_A 1G4F_A.
Probab=21.58 E-value=63 Score=21.80 Aligned_cols=26 Identities=15% Similarity=0.132 Sum_probs=17.9
Q ss_pred CCceEEcCEEcc----eeEEcCCCCEEEEe
Q psy5454 80 EAETFVNGQRIF----ETTILQVVVAASAV 105 (129)
Q Consensus 80 ~~~t~VNG~~I~----~~~~L~~GDrI~~~ 105 (129)
.+.+..||+++. .+-...|||.|.+=
T Consensus 10 ra~Vly~g~k~~i~d~~~~~v~Hge~Vsff 39 (85)
T PF09014_consen 10 RARVLYNGEKVWIQDLFKNGVLHGEIVSFF 39 (85)
T ss_dssp S-EEEETTEEEEHHHHTTT-BETT-EEEEE
T ss_pred EEEEEECCEEechhhcccCceeeCCEEEEE
Confidence 578999999885 33468899999873
No 119
>COG1977 MoaD Molybdopterin converting factor, small subunit [Coenzyme metabolism]
Probab=21.51 E-value=96 Score=20.17 Aligned_cols=19 Identities=11% Similarity=-0.244 Sum_probs=14.4
Q ss_pred EEcceeEEcCCCCEEEEec
Q psy5454 88 QRIFETTILQVVVAASAVA 106 (129)
Q Consensus 88 ~~I~~~~~L~~GDrI~~~~ 106 (129)
......+.|++||.|.|-.
T Consensus 61 ~~~~~~t~L~dGDeVa~~P 79 (84)
T COG1977 61 FLVGLDTPLKDGDEVAFFP 79 (84)
T ss_pred eeccccccCCCCCEEEEeC
Confidence 3444668999999998754
No 120
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=21.29 E-value=1.6e+02 Score=18.75 Aligned_cols=36 Identities=14% Similarity=0.204 Sum_probs=25.3
Q ss_pred CCEEEEE-eCCCCCceEEcCEEcceeEEcCCCCEEEE
Q psy5454 69 EGIVTVT-PCSREAETFVNGQRIFETTILQVVVAASA 104 (129)
Q Consensus 69 ~g~v~L~-p~ss~~~t~VNG~~I~~~~~L~~GDrI~~ 104 (129)
++.+.|. +.++.-.++|||+++.....-..|++..+
T Consensus 32 Gdvi~L~~~~~~~v~l~v~g~~~~~g~lg~~~~~~av 68 (77)
T TIGR02480 32 GSVIELDKLAGEPLDILVNGRLIARGEVVVVEDKFGI 68 (77)
T ss_pred CCEEEcCCCCCCcEEEEECCEEEEEEEEEEECCEEEE
Confidence 4455553 34456789999999987667777777665
No 121
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=20.95 E-value=1.7e+02 Score=20.51 Aligned_cols=43 Identities=14% Similarity=0.051 Sum_probs=27.3
Q ss_pred CCCcEEEEEcCCEEEEEeCCCCCceEEcCEEcceeEEcCCCCEEEEec
Q psy5454 59 QPRHCVIAHTEGIVTVTPCSREAETFVNGQRIFETTILQVVVAASAVA 106 (129)
Q Consensus 59 ~~~Hc~I~~~~g~v~L~p~ss~~~t~VNG~~I~~~~~L~~GDrI~~~~ 106 (129)
...|+.+.+..+.....+. ..-+.+++.. ...|+.||.|..--
T Consensus 24 ~~~~~lV~f~~~~~~~v~~--~~iI~~~~~~---~~~L~~GD~VLA~~ 66 (124)
T PF15057_consen 24 SSGQFLVEFDDGDTQEVPI--SDIIALSDAM---RHSLQVGDKVLAPW 66 (124)
T ss_pred CCCEEEEEECCCCEEEeCh--HHeEEccCcc---cCcCCCCCEEEEec
Confidence 6677777776665555554 2355665554 35788888876543
No 122
>PF09138 Urm1: Urm1 (Ubiquitin related modifier); InterPro: IPR015221 Ubiquitin related modifier 1 (Urm1) is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like urmylation pathway []. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily []. ; GO: 0034227 tRNA thio-modification, 0005737 cytoplasm; PDB: 2AX5_A 2QJL_A 2PKO_A 1WGK_A 1XO3_A 2K9X_A.
