Query 023552
Match_columns 280
No_of_seqs 119 out of 149
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 04:55:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023552.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023552hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK03954 ribonuclease P protei 99.9 6.2E-23 1.3E-27 170.9 7.8 88 39-142 17-106 (121)
2 COG2023 RPR2 RNase P subunit R 99.9 2.1E-22 4.5E-27 164.5 7.5 85 39-142 9-95 (105)
3 PF04032 Rpr2: RNAse P Rpr2/Rp 99.9 4.8E-22 1E-26 150.4 8.6 82 42-137 1-85 (85)
4 KOG4394 RNase P subunit that i 99.5 2E-14 4.4E-19 118.4 5.4 105 35-148 5-112 (116)
5 PF02150 RNA_POL_M_15KD: RNA p 78.4 1 2.2E-05 30.4 0.8 31 87-141 2-32 (35)
6 PF10122 Mu-like_Com: Mu-like 77.1 1.9 4.1E-05 32.1 2.0 36 86-144 4-39 (51)
7 PF10058 DUF2296: Predicted in 76.4 2.1 4.6E-05 31.5 2.1 31 86-139 22-54 (54)
8 PF07754 DUF1610: Domain of un 74.8 2.6 5.7E-05 26.9 2.0 12 126-137 13-24 (24)
9 PF01927 Mut7-C: Mut7-C RNAse 72.3 7.2 0.00016 33.0 4.7 65 66-142 69-137 (147)
10 PF04810 zf-Sec23_Sec24: Sec23 70.4 1.7 3.8E-05 29.7 0.5 34 88-142 4-37 (40)
11 KOG2846 Predicted membrane pro 70.3 18 0.00039 35.7 7.4 25 125-149 238-262 (328)
12 PF04690 YABBY: YABBY protein; 69.9 1.6 3.4E-05 39.1 0.2 34 86-138 12-45 (170)
13 PF01921 tRNA-synt_1f: tRNA sy 68.4 6 0.00013 39.1 3.9 56 69-142 152-212 (360)
14 COG3478 Predicted nucleic-acid 67.2 6 0.00013 31.0 2.9 38 87-140 5-51 (68)
15 cd00674 LysRS_core_class_I cat 66.5 9.7 0.00021 37.2 4.8 36 86-141 169-204 (353)
16 smart00661 RPOL9 RNA polymeras 66.2 6.4 0.00014 27.1 2.6 33 87-142 1-33 (52)
17 TIGR00467 lysS_arch lysyl-tRNA 64.9 11 0.00024 38.7 5.0 35 86-141 168-202 (515)
18 PF04502 DUF572: Family of unk 64.0 10 0.00022 36.3 4.4 56 85-148 39-96 (324)
19 PRK00750 lysK lysyl-tRNA synth 62.9 12 0.00026 38.0 4.9 37 86-141 175-211 (510)
20 COG1594 RPB9 DNA-directed RNA 62.6 6.1 0.00013 32.8 2.3 36 86-144 2-37 (113)
21 PRK00398 rpoP DNA-directed RNA 61.4 7.6 0.00017 26.9 2.3 15 129-143 21-35 (46)
22 COG1579 Zn-ribbon protein, pos 60.9 3.7 8.1E-05 38.5 0.8 58 60-138 173-230 (239)
23 COG1656 Uncharacterized conser 54.4 10 0.00022 34.1 2.4 67 68-146 77-147 (165)
24 KOG1986 Vesicle coat complex C 51.9 9.2 0.0002 41.1 2.0 50 86-156 53-102 (745)
25 PF14803 Nudix_N_2: Nudix N-te 50.7 14 0.00031 25.0 2.1 32 87-139 1-32 (34)
26 PF01430 HSP33: Hsp33 protein; 50.4 9.2 0.0002 35.6 1.6 17 125-141 262-278 (280)
27 COG1384 LysS Lysyl-tRNA synthe 49.8 28 0.0006 36.3 5.0 97 25-141 84-206 (521)
28 PRK00241 nudC NADH pyrophospha 49.7 12 0.00026 34.7 2.2 14 86-99 99-112 (256)
29 TIGR01384 TFS_arch transcripti 48.3 14 0.00031 29.1 2.2 13 87-99 1-13 (104)
30 COG1198 PriA Primosomal protei 47.8 16 0.00035 39.2 3.1 39 86-140 435-473 (730)
31 PLN00162 transport protein sec 47.7 15 0.00033 39.2 2.9 37 87-144 54-90 (761)
32 PRK00432 30S ribosomal protein 47.3 13 0.00028 26.9 1.6 14 86-99 20-34 (50)
33 PF09855 DUF2082: Nucleic-acid 45.8 29 0.00063 26.5 3.4 19 126-144 33-51 (64)
34 PF07282 OrfB_Zn_ribbon: Putat 44.8 41 0.00089 24.5 4.0 47 67-138 4-55 (69)
35 KOG2691 RNA polymerase II subu 42.9 16 0.00034 31.1 1.7 33 86-139 4-36 (113)
36 COG4321 Uncharacterized protei 42.1 8.2 0.00018 32.3 -0.1 13 252-264 34-46 (102)
37 cd00498 Hsp33 Heat shock prote 41.9 14 0.00031 34.4 1.5 17 125-141 258-274 (275)
38 COG2888 Predicted Zn-ribbon RN 41.7 23 0.00049 27.3 2.2 19 86-104 9-27 (61)
39 PRK01402 hslO Hsp33-like chape 39.8 16 0.00036 35.4 1.6 18 125-142 304-321 (328)
40 PRK00114 hslO Hsp33-like chape 39.5 16 0.00035 34.4 1.4 19 125-143 264-282 (293)
41 PF02591 DUF164: Putative zinc 39.2 7.4 0.00016 27.9 -0.7 35 85-138 21-55 (56)
42 PF13453 zf-TFIIB: Transcripti 39.1 38 0.00082 22.9 2.8 18 126-143 16-33 (41)
43 PF13717 zinc_ribbon_4: zinc-r 38.9 21 0.00045 24.0 1.5 14 125-138 21-34 (36)
44 PRK04136 rpl40e 50S ribosomal 37.0 20 0.00042 26.5 1.2 15 85-99 13-27 (48)
45 PHA02130 hypothetical protein 35.6 21 0.00045 28.4 1.2 28 250-278 12-39 (81)
46 KOG4217 Nuclear receptors of t 34.3 22 0.00048 37.1 1.6 38 131-170 323-370 (605)
47 KOG2989 Uncharacterized conser 33.7 25 0.00053 33.6 1.6 64 83-152 37-100 (253)
48 PF12773 DZR: Double zinc ribb 33.4 23 0.0005 24.3 1.1 14 84-97 10-23 (50)
49 COG2816 NPY1 NTP pyrophosphohy 33.1 34 0.00073 33.0 2.5 40 85-149 110-149 (279)
50 COG4888 Uncharacterized Zn rib 32.8 61 0.0013 27.4 3.6 38 83-139 19-56 (104)
51 PF14599 zinc_ribbon_6: Zinc-r 32.8 19 0.00042 27.3 0.6 47 70-141 10-60 (61)
52 smart00659 RPOLCX RNA polymera 31.5 26 0.00056 24.8 1.1 15 128-142 1-15 (44)
53 PF04981 NMD3: NMD3 family ; 31.2 26 0.00057 31.8 1.4 24 79-102 28-51 (236)
54 PRK14892 putative transcriptio 31.1 52 0.0011 27.1 2.9 33 85-139 20-52 (99)
55 TIGR00595 priA primosomal prot 30.9 35 0.00075 34.6 2.3 40 86-141 213-252 (505)
56 PF13408 Zn_ribbon_recom: Reco 29.9 45 0.00097 23.0 2.1 39 130-170 6-44 (58)
57 TIGR01385 TFSII transcription 29.9 1.3E+02 0.0028 29.0 5.8 41 86-141 258-298 (299)
58 TIGR00375 conserved hypothetic 29.8 20 0.00042 35.6 0.3 48 79-153 230-280 (374)
59 COG5134 Uncharacterized conser 29.0 55 0.0012 31.2 3.1 72 86-163 42-121 (272)
60 COG4332 Uncharacterized protei 28.9 41 0.00089 31.1 2.2 42 86-141 17-61 (203)
61 cd00729 rubredoxin_SM Rubredox 28.5 32 0.00069 22.9 1.1 13 128-140 1-13 (34)
62 PRK14873 primosome assembly pr 28.3 42 0.0009 35.5 2.4 22 86-108 383-404 (665)
63 KOG0970 DNA polymerase alpha, 27.2 59 0.0013 37.3 3.4 90 39-146 1179-1274(1429)
64 PF01641 SelR: SelR domain; I 24.8 94 0.002 26.6 3.5 39 86-137 37-94 (124)
65 COG5028 Vesicle coat complex C 24.3 36 0.00077 37.3 1.1 40 87-147 200-239 (861)
66 PF01873 eIF-5_eIF-2B: Domain 23.8 96 0.0021 26.3 3.4 14 126-139 111-124 (125)
67 PF13719 zinc_ribbon_5: zinc-r 23.4 49 0.0011 22.2 1.3 13 127-139 23-35 (37)
68 PF09297 zf-NADH-PPase: NADH p 23.4 51 0.0011 21.2 1.3 13 86-98 3-15 (32)
69 PRK05580 primosome assembly pr 23.2 56 0.0012 34.3 2.2 21 86-107 381-401 (679)
70 PF14319 Zn_Tnp_IS91: Transpos 22.7 78 0.0017 26.0 2.6 28 125-155 38-65 (111)
71 COG3058 FdhE Uncharacterized p 22.7 1E+02 0.0023 30.2 3.7 50 84-139 183-235 (308)
72 PF13467 RHH_4: Ribbon-helix-h 22.6 44 0.00095 25.8 1.0 14 253-266 22-35 (67)
73 smart00653 eIF2B_5 domain pres 22.4 1.1E+02 0.0024 25.4 3.4 44 68-138 66-110 (110)
74 COG1998 RPS31 Ribosomal protei 22.2 65 0.0014 24.1 1.8 13 85-97 18-32 (51)
75 PF04828 GFA: Glutathione-depe 22.2 34 0.00073 25.1 0.3 16 82-97 44-59 (92)
76 PRK03988 translation initiatio 21.9 1.1E+02 0.0025 26.4 3.5 34 86-141 102-135 (138)
77 PRK00222 methionine sulfoxide 21.6 1.2E+02 0.0025 26.8 3.5 12 86-97 43-54 (142)
78 COG2051 RPS27A Ribosomal prote 21.3 55 0.0012 25.7 1.3 26 126-151 35-60 (67)
79 COG1281 Disulfide bond chapero 20.9 52 0.0011 31.9 1.3 17 126-142 263-279 (286)
80 COG3809 Uncharacterized protei 20.8 60 0.0013 26.5 1.5 40 87-149 2-41 (88)
81 PTZ00396 Casein kinase II subu 20.6 3.6E+02 0.0077 25.7 6.8 62 69-150 106-169 (251)
82 PF01020 Ribosomal_L40e: Ribos 20.4 61 0.0013 24.3 1.3 26 71-100 6-31 (52)
83 PF01096 TFIIS_C: Transcriptio 20.4 58 0.0012 22.2 1.1 13 127-139 26-38 (39)
84 KOG3507 DNA-directed RNA polym 20.2 72 0.0016 24.7 1.7 17 125-141 16-32 (62)
85 PF13005 zf-IS66: zinc-finger 20.1 1.3E+02 0.0027 20.4 2.8 21 87-107 3-25 (47)
86 COG4481 Uncharacterized protei 20.1 61 0.0013 24.9 1.3 14 126-139 31-44 (60)
87 PF02148 zf-UBP: Zn-finger in 20.0 57 0.0012 23.8 1.1 22 129-151 11-32 (63)
No 1
>PRK03954 ribonuclease P protein component 4; Validated
Probab=99.88 E-value=6.2e-23 Score=170.86 Aligned_cols=88 Identities=23% Similarity=0.320 Sum_probs=77.3
Q ss_pred ccHHHHHHHHHHHHHHhhcCCCChHHHHHHHHHHHHHHHh--CCCCCcccccCcCCCcccccCCceEEEEEecchhcccc
Q 023552 39 KSKLELEHLQRLAVWASSETSVPSLAALFGHRLASANEVL--GLQPDPSFFSCQRCETVLQPGFNCTIRIEKNQVKSRRR 116 (280)
Q Consensus 39 ~s~lRiehL~nLA~~A~~ea~~PsLSr~Y~r~l~~vseK~--~Lpp~~kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr 116 (280)
..++||++||++|+.+.. ..|+||++|+..++.|++++ +|||+++|+||++|+++||||+||+|||+++
T Consensus 17 iA~eRi~~L~~~A~~~~~--~~pelar~Yv~lar~Is~K~rirlp~~~KR~~CK~C~t~LiPG~n~~vRi~~~------- 87 (121)
T PRK03954 17 IARERIDTLFTLAERVFP--YSPELANRYVELALAVQQKAKVKLPRKWKRRYCKRCHSFLVPGVNARVRLRQK------- 87 (121)
T ss_pred HHHHHHHHHHHHHHHHhh--cCHHHHHHHHHHHHHHHHHhccCCCHHHHHHHhhcCCCeeecCCceEEEEecC-------
Confidence 457899999999987663 36899999999999999999 7788888999999999999999999999931
Q ss_pred cCCCCCCCCCeEEEecCCCCCccccc
Q 023552 117 WKKPKTSMQNTVVYKCHFCSHHNLKR 142 (280)
Q Consensus 117 ~Kk~~~~~~n~VV~tCl~CG~~n~~r 142 (280)
...+||++|++||++++|.
