Query 013381
Match_columns 444
No_of_seqs 205 out of 411
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 03:16:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013381.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013381hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0909 Peptide:N-glycanase [P 100.0 7E-107 2E-111 823.8 20.2 354 3-434 145-500 (500)
2 PF03835 Rad4: Rad4 transgluta 99.9 6.4E-23 1.4E-27 183.4 7.5 102 103-215 33-145 (145)
3 TIGR00605 rad4 DNA repair prot 99.8 1.9E-20 4.2E-25 203.8 8.0 137 73-218 256-477 (713)
4 PF01841 Transglut_core: Trans 99.5 4.2E-14 9.2E-19 117.4 6.0 81 43-124 16-113 (113)
5 smart00460 TGc Transglutaminas 99.4 5.1E-13 1.1E-17 102.7 6.0 53 71-125 1-67 (68)
6 COG1305 Transglutaminase-like 99.2 1.6E-11 3.4E-16 116.4 7.9 78 62-140 180-275 (319)
7 KOG2179 Nucleotide excision re 99.2 7E-12 1.5E-16 135.4 4.2 129 76-217 263-428 (669)
8 COG5535 RAD4 DNA repair protei 98.5 9.6E-09 2.1E-13 110.0 -3.1 124 70-193 241-399 (650)
9 PF04473 DUF553: Transglutamin 97.2 0.0014 3E-08 60.7 8.2 68 60-129 59-131 (153)
10 PF13369 Transglut_core2: Tran 94.0 0.17 3.7E-06 45.9 6.9 63 60-126 48-110 (152)
11 COG5279 CYK3 Uncharacterized p 93.7 0.16 3.4E-06 55.2 6.9 64 60-125 189-268 (521)
12 PF14381 EDR1: Ethylene-respon 90.6 0.46 1E-05 46.1 5.4 53 71-124 137-195 (204)
13 COG1571 Predicted DNA-binding 87.8 0.33 7.1E-06 51.8 2.3 35 17-66 349-383 (421)
14 PF14402 7TM_transglut: 7 tran 86.2 0.71 1.5E-05 47.6 3.6 47 85-133 2-57 (313)
15 PF12760 Zn_Tnp_IS1595: Transp 85.7 0.54 1.2E-05 35.0 1.9 33 13-58 13-45 (46)
16 PF13471 Transglut_core3: Tran 85.7 1.3 2.9E-05 38.2 4.6 37 75-111 54-97 (117)
17 COG2816 NPY1 NTP pyrophosphohy 83.1 0.5 1.1E-05 48.0 0.9 53 4-78 103-155 (279)
18 PRK00464 nrdR transcriptional 75.6 2.2 4.7E-05 39.9 2.5 35 20-58 2-36 (154)
19 TIGR03655 anti_R_Lar restricti 74.8 5.3 0.00011 30.5 4.1 36 20-62 3-38 (53)
20 PF13453 zf-TFIIB: Transcripti 73.8 2.7 5.8E-05 30.5 2.1 28 20-59 1-28 (41)
21 PRK09710 lar restriction allev 69.4 4.3 9.3E-05 33.1 2.6 34 18-62 6-39 (64)
22 PF00797 Acetyltransf_2: N-ace 68.2 5 0.00011 38.3 3.2 68 69-138 38-120 (240)
23 PF06035 Peptidase_C93: Bacter 64.3 5.3 0.00011 38.1 2.5 25 73-97 74-98 (170)
24 PF14354 Lar_restr_allev: Rest 63.1 8.9 0.00019 29.4 3.2 34 19-58 4-37 (61)
25 PRK00241 nudC NADH pyrophospha 62.4 8.5 0.00018 38.3 3.7 45 3-68 90-134 (256)
26 PF09862 DUF2089: Protein of u 61.6 7.5 0.00016 34.9 2.8 16 46-61 8-23 (113)
27 PHA02998 RNA polymerase subuni 61.4 6.2 0.00014 38.2 2.4 45 19-68 144-189 (195)
28 PF08274 PhnA_Zn_Ribbon: PhnA 61.0 2.6 5.6E-05 29.5 -0.1 27 18-59 2-28 (30)
29 TIGR00686 phnA alkylphosphonat 60.8 5.8 0.00013 35.4 2.0 28 17-59 1-28 (109)
30 PF14353 CpXC: CpXC protein 60.6 6.1 0.00013 34.7 2.1 43 19-62 2-50 (128)
31 PRK10220 hypothetical protein; 59.2 7.2 0.00016 35.0 2.3 30 16-60 1-30 (111)
32 PRK10941 hypothetical protein; 55.6 37 0.00081 34.2 6.9 65 63-129 82-146 (269)
33 PF06397 Desulfoferrod_N: Desu 55.4 6.9 0.00015 28.5 1.3 14 47-60 3-16 (36)
34 PF14803 Nudix_N_2: Nudix N-te 53.1 7.6 0.00017 27.8 1.2 29 21-59 3-31 (34)
35 PRK15047 N-hydroxyarylamine O- 52.9 13 0.00028 37.6 3.2 65 70-136 59-137 (281)
36 COG1997 RPL43A Ribosomal prote 52.4 12 0.00027 32.3 2.5 30 17-61 34-64 (89)
37 PF04216 FdhE: Protein involve 50.4 6.7 0.00015 39.3 0.8 45 14-66 169-213 (290)
38 TIGR02667 moaB_proteo molybden 49.2 15 0.00033 34.0 2.8 60 328-387 88-159 (163)
39 COG2888 Predicted Zn-ribbon RN 48.2 11 0.00024 30.5 1.5 35 18-57 9-45 (61)
40 PF13005 zf-IS66: zinc-finger 48.0 15 0.00032 26.8 2.1 39 18-57 2-47 (47)
41 cd00886 MogA_MoaB MogA_MoaB fa 46.9 25 0.00054 31.9 3.8 52 332-383 90-151 (152)
42 PF12386 Peptidase_C71: Pseudo 46.1 20 0.00043 33.1 3.0 29 73-101 51-79 (142)
43 PF04721 DUF750: Domain of unk 45.2 0.28 6.2E-06 39.5 -7.9 57 267-325 3-59 (62)
44 PF14169 YdjO: Cold-inducible 44.5 12 0.00026 30.1 1.2 23 7-29 28-50 (59)
45 PF03811 Zn_Tnp_IS1: InsA N-te 43.3 22 0.00049 25.7 2.3 29 19-57 6-36 (36)
46 PF04981 NMD3: NMD3 family ; 43.3 85 0.0018 30.7 7.1 135 21-174 1-143 (236)
47 smart00440 ZnF_C2C2 C2C2 Zinc 41.6 25 0.00053 25.7 2.4 35 20-59 2-37 (40)
48 COG1594 RPB9 DNA-directed RNA 41.4 20 0.00044 31.8 2.3 39 19-62 73-112 (113)
49 cd04476 RPA1_DBD_C RPA1_DBD_C: 41.2 14 0.00031 33.6 1.3 64 14-123 31-97 (166)
50 TIGR03696 Rhs_assc_core RHS re 41.0 28 0.00061 28.2 2.9 39 106-145 32-70 (76)
51 TIGR01562 FdhE formate dehydro 40.9 24 0.00052 36.5 3.0 49 16-81 182-232 (305)
52 TIGR02159 PA_CoA_Oxy4 phenylac 40.8 13 0.00029 34.3 1.1 34 18-59 105-139 (146)
53 TIGR00319 desulf_FeS4 desulfof 40.6 16 0.00035 25.4 1.2 14 47-60 4-17 (34)
54 PRK02935 hypothetical protein; 40.5 20 0.00043 32.1 2.0 31 18-64 70-100 (110)
55 PHA00626 hypothetical protein 40.2 17 0.00038 29.2 1.5 29 20-58 2-31 (59)
56 COG3672 Predicted transglutami 40.2 78 0.0017 31.0 6.1 32 60-97 97-128 (191)
57 PF11672 DUF3268: Protein of u 39.5 29 0.00062 30.7 2.9 45 18-68 2-50 (102)
58 PF14690 zf-ISL3: zinc-finger 38.7 27 0.00058 25.3 2.2 39 18-56 2-47 (47)
59 PF13240 zinc_ribbon_2: zinc-r 37.6 16 0.00035 23.9 0.8 8 20-27 1-8 (23)
60 TIGR00244 transcriptional regu 37.2 16 0.00036 34.2 1.1 55 20-78 2-57 (147)
61 PF01096 TFIIS_C: Transcriptio 36.7 19 0.0004 26.2 1.1 35 20-59 2-37 (39)
62 COG2912 Uncharacterized conser 33.9 73 0.0016 32.6 5.1 67 60-129 80-146 (269)
63 cd00974 DSRD Desulforedoxin (D 33.5 23 0.00051 24.7 1.1 13 48-60 2-14 (34)
64 TIGR00340 zpr1_rel ZPR1-relate 33.4 39 0.00085 31.9 2.9 34 21-59 1-37 (163)
65 COG4332 Uncharacterized protei 33.3 27 0.00059 34.0 1.9 44 20-65 19-64 (203)
66 KOG4477 RING1 interactor RYBP 32.9 16 0.00034 35.8 0.2 38 32-69 14-61 (228)
67 PF11023 DUF2614: Protein of u 32.5 20 0.00044 32.3 0.9 31 18-64 69-99 (114)
68 COG2162 NhoA Arylamine N-acety 31.4 1E+02 0.0022 31.8 5.6 63 72-136 63-139 (275)
69 PF11781 RRN7: RNA polymerase 30.9 39 0.00084 24.4 1.9 31 15-60 3-35 (36)
70 PF04216 FdhE: Protein involve 30.8 27 0.00059 35.0 1.5 39 17-61 210-249 (290)
71 TIGR01384 TFS_arch transcripti 30.7 46 0.00099 28.2 2.7 36 19-59 63-99 (104)
72 PRK03564 formate dehydrogenase 30.5 44 0.00096 34.7 3.0 51 15-81 184-234 (309)
73 TIGR03830 CxxCG_CxxCG_HTH puta 30.1 32 0.00069 29.5 1.6 38 21-59 1-40 (127)
74 PRK15312 antimicrobial resista 30.0 1.6E+02 0.0034 30.7 6.8 81 70-150 174-277 (298)
75 PF06044 DRP: Dam-replacing fa 28.5 27 0.00059 35.3 1.1 35 14-59 26-62 (254)
76 COG3809 Uncharacterized protei 28.3 32 0.00069 29.5 1.3 28 20-59 3-30 (88)
77 smart00709 Zpr1 Duplicated dom 28.1 48 0.001 31.1 2.6 34 20-58 2-37 (160)
78 smart00661 RPOL9 RNA polymeras 28.0 52 0.0011 24.2 2.3 14 49-62 19-32 (52)
79 PF08646 Rep_fac-A_C: Replicat 27.7 16 0.00034 32.8 -0.7 66 14-125 15-85 (146)
80 COG0521 MoaB Molybdopterin bio 27.6 46 0.001 31.8 2.4 60 319-378 83-154 (169)
81 TIGR00310 ZPR1_znf ZPR1 zinc f 27.6 44 0.00094 32.4 2.2 34 20-58 2-38 (192)
82 PRK00398 rpoP DNA-directed RNA 27.1 42 0.00091 24.7 1.6 11 50-60 21-31 (46)
83 PF12390 Se-cys_synth_N: Selen 26.7 38 0.00083 24.5 1.3 37 332-384 3-39 (40)
84 COG0675 Transposase and inacti 25.7 43 0.00093 32.3 1.9 22 19-59 310-331 (364)
85 PRK03564 formate dehydrogenase 24.8 53 0.0012 34.1 2.4 39 17-61 225-263 (309)
86 PRK00432 30S ribosomal protein 24.2 55 0.0012 25.2 1.8 40 4-59 4-46 (50)
87 PRK03954 ribonuclease P protei 23.7 42 0.00092 30.4 1.3 22 47-70 91-112 (121)
88 TIGR01206 lysW lysine biosynth 23.3 58 0.0013 25.6 1.8 32 19-62 3-34 (54)
89 COG1327 Predicted transcriptio 23.2 26 0.00055 33.2 -0.2 42 20-65 2-44 (156)
90 COG1571 Predicted DNA-binding 23.1 57 0.0012 35.3 2.3 62 308-369 48-111 (421)
91 PF10058 DUF2296: Predicted in 22.8 64 0.0014 25.3 2.0 31 19-59 23-53 (54)
92 PF14951 DUF4503: Domain of un 22.5 32 0.00068 36.7 0.3 36 13-63 272-307 (389)
93 TIGR03831 YgiT_finger YgiT-typ 22.5 27 0.0006 24.8 -0.1 38 21-59 1-41 (46)
94 PF12172 DUF35_N: Rubredoxin-l 22.5 65 0.0014 22.6 1.8 21 45-65 6-26 (37)
95 PRK14714 DNA polymerase II lar 22.4 44 0.00095 40.7 1.4 68 18-98 667-745 (1337)
96 COG1326 Uncharacterized archae 22.3 46 0.001 32.7 1.3 34 19-60 7-40 (201)
97 PF09855 DUF2082: Nucleic-acid 22.3 77 0.0017 25.8 2.4 41 20-60 2-46 (64)
98 PF09986 DUF2225: Uncharacteri 22.2 52 0.0011 31.9 1.7 50 18-67 5-68 (214)
99 PRK05978 hypothetical protein; 22.0 65 0.0014 30.2 2.2 32 19-63 34-65 (148)
100 TIGR00617 rpa1 replication fac 22.0 1.2E+02 0.0026 34.1 4.6 24 101-124 517-540 (608)
101 PF08271 TF_Zn_Ribbon: TFIIB z 21.6 28 0.00061 25.4 -0.2 30 20-62 2-31 (43)
102 TIGR00311 aIF-2beta translatio 21.6 70 0.0015 29.3 2.3 28 20-59 99-127 (133)
103 COG3677 Transposase and inacti 21.6 53 0.0012 29.7 1.5 37 13-59 24-62 (129)
104 PF01780 Ribosomal_L37ae: Ribo 20.6 56 0.0012 28.4 1.3 26 19-59 36-62 (90)
105 PF08421 Methyltransf_13: Puta 20.5 63 0.0014 25.5 1.6 39 21-59 1-49 (62)
106 PF09151 DUF1936: Domain of un 20.3 43 0.00092 24.2 0.5 26 20-54 3-28 (36)
107 TIGR01562 FdhE formate dehydro 20.2 71 0.0015 33.1 2.3 41 17-61 223-263 (305)
No 1
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.1e-107 Score=823.81 Aligned_cols=354 Identities=42% Similarity=0.724 Sum_probs=332.4
Q ss_pred chhHHhhccC-ceeecCCCCCCCCCCC-ccccCCCCChhhhhcCccEEEEEecCCCCCccccCCCCCHHHHHHhCCccch
Q 013381 3 LICVLFILQY-CRWVNAPPCDGCSNET-VGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCG 80 (444)
Q Consensus 3 ~~LL~WFK~~-F~Wvn~P~C~~Cg~~t-~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~kLL~tR~GrCg 80 (444)
|+||+|||++ |+|||+|+|+.||++| ...|.++|+.+|.++||+|||+|+|+.||+.+||||||||.|||+||+||||
T Consensus 145 leLL~WFKq~FF~WvN~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPRYNdp~kLLeTRkGRCG 224 (500)
T KOG0909|consen 145 LELLNWFKQDFFKWVNNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPRYNDPIKLLETRKGRCG 224 (500)
T ss_pred HHHHHHHHHhhheecCCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCcccCCHHHHHhhccCccc
Confidence 5799999985 8999999999999999 5777788999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHcCCCeEEEEeCCCceEEEEeeCCCCCeEEeccCCCccCCCeeeecCccCccceEEeecCCcceechhh
Q 013381 81 EWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKR 160 (444)
Q Consensus 81 E~AnlF~~l~RAlG~~aR~V~d~~dHvW~EVys~~~~rWIhVDPceg~iD~Pllye~gwgK~lsYVIAFs~DGv~DVTrR 160 (444)
|||||||++|||+|++||||||.+||||+||||+.++|||||||||+++|+|+||+.||||+|+|||||++|||+|||||
T Consensus 225 EWANCFTllcralg~daR~i~d~tDHVWtEvYS~~qqRW~HvDpcE~v~D~PllYe~GW~KklsY~iafgkD~VvDVT~R 304 (500)
T KOG0909|consen 225 EWANCFTLLCRALGLDARYIWDRTDHVWTEVYSNAQQRWVHVDPCENVFDKPLLYEIGWGKKLSYCIAFGKDGVVDVTWR 304 (500)
T ss_pred hHHHHHHHHHHHcCCcceEEeecCcchhHHhhhhhhheeEeecccccccccceeeecccCcccceEEEeccCceEeeehh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccChHHHhhccccccHHHHHHHHHHHHHHHHccCCHHHhhhhhhhcHHHHHHHHhhccCCCCCCCCCCCcccccHHHHH
Q 013381 161 YTRKWHEVLSRRNIATEQTVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAMERDLYSTDDAPVSLPGRQSGDKEWRI 240 (444)
Q Consensus 161 Yt~~~~~~~~RR~rv~Eewl~~~L~~l~~~~R~~ls~~~~~~Le~RD~~E~~EL~~~~~~~~~~~~~l~GRqSGs~eWr~ 240 (444)
|+.+|.+++.+|+.|.|+.|+.+|..||+++|.++++++++.|++||.+|..||.+.+.+..++..+||||||||++||.
