Query 027811
Match_columns 218
No_of_seqs 114 out of 1152
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 15:32:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027811.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027811hhsearch_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 7.9E-60 1.7E-64 398.7 21.2 156 58-213 1-156 (185)
2 PRK14578 elongation factor P; 100.0 6.8E-58 1.5E-62 387.6 21.3 156 58-213 1-158 (187)
3 PRK04542 elongation factor P; 100.0 8.9E-58 1.9E-62 387.4 20.9 156 58-213 1-159 (189)
4 TIGR02178 yeiP elongation fact 100.0 1.8E-56 4E-61 378.5 21.3 153 61-213 2-157 (186)
5 PRK00529 elongation factor P; 100.0 1.6E-55 3.6E-60 372.7 21.3 156 58-213 1-156 (186)
6 TIGR00038 efp translation elon 100.0 2.7E-55 5.8E-60 370.9 21.1 155 59-213 1-155 (184)
7 COG0231 Efp Translation elonga 100.0 2E-45 4.4E-50 296.0 16.7 130 57-186 2-131 (131)
8 TIGR00037 eIF_5A translation i 100.0 5.1E-37 1.1E-41 246.9 16.1 120 57-178 5-125 (130)
9 PRK03999 translation initiatio 100.0 2.1E-35 4.6E-40 237.2 16.1 117 58-176 5-122 (129)
10 PLN03107 eukaryotic translatio 100.0 1.5E-31 3.2E-36 221.8 16.4 120 57-176 19-147 (159)
11 cd04470 S1_EF-P_repeat_1 S1_EF 99.9 1E-23 2.2E-28 149.2 7.3 61 123-183 1-61 (61)
12 PF08207 EFP_N: Elongation fac 99.8 3.5E-21 7.6E-26 135.0 8.5 58 60-117 1-58 (58)
13 PF01132 EFP: Elongation facto 99.8 2.6E-21 5.6E-26 134.3 6.4 55 124-178 1-55 (55)
14 PTZ00328 eukaryotic initiation 99.8 4.1E-18 9E-23 141.7 13.8 118 57-174 21-150 (166)
15 cd04463 S1_EF_like S1_EF_like: 99.7 9E-18 1.9E-22 115.7 6.0 55 125-180 1-55 (55)
16 KOG3271 Translation initiation 99.5 8.9E-14 1.9E-18 113.1 9.7 112 59-170 21-136 (156)
17 smart00841 Elong-fact-P_C Elon 98.8 3.7E-09 8E-14 73.9 2.8 28 186-213 1-28 (56)
18 cd05794 S1_EF-P_repeat_2 S1_EF 98.8 5.1E-09 1.1E-13 73.2 2.8 28 186-213 1-28 (56)
19 PF09285 Elong-fact-P_C: Elong 98.7 1.5E-08 3.3E-13 70.8 3.0 28 186-213 1-28 (56)
20 cd04467 S1_aIF5A S1_aIF5A: Arc 98.6 8.7E-08 1.9E-12 67.2 5.6 54 122-177 1-54 (57)
21 COG1499 NMD3 NMD protein affec 98.4 5.3E-06 1.1E-10 77.1 12.4 130 36-181 215-352 (355)
22 PF01287 eIF-5a: Eukaryotic el 96.9 0.0053 1.1E-07 44.6 7.0 55 121-176 1-62 (69)
23 cd04468 S1_eIF5A S1_eIF5A: Euk 90.4 1.2 2.5E-05 32.5 6.0 50 122-172 1-54 (69)
24 PF08605 Rad9_Rad53_bind: Fung 83.6 2.6 5.7E-05 34.2 5.1 39 59-97 55-103 (131)
25 PF02941 FeThRed_A: Ferredoxin 75.0 1.5 3.3E-05 31.8 1.0 26 164-189 30-56 (67)
26 cd04469 S1_Hex1 S1_Hex1: Hex1, 74.8 17 0.00036 26.9 6.6 51 125-176 3-61 (75)
27 PRK05338 rplS 50S ribosomal pr 56.3 69 0.0015 25.5 7.2 66 59-125 14-88 (116)
28 PF13275 S4_2: S4 domain; PDB: 55.0 13 0.00029 26.6 2.7 19 62-80 47-65 (65)
29 PF01245 Ribosomal_L19: Riboso 54.6 63 0.0014 25.5 6.7 68 58-126 13-89 (113)
30 TIGR01024 rplS_bact ribosomal 48.2 95 0.0021 24.6 6.8 65 58-123 13-86 (113)
31 PRK11507 ribosome-associated p 47.9 23 0.00051 25.8 3.1 19 62-80 51-69 (70)
32 CHL00084 rpl19 ribosomal prote 47.4 1.2E+02 0.0025 24.3 7.2 66 58-124 17-91 (117)
33 PF04014 Antitoxin-MazE: Antid 46.5 33 0.00071 22.3 3.4 31 146-178 7-38 (47)
34 PF01079 Hint: Hint module; I 46.3 38 0.00083 29.5 4.7 45 55-99 23-72 (217)
35 KOG3297 DNA-directed RNA polym 43.6 2.2E+02 0.0048 24.8 12.2 107 67-193 43-156 (202)
36 PF13509 S1_2: S1 domain; PDB: 42.7 31 0.00068 23.7 3.0 36 137-175 16-51 (61)
37 PF05521 Phage_H_T_join: Phage 42.0 51 0.0011 23.2 4.2 24 63-86 62-85 (95)
38 PF11948 DUF3465: Protein of u 39.2 32 0.00069 28.1 2.9 32 58-89 80-116 (131)
39 PRK07018 flgA flagellar basal 38.4 88 0.0019 27.2 5.8 25 95-119 209-233 (235)
40 PRK10377 PTS system glucitol/s 37.6 46 0.001 26.6 3.6 24 61-84 49-72 (120)
41 TIGR03170 flgA_cterm flagella 37.5 91 0.002 23.8 5.2 24 95-118 98-121 (122)
42 COG2501 S4-like RNA binding pr 37.3 36 0.00079 25.1 2.7 21 62-82 51-71 (73)
43 PF03829 PTSIIA_gutA: PTS syst 36.8 42 0.0009 26.6 3.2 23 61-83 49-71 (117)
44 PF02839 CBM_5_12: Carbohydrat 36.6 40 0.00086 21.1 2.5 19 64-82 10-28 (41)
45 PF13856 Gifsy-2: ATP-binding 36.6 48 0.0011 24.7 3.4 22 64-85 66-87 (95)
46 TIGR00849 gutA PTS system, glu 36.1 51 0.0011 26.4 3.6 23 62-84 50-72 (121)
47 cd05829 Sortase_E Sortase E (S 35.7 1.1E+02 0.0024 24.5 5.6 72 133-217 49-126 (144)
48 PF12158 DUF3592: Protein of u 35.6 95 0.0021 23.9 5.1 49 127-183 65-113 (148)
49 PF11694 DUF3290: Protein of u 34.1 49 0.0011 27.3 3.3 28 56-83 98-125 (149)
50 TIGR01646 vgr_GE Rhs element V 33.2 2.4E+02 0.0052 26.9 8.3 120 58-177 275-423 (483)
51 smart00676 DM10 Domains in hyp 32.6 43 0.00094 25.8 2.6 28 57-84 67-94 (104)
52 COG1326 Uncharacterized archae 31.6 2.5E+02 0.0054 24.6 7.3 22 62-83 73-94 (201)
53 PRK11354 kil FtsZ inhibitor pr 31.2 63 0.0014 23.8 3.1 27 57-83 9-35 (73)
54 PF09465 LBR_tudor: Lamin-B re 30.8 1.7E+02 0.0036 20.5 5.0 37 101-137 6-47 (55)
55 PRK13480 3'-5' exoribonuclease 30.5 1.5E+02 0.0032 27.4 6.2 53 59-115 3-55 (314)
56 PF13785 DUF4178: Domain of un 29.8 2.6E+02 0.0057 21.6 12.2 23 64-86 1-23 (140)
57 PF13144 SAF_2: SAF-like 29.5 1.5E+02 0.0033 24.5 5.7 24 95-118 172-195 (196)
58 PF10665 Minor_capsid_1: Minor 29.2 1.5E+02 0.0032 23.3 5.2 26 61-86 74-99 (114)
59 PF02182 SAD_SRA: SAD/SRA doma 29.1 1.3E+02 0.0027 24.9 5.0 46 55-101 107-152 (155)
60 PF08292 RNA_pol_Rbc25: RNA po 28.4 3E+02 0.0066 21.8 7.0 65 128-194 10-75 (122)
61 cd01763 Sumo Small ubiquitin-r 28.4 74 0.0016 23.2 3.2 57 90-150 8-72 (87)
62 COG4043 Preprotein translocase 27.3 90 0.0019 24.6 3.5 23 61-83 31-55 (111)
63 cd00004 Sortase Sortases are c 26.5 1.8E+02 0.0039 22.3 5.3 48 160-216 63-114 (128)
64 PF07591 PT-HINT: Pretoxin HIN 25.8 67 0.0014 25.5 2.7 27 58-84 71-98 (130)
65 TIGR01363 strep_his_triad stre 25.3 30 0.00065 32.2 0.7 22 61-82 118-139 (348)
66 TIGR02609 doc_partner putative 25.3 99 0.0021 22.2 3.3 30 147-178 11-40 (74)
67 KOG1999 RNA polymerase II tran 24.5 1.9E+02 0.0041 31.0 6.2 79 100-181 397-484 (1024)
68 PF11871 DUF3391: Domain of un 23.0 42 0.00091 25.7 1.0 21 57-77 3-23 (128)
69 PF14306 PUA_2: PUA-like domai 22.7 45 0.00097 27.8 1.2 43 138-180 55-111 (160)
70 COG0335 RplS Ribosomal protein 22.5 4.1E+02 0.0088 21.3 7.7 65 59-124 16-89 (115)
71 cd05830 Sortase_D_5 Sortase D 22.2 3.2E+02 0.007 21.5 6.0 55 159-217 63-123 (137)
72 cd01771 Faf1_UBX Faf1 UBX doma 21.7 86 0.0019 22.9 2.4 29 89-120 2-30 (80)
73 TIGR03361 VI_Rhs_Vgr type VI s 21.3 6.7E+02 0.015 24.0 9.1 116 58-177 283-434 (513)
74 KOG0272 U4/U6 small nuclear ri 21.1 2E+02 0.0043 28.0 5.2 90 33-132 311-405 (459)
75 PF12385 Peptidase_C70: Papain 20.8 68 0.0015 27.2 1.9 34 128-161 130-163 (166)
76 PRK06005 flgA flagellar basal 20.4 2.6E+02 0.0057 23.1 5.3 24 95-118 133-156 (160)
77 COG5406 Nucleosome binding fac 20.3 1.2E+02 0.0026 31.3 3.8 87 4-92 476-582 (1001)
78 PF05354 Phage_attach: Phage H 20.3 76 0.0016 25.5 2.0 26 59-87 70-95 (117)
79 TIGR03784 marine_sortase sorta 20.2 1.5E+02 0.0033 24.8 4.0 27 61-87 106-137 (174)
80 PF05951 Peptidase_M15_2: Bact 20.2 61 0.0013 27.0 1.5 54 95-150 7-62 (152)
No 1
>PRK12426 elongation factor P; Provisional
Probab=100.00 E-value=7.9e-60 Score=398.65 Aligned_cols=156 Identities=17% Similarity=0.335 Sum_probs=154.5
Q ss_pred eEecCCCCCccEEEECCeEEEEEEeEEeeCCCCCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCCeE
Q 027811 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTA 137 (218)
Q Consensus 58 ~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGkG~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd~~ 137 (218)
|+++||||+|++|++||+||+|++++|+|||||+|++|+|||||.||+++++||+++|++|.|+++++++||||.||+.|
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 EEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCcccEEEEe
Q 027811 138 FVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYGPTISKH 213 (218)
Q Consensus 138 vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V~LP~~V~l~V~etep~vKGdTat~~~K~A~Let 213 (218)
+|||+|||||++|+++.+|++.+||+|||+|+|.+|+|+||+|+||.+|+|+|+||+|++|||||++++|||+|||
T Consensus 81 ~FMd~etyeQi~i~~~~lgd~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~kgdTat~~~KpAtLeT 156 (185)
T PRK12426 81 LFLDLGNYDKIYIPKEIMKDNFLFLKAGVTVSALVYDGTVFSVELPHFLELMVSKTDFPGDSLSLSGGAKKALLET 156 (185)
T ss_pred EEecCCCceEEEeCHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCcccCCCcccEEEcC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998
No 2
>PRK14578 elongation factor P; Provisional
Probab=100.00 E-value=6.8e-58 Score=387.62 Aligned_cols=156 Identities=24% Similarity=0.391 Sum_probs=153.1
Q ss_pred eEecCCCCCccEEEECCeEEEEEEeEEeeCCCC--CeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCC
Q 027811 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRG--GAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (218)
Q Consensus 58 ~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGkG--~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd 135 (218)
|+++|+||+|++|++||+||+|++++|+|||+| +|++|+|||||.||++++++|+++|++|.|+++++++||||.||+
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 578999999999999999999999999999987 569999999999999999999999999999999999999999999
Q ss_pred eEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCcccEEEEe
Q 027811 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYGPTISKH 213 (218)
Q Consensus 136 ~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V~LP~~V~l~V~etep~vKGdTat~~~K~A~Let 213 (218)
.|+|||+|||||++|+++.+|++.+||+|||+|.|.+|+|+||+|+||.+|+|+|++|+|++|||||++++|||+|||
T Consensus 81 ~~~FMD~etyEQ~~i~~~~~g~~~~fL~e~~~v~v~~~~~~~i~v~lP~~V~l~V~~tep~~KGdT~t~~~KpA~leT 158 (187)
T PRK14578 81 RGVFMDLETYEQFEMEEDAFSAIAPFLLDGTEVQLGLFQGRMVNVDLPMTVELTVTDTAPVMKNATATAQTKEAVLET 158 (187)
