Query 009894
Match_columns 523
No_of_seqs 251 out of 594
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 18:36:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009894.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009894hhsearch_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 4E-116 8E-121 906.7 23.0 419 13-513 79-500 (500)
2 PF03835 Rad4: Rad4 transgluta 99.8 2E-21 4.4E-26 177.4 7.7 101 182-293 33-144 (145)
3 TIGR00605 rad4 DNA repair prot 99.8 4.1E-19 8.8E-24 197.2 8.1 105 184-297 370-477 (713)
4 PF01841 Transglut_core: Trans 99.5 3.5E-14 7.5E-19 120.5 6.7 80 123-203 17-113 (113)
5 COG1305 Transglutaminase-like 99.4 9.9E-13 2.1E-17 127.5 10.3 99 78-219 159-275 (319)
6 smart00460 TGc Transglutaminas 99.4 5E-13 1.1E-17 105.0 6.2 53 150-204 1-67 (68)
7 KOG2179 Nucleotide excision re 99.0 1E-10 2.2E-15 128.8 4.3 181 155-357 263-484 (669)
8 COG5535 RAD4 DNA repair protei 98.1 1.3E-07 2.8E-12 103.3 -4.0 124 149-272 241-399 (650)
9 PF04473 DUF553: Transglutamin 97.2 0.0013 2.9E-08 62.0 8.3 68 139-208 59-131 (153)
10 COG5279 CYK3 Uncharacterized p 94.7 0.076 1.6E-06 58.6 7.1 64 139-204 189-268 (521)
11 PF13369 Transglut_core2: Tran 93.6 0.23 5E-06 46.1 7.1 59 143-205 52-110 (152)
12 PF14381 EDR1: Ethylene-respon 91.8 0.24 5.2E-06 49.0 4.8 54 150-204 137-196 (204)
13 PF14402 7TM_transglut: 7 tran 90.8 0.23 4.9E-06 52.1 3.6 48 164-213 2-58 (313)
14 TIGR01385 TFSII transcription 90.5 0.95 2.1E-05 47.3 7.9 127 3-141 167-298 (299)
15 PF13471 Transglut_core3: Tran 87.6 0.93 2E-05 40.1 4.7 37 154-190 54-97 (117)
16 COG1571 Predicted DNA-binding 85.8 0.43 9.4E-06 51.9 1.9 35 96-145 349-383 (421)
17 PRK10941 hypothetical protein; 82.2 13 0.00029 38.3 10.7 60 147-208 87-146 (269)
18 PF12760 Zn_Tnp_IS1595: Transp 81.0 1.1 2.3E-05 34.1 1.8 34 91-137 12-45 (46)
19 COG2816 NPY1 NTP pyrophosphohy 78.7 2.7 5.8E-05 43.8 4.4 54 80-156 100-154 (279)
20 TIGR03655 anti_R_Lar restricti 76.1 4.5 9.8E-05 31.6 4.1 36 99-141 3-38 (53)
21 PF13453 zf-TFIIB: Transcripti 69.7 3.6 7.8E-05 30.5 2.0 27 99-137 1-27 (41)
22 PRK00464 nrdR transcriptional 68.8 3.7 8.1E-05 39.2 2.5 35 99-137 2-36 (154)
23 PRK03564 formate dehydrogenase 68.7 38 0.00081 36.0 10.0 113 23-145 103-228 (309)
24 PRK09710 lar restriction allev 68.1 4.7 0.0001 33.6 2.6 34 97-141 6-39 (64)
25 PRK06556 vitamin B12-dependent 64.1 4.1 8.8E-05 48.8 2.1 31 93-139 920-950 (953)
26 PF14353 CpXC: CpXC protein 63.8 4.4 9.6E-05 36.4 1.8 42 98-140 2-49 (128)
27 PRK15047 N-hydroxyarylamine O- 63.6 21 0.00045 37.0 6.9 67 148-216 58-138 (281)
28 PF08274 PhnA_Zn_Ribbon: PhnA 63.6 2.6 5.7E-05 30.1 0.3 27 97-138 2-28 (30)
29 PF06035 Peptidase_C93: Bacter 63.4 6.5 0.00014 38.3 3.0 25 152-176 74-98 (170)
30 PF14354 Lar_restr_allev: Rest 62.8 9.3 0.0002 30.0 3.3 33 98-137 4-37 (61)
31 PF00797 Acetyltransf_2: N-ace 61.2 7.8 0.00017 37.8 3.2 68 148-217 38-120 (240)
32 PF09862 DUF2089: Protein of u 61.2 6.8 0.00015 35.8 2.6 26 222-247 39-66 (113)
33 TIGR00686 phnA alkylphosphonat 61.2 5.5 0.00012 36.3 1.9 26 97-137 2-27 (109)
34 PRK00241 nudC NADH pyrophospha 60.8 12 0.00026 38.1 4.5 47 80-147 88-134 (256)
35 PRK10220 hypothetical protein; 58.7 7 0.00015 35.7 2.1 28 96-138 2-29 (111)
36 PHA02998 RNA polymerase subuni 53.0 11 0.00024 37.2 2.7 45 98-147 144-189 (195)
37 COG1997 RPL43A Ribosomal prote 47.5 16 0.00034 32.4 2.4 31 96-140 34-64 (89)
38 PRK02935 hypothetical protein; 47.4 13 0.00028 33.9 2.0 31 97-143 70-100 (110)
39 PF06397 Desulfoferrod_N: Desu 47.1 11 0.00023 28.2 1.2 14 126-139 3-16 (36)
40 PF04981 NMD3: NMD3 family ; 45.9 61 0.0013 32.4 6.7 111 124-253 30-143 (236)
41 PF14803 Nudix_N_2: Nudix N-te 44.4 14 0.0003 27.1 1.4 29 100-138 3-31 (34)
42 PF03811 Zn_Tnp_IS1: InsA N-te 44.3 21 0.00045 26.5 2.3 31 98-136 6-36 (36)
43 PF04216 FdhE: Protein involve 43.6 11 0.00023 38.7 1.0 44 93-145 169-213 (290)
44 COG2912 Uncharacterized conser 42.9 44 0.00094 34.9 5.2 63 142-207 83-145 (269)
45 PF13005 zf-IS66: zinc-finger 41.0 21 0.00046 26.6 2.0 38 98-136 3-47 (47)
46 COG3672 Predicted transglutami 40.6 68 0.0015 32.0 5.9 23 153-175 105-127 (191)
47 COG1656 Uncharacterized conser 39.6 64 0.0014 31.5 5.5 90 36-138 34-139 (165)
48 KOG1105 Transcription elongati 39.2 1E+02 0.0022 32.7 7.3 126 4-141 165-295 (296)
49 COG2162 NhoA Arylamine N-acety 39.1 89 0.0019 32.8 6.7 66 148-215 59-139 (275)
50 cd00886 MogA_MoaB MogA_MoaB fa 38.2 43 0.00092 31.1 4.0 50 412-461 91-150 (152)
51 TIGR01562 FdhE formate dehydro 38.0 28 0.00061 36.8 3.0 43 95-145 182-226 (305)
52 PF11023 DUF2614: Protein of u 37.8 15 0.00034 33.7 1.0 32 96-143 68-99 (114)
53 COG1594 RPB9 DNA-directed RNA 37.5 28 0.0006 31.6 2.6 41 97-141 72-112 (113)
54 PHA00626 hypothetical protein 37.3 19 0.00041 29.6 1.3 29 99-137 2-31 (59)
55 smart00440 ZnF_C2C2 C2C2 Zinc 36.4 34 0.00073 25.6 2.4 35 99-138 2-37 (40)
56 TIGR00340 zpr1_rel ZPR1-relate 36.4 27 0.00058 33.7 2.4 34 100-137 1-36 (163)
57 PF06044 DRP: Dam-replacing fa 35.8 17 0.00037 37.5 1.1 29 99-138 33-62 (254)
58 PF14169 YdjO: Cold-inducible 34.9 19 0.00041 29.6 1.0 23 86-108 28-50 (59)
59 COG2888 Predicted Zn-ribbon RN 34.4 17 0.00037 30.1 0.6 10 97-106 9-18 (61)
60 PF01096 TFIIS_C: Transcriptio 34.2 27 0.00058 25.9 1.6 35 99-138 2-37 (39)
61 TIGR02667 moaB_proteo molybden 34.0 32 0.00068 32.6 2.5 58 409-466 90-159 (163)
62 PF11781 RRN7: RNA polymerase 33.8 31 0.00067 25.5 1.8 31 94-139 3-35 (36)
63 COG4332 Uncharacterized protei 33.6 27 0.00059 34.7 2.0 44 100-145 20-65 (203)
64 TIGR02159 PA_CoA_Oxy4 phenylac 33.5 20 0.00043 33.9 1.0 66 53-138 73-139 (146)
65 PF09297 zf-NADH-PPase: NADH p 33.1 28 0.00062 24.5 1.5 14 97-110 3-16 (32)
66 TIGR00319 desulf_FeS4 desulfof 32.7 24 0.00052 25.1 1.1 14 126-139 4-17 (34)
67 TIGR00244 transcriptional regu 32.2 35 0.00076 32.7 2.4 26 250-275 75-100 (147)
68 PF01927 Mut7-C: Mut7-C RNAse 30.8 79 0.0017 29.4 4.5 54 79-138 72-133 (147)
69 PF13240 zinc_ribbon_2: zinc-r 29.7 27 0.00059 23.3 0.9 8 100-107 2-9 (23)
70 COG3877 Uncharacterized protei 29.6 44 0.00095 30.8 2.5 26 97-140 6-31 (122)
71 PF14690 zf-ISL3: zinc-finger 29.5 38 0.00083 25.1 1.8 11 98-108 3-13 (47)
72 PF04216 FdhE: Protein involve 29.0 38 0.00083 34.7 2.3 42 92-139 205-248 (290)
73 TIGR00310 ZPR1_znf ZPR1 zinc f 28.8 38 0.00082 33.5 2.1 34 99-137 2-38 (192)
74 PF12386 Peptidase_C71: Pseudo 28.5 55 0.0012 30.9 3.0 28 152-179 51-78 (142)
75 cd04476 RPA1_DBD_C RPA1_DBD_C: 28.4 30 0.00066 32.2 1.3 61 93-201 31-96 (166)
76 cd01675 RNR_III Class III ribo 28.3 57 0.0012 36.9 3.7 41 80-138 496-541 (555)
77 TIGR03696 Rhs_assc_core RHS re 28.1 61 0.0013 26.9 3.0 39 185-224 32-70 (76)
78 PF11672 DUF3268: Protein of u 27.3 57 0.0012 29.5 2.8 42 98-145 3-48 (102)
79 COG1998 RPS31 Ribosomal protei 26.9 41 0.00088 27.1 1.5 28 96-137 18-45 (51)
80 cd00974 DSRD Desulforedoxin (D 26.7 33 0.00072 24.5 1.0 13 127-139 2-14 (34)
81 smart00709 Zpr1 Duplicated dom 26.6 43 0.00093 32.2 2.0 34 99-137 2-37 (160)
82 COG3809 Uncharacterized protei 26.0 37 0.0008 29.8 1.3 27 99-137 3-29 (88)
83 PF04721 DUF750: Domain of unk 25.4 1.1 2.4E-05 36.9 -7.7 54 346-401 3-56 (62)
84 COG1327 Predicted transcriptio 25.3 30 0.00064 33.5 0.7 25 250-274 75-99 (156)
85 PF01921 tRNA-synt_1f: tRNA sy 25.2 19 0.0004 38.9 -0.8 54 81-143 154-213 (360)
86 PRK00398 rpoP DNA-directed RNA 25.1 44 0.00095 25.2 1.4 11 129-139 21-31 (46)
87 PRK03564 formate dehydrogenase 25.0 54 0.0012 34.8 2.6 42 92-139 220-262 (309)
88 PF14726 RTTN_N: Rotatin, an a 25.0 86 0.0019 28.0 3.5 17 77-100 28-44 (98)
89 KOG4477 RING1 interactor RYBP 24.5 30 0.00065 34.6 0.6 35 112-146 15-59 (228)
90 TIGR03830 CxxCG_CxxCG_HTH puta 24.4 44 0.00095 29.3 1.5 38 100-138 1-40 (127)
91 TIGR01384 TFS_arch transcripti 23.5 74 0.0016 27.6 2.8 36 98-138 63-99 (104)
92 TIGR00311 aIF-2beta translatio 22.6 63 0.0014 30.3 2.2 44 79-138 84-127 (133)
93 PRK15312 antimicrobial resista 22.5 2.4E+02 0.0053 30.0 6.7 92 148-244 173-287 (298)
94 PF01780 Ribosomal_L37ae: Ribo 22.5 51 0.0011 29.3 1.5 26 99-138 37-62 (90)
95 PRK03954 ribonuclease P protei 22.4 42 0.00092 31.1 1.1 17 126-143 91-107 (121)
96 PF07282 OrfB_Zn_ribbon: Putat 22.4 62 0.0013 25.9 1.9 29 96-138 27-55 (69)
97 PRK00432 30S ribosomal protein 22.4 59 0.0013 25.6 1.7 28 96-138 19-46 (50)
98 PTZ00326 phenylalanyl-tRNA syn 22.2 96 0.0021 35.0 3.9 104 137-242 373-490 (494)
99 PF08271 TF_Zn_Ribbon: TFIIB z 22.2 43 0.00092 25.0 0.9 30 99-141 2-31 (43)
100 PLN02678 seryl-tRNA synthetase 21.9 1.6E+02 0.0034 32.8 5.5 47 163-209 310-364 (448)
101 PF12390 Se-cys_synth_N: Selen 21.9 54 0.0012 24.3 1.3 37 411-463 3-39 (40)
102 COG0675 Transposase and inacti 21.6 55 0.0012 32.4 1.8 41 79-138 283-331 (364)
103 COG1779 C4-type Zn-finger prot 21.1 61 0.0013 32.6 1.9 37 97-137 14-51 (201)
104 smart00661 RPOL9 RNA polymeras 21.1 68 0.0015 24.2 1.8 14 128-141 19-32 (52)
105 PF09986 DUF2225: Uncharacteri 21.0 59 0.0013 32.3 1.8 24 124-147 43-69 (214)
106 COG5525 Bacteriophage tail ass 21.0 60 0.0013 37.4 2.1 55 84-141 214-271 (611)
107 PRK00420 hypothetical protein; 21.0 71 0.0015 29.3 2.2 41 80-138 7-49 (112)
108 PF05876 Terminase_GpA: Phage 21.0 74 0.0016 36.0 2.8 28 450-477 468-495 (557)
109 COG1384 LysS Lysyl-tRNA synthe 21.0 70 0.0015 36.3 2.6 62 335-400 365-433 (521)
110 TIGR01562 FdhE formate dehydro 20.9 73 0.0016 33.7 2.6 44 92-139 218-262 (305)
111 PRK10445 endonuclease VIII; Pr 20.9 57 0.0012 33.3 1.7 26 98-137 236-263 (263)
112 PF08646 Rep_fac-A_C: Replicat 20.8 27 0.00059 31.9 -0.5 26 180-205 61-86 (146)
113 cd00674 LysRS_core_class_I cat 20.7 49 0.0011 35.5 1.3 45 97-150 169-213 (353)
114 PHA02942 putative transposase; 20.5 73 0.0016 34.4 2.5 44 80-138 300-351 (383)
115 PF13912 zf-C2H2_6: C2H2-type 20.4 56 0.0012 21.4 1.1 23 129-156 1-23 (27)
116 PF09855 DUF2082: Nucleic-acid 20.4 89 0.0019 26.0 2.5 41 99-139 2-46 (64)
117 PRK05978 hypothetical protein; 20.2 75 0.0016 30.5 2.2 41 80-141 24-64 (148)
No 1
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.6e-116 Score=906.70 Aligned_cols=419 Identities=42% Similarity=0.725 Sum_probs=384.3
Q ss_pred HhhccCchhhHHHHHhhhhhhchhcCCHHHHHHHhccCChHHHHHHHHHHHHHcCCCCCCCchhHHHHHHHHHHHHhhc-
Q 009894 13 QHAVGENSGQFEETVHPYISKVLMYEDPIRQEAAKKTVPVERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLLFWFKQT- 91 (523)
Q Consensus 13 q~~~~~~~~~f~~~l~~~~~~v~~YEd~~lq~~Al~~IPl~~L~~~a~~~l~~~g~~~~~~~~~~~~~l~~LL~WFK~~- 91 (523)
+.++...+++|++.|.+|++||++||||.||++||++||+|+|+++|++++++ ..+++.+.|..+..+||+|||++
T Consensus 79 ~f~a~~~~~~Fle~l~~~sqhvlvYEDP~lq~~Als~iPvdEL~~kA~ekla~---~eg~ki~kdy~i~leLL~WFKq~F 155 (500)
T KOG0909|consen 79 SFSALRATNAFLEVLRSYSQHVLVYEDPVLQAKALSTIPVDELKEKASEKLAK---AEGEKIYKDYLIKLELLNWFKQDF 155 (500)
T ss_pred hhhhhhcchHHHHHHHHhccCceeecCHHHHHHHHhcCCHHHHHHHHHHhhcc---cchhhhhcchHHHHHHHHHHHHhh
Confidence 33445578899999999999999999999999999999999999999998876 22345555555557999999998
Q ss_pred CeeecCCCCCCCCCCc-cccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHHHHhcCccchhhHHHHHHHHH
Q 009894 92 FRWVNAPPCDGCSNET-VGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCR 170 (523)
Q Consensus 92 F~wv~~P~C~~Cg~~t-~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~GrCge~A~lF~~l~R 170 (523)
|+|||+|||+.||++| ...|.++|+.+|.++||++||+|+|+.||+.+||||||+|.+||+||+||||||||||+++||
T Consensus 156 F~WvN~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPRYNdp~kLLeTRkGRCGEWANCFTllcr 235 (500)
T KOG0909|consen 156 FKWVNNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPRYNDPIKLLETRKGRCGEWANCFTLLCR 235 (500)
T ss_pred heecCCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCcccCCHHHHHhhccCccchHHHHHHHHHH
Confidence 7999999999999999 567888899999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCCCcCCCCeeeecCccCccceEEeecCCcceechhhhccChHHhhhh
Q 009894 171 AFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSR 250 (523)
Q Consensus 171 alGl~aR~V~d~~dHvW~EVy~~~~~rWI~vDP~~~~vD~Pllye~gwgK~lsYVIAFs~dGv~DVTrRYt~~~~~~~~R 250 (523)
|+|++||||||.+||||+|||++.++|||||||||+++|+|+||+.||||+|+|||||++|||+||||||+.+|.+++.+
T Consensus 236 alg~daR~i~d~tDHVWtEvYS~~qqRW~HvDpcE~v~D~PllYe~GW~KklsY~iafgkD~VvDVT~RYi~~h~e~~~~ 315 (500)
T KOG0909|consen 236 ALGLDARYIWDRTDHVWTEVYSNAQQRWVHVDPCENVFDKPLLYEIGWGKKLSYCIAFGKDGVVDVTWRYILDHKENLLP 315 (500)
T ss_pred HcCCcceEEeecCcchhHHhhhhhhheeEeecccccccccceeeecccCcccceEEEeccCceEeeehhhhccchhhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccHHHHHHHHHHHHHHHHccCCHHHhhhhhhhcHHHHHHHHhhhcCCCCCCCCCCCCccccHHHHHhhcCCCCCCCC
Q 009894 251 RNIATEQTVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAMERDLYSTDDAPVSLPGRQSGDKEWRISRSEIGSDDNC 330 (523)
Q Consensus 251 R~rv~E~wl~~~L~~l~~~~r~~ls~~e~~~Le~Rd~~E~~EL~~~~~~~~~~~~~l~GRqSGS~eWr~aRGE~G~~~~~ 330 (523)
|+.|.|+.|+++|..||+++|.++++++++.|++||.+|+.||.+...+.+++..+||||||||++||.+|||+|.