T Consensus 305 Yi~~h~e~~~~R~~~~E~~l~~~l~~in~~rr~~lt~~r~~~L~~rd~~e~~El~~~~~~~~~~~~~L~GR~SGs~eWr~ 384 (500)
T KOG0909|consen 305 YILDHKENLLPRDLCKESVLQQTLQFINKRRRYSLTDDRKKELAQRDEREQIELIRGKTPETPTKSSLPGRQSGSVEWRA 384 (500)
T ss_pred hhccchhhccchhhcchHHHHHHHHHHHHHHHhhcChHHHHHHHhhhHHHHHHHHhccccCCCCCCCCCCcccccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999988888889999999999999999
Q ss_pred hhcCCCCCCCCCccCCCCCceeecccceeeEeecchhhhhccccCCCchhhHHHHHHHHHHHHhhccCCCcccccccccC
Q 013381 241 SRSEIGSDDNCSLSCSSCPVRVCIDEHVTTIYNAFSSVLSHFVENNVPKSGAIELLKILKGILGDLKKSPYKTRRVSLNS 320 (444)
Q Consensus 241 aRGE~G~~~~~s~~~s~cp~r~c~dehv~~iY~a~~~~ls~~~~~~~~~~~a~~~~~~~r~~~~dlk~~~f~~R~~~~~~ 320 (444)
+|||+|. |++ ||+.+- + |.++||++..|||++|.||||+ |++|.+--+-
T Consensus 385 ~RGE~G~-------------------h~~-i~D~~~-------~---~~~~~~e~~~i~r~ve~Dw~mt-ylaR~~~~s~ 433 (500)
T KOG0909|consen 385 QRGEDGK-------------------HNT-IYDSYT-------E---WSAQAFELENIFRKVETDWKMT-YLARLEGDSP 433 (500)
T ss_pred hhccccc-------------------cce-ehhhhh-------h---HHHHHHHHHHHHHHHHhhHHHH-HHHHhcCCCC
Confidence 9999998 777 888765 1 8999999999999999999999 9999998777
Q ss_pred CCCchhHHHHhhhccHHHHHHhhccccccCCCCCeEEEecCCccccccchhhhHHHHHHHHHhcccccCCCCCccccccc
Q 013381 321 VPNNGQKIVHQLLPSIGHLLRVLSLKSELNTDGRVDIVLAGDPVKTSLSLPVVFKALDDMIHDLNNCDNFGKGSFCLPLL 400 (444)
Q Consensus 321 ~~~~~~~~~~~~lps~~~ll~~lslk~~~~~~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 400 (444)
..+++ .| +++ +.+.++.++||+.++.|.|+= ++||.+||.+.. .++++-.++.
T Consensus 434 ~~isw--~f-d~~-~~~~~~~~~~l~~~~qtf~~g-------------~~~v~~D~s~~s-ad~~~a~~l~--------- 486 (500)
T KOG0909|consen 434 GNISW--HF-DFK-LKGLKVKSESLMAEIQTFGKG-------------CMRVTIDASALS-ADPSNATILK--------- 486 (500)
T ss_pred ccccc--hh-hhh-hcccHHHHHHHHhhhhhcCCC-------------ceEeeechhccc-CCcccCceee---------
Confidence 77777 23 233 889999999999999999874 889999999888 7777744432
Q ss_pred ccccccccceeecccccccceeeccccCCCcccc
Q 013381 401 KLNRIHSGSVLASGEEFPFGIVTSAFDGIRPSKW 434 (444)
Q Consensus 401 ~~~~~~~g~~~a~~e~~p~g~~~~af~g~~~~kw 434 (444)
|+|.+|+|+.-.||
T Consensus 487 --------------------i~t~~~~g~~~~~w 500 (500)
T KOG0909|consen 487 --------------------IRTELFSGKGDVKW 500 (500)
T ss_pred --------------------eehhhcCCccccCC
Confidence 99999999999998
No 2
>PF03835 Rad4: Rad4 transglutaminase-like domain; InterPro: IPR018325 RAD4/Xp-C proteins contain an ancient transglutaminase fold that is also found in peptide-N-glycanases (PNGases), which remove glycans from glycoproteins during their degradation. The PNGases retain the catalytic triad that is typical of this fold and are predicted to have a reaction mechanism similar to that involved in transglutamination. In contrast, the RAD4/Xp-C proteins are predicted to be inactive and are likely to only possess the interaction function in DNA repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A 1X3W_A 1X3Z_A 3ESW_A.
Probab=99.88 E-value=6.4e-23 Score=183.44 Aligned_cols=102 Identities=36% Similarity=0.564 Sum_probs=74.0
Q ss_pred CCCceEEEEeeCCCCCeEEeccCCC-----ccCCCeeeecCccCccceEEeecCCc-ceechhhhccChHHHhhcccccc
Q 013381 103 FTDHVWTECFSQSLGRWMHLDPCEG-----IYDRPLLYEKGWNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSRRNIAT 176 (444)
Q Consensus 103 ~~dHvW~EVys~~~~rWIhVDPceg-----~iD~Pllye~gwgK~lsYVIAFs~DG-v~DVTrRYt~~~~~~~~RR~rv~ 176 (444)
..+|+|+|||++.++||||||||++ .++.|. ..+|+++|+|||||+.|| ++|||+||+.++.....+|.|+.
T Consensus 33 ~~~~~W~EV~~~~~~rWI~VDp~~~~~~~~~~~ep~--~~~~~~~~~YViA~d~~~~~kDVT~RY~~~~~~~~~~r~R~~ 110 (145)
T PF03835_consen 33 PYPNFWVEVYSPEEKRWIHVDPVVGKIIKVSCDEPL--EENANNPMSYVIAFDNDGYAKDVTRRYASNYWNSKTRRLRVD 110 (145)
T ss_dssp TTTCEEEEEEETTTTEEEEEETTTS-EESTBTTSTC--CCCCS--B-EEEEE-CTTEEEE-HHHH-T-TCCCCCGGGSGG
T ss_pred CCCeEEEEEEecCCCeEEEeeeeccccccccccCch--hhccCCceEEEEEEeCCCCEEEchHhhcccccccccccccCC
Confidence 3689999999999999999999997 667777 778999999999996555 69999999998334446888888
Q ss_pred -----HHHHHHHHHHHHHHHHccCCHHHhhhhhhhcHHHHHHHH
Q 013381 177 -----EQTVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAME 215 (444)
Q Consensus 177 -----Eewl~~~L~~l~~~~R~~ls~~~~~~Le~RD~~E~~EL~ 215 (444)
++||..+|+.++...+... .||..|++||.
T Consensus 111 ~~~~~~~W~~~~l~~~~~~~~~~~---------~~d~~Ed~el~ 145 (145)
T PF03835_consen 111 RSYEEEDWWEKVLRPYNRPRRDRT---------IRDKKEDEELH 145 (145)
T ss_dssp GSHHHHHHHHHHHHHH--S---H-----------HHHHHHHHH-
T ss_pred ccccHHHHHHHHHHHHhccccccc---------chHHHHHhhcC
Confidence 9999999998885443311 57888988873
No 3
>TIGR00605 rad4 DNA repair protein rad4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.81 E-value=1.9e-20 Score=203.75 Aligned_cols=137 Identities=19% Similarity=0.292 Sum_probs=109.1
Q ss_pred HhCCccchhhHHHHHHHHHHcCCCeEEEEeC-------------------------------------------------
Q 013381 73 ETKRGRCGEWANCFTLYCRAFGYESRLILDF------------------------------------------------- 103 (444)
Q Consensus 73 ~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d~------------------------------------------------- 103 (444)
.++.|+.+--|++|++++|++|.+||+|.+.
T Consensus 256 ~~~~gsrd~~aql~~allr~~~~~~rlv~slqpl~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~s~~S~~~tsR~~l~~ 335 (713)
T TIGR00605 256 NRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHNDPEISSEGFVPKLSACNANQRLIMSCESADRTSRFRMKK 335 (713)
T ss_pred hccccccchhhhHHHHHHhhhcccccccccccccCcccCCCCcccccccccccccccccccccccccCCCCccccccccc
Confidence 4667888889999999999999999999420
Q ss_pred ---------------------------------CCceEEEEeeCCCCCeEEeccCC-CccCCCeeeecCccCccceEEee
Q 013381 104 ---------------------------------TDHVWTECFSQSLGRWMHLDPCE-GIYDRPLLYEKGWNKKLNYVIAI 149 (444)
Q Consensus 104 ---------------------------------~dHvW~EVys~~~~rWIhVDPce-g~iD~Pllye~gwgK~lsYVIAF 149 (444)
.+++|+|||++..++||||||++ +++|+|..|..+|+++|+|||||
T Consensus 336 ~l~~P~fs~~~~~~k~~~~~~~~~~~~~~~~~~~p~~W~Ev~~~~~~rWI~VD~~~~~~~~~~~~~~e~~~~~m~YVvAf 415 (713)
T TIGR00605 336 DPSLPGFSAYSDMDKSPIFTCEEGDKFIDRWITYVDFWVEVFIEQEEKWVCVDAVHSGVVPKGVTCFEPATLMMTYVFAY 415 (713)
T ss_pred cCCCCCccccccCCCCCccchhcccccccccCCCCeeEEEEeecccceeEEeccccccccCCchhhccCCCCceEEEEEE
Confidence 03899999999999999999999 99999998889999999999999
Q ss_pred cCCc-ceechhhhccChHHHhhccccccHHHHHHH-HHHHHHHHHccCCHHHhhhhhhhcHHHHHHHHhhc
Q 013381 150 SKDG-VFDVTKRYTRKWHEVLSRRNIATEQTVSAV-LAKMTRECRRSFASETLSTLEDRDKCEREAMERDL 218 (444)
Q Consensus 150 s~DG-v~DVTrRYt~~~~~~~~RR~rv~Eewl~~~-L~~l~~~~R~~ls~~~~~~Le~RD~~E~~EL~~~~ 218 (444)
+.|| ++|||+||+.+|+.. .|+.||+..|+.++ ++.+-..... + ... +|..|+.||....
T Consensus 416 ~~d~~~kDVT~RY~~~~~~k-~r~~Rv~~~w~~~~w~~~~~~~~~~------r-~~~-~d~~Ed~el~~~~ 477 (713)
T TIGR00605 416 DRDGYVKDVTRRYCDQWSTK-VRKRRVEKADFGETWFRPIFGALHK------R-KRT-IDDIEDQEFLRRH 477 (713)
T ss_pred cCCCceeechhhHhhhhhhh-hheeeecccchHHHHHHHHhhhhcc------C-ccc-hhhhhhhHhhhhh
Confidence 9985 799999999999763 57888886666665 5544432211 1 111 5677888876543
No 4
>PF01841 Transglut_core: Transglutaminase-like superfamily; InterPro: IPR002931 This domain is found in many proteins known to have transglutaminase activity, i.e. which cross-link proteins through an acyl-transfer reaction between the gamma-carboxamide group of peptide-bound glutamine and the epsilon-amino group of peptide-bound lysine, resulting in a epsilon-(gamma-glutamyl)lysine isopeptide bond. Tranglutaminases have been found in a diverse range of species, from bacteria through to mammals. The enzymes require calcium binding and their activity leads to post-translational modification of proteins through acyl-transfer reactions, involving peptidyl glutamine residues as acyl donors and a variety of primary amines as acyl acceptors, with the generation of proteinase resistant isopeptide bonds []. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' []. On the basis of the experimentally demonstrated activity of the Methanobacterium phage psiM2 pseudomurein endoisopeptidase [], it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease []. A subunit of plasma Factor XIII revealed that each Factor XIIIA subunit is composed of four domains (termed N-terminal beta-sandwich, core domain (containing the catalytic and the regulatory sites), and C-terminal beta-barrels 1 and 2) and that two monomers assemble into the native dimer through the surfaces in domains 1 and 2, in opposite orientation. This organisation in four domains is highly conserved during evolution among transglutaminase isoforms [].; PDB: 2F4M_A 2F4O_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B ....
Probab=99.48 E-value=4.2e-14 Score=117.41 Aligned_cols=81 Identities=25% Similarity=0.503 Sum_probs=64.9
Q ss_pred cCccEEEEEecCCCCCc--cccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeC---------------CC
Q 013381 43 YGAARVELFRCKVCSKI--TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDF---------------TD 105 (444)
Q Consensus 43 ~ga~rVE~y~C~~C~~~--~RFPRYn~p~kLL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d~---------------~d 105 (444)
..+-.+-.|..+.+.-. ...+...+|..+|++++|.|.++|.+|++|||++|++||+|... ..
T Consensus 16 ~~~~~i~~~v~~~~~y~~~~~~~~~~~~~~~l~~~~G~C~~~a~l~~allr~~Gipar~v~g~~~~~~~~~~~~~~~~~~ 95 (113)
T PF01841_consen 16 EKAKAIYDWVRSNIRYDDPNYSPGPRDASEVLRSGRGDCEDYASLFVALLRALGIPARVVSGYVKGPDPDGDYSVDGNDN 95 (113)
T ss_dssp CCCCCCCCCCCCCCCEC-TCCCCCCTTHHHHHHCEEESHHHHHHHHHHHHHHHT--EEEEEEEEEECSSTTCTSTSSEEE
T ss_pred HHHHHHHHHHHhCcEEeCCCCCCCCCCHHHHHHcCCCccHHHHHHHHHHHhhCCCceEEEEEEcCCccccccccCCCCCC
Confidence 45556666666655544 57788889999999999999999999999999999999999642 13
Q ss_pred ceEEEEeeCCCCCeEEecc
Q 013381 106 HVWTECFSQSLGRWMHLDP 124 (444)
Q Consensus 106 HvW~EVys~~~~rWIhVDP 124 (444)
|+|+|||.+. ++|+++||
T Consensus 96 H~w~ev~~~~-~~W~~~Dp 113 (113)
T PF01841_consen 96 HAWVEVYLPG-GGWIPLDP 113 (113)
T ss_dssp EEEEEEEETT-TEEEEEET
T ss_pred EEEEEEEEcC-CcEEEcCC
Confidence 9999999954 56999998
No 5
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=99.39 E-value=5.1e-13 Score=102.70 Aligned_cols=53 Identities=36% Similarity=0.853 Sum_probs=48.3
Q ss_pred HHHhCCccchhhHHHHHHHHHHcCCCeEEEEe--------------CCCceEEEEeeCCCCCeEEeccC
Q 013381 71 LVETKRGRCGEWANCFTLYCRAFGYESRLILD--------------FTDHVWTECFSQSLGRWMHLDPC 125 (444)
Q Consensus 71 LL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d--------------~~dHvW~EVys~~~~rWIhVDPc 125 (444)
+|++|.|.|.++|++|+++||++|++||+|.. ...|+|+|||.+ ++|+.+||+
T Consensus 1 ~~~~~~G~C~~~a~l~~~llr~~GIpar~v~g~~~~~~~~~~~~~~~~~H~W~ev~~~--~~W~~~D~~ 67 (68)
T smart00460 1 LLKTKYGTCGEFAALFVALLRSLGIPARVVSGYLKAPDTIGGLRSIWEAHAWAEVYLE--GGWVPVDPT 67 (68)
T ss_pred CCcccceeeHHHHHHHHHHHHHCCCCeEEEeeeecCCCCCcccccCCCcEEEEEEEEC--CCeEEEeCC
Confidence 47899999999999999999999999999964 367999999997 789999996
No 6
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=99.24 E-value=1.6e-11 Score=116.44 Aligned_cols=78 Identities=23% Similarity=0.516 Sum_probs=64.7
Q ss_pred cCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeC-----------------CCceEEEEeeCCCCCeEEecc
Q 013381 62 FPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDF-----------------TDHVWTECFSQSLGRWMHLDP 124 (444)
Q Consensus 62 FPRYn~p~kLL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d~-----------------~dHvW~EVys~~~~rWIhVDP 124 (444)
-+-..++...|++++|.|.++|++|+++||++|++||+|.++ ..|+|+|||.+.. .|+++||
T Consensus 180 ~~~~~~~~~~l~~~~G~C~d~a~l~val~Ra~GIpAR~V~Gy~~~~~~~~~~~~~~~~~~~Haw~ev~~~~~-gW~~~Dp 258 (319)
T COG1305 180 TPVTGSASDALRLGRGVCRDFAHLLVALLRAAGIPARYVSGYLGAEVEPLSGRPLVRNDDAHAWAEVYLPGR-GWVPLDP 258 (319)
T ss_pred CCCCCCHHHHHHhCCcccccHHHHHHHHHHHcCCcceeeeccccCCCCcccccccccCcccceeeeeecCCC-ccEeecC
Confidence 566778999999999999999999999999999999999742 2499999999977 5999999
Q ss_pred CCCccCCCee-eecCcc
Q 013381 125 CEGIYDRPLL-YEKGWN 140 (444)
Q Consensus 125 ceg~iD~Pll-ye~gwg 140 (444)
+.+..-.... +..+|+
T Consensus 259 t~~~~~~~~~~~~~~~~ 275 (319)
T COG1305 259 TNGLLAGGRYSILAAWG 275 (319)
T ss_pred CCCCccCcccccccccc
Confidence 9776544443 444554
No 7
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=99.21 E-value=7e-12 Score=135.41 Aligned_cols=129 Identities=26% Similarity=0.398 Sum_probs=99.7
Q ss_pred CccchhhHHHHHHHHHHcCCCeEEEEe-----------------------------CCCceEEEEeeCCCCCeEEecc--
Q 013381 76 RGRCGEWANCFTLYCRAFGYESRLILD-----------------------------FTDHVWTECFSQSLGRWMHLDP-- 124 (444)
Q Consensus 76 ~GrCgE~AnlF~~l~RAlG~~aR~V~d-----------------------------~~dHvW~EVys~~~~rWIhVDP-- 124 (444)
+|+-.--+..|.+++|..+ ++|...+ ..+.+|+|||+..+++||||||
T Consensus 263 ~g~~d~~~q~~~~l~~~~n-~~r~~~~l~p~~~~~~~~~~~s~~~~~~~s~~~~~~~~p~~W~ev~~~~e~kwV~vd~~~ 341 (669)
T KOG2179|consen 263 KGDADVSSQIIHALLRTPN-NARLAPSLQPPVFSNLSVKDLSDTSLYGNSLENIDGAGPVFWLEVLDKFEKKWVCVDPPS 341 (669)
T ss_pred CCCcchHHHHHHHHhhccc-hhhcccccCCcchhhccccccccccccccchhhcCCcccchhHHHHHhhcceEEEecchh
Confidence 7888888999999999998 5555421 0247899999999999999995
Q ss_pred CCCccCCCeeeecC---ccCccceEEeecCCc-ceechhhhccChHHHhhcc--ccccHHHHHHHHHHHHHHHHccCCHH
Q 013381 125 CEGIYDRPLLYEKG---WNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSRR--NIATEQTVSAVLAKMTRECRRSFASE 198 (444)
Q Consensus 125 ceg~iD~Pllye~g---wgK~lsYVIAFs~DG-v~DVTrRYt~~~~~~~~RR--~rv~Eewl~~~L~~l~~~~R~~ls~~ 198 (444)
..+.++.++..... -+..|.||+||+.|| ++|||+||+..|+.....| .+++..||..+++.+.+.