T ss_pred EEEEecCCCcEEEEecHHHhhhHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCccccCccCCCcceEEEcC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999998
No 3
>PRK04542 elongation factor P; Provisional
Probab=100.00 E-value=8.9e-58 Score=387.38 Aligned_cols=156 Identities=25% Similarity=0.429 Sum_probs=153.1
Q ss_pred eEecCCCCCccEEEECCeEEEEEEeEEeeC-CCC-CeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCC
Q 027811 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQR-GRG-GAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (218)
Q Consensus 58 ~i~andiRkG~~I~~dG~~y~Vl~~~h~kp-GkG-~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd 135 (218)
|+++|+||+|++|++||+||+|++++|+|| ||| +|++|+|||||.||+++++||+++|+||.|++++++|||||.||+
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 559999999999999999999999999999999999999999999
Q ss_pred eEEEecCCCccccccCchhhhhhhhhcCCCCE-EEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCcccEEEEe
Q 027811 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYGPTISKH 213 (218)
Q Consensus 136 ~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~-V~V~~~eg~~i~V~LP~~V~l~V~etep~vKGdTat~~~K~A~Let 213 (218)
.|+|||+|||||++|+++.+|++.+||+|||+ |+|.+|+|+||+|+||.+|+|+|++|+|++||||+++++|||+|||
T Consensus 81 ~~~FMd~etyEQ~~i~~~~lgd~~~~L~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~kGdT~~~~~KpAtLet 159 (189)
T PRK04542 81 EYVFMDNEDYTPYTFKKDQIEDELLFIPEGMPGMQVLTVDGQPVALELPQTVDLEIVETAPSIKGASASARTKPATLST 159 (189)
T ss_pred EEEEecCCCceEEEECHHHhhhHhhhhhcCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCccccccCCCCccEEEcC
Confidence 99999999999999999999999999999998 9999999999999999999999999999999999999999999998
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=1.8e-56 Score=378.51 Aligned_cols=153 Identities=22% Similarity=0.404 Sum_probs=149.9
Q ss_pred cCCCCCccEEEECCeEEEEEEeEEeeCCCCCe--eEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCCeEE
Q 027811 61 ASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGA--MMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAF 138 (218)
Q Consensus 61 andiRkG~~I~~dG~~y~Vl~~~h~kpGkG~A--~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd~~v 138 (218)
+|+||+|++|++||+||+|++++|+|||+|+| ++|+|||||.||+++++||+++|+||.|+++++++||||.||+.|+
T Consensus 2 ~~~lk~G~~i~~dg~~~~V~~~~~~kpg~~ga~~~vk~klknl~tG~~~e~tf~s~e~ve~a~le~~~~qylY~dg~~~~ 81 (186)
T TIGR02178 2 ASEMKKGSIVEYNGKTLLIKDIQRSSPQGRGGNVRYKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKDGEEYV 81 (186)
T ss_pred cccccCCCEEEECCEEEEEEEEEEECCCCCCCcEEEEEEEeEcCCCCeEEEEECCCCeEEEEEEEEeEeEEEEeCCCeEE
Confidence 79999999999999999999999999987666 8999999999999999999999999999999999999999999999
Q ss_pred EecCCCccccccCchhhhhhhhhcCCCCE-EEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCcccEEEEe
Q 027811 139 VIESETFEQLEVPLDVFGKAGAYLQEGMK-VWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYGPTISKH 213 (218)
Q Consensus 139 FMD~ETyEQi~v~~d~lg~~~~fL~eg~~-V~V~~~eg~~i~V~LP~~V~l~V~etep~vKGdTat~~~K~A~Let 213 (218)
|||+|||||++|+++.+|++.+||+|||+ |+|.+|+|+||+|+||.+|+|+|++|+|++|||||++++|||+|||
T Consensus 82 FMD~etyEQ~~i~~~~lgd~~~fL~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~~KGdT~~~~~KpA~LeT 157 (186)
T TIGR02178 82 FMDEEDYTPYTFDKDAIEDELLFISEGLSGMYVQLIDGSPVALELPQHVVLEIVETPPEIKGASASKRPKPAKLIT 157 (186)
T ss_pred EccCCCcEEEEeCHHHhhhhhhhhhCCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCcccccCCCCcccEEEcC
Confidence 99999999999999999999999999997 9999999999999999999999999999999999999999999998
No 5
>PRK00529 elongation factor P; Validated
Probab=100.00 E-value=1.6e-55 Score=372.67 Aligned_cols=156 Identities=33% Similarity=0.571 Sum_probs=154.4
Q ss_pred eEecCCCCCccEEEECCeEEEEEEeEEeeCCCCCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCCeE
Q 027811 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTA 137 (218)
Q Consensus 58 ~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGkG~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd~~ 137 (218)
|+++|+||+|++|+++|+||+|++++|+|||||+|++|+++|||.||++++.+|+++|+++.+.++++++||||.||+.|
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 EEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCcccEEEEe
Q 027811 138 FVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYGPTISKH 213 (218)
Q Consensus 138 vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V~LP~~V~l~V~etep~vKGdTat~~~K~A~Let 213 (218)
+|||+|||||++||++.++++.+||+|||+|+|.+|+|+||+|+||.+|+|+|++|+|++||||+++++|||+|||
T Consensus 81 ~fMD~etyeq~~l~~~~lg~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~let 156 (186)
T PRK00529 81 VFMDTETYEQIEVPADQVGDAAKFLKEGMEVTVVFYNGEPISVELPNFVELEVTETEPGVKGDTASGGTKPATLET 156 (186)
T ss_pred EEecCCCceeeEcCHHHhHHHHhhccCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCccCcccCCCcccEEEcC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998
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=2.7e-55 Score=370.94 Aligned_cols=155 Identities=31% Similarity=0.582 Sum_probs=153.2
Q ss_pred EecCCCCCccEEEECCeEEEEEEeEEeeCCCCCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCCeEE
Q 027811 59 VNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAF 138 (218)
Q Consensus 59 i~andiRkG~~I~~dG~~y~Vl~~~h~kpGkG~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd~~v 138 (218)
+++|+||+|++|+++|+||+|++++|+|||||+|++|+++|||.||++++++|+++|+++.+.++++++||||.||+.|+
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 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCccCCCCcccEEEEe
Q 027811 139 VIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPTVTPRYGPTISKH 213 (218)
Q Consensus 139 FMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V~LP~~V~l~V~etep~vKGdTat~~~K~A~Let 213 (218)
|||+|||||++|+++.++++.+||+|||+|+|.+|+|+||+|+||.+|+|+|++|+|++|||||++++|||+|||
T Consensus 81 fMD~etyeq~~i~~~~l~~~~~~L~eg~~v~v~~~~~~~i~v~lP~~v~l~V~~t~p~~kg~t~~~~~K~A~let 155 (184)
T TIGR00038 81 FMDTETYEQIELPKDLLGDAAKFLKENMEVSVTFYNGEPIGVELPNFVELEVTETEPGVKGDTASGGTKPATLET 155 (184)
T ss_pred EeCCCCccceEcCHHHHHHHHhhcCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCccccccCCCcccEEEcC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999998
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=2e-45 Score=296.04 Aligned_cols=130 Identities=35% Similarity=0.619 Sum_probs=128.1
Q ss_pred eeEecCCCCCccEEEECCeEEEEEEeEEeeCCCCCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCCe
Q 027811 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDT 136 (218)
Q Consensus 57 ~~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGkG~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd~ 136 (218)
.|+++++||+|++|.+||+||+|++++|+|||||+|++|+++|||.||++++.+|+++|++|.|.++++++||||.||+.
T Consensus 2 ~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGKg~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~dg~~ 81 (131)
T COG0231 2 AMISASELRKGLYIVIDGEPYVVVEISHVKPGKGGAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYIDGDF 81 (131)
T ss_pred ceeeHHHccCCCEEEECCeEEEEEEEEEccCCCCCcEEEEEEEEccCCCEEEEEEcCCCEEEEeEEeeeeEEEEEcCCCe
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEEeCCCeE
Q 027811 137 AFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRV 186 (218)
Q Consensus 137 ~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V~LP~~V 186 (218)
|+|||+|||||++|+++.+++..+||+|||+|+|++|+|++++|+||.+|
T Consensus 82 ~~FMD~etyeq~~v~~~~~~d~~~~l~eg~~v~v~~~~g~~i~v~lP~~v 131 (131)
T COG0231 82 YVFMDLETYEQYELPKDQIGDAAKFLKEGMEVEVLLYNGEPIAVELPNFV 131 (131)
T ss_pred EEEccCCCceEEEecchhhhhHHHhcCCCCEEEEEEECCEEEEEECCCCC
Confidence 99999999999999999999999999999999999999999999999975
No 8
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=100.00 E-value=5.1e-37 Score=246.92 Aligned_cols=120 Identities=22% Similarity=0.321 Sum_probs=114.5
Q ss_pred eeEecCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCC
Q 027811 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (218)
Q Consensus 57 ~~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGk-G~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd 135 (218)
..+++++||+|++|++||+||+|++++|+|||| |+|++|+++|||.||++++.+|+++|++|.|.++++++||||.||+
T Consensus 5 ~~~~~~~irkG~~i~~~g~p~~V~e~~~~kpGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ve~~~ve~~~~qylY~dg~ 84 (130)
T TIGR00037 5 KQVQVSALRVGGYVVIDGRPCKIVDISTSKPGKHGHAKARVVAIGIFTGKKLEFVSPSTSKVEVPIVDRREYQVLAIMGG 84 (130)
T ss_pred eeccHHHccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEECCCCEEEEeEEEEEEEEEEEecCC
Confidence 347899999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred eEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEE
Q 027811 136 TAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 178 (218)
Q Consensus 136 ~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i 178 (218)
.|+|||+|||||++|+.+. +..+||+||++|.|+-..|+..
T Consensus 85 ~~~fMd~etyeq~~i~~~~--~~~~~Lke~~~V~v~~~~g~~~ 125 (130)
T TIGR00037 85 MVQLMDLDTYETDELPIPE--ELGDSLEPGFEVEYIEAMGQEK 125 (130)
T ss_pred EEEEEcCCCcEEEEecCCh--hHHHHhhcCCEEEEEecCCeEE
Confidence 9999999999999999985 8899999999999998877643
No 9
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=100.00 E-value=2.1e-35 Score=237.21 Aligned_cols=117 Identities=23% Similarity=0.341 Sum_probs=111.4
Q ss_pred eEecCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCCe
Q 027811 58 KVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDT 136 (218)
Q Consensus 58 ~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGk-G~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd~ 136 (218)
.+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||.||++++.+|+++|++|.+.++++++||||.||+.