Probab=20.65 E-value=55 Score=22.43 Aligned_cols=26 Identities=12% Similarity=0.037 Sum_probs=17.2
Q ss_pred CceEEcCEEcc----eeEEcCCCCEEEEec
Q psy5454 81 AETFVNGQRIF----ETTILQVVVAASAVA 106 (129)
Q Consensus 81 ~~t~VNG~~I~----~~~~L~~GDrI~~~~ 106 (129)
--+.||+.--. ....|++||.|.|.+
T Consensus 62 ILvLINd~DwEl~g~~~y~l~~~D~I~FiS 91 (96)
T PF09138_consen 62 ILVLINDADWELLGEEDYVLKDGDNITFIS 91 (96)
T ss_dssp EEEEETTCEHHHHTCCCSB--TTEEEEEEE
T ss_pred EEEEEcCccceeecCcceEcCCCCEEEEEc
Confidence 46777876543 457999999998865
No 123
>PF06241 DUF1012: Protein of unknown function (DUF1012); InterPro: IPR010420 This entry represents the CASTOR/POLLUX/SYM8 family of ion channels, which are found in plants. They have been implicated in modulating the nuclear membrane envelope potential [].
Probab=20.16 E-value=1e+02 Score=24.00 Aligned_cols=28 Identities=14% Similarity=0.161 Sum_probs=20.2
Q ss_pred CceEEcCEEcc---eeEEcCCCCEEEEecCc
Q psy5454 81 AETFVNGQRIF---ETTILQVVVAASAVAEK 108 (129)
Q Consensus 81 ~~t~VNG~~I~---~~~~L~~GDrI~~~~~~ 108 (129)
+|++-||+-+- +...|+.||.+.+.|++
T Consensus 120 CGv~r~GkI~fhP~Dd~vL~e~DklLvIa~~ 150 (206)
T PF06241_consen 120 CGVKRDGKIVFHPDDDYVLREGDKLLVIAPV 150 (206)
T ss_pred eeeeeCCeeEECCCCCceeecCCEEEEEeec
Confidence 46677776553 33578999999998866
No 124
>PRK09890 cold shock protein CspG; Provisional
Probab=20.16 E-value=2.2e+02 Score=17.84 Aligned_cols=42 Identities=21% Similarity=0.193 Sum_probs=29.5
Q ss_pred CCEEEEEeCCCCCceEEcCEEccee--EEcCCCCEEEEecCchh
Q psy5454 69 EGIVTVTPCSREAETFVNGQRIFET--TILQVVVAASAVAEKQQ 110 (129)
Q Consensus 69 ~g~v~L~p~ss~~~t~VNG~~I~~~--~~L~~GDrI~~~~~~~~ 110 (129)
.|-=||+|.+....+||.=..+... ..|..||+|.+..+.-+
T Consensus 16 kGfGFI~~~~g~~dvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~ 59 (70)
T PRK09890 16 KGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQ 59 (70)
T ss_pred CCcEEEecCCCCceEEEEEeeeccCCCCCCCCCCEEEEEEEECC
Confidence 4555888875456788877666532 57999999998765443
No 125
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=20.04 E-value=1.2e+02 Score=21.22 Aligned_cols=20 Identities=10% Similarity=-0.004 Sum_probs=13.7
Q ss_pred CCceEEcCEEcceeEEcCCC
Q psy5454 80 EAETFVNGQRIFETTILQVV 99 (129)
Q Consensus 80 ~~~t~VNG~~I~~~~~L~~G 99 (129)
.+.+.|||+.-.....+.++
T Consensus 7 ~G~i~i~g~~y~~~viv~p~ 26 (117)
T cd05126 7 FGSITVGGETYEHDIVVYPD 26 (117)
T ss_pred CCEEEECCEEEcCCEEEeCC
Confidence 46777888777666666555
Done!