T Consensus 342 v~~~~~~~~~~~~~a~~~~~~~~yVva~da~~~~kDVT~RY~~~~~s~~~~~~k~~~~~~w~~~~l~~~~~~-------- 413 (669)
T KOG2179|consen 342 VIGKYHLFQPIGAVAEINGRHLAYVVAYDADGYVKDVTRRYCESWSSILRKRSKVRFSKKWFDKVLAPLGKL-------- 413 (669)
T ss_pred hcceeccccccchhhhhccccceEEEEecCCCccchhHHHHhhhhhhhhhccccccHHHHHhhhhHhhhccc--------
Confidence 45666666655543 355999999999999 7999999999998776433 567899999999999865
Q ss_pred HhhhhhhhcHHHHHHHHhh
Q 013381 199 TLSTLEDRDKCEREAMERD 217 (444)
Q Consensus 199 ~~~~Le~RD~~E~~EL~~~ 217 (444)
...|+..|+.|+...
T Consensus 414 ----~~~~e~~ed~~~~~~ 428 (669)
T KOG2179|consen 414 ----RKDREDTEDIELLRR 428 (669)
T ss_pred ----cchHHHHHHHHHHHH
Confidence 124566666665443
No 8
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=98.48 E-value=9.6e-09 Score=109.97 Aligned_cols=124 Identities=21% Similarity=0.259 Sum_probs=94.2
Q ss_pred HHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeC--------------------------CCceEEEEeeCCCCCeEEec
Q 013381 70 KLVETKRGRCGEWANCFTLYCRAFGYESRLILDF--------------------------TDHVWTECFSQSLGRWMHLD 123 (444)
Q Consensus 70 kLL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d~--------------------------~dHvW~EVys~~~~rWIhVD 123 (444)
.-+-...|+-.--+.||++++|++.+.+|++.+. .+-+|+|||....++||.||
T Consensus 241 ~~~~~~~~~~D~~vrgf~a~~r~~~v~~Rli~~l~~P~Fs~~~~~~~~~e~~~~~iD~l~~p~fw~ev~~~~~~kwv~vd 320 (650)
T COG5535 241 VPLKSADGRRDADVRGFEAEHRILNVFARLIASLIQPVFSNNSDLDVLSEGLLEYIDSLEYPGFWGEVVDKFEKKWVFVD 320 (650)
T ss_pred hhHhhccCCCcchhHHHHHHHHHhccchhhhccccCcccccccccccCccccceeccchhcchHHHHHHHHHHhceEecc
Confidence 3355677887888899999999999999999531 24789999999999999999
Q ss_pred cCC--CccCC-Ceeeec---CccCccceEEeecCCc-ceechhhhccChHHHhhc--cccccHHHHHHHHHHHHHHHHc
Q 013381 124 PCE--GIYDR-PLLYEK---GWNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSR--RNIATEQTVSAVLAKMTRECRR 193 (444)
Q Consensus 124 Pce--g~iD~-Pllye~---gwgK~lsYVIAFs~DG-v~DVTrRYt~~~~~~~~R--R~rv~Eewl~~~L~~l~~~~R~ 193 (444)
|.. .++.. -.-+|. --.+.|.||+|++.++ ++|||+||+......+.| +...++.|+...+..+++..+.
T Consensus 321 p~~l~~v~~~l~~kfepa~~~~~n~~~~V~ayd~~~y~~DVt~RY~d~~~s~~kritk~~fs~qy~~r~~~~l~~~k~~ 399 (650)
T COG5535 321 PVRLYIVYSELKCKFEPAASIHLNIMEYVGAYDACVYVKDVTLRYRDQSYSFLKRITKHLFSVQYFVRQFPGLGKCKEA 399 (650)
T ss_pred cchhhhhhhhhhheechhHHHHHHHHHHhhhhccCccchhHHHHHHHHHhhhhhhhhccchHHHHHHHHhcccCccccc
Confidence 984 34432 111222 1357899999999776 599999999987655432 3345899999999999976654
No 9
>PF04473 DUF553: Transglutaminase-like domain; InterPro: IPR007562 This entry represents a transglutaminase-like domain found in a family of uncharacterised archaeal proteins that had previously been called DUF553 and UPF0252.
Probab=97.21 E-value=0.0014 Score=60.69 Aligned_cols=68 Identities=22% Similarity=0.343 Sum_probs=57.1
Q ss_pred cccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEe--CC---CceEEEEeeCCCCCeEEeccCCCcc
Q 013381 60 TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILD--FT---DHVWTECFSQSLGRWMHLDPCEGIY 129 (444)
Q Consensus 60 ~RFPRYn~p~kLL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d--~~---dHvW~EVys~~~~rWIhVDPceg~i 129 (444)
...+++++|.++|..|+|.|++||.+..++|-.+|+..=+|+. +. .|+|+-|-.. +.|-.+|.---.+
T Consensus 59 ~~~~~i~tp~etl~~k~GiC~DYA~Lta~lLl~~g~~~~yi~~~~~~~~~~Haa~aV~in--g~~yvlDq~~p~~ 131 (153)
T PF04473_consen 59 KNSTYIQTPYETLKYKKGICGDYAILTAALLLNMGYSPVYILHIEFDNDPGHAAVAVKIN--GKYYVLDQHLPPI 131 (153)
T ss_pred cccccccCHHHHHHcCCeeeHHHHHHHHHHHHHCCCCceEEEEEecCCCCCeEEEEEEEC--CEEEEEeCCCCCc
Confidence 4456778999999999999999999999999999999878864 33 5999999886 5799999874433
No 10
>PF13369 Transglut_core2: Transglutaminase-like superfamily
Probab=94.03 E-value=0.17 Score=45.91 Aligned_cols=63 Identities=22% Similarity=0.233 Sum_probs=51.7
Q ss_pred cccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeCCCceEEEEeeCCCCCeEEeccCC
Q 013381 60 TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCE 126 (444)
Q Consensus 60 ~RFPRYn~p~kLL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d~~dHvW~EVys~~~~rWIhVDPce 126 (444)
..=|......++|++|+|-|.-.|.+|..++|.+|+++.-|. +..|+.+-+-+ . + -+=|||.+
T Consensus 48 y~~~~n~~l~~vL~~r~G~Pi~L~ily~~va~rlGl~~~~v~-~Pgh~l~r~~~-~-~-~~~iDpf~ 110 (152)
T PF13369_consen 48 YYDPENSFLHKVLERRRGIPISLAILYLEVARRLGLPAEPVN-FPGHFLVRVRS-D-G-EFYIDPFN 110 (152)
T ss_pred cCChHhhhHHHHHhcCCCCcHHHHHHHHHHHHHcCCeEEEEe-cCCEEEEEEec-C-C-cEEEccCC
Confidence 334556778999999999999999999999999999998764 77788877774 2 2 26789986
No 11
>COG5279 CYK3 Uncharacterized protein involved in cytokinesis, contains TGc (transglutaminase/protease-like) domain [Cell division and chromosome partitioning]
Probab=93.70 E-value=0.16 Score=55.16 Aligned_cols=64 Identities=23% Similarity=0.512 Sum_probs=53.5
Q ss_pred cccCCCCCHH----HHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeC------------CCceEEEEeeCCCCCeEEec
Q 013381 60 TRFPRYNDPL----KLVETKRGRCGEWANCFTLYCRAFGYESRLILDF------------TDHVWTECFSQSLGRWMHLD 123 (444)
Q Consensus 60 ~RFPRYn~p~----kLL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d~------------~dHvW~EVys~~~~rWIhVD 123 (444)
++-|||.... -.+..+++.|--||++|-+||.++|++|=+|.++ -+|+|.-|=..+ .|--||
T Consensus 189 i~d~~ytt~l~~~r~~~I~heavCtgYa~lfK~lcn~lgIp~~iIegf~k~~~~~~~~~~iNHaWN~VkiD~--~yy~VD 266 (521)
T COG5279 189 IQDPRYTTVLAQMRSVLINHEAVCTGYAELFKELCNALGIPCEIIEGFLKSPIYYTRDININHAWNIVKIDN--EYYLVD 266 (521)
T ss_pred CCcchhhhhhhhhhhhhhhcccccchHHHHHHHHHHhcCCceEEEeecccccccccCCccccceeeEEEECC--eEEEEe
Confidence 3447776554 2456689999999999999999999999999886 369999999876 699999
Q ss_pred cC
Q 013381 124 PC 125 (444)
Q Consensus 124 Pc 125 (444)
.+
T Consensus 267 tT 268 (521)
T COG5279 267 TT 268 (521)
T ss_pred ee
Confidence 88
No 12
>PF14381 EDR1: Ethylene-responsive protein kinase Le-CTR1
Probab=90.64 E-value=0.46 Score=46.10 Aligned_cols=53 Identities=19% Similarity=0.231 Sum_probs=42.8
Q ss_pred HHHhCCccchhhHHHHHHHHHHcCCCeEEEEe-----C-CCceEEEEeeCCCCCeEEecc
Q 013381 71 LVETKRGRCGEWANCFTLYCRAFGYESRLILD-----F-TDHVWTECFSQSLGRWMHLDP 124 (444)
Q Consensus 71 LL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d-----~-~dHvW~EVys~~~~rWIhVDP 124 (444)
|=.-+.|.|.+-|.||-.+|-++|+++|+|-. + .++.|+.|-......+ =||-
T Consensus 137 lG~l~~G~~rhRALLFKvLAD~iglpCrLvrG~~y~g~~~~~a~~~V~~~~~~ey-iVDL 195 (204)
T PF14381_consen 137 LGSLRIGLCRHRALLFKVLADRIGLPCRLVRGCYYCGWDDDDASNLVKFDDGREY-IVDL 195 (204)
T ss_pred EeeecccchHHHHHHHHHHHHhcCCCceEEeeccCCccCCCCceEEEEcCCCcEE-EEEc
Confidence 44568999999999999999999999999975 3 5789999987764444 2444
No 13
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=87.76 E-value=0.33 Score=51.81 Aligned_cols=35 Identities=29% Similarity=0.556 Sum_probs=28.2
Q ss_pred cCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccCCCC
Q 013381 17 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 66 (444)
Q Consensus 17 n~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPRYn 66 (444)
.+|.|+.||..|.+.|.. -|+|++||...+-.++-
T Consensus 349 ~~p~Cp~Cg~~m~S~G~~---------------g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 349 VNPVCPRCGGRMKSAGRN---------------GFRCKKCGTRARETLIK 383 (421)
T ss_pred cCCCCCccCCchhhcCCC---------------CcccccccccCCccccc
Confidence 469999999999888742 39999999877766655
No 14
>PF14402 7TM_transglut: 7 transmembrane helices usually fused to an inactive transglutaminase
Probab=86.20 E-value=0.71 Score=47.58 Aligned_cols=47 Identities=21% Similarity=0.434 Sum_probs=38.6
Q ss_pred HHHHHHHHcCCCeEEEEe---------CCCceEEEEeeCCCCCeEEeccCCCccCCCe
Q 013381 85 CFTLYCRAFGYESRLILD---------FTDHVWTECFSQSLGRWMHLDPCEGIYDRPL 133 (444)
Q Consensus 85 lF~~l~RAlG~~aR~V~d---------~~dHvW~EVys~~~~rWIhVDPceg~iD~Pl 133 (444)
++..+++.-|++||.|.. ...+.|.|||+. ++|+.+||..+....|.
T Consensus 2 ~~~~lL~~a~Ipar~v~gl~Led~rr~q~l~~~lev~~~--~~W~~f~p~tg~~g~p~ 57 (313)
T PF14402_consen 2 LIVKLLAMAGIPARVVHGLKLEDGRRRQSLEPWLEVFNG--GKWVLFNPRTGEQGLPE 57 (313)
T ss_pred HHHHHHHhCCCCccEeeeEEecCCccccCcHhHHheeeC--CeEEEECCCCCCcCCCC
Confidence 567889999999999952 345889999986 67999999988776663
No 15
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=85.74 E-value=0.54 Score=34.98 Aligned_cols=33 Identities=27% Similarity=0.586 Sum_probs=24.7
Q ss_pred ceeecCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCC
Q 013381 13 CRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 58 (444)
Q Consensus 13 F~Wvn~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~ 58 (444)
++|=|.+.|+.||+.....-.. .-.|+|..|+.
T Consensus 13 ~RW~~g~~CP~Cg~~~~~~~~~-------------~~~~~C~~C~~ 45 (46)
T PF12760_consen 13 IRWPDGFVCPHCGSTKHYRLKT-------------RGRYRCKACRK 45 (46)
T ss_pred hcCCCCCCCCCCCCeeeEEeCC-------------CCeEECCCCCC
Confidence 6899999999999973322211 45799999985
No 16
>PF13471 Transglut_core3: Transglutaminase-like superfamily
Probab=85.69 E-value=1.3 Score=38.23 Aligned_cols=37 Identities=30% Similarity=0.608 Sum_probs=32.4
Q ss_pred CCccchhhHHHHHHHHHHcCCCeEEEEe-------CCCceEEEE
Q 013381 75 KRGRCGEWANCFTLYCRAFGYESRLILD-------FTDHVWTEC 111 (444)
Q Consensus 75 R~GrCgE~AnlF~~l~RAlG~~aR~V~d-------~~dHvW~EV 111 (444)
.+..|-+.|.....+||..|+++.+|++ +..|+|+|+
T Consensus 54 ~~~~CL~~ala~~~~L~~~gi~~~l~iGv~~~~~~~~aHAWve~ 97 (117)
T PF13471_consen 54 WRSKCLPRALALQRLLRRRGIPATLVIGVRKDDDPFAAHAWVEC 97 (117)
T ss_pred CCCChHHHHHHHHHHHHhcCCCcEEEEEEeeCCCCceEEEEEEE
Confidence 3569999999999999999999999985 346999994
No 17
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=83.10 E-value=0.5 Score=48.03 Aligned_cols=53 Identities=26% Similarity=0.451 Sum_probs=38.8
Q ss_pred hhHHhhccCceeecCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccCCCCCHHHHHHhCCcc
Q 013381 4 ICVLFILQYCRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGR 78 (444)
Q Consensus 4 ~LL~WFK~~F~Wvn~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~kLL~tR~Gr 78 (444)
+|++|.+.. .-|..||++|...-.+ . ..+|++||.. -|||. ||.-++-+++|-
T Consensus 103 ~l~~w~~~~------RFCg~CG~~~~~~~~g------~--------~~~C~~cg~~-~fPR~-dP~vIv~v~~~~ 155 (279)
T COG2816 103 QLLEWYRSH------RFCGRCGTKTYPREGG------W--------ARVCPKCGHE-HFPRI-DPCVIVAVIRGD 155 (279)
T ss_pred HHHHHHhhC------cCCCCCCCcCccccCc------e--------eeeCCCCCCc-cCCCC-CCeEEEEEecCC
Confidence 688999863 3399999988743211 1 3689999764 59997 488888888874
No 18
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=75.58 E-value=2.2 Score=39.90 Aligned_cols=35 Identities=23% Similarity=0.355 Sum_probs=21.0
Q ss_pred CCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCC
Q 013381 20 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 58 (444)
Q Consensus 20 ~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~ 58 (444)
.||.||++.+.+-...+. ..|-..-..|+|+.||.