T Consensus 5 ~~~~~~lrkG~~i~~~g~p~~V~~~~~~kpGkhg~a~vr~k~knL~tG~~~e~~~~s~d~~e~~~ve~~~~qylY~dg~~ 84 (129)
T PRK03999 5 QVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIMGDV 84 (129)
T ss_pred cccHHHccCCCEEEECCEEEEEEEEEeecCCCCCcEEEEEEEEECCCCCEEEEEecCCCceeeeeEEeEEEEEEEecCCE
Confidence 46789999999999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCE
Q 027811 137 AFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGR 176 (218)
Q Consensus 137 ~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~ 176 (218)
|+|||+|||||++|+++ +++..||+||++|+|+--.|+
T Consensus 85 ~~fMd~eTyeq~~i~~~--~d~~~~l~eg~~v~v~~~~g~ 122 (129)
T PRK03999 85 VQLMDLETYETFEIPIP--EELKDKLEPGVEVEYWEAMGR 122 (129)
T ss_pred EEEecCCCceEEEecCC--hhHHhhCcCCCEEEEEhhCCe
Confidence 99999999999999998 888999999999998764454
No 10
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=99.98 E-value=1.5e-31 Score=221.76 Aligned_cols=120 Identities=18% Similarity=0.288 Sum_probs=106.4
Q ss_pred eeEecCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCC
Q 027811 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (218)
Q Consensus 57 ~~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGk-G~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd 135 (218)
+|+++++||+|++|+++|+||+|++++|+|||| |+|++|+++|||+||++++.+|++++++|.|+++++++||||.||+
T Consensus 19 ~m~~~~~lKkG~~I~~~g~pc~V~e~~~~KpGKHG~A~vr~k~knl~TG~k~e~~f~s~~~ve~~~ve~~~~qyly~dgd 98 (159)
T PLN03107 19 YPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNCDVPHVNRTDYQLIDISED 98 (159)
T ss_pred eccchHhccCCCEEEECCEEEEEEEEEecCCCCCCcEEEEEEEEECCCCCEEEEEecCCCEEEEEEEEEEEEEEEEEcCC
Confidence 489999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred eE-EEecC--CCccccccCc---hhhhhhhhhcCCCCEEEEEEEC--CE
Q 027811 136 TA-FVIES--ETFEQLEVPL---DVFGKAGAYLQEGMKVWLQLYD--GR 176 (218)
Q Consensus 136 ~~-vFMD~--ETyEQi~v~~---d~lg~~~~fL~eg~~V~V~~~e--g~ 176 (218)
.| +|||+ +||||+.||+ ++.........+|.++.|..|. |+
T Consensus 99 ~y~~fMD~~get~eqi~v~~~~~el~~~i~~~f~~g~~~~v~v~~~mg~ 147 (159)
T PLN03107 99 GFVSLMDESGNTKDDLKLPTEDDTLAEQIKDGFDEGKDLVVTVMSAMGE 147 (159)
T ss_pred ceEEEEcCCCCcceeEEccCcchHHHHHHHHHHhCCCeEEEEEEecCCe
Confidence 95 99999 6999999986 3333334445779885555543 65
No 11
>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=99.90 E-value=1e-23 Score=149.22 Aligned_cols=61 Identities=33% Similarity=0.758 Sum_probs=59.7
Q ss_pred EeeEEEEEEEeCCeEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEEeCC
Q 027811 123 EDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 183 (218)
Q Consensus 123 e~k~~qyLY~Dgd~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V~LP 183 (218)
++|++||||.||+.|+|||+|||||++|+++.+|++.+||+|||+|+|.+|+|+||+|+||
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 4789999999999999999999999999999999999999999999999999999999999
No 12
>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=3.5e-21 Score=134.96 Aligned_cols=58 Identities=40% Similarity=0.708 Sum_probs=53.6
Q ss_pred ecCCCCCccEEEECCeEEEEEEeEEeeCCCCCeeEEEEEeeCCCCCEEEEEecCCCcE
Q 027811 60 NASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAV 117 (218)
Q Consensus 60 ~andiRkG~~I~~dG~~y~Vl~~~h~kpGkG~A~vr~klknL~TG~k~e~tf~s~dkv 117 (218)
+|+|||+|++|++||+||+|++++|++||||+|+||+|||||.||+++|++|+++|+|
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 13
>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=99.84 E-value=2.6e-21 Score=134.29 Aligned_cols=55 Identities=36% Similarity=0.748 Sum_probs=49.9
Q ss_pred eeEEEEEEEeCCeEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEE
Q 027811 124 DKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 178 (218)
Q Consensus 124 ~k~~qyLY~Dgd~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i 178 (218)
+|++||||.||+.|||||+|||||++|+++.+|++.+||+||++|+|.+|+|+||
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 14
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=99.78 E-value=4.1e-18 Score=141.74 Aligned_cols=118 Identities=19% Similarity=0.297 Sum_probs=103.2
Q ss_pred eeEecCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCC
Q 027811 57 VKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTEND 135 (218)
Q Consensus 57 ~~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGk-G~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd 135 (218)
+-++++.||+|.+|.++|+||+|+++..+|||| |+|.+++...||+||++.+...++.++++++.+++++||++..++|
T Consensus 21 ~p~q~~~LkkG~yvvIkGrPCKIveistSKtGKHGhAK~~ivaidIFTgkK~edi~Ps~hnv~VP~V~r~~yqli~I~~d 100 (166)
T PTZ00328 21 YPLPAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPN 100 (166)
T ss_pred ecccccceeECCEEEECCeeeEEEEEecCCCCcCCceEEEEEEEecCCCCEEeeecCccceeEeeeEEeeEEEEEEEcCC
Confidence 456789999999999999999999999999999 9999999999999999999999999999999999999999999886
Q ss_pred -------eEEEecCCCccccccCc---hhhhh-hhhhcCCCCEEEEEEEC
Q 027811 136 -------TAFVIESETFEQLEVPL---DVFGK-AGAYLQEGMKVWLQLYD 174 (218)
Q Consensus 136 -------~~vFMD~ETyEQi~v~~---d~lg~-~~~fL~eg~~V~V~~~e 174 (218)
...+||.++|+-..|+. +.++. ....+.+|.+|.|.+|.
T Consensus 101 ~~~~~~g~v~LMd~~g~~k~dl~lp~~~el~~~ik~~f~~g~ev~v~vi~ 150 (166)
T PTZ00328 101 EDPSLPAHLSLMDDEGESREDLDMPPDAALATQIKEQFDSGKEVLVVVVS 150 (166)
T ss_pred CcccccceEEEEcCCCCeeecccCCChhHHHHHHHHHhcCCCeEEEEEEh
Confidence 37999999887766543 23333 34566999999987775
No 15
>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=99.72 E-value=9e-18 Score=115.67 Aligned_cols=55 Identities=18% Similarity=0.269 Sum_probs=51.4
Q ss_pred eEEEEEEEeCCeEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEE
Q 027811 125 KSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSG 180 (218)
Q Consensus 125 k~~qyLY~Dgd~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V 180 (218)
|++||||.||+.|+|||+|||||++++++.. +..+||+||++|.|++|+|+|++|
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 5799999999999999999999999999985 589999999999999999999874
No 16
>KOG3271 consensus Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=99.51 E-value=8.9e-14 Score=113.06 Aligned_cols=112 Identities=17% Similarity=0.279 Sum_probs=98.6
Q ss_pred EecCCCCCccEEEECCeEEEEEEeEEeeCCC-CCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCCeE
Q 027811 59 VNASHVRPGNVIEKSGKMYQVIDAEHKQRGR-GGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTA 137 (218)
Q Consensus 59 i~andiRkG~~I~~dG~~y~Vl~~~h~kpGk-G~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd~~ 137 (218)
.+.+.||++-.|.++|+||+|+++.-+|.|| |+|.+.+..++|+||++.+..++++++++++.++|++||.+-.+++..
T Consensus 21 ~q~salrkNG~vviK~rpckivEmSTsKtGKHGhAKvh~vaidifTgkk~edI~psthn~dVp~vkr~~yqLidIsd~~~ 100 (156)
T KOG3271|consen 21 MQCSALRKNGHVVIKGRPCKIVEMSTSKTGKHGHAKVHIVAIDIFTGKKLEDICPSTHNMDVPVVKRVDYQLIDISDGYL 100 (156)
T ss_pred chhhheeeCCEEEEcCCCceEEEeecccCCcCCceEEEEEEEEeecCcccccccCCCCccccCccccceeEEEEecCCeE
Confidence 3467899999999999999999999999999 999999999999999999999999999999999999999999999988
Q ss_pred EEecC--CCccccccCchhhhhhhh-hcCCCCEEEE
Q 027811 138 FVIES--ETFEQLEVPLDVFGKAGA-YLQEGMKVWL 170 (218)
Q Consensus 138 vFMD~--ETyEQi~v~~d~lg~~~~-fL~eg~~V~V 170 (218)
.|||+ ++-+++.+|...+++.+. =..+|..+.|
T Consensus 101 sl~t~sG~~kdDlklp~~el~~~i~~~~e~g~dl~v 136 (156)
T KOG3271|consen 101 SLMTDSGETKDDLKLPEGELGNQIRQGFEEGKDLLV 136 (156)
T ss_pred EEEcCCCCcchhccCcchhHHHHHHHhhcCCCcEEE
Confidence 99998 467888889888887753 2345543333
No 17
>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=98.78 E-value=3.7e-09 Score=73.90 Aligned_cols=28 Identities=21% Similarity=0.277 Sum_probs=27.0
Q ss_pred EEEEEEEeCCCCCCccCCCCcccEEEEe
Q 027811 186 VACTIKEIHASTKGPTVTPRYGPTISKH 213 (218)
Q Consensus 186 V~l~V~etep~vKGdTat~~~K~A~Let 213 (218)
|+|+|+||+|++||||+++++|||+|||
T Consensus 1 V~l~V~etep~vkG~T~~~~~K~A~let 28 (56)
T smart00841 1 VELEVTETEPGVKGDTASGGTKPATLET 28 (56)
T ss_pred CEEEEEECCCCccccccCCCcceEEECC
Confidence 6899999999999999999999999997
No 18
>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=98.75 E-value=5.1e-09 Score=73.19 Aligned_cols=28 Identities=21% Similarity=0.300 Sum_probs=27.0
Q ss_pred EEEEEEEeCCCCCCccCCCCcccEEEEe
Q 027811 186 VACTIKEIHASTKGPTVTPRYGPTISKH 213 (218)
Q Consensus 186 V~l~V~etep~vKGdTat~~~K~A~Let 213 (218)
|+|+|++|+|++||||+++++|||+|||
T Consensus 1 v~l~V~etep~~kG~T~~~~~K~A~let 28 (56)
T cd05794 1 VELEVTETEPGVKGDTASSGTKPATLET 28 (56)
T ss_pred CEEEEEECCCCccccccCCCcceEEECC
Confidence 5899999999999999999999999998
No 19
>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=98.67 E-value=1.5e-08 Score=70.78 Aligned_cols=28 Identities=25% Similarity=0.412 Sum_probs=26.1
Q ss_pred EEEEEEEeCCCCCCccCCCCcccEEEEe
Q 027811 186 VACTIKEIHASTKGPTVTPRYGPTISKH 213 (218)
Q Consensus 186 V~l~V~etep~vKGdTat~~~K~A~Let 213 (218)
|+|+|+||+|++||||+++++|||+|||
T Consensus 1 V~l~V~etep~~kg~t~~~~~K~A~let 28 (56)
T PF09285_consen 1 VELEVVETEPAVKGDTASSSYKPATLET 28 (56)
T ss_dssp EEEEEEEE-SSSTTSSSSTTEEEEEETT
T ss_pred CEEEEEECCCCccCcccCCCccEEEEcC
Confidence 7899999999999999999999999997
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=98.61 E-value=8.7e-08 Score=67.24 Aligned_cols=54 Identities=26% Similarity=0.319 Sum_probs=46.0
Q ss_pred EEeeEEEEEEEeCCeEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEE
Q 027811 122 VEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRA 177 (218)
Q Consensus 122 le~k~~qyLY~Dgd~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~ 177 (218)
|+||..|.++.+|+...+||+||||.++++.. .+...-+++|.+|.++-..|+.