T Consensus 88 -------~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 88 -------RMPHVVITCLECGHIMRYP 106 (121)
T ss_pred -------CcceEEEECccCCCEEeec
Confidence 1357999999999999975
No 2
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=2.1e-22 Score=164.49 Aligned_cols=85 Identities=22% Similarity=0.271 Sum_probs=74.6
Q ss_pred ccHHHHHHHHHHHHHHhhcCCCChHHHHHHHHHHHHHHHh--CCCCCcccccCcCCCcccccCCceEEEEEecchhcccc
Q 023552 39 KSKLELEHLQRLAVWASSETSVPSLAALFGHRLASANEVL--GLQPDPSFFSCQRCETVLQPGFNCTIRIEKNQVKSRRR 116 (280)
Q Consensus 39 ~s~lRiehL~nLA~~A~~ea~~PsLSr~Y~r~l~~vseK~--~Lpp~~kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr 116 (280)
.-.+||++||+||..+... .|+||++|...+..|++++ .||++++|+||++|++||+||.||+|||.
T Consensus 9 ia~eRi~~L~~lA~~~~~~--~~~laRrYv~la~~Is~K~rv~lp~~iKR~~CkkC~t~Lvpg~n~rvR~~--------- 77 (105)
T COG2023 9 IAAERIDYLYSLAEETFRT--GPDLARRYVKLARRISMKYRVRLPREIKRTICKKCYTPLVPGKNARVRLR--------- 77 (105)
T ss_pred HHHHHHHHHHHHHHHHHhc--CcHHHHHHHHHHHHHHHhhccccCHHHHHHhccccCcccccCcceEEEEc---------
Confidence 4467788888887665542 2799999999999999999 78999999999999999999999999999
Q ss_pred cCCCCCCCCCeEEEecCCCCCccccc
Q 023552 117 WKKPKTSMQNTVVYKCHFCSHHNLKR 142 (280)
Q Consensus 117 ~Kk~~~~~~n~VV~tCl~CG~~n~~r 142 (280)
.+.|+++|+.||+++++.
T Consensus 78 --------~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 78 --------KGRVVVTCLECGTIRRYP 95 (105)
T ss_pred --------CCeEEEEecCCCcEEEec
Confidence 467999999999999985
No 3
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=99.87 E-value=4.8e-22 Score=150.41 Aligned_cols=82 Identities=28% Similarity=0.565 Sum_probs=63.3
Q ss_pred HHHHHHHHHHH-HHhhcCCCChHHHHHHHHHHHHHHHh--CCCCCcccccCcCCCcccccCCceEEEEEecchhcccccC
Q 023552 42 LELEHLQRLAV-WASSETSVPSLAALFGHRLASANEVL--GLQPDPSFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWK 118 (280)
Q Consensus 42 lRiehL~nLA~-~A~~ea~~PsLSr~Y~r~l~~vseK~--~Lpp~~kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~K 118 (280)
+|++|||++|+ +.. ...|+||+.|+++|..+++++ +|||+++++||++|+++||||+||+|||+++
T Consensus 1 ~Ri~~L~~~a~~~~~--~~~~~lsr~y~~~~~~i~~k~~~~l~~~~kr~~Ck~C~~~liPG~~~~vri~~~--------- 69 (85)
T PF04032_consen 1 QRINFLYQAAHLLLA--DGSPSLSRHYMKLMRKISKKTRIRLPPEIKRTICKKCGSLLIPGVNCSVRIRKK--------- 69 (85)
T ss_dssp HHHHHHHHHHH-HHC--CC-HHHHHHHHHHHHHHHHHCT---STTCCCTB-TTT--B--CTTTEEEEEE-----------
T ss_pred CHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHHHHHhCCCCChHHhcccccCCCCEEeCCCccEEEEEec---------
Confidence 69999999999 433 457999999999999999998 6789999999999999999999999999931
Q ss_pred CCCCCCCCeEEEecCCCCC
Q 023552 119 KPKTSMQNTVVYKCHFCSH 137 (280)
Q Consensus 119 k~~~~~~n~VV~tCl~CG~ 137 (280)
....+.|+|+|+.|||
T Consensus 70 ---~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 70 ---KKKKNFLVYTCLNCGH 85 (85)
T ss_dssp ----SSS-EEEEEETTTTE
T ss_pred ---CCCCCEEEEEccccCC
Confidence 1126899999999996
No 4
>KOG4394 consensus RNase P subunit that is not also a subunit of RNase MRP, involved in pre-tRNA processing [RNA processing and modification]
Probab=99.50 E-value=2e-14 Score=118.44 Aligned_cols=105 Identities=19% Similarity=0.228 Sum_probs=88.0
Q ss_pred CCCcccHHHHHHHHHHHHHHhhcCCCC-hHHHHHHHHHHHHHHHh--CCCCCcccccCcCCCcccccCCceEEEEEecch
Q 023552 35 TTNVKSKLELEHLQRLAVWASSETSVP-SLAALFGHRLASANEVL--GLQPDPSFFSCQRCETVLQPGFNCTIRIEKNQV 111 (280)
Q Consensus 35 ~~n~~s~lRiehL~nLA~~A~~ea~~P-sLSr~Y~r~l~~vseK~--~Lpp~~kR~iCKrC~tiLiPG~NcrVRI~nnkk 111 (280)
+.|.+.+.|+.+||+.++....+...+ +|||.|..-++.|++++ ++.|+++|+||+.|+++|+||.+|++|-+.-.+
T Consensus 5 ik~~d~f~RlnyLYQas~~~~r~~qe~t~LaR~Yi~t~~~Iskk~v~r~~P~iKRTiCkgC~sLLvpgk~c~ir~~~~~r 84 (116)
T KOG4394|consen 5 IKNQDHFHRLNYLYQASAYQTRARQEATPLARNYIKTMDLISKKTVTRLLPTIKRTICKGCHSLLVPGKKCEIRSDGALR 84 (116)
T ss_pred cccHHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhhhhhhCchHHHHHHhchhhhccCCcceeEeecchhh
Confidence 457789999999999999877655554 79999999999999998 888999999999999999999999999975322
Q ss_pred hcccccCCCCCCCCCeEEEecCCCCCcccccCCCCCc
Q 023552 112 KSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPVGH 148 (280)
Q Consensus 112 K~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k~~ 148 (280)
+ .-..+.|+.+|..|..-.+|--+.-|-
T Consensus 85 ~---------~~g~~~v~~~c~~c~~~~Rf~~~~~~~ 112 (116)
T KOG4394|consen 85 V---------MCGCGTVKRFCIGCDPNYRFYSEREGN 112 (116)
T ss_pred h---------CCCcchHHHHhhccCcccccccCcccc
Confidence 2 224788999999999999987665543
No 5
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=78.44 E-value=1 Score=30.40 Aligned_cols=31 Identities=23% Similarity=0.503 Sum_probs=20.2
Q ss_pred ccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 87 FSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 87 ~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
.||..|+.+|+|-- . ....+ .|..||++...
T Consensus 2 ~FCp~C~nlL~p~~------~----------------~~~~~--~C~~C~Y~~~~ 32 (35)
T PF02150_consen 2 RFCPECGNLLYPKE------D----------------KEKRV--ACRTCGYEEPI 32 (35)
T ss_dssp -BETTTTSBEEEEE------E----------------TTTTE--EESSSS-EEE-
T ss_pred eeCCCCCccceEcC------C----------------CccCc--CCCCCCCccCC
Confidence 69999999999731 1 02233 99999998654
No 6
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=77.13 E-value=1.9 Score=32.06 Aligned_cols=36 Identities=25% Similarity=0.381 Sum_probs=27.0
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCC
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGT 144 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt 144 (280)
..-|.+|+-+|--+- ....|.|+|.-||..|..++.
T Consensus 4 eiRC~~CnklLa~~g-----------------------~~~~leIKCpRC~tiN~~~a~ 39 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAG-----------------------EVIELEIKCPRCKTINHVRAT 39 (51)
T ss_pred ceeccchhHHHhhhc-----------------------CccEEEEECCCCCccceEecc
Confidence 345999999887631 134688999999999887765
No 7
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=76.40 E-value=2.1 Score=31.51 Aligned_cols=31 Identities=29% Similarity=0.773 Sum_probs=22.6
Q ss_pred cccCcCCCc--ccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcc
Q 023552 86 FFSCQRCET--VLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHN 139 (280)
Q Consensus 86 R~iCKrC~t--iLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n 139 (280)
-.||++|.. -|.| +.+ ...|.|.|-.||..|
T Consensus 22 aLIC~~C~~hNGla~------~~~-----------------~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 22 ALICSKCFSHNGLAP------KEE-----------------FEEIQYRCPYCGALN 54 (54)
T ss_pred eEECcccchhhcccc------ccc-----------------CCceEEEcCCCCCcC
Confidence 789999976 3343 222 457899999999865
No 8
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=74.82 E-value=2.6 Score=26.85 Aligned_cols=12 Identities=25% Similarity=0.736 Sum_probs=10.0
Q ss_pred CeEEEecCCCCC
Q 023552 126 NTVVYKCHFCSH 137 (280)
Q Consensus 126 n~VV~tCl~CG~ 137 (280)
..|.|.|-+||.