T Consensus 2 ~cp~c~~~~~~~~~s~~~----~~~~~~~~~~~c~~c~~ 36 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPA----EDGNAIRRRRECLACGK 36 (154)
T ss_pred cCCCCCCCCCEeEecccc----CCCCceeeeeeccccCC
Confidence 699999976433222111 12323334699999985
No 19
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=74.81 E-value=5.3 Score=30.53 Aligned_cols=36 Identities=22% Similarity=0.400 Sum_probs=22.5
Q ss_pred CCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCcccc
Q 013381 20 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 62 (444)
Q Consensus 20 ~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RF 62 (444)
|||.||+.....-... ..-.....|.|..||....+
T Consensus 3 PCPfCGg~~~~~~~~~-------~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGF-------DPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEecc-------CCCCCEEEEECCCCCCCccc
Confidence 8999999766322111 01122334699999998776
No 20
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=73.79 E-value=2.7 Score=30.49 Aligned_cols=28 Identities=29% Similarity=0.583 Sum_probs=19.6
Q ss_pred CCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 20 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 20 ~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
.||.|+.+...... .-|+++.|.+|+-.
T Consensus 1 ~CP~C~~~l~~~~~------------~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRL------------GDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEE------------CCEEEEECCCCCeE
Confidence 48999885442221 44999999999853
No 21
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=69.37 E-value=4.3 Score=33.15 Aligned_cols=34 Identities=21% Similarity=0.372 Sum_probs=24.8
Q ss_pred CCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCcccc
Q 013381 18 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 62 (444)
Q Consensus 18 ~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RF 62 (444)
--|||.||.++...+.. +.-+...|.+|++..-|
T Consensus 6 lKPCPFCG~~~~~v~~~-----------~g~~~v~C~~CgA~~~~ 39 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAI-----------SGYYRAKCNGCESRTGY 39 (64)
T ss_pred ccCCCCCCCceeEEEec-----------CceEEEEcCCCCcCccc
Confidence 45899999987765531 33667899999986543
No 22
>PF00797 Acetyltransf_2: N-acetyltransferase; InterPro: IPR001447 Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30 kDa. It facilitates the transfer of an acetyl group from acetyl coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (Mycobacterium tuberculosis, Mycobacterium smegmatis etc) to Homo sapiens (Human). It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid. NAT catalyses the reaction: Acetyl-coA + arylamine = coA + N-acetylarylamine NAT is the target of a common genetic polymorphism of clinical relevance in humans. The N-acetylation polymorphism is determined by low or high NAT activity in liver. NAT has been implicated in the action and toxicity of amine-containing drugs, and in the susceptibility to cancer and systematic lupus erythematosus. Two highly similar human genes for NAT, termed NAT1 and NAT2, encode genetically invariant and variant NAT proteins, respectively. ; GO: 0016407 acetyltransferase activity, 0008152 metabolic process; PDB: 1W6F_A 1W5R_A 1GX3_D 2PQT_A 2IJA_A 1W4T_A 2BSZ_B 3D9W_B 3LTW_A 3LNB_A ....
Probab=68.23 E-value=5 Score=38.27 Aligned_cols=68 Identities=25% Similarity=0.309 Sum_probs=41.2
Q ss_pred HHHH-HhCCccchhhHHHHHHHHHHcCCCeEEEEe------------CCCceEEEEeeCCCCCeEEeccCCCc--cCCCe
Q 013381 69 LKLV-ETKRGRCGEWANCFTLYCRAFGYESRLILD------------FTDHVWTECFSQSLGRWMHLDPCEGI--YDRPL 133 (444)
Q Consensus 69 ~kLL-~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d------------~~dHvW~EVys~~~~rWIhVDPceg~--iD~Pl 133 (444)
.|++ +.|-|-|-|-..+|..+|++|||+++++.. ..+|.=.=|-.++. +| =||+.-|. .-.|+
T Consensus 38 ~kiv~~~rGG~C~elN~lf~~lL~~lGf~v~~~~arv~~~~~~~~~~~~~H~~liV~~~~~-~y-lvDvGfG~~~~~~Pl 115 (240)
T PF00797_consen 38 DKIVRRGRGGYCFELNGLFYWLLRELGFDVTLVSARVYSPGGPDYWPPRTHLVLIVTLDGE-RY-LVDVGFGGPSPREPL 115 (240)
T ss_dssp HHHTTTT--B-HHHHHHHHHHHHHHCT-EEEEEEEEEETTTTTCCSSSEEEEEEEEEETTE-EE-EE-SSSTTC--SS-E
T ss_pred HHHHhcCCCeEhHHHHHHHHHHHHHCCCeEEEEEEEEEeCCCCCCCCCCceEEEEEEECCE-EE-EEeccCCCcCcccce
Confidence 3544 577899999999999999999999999952 11466555555543 56 46776544 34555
Q ss_pred eeecC
Q 013381 134 LYEKG 138 (444)
Q Consensus 134 lye~g 138 (444)
....+
T Consensus 116 ~l~~~ 120 (240)
T PF00797_consen 116 PLEDG 120 (240)
T ss_dssp ESSST
T ss_pred EccCC
Confidence 55443
No 23
>PF06035 Peptidase_C93: Bacterial transglutaminase-like cysteine proteinase BTLCP; InterPro: IPR010319 Structural analysis predicts that this family of proteins are bacterial transglutaminase-like cysteine peptidases (BTLCPs) with an invariant Cys-His-Asp catalytic triad and an N-terminal signal sequence. They are predicted to possess the papain-like cysteine proteinase fold and catalyse post-translational protein modification through transamidase, acetylase or hydrolase activity. Inspection of neighbouring genes suggests a link between this predicted activity and a type-I secretion system resembling ATP-binding cassette exporters of toxins and proteases involved in bacterial pathogenicity [].; PDB: 4FGQ_B 4FGP_B 4FGO_A.
Probab=64.29 E-value=5.3 Score=38.07 Aligned_cols=25 Identities=16% Similarity=0.301 Sum_probs=20.3
Q ss_pred HhCCccchhhHHHHHHHHHHcCCCe
Q 013381 73 ETKRGRCGEWANCFTLYCRAFGYES 97 (444)
Q Consensus 73 ~tR~GrCgE~AnlF~~l~RAlG~~a 97 (444)
..+.|.|-|||..=-..|+++|++.
T Consensus 74 ~~g~GDCEDyai~K~~~L~~~G~p~ 98 (170)
T PF06035_consen 74 ARGAGDCEDYAIAKRFALIELGVPA 98 (170)
T ss_dssp HHTEE-HHHHHHHHHHHHHHHT--G
T ss_pred CCCcCCcHhHHHHHHHHHHHcCCCH
Confidence 5799999999999999999999984
No 24
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=63.07 E-value=8.9 Score=29.44 Aligned_cols=34 Identities=24% Similarity=0.435 Sum_probs=18.3
Q ss_pred CCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCC
Q 013381 19 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 58 (444)
Q Consensus 19 P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~ 58 (444)
.|||.||.+............. .+ ..| .|..||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~-~~--~~V---~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYG-MY--YYV---ECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCC-CE--EEE---EcCCCCC
Confidence 5899998876644332111100 00 223 3999998
No 25
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=62.41 E-value=8.5 Score=38.30 Aligned_cols=45 Identities=16% Similarity=0.245 Sum_probs=30.5
Q ss_pred chhHHhhccCceeecCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccCCCCCH
Q 013381 3 LICVLFILQYCRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 68 (444)
Q Consensus 3 ~~LL~WFK~~F~Wvn~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p 68 (444)
.+|++|-++. --|+.||+++.... +.. .-.|..|+ .+-|||....
T Consensus 90 ~~l~~w~~~~------~fC~~CG~~~~~~~-------------~~~-~~~C~~c~-~~~yp~~~pa 134 (256)
T PRK00241 90 VQLAEFYRSH------RFCGYCGHPMHPSK-------------TEW-AMLCPHCR-ERYYPRIAPC 134 (256)
T ss_pred HHHHHHhhcC------ccccccCCCCeecC-------------Cce-eEECCCCC-CEECCCCCCE
Confidence 4688888863 23999999876421 112 24699997 5789997644
No 26
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=61.64 E-value=7.5 Score=34.85 Aligned_cols=16 Identities=19% Similarity=0.451 Sum_probs=13.0
Q ss_pred cEEEEEecCCCCCccc
Q 013381 46 ARVELFRCKVCSKITR 61 (444)
Q Consensus 46 ~rVE~y~C~~C~~~~R 61 (444)
-.|.-++|++|++.++
T Consensus 8 l~vt~l~C~~C~t~i~ 23 (113)
T PF09862_consen 8 LVVTRLKCPSCGTEIE 23 (113)
T ss_pred eEEEEEEcCCCCCEEE
Confidence 4678899999998764
No 27
>PHA02998 RNA polymerase subunit; Provisional
Probab=61.38 E-value=6.2 Score=38.19 Aligned_cols=45 Identities=22% Similarity=0.520 Sum_probs=31.0
Q ss_pred CCCCCCCCCC-ccccCCCCChhhhhcCccEEEEEecCCCCCccccCCCCCH
Q 013381 19 PPCDGCSNET-VGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 68 (444)
Q Consensus 19 P~C~~Cg~~t-~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p 68 (444)
.+|+.|++.. ...-++.=++|| .-.=-|+|..||...+=|||-+.
T Consensus 144 v~CPkCg~~~A~f~qlQTRSADE-----PmT~FYkC~~CG~~wkppkf~~~ 189 (195)
T PHA02998 144 TPCPNCKSKNTTPMMIQTRAADE-----PPLVRHACRDCKKHFKPPKFRDK 189 (195)
T ss_pred CCCCCCCCCceEEEEEeeccCCC-----CceEEEEcCCCCCccCCcccccc
Confidence 6899999863 322222223344 33457999999999999998765
No 28
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=60.98 E-value=2.6 Score=29.53 Aligned_cols=27 Identities=33% Similarity=0.710 Sum_probs=12.8
Q ss_pred CCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 18 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 18 ~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
-|+|+.|+++..... | ++|.|+.|+..
T Consensus 2 ~p~Cp~C~se~~y~D-----------~----~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYTYED-----------G----ELLVCPECGHE 28 (30)
T ss_dssp S---TTT-----EE------------S----SSEEETTTTEE
T ss_pred CCCCCCCCCcceecc-----------C----CEEeCCccccc
Confidence 389999999866522 1 36889999865
No 29
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=60.79 E-value=5.8 Score=35.43 Aligned_cols=28 Identities=29% Similarity=0.681 Sum_probs=20.5
Q ss_pred cCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 17 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 17 n~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
+-|+||.|+++-.... | ++|-|+.|++.
T Consensus 1 ~lp~CP~C~seytY~d-----------g----~~~iCpeC~~E 28 (109)
T TIGR00686 1 DLPPCPKCNSEYTYHD-----------G----TQLICPSCLYE 28 (109)
T ss_pred CCCcCCcCCCcceEec-----------C----CeeECcccccc
Confidence 3599999999755432 1 47999999864
No 30
>PF14353 CpXC: CpXC protein
Probab=60.58 E-value=6.1 Score=34.73 Aligned_cols=43 Identities=21% Similarity=0.295 Sum_probs=26.7
Q ss_pred CCCCCCCCCCccc------cCCCCChhhhhcCccEEEEEecCCCCCcccc
Q 013381 19 PPCDGCSNETVGQ------GMGTPLPSEIQYGAARVELFRCKVCSKITRF 62 (444)
Q Consensus 19 P~C~~Cg~~t~~~------g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RF 62 (444)
..|+.||.+.... ....|-.-|+- -.+..=.|.|++||+..+.
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~i-l~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKI-LDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHH-HcCCcCEEECCCCCCceec
Confidence 4799999864311 11223223322 2567778999999988764
No 31
>PRK10220 hypothetical protein; Provisional
Probab=59.21 E-value=7.2 Score=34.95 Aligned_cols=30 Identities=20% Similarity=0.543 Sum_probs=21.7
Q ss_pred ecCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCcc
Q 013381 16 VNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 60 (444)
Q Consensus 16 vn~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~ 60 (444)
++-|+|+.|+++-..... ++|-|+.|++.-
T Consensus 1 m~lP~CP~C~seytY~d~---------------~~~vCpeC~hEW 30 (111)
T PRK10220 1 MSLPHCPKCNSEYTYEDN---------------GMYICPECAHEW 30 (111)
T ss_pred CCCCcCCCCCCcceEcCC---------------CeEECCcccCcC
Confidence 356999999997553321 279999998753
No 32
>PRK10941 hypothetical protein; Provisional
Probab=55.65 E-value=37 Score=34.25 Aligned_cols=65 Identities=11% Similarity=0.073 Sum_probs=48.5
Q ss_pred CCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeCCCceEEEEeeCCCCCeEEeccCCCcc
Q 013381 63 PRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIY 129 (444)
Q Consensus 63 PRYn~p~kLL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d~~dHvW~EVys~~~~rWIhVDPceg~i 129 (444)
|+=....++|++|+|.=.--|.+|+.++|.+|+++.-| ++..|+=.-+=.+..+.| =+||++|.+
T Consensus 82 p~ns~L~~VL~~R~G~PisL~il~l~iA~~lglp~~gV-~fPghfllr~~~~d~~~~-~IDPf~G~~ 146 (269)
T PRK10941 82 SDALWLDKVLKTRQGSAVSLGAILLWIANRLDLPLMPV-IFPTQLILRADWLDGEMW-LINPFNGET 146 (269)
T ss_pred chhhHHHHHHHccCCCcHHHHHHHHHHHHHcCCCeeee-ecCchheeeeecCCCceE-EEeCCCCCC
Confidence 33334678999999999999999999999999998665 566666665533333334 489998765
No 33
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=55.41 E-value=6.9 Score=28.54 Aligned_cols=14 Identities=29% Similarity=0.956 Sum_probs=8.8
Q ss_pred EEEEEecCCCCCcc
Q 013381 47 RVELFRCKVCSKIT 60 (444)
Q Consensus 47 rVE~y~C~~C~~~~ 60 (444)
.-|+|+|..||..+
T Consensus 3 ~~~~YkC~~CGniV 16 (36)
T PF06397_consen 3 KGEFYKCEHCGNIV 16 (36)
T ss_dssp TTEEEE-TTT--EE
T ss_pred cccEEEccCCCCEE
Confidence 34899999999865
No 34
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=53.08 E-value=7.6 Score=27.82 Aligned_cols=29 Identities=24% Similarity=0.544 Sum_probs=14.1
Q ss_pred CCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 21 CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 21 C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
|+.||++.... -|..|++ |.+.|+.||.+
T Consensus 3 C~~CG~~l~~~---ip~gd~r-------~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERR---IPEGDDR-------ERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE-----TT-SS--------EEEETTTTEE
T ss_pred cccccChhhhh---cCCCCCc-------cceECCCCCCE
Confidence 89999975421 1222333 77899999864
No 35
>PRK15047 N-hydroxyarylamine O-acetyltransferase; Provisional
Probab=52.85 E-value=13 Score=37.62 Aligned_cols=65 Identities=25% Similarity=0.336 Sum_probs=43.2
Q ss_pred HHH-HhCCccchhhHHHHHHHHHHcCCCeEEEEe-------C----CCceEEEEeeCCCCCeEEeccCCC--ccCCCeee
Q 013381 70 KLV-ETKRGRCGEWANCFTLYCRAFGYESRLILD-------F----TDHVWTECFSQSLGRWMHLDPCEG--IYDRPLLY 135 (444)
Q Consensus 70 kLL-~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d-------~----~dHvW~EVys~~~~rWIhVDPceg--~iD~Plly 135 (444)
||+ +.|-|-|-|-..+|..++|+|||+++.+.. . ..|.=.=|..++ ++| =+|.--| ..-.|+..
T Consensus 59 KlV~~~RGGyCfE~N~Lf~~~L~~LGF~v~~~~arV~~~~~~~~~~~tH~~l~V~i~~-~~y-LvDVGFG~~~~~~Pl~L 136 (281)
T PRK15047 59 KLVIARRGGYCFEQNGLFERVLRELGFNVRSLLGRVVLSNPPALPPRTHRLLLVELEG-EKW-IADVGFGGQTLTAPIRL 136 (281)
T ss_pred HHhcCCCCEEcHhHHHHHHHHHHHcCCcEEEEEEEEEecCCCCCCCcCcEEEEEEECC-eeE-EEEecCCCCCCCccEEC
Confidence 444 367789999999999999999999876632 1 146666666654 346 3566544 23455554
Q ss_pred e
Q 013381 136 E 136 (444)
Q Consensus 136 e 136 (444)
+
T Consensus 137 ~ 137 (281)
T PRK15047 137 V 137 (281)
T ss_pred C
Confidence 3
No 36
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=52.37 E-value=12 Score=32.33 Aligned_cols=30 Identities=20% Similarity=0.500 Sum_probs=21.9
Q ss_pred cCCCCCCCCCCCcc-ccCCCCChhhhhcCccEEEEEecCCCCCccc
Q 013381 17 NAPPCDGCSNETVG-QGMGTPLPSEIQYGAARVELFRCKVCSKITR 61 (444)
Q Consensus 17 n~P~C~~Cg~~t~~-~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~R 61 (444)
+.+.|+.|+.+++. .+ +=+.+|.+||...-
T Consensus 34 ~~~~Cp~C~~~~VkR~a---------------~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTTVKRIA---------------TGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCcceeeec---------------cCeEEcCCCCCeec
Confidence 57899999998652 22 22799999997654
No 37
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=50.42 E-value=6.7 Score=39.27 Aligned_cols=45 Identities=22% Similarity=0.476 Sum_probs=19.9
Q ss_pred eeecCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccCCCC
Q 013381 14 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 66 (444)
Q Consensus 14 ~Wvn~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPRYn 66 (444)
.| +...||.||+.-...-... ++. . +. --..|..|++.-+|+|..