T Consensus 1 i~k~~aqVisi~g~~vQlMD~eTYeT~ev~~p--~~~~~~i~~G~eV~y~~~~g~~ 54 (57)
T cd04467 1 IERKTGQVLSIMGDVVQLMDLETYETFEVPIP--EEIKDKLEPGKEVEYWESMGKR 54 (57)
T ss_pred CcceEEEEEEEcCCEEEEeccccceeEEEecc--hhhcccCCCCCEEEEEeecCeE
Confidence 58999999999999999999999999999986 2222348999999988877863
No 21
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=98.37 E-value=5.3e-06 Score=77.11 Aligned_cols=130 Identities=19% Similarity=0.226 Sum_probs=98.7
Q ss_pred CCCCcccccccc---ccceeeee-eeeEecCCCCCccEEEECCeEEEEEEeEEeeCCCCCeeEEEEEeeCCCCCEEEEEe
Q 027811 36 SSGDRDTCLLRF---PWSATQQR-AVKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRF 111 (218)
Q Consensus 36 ~~~~~~~~~~~~---~~~~~~~R-~~~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGkG~A~vr~klknL~TG~k~e~tf 111 (218)
||....+.-|.+ +.....|| .+.+...++|+|++|.++|+.+.++... |+ .+.++|+.||...+.+|
T Consensus 215 ~~~v~eS~~Lvg~d~~tgk~~yR~t~Svrip~~~~gDiV~~~~~~~~~v~~~----~~-----~~~~~dl~t~e~~~~~~ 285 (355)
T COG1499 215 GGEVKESEKLVGRDRFTGKRVYRFTYSVRIPEFRPGDIVSVRGRQLVLVRSI----GK-----GIVVLDLETGEPVEITW 285 (355)
T ss_pred CcEEEecceeEEEecCCCceEEEEEEEEECCCCCCCCEEEECCCeEEEEEEe----cC-----ceEEEecccCCccccCh
Confidence 444444444433 24555688 5889999999999999999766666555 56 68999999999888887
Q ss_pred cCCCcEE--e--eeEEeeEEEEEEEeCCeEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEEe
Q 027811 112 GTEEAVE--R--VFVEDKSFTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGS 181 (218)
Q Consensus 112 ~s~dkvE--~--v~le~k~~qyLY~Dgd~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V~ 181 (218)
.....-+ . ..-+-+.+.++..+++..+|||++|||-+++..+ =|.+|.+|.++.++|...-++
T Consensus 286 ~~~~~~~~~~~~~~~~~~~~~vvs~~~~~~~v~d~et~e~~~~~~~-------~~~~g~~v~v~~~~~~~~~~~ 352 (355)
T COG1499 286 SVYKRNEGKVAVKEPRLKKAVVVSRDPSAIQVLDPETYEARTVKGP-------SLEEGDEVKVFKVRGRNYVVE 352 (355)
T ss_pred hhcccCcceeeeccccceEEEEEecCCCceEEEecceEEEEeccCC-------CCCCCCEEEEEEEeceEEeec
Confidence 5544444 2 2233378899999999999999999999999766 368999999999999876543
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=96.88 E-value=0.0053 Score=44.60 Aligned_cols=55 Identities=24% Similarity=0.283 Sum_probs=39.6
Q ss_pred eEEeeEEEEEEEeCC-eEEEecCCCccccc---cCchhhhhhh-hhcCCCCE--EEEEEECCE
Q 027811 121 FVEDKSFTCLYTEND-TAFVIESETFEQLE---VPLDVFGKAG-AYLQEGMK--VWLQLYDGR 176 (218)
Q Consensus 121 ~le~k~~qyLY~Dgd-~~vFMD~ETyEQi~---v~~d~lg~~~-~fL~eg~~--V~V~~~eg~ 176 (218)
.++|++||.+..++| ...+|| |+||..+ +|..-+++.+ .-+.+|.+ |+|+---|+
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 679999 7766655 8855565543 44589988 666655564
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=90.37 E-value=1.2 Score=32.46 Aligned_cols=50 Identities=22% Similarity=0.400 Sum_probs=37.9
Q ss_pred EEeeEEEEEEEeCCeEEEecC--CCccccccCchhhhhhh--hhcCCCCEEEEEE
Q 027811 122 VEDKSFTCLYTENDTAFVIES--ETFEQLEVPLDVFGKAG--AYLQEGMKVWLQL 172 (218)
Q Consensus 122 le~k~~qyLY~Dgd~~vFMD~--ETyEQi~v~~d~lg~~~--~fL~eg~~V~V~~ 172 (218)
+.|++||.+..+++...+||. ++-|++.+|.+.++..+ .| .+|..+-|..
T Consensus 1 V~R~eYqLidI~dGflsLm~e~G~~k~DlklP~~elg~~I~~~f-~~gk~~~vtV 54 (69)
T cd04468 1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKF-DEGKDVLVTV 54 (69)
T ss_pred CcceeEEEEeecCCeEEEEcCCCCcccCCcCCcHHHHHHHHHHH-hCCCcEEEEE
Confidence 468899999998777799975 57899999998888765 35 5565544443
No 24
>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=83.63 E-value=2.6 Score=34.18 Aligned_cols=39 Identities=26% Similarity=0.405 Sum_probs=31.7
Q ss_pred EecCCCCCccEEEECCe--EEEEEEeEEee--CC------CCCeeEEEE
Q 027811 59 VNASHVRPGNVIEKSGK--MYQVIDAEHKQ--RG------RGGAMMQME 97 (218)
Q Consensus 59 i~andiRkG~~I~~dG~--~y~Vl~~~h~k--pG------kG~A~vr~k 97 (218)
+..=|||.|+.|.+++. +|.|+.+.+.- +. ||.+.|.+|
T Consensus 55 v~~LDlRIGD~Vkv~~~k~~yiV~Gl~~~~~~~~~~i~cirGy~tV~Lk 103 (131)
T PF08605_consen 55 VKYLDLRIGDTVKVDGPKVTYIVVGLECKISSEDNIITCIRGYNTVYLK 103 (131)
T ss_pred EeeeeeecCCEEEECCCCccEEEEEeeecCCCCCCceEEcCCCcEEEEE
Confidence 45568999999999998 99999999872 33 588888774
No 25
>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=74.97 E-value=1.5 Score=31.78 Aligned_cols=26 Identities=27% Similarity=0.460 Sum_probs=14.9
Q ss_pred CCCEEEEE-EECCEEEEEeCCCeEEEE
Q 027811 164 EGMKVWLQ-LYDGRALSGSIPKRVACT 189 (218)
Q Consensus 164 eg~~V~V~-~~eg~~i~V~LP~~V~l~ 189 (218)
||..+++. .|+|+||+.+||-.|.+.
T Consensus 30 EGev~~~v~~wkGr~iSanlP~~V~F~ 56 (67)
T PF02941_consen 30 EGEVKQIVTDWKGRPISANLPVKVQFD 56 (67)
T ss_dssp EEEEEEE-SEETTEE---SS-EEEEET
T ss_pred EEEEEEEEeecCCcEecCCCcEEEEEe
Confidence 44444433 499999999999988764
No 26
>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=74.85 E-value=17 Score=26.89 Aligned_cols=51 Identities=18% Similarity=0.238 Sum_probs=35.2
Q ss_pred eEEEEEEEeCCeEEEecC--CCccccccC-chhhhhhh--hhcCCCC---EEEEEEECCE
Q 027811 125 KSFTCLYTENDTAFVIES--ETFEQLEVP-LDVFGKAG--AYLQEGM---KVWLQLYDGR 176 (218)
Q Consensus 125 k~~qyLY~Dgd~~vFMD~--ETyEQi~v~-~d~lg~~~--~fL~eg~---~V~V~~~eg~ 176 (218)
++||.+..+++...+||. ++-|++.|| ...++..+ .| .+|. .|.|+--.|+
T Consensus 3 ~eYqLidI~DG~lsLM~e~G~~kdDl~lP~~~~l~~~I~~~f-~~gk~~v~VtVlsAmGe 61 (75)
T cd04469 3 KQYRVLDIQDGSIVAMTETGDVKQGLPVIDQSNLWTRLKTAF-ESGRGSVRVLVVNDGGR 61 (75)
T ss_pred eEEEEEEecCCeEEEEcCCCCcccCccCCCcchHHHHHHHHH-HCCCCcEEEEEEccCCe
Confidence 689999996667799975 578899999 66666654 35 6666 4444444443
No 27
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=56.29 E-value=69 Score=25.55 Aligned_cols=66 Identities=23% Similarity=0.374 Sum_probs=43.0
Q ss_pred EecCCCCCccEEEE-----CCeEEEEEEeEE---eeCCCCCeeEEEEEeeCCCCCEEEEEecCCCc-EEeeeEEee
Q 027811 59 VNASHVRPGNVIEK-----SGKMYQVIDAEH---KQRGRGGAMMQMELRDIDTGNKVSLRFGTEEA-VERVFVEDK 125 (218)
Q Consensus 59 i~andiRkG~~I~~-----dG~~y~Vl~~~h---~kpGkG~A~vr~klknL~TG~k~e~tf~s~dk-vE~v~le~k 125 (218)
.+..++++||+|.. +|.--++..++- .+.++|- .-.+.+|++..|-=+|.+|+-... ++.+.+-++
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 KDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGL-NETFTVRKISYGVGVERTFPLHSPRIDSIEVVRR 88 (116)
T ss_pred cCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCC-CceEEEEEcccCccEEEEecCCCCcccEEEEEEe
Confidence 56789999999876 455444444432 1123433 336889999999999999976443 555555443
No 28
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=55.00 E-value=13 Score=26.58 Aligned_cols=19 Identities=42% Similarity=0.941 Sum_probs=14.0
Q ss_pred CCCCCccEEEECCeEEEEE
Q 027811 62 SHVRPGNVIEKSGKMYQVI 80 (218)
Q Consensus 62 ndiRkG~~I~~dG~~y~Vl 80 (218)
-.|++|++|..+|..|+|+
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 4689999999999999985
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=54.56 E-value=63 Score=25.50 Aligned_cols=68 Identities=22% Similarity=0.275 Sum_probs=44.2
Q ss_pred eEecCCCCCccEEEE-----CCeEEEEEEeEEe---eCCCCCeeEEEEEeeCCCCCEEEEEecCCCc-EEeeeEEeeE
Q 027811 58 KVNASHVRPGNVIEK-----SGKMYQVIDAEHK---QRGRGGAMMQMELRDIDTGNKVSLRFGTEEA-VERVFVEDKS 126 (218)
Q Consensus 58 ~i~andiRkG~~I~~-----dG~~y~Vl~~~h~---kpGkG~A~vr~klknL~TG~k~e~tf~s~dk-vE~v~le~k~ 126 (218)
..+..++++||+|.+ +|..-++..|+-+ ..++|- .-.+.++|+..|.-+|.+|+-... ++.+.+-++.
T Consensus 13 ~~~~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 13 KKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGL-NSSFTLRNISQGVGVERVFPLYSPLIKSIEVLRRG 89 (113)
T ss_dssp SSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSST-SSEEEEEEEETTEEEEEEEETTSTTEEEEEEEEEB
T ss_pred hcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCC-CeeEEEEEEecCccEEEEEEcCCCCeEEEEEEEec
Confidence 467889999999865 3433344344321 123332 226778999999999999987554 6666666543
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=48.22 E-value=95 Score=24.64 Aligned_cols=65 Identities=23% Similarity=0.285 Sum_probs=41.3
Q ss_pred eEecCCCCCccEEEE-----CCeEEEEEEeEE---eeCCCCCeeEEEEEeeCCCCCEEEEEecCCCc-EEeeeEE
Q 027811 58 KVNASHVRPGNVIEK-----SGKMYQVIDAEH---KQRGRGGAMMQMELRDIDTGNKVSLRFGTEEA-VERVFVE 123 (218)
Q Consensus 58 ~i~andiRkG~~I~~-----dG~~y~Vl~~~h---~kpGkG~A~vr~klknL~TG~k~e~tf~s~dk-vE~v~le 123 (218)
..+..++++||+|.+ +|.--++..++- .+.++|- .-.+.+|++..|-=+|.+|+-... ++.+.+-
T Consensus 13 ~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~-~~tftvR~i~~gvGVEr~fpl~SP~I~~IeVl 86 (113)
T TIGR01024 13 KKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGI-GETFTVRKISYGVGVERIFPLHSPNIDSIEVV 86 (113)
T ss_pred hcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCC-ceEEEEEEeccCccEEEEEEcCCCccceEEEE
Confidence 456889999999977 333333333331 1124443 336889999999999999976443 4444444
No 31
>PRK11507 ribosome-associated protein; Provisional
Probab=47.93 E-value=23 Score=25.83 Aligned_cols=19 Identities=21% Similarity=0.429 Sum_probs=17.0
Q ss_pred CCCCCccEEEECCeEEEEE
Q 027811 62 SHVRPGNVIEKSGKMYQVI 80 (218)
Q Consensus 62 ndiRkG~~I~~dG~~y~Vl 80 (218)
-.|++|++|.++|.-|+|.
T Consensus 51 kKl~~GD~V~~~g~~~~v~ 69 (70)
T PRK11507 51 CKIVAGQTVSFAGHSVQVV 69 (70)
T ss_pred CCCCCCCEEEECCEEEEEe
Confidence 5699999999999999886
No 32
>CHL00084 rpl19 ribosomal protein L19
Probab=47.42 E-value=1.2e+02 Score=24.30 Aligned_cols=66 Identities=20% Similarity=0.220 Sum_probs=42.1
Q ss_pred eEecCCCCCccEEEE-----CCeEEEEEEeEE---eeCCCCCeeEEEEEeeCCCCCEEEEEecCCCc-EEeeeEEe
Q 027811 58 KVNASHVRPGNVIEK-----SGKMYQVIDAEH---KQRGRGGAMMQMELRDIDTGNKVSLRFGTEEA-VERVFVED 124 (218)
Q Consensus 58 ~i~andiRkG~~I~~-----dG~~y~Vl~~~h---~kpGkG~A~vr~klknL~TG~k~e~tf~s~dk-vE~v~le~ 124 (218)
..+..++++||+|.+ +|.--++-.++- ...|+|-.. .+-+|++..|-=+|.+|+-... ++.+.+-+
T Consensus 17 ~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~-tftvRki~~gvGVEr~fpl~SP~I~~IeV~r 91 (117)
T CHL00084 17 KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNT-TITVRKVFQGIGVERVFLLHSPKLASIEVLR 91 (117)
T ss_pred hcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCe-eEEEEEeccCccEEEEEecCCCccceEEEEE
Confidence 457889999999875 454333333331 122444332 5889999999999999976443 44444443
No 33
>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=46.48 E-value=33 Score=22.28 Aligned_cols=31 Identities=19% Similarity=0.307 Sum_probs=23.0
Q ss_pred cccccCchhhhhhhhhcCCCCEEEEEEECC-EEE
Q 027811 146 EQLEVPLDVFGKAGAYLQEGMKVWLQLYDG-RAL 178 (218)
Q Consensus 146 EQi~v~~d~lg~~~~fL~eg~~V~V~~~eg-~~i 178 (218)
-|+.||+++... .-|++|++|.+...+| +.+
T Consensus 7 ~~v~iPk~~~~~--l~l~~Gd~v~i~~~~~g~i~ 38 (47)
T PF04014_consen 7 GQVTIPKEIREK--LGLKPGDEVEIEVEGDGKIV 38 (47)
T ss_dssp SEEEE-HHHHHH--TTSSTTTEEEEEEETTSEEE
T ss_pred ceEECCHHHHHH--cCCCCCCEEEEEEeCCCEEE
Confidence 378899887643 3589999999999987 443
No 34
>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=46.35 E-value=38 Score=29.54 Aligned_cols=45 Identities=18% Similarity=0.237 Sum_probs=31.6
Q ss_pred eeeeEecCCCCCccEEEE---CCe--EEEEEEeEEeeCCCCCeeEEEEEe
Q 027811 55 RAVKVNASHVRPGNVIEK---SGK--MYQVIDAEHKQRGRGGAMMQMELR 99 (218)
Q Consensus 55 R~~~i~andiRkG~~I~~---dG~--~y~Vl~~~h~kpGkG~A~vr~klk 99 (218)
.+-.+.+.||+.|+.|.- +|+ .-.|+-+-|..|..-+-|++++..