T Consensus 316 R~~~~E~~l~~~l~~in~~rr~~lt~~r~~~L~~rd~~e~~El~~~~~~~~~~~~~L~GR~SGs~eWr~~RGE~G~---- 391 (500)
T KOG0909|consen 316 RDLCKESVLQQTLQFINKRRRYSLTDDRKKELAQRDEREQIELIRGKTPETPTKSSLPGRQSGSVEWRAQRGEDGK---- 391 (500)
T ss_pred hhhcchHHHHHHHHHHHHHHHhhcChHHHHHHHhhhHHHHHHHHhccccCCCCCCCCCCcccccHHHHHhhccccc----
Confidence 9999999999999999999999999999999999999999999999988888899999999999999999999998
Q ss_pred CcCCCCCCceeecccceeeEeeccchhhhccccCCCchhhHHHHHHHHHHHHhhccCCCcccccccccCCCCchhHHHHh
Q 009894 331 SLSCSSCPVRVCIDEHVTTIYNAFSSVLSHFVENNVPKSGAIELLKILKGILGDLKKSPYKTRRVSLNSVPNNGQKIVHQ 410 (523)
Q Consensus 331 s~~~s~cp~~~c~d~hv~~iY~a~~~~ls~~~~~~~~~~~a~~~~~~~r~~~~dlk~~~f~~R~~~~~~~~~~~~~~~~~ 410 (523)
|++ ||+..- + |.+++|++..|||+++.||||+ |++|.+--+-..++ +.
T Consensus 392 ---------------h~~-i~D~~~-------~---~~~~~~e~~~i~r~ve~Dw~mt-ylaR~~~~s~~~is-----w~ 439 (500)
T KOG0909|consen 392 ---------------HNT-IYDSYT-------E---WSAQAFELENIFRKVETDWKMT-YLARLEGDSPGNIS-----WH 439 (500)
T ss_pred ---------------cce-ehhhhh-------h---HHHHHHHHHHHHHHHHhhHHHH-HHHHhcCCCCcccc-----ch
Confidence 777 887765 1 8999999999999999999999 99999865555544 44
Q ss_pred h-ccchHHHHHhhccccccCCCCCeEEEecCCCccccchhhHhHHHHHHHHHhcccCcCCCCCcccccccccccccccce
Q 009894 411 L-LPSIGHLLRVLSLKSELNTDGRVDIVLAGDPVKTSLSLPVVFKALDDMIHDLNNCDNFGKGSFCLPLLKLNRIHSGSV 489 (523)
Q Consensus 411 ~-lps~~~ll~~lslk~~~~~~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 489 (523)
| +-+.+.++.++||+.++.|.|+= ++||.+||.+.. .++++-.++.
T Consensus 440 fd~~~~~~~~~~~~l~~~~qtf~~g-------------~~~v~~D~s~~s-ad~~~a~~l~------------------- 486 (500)
T KOG0909|consen 440 FDFKLKGLKVKSESLMAEIQTFGKG-------------CMRVTIDASALS-ADPSNATILK------------------- 486 (500)
T ss_pred hhhhhcccHHHHHHHHhhhhhcCCC-------------ceEeeechhccc-CCcccCceee-------------------
Confidence 4 34889999999999999999874 888999999887 7777744331
Q ss_pred eccccccccceeeccccCCCcccc
Q 009894 490 LASGEEFPFGIVTSAFDGIRPSKW 513 (523)
Q Consensus 490 ~a~~e~~p~g~~~~af~g~~~~kw 513 (523)
|+|.+|+|+.-.||
T Consensus 487 ----------i~t~~~~g~~~~~w 500 (500)
T KOG0909|consen 487 ----------IRTELFSGKGDVKW 500 (500)
T ss_pred ----------eehhhcCCccccCC
Confidence 99999999999999
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=99.84 E-value=2e-21 Score=177.41 Aligned_cols=101 Identities=36% Similarity=0.534 Sum_probs=73.6
Q ss_pred CCCeeEEEEEeCCCCCeEEeccCCC-----cCCCCeeeecCccCccceEEeecCC-cceechhhhccChHHhhhhccccc
Q 009894 182 FTDHVWTECFSQSLGRWMHLDPCEG-----IYDRPLLYEKGWNKKLNYVIAISKD-GVFDVTKRYTRKWHEVLSRRNIAT 255 (523)
Q Consensus 182 ~~dHvW~EVy~~~~~rWI~vDP~~~-----~vD~Pllye~gwgK~lsYVIAFs~d-Gv~DVTrRYt~~~~~~~~RR~rv~ 255 (523)
..+|+|+|||++.+++||||||+.+ .++.|. ..+|+++|+|||||+.| +++|||+||+.++.....+|.|+.
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 4689999999999999999999997 667777 77899999999999655 579999999998334456888888
Q ss_pred -----HHHHHHHHHHHHHHHHccCCHHHhhhhhhhcHHHHHHH
Q 009894 256 -----EQTVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAM 293 (523)
Q Consensus 256 -----E~wl~~~L~~l~~~~r~~ls~~e~~~Le~Rd~~E~~EL 293 (523)
++||..+|+.++...+... .||..|..||
T Consensus 111 ~~~~~~~W~~~~l~~~~~~~~~~~---------~~d~~Ed~el 144 (145)
T PF03835_consen 111 RSYEEEDWWEKVLRPYNRPRRDRT---------IRDKKEDEEL 144 (145)
T ss_dssp GSHHHHHHHHHHHHHH--S---H-----------HHHHHHHHH
T ss_pred ccccHHHHHHHHHHHHhccccccc---------chHHHHHhhc
Confidence 9999999998885443221 5688888887
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=99.77 E-value=4.1e-19 Score=197.25 Aligned_cols=105 Identities=20% Similarity=0.358 Sum_probs=81.8
Q ss_pred CeeEEEEEeCCCCCeEEeccCC-CcCCCCeeeecCccCccceEEeecCC-cceechhhhccChHHhhhhcccccHHHHHH
Q 009894 184 DHVWTECFSQSLGRWMHLDPCE-GIYDRPLLYEKGWNKKLNYVIAISKD-GVFDVTKRYTRKWHEVLSRRNIATEQTVSA 261 (523)
Q Consensus 184 dHvW~EVy~~~~~rWI~vDP~~-~~vD~Pllye~gwgK~lsYVIAFs~d-Gv~DVTrRYt~~~~~~~~RR~rv~E~wl~~ 261 (523)
+++|+|||++..++||||||++ +++|+|..|..+|+++|+|||||+.| +++|||+||+.+|+. ..|+.||+..||.+
T Consensus 370 p~~W~Ev~~~~~~rWI~VD~~~~~~~~~~~~~~e~~~~~m~YVvAf~~d~~~kDVT~RY~~~~~~-k~r~~Rv~~~w~~~ 448 (713)
T TIGR00605 370 VDFWVEVFIEQEEKWVCVDAVHSGVVPKGVTCFEPATLMMTYVFAYDRDGYVKDVTRRYCDQWST-KVRKRRVEKADFGE 448 (713)
T ss_pred CeeEEEEeecccceeEEeccccccccCCchhhccCCCCceEEEEEEcCCCceeechhhHhhhhhh-hhheeeecccchHH
Confidence 3899999999999999999999 99999999999999999999999998 579999999999976 35777887666666
Q ss_pred H-HHHHHHHHHccCCHHHhhhhhhhcHHHHHHHHhhh
Q 009894 262 V-LAKMTRECRRSFASETLSTLEDRDKCEREAMERDL 297 (523)
Q Consensus 262 ~-L~~l~~~~r~~ls~~e~~~Le~Rd~~E~~EL~~~~ 297 (523)
+ ++.+-..... + ... +|..|..||....
T Consensus 449 ~w~~~~~~~~~~------r-~~~-~d~~Ed~el~~~~ 477 (713)
T TIGR00605 449 TWFRPIFGALHK------R-KRT-IDDIEDQEFLRRH 477 (713)
T ss_pred HHHHHHhhhhcc------C-ccc-hhhhhhhHhhhhh
Confidence 5 5544332211 1 111 5566777776543
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=99.50 E-value=3.5e-14 Score=120.53 Aligned_cols=80 Identities=25% Similarity=0.483 Sum_probs=62.7
Q ss_pred CCceEEEeeeCCCCcc--cccCCCCCHHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEEe----C-----------CCe
Q 009894 123 GAARVELFRCKVCSKI--TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILD----F-----------TDH 185 (523)
Q Consensus 123 ga~rVE~y~C~~C~~~--~RFPRYn~p~~LL~tR~GrCge~A~lF~~l~RalGl~aR~V~d----~-----------~dH 185 (523)
.+..+-.|..+++.-. ...+...+|..+|.+++|.|.++|.+|+++||++|||||+|+. . ..|
T Consensus 17 ~~~~i~~~v~~~~~y~~~~~~~~~~~~~~~l~~~~G~C~~~a~l~~allr~~Gipar~v~g~~~~~~~~~~~~~~~~~~H 96 (113)
T PF01841_consen 17 KAKAIYDWVRSNIRYDDPNYSPGPRDASEVLRSGRGDCEDYASLFVALLRALGIPARVVSGYVKGPDPDGDYSVDGNDNH 96 (113)
T ss_dssp CCCCCCCCCCCCCCEC-TCCCCCCTTHHHHHHCEEESHHHHHHHHHHHHHHHT--EEEEEEEEEECSSTTCTSTSSEEEE
T ss_pred HHHHHHHHHHhCcEEeCCCCCCCCCCHHHHHHcCCCccHHHHHHHHHHHhhCCCceEEEEEEcCCccccccccCCCCCCE
Confidence 3444445555555443 5778888999999999999999999999999999999999953 1 239
Q ss_pred eEEEEEeCCCCCeEEecc
Q 009894 186 VWTECFSQSLGRWMHLDP 203 (523)
Q Consensus 186 vW~EVy~~~~~rWI~vDP 203 (523)
+|+|||.++ ++|+++||
T Consensus 97 ~w~ev~~~~-~~W~~~Dp 113 (113)
T PF01841_consen 97 AWVEVYLPG-GGWIPLDP 113 (113)
T ss_dssp EEEEEEETT-TEEEEEET
T ss_pred EEEEEEEcC-CcEEEcCC
Confidence 999999965 57999998
No 5
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=99.40 E-value=9.9e-13 Score=127.53 Aligned_cols=99 Identities=20% Similarity=0.407 Sum_probs=78.4
Q ss_pred HHHHHHHHHHHhhcCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHHHHhcCcc
Q 009894 78 HAFLLQLLFWFKQTFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGR 157 (523)
Q Consensus 78 ~~~l~~LL~WFK~~F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~Gr 157 (523)
...+..+..|+...|.|...+.+ . ..++..+|.+++|.
T Consensus 159 ~~~~~~~~~~~~~~~~y~~~~~~---------~---------------------------------~~~~~~~l~~~~G~ 196 (319)
T COG1305 159 REKAAALFDYVNSKIRYSPGPTP---------V---------------------------------TGSASDALRLGRGV 196 (319)
T ss_pred HHHHHHHHHHHhhcceeecCCCC---------C---------------------------------CCCHHHHHHhCCcc
Confidence 35788999999976888766543 1 13468999999999
Q ss_pred chhhHHHHHHHHHHcCCCeEEEEe-----------------CCCeeEEEEEeCCCCCeEEeccCCCcCCCCee-eecCcc
Q 009894 158 CGEWANCFTLYCRAFGYESRLILD-----------------FTDHVWTECFSQSLGRWMHLDPCEGIYDRPLL-YEKGWN 219 (523)
Q Consensus 158 Cge~A~lF~~l~RalGl~aR~V~d-----------------~~dHvW~EVy~~~~~rWI~vDP~~~~vD~Pll-ye~gwg 219 (523)
|.|+|++|+++||++|||||||.+ ...|+|+|||.++. +|+++||+.+..-.... +..+|+
T Consensus 197 C~d~a~l~val~Ra~GIpAR~V~Gy~~~~~~~~~~~~~~~~~~~Haw~ev~~~~~-gW~~~Dpt~~~~~~~~~~~~~~~~ 275 (319)
T COG1305 197 CRDFAHLLVALLRAAGIPARYVSGYLGAEVEPLSGRPLVRNDDAHAWAEVYLPGR-GWVPLDPTNGLLAGGRYSILAAWG 275 (319)
T ss_pred cccHHHHHHHHHHHcCCcceeeeccccCCCCcccccccccCcccceeeeeecCCC-ccEeecCCCCCccCcccccccccc
Confidence 999999999999999999999942 23599999999986 79999999876644443 444554
No 6
>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=99.40 E-value=5e-13 Score=104.99 Aligned_cols=53 Identities=36% Similarity=0.853 Sum_probs=47.9
Q ss_pred HHHhcCccchhhHHHHHHHHHHcCCCeEEEEe--------------CCCeeEEEEEeCCCCCeEEeccC
Q 009894 150 LVETKRGRCGEWANCFTLYCRAFGYESRLILD--------------FTDHVWTECFSQSLGRWMHLDPC 204 (523)
Q Consensus 150 LL~tR~GrCge~A~lF~~l~RalGl~aR~V~d--------------~~dHvW~EVy~~~~~rWI~vDP~ 204 (523)
+|++|.|.|.++|++|+++||++|||||+|.. ...|+|+|||.+ ++|+.+||+
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 47899999999999999999999999999942 467999999998 589999997
No 7
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=99.05 E-value=1e-10 Score=128.84 Aligned_cols=181 Identities=23% Similarity=0.312 Sum_probs=118.9
Q ss_pred CccchhhHHHHHHHHHHcCCCeEEEE-------e----------------------CCCeeEEEEEeCCCCCeEEecc--
Q 009894 155 RGRCGEWANCFTLYCRAFGYESRLIL-------D----------------------FTDHVWTECFSQSLGRWMHLDP-- 203 (523)
Q Consensus 155 ~GrCge~A~lF~~l~RalGl~aR~V~-------d----------------------~~dHvW~EVy~~~~~rWI~vDP-- 203 (523)
+|+-.--+..|.+++|..+ ++|... . ..+..|+|||+..++.||+|||
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 6776778999999999998 555441 0 1247899999999999999995
Q ss_pred CCCcCCCCeeeecC---ccCccceEEeecCCc-ceechhhhccChHHhhhhc--ccccHHHHHHHHHHHHHHHHccCCHH
Q 009894 204 CEGIYDRPLLYEKG---WNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSRR--NIATEQTVSAVLAKMTRECRRSFASE 277 (523)
Q Consensus 204 ~~~~vD~Pllye~g---wgK~lsYVIAFs~dG-v~DVTrRYt~~~~~~~~RR--~rv~E~wl~~~L~~l~~~~r~~ls~~ 277 (523)
..+.++.++..... -+..|.|||||+.+| ++|||+||+..|+.....| .+++..||..+++.++..