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 378899999994
No 9
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=72.28 E-value=7.2 Score=32.98 Aligned_cols=65 Identities=17% Similarity=0.269 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHhCCCCCcc--cccCcCCCcccccCCceEEE--EEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 66 LFGHRLASANEVLGLQPDPS--FFSCQRCETVLQPGFNCTIR--IEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 66 ~Y~r~l~~vseK~~Lpp~~k--R~iCKrC~tiLiPG~NcrVR--I~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
....||..+.+.++|.+.+. .+-|..|+..|+|=-.-.|+ |. - ..-......+.|..||.+.=.
T Consensus 69 ~~~~QL~ev~~~~~l~~~~~~~~sRC~~CN~~L~~v~~~~v~~~vp---------~---~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 69 DPEEQLREVLERFGLKLRLDPIFSRCPKCNGPLRPVSKEEVKDRVP---------P---YVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred CHHHHHHHHHHHcCCccccCCCCCccCCCCcEeeechhhccccccC---------c---cccccCCeEEECCCCCCEecc
Confidence 34568899888888766555 79999999988875333231 11 0 011123458999999998754
Q ss_pred c
Q 023552 142 R 142 (280)
Q Consensus 142 r 142 (280)
.
T Consensus 137 G 137 (147)
T PF01927_consen 137 G 137 (147)
T ss_pred c
Confidence 3
No 10
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=70.44 E-value=1.7 Score=29.69 Aligned_cols=34 Identities=26% Similarity=0.699 Sum_probs=18.2
Q ss_pred cCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCccccc
Q 023552 88 SCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKR 142 (280)
Q Consensus 88 iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~r 142 (280)
.|++|.+||=|=. .|. .+.-.++|.+|++.|...
T Consensus 4 rC~~C~aylNp~~----~~~-----------------~~~~~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 4 RCRRCRAYLNPFC----QFD-----------------DGGKTWICNFCGTKNPLP 37 (40)
T ss_dssp B-TTT--BS-TTS----EEE-----------------TTTTEEEETTT--EEE--
T ss_pred ccCCCCCEECCcc----eEc-----------------CCCCEEECcCCCCcCCCC
Confidence 5999999997753 455 223347999999988654
No 11
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=70.32 E-value=18 Score=35.66 Aligned_cols=25 Identities=16% Similarity=0.549 Sum_probs=19.8
Q ss_pred CCeEEEecCCCCCcccccCCCCCcc
Q 023552 125 QNTVVYKCHFCSHHNLKRGTPVGHM 149 (280)
Q Consensus 125 ~n~VV~tCl~CG~~n~~rGt~k~~~ 149 (280)
..++.|.|.+|++-|.-+-++-.-|
T Consensus 238 ~~yi~F~C~~Cn~LN~~~k~~e~s~ 262 (328)
T KOG2846|consen 238 YEYITFRCPHCNALNPAKKSPENSL 262 (328)
T ss_pred cCceEEECccccccCCCcCCccccc
Confidence 5789999999999998877744433
No 12
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=69.85 E-value=1.6 Score=39.12 Aligned_cols=34 Identities=26% Similarity=0.702 Sum_probs=27.7
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCc
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHH 138 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~ 138 (280)
..-|-.|+|+|.-|+-|+-- -+.|.++|..|...
T Consensus 12 YVhCnFC~TiLaVsVP~ssL-------------------~~~VTVRCGHCtNL 45 (170)
T PF04690_consen 12 YVHCNFCNTILAVSVPCSSL-------------------LKTVTVRCGHCTNL 45 (170)
T ss_pred EEEcCCcCeEEEEecchhhh-------------------hhhhceeccCccce
Confidence 66799999999988877652 35899999999864
No 13
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=68.38 E-value=6 Score=39.10 Aligned_cols=56 Identities=16% Similarity=0.358 Sum_probs=26.7
Q ss_pred HHHHHHHHHh---CCCCCcc--cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCccccc
Q 023552 69 HRLASANEVL---GLQPDPS--FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKR 142 (280)
Q Consensus 69 r~l~~vseK~---~Lpp~~k--R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~r 142 (280)
..++.|...+ .++.+.. .-+|.+|+.++. +.|.. + +...+.|.|.|..|||.-...
T Consensus 152 ~~I~~Il~~~~~~~~~~~y~Pf~piC~~cGri~t------t~v~~--------~----d~~~~~v~Y~c~~cG~~g~~~ 212 (360)
T PF01921_consen 152 DEIREILNEYRGRERPETYSPFLPICEKCGRIDT------TEVTE--------Y----DPEGGTVTYRCEECGHEGEVD 212 (360)
T ss_dssp HHHHHHHHHHHHHT--TT--SEEEEETTTEE--E------EEEEE--------E------SSSEEEEE--TTS---EEE
T ss_pred HHHHHHHHHhcCcCCCCCeeeeeeeccccCCccc------ceeeE--------e----ecCCCEEEEEecCCCCEEEEe
Confidence 3444444444 4444433 889999998764 22221 0 112578999999999976543
No 14
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=67.25 E-value=6 Score=30.95 Aligned_cols=38 Identities=18% Similarity=0.603 Sum_probs=25.6
Q ss_pred ccCcCCCc-------ccccCCceE--EEEEecchhcccccCCCCCCCCCeEEEecCCCCCccc
Q 023552 87 FSCQRCET-------VLQPGFNCT--IRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNL 140 (280)
Q Consensus 87 ~iCKrC~t-------iLiPG~Ncr--VRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~ 140 (280)
.-|.+|+. +..||-..+ +-|++ +..++++|..||+.-.
T Consensus 5 ~kCpKCgn~~~~ekei~~tg~~lskifdvq~----------------n~f~~itCk~CgYtEf 51 (68)
T COG3478 5 FKCPKCGNTNYEEKEIAATGGGLSKIFDVQN----------------NKFIVITCKNCGYTEF 51 (68)
T ss_pred ccCCCcCCcchhhceeeccCCCcceeEEecc----------------cEEEEEEeccCCchhh
Confidence 34999974 455655544 44443 3579999999998644
No 15
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=66.53 E-value=9.7 Score=37.22 Aligned_cols=36 Identities=28% Similarity=0.535 Sum_probs=23.2
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
.-+|.+|+ .|. .+| +.. +...+.|.|.| .|||.-..
T Consensus 169 ~p~c~~cg-~~~----~~v-~~~-------------d~~~~~v~y~c-~cG~~g~~ 204 (353)
T cd00674 169 MPYCEKCG-KDT----TTV-EAY-------------DAKAGTVTYKC-ECGHEETV 204 (353)
T ss_pred eeecCCcC-cce----eEE-EEE-------------eCCCCeEEEEc-CCCCEEEE
Confidence 88999999 442 222 221 11246799999 79997654
No 16
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=66.16 E-value=6.4 Score=27.15 Aligned_cols=33 Identities=18% Similarity=0.428 Sum_probs=22.2
Q ss_pred ccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCccccc
Q 023552 87 FSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKR 142 (280)
Q Consensus 87 ~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~r 142 (280)
.||..|+.+|.+=. . .+.-.+.|..||+.....
T Consensus 1 ~FCp~Cg~~l~~~~------~-----------------~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 1 KFCPKCGNMLIPKE------G-----------------KEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCCcccccc------C-----------------CCCCEEECCcCCCeEECC
Confidence 48999999886531 0 111256799999986653
No 17
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=64.94 E-value=11 Score=38.67 Aligned_cols=35 Identities=14% Similarity=0.458 Sum_probs=24.3
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
.-+|.+|+.++.| .. -+. . ...|.|.| .|||....
T Consensus 168 ~pic~~cGrv~~~---~~-~~~---------------~-~~~v~Y~c-~cG~~g~~ 202 (515)
T TIGR00467 168 SVFCENCGRDTTT---VN-NYD---------------N-EYSIEYSC-ECGNQESV 202 (515)
T ss_pred eeecCCcCccCce---EE-Eec---------------C-CceEEEEc-CCCCEEEE
Confidence 8899999999772 11 111 0 12699999 79998654
No 18
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=63.96 E-value=10 Score=36.32 Aligned_cols=56 Identities=18% Similarity=0.199 Sum_probs=36.7
Q ss_pred ccccCcCCCcccccCC--ceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCCCCCc
Q 023552 85 SFFSCQRCETVLQPGF--NCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPVGH 148 (280)
Q Consensus 85 kR~iCKrC~tiLiPG~--NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k~~ 148 (280)
....|..|+.++.=|+ |++.+-.. ..+-=+..-=.+.++|+.|++.--|+.+|++.
T Consensus 39 f~i~C~~C~~~I~kG~rFNA~Ke~v~--------~E~Yls~~I~rF~~kC~~C~~~i~~kTDPkn~ 96 (324)
T PF04502_consen 39 FNIWCNTCGEYIYKGVRFNARKEKVG--------NEKYLSTPIYRFYIKCPRCSNEIEFKTDPKNT 96 (324)
T ss_pred ccCcCCCCccccccceeeeeeeEecC--------CCccccceEEEEEEEcCCCCCEEeeecCCCCC
Confidence 3678999999988885 33333110 00000011124788999999999999999984
No 19
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=62.89 E-value=12 Score=38.02 Aligned_cols=37 Identities=30% Similarity=0.583 Sum_probs=24.8
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
.-+|.+|+.++.-.+ +.. +...+.|.|.| .|||.-..
T Consensus 175 ~pic~~cg~~~~~~~-----~~~-------------d~~~~~v~y~~-~cG~~~~~ 211 (510)
T PRK00750 175 LPICPKCGKVLTTPV-----ISY-------------DAEAGTVTYDC-ECGHEGEV 211 (510)
T ss_pred eeeCCCCCccceEEE-----EEE-------------eCCCCEEEEEc-CCCCEEEE
Confidence 889999999864221 121 11145799999 69998654
No 20
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=62.60 E-value=6.1 Score=32.81 Aligned_cols=36 Identities=17% Similarity=0.397 Sum_probs=26.1
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCC
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGT 144 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt 144 (280)
..||..|+++|+|=. . ...-+..|-.||+...+...
T Consensus 2 m~FCp~Cgsll~p~~------~-----------------~~~~~l~C~kCgye~~~~~~ 37 (113)
T COG1594 2 MRFCPKCGSLLYPKK------D-----------------DEGGKLVCRKCGYEEEASNK 37 (113)
T ss_pred ccccCCccCeeEEeE------c-----------------CCCcEEECCCCCcchhcccc
Confidence 469999999999821 0 01126799999999887753
No 21
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=61.45 E-value=7.6 Score=26.86 Aligned_cols=15 Identities=20% Similarity=0.532 Sum_probs=11.3
Q ss_pred EEecCCCCCcccccC
Q 023552 129 VYKCHFCSHHNLKRG 143 (280)
Q Consensus 129 V~tCl~CG~~n~~rG 143 (280)
.++|.+||.......
