Query 027058
Match_columns 229
No_of_seqs 149 out of 1244
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 04:22:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027058.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027058hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK12426 elongation factor P; 100.0 5.5E-76 1.2E-80 499.7 25.5 185 45-229 1-185 (185)
2 PRK14578 elongation factor P; 100.0 9.2E-74 2E-78 487.2 25.7 185 45-229 1-187 (187)
3 PRK04542 elongation factor P; 100.0 1.2E-73 2.5E-78 487.1 25.1 185 45-229 1-188 (189)
4 TIGR02178 yeiP elongation fact 100.0 1.3E-72 2.9E-77 479.5 25.3 183 47-229 1-186 (186)
5 PRK00529 elongation factor P; 100.0 1.8E-71 4E-76 473.0 25.3 185 45-229 1-185 (186)
6 TIGR00038 efp translation elon 100.0 2.6E-71 5.7E-76 471.5 25.0 184 46-229 1-184 (184)
7 COG0231 Efp Translation elonga 100.0 6.3E-46 1.4E-50 300.6 17.5 131 43-173 1-131 (131)
8 TIGR00037 eIF_5A translation i 100.0 1.3E-37 2.9E-42 251.7 17.3 121 43-165 4-125 (130)
9 PRK03999 translation initiatio 100.0 5.1E-36 1.1E-40 242.1 15.8 118 44-163 4-122 (129)
10 PLN03107 eukaryotic translatio 100.0 8.9E-33 1.9E-37 230.3 17.5 126 38-163 13-147 (159)
11 PF09285 Elong-fact-P_C: Elong 99.9 4.3E-27 9.3E-32 164.5 7.1 56 173-228 1-56 (56)
12 smart00841 Elong-fact-P_C Elon 99.9 3.4E-27 7.4E-32 165.0 6.5 56 173-228 1-56 (56)
13 cd05794 S1_EF-P_repeat_2 S1_EF 99.9 3.6E-27 7.8E-32 164.9 6.6 56 173-228 1-56 (56)
14 cd04470 S1_EF-P_repeat_1 S1_EF 99.9 5.2E-23 1.1E-27 146.3 7.8 61 110-170 1-61 (61)
15 PTZ00328 eukaryotic initiation 99.9 3.5E-21 7.5E-26 160.8 14.8 122 40-161 17-150 (166)
16 PF08207 EFP_N: Elongation fac 99.9 3.8E-21 8.2E-26 135.4 9.0 58 47-104 1-58 (58)
17 PF01132 EFP: Elongation facto 99.8 1.1E-20 2.3E-25 131.8 6.5 55 111-165 1-55 (55)
18 KOG3271 Translation initiation 99.7 4.2E-17 9.1E-22 132.8 9.1 112 43-154 18-133 (156)
19 cd04463 S1_EF_like S1_EF_like: 99.7 4.7E-17 1E-21 112.7 6.5 55 112-167 1-55 (55)
20 cd04467 S1_aIF5A S1_aIF5A: Arc 98.7 3.8E-08 8.2E-13 69.3 6.3 54 109-164 1-54 (57)
21 COG1499 NMD3 NMD protein affec 98.3 6.9E-06 1.5E-10 76.8 12.1 110 43-168 239-352 (355)
22 PF01287 eIF-5a: Eukaryotic el 97.3 0.0011 2.4E-08 48.3 6.6 55 108-163 1-62 (69)
23 cd04468 S1_eIF5A S1_eIF5A: Euk 93.9 0.17 3.7E-06 37.0 5.4 51 109-159 1-54 (69)
24 cd04469 S1_Hex1 S1_Hex1: Hex1, 85.5 3.5 7.7E-05 30.6 6.1 52 112-163 3-61 (75)
25 PF00900 Ribosomal_S4e: Riboso 77.9 2.6 5.7E-05 31.2 3.1 32 193-224 43-75 (77)
26 PF08605 Rad9_Rad53_bind: Fung 75.5 6.8 0.00015 32.0 5.1 40 45-84 54-103 (131)
27 PRK05338 rplS 50S ribosomal pr 69.3 26 0.00056 28.1 7.0 67 46-112 14-88 (116)
28 PF02941 FeThRed_A: Ferredoxin 67.4 2.6 5.7E-05 30.6 0.9 18 159-176 39-56 (67)
29 PF01245 Ribosomal_L19: Riboso 63.6 25 0.00055 27.9 5.9 68 46-113 14-89 (113)
30 TIGR01024 rplS_bact ribosomal 62.0 40 0.00086 26.9 6.8 65 46-111 14-87 (113)
31 CHL00084 rpl19 ribosomal prote 60.9 50 0.0011 26.5 7.1 66 46-112 18-92 (117)
32 PF13275 S4_2: S4 domain; PDB: 52.8 14 0.00031 26.5 2.6 19 49-67 47-65 (65)
33 PF13509 S1_2: S1 domain; PDB: 52.4 23 0.00051 24.5 3.6 36 123-161 15-50 (61)
34 KOG1999 RNA polymerase II tran 52.3 1.2E+02 0.0027 32.4 10.1 173 45-222 334-545 (1024)
35 PRK11507 ribosome-associated p 47.6 19 0.00041 26.4 2.6 20 48-67 50-69 (70)
36 PF09262 PEX-1N: Peroxisome bi 46.0 14 0.0003 27.6 1.7 63 130-206 12-78 (80)
37 PF13785 DUF4178: Domain of un 43.2 1.6E+02 0.0034 23.0 14.0 23 51-73 1-23 (140)
38 TIGR00523 eIF-1A eukaryotic/ar 42.6 1.1E+02 0.0024 23.6 6.4 52 162-221 6-69 (99)
39 PRK14560 putative RNA-binding 42.3 64 0.0014 26.6 5.3 71 150-227 39-125 (160)
40 COG0335 RplS Ribosomal protein 40.2 1.9E+02 0.0042 23.2 7.7 65 48-112 18-90 (115)
41 COG4043 Preprotein translocase 39.6 43 0.00093 26.5 3.6 24 47-70 30-55 (111)
42 PRK10377 PTS system glucitol/s 39.6 38 0.00082 27.2 3.4 24 48-71 49-72 (120)
43 PF10665 Minor_capsid_1: Minor 38.7 83 0.0018 24.9 5.2 26 48-73 74-99 (114)
44 cd02786 MopB_CT_3 The MopB_CT_ 38.2 25 0.00055 26.6 2.2 21 208-228 43-63 (116)
45 COG2996 Predicted RNA-bindinin 38.2 3.3E+02 0.0071 25.2 10.9 87 121-219 17-124 (287)
46 PF05521 Phage_H_T_join: Phage 38.1 60 0.0013 23.0 4.1 30 44-73 55-85 (95)
47 PF03829 PTSIIA_gutA: PTS syst 38.0 36 0.00079 27.1 3.1 23 48-70 49-71 (117)
48 TIGR00849 gutA PTS system, glu 37.9 42 0.00091 27.0 3.4 23 49-71 50-72 (121)
49 TIGR01646 vgr_GE Rhs element V 37.7 1.9E+02 0.004 27.8 8.5 119 45-163 275-422 (483)
50 PRK00364 groES co-chaperonin G 37.7 91 0.002 23.7 5.1 37 24-60 19-68 (95)
51 PF04014 Antitoxin-MazE: Antid 37.2 65 0.0014 20.9 3.7 30 134-165 8-38 (47)
52 PRK12366 replication factor A; 36.3 4.8E+02 0.01 26.5 11.9 55 45-100 63-120 (637)
53 COG2016 Predicted RNA-binding 35.9 61 0.0013 27.5 4.2 69 147-222 36-119 (161)
54 TIGR00451 unchar_dom_2 unchara 35.5 89 0.0019 23.8 4.8 29 200-228 45-80 (107)
55 COG2501 S4-like RNA binding pr 35.4 39 0.00084 25.0 2.6 22 48-69 50-71 (73)
56 PF12158 DUF3592: Protein of u 35.1 1E+02 0.0022 23.9 5.3 49 114-170 65-113 (148)
57 cd02790 MopB_CT_Formate-Dh_H F 35.0 29 0.00063 26.1 2.0 21 208-228 47-67 (116)
58 PRK04313 30S ribosomal protein 34.5 64 0.0014 29.0 4.3 32 193-224 132-165 (237)
59 PRK13480 3'-5' exoribonuclease 34.5 1.1E+02 0.0024 28.4 6.1 54 45-102 2-55 (314)
60 cd02779 MopB_CT_Arsenite-Ox Th 34.1 30 0.00065 26.5 2.0 22 208-229 45-66 (115)
61 PF05354 Phage_attach: Phage H 34.1 36 0.00079 27.4 2.5 27 45-74 69-95 (117)
62 PF02839 CBM_5_12: Carbohydrat 33.3 44 0.00096 20.9 2.4 19 51-69 10-28 (41)
63 PF13856 Gifsy-2: ATP-binding 32.3 58 0.0013 24.4 3.3 22 51-72 66-87 (95)
64 PRK04012 translation initiatio 32.2 2E+02 0.0042 22.3 6.2 44 171-222 21-72 (100)
65 KOG0267 Microtubule severing p 31.7 1.1E+02 0.0024 31.9 5.9 152 45-203 135-302 (825)
66 cd04458 CSP_CDS Cold-Shock Pro 31.6 1.6E+02 0.0034 20.0 5.2 45 118-162 8-54 (65)
67 cd02778 MopB_CT_Thiosulfate-R- 31.5 37 0.0008 25.9 2.1 20 209-228 43-62 (123)
68 KOG1708 Mitochondrial/chloropl 31.3 68 0.0015 28.4 3.8 52 160-226 122-173 (236)
69 PF06988 NifT: NifT/FixU prote 30.4 2.1E+02 0.0046 20.6 6.1 49 154-209 2-52 (64)
70 PF01568 Molydop_binding: Moly 30.2 35 0.00076 25.4 1.7 19 210-228 44-62 (110)
71 PF15415 DUF4622: Protein of u 30.1 59 0.0013 29.7 3.4 72 148-226 39-128 (310)
72 PF09465 LBR_tudor: Lamin-B re 29.8 2E+02 0.0043 20.2 5.5 38 89-126 7-49 (55)
73 smart00359 PUA Putative RNA-bi 29.4 65 0.0014 22.3 2.9 25 204-228 25-49 (77)
74 cd02792 MopB_CT_Formate-Dh-Na- 29.3 45 0.00098 25.3 2.2 20 209-228 48-67 (122)
75 PF05951 Peptidase_M15_2: Bact 29.2 37 0.0008 28.4 1.8 52 82-135 7-60 (152)
76 cd02787 MopB_CT_ydeP The MopB_ 29.1 35 0.00076 25.8 1.6 21 208-228 43-63 (112)
77 PF02182 SAD_SRA: SAD/SRA doma 29.1 1.3E+02 0.0028 25.0 5.1 36 52-88 117-152 (155)
78 cd01752 PLAT_polycystin PLAT/L 28.7 2.1E+02 0.0045 22.2 6.0 31 67-97 67-99 (120)
79 PLN00036 40S ribosomal protein 28.6 69 0.0015 29.1 3.6 30 96-126 80-111 (261)
80 PRK15463 cold shock-like prote 28.5 1.1E+02 0.0023 22.0 4.0 45 118-162 12-58 (70)
81 PRK14533 groES co-chaperonin G 27.9 1.5E+02 0.0033 22.5 4.9 37 24-60 19-63 (91)
82 PF11948 DUF3465: Protein of u 27.5 61 0.0013 26.6 2.7 30 47-76 82-116 (131)
83 TIGR03170 flgA_cterm flagella 27.4 1.7E+02 0.0037 22.4 5.3 24 82-105 98-121 (122)
84 cd00320 cpn10 Chaperonin 10 Kd 27.4 1.6E+02 0.0035 22.2 4.9 40 22-61 16-68 (93)
85 cd02788 MopB_CT_NDH-1_NuoG2-N7 27.3 47 0.001 24.7 2.0 18 209-226 42-59 (96)
86 cd05706 S1_Rrp5_repeat_sc10 S1 27.2 2.1E+02 0.0045 19.6 6.0 55 149-219 1-57 (73)
87 PF07076 DUF1344: Protein of u 27.1 1.9E+02 0.0042 20.6 4.9 39 172-219 4-47 (61)
88 cd01763 Sumo Small ubiquitin-r 26.7 73 0.0016 23.4 2.9 56 77-136 8-71 (87)
89 cd07387 MPP_PolD2_C PolD2 (DNA 26.6 79 0.0017 28.5 3.6 40 186-225 210-252 (257)
90 PRK07018 flgA flagellar basal 26.5 1.9E+02 0.0042 25.3 6.0 25 82-106 209-233 (235)
91 cd02794 MopB_CT_DmsA-EC The Mo 26.3 54 0.0012 25.1 2.2 19 210-228 44-62 (121)
92 PF02470 MCE: mce related prot 26.2 2.2E+02 0.0048 20.1 5.4 40 46-86 10-50 (81)
93 cd02783 MopB_CT_2 The MopB_CT_ 26.1 51 0.0011 26.9 2.2 21 209-229 45-65 (156)
94 PRK08572 rps17p 30S ribosomal 25.6 3.2E+02 0.0069 21.6 6.4 78 135-219 7-87 (108)
95 PF01079 Hint: Hint module; I 25.3 1.1E+02 0.0024 26.8 4.2 41 45-85 26-71 (217)
96 PF10703 MoaF: Molybdenum cofa 25.3 4.6E+02 0.0099 24.0 8.2 84 82-172 21-111 (265)
97 PTZ00414 10 kDa heat shock pro 24.6 1.9E+02 0.0042 22.5 5.0 37 23-59 27-71 (100)
98 TIGR03784 marine_sortase sorta 24.5 63 0.0014 27.3 2.4 17 210-226 109-125 (174)
99 cd02785 MopB_CT_4 The MopB_CT_ 24.0 63 0.0014 24.9 2.2 20 209-228 45-64 (124)
100 PF14289 DUF4369: Domain of un 24.0 2.8E+02 0.0061 20.0 6.6 29 195-224 61-91 (106)
101 cd02781 MopB_CT_Acetylene-hydr 23.6 67 0.0015 24.7 2.3 19 210-228 47-65 (130)
102 COG1153 FwdD Formylmethanofura 23.6 56 0.0012 26.6 1.9 22 208-229 43-64 (128)
103 COG0090 RplB Ribosomal protein 23.5 2.2E+02 0.0048 26.1 5.8 31 50-80 123-154 (275)
104 COG1047 SlpA FKBP-type peptidy 23.5 1.9E+02 0.0041 24.8 5.1 43 49-98 89-135 (174)
105 smart00652 eIF1a eukaryotic tr 23.4 2.9E+02 0.0062 20.5 5.6 43 172-222 6-56 (83)
106 smart00676 DM10 Domains in hyp 23.3 56 0.0012 25.3 1.8 27 45-71 68-94 (104)
107 PF07591 PT-HINT: Pretoxin HIN 23.1 69 0.0015 25.6 2.3 27 45-71 71-98 (130)
108 PF11871 DUF3391: Domain of un 22.9 49 0.0011 25.5 1.4 20 45-64 4-23 (128)
109 PRK10354 RNA chaperone/anti-te 22.8 2.6E+02 0.0056 19.8 5.1 45 118-162 12-58 (70)
110 PRK12617 flgA flagellar basal 22.5 2.1E+02 0.0045 25.1 5.4 77 29-106 128-212 (214)
111 PF01472 PUA: PUA domain; Int 22.3 1.2E+02 0.0025 21.6 3.2 24 205-228 26-49 (74)
112 PF08292 RNA_pol_Rbc25: RNA po 21.5 4.2E+02 0.0092 21.1 8.6 64 115-180 10-74 (122)
113 cd02782 MopB_CT_1 The MopB_CT_ 21.3 77 0.0017 24.4 2.3 20 209-228 46-65 (129)
114 cd02793 MopB_CT_DMSOR-BSOR-TMA 21.1 72 0.0016 24.9 2.0 20 209-228 46-65 (129)
115 cd02776 MopB_CT_Nitrate-R-NarG 21.0 71 0.0015 25.8 2.0 20 209-228 44-63 (141)
116 PF00207 A2M: Alpha-2-macroglo 20.8 85 0.0019 23.1 2.3 17 203-219 59-75 (92)
117 PTZ00118 40S ribosomal protein 20.7 1.3E+02 0.0028 27.4 3.8 29 96-125 80-110 (262)
118 PRK11354 kil FtsZ inhibitor pr 20.6 1.3E+02 0.0027 22.3 3.0 49 45-105 10-58 (73)
119 PF01176 eIF-1a: Translation i 20.6 3E+02 0.0065 19.2 5.0 31 193-223 17-55 (65)
120 KOG3048 Molecular chaperone Pr 20.4 1.5E+02 0.0032 24.9 3.7 37 192-228 61-97 (153)
No 1
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=5.5e-76 Score=499.68 Aligned_cols=185 Identities=32% Similarity=0.523 Sum_probs=183.4
Q ss_pred EEEccccCCccEEEECCcEEEEEEEeEeeCCCCceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeCCeE
Q 027058 45 AFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGKGAAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDGSMF 124 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dgd~~ 124 (229)
|+++||||+|++|++||+||+|++++|+|||||+|++|+|||||.||+++|++|+++|++|.++++++++||||.||+.|
T Consensus 1 m~~~~dik~G~~i~~~g~~~~V~~~~h~kPGkg~A~vr~klknl~tG~~~e~tf~s~ek~e~a~ve~~~~qylY~dg~~~ 80 (185)
T PRK12426 1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPKGETFIKVSLQAADSDVVVERNFKAGQEVKEAQFEPRNLEYLYLEGDEY 80 (185)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEecCCCCceEEEEEEEEcCCCCeEEEEECCCCeEEEeEEEeeEeEEEEECCCeE
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCCcEE
Q 027058 125 VFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTGAVV 204 (229)
Q Consensus 125 ~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v 204 (229)
+|||+|||||++|+++.+||+.+||+|||+|++++|+|+||+|+||++|+|+|+||+|++|||||++++|||+||||++|
T Consensus 81 ~FMd~etyeQi~i~~~~lgd~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~kgdTat~~~KpAtLeTG~~V 160 (185)
T PRK12426 81 LFLDLGNYDKIYIPKEIMKDNFLFLKAGVTVSALVYDGTVFSVELPHFLELMVSKTDFPGDSLSLSGGAKKALLETGVEV 160 (185)
T ss_pred EEecCCCceEEEeCHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCcccCCCcccEEEcCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcccCeecCCEEEEEcCCCeeeecC
Q 027058 205 NVPLFVNIGDEILVDTRTGQYMTRA 229 (229)
Q Consensus 205 ~VP~FI~~Gd~I~V~T~~g~Y~~R~ 229 (229)
+||+||++||+|+||||||+|++||
T Consensus 161 ~VP~FI~~Gd~IkVdT~~geY~~R~ 185 (185)
T PRK12426 161 LVPPFVEIGDVIKVDTRTCEYIQRV 185 (185)
T ss_pred EeCCcccCCCEEEEECCCCeEEeeC
Confidence 9999999999999999999999997
No 2
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=9.2e-74 Score=487.15 Aligned_cols=185 Identities=38% Similarity=0.677 Sum_probs=182.1
Q ss_pred EEEccccCCccEEEECCcEEEEEEEeEeeCCCC--ceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeCC
Q 027058 45 AFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGKG--AAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDGS 122 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG--~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dgd 122 (229)
|++++|||+|++|++||+||+|++++|+|||+| +|++|+|||||.||+++|++|+++|++|.++++++++||||.||+
T Consensus 1 m~~~~dik~G~~i~~dg~~~~V~~~~~~kpg~~g~~a~vr~klknl~tG~~~e~tf~s~d~ve~a~ve~~~~qylY~dg~ 80 (187)
T PRK14578 1 MYTTSDFKKGLVIQLDGAPCLLLDVTFQSPSARGANTMVKTKYRNLLTGQVLEKTFRSGDKVEEADFERHKGQFLYADGD 80 (187)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEEcCCCCCCceEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEeEeEEEEeCCC
Confidence 678999999999999999999999999999887 569999999999999999999999999999999999999999999
Q ss_pred eEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCCc
Q 027058 123 MFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTGA 202 (229)
Q Consensus 123 ~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG~ 202 (229)
.|+|||+|||||++|+++.+|++.+||+|||+|.+.+|+|+||+|+||++|+|+|++|+|++||||+++++|||+||||+
T Consensus 81 ~~~FMD~etyEQ~~i~~~~~g~~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V~~tep~~KGdT~t~~~KpA~leTG~ 160 (187)
T PRK14578 81 RGVFMDLETYEQFEMEEDAFSAIAPFLLDGTEVQLGLFQGRMVNVDLPMTVELTVTDTAPVMKNATATAQTKEAVLETGL 160 (187)
T ss_pred EEEEecCCCcEEEEecHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCccccCccCCCcceEEEcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEcccCeecCCEEEEEcCCCeeeecC
Q 027058 203 VVNVPLFVNIGDEILVDTRTGQYMTRA 229 (229)
Q Consensus 203 ~v~VP~FI~~Gd~I~V~T~~g~Y~~R~ 229 (229)
+|+||+||++||+|+||||||+|++||
T Consensus 161 ~v~VP~FI~~Gd~I~VdT~~g~Y~~R~ 187 (187)
T PRK14578 161 RLQVPPYLESGEKIKVDTRDGRFISRA 187 (187)
T ss_pred EEEeCCcccCCCEEEEECCCCcEEeeC
Confidence 999999999999999999999999997
No 3
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=1.2e-73 Score=487.10 Aligned_cols=185 Identities=31% Similarity=0.573 Sum_probs=182.1
Q ss_pred EEEccccCCccEEEECCcEEEEEEEeEeeC-CCC-ceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeCC
Q 027058 45 AFSSNDIKVGSNIEVDGAPWRVLEFLHVKP-GKG-AAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDGS 122 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~py~Vv~~~~~kp-GKG-~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dgd 122 (229)
|+++||||+|++|++||+||+|++++|+|| ||| +|++|+|||||.||++++++|+++|++|.++++++++||||.||+
T Consensus 1 mi~~~dik~G~~i~~~g~~~~V~~~~h~kp~Gkg~~a~vr~klknl~tG~~~e~tfrs~ekve~a~~~~~~~qylY~dg~ 80 (189)
T PRK04542 1 MPKANEIKKGMVVEYNGKLLLVKDIDRQSPSGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVDLTRRPVTFSYIDGD 80 (189)
T ss_pred CCchhhcCCCCEEEECCEEEEEEEEEEECCCCCCcceEEEEEEEEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCC
Confidence 688999999999999999999999999999 798 459999999999999999999999999999999999999999999
Q ss_pred eEEEecCCCceeeecCccchhhhhhccCCCCe-EEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCC
Q 027058 123 MFVFMDLTTFEEVRLNETDVGDKKKWLKEGMD-CNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTG 201 (229)
Q Consensus 123 ~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~-v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG 201 (229)
.|+|||+|||||++|+++.+||+.+||+||++ |++++|+|+||+|+||++|+|+|++|+|++||||+++++|||+||||
T Consensus 81 ~~~FMd~etyEQ~~i~~~~lgd~~~~L~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~kGdT~~~~~KpAtLetG 160 (189)
T PRK04542 81 EYVFMDNEDYTPYTFKKDQIEDELLFIPEGMPGMQVLTVDGQPVALELPQTVDLEIVETAPSIKGASASARTKPATLSTG 160 (189)
T ss_pred EEEEecCCCceEEEECHHHhhhHhhhhhcCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCccccccCCCCccEEEcCC
Confidence 99999999999999999999999999999998 99999999999999999999999999999999999999999999999
Q ss_pred cEEEcccCeecCCEEEEEcCCCeeeecC
Q 027058 202 AVVNVPLFVNIGDEILVDTRTGQYMTRA 229 (229)
Q Consensus 202 ~~v~VP~FI~~Gd~I~V~T~~g~Y~~R~ 229 (229)
++|+||+||++||+|+||||||+|++||
T Consensus 161 ~~v~VP~FI~~Gd~I~VdT~tgeYv~R~ 188 (189)
T PRK04542 161 LVIQVPEYISTGEKIRINTEERKFMGRA 188 (189)
T ss_pred CEEEeCCcccCCCEEEEECCCCcEEeec
Confidence 9999999999999999999999999997
No 4
>TIGR02178 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae.