T Consensus 169 ~w-~~g~CPvCGs~P~~s~l~~---~~~-~--G~-R~L~Cs~C~t~W~~~R~~ 213 (290)
T PF04216_consen 169 GW-QRGYCPVCGSPPVLSVLRG---GER-E--GK-RYLHCSLCGTEWRFVRIK 213 (290)
T ss_dssp -T-T-SS-TTT---EEEEEEE------------E-EEEEETTT--EEE--TTS
T ss_pred Cc-cCCcCCCCCCcCceEEEec---CCC-C--cc-EEEEcCCCCCeeeecCCC
Confidence 45 5689999999643211100 000 1 22 667899999999999954
No 38
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial. This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA.
Probab=49.19 E-value=15 Score=33.97 Aligned_cols=60 Identities=18% Similarity=0.270 Sum_probs=46.7
Q ss_pred HHHhhhccHHHHHHhhcccc-c---------cC-CCCCeEEEecCCccccccch-hhhHHHHHHHHHhcccc
Q 013381 328 IVHQLLPSIGHLLRVLSLKS-E---------LN-TDGRVDIVLAGDPVKTSLSL-PVVFKALDDMIHDLNNC 387 (444)
Q Consensus 328 ~~~~~lps~~~ll~~lslk~-~---------~~-~~g~~~~~~~~~p~~tsl~l-~~~~~~~~~~~~~~~~~ 387 (444)
++++.||-++.++..+++|. - ++ .+|..-++|-|+|+....++ -.+..+|+.+++..++-
T Consensus 88 l~~~~l~G~~~~~~~i~~~p~G~~~~lsr~~~g~~~~~~v~~LPG~P~aa~~~~~~~v~P~l~~~~~~~~~~ 159 (163)
T TIGR02667 88 LFDKTVEGFGELFRQLSYEEIGTSTIQSRALAGLANGTFVFCLPGSTGACRTAWDKIIAAQLDARHRPCNFV 159 (163)
T ss_pred HHCCcCCcHHHHHHHHhhcccCHHHHHhhhhheeeCCeEEEECCCCHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 44555788889999999986 2 22 25779999999999998888 46888888887777663
No 39
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=48.18 E-value=11 Score=30.53 Aligned_cols=35 Identities=34% Similarity=0.879 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCc-cccC-CCCChhhhhcCccEEEEEecCCCC
Q 013381 18 APPCDGCSNETV-GQGM-GTPLPSEIQYGAARVELFRCKVCS 57 (444)
Q Consensus 18 ~P~C~~Cg~~t~-~~g~-~~Pt~~E~~~ga~rVE~y~C~~C~ 57 (444)
.|.|.+||..-. ..+. .-|=| .++-+++|||..|.
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CP-----nCGe~~I~Rc~~CR 45 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCP-----NCGEVEIYRCAKCR 45 (61)
T ss_pred CceeccCCCEeccCCceeEeeCC-----CCCceeeehhhhHH
Confidence 678888887532 1111 11211 34556777776664
No 40
>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=47.96 E-value=15 Score=26.84 Aligned_cols=39 Identities=15% Similarity=0.405 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCccccCCCCChhhhhc-------CccEEEEEecCCCC
Q 013381 18 APPCDGCSNETVGQGMGTPLPSEIQY-------GAARVELFRCKVCS 57 (444)
Q Consensus 18 ~P~C~~Cg~~t~~~g~~~Pt~~E~~~-------ga~rVE~y~C~~C~ 57 (444)
...|+.||+.....|... ..++... ---+...|.|..|+
T Consensus 2 ~~~C~~Cg~~l~~ig~~~-~~q~l~~~p~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 2 PRACPDCGGELKEIGEEK-VRQVLDLPPAKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred CCcCCCCCceeeECCcee-eEEEEeecccceEEEEEEeceEECCCCC
Confidence 457999999876555420 1222221 12345678999986
No 41
>cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
Probab=46.88 E-value=25 Score=31.85 Aligned_cols=52 Identities=27% Similarity=0.427 Sum_probs=39.4
Q ss_pred hhccHHHHHHhhccccccCC----------CCCeEEEecCCccccccchhhhHHHHHHHHHh
Q 013381 332 LLPSIGHLLRVLSLKSELNT----------DGRVDIVLAGDPVKTSLSLPVVFKALDDMIHD 383 (444)
Q Consensus 332 ~lps~~~ll~~lslk~~~~~----------~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~~ 383 (444)
-||-++..+..+++|.--.. +|+..++|-|+|+.+..++=+++++|+.++.-
T Consensus 90 ~l~g~~~~~~~~~~~pg~~~~~~~~~~g~~~~~~v~~LPG~P~aa~~~~~~v~P~l~~~~~~ 151 (152)
T cd00886 90 ELPGFGEAFRALSLEETGTAMLSRAVAGIRGGTLIFNLPGSPKAVREALEVILPELPHLLDL 151 (152)
T ss_pred cCccHHHHHHHhhcccCCcEEEechhheEECCEEEEECCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 35566778888888864322 68899999999998877776688888777653
No 42
>PF12386 Peptidase_C71: Pseudomurein endo-isopeptidase Pei; InterPro: IPR022119 This peptidase has the catalytic triad C-H-D at the C-terminal end, a triad similar to that in thiol proteases and animal transglutaminases. It catalyses the in vitro lysis of M. marburgensis cells under reducing conditions and exhibits characteristics of metal-activated peptidases.
Probab=46.13 E-value=20 Score=33.11 Aligned_cols=29 Identities=17% Similarity=0.303 Sum_probs=24.7
Q ss_pred HhCCccchhhHHHHHHHHHHcCCCeEEEE
Q 013381 73 ETKRGRCGEWANCFTLYCRAFGYESRLIL 101 (444)
Q Consensus 73 ~tR~GrCgE~AnlF~~l~RAlG~~aR~V~ 101 (444)
.|.---|-+|+++|.-++.+|||++|++.
T Consensus 51 ~~~GiNCtD~~Qlf~~v~~~lGY~Vq~~H 79 (142)
T PF12386_consen 51 RTSGINCTDACQLFYRVIESLGYDVQFEH 79 (142)
T ss_pred HhcCCCchhHHHHHHHHHHhcCceEEEEE
Confidence 34334599999999999999999999994
No 43
>PF04721 DUF750: Domain of unknown function (DUF750) ; InterPro: IPR006588 The PAW domain (present in PNGases and other worm proteins) is found as a single copy at the C terminus of metazoan peptide:N-glycanase (PNGase) and in multiple copies in hypothetical Caenorhabditis elegans proteins peptide:N-glycanases (PNGases) []. The C-terminal PAW domain of PNGase binds to the mannose moieties of N-linked oligosaccharide chains []. The PAW domain is a slightly elongated molecule and displays a beta-sandwich architecture, which is composed of two layers, containing nine and eight antiparallel beta-strands, respectively, and three additional short helices []. Some proteins known to contain a PAW domain are listed below: Animal peptide:N-glycanase (PNGase) 3.5.1.52 from EC, catalyses the deglycosylation of several misfolded N-linked glycoproteins by cleaving the bulky glycan chain before the proteins are degraded by the proteasome. Caenorhabditis elegans putative uncharacterised protein C17B7.5. ; GO: 0006516 glycoprotein catabolic process, 0005737 cytoplasm; PDB: 2G9F_A 2I74_B 2G9G_A.
Probab=45.19 E-value=0.28 Score=39.47 Aligned_cols=57 Identities=18% Similarity=0.113 Sum_probs=37.5
Q ss_pred ceeeEeecchhhhhccccCCCchhhHHHHHHHHHHHHhhccCCCcccccccccCCCCch
Q 013381 267 HVTTIYNAFSSVLSHFVENNVPKSGAIELLKILKGILGDLKKSPYKTRRVSLNSVPNNG 325 (444)
Q Consensus 267 hv~~iY~a~~~~ls~~~~~~~~~~~a~~~~~~~r~~~~dlk~~~f~~R~~~~~~~~~~~ 325 (444)
++..-|+-..-.-||-.++ .|...++.+..|.|+++.||+|+ |.+|+...+...++|
T Consensus 3 y~~FtYdii~d~YS~~~~d-Gs~~~~~~~~nI~R~ve~d~~~v-YL~r~~~~~~g~I~W 59 (62)
T PF04721_consen 3 YVKFTYDIISDTYSHTNED-GSPIQPWKVENIERKVERDWNMV-YLHRKEGSEEGNISW 59 (62)
T ss_dssp ----EEETTTTEEEECCGT-TEEEE-SSEESEEEEEETTTTEE-EEEE-TT-SEEEEEE
T ss_pred ccceeEEeccCEEEeeCCC-CeEEeeEEeeeEEEEEeCCCcEE-EEEEcCCCccceEEE
Confidence 4555666666555554332 46667888899999999999999 999998877666554
No 44
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=44.48 E-value=12 Score=30.12 Aligned_cols=23 Identities=17% Similarity=0.401 Sum_probs=19.9
Q ss_pred HhhccCceeecCCCCCCCCCCCc
Q 013381 7 LFILQYCRWVNAPPCDGCSNETV 29 (444)
Q Consensus 7 ~WFK~~F~Wvn~P~C~~Cg~~t~ 29 (444)
-|-+..|+--+.|.|+-|++++.
T Consensus 28 gWmR~nFs~~~~p~CPlC~s~M~ 50 (59)
T PF14169_consen 28 GWMRDNFSFEEEPVCPLCKSPMV 50 (59)
T ss_pred cccccccccCCCccCCCcCCccc
Confidence 47777899999999999999876
No 45
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=43.32 E-value=22 Score=25.72 Aligned_cols=29 Identities=28% Similarity=0.675 Sum_probs=20.2
Q ss_pred CCCCCCCCCC-c-cccCCCCChhhhhcCccEEEEEecCCCC
Q 013381 19 PPCDGCSNET-V-GQGMGTPLPSEIQYGAARVELFRCKVCS 57 (444)
Q Consensus 19 P~C~~Cg~~t-~-~~g~~~Pt~~E~~~ga~rVE~y~C~~C~ 57 (444)
..|+.|++.. + ..|.. ...-..|+|..|.
T Consensus 6 v~CP~C~s~~~v~k~G~~----------~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTEGVKKNGKS----------PSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCCcceeCCCC----------CCCCEeEecCcCC
Confidence 6799999976 2 33432 2456789999984
No 46
>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=43.26 E-value=85 Score=30.70 Aligned_cols=135 Identities=18% Similarity=0.277 Sum_probs=65.7
Q ss_pred CCCCCCCCcc--ccCCCC-Chh--hhhcCccEEEEEecCCCCCccccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCC
Q 013381 21 CDGCSNETVG--QGMGTP-LPS--EIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGY 95 (444)
Q Consensus 21 C~~Cg~~t~~--~g~~~P-t~~--E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~kLL~tR~GrCgE~AnlF~~l~RAlG~ 95 (444)
|+.||.++.. .|+.+. ..+ +...=..++++..|+.||+...=-++.++ +.+ ..-+.|+-.+-+.+.-
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~W~~~----~~~----el~~~~lk~v~~~l~~ 72 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGRWVDP----ESR----ELEELCLKKVERGLKK 72 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCCEeeec----Ccc----cHHHHHHHHHHHHHHH
Confidence 8899986542 355221 000 11112356899999999976433477766 110 1112222222232221
Q ss_pred CeEEEEeCCCceEEEEeeCCCCCeEEeccCCCccC-CCeeeecCccCccceEEeec--CCcceechhhhccChHHHhhcc
Q 013381 96 ESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYD-RPLLYEKGWNKKLNYVIAIS--KDGVFDVTKRYTRKWHEVLSRR 172 (444)
Q Consensus 96 ~aR~V~d~~dHvW~EVys~~~~rWIhVDPceg~iD-~Pllye~gwgK~lsYVIAFs--~DGv~DVTrRYt~~~~~~~~RR 172 (444)
. ..+......+|+|..+. .--+.|--...+.+ .| -..+|.+-|. ..-+-|=+++.-..|..+++-|
T Consensus 73 ~-~~~~~d~~~v~~e~~~~--r~~v~v~v~~~v~~~~~--------~~~~~~v~~~v~~~~C~~C~r~~~~~~eaiVQvR 141 (236)
T PF04981_consen 73 N-IKVHVDAEFVWTEPHSK--RIKVKVTVQGEVHGGTP--------VEQEYEVEVRVKRQQCPDCSRIAGGYYEAIVQVR 141 (236)
T ss_pred h-hcccccccEEEEEeeCC--EEEEEEEEEEEEcccce--------EEEEEEEEEEEEcCCChhHHhhhCCCccEEEEEE
Confidence 1 11233455678888332 22333333322222 22 2234555554 3334666777766777777767
Q ss_pred cc
Q 013381 173 NI 174 (444)
Q Consensus 173 ~r 174 (444)
..
T Consensus 142 ~~ 143 (236)
T PF04981_consen 142 QR 143 (236)
T ss_pred ec
Confidence 55
No 47
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=41.65 E-value=25 Score=25.72 Aligned_cols=35 Identities=23% Similarity=0.497 Sum_probs=21.1
Q ss_pred CCCCCCCCCc-cccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 20 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 20 ~C~~Cg~~t~-~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
+|+.||+... ..-...=++|| .-.=-|.|..|+..
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE-----~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADE-----PMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCC-----CCeEEEEeCCCCCE
Confidence 6999998643 22221112344 33457999999974
No 48
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=41.43 E-value=20 Score=31.77 Aligned_cols=39 Identities=21% Similarity=0.417 Sum_probs=25.4
Q ss_pred CCCCCCCCCCcc-ccCCCCChhhhhcCccEEEEEecCCCCCcccc
Q 013381 19 PPCDGCSNETVG-QGMGTPLPSEIQYGAARVELFRCKVCSKITRF 62 (444)
Q Consensus 19 P~C~~Cg~~t~~-~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RF 62 (444)
..|+.||++... -=...=.+|| .-+.-|+|..||..-||
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDE-----p~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADE-----PETRFYKCTRCGYRWRE 112 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCC-----CceEEEEecccCCEeec
Confidence 569999997541 1111112233 56789999999988775
No 49
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=41.20 E-value=14 Score=33.65 Aligned_cols=64 Identities=28% Similarity=0.596 Sum_probs=43.0
Q ss_pred eeecCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCcc--ccCCCCCHHHHHHhCCccchhhHHHHHHHHH
Q 013381 14 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT--RFPRYNDPLKLVETKRGRCGEWANCFTLYCR 91 (444)
Q Consensus 14 ~Wvn~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~--RFPRYn~p~kLL~tR~GrCgE~AnlF~~l~R 91 (444)
.|+. +.|+.|+++....+. -.|.|..|+... --|||-
T Consensus 31 ~~~Y-~aC~~C~kkv~~~~~---------------~~~~C~~C~~~~~~~~~ry~------------------------- 69 (166)
T cd04476 31 NWWY-PACPGCNKKVVEEGN---------------GTYRCEKCNKSVPNPEYRYI------------------------- 69 (166)
T ss_pred CeEE-ccccccCcccEeCCC---------------CcEECCCCCCcCCCccEEEE-------------------------
Confidence 5665 889999986543331 579999999874 233332
Q ss_pred HcCCCeEEE-EeCCCceEEEEeeCCCCCeEEec
Q 013381 92 AFGYESRLI-LDFTDHVWTECFSQSLGRWMHLD 123 (444)
Q Consensus 92 AlG~~aR~V-~d~~dHvW~EVys~~~~rWIhVD 123 (444)
..+. .|.++.+|+-+|.....+=++..
T Consensus 70 -----l~~~i~D~Tg~~~~~~F~~~ae~l~G~s 97 (166)
T cd04476 70 -----LSLNVADHTGEAWLTLFDEVAEQIFGKS 97 (166)
T ss_pred -----EEEEEEeCCCCEEEEEehHHHHHHhCCC
Confidence 1122 47899999999987666566653
No 50
>TIGR03696 Rhs_assc_core RHS repeat-associated core domain. This model represents a conserved unique core sequence shared by large numbers of proteins. It is occasional in the Archaea Methanosarcina barkeri) but common in bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (pfam01839) class, and an RHS repeat (pfam05593) or YD repeat (TIGR01643). This class includes secreted bacterial insecticidal toxins and intercellular signalling proteins such as the teneurins in animals. The other class consists of uncharacterized proteins shorter than 400 amino acids, where this core domain of about 75 amino acids tends to occur in the N-terminal half. Over twenty such proteins are found in Pseudomonas putida alone; little sequence similarity or repeat structure is found among these proteins outside the region modeled by this domain.