T Consensus 21 ~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 21 GVRCPYCGYRILFKE 35 (46)
T ss_pred ceECCCCCCeEEEcc
Confidence 579999998766533
No 22
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=60.86 E-value=3.7 Score=38.49 Aligned_cols=58 Identities=17% Similarity=0.352 Sum_probs=40.2
Q ss_pred CChHHHHHHHHHHHHHHHhCCCCCcccccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCc
Q 023552 60 VPSLAALFGHRLASANEVLGLQPDPSFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHH 138 (280)
Q Consensus 60 ~PsLSr~Y~r~l~~vseK~~Lpp~~kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~ 138 (280)
.|.|...|-+.+.. .+-.++-| +.-..|-.|+-.|-+++-.-||-. |. +++|-.||.+
T Consensus 173 ~~ell~~yeri~~~-~kg~gvvp-l~g~~C~GC~m~l~~~~~~~V~~~------------------d~-iv~CP~CgRI 230 (239)
T COG1579 173 DPELLSEYERIRKN-KKGVGVVP-LEGRVCGGCHMKLPSQTLSKVRKK------------------DE-IVFCPYCGRI 230 (239)
T ss_pred CHHHHHHHHHHHhc-CCCceEEe-ecCCcccCCeeeecHHHHHHHhcC------------------CC-CccCCccchH
Confidence 35677777766655 22234433 457899999999999987777653 33 4699999976
No 23
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=54.40 E-value=10 Score=34.07 Aligned_cols=67 Identities=24% Similarity=0.354 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhCCCC--CcccccCcCCCcccccCCceEE--EEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccC
Q 023552 68 GHRLASANEVLGLQP--DPSFFSCQRCETVLQPGFNCTI--RIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRG 143 (280)
Q Consensus 68 ~r~l~~vseK~~Lpp--~~kR~iCKrC~tiLiPG~NcrV--RI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rG 143 (280)
-.||+.+..++++.+ .+...-|-.|++.|++=.---| +|. -+ .-..-...+.|..||.+.=..+
T Consensus 77 ~~Ql~e~~~~~~l~~~~~~e~~RCp~CN~~L~~vs~eev~~~Vp---------~~---~~~~~~~f~~C~~CgkiYW~Gs 144 (165)
T COG1656 77 EEQLAEFLARLGLKPRLFPEFSRCPECNGELEKVSREEVKEKVP---------EK---VYRNYEEFYRCPKCGKIYWKGS 144 (165)
T ss_pred HHHHHHHHHHhccchhcccccccCcccCCEeccCcHHHHhhccc---------hh---hhhcccceeECCCCcccccCch
Confidence 357788777777766 4558889999999875321111 111 00 0012356789999999987654
Q ss_pred CCC
Q 023552 144 TPV 146 (280)
Q Consensus 144 t~k 146 (280)
--.
T Consensus 145 Hw~ 147 (165)
T COG1656 145 HWR 147 (165)
T ss_pred HHH
Confidence 333
No 24
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.91 E-value=9.2 Score=41.09 Aligned_cols=50 Identities=24% Similarity=0.545 Sum_probs=40.2
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCCCCCcccccccCC
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPVGHMKEICPMK 156 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k~~~k~~~~~~ 156 (280)
-..|.+|+++|-|= |+|.+.. -++.|.+|-+.|.+.+.-.|.=..-+|.-
T Consensus 53 P~~C~~C~AvlNPy--c~vd~~a-------------------~~W~CpfC~qrN~~p~~Y~~is~~n~P~e 102 (745)
T KOG1986|consen 53 PLRCSKCGAVLNPY--CSVDFRA-------------------KSWICPFCNQRNPFPPHYSGISENNLPPE 102 (745)
T ss_pred CchhccchhhcCcc--eeecccC-------------------ceEeccccccCCCCChhhcccCccCCChh
Confidence 77899999999996 7777762 24699999999999988877766665554
No 25
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=50.68 E-value=14 Score=24.96 Aligned_cols=32 Identities=22% Similarity=0.398 Sum_probs=16.3
Q ss_pred ccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcc
Q 023552 87 FSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHN 139 (280)
Q Consensus 87 ~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n 139 (280)
.||..|+..| ..+|-. ..+.....|..||++.
T Consensus 1 kfC~~CG~~l------~~~ip~---------------gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 1 KFCPQCGGPL------ERRIPE---------------GDDRERLVCPACGFIH 32 (34)
T ss_dssp -B-TTT--B-------EEE--T---------------T-SS-EEEETTTTEEE
T ss_pred CccccccChh------hhhcCC---------------CCCccceECCCCCCEE
Confidence 4899998876 334431 1456778999999863
No 26
>PF01430 HSP33: Hsp33 protein; InterPro: IPR000397 Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidizing conditions like H2O2 cause disulphide bonds to form in Hsp33, a process that leads to the activation of its chaperone function [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0005737 cytoplasm; PDB: 1VZY_B 1VQ0_A 1I7F_A 3M7M_X 1XJH_A 1HW7_A.
Probab=50.41 E-value=9.2 Score=35.58 Aligned_cols=17 Identities=18% Similarity=0.520 Sum_probs=12.1
Q ss_pred CCeEEEecCCCCCcccc
Q 023552 125 QNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 125 ~n~VV~tCl~CG~~n~~ 141 (280)
.+.+.++|+|||..+.|
T Consensus 262 ~~~iev~C~fC~~~Y~f 278 (280)
T PF01430_consen 262 NGKIEVTCEFCGKKYRF 278 (280)
T ss_dssp CSEEEEE-TTT--EEEE
T ss_pred CCCEEEEeeCCCCEEEe
Confidence 47899999999998876
No 27
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=49.76 E-value=28 Score=36.29 Aligned_cols=97 Identities=23% Similarity=0.367 Sum_probs=52.6
Q ss_pred hhhcccccccCCCccc--HHHHHHHHHHHHHHhhcCCCCh----HHHHH-----HHH----------HHHHHHHh-C--C
Q 023552 25 DEKAGKKLVNTTNVKS--KLELEHLQRLAVWASSETSVPS----LAALF-----GHR----------LASANEVL-G--L 80 (280)
Q Consensus 25 ~e~~g~~~~~~~n~~s--~lRiehL~nLA~~A~~ea~~Ps----LSr~Y-----~r~----------l~~vseK~-~--L 80 (280)
|+-.|.-...+|++.. .-=.+|..+.+..+...+.++. =+..| ... |+.|...+ + +
T Consensus 84 e~Ylg~Plt~IPdP~G~~~Sya~hf~~~f~~~l~~~Gi~~E~~s~se~Yk~G~~~~~i~~ale~rdeI~~il~~~~~~~~ 163 (521)
T COG1384 84 EQYLGMPLTEIPDPFGCCDSYAEHFLRPFEEFLDEFGIEVEFVSATELYKSGLYDEAIRIALERRDEIMEILNEYRGREL 163 (521)
T ss_pred HHHcCCccccCCCCccccchHHHHHHHHHHHHHHhcCCceEEEEhHHhhhcccHHHHHHHHHhhHHHHHHHHHHhcCCcc
Confidence 3445555566665543 1224566666666665555431 22222 222 33333444 2 3
Q ss_pred CCCcc--cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 81 QPDPS--FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 81 pp~~k--R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
+-+.+ .-+|-+|+.++ ++.|.. | +.. ..|.|.| .|||...-
T Consensus 164 ~e~~~P~~piC~kcGri~------~t~v~~--------~----d~~-~~v~Y~C-e~Gh~g~v 206 (521)
T COG1384 164 EEDWSPFMPICEKCGRIL------TTPVIE--------W----DGE-GTVEYRC-ECGHEGEV 206 (521)
T ss_pred cCCceeccccccccCCcc------eeEEEE--------e----cCC-ceEEEEe-cCCcccee
Confidence 33333 88999998875 334442 1 222 5899999 89997643
No 28
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=49.73 E-value=12 Score=34.73 Aligned_cols=14 Identities=21% Similarity=0.553 Sum_probs=11.8
Q ss_pred cccCcCCCcccccC
Q 023552 86 FFSCQRCETVLQPG 99 (280)
Q Consensus 86 R~iCKrC~tiLiPG 99 (280)
+.||.+|++.+.+.
T Consensus 99 ~~fC~~CG~~~~~~ 112 (256)
T PRK00241 99 HRFCGYCGHPMHPS 112 (256)
T ss_pred CccccccCCCCeec
Confidence 88999999988753
No 29
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=48.30 E-value=14 Score=29.09 Aligned_cols=13 Identities=23% Similarity=0.800 Sum_probs=10.9
Q ss_pred ccCcCCCcccccC
Q 023552 87 FSCQRCETVLQPG 99 (280)
Q Consensus 87 ~iCKrC~tiLiPG 99 (280)
.||..|+++|.|.
T Consensus 1 ~fC~~Cg~~l~~~ 13 (104)
T TIGR01384 1 KFCPKCGSLMTPK 13 (104)
T ss_pred CCCcccCcccccC
Confidence 3899999999763
No 30
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.80 E-value=16 Score=39.23 Aligned_cols=39 Identities=21% Similarity=0.602 Sum_probs=24.3
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCccc
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNL 140 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~ 140 (280)
...|+.|+.++.== ||.+-+..- +..=...||.||++..
T Consensus 435 ~l~C~~Cg~v~~Cp-~Cd~~lt~H---------------~~~~~L~CH~Cg~~~~ 473 (730)
T COG1198 435 LLLCRDCGYIAECP-NCDSPLTLH---------------KATGQLRCHYCGYQEP 473 (730)
T ss_pred eeecccCCCcccCC-CCCcceEEe---------------cCCCeeEeCCCCCCCC
Confidence 78899998876522 566555541 1222357888888743
No 31
>PLN00162 transport protein sec23; Provisional
Probab=47.70 E-value=15 Score=39.17 Aligned_cols=37 Identities=27% Similarity=0.661 Sum_probs=26.7
Q ss_pred ccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCC
Q 023552 87 FSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGT 144 (280)
Q Consensus 87 ~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt 144 (280)
..|++|.+||=|= +++.. +.-.+.|.+|+..|-+...
T Consensus 54 vRC~~CraylNPf----~~~d~-----------------~~~~W~C~~C~~~N~~P~~ 90 (761)
T PLN00162 54 LRCRTCRAVLNPY----CRVDF-----------------QAKIWICPFCFQRNHFPPH 90 (761)
T ss_pred CccCCCcCEECCc----eEEec-----------------CCCEEEccCCCCCCCCchH
Confidence 5699999999664 44552 1223699999999987643
No 32
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=47.29 E-value=13 Score=26.95 Aligned_cols=14 Identities=21% Similarity=0.472 Sum_probs=11.6
Q ss_pred cccCcCCCc-ccccC
Q 023552 86 FFSCQRCET-VLQPG 99 (280)
Q Consensus 86 R~iCKrC~t-iLiPG 99 (280)
+.+|.+|++ ||.+.