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 35666666655543 456999999999998 7999999999998776544 466899999999999864
Q ss_pred HhhhhhhhcHHHHHHHHhhhcCCCCCCCCCCCCccccHHHHHh---hcCCCCCCCCCcCC-CCCCceeecccceeeEeec
Q 009894 278 TLSTLEDRDKCEREAMERDLYSTDDAPVSLPGRQSGDKEWRIS---RSEIGSDDNCSLSC-SSCPVRVCIDEHVTTIYNA 353 (523)
Q Consensus 278 e~~~Le~Rd~~E~~EL~~~~~~~~~~~~~l~GRqSGS~eWr~a---RGE~G~~~~~s~~~-s~cp~~~c~d~hv~~iY~a 353 (523)
...|+..|..++...... ..+|-=++ +-+.. --|-=...+..+.| ..|-++.|... |..||..
T Consensus 414 ----~~~~e~~ed~~~~~~~~~-----~~lP~sv~---~~K~Hp~fvler~Lkk~q~l~P~k~p~~g~~kG~-~E~VY~R 480 (669)
T KOG2179|consen 414 ----RKDREDTEDIELLRRHTS-----EGLPTSVQ---DLKNHPLFVLERHLKKNQALKPCKKPTLGFTKGD-VEAVYLR 480 (669)
T ss_pred ----cchHHHHHHHHHHHHhcc-----CCCCchHH---HhccCchhhhHHHHhhcccccccccceeeeecCC-ceeeeeh
Confidence 134455555555433221 12221000 11100 00000011223344 67778888886 7789987
Q ss_pred cchh
Q 009894 354 FSSV 357 (523)
Q Consensus 354 ~~~~ 357 (523)
.-.+
T Consensus 481 ~~V~ 484 (669)
T KOG2179|consen 481 RDVV 484 (669)
T ss_pred hhHH
Confidence 6533
No 8
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=98.14 E-value=1.3e-07 Score=103.28 Aligned_cols=124 Identities=21% Similarity=0.243 Sum_probs=91.5
Q ss_pred HHHHhcCccchhhHHHHHHHHHHcCCCeEEEEe--------------------------CCCeeEEEEEeCCCCCeEEec
Q 009894 149 KLVETKRGRCGEWANCFTLYCRAFGYESRLILD--------------------------FTDHVWTECFSQSLGRWMHLD 202 (523)
Q Consensus 149 ~LL~tR~GrCge~A~lF~~l~RalGl~aR~V~d--------------------------~~dHvW~EVy~~~~~rWI~vD 202 (523)
--+-...|+-.--+.+|+++||++.+++|++.+ ..+-.|+|||....+.||.+|
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 334556777777788999999999999999831 124679999999999999999
Q ss_pred cCC--CcCCC-Ceeeec---CccCccceEEeecCCc-ceechhhhccChHHhhhh--cccccHHHHHHHHHHHHHHHHc
Q 009894 203 PCE--GIYDR-PLLYEK---GWNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSR--RNIATEQTVSAVLAKMTRECRR 272 (523)
Q Consensus 203 P~~--~~vD~-Pllye~---gwgK~lsYVIAFs~dG-v~DVTrRYt~~~~~~~~R--R~rv~E~wl~~~L~~l~~~~r~ 272 (523)
|.. .++.. ---+|. --.+.|.||+|++.++ ++|||+||+......+.| +...++.|+...+..++...+.
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 22231 001111 2367899999999775 699999999987655432 2345799999999999876653
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=97.22 E-value=0.0013 Score=62.05 Aligned_cols=68 Identities=21% Similarity=0.324 Sum_probs=56.9
Q ss_pred cccCCCCCHHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEE--eCC---CeeEEEEEeCCCCCeEEeccCCCcC
Q 009894 139 TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLIL--DFT---DHVWTECFSQSLGRWMHLDPCEGIY 208 (523)
Q Consensus 139 ~RFPRYn~p~~LL~tR~GrCge~A~lF~~l~RalGl~aR~V~--d~~---dHvW~EVy~~~~~rWI~vDP~~~~v 208 (523)
...+++++|.+++..|+|.|+|||.+..++|-.+|+..=||+ +.. .|+|+-|-..+ .|-.+|..--.+
T Consensus 59 ~~~~~i~tp~etl~~k~GiC~DYA~Lta~lLl~~g~~~~yi~~~~~~~~~~Haa~aV~ing--~~yvlDq~~p~~ 131 (153)
T PF04473_consen 59 KNSTYIQTPYETLKYKKGICGDYAILTAALLLNMGYSPVYILHIEFDNDPGHAAVAVKING--KYYVLDQHLPPI 131 (153)
T ss_pred cccccccCHHHHHHcCCeeeHHHHHHHHHHHHHCCCCceEEEEEecCCCCCeEEEEEEECC--EEEEEeCCCCCc
Confidence 345677899999999999999999999999999999887774 323 59999999986 599999874433
No 10
>COG5279 CYK3 Uncharacterized protein involved in cytokinesis, contains TGc (transglutaminase/protease-like) domain [Cell division and chromosome partitioning]
Probab=94.69 E-value=0.076 Score=58.62 Aligned_cols=64 Identities=23% Similarity=0.512 Sum_probs=53.9
Q ss_pred cccCCCCCHH----HHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeC------------CCeeEEEEEeCCCCCeEEec
Q 009894 139 TRFPRYNDPL----KLVETKRGRCGEWANCFTLYCRAFGYESRLILDF------------TDHVWTECFSQSLGRWMHLD 202 (523)
Q Consensus 139 ~RFPRYn~p~----~LL~tR~GrCge~A~lF~~l~RalGl~aR~V~d~------------~dHvW~EVy~~~~~rWI~vD 202 (523)
++-|||.... ..+-..++.|.-||.+|-+||.++||||=+|-++ -+|+|.-|=..+ .|-.||
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 4458887655 2456689999999999999999999999999653 369999999987 599999
Q ss_pred cC
Q 009894 203 PC 204 (523)
Q Consensus 203 P~ 204 (523)
.+
T Consensus 267 tT 268 (521)
T COG5279 267 TT 268 (521)
T ss_pred ee
Confidence 98
No 11
>PF13369 Transglut_core2: Transglutaminase-like superfamily
Probab=93.60 E-value=0.23 Score=46.06 Aligned_cols=59 Identities=20% Similarity=0.209 Sum_probs=48.8
Q ss_pred CCCCHHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCC
Q 009894 143 RYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCE 205 (523)
Q Consensus 143 RYn~p~~LL~tR~GrCge~A~lF~~l~RalGl~aR~V~d~~dHvW~EVy~~~~~rWI~vDP~~ 205 (523)
......++|++|+|-|.-.|.+|+.+||.+|+++.-|. ...|+.+-+-. + ..+=|||.+
T Consensus 52 ~n~~l~~vL~~r~G~Pi~L~ily~~va~rlGl~~~~v~-~Pgh~l~r~~~-~--~~~~iDpf~ 110 (152)
T PF13369_consen 52 ENSFLHKVLERRRGIPISLAILYLEVARRLGLPAEPVN-FPGHFLVRVRS-D--GEFYIDPFN 110 (152)
T ss_pred HhhhHHHHHhcCCCCcHHHHHHHHHHHHHcCCeEEEEe-cCCEEEEEEec-C--CcEEEccCC
Confidence 34567999999999999999999999999999998774 67788777774 3 236789986
No 12
>PF14381 EDR1: Ethylene-responsive protein kinase Le-CTR1
Probab=91.83 E-value=0.24 Score=49.04 Aligned_cols=54 Identities=19% Similarity=0.201 Sum_probs=43.3
Q ss_pred HHHhcCccchhhHHHHHHHHHHcCCCeEEEE----e-C-CCeeEEEEEeCCCCCeEEeccC
Q 009894 150 LVETKRGRCGEWANCFTLYCRAFGYESRLIL----D-F-TDHVWTECFSQSLGRWMHLDPC 204 (523)
Q Consensus 150 LL~tR~GrCge~A~lF~~l~RalGl~aR~V~----d-~-~dHvW~EVy~~~~~rWI~vDP~ 204 (523)
|=.-+.|.|.|=|.||-.+|-.+|+|+|+|- . + .+|+|+.|-..+...+ =||-+
T Consensus 137 lG~l~~G~~rhRALLFKvLAD~iglpCrLvrG~~y~g~~~~~a~~~V~~~~~~ey-iVDLm 196 (204)
T PF14381_consen 137 LGSLRIGLCRHRALLFKVLADRIGLPCRLVRGCYYCGWDDDDASNLVKFDDGREY-IVDLM 196 (204)
T ss_pred EeeecccchHHHHHHHHHHHHhcCCCceEEeeccCCccCCCCceEEEEcCCCcEE-EEEcC
Confidence 4456899999999999999999999999993 2 4 6899999998765444 35544
No 13
>PF14402 7TM_transglut: 7 transmembrane helices usually fused to an inactive transglutaminase
Probab=90.76 E-value=0.23 Score=52.11 Aligned_cols=48 Identities=19% Similarity=0.362 Sum_probs=39.6
Q ss_pred HHHHHHHHcCCCeEEEEe---------CCCeeEEEEEeCCCCCeEEeccCCCcCCCCee
Q 009894 164 CFTLYCRAFGYESRLILD---------FTDHVWTECFSQSLGRWMHLDPCEGIYDRPLL 213 (523)
Q Consensus 164 lF~~l~RalGl~aR~V~d---------~~dHvW~EVy~~~~~rWI~vDP~~~~vD~Pll 213 (523)
++..+++..|+|||.|.. ...+-|.|||+.+ +|+-+||..+....|.-
T Consensus 2 ~~~~lL~~a~Ipar~v~gl~Led~rr~q~l~~~lev~~~~--~W~~f~p~tg~~g~p~n 58 (313)
T PF14402_consen 2 LIVKLLAMAGIPARVVHGLKLEDGRRRQSLEPWLEVFNGG--KWVLFNPRTGEQGLPEN 58 (313)
T ss_pred HHHHHHHhCCCCccEeeeEEecCCccccCcHhHHheeeCC--eEEEECCCCCCcCCCCC
Confidence 567899999999999952 3558899999974 69999999988876643
No 14
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=90.53 E-value=0.95 Score=47.26 Aligned_cols=127 Identities=13% Similarity=0.195 Sum_probs=74.9
Q ss_pred hHHHHHHHHHHhhccCchhhHHHHHhhhhhhchhcCCHHHHHHHhcc-CChHHHHHHHHHHHHHcCCCCCCCchhHHHHH
Q 009894 3 QAEEEALLFQQHAVGENSGQFEETVHPYISKVLMYEDPIRQEAAKKT-VPVERLEEKSLVSLAREGNFKPSKTEQDHAFL 81 (523)
Q Consensus 3 q~e~~~~~~qq~~~~~~~~~f~~~l~~~~~~v~~YEd~~lq~~Al~~-IPl~~L~~~a~~~l~~~g~~~~~~~~~~~~~l 81 (523)
-+|+|..++..+.. +...+..++++.+..+.-=.||.|....+.- |+.++|-......++.+ +...+...+.
T Consensus 167 A~~iE~~~f~~~~~--~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~-----e~k~~~e~~~ 239 (299)
T TIGR01385 167 AIQIEELKFNNLGT--TEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASA-----ELKQEREEIT 239 (299)
T ss_pred HHHHHHHHHHHcCC--CcHHHHHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCH-----HHHHHHHHHH
Confidence 45677777776553 4456888999888877777899998888775 88888854433322210 0001112233
Q ss_pred HHHHHHHh---hcCeeecCCCCCCCCCC-ccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009894 82 LQLLFWFK---QTFRWVNAPPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (523)
Q Consensus 82 ~~LL~WFK---~~F~wv~~P~C~~Cg~~-t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (523)
++-|+==. ..-+=++..+|+.||+. +.+.-...=++|| ...=.|.|..||+.-+|
T Consensus 240 ke~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~QtrsaDE-----pmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 240 KENLFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADE-----PMTTFVTCEECGNRWKF 298 (299)
T ss_pred HHHHHHHHhhhhhcCCcccccCCCCCCccceEEEecccCCCC-----CCeEEEEcCCCCCeeee
Confidence 33222100 11345677899999985 3322221122332 33447899999998877
No 15
>PF13471 Transglut_core3: Transglutaminase-like superfamily
Probab=87.60 E-value=0.93 Score=40.07 Aligned_cols=37 Identities=30% Similarity=0.608 Sum_probs=32.3
Q ss_pred cCccchhhHHHHHHHHHHcCCCeEEEEe-------CCCeeEEEE
Q 009894 154 KRGRCGEWANCFTLYCRAFGYESRLILD-------FTDHVWTEC 190 (523)
Q Consensus 154 R~GrCge~A~lF~~l~RalGl~aR~V~d-------~~dHvW~EV 190 (523)
.+..|-..|.....+||..|+++.+|+. +..|+|+|+
T Consensus 54 ~~~~CL~~ala~~~~L~~~gi~~~l~iGv~~~~~~~~aHAWve~ 97 (117)
T PF13471_consen 54 WRSKCLPRALALQRLLRRRGIPATLVIGVRKDDDPFAAHAWVEC 97 (117)
T ss_pred CCCChHHHHHHHHHHHHhcCCCcEEEEEEeeCCCCceEEEEEEE
Confidence 3568999999999999999999999963 467999993
No 16
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=85.81 E-value=0.43 Score=51.95 Aligned_cols=35 Identities=29% Similarity=0.549 Sum_probs=28.3
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCC
Q 009894 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 145 (523)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn 145 (523)
.+|.|+.||..|.+.|. + -|+|++||...+-.++-
T Consensus 349 ~~p~Cp~Cg~~m~S~G~------------~---g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 349 VNPVCPRCGGRMKSAGR------------N---GFRCKKCGTRARETLIK 383 (421)
T ss_pred cCCCCCccCCchhhcCC------------C---CcccccccccCCccccc
Confidence 46999999999998873 1 49999999877766655
No 17
>PRK10941 hypothetical protein; Provisional
Probab=82.16 E-value=13 Score=38.26 Aligned_cols=60 Identities=12% Similarity=0.135 Sum_probs=45.6
Q ss_pred HHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCCCcC
Q 009894 147 PLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIY 208 (523)
Q Consensus 147 p~~LL~tR~GrCge~A~lF~~l~RalGl~aR~V~d~~dHvW~EVy~~~~~rWI~vDP~~~~v 208 (523)
..++|++|+|.---.|.+|+.++|.+|+|+.=| ++..|.=.-+=.++...| =+||++|-+
T Consensus 87 L~~VL~~R~G~PisL~il~l~iA~~lglp~~gV-~fPghfllr~~~~d~~~~-~IDPf~G~~ 146 (269)
T PRK10941 87 LDKVLKTRQGSAVSLGAILLWIANRLDLPLMPV-IFPTQLILRADWLDGEMW-LINPFNGET 146 (269)
T ss_pred HHHHHHccCCCcHHHHHHHHHHHHHcCCCeeee-ecCchheeeeecCCCceE-EEeCCCCCC
Confidence 478999999999999999999999999998765 455566555533332334 589987654
No 18
>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=80.97 E-value=1.1 Score=34.11 Aligned_cols=34 Identities=26% Similarity=0.598 Sum_probs=25.0
Q ss_pred cCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009894 91 TFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 91 ~F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
+++|-+.+.|+.||+.....-. ..-.|+|..|+.
T Consensus 12 ~~RW~~g~~CP~Cg~~~~~~~~-------------~~~~~~C~~C~~ 45 (46)
T PF12760_consen 12 EIRWPDGFVCPHCGSTKHYRLK-------------TRGRYRCKACRK 45 (46)
T ss_pred HhcCCCCCCCCCCCCeeeEEeC-------------CCCeEECCCCCC
Confidence 3689999999999997332211 145799999985
No 19
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=78.68 E-value=2.7 Score=43.80 Aligned_cols=54 Identities=33% Similarity=0.698 Sum_probs=38.5
Q ss_pred HHHHHHHHHhhc-CeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHHHHhcCc
Q 009894 80 FLLQLLFWFKQT-FRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRG 156 (523)
Q Consensus 80 ~l~~LL~WFK~~-F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~G 156 (523)
.-.+|++|.++. | |..||++|.....+ -...|++||. .-|||.. |.-+.-+++|
T Consensus 100 ~a~~l~~w~~~~RF-------Cg~CG~~~~~~~~g--------------~~~~C~~cg~-~~fPR~d-P~vIv~v~~~ 154 (279)
T COG2816 100 RAVQLLEWYRSHRF-------CGRCGTKTYPREGG--------------WARVCPKCGH-EHFPRID-PCVIVAVIRG 154 (279)
T ss_pred HHHHHHHHHhhCcC-------CCCCCCcCccccCc--------------eeeeCCCCCC-ccCCCCC-CeEEEEEecC
Confidence 457899999864 5 99999988755211 1468999987 4699975 5556666665
No 20
>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=76.14 E-value=4.5 Score=31.60 Aligned_cols=36 Identities=22% Similarity=0.400 Sum_probs=22.5
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009894 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (523)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (523)
|||.||+....+..+. ..-+....|.|..||....+
T Consensus 3 PCPfCGg~~~~~~~~~-------~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGF-------DPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEecc-------CCCCCEEEEECCCCCCCccc
Confidence 6999999766332110 01223445699999998776
No 21
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=69.66 E-value=3.6 Score=30.50 Aligned_cols=27 Identities=26% Similarity=0.506 Sum_probs=19.4
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009894 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
.||.|+....... .+.|+++.|.+|+-
T Consensus 1 ~CP~C~~~l~~~~------------~~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGTELEPVR------------LGDVEIDVCPSCGG 27 (41)
T ss_pred CcCCCCcccceEE------------ECCEEEEECCCCCe
Confidence 4889988544321 14599999999985
No 22
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=68.84 E-value=3.7 Score=39.19 Aligned_cols=35 Identities=23% Similarity=0.355 Sum_probs=20.1
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009894 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
.||.||++.+.+-...+. ..|-..-..|+|+.||.