Probab=40.97 E-value=28 Score=28.23 Aligned_cols=39 Identities=23% Similarity=0.309 Sum_probs=26.5
Q ss_pred ceEEEEeeCCCCCeEEeccCCCccCCCeeeecCccCccce
Q 013381 106 HVWTECFSQSLGRWMHLDPCEGIYDRPLLYEKGWNKKLNY 145 (444)
Q Consensus 106 HvW~EVys~~~~rWIhVDPceg~iD~Pllye~gwgK~lsY 145 (444)
+...-.|++..+||+..||.. ..+....|.=..+.++++
T Consensus 32 ~~~~R~Ydp~~Grf~~~DP~~-~~~~~n~Y~Y~~nnP~~~ 70 (76)
T TIGR03696 32 YNGARYYDPELGRFLSPDPIG-LGGGLNLYAYVGNNPVNW 70 (76)
T ss_pred eeCCEeEeCCCCceeccCccc-cCCCceeeeeeCCCCCcc
Confidence 467788999999999999973 334344444444555554
No 51
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=40.91 E-value=24 Score=36.46 Aligned_cols=49 Identities=22% Similarity=0.549 Sum_probs=33.4
Q ss_pred ecCCCCCCCCCCCccccCCCCChhhhhcC--ccEEEEEecCCCCCccccCCCCCHHHHHHhCCccchh
Q 013381 16 VNAPPCDGCSNETVGQGMGTPLPSEIQYG--AARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGE 81 (444)
Q Consensus 16 vn~P~C~~Cg~~t~~~g~~~Pt~~E~~~g--a~rVE~y~C~~C~~~~RFPRYn~p~kLL~tR~GrCgE 81 (444)
-+...|+.||+.-+ ......+ ....--..|..|++.-+|+|- +.-.||+
T Consensus 182 ~~~~~CPvCGs~P~--------~s~~~~~~~~~G~RyL~CslC~teW~~~R~---------~C~~Cg~ 232 (305)
T TIGR01562 182 ESRTLCPACGSPPV--------ASMVRQGGKETGLRYLSCSLCATEWHYVRV---------KCSHCEE 232 (305)
T ss_pred CCCCcCCCCCChhh--------hhhhcccCCCCCceEEEcCCCCCcccccCc---------cCCCCCC
Confidence 46779999999532 2222221 234557899999999999994 4666775
No 52
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=40.82 E-value=13 Score=34.32 Aligned_cols=34 Identities=24% Similarity=0.605 Sum_probs=21.9
Q ss_pred CCCCCCCCCC-CccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 18 APPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 18 ~P~C~~Cg~~-t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
...|++||+. |.....-.||+=-+ +|+|..|...
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka--------~~~c~~c~ep 139 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKA--------LYRCRACKEP 139 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHH--------HhhhhhhCCc
Confidence 4789999995 44333333444332 7999999764
No 53
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=40.62 E-value=16 Score=25.44 Aligned_cols=14 Identities=29% Similarity=0.980 Sum_probs=11.6
Q ss_pred EEEEEecCCCCCcc
Q 013381 47 RVELFRCKVCSKIT 60 (444)
Q Consensus 47 rVE~y~C~~C~~~~ 60 (444)
+.|.|+|..||..+
T Consensus 4 ~~~~ykC~~Cgniv 17 (34)
T TIGR00319 4 EGQVYKCEVCGNIV 17 (34)
T ss_pred cCcEEEcCCCCcEE
Confidence 46899999999764
No 54
>PRK02935 hypothetical protein; Provisional
Probab=40.50 E-value=20 Score=32.13 Aligned_cols=31 Identities=23% Similarity=0.429 Sum_probs=24.3
Q ss_pred CCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccCC
Q 013381 18 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 64 (444)
Q Consensus 18 ~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPR 64 (444)
+-.||.|+++|...|. +..|-.|+++..-++
T Consensus 70 qV~CP~C~K~TKmLGr----------------vD~CM~C~~PLTLd~ 100 (110)
T PRK02935 70 QVICPSCEKPTKMLGR----------------VDACMHCNQPLTLDR 100 (110)
T ss_pred eeECCCCCchhhhccc----------------eeecCcCCCcCCcCc
Confidence 3579999999998884 348999998876544
No 55
>PHA00626 hypothetical protein
Probab=40.23 E-value=17 Score=29.20 Aligned_cols=29 Identities=14% Similarity=0.417 Sum_probs=18.3
Q ss_pred CCCCCCCCCc-cccCCCCChhhhhcCccEEEEEecCCCCC
Q 013381 20 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSK 58 (444)
Q Consensus 20 ~C~~Cg~~t~-~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~ 58 (444)
.||.||+.++ ..|... .-.-.|+|+.||-
T Consensus 2 ~CP~CGS~~Ivrcg~cr----------~~snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR----------GWSDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCceeeeeceec----------ccCcceEcCCCCC
Confidence 5999999654 333321 0013699999994
No 56
>COG3672 Predicted transglutaminase-like cysteine proteinase [General function prediction only]
Probab=40.22 E-value=78 Score=30.98 Aligned_cols=32 Identities=22% Similarity=0.200 Sum_probs=25.9
Q ss_pred cccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCe
Q 013381 60 TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYES 97 (444)
Q Consensus 60 ~RFPRYn~p~kLL~tR~GrCgE~AnlF~~l~RAlG~~a 97 (444)
..+..|.. +..|.|.+||..=-.-|..+|+++
T Consensus 97 ed~Wa~P~------~~~GDCEDyal~KRr~L~~~G~s~ 128 (191)
T COG3672 97 EDYWAYPV------TGAGDCEDYALEKRRRLMEAGVSS 128 (191)
T ss_pred cccccCCC------CCcccHHHHHHHHHHHHHHcCCCh
Confidence 44555554 899999999999999999999874
No 57
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=39.54 E-value=29 Score=30.67 Aligned_cols=45 Identities=27% Similarity=0.421 Sum_probs=26.2
Q ss_pred CCCCCCCCCCCccccCCCCChhhhhcC--cc-EEEEEecCCCCCccc-cCCCCCH
Q 013381 18 APPCDGCSNETVGQGMGTPLPSEIQYG--AA-RVELFRCKVCSKITR-FPRYNDP 68 (444)
Q Consensus 18 ~P~C~~Cg~~t~~~g~~~Pt~~E~~~g--a~-rVE~y~C~~C~~~~R-FPRYn~p 68 (444)
...|+.||.+...... ++. +| .+ .=-+|.|+.|++.+- +|.=+-|
T Consensus 2 p~~CpYCg~~~~l~~~-----~~i-Yg~~~~~~~~~y~C~~C~AyVG~H~~t~~P 50 (102)
T PF11672_consen 2 PIICPYCGGPAELVDG-----SEI-YGHRYDDGPYLYVCTPCDAYVGCHPGTDIP 50 (102)
T ss_pred CcccCCCCCeeEEccc-----chh-cCccCCCCceeEECCCCCceeeeeCCCCCc
Confidence 3579999998764432 111 22 00 113499999998654 5544333
No 58
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=38.70 E-value=27 Score=25.31 Aligned_cols=39 Identities=31% Similarity=0.686 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCccc-cCC------CCChhhhhcCccEEEEEecCCC
Q 013381 18 APPCDGCSNETVGQ-GMG------TPLPSEIQYGAARVELFRCKVC 56 (444)
Q Consensus 18 ~P~C~~Cg~~t~~~-g~~------~Pt~~E~~~ga~rVE~y~C~~C 56 (444)
.+.|+.||+.+... |.. .|.......=--++-.|+|+.|
T Consensus 2 ~~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred CccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 46799999987422 442 1222211122234556778776
No 59
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=37.58 E-value=16 Score=23.88 Aligned_cols=8 Identities=38% Similarity=0.970 Sum_probs=5.9
Q ss_pred CCCCCCCC
Q 013381 20 PCDGCSNE 27 (444)
Q Consensus 20 ~C~~Cg~~ 27 (444)
.|+.||.+
T Consensus 1 ~Cp~CG~~ 8 (23)
T PF13240_consen 1 YCPNCGAE 8 (23)
T ss_pred CCcccCCC
Confidence 38888874
No 60
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=37.22 E-value=16 Score=34.17 Aligned_cols=55 Identities=18% Similarity=0.199 Sum_probs=31.5
Q ss_pred CCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCC-ccccCCCCCHHHHHHhCCcc
Q 013381 20 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK-ITRFPRYNDPLKLVETKRGR 78 (444)
Q Consensus 20 ~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~-~~RFPRYn~p~kLL~tR~Gr 78 (444)
.||.||.+...+=...|+. .|.+.=-.=.|..||. .|-|-|.....-+.-.+-|+
T Consensus 2 ~CP~C~~~dtkViDSR~~~----dg~~IRRRReC~~C~~RFTTyErve~~~l~ViKkdG~ 57 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVE----DGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGV 57 (147)
T ss_pred CCCCCCCCCCEeeeccccC----CCCeeeecccCCccCCccceeeeccccccEEEcCCCC
Confidence 6999999766554433332 3545545678999994 33444443333334455555
No 61
>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=36.68 E-value=19 Score=26.17 Aligned_cols=35 Identities=17% Similarity=0.356 Sum_probs=18.1
Q ss_pred CCCCCCCCCc-cccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 20 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 20 ~C~~Cg~~t~-~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
+|+.||++.. ..-...=.+|| ...=.|.|..||+.
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE-----~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADE-----PMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSS-----SSEEEEEESSSTEE
T ss_pred CCcCCCCCeEEEEEeeccCCCC-----CCeEEEEeCCCCCe
Confidence 6999999643 22111112233 34457999999874
No 62
>COG2912 Uncharacterized conserved protein [Function unknown]
Probab=33.90 E-value=73 Score=32.60 Aligned_cols=67 Identities=13% Similarity=0.085 Sum_probs=55.9
Q ss_pred cccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeCCCceEEEEeeCCCCCeEEeccCCCcc
Q 013381 60 TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIY 129 (444)
Q Consensus 60 ~RFPRYn~p~kLL~tR~GrCgE~AnlF~~l~RAlG~~aR~V~d~~dHvW~EVys~~~~rWIhVDPceg~i 129 (444)
-.-||---...++++|+|.=-.-|..++.+++++|++- +=+++.+|+=.-+..+. +-| -+||++|-+
T Consensus 80 y~~~~n~~l~~Vl~~R~G~pvsLa~vll~ia~~l~lpl-~gV~FP~~flLR~~~~~-~~~-~idP~ng~~ 146 (269)
T COG2912 80 YFDPRNLYLNQVLQRRQGIPVSLAVVLLEIARRLDLPL-YGVNFPTQLLLRAEVED-EPL-LIDPFNGGT 146 (269)
T ss_pred ccCchhhhHHHHHHHcCCCcchHHHHHHHHHHHcCCCC-CccCCccceeEeeccCC-Cce-eeCCCCCCc
Confidence 44577667789999999999999999999999999997 55788999988888877 434 899997643
No 63
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=33.48 E-value=23 Score=24.65 Aligned_cols=13 Identities=31% Similarity=1.216 Sum_probs=10.5
Q ss_pred EEEEecCCCCCcc
Q 013381 48 VELFRCKVCSKIT 60 (444)
Q Consensus 48 VE~y~C~~C~~~~ 60 (444)
.|.|+|..||...
T Consensus 2 ~~~ykC~~CGniv 14 (34)
T cd00974 2 LEVYKCEICGNIV 14 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4789999999765
No 64
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=33.37 E-value=39 Score=31.91 Aligned_cols=34 Identities=21% Similarity=0.590 Sum_probs=22.8
Q ss_pred CCCCCCCCccc-c--CCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 21 CDGCSNETVGQ-G--MGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 21 C~~Cg~~t~~~-g--~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
|+.||+++... . ..-|- ++-..+--|.|++||-.
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~-----F~evii~sf~C~~CGyr 37 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPY-----FGKIMLSTYICEKCGYR 37 (163)
T ss_pred CCCCCCcceEeeeEeccCCC-----cceEEEEEEECCCCCCc
Confidence 99999874322 1 12232 35578889999999953
No 65
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.34 E-value=27 Score=34.05 Aligned_cols=44 Identities=11% Similarity=0.227 Sum_probs=28.6
Q ss_pred CCCCCCCCCcc--ccCCCCChhhhhcCccEEEEEecCCCCCccccCCC
Q 013381 20 PCDGCSNETVG--QGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRY 65 (444)
Q Consensus 20 ~C~~Cg~~t~~--~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPRY 65 (444)
.|+.||..+.+ .|+-.-++.-+ --..==+|+|.+|+..--||-|
T Consensus 19 ~C~~Cg~kr~f~cSg~fRvNAq~K--~LDvWlIYkC~~Cd~tWN~~If 64 (203)
T COG4332 19 RCNSCGVKRAFTCSGKFRVNAQGK--VLDVWLIYKCTHCDYTWNISIF 64 (203)
T ss_pred hCcccCCcceeeecCcEEEcCCCc--EEEEEEEEEeeccCCccchhhh
Confidence 49999998764 46544443321 2344568999999987665544
No 66
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=32.90 E-value=16 Score=35.79 Aligned_cols=38 Identities=34% Similarity=0.572 Sum_probs=28.6
Q ss_pred cCCCCChhhhhcCcc------EEEEEecCCCC----CccccCCCCCHH
Q 013381 32 GMGTPLPSEIQYGAA------RVELFRCKVCS----KITRFPRYNDPL 69 (444)
Q Consensus 32 g~~~Pt~~E~~~ga~------rVE~y~C~~C~----~~~RFPRYn~p~ 69 (444)
..+-|+.||-.+.|+ +.|-|+|..|+ +.||=||.|+-.
T Consensus 14 r~akp~~Deg~WdCsvCTFrNsAeAfkC~vCdvRKGTSTRkpr~nsql 61 (228)
T KOG4477|consen 14 RDAKPNDDEGKWDCSVCTFRNSAEAFKCFVCDVRKGTSTRKPRCNSQL 61 (228)
T ss_pred ccCCCccccCceeeeeeeecchhhhhheeeecccccccccCCcchHHH
Confidence 345688888877775 56999999996 568888888643
No 67
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=32.51 E-value=20 Score=32.31 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=24.0
Q ss_pred CCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccCC
Q 013381 18 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 64 (444)
Q Consensus 18 ~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPR 64 (444)
.-.||.|+..|...|. | ..|-.|+++....|
T Consensus 69 ~V~CP~C~K~TKmLGr--------------~--D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGR--------------V--DACMHCKEPLTLDP 99 (114)
T ss_pred eeECCCCCChHhhhch--------------h--hccCcCCCcCccCc
Confidence 4579999999988873 2 47999998766554
No 68
>COG2162 NhoA Arylamine N-acetyltransferase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=31.39 E-value=1e+02 Score=31.79 Aligned_cols=63 Identities=22% Similarity=0.375 Sum_probs=42.0
Q ss_pred HHhCCccchhhHHHHHHHHHHcCCCeEE-----EEeC-------CCceEEEEeeCCCCCeEEeccCCC--ccCCCeeee
Q 013381 72 VETKRGRCGEWANCFTLYCRAFGYESRL-----ILDF-------TDHVWTECFSQSLGRWMHLDPCEG--IYDRPLLYE 136 (444)
Q Consensus 72 L~tR~GrCgE~AnlF~~l~RAlG~~aR~-----V~d~-------~dHvW~EVys~~~~rWIhVDPceg--~iD~Pllye 136 (444)
+..|-|-|-|---+|..+++++||+.|. +|.. ..|.=.=|..+.. -|+ +|.--| +.-.|+-.+
T Consensus 63 ~~rRGGyCfElNglf~~vL~~lGF~v~~l~arV~~g~~~~a~~~~tH~~L~v~~~~~-~~l-~DvGFGg~~l~APlrL~ 139 (275)
T COG2162 63 LARRGGYCFELNGLFGRVLRELGFNVRLLLARVVWGLAPDALPPRTHRLLLVELEGE-TWL-ADVGFGGQTLTAPIRLE 139 (275)
T ss_pred hccccceehhhhhHHHHHHHHcCCcceeeEEEEEecCCCCCCCcccceEEEEEecCc-eeE-EecCCCCCCcCCCcccC
Confidence 4467889999999999999999998655 4543 2577666666654 474 455433 223354444
No 69
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=30.90 E-value=39 Score=24.38 Aligned_cols=31 Identities=23% Similarity=0.730 Sum_probs=19.2
Q ss_pred eecCCC--CCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCcc
Q 013381 15 WVNAPP--CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 60 (444)
Q Consensus 15 Wvn~P~--C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~ 60 (444)
|+-.|. |+.|++.......+ .|-|..||+.+
T Consensus 3 ~~~~~~~~C~~C~~~~~~~~dG---------------~~yC~~cG~~~ 35 (36)
T PF11781_consen 3 WMRGPNEPCPVCGSRWFYSDDG---------------FYYCDRCGHQS 35 (36)
T ss_pred ccccCCCcCCCCCCeEeEccCC---------------EEEhhhCceEc
Confidence 444555 99999862211111 58899998764
No 70
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=30.80 E-value=27 Score=35.00 Aligned_cols=39 Identities=18% Similarity=0.255 Sum_probs=18.4
Q ss_pred cCCCCCCCCCCCc-cccCCCCChhhhhcCccEEEEEecCCCCCccc
Q 013381 17 NAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITR 61 (444)
Q Consensus 17 n~P~C~~Cg~~t~-~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~R 61 (444)
....|+.||+... ....-. ..+...+.++.|..|+..+.