Probab=100.00 E-value=1.3e-72 Score=479.50 Aligned_cols=183 Identities=28% Similarity=0.538 Sum_probs=179.1
Q ss_pred EccccCCccEEEECCcEEEEEEEeEeeCCCCce--EEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeCCeE
Q 027058 47 SSNDIKVGSNIEVDGAPWRVLEFLHVKPGKGAA--FVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDGSMF 124 (229)
Q Consensus 47 ~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG~A--~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dgd~~ 124 (229)
.+||||+|++|++||+||+|++++|+|||+|+| ++|+|||||.||++++++|+++|++|.++++++++||||.||+.|
T Consensus 1 ~~~~lk~G~~i~~dg~~~~V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le~~~~qylY~dg~~~ 80 (186)
T TIGR02178 1 KASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKDGEEY 80 (186)
T ss_pred CcccccCCCEEEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCCeE
Confidence 378999999999999999999999999977666 899999999999999999999999999999999999999999999
Q ss_pred EEecCCCceeeecCccchhhhhhccCCCCe-EEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCCcE
Q 027058 125 VFMDLTTFEEVRLNETDVGDKKKWLKEGMD-CNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTGAV 203 (229)
Q Consensus 125 ~FMD~etyEQi~v~~~~lgd~~~fL~eG~~-v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG~~ 203 (229)
+|||+|||||++|+++.+|++.+||+|||+ |++.+|+|+||+|+||++|+|+|++|+|++||||+++++|||+||||++
T Consensus 81 ~FMD~etyEQ~~i~~~~lgd~~~fL~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~KGdT~~~~~KpA~LeTG~~ 160 (186)
T TIGR02178 81 VFMDEEDYTPYTFDKDAIEDELLFISEGLSGMYVQLIDGSPVALELPQHVVLEIVETPPEIKGASASKRPKPAKLITGLV 160 (186)
T ss_pred EEccCCCcEEEEeCHHHhhhhhhhhhCCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCcccccCCCCcccEEEcCCCE
Confidence 999999999999999999999999999997 9999999999999999999999999999999999999999999999999
Q ss_pred EEcccCeecCCEEEEEcCCCeeeecC
Q 027058 204 VNVPLFVNIGDEILVDTRTGQYMTRA 229 (229)
Q Consensus 204 v~VP~FI~~Gd~I~V~T~~g~Y~~R~ 229 (229)
|+||+||++||+|+||||||+|++||
T Consensus 161 v~VP~FI~~Gd~IkVdTrtg~Y~~R~ 186 (186)
T TIGR02178 161 VQVPEYITTGERILINTTERAFMGRA 186 (186)
T ss_pred EEeCCeecCCCEEEEECCCCcEEccC
Confidence 99999999999999999999999997
No 5
>PRK00529 elongation factor P; Validated
Probab=100.00 E-value=1.8e-71 Score=473.04 Aligned_cols=185 Identities=56% Similarity=0.948 Sum_probs=183.4
Q ss_pred EEEccccCCccEEEECCcEEEEEEEeEeeCCCCceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeCCeE
Q 027058 45 AFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGKGAAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDGSMF 124 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dgd~~ 124 (229)
|+++|+||+|++|+++|+||+|++++|+|||||+|++|+++|||.||++++.+|+++|+++.+.++++++||+|.||+.|
T Consensus 1 ~~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGkg~A~vrvk~knL~tG~~~e~~f~~~e~ve~~~ve~~~~q~ly~dgd~~ 80 (186)
T PRK00529 1 MISANDLRKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLLTGSVVEKTFKAGDKVERADVERREMQYLYNDGDGY 80 (186)
T ss_pred CcchhhcCCCCEEEECCEEEEEEEEEEeeCCCCceEEEEEEEECCCCCeEEEEeCCCCEEEeccEEeEEEEEEEECCCEE
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCCcEE
Q 027058 125 VFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTGAVV 204 (229)
Q Consensus 125 ~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v 204 (229)
+|||+|||||++++.+.+|++.+||+||++|++++|+|+||+|+||++|+|+|+||+|++||||+++++|||+||||++|
T Consensus 81 ~fMD~etyeq~~l~~~~lg~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v 160 (186)
T PRK00529 81 VFMDTETYEQIEVPADQVGDAAKFLKEGMEVTVVFYNGEPISVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVV 160 (186)
T ss_pred EEecCCCceeeEcCHHHhHHHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCccCcccCCCcccEEEcCCCEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcccCeecCCEEEEEcCCCeeeecC
Q 027058 205 NVPLFVNIGDEILVDTRTGQYMTRA 229 (229)
Q Consensus 205 ~VP~FI~~Gd~I~V~T~~g~Y~~R~ 229 (229)
+||+||++||+|+|||++|+|++||
T Consensus 161 ~VP~fI~~Gd~I~v~T~~g~y~~R~ 185 (186)
T PRK00529 161 QVPLFINEGEKIKVDTRTGEYVERA 185 (186)
T ss_pred EeCCeecCCCEEEEECCCCcEEeec
Confidence 9999999999999999999999997
No 6
>TIGR00038 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria.
Probab=100.00 E-value=2.6e-71 Score=471.45 Aligned_cols=184 Identities=54% Similarity=0.925 Sum_probs=182.2
Q ss_pred EEccccCCccEEEECCcEEEEEEEeEeeCCCCceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeCCeEE
Q 027058 46 FSSNDIKVGSNIEVDGAPWRVLEFLHVKPGKGAAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDGSMFV 125 (229)
Q Consensus 46 i~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dgd~~~ 125 (229)
+++|+||+|++|+++|+||+|++++|+|||||+|++|+++|||.||++++++|+++|+++.+.++++++||+|.||+.|+
T Consensus 1 ~~a~~ik~G~~I~~~g~~~~V~~~~~~kpGkg~A~~rvk~knL~tG~~~e~~f~~~~kve~~~~e~~~~q~ly~dgd~~~ 80 (184)
T TIGR00038 1 ISANDLRKGLVIELDGEPYVVLEFEHVKPGKGQAFVRVKLKNLLTGKVLEKTFRSGEKVEKADVEEREMQYLYKDGDSYV 80 (184)
T ss_pred CchhhccCCCEEEECCEEEEEEEEEEeeCCCCceEEEEEEEECCCCCEEEEEeCCCCEEEcccEEeEEEEEEEECCCEEE
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCCcEEE
Q 027058 126 FMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTGAVVN 205 (229)
Q Consensus 126 FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~ 205 (229)
|||+|||||++++.+.+|+..+||+|||+|.+.+|+|+||+|+||++|+|+|+||+|++||||+++++|||+||||++|+
T Consensus 81 fMD~etyeq~~i~~~~l~~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~letG~~v~ 160 (184)
T TIGR00038 81 FMDTETYEQIELPKDLLGDAAKFLKENMEVSVTFYNGEPIGVELPNFVELEVTETEPGVKGDTASGGTKPATLETGAVVQ 160 (184)
T ss_pred EeCCCCccceEcCHHHHHHHHhhcCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCccccccCCCcccEEEcCCCEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCeecCCEEEEEcCCCeeeecC
Q 027058 206 VPLFVNIGDEILVDTRTGQYMTRA 229 (229)
Q Consensus 206 VP~FI~~Gd~I~V~T~~g~Y~~R~ 229 (229)
||+||++||+|+|||++|+|++||
T Consensus 161 VP~fi~~Gd~I~v~T~~g~y~~R~ 184 (184)
T TIGR00038 161 VPLFIEEGEKIKVDTRTGEYVERA 184 (184)
T ss_pred eCCcccCCCEEEEECCCCcEEecC
Confidence 999999999999999999999997
No 7
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.3e-46 Score=300.59 Aligned_cols=131 Identities=45% Similarity=0.780 Sum_probs=128.6
Q ss_pred EEEEEccccCCccEEEECCcEEEEEEEeEeeCCCCceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeCC
Q 027058 43 IYAFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGKGAAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDGS 122 (229)
Q Consensus 43 ~~~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dgd 122 (229)
++|+++++||+|++|++||+||+|++++|+|||||+|++|+++|||+||++++.+|+++|++|.|.++++++||||.||+
T Consensus 1 ~~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGKg~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~dg~ 80 (131)
T COG0231 1 MAMISASELRKGLYIVIDGEPYVVVEISHVKPGKGGAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYIDGD 80 (131)
T ss_pred CceeeHHHccCCCEEEECCeEEEEEEEEEccCCCCCcEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeeeEEEEEcCCC
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEEEEECCceE
Q 027058 123 MFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKIIDFEVPITV 173 (229)
Q Consensus 123 ~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i~v~lP~~V 173 (229)
.|+|||+|||||++++.+.++|+.+||+|||+|++++|+|++++++||++|
T Consensus 81 ~~~FMD~etyeq~~v~~~~~~d~~~~l~eg~~v~v~~~~g~~i~v~lP~~v 131 (131)
T COG0231 81 FYVFMDLETYEQYELPKDQIGDAAKFLKEGMEVEVLLYNGEPIAVELPNFV 131 (131)
T ss_pred eEEEccCCCceEEEecchhhhhHHHhcCCCCEEEEEEECCEEEEEECCCCC
Confidence 999999999999999999999999999999999999999999999999975
No 8
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=1.3e-37 Score=251.71 Aligned_cols=121 Identities=24% Similarity=0.319 Sum_probs=115.8
Q ss_pred EEEEEccccCCccEEEECCcEEEEEEEeEeeCCC-CceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeC
Q 027058 43 IYAFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGK-GAAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDG 121 (229)
Q Consensus 43 ~~~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGK-G~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dg 121 (229)
++.+++++||+|++|++||+||+|++++|+|||| |+|++|+++|||+||+++|.+|+++|++|.|.++++++||||.||
T Consensus 4 ~~~~~~~~irkG~~i~~~g~p~~V~e~~~~kpGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ve~~~ve~~~~qylY~dg 83 (130)
T TIGR00037 4 TKQVQVSALRVGGYVVIDGRPCKIVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSKVEVPIVDRREYQVLAIMG 83 (130)
T ss_pred ceeccHHHccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEEEEEEEEecC
Confidence 4578999999999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred CeEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEE
Q 027058 122 SMFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKII 165 (229)
Q Consensus 122 d~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i 165 (229)
+.|+|||+|||||++|+.+. +..+||+||++|.++-..|+..
T Consensus 84 ~~~~fMd~etyeq~~i~~~~--~~~~~Lke~~~V~v~~~~g~~~ 125 (130)
T TIGR00037 84 GMVQLMDLDTYETDELPIPE--ELGDSLEPGFEVEYIEAMGQEK 125 (130)
T ss_pred CEEEEEcCCCcEEEEecCCh--hHHHHhhcCCEEEEEecCCeEE
Confidence 99999999999999999885 8899999999999998877643
No 9
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=5.1e-36 Score=242.15 Aligned_cols=118 Identities=25% Similarity=0.342 Sum_probs=112.8
Q ss_pred EEEEccccCCccEEEECCcEEEEEEEeEeeCCC-CceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeCC
Q 027058 44 YAFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGK-GAAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDGS 122 (229)
Q Consensus 44 ~~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGK-G~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dgd 122 (229)
-.+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||.||++++.+|+++|++|.+.++++++||+|.||+
T Consensus 4 ~~~~~~~lrkG~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~qylY~dg~ 83 (129)
T PRK03999 4 KQVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMGD 83 (129)
T ss_pred ccccHHHccCCCEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEEEEEecCC
Confidence 368999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred eEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCe
Q 027058 123 MFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGK 163 (229)
Q Consensus 123 ~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~ 163 (229)
.|+|||+|||||++|+.+ +++..||+||++|.++--.|+
T Consensus 84 ~~~fMd~eTyeq~~i~~~--~d~~~~l~eg~~v~v~~~~g~ 122 (129)
T PRK03999 84 VVQLMDLETYETFEIPIP--EELKDKLEPGVEVEYWEAMGR 122 (129)
T ss_pred EEEEecCCCceEEEecCC--hhHHhhCcCCCEEEEEhhCCe
Confidence 999999999999999988 888999999999998775554
No 10
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=100.00 E-value=8.9e-33 Score=230.30 Aligned_cols=126 Identities=21% Similarity=0.309 Sum_probs=110.2
Q ss_pred CCCceEEEEEccccCCccEEEECCcEEEEEEEeEeeCCC-CceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEE
Q 027058 38 SKFPRIYAFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGK-GAAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQF 116 (229)
Q Consensus 38 ~~~~~~~~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGK-G~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qy 116 (229)
+....++|+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||+++|.+|+++++++.|+++++++||
T Consensus 13 ~~~~~t~m~~~~~lKkG~~I~~~g~pc~V~e~~~~KpGKHG~A~vr~k~knl~TG~k~e~~f~s~~~ve~~~ve~~~~qy 92 (159)
T PLN03107 13 AGASKTYPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNCDVPHVNRTDYQL 92 (159)
T ss_pred cCCCceeccchHhccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEecCCCEEEEEEEEEEEEEE
Confidence 444567899999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred EEEeCCeE-EEecC--CCceeeecCc--cchhh-hhhccCCCCeEEEEEE--CCe
Q 027058 117 TYKDGSMF-VFMDL--TTFEEVRLNE--TDVGD-KKKWLKEGMDCNLLFW--KGK 163 (229)
Q Consensus 117 lY~Dgd~~-~FMD~--etyEQi~v~~--~~lgd-~~~fL~eG~~v~v~~~--~g~ 163 (229)
||.||+.| +|||+ ++|||+.||. +.+++ ...+..+|.++.|..| .|+
T Consensus 93 ly~dgd~y~~fMD~~get~eqi~v~~~~~el~~~i~~~f~~g~~~~v~v~~~mg~ 147 (159)
T PLN03107 93 IDISEDGFVSLMDESGNTKDDLKLPTEDDTLAEQIKDGFDEGKDLVVTVMSAMGE 147 (159)
T ss_pred EEEcCCceEEEEcCCCCcceeEEccCcchHHHHHHHHHHhCCCeEEEEEEecCCe
Confidence 99999996 99999 6999999985 34544 3345577988544444 455
No 11
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=99.94 E-value=4.3e-27 Score=164.50 Aligned_cols=56 Identities=59% Similarity=0.959 Sum_probs=50.2
Q ss_pred EEEEEEEcCCCcccccCCCCcccEEecCCcEEEcccCeecCCEEEEEcCCCeeeec
Q 027058 173 VQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNVPLFVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 173 V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~g~Y~~R 228 (229)
|+|+|+||+|++||||+++++|+|+||||++|+||+||++||+|+|||++|+|++|
T Consensus 1 V~l~V~etep~~kg~t~~~~~K~A~letG~~i~VP~FI~~Gd~I~VdT~~g~Yv~R 56 (56)
T PF09285_consen 1 VELEVVETEPAVKGDTASSSYKPATLETGAEIQVPLFIEEGDKIKVDTRDGSYVER 56 (56)
T ss_dssp EEEEEEEE-SSSTTSSSSTTEEEEEETTS-EEEEETT--TT-EEEEETTTTEEEEE
T ss_pred CEEEEEECCCCccCcccCCCccEEEEcCCCEEEccceecCCCEEEEECCCCeEeCC
Confidence 68999999999999999999999999999999999999999999999999999998
No 12
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=99.94 E-value=3.4e-27 Score=165.01 Aligned_cols=56 Identities=70% Similarity=1.152 Sum_probs=55.0
Q ss_pred EEEEEEEcCCCcccccCCCCcccEEecCCcEEEcccCeecCCEEEEEcCCCeeeec
Q 027058 173 VQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNVPLFVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 173 V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~g~Y~~R 228 (229)
|+|+|+||+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++|
T Consensus 1 V~l~V~etep~vkG~T~~~~~K~A~letG~~i~VP~FI~~Gd~I~V~T~~g~Y~~R 56 (56)
T smart00841 1 VELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGDKIKVDTRTGEYVSR 56 (56)
T ss_pred CEEEEEECCCCccccccCCCcceEEECCCCEEEcCCcccCCCEEEEECCCCcEEcC
Confidence 58999999999999999999999999999999999999999999999999999998
No 13
>cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=99.94 E-value=3.6e-27 Score=164.88 Aligned_cols=56 Identities=63% Similarity=1.045 Sum_probs=55.0
Q ss_pred EEEEEEEcCCCcccccCCCCcccEEecCCcEEEcccCeecCCEEEEEcCCCeeeec
Q 027058 173 VQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNVPLFVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 173 V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~g~Y~~R 228 (229)
|+|+|+||+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++|
T Consensus 1 v~l~V~etep~~kG~T~~~~~K~A~letG~~i~VP~FI~~Gd~I~V~T~~g~Y~~R 56 (56)
T cd05794 1 VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER 56 (56)
T ss_pred CEEEEEECCCCccccccCCCcceEEECCCCEEEcCCeecCCCEEEEECCCCcEecC
Confidence 58999999999999999999999999999999999999999999999999999998
No 14
>cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P
Probab=99.88 E-value=5.2e-23 Score=146.33 Aligned_cols=61 Identities=43% Similarity=0.806 Sum_probs=59.8
Q ss_pred eeeeeEEEEEeCCeEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEEEEECC
Q 027058 110 FKETKQFTYKDGSMFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKIIDFEVP 170 (229)
Q Consensus 110 erk~~qylY~Dgd~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i~v~lP 170 (229)
+++++||||.||+.|+|||++||||++|+++.+|++.+||+||++|++++|+|+||+|+||
T Consensus 1 e~~~~qylY~dg~~~~FMd~etyeQ~~i~~~~igd~~~~L~e~~~v~v~~~~~~~i~v~lP 61 (61)
T cd04470 1 EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVELP 61 (61)
T ss_pred CCceEEEEEeCCCEEEEeCCCCceEEEECHHHhhhHHhhCcCCCEEEEEEECCEEEEEECc
Confidence 5789999999999999999999999999999999999999999999999999999999999
No 15
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=99.87 E-value=3.5e-21 Score=160.76 Aligned_cols=122 Identities=19% Similarity=0.229 Sum_probs=107.6
Q ss_pred CceEEEEEccccCCccEEEECCcEEEEEEEeEeeCCC-CceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEE
Q 027058 40 FPRIYAFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGK-GAAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTY 118 (229)
Q Consensus 40 ~~~~~~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGK-G~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY 118 (229)
.+.++.++++.||+|.+|.++|+||+|++++.+|||| |+|++++...+|+||+++|...|+.++++.|.++|+++|++.