T Consensus 2 ~cp~c~~~~~~~~~s~~~----~~~~~~~~~~~c~~c~~ 36 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPA----EDGNAIRRRRECLACGK 36 (154)
T ss_pred cCCCCCCCCCEeEecccc----CCCCceeeeeeccccCC
Confidence 599999976433211111 11222224699999986
No 23
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=68.72 E-value=38 Score=35.95 Aligned_cols=113 Identities=12% Similarity=0.192 Sum_probs=58.3
Q ss_pred HHHHHhhhhhhchhcCCHHHHHHH--hccCChHHHHHHHHHHHHHcCCCCCCCchhHHHHHHHHHHHHhh---cC-----
Q 009894 23 FEETVHPYISKVLMYEDPIRQEAA--KKTVPVERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLLFWFKQ---TF----- 92 (523)
Q Consensus 23 f~~~l~~~~~~v~~YEd~~lq~~A--l~~IPl~~L~~~a~~~l~~~g~~~~~~~~~~~~~l~~LL~WFK~---~F----- 92 (523)
....|..+.+.+.-.-.+.++... +...+-++|+..|...+. |.+........-.+..+|--||.+ .+
T Consensus 103 w~~~L~~Ll~~l~~~~~~~~~~~l~~L~~~~~~~l~~~A~~Ll~--~~~~~v~~~~a~Fi~AALqv~wa~~a~~l~~~~~ 180 (309)
T PRK03564 103 WQKLLMALIAELKPEASGPALAVIENLEKASTQELEDMASALLA--SDFSSVSSDKAPFIWAALSLYWAQMAQQIPGKAR 180 (309)
T ss_pred HHHHHHHHHHHhcccCCHHHHHHHHHHHhCCHHHHHHHHHHHhc--CCccccchhHHHHHHHHHHHHHHHHHhhCCcccc
Confidence 445555555555444444443322 122445566666665443 332222122222233344445544 12
Q ss_pred --eeecCCCCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCC
Q 009894 93 --RWVNAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 145 (523)
Q Consensus 93 --~wv~~P~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn 145 (523)
.|-+...||.||+.-. .+-. ..+....--..|.-|++.-+|+|..
T Consensus 181 ~~~~~~~~~CPvCGs~P~~s~v~--------~~~~~G~RyL~CslC~teW~~~R~~ 228 (309)
T PRK03564 181 AEYGEQRQFCPVCGSMPVSSVVQ--------IGTTQGLRYLHCNLCESEWHVVRVK 228 (309)
T ss_pred cccccCCCCCCCCCCcchhheee--------ccCCCCceEEEcCCCCCcccccCcc
Confidence 2456788999999643 2110 0112344567899999999999954
No 24
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=68.10 E-value=4.7 Score=33.64 Aligned_cols=34 Identities=21% Similarity=0.408 Sum_probs=24.3
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009894 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (523)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (523)
--|||.||.+...+.. .+..+...|.+|+...-|
T Consensus 6 lKPCPFCG~~~~~v~~-----------~~g~~~v~C~~CgA~~~~ 39 (64)
T PRK09710 6 VKPCPFCGCPSVTVKA-----------ISGYYRAKCNGCESRTGY 39 (64)
T ss_pred ccCCCCCCCceeEEEe-----------cCceEEEEcCCCCcCccc
Confidence 3469999998776642 144667889999986443
No 25
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=64.07 E-value=4.1 Score=48.79 Aligned_cols=31 Identities=26% Similarity=0.664 Sum_probs=25.6
Q ss_pred eeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009894 93 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (523)
Q Consensus 93 ~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (523)
.-++.|+|+.||+.+...|. -|.|..||+.+
T Consensus 920 ~~~~~~~c~~c~~~~~~~g~----------------c~~c~~cg~t~ 950 (953)
T PRK06556 920 EAADAPLCPTCGTKMVRNGS----------------CYVCEGCGSTS 950 (953)
T ss_pred ccccCCcCCCccCeeeECCc----------------eEeccCCCCCC
Confidence 45799999999987777775 49999999864
No 26
>PF14353 CpXC: CpXC protein
Probab=63.78 E-value=4.4 Score=36.43 Aligned_cols=42 Identities=21% Similarity=0.293 Sum_probs=25.6
Q ss_pred CCCCCCCCCccc-----c-CCCCCChhhhccCCceEEEeeeCCCCcccc
Q 009894 98 PPCDGCSNETVG-----Q-GMGTPLPSEIQYGAARVELFRCKVCSKITR 140 (523)
Q Consensus 98 P~C~~Cg~~t~~-----~-g~~~P~~~E~~~ga~rVE~y~C~~C~~~~R 140 (523)
..||.||.+... + ....|..-|.-- .+..=.|.|++||+..+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il-~g~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKIL-DGSLFSFTCPSCGHKFR 49 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHH-cCCcCEEECCCCCCcee
Confidence 469999987431 1 122333233222 56777899999998654
No 27
>PRK15047 N-hydroxyarylamine O-acetyltransferase; Provisional
Probab=63.60 E-value=21 Score=36.99 Aligned_cols=67 Identities=24% Similarity=0.283 Sum_probs=48.9
Q ss_pred HHHH-HhcCccchhhHHHHHHHHHHcCCCeEEE-----Ee------CCCeeEEEEEeCCCCCeEEeccCCCc--CCCCee
Q 009894 148 LKLV-ETKRGRCGEWANCFTLYCRAFGYESRLI-----LD------FTDHVWTECFSQSLGRWMHLDPCEGI--YDRPLL 213 (523)
Q Consensus 148 ~~LL-~tR~GrCge~A~lF~~l~RalGl~aR~V-----~d------~~dHvW~EVy~~~~~rWI~vDP~~~~--vD~Pll 213 (523)
.|++ .-|-|.|-|...+|..++|++|++++.+ ++ ...|.=.=|..+++ .| =+|+--|. .-.|+.
T Consensus 58 ~KlV~~~RGGyCfE~N~Lf~~~L~~LGF~v~~~~arV~~~~~~~~~~~tH~~l~V~i~~~-~y-LvDVGFG~~~~~~Pl~ 135 (281)
T PRK15047 58 EKLVIARRGGYCFEQNGLFERVLRELGFNVRSLLGRVVLSNPPALPPRTHRLLLVELEGE-KW-IADVGFGGQTLTAPIR 135 (281)
T ss_pred HHHhcCCCCEEcHhHHHHHHHHHHHcCCcEEEEEEEEEecCCCCCCCcCcEEEEEEECCe-eE-EEEecCCCCCCCccEE
Confidence 4555 3577899999999999999999997766 21 12488777888764 68 57887663 467776
Q ss_pred eec
Q 009894 214 YEK 216 (523)
Q Consensus 214 ye~ 216 (523)
.+.
T Consensus 136 L~~ 138 (281)
T PRK15047 136 LVA 138 (281)
T ss_pred CCC
Confidence 643
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=63.56 E-value=2.6 Score=30.14 Aligned_cols=27 Identities=30% Similarity=0.586 Sum_probs=13.2
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
-|+|+.|+++...... ++|-|+.|+..
T Consensus 2 ~p~Cp~C~se~~y~D~---------------~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYTYEDG---------------ELLVCPECGHE 28 (30)
T ss_dssp S---TTT-----EE-S---------------SSEEETTTTEE
T ss_pred CCCCCCCCCcceeccC---------------CEEeCCccccc
Confidence 3899999998765421 36899999874
No 29
>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=63.40 E-value=6.5 Score=38.27 Aligned_cols=25 Identities=16% Similarity=0.301 Sum_probs=20.2
Q ss_pred HhcCccchhhHHHHHHHHHHcCCCe
Q 009894 152 ETKRGRCGEWANCFTLYCRAFGYES 176 (523)
Q Consensus 152 ~tR~GrCge~A~lF~~l~RalGl~a 176 (523)
..+.|-|.|||.+=-..|+.+|+|.
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 4799999999999999999999983
No 30
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=62.77 E-value=9.3 Score=30.03 Aligned_cols=33 Identities=27% Similarity=0.480 Sum_probs=18.0
Q ss_pred CCCCCCCCCccccCCCCCChhhhccCC-ceEEEeeeCCCCc
Q 009894 98 PPCDGCSNETVGQGMGTPLPSEIQYGA-ARVELFRCKVCSK 137 (523)
Q Consensus 98 P~C~~Cg~~t~~~g~~~P~~~E~~~ga-~rVE~y~C~~C~~ 137 (523)
.|||.||.............. +. ..|+ |..||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~----~~~~~V~---C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDY----GMYYYVE---CTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCC----CCEEEEE---cCCCCC
Confidence 469999877654432111000 11 3343 999998
No 31
>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=61.20 E-value=7.8 Score=37.81 Aligned_cols=68 Identities=25% Similarity=0.309 Sum_probs=45.3
Q ss_pred HHHH-HhcCccchhhHHHHHHHHHHcCCCeEEEEe------------CCCeeEEEEEeCCCCCeEEeccCCCcC--CCCe
Q 009894 148 LKLV-ETKRGRCGEWANCFTLYCRAFGYESRLILD------------FTDHVWTECFSQSLGRWMHLDPCEGIY--DRPL 212 (523)
Q Consensus 148 ~~LL-~tR~GrCge~A~lF~~l~RalGl~aR~V~d------------~~dHvW~EVy~~~~~rWI~vDP~~~~v--D~Pl 212 (523)
.+++ ..|-|.|-|...+|..+++.+|++++++.. ..+|.=.=|-.++. +| =||+.-|.. -.|+
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 4555 567789999999999999999999999841 12477777777764 67 588886653 5666
Q ss_pred eeecC
Q 009894 213 LYEKG 217 (523)
Q Consensus 213 lye~g 217 (523)
....+
T Consensus 116 ~l~~~ 120 (240)
T PF00797_consen 116 PLEDG 120 (240)
T ss_dssp ESSST
T ss_pred EccCC
Confidence 65544
No 32
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=61.19 E-value=6.8 Score=35.85 Aligned_cols=26 Identities=15% Similarity=0.282 Sum_probs=16.7
Q ss_pred cceEEeecC--CcceechhhhccChHHh
Q 009894 222 LNYVIAISK--DGVFDVTKRYTRKWHEV 247 (523)
Q Consensus 222 lsYVIAFs~--dGv~DVTrRYt~~~~~~ 247 (523)
+.+|..|=. .-++||.+-|--.|..+
T Consensus 39 ~~Fi~~Fi~~rGnlKe~e~~lgiSYPTv 66 (113)
T PF09862_consen 39 LEFIKLFIKNRGNLKEMEKELGISYPTV 66 (113)
T ss_pred HHHHHHHHHhcCCHHHHHHHHCCCcHHH
Confidence 445555542 23688888888888744
No 33
>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=61.18 E-value=5.5 Score=36.33 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=20.2
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009894 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
-|+||.|+++-.+... ++|-|+.|++
T Consensus 2 lp~CP~C~seytY~dg---------------~~~iCpeC~~ 27 (109)
T TIGR00686 2 LPPCPKCNSEYTYHDG---------------TQLICPSCLY 27 (109)
T ss_pred CCcCCcCCCcceEecC---------------CeeECccccc
Confidence 5999999998665421 3799999987
No 34
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=60.77 E-value=12 Score=38.09 Aligned_cols=47 Identities=19% Similarity=0.443 Sum_probs=31.6
Q ss_pred HHHHHHHHHhhcCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCH
Q 009894 80 FLLQLLFWFKQTFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 147 (523)
Q Consensus 80 ~l~~LL~WFK~~F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p 147 (523)
...+|++|-++. ++ |+.||+++.... +.. .-.|..|+. .-|||....
T Consensus 88 ~a~~l~~w~~~~-~f-----C~~CG~~~~~~~-------------~~~-~~~C~~c~~-~~yp~~~pa 134 (256)
T PRK00241 88 RAVQLAEFYRSH-RF-----CGYCGHPMHPSK-------------TEW-AMLCPHCRE-RYYPRIAPC 134 (256)
T ss_pred HHHHHHHHhhcC-cc-----ccccCCCCeecC-------------Cce-eEECCCCCC-EECCCCCCE
Confidence 346788888763 22 999999876431 112 246999984 789997654
No 35
>PRK10220 hypothetical protein; Provisional
Probab=58.71 E-value=7 Score=35.74 Aligned_cols=28 Identities=21% Similarity=0.604 Sum_probs=21.3
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
+-|+||.|+++-.+... ++|-|+.|++.
T Consensus 2 ~lP~CP~C~seytY~d~---------------~~~vCpeC~hE 29 (111)
T PRK10220 2 SLPHCPKCNSEYTYEDN---------------GMYICPECAHE 29 (111)
T ss_pred CCCcCCCCCCcceEcCC---------------CeEECCcccCc
Confidence 56999999997665421 27999999974
No 36
>PHA02998 RNA polymerase subunit; Provisional
Probab=53.04 E-value=11 Score=37.22 Aligned_cols=45 Identities=22% Similarity=0.520 Sum_probs=29.7
Q ss_pred CCCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCH
Q 009894 98 PPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 147 (523)
Q Consensus 98 P~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p 147 (523)
.+|+.|++... ..-...=++|| ...=-|+|..||...+=||+.+.
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 56999998632 22111122333 33456999999999999998765
No 37
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=47.47 E-value=16 Score=32.38 Aligned_cols=31 Identities=19% Similarity=0.500 Sum_probs=21.7
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccc
Q 009894 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR 140 (523)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~R 140 (523)
..+.|+.|+.++..- ..+-+++|.+||...-
T Consensus 34 ~~~~Cp~C~~~~VkR--------------~a~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRTTVKR--------------IATGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCcceee--------------eccCeEEcCCCCCeec
Confidence 567899999985422 1123799999997543
No 38
>PRK02935 hypothetical protein; Provisional
Probab=47.41 E-value=13 Score=33.92 Aligned_cols=31 Identities=23% Similarity=0.429 Sum_probs=24.2
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCC
Q 009894 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 143 (523)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPR 143 (523)
+-.||.|+..|...|. +..|-.|+++..-++
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 4569999999999983 348999999766543
No 39
>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=47.10 E-value=11 Score=28.19 Aligned_cols=14 Identities=29% Similarity=0.956 Sum_probs=8.8
Q ss_pred eEEEeeeCCCCccc
Q 009894 126 RVELFRCKVCSKIT 139 (523)
Q Consensus 126 rVE~y~C~~C~~~~ 139 (523)
.-|+|+|..||..+
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 35899999999865
No 40
>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=45.87 E-value=61 Score=32.41 Aligned_cols=111 Identities=17% Similarity=0.263 Sum_probs=55.7
Q ss_pred CceEEEeeeCCCCcccccCCCCCHHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeCCCeeEEEEEeCCCCCeEEecc
Q 009894 124 AARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDP 203 (523)
Q Consensus 124 a~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~GrCge~A~lF~~l~RalGl~aR~V~d~~dHvW~EVy~~~~~rWI~vDP 203 (523)
...+++..|+.||+.-.=-++.++ +.+ ..-+.|+-.+-+.+.-.. .+......+|+|..+. .-.+.|..
T Consensus 30 ~~~i~v~~C~~Cg~~~~~~~W~~~----~~~----el~~~~lk~v~~~l~~~~-~~~~d~~~v~~e~~~~--r~~v~v~v 98 (236)
T PF04981_consen 30 PDRIEVTICPKCGRYRIGGRWVDP----ESR----ELEELCLKKVERGLKKNI-KVHVDAEFVWTEPHSK--RIKVKVTV 98 (236)
T ss_pred CCccCceECCCCCCEECCCEeeec----Ccc----cHHHHHHHHHHHHHHHhh-cccccccEEEEEeeCC--EEEEEEEE
Confidence 356899999999985433466655 100 111222222222222111 1223344678888332 23455544
Q ss_pred CCCcCC-CCeeeecCccCccceEEeec--CCcceechhhhccChHHhhhhccc
Q 009894 204 CEGIYD-RPLLYEKGWNKKLNYVIAIS--KDGVFDVTKRYTRKWHEVLSRRNI 253 (523)
Q Consensus 204 ~~~~vD-~Pllye~gwgK~lsYVIAFs--~dGv~DVTrRYt~~~~~~~~RR~r 253 (523)
...+.+ .|+- .+|.+-|. ..-+-|=+++....|..+++-|..