T Consensus 20 ~~fCP~Cg~~~m~~~ 34 (50)
T PRK00432 20 NKFCPRCGSGFMAEH 34 (50)
T ss_pred cCcCcCCCcchhecc
Confidence 679999998 87765
No 33
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=45.80 E-value=29 Score=26.54 Aligned_cols=19 Identities=11% Similarity=0.338 Sum_probs=15.5
Q ss_pred CeEEEecCCCCCcccccCC
Q 023552 126 NTVVYKCHFCSHHNLKRGT 144 (280)
Q Consensus 126 n~VV~tCl~CG~~n~~rGt 144 (280)
...++.|..||+.-...+.
T Consensus 33 ~f~~v~C~~CGYTE~Y~~~ 51 (64)
T PF09855_consen 33 KFTTVSCTNCGYTEFYKAK 51 (64)
T ss_pred EEEEEECCCCCCEEEEeec
Confidence 4689999999999777643
No 34
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=44.75 E-value=41 Score=24.47 Aligned_cols=47 Identities=26% Similarity=0.521 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhCC-----CCCcccccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCc
Q 023552 67 FGHRLASANEVLGL-----QPDPSFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHH 138 (280)
Q Consensus 67 Y~r~l~~vseK~~L-----pp~~kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~ 138 (280)
+...|...++..|+ +|...-..|-.|+....- + ...-++.|..||..
T Consensus 4 ~~~~L~yka~~~G~~v~~v~~~~TSq~C~~CG~~~~~------~-------------------~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 4 FRQRLEYKAEEYGIQVVEVDEAYTSQTCPRCGHRNKK------R-------------------RSGRVFTCPNCGFE 55 (69)
T ss_pred HHHHHHHHHHHhCCEEEEECCCCCccCccCccccccc------c-------------------cccceEEcCCCCCE
Confidence 44566666666654 455557889999887654 1 12345799999986
No 35
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=42.88 E-value=16 Score=31.13 Aligned_cols=33 Identities=18% Similarity=0.480 Sum_probs=26.6
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcc
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHN 139 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n 139 (280)
.+||+-|+.+|.|-- +.-.+.|++-|-+|.++-
T Consensus 4 ~rfC~eCNNmLYPkE---------------------Dked~~L~laCrnCd~ve 36 (113)
T KOG2691|consen 4 IRFCRECNNMLYPKE---------------------DKEDRILLLACRNCDYVE 36 (113)
T ss_pred cchhhhhhccccccc---------------------cccccEEEEEecCCcceE
Confidence 479999999999952 223678999999999874
No 36
>COG4321 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]
Probab=42.08 E-value=8.2 Score=32.33 Aligned_cols=13 Identities=62% Similarity=0.897 Sum_probs=11.0
Q ss_pred cchhhHHHHHhhc
Q 023552 252 TSWTSLKEIAERS 264 (280)
Q Consensus 252 kswtslkeia~~~ 264 (280)
-=|+.|||||+..
T Consensus 34 ~FW~~L~eIA~~r 46 (102)
T COG4321 34 PFWDILKEIAERR 46 (102)
T ss_pred HHHHHHHHHHHhc
Confidence 3499999999975
No 37
>cd00498 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form.
Probab=41.94 E-value=14 Score=34.43 Aligned_cols=17 Identities=18% Similarity=0.503 Sum_probs=14.7
Q ss_pred CCeEEEecCCCCCcccc
Q 023552 125 QNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 125 ~n~VV~tCl~CG~~n~~ 141 (280)
.+.+.++|+|||..+.|
T Consensus 258 ~g~iev~C~FC~~~Y~f 274 (275)
T cd00498 258 DGGIEVTCEFCGEKYHF 274 (275)
T ss_pred CCCEEEEEeCCCCEEec
Confidence 35799999999999876
No 38
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=41.65 E-value=23 Score=27.33 Aligned_cols=19 Identities=21% Similarity=0.406 Sum_probs=15.1
Q ss_pred cccCcCCCcccccCCceEE
Q 023552 86 FFSCQRCETVLQPGFNCTI 104 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrV 104 (280)
-..|-.|+..|.||-+..+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~ 27 (61)
T COG2888 9 PPVCTSCGREIAPGETAVK 27 (61)
T ss_pred CceeccCCCEeccCCceeE
Confidence 3579999999999976654
No 39
>PRK01402 hslO Hsp33-like chaperonin; Reviewed
Probab=39.82 E-value=16 Score=35.38 Aligned_cols=18 Identities=22% Similarity=0.492 Sum_probs=15.6
Q ss_pred CCeEEEecCCCCCccccc
Q 023552 125 QNTVVYKCHFCSHHNLKR 142 (280)
Q Consensus 125 ~n~VV~tCl~CG~~n~~r 142 (280)
.+.+.++|+|||..+.|.
T Consensus 304 ~g~iev~CeFC~~~Y~f~ 321 (328)
T PRK01402 304 DGKISVTCEFCSRVYRFD 321 (328)
T ss_pred CCCEEEEeeCCCCEEEeC
Confidence 367999999999999875
No 40
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=39.51 E-value=16 Score=34.44 Aligned_cols=19 Identities=21% Similarity=0.494 Sum_probs=16.1
Q ss_pred CCeEEEecCCCCCcccccC
Q 023552 125 QNTVVYKCHFCSHHNLKRG 143 (280)
Q Consensus 125 ~n~VV~tCl~CG~~n~~rG 143 (280)
.+.+.++|+|||..+.|.-
T Consensus 264 ~~~iev~C~FC~~~Y~f~~ 282 (293)
T PRK00114 264 DGGAEMVCQFCGNKYLFDE 282 (293)
T ss_pred CCCEEEEEeCCCCEEEeCH
Confidence 3679999999999998853
No 41
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=39.18 E-value=7.4 Score=27.93 Aligned_cols=35 Identities=23% Similarity=0.329 Sum_probs=26.5
Q ss_pred ccccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCc
Q 023552 85 SFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHH 138 (280)
Q Consensus 85 kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~ 138 (280)
....|..|+.-|-|..-..|+- +.-+++|-+||.+
T Consensus 21 ~~~~C~gC~~~l~~~~~~~i~~-------------------~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 21 EGGTCSGCHMELPPQELNEIRK-------------------GDEIVFCPNCGRI 55 (56)
T ss_pred eCCccCCCCEEcCHHHHHHHHc-------------------CCCeEECcCCCcc
Confidence 3779999999999987555532 2446799999975
No 42
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=39.08 E-value=38 Score=22.94 Aligned_cols=18 Identities=17% Similarity=0.366 Sum_probs=14.1
Q ss_pred CeEEEecCCCCCcccccC
Q 023552 126 NTVVYKCHFCSHHNLKRG 143 (280)
Q Consensus 126 n~VV~tCl~CG~~n~~rG 143 (280)
+..+..|..||.+-+-.|
T Consensus 16 ~~~id~C~~C~G~W~d~~ 33 (41)
T PF13453_consen 16 DVEIDVCPSCGGIWFDAG 33 (41)
T ss_pred CEEEEECCCCCeEEccHH
Confidence 588899999998766444
No 43
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=38.93 E-value=21 Score=24.05 Aligned_cols=14 Identities=21% Similarity=0.508 Sum_probs=11.1
Q ss_pred CCeEEEecCCCCCc
Q 023552 125 QNTVVYKCHFCSHH 138 (280)
Q Consensus 125 ~n~VV~tCl~CG~~ 138 (280)
...+.++|-.|||+
T Consensus 21 ~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 21 PKGRKVRCSKCGHV 34 (36)
T ss_pred CCCcEEECCCCCCE
Confidence 44567899999986
No 44
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=37.00 E-value=20 Score=26.49 Aligned_cols=15 Identities=20% Similarity=0.213 Sum_probs=12.4
Q ss_pred ccccCcCCCcccccC
Q 023552 85 SFFSCQRCETVLQPG 99 (280)
Q Consensus 85 kR~iCKrC~tiLiPG 99 (280)
...||.+|+.-+-|+
T Consensus 13 ~k~ICrkC~ARnp~~ 27 (48)
T PRK04136 13 NKKICMRCNARNPWR 27 (48)
T ss_pred cccchhcccCCCCcc
Confidence 478999999887776
No 45
>PHA02130 hypothetical protein
Probab=35.60 E-value=21 Score=28.40 Aligned_cols=28 Identities=36% Similarity=0.479 Sum_probs=20.4
Q ss_pred cccchhhHHHHHhhcccccccccceeccc
Q 023552 250 RRTSWTSLKEIAERSEDDNGRMANLTIPF 278 (280)
Q Consensus 250 ~rkswtslkeia~~~e~~~~~~~n~~ipf 278 (280)
--|||.||+|-...+ -|+=.-.-|.|||
T Consensus 12 tfks~~sl~~wl~~~-~dswdddil~ipf 39 (81)
T PHA02130 12 TFKSWESLREWLDER-FDSWDDDILSIPF 39 (81)
T ss_pred hhHHHHHHHHHHHhc-ccccccchhcccc
Confidence 358999999987655 4554456688888
No 46
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=34.27 E-value=22 Score=37.09 Aligned_cols=38 Identities=21% Similarity=0.509 Sum_probs=23.2
Q ss_pred ecCCCCCcc----------cccCCCCCcccccccCCCCCCCCCCCCCCCc
Q 023552 131 KCHFCSHHN----------LKRGTPVGHMKEICPMKAKPSSRPQCGSKSP 170 (280)
Q Consensus 131 tCl~CG~~n----------~~rGt~k~~~k~~~~~~~k~~~~~~~~~~~~ 170 (280)
+|.+|..++ -..++-||. .+-+|+|+|.. .+.||+-||
T Consensus 323 RCQyCRfQKCL~VGMVKEVVRtdSLkGR-RGRLpSKpKs~-q~sppSpPi 370 (605)
T KOG4217|consen 323 RCQYCRFQKCLAVGMVKEVVRTDSLKGR-RGRLPSKPKSR-QPSPPSPPI 370 (605)
T ss_pred hchhhhHhHHHHhhhhhhheeccccccc-cCCCCCCCCCC-CCCCCCCch
Confidence 677776554 234555555 45689999987 444555444
No 47
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.72 E-value=25 Score=33.62 Aligned_cols=64 Identities=19% Similarity=0.175 Sum_probs=40.7
Q ss_pred CcccccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCCCCCccccc
Q 023552 83 DPSFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPVGHMKEI 152 (280)
Q Consensus 83 ~~kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k~~~k~~ 152 (280)
.+.+.-|.-|+.|..=|.-..-|-+.-.-+ .-=....=.+.+.|..|++...|+.+++|..-.|
T Consensus 37 ~Pf~~rC~tCgeyi~kg~kfN~r~E~~~~e------~yLgiki~Rf~i~Ct~cl~el~~rTDp~N~dY~~ 100 (253)
T KOG2989|consen 37 TPFRLRCNTCGEYIYKGKKFNAREEDVIEE------TYLGIKIFRFYIKCTRCLRELSFRTDPKNSDYVI 100 (253)
T ss_pred ccceeecccccchhhcCCCcchhHHhhhcc------ccccceeeeeeeeccchHhhhhhhcCCcchHHHH
Confidence 355889999999998874322222210000 0000012357899999999999999999976544
No 48
>PF12773 DZR: Double zinc ribbon
Probab=33.44 E-value=23 Score=24.33 Aligned_cols=14 Identities=29% Similarity=0.441 Sum_probs=11.5
Q ss_pred cccccCcCCCcccc
Q 023552 84 PSFFSCQRCETVLQ 97 (280)
Q Consensus 84 ~kR~iCKrC~tiLi 97 (280)
....||..|++.|.