T Consensus 17 as~t~p~q~~~LkkG~yvvIkGrPCKIveistSKtGKHGhAK~~ivaidIFTgkK~edi~Ps~hnv~VP~V~r~~yqli~ 96 (166)
T PTZ00328 17 ASKTYPLPAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLD 96 (166)
T ss_pred CCceecccccceeECCEEEECCeeeEEEEEecCCCCcCCceEEEEEEEecCCCCEEeeecCccceeEeeeEEeeEEEEEE
Confidence 3457899999999999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred EeCC-------eEEEecCCCceeeec--Cc-cchhh-hhhccCCCCeEEEEEEC
Q 027058 119 KDGS-------MFVFMDLTTFEEVRL--NE-TDVGD-KKKWLKEGMDCNLLFWK 161 (229)
Q Consensus 119 ~Dgd-------~~~FMD~etyEQi~v--~~-~~lgd-~~~fL~eG~~v~v~~~~ 161 (229)
.++| ..++||.+.|+...| |. +.|+. ....+.+|.+|.|.+|.
T Consensus 97 I~~d~~~~~~g~v~LMd~~g~~k~dl~lp~~~el~~~ik~~f~~g~ev~v~vi~ 150 (166)
T PTZ00328 97 IQPNEDPSLPAHLSLMDDEGESREDLDMPPDAALATQIKEQFDSGKEVLVVVVS 150 (166)
T ss_pred EcCCCcccccceEEEEcCCCCeeecccCCChhHHHHHHHHHhcCCCeEEEEEEh
Confidence 9876 378999998887765 43 34444 34567999999877774
No 16
>PF08207 EFP_N: Elongation factor P (EF-P) KOW-like domain; InterPro: IPR013185 This entry represents the N-terminal domain of homologues of elongation factor P, which probably are translation initiation factors. ; PDB: 3TRE_A 1YBY_A 1IZ6_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H 3OYY_B.
Probab=99.85 E-value=3.8e-21 Score=135.42 Aligned_cols=58 Identities=57% Similarity=0.979 Sum_probs=53.7
Q ss_pred EccccCCccEEEECCcEEEEEEEeEeeCCCCceEEEEEEEECCCCCEEEEEecCCCeE
Q 027058 47 SSNDIKVGSNIEVDGAPWRVLEFLHVKPGKGAAFVRTKLRNYMSGTTVERTFRAGITV 104 (229)
Q Consensus 47 ~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG~A~vriklknL~TG~~~e~tf~s~dkv 104 (229)
+|+|||+|++|++||+||+|++++|++||||+|+||+|||||.||+++|.+|+++|+|
T Consensus 1 sa~dlr~G~~i~~~g~~~~V~~~~~~k~gkg~a~v~~klknl~tG~~~e~tf~s~d~v 58 (58)
T PF08207_consen 1 SASDLRKGMVIEIDGEPYVVLDFQHVKPGKGGAFVRVKLKNLRTGSKVEKTFRSGDKV 58 (58)
T ss_dssp EGGG--TTSEEEETTEEEEEEEEEEECCTTSSSEEEEEEEETTTTEEEEEEEETT-EE
T ss_pred CHHHccCCCEEEECCEEEEEEEEEEECCCCCCeEEEEEEEECCCCCEEEEEECCCCcC
Confidence 5899999999999999999999999999999999999999999999999999999986
No 17
>PF01132 EFP: Elongation factor P (EF-P) OB domain; InterPro: IPR001059 Elongation factor P (EF-P) is a prokaryotic protein translation factor required for efficient peptide bond synthesis on 70S ribosomes from fMet-tRNAfMet []. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase. This entry reresents the central domain of elongation factor P and its homologues. It forms an oligonucleotide-binding (OB) fold, though it is not clear if this region is involved in binding nucleic acids [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation; PDB: 1YBY_A 3A5Z_H 3TRE_A 1UEB_B 3HUW_V 3HUY_V 3OYY_B.
Probab=99.83 E-value=1.1e-20 Score=131.78 Aligned_cols=55 Identities=44% Similarity=0.866 Sum_probs=49.9
Q ss_pred eeeeEEEEEeCCeEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEE
Q 027058 111 KETKQFTYKDGSMFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKII 165 (229)
Q Consensus 111 rk~~qylY~Dgd~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i 165 (229)
||++||||.||+.|+|||++||||++|+++.+|++.+||+||++|++++|+|+||
T Consensus 1 ~r~~qylY~dgd~~~FMd~etyeQi~v~~~~~g~~~~~L~eg~~v~v~~~~~~~I 55 (55)
T PF01132_consen 1 RREMQYLYKDGDNYVFMDTETYEQIEVPKDQLGDALKFLKEGMEVQVLFYEGKPI 55 (55)
T ss_dssp EEEEEEEEEESSEEEEEETTT--EEEEEHHHHTTTGCC--TTEEEEEEEETTEEE
T ss_pred CceEEEEEeCCCEEEEecCCCceEEEecHHHhChHHhhCcCCCEEEEEEECCEEC
Confidence 6899999999999999999999999999999999999999999999999999997
No 18
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.71 E-value=4.2e-17 Score=132.76 Aligned_cols=112 Identities=20% Similarity=0.346 Sum_probs=101.4
Q ss_pred EEEEEccccCCccEEEECCcEEEEEEEeEeeCCC-CceEEEEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeC
Q 027058 43 IYAFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGK-GAAFVRTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDG 121 (229)
Q Consensus 43 ~~~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGK-G~A~vriklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dg 121 (229)
++.++++.||++-+|.++|+||+|++++.+|.|| |+|++++..++|+||+++|.-++|+++++++.++|.++|.+-.++
T Consensus 18 t~p~q~salrkNG~vviK~rpckivEmSTsKtGKHGhAKvh~vaidifTgkk~edI~psthn~dVp~vkr~~yqLidIsd 97 (156)
T KOG3271|consen 18 TYPMQCSALRKNGHVVIKGRPCKIVEMSTSKTGKHGHAKVHIVAIDIFTGKKLEDICPSTHNMDVPVVKRVDYQLIDISD 97 (156)
T ss_pred cccchhhheeeCCEEEEcCCCceEEEeecccCCcCCceEEEEEEEEeecCcccccccCCCCccccCccccceeEEEEecC
Confidence 4688999999999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred CeEEEecC--CCceeeecCccchhhhhh-ccCCCCe
Q 027058 122 SMFVFMDL--TTFEEVRLNETDVGDKKK-WLKEGMD 154 (229)
Q Consensus 122 d~~~FMD~--etyEQi~v~~~~lgd~~~-fL~eG~~ 154 (229)
+...|||+ ++-+++.+|...++++.. -..+|..
T Consensus 98 ~~~sl~t~sG~~kdDlklp~~el~~~i~~~~e~g~d 133 (156)
T KOG3271|consen 98 GYLSLMTDSGETKDDLKLPEGELGNQIRQGFEEGKD 133 (156)
T ss_pred CeEEEEcCCCCcchhccCcchhHHHHHHHhhcCCCc
Confidence 98889998 577888899888887553 3344443
No 19
>cd04463 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication.
Probab=99.69 E-value=4.7e-17 Score=112.70 Aligned_cols=55 Identities=22% Similarity=0.148 Sum_probs=51.4
Q ss_pred eeeEEEEEeCCeEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEEEE
Q 027058 112 ETKQFTYKDGSMFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKIIDF 167 (229)
Q Consensus 112 k~~qylY~Dgd~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i~v 167 (229)
+++||||.||+.|+|||+|||||++++++.. +..+||+||++|.|++|+|+|+++
T Consensus 1 ~~~qylY~dg~~~~fMd~etyeq~~v~~~~~-~~~~~l~eg~~v~v~~~~g~~i~~ 55 (55)
T cd04463 1 RELQVLDIQGSKPVTMDLETYEVVQVPPPVD-QSFESFEPGEVVLVDTRTGQYVGV 55 (55)
T ss_pred CCEEEEEcCCCEeEEecCCCceEEEeCHHHh-hHHhhCCCCCEEEEEEECCEEEeC
Confidence 5799999999999999999999999999874 589999999999999999999874
No 20
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=98.72 E-value=3.8e-08 Score=69.27 Aligned_cols=54 Identities=24% Similarity=0.287 Sum_probs=46.1
Q ss_pred eeeeeeEEEEEeCCeEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeE
Q 027058 109 VFKETKQFTYKDGSMFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKI 164 (229)
Q Consensus 109 verk~~qylY~Dgd~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~ 164 (229)
++||..|.++.+|+..++||+||||.++++... +...-+++|.+|.++...|+.
T Consensus 1 i~k~~aqVisi~g~~vQlMD~eTYeT~ev~~p~--~~~~~i~~G~eV~y~~~~g~~ 54 (57)
T cd04467 1 IERKTGQVLSIMGDVVQLMDLETYETFEVPIPE--EIKDKLEPGKEVEYWESMGKR 54 (57)
T ss_pred CcceEEEEEEEcCCEEEEeccccceeEEEecch--hhcccCCCCCEEEEEeecCeE
Confidence 589999999999999999999999999999752 223458999999988887863
No 21
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=98.32 E-value=6.9e-06 Score=76.77 Aligned_cols=110 Identities=18% Similarity=0.225 Sum_probs=88.1
Q ss_pred EEEEEccccCCccEEEECCcEEEEEEEeEeeCCCCceEEEEEEEECCCCCEEEEEecCCCeEE----EeeeeeeeeEEEE
Q 027058 43 IYAFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGKGAAFVRTKLRNYMSGTTVERTFRAGITVE----EADVFKETKQFTY 118 (229)
Q Consensus 43 ~~~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG~A~vriklknL~TG~~~e~tf~s~dkve----~~~verk~~qylY 118 (229)
.+.+.+.++|+|++|.++|..+.++...+ + ++.++|+.|++..+.+|.....-+ ..+-+-+.+.++.
T Consensus 239 t~Svrip~~~~gDiV~~~~~~~~~v~~~~----~-----~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~~~~~~~vvs 309 (355)
T COG1499 239 TYSVRIPEFRPGDIVSVRGRQLVLVRSIG----K-----GIVVLDLETGEPVEITWSVYKRNEGKVAVKEPRLKKAVVVS 309 (355)
T ss_pred EEEEECCCCCCCCEEEECCCeEEEEEEec----C-----ceEEEecccCCccccChhhcccCcceeeeccccceEEEEEe
Confidence 58999999999999999996665555432 3 589999999988888775544433 3333336888899
Q ss_pred EeCCeEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEEEEE
Q 027058 119 KDGSMFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKIIDFE 168 (229)
Q Consensus 119 ~Dgd~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i~v~ 168 (229)
.+++..+|||++|||-+++..+ =|.+|.+|.++.++++...++
T Consensus 310 ~~~~~~~v~d~et~e~~~~~~~-------~~~~g~~v~v~~~~~~~~~~~ 352 (355)
T COG1499 310 RDPSAIQVLDPETYEARTVKGP-------SLEEGDEVKVFKVRGRNYVVE 352 (355)
T ss_pred cCCCceEEEecceEEEEeccCC-------CCCCCCEEEEEEEeceEEeec
Confidence 9999999999999999999876 368999999999999876554
No 22
>PF01287 eIF-5a: Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; InterPro: IPR020189 A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands []. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case []. There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 []. This entry represents the RNA-binding domain of translation elongation factor IF5A [].; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0043022 ribosome binding, 0006452 translational frameshifting, 0045901 positive regulation of translational elongation, 0045905 positive regulation of translational termination; PDB: 1IZ6_B 3CPF_A 1KHI_A 1BKB_A 1XTD_A 3ER0_A 3HKS_B 1X6O_A 2EIF_A 1EIF_A.
Probab=97.27 E-value=0.0011 Score=48.35 Aligned_cols=55 Identities=24% Similarity=0.328 Sum_probs=39.6
Q ss_pred eeeeeeeEEEEEeCC-eEEEecCCCceeee---cCccchhhhh-hccCCCCe--EEEEEECCe
Q 027058 108 DVFKETKQFTYKDGS-MFVFMDLTTFEEVR---LNETDVGDKK-KWLKEGMD--CNLLFWKGK 163 (229)
Q Consensus 108 ~verk~~qylY~Dgd-~~~FMD~etyEQi~---v~~~~lgd~~-~fL~eG~~--v~v~~~~g~ 163 (229)
.|+|+++|.+..++| ...+|| ++||+.+ +|...+++.. ..+.+|.+ |.++...|+
T Consensus 1 ~V~r~eyqli~I~~Dg~lsLMd-e~get~eDl~lP~~el~~ei~~~~~~g~~~~Vtv~~amG~ 62 (69)
T PF01287_consen 1 IVKRKEYQLIDIDGDGFLSLMD-EDGETREDLKLPDGELGEEIKAKFEEGKEVLVTVLSAMGE 62 (69)
T ss_dssp -EEEEEEEEEEEETTTEEEEEE-TTS-EEEEEECCSHHHHHHHHHHHHTTCEEEEEEEEETTE
T ss_pred CeEEEEEEEEEEccCcEEEEEc-CCCCeeccEEecccchhHHHHhhccCCCeEEEEEEeeCCc
Confidence 478999999999987 678999 6666555 8866776643 45589988 555555554
No 23
>cd04468 S1_eIF5A S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=93.91 E-value=0.17 Score=36.97 Aligned_cols=51 Identities=25% Similarity=0.352 Sum_probs=38.2
Q ss_pred eeeeeeEEEEEeCCeEEEecC--CCceeeecCccchhhhhh-ccCCCCeEEEEE
Q 027058 109 VFKETKQFTYKDGSMFVFMDL--TTFEEVRLNETDVGDKKK-WLKEGMDCNLLF 159 (229)
Q Consensus 109 verk~~qylY~Dgd~~~FMD~--etyEQi~v~~~~lgd~~~-fL~eG~~v~v~~ 159 (229)
|.|++||++..+++...+|+. ++-|++.+|.+.++...+ -..+|..+.+..
T Consensus 1 V~R~eYqLidI~dGflsLm~e~G~~k~DlklP~~elg~~I~~~f~~gk~~~vtV 54 (69)
T cd04468 1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKFDEGKDVLVTV 54 (69)
T ss_pred CcceeEEEEeecCCeEEEEcCCCCcccCCcCCcHHHHHHHHHHHhCCCcEEEEE
Confidence 468999999998777789976 679999999988888543 225566544443
No 24
>cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.
Probab=85.47 E-value=3.5 Score=30.56 Aligned_cols=52 Identities=10% Similarity=0.056 Sum_probs=35.7
Q ss_pred eeeEEEEEeCCeEEEecC--CCceeeecC-ccchhhhhh-ccCCCC-e--EEEEEECCe
Q 027058 112 ETKQFTYKDGSMFVFMDL--TTFEEVRLN-ETDVGDKKK-WLKEGM-D--CNLLFWKGK 163 (229)
Q Consensus 112 k~~qylY~Dgd~~~FMD~--etyEQi~v~-~~~lgd~~~-fL~eG~-~--v~v~~~~g~ 163 (229)
++||.+..+++...+||. ++-+++.+| .+.++...+ -..+|. + |.|+-..|+
T Consensus 3 ~eYqLidI~DG~lsLM~e~G~~kdDl~lP~~~~l~~~I~~~f~~gk~~v~VtVlsAmGe 61 (75)
T cd04469 3 KQYRVLDIQDGSIVAMTETGDVKQGLPVIDQSNLWTRLKTAFESGRGSVRVLVVNDGGR 61 (75)
T ss_pred eEEEEEEecCCeEEEEcCCCCcccCccCCCcchHHHHHHHHHHCCCCcEEEEEEccCCe
Confidence 589999996667789975 678999999 777877543 126666 4 444444443
No 25
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=77.94 E-value=2.6 Score=31.22 Aligned_cols=32 Identities=16% Similarity=0.277 Sum_probs=26.0
Q ss_pred cccEEecCCcEEEcc-cCeecCCEEEEEcCCCe
Q 027058 193 SKPATLDTGAVVNVP-LFVNIGDEILVDTRTGQ 224 (229)
Q Consensus 193 ~K~A~LetG~~v~VP-~FI~~Gd~I~V~T~~g~ 224 (229)
-=...+..|..|..| +-|++||.|+++..+++
T Consensus 43 ~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~k 75 (77)
T PF00900_consen 43 KPQLNTHDGRNIRYPDPDIKTNDTVVIDLPTQK 75 (77)
T ss_dssp EEEEEETTTEEEES-SST--TTEEEEEETTTTE
T ss_pred cEEEEecCceEEEcCcCCccCCCEEEEECCCCc
Confidence 446778999999999 99999999999999886
No 26
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=75.47 E-value=6.8 Score=31.95 Aligned_cols=40 Identities=23% Similarity=0.361 Sum_probs=31.3
Q ss_pred EEEccccCCccEEEECCc--EEEEEEEeEee--CC------CCceEEEEE
Q 027058 45 AFSSNDIKVGSNIEVDGA--PWRVLEFLHVK--PG------KGAAFVRTK 84 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~--py~Vv~~~~~k--pG------KG~A~vrik 84 (229)
-+..=|||.|+.|..++. +|.|+.+++.- +. ||.+.|.+|
T Consensus 54 dv~~LDlRIGD~Vkv~~~k~~yiV~Gl~~~~~~~~~~i~cirGy~tV~Lk 103 (131)
T PF08605_consen 54 DVKYLDLRIGDTVKVDGPKVTYIVVGLECKISSEDNIITCIRGYNTVYLK 103 (131)
T ss_pred cEeeeeeecCCEEEECCCCccEEEEEeeecCCCCCCceEEcCCCcEEEEE
Confidence 345568999999999998 99999999872 22 577777764
No 27
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=69.27 E-value=26 Score=28.06 Aligned_cols=67 Identities=21% Similarity=0.297 Sum_probs=44.1
Q ss_pred EEccccCCccEEEE-----CCcEEEEEEEeEeeCCC--CceEEEEEEEECCCCCEEEEEecCCCe-EEEeeeeee
Q 027058 46 FSSNDIKVGSNIEV-----DGAPWRVLEFLHVKPGK--GAAFVRTKLRNYMSGTTVERTFRAGIT-VEEADVFKE 112 (229)
Q Consensus 46 i~a~dirkG~~I~~-----dG~py~Vv~~~~~kpGK--G~A~vriklknL~TG~~~e~tf~s~dk-ve~~~verk 112 (229)
-+..+++.||+|.+ +|.-.++..++-.--++ ++..-.+.+||+..|-=+|..|+-... ++.+.+.++
T Consensus 14 ~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~ 88 (116)
T PRK05338 14 KDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPLHSPRIDSIEVVRR 88 (116)
T ss_pred cCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEecCCCCcccEEEEEEe
Confidence 35778999999976 56544444444332221 222446899999999999999976553 555555544
No 28
>PF02941 FeThRed_A: Ferredoxin thioredoxin reductase variable alpha chain; InterPro: IPR004207 Ferredoxin thioredoxin reductase is a [4FE-4S] protein which plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit a and subunit b. Subunit a is the variable subunit, and b is the catalytic chain. This family is the alpha chain.; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0015979 photosynthesis, 0009536 plastid; PDB: 2PUK_B 2PVO_B 2PVG_B 1DJ7_B 2PVD_B 2PU9_B 2PUO_B.