T Consensus 23 ~G~~k~m~~L~iGD~Vla~d~~G~~~yS~V~~flhr~~~~~~~F~~i~te 72 (217)
T PF01079_consen 23 DGGRKRMSDLKIGDRVLAVDSDGKLVYSPVIMFLHRDPEQRAEFVVIETE 72 (217)
T ss_dssp TS-EEEGGG--TT-EEEEE-TTS-EEEEEEEEEEEEEEEEEEEEEEEEET
T ss_pred CCCEeEHHHCCCCCEEEEecCCCcEEEEeEEEEeccCccccEEEEEEEcC
Confidence 366788999999998865 564 448999999999887788887653
No 35
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=43.63 E-value=2.2e+02 Score=24.78 Aligned_cols=107 Identities=16% Similarity=0.284 Sum_probs=65.7
Q ss_pred ccEEEECCeEEEEEEeE--EeeCCCCCeeEEEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEeCCeEEEecCCC
Q 027811 67 GNVIEKSGKMYQVIDAE--HKQRGRGGAMMQMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTENDTAFVIESET 144 (218)
Q Consensus 67 G~~I~~dG~~y~Vl~~~--h~kpGkG~A~vr~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~Dgd~~vFMD~ET 144 (218)
|..|-+ |.|+++. .++||-|++..++.+|=+. .+.=-|+-+.. .+.-.+.++.++== --
T Consensus 43 GLCI~v----yDi~~v~e~~v~pGDGas~~~V~FR~vV------FrPF~gEVi~g--------ki~~cs~eG~rvtl-~F 103 (202)
T KOG3297|consen 43 GLCICV----YDILEVEEGIVLPGDGASYARVWFRVVV------FRPFVGEVITG--------KIKECSEEGLRVTL-GF 103 (202)
T ss_pred cEEEEE----eEeeeecceEEecCCCceEEEEEEEEEE------EecccceEEEE--------EeecCCccceEEEE-Ee
Confidence 555543 6676765 6889999999999887542 22222332221 11112222222111 14
Q ss_pred ccccccCchhhhhhhhhcCCCCEEEEEEEC-----CEEEEEeCCCeEEEEEEEe
Q 027811 145 FEQLEVPLDVFGKAGAYLQEGMKVWLQLYD-----GRALSGSIPKRVACTIKEI 193 (218)
Q Consensus 145 yEQi~v~~d~lg~~~~fL~eg~~V~V~~~e-----g~~i~V~LP~~V~l~V~et 193 (218)
||+|-||++.|.+...| .|...+-|+-|+ +.-+-+..-..|-+.|++-
T Consensus 104 FdDI~IP~~~L~~p~~f-~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 104 FDDIFIPKEMLPEPCVF-EPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred eeceeechhhCCCCccc-ccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 78899999999887766 555788888886 3446667777777777654
No 36
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=42.75 E-value=31 Score=23.75 Aligned_cols=36 Identities=14% Similarity=0.198 Sum_probs=21.7
Q ss_pred EEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECC
Q 027811 137 AFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDG 175 (218)
Q Consensus 137 ~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg 175 (218)
-.|+|.+..+++.+|..... .=+++|.+|.|+.|.|
T Consensus 16 g~fL~~~~~~~vlLp~~e~~---~~~~~Gd~v~VFvY~D 51 (61)
T PF13509_consen 16 GYFLDDGEGKEVLLPKSEVP---EPLKVGDEVEVFVYLD 51 (61)
T ss_dssp EEEEEETT-EEEEEEGGG---------TTSEEEEEEEE-
T ss_pred EEEEECCCCCEEEechHHcC---CCCCCCCEEEEEEEEC
Confidence 34466666788888876553 2378999999999854
No 37
>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=41.96 E-value=51 Score=23.18 Aligned_cols=24 Identities=21% Similarity=0.473 Sum_probs=18.5
Q ss_pred CCCCccEEEECCeEEEEEEeEEee
Q 027811 63 HVRPGNVIEKSGKMYQVIDAEHKQ 86 (218)
Q Consensus 63 diRkG~~I~~dG~~y~Vl~~~h~k 86 (218)
+|..++.|.++|+.|.|..+....
T Consensus 62 ~I~~~~ri~~~g~~y~I~~i~~~~ 85 (95)
T PF05521_consen 62 DITPDMRIKYDGKVYNIKSIDPDD 85 (95)
T ss_dssp TSSTTEEEEECTEEEEE-S--EE-
T ss_pred CCCcceEEEECCEEEEEEEECCCC
Confidence 799999999999999999977554
No 38
>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=39.24 E-value=32 Score=28.09 Aligned_cols=32 Identities=19% Similarity=0.221 Sum_probs=27.3
Q ss_pred eEecCCCCCccEEEECCeEE-----EEEEeEEeeCCC
Q 027811 58 KVNASHVRPGNVIEKSGKMY-----QVIDAEHKQRGR 89 (218)
Q Consensus 58 ~i~andiRkG~~I~~dG~~y-----~Vl~~~h~kpGk 89 (218)
+-....|++|+.|+..|+++ .|+.+.|.-|+.
T Consensus 80 aprip~l~~GD~V~f~GeYe~n~kggvIHWTH~dp~~ 116 (131)
T PF11948_consen 80 APRIPWLQKGDQVEFYGEYEWNPKGGVIHWTHHDPRG 116 (131)
T ss_pred cccCcCcCCCCEEEEEEEEEECCCCCEEEeeccCCCC
Confidence 34567899999999999987 799999998865
No 39
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=38.42 E-value=88 Score=27.23 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=21.0
Q ss_pred EEEEeeCCCCCEEEEEecCCCcEEe
Q 027811 95 QMELRDIDTGNKVSLRFGTEEAVER 119 (218)
Q Consensus 95 r~klknL~TG~k~e~tf~s~dkvE~ 119 (218)
.+++||+.||+.+.-+..+...|+.
T Consensus 209 ~IrVrN~~Sgk~i~g~V~~~g~V~V 233 (235)
T PRK07018 209 QIRVRNMASGQVVSGIVTGDGEVEV 233 (235)
T ss_pred eEEEEECCCCCEEEEEEeCCCEEEE
Confidence 7888999999999988877777664
No 40
>PRK10377 PTS system glucitol/sorbitol-specific transporter subunit IIA; Provisional
Probab=37.60 E-value=46 Score=26.56 Aligned_cols=24 Identities=21% Similarity=0.310 Sum_probs=21.1
Q ss_pred cCCCCCccEEEECCeEEEEEEeEE
Q 027811 61 ASHVRPGNVIEKSGKMYQVIDAEH 84 (218)
Q Consensus 61 andiRkG~~I~~dG~~y~Vl~~~h 84 (218)
..+|++|+.+.++|+-|.|..+--
T Consensus 49 ~~~i~~Gd~l~i~~~~Y~ItaVG~ 72 (120)
T PRK10377 49 KGALQPGLQFELGQHRYPVTAVGS 72 (120)
T ss_pred cCccCCCCEEEECCEEEEEEEEhH
Confidence 467999999999999999988753
No 41
>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=37.48 E-value=91 Score=23.84 Aligned_cols=24 Identities=25% Similarity=0.378 Sum_probs=19.2
Q ss_pred EEEEeeCCCCCEEEEEecCCCcEE
Q 027811 95 QMELRDIDTGNKVSLRFGTEEAVE 118 (218)
Q Consensus 95 r~klknL~TG~k~e~tf~s~dkvE 118 (218)
.++++|+.+|+.+.-+.-....++
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 788999999999988876655554
No 42
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=37.33 E-value=36 Score=25.06 Aligned_cols=21 Identities=38% Similarity=0.740 Sum_probs=18.2
Q ss_pred CCCCCccEEEECCeEEEEEEe
Q 027811 62 SHVRPGNVIEKSGKMYQVIDA 82 (218)
Q Consensus 62 ndiRkG~~I~~dG~~y~Vl~~ 82 (218)
-.||.|++|++.|..|.|...
T Consensus 51 kKlr~gd~V~i~~~~~~v~~~ 71 (73)
T COG2501 51 KKLRDGDVVEIPGQRYQVVAQ 71 (73)
T ss_pred CEeecCCEEEECCEEEEEEec
Confidence 348999999999999999864
No 43
>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=36.78 E-value=42 Score=26.63 Aligned_cols=23 Identities=17% Similarity=0.528 Sum_probs=15.9
Q ss_pred cCCCCCccEEEECCeEEEEEEeE
Q 027811 61 ASHVRPGNVIEKSGKMYQVIDAE 83 (218)
Q Consensus 61 andiRkG~~I~~dG~~y~Vl~~~ 83 (218)
..+|++|+.+.++++.|.|..+-
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 46899999999999999998875
No 44
>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=36.61 E-value=40 Score=21.06 Aligned_cols=19 Identities=26% Similarity=0.365 Sum_probs=14.2
Q ss_pred CCCccEEEECCeEEEEEEe
Q 027811 64 VRPGNVIEKSGKMYQVIDA 82 (218)
Q Consensus 64 iRkG~~I~~dG~~y~Vl~~ 82 (218)
-..|++|.++|..|+..-.
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 4679999999999998443
No 45
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=36.56 E-value=48 Score=24.70 Aligned_cols=22 Identities=23% Similarity=0.397 Sum_probs=17.2
Q ss_pred CCCccEEEECCeEEEEEEeEEe
Q 027811 64 VRPGNVIEKSGKMYQVIDAEHK 85 (218)
Q Consensus 64 iRkG~~I~~dG~~y~Vl~~~h~ 85 (218)
.|+|+.|.+||+-|.|.+++.-
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 5699999999999999998743
No 46
>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=36.11 E-value=51 Score=26.38 Aligned_cols=23 Identities=26% Similarity=0.491 Sum_probs=20.5
Q ss_pred CCCCCccEEEECCeEEEEEEeEE
Q 027811 62 SHVRPGNVIEKSGKMYQVIDAEH 84 (218)
Q Consensus 62 ndiRkG~~I~~dG~~y~Vl~~~h 84 (218)
.+|++|+.+.++|+-|.|..+--
T Consensus 50 ~~i~~Gd~l~i~~~~Y~ItaVG~ 72 (121)
T TIGR00849 50 GTLKPGQVFMIGGIAYPVTAVGD 72 (121)
T ss_pred CCcCCCCEEEECCEEEEEEEEhH
Confidence 47999999999999999988753
No 47
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=35.72 E-value=1.1e+02 Score=24.51 Aligned_cols=72 Identities=14% Similarity=0.051 Sum_probs=40.6
Q ss_pred eCCeEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCcc------CCCCc
Q 027811 133 ENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGPT------VTPRY 206 (218)
Q Consensus 133 Dgd~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V~LP~~V~l~V~etep~vKGdT------at~~~ 206 (218)
.|+..+..+..++- ....|.+ ..=|+.|++|.|..-+|+ ..+++|++++--.|.+. .....