T Consensus 10 ~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP 23 (50)
T ss_pred ccccCChhhcCChh
Confidence 34789999999888
No 49
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.10 E-value=34 Score=33.03 Aligned_cols=40 Identities=28% Similarity=0.445 Sum_probs=30.6
Q ss_pred ccccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCCCCCcc
Q 023552 85 SFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPVGHM 149 (280)
Q Consensus 85 kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k~~~ 149 (280)
.++||-+|++-+.|. .+-...-|..||+.---|-+|-=+|
T Consensus 110 ~~RFCg~CG~~~~~~-------------------------~~g~~~~C~~cg~~~fPR~dP~vIv 149 (279)
T COG2816 110 SHRFCGRCGTKTYPR-------------------------EGGWARVCPKCGHEHFPRIDPCVIV 149 (279)
T ss_pred hCcCCCCCCCcCccc-------------------------cCceeeeCCCCCCccCCCCCCeEEE
Confidence 399999999987765 3456678999999887777765443
No 50
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=32.80 E-value=61 Score=27.35 Aligned_cols=38 Identities=26% Similarity=0.510 Sum_probs=26.9
Q ss_pred CcccccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcc
Q 023552 83 DPSFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHN 139 (280)
Q Consensus 83 ~~kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n 139 (280)
-++.+.|-+|+...+- .|+|-.. .+.-+..|..||...
T Consensus 19 L~k~FtCp~Cghe~vs--~ctvkk~-----------------~~~g~~~Cg~CGls~ 56 (104)
T COG4888 19 LPKTFTCPRCGHEKVS--SCTVKKT-----------------VNIGTAVCGNCGLSF 56 (104)
T ss_pred CCceEecCccCCeeee--EEEEEec-----------------CceeEEEcccCcceE
Confidence 3449999999997763 3555333 356677999999754
No 51
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=32.75 E-value=19 Score=27.29 Aligned_cols=47 Identities=15% Similarity=0.384 Sum_probs=14.4
Q ss_pred HHHHHHHHhCCCCCcc----cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 70 RLASANEVLGLQPDPS----FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 70 ~l~~vseK~~Lpp~~k----R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
.|++..+...+|++.. ..+|..|+. ++.|..+ .|-.+|..||.-|..
T Consensus 10 ~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~------~s~v~fH-------------------~lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 10 MLDAEIAATPMPEEYRNKKVWILCNDCNA------KSEVPFH-------------------FLGHKCSHCGSYNTR 60 (61)
T ss_dssp ------------------EEEEEESSS--------EEEEE---------------------TT----TTTS---EE
T ss_pred HHHHHHHhCCCCHHHhCCEEEEECCCCCC------ccceeee-------------------HhhhcCCCCCCcccC
Confidence 4444444446777655 678999964 4445444 566799999987754
No 52
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=31.51 E-value=26 Score=24.77 Aligned_cols=15 Identities=27% Similarity=0.691 Sum_probs=11.5
Q ss_pred EEEecCCCCCccccc
Q 023552 128 VVYKCHFCSHHNLKR 142 (280)
Q Consensus 128 VV~tCl~CG~~n~~r 142 (280)
|+|.|..||......
T Consensus 1 ~~Y~C~~Cg~~~~~~ 15 (44)
T smart00659 1 MIYICGECGRENEIK 15 (44)
T ss_pred CEEECCCCCCEeecC
Confidence 578899999876654
No 53
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=31.25 E-value=26 Score=31.80 Aligned_cols=24 Identities=13% Similarity=0.169 Sum_probs=19.8
Q ss_pred CCCCCcccccCcCCCcccccCCce
Q 023552 79 GLQPDPSFFSCQRCETVLQPGFNC 102 (280)
Q Consensus 79 ~Lpp~~kR~iCKrC~tiLiPG~Nc 102 (280)
.+|......+|+.|+.++++|.=.
T Consensus 28 ei~~~i~v~~C~~Cg~~~~~~~W~ 51 (236)
T PF04981_consen 28 EIPDRIEVTICPKCGRYRIGGRWV 51 (236)
T ss_pred ecCCccCceECCCCCCEECCCEee
Confidence 467778899999999999997433
No 54
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=31.14 E-value=52 Score=27.14 Aligned_cols=33 Identities=27% Similarity=0.741 Sum_probs=20.8
Q ss_pred ccccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcc
Q 023552 85 SFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHN 139 (280)
Q Consensus 85 kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n 139 (280)
..+.|.+|+.. .++|.|. .+...+.|..||.-+
T Consensus 20 t~f~CP~Cge~-----~v~v~~~-----------------k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKV-----SISVKIK-----------------KNIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCe-----EeeeecC-----------------CCcceEECCCCCCcc
Confidence 47788888742 3444444 235556888888764
No 55
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.94 E-value=35 Score=34.57 Aligned_cols=40 Identities=25% Similarity=0.664 Sum_probs=24.0
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
..+|..|+..+.=- +|.+.+.+- +. .+. ..||.||+....
T Consensus 213 ~~~C~~Cg~~~~C~-~C~~~l~~h--------~~-----~~~--l~Ch~Cg~~~~~ 252 (505)
T TIGR00595 213 NLLCRSCGYILCCP-NCDVSLTYH--------KK-----EGK--LRCHYCGYQEPI 252 (505)
T ss_pred eeEhhhCcCccCCC-CCCCceEEe--------cC-----CCe--EEcCCCcCcCCC
Confidence 56899998877633 455555431 01 232 478888877653
No 56
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=29.90 E-value=45 Score=22.96 Aligned_cols=39 Identities=18% Similarity=0.330 Sum_probs=25.4
Q ss_pred EecCCCCCcccccCCCCCcccccccCCCCCCCCCCCCCCCc
Q 023552 130 YKCHFCSHHNLKRGTPVGHMKEICPMKAKPSSRPQCGSKSP 170 (280)
Q Consensus 130 ~tCl~CG~~n~~rGt~k~~~k~~~~~~~k~~~~~~~~~~~~ 170 (280)
+.|..||+.+..+...+++.-=.|....+... .++..+|
T Consensus 6 l~C~~CG~~m~~~~~~~~~~yy~C~~~~~~~~--~C~~~~i 44 (58)
T PF13408_consen 6 LRCGHCGSKMTRRKRKGKYRYYRCSNRRRKGK--GCPNKSI 44 (58)
T ss_pred EEcccCCcEeEEEECCCCceEEEcCCCcCCCC--CCCCCEe
Confidence 58999999988876665666666776654433 3544333
No 57
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=29.88 E-value=1.3e+02 Score=29.03 Aligned_cols=41 Identities=22% Similarity=0.459 Sum_probs=24.6
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
.+-|.+|+ +..|+..-... | ..+ ..=.+.|+|..|||.-.|
T Consensus 258 ~~~C~~C~-----~~~~~~~q~Qt----r-----saD-EpmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 258 LFTCGKCK-----QKKCTYYQLQT----R-----SAD-EPMTTFVTCEECGNRWKF 298 (299)
T ss_pred cccCCCCC-----CccceEEEecc----c-----CCC-CCCeEEEEcCCCCCeeee
Confidence 78999997 34555433211 0 001 112588999999997655
No 58
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=29.81 E-value=20 Score=35.63 Aligned_cols=48 Identities=23% Similarity=0.485 Sum_probs=32.8
Q ss_pred CCCCCcc---cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCCCCCcccccc
Q 023552 79 GLQPDPS---FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPVGHMKEIC 153 (280)
Q Consensus 79 ~Lpp~~k---R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k~~~k~~~ 153 (280)
++.|++- ++.|.+|+..+-|.-+.. ....|- ||.. +..|= ...|.+|.
T Consensus 230 g~~P~~GKYh~~~c~~C~~~~~~~~~~~------------------------~~~~Cp-CG~~-i~~GV-~~Rv~eLa 280 (374)
T TIGR00375 230 GLDPLLGKYHQTACEACGEPAVSEDAET------------------------ACANCP-CGGR-IKKGV-SDRLRELS 280 (374)
T ss_pred eECcCCCccchhhhcccCCcCCchhhhh------------------------cCCCCC-CCCc-ceech-HHHHHHHh
Confidence 6666554 999999999988874322 235899 9999 66552 33455554
No 59
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=29.00 E-value=55 Score=31.22 Aligned_cols=72 Identities=25% Similarity=0.326 Sum_probs=42.5
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCCCCC--------cccccccCCC
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPVG--------HMKEICPMKA 157 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k~--------~~k~~~~~~~ 157 (280)
-.-|=.|+.|+.-|.-.. -.+.=-.-|---....=.+.|.|+-||..--+|.+|+| -+..|-|-++
T Consensus 42 ~~RCL~C~~YI~K~~rfN------avkE~~~dK~y~~~kiYRf~I~C~~C~n~i~~RTDPkN~~YV~EsGg~R~i~pq~~ 115 (272)
T COG5134 42 PVRCLNCENYIQKGTRFN------AVKEEIGDKSYYTTKIYRFSIKCHLCSNPIDVRTDPKNTEYVVESGGRRKIEPQDI 115 (272)
T ss_pred ceeecchhhhhhcccchh------HHHHHhcccccceeEEEEEEEEccCCCCceeeecCCCCceEEEecCceeecCcccc
Confidence 556999999987663111 00000000000000122578999999999999999986 3556777776
Q ss_pred CCCCCC
Q 023552 158 KPSSRP 163 (280)
Q Consensus 158 k~~~~~ 163 (280)
+.-+..
T Consensus 116 n~D~~k 121 (272)
T COG5134 116 NEDPAK 121 (272)
T ss_pred ccChhh
Confidence 665544
No 60
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.92 E-value=41 Score=31.14 Aligned_cols=42 Identities=21% Similarity=0.551 Sum_probs=25.5
Q ss_pred cccCcCCCcccccCCceE--EEEEecchhcccccCCCCCCCCCe-EEEecCCCCCcccc
Q 023552 86 FFSCQRCETVLQPGFNCT--IRIEKNQVKSRRRWKKPKTSMQNT-VVYKCHFCSHHNLK 141 (280)
Q Consensus 86 R~iCKrC~tiLiPG~Ncr--VRI~nnkkK~Kkr~Kk~~~~~~n~-VV~tCl~CG~~n~~ 141 (280)
-.-|.+|+..= -|+|+ .||.-+ +++ -++ ++|+|..|.+.--+
T Consensus 17 ~k~C~~Cg~kr--~f~cSg~fRvNAq--~K~----------LDvWlIYkC~~Cd~tWN~ 61 (203)
T COG4332 17 AKRCNSCGVKR--AFTCSGKFRVNAQ--GKV----------LDVWLIYKCTHCDYTWNI 61 (203)
T ss_pred hhhCcccCCcc--eeeecCcEEEcCC--CcE----------EEEEEEEEeeccCCccch
Confidence 45699998632 33444 566522 111 243 89999999986544
No 61
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=28.48 E-value=32 Score=22.94 Aligned_cols=13 Identities=23% Similarity=0.526 Sum_probs=10.7
Q ss_pred EEEecCCCCCccc
Q 023552 128 VVYKCHFCSHHNL 140 (280)
Q Consensus 128 VV~tCl~CG~~n~ 140 (280)
++|.|..||++..