T Consensus 99 ~~~v~~~~~~~--------~~~~v~~~v~~~~C~~C~r~~~~~~eaiVQvR~~ 143 (236)
T PF04981_consen 99 QGEVHGGTPVE--------QEYEVEVRVKRQQCPDCSRIAGGYYEAIVQVRQR 143 (236)
T ss_pred EEEEcccceEE--------EEEEEEEEEEcCCChhHHhhhCCCccEEEEEEec
Confidence 433333 3322 34555554 334567777776677777777754
No 41
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=44.43 E-value=14 Score=27.06 Aligned_cols=29 Identities=24% Similarity=0.515 Sum_probs=14.2
Q ss_pred CCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 100 CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 100 C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
|+.||++.... -|..| .-|.+.|+.||.+
T Consensus 3 C~~CG~~l~~~---ip~gd-------~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERR---IPEGD-------DRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE-----TT--------SS-EEEETTTTEE
T ss_pred cccccChhhhh---cCCCC-------CccceECCCCCCE
Confidence 89999975432 12222 3367899999864
No 42
>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=44.30 E-value=21 Score=26.45 Aligned_cols=31 Identities=23% Similarity=0.502 Sum_probs=20.4
Q ss_pred CCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCC
Q 009894 98 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCS 136 (523)
Q Consensus 98 P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~ 136 (523)
..||.|++.......| .+...-..|+|..|.
T Consensus 6 v~CP~C~s~~~v~k~G--------~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTEGVKKNG--------KSPSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCCcceeCC--------CCCCCCEeEecCcCC
Confidence 5699999976332221 124567789999984
No 43
>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=43.62 E-value=11 Score=38.73 Aligned_cols=44 Identities=23% Similarity=0.508 Sum_probs=19.4
Q ss_pred eeecCCCCCCCCCCccccCCCCCChhhhccCC-ceEEEeeeCCCCcccccCCCC
Q 009894 93 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGA-ARVELFRCKVCSKITRFPRYN 145 (523)
Q Consensus 93 ~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga-~rVE~y~C~~C~~~~RFPRYn 145 (523)
.| +..-||.||+.-... .+..+. ..---..|.-|++.-+|+|..
T Consensus 169 ~w-~~g~CPvCGs~P~~s--------~l~~~~~~G~R~L~Cs~C~t~W~~~R~~ 213 (290)
T PF04216_consen 169 GW-QRGYCPVCGSPPVLS--------VLRGGEREGKRYLHCSLCGTEWRFVRIK 213 (290)
T ss_dssp -T-T-SS-TTT---EEEE--------EEE------EEEEEETTT--EEE--TTS
T ss_pred Cc-cCCcCCCCCCcCceE--------EEecCCCCccEEEEcCCCCCeeeecCCC
Confidence 44 457899999964321 111111 123667999999999999965
No 44
>COG2912 Uncharacterized conserved protein [Function unknown]
Probab=42.89 E-value=44 Score=34.91 Aligned_cols=63 Identities=14% Similarity=0.151 Sum_probs=52.3
Q ss_pred CCCCCHHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCCCc
Q 009894 142 PRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGI 207 (523)
Q Consensus 142 PRYn~p~~LL~tR~GrCge~A~lF~~l~RalGl~aR~V~d~~dHvW~EVy~~~~~rWI~vDP~~~~ 207 (523)
||----..++++|+|.--..|..++.+++++|+|- +=.++.+|.=.-+..++ +-| -+||+++-
T Consensus 83 ~~n~~l~~Vl~~R~G~pvsLa~vll~ia~~l~lpl-~gV~FP~~flLR~~~~~-~~~-~idP~ng~ 145 (269)
T COG2912 83 PRNLYLNQVLQRRQGIPVSLAVVLLEIARRLDLPL-YGVNFPTQLLLRAEVED-EPL-LIDPFNGG 145 (269)
T ss_pred chhhhHHHHHHHcCCCcchHHHHHHHHHHHcCCCC-CccCCccceeEeeccCC-Cce-eeCCCCCC
Confidence 44445588999999999999999999999999997 33578889888888887 445 89999764
No 45
>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=40.97 E-value=21 Score=26.63 Aligned_cols=38 Identities=16% Similarity=0.407 Sum_probs=22.4
Q ss_pred CCCCCCCCCccccCCCCCChhhhcc-------CCceEEEeeeCCCC
Q 009894 98 PPCDGCSNETVGQGMGTPLPSEIQY-------GAARVELFRCKVCS 136 (523)
Q Consensus 98 P~C~~Cg~~t~~~g~~~P~~~E~~~-------ga~rVE~y~C~~C~ 136 (523)
.-|+.||+....+|.. ...++... --.+...|.|..|+
T Consensus 3 ~~C~~Cg~~l~~ig~~-~~~q~l~~~p~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 3 RACPDCGGELKEIGEE-KVRQVLDLPPAKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred CcCCCCCceeeECCce-eeEEEEeecccceEEEEEEeceEECCCCC
Confidence 4699999987655532 01222221 13455678999986
No 46
>COG3672 Predicted transglutaminase-like cysteine proteinase [General function prediction only]
Probab=40.62 E-value=68 Score=32.04 Aligned_cols=23 Identities=22% Similarity=0.200 Sum_probs=21.9
Q ss_pred hcCccchhhHHHHHHHHHHcCCC
Q 009894 153 TKRGRCGEWANCFTLYCRAFGYE 175 (523)
Q Consensus 153 tR~GrCge~A~lF~~l~RalGl~ 175 (523)
+..|-|.|||..=-.-+..+|++
T Consensus 105 ~~~GDCEDyal~KRr~L~~~G~s 127 (191)
T COG3672 105 TGAGDCEDYALEKRRRLMEAGVS 127 (191)
T ss_pred CCcccHHHHHHHHHHHHHHcCCC
Confidence 89999999999999999999998
No 47
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.55 E-value=64 Score=31.52 Aligned_cols=90 Identities=21% Similarity=0.169 Sum_probs=47.2
Q ss_pred hcCCHHHHHHHhc--cCChHH---HHHHHHHHHHHcCCC---CCCCchhHHHHHHHHHHHHhhcCeeec--CCCCCCCCC
Q 009894 36 MYEDPIRQEAAKK--TVPVER---LEEKSLVSLAREGNF---KPSKTEQDHAFLLQLLFWFKQTFRWVN--APPCDGCSN 105 (523)
Q Consensus 36 ~YEd~~lq~~Al~--~IPl~~---L~~~a~~~l~~~g~~---~~~~~~~~~~~l~~LL~WFK~~F~wv~--~P~C~~Cg~ 105 (523)
.++|+..+..|.. -|=+.+ |+.++ + .|-. -++.. ....+.+++.-|.-.+ |+. .-.|+.|++
T Consensus 34 ~~~d~~i~~i~~~e~rIllTRDr~L~~r~-k----~g~~~i~i~~~s--~~~Ql~e~~~~~~l~~-~~~~e~~RCp~CN~ 105 (165)
T COG1656 34 NESDDEIILIAKKEGRILLTRDRELYKRA-K----LGIKAILIRSDS--IEEQLAEFLARLGLKP-RLFPEFSRCPECNG 105 (165)
T ss_pred cCCcHHHHHHHhcCCeEEEeccHHHHHHh-h----ccCceEEEeCCC--HHHHHHHHHHHhccch-hcccccccCcccCC
Confidence 4889999998888 454433 44444 2 2210 01111 1123555555454433 433 246999998
Q ss_pred Ccccc------CCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 106 ETVGQ------GMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 106 ~t~~~------g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
+-..+ +..+|- .--.--|.|+|++||..
T Consensus 106 ~L~~vs~eev~~~Vp~~-----~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 106 ELEKVSREEVKEKVPEK-----VYRNYEEFYRCPKCGKI 139 (165)
T ss_pred EeccCcHHHHhhccchh-----hhhcccceeECCCCccc
Confidence 64322 112211 11234568999999974
No 48
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=39.20 E-value=1e+02 Score=32.74 Aligned_cols=126 Identities=16% Similarity=0.233 Sum_probs=74.2
Q ss_pred HHHHHHHHHHhhccCchhhHHHHHhhhhhhchhcCCHHHHHHHhcc-CChHHHHHHHHHHHHHcCCCCCCCchhHHHHHH
Q 009894 4 AEEEALLFQQHAVGENSGQFEETVHPYISKVLMYEDPIRQEAAKKT-VPVERLEEKSLVSLAREGNFKPSKTEQDHAFLL 82 (523)
Q Consensus 4 ~e~~~~~~qq~~~~~~~~~f~~~l~~~~~~v~~YEd~~lq~~Al~~-IPl~~L~~~a~~~l~~~g~~~~~~~~~~~~~l~ 82 (523)
.++|.+|++. ...+......++++-+..+--=.||.|+..++.- |+-++|-....+.++.+ +.-+....+++
T Consensus 165 ~~iE~~~~~~--~g~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~-----~lk~~~~k~~k 237 (296)
T KOG1105|consen 165 VQIEEAIFEK--LGNTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASE-----ELKEERQKLTK 237 (296)
T ss_pred HHHHHHHHHH--hCCCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccH-----HHHHHHHHHHH
Confidence 4566777773 3445566778888878888888999999988876 66677743332222110 11122334555
Q ss_pred HHHHHH-hh--cCeeecCCCCCCCCCC-ccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009894 83 QLLFWF-KQ--TFRWVNAPPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (523)
Q Consensus 83 ~LL~WF-K~--~F~wv~~P~C~~Cg~~-t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (523)
+-|+.= -. +=+=++...|..|+.. ....-...+++||- -..-| .|+.||..-.|
T Consensus 238 eal~~~q~~~~~gt~td~fkcgkckk~~cty~q~Qtrs~DeP--mtTfv---~C~ecgnrWkf 295 (296)
T KOG1105|consen 238 EALREHQMAKIQGTQTDLFKCGKCKKKNCTYTQLQTRSADEP--MTTFV---TCNECGNRWKF 295 (296)
T ss_pred HHHHHHhhcccccccccceeeccccccceeEEeeccCCCCCC--cceee---eecccCCcccc
Confidence 554421 11 1244567789999985 33444455566653 12333 59999986655
No 49
>COG2162 NhoA Arylamine N-acetyltransferase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=39.13 E-value=89 Score=32.85 Aligned_cols=66 Identities=26% Similarity=0.382 Sum_probs=45.7
Q ss_pred HHHH-HhcCccchhhHHHHHHHHHHcCCCeEE-----EEeC-------CCeeEEEEEeCCCCCeEEeccCCC--cCCCCe
Q 009894 148 LKLV-ETKRGRCGEWANCFTLYCRAFGYESRL-----ILDF-------TDHVWTECFSQSLGRWMHLDPCEG--IYDRPL 212 (523)
Q Consensus 148 ~~LL-~tR~GrCge~A~lF~~l~RalGl~aR~-----V~d~-------~dHvW~EVy~~~~~rWI~vDP~~~--~vD~Pl 212 (523)
.||+ ..|-|.|-|.--+|..+++++|+.+|. +|.. ..|.=.-|..++. -|+ +|.-.| ..-.|+
T Consensus 59 ~KLv~~rRGGyCfElNglf~~vL~~lGF~v~~l~arV~~g~~~~a~~~~tH~~L~v~~~~~-~~l-~DvGFGg~~l~APl 136 (275)
T COG2162 59 DKLVLARRGGYCFELNGLFGRVLRELGFNVRLLLARVVWGLAPDALPPRTHRLLLVELEGE-TWL-ADVGFGGQTLTAPI 136 (275)
T ss_pred HHHHhccccceehhhhhHHHHHHHHcCCcceeeEEEEEecCCCCCCCcccceEEEEEecCc-eeE-EecCCCCCCcCCCc
Confidence 4444 456789999999999999999998655 4532 3588777777775 584 666555 334465
Q ss_pred eee
Q 009894 213 LYE 215 (523)
Q Consensus 213 lye 215 (523)
..+
T Consensus 137 rL~ 139 (275)
T COG2162 137 RLE 139 (275)
T ss_pred ccC
Confidence 555
No 50
>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=38.20 E-value=43 Score=31.06 Aligned_cols=50 Identities=28% Similarity=0.484 Sum_probs=38.1
Q ss_pred ccchHHHHHhhccccccC----------CCCCeEEEecCCCccccchhhHhHHHHHHHHH
Q 009894 412 LPSIGHLLRVLSLKSELN----------TDGRVDIVLAGDPVKTSLSLPVVFKALDDMIH 461 (523)
Q Consensus 412 lps~~~ll~~lslk~~~~----------~~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~ 461 (523)
||-++.++..+++|.--. .+|+..++|-|+|+.+..++=+++++|+.++.
T Consensus 91 l~g~~~~~~~~~~~pg~~~~~~~~~~g~~~~~~v~~LPG~P~aa~~~~~~v~P~l~~~~~ 150 (152)
T cd00886 91 LPGFGEAFRALSLEETGTAMLSRAVAGIRGGTLIFNLPGSPKAVREALEVILPELPHLLD 150 (152)
T ss_pred CccHHHHHHHhhcccCCcEEEechhheEECCEEEEECCCCHHHHHHHHHHHHHHHHHHHH
Confidence 456667788888886432 26889999999999887777778888877765
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=37.99 E-value=28 Score=36.78 Aligned_cols=43 Identities=16% Similarity=0.446 Sum_probs=29.1
Q ss_pred ecCCCCCCCCCCccccCCCCCChhhhcc--CCceEEEeeeCCCCcccccCCCC
Q 009894 95 VNAPPCDGCSNETVGQGMGTPLPSEIQY--GAARVELFRCKVCSKITRFPRYN 145 (523)
Q Consensus 95 v~~P~C~~Cg~~t~~~g~~~P~~~E~~~--ga~rVE~y~C~~C~~~~RFPRYn 145 (523)
-+..-||.||+.-. ...... +..+.-...|..|++.-+|+|..
T Consensus 182 ~~~~~CPvCGs~P~--------~s~~~~~~~~~G~RyL~CslC~teW~~~R~~ 226 (305)
T TIGR01562 182 ESRTLCPACGSPPV--------ASMVRQGGKETGLRYLSCSLCATEWHYVRVK 226 (305)
T ss_pred CCCCcCCCCCChhh--------hhhhcccCCCCCceEEEcCCCCCcccccCcc
Confidence 45678999999532 111111 13455677999999999999954
No 52
>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=37.77 E-value=15 Score=33.72 Aligned_cols=32 Identities=22% Similarity=0.387 Sum_probs=24.5
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCC
Q 009894 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 143 (523)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPR 143 (523)
-.-.||.|+..|...|. + ..|-+|+++....|
T Consensus 68 v~V~CP~C~K~TKmLGr--------------~--D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGR--------------V--DACMHCKEPLTLDP 99 (114)
T ss_pred eeeECCCCCChHhhhch--------------h--hccCcCCCcCccCc
Confidence 34569999999999973 2 48999998765544
No 53
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=37.54 E-value=28 Score=31.60 Aligned_cols=41 Identities=15% Similarity=0.271 Sum_probs=25.7
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009894 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (523)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (523)
...|+.||+.....-. ...+..+-.-+.-|+|..||..-||
T Consensus 72 ~~~CpkCg~~ea~y~~----~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQ----LQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEe----eehhccCCCceEEEEecccCCEeec
Confidence 4669999997542210 0111122356778999999997775
No 54
>PHA00626 hypothetical protein
Probab=37.35 E-value=19 Score=29.57 Aligned_cols=29 Identities=14% Similarity=0.433 Sum_probs=18.3
Q ss_pred CCCCCCCCcccc-CCCCCChhhhccCCceEEEeeeCCCCc
Q 009894 99 PCDGCSNETVGQ-GMGTPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 99 ~C~~Cg~~t~~~-g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
.||.||+.+... |... ...-.|+|+.||-
T Consensus 2 ~CP~CGS~~Ivrcg~cr----------~~snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR----------GWSDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCceeeeeceec----------ccCcceEcCCCCC
Confidence 599999965432 3211 1124699999995
No 55
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=36.42 E-value=34 Score=25.58 Aligned_cols=35 Identities=23% Similarity=0.497 Sum_probs=20.5
Q ss_pred CCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 99 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 99 ~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
+|+.||+... ..-...=++|| ...=.|.|..||..
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 22111112332 33457999999974
No 56
>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=36.35 E-value=27 Score=33.71 Aligned_cols=34 Identities=21% Similarity=0.582 Sum_probs=22.0
Q ss_pred CCCCCCCcccc-CCCCCChhhhc-cCCceEEEeeeCCCCc
Q 009894 100 CDGCSNETVGQ-GMGTPLPSEIQ-YGAARVELFRCKVCSK 137 (523)
Q Consensus 100 C~~Cg~~t~~~-g~~~P~~~E~~-~ga~rVE~y~C~~C~~ 137 (523)
|+.||+++... .. ..++. ++--.+--|.|++||-
T Consensus 1 CP~Cg~~~~~~~~~----~~~IP~F~evii~sf~C~~CGy 36 (163)
T TIGR00340 1 CPVCGSRTLKAVTY----DYDIPYFGKIMLSTYICEKCGY 36 (163)
T ss_pred CCCCCCcceEeeeE----eccCCCcceEEEEEEECCCCCC
Confidence 99999874322 11 11222 3557788999999996
No 57
>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=35.81 E-value=17 Score=37.46 Aligned_cols=29 Identities=21% Similarity=0.504 Sum_probs=10.5
Q ss_pred CCCCCCCC-ccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 99 PCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 99 ~C~~Cg~~-t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
.|+.||+. ....+...|.+ -|.|..|+..