Probab=67.38 E-value=2.6 Score=30.62 Aligned_cols=18 Identities=39% Similarity=0.803 Sum_probs=12.1
Q ss_pred EECCeEEEEECCceEEEE
Q 027058 159 FWKGKIIDFEVPITVQLT 176 (229)
Q Consensus 159 ~~~g~~i~v~lP~~V~l~ 176 (229)
.|+|++||..||-.|.+.
T Consensus 39 ~wkGr~iSanlP~~V~F~ 56 (67)
T PF02941_consen 39 DWKGRPISANLPVKVQFD 56 (67)
T ss_dssp EETTEE---SS-EEEEET
T ss_pred ecCCcEecCCCcEEEEEe
Confidence 489999999999998874
No 29
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=63.63 E-value=25 Score=27.89 Aligned_cols=68 Identities=24% Similarity=0.320 Sum_probs=44.6
Q ss_pred EEccccCCccEEEE-----CCcEEEEEEEeEeeCCC--CceEEEEEEEECCCCCEEEEEecCCCe-EEEeeeeeee
Q 027058 46 FSSNDIKVGSNIEV-----DGAPWRVLEFLHVKPGK--GAAFVRTKLRNYMSGTTVERTFRAGIT-VEEADVFKET 113 (229)
Q Consensus 46 i~a~dirkG~~I~~-----dG~py~Vv~~~~~kpGK--G~A~vriklknL~TG~~~e~tf~s~dk-ve~~~verk~ 113 (229)
.+..+|++||+|.+ +|....+..|+-.--++ .+-.-.+.++|+..|.-+|..|+-... ++.+++-++.
T Consensus 14 ~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l~SP~I~~IeV~~~~ 89 (113)
T PF01245_consen 14 KDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPLYSPLIKSIEVLRRG 89 (113)
T ss_dssp SSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEETTSTTEEEEEEEEEB
T ss_pred cCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEcCCCCeEEEEEEEec
Confidence 45679999999965 35444444444332222 112336788999999999999987665 6666666654
No 30
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=62.04 E-value=40 Score=26.90 Aligned_cols=65 Identities=26% Similarity=0.352 Sum_probs=42.0
Q ss_pred EEccccCCccEEEE-----CCcEEEEEEEeEeeC---CCCceEEEEEEEECCCCCEEEEEecCCCe-EEEeeeee
Q 027058 46 FSSNDIKVGSNIEV-----DGAPWRVLEFLHVKP---GKGAAFVRTKLRNYMSGTTVERTFRAGIT-VEEADVFK 111 (229)
Q Consensus 46 i~a~dirkG~~I~~-----dG~py~Vv~~~~~kp---GKG~A~vriklknL~TG~~~e~tf~s~dk-ve~~~ver 111 (229)
.+..++++||+|.+ +|.-.++..++-+-- ++|- .-.+.+||+..|-=+|.+|+-... ++.+.+.+
T Consensus 14 ~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~-~~tftvR~i~~gvGVEr~fpl~SP~I~~IeVl~ 87 (113)
T TIGR01024 14 KDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGI-GETFTVRKISYGVGVERIFPLHSPNIDSIEVVR 87 (113)
T ss_pred cCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCC-ceEEEEEEeccCccEEEEEEcCCCccceEEEEE
Confidence 46788999999976 444334333433222 2332 346899999999999999976553 44454444
No 31
>CHL00084 rpl19 ribosomal protein L19
Probab=60.86 E-value=50 Score=26.52 Aligned_cols=66 Identities=23% Similarity=0.332 Sum_probs=42.5
Q ss_pred EEccccCCccEEEE-----CCcEEEEEEEeEee---CCCCceEEEEEEEECCCCCEEEEEecCCCe-EEEeeeeee
Q 027058 46 FSSNDIKVGSNIEV-----DGAPWRVLEFLHVK---PGKGAAFVRTKLRNYMSGTTVERTFRAGIT-VEEADVFKE 112 (229)
Q Consensus 46 i~a~dirkG~~I~~-----dG~py~Vv~~~~~k---pGKG~A~vriklknL~TG~~~e~tf~s~dk-ve~~~verk 112 (229)
.+..++++||+|.+ +|.-..+-.++-+- -|+|- .-.+.+|++..|-=+|..|+-... ++.+++-++
T Consensus 18 ~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~-~~tftvRki~~gvGVEr~fpl~SP~I~~IeV~r~ 92 (117)
T CHL00084 18 KNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGL-NTTITVRKVFQGIGVERVFLLHSPKLASIEVLRR 92 (117)
T ss_pred cCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCC-CeeEEEEEeccCccEEEEEecCCCccceEEEEEe
Confidence 46789999999975 55433333333222 23333 336899999999999999976543 555555543
No 32
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=52.84 E-value=14 Score=26.54 Aligned_cols=19 Identities=32% Similarity=0.781 Sum_probs=14.0
Q ss_pred cccCCccEEEECCcEEEEE
Q 027058 49 NDIKVGSNIEVDGAPWRVL 67 (229)
Q Consensus 49 ~dirkG~~I~~dG~py~Vv 67 (229)
..|++|++|.++|..|+|+
T Consensus 47 ~Kl~~GD~V~~~~~~~~Vv 65 (65)
T PF13275_consen 47 KKLRPGDVVEIDGEEYRVV 65 (65)
T ss_dssp ----SSEEEEETTEEEEEE
T ss_pred CcCCCCCEEEECCEEEEEC
Confidence 4789999999999999885
No 33
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=52.42 E-value=23 Score=24.52 Aligned_cols=36 Identities=25% Similarity=0.282 Sum_probs=23.1
Q ss_pred eEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEEC
Q 027058 123 MFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWK 161 (229)
Q Consensus 123 ~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~ 161 (229)
.-.|+|.+..+.+.+|...+. .=++.|.+|.++.|.
T Consensus 15 ~g~fL~~~~~~~vlLp~~e~~---~~~~~Gd~v~VFvY~ 50 (61)
T PF13509_consen 15 FGYFLDDGEGKEVLLPKSEVP---EPLKVGDEVEVFVYL 50 (61)
T ss_dssp SEEEEEETT-EEEEEEGGG---------TTSEEEEEEEE
T ss_pred CEEEEECCCCCEEEechHHcC---CCCCCCCEEEEEEEE
Confidence 345567677788999887663 338999999999984
No 34
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=52.30 E-value=1.2e+02 Score=32.42 Aligned_cols=173 Identities=17% Similarity=0.221 Sum_probs=107.6
Q ss_pred EEEccccCCccEEEEC-------CcEEEEEEEeE-----eeCC-----C-----CceEEEEEEEECCCCCEEEEEecCCC
Q 027058 45 AFSSNDIKVGSNIEVD-------GAPWRVLEFLH-----VKPG-----K-----GAAFVRTKLRNYMSGTTVERTFRAGI 102 (229)
Q Consensus 45 ~i~a~dirkG~~I~~d-------G~py~Vv~~~~-----~kpG-----K-----G~A~vriklknL~TG~~~e~tf~s~d 102 (229)
.....+-+.|+++++. |-+|+=+.+++ ++|- | ...-+.... -+.+.++.+..|..+|
T Consensus 334 ~~~~~~~~~Gd~l~~~gn~~~~dGFLyK~v~i~sI~t~gV~PT~dELekF~~~~e~~Dl~~~s-t~~~~r~~~~~F~~GD 412 (1024)
T KOG1999|consen 334 SEGRRDHSRGDYLEFEGNELFKDGFLYKDVSISSIITDGVKPTLDELEKFNPSNEEGDLEWVS-TLKSNRKKKHLFSPGD 412 (1024)
T ss_pred hccccccccCceEEecCCceeccceeeeeeecceeeecCcccCHHHHHhhcCCCccccceeee-eeccccccccccCCCC
Confidence 3455566778888764 44666555544 3442 1 111122222 5678888888899999
Q ss_pred eEEEeeeeeeeeEEE--EEeCCeEEEecC--CCceeeecCccchhhhhhccCCCCeEEEEE--EC---CeEEEEECCceE
Q 027058 103 TVEEADVFKETKQFT--YKDGSMFVFMDL--TTFEEVRLNETDVGDKKKWLKEGMDCNLLF--WK---GKIIDFEVPITV 173 (229)
Q Consensus 103 kve~~~verk~~qyl--Y~Dgd~~~FMD~--etyEQi~v~~~~lgd~~~fL~eG~~v~v~~--~~---g~~i~v~lP~~V 173 (229)
.+++..-|-+.++=. -.||+..+.|-. +--+-++++...| .+|+++|.-|+|.- |+ |-++-|+==.-+
T Consensus 413 ~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eL---rKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi 489 (1024)
T KOG1999|consen 413 AVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASEL---RKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVI 489 (1024)
T ss_pred eEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhh---hhhccCCCeEEEEeccccCCcceEEEEeCCeEE
Confidence 999999999988766 568988888875 3456778887777 79999998888775 44 345555532222
Q ss_pred --------EEEEEEcCCCcccccCCCCcccEEecCCcEEEcccCeecCCEEEEEcCC
Q 027058 174 --------QLTVVDVDPGLKGDTASGGSKPATLDTGAVVNVPLFVNIGDEILVDTRT 222 (229)
Q Consensus 174 --------~l~V~et~p~~kgdta~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~ 222 (229)
+|+|--..-..--+.+++..|---.|=+--||.+.+ +.|-+|++.-++
T Consensus 490 ~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hdlVqLd~~-~vgvI~rle~e~ 545 (1024)
T KOG1999|consen 490 LLSDLTMEELKVFARDLQLCSEVTLGVEKSGEYELHDLVQLDNQ-NVGVIVRLERET 545 (1024)
T ss_pred EEecCccceeeEEehhcccchheeecccccccccccceeecCCC-cEEEEEEecchh
Confidence 333332222211222333333334455566788888 888888876543
No 35
>PRK11507 ribosome-associated protein; Provisional
Probab=47.58 E-value=19 Score=26.38 Aligned_cols=20 Identities=20% Similarity=0.361 Sum_probs=17.3
Q ss_pred ccccCCccEEEECCcEEEEE
Q 027058 48 SNDIKVGSNIEVDGAPWRVL 67 (229)
Q Consensus 48 a~dirkG~~I~~dG~py~Vv 67 (229)
-..|++|++|.++|+-++|.
T Consensus 50 gkKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 50 RCKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred CCCCCCCCEEEECCEEEEEe
Confidence 34789999999999998875
No 36
>PF09262 PEX-1N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015342 This domain adopts a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; GO: 0005524 ATP binding, 0007031 peroxisome organization, 0005777 peroxisome; PDB: 1WLF_A.
Probab=45.96 E-value=14 Score=27.59 Aligned_cols=63 Identities=17% Similarity=0.240 Sum_probs=33.6
Q ss_pred CCceeeecCccchhh----hhhccCCCCeEEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCCcEEE
Q 027058 130 TTFEEVRLNETDVGD----KKKWLKEGMDCNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTGAVVN 205 (229)
Q Consensus 130 etyEQi~v~~~~lgd----~~~fL~eG~~v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~ 205 (229)
+++|-+++..+.+++ +.+.+.+|+.+.++..++ ..+.++|..++|....+ -.|.|++|.+|-
T Consensus 12 dDWEIlEl~A~~lE~~lL~QiRvv~~~~~~~v~v~~~--------~~i~~~V~~i~p~~~~~------~~~~L~~~TEv~ 77 (80)
T PF09262_consen 12 DDWEILELHAEFLEDQLLSQIRVVFPGQVFPVWVSQN--------TVIKFKVVSIEPSSSAE------GCARLSPDTEVI 77 (80)
T ss_dssp HHHHHHHHS-SSHHHHHHHH--EE-TT-EEEEESSSS---------EEEEEEEEEES--S---------SEE--TT-EEE
T ss_pred cHHHHHHHhHHHHHHHHHHhheeecCCCEEEEEEcCC--------eEEEEEEEEccCCCCce------eEEEeCCCcEEE
Confidence 457777777766655 334555666666554333 35678899998863211 379999999987
Q ss_pred c
Q 027058 206 V 206 (229)
Q Consensus 206 V 206 (229)
|
T Consensus 78 V 78 (80)
T PF09262_consen 78 V 78 (80)
T ss_dssp E
T ss_pred E
Confidence 6
No 37
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=43.20 E-value=1.6e+02 Score=23.00 Aligned_cols=23 Identities=17% Similarity=0.423 Sum_probs=20.1
Q ss_pred cCCccEEEECCcEEEEEEEeEee
Q 027058 51 IKVGSNIEVDGAPWRVLEFLHVK 73 (229)
Q Consensus 51 irkG~~I~~dG~py~Vv~~~~~k 73 (229)
|++|+++.++|++|.|+-...-+
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 68999999999999999876643
No 38
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=42.57 E-value=1.1e+02 Score=23.61 Aligned_cols=52 Identities=15% Similarity=0.222 Sum_probs=35.1
Q ss_pred CeEEEEECCc----eEEEEEEEcCCCcccccCCCCcccEEecCCcEEEc--c------cCeecCCEEEEEcC
Q 027058 162 GKIIDFEVPI----TVQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNV--P------LFVNIGDEILVDTR 221 (229)
Q Consensus 162 g~~i~v~lP~----~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~V--P------~FI~~Gd~I~V~T~ 221 (229)
+....++||. .+..+|++.-++ ..=.+.+++|.++.+ | ..|+.||.|.|+..
T Consensus 6 ~~~~~~~~p~~~e~e~~g~V~~~lG~--------~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp~ 69 (99)
T TIGR00523 6 EQQIRVRLPRKEEGEILGVIEQMLGA--------GRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPW 69 (99)
T ss_pred cCcceeeCCCCCCCEEEEEEEEEcCC--------CEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEEc
Confidence 3455677774 678888877553 234667788877643 4 36889999999543
No 39
>PRK14560 putative RNA-binding protein; Provisional
Probab=42.30 E-value=64 Score=26.56 Aligned_cols=71 Identities=21% Similarity=0.305 Sum_probs=39.3
Q ss_pred CCCCeEEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCC-cccEEe--------cCCcEEEcccC------eecCC
Q 027058 150 KEGMDCNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGG-SKPATL--------DTGAVVNVPLF------VNIGD 214 (229)
Q Consensus 150 ~eG~~v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~-~K~A~L--------etG~~v~VP~F------I~~Gd 214 (229)
+.+..+.+.+.+|+|+-++.=..+ -|.+.|.-.-.. .+.+++ ..|+.++.|-. ++.||
T Consensus 39 ~~~~~~~~~~~~~~p~~f~~d~~~-------~Ptl~~~~~~~~~~~~v~Vd~~a~~~i~~Ga~lm~pGV~~~~~~~~~Gd 111 (160)
T PRK14560 39 ETDKKEEIYLVDGEPLFFKVDDEL-------FPTLRGALKLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGD 111 (160)
T ss_pred EcCCcEEEEEECCEEEEEEeCCcc-------cccHHHHHhCCccCCEEEEeccHHHHHHCCCceecCeeeeCCCCCCCCC
Confidence 345567777778888776541112 222222111111 122222 36788777744 46799
Q ss_pred EEEEEcCC-Ceeee
Q 027058 215 EILVDTRT-GQYMT 227 (229)
Q Consensus 215 ~I~V~T~~-g~Y~~ 227 (229)
.|.|-++. |+.+.
T Consensus 112 ~V~I~~~~~~~~va 125 (160)
T PRK14560 112 IVFVVEETHGKPLA 125 (160)
T ss_pred EEEEEECCCCeEEE
Confidence 99998876 77664
No 40
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=40.22 E-value=1.9e+02 Score=23.16 Aligned_cols=65 Identities=23% Similarity=0.313 Sum_probs=43.7
Q ss_pred ccccCCccEEEE-----CCcEEEEEEEeEeeCCC--CceEEEEEEEECCCCCEEEEEecCCCe-EEEeeeeee
Q 027058 48 SNDIKVGSNIEV-----DGAPWRVLEFLHVKPGK--GAAFVRTKLRNYMSGTTVERTFRAGIT-VEEADVFKE 112 (229)
Q Consensus 48 a~dirkG~~I~~-----dG~py~Vv~~~~~kpGK--G~A~vriklknL~TG~~~e~tf~s~dk-ve~~~verk 112 (229)
+.++++||.|.. +|.-+.+-.|+-+--.+ ++..=.+.++.+..|-=+|.+|+-... +|.+++-++
T Consensus 18 iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~Fp~~SP~Ie~IeV~rr 90 (115)
T COG0335 18 IPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVFPLHSPLIESIEVVRR 90 (115)
T ss_pred CCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecCceEEEEeecCCCceeEEEEEec
Confidence 678888888753 67777777776543322 222335677888999999999976543 666666554
No 41
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.60 E-value=43 Score=26.48 Aligned_cols=24 Identities=25% Similarity=0.394 Sum_probs=17.0
Q ss_pred EccccCCccEEEECCc--EEEEEEEe
Q 027058 47 SSNDIKVGSNIEVDGA--PWRVLEFL 70 (229)
Q Consensus 47 ~a~dirkG~~I~~dG~--py~Vv~~~ 70 (229)
+-.++++|++|+++|. +.+|+++.
T Consensus 30 krr~ik~GD~IiF~~~~l~v~V~~vr 55 (111)
T COG4043 30 KRRQIKPGDKIIFNGDKLKVEVIDVR 55 (111)
T ss_pred hhcCCCCCCEEEEcCCeeEEEEEEEe
Confidence 3458999999999974 44555543
No 42
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=39.56 E-value=38 Score=27.16 Aligned_cols=24 Identities=13% Similarity=0.176 Sum_probs=21.1
Q ss_pred ccccCCccEEEECCcEEEEEEEeE
Q 027058 48 SNDIKVGSNIEVDGAPWRVLEFLH 71 (229)
Q Consensus 48 a~dirkG~~I~~dG~py~Vv~~~~ 71 (229)
-.+|++|+.+.++|+-|.|..+--
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaVG~ 72 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAVGS 72 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEEhH
Confidence 467999999999999999998743
No 43
>PF10665 Minor_capsid_1: Minor capsid protein; InterPro: IPR019612 This entry is represented by Bacteriophage A118, Gp9. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a putative tail-knob protein from Listeria phage A118.
Probab=38.68 E-value=83 Score=24.89 Aligned_cols=26 Identities=27% Similarity=0.275 Sum_probs=23.1
Q ss_pred ccccCCccEEEECCcEEEEEEEeEee
Q 027058 48 SNDIKVGSNIEVDGAPWRVLEFLHVK 73 (229)
Q Consensus 48 a~dirkG~~I~~dG~py~Vv~~~~~k 73 (229)
+-+++.|+.|.+||+.|.|.++...-
T Consensus 74 ~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 74 FPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred ccccCCCCEEEECCceEEEEEEEecc
Confidence 35899999999999999999998765
No 44
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=38.24 E-value=25 Score=26.59 Aligned_cols=21 Identities=24% Similarity=0.199 Sum_probs=17.2
Q ss_pred cCeecCCEEEEEcCCCeeeec
Q 027058 208 LFVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 208 ~FI~~Gd~I~V~T~~g~Y~~R 228 (229)
+=|+.||+|+|.++.|+..-|
T Consensus 43 lgi~~Gd~V~v~s~~G~~~~~ 63 (116)
T cd02786 43 RGIADGDLVVVFNDRGSVTLR 63 (116)
T ss_pred cCCCCCCEEEEEcCCeEEEEE
Confidence 347789999999999987654
No 45
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=38.19 E-value=3.3e+02 Score=25.20 Aligned_cols=87 Identities=26% Similarity=0.345 Sum_probs=56.0
Q ss_pred CCeEEEecCCCce-eeecCccchhhhhhccCCCCeEEEEEE---CCeEEE------EECCceEEEEEEEcCCCcccccCC
Q 027058 121 GSMFVFMDLTTFE-EVRLNETDVGDKKKWLKEGMDCNLLFW---KGKIID------FEVPITVQLTVVDVDPGLKGDTAS 190 (229)
Q Consensus 121 gd~~~FMD~etyE-Qi~v~~~~lgd~~~fL~eG~~v~v~~~---~g~~i~------v~lP~~V~l~V~et~p~~kgdta~ 190 (229)
.+...|++.++++ .+-+++.... -.=++.|.+|+++.| +++++. +..=..=-++|+++.+.+
T Consensus 17 ~~~g~fL~~~~~~~~ilL~k~~~~--~~e~evGdev~vFiY~D~~~rl~aTt~~p~~tvg~~g~~~Vv~v~~~l------ 88 (287)
T COG2996 17 SDFGYFLDAGEDGTTILLPKSEPE--EDELEVGDEVTVFIYVDSEDRLIATTREPKATVGEYGWLKVVEVNKDL------ 88 (287)
T ss_pred eceeEEEecCCCceEEeccccCCc--CCccccCcEEEEEEEECCCCceeheeecceEeecceeEEEEEEEcCCc------
Confidence 3556777777775 6666665432 123789999999987 566653 333344468999997753
Q ss_pred CCcccEEecCCcE--EEcc---------cCeecCCEEEEE
Q 027058 191 GGSKPATLDTGAV--VNVP---------LFVNIGDEILVD 219 (229)
Q Consensus 191 ~~~K~A~LetG~~--v~VP---------~FI~~Gd~I~V~ 219 (229)
-|-|++|+. +.|| +..+.||+.-|.