T Consensus 49 ~Gn~viaGH~~~~g----~~~~F~~-L~~l~~GD~I~v~~~~g~--------~~~Y~V~~~~~v~~~~~~~~~~~~~~~~ 115 (144)
T cd05829 49 KGTAVLAGHVDSRG----GPAVFFR-LGDLRKGDKVEVTRADGQ--------TATFRVDRVEVYPKDAFPTDAVYGDTGP 115 (144)
T ss_pred CCCEEEEEecCCCC----CChhhcc-hhcCCCCCEEEEEECCCC--------EEEEEEeEEEEECcccCChhheecCCCC
Confidence 34445555554442 2222322 223789999988764554 35666666554444332 12445
Q ss_pred ccEEEEeeccc
Q 027811 207 GPTISKHIEGL 217 (218)
Q Consensus 207 K~A~Let~~~~ 217 (218)
...+|-||.+-
T Consensus 116 ~~LtLiTC~~~ 126 (144)
T cd05829 116 PRLRLITCGGP 126 (144)
T ss_pred CEEEEEEeCCC
Confidence 78999999863
No 48
>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=35.63 E-value=95 Score=23.92 Aligned_cols=49 Identities=14% Similarity=0.072 Sum_probs=28.4
Q ss_pred EEEEEEeCCeEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEECCEEEEEeCC
Q 027811 127 FTCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLYDGRALSGSIP 183 (218)
Q Consensus 127 ~qyLY~Dgd~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i~V~LP 183 (218)
++|-|.||..+. ++.-+.+...+..+-.+.|.+|+|.+.-++|=...++
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 677777664444 1111111133333336799999998888887665444
No 49
>PF11694 DUF3290: Protein of unknown function (DUF3290); InterPro: IPR021707 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=34.07 E-value=49 Score=27.32 Aligned_cols=28 Identities=29% Similarity=0.465 Sum_probs=25.1
Q ss_pred eeeEecCCCCCccEEEECCeEEEEEEeE
Q 027811 56 AVKVNASHVRPGNVIEKSGKMYQVIDAE 83 (218)
Q Consensus 56 ~~~i~andiRkG~~I~~dG~~y~Vl~~~ 83 (218)
-+.++...++-|++|+.+++.|+|.-..
T Consensus 98 ~v~VNst~l~dG~iVki~~~yYrV~~n~ 125 (149)
T PF11694_consen 98 EVYVNSTALTDGMIVKIGDKYYRVIFND 125 (149)
T ss_pred eEEEecccccCCeEEEECCccEEEEEcC
Confidence 5789999999999999999999997654
No 50
>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=33.23 E-value=2.4e+02 Score=26.86 Aligned_cols=120 Identities=17% Similarity=0.138 Sum_probs=63.5
Q ss_pred eEecCCCCCccEEEECCeE-------EEEEEeEEeeCC------CCCeeEEEEEeeCCCCCEEEEE---ecCCCcEEeee
Q 027811 58 KVNASHVRPGNVIEKSGKM-------YQVIDAEHKQRG------RGGAMMQMELRDIDTGNKVSLR---FGTEEAVERVF 121 (218)
Q Consensus 58 ~i~andiRkG~~I~~dG~~-------y~Vl~~~h~kpG------kG~A~vr~klknL~TG~k~e~t---f~s~dkvE~v~ 121 (218)
..++..|++|..|.+.|.| |.|+++.|.--. -..+.++..+.-+-.+...--. .+.-.-+..+.
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 3456779999999997753 899999987221 1134455555555444321110 11111134455
Q ss_pred EEeeEEEEEEEeCCe---EEE-ecCCCc-c-----ccccCchhhhhh--hhh-cCCCCEEEEEEECCEE
Q 027811 122 VEDKSFTCLYTENDT---AFV-IESETF-E-----QLEVPLDVFGKA--GAY-LQEGMKVWLQLYDGRA 177 (218)
Q Consensus 122 le~k~~qyLY~Dgd~---~vF-MD~ETy-E-----Qi~v~~d~lg~~--~~f-L~eg~~V~V~~~eg~~ 177 (218)
|..-.-++.|.|+.+ ..| .|.... + =+.+....-|+. .-| +..|++|-|.|.+|.|
T Consensus 355 V~g~~~~~~~~d~~GRvkV~f~wd~~~~~~~~~S~W~Rvaqp~AG~~~G~~f~PrvG~EVlV~F~~GDp 423 (483)
T TIGR01646 355 VVGAQGEEIHTDKYGRIRVHFHWDRYGQSNDYSSCWIRVAQPWAGKNWGSLAIPRVGQEVIVGFLDGDP 423 (483)
T ss_pred EECCCCCeeccCCCCcEEEEeecCCCCCCCCCCceEEEEeccccCCCccccccCCCCCEEEEEEeCCCC
Confidence 554333477777643 222 222211 1 133333222221 223 4889999999998754
No 51
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=32.56 E-value=43 Score=25.81 Aligned_cols=28 Identities=21% Similarity=0.412 Sum_probs=24.8
Q ss_pred eeEecCCCCCccEEEECCeEEEEEEeEE
Q 027811 57 VKVNASHVRPGNVIEKSGKMYQVIDAEH 84 (218)
Q Consensus 57 ~~i~andiRkG~~I~~dG~~y~Vl~~~h 84 (218)
..+...||..|..|.+.|+.+.|.+++.
T Consensus 67 ~~y~~~Dl~vG~~v~i~gr~f~I~d~D~ 94 (104)
T smart00676 67 EYYHASDLNVGTTINVFGRQFRIYDCDE 94 (104)
T ss_pred CccCHHHcCCCCEEEEeCEEEEEEECCH
Confidence 3477899999999999999999999853
No 52
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=31.57 E-value=2.5e+02 Score=24.56 Aligned_cols=22 Identities=23% Similarity=0.427 Sum_probs=20.3
Q ss_pred CCCCCccEEEECCeEEEEEEeE
Q 027811 62 SHVRPGNVIEKSGKMYQVIDAE 83 (218)
Q Consensus 62 ndiRkG~~I~~dG~~y~Vl~~~ 83 (218)
-.|++|+.|..+|+-++|.+++
T Consensus 73 E~l~vGDei~vd~e~veITSIE 94 (201)
T COG1326 73 ETLKVGDEIEVDGEEVEITSIE 94 (201)
T ss_pred CeEecCCEEEEcCCEEEEEEEe
Confidence 5689999999999999999998
No 53
>PRK11354 kil FtsZ inhibitor protein; Reviewed
Probab=31.17 E-value=63 Score=23.78 Aligned_cols=27 Identities=19% Similarity=0.391 Sum_probs=21.5
Q ss_pred eeEecCCCCCccEEEECCeEEEEEEeE
Q 027811 57 VKVNASHVRPGNVIEKSGKMYQVIDAE 83 (218)
Q Consensus 57 ~~i~andiRkG~~I~~dG~~y~Vl~~~ 83 (218)
..+.=..+.+||.++++|+.|+.....
T Consensus 9 ~~v~Rq~V~PG~~v~~~grty~ASAN~ 35 (73)
T PRK11354 9 DEIPRQCVTPGDYVLHEGRTYIASANN 35 (73)
T ss_pred eeecccccCCceEEEEcCcEEEEEech
Confidence 345556789999999999999987653
No 54
>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=30.78 E-value=1.7e+02 Score=20.50 Aligned_cols=37 Identities=19% Similarity=0.281 Sum_probs=23.5
Q ss_pred CCCCCEEEEEecCCCcEEeeeE-----EeeEEEEEEEeCCeE
Q 027811 101 IDTGNKVSLRFGTEEAVERVFV-----EDKSFTCLYTENDTA 137 (218)
Q Consensus 101 L~TG~k~e~tf~s~dkvE~v~l-----e~k~~qyLY~Dgd~~ 137 (218)
...|.++.-+|+.+...-++.| ..+.++.+|.||+..
T Consensus 6 ~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel 47 (55)
T PF09465_consen 6 FAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTEL 47 (55)
T ss_dssp S-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EE
T ss_pred ccCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEE
Confidence 3568899999988877533333 357889999999874
No 55
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=30.55 E-value=1.5e+02 Score=27.38 Aligned_cols=53 Identities=11% Similarity=0.258 Sum_probs=40.3
Q ss_pred EecCCCCCccEEEECCeEEEEEEeEEeeCCCCCeeEEEEEeeCCCCCEEEEEecCCC
Q 027811 59 VNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDIDTGNKVSLRFGTEE 115 (218)
Q Consensus 59 i~andiRkG~~I~~dG~~y~Vl~~~h~kpGkG~A~vr~klknL~TG~k~e~tf~s~d 115 (218)
..+++++.|+.|.. +|.|.+.+-...-.|..+..+.+.| .||...-+-|...+
T Consensus 3 ~~i~~l~~g~~v~~---~~lv~~~~~~~~knG~~yl~l~l~D-~tG~I~ak~W~~~~ 55 (314)
T PRK13480 3 KGIEELEVGEQVDH---FLLIKSATKGVASNGKPFLTLILQD-KSGDIEAKLWDVSP 55 (314)
T ss_pred chHhhcCCCCEeeE---EEEEEEceeeecCCCCeEEEEEEEc-CCcEEEEEeCCCCh
Confidence 35789999986643 6677777654444488999999999 99999888886653
No 56
>PF13785 DUF4178: Domain of unknown function (DUF4178)
Probab=29.75 E-value=2.6e+02 Score=21.56 Aligned_cols=23 Identities=26% Similarity=0.378 Sum_probs=20.2
Q ss_pred CCCccEEEECCeEEEEEEeEEee
Q 027811 64 VRPGNVIEKSGKMYQVIDAEHKQ 86 (218)
Q Consensus 64 iRkG~~I~~dG~~y~Vl~~~h~k 86 (218)
|++|+++.++|+.|+|+-...-+
T Consensus 1 L~~G~~~~~~g~~~~ViG~~~~~ 23 (140)
T PF13785_consen 1 LQLGDIGRIDGKDYTVIGRIQYD 23 (140)
T ss_pred CCCCCEEEECCeEEEEEEEEEEE
Confidence 68999999999999998877653
No 57
>PF13144 SAF_2: SAF-like
Probab=29.51 E-value=1.5e+02 Score=24.48 Aligned_cols=24 Identities=21% Similarity=0.340 Sum_probs=19.7
Q ss_pred EEEEeeCCCCCEEEEEecCCCcEE
Q 027811 95 QMELRDIDTGNKVSLRFGTEEAVE 118 (218)
Q Consensus 95 r~klknL~TG~k~e~tf~s~dkvE 118 (218)
.++++|+.||+.+.-+.-+...|+
T Consensus 172 ~I~V~N~~S~k~v~g~V~~~~~V~ 195 (196)
T PF13144_consen 172 TIRVKNLSSGKIVQGRVIGPGTVE 195 (196)
T ss_pred EEEEEECCCCCEEEEEEecCCEEE
Confidence 788999999999988887666655
No 58
>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=29.16 E-value=1.5e+02 Score=23.35 Aligned_cols=26 Identities=23% Similarity=0.270 Sum_probs=22.9
Q ss_pred cCCCCCccEEEECCeEEEEEEeEEee
Q 027811 61 ASHVRPGNVIEKSGKMYQVIDAEHKQ 86 (218)
Q Consensus 61 andiRkG~~I~~dG~~y~Vl~~~h~k 86 (218)
+-+++.|..|..||+.|.|.++...-
T Consensus 74 ~~~~~~~skI~fdG~ey~V~~v~~~y 99 (114)
T PF10665_consen 74 FPDFTEGSKIVFDGKEYTVTKVNPNY 99 (114)
T ss_pred ccccCCCCEEEECCceEEEEEEEecc
Confidence 35889999999999999999998755
No 59
>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=29.13 E-value=1.3e+02 Score=24.90 Aligned_cols=46 Identities=20% Similarity=0.371 Sum_probs=29.8
Q ss_pred eeeeEecCCCCCccEEEECCeEEEEEEeEEeeCCCCCeeEEEEEeeC
Q 027811 55 RAVKVNASHVRPGNVIEKSGKMYQVIDAEHKQRGRGGAMMQMELRDI 101 (218)
Q Consensus 55 R~~~i~andiRkG~~I~~dG~~y~Vl~~~h~kpGkG~A~vr~klknL 101 (218)
|+.......-.++-++.+|| +|+|+++...+-..|....+.+|+-+
T Consensus 107 R~~~~~~~~ap~~g~yrYDG-LY~V~~~w~~~g~~G~~v~kF~L~R~ 152 (155)
T PF02182_consen 107 RGYKLKSSYAPKGGIYRYDG-LYKVVKYWREKGKSGFKVFKFKLVRL 152 (155)
T ss_dssp EEGGGGGTTS-SSS-EEEEE-EEEEEEEEEEE-TTSSEEEEEEEEE-
T ss_pred eecCCCCccCCcCCCEEeCc-EEEEEEEEEEeCCCCcEEEEEEEEEC
Confidence 33333333335566788988 99999999876555777888888755
No 60
>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=28.40 E-value=3e+02 Score=21.81 Aligned_cols=65 Identities=11% Similarity=0.241 Sum_probs=46.6
Q ss_pred EEEEEeCCeEEEecCCCccccccCchhhhhhhhhcCCCCEEEEEEE-CCEEEEEeCCCeEEEEEEEeC
Q 027811 128 TCLYTENDTAFVIESETFEQLEVPLDVFGKAGAYLQEGMKVWLQLY-DGRALSGSIPKRVACTIKEIH 194 (218)
Q Consensus 128 qyLY~Dgd~~vFMD~ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~~-eg~~i~V~LP~~V~l~V~ete 194 (218)
.....+.++. -...+=|++|-||++.|-+...| .++..+-++-+ ++.-+-+++-..|-++|.+..