T Consensus 33 yCP~Cg~~~L~~f~NN~PVa-----------DF~C~~C~ee 62 (254)
T PF06044_consen 33 YCPNCGSKPLSKFENNRPVA-----------DFYCPNCNEE 62 (254)
T ss_dssp --TTT--SS-EE-------------------EEE-TTT--E
T ss_pred cCCCCCChhHhhccCCCccc-----------eeECCCCchH
Confidence 49999997 55556554544 4999999863
No 58
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=34.91 E-value=19 Score=29.63 Aligned_cols=23 Identities=26% Similarity=0.741 Sum_probs=19.8
Q ss_pred HHHhhcCeeecCCCCCCCCCCcc
Q 009894 86 FWFKQTFRWVNAPPCDGCSNETV 108 (523)
Q Consensus 86 ~WFK~~F~wv~~P~C~~Cg~~t~ 108 (523)
-|-+..|+.-..|.|+-|++++.
T Consensus 28 gWmR~nFs~~~~p~CPlC~s~M~ 50 (59)
T PF14169_consen 28 GWMRDNFSFEEEPVCPLCKSPMV 50 (59)
T ss_pred cccccccccCCCccCCCcCCccc
Confidence 47777799999999999999875
No 59
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=34.43 E-value=17 Score=30.12 Aligned_cols=10 Identities=40% Similarity=1.125 Sum_probs=7.3
Q ss_pred CCCCCCCCCC
Q 009894 97 APPCDGCSNE 106 (523)
Q Consensus 97 ~P~C~~Cg~~ 106 (523)
.|.|.+||..
T Consensus 9 ~~~CtSCg~~ 18 (61)
T COG2888 9 PPVCTSCGRE 18 (61)
T ss_pred CceeccCCCE
Confidence 5678888874
No 60
>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=34.16 E-value=27 Score=25.93 Aligned_cols=35 Identities=17% Similarity=0.356 Sum_probs=18.1
Q ss_pred CCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 99 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 99 ~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
+|+.||++.. ..-...=.+|| ...=.|.|..||+.
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 6999999743 22111112232 34557999999974
No 61
>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=33.98 E-value=32 Score=32.63 Aligned_cols=58 Identities=19% Similarity=0.263 Sum_probs=44.8
Q ss_pred HhhccchHHHHHhhcccc-c---------cC-CCCCeEEEecCCCccccchh-hHhHHHHHHHHHhcccC
Q 009894 409 HQLLPSIGHLLRVLSLKS-E---------LN-TDGRVDIVLAGDPVKTSLSL-PVVFKALDDMIHDLNNC 466 (523)
Q Consensus 409 ~~~lps~~~ll~~lslk~-~---------~~-~~g~~~~~~~~~p~~tsl~l-~~~~~~~~~~~~~~~~~ 466 (523)
++-+|-++.++..+++|. - ++ .+|..-++|-|+|+....++ -.+..+|+.+++..++-
T Consensus 90 ~~~l~G~~~~~~~i~~~p~G~~~~lsr~~~g~~~~~~v~~LPG~P~aa~~~~~~~v~P~l~~~~~~~~~~ 159 (163)
T TIGR02667 90 DKTVEGFGELFRQLSYEEIGTSTIQSRALAGLANGTFVFCLPGSTGACRTAWDKIIAAQLDARHRPCNFV 159 (163)
T ss_pred CCcCCcHHHHHHHHhhcccCHHHHHhhhhheeeCCeEEEECCCCHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 333778888999999986 2 22 25679999999999998888 56888888887777663
No 62
>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=33.78 E-value=31 Score=25.46 Aligned_cols=31 Identities=23% Similarity=0.730 Sum_probs=19.5
Q ss_pred eecCCC--CCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009894 94 WVNAPP--CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (523)
Q Consensus 94 wv~~P~--C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (523)
|+-.|. |+.|++.......| .|-|..||+.+
T Consensus 3 ~~~~~~~~C~~C~~~~~~~~dG---------------~~yC~~cG~~~ 35 (36)
T PF11781_consen 3 WMRGPNEPCPVCGSRWFYSDDG---------------FYYCDRCGHQS 35 (36)
T ss_pred ccccCCCcCCCCCCeEeEccCC---------------EEEhhhCceEc
Confidence 444455 99999962222111 58899999864
No 63
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.60 E-value=27 Score=34.72 Aligned_cols=44 Identities=11% Similarity=0.241 Sum_probs=27.7
Q ss_pred CCCCCCCccc--cCCCCCChhhhccCCceEEEeeeCCCCcccccCCCC
Q 009894 100 CDGCSNETVG--QGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 145 (523)
Q Consensus 100 C~~Cg~~t~~--~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn 145 (523)
|+.||..+.+ .|+-.-++.- ---+.==+|+|.+|...-.||-|.
T Consensus 20 C~~Cg~kr~f~cSg~fRvNAq~--K~LDvWlIYkC~~Cd~tWN~~Ife 65 (203)
T COG4332 20 CNSCGVKRAFTCSGKFRVNAQG--KVLDVWLIYKCTHCDYTWNISIFE 65 (203)
T ss_pred CcccCCcceeeecCcEEEcCCC--cEEEEEEEEEeeccCCccchhhhh
Confidence 9999997654 3543333321 112445689999999877666553
No 64
>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=33.51 E-value=20 Score=33.93 Aligned_cols=66 Identities=18% Similarity=0.308 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHcCCCCCCCchhHHHHHHHHHHHHhhcCeeecCCCCCCCCCC-ccccCCCCCChhhhccCCceEEEee
Q 009894 53 ERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLLFWFKQTFRWVNAPPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFR 131 (523)
Q Consensus 53 ~~L~~~a~~~l~~~g~~~~~~~~~~~~~l~~LL~WFK~~F~wv~~P~C~~Cg~~-t~~~g~~~P~~~E~~~ga~rVE~y~ 131 (523)
|.|.+.+..+|..-|-.-|....... . ..+.| ...|++||+. |.....-.||+=- -+|+
T Consensus 73 d~it~~gr~~l~~~giapp~~~~~~~--~--------~~~~~--~~~cp~c~s~~t~~~s~fg~t~ck--------a~~~ 132 (146)
T TIGR02159 73 DWITEDAREKLREYGIAPPAGHYVVG--V--------SPEPP--SVQCPRCGSADTTITSIFGPTACK--------ALYR 132 (146)
T ss_pred HHCCHHHHHHHHhcCccCCCccCCCc--c--------cCCCC--CCcCCCCCCCCcEeecCCCChhhH--------HHhh
Confidence 66777777667655543333221111 0 12344 5789999995 4433222233322 3799
Q ss_pred eCCCCcc
Q 009894 132 CKVCSKI 138 (523)
Q Consensus 132 C~~C~~~ 138 (523)
|..|...
T Consensus 133 c~~c~ep 139 (146)
T TIGR02159 133 CRACKEP 139 (146)
T ss_pred hhhhCCc
Confidence 9999764
No 65
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=33.13 E-value=28 Score=24.46 Aligned_cols=14 Identities=21% Similarity=0.363 Sum_probs=7.4
Q ss_pred CCCCCCCCCCcccc
Q 009894 97 APPCDGCSNETVGQ 110 (523)
Q Consensus 97 ~P~C~~Cg~~t~~~ 110 (523)
..-|+.||++|...
T Consensus 3 ~rfC~~CG~~t~~~ 16 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA 16 (32)
T ss_dssp TSB-TTT--BEEE-
T ss_pred CcccCcCCccccCC
Confidence 34599999998765
No 66
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=32.72 E-value=24 Score=25.12 Aligned_cols=14 Identities=29% Similarity=0.980 Sum_probs=11.4
Q ss_pred eEEEeeeCCCCccc
Q 009894 126 RVELFRCKVCSKIT 139 (523)
Q Consensus 126 rVE~y~C~~C~~~~ 139 (523)
+.++|+|..||..+
T Consensus 4 ~~~~ykC~~Cgniv 17 (34)
T TIGR00319 4 EGQVYKCEVCGNIV 17 (34)
T ss_pred cCcEEEcCCCCcEE
Confidence 46799999999754
No 67
>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=32.15 E-value=35 Score=32.74 Aligned_cols=26 Identities=4% Similarity=0.065 Sum_probs=19.8
Q ss_pred hcccccHHHHHHHHHHHHHHHHccCC
Q 009894 250 RRNIATEQTVSAVLAKMTRECRRSFA 275 (523)
Q Consensus 250 RR~rv~E~wl~~~L~~l~~~~r~~ls 275 (523)
++..|+.+.+..++..|...++....
T Consensus 75 ~KRpVs~e~ie~~v~~Ie~~l~~~~~ 100 (147)
T TIGR00244 75 EKRPVSFDDLEHAINHIEAQLRAQGE 100 (147)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 44468999999999998888776443
No 68
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=30.83 E-value=79 Score=29.40 Aligned_cols=54 Identities=22% Similarity=0.362 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhhcCeeec--CCCCCCCCCCcccc------CCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 79 AFLLQLLFWFKQTFRWVN--APPCDGCSNETVGQ------GMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 79 ~~l~~LL~WFK~~F~wv~--~P~C~~Cg~~t~~~------g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
..|.+++.-|.=.+ +.+ --.|+.|++.-..+ +..+|..- ...-+.|+|+.||+.
T Consensus 72 ~QL~ev~~~~~l~~-~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~-----~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 72 EQLREVLERFGLKL-RLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVY-----ETYDEFWRCPGCGKI 133 (147)
T ss_pred HHHHHHHHHcCCcc-ccCCCCCccCCCCcEeeechhhccccccCcccc-----ccCCeEEECCCCCCE
Confidence 45778887774333 222 13799999854322 22222211 123358999999974
No 69
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=29.67 E-value=27 Score=23.33 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=5.8
Q ss_pred CCCCCCCc
Q 009894 100 CDGCSNET 107 (523)
Q Consensus 100 C~~Cg~~t 107 (523)
|+.||.+.
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 78888743
No 70
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.62 E-value=44 Score=30.79 Aligned_cols=26 Identities=23% Similarity=0.649 Sum_probs=18.7
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccc
Q 009894 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR 140 (523)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~R 140 (523)
-|+||.||.+.. |---+|+.|++.+|
T Consensus 6 ~~~cPvcg~~~i------------------VTeL~c~~~etTVr 31 (122)
T COG3877 6 INRCPVCGRKLI------------------VTELKCSNCETTVR 31 (122)
T ss_pred CCCCCcccccce------------------eEEEecCCCCceEe
Confidence 478999998443 33357999988765
No 71
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=29.45 E-value=38 Score=25.07 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=8.9
Q ss_pred CCCCCCCCCcc
Q 009894 98 PPCDGCSNETV 108 (523)
Q Consensus 98 P~C~~Cg~~t~ 108 (523)
+.|+.||+.+.
T Consensus 3 ~~Cp~Cg~~~~ 13 (47)
T PF14690_consen 3 PRCPHCGSPSV 13 (47)
T ss_pred ccCCCcCCCce
Confidence 56999999874
No 72
>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=29.03 E-value=38 Score=34.73 Aligned_cols=42 Identities=19% Similarity=0.315 Sum_probs=19.5
Q ss_pred Cee-ecCCCCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009894 92 FRW-VNAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (523)
Q Consensus 92 F~w-v~~P~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (523)
+.| +....|+.||+... ....-. ..+...+.++.|..|+..+
T Consensus 205 t~W~~~R~~Cp~Cg~~~~~~l~~~~------~e~~~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 205 TEWRFVRIKCPYCGNTDHEKLEYFT------VEGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp -EEE--TTS-TTT---SS-EEE--------------SEEEEEETTTTEEE
T ss_pred CeeeecCCCCcCCCCCCCcceeeEe------cCCCCcEEEEECCcccchH
Confidence 477 66778999998643 222210 1233467777999999753
No 73
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=28.79 E-value=38 Score=33.51 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=21.9
Q ss_pred CCCCCCCCcc--ccCCC-CCChhhhccCCceEEEeeeCCCCc
Q 009894 99 PCDGCSNETV--GQGMG-TPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 99 ~C~~Cg~~t~--~~g~~-~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
+|+.||.+.. ..-.. -|- ++-..+--+.|++||-
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 6999997532 22111 122 3567778999999986
No 74
>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=28.51 E-value=55 Score=30.90 Aligned_cols=28 Identities=18% Similarity=0.336 Sum_probs=24.2
Q ss_pred HhcCccchhhHHHHHHHHHHcCCCeEEE
Q 009894 152 ETKRGRCGEWANCFTLYCRAFGYESRLI 179 (523)
Q Consensus 152 ~tR~GrCge~A~lF~~l~RalGl~aR~V 179 (523)
.|.---|-|++++|--++.+||+.+|++
T Consensus 51 ~~~GiNCtD~~Qlf~~v~~~lGY~Vq~~ 78 (142)
T PF12386_consen 51 RTSGINCTDACQLFYRVIESLGYDVQFE 78 (142)
T ss_pred HhcCCCchhHHHHHHHHHHhcCceEEEE
Confidence 3433459999999999999999999999
No 75
>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=28.42 E-value=30 Score=32.24 Aligned_cols=61 Identities=31% Similarity=0.695 Sum_probs=40.2
Q ss_pred eeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHHHHhcCccchhhHHHHHHHHHHc
Q 009894 93 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAF 172 (523)
Q Consensus 93 ~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~GrCge~A~lF~~l~Ral 172 (523)
.|+. +-|+.|+.+....+. ..|+|..|+...-=|
T Consensus 31 ~~~Y-~aC~~C~kkv~~~~~---------------~~~~C~~C~~~~~~~------------------------------ 64 (166)
T cd04476 31 NWWY-PACPGCNKKVVEEGN---------------GTYRCEKCNKSVPNP------------------------------ 64 (166)
T ss_pred CeEE-ccccccCcccEeCCC---------------CcEECCCCCCcCCCc------------------------------
Confidence 4555 669999886443321 579999999864212
Q ss_pred CCCeEEE-----EeCCCeeEEEEEeCCCCCeEEe
Q 009894 173 GYESRLI-----LDFTDHVWTECFSQSLGRWMHL 201 (523)
Q Consensus 173 Gl~aR~V-----~d~~dHvW~EVy~~~~~rWI~v 201 (523)
..||. -|.++.+|+-+|.+....=++.
T Consensus 65 --~~ry~l~~~i~D~Tg~~~~~~F~~~ae~l~G~ 96 (166)
T cd04476 65 --EYRYILSLNVADHTGEAWLTLFDEVAEQIFGK 96 (166)
T ss_pred --cEEEEEEEEEEeCCCCEEEEEehHHHHHHhCC
Confidence 12344 3688899999998765555555
No 76
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=28.32 E-value=57 Score=36.87 Aligned_cols=41 Identities=27% Similarity=0.425 Sum_probs=26.7
Q ss_pred HHHHHHHH-Hhhc--CeeecCCC--CCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 80 FLLQLLFW-FKQT--FRWVNAPP--CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 80 ~l~~LL~W-FK~~--F~wv~~P~--C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
-+++|++. |++. +-|++.|. |..||.... -+.+.|+.||..
T Consensus 496 al~~lv~~a~~~~~~y~~~~~p~~~C~~CG~~~~------------------~~~~~CP~CGs~ 541 (555)
T cd01675 496 ALEALVKKAAKRGVIYFGINTPIDICNDCGYIGE------------------GEGFKCPKCGSE 541 (555)
T ss_pred HHHHHHHHHHHcCCceEEEecCCccCCCCCCCCc------------------CCCCCCcCCCCc
Confidence 56677776 6663 45666665 888886222 234899999953
No 77
>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=28.12 E-value=61 Score=26.90 Aligned_cols=39 Identities=23% Similarity=0.309 Sum_probs=25.5
Q ss_pred eeEEEEEeCCCCCeEEeccCCCcCCCCeeeecCccCccce
Q 009894 185 HVWTECFSQSLGRWMHLDPCEGIYDRPLLYEKGWNKKLNY 224 (523)
Q Consensus 185 HvW~EVy~~~~~rWI~vDP~~~~vD~Pllye~gwgK~lsY 224 (523)
+...-.|++..+||+..||.. ..+..-.|.=..+.++++
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 455667999999999999963 334334444344555544
No 78
>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=27.32 E-value=57 Score=29.46 Aligned_cols=42 Identities=26% Similarity=0.430 Sum_probs=24.5
Q ss_pred CCCCCCCCCccccCCCCCChhhhccCC---ceEEEeeeCCCCcccc-cCCCC
Q 009894 98 PPCDGCSNETVGQGMGTPLPSEIQYGA---ARVELFRCKVCSKITR-FPRYN 145 (523)
Q Consensus 98 P~C~~Cg~~t~~~g~~~P~~~E~~~ga---~rVE~y~C~~C~~~~R-FPRYn 145 (523)
..|+.||.+...+.. ++. +|- ..=-+|.|..|++.+- +|.=+
T Consensus 3 ~~CpYCg~~~~l~~~-----~~i-Yg~~~~~~~~~y~C~~C~AyVG~H~~t~ 48 (102)
T PF11672_consen 3 IICPYCGGPAELVDG-----SEI-YGHRYDDGPYLYVCTPCDAYVGCHPGTD 48 (102)
T ss_pred cccCCCCCeeEEccc-----chh-cCccCCCCceeEECCCCCceeeeeCCCC
Confidence 459999998765431 111 221 1123599999998653 45433
No 79
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=26.89 E-value=41 Score=27.06 Aligned_cols=28 Identities=14% Similarity=0.396 Sum_probs=19.5
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009894 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
.++.||+||..+.... --+.|.|..||-
T Consensus 18 k~~~CPrCG~gvfmA~--------------H~dR~~CGkCgy 45 (51)
T COG1998 18 KNRFCPRCGPGVFMAD--------------HKDRWACGKCGY 45 (51)
T ss_pred ccccCCCCCCcchhhh--------------cCceeEeccccc
Confidence 4577999997555432 223788999985
No 80
>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=26.71 E-value=33 Score=24.46 Aligned_cols=13 Identities=31% Similarity=1.216 Sum_probs=10.5
Q ss_pred EEEeeeCCCCccc
Q 009894 127 VELFRCKVCSKIT 139 (523)
Q Consensus 127 VE~y~C~~C~~~~ 139 (523)
.+.|+|..||...