T Consensus 210 ~R~~Cp~Cg~~~~~~l~~~~------~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 210 VRIKCPYCGNTDHEKLEYFT------VEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp -TTS-TTT---SS-EEE--------------SEEEEEETTTTEEEE
T ss_pred cCCCCcCCCCCCCcceeeEe------cCCCCcEEEEECCcccchHH
Confidence 3467999998643 222211 11224677888999998643
No 71
>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=30.71 E-value=46 Score=28.21 Aligned_cols=36 Identities=17% Similarity=0.463 Sum_probs=23.0
Q ss_pred CCCCCCCCCCc-cccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 19 PPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 19 P~C~~Cg~~t~-~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
-+|+.||++.. +.-+..-++|| ...=.|.|..|+..
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q~RsadE-----~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQTRRADE-----PETRFYKCTKCGYV 99 (104)
T ss_pred CCCCCCCCCeeEEEEeccCCCCC-----CcEEEEEeCCCCCe
Confidence 57999998643 33222233454 34558999999974
No 72
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=30.46 E-value=44 Score=34.68 Aligned_cols=51 Identities=16% Similarity=0.287 Sum_probs=33.4
Q ss_pred eecCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccCCCCCHHHHHHhCCccchh
Q 013381 15 WVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGE 81 (444)
Q Consensus 15 Wvn~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~kLL~tR~GrCgE 81 (444)
|-+...|+.||+.-... +... .+....--..|..|++.-+|+|- +.-.||+
T Consensus 184 ~~~~~~CPvCGs~P~~s-~v~~------~~~~G~RyL~CslC~teW~~~R~---------~C~~Cg~ 234 (309)
T PRK03564 184 GEQRQFCPVCGSMPVSS-VVQI------GTTQGLRYLHCNLCESEWHVVRV---------KCSNCEQ 234 (309)
T ss_pred ccCCCCCCCCCCcchhh-eeec------cCCCCceEEEcCCCCCcccccCc---------cCCCCCC
Confidence 45789999999964311 1000 11123356789999999999994 4666775
No 73
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=30.08 E-value=32 Score=29.50 Aligned_cols=38 Identities=13% Similarity=0.255 Sum_probs=20.6
Q ss_pred CCCCCCCCccccCCCCChhhhhcC--ccEEEEEecCCCCCc
Q 013381 21 CDGCSNETVGQGMGTPLPSEIQYG--AARVELFRCKVCSKI 59 (444)
Q Consensus 21 C~~Cg~~t~~~g~~~Pt~~E~~~g--a~rVE~y~C~~C~~~ 59 (444)
|+.|++.+...+...=+-+. .+. .-.++.+.|+.||..
T Consensus 1 C~~C~~~~~~~~~~~~~~~~-~G~~~~v~~~~~~C~~CGe~ 40 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTY-KGESITIGVPGWYCPACGEE 40 (127)
T ss_pred CCCCCCccceeeeecceEEE-cCEEEEEeeeeeECCCCCCE
Confidence 89998654333322111111 111 125688999999975
No 74
>PRK15312 antimicrobial resistance protein Mig-14; Provisional
Probab=30.03 E-value=1.6e+02 Score=30.73 Aligned_cols=81 Identities=17% Similarity=0.155 Sum_probs=53.9
Q ss_pred HHHHhCCccch---hhHHH--HHHHHHHcCCCeEEEEeCCCceEEEEeeCCCCCeEEeccCCCccCCCee-eecC-----
Q 013381 70 KLVETKRGRCG---EWANC--FTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDRPLL-YEKG----- 138 (444)
Q Consensus 70 kLL~tR~GrCg---E~Anl--F~~l~RAlG~~aR~V~d~~dHvW~EVys~~~~rWIhVDPceg~iD~Pll-ye~g----- 138 (444)
+|++.|-|.+. +.+++ |...+|-+=+-.=+-+|..+.+=.=||--....||.+|-++|-+|.-.. +..|
T Consensus 174 ~Lf~~Rwg~~~~~~~~~~l~e~f~~Lr~l~fG~VLfl~~~PcA~qlv~k~eSp~wi~~D~iNgG~Dpe~~~~spGSIL~W 253 (298)
T PRK15312 174 ELFRSRFGNTLSCYPADNLANFFSQLRHLLFGHILYIEGIPCAFDIVLKSESQMNVYFDVPNGAVKNECMPLSPGSILMW 253 (298)
T ss_pred HHHHHHhCCCCCcccHHHHHHHHHHhHHhheeeEEEECCcceEEEEEEEecCCCcEEEecccCccCcccccCCCccEEEE
Confidence 46666776433 33333 3334455545444556888888888888888899999999999986533 3333
Q ss_pred ------------ccCccceEEeec
Q 013381 139 ------------WNKKLNYVIAIS 150 (444)
Q Consensus 139 ------------wgK~lsYVIAFs 150 (444)
-+|+|.|-||..
T Consensus 254 lNi~~A~~~~~~~~K~lrfSfG~~ 277 (298)
T PRK15312 254 LNISRARHYCQERQKKLIFSIGIL 277 (298)
T ss_pred ecHHHHHHHHHhcCCcEEEEecCC
Confidence 378899988843
No 75
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=28.52 E-value=27 Score=35.35 Aligned_cols=35 Identities=23% Similarity=0.565 Sum_probs=12.7
Q ss_pred eee-cCCCCCCCCCC-CccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 14 RWV-NAPPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 14 ~Wv-n~P~C~~Cg~~-t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
.|| .+-.|+.||+. ...-+...|.+ -|.|..|+..
T Consensus 26 ~Wv~~n~yCP~Cg~~~L~~f~NN~PVa-----------DF~C~~C~ee 62 (254)
T PF06044_consen 26 DWVAENMYCPNCGSKPLSKFENNRPVA-----------DFYCPNCNEE 62 (254)
T ss_dssp HHHHHH---TTT--SS-EE-------------------EEE-TTT--E
T ss_pred HHHHHCCcCCCCCChhHhhccCCCccc-----------eeECCCCchH
Confidence 344 34679999997 55556655544 5999999965
No 76
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.32 E-value=32 Score=29.54 Aligned_cols=28 Identities=29% Similarity=0.453 Sum_probs=21.1
Q ss_pred CCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 20 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 20 ~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
.|+.|+-+..+.- -+.||+=.|+.|+-.
T Consensus 3 lCP~C~v~l~~~~------------rs~vEiD~CPrCrGV 30 (88)
T COG3809 3 LCPICGVELVMSV------------RSGVEIDYCPRCRGV 30 (88)
T ss_pred ccCcCCceeeeee------------ecCceeeeCCccccE
Confidence 5999998765432 267999999999753
No 77
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=28.10 E-value=48 Score=31.15 Aligned_cols=34 Identities=18% Similarity=0.477 Sum_probs=22.7
Q ss_pred CCCCCCCCCc--cccCCCCChhhhhcCccEEEEEecCCCCC
Q 013381 20 PCDGCSNETV--GQGMGTPLPSEIQYGAARVELFRCKVCSK 58 (444)
Q Consensus 20 ~C~~Cg~~t~--~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~ 58 (444)
.|+.||.+.. ..-..-|- ++-..+--|.|++||-
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~-----F~evii~sf~C~~CGy 37 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPY-----FREVIIMSFECEHCGY 37 (160)
T ss_pred cCCCCCCCCEEEEEEecCCC-----cceEEEEEEECCCCCC
Confidence 5999997632 22222333 3457888999999995
No 78
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.01 E-value=52 Score=24.20 Aligned_cols=14 Identities=21% Similarity=0.543 Sum_probs=10.9
Q ss_pred EEEecCCCCCcccc
Q 013381 49 ELFRCKVCSKITRF 62 (444)
Q Consensus 49 E~y~C~~C~~~~RF 62 (444)
+.|.|+.||...+-
T Consensus 19 ~~~vC~~Cg~~~~~ 32 (52)
T smart00661 19 RRFVCRKCGYEEPI 32 (52)
T ss_pred CEEECCcCCCeEEC
Confidence 48999999976554
No 79
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=27.72 E-value=16 Score=32.75 Aligned_cols=66 Identities=27% Similarity=0.636 Sum_probs=41.2
Q ss_pred eeecCCCCC--CCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccc--cCCCCCHHHHHHhCCccchhhHHHHHHH
Q 013381 14 RWVNAPPCD--GCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR--FPRYNDPLKLVETKRGRCGEWANCFTLY 89 (444)
Q Consensus 14 ~Wvn~P~C~--~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~R--FPRYn~p~kLL~tR~GrCgE~AnlF~~l 89 (444)
.|+. |.|+ .|+++....+.+ .|+|.+|+.... -|||-
T Consensus 15 ~~~Y-~aC~~~~C~kKv~~~~~~---------------~y~C~~C~~~~~~~~~ry~----------------------- 55 (146)
T PF08646_consen 15 NWYY-PACPNEKCNKKVTENGDG---------------SYRCEKCNKTVENPKYRYR----------------------- 55 (146)
T ss_dssp TTEE-EE-TSTTTS-B-EEETTT---------------EEEETTTTEEESS-EEEEE-----------------------
T ss_pred CcEE-CCCCCccCCCEeecCCCc---------------EEECCCCCCcCCCeeEEEE-----------------------
Confidence 3433 7899 999875544422 299999998752 33332
Q ss_pred HHHcCCCeEE-EEeCCCceEEEEeeCCCCCeEEeccC
Q 013381 90 CRAFGYESRL-ILDFTDHVWTECFSQSLGRWMHLDPC 125 (444)
Q Consensus 90 ~RAlG~~aR~-V~d~~dHvW~EVys~~~~rWIhVDPc 125 (444)
..+ |.|.++..|+-+|.....+=++.+..
T Consensus 56 -------l~~~i~D~tg~~~~~~F~~~a~~l~G~~a~ 85 (146)
T PF08646_consen 56 -------LSLKISDGTGSIWVTLFDEEAEQLLGMSAD 85 (146)
T ss_dssp -------EEEEEEETTEEEEEEEEHHHHHHHHCCHHC
T ss_pred -------EEEEEEeCCCeEEEEEEhHHHHHHhCCCHH
Confidence 111 24789999999999876666666654
No 80
>COG0521 MoaB Molybdopterin biosynthesis enzymes [Coenzyme metabolism]
Probab=27.60 E-value=46 Score=31.81 Aligned_cols=60 Identities=25% Similarity=0.447 Sum_probs=44.7
Q ss_pred cCCCCchhHHHHhhhccHHHHHHhhccccc-c----------CCCCCeEEEecCCccccccchh-hhHHHHH
Q 013381 319 NSVPNNGQKIVHQLLPSIGHLLRVLSLKSE-L----------NTDGRVDIVLAGDPVKTSLSLP-VVFKALD 378 (444)
Q Consensus 319 ~~~~~~~~~~~~~~lps~~~ll~~lslk~~-~----------~~~g~~~~~~~~~p~~tsl~l~-~~~~~~~ 378 (444)
|-+.++-..+|++.+|-|++++..+|++.. - --+|...++|-|.|----+||= +++++|+
T Consensus 83 DvTpEA~~~~~dKeipGFgE~fR~~S~~~~g~~AiLSRa~aGv~~~tlIf~LPGSp~Avr~~l~~iI~p~l~ 154 (169)
T COG0521 83 DVTPEATRPLFDKEIPGFGELFRRLSLEEIGPTAILSRAVAGVRNGTLIFNLPGSPGAVRDALEGIILPELD 154 (169)
T ss_pred cCCHHHHHHHHhccCCcHHHHHHHhhhhcCCCcEEEeeeeeEEeCCeEEEEcCCChhhHHHHHHHHHHHhcc
Confidence 344455456899999999999999999982 1 1245688899998887777775 6666666
No 81
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=27.55 E-value=44 Score=32.37 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=22.5
Q ss_pred CCCCCCCCCc--cccCC-CCChhhhhcCccEEEEEecCCCCC
Q 013381 20 PCDGCSNETV--GQGMG-TPLPSEIQYGAARVELFRCKVCSK 58 (444)
Q Consensus 20 ~C~~Cg~~t~--~~g~~-~Pt~~E~~~ga~rVE~y~C~~C~~ 58 (444)
+|+.||.+.. ..-.. -|- ++-..+--|.|++||-
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~-----F~evii~sf~C~~CGy 38 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPY-----FGEVLETSTICEHCGY 38 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCC-----cceEEEEEEECCCCCC
Confidence 6999997632 22112 232 3557888999999995
No 82
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=27.05 E-value=42 Score=24.75 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=8.1
Q ss_pred EEecCCCCCcc
Q 013381 50 LFRCKVCSKIT 60 (444)
Q Consensus 50 ~y~C~~C~~~~ 60 (444)
..+|+.||...
T Consensus 21 ~~~Cp~CG~~~ 31 (46)
T PRK00398 21 GVRCPYCGYRI 31 (46)
T ss_pred ceECCCCCCeE
Confidence 57888888744
No 83
>PF12390 Se-cys_synth_N: Selenocysteine synthase N terminal
Probab=26.73 E-value=38 Score=24.54 Aligned_cols=37 Identities=30% Similarity=0.602 Sum_probs=27.6
Q ss_pred hhccHHHHHHhhccccccCCCCCeEEEecCCccccccchhhhHHHHHHHHHhc
Q 013381 332 LLPSIGHLLRVLSLKSELNTDGRVDIVLAGDPVKTSLSLPVVFKALDDMIHDL 384 (444)
Q Consensus 332 ~lps~~~ll~~lslk~~~~~~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~~~ 384 (444)
-|||.+.+|....++.-+..-|+ +++.+++.+++..+
T Consensus 3 ~LPsVD~lL~~~~~~~l~~~~~r----------------~~v~~~vR~~ld~~ 39 (40)
T PF12390_consen 3 QLPSVDELLQEPEIQDLIERYGR----------------PLVVDAVREVLDEL 39 (40)
T ss_pred CCchHHHHHhChhhHHHHHHcCH----------------HHHHHHHHHHHHHh
Confidence 38999999999888877665554 66777777776653
No 84
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.75 E-value=43 Score=32.33 Aligned_cols=22 Identities=27% Similarity=0.779 Sum_probs=16.8
Q ss_pred CCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 19 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 19 P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
-.|+.||. -....|.|+.||..
T Consensus 310 ~~C~~cg~-------------------~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH-------------------LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC-------------------ccceeEECCCCCCe
Confidence 56888887 23578999999964
No 85
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.82 E-value=53 Score=34.09 Aligned_cols=39 Identities=15% Similarity=0.214 Sum_probs=23.3
Q ss_pred cCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccc
Q 013381 17 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR 61 (444)
Q Consensus 17 n~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~R 61 (444)
....|+.||+. ...++- +.++ +-..+.++.|..|++...
T Consensus 225 ~R~~C~~Cg~~-~~l~y~--~~~~---~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 225 VRVKCSNCEQS-GKLHYW--SLDS---EQAAVKAESCGDCGTYLK 263 (309)
T ss_pred cCccCCCCCCC-Cceeee--eecC---CCcceEeeecccccccce
Confidence 45689999873 222221 1111 113478889999998755
No 86
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=24.16 E-value=55 Score=25.20 Aligned_cols=40 Identities=10% Similarity=0.220 Sum_probs=24.9
Q ss_pred hhHHhhccC---ceeecCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 4 ICVLFILQY---CRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 4 ~LL~WFK~~---F~Wvn~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
+.|.||+=+ ++ .+..-||.||+. ...-. -..+.|..||-.
T Consensus 4 ~~~~~y~v~~~~v~-~~~~fCP~Cg~~-~m~~~--------------~~r~~C~~Cgyt 46 (50)
T PRK00432 4 AKREYYEVDGGKVK-RKNKFCPRCGSG-FMAEH--------------LDRWHCGKCGYT 46 (50)
T ss_pred ceeeeEEECCCEEE-EccCcCcCCCcc-hhecc--------------CCcEECCCcCCE
Confidence 456777732 33 356799999985 32111 036889999853
No 87
>PRK03954 ribonuclease P protein component 4; Validated
Probab=23.71 E-value=42 Score=30.43 Aligned_cols=22 Identities=36% Similarity=0.854 Sum_probs=17.5
Q ss_pred EEEEEecCCCCCccccCCCCCHHH
Q 013381 47 RVELFRCKVCSKITRFPRYNDPLK 70 (444)
Q Consensus 47 rVE~y~C~~C~~~~RFPRYn~p~k 70 (444)
.| ++.|..||...||| |....+
T Consensus 91 ~v-vitCl~CG~~kR~P-~~~~~k 112 (121)
T PRK03954 91 HV-VITCLECGHIMRYP-YLREVK 112 (121)
T ss_pred eE-EEECccCCCEEeec-cchhhh
Confidence 46 89999999999998 444444
No 88
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=23.27 E-value=58 Score=25.64 Aligned_cols=32 Identities=25% Similarity=0.446 Sum_probs=20.1
Q ss_pred CCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCcccc
Q 013381 19 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 62 (444)
Q Consensus 19 P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RF 62 (444)
..|+.||.+-...+ .. +=|+..|..||+..+-
T Consensus 3 ~~CP~CG~~iev~~-----~~-------~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECPDCGAEIELEN-----PE-------LGELVICDECGAELEV 34 (54)
T ss_pred cCCCCCCCEEecCC-----Cc-------cCCEEeCCCCCCEEEE
Confidence 47999999532211 10 1246699999987654
No 89
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=23.17 E-value=26 Score=33.22 Aligned_cols=42 Identities=26% Similarity=0.379 Sum_probs=26.5
Q ss_pred CCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCC-ccccCCC
Q 013381 20 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK-ITRFPRY 65 (444)
Q Consensus 20 ~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~-~~RFPRY 65 (444)
.||.|+.+...+=...|+. .|++.=-.=.|..||. .|-|-|.