T Consensus 10 ~I~~~~~~Gi-~vslgFFddI~IP~~~L~~ps~f-d~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 10 KIKSSTAEGI-RVSLGFFDDIFIPPSLLPEPSRF-DEEEQAWVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp EEEEEETTEE-EEEECCEEEEEEECCCC-TTEEE-ECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred EEEecCCCcE-EEEecccccEEECHHHCCCCCcc-CccCCEEEEECCCCceeEccCCCEEEEEEeEEE
Confidence 3444555543 33446799999999999887777 66678888888 889999999999988887653
No 61
>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=28.39 E-value=74 Score=23.25 Aligned_cols=57 Identities=12% Similarity=0.262 Sum_probs=39.2
Q ss_pred CCeeEEEEEeeCCCCCEEEEEecCCCcEEe--------eeEEeeEEEEEEEeCCeEEEecCCCcccccc
Q 027811 90 GGAMMQMELRDIDTGNKVSLRFGTEEAVER--------VFVEDKSFTCLYTENDTAFVIESETFEQLEV 150 (218)
Q Consensus 90 G~A~vr~klknL~TG~k~e~tf~s~dkvE~--------v~le~k~~qyLY~Dgd~~vFMD~ETyEQi~v 150 (218)
-..+|++++++. +|+.+....+.+++++. ..+......|+| +|. .+.|.+|-+++.+
T Consensus 8 ~~~~i~I~v~~~-~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f-~G~--~L~~~~T~~~l~m 72 (87)
T cd01763 8 ISEHINLKVKGQ-DGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLF-DGQ--RIRDNQTPDDLGM 72 (87)
T ss_pred CCCeEEEEEECC-CCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEE-CCe--ECCCCCCHHHcCC
Confidence 467899999999 89999999999998764 344555666666 443 3444455444443
No 62
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.31 E-value=90 Score=24.64 Aligned_cols=23 Identities=30% Similarity=0.561 Sum_probs=16.0
Q ss_pred cCCCCCccEEEECCe--EEEEEEeE
Q 027811 61 ASHVRPGNVIEKSGK--MYQVIDAE 83 (218)
Q Consensus 61 andiRkG~~I~~dG~--~y~Vl~~~ 83 (218)
--++++|++|..+|. +.+|+++.
T Consensus 31 rr~ik~GD~IiF~~~~l~v~V~~vr 55 (111)
T COG4043 31 RRQIKPGDKIIFNGDKLKVEVIDVR 55 (111)
T ss_pred hcCCCCCCEEEEcCCeeEEEEEEEe
Confidence 457899999999974 33444444
No 63
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=26.49 E-value=1.8e+02 Score=22.32 Aligned_cols=48 Identities=15% Similarity=0.075 Sum_probs=27.2
Q ss_pred hhcCCCCEEEEEEECCEEEEEeCCCeEEEEEEEeCCCCCCc----cCCCCcccEEEEeecc
Q 027811 160 AYLQEGMKVWLQLYDGRALSGSIPKRVACTIKEIHASTKGP----TVTPRYGPTISKHIEG 216 (218)
Q Consensus 160 ~fL~eg~~V~V~~~eg~~i~V~LP~~V~l~V~etep~vKGd----Tat~~~K~A~Let~~~ 216 (218)
+-|++|..|.|..- ++. .+++|.+.+---+.+ ......+..||-||.+
T Consensus 63 ~~l~~Gd~v~v~~~-~~~--------~~Y~V~~~~~v~~~~~~~~~~~~~~~~LtLiTC~~ 114 (128)
T cd00004 63 DNLKKGDKIYLTDG-GKT--------YVYKVTSILTVTPTDVVVVNPPTGDPILTLITCTP 114 (128)
T ss_pred HHCCCCCEEEEEEC-CEE--------EEEEEEEEEEECCCceEEeccCCCCCEEEEEEcCC
Confidence 34678888887653 332 334444333222222 2234568999999987
No 64
>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=25.76 E-value=67 Score=25.48 Aligned_cols=27 Identities=19% Similarity=0.300 Sum_probs=15.6
Q ss_pred eEecCCCCCccEE-EECCeEEEEEEeEE
Q 027811 58 KVNASHVRPGNVI-EKSGKMYQVIDAEH 84 (218)
Q Consensus 58 ~i~andiRkG~~I-~~dG~~y~Vl~~~h 84 (218)
-+.|.+|++|+.| ..+|+...|.+...
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 3569999999998 45888877777654
No 65
>TIGR01363 strep_his_triad streptococcal histidine triad protein. This model represents the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Three repeats are found in the seed alignment. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice.
Probab=25.33 E-value=30 Score=32.24 Aligned_cols=22 Identities=27% Similarity=0.552 Sum_probs=19.3
Q ss_pred cCCCCCccEEEECCeEEEEEEe
Q 027811 61 ASHVRPGNVIEKSGKMYQVIDA 82 (218)
Q Consensus 61 andiRkG~~I~~dG~~y~Vl~~ 82 (218)
.++++.|=+|+++|+.|..++-
T Consensus 118 v~e~~~GYvIkv~~~Yy~ylKd 139 (348)
T TIGR01363 118 VNEIKGGYVIKVNGKYYVYLKD 139 (348)
T ss_pred HhhhcCceEEEECCEEEEEEcC
Confidence 5899999999999999987654
No 66
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=25.32 E-value=99 Score=22.18 Aligned_cols=30 Identities=20% Similarity=0.367 Sum_probs=22.7
Q ss_pred ccccCchhhhhhhhhcCCCCEEEEEEECCEEE
Q 027811 147 QLEVPLDVFGKAGAYLQEGMKVWLQLYDGRAL 178 (218)
Q Consensus 147 Qi~v~~d~lg~~~~fL~eg~~V~V~~~eg~~i 178 (218)
.+.||++++. ... |.+|.+|.+...+|..+
T Consensus 11 ~vtIPk~i~~-~lg-l~~Gd~v~v~~~~~~ii 40 (74)
T TIGR02609 11 VVTLPKEVLE-SLG-LKEGDTLYVDEEEGGLK 40 (74)
T ss_pred EEEECHHHHH-HcC-cCCCCEEEEEEECCEEE
Confidence 5688998874 333 79999999988887643
No 67
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=24.46 E-value=1.9e+02 Score=30.99 Aligned_cols=79 Identities=20% Similarity=0.285 Sum_probs=58.3
Q ss_pred eCCCCCEEEEEecCCCcEEeeeEEeeEEEEEE--EeCCeEEEecC--CCccccccCchhhhhhhhhcCCCCEEEEEE--E
Q 027811 100 DIDTGNKVSLRFGTEEAVERVFVEDKSFTCLY--TENDTAFVIES--ETFEQLEVPLDVFGKAGAYLQEGMKVWLQL--Y 173 (218)
Q Consensus 100 nL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY--~Dgd~~vFMD~--ETyEQi~v~~d~lg~~~~fL~eg~~V~V~~--~ 173 (218)
-+.+.++....|..+|.||++.-|-+.++-.- .||+..+.|-. .--+.++++..-| .+|+++|.-|+|.- |
T Consensus 397 t~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eL---rKyF~~GDhVKVi~G~~ 473 (1024)
T KOG1999|consen 397 TLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASEL---RKYFEPGDHVKVIAGRY 473 (1024)
T ss_pred eeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhh---hhhccCCCeEEEEeccc
Confidence 66778888888999999999999998876544 47777777654 2355677776555 68999999888876 5
Q ss_pred CC---EEEEEe
Q 027811 174 DG---RALSGS 181 (218)
Q Consensus 174 eg---~~i~V~ 181 (218)
+| -+|.|+
T Consensus 474 eG~tGlVvrVe 484 (1024)
T KOG1999|consen 474 EGDTGLVVRVE 484 (1024)
T ss_pred cCCcceEEEEe
Confidence 54 344444
No 68
>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=22.97 E-value=42 Score=25.69 Aligned_cols=21 Identities=14% Similarity=0.482 Sum_probs=15.9
Q ss_pred eeEecCCCCCccEEEECCeEE
Q 027811 57 VKVNASHVRPGNVIEKSGKMY 77 (218)
Q Consensus 57 ~~i~andiRkG~~I~~dG~~y 77 (218)
.+|.+++|++||+|..-..+|
T Consensus 3 kkI~v~~L~~GM~V~~~~~~w 23 (128)
T PF11871_consen 3 KKIPVDQLKPGMYVSRLDRSW 23 (128)
T ss_pred eEEEHHHCCCCcEEEecCCCc
Confidence 368899999999997644443
No 69
>PF14306 PUA_2: PUA-like domain; PDB: 1M8P_C 1I2D_B 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2QJF_A 2OFX_B 1J70_B 1G8F_A ....
Probab=22.66 E-value=45 Score=27.78 Aligned_cols=43 Identities=30% Similarity=0.405 Sum_probs=26.7
Q ss_pred EEecCCCccccc----c--------C--chhhhhhhhhcCCCCEEEEEEECCEEEEE
Q 027811 138 FVIESETFEQLE----V--------P--LDVFGKAGAYLQEGMKVWLQLYDGRALSG 180 (218)
Q Consensus 138 vFMD~ETyEQi~----v--------~--~d~lg~~~~fL~eg~~V~V~~~eg~~i~V 180 (218)
-||+.+.|+++. + | .+.-.+.++=|++|..|.+..-+|+++++
T Consensus 55 GFM~~~dy~~V~~~~rL~~G~~wpiPI~L~v~~e~~~~l~~G~~v~L~~~~G~~~a~ 111 (160)
T PF14306_consen 55 GFMNEEDYESVLETMRLPDGTLWPIPIVLDVSEEEAKSLKEGDKVALRDPEGKPVAI 111 (160)
T ss_dssp EE--HHHHHHHHHHSBETTSSB--S---EEECHHHHTTCTTTSEEEEEETTTEEEEE
T ss_pred cccCHHHHHHHHhhCCcCCCCEEeEEEEEECCHHHHHhccCCCEEEEECCCCCEEEE
Confidence 588888777652 1 1 12222333448999999998777999884
No 70
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=22.50 E-value=4.1e+02 Score=21.27 Aligned_cols=65 Identities=26% Similarity=0.358 Sum_probs=42.2
Q ss_pred EecCCCCCccEEEE-----CCeEEEEEEeEEe---eCCCCCeeEEEEEeeCCCCCEEEEEecCCC-cEEeeeEEe
Q 027811 59 VNASHVRPGNVIEK-----SGKMYQVIDAEHK---QRGRGGAMMQMELRDIDTGNKVSLRFGTEE-AVERVFVED 124 (218)
Q Consensus 59 i~andiRkG~~I~~-----dG~~y~Vl~~~h~---kpGkG~A~vr~klknL~TG~k~e~tf~s~d-kvE~v~le~ 124 (218)
-.+.++++||.|.. +|.-.++-.|+-+ ..|+|-. =..-++.+..|-=+|.+|+-.- .+|.+++-+
T Consensus 16 ~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~-~tftvRkis~G~GVEr~Fp~~SP~Ie~IeV~r 89 (115)
T COG0335 16 KDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGIS-ETFTVRKISYGVGVERVFPLHSPLIESIEVVR 89 (115)
T ss_pred hhCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCcc-ceEEEEEeecCceEEEEeecCCCceeEEEEEe
Confidence 34788899988764 5666666666632 2343322 2456778899999999997643 355555544
No 71
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=22.18 E-value=3.2e+02 Score=21.49 Aligned_cols=55 Identities=18% Similarity=0.110 Sum_probs=26.9
Q ss_pred hhhcCCCCEEEEEEECCE----EEE--EeCCCeEEEEEEEeCCCCCCccCCCCcccEEEEeeccc
Q 027811 159 GAYLQEGMKVWLQLYDGR----ALS--GSIPKRVACTIKEIHASTKGPTVTPRYGPTISKHIEGL 217 (218)
Q Consensus 159 ~~fL~eg~~V~V~~~eg~----~i~--V~LP~~V~l~V~etep~vKGdTat~~~K~A~Let~~~~ 217 (218)
.+-|++|+.|.+...++. +.+ +.-|..+ .+.+..++ +...++..+..||-||++-
T Consensus 63 L~~l~~Gd~i~v~~~~~~~~Y~V~~~~~v~~~~~--~~~~~~~~--~~~~~~~~~~LTLiTC~~~ 123 (137)
T cd05830 63 LDKLRPGDKIVVETADGWYTYVVRSSEIVLPTDV--EVIAPVPG--QPGAEPTDRYLTLTTCHPK 123 (137)
T ss_pred HhhCCCCCEEEEEECCeEEEEEEeEEEEECCCcc--eEeeecCC--CcCCCCCCCEEEEEeeCCC
Confidence 345789998888654432 111 1222222 11111111 1112334578999999874
No 72
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=21.69 E-value=86 Score=22.92 Aligned_cols=29 Identities=10% Similarity=0.211 Sum_probs=21.3
Q ss_pred CCCeeEEEEEeeCCCCCEEEEEecCCCcEEee
Q 027811 89 RGGAMMQMELRDIDTGNKVSLRFGTEEAVERV 120 (218)
Q Consensus 89 kG~A~vr~klknL~TG~k~e~tf~s~dkvE~v 120 (218)
+|...++++ +-+|+.++.+|.++++++.+
T Consensus 2 ~~~~~i~iR---lP~G~r~~rrF~~t~~L~~l 30 (80)
T cd01771 2 EPISKLRVR---TPSGDFLERRFLGDTPLQVL 30 (80)
T ss_pred CCeEEEEEE---CCCCCEEEEEeCCCCcHHHH
Confidence 344444444 56899999999999998754
No 73
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=21.31 E-value=6.7e+02 Score=24.03 Aligned_cols=116 Identities=18% Similarity=0.237 Sum_probs=60.1
Q ss_pred eEecCCCCCccEEEECCe-------EEEEEEeEEeeCC--------CCCeeEEEEEeeCCCCCEEEEEecCCC-------
Q 027811 58 KVNASHVRPGNVIEKSGK-------MYQVIDAEHKQRG--------RGGAMMQMELRDIDTGNKVSLRFGTEE------- 115 (218)
Q Consensus 58 ~i~andiRkG~~I~~dG~-------~y~Vl~~~h~kpG--------kG~A~vr~klknL~TG~k~e~tf~s~d------- 115 (218)
..++-.|++|..|.+.|. -|.|++++|.--. -+...++.++.=+-... .|++..