T Consensus 2 ~~~ykC~~CGniv 14 (34)
T cd00974 2 LEVYKCEICGNIV 14 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4689999999764
No 81
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=26.65 E-value=43 Score=32.15 Aligned_cols=34 Identities=18% Similarity=0.477 Sum_probs=21.9
Q ss_pred CCCCCCCCcc--ccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009894 99 PCDGCSNETV--GQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 99 ~C~~Cg~~t~--~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
.|+.||.+.. ..-..-|- ++-..+--|.|++||-
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 5999997532 22211222 3556778999999995
No 82
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.96 E-value=37 Score=29.76 Aligned_cols=27 Identities=30% Similarity=0.432 Sum_probs=21.2
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009894 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
.|+.|+-+..+.. -+.||+=.|+.|+.
T Consensus 3 lCP~C~v~l~~~~------------rs~vEiD~CPrCrG 29 (88)
T COG3809 3 LCPICGVELVMSV------------RSGVEIDYCPRCRG 29 (88)
T ss_pred ccCcCCceeeeee------------ecCceeeeCCcccc
Confidence 4999998766542 37799999999975
No 83
>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=25.41 E-value=1.1 Score=36.92 Aligned_cols=54 Identities=19% Similarity=0.155 Sum_probs=34.8
Q ss_pred ceeeEeeccchhhhccccCCCchhhHHHHHHHHHHHHhhccCCCcccccccccCCC
Q 009894 346 HVTTIYNAFSSVLSHFVENNVPKSGAIELLKILKGILGDLKKSPYKTRRVSLNSVP 401 (523)
Q Consensus 346 hv~~iY~a~~~~ls~~~~~~~~~~~a~~~~~~~r~~~~dlk~~~f~~R~~~~~~~~ 401 (523)
+|..-|+-..-.-|+-.++ .|...++.+..|.|+++.||+|+ |.+|+...+...
T Consensus 3 y~~FtYdii~d~YS~~~~d-Gs~~~~~~~~nI~R~ve~d~~~v-YL~r~~~~~~g~ 56 (62)
T PF04721_consen 3 YVKFTYDIISDTYSHTNED-GSPIQPWKVENIERKVERDWNMV-YLHRKEGSEEGN 56 (62)
T ss_dssp ----EEETTTTEEEECCGT-TEEEE-SSEESEEEEEETTTTEE-EEEE-TT-SEEE
T ss_pred ccceeEEeccCEEEeeCCC-CeEEeeEEeeeEEEEEeCCCcEE-EEEEcCCCccce
Confidence 4556666666555554332 46667888899999999999999 999988765544
No 84
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=25.32 E-value=30 Score=33.49 Aligned_cols=25 Identities=12% Similarity=0.268 Sum_probs=20.4
Q ss_pred hcccccHHHHHHHHHHHHHHHHccC
Q 009894 250 RRNIATEQTVSAVLAKMTRECRRSF 274 (523)
Q Consensus 250 RR~rv~E~wl~~~L~~l~~~~r~~l 274 (523)
++..|+.+.++.+++.+-.++|..-
T Consensus 75 ~KRpVs~e~ie~~v~~ie~~Lr~~g 99 (156)
T COG1327 75 EKRPVSSEQIEEAVSHIERQLRSSG 99 (156)
T ss_pred hcCCCCHHHHHHHHHHHHHHHHhcC
Confidence 5567899999999999998888653
No 85
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=25.19 E-value=19 Score=38.94 Aligned_cols=54 Identities=17% Similarity=0.372 Sum_probs=26.9
Q ss_pred HHHHHHHH-hhc-C-ee-ecCCCCCCCCC-Ccc-ccCCCCCChhhhccCCceEEEeeeCCCCcccccCC
Q 009894 81 LLQLLFWF-KQT-F-RW-VNAPPCDGCSN-ETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 143 (523)
Q Consensus 81 l~~LL~WF-K~~-F-~w-v~~P~C~~Cg~-~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPR 143 (523)
|.++|.=+ .+. - +| --.|.|+.||. .|+ .... ..+...|+ |+|..||+....+-
T Consensus 154 I~~Il~~~~~~~~~~~y~Pf~piC~~cGri~tt~v~~~--------d~~~~~v~-Y~c~~cG~~g~~~i 213 (360)
T PF01921_consen 154 IREILNEYRGRERPETYSPFLPICEKCGRIDTTEVTEY--------DPEGGTVT-YRCEECGHEGEVDI 213 (360)
T ss_dssp HHHHHHHHHHHT--TT--SEEEEETTTEE--EEEEEEE----------SSSEEE-EE--TTS---EEET
T ss_pred HHHHHHHhcCcCCCCCeeeeeeeccccCCcccceeeEe--------ecCCCEEE-EEecCCCCEEEEec
Confidence 45544444 333 2 55 33688999998 444 3321 11356676 99999999665543
No 86
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=25.13 E-value=44 Score=25.23 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=8.0
Q ss_pred EeeeCCCCccc
Q 009894 129 LFRCKVCSKIT 139 (523)
Q Consensus 129 ~y~C~~C~~~~ 139 (523)
..+|+.||...
T Consensus 21 ~~~Cp~CG~~~ 31 (46)
T PRK00398 21 GVRCPYCGYRI 31 (46)
T ss_pred ceECCCCCCeE
Confidence 56888888743
No 87
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=25.04 E-value=54 Score=34.79 Aligned_cols=42 Identities=19% Similarity=0.290 Sum_probs=25.8
Q ss_pred Cee-ecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009894 92 FRW-VNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (523)
Q Consensus 92 F~w-v~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (523)
..| +....|+.||+. ...++ -+.++ +...+.++.|..|++..
T Consensus 220 teW~~~R~~C~~Cg~~-~~l~y--~~~~~---~~~~~r~e~C~~C~~Yl 262 (309)
T PRK03564 220 SEWHVVRVKCSNCEQS-GKLHY--WSLDS---EQAAVKAESCGDCGTYL 262 (309)
T ss_pred CcccccCccCCCCCCC-Cceee--eeecC---CCcceEeeecccccccc
Confidence 477 667889999973 22332 11121 11346777999999864
No 88
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=25.03 E-value=86 Score=27.96 Aligned_cols=17 Identities=53% Similarity=0.993 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHhhcCeeecCCCC
Q 009894 77 DHAFLLQLLFWFKQTFRWVNAPPC 100 (523)
Q Consensus 77 ~~~~l~~LL~WFK~~F~wv~~P~C 100 (523)
...++++||+|| |-|++
T Consensus 28 ~~~Ll~~LleWF-------nf~~~ 44 (98)
T PF14726_consen 28 ERLLLKQLLEWF-------NFPPV 44 (98)
T ss_pred HHHHHHHHHHHh-------CCCCC
Confidence 446899999999 66665
No 89
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=24.50 E-value=30 Score=34.56 Aligned_cols=35 Identities=34% Similarity=0.594 Sum_probs=26.3
Q ss_pred CCCCChhhhccCCc------eEEEeeeCCCC----cccccCCCCC
Q 009894 112 MGTPLPSEIQYGAA------RVELFRCKVCS----KITRFPRYND 146 (523)
Q Consensus 112 ~~~P~~~E~~~ga~------rVE~y~C~~C~----~~~RFPRYn~ 146 (523)
.+-|+.||-.|.|+ +.|-|+|..|+ +.+|=||.|+
T Consensus 15 ~akp~~Deg~WdCsvCTFrNsAeAfkC~vCdvRKGTSTRkpr~ns 59 (228)
T KOG4477|consen 15 DAKPNDDEGKWDCSVCTFRNSAEAFKCFVCDVRKGTSTRKPRCNS 59 (228)
T ss_pred cCCCccccCceeeeeeeecchhhhhheeeecccccccccCCcchH
Confidence 34577777777764 57999999997 5678888774
No 90
>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=24.35 E-value=44 Score=29.32 Aligned_cols=38 Identities=13% Similarity=0.277 Sum_probs=20.1
Q ss_pred CCCCCCCccccCCCCCChhhhccCC--ceEEEeeeCCCCcc
Q 009894 100 CDGCSNETVGQGMGTPLPSEIQYGA--ARVELFRCKVCSKI 138 (523)
Q Consensus 100 C~~Cg~~t~~~g~~~P~~~E~~~ga--~rVE~y~C~~C~~~ 138 (523)
|+.|++.+...+...-+-+ ..+.. -.|..+.|+.||..
T Consensus 1 C~~C~~~~~~~~~~~~~~~-~~G~~~~v~~~~~~C~~CGe~ 40 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYT-YKGESITIGVPGWYCPACGEE 40 (127)
T ss_pred CCCCCCccceeeeecceEE-EcCEEEEEeeeeeECCCCCCE
Confidence 8999864433322111111 11111 25678999999974
No 91
>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=23.54 E-value=74 Score=27.60 Aligned_cols=36 Identities=17% Similarity=0.463 Sum_probs=22.4
Q ss_pred CCCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 98 PPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 98 P~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
-.|+.||+... ..-...-++|| ...=.|.|.+||..
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 22222223343 34567999999974
No 92
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=22.62 E-value=63 Score=30.29 Aligned_cols=44 Identities=20% Similarity=0.453 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhcCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 79 AFLLQLLFWFKQTFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 79 ~~l~~LL~WFK~~F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
..+.++|+=|=. .||. |+.|+++.+..-. -+++-.-+|..||+.
T Consensus 84 ~~i~~~L~~yI~--~yVl---C~~C~sPdT~l~k-----------~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 84 FLLNERIEDYVR--KYVI---CRECNRPDTRIIK-----------EGRVSLLKCEACGAK 127 (133)
T ss_pred HHHHHHHHHHHh--heEE---CCCCCCCCcEEEE-----------eCCeEEEecccCCCC
Confidence 457777766544 4455 9999996443211 156767799999974
No 93
>PRK15312 antimicrobial resistance protein Mig-14; Provisional
Probab=22.52 E-value=2.4e+02 Score=30.05 Aligned_cols=92 Identities=20% Similarity=0.236 Sum_probs=57.5
Q ss_pred HHHHHhcCccch---hhHHH--HHHHHHHcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCCCcCCCCee-eecC----
Q 009894 148 LKLVETKRGRCG---EWANC--FTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDRPLL-YEKG---- 217 (523)
Q Consensus 148 ~~LL~tR~GrCg---e~A~l--F~~l~RalGl~aR~V~d~~dHvW~EVy~~~~~rWI~vDP~~~~vD~Pll-ye~g---- 217 (523)
..|++.|-|.+- +.+++ |...+|-+=+-.=+-+|..+-+=.=|+--....||.+|-.++-+|.-.. +..|
T Consensus 173 ~~Lf~~Rwg~~~~~~~~~~l~e~f~~Lr~l~fG~VLfl~~~PcA~qlv~k~eSp~wi~~D~iNgG~Dpe~~~~spGSIL~ 252 (298)
T PRK15312 173 IELFRSRFGNTLSCYPADNLANFFSQLRHLLFGHILYIEGIPCAFDIVLKSESQMNVYFDVPNGAVKNECMPLSPGSILM 252 (298)
T ss_pred HHHHHHHhCCCCCcccHHHHHHHHHHhHHhheeeEEEECCcceEEEEEEEecCCCcEEEecccCccCcccccCCCccEEE
Confidence 467777877433 33333 2333444433333336778888777887777889999999999986633 3322
Q ss_pred -------------ccCccceEEeecCCcceechhhhccCh
Q 009894 218 -------------WNKKLNYVIAISKDGVFDVTKRYTRKW 244 (523)
Q Consensus 218 -------------wgK~lsYVIAFs~dGv~DVTrRYt~~~ 244 (523)
-+|+|.|-||..+- |+.|-..|
T Consensus 253 WlNi~~A~~~~~~~~K~lrfSfG~~r~-----~~~YK~RW 287 (298)
T PRK15312 253 WLNISRARHYCQERQKKLIFSIGILKP-----EWEYKRMW 287 (298)
T ss_pred EecHHHHHHHHHhcCCcEEEEecCCCC-----ChhHHhhc
Confidence 27899999984322 34555555
No 94
>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=22.47 E-value=51 Score=29.26 Aligned_cols=26 Identities=27% Similarity=0.736 Sum_probs=17.1
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
.|+.||.....- ..+=+++|.+|+..
T Consensus 37 ~Cp~Cgk~~vkR--------------~a~GIW~C~~C~~~ 62 (90)
T PF01780_consen 37 TCPFCGKTSVKR--------------VATGIWKCKKCGKK 62 (90)
T ss_dssp EESSSSSSEEEE--------------EETTEEEETTTTEE
T ss_pred cCCCCCCceeEE--------------eeeEEeecCCCCCE
Confidence 499999965311 11126999999964
No 95
>PRK03954 ribonuclease P protein component 4; Validated
Probab=22.43 E-value=42 Score=31.10 Aligned_cols=17 Identities=35% Similarity=0.893 Sum_probs=15.0
Q ss_pred eEEEeeeCCCCcccccCC
Q 009894 126 RVELFRCKVCSKITRFPR 143 (523)
Q Consensus 126 rVE~y~C~~C~~~~RFPR 143 (523)
.| ++.|..||...|||=
T Consensus 91 ~v-vitCl~CG~~kR~P~ 107 (121)
T PRK03954 91 HV-VITCLECGHIMRYPY 107 (121)
T ss_pred eE-EEECccCCCEEeecc
Confidence 45 889999999999984
No 96
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.40 E-value=62 Score=25.92 Aligned_cols=29 Identities=17% Similarity=0.477 Sum_probs=19.9
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
-+-.|+.||..... ...-..|.|+.||..
T Consensus 27 TSq~C~~CG~~~~~--------------~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--------------RRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCccccccc--------------ccccceEEcCCCCCE
Confidence 45569999985443 123357999999975
No 97
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.35 E-value=59 Score=25.62 Aligned_cols=28 Identities=14% Similarity=0.437 Sum_probs=18.5
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
+..-||.||+. ..... -..+.|..||-.
T Consensus 19 ~~~fCP~Cg~~-~m~~~--------------~~r~~C~~Cgyt 46 (50)
T PRK00432 19 KNKFCPRCGSG-FMAEH--------------LDRWHCGKCGYT 46 (50)
T ss_pred ccCcCcCCCcc-hhecc--------------CCcEECCCcCCE
Confidence 45679999986 32211 146889999853
No 98
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=22.22 E-value=96 Score=35.02 Aligned_cols=104 Identities=16% Similarity=0.324 Sum_probs=60.5
Q ss_pred cccccCCCCCHHHHHHhcCccchhhHHHHHHHHHHcCC-CeEEE--EeC--CCeeEEEEEeCCCCCeEEeccCCCcCCCC
Q 009894 137 KITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGY-ESRLI--LDF--TDHVWTECFSQSLGRWMHLDPCEGIYDRP 211 (523)
Q Consensus 137 ~~~RFPRYn~p~~LL~tR~GrCge~A~lF~~l~RalGl-~aR~V--~d~--~dHvW~EVy~~~~~rWI~vDP~~~~vD~P 211 (523)
..+++|-|+...-++--+.-.-+|.-.++..+++++|+ ..||. |.. ++-+=+++|.+..++||-|=-| |++..-
T Consensus 373 DatH~~eFhQ~Eg~vi~~~~s~~~L~~~l~~f~~~lG~~~~RfrP~yfPfTEPS~Ev~v~~~~~gkWIEIgg~-Gm~rpe 451 (494)
T PTZ00326 373 DATHLAEFHQVEGFVIDRNLTLGDLIGTIREFFRRIGITKLRFKPAFNPYTEPSMEIFGYHPGLKKWVEVGNS-GIFRPE 451 (494)
T ss_pred CCCcCceeEEEEEEEEeCCCCHHHHHHHHHHHHHhcCCCceEEecCCCCCCCCeeEEEEEecCCCcEEEEeCc-CccCHH
Confidence 34555555544333222222334555666788899998 68998 542 3334455566666679999888 777655
Q ss_pred eeeecCccCccceEEeec---------CCcceechhhhcc
Q 009894 212 LLYEKGWNKKLNYVIAIS---------KDGVFDVTKRYTR 242 (523)
Q Consensus 212 llye~gwgK~lsYVIAFs---------~dGv~DVTrRYt~ 242 (523)
.+-..|-..+. -|+||+ +.|+.|+--=|..