T Consensus 2 ~CPfC~~~~tkViDSR~~e----dg~aIRRRReC~~C~~RFTTfE~~ 44 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAE----EGNAIRRRRECLECGERFTTFERA 44 (156)
T ss_pred CCCCCCCCCCeeeeccccc----ccchhhhhhcccccccccchhhee
Confidence 6999999866555444443 3555555667999985 3334333
No 90
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.08 E-value=57 Score=35.34 Aligned_cols=62 Identities=19% Similarity=0.142 Sum_probs=40.6
Q ss_pred CCCccccccc-ccCCCCchhHHHHhhhccHHHHHHhhccccccCCCCCeEEEec-CCccccccc
Q 013381 308 KSPYKTRRVS-LNSVPNNGQKIVHQLLPSIGHLLRVLSLKSELNTDGRVDIVLA-GDPVKTSLS 369 (444)
Q Consensus 308 ~~~f~~R~~~-~~~~~~~~~~~~~~~lps~~~ll~~lslk~~~~~~g~~~~~~~-~~p~~tsl~ 369 (444)
+.|||+|... +.-.......-.+.++--.-.+...++++...+|+|.+.|... ++++.+|++
T Consensus 48 ~ipyKTRGN~av~l~~~~~~~d~~~~~~~~~~~ve~~~~~~~~~t~PG~vv~~~~~~ev~~~~~ 111 (421)
T COG1571 48 NIPYKTRGNAAVLLLVARRRGDANDIFYLAREGVEKLALKDSENTNPGEVVAVGELPEVLRSFY 111 (421)
T ss_pred CCceeccCCceeEEEeecCccchHHHHHHHHHHHHHhhccccccCCCcEEEEecCCcHHHHHHH
Confidence 5799999988 2111111000001222234678889999999999999999999 777765544
No 91
>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=22.75 E-value=64 Score=25.25 Aligned_cols=31 Identities=23% Similarity=0.682 Sum_probs=19.1
Q ss_pred CCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 19 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 19 P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
.-|+.|.+- .|+.+ .+| ..-| .|+|..||..
T Consensus 23 LIC~~C~~h---NGla~--~~~----~~~i-~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSH---NGLAP--KEE----FEEI-QYRCPYCGAL 53 (54)
T ss_pred EECcccchh---hcccc--ccc----CCce-EEEcCCCCCc
Confidence 458888763 34443 222 2345 8999999863
No 92
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=22.55 E-value=32 Score=36.70 Aligned_cols=36 Identities=33% Similarity=0.786 Sum_probs=22.8
Q ss_pred ceeecCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccC
Q 013381 13 CRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFP 63 (444)
Q Consensus 13 F~Wvn~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFP 63 (444)
|.| |.|+.||+..--+.. + .=..|.|..|...+-=|
T Consensus 272 fSW---PvCd~CGn~rLe~~p-----e-------~rg~~~C~~Cs~~V~sP 307 (389)
T PF14951_consen 272 FSW---PVCDRCGNGRLEQSP-----E-------DRGAFSCGDCSRVVTSP 307 (389)
T ss_pred ccC---ccccccCCccceeCc-----c-------CCCceeccchhhhccCc
Confidence 899 999999995432211 1 11358888888765433
No 93
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=22.50 E-value=27 Score=24.78 Aligned_cols=38 Identities=16% Similarity=0.257 Sum_probs=18.1
Q ss_pred CCCCCCCCccccCCCCChhhhhcCccEE---EEEecCCCCCc
Q 013381 21 CDGCSNETVGQGMGTPLPSEIQYGAARV---ELFRCKVCSKI 59 (444)
Q Consensus 21 C~~Cg~~t~~~g~~~Pt~~E~~~ga~rV---E~y~C~~C~~~ 59 (444)
|+.|++++...... ...-+..+....+ -.+.|+.||..
T Consensus 1 C~~C~~~~~~~~~~-~~~~~~~~~~~~i~~vp~~~C~~CGE~ 41 (46)
T TIGR03831 1 CPICGGEELEGKTT-TETYEYGGELIVIENVPALVCPQCGEE 41 (46)
T ss_pred CCCCCCceecceEE-EEEEEeCCEEEEEeCCCccccccCCCE
Confidence 88897655433221 1111222222333 23569999864
No 94
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=22.46 E-value=65 Score=22.64 Aligned_cols=21 Identities=29% Similarity=0.526 Sum_probs=12.4
Q ss_pred ccEEEEEecCCCCCccccCCC
Q 013381 45 AARVELFRCKVCSKITRFPRY 65 (444)
Q Consensus 45 a~rVE~y~C~~C~~~~RFPRY 65 (444)
..++.+.+|..||...=.||.
T Consensus 6 ~~~l~~~rC~~Cg~~~~pPr~ 26 (37)
T PF12172_consen 6 EGRLLGQRCRDCGRVQFPPRP 26 (37)
T ss_dssp TT-EEEEE-TTT--EEES--S
T ss_pred CCEEEEEEcCCCCCEecCCCc
Confidence 368899999999998877774
No 95
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.44 E-value=44 Score=40.72 Aligned_cols=68 Identities=16% Similarity=0.274 Sum_probs=34.5
Q ss_pred CCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccCCCCCHHHHHHhCCccchh-----------hHHHH
Q 013381 18 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGE-----------WANCF 86 (444)
Q Consensus 18 ~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~kLL~tR~GrCgE-----------~AnlF 86 (444)
...|+.||..+.. ...+ .-|+...-+|.|+.||+.+-. ++.. .++..+||- -...+
T Consensus 667 ~rkCPkCG~~t~~-~fCP------~CGs~te~vy~CPsCGaev~~----des~--a~~CP~CGtplv~~~~~~i~~~~~~ 733 (1337)
T PRK14714 667 RRRCPSCGTETYE-NRCP------DCGTHTEPVYVCPDCGAEVPP----DESG--RVECPRCDVELTPYQRRTINVKEEY 733 (1337)
T ss_pred EEECCCCCCcccc-ccCc------ccCCcCCCceeCccCCCccCC----Cccc--cccCCCCCCcccccceEEecHHHHH
Confidence 4678888886542 1110 011111225788888885432 2212 555666663 23445
Q ss_pred HHHHHHcCCCeE
Q 013381 87 TLYCRAFGYESR 98 (444)
Q Consensus 87 ~~l~RAlG~~aR 98 (444)
-..+..+|...+
T Consensus 734 ~~A~~~~g~~~~ 745 (1337)
T PRK14714 734 RSALENVGEREN 745 (1337)
T ss_pred HHHHHHhCcccc
Confidence 555666676644
No 96
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=22.31 E-value=46 Score=32.70 Aligned_cols=34 Identities=29% Similarity=0.662 Sum_probs=19.2
Q ss_pred CCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCcc
Q 013381 19 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 60 (444)
Q Consensus 19 P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~ 60 (444)
..|+.||++...+... -+ .|-+ =+++|..||+..
T Consensus 7 ~~Cp~Cg~eev~hEVi----k~--~g~~--~lvrC~eCG~V~ 40 (201)
T COG1326 7 IECPSCGSEEVSHEVI----KE--RGRE--PLVRCEECGTVH 40 (201)
T ss_pred EECCCCCcchhhHHHH----Hh--cCCc--eEEEccCCCcEe
Confidence 4799999654322110 00 0111 478999999875
No 97
>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=22.28 E-value=77 Score=25.75 Aligned_cols=41 Identities=20% Similarity=0.380 Sum_probs=22.5
Q ss_pred CCCCCCCCCccccCCCCChhh---h-hcCccEEEEEecCCCCCcc
Q 013381 20 PCDGCSNETVGQGMGTPLPSE---I-QYGAARVELFRCKVCSKIT 60 (444)
Q Consensus 20 ~C~~Cg~~t~~~g~~~Pt~~E---~-~~ga~rVE~y~C~~C~~~~ 60 (444)
.|+.||++.--.+....+-.- . .-+-.+--..-|+.||-..
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE 46 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTE 46 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEE
Confidence 599999975433322111111 1 1122355677899998764
No 98
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=22.19 E-value=52 Score=31.92 Aligned_cols=50 Identities=16% Similarity=0.298 Sum_probs=28.0
Q ss_pred CCCCCCCCCCC--c--cccCCCCChhhh-------hcCccEEEEEecCCCCCc---cccCCCCC
Q 013381 18 APPCDGCSNET--V--GQGMGTPLPSEI-------QYGAARVELFRCKVCSKI---TRFPRYND 67 (444)
Q Consensus 18 ~P~C~~Cg~~t--~--~~g~~~Pt~~E~-------~~ga~rVE~y~C~~C~~~---~RFPRYn~ 67 (444)
+-.||.|+++- . ..|......-+. .-..---++..|++||-+ .-|++...
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~~ 68 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLSP 68 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccCCH
Confidence 45799999862 2 223221111110 023456788999999943 34887664
No 99
>PRK05978 hypothetical protein; Provisional
Probab=22.01 E-value=65 Score=30.20 Aligned_cols=32 Identities=16% Similarity=0.449 Sum_probs=20.9
Q ss_pred CCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccccC
Q 013381 19 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFP 63 (444)
Q Consensus 19 P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RFP 63 (444)
-.|++||....+.|.-...+ +|+.||....+-
T Consensus 34 grCP~CG~G~LF~g~Lkv~~-------------~C~~CG~~~~~~ 65 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVD-------------HCAACGEDFTHH 65 (148)
T ss_pred CcCCCCCCCcccccccccCC-------------CccccCCccccC
Confidence 36899998777666543222 588998765443
No 100
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.01 E-value=1.2e+02 Score=34.07 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=18.4
Q ss_pred EeCCCceEEEEeeCCCCCeEEecc
Q 013381 101 LDFTDHVWTECFSQSLGRWMHLDP 124 (444)
Q Consensus 101 ~d~~dHvW~EVys~~~~rWIhVDP 124 (444)
.|.+...|+-+|.+...+=++...
T Consensus 517 ~D~Tg~~~~t~F~~~ae~llG~sA 540 (608)
T TIGR00617 517 SDETGQLWVTAFNDQAEQILGKSA 540 (608)
T ss_pred EeCCCCEEEEEEhHHHHHHcCCCH
Confidence 378999999999987666666544
No 101
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (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 seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.59 E-value=28 Score=25.37 Aligned_cols=30 Identities=20% Similarity=0.489 Sum_probs=16.5
Q ss_pred CCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCcccc
Q 013381 20 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 62 (444)
Q Consensus 20 ~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~RF 62 (444)
.|+.||+...... ..+=| +.|..||.....
T Consensus 2 ~Cp~Cg~~~~~~D------------~~~g~-~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKEIVFD------------PERGE-LVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSEEEEE------------TTTTE-EEETTT-BBEE-
T ss_pred CCcCCcCCceEEc------------CCCCe-EECCCCCCEeec
Confidence 5999999652111 01112 489999987653
No 102
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.57 E-value=70 Score=29.31 Aligned_cols=28 Identities=25% Similarity=0.598 Sum_probs=20.0
Q ss_pred CCCCCCCCCc-cccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 20 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 20 ~C~~Cg~~t~-~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
.|+.|+++.+ ..-. +++-.-+|..||+.
T Consensus 99 lC~~C~sPdT~l~k~------------~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 99 ICRECNRPDTRIIKE------------GRVSLLKCEACGAK 127 (133)
T ss_pred ECCCCCCCCcEEEEe------------CCeEEEecccCCCC
Confidence 5999999643 3321 46767799999975
No 103
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.56 E-value=53 Score=29.74 Aligned_cols=37 Identities=22% Similarity=0.423 Sum_probs=23.2
Q ss_pred ceeecC-CCCCCCCCCC-ccccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 13 CRWVNA-PPCDGCSNET-VGQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 13 F~Wvn~-P~C~~Cg~~t-~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
|.+... +.||.|++.. .-.|... ...=.|+|+.|+..
T Consensus 24 ~~~~~~~~~cP~C~s~~~~k~g~~~----------~~~qRyrC~~C~~t 62 (129)
T COG3677 24 IRMQITKVNCPRCKSSNVVKIGGIR----------RGHQRYKCKSCGST 62 (129)
T ss_pred HhhhcccCcCCCCCccceeeECCcc----------ccccccccCCcCcc
Confidence 334444 8899999976 2333211 11557999999964
No 104
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=20.62 E-value=56 Score=28.41 Aligned_cols=26 Identities=27% Similarity=0.664 Sum_probs=17.3
Q ss_pred CCCCCCCCCCc-cccCCCCChhhhhcCccEEEEEecCCCCCc
Q 013381 19 PPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 19 P~C~~Cg~~t~-~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~ 59 (444)
-.|+.||...+ -++. =+++|.+|+..
T Consensus 36 y~Cp~Cgk~~vkR~a~---------------GIW~C~~C~~~ 62 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVAT---------------GIWKCKKCGKK 62 (90)
T ss_dssp BEESSSSSSEEEEEET---------------TEEEETTTTEE
T ss_pred CcCCCCCCceeEEeee---------------EEeecCCCCCE
Confidence 35999998654 1111 15999999864
No 105
>PF08421 Methyltransf_13: Putative zinc binding domain; InterPro: IPR013630 This domain is found at the N terminus of bacterial methyltransferases. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=20.53 E-value=63 Score=25.50 Aligned_cols=39 Identities=18% Similarity=0.428 Sum_probs=18.3
Q ss_pred CCCCCCCCc----cccCCC-----CCh-hhhhcCccEEEEEecCCCCCc
Q 013381 21 CDGCSNETV----GQGMGT-----PLP-SEIQYGAARVELFRCKVCSKI 59 (444)
Q Consensus 21 C~~Cg~~t~----~~g~~~-----Pt~-~E~~~ga~rVE~y~C~~C~~~ 59 (444)
|..||++.. ..|..| +.+ .....-.--.++|.|..|+..
T Consensus 1 CR~Cgs~~l~~vldLG~~Pl~~~f~~~~~~~~e~~~pL~l~~C~~Cglv 49 (62)
T PF08421_consen 1 CRICGSSDLKPVLDLGDQPLANSFLKPELDEPEPRYPLDLYVCEDCGLV 49 (62)
T ss_dssp -TTTS-E-EEEEEEEEEEE-TT--B-TTS-S---EEEEEEEEETTT--E
T ss_pred CCCCCCCccceEeecCCCCccccccChhhCCCceEECCEEEECCCCCch
Confidence 788998621 223321 222 233345677899999999853
No 106
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=20.31 E-value=43 Score=24.18 Aligned_cols=26 Identities=27% Similarity=0.742 Sum_probs=14.4
Q ss_pred CCCCCCCCCccccCCCCChhhhhcCccEEEEEecC
Q 013381 20 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCK 54 (444)
Q Consensus 20 ~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~ 54 (444)
.|+.||- |.-.|.-+|. +-+.+|+|+
T Consensus 3 lcpkcgv-----gvl~pvy~~k----geikvfrcs 28 (36)
T PF09151_consen 3 LCPKCGV-----GVLEPVYNQK----GEIKVFRCS 28 (36)
T ss_dssp B-TTTSS-----SBEEEEE-TT----S-EEEEEES
T ss_pred cCCccCc-----eEEEEeecCC----CcEEEEEcC
Confidence 4888875 3333433443 678899997
No 107
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.17 E-value=71 Score=33.09 Aligned_cols=41 Identities=12% Similarity=0.237 Sum_probs=23.8
Q ss_pred cCCCCCCCCCCCccccCCCCChhhhhcCccEEEEEecCCCCCccc
Q 013381 17 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR 61 (444)
Q Consensus 17 n~P~C~~Cg~~t~~~g~~~Pt~~E~~~ga~rVE~y~C~~C~~~~R 61 (444)
....|+.||+.. ..++-. .++ ..+-..+.++.|..|++...
T Consensus 223 ~R~~C~~Cg~~~-~l~y~~--~e~-~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 223 VRVKCSHCEESK-HLAYLS--LEH-DAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred cCccCCCCCCCC-ceeeEe--ecC-CCCCcceEEeeccccccchh
Confidence 457899999842 233221 111 01224577888999998654
Done!