T Consensus 1 ~~~~C~~CG~i~~ 13 (34)
T cd00729 1 KVWVCPVCGYIHE 13 (34)
T ss_pred CeEECCCCCCEeE
Confidence 3689999999865
No 62
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.35 E-value=42 Score=35.55 Aligned_cols=22 Identities=27% Similarity=0.528 Sum_probs=15.5
Q ss_pred cccCcCCCcccccCCceEEEEEe
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEK 108 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~n 108 (280)
..+|+.|+..+.=. +|.+.+..
T Consensus 383 ~l~C~~Cg~~~~C~-~C~~~L~~ 404 (665)
T PRK14873 383 SLACARCRTPARCR-HCTGPLGL 404 (665)
T ss_pred eeEhhhCcCeeECC-CCCCceeE
Confidence 66899998877644 56666554
No 63
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=27.16 E-value=59 Score=37.30 Aligned_cols=90 Identities=20% Similarity=0.227 Sum_probs=60.5
Q ss_pred ccHHHHHHHHHHHHHHhhcCCCChHHHHH----HHHHHHHHHHhCCCCCcccc--cCcCCCcccccCCceEEEEEecchh
Q 023552 39 KSKLELEHLQRLAVWASSETSVPSLAALF----GHRLASANEVLGLQPDPSFF--SCQRCETVLQPGFNCTIRIEKNQVK 112 (280)
Q Consensus 39 ~s~lRiehL~nLA~~A~~ea~~PsLSr~Y----~r~l~~vseK~~Lpp~~kR~--iCKrC~tiLiPG~NcrVRI~nnkkK 112 (280)
.+.+.|++.|.|+++. .|+++|.. +-....+++-.||.+...|. .=+.=.+.|.||-...--.+.
T Consensus 1179 ~~~l~iD~~YYLa~QI-----hPvV~Rlve~Iegt~a~riae~LGlDstkyr~~~~~q~~~~a~s~~~s~~td~~~---- 1249 (1429)
T KOG0970|consen 1179 EDNLAIDYNYYLAQQI-----HPVVERLVEPIEGTDAVRIAECLGLDSTKYRRHEGNQKENSALSPDESTLTDVER---- 1249 (1429)
T ss_pred CcceeechhhHhhhhc-----chhHHHHhhhhcccCHHHHHHHhCCCchhhhhhhcchhhhhhhCCCcchhcchhh----
Confidence 4448899999999853 37788776 45667778888997755533 235667788888544432220
Q ss_pred cccccCCCCCCCCCeEEEecCCCCCcccccCCCC
Q 023552 113 SRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPV 146 (280)
Q Consensus 113 ~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k 146 (280)
. .-.-.+...|-.|++.+.+.+...
T Consensus 1250 -------~--~~ce~~~l~CptC~~~~~~~~~~~ 1274 (1429)
T KOG0970|consen 1250 -------F--KDCEPLTLRCPTCSTENSRAFAVD 1274 (1429)
T ss_pred -------h--ccccceEEECCCCCCccccccccc
Confidence 0 003357789999999998887654
No 64
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=24.85 E-value=94 Score=26.63 Aligned_cols=39 Identities=23% Similarity=0.423 Sum_probs=27.3
Q ss_pred cccCcCCCccc-------------------ccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCC
Q 023552 86 FFSCQRCETVL-------------------QPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSH 137 (280)
Q Consensus 86 R~iCKrC~tiL-------------------iPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~ 137 (280)
...|..|++.| +++-++..+... +-...++.+.|..||.
T Consensus 37 ~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~v~~~~D~-------------s~g~~R~Ev~C~~Cg~ 94 (124)
T PF01641_consen 37 IYVCAVCGTPLFSSDTKFDSGCGWPSFWQPIPGDAVKEREDF-------------SHGMVRTEVRCARCGS 94 (124)
T ss_dssp EEEETTTS-EEEEGGGEETSSSSSSEESSCSSTTSEEEEEEE-------------CTSSEEEEEEETTTCC
T ss_pred EEEcCCCCCccccCcccccCCcCCccccCcCChHHEEEeccc-------------cCCceEEEEEecCCCC
Confidence 77899999988 466565555552 1135679999999985
No 65
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=24.31 E-value=36 Score=37.33 Aligned_cols=40 Identities=23% Similarity=0.463 Sum_probs=31.5
Q ss_pred ccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCCCCC
Q 023552 87 FSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPVG 147 (280)
Q Consensus 87 ~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k~ 147 (280)
.-|++|.+|+-|=+ ++|+ +-.+++|+.|+..|-.++..-+
T Consensus 200 vRCrrCrsYiNPfv---~fi~------------------~g~kw~CNiC~~kN~vp~~~~~ 239 (861)
T COG5028 200 VRCRRCRSYINPFV---QFIE------------------QGRKWRCNICRSKNDVPEGFDN 239 (861)
T ss_pred hhhhhhHhhcCceE---EEec------------------CCcEEEEeeccccccCcccccC
Confidence 56999999997754 5566 2345799999999999887766
No 66
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=23.84 E-value=96 Score=26.28 Aligned_cols=14 Identities=21% Similarity=0.629 Sum_probs=11.7
Q ss_pred CeEEEecCCCCCcc
Q 023552 126 NTVVYKCHFCSHHN 139 (280)
Q Consensus 126 n~VV~tCl~CG~~n 139 (280)
..+...|..||...
T Consensus 111 r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 111 RLIFLKCKACGASR 124 (125)
T ss_dssp TCCEEEETTTSCEE
T ss_pred CEEEEEecccCCcC
Confidence 57889999999864
No 67
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.43 E-value=49 Score=22.20 Aligned_cols=13 Identities=23% Similarity=0.429 Sum_probs=10.1
Q ss_pred eEEEecCCCCCcc
Q 023552 127 TVVYKCHFCSHHN 139 (280)
Q Consensus 127 ~VV~tCl~CG~~n 139 (280)
...++|..|+|+-
T Consensus 23 ~~~vrC~~C~~~f 35 (37)
T PF13719_consen 23 GRKVRCPKCGHVF 35 (37)
T ss_pred CcEEECCCCCcEe
Confidence 3467999999864
No 68
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.42 E-value=51 Score=21.25 Aligned_cols=13 Identities=31% Similarity=0.677 Sum_probs=7.7
Q ss_pred cccCcCCCccccc
Q 023552 86 FFSCQRCETVLQP 98 (280)
Q Consensus 86 R~iCKrC~tiLiP 98 (280)
+.||-+|++.+++
T Consensus 3 ~rfC~~CG~~t~~ 15 (32)
T PF09297_consen 3 HRFCGRCGAPTKP 15 (32)
T ss_dssp TSB-TTT--BEEE
T ss_pred CcccCcCCccccC
Confidence 6799999987654
No 69
>PRK05580 primosome assembly protein PriA; Validated
Probab=23.20 E-value=56 Score=34.34 Aligned_cols=21 Identities=24% Similarity=0.642 Sum_probs=13.4
Q ss_pred cccCcCCCcccccCCceEEEEE
Q 023552 86 FFSCQRCETVLQPGFNCTIRIE 107 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~ 107 (280)
..+|..|+..+.=. +|.+-+.
T Consensus 381 ~~~C~~Cg~~~~C~-~C~~~l~ 401 (679)
T PRK05580 381 FLLCRDCGWVAECP-HCDASLT 401 (679)
T ss_pred ceEhhhCcCccCCC-CCCCcee
Confidence 67888888776533 4554444
No 70
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=22.74 E-value=78 Score=26.02 Aligned_cols=28 Identities=21% Similarity=0.507 Sum_probs=22.8
Q ss_pred CCeEEEecCCCCCcccccCCCCCcccccccC
Q 023552 125 QNTVVYKCHFCSHHNLKRGTPVGHMKEICPM 155 (280)
Q Consensus 125 ~n~VV~tCl~CG~~n~~rGt~k~~~k~~~~~ 155 (280)
.|..++.|..||+....--+=|+. .||+
T Consensus 38 ~G~~~~~C~~Cg~~~~~~~SCk~R---~CP~ 65 (111)
T PF14319_consen 38 LGFHRYRCEDCGHEKIVYNSCKNR---HCPS 65 (111)
T ss_pred CCcceeecCCCCceEEecCcccCc---CCCC
Confidence 578889999999999888887776 5654
No 71
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=22.68 E-value=1e+02 Score=30.25 Aligned_cols=50 Identities=18% Similarity=0.265 Sum_probs=27.8
Q ss_pred cccccCcCCCcccccCCceEEEEEecchhcccccCCCCCCC---CCeEEEecCCCCCcc
Q 023552 84 PSFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSM---QNTVVYKCHFCSHHN 139 (280)
Q Consensus 84 ~kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~---~n~VV~tCl~CG~~n 139 (280)
..+.+|.-|++.-+-++ |++-..--+.|==+ .+-| =++|.++|.+||...
T Consensus 183 e~~~~CPvCGS~PvaSm---V~~g~~~~GlRYL~---CslC~teW~~VR~KC~nC~~t~ 235 (308)
T COG3058 183 ESRQYCPVCGSMPVASM---VQIGETEQGLRYLH---CSLCETEWHYVRVKCSNCEQSK 235 (308)
T ss_pred cccccCCCcCCCCccee---eeecCccccchhhh---hhhHHHHHHHHHHHhccccccC
Confidence 34789999999766543 44441111111000 0000 167999999999764
No 72
>PF13467 RHH_4: Ribbon-helix-helix domain; PDB: 3KK4_C.
Probab=22.65 E-value=44 Score=25.78 Aligned_cols=14 Identities=43% Similarity=0.662 Sum_probs=11.4
Q ss_pred chhhHHHHHhhccc
Q 023552 253 SWTSLKEIAERSED 266 (280)
Q Consensus 253 swtslkeia~~~e~ 266 (280)
-|..|+|||+....
T Consensus 22 FW~~L~eiA~~~g~ 35 (67)
T PF13467_consen 22 FWDALEEIAAREGL 35 (67)
T ss_dssp HHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHcCC
Confidence 49999999998743
No 73
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=22.38 E-value=1.1e+02 Score=25.42 Aligned_cols=44 Identities=16% Similarity=0.365 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhCCCCCcc-cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCc
Q 023552 68 GHRLASANEVLGLQPDPS-FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHH 138 (280)
Q Consensus 68 ~r~l~~vseK~~Lpp~~k-R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~ 138 (280)
..+|..+-.+ .+. .-+|..|++. ...+-.+ .+.+...|..||..