T Consensus 452 vL~~~Gi~~~~-~~~A~GlGleRlaMi~ygi~DIR~l~~~ 490 (494)
T PTZ00326 452 MLRPMGFPEDV-TVIAWGLSLERPTMIKYGIKNIRDLFGH 490 (494)
T ss_pred HHHhcCCCCcc-eEEEEEecHHHHHHHHhCCcHHHHHhcc
Confidence 55444443343 266665 3677776554443
No 99
>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=22.20 E-value=43 Score=24.99 Aligned_cols=30 Identities=20% Similarity=0.489 Sum_probs=17.1
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009894 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (523)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (523)
.|+.||+...... ..+=| +.|..||.....
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 4899999653221 11112 589999987653
No 100
>PLN02678 seryl-tRNA synthetase
Probab=21.88 E-value=1.6e+02 Score=32.82 Aligned_cols=47 Identities=11% Similarity=0.152 Sum_probs=35.3
Q ss_pred HHHHHHHHHcCCCeEEEE----e----CCCeeEEEEEeCCCCCeEEeccCCCcCC
Q 009894 163 NCFTLYCRAFGYESRLIL----D----FTDHVWTECFSQSLGRWMHLDPCEGIYD 209 (523)
Q Consensus 163 ~lF~~l~RalGl~aR~V~----d----~~dHvW~EVy~~~~~rWI~vDP~~~~vD 209 (523)
..-..+...||||.|.|. | ..-.+=.|||.|++++|.-|-.|.+.-|
T Consensus 310 ~~~~~i~~~L~lpyrvv~~~sgdlg~~a~~~yDiE~W~P~~~~y~EvsS~Snc~D 364 (448)
T PLN02678 310 KNSEDFYQSLGIPYQVVSIVSGALNDAAAKKYDLEAWFPASKTYRELVSCSNCTD 364 (448)
T ss_pred HHHHHHHHHcCCCeEEEeecccccCCchhhceeeEeeccccCCceEEeeeccccc
Confidence 344556788999999984 2 1113348999999999999999977665
No 101
>PF12390 Se-cys_synth_N: Selenocysteine synthase N terminal
Probab=21.87 E-value=54 Score=24.31 Aligned_cols=37 Identities=30% Similarity=0.602 Sum_probs=27.1
Q ss_pred hccchHHHHHhhccccccCCCCCeEEEecCCCccccchhhHhHHHHHHHHHhc
Q 009894 411 LLPSIGHLLRVLSLKSELNTDGRVDIVLAGDPVKTSLSLPVVFKALDDMIHDL 463 (523)
Q Consensus 411 ~lps~~~ll~~lslk~~~~~~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~~~ 463 (523)
-|||.+.+|....++.-+..-|+ +++.+++.+++..+
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 38999999998888777665554 56777777776543
No 102
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.56 E-value=55 Score=32.40 Aligned_cols=41 Identities=22% Similarity=0.370 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhhc---Ceeec-----CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 79 AFLLQLLFWFKQT---FRWVN-----APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 79 ~~l~~LL~WFK~~---F~wv~-----~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
..+++.|.|.-.. +..++ +-.|+.||. -....|.|+.||..
T Consensus 283 ~~~~~~l~yka~~~~~~v~~~~~~~tS~~C~~cg~-------------------~~~r~~~C~~cg~~ 331 (364)
T COG0675 283 GELRRQLEYKAEWGGIVVKVVPPYYTSKTCPCCGH-------------------LSGRLFKCPRCGFV 331 (364)
T ss_pred HHHHHHHHHHHHhCCeEEEECCCCCCcccccccCC-------------------ccceeEECCCCCCe
Confidence 3466666666643 22222 245888888 12467999999973
No 103
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=21.14 E-value=61 Score=32.58 Aligned_cols=37 Identities=16% Similarity=0.325 Sum_probs=23.7
Q ss_pred CCCCCCCCCCccccCCCCCChhhhc-cCCceEEEeeeCCCCc
Q 009894 97 APPCDGCSNETVGQGMGTPLPSEIQ-YGAARVELFRCKVCSK 137 (523)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~-~ga~rVE~y~C~~C~~ 137 (523)
...||.||+........ .+.. +|--.+=.+.|.+||-
T Consensus 14 ~~~CPvCg~~l~~~~~~----~~IPyFG~V~i~t~~C~~CgY 51 (201)
T COG1779 14 RIDCPVCGGTLKAHMYL----YDIPYFGEVLISTGVCERCGY 51 (201)
T ss_pred eecCCcccceeeEEEee----ecCCccceEEEEEEEccccCC
Confidence 35699999954333322 2222 3566777899999985
No 104
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.06 E-value=68 Score=24.15 Aligned_cols=14 Identities=21% Similarity=0.543 Sum_probs=10.5
Q ss_pred EEeeeCCCCccccc
Q 009894 128 ELFRCKVCSKITRF 141 (523)
Q Consensus 128 E~y~C~~C~~~~RF 141 (523)
..|.|+.||...+-
T Consensus 19 ~~~vC~~Cg~~~~~ 32 (52)
T smart00661 19 RRFVCRKCGYEEPI 32 (52)
T ss_pred CEEECCcCCCeEEC
Confidence 37899999975443
No 105
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=21.05 E-value=59 Score=32.29 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=16.5
Q ss_pred CceEEEeeeCCCCcc---cccCCCCCH
Q 009894 124 AARVELFRCKVCSKI---TRFPRYNDP 147 (523)
Q Consensus 124 a~rVE~y~C~~C~~~---~RFPRYn~p 147 (523)
.---++..|++||-. ..|+.....
T Consensus 43 P~~Y~V~vCP~CgyA~~~~~F~~l~~~ 69 (214)
T PF09986_consen 43 PLFYEVWVCPHCGYAAFEEDFEKLSPE 69 (214)
T ss_pred CeeeeEEECCCCCCcccccccccCCHH
Confidence 345688899999943 348866643
No 106
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=21.05 E-value=60 Score=37.42 Aligned_cols=55 Identities=20% Similarity=0.423 Sum_probs=29.1
Q ss_pred HHHHHhh-cCeeecCCCCCCCCCCcccc-C-CCCCChhhhccCCceEEEeeeCCCCccccc
Q 009894 84 LLFWFKQ-TFRWVNAPPCDGCSNETVGQ-G-MGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (523)
Q Consensus 84 LL~WFK~-~F~wv~~P~C~~Cg~~t~~~-g-~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (523)
+++=|.. +|+|..- +|+.||...... | +..| .-..+-+.--=.|+|.+|+..++-
T Consensus 214 Ie~~y~~gd~rr~yv-pCPHCGe~q~l~~~e~~~~--~g~~~~~~~~~~~~c~h~~~~i~~ 271 (611)
T COG5525 214 IERAYNAGDQRRFYV-PCPHCGEEQQLKFGEKSGP--RGLKDTPAEAAFIQCEHCGCVIRP 271 (611)
T ss_pred HHHHhhhccceeEEe-eCCCCCchhhccccccCCC--cCcccchhhhhhhhccccCceeee
Confidence 3333444 4755553 599999864321 1 1111 111111122235799999999987
No 107
>PRK00420 hypothetical protein; Validated
Probab=21.04 E-value=71 Score=29.29 Aligned_cols=41 Identities=15% Similarity=0.227 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhcCeeecCCCCCCCCCCccc--cCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 80 FLLQLLFWFKQTFRWVNAPPCDGCSNETVG--QGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 80 ~l~~LL~WFK~~F~wv~~P~C~~Cg~~t~~--~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
.++.+-.+..+-.+- ..-.||.||.+-.. .| ...|+.||..
T Consensus 7 ~~k~~a~~Ll~Ga~m-l~~~CP~Cg~pLf~lk~g-----------------~~~Cp~Cg~~ 49 (112)
T PRK00420 7 IVKKAAELLLKGAKM-LSKHCPVCGLPLFELKDG-----------------EVVCPVHGKV 49 (112)
T ss_pred HHHHHHHHHHhHHHH-ccCCCCCCCCcceecCCC-----------------ceECCCCCCe
Confidence 444444444443222 44779999987553 33 2579999974
No 108
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=20.99 E-value=74 Score=36.01 Aligned_cols=28 Identities=21% Similarity=0.173 Sum_probs=18.3
Q ss_pred hHhHHHHHHHHHhcccCcCCCCCccccc
Q 009894 450 PVVFKALDDMIHDLNNCDNFGKGSFCLP 477 (523)
Q Consensus 450 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 477 (523)
+|=.|.++++++.-=+-...+.|.++||
T Consensus 468 ~vgt~~~K~~l~~rL~~~~~~~g~~hfp 495 (557)
T PF05876_consen 468 LVGTDAAKDTLYGRLRREEPGPGYVHFP 495 (557)
T ss_pred EEccHHHHHHHHHhhcccCCCCceEEcC
Confidence 4446788888875444344566778888
No 109
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=20.99 E-value=70 Score=36.29 Aligned_cols=62 Identities=19% Similarity=0.182 Sum_probs=35.8
Q ss_pred CCCCceeecccceeeEeeccc-hhhh----ccccCC--CchhhHHHHHHHHHHHHhhccCCCcccccccccCC
Q 009894 335 SSCPVRVCIDEHVTTIYNAFS-SVLS----HFVENN--VPKSGAIELLKILKGILGDLKKSPYKTRRVSLNSV 400 (523)
Q Consensus 335 s~cp~~~c~d~hv~~iY~a~~-~~ls----~~~~~~--~~~~~a~~~~~~~r~~~~dlk~~~f~~R~~~~~~~ 400 (523)
.--|+|.|.+ +..|+++.. -+|. +...+. .....+.+.+..-++-..|. +|.+.+.+-.+..
T Consensus 365 ~~vpFr~l~~--l~qi~~~~~e~il~~~~~~~~~~~~~~~~~~l~~~i~~A~~W~~~y--aP~~~kf~~~e~~ 433 (521)
T COG1384 365 YQVPFRHLAV--LVQIANAEEEDILEILIRRYLPDADPDTIEDLDERIEYAINWLRDY--APEKVKFSILEKP 433 (521)
T ss_pred CCCCHHHHHH--HHHHcCCchHHHHHHHHHhccCCCChhhHHHHHHHHHHHHHHHHHh--Cccceeecccccc
Confidence 3578888888 778887764 2221 222222 24555566666666666666 6666665555444
No 110
>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=20.87 E-value=73 Score=33.74 Aligned_cols=44 Identities=14% Similarity=0.258 Sum_probs=26.1
Q ss_pred Cee-ecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009894 92 FRW-VNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (523)
Q Consensus 92 F~w-v~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (523)
..| +....|+.||+.. ..++- +.++ ..+...+.++.|..|++..
T Consensus 218 teW~~~R~~C~~Cg~~~-~l~y~--~~e~-~~~~~~~r~e~C~~C~~Yl 262 (305)
T TIGR01562 218 TEWHYVRVKCSHCEESK-HLAYL--SLEH-DAEKAVLKAETCDSCQGYL 262 (305)
T ss_pred CcccccCccCCCCCCCC-ceeeE--eecC-CCCCcceEEeeccccccch
Confidence 467 6678899999853 23321 1111 0122456777999999863
No 111
>PRK10445 endonuclease VIII; Provisional
Probab=20.86 E-value=57 Score=33.32 Aligned_cols=26 Identities=19% Similarity=0.538 Sum_probs=17.5
Q ss_pred CCCCCCCCCcc--ccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009894 98 PPCDGCSNETV--GQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (523)
Q Consensus 98 P~C~~Cg~~t~--~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (523)
-+|+.||.+-. .+|. =-.|-|+.|+.
T Consensus 236 ~~Cp~Cg~~I~~~~~~g--------------R~t~~CP~CQ~ 263 (263)
T PRK10445 236 EACERCGGIIEKTTLSS--------------RPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCEeEEEEECC--------------CCcEECCCCcC
Confidence 67999998643 2331 12599999974
No 112
>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=20.82 E-value=27 Score=31.93 Aligned_cols=26 Identities=19% Similarity=0.374 Sum_probs=19.2
Q ss_pred EeCCCeeEEEEEeCCCCCeEEeccCC
Q 009894 180 LDFTDHVWTECFSQSLGRWMHLDPCE 205 (523)
Q Consensus 180 ~d~~dHvW~EVy~~~~~rWI~vDP~~ 205 (523)
.|.++..|+-+|.+....-++.+..+
T Consensus 61 ~D~tg~~~~~~F~~~a~~l~G~~a~e 86 (146)
T PF08646_consen 61 SDGTGSIWVTLFDEEAEQLLGMSADE 86 (146)
T ss_dssp EETTEEEEEEEEHHHHHHHHCCHHCC
T ss_pred EeCCCeEEEEEEhHHHHHHhCCCHHH
Confidence 37899999999987655566666543
No 113
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=20.75 E-value=49 Score=35.51 Aligned_cols=45 Identities=22% Similarity=0.445 Sum_probs=0.0
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHH
Q 009894 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKL 150 (523)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~L 150 (523)
.|.|+.||.-++.+ .+....+..|+ |+| .||+...-+-.+.-.||
T Consensus 169 ~p~c~~cg~~~~~v-------~~~d~~~~~v~-y~c-~cG~~g~~~~~~g~~KL 213 (353)
T cd00674 169 MPYCEKCGKDTTTV-------EAYDAKAGTVT-YKC-ECGHEETVDIRTGRGKL 213 (353)
T ss_pred eeecCCcCcceeEE-------EEEeCCCCeEE-EEc-CCCCEEEEeecCCCccc
No 114
>PHA02942 putative transposase; Provisional
Probab=20.50 E-value=73 Score=34.43 Aligned_cols=44 Identities=23% Similarity=0.534 Sum_probs=26.1
Q ss_pred HHHHHHHHHhhc----Ceee----cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009894 80 FLLQLLFWFKQT----FRWV----NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (523)
Q Consensus 80 ~l~~LL~WFK~~----F~wv----~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (523)
.|.+.|.|=... +..| -+-.|+.||..+... ..| .|.|..||..
T Consensus 300 ~l~~~LeYKA~~~G~~Vv~V~p~yTSq~Cs~CG~~~~~l-------------~~r--~f~C~~CG~~ 351 (383)
T PHA02942 300 RIQYWIEWQAKKHGMIVEFVNPSYSSVSCPKCGHKMVEI-------------AHR--YFHCPSCGYE 351 (383)
T ss_pred HHHHHHHHHHHHhCCEEEEECCCCCCccCCCCCCccCcC-------------CCC--EEECCCCCCE
Confidence 455666665432 2333 335599999854211 122 6999999985
No 115
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=20.42 E-value=56 Score=21.38 Aligned_cols=23 Identities=35% Similarity=0.658 Sum_probs=14.9
Q ss_pred EeeeCCCCcccccCCCCCHHHHHHhcCc
Q 009894 129 LFRCKVCSKITRFPRYNDPLKLVETKRG 156 (523)
Q Consensus 129 ~y~C~~C~~~~RFPRYn~p~~LL~tR~G 156 (523)
+|+|..|+. .|++-..+.+-++-
T Consensus 1 ~~~C~~C~~-----~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 1 PFECDECGK-----TFSSLSALREHKRS 23 (27)
T ss_dssp SEEETTTTE-----EESSHHHHHHHHCT
T ss_pred CCCCCccCC-----ccCChhHHHHHhHH
Confidence 489999997 34555555555443
No 116
>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=20.40 E-value=89 Score=25.98 Aligned_cols=41 Identities=20% Similarity=0.396 Sum_probs=22.6
Q ss_pred CCCCCCCCccccCCCCCChh---hh-ccCCceEEEeeeCCCCccc
Q 009894 99 PCDGCSNETVGQGMGTPLPS---EI-QYGAARVELFRCKVCSKIT 139 (523)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~---E~-~~ga~rVE~y~C~~C~~~~ 139 (523)
.|+.||++.--.+....+-. .. .-+-.+--...|+.||-..
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 59999997543332211111 11 1123456678899999753
No 117
>PRK05978 hypothetical protein; Provisional
Probab=20.17 E-value=75 Score=30.45 Aligned_cols=41 Identities=15% Similarity=0.343 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhcCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009894 80 FLLQLLFWFKQTFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (523)
Q Consensus 80 ~l~~LL~WFK~~F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (523)
..+.+++=++ -.||+||......|.-...+ +|+.||....+
T Consensus 24 ~~~~~~rGl~--------grCP~CG~G~LF~g~Lkv~~-------------~C~~CG~~~~~ 64 (148)
T PRK05978 24 VGRAMWRGFR--------GRCPACGEGKLFRAFLKPVD-------------HCAACGEDFTH 64 (148)
T ss_pred hHHHHHHHHc--------CcCCCCCCCcccccccccCC-------------CccccCCcccc
Confidence 4555555443 46999999766555432221 59999975443
Done!