T Consensus 89 ----GaFlD~Gl~KDl~vp~~elp~~~~~wpq~Gd~l~v~ 124 (287)
T COG2996 89 ----GAFLDWGLPKDLLVPLDELPTLKSLWPQKGDKLLVY 124 (287)
T ss_pred ----ceEEecCCCcceeeehhhcccccccCCCCCCEEEEE
Confidence 356666654 3333 337889988765
No 46
>PF05521 Phage_H_T_join: Phage head-tail joining protein ; InterPro: IPR008767 This entry describes the head-tail adaptor protein of bacteriophage SPP1 and related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg7 (RCAP_rcc01689) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2KCA_A 2KZ4_A.
Probab=38.05 E-value=60 Score=22.97 Aligned_cols=30 Identities=17% Similarity=0.265 Sum_probs=21.1
Q ss_pred EEEEc-cccCCccEEEECCcEEEEEEEeEee
Q 027058 44 YAFSS-NDIKVGSNIEVDGAPWRVLEFLHVK 73 (229)
Q Consensus 44 ~~i~a-~dirkG~~I~~dG~py~Vv~~~~~k 73 (229)
+.+.- .+|..++.|.++|+.|.|..+....
T Consensus 55 ~~iR~~~~I~~~~ri~~~g~~y~I~~i~~~~ 85 (95)
T PF05521_consen 55 FTIRYRKDITPDMRIKYDGKVYNIKSIDPDD 85 (95)
T ss_dssp EEECS-TTSSTTEEEEECTEEEEE-S--EE-
T ss_pred EEEecCcCCCcceEEEECCEEEEEEEECCCC
Confidence 34433 3799999999999999999977654
No 47
>PF03829 PTSIIA_gutA: PTS system glucitol/sorbitol-specific IIA component; InterPro: IPR004716 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria. The system in Escherichia coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2F9H_A.
Probab=37.99 E-value=36 Score=27.10 Aligned_cols=23 Identities=22% Similarity=0.419 Sum_probs=15.8
Q ss_pred ccccCCccEEEECCcEEEEEEEe
Q 027058 48 SNDIKVGSNIEVDGAPWRVLEFL 70 (229)
Q Consensus 48 a~dirkG~~I~~dG~py~Vv~~~ 70 (229)
..+|++|+.+.++++.|.|..+-
T Consensus 49 ~~~i~~Gd~l~i~~~~y~ItaVG 71 (117)
T PF03829_consen 49 KGDIKPGDTLIIGGQEYTITAVG 71 (117)
T ss_dssp G----TT-EEEETTEEEEEEEE-
T ss_pred cCCcCCCCEEEECCeEEEEEEEh
Confidence 46899999999999999999874
No 48
>TIGR00849 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component.
Probab=37.89 E-value=42 Score=26.96 Aligned_cols=23 Identities=17% Similarity=0.276 Sum_probs=20.5
Q ss_pred cccCCccEEEECCcEEEEEEEeE
Q 027058 49 NDIKVGSNIEVDGAPWRVLEFLH 71 (229)
Q Consensus 49 ~dirkG~~I~~dG~py~Vv~~~~ 71 (229)
.+|++|+.+.++|+-|.|..+--
T Consensus 50 ~~i~~Gd~l~i~~~~Y~ItaVG~ 72 (121)
T TIGR00849 50 GTLKPGQVFMIGGIAYPVTAVGD 72 (121)
T ss_pred CCcCCCCEEEECCEEEEEEEEhH
Confidence 48999999999999999998743
No 49
>TIGR01646 vgr_GE Rhs element Vgr protein. This model represents the Vgr family of proteins, associated with some classes of Rhs elements. This model does not include a large octapeptide repeat region, VGXXXXXX, found in the Vgr of Rhs classes G and E.
Probab=37.67 E-value=1.9e+02 Score=27.82 Aligned_cols=119 Identities=12% Similarity=0.056 Sum_probs=64.2
Q ss_pred EEEccccCCccEEEECCcE-------EEEEEEeEeeCC------CCceEEEEEEEECCCCCEEEE---EecCCCeEEEee
Q 027058 45 AFSSNDIKVGSNIEVDGAP-------WRVLEFLHVKPG------KGAAFVRTKLRNYMSGTTVER---TFRAGITVEEAD 108 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~p-------y~Vv~~~~~kpG------KG~A~vriklknL~TG~~~e~---tf~s~dkve~~~ 108 (229)
..++..|+.|..|.+.|.| |.|+++.|.--. -..+.++..+.-+..+...-- ..+.-.-+..+.
T Consensus 275 ~~~~~~L~~G~~~~l~~~~~~~~~~~~~v~~v~h~~~~~~~~~~~~~~~y~~~f~~~p~~~~~rp~~~~~p~i~G~~~a~ 354 (483)
T TIGR01646 275 EGNAAGLAPGQLFVLSGHPRNDQNNGYLIVSAIHSIVQLGWDTGIQGYELPNQFIAIEVDVIWRPAATPLPKVNGPQIAV 354 (483)
T ss_pred EeCCCeecCCCEEEecCCCCcccCCCEEEEEEEEEEEcCccccCCCCceEEEEEEEEECCCccCCCCCCCCCCCCcceEE
Confidence 3356779999999998764 999999987211 112446666655544432111 111112234555
Q ss_pred eeeeeeEEEEEeCCe---EEEe-cCCCc----ee--eecCccchhhh--hhc-cCCCCeEEEEEECCe
Q 027058 109 VFKETKQFTYKDGSM---FVFM-DLTTF----EE--VRLNETDVGDK--KKW-LKEGMDCNLLFWKGK 163 (229)
Q Consensus 109 verk~~qylY~Dgd~---~~FM-D~ety----EQ--i~v~~~~lgd~--~~f-L~eG~~v~v~~~~g~ 163 (229)
|.--+-+++|.|+.. ..|. |.... +. +.+....-|+. ..| +..|+||-|-|.+|.
T Consensus 355 V~g~~~~~~~~d~~GRvkV~f~wd~~~~~~~~~S~W~Rvaqp~AG~~~G~~f~PrvG~EVlV~F~~GD 422 (483)
T TIGR01646 355 VVGAQGEEIHTDKYGRIRVHFHWDRYGQSNDYSSCWIRVAQPWAGKNWGSLAIPRVGQEVIVGFLDGD 422 (483)
T ss_pred EECCCCCeeccCCCCcEEEEeecCCCCCCCCCCceEEEEeccccCCCccccccCCCCCEEEEEEeCCC
Confidence 554444577777653 2232 22211 11 33333222221 223 378999999999864
No 50
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=37.67 E-value=91 Score=23.70 Aligned_cols=37 Identities=22% Similarity=0.243 Sum_probs=22.9
Q ss_pred ccCCCCccCCCCCCCCCceEEEEEcc-------------ccCCccEEEEC
Q 027058 24 TLSSKPSVLPMRPRSKFPRIYAFSSN-------------DIKVGSNIEVD 60 (229)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~i~a~-------------dirkG~~I~~d 60 (229)
.-.+.|-++|+-++.+......+.++ ++|+|+.|.++
T Consensus 19 ~~T~gGI~Lp~~a~~k~~~G~VvaVG~G~~~~~G~~~~~~vk~GD~Vlf~ 68 (95)
T PRK00364 19 EKTAGGIVLPDSAKEKPQEGEVVAVGPGRRLDNGERVPLDVKVGDKVLFG 68 (95)
T ss_pred ccccceEEcCccccCCcceEEEEEECCCeECCCCCEeecccCCCCEEEEc
Confidence 34456777888766665543333333 48888888774
No 51
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=37.18 E-value=65 Score=20.94 Aligned_cols=30 Identities=20% Similarity=0.165 Sum_probs=22.1
Q ss_pred eeecCccchhhhhhccCCCCeEEEEEECC-eEE
Q 027058 134 EVRLNETDVGDKKKWLKEGMDCNLLFWKG-KII 165 (229)
Q Consensus 134 Qi~v~~~~lgd~~~fL~eG~~v~v~~~~g-~~i 165 (229)
|+.||++.... .-|++|+++.+...++ +++
T Consensus 8 ~v~iPk~~~~~--l~l~~Gd~v~i~~~~~g~i~ 38 (47)
T PF04014_consen 8 QVTIPKEIREK--LGLKPGDEVEIEVEGDGKIV 38 (47)
T ss_dssp EEEE-HHHHHH--TTSSTTTEEEEEEETTSEEE
T ss_pred eEECCHHHHHH--cCCCCCCEEEEEEeCCCEEE
Confidence 78889877532 2589999999999887 443
No 52
>PRK12366 replication factor A; Reviewed
Probab=36.34 E-value=4.8e+02 Score=26.54 Aligned_cols=55 Identities=16% Similarity=0.286 Sum_probs=38.7
Q ss_pred EEEccccCCccE-EEECCcEEEEEEEeEeeCCCC--ceEEEEEEEECCCCCEEEEEecC
Q 027058 45 AFSSNDIKVGSN-IEVDGAPWRVLEFLHVKPGKG--AAFVRTKLRNYMSGTTVERTFRA 100 (229)
Q Consensus 45 ~i~a~dirkG~~-I~~dG~py~Vv~~~~~kpGKG--~A~vriklknL~TG~~~e~tf~s 100 (229)
.+.+++|.+|+. +.+.++...+-+....+-.+| +-...+.+-| .||++.=--|..
T Consensus 63 ~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~D-etG~Ir~t~W~~ 120 (637)
T PRK12366 63 DFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIAD-NTGTIRLTLWND 120 (637)
T ss_pred eeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEc-CCCEEEEEEEch
Confidence 567899999995 888888777766665544444 2355777888 888766556643
No 53
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=35.92 E-value=61 Score=27.47 Aligned_cols=69 Identities=20% Similarity=0.158 Sum_probs=41.3
Q ss_pred hccCCCCeEEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcc-cEE--------ecCCcEEEcccCe------e
Q 027058 147 KWLKEGMDCNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSK-PAT--------LDTGAVVNVPLFV------N 211 (229)
Q Consensus 147 ~fL~eG~~v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K-~A~--------LetG~~v~VP~FI------~ 211 (229)
...+...+.++++.||+|+-++.-..+. |.+++--..+..+ .++ +-||+-|+.|-.+ +
T Consensus 36 ~v~~~~~~~~ii~vdG~pl~f~~~~~~i-------PTl~~l~~~~~~~~~V~VD~GAvk~v~nGADvM~PGIv~~~~~ik 108 (161)
T COG2016 36 EVAKCDDKFEIILVDGEPLLFQRDDRLI-------PTLRLLLKLPPGKYVVVVDEGAVKFVLNGADVMAPGIVSADGEIK 108 (161)
T ss_pred EEEecCCcEEEEEECCEEEEEEeCCeec-------hhhHHHHhCCCCccEEEEcCccHhhhcCCCceeccceeecCCCcc
Confidence 3445666888889999999887665332 2222222222111 222 4577889999765 4
Q ss_pred cCCEEEEEcCC
Q 027058 212 IGDEILVDTRT 222 (229)
Q Consensus 212 ~Gd~I~V~T~~ 222 (229)
.||.|.|.-+.
T Consensus 109 ~Gd~VvV~~e~ 119 (161)
T COG2016 109 EGDIVVVVDEK 119 (161)
T ss_pred CCCEEEEEEcC
Confidence 57777766443
No 54
>TIGR00451 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.
Probab=35.54 E-value=89 Score=23.80 Aligned_cols=29 Identities=24% Similarity=0.299 Sum_probs=22.3
Q ss_pred CCcEEEccc------CeecCCEEEEEcCC-Ceeeec
Q 027058 200 TGAVVNVPL------FVNIGDEILVDTRT-GQYMTR 228 (229)
Q Consensus 200 tG~~v~VP~------FI~~Gd~I~V~T~~-g~Y~~R 228 (229)
.|+.++.|- -++.||.|.|-+.+ |+.+.+
T Consensus 45 ~Ga~L~~pGV~~~~~~~~~gd~V~I~~~~~~~~iav 80 (107)
T TIGR00451 45 NGADVMRPGIVDADEDIKEGDDVVVVDENKDRPLAV 80 (107)
T ss_pred CCccccCCeeEeCCCCcCCCCEEEEEECCCCeEEEE
Confidence 688888884 45779999998776 887753
No 55
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=35.41 E-value=39 Score=24.99 Aligned_cols=22 Identities=18% Similarity=0.486 Sum_probs=18.9
Q ss_pred ccccCCccEEEECCcEEEEEEE
Q 027058 48 SNDIKVGSNIEVDGAPWRVLEF 69 (229)
Q Consensus 48 a~dirkG~~I~~dG~py~Vv~~ 69 (229)
-..||.|+.|++.|..|.|...
T Consensus 50 gkKlr~gd~V~i~~~~~~v~~~ 71 (73)
T COG2501 50 GKKLRDGDVVEIPGQRYQVVAQ 71 (73)
T ss_pred CCEeecCCEEEECCEEEEEEec
Confidence 3578899999999999999864
No 56
>PF12158 DUF3592: Protein of unknown function (DUF3592); InterPro: IPR021994 This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=35.06 E-value=1e+02 Score=23.92 Aligned_cols=49 Identities=12% Similarity=0.205 Sum_probs=27.3
Q ss_pred eEEEEEeCCeEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEECCeEEEEECC
Q 027058 114 KQFTYKDGSMFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFWKGKIIDFEVP 170 (229)
Q Consensus 114 ~qylY~Dgd~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~~g~~i~v~lP 170 (229)
++|.|.||..+. ++.-+.....+..+..+.|.+|++.+.-++|=...++
T Consensus 65 v~y~~~~G~~~~--------~~~~~~~~~~~~~~~~~~G~~V~V~Y~P~~P~~~~l~ 113 (148)
T PF12158_consen 65 VEYTYQDGRTYS--------RFYSGSDNFGSYWPKYPIGDTVTVYYNPNNPEEARLE 113 (148)
T ss_pred EEEEECCCcEEE--------EeccCCcccccCCccCCCcCEEEEEECCcCCCeEEEe
Confidence 667777663333 1111111233334447789999998877776554443
No 57
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=35.04 E-value=29 Score=26.08 Aligned_cols=21 Identities=29% Similarity=0.457 Sum_probs=16.5
Q ss_pred cCeecCCEEEEEcCCCeeeec
Q 027058 208 LFVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 208 ~FI~~Gd~I~V~T~~g~Y~~R 228 (229)
+=|+.||+|+|.+..|+..-+
T Consensus 47 lgi~~Gd~V~v~~~~G~~~~~ 67 (116)
T cd02790 47 LGIEDGEKVRVSSRRGSVEVR 67 (116)
T ss_pred cCCCCCCEEEEEcCCEEEEEE
Confidence 346889999999999986543
No 58
>PRK04313 30S ribosomal protein S4e; Validated
Probab=34.54 E-value=64 Score=28.95 Aligned_cols=32 Identities=19% Similarity=0.200 Sum_probs=21.4
Q ss_pred cccEEecCCcEEEcc--cCeecCCEEEEEcCCCe
Q 027058 193 SKPATLDTGAVVNVP--LFVNIGDEILVDTRTGQ 224 (229)
Q Consensus 193 ~K~A~LetG~~v~VP--~FI~~Gd~I~V~T~~g~ 224 (229)
--...|..|..|.+| .-+++||.|+|+-.+++
T Consensus 132 ~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~k 165 (237)
T PRK04313 132 KIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQE 165 (237)
T ss_pred EEEEEecCCceEEccCccccccCCEEEEECCCCc
Confidence 335566677777777 56777777777776664
No 59
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=34.46 E-value=1.1e+02 Score=28.36 Aligned_cols=54 Identities=13% Similarity=0.206 Sum_probs=41.3
Q ss_pred EEEccccCCccEEEECCcEEEEEEEeEeeCCCCceEEEEEEEECCCCCEEEEEecCCC
Q 027058 45 AFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGKGAAFVRTKLRNYMSGTTVERTFRAGI 102 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG~A~vriklknL~TG~~~e~tf~s~d 102 (229)
|..++|++.|..|. .+|.|.+.+-...-+|+.+..+.+.| .||.+.-+-|...+
T Consensus 2 m~~i~~l~~g~~v~---~~~lv~~~~~~~~knG~~yl~l~l~D-~tG~I~ak~W~~~~ 55 (314)
T PRK13480 2 MKGIEELEVGEQVD---HFLLIKSATKGVASNGKPFLTLILQD-KSGDIEAKLWDVSP 55 (314)
T ss_pred cchHhhcCCCCEee---EEEEEEEceeeecCCCCeEEEEEEEc-CCcEEEEEeCCCCh
Confidence 44789999998654 36777777654433488899999999 99999888887653
No 60
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=34.15 E-value=30 Score=26.46 Aligned_cols=22 Identities=23% Similarity=0.080 Sum_probs=17.9
Q ss_pred cCeecCCEEEEEcCCCeeeecC
Q 027058 208 LFVNIGDEILVDTRTGQYMTRA 229 (229)
Q Consensus 208 ~FI~~Gd~I~V~T~~g~Y~~R~ 229 (229)
+=|+.||.|+|.++.|+..-||
T Consensus 45 lgi~~Gd~V~v~s~~G~i~~~~ 66 (115)
T cd02779 45 EGLKNGDLVEVYNDYGSTTAMA 66 (115)
T ss_pred cCCCCCCEEEEEeCCEEEEEEE
Confidence 4578899999999999876553
No 61
>PF05354 Phage_attach: Phage Head-Tail Attachment; InterPro: IPR008018 This entry is represented by Bacteriophage lambda, FII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The phage head-tail attachment protein is required for the joining of phage heads and tails at the last step of morphogenesis [].; GO: 0042963 phage assembly, 0019028 viral capsid; PDB: 2KX4_A 1K0H_A.
Probab=34.13 E-value=36 Score=27.36 Aligned_cols=27 Identities=19% Similarity=0.346 Sum_probs=19.3
Q ss_pred EEEccccCCccEEEECCcEEEEEEEeEeeC
Q 027058 45 AFSSNDIKVGSNIEVDGAPWRVLEFLHVKP 74 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~py~Vv~~~~~kp 74 (229)
...+..||+++.+.+.|++|.|.+ +.|
T Consensus 69 t~dv~~L~r~DtL~I~g~~y~Vd~---v~p 95 (117)
T PF05354_consen 69 TADVSGLKRRDTLTIGGESYWVDR---VGP 95 (117)
T ss_dssp CCCCCTS-TT-EEEETTTEEEBS------S
T ss_pred ehHhhhhhcCCeEEECCEEEEEEe---ecc
Confidence 457889999999999999999944 556
No 62
>PF02839 CBM_5_12: Carbohydrate binding domain; InterPro: IPR003610 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM5 from CAZY and CBM12 from CAZY. These modules have a core structure consisting of a 3-stranded meander beta-sheet, which contain six aromatic groups that may be important for binding. CBM5/12 is found in proteins such as chitinase A1, chitinase B [], and endoglucanase Z []. The overall topology of the CBM is structurally similar to the C-terminal chitin-binding domains (ChBD) of chitinase A1 and chitinase B, however the binding mechanism for the ChBD may be different from that of the CBM [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process, 0005576 extracellular region; PDB: 1ED7_A 1W1V_A 1E15_B 1UR8_A 1E6Z_B 1E6P_A 1W1T_A 1W1P_B 1UR9_A 1E6R_A ....
Probab=33.31 E-value=44 Score=20.95 Aligned_cols=19 Identities=11% Similarity=0.331 Sum_probs=14.3
Q ss_pred cCCccEEEECCcEEEEEEE
Q 027058 51 IKVGSNIEVDGAPWRVLEF 69 (229)
Q Consensus 51 irkG~~I~~dG~py~Vv~~ 69 (229)
...|++|.++|..|+..-.