T Consensus 283 ~s~~~~l~~G~~~~l~~~~~~~~~g~ylVt~v~H~~~~~~~~~~~~~~~~~y~~~f~~ip~~~----~~rp~~~~~~P~i 358 (513)
T TIGR03361 283 ESNCRRLAPGYLFTLSGHPRAALNREYLVVSVHHHGRQPQVLEESGGSGAGYRNSFQCIPADV----PFRPPRRTPKPRI 358 (513)
T ss_pred EeCcCeEcCCCEEEeCCCCCcccCCCEEEEEEEEEEEeCcccccccCCCceEEEEEEEEECCC----cccCCCCCCCCcC
Confidence 344568999999999764 3999999996520 12234444443333222 222211
Q ss_pred -cEEeeeEEeeEEEEEEEeCCe---EEEe-cCC----Cccc--cccCchhhhhh--hhh-cCCCCEEEEEEECCEE
Q 027811 116 -AVERVFVEDKSFTCLYTENDT---AFVI-ESE----TFEQ--LEVPLDVFGKA--GAY-LQEGMKVWLQLYDGRA 177 (218)
Q Consensus 116 -kvE~v~le~k~~qyLY~Dgd~---~vFM-D~E----TyEQ--i~v~~d~lg~~--~~f-L~eg~~V~V~~~eg~~ 177 (218)
-+..+.|...+-+.+|.|+.+ ..|. |.+ ..+. +.+-...-|.. .-| ...|++|-|.|.+|.|
T Consensus 359 ~G~q~A~V~g~~~~~i~~D~~GRvkV~f~wd~~~~~~~~~S~wvRvaqp~AG~~~G~~f~PrvG~EVlV~F~~GDp 434 (513)
T TIGR03361 359 DGPQTATVVGPAGEEIYTDEYGRVKVQFHWDRYGKRDEKSSCWVRVAQPWAGNGWGSVAIPRVGQEVVVDFLEGDP 434 (513)
T ss_pred CCCeEEEEECCCCCEEeECCCCCEEEEecccCCCCCCCCCceEEEecccccCCCcccccCCCCCCEEEEEEcCCCC
Confidence 144555555444556666533 1222 111 1111 22222222221 223 3789999999998754
No 74
>KOG0272 consensus U4/U6 small nuclear ribonucleoprotein Prp4 (contains WD40 repeats) [RNA processing and modification]
Probab=21.06 E-value=2e+02 Score=28.04 Aligned_cols=90 Identities=14% Similarity=0.095 Sum_probs=55.4
Q ss_pred CCCCCCCccccccccccceeeeeeeeEecCCCCCccEEE-ECCeEEEEEEeEEeeCCC----CCeeEEEEEeeCCCCCEE
Q 027811 33 CHRSSGDRDTCLLRFPWSATQQRAVKVNASHVRPGNVIE-KSGKMYQVIDAEHKQRGR----GGAMMQMELRDIDTGNKV 107 (218)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~R~~~i~andiRkG~~I~-~dG~~y~Vl~~~h~kpGk----G~A~vr~klknL~TG~k~ 107 (218)
++-.||++++.-+++--..| |+|.|..|+ .+|-.-+|..+.++.-|- |++-..+|+=||.-.+-.
T Consensus 311 f~~DGSL~~tGGlD~~~RvW----------DlRtgr~im~L~gH~k~I~~V~fsPNGy~lATgs~Dnt~kVWDLR~r~~l 380 (459)
T KOG0272|consen 311 FQPDGSLAATGGLDSLGRVW----------DLRTGRCIMFLAGHIKEILSVAFSPNGYHLATGSSDNTCKVWDLRMRSEL 380 (459)
T ss_pred ecCCCceeeccCccchhhee----------ecccCcEEEEecccccceeeEeECCCceEEeecCCCCcEEEeeecccccc
Confidence 45567888888777654443 556666663 467777888888776554 666667777777766664
Q ss_pred EEEecCCCcEEeeeEEeeEEEEEEE
Q 027811 108 SLRFGTEEAVERVFVEDKSFTCLYT 132 (218)
Q Consensus 108 e~tf~s~dkvE~v~le~k~~qyLY~ 132 (218)
...-...+-|..|..+...-.||-.
T Consensus 381 y~ipAH~nlVS~Vk~~p~~g~fL~T 405 (459)
T KOG0272|consen 381 YTIPAHSNLVSQVKYSPQEGYFLVT 405 (459)
T ss_pred eecccccchhhheEecccCCeEEEE
Confidence 3333333445566655544444443
No 75
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=20.75 E-value=68 Score=27.19 Aligned_cols=34 Identities=29% Similarity=0.401 Sum_probs=26.0
Q ss_pred EEEEEeCCeEEEecCCCccccccCchhhhhhhhh
Q 027811 128 TCLYTENDTAFVIESETFEQLEVPLDVFGKAGAY 161 (218)
Q Consensus 128 qyLY~Dgd~~vFMD~ETyEQi~v~~d~lg~~~~f 161 (218)
+=+|.|++.++|+|+|.--...++.|.|.....|
T Consensus 130 TGI~~dg~~i~~~DP~~gP~~~m~l~~fn~~~~w 163 (166)
T PF12385_consen 130 TGIDGDGDSIHVHDPEQGPNLRMSLDMFNQALAW 163 (166)
T ss_pred EeecCCCCeEEecCcccCCCceecHHHHhhhhcc
Confidence 5568888999999999877777777777554443
No 76
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.41 E-value=2.6e+02 Score=23.07 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=19.3
Q ss_pred EEEEeeCCCCCEEEEEecCCCcEE
Q 027811 95 QMELRDIDTGNKVSLRFGTEEAVE 118 (218)
Q Consensus 95 r~klknL~TG~k~e~tf~s~dkvE 118 (218)
.++.||+.+|+.+.-+....-.|.
T Consensus 133 ~IrVrN~~Sgkiv~g~V~~~g~V~ 156 (160)
T PRK06005 133 LIRVRNVDSGVIVSGTVLADGTIQ 156 (160)
T ss_pred EEEEEECCCCCEEEEEEecCCEEE
Confidence 789999999999988876655544
No 77
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=20.34 E-value=1.2e+02 Score=31.29 Aligned_cols=87 Identities=20% Similarity=0.245 Sum_probs=46.8
Q ss_pred hHHHHHH-----HhhhhccccccccCCCCCCCCCCCCCCCCcccccccc---------cccee------eeeeeeEecCC
Q 027811 4 VEVSKRL-----SRALFSFSSYSRSLPNFLPSPDCHRSSGDRDTCLLRF---------PWSAT------QQRAVKVNASH 63 (218)
Q Consensus 4 ~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~------~~R~~~i~and 63 (218)
++|+|.| .+-|-+|++.+-+-|..++.+.-++=-|+.--..+++ -|.++ -.|.|-.-++.
T Consensus 476 ~EhQK~L~~k~~~egL~rf~~a~~~gpds~~~~~~kr~esY~rdSqlP~~i~elRi~VD~~~qsIilPI~grpVPFHiss 555 (1001)
T COG5406 476 VEHQKELLDKIIEEGLERFRNASDAGPDSIEEKSEKRIESYSRDSQLPRQIGELRIIVDFARQSIILPIGGRPVPFHISS 555 (1001)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhcccCCccccchhhhhhccccccccccccccceEEEEEeccceEEEeecCcccceeehh
Confidence 3556554 3678888877765555444432222222222222221 12221 13556666777
Q ss_pred CCCccEEEECCeEEEEEEeEEeeCCCCCe
Q 027811 64 VRPGNVIEKSGKMYQVIDAEHKQRGRGGA 92 (218)
Q Consensus 64 iRkG~~I~~dG~~y~Vl~~~h~kpGkG~A 92 (218)
+|.|..= |..-|..+...+..||+|++
T Consensus 556 ~Knaskn--deg~~~yLRlNF~spg~~gg 582 (1001)
T COG5406 556 IKNASKN--DEGNFVYLRLNFKSPGKGGG 582 (1001)
T ss_pred hcccccc--CCCceEEEEEeccCCCCCCC
Confidence 8777643 33456777788888888665
No 78
>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=20.29 E-value=76 Score=25.45 Aligned_cols=26 Identities=15% Similarity=0.210 Sum_probs=18.1
Q ss_pred EecCCCCCccEEEECCeEEEEEEeEEeeC
Q 027811 59 VNASHVRPGNVIEKSGKMYQVIDAEHKQR 87 (218)
Q Consensus 59 i~andiRkG~~I~~dG~~y~Vl~~~h~kp 87 (218)
..+..||+++.+.+.|+.|.|-+ +.|
T Consensus 70 ~dv~~L~r~DtL~I~g~~y~Vd~---v~p 95 (117)
T PF05354_consen 70 ADVSGLKRRDTLTIGGESYWVDR---VGP 95 (117)
T ss_dssp CCCCTS-TT-EEEETTTEEEBS------S
T ss_pred hHhhhhhcCCeEEECCEEEEEEe---ecc
Confidence 34788999999999999999944 555
No 79
>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=20.25 E-value=1.5e+02 Score=24.80 Aligned_cols=27 Identities=33% Similarity=0.583 Sum_probs=0.0
Q ss_pred cCCCCCccEEEE---CCeE--EEEEEeEEeeC
Q 027811 61 ASHVRPGNVIEK---SGKM--YQVIDAEHKQR 87 (218)
Q Consensus 61 andiRkG~~I~~---dG~~--y~Vl~~~h~kp 87 (218)
..+|++|+.|.+ +|+. |+|.+.+.+.|
T Consensus 106 L~~L~~GD~I~v~~~~g~~~~Y~V~~~~iV~~ 137 (174)
T TIGR03784 106 LQELRPGDVIRLQTPDGQWQSYQVTATRVVDE 137 (174)
T ss_pred hhhCCCCCEEEEEECCCeEEEEEEeEEEEECC
No 80
>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=20.21 E-value=61 Score=27.03 Aligned_cols=54 Identities=11% Similarity=0.285 Sum_probs=35.2
Q ss_pred EEEEeeCCCCCEEEEEecCCCcEEeeeEEeeEEEEEEEe--CCeEEEecCCCcccccc
Q 027811 95 QMELRDIDTGNKVSLRFGTEEAVERVFVEDKSFTCLYTE--NDTAFVIESETFEQLEV 150 (218)
Q Consensus 95 r~klknL~TG~k~e~tf~s~dkvE~v~le~k~~qyLY~D--gd~~vFMD~ETyEQi~v 150 (218)
.+.|.|+.||...+.+|..+-.+....+.+ ..++-.| .+..+-||+..||.+..
T Consensus 7 ~L~l~~~hTgE~~~~~y~~~g~y~~~al~~--l~~~lRD~r~~~~~~iDp~L~d~L~~ 62 (152)
T PF05951_consen 7 SLSLYNLHTGERLDIVYWADGRYDPEALAQ--LNHLLRDHRTNEVHPIDPRLLDLLYE 62 (152)
T ss_pred EEEEEeCCCCCEEEEEEecCCEECHHHHHH--HHHHHcCCCCCCceecCHHHHHHHHH
Confidence 789999999999999987665554444332 2223333 24567888876655443
Done!