T Consensus 66 ~~~i~~~l~~-----yI~~yVlC~~C~sp-----dT~l~k~-----------------~r~~~l~C~aCGa~ 110 (110)
T smart00653 66 PKKLQDLLRR-----YIKEYVLCPECGSP-----DTELIKE-----------------NRLFFLKCEACGAR 110 (110)
T ss_pred HHHHHHHHHH-----HHHhcEECCCCCCC-----CcEEEEe-----------------CCeEEEEccccCCC
Confidence 3455554333 334 6789999874 1222222 35788899999973
No 74
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=22.19 E-value=65 Score=24.11 Aligned_cols=13 Identities=23% Similarity=0.524 Sum_probs=10.1
Q ss_pred ccccCcCCC--cccc
Q 023552 85 SFFSCQRCE--TVLQ 97 (280)
Q Consensus 85 kR~iCKrC~--tiLi 97 (280)
++.+|.+|+ +||.
T Consensus 18 k~~~CPrCG~gvfmA 32 (51)
T COG1998 18 KNRFCPRCGPGVFMA 32 (51)
T ss_pred ccccCCCCCCcchhh
Confidence 378999998 6664
No 75
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=22.16 E-value=34 Score=25.11 Aligned_cols=16 Identities=19% Similarity=0.416 Sum_probs=10.9
Q ss_pred CCcccccCcCCCcccc
Q 023552 82 PDPSFFSCQRCETVLQ 97 (280)
Q Consensus 82 p~~kR~iCKrC~tiLi 97 (280)
+...|.||..|++.|-
T Consensus 44 ~~~~r~FC~~CGs~l~ 59 (92)
T PF04828_consen 44 KGVERYFCPTCGSPLF 59 (92)
T ss_dssp SSCEEEEETTT--EEE
T ss_pred CcCcCcccCCCCCeee
Confidence 4455999999999775
No 76
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=21.90 E-value=1.1e+02 Score=26.36 Aligned_cols=34 Identities=24% Similarity=0.523 Sum_probs=23.3
Q ss_pred cccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccc
Q 023552 86 FFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 86 R~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~ 141 (280)
.-+|..|++ |-.... .+ .+.+...|..||.....
T Consensus 102 yVlC~~C~s---pdT~l~--k~-----------------~r~~~l~C~ACGa~~~V 135 (138)
T PRK03988 102 YVICPECGS---PDTKLI--KE-----------------GRIWVLKCEACGAETPV 135 (138)
T ss_pred cEECCCCCC---CCcEEE--Ec-----------------CCeEEEEcccCCCCCcC
Confidence 678999987 442221 12 34678999999997654
No 77
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=21.55 E-value=1.2e+02 Score=26.78 Aligned_cols=12 Identities=25% Similarity=0.636 Sum_probs=10.5
Q ss_pred cccCcCCCcccc
Q 023552 86 FFSCQRCETVLQ 97 (280)
Q Consensus 86 R~iCKrC~tiLi 97 (280)
...|..|++.|-
T Consensus 43 ~Y~C~~Cg~pLF 54 (142)
T PRK00222 43 IYVCIVCGEPLF 54 (142)
T ss_pred EEEecCCCchhc
Confidence 679999999884
No 78
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=21.30 E-value=55 Score=25.65 Aligned_cols=26 Identities=12% Similarity=0.245 Sum_probs=19.2
Q ss_pred CeEEEecCCCCCcccccCCCCCcccc
Q 023552 126 NTVVYKCHFCSHHNLKRGTPVGHMKE 151 (280)
Q Consensus 126 n~VV~tCl~CG~~n~~rGt~k~~~k~ 151 (280)
..-+++|+.||.+=....-.|+.|++
T Consensus 35 ast~V~C~~CG~~l~~PTGGka~i~~ 60 (67)
T COG2051 35 ASTVVTCLICGTTLAEPTGGKAKISG 60 (67)
T ss_pred CceEEEecccccEEEecCCCeEEeee
Confidence 45667999999987777666666654
No 79
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=20.94 E-value=52 Score=31.88 Aligned_cols=17 Identities=24% Similarity=0.581 Sum_probs=15.0
Q ss_pred CeEEEecCCCCCccccc
Q 023552 126 NTVVYKCHFCSHHNLKR 142 (280)
Q Consensus 126 n~VV~tCl~CG~~n~~r 142 (280)
+.+.++|+|||..+.|-
T Consensus 263 g~iev~C~FC~~~Y~f~ 279 (286)
T COG1281 263 GGIEVTCEFCGTKYLFD 279 (286)
T ss_pred CCeEEEeeccCCEEecC
Confidence 57999999999999874
No 80
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.82 E-value=60 Score=26.55 Aligned_cols=40 Identities=20% Similarity=0.308 Sum_probs=29.4
Q ss_pred ccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCCCCCcc
Q 023552 87 FSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPVGHM 149 (280)
Q Consensus 87 ~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k~~~ 149 (280)
.+|..|+.-|++-.-. +.=+--|-.|+.+-|-||...-.|
T Consensus 2 llCP~C~v~l~~~~rs-----------------------~vEiD~CPrCrGVWLDrGELdKli 41 (88)
T COG3809 2 LLCPICGVELVMSVRS-----------------------GVEIDYCPRCRGVWLDRGELDKLI 41 (88)
T ss_pred cccCcCCceeeeeeec-----------------------CceeeeCCccccEeecchhHHHHH
Confidence 4799998888765433 344447999999999999865444
No 81
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=20.63 E-value=3.6e+02 Score=25.74 Aligned_cols=62 Identities=18% Similarity=0.229 Sum_probs=40.3
Q ss_pred HHHHHHHHHh--CCCCCcccccCcCCCcccccCCceEEEEEecchhcccccCCCCCCCCCeEEEecCCCCCcccccCCCC
Q 023552 69 HRLASANEVL--GLQPDPSFFSCQRCETVLQPGFNCTIRIEKNQVKSRRRWKKPKTSMQNTVVYKCHFCSHHNLKRGTPV 146 (280)
Q Consensus 69 r~l~~vseK~--~Lpp~~kR~iCKrC~tiLiPG~NcrVRI~nnkkK~Kkr~Kk~~~~~~n~VV~tCl~CG~~n~~rGt~k 146 (280)
+=|....+|+ +.-..--|..|++|. +|--|++=..+ ...|-+-|-.|..+..-+-+.-
T Consensus 106 ~Gl~~M~eKY~~g~FG~CPRv~C~~q~-~LPvGlSd~~g-------------------~~~VKlyCP~C~DvY~p~s~~~ 165 (251)
T PTZ00396 106 KGLALMREKYLQGKFGHCPRVLCEGQN-VLPIGLSDVLK-------------------TSRVKVYCPRCQEVYHPKKSSL 165 (251)
T ss_pred HHHHHHHHHhhCCCCCCCCCccCCCCc-ccccccCCCcC-------------------cCceeEeCCCchhhcCCCCccc
Confidence 4455556777 565656699999985 44448644333 3478889999999986554333
Q ss_pred Cccc
Q 023552 147 GHMK 150 (280)
Q Consensus 147 ~~~k 150 (280)
.+|-
T Consensus 166 ~~iD 169 (251)
T PTZ00396 166 LDID 169 (251)
T ss_pred cccc
Confidence 3443
No 82
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 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 [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=20.39 E-value=61 Score=24.29 Aligned_cols=26 Identities=19% Similarity=0.367 Sum_probs=14.5
Q ss_pred HHHHHHHhCCCCCcccccCcCCCcccccCC
Q 023552 71 LASANEVLGLQPDPSFFSCQRCETVLQPGF 100 (280)
Q Consensus 71 l~~vseK~~Lpp~~kR~iCKrC~tiLiPG~ 100 (280)
|..+++++. ....||++|++-|-|..
T Consensus 6 l~~la~K~n----~~k~ICrkCyarl~~~A 31 (52)
T PF01020_consen 6 LRALAQKYN----CDKMICRKCYARLPPRA 31 (52)
T ss_dssp HHHHHHHHH----TS-EEETTT--EE-TTS
T ss_pred HHHHHHHHc----ccceecccccCcCCCCc
Confidence 344566643 25789999999888763
No 83
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=20.38 E-value=58 Score=22.18 Aligned_cols=13 Identities=38% Similarity=0.833 Sum_probs=11.2
Q ss_pred eEEEecCCCCCcc
Q 023552 127 TVVYKCHFCSHHN 139 (280)
Q Consensus 127 ~VV~tCl~CG~~n 139 (280)
.+.|.|..|||.-
T Consensus 26 T~fy~C~~C~~~w 38 (39)
T PF01096_consen 26 TLFYVCCNCGHRW 38 (39)
T ss_dssp EEEEEESSSTEEE
T ss_pred eEEEEeCCCCCee
Confidence 6999999999863
No 84
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=20.20 E-value=72 Score=24.69 Aligned_cols=17 Identities=29% Similarity=0.630 Sum_probs=13.5
Q ss_pred CCeEEEecCCCCCcccc
Q 023552 125 QNTVVYKCHFCSHHNLK 141 (280)
Q Consensus 125 ~n~VV~tCl~CG~~n~~ 141 (280)
...|+|-|..||..|..
T Consensus 16 ~~~miYiCgdC~~en~l 32 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTL 32 (62)
T ss_pred cccEEEEeccccccccc
Confidence 45789999999988753
No 85
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=20.15 E-value=1.3e+02 Score=20.41 Aligned_cols=21 Identities=19% Similarity=0.423 Sum_probs=14.4
Q ss_pred ccCcCCCccccc-CCc-eEEEEE
Q 023552 87 FSCQRCETVLQP-GFN-CTIRIE 107 (280)
Q Consensus 87 ~iCKrC~tiLiP-G~N-crVRI~ 107 (280)
..|..|+.-|.+ |.. .+-.++
T Consensus 3 ~~C~~Cg~~l~~ig~~~~~q~l~ 25 (47)
T PF13005_consen 3 RACPDCGGELKEIGEEKVRQVLD 25 (47)
T ss_pred CcCCCCCceeeECCceeeEEEEe
Confidence 579999998875 665 444444
No 86
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.06 E-value=61 Score=24.85 Aligned_cols=14 Identities=29% Similarity=0.665 Sum_probs=11.6
Q ss_pred CeEEEecCCCCCcc
Q 023552 126 NTVVYKCHFCSHHN 139 (280)
Q Consensus 126 n~VV~tCl~CG~~n 139 (280)
-.+.++|..|||.-
T Consensus 31 aDIkikC~nC~h~v 44 (60)
T COG4481 31 ADIKIKCENCGHSV 44 (60)
T ss_pred CcEEEEecCCCcEE
Confidence 46899999999963
No 87
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=20.05 E-value=57 Score=23.83 Aligned_cols=22 Identities=23% Similarity=0.440 Sum_probs=15.8
Q ss_pred EEecCCCCCcccccCCCCCcccc
Q 023552 129 VYKCHFCSHHNLKRGTPVGHMKE 151 (280)
Q Consensus 129 V~tCl~CG~~n~~rGt~k~~~k~ 151 (280)
++.||+||++.=-++.. ||+..
T Consensus 11 lw~CL~Cg~~~C~~~~~-~Ha~~ 32 (63)
T PF02148_consen 11 LWLCLTCGYVGCGRYSN-GHALK 32 (63)
T ss_dssp EEEETTTS-EEETTTST-SHHHH
T ss_pred eEEeCCCCcccccCCcC-cHHHH
Confidence 56799999998877665 77653
Done!