T Consensus 10 Y~~Gd~V~~~g~~y~a~~~ 28 (41)
T PF02839_consen 10 YNAGDRVSYNGKLYQAKWW 28 (41)
T ss_dssp E-TT-EEEETTEEEEESSS
T ss_pred EcCCCEEEECCCEEEEeec
Confidence 4679999999999998543
No 63
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=32.30 E-value=58 Score=24.41 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=17.5
Q ss_pred cCCccEEEECCcEEEEEEEeEe
Q 027058 51 IKVGSNIEVDGAPWRVLEFLHV 72 (229)
Q Consensus 51 irkG~~I~~dG~py~Vv~~~~~ 72 (229)
.|+|+.|.+||+-|.|.+++.-
T Consensus 66 P~~gd~v~~dG~~y~V~~~~~~ 87 (95)
T PF13856_consen 66 PRRGDRVVIDGESYTVTRFQEE 87 (95)
T ss_dssp --TT-EEEETTEEEEEEEEEEE
T ss_pred CCCCCEEEECCeEEEEeEEecC
Confidence 5699999999999999998864
No 64
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=32.24 E-value=2e+02 Score=22.35 Aligned_cols=44 Identities=16% Similarity=0.098 Sum_probs=28.8
Q ss_pred ceEEEEEEEcCCCcccccCCCCcccEEecCCcEEEc--c------cCeecCCEEEEEcCC
Q 027058 171 ITVQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNV--P------LFVNIGDEILVDTRT 222 (229)
Q Consensus 171 ~~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~V--P------~FI~~Gd~I~V~T~~ 222 (229)
..+...|++.-++ ..=.+.+++|.++.+ | ..|..||.|.|....
T Consensus 21 ~e~~g~V~~~lG~--------~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~ 72 (100)
T PRK04012 21 GEVFGVVEQMLGA--------NRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWD 72 (100)
T ss_pred CEEEEEEEEEcCC--------CEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEecc
Confidence 4566667766443 233566677776533 4 578899999998654
No 65
>KOG0267 consensus Microtubule severing protein katanin p80 subunit B (contains WD40 repeats) [Cell cycle control, cell division, chromosome partitioning]
Probab=31.68 E-value=1.1e+02 Score=31.86 Aligned_cols=152 Identities=16% Similarity=0.212 Sum_probs=93.8
Q ss_pred EEEccccC-CccEEEECCcEEEEEEEeEeeCCC----CceEEEEEEEECCCCCEEEEEecCC-CeEEEeeeeeeeeEEEE
Q 027058 45 AFSSNDIK-VGSNIEVDGAPWRVLEFLHVKPGK----GAAFVRTKLRNYMSGTTVERTFRAG-ITVEEADVFKETKQFTY 118 (229)
Q Consensus 45 ~i~a~dir-kG~~I~~dG~py~Vv~~~~~kpGK----G~A~vriklknL~TG~~~e~tf~s~-dkve~~~verk~~qylY 118 (229)
-..+.|+| +|-.-.++|.++.|--..+.--|| |+--.-+++=|+.-|+.. ..|++. .++.. +|-.+..||-
T Consensus 135 d~~iwD~Rk~Gc~~~~~s~~~vv~~l~lsP~Gr~v~~g~ed~tvki~d~~agk~~-~ef~~~e~~v~s--le~hp~e~Ll 211 (825)
T KOG0267|consen 135 DLKIWDIRKKGCSHTYKSHTRVVDVLRLSPDGRWVASGGEDNTVKIWDLTAGKLS-KEFKSHEGKVQS--LEFHPLEVLL 211 (825)
T ss_pred cceehhhhccCceeeecCCcceeEEEeecCCCceeeccCCcceeeeecccccccc-cccccccccccc--cccCchhhhh
Confidence 45678999 788888999776655555544476 444577888888888776 456532 23333 3355556665
Q ss_pred EeC---CeEEEecCCCceeeecCc-cchhh-hhhccCCCCeE----EEEEECCeEEEEECCceEEEEEEEcCCCcccccC
Q 027058 119 KDG---SMFVFMDLTTFEEVRLNE-TDVGD-KKKWLKEGMDC----NLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTA 189 (229)
Q Consensus 119 ~Dg---d~~~FMD~etyEQi~v~~-~~lgd-~~~fL~eG~~v----~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta 189 (229)
.-| ...-|-|.||||-|.=.+ +..|- ...|=-+|+.+ ++.+-+.+ .--.+|..++..+||-..|+++
T Consensus 212 a~Gs~d~tv~f~dletfe~I~s~~~~~~~v~~~~fn~~~~~~~~G~q~sl~~~~----~a~ah~~~~~~~~Ep~~~~~~v 287 (825)
T KOG0267|consen 212 APGSSDRTVRFWDLETFEVISSGKPETDGVRSLAFNPDGKIVLSGEQISLSESR----TASAHVRKTLARWEPEMDGAVV 287 (825)
T ss_pred ccCCCCceeeeeccceeEEeeccCCccCCceeeeecCCceeeecCchhhhhhhh----cccceeecccccccccccccee
Confidence 544 356799999998885433 32222 22343444332 11122222 2238999999999999888886
Q ss_pred CC-CcccEEecCCcE
Q 027058 190 SG-GSKPATLDTGAV 203 (229)
Q Consensus 190 ~~-~~K~A~LetG~~ 203 (229)
+. ..|+..+.-|..
T Consensus 288 qs~~~~ek~v~v~~d 302 (825)
T KOG0267|consen 288 QSNSHKEKVVAVGRD 302 (825)
T ss_pred eecCCcccccccccC
Confidence 64 577777755543
No 66
>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=31.65 E-value=1.6e+02 Score=20.04 Aligned_cols=45 Identities=20% Similarity=0.262 Sum_probs=33.0
Q ss_pred EEeCCeEEEecCCC-ceeeecCccchhhh-hhccCCCCeEEEEEECC
Q 027058 118 YKDGSMFVFMDLTT-FEEVRLNETDVGDK-KKWLKEGMDCNLLFWKG 162 (229)
Q Consensus 118 Y~Dgd~~~FMD~et-yEQi~v~~~~lgd~-~~fL~eG~~v~v~~~~g 162 (229)
|.+...|=|+..+. -+++-+....+... ..-|++|+.|......+
T Consensus 8 ~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 8 FDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEG 54 (65)
T ss_pred EECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEEC
Confidence 45556677777765 78888888887665 56789999988877543
No 67
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.49 E-value=37 Score=25.91 Aligned_cols=20 Identities=20% Similarity=0.326 Sum_probs=16.7
Q ss_pred CeecCCEEEEEcCCCeeeec
Q 027058 209 FVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 209 FI~~Gd~I~V~T~~g~Y~~R 228 (229)
=|+.||+|+|.++.|+..-+
T Consensus 43 gi~~Gd~V~v~s~~G~i~~~ 62 (123)
T cd02778 43 GIKDGDRVEVSSARGKVTGK 62 (123)
T ss_pred CCCCCCEEEEEeCCCcEEEE
Confidence 57889999999999987644
No 68
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=31.29 E-value=68 Score=28.43 Aligned_cols=52 Identities=31% Similarity=0.498 Sum_probs=34.8
Q ss_pred ECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCCcEEEcccCeecCCEEEEEcCCCeee
Q 027058 160 WKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNVPLFVNIGDEILVDTRTGQYM 226 (229)
Q Consensus 160 ~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~g~Y~ 226 (229)
+.|.++..|-|-++.-.|.=.+|.= - +|. |-+. -|-+.|++|+|.||+|.-+
T Consensus 122 ~pgtivk~EaPlhvsk~VmLvdp~d---~-----q~t--e~~w-----r~~e~GekVRvstrSG~iI 173 (236)
T KOG1708|consen 122 EPGTIVKSEAPLHVSKQVMLVDPED---D-----QPT--EVEW-----RFTEDGEKVRVSTRSGRII 173 (236)
T ss_pred CCceEEeecCCceecceeEEECccc---c-----CCc--eeeE-----EEcCCCcEEEEEecccccc
Confidence 4678888888988877777677731 0 111 1112 2667899999999998643
No 69
>PF06988 NifT: NifT/FixU protein; InterPro: IPR009727 This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in Klebsiella pneumoniae has only a limited effect on nitrogen fixation [].; GO: 0009399 nitrogen fixation; PDB: 2JN4_A.
Probab=30.42 E-value=2.1e+02 Score=20.63 Aligned_cols=49 Identities=20% Similarity=0.199 Sum_probs=26.7
Q ss_pred eEEEEEECCeEEEEECCce-EEEEEEEcC-CCcccccCCCCcccEEecCCcEEEcccC
Q 027058 154 DCNLLFWKGKIIDFEVPIT-VQLTVVDVD-PGLKGDTASGGSKPATLDTGAVVNVPLF 209 (229)
Q Consensus 154 ~v~v~~~~g~~i~v~lP~~-V~l~V~et~-p~~kgdta~~~~K~A~LetG~~v~VP~F 209 (229)
.|.+...+.--+++-+|.+ ++=.|++.| |..= -+.++|.||.+..+|..
T Consensus 2 kVmiR~~~~G~ls~YVpKKDLEE~Vv~~E~~~~w-------GG~v~L~NGw~l~lp~~ 52 (64)
T PF06988_consen 2 KVMIRKNGAGGLSAYVPKKDLEEPVVSMEKPELW-------GGEVTLANGWELYLPPL 52 (64)
T ss_dssp -EEEEE-SS--EEEEETTTTEEEEEEEESSSSS--------SSEEEETTS-EEE----
T ss_pred eEEEEeCCCcCEEEEEeCCccccceeeeeccCcc-------CCEEEECCcCEEEeCCC
Confidence 3444433333777777765 677777774 3322 46899999999999875
No 70
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=30.19 E-value=35 Score=25.43 Aligned_cols=19 Identities=26% Similarity=0.365 Sum_probs=14.6
Q ss_pred eecCCEEEEEcCCCeeeec
Q 027058 210 VNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 210 I~~Gd~I~V~T~~g~Y~~R 228 (229)
|+.||+|+|.++.|+-.-+
T Consensus 44 i~~Gd~V~v~s~~G~v~~~ 62 (110)
T PF01568_consen 44 IKDGDWVRVSSPRGSVEVR 62 (110)
T ss_dssp --TTCEEEEEETTEEEEEE
T ss_pred CcCCCEEEEEeccceEeee
Confidence 7899999999999986654
No 71
>PF15415 DUF4622: Protein of unknown function (DUF4622)
Probab=30.12 E-value=59 Score=29.65 Aligned_cols=72 Identities=22% Similarity=0.357 Sum_probs=44.6
Q ss_pred ccCCCCeEEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEe-cCCcEEEc---ccCeecCC---------
Q 027058 148 WLKEGMDCNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATL-DTGAVVNV---PLFVNIGD--------- 214 (229)
Q Consensus 148 fL~eG~~v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~L-etG~~v~V---P~FI~~Gd--------- 214 (229)
.|.+|..+-+.++++.-=.-+--+ .=-|+.| |+.-.+...|+.+ |||..|.+ |+|.++|-
T Consensus 39 lL~~GSTlwL~~~~~ak~gtt~~t--qgYvVrt-----gtgG~~~LYPC~~deNG~~i~~s~tPLyl~aGtY~F~~iSPA 111 (310)
T PF15415_consen 39 LLPIGSTLWLFYYDQAKNGTTYYT--QGYVVRT-----GTGGYNSLYPCQFDENGKYINSSSTPLYLNAGTYYFRMISPA 111 (310)
T ss_pred EccCCCEEEEEEeccccccceeee--eEEEEEe-----cCCCcceeeeeEEcCCCcEEeccCCceEEecceEEEEEeccc
Confidence 467889988888764322111111 1112222 3333456889988 79988765 99999995
Q ss_pred -----EEEEEcCCCeee
Q 027058 215 -----EILVDTRTGQYM 226 (229)
Q Consensus 215 -----~I~V~T~~g~Y~ 226 (229)
+-+++..+|+|+
T Consensus 112 ka~~~dgk~~I~NGeYl 128 (310)
T PF15415_consen 112 KASNSDGKMNIDNGEYL 128 (310)
T ss_pred cccccCceEEeCCceEE
Confidence 345677778876
No 72
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=29.76 E-value=2e+02 Score=20.15 Aligned_cols=38 Identities=18% Similarity=0.228 Sum_probs=23.7
Q ss_pred CCCCEEEEEecCCCeEEEeee-----eeeeeEEEEEeCCeEEE
Q 027058 89 MSGTTVERTFRAGITVEEADV-----FKETKQFTYKDGSMFVF 126 (229)
Q Consensus 89 ~TG~~~e~tf~s~dkve~~~v-----erk~~qylY~Dgd~~~F 126 (229)
..|..+.-+||.+...-++.| ..+.++.+|.||+..-+
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~l 49 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELEL 49 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEEE
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEEe
Confidence 468888899988887533333 35778999999987443
No 73
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=29.39 E-value=65 Score=22.30 Aligned_cols=25 Identities=20% Similarity=0.235 Sum_probs=20.8
Q ss_pred EEcccCeecCCEEEEEcCCCeeeec
Q 027058 204 VNVPLFVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 204 v~VP~FI~~Gd~I~V~T~~g~Y~~R 228 (229)
+.++.-++.||.|.|-+++|+++.+
T Consensus 25 ~~~~~~~~~g~~V~v~~~~g~~vg~ 49 (77)
T smart00359 25 VRVDGGIKEGDVVVIVDEKGEPLGI 49 (77)
T ss_pred EEEeCCcCCCCEEEEEcCCCCEEEE
Confidence 4565567789999999999999876
No 74
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=29.26 E-value=45 Score=25.30 Aligned_cols=20 Identities=20% Similarity=0.345 Sum_probs=15.9
Q ss_pred CeecCCEEEEEcCCCeeeec
Q 027058 209 FVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 209 FI~~Gd~I~V~T~~g~Y~~R 228 (229)
=|+.||+|+|.+..|+..-+
T Consensus 48 gi~~Gd~V~v~s~~G~~~~~ 67 (122)
T cd02792 48 GIKNGDMVWVSSPRGKIKVK 67 (122)
T ss_pred CCCCCCEEEEEcCCceEEEE
Confidence 36789999999999986544
No 75
>PF05951 Peptidase_M15_2: Bacterial protein of unknown function (DUF882); InterPro: IPR010275 This family consists of proteins related to metallopeptidases belong to MEROPS peptidase family M15A. They are classed as non-peptidase homologues (M15A.UNA) and include A3D3U2 from SWISSPROT, where the metal ligands (marked by *) are conserved but the catalytic Asn has been replaced by Asp (+): 70 80 90 100 110 120 A3D3U2: QSKVLNDFNHLLRDHRQNVAAPMDKRLFDLLYSLKTTLNVDDEIHVISGYRSPKTNAMLA : .:. .:. : :.: ::.:: . :: . B1W1A6: PELNTCNSTWAGGKVAAGTARANALSSMWKLEALRHALG-DRSIRVTSGFRSASCNAAV- 20 30 40 50 60 70 * 130 * 140 150 160 170 * + A3D3U2: SNSGGVAKKSYHMRGMAMDIAIPSVKLKTLREAALSLKLGGV---GYYPNSGFVHVDCGP :: :..: :: : :.:.. .: :: . : . :. :: .. :::. :: B1W1A6: ---GG-ASNSRHMYGDAVDLGASPHSLCTLAKQARYHGFRGILGPGYVGHNDHVHVNQGP 80 90 100 110 120 B1W1A6 from SWISSPROT belongs to IPR013230 from INTERPRO, whcih contains peptidases belonging to the M15A family. The function of the proteins in this entry are not known.
Probab=29.24 E-value=37 Score=28.42 Aligned_cols=52 Identities=12% Similarity=0.131 Sum_probs=33.7
Q ss_pred EEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEe--CCeEEEecCCCceee
Q 027058 82 RTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKD--GSMFVFMDLTTFEEV 135 (229)
Q Consensus 82 riklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~D--gd~~~FMD~etyEQi 135 (229)
.+.|.|+.||..++.+|..+.......+.+ ..++..| .+..+-||+..|+.+
T Consensus 7 ~L~l~~~hTgE~~~~~y~~~g~y~~~al~~--l~~~lRD~r~~~~~~iDp~L~d~L 60 (152)
T PF05951_consen 7 SLSLYNLHTGERLDIVYWADGRYDPEALAQ--LNHLLRDHRTNEVHPIDPRLLDLL 60 (152)
T ss_pred EEEEEeCCCCCEEEEEEecCCEECHHHHHH--HHHHHcCCCCCCceecCHHHHHHH
Confidence 789999999999999997776655443332 2233333 344677777655443
No 76
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=29.15 E-value=35 Score=25.83 Aligned_cols=21 Identities=24% Similarity=0.330 Sum_probs=16.3
Q ss_pred cCeecCCEEEEEcCCCeeeec
Q 027058 208 LFVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 208 ~FI~~Gd~I~V~T~~g~Y~~R 228 (229)
+=|+.||+|+|.++.|+-.-|
T Consensus 43 lgI~dGd~V~v~s~~G~i~~~ 63 (112)
T cd02787 43 LGLKAGDRVDLESAFGDGQGR 63 (112)
T ss_pred hCCCCCCEEEEEecCCCCeEE
Confidence 346799999999999985433
No 77
>PF02182 SAD_SRA: SAD/SRA domain; InterPro: IPR003105 This domain has been termed SRA-YDG, for SET and Ring finger Associated, and because of the conserved YDG motif within the domain. Further characteristics of the domain are the conservation of up to 13 evenly spaced glycine residues and a VRV(I/V)RG motif. The domain is mainly found in plants and animals and in bacteria. In animals, this domain is associated with the Np95-like ring finger protein and the related gene product Np97, which contains PHD and RING FINGER domains and which is an important determinant in cell cycle progression. Np95 is a chromatin-associated ubiquitin ligase, binding to histones is direct and shows a remarkable preference for histone H3 and its N-terminal tail. The SRA-YDG domain contained in Np95 is indispensable both for the interaction with histones and for chromatin binding in vivo [, ]. In plants the SRA-YDG domain is associated with the SET domain, found in a family of histone methyl transferases, and in bacteria it is found in association with HNH, a non-specific nuclease motif [, ].; GO: 0042393 histone binding; PDB: 2ZO1_B 2ZKD_A 2ZO0_B 2ZKF_A 2ZKG_B 3FDE_A 3F8I_A 2ZO2_B 3F8J_B 2ZKE_A ....
Probab=29.07 E-value=1.3e+02 Score=24.95 Aligned_cols=36 Identities=22% Similarity=0.339 Sum_probs=26.4
Q ss_pred CCccEEEECCcEEEEEEEeEeeCCCCceEEEEEEEEC
Q 027058 52 KVGSNIEVDGAPWRVLEFLHVKPGKGAAFVRTKLRNY 88 (229)
Q Consensus 52 rkG~~I~~dG~py~Vv~~~~~kpGKG~A~vriklknL 88 (229)
.++-++.||| +|+|+++...+-..|...+|.+|+-+
T Consensus 117 p~~g~yrYDG-LY~V~~~w~~~g~~G~~v~kF~L~R~ 152 (155)
T PF02182_consen 117 PKGGIYRYDG-LYKVVKYWREKGKSGFKVFKFKLVRL 152 (155)
T ss_dssp -SSS-EEEEE-EEEEEEEEEEE-TTSSEEEEEEEEE-
T ss_pred CcCCCEEeCc-EEEEEEEEEEeCCCCcEEEEEEEEEC
Confidence 3456688988 99999998866555888889999865
No 78
>cd01752 PLAT_polycystin PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological functions remain poorly defined. In human, mutations in polycystin-1 (PKD1) and polycystin-2 (PKD2) have been shown to be the cause for autosomal dominant polycystic kidney disease (ADPKD). The generally proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
Probab=28.67 E-value=2.1e+02 Score=22.17 Aligned_cols=31 Identities=16% Similarity=0.320 Sum_probs=21.4
Q ss_pred EEEeEeeCCCCce-EE-EEEEEECCCCCEEEEE
Q 027058 67 LEFLHVKPGKGAA-FV-RTKLRNYMSGTTVERT 97 (229)
Q Consensus 67 v~~~~~kpGKG~A-~v-riklknL~TG~~~e~t 97 (229)
+.+.|-..|.+.+ ++ ++++++..||+....-
T Consensus 67 i~l~hd~~g~~~~W~l~~V~V~~~~t~~~~~F~ 99 (120)
T cd01752 67 IRLWHDNSGLSPSWYLSRVIVRDLQTGKKWFFL 99 (120)
T ss_pred EEEEECCCCCCCCeEEEEEEEEECCCCcEEEEE
Confidence 3456666677666 44 8889999998776543
No 79
>PLN00036 40S ribosomal protein S4; Provisional
Probab=28.65 E-value=69 Score=29.15 Aligned_cols=30 Identities=23% Similarity=0.409 Sum_probs=15.3
Q ss_pred EEecCCCeEEEeeeee--eeeEEEEEeCCeEEE
Q 027058 96 RTFRAGITVEEADVFK--ETKQFTYKDGSMFVF 126 (229)
Q Consensus 96 ~tf~s~dkve~~~ver--k~~qylY~Dgd~~~F 126 (229)
.+|+.| -++.+.+++ ..|-.+|.....|.+
T Consensus 80 ~~fPvG-~mDVIsI~kt~e~yRvl~D~kGrf~l 111 (261)
T PLN00036 80 KTYPAG-FMDVISIPKTNENFRLLYDTKGRFRL 111 (261)
T ss_pred CCCCCc-eeEEEEEcCCCCeEEEEECCCceEEE
Confidence 345554 456666643 344445555554444
No 80
>PRK15463 cold shock-like protein CspF; Provisional
Probab=28.51 E-value=1.1e+02 Score=21.99 Aligned_cols=45 Identities=11% Similarity=0.164 Sum_probs=33.4
Q ss_pred EEeCCeEEEecCCC-ceeeecCccchhhh-hhccCCCCeEEEEEECC
Q 027058 118 YKDGSMFVFMDLTT-FEEVRLNETDVGDK-KKWLKEGMDCNLLFWKG 162 (229)
Q Consensus 118 Y~Dgd~~~FMD~et-yEQi~v~~~~lgd~-~~fL~eG~~v~v~~~~g 162 (229)
|.+...|=|+.++. -+++-+....|... ...|++|+.|+....++
T Consensus 12 fn~~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15463 12 FDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRING 58 (70)
T ss_pred EeCCCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEEC
Confidence 44456788887755 57899988888654 56799999998877654
No 81
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=27.86 E-value=1.5e+02 Score=22.49 Aligned_cols=37 Identities=24% Similarity=0.284 Sum_probs=22.8
Q ss_pred ccCCCCccCCCCCCCCCceEEEEEcc--------ccCCccEEEEC
Q 027058 24 TLSSKPSVLPMRPRSKFPRIYAFSSN--------DIKVGSNIEVD 60 (229)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~i~a~--------dirkG~~I~~d 60 (229)
.-.+.|-++|+-++.+......+.++ ++|.|+.+.+.
T Consensus 19 ~~T~gGI~Lp~~a~ek~~~G~VvavG~g~~~~~~~Vk~GD~Vl~~ 63 (91)
T PRK14533 19 KKTEGGIVLPDSAKEKPMKAEVVAVGKLDDEEDFDIKVGDKVIFS 63 (91)
T ss_pred ceecccEEecccccCCcceEEEEEECCCCccccccccCCCEEEEc
Confidence 33466777888777766544344333 47777777663
No 82
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=27.54 E-value=61 Score=26.59 Aligned_cols=30 Identities=20% Similarity=0.262 Sum_probs=25.5
Q ss_pred EccccCCccEEEECCcEE-----EEEEEeEeeCCC
Q 027058 47 SSNDIKVGSNIEVDGAPW-----RVLEFLHVKPGK 76 (229)
Q Consensus 47 ~a~dirkG~~I~~dG~py-----~Vv~~~~~kpGK 76 (229)
.+.+|++|+.|++.|+.+ -|+.+.|..|+.
T Consensus 82 rip~l~~GD~V~f~GeYe~n~kggvIHWTH~dp~~ 116 (131)
T PF11948_consen 82 RIPWLQKGDQVEFYGEYEWNPKGGVIHWTHHDPRG 116 (131)
T ss_pred cCcCcCCCCEEEEEEEEEECCCCCEEEeeccCCCC
Confidence 456799999999999976 689999988864
No 83
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=27.44 E-value=1.7e+02 Score=22.43 Aligned_cols=24 Identities=29% Similarity=0.367 Sum_probs=18.9
Q ss_pred EEEEEECCCCCEEEEEecCCCeEE
Q 027058 82 RTKLRNYMSGTTVERTFRAGITVE 105 (229)
Q Consensus 82 riklknL~TG~~~e~tf~s~dkve 105 (229)
.++.+|+.+|+.+.-+--+..+++
T Consensus 98 ~I~V~N~~s~k~i~~~V~~~g~V~ 121 (122)
T TIGR03170 98 QIRVRNLSSGKIISGIVTGPGTVE 121 (122)
T ss_pred EEEEEECCCCCEEEEEEeCCCEEE
Confidence 688899999999988776665553
No 84
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=27.37 E-value=1.6e+02 Score=22.22 Aligned_cols=40 Identities=15% Similarity=0.149 Sum_probs=24.2
Q ss_pred ccccCCCCccCCCCCCCCCceEEEEEcc-------------ccCCccEEEECC
Q 027058 22 FTTLSSKPSVLPMRPRSKFPRIYAFSSN-------------DIKVGSNIEVDG 61 (229)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~i~a~-------------dirkG~~I~~dG 61 (229)
.-.-.+.|-++|..++.+......+.++ +++.|+.|.+..
T Consensus 16 ~e~~T~~GI~Lp~~~~~k~~~g~VvAVG~g~~~~~g~~~~~~vk~GD~Vl~~~ 68 (93)
T cd00320 16 AEEKTKGGIILPDSAKEKPQEGKVVAVGPGRRNENGERVPLSVKVGDKVLFPK 68 (93)
T ss_pred ccceecceEEeCCCcCCCceEEEEEEECCCeECCCCCCccccccCCCEEEECC
Confidence 3334466777888777666543333222 488888887754
No 85
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=27.27 E-value=47 Score=24.72 Aligned_cols=18 Identities=17% Similarity=0.106 Sum_probs=14.8
Q ss_pred CeecCCEEEEEcCCCeee
Q 027058 209 FVNIGDEILVDTRTGQYM 226 (229)
Q Consensus 209 FI~~Gd~I~V~T~~g~Y~ 226 (229)
=|+.||+|+|.++.|+-.
T Consensus 42 Gi~~Gd~V~v~s~~G~i~ 59 (96)
T cd02788 42 GLADGDLVEFSLGDGTLT 59 (96)
T ss_pred CCCCCCEEEEEECCeEEE
Confidence 367899999999998854
No 86
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=27.21 E-value=2.1e+02 Score=19.56 Aligned_cols=55 Identities=15% Similarity=-0.012 Sum_probs=32.4
Q ss_pred cCCCCeE--EEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCCcEEEcccCeecCCEEEEE
Q 027058 149 LKEGMDC--NLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNVPLFVNIGDEILVD 219 (229)
Q Consensus 149 L~eG~~v--~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~VP~FI~~Gd~I~V~ 219 (229)
|+.|+.+ .|.-..+.-+.++|+..++-.|--++-.- +.. -..+.+++.||.|++.
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~--~~~--------------~~~~~~~~~Gd~v~~~ 57 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALD--DYS--------------EALPYKFKKNDIVRAC 57 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccC--ccc--------------cccccccCCCCEEEEE
Confidence 4567765 44445667778888877766665443211 100 0125778889988774
No 87
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=27.06 E-value=1.9e+02 Score=20.63 Aligned_cols=39 Identities=28% Similarity=0.399 Sum_probs=30.0
Q ss_pred eEEEEEEEcCCCcccccCCCCcccEEecCCcEEEcccC-----eecCCEEEEE
Q 027058 172 TVQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNVPLF-----VNIGDEILVD 219 (229)
Q Consensus 172 ~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~VP~F-----I~~Gd~I~V~ 219 (229)
.++=+|.+.+|. +...+|+.|..-+.|.= +++|.+|+|-
T Consensus 4 ~veG~I~~id~~---------~~titLdDGksy~lp~ef~~~~L~~G~kV~V~ 47 (61)
T PF07076_consen 4 DVEGTIKSIDPE---------TMTITLDDGKSYKLPEEFDFDGLKPGMKVVVF 47 (61)
T ss_pred cceEEEEEEcCC---------ceEEEecCCCEEECCCcccccccCCCCEEEEE
Confidence 345566666664 56899999999999863 7889999885
No 88
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=26.71 E-value=73 Score=23.41 Aligned_cols=56 Identities=13% Similarity=0.204 Sum_probs=36.4
Q ss_pred CceEEEEEEEECCCCCEEEEEecCCCeEEEe--------eeeeeeeEEEEEeCCeEEEecCCCceeee
Q 027058 77 GAAFVRTKLRNYMSGTTVERTFRAGITVEEA--------DVFKETKQFTYKDGSMFVFMDLTTFEEVR 136 (229)
Q Consensus 77 G~A~vriklknL~TG~~~e~tf~s~dkve~~--------~verk~~qylY~Dgd~~~FMD~etyEQi~ 136 (229)
-+.++.+++++. +|+.+....+.+++++.+ .+......|+|. | -.+.|.+|-+++.
T Consensus 8 ~~~~i~I~v~~~-~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~-G--~~L~~~~T~~~l~ 71 (87)
T cd01763 8 ISEHINLKVKGQ-DGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFD-G--QRIRDNQTPDDLG 71 (87)
T ss_pred CCCeEEEEEECC-CCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEEC-C--eECCCCCCHHHcC
Confidence 456899999999 899999999999986543 344445555553 3 2333444444433
No 89
>cd07387 MPP_PolD2_C PolD2 (DNA polymerase delta, subunit 2), C-terminal domain. PolD2 (DNA polymerase delta, subunit 2) is an auxiliary subunit of the eukaryotic DNA polymerase delta (PolD) complex thought to play a regulatory role and to serve as a scaffold for PolD assembly by interacting simultaneously with all of the other three subunits. PolD2 is catalytically inactive and lacks the active site residues required for phosphoesterase activity in other members of this superfamily. PolD2 is also involved in the recruitment of several proteins regulating DNA metabolism, including p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3), and p12(PolD4). PolD is one of three major replicases in eukaryotes. PolD also plays an essential role in translesion DNA synthesis, homologous recombination, and DNA repair. Within the PolD complex, PolD2 tightly associates with PolD3. PolD2 belongs to the metallophosphatase (MPP) superfamily
Probab=26.60 E-value=79 Score=28.47 Aligned_cols=40 Identities=33% Similarity=0.454 Sum_probs=29.3
Q ss_pred cccCCCCcccEEecCCcE---EEcccCeecCCEEEEEcCCCee
Q 027058 186 GDTASGGSKPATLDTGAV---VNVPLFVNIGDEILVDTRTGQY 225 (229)
Q Consensus 186 gdta~~~~K~A~LetG~~---v~VP~FI~~Gd~I~V~T~~g~Y 225 (229)
|+...-++|...-++|.. |.||.|-++|..+.||.+|-+.
T Consensus 210 Gnq~~f~t~~~~~~~~~~v~lv~vP~Fs~t~~~vlvdl~tLe~ 252 (257)
T cd07387 210 GNQPKFGTKLVEGEEGQRVLLVCVPSFSKTGTAVLVNLRTLEC 252 (257)
T ss_pred CCCcceeeeEEEcCCCCeEEEEEeCCcCcCCEEEEEECCcCcE
Confidence 444444455555554544 6889999999999999998764
No 90
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.52 E-value=1.9e+02 Score=25.28 Aligned_cols=25 Identities=28% Similarity=0.332 Sum_probs=21.0
Q ss_pred EEEEEECCCCCEEEEEecCCCeEEE
Q 027058 82 RTKLRNYMSGTTVERTFRAGITVEE 106 (229)
Q Consensus 82 riklknL~TG~~~e~tf~s~dkve~ 106 (229)
.++.||+.||+.+.-+..+...++.
T Consensus 209 ~IrVrN~~Sgk~i~g~V~~~g~V~V 233 (235)
T PRK07018 209 QIRVRNMASGQVVSGIVTGDGEVEV 233 (235)
T ss_pred eEEEEECCCCCEEEEEEeCCCEEEE
Confidence 7888899999999988877777764
No 91
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=26.26 E-value=54 Score=25.14 Aligned_cols=19 Identities=26% Similarity=0.461 Sum_probs=15.2
Q ss_pred eecCCEEEEEcCCCeeeec
Q 027058 210 VNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 210 I~~Gd~I~V~T~~g~Y~~R 228 (229)
|+.||+|+|.++.|+-.-|
T Consensus 44 i~~Gd~V~v~s~~g~i~~~ 62 (121)
T cd02794 44 IKDGDRVLVFNDRGKVIRP 62 (121)
T ss_pred CCCCCEEEEEcCCceEEEE
Confidence 5679999999999876544
No 92
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=26.19 E-value=2.2e+02 Score=20.09 Aligned_cols=40 Identities=18% Similarity=0.226 Sum_probs=29.0
Q ss_pred EEccccCCccEEEECC-cEEEEEEEeEeeCCCCceEEEEEEE
Q 027058 46 FSSNDIKVGSNIEVDG-APWRVLEFLHVKPGKGAAFVRTKLR 86 (229)
Q Consensus 46 i~a~dirkG~~I~~dG-~py~Vv~~~~~kpGKG~A~vriklk 86 (229)
-+++-|.+|+-|.+.| +.=+|.+++. .+..+++.+.+++.
T Consensus 10 ~~~~GL~~gs~V~~~Gv~VG~V~~i~l-~~~~~~v~v~~~i~ 50 (81)
T PF02470_consen 10 DDAGGLSVGSPVRYRGVEVGKVTSIEL-DPDGNRVRVTLRID 50 (81)
T ss_pred CCcCCCCCcCEEEECCEEEEEEEEEEE-cCCCCEEEEEEEEc
Confidence 3778899999999999 5668888876 44445555555554
No 93
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=26.05 E-value=51 Score=26.90 Aligned_cols=21 Identities=24% Similarity=0.300 Sum_probs=16.9
Q ss_pred CeecCCEEEEEcCCCeeeecC
Q 027058 209 FVNIGDEILVDTRTGQYMTRA 229 (229)
Q Consensus 209 FI~~Gd~I~V~T~~g~Y~~R~ 229 (229)
=|+.||+|+|.++.|+-.-||
T Consensus 45 GI~dGd~V~v~s~~G~~~~~a 65 (156)
T cd02783 45 GIKDGDWVWVESVNGRVKGQA 65 (156)
T ss_pred CCCCCCEEEEEcCCeeEEEEE
Confidence 377899999999999876553
No 94
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=25.64 E-value=3.2e+02 Score=21.61 Aligned_cols=78 Identities=13% Similarity=0.127 Sum_probs=51.0
Q ss_pred eecCccchhh-hhhccCCCCeEEEEEECCeEEEEECCceEEEEEEEcCCCcccccCCCCcccEEecCCcEEEccc-C-ee
Q 027058 135 VRLNETDVGD-KKKWLKEGMDCNLLFWKGKIIDFEVPITVQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNVPL-F-VN 211 (229)
Q Consensus 135 i~v~~~~lgd-~~~fL~eG~~v~v~~~~g~~i~v~lP~~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~VP~-F-I~ 211 (229)
+..|.+...| ..+|-- ...+.-....|.+++-.+..+|..+|...-.--+ ..|-..-.+-.-+.-|. + ++
T Consensus 7 ~~~p~~~~~d~~cP~~g-~l~irgk~l~G~VvS~Km~KTvvV~v~r~~~hpk------Y~K~i~r~kky~aHDe~cn~~k 79 (108)
T PRK08572 7 VKPPEEECDDPNCPFHG-TLPVRGQVLEGTVVSDKMHKTVVVEREYLHYVPK------YERYEKRRSRIHAHNPPCIDAK 79 (108)
T ss_pred CCCCcccccCCCCCCcc-eeeeeeEEEEEEEEecCCCceEEEEEEEEEecCC------ccEEEEEeeeEEEECCCCCCCC
Confidence 3444444433 344443 2556667789999999999999999988742111 13444445556666676 4 89
Q ss_pred cCCEEEEE
Q 027058 212 IGDEILVD 219 (229)
Q Consensus 212 ~Gd~I~V~ 219 (229)
+||.|.|.
T Consensus 80 vGD~V~I~ 87 (108)
T PRK08572 80 VGDKVKIA 87 (108)
T ss_pred CCCEEEEE
Confidence 99999986
No 95
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=25.34 E-value=1.1e+02 Score=26.81 Aligned_cols=41 Identities=32% Similarity=0.470 Sum_probs=29.6
Q ss_pred EEEccccCCccEEEE---CCc--EEEEEEEeEeeCCCCceEEEEEE
Q 027058 45 AFSSNDIKVGSNIEV---DGA--PWRVLEFLHVKPGKGAAFVRTKL 85 (229)
Q Consensus 45 ~i~a~dirkG~~I~~---dG~--py~Vv~~~~~kpGKG~A~vrikl 85 (229)
.+.+.||+.|+.|.- +|+ ...|+-+.|..|..-+-|++++.
T Consensus 26 ~k~m~~L~iGD~Vla~d~~G~~~yS~V~~flhr~~~~~~~F~~i~t 71 (217)
T PF01079_consen 26 RKRMSDLKIGDRVLAVDSDGKLVYSPVIMFLHRDPEQRAEFVVIET 71 (217)
T ss_dssp EEEGGG--TT-EEEEE-TTS-EEEEEEEEEEEEEEEEEEEEEEEEE
T ss_pred EeEHHHCCCCCEEEEecCCCcEEEEeEEEEeccCccccEEEEEEEc
Confidence 678899999998866 454 66999999999987777777764
No 96
>PF10703 MoaF: Molybdenum cofactor biosynthesis protein F; InterPro: IPR024724 Molybdenum cofactor biosynthesis protein F (MoaF) is essential for the production of the monoamine-inducible 30kDa protein in Klebsiella []. It is necessary for reconstituting organoautotrophic growth in Ralstonia eutropha []. MoaF is conserved in proteobacteria and some lower eukaryotes. The operon regulating the Moa genes is responsible for molybdenum cofactor biosynthesis.
Probab=25.25 E-value=4.6e+02 Score=23.96 Aligned_cols=84 Identities=15% Similarity=0.194 Sum_probs=59.9
Q ss_pred EEEEEECCCCCEEEEEecCCCeEEEeeeeeeeeEEEEEeCCeEEEecCCCceeeecCccchhhhhhccCCCC---eEEEE
Q 027058 82 RTKLRNYMSGTTVERTFRAGITVEEADVFKETKQFTYKDGSMFVFMDLTTFEEVRLNETDVGDKKKWLKEGM---DCNLL 158 (229)
Q Consensus 82 riklknL~TG~~~e~tf~s~dkve~~~verk~~qylY~Dgd~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~---~v~v~ 158 (229)
++--.+-.+|+.++.+|..+.+++-...+...++.-+.++. -.+-|+-+++-++.+ -.+|++++. .|+++
T Consensus 21 ~lp~~~~L~G~~~tl~~~~G~~~~~~F~d~~~l~W~~~~~~-----g~~~y~a~evrpgif--fVdf~~~~~~~~svSlV 93 (265)
T PF10703_consen 21 RLPATDDLAGRTLTLRFDNGWTIEHRFGDDDRLTWRGVEGS-----GEAPYRATEVRPGIF--FVDFIKPERPEASVSLV 93 (265)
T ss_pred cCCCCcccCCcEEEEEeCCCCEEEEEecCCceEEEeeccCC-----CccceEEEEecCCeE--EEEeEcCCCCCceEEEE
Confidence 45556778999999999999888877777777777777766 557799999998874 257887763 26665
Q ss_pred EE--CCeEEEEE--CCce
Q 027058 159 FW--KGKIIDFE--VPIT 172 (229)
Q Consensus 159 ~~--~g~~i~v~--lP~~ 172 (229)
+. .++.+.|. ||..
T Consensus 94 lDl~~g~a~~v~~~l~~~ 111 (265)
T PF10703_consen 94 LDLTTGRATAVIGQLPDE 111 (265)
T ss_pred EECCCCeEEEEEeeccCc
Confidence 54 46655543 5544
No 97
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=24.63 E-value=1.9e+02 Score=22.45 Aligned_cols=37 Identities=14% Similarity=0.211 Sum_probs=23.3
Q ss_pred cccCCCCccCCCCCCCCCceEEEEEcc--------ccCCccEEEE
Q 027058 23 TTLSSKPSVLPMRPRSKFPRIYAFSSN--------DIKVGSNIEV 59 (229)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~i~a~--------dirkG~~I~~ 59 (229)
-.-.+.|-++|+-++.+......+.++ ++|+|+.|.+
T Consensus 27 e~kT~gGIiLP~sakekp~~g~VvAVG~G~~~~~~~Vk~GD~Vl~ 71 (100)
T PTZ00414 27 AKQTKAGVLIPEQVAGKVNEGTVVAVAAATKDWTPTVKVGDTVLL 71 (100)
T ss_pred ccccccCEEcccccccCCceeEEEEECCCCccccceecCCCEEEE
Confidence 344467788898777776653333222 3788887765
No 98
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=24.51 E-value=63 Score=27.32 Aligned_cols=17 Identities=35% Similarity=0.538 Sum_probs=15.0
Q ss_pred eecCCEEEEEcCCCeee
Q 027058 210 VNIGDEILVDTRTGQYM 226 (229)
Q Consensus 210 I~~Gd~I~V~T~~g~Y~ 226 (229)
+++||.|.|.+.+|+|.
T Consensus 109 L~~GD~I~v~~~~g~~~ 125 (174)
T TIGR03784 109 LRPGDVIRLQTPDGQWQ 125 (174)
T ss_pred CCCCCEEEEEECCCeEE
Confidence 78999999999999753
No 99
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.98 E-value=63 Score=24.89 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=16.2
Q ss_pred CeecCCEEEEEcCCCeeeec
Q 027058 209 FVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 209 FI~~Gd~I~V~T~~g~Y~~R 228 (229)
=|+.||+|+|.++.|+-.-|
T Consensus 45 gi~~Gd~V~v~s~~G~i~~~ 64 (124)
T cd02785 45 GIAHGDLVEVYNDRGSVVCK 64 (124)
T ss_pred CCCCCCEEEEEeCCCEEEEE
Confidence 46789999999999986544
No 100
>PF14289 DUF4369: Domain of unknown function (DUF4369)
Probab=23.98 E-value=2.8e+02 Score=19.97 Aligned_cols=29 Identities=28% Similarity=0.370 Sum_probs=21.1
Q ss_pred cEEe--cCCcEEEcccCeecCCEEEEEcCCCe
Q 027058 195 PATL--DTGAVVNVPLFVNIGDEILVDTRTGQ 224 (229)
Q Consensus 195 ~A~L--etG~~v~VP~FI~~Gd~I~V~T~~g~ 224 (229)
.+.| ..+..-.+|.|+++|+ |.|+.....
T Consensus 61 ~~~l~~~~~~~~~~~~~le~g~-i~i~~d~~~ 91 (106)
T PF14289_consen 61 FYYLSIFKGGKGYVPFFLEPGD-ITINGDANN 91 (106)
T ss_pred EEEEEEECCCCeEEEEEEeCCE-EEEEEeccc
Confidence 4555 4556668899999999 999875443
No 101
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.62 E-value=67 Score=24.73 Aligned_cols=19 Identities=26% Similarity=0.401 Sum_probs=15.1
Q ss_pred eecCCEEEEEcCCCeeeec
Q 027058 210 VNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 210 I~~Gd~I~V~T~~g~Y~~R 228 (229)
|+.||+|+|.++.|+-.-|
T Consensus 47 i~~Gd~V~v~s~~G~~~~~ 65 (130)
T cd02781 47 IADGDWVWVETPRGRARQK 65 (130)
T ss_pred CCCCCEEEEECCCCEEEEE
Confidence 5789999999999876543
No 102
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=23.62 E-value=56 Score=26.56 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=17.5
Q ss_pred cCeecCCEEEEEcCCCeeeecC
Q 027058 208 LFVNIGDEILVDTRTGQYMTRA 229 (229)
Q Consensus 208 ~FI~~Gd~I~V~T~~g~Y~~R~ 229 (229)
|=+++||+++|.++-|+-+=||
T Consensus 43 Lgv~EGD~VkVkse~GeVVV~A 64 (128)
T COG1153 43 LGVSEGDKVKVKSEFGEVVVKA 64 (128)
T ss_pred hCCCcCCeEEEEecCccEEEEE
Confidence 4578899999999999866543
No 103
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=23.50 E-value=2.2e+02 Score=26.13 Aligned_cols=31 Identities=29% Similarity=0.616 Sum_probs=12.5
Q ss_pred ccCCccEEEECCcEE-EEEEEeEeeCCCCceE
Q 027058 50 DIKVGSNIEVDGAPW-RVLEFLHVKPGKGAAF 80 (229)
Q Consensus 50 dirkG~~I~~dG~py-~Vv~~~~~kpGKG~A~ 80 (229)
+|+.|+++-+.+-|- .++-.-..+||+|+.+
T Consensus 123 ~ik~GN~lpL~~IP~Gt~VhNVE~~pG~GGq~ 154 (275)
T COG0090 123 DIKPGNALPLGNIPEGTIVHNVELKPGDGGQL 154 (275)
T ss_pred CcCCcceeeeccCCCCceEEeeeeccCCCceE
Confidence 444444444433322 2222223455554433
No 104
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=23.46 E-value=1.9e+02 Score=24.79 Aligned_cols=43 Identities=23% Similarity=0.402 Sum_probs=33.6
Q ss_pred cccCCccEEEECCc----EEEEEEEeEeeCCCCceEEEEEEEECCCCCEEEEEe
Q 027058 49 NDIKVGSNIEVDGA----PWRVLEFLHVKPGKGAAFVRTKLRNYMSGTTVERTF 98 (229)
Q Consensus 49 ~dirkG~~I~~dG~----py~Vv~~~~~kpGKG~A~vriklknL~TG~~~e~tf 98 (229)
+++.+|+.+..++. |.+|+++. ...|.+.+.+-.-|+.+...+
T Consensus 89 ~~~~vGm~~~~~~~~~~~~~~V~~V~-------~~~V~VDfNHpLAGktL~fev 135 (174)
T COG1047 89 GELEVGMEVEAEGGDGEIPGVVTEVS-------GDRVTVDFNHPLAGKTLHFEV 135 (174)
T ss_pred CCCCCCcEEEEcCCCceeeEEEEEEc-------CCEEEEeCCCcCCCCeEEEEE
Confidence 37899999999997 99999874 345677777777777776655
No 105
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=23.41 E-value=2.9e+02 Score=20.53 Aligned_cols=43 Identities=23% Similarity=0.280 Sum_probs=26.1
Q ss_pred eEEEEEEEcCCCcccccCCCCcccEEecCCcEEEc--c------cCeecCCEEEEEcCC
Q 027058 172 TVQLTVVDVDPGLKGDTASGGSKPATLDTGAVVNV--P------LFVNIGDEILVDTRT 222 (229)
Q Consensus 172 ~V~l~V~et~p~~kgdta~~~~K~A~LetG~~v~V--P------~FI~~Gd~I~V~T~~ 222 (229)
.+..+|++.-++ ..=.+.+++|.++.+ | ..|+.||.|.|+..+
T Consensus 6 q~~g~V~~~lG~--------~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~~ 56 (83)
T smart00652 6 QEIAQVVKMLGN--------GRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWD 56 (83)
T ss_pred cEEEEEEEEcCC--------CEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEecC
Confidence 445555555432 234566677766533 3 368889999998654
No 106
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=23.33 E-value=56 Score=25.30 Aligned_cols=27 Identities=26% Similarity=0.548 Sum_probs=24.0
Q ss_pred EEEccccCCccEEEECCcEEEEEEEeE
Q 027058 45 AFSSNDIKVGSNIEVDGAPWRVLEFLH 71 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~py~Vv~~~~ 71 (229)
.++..||..|..|.+.|+.+.|.+.+.
T Consensus 68 ~y~~~Dl~vG~~v~i~gr~f~I~d~D~ 94 (104)
T smart00676 68 YYHASDLNVGTTINVFGRQFRIYDCDE 94 (104)
T ss_pred ccCHHHcCCCCEEEEeCEEEEEEECCH
Confidence 467889999999999999999998753
No 107
>PF07591 PT-HINT: Pretoxin HINT domain; InterPro: IPR011451 This entry represents a cluster of homologous proteins identified in Leptospira interrogans. One member (Q8EZX6 from SWISSPROT) has been predicted to be a phenazine biosynthesis family protein.; PDB: 2JNQ_A 2JMZ_A.
Probab=23.10 E-value=69 Score=25.57 Aligned_cols=27 Identities=26% Similarity=0.330 Sum_probs=15.9
Q ss_pred EEEccccCCccEEE-ECCcEEEEEEEeE
Q 027058 45 AFSSNDIKVGSNIE-VDGAPWRVLEFLH 71 (229)
Q Consensus 45 ~i~a~dirkG~~I~-~dG~py~Vv~~~~ 71 (229)
-+.|.+|++|+.|. .+|+...|.+++.
T Consensus 71 Wv~A~~L~~GD~L~~~~G~~~~v~~i~~ 98 (130)
T PF07591_consen 71 WVEAEDLKVGDRLLTADGSWVTVTSIRR 98 (130)
T ss_dssp -EEGGG--TTSEEEEE-SSEEEEE----
T ss_pred hhhHhhCCCCCEEEcCCCCEEEEEEEEe
Confidence 57899999999994 4788877777654
No 108
>PF11871 DUF3391: Domain of unknown function (DUF3391); InterPro: IPR021812 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is typically between 122 to 139 amino acids in length. This domain is found associated with PF01966 from PFAM.
Probab=22.91 E-value=49 Score=25.51 Aligned_cols=20 Identities=15% Similarity=0.376 Sum_probs=15.9
Q ss_pred EEEccccCCccEEEECCcEE
Q 027058 45 AFSSNDIKVGSNIEVDGAPW 64 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~py 64 (229)
.|.+++|+.||+|..-..+|
T Consensus 4 kI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 4 KIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred EEEHHHCCCCcEEEecCCCc
Confidence 68899999999997655444
No 109
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=22.77 E-value=2.6e+02 Score=19.79 Aligned_cols=45 Identities=18% Similarity=0.255 Sum_probs=30.6
Q ss_pred EEeCCeEEEecCCCc-eeeecCccchhhh-hhccCCCCeEEEEEECC
Q 027058 118 YKDGSMFVFMDLTTF-EEVRLNETDVGDK-KKWLKEGMDCNLLFWKG 162 (229)
Q Consensus 118 Y~Dgd~~~FMD~ety-EQi~v~~~~lgd~-~~fL~eG~~v~v~~~~g 162 (229)
|.+...|=|+.++.- +++-+..+.+... ..-|++|+.|+...-.+
T Consensus 12 f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~ 58 (70)
T PRK10354 12 FNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESG 58 (70)
T ss_pred EeCCCCcEEEecCCCCccEEEEEeeccccCCCCCCCCCEEEEEEEEC
Confidence 344456777776554 6888887777543 35689999988776543
No 110
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=22.54 E-value=2.1e+02 Score=25.10 Aligned_cols=77 Identities=18% Similarity=0.150 Sum_probs=42.5
Q ss_pred CccCCCCCCCCCceEEEEEccccCCccEEEECCcEEEEEE----EeEeeCCC----CceEEEEEEEECCCCCEEEEEecC
Q 027058 29 PSVLPMRPRSKFPRIYAFSSNDIKVGSNIEVDGAPWRVLE----FLHVKPGK----GAAFVRTKLRNYMSGTTVERTFRA 100 (229)
Q Consensus 29 ~~~~~~~~~~~~~~~~~i~a~dirkG~~I~~dG~py~Vv~----~~~~kpGK----G~A~vriklknL~TG~~~e~tf~s 100 (229)
..+.+++.|..-.....+..++|+. -.+...|+...|+- ++-+.+|+ |+-==.++.||+.+|++++-+-.+
T Consensus 128 ~~~vG~~~~r~l~aGq~i~~~~L~~-p~lV~rG~~V~I~a~~~g~~Vs~~G~AL~~G~~Ge~IrVrN~~SgrvV~g~V~~ 206 (214)
T PRK12617 128 VAAVGKTARRILPAGSLLSANDLVS-QRLVRRGDTVPLVSRNGGLEVRMSGRALSDAGENERVSVENSSSRRVVQGIVEA 206 (214)
T ss_pred HHhccceeeeecCCCCeeCHHHcCC-cceEcCCCEEEEEEecCCEEEEEEEEEccCCCCCCEEEEEECCCCCEEEEEEeC
Confidence 3444554444444344555555542 22333344444332 22233333 333337889999999999998877
Q ss_pred CCeEEE
Q 027058 101 GITVEE 106 (229)
Q Consensus 101 ~dkve~ 106 (229)
.-.++.
T Consensus 207 ~G~V~V 212 (214)
T PRK12617 207 SGTVVV 212 (214)
T ss_pred CcEEEE
Confidence 777764
No 111
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=22.26 E-value=1.2e+02 Score=21.60 Aligned_cols=24 Identities=21% Similarity=0.261 Sum_probs=17.7
Q ss_pred EcccCeecCCEEEEEcCCCeeeec
Q 027058 205 NVPLFVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 205 ~VP~FI~~Gd~I~V~T~~g~Y~~R 228 (229)
.+-.-++.||.|.|-+.+|+.+.+
T Consensus 26 ~~~~~f~~gd~V~i~~~~g~~ia~ 49 (74)
T PF01472_consen 26 EVDGDFRKGDEVAIVDEDGEVIAV 49 (74)
T ss_dssp EEETT--TTSEEEEEETTSSEEEE
T ss_pred ECCCCcCCCCEEEEEcCCCeEEEE
Confidence 343445889999999999998875
No 112
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=21.47 E-value=4.2e+02 Score=21.08 Aligned_cols=64 Identities=8% Similarity=0.171 Sum_probs=44.8
Q ss_pred EEEEEeCCeEEEecCCCceeeecCccchhhhhhccCCCCeEEEEEE-CCeEEEEECCceEEEEEEEc
Q 027058 115 QFTYKDGSMFVFMDLTTFEEVRLNETDVGDKKKWLKEGMDCNLLFW-KGKIIDFEVPITVQLTVVDV 180 (229)
Q Consensus 115 qylY~Dgd~~~FMD~etyEQi~v~~~~lgd~~~fL~eG~~v~v~~~-~g~~i~v~lP~~V~l~V~et 180 (229)
..+..+.+..+ ...+-|++|.||++.|-+-+.| .+...+=++.| ++.-+-+++-..|-++|.+.
T Consensus 10 ~I~~~~~~Gi~-vslgFFddI~IP~~~L~~ps~f-d~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~ 74 (122)
T PF08292_consen 10 KIKSSTAEGIR-VSLGFFDDIFIPPSLLPEPSRF-DEEEQAWVWEYDEEQELFFDIGEEIRFRVESE 74 (122)
T ss_dssp EEEEEETTEEE-EEECCEEEEEEECCCC-TTEEE-ECCCTEEEEEESSSEEEEE-TT-EEEEEEEEE
T ss_pred EEEecCCCcEE-EEecccccEEECHHHCCCCCcc-CccCCEEEEECCCCceeEccCCCEEEEEEeEE
Confidence 34444544432 3336899999999999877777 44466777778 89999999999999998765
No 113
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.32 E-value=77 Score=24.44 Aligned_cols=20 Identities=20% Similarity=0.260 Sum_probs=15.6
Q ss_pred CeecCCEEEEEcCCCeeeec
Q 027058 209 FVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 209 FI~~Gd~I~V~T~~g~Y~~R 228 (229)
=|+.||.|+|.+..|+-.-|
T Consensus 46 gi~~Gd~V~v~s~~g~~~~~ 65 (129)
T cd02782 46 GLADGDKVRVTSAAGSVEAE 65 (129)
T ss_pred CCCCCCEEEEEcCCCeEEEE
Confidence 36789999999998876544
No 114
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.10 E-value=72 Score=24.90 Aligned_cols=20 Identities=20% Similarity=0.177 Sum_probs=15.5
Q ss_pred CeecCCEEEEEcCCCeeeec
Q 027058 209 FVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 209 FI~~Gd~I~V~T~~g~Y~~R 228 (229)
=|+.||.|+|.++.|+-.-|
T Consensus 46 gi~~Gd~V~v~s~~G~~~~~ 65 (129)
T cd02793 46 GIADGDIVRVFNDRGACLAG 65 (129)
T ss_pred CCCCCCEEEEEcCCEEEEEE
Confidence 46789999999998876544
No 115
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.97 E-value=71 Score=25.77 Aligned_cols=20 Identities=20% Similarity=0.111 Sum_probs=16.4
Q ss_pred CeecCCEEEEEcCCCeeeec
Q 027058 209 FVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 209 FI~~Gd~I~V~T~~g~Y~~R 228 (229)
=|+.||.|+|.++.|+-.-|
T Consensus 44 gI~dGd~V~v~~~~G~v~~~ 63 (141)
T cd02776 44 GIKDNDWVEVFNDNGVVVAR 63 (141)
T ss_pred CCCCCCEEEEEeCCeEEEEE
Confidence 57889999999999887644
No 116
>PF00207 A2M: Alpha-2-macroglobulin family; InterPro: IPR001599 This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; GO: 0004866 endopeptidase inhibitor activity; PDB: 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 2PN5_A 3FRP_G 3HRZ_B ....
Probab=20.75 E-value=85 Score=23.06 Aligned_cols=17 Identities=29% Similarity=0.511 Sum_probs=12.7
Q ss_pred EEEcccCeecCCEEEEE
Q 027058 203 VVNVPLFVNIGDEILVD 219 (229)
Q Consensus 203 ~v~VP~FI~~Gd~I~V~ 219 (229)
....|.|+..||.+.|.
T Consensus 59 ~~~lP~~l~~GD~~~i~ 75 (92)
T PF00207_consen 59 QLNLPRSLRRGDQIQIP 75 (92)
T ss_dssp EEE--SEEETTSEEEEE
T ss_pred EcCCCcEEecCCEEEEE
Confidence 46789999999999875
No 117
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=20.67 E-value=1.3e+02 Score=27.42 Aligned_cols=29 Identities=24% Similarity=0.366 Sum_probs=14.1
Q ss_pred EEecCCCeEEEeeeee--eeeEEEEEeCCeEE
Q 027058 96 RTFRAGITVEEADVFK--ETKQFTYKDGSMFV 125 (229)
Q Consensus 96 ~tf~s~dkve~~~ver--k~~qylY~Dgd~~~ 125 (229)
.+|+.| -++.+.+++ ..|-.+|.....|.
T Consensus 80 ~~fPvG-~mDVIsI~kt~e~yRvl~D~kGr~~ 110 (262)
T PTZ00118 80 CTYPVG-FMDVVSLTKTNEYFRLLYDTKGRFV 110 (262)
T ss_pred CCCCCc-eeEEEEEcCCCCeEEEEECCCccEE
Confidence 345554 456666653 33444454444333
No 118
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=20.60 E-value=1.3e+02 Score=22.28 Aligned_cols=49 Identities=10% Similarity=0.123 Sum_probs=31.3
Q ss_pred EEEccccCCccEEEECCcEEEEEEEeEeeCCCCceEEEEEEEECCCCCEEEEEecCCCeEE
Q 027058 45 AFSSNDIKVGSNIEVDGAPWRVLEFLHVKPGKGAAFVRTKLRNYMSGTTVERTFRAGITVE 105 (229)
Q Consensus 45 ~i~a~dirkG~~I~~dG~py~Vv~~~~~kpGKG~A~vriklknL~TG~~~e~tf~s~dkve 105 (229)
.+.=..+.+||.+.++|+.|..-.... +-| ++.+.++. |.+.-.++-+|
T Consensus 10 ~v~Rq~V~PG~~v~~~grty~ASAN~~-~r~------~LYl~~~~-----e~~~i~d~~Ie 58 (73)
T PRK11354 10 EIPRQCVTPGDYVLHEGRTYIASANNI-KKR------KLYIRTLT-----TKTCITDCMIK 58 (73)
T ss_pred eecccccCCceEEEEcCcEEEEEechh-hCc------eEEEEeee-----EEEEEeeeEEE
Confidence 445567899999999999998766532 222 35555543 44444455555
No 119
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=20.55 E-value=3e+02 Score=19.15 Aligned_cols=31 Identities=19% Similarity=0.294 Sum_probs=18.9
Q ss_pred cccEEecCCcEEEc--c------cCeecCCEEEEEcCCC
Q 027058 193 SKPATLDTGAVVNV--P------LFVNIGDEILVDTRTG 223 (229)
Q Consensus 193 ~K~A~LetG~~v~V--P------~FI~~Gd~I~V~T~~g 223 (229)
.=.+.+++|.++.+ | ..|+.||.|.|+....
T Consensus 17 ~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~ 55 (65)
T PF01176_consen 17 LFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPY 55 (65)
T ss_dssp EEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTT
T ss_pred EEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEeccc
Confidence 44566777766543 3 5899999999997653
No 120
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=20.39 E-value=1.5e+02 Score=24.90 Aligned_cols=37 Identities=24% Similarity=0.309 Sum_probs=28.7
Q ss_pred CcccEEecCCcEEEcccCeecCCEEEEEcCCCeeeec
Q 027058 192 GSKPATLDTGAVVNVPLFVNIGDEILVDTRTGQYMTR 228 (229)
Q Consensus 192 ~~K~A~LetG~~v~VP~FI~~Gd~I~V~T~~g~Y~~R 228 (229)
..|.+.+.=-...=||-=+.-.+++.||.-||=|+|+
T Consensus 61 eGk~~LVPLTsSlYVPGkl~d~~k~lVDIGTGYyVEK 97 (153)
T KOG3048|consen 61 EGKKLLVPLTSSLYVPGKLSDNSKFLVDIGTGYYVEK 97 (153)
T ss_pred CCCeEEEecccceeccceeccccceeEeccCceEEee
Confidence 3455555555566777788889999999999999986
Done!