Query 009800
Match_columns 525
No_of_seqs 241 out of 592
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 17:29:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009800.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009800hhsearch_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 1E-117 3E-122 918.1 23.0 419 13-513 79-500 (500)
2 PF03835 Rad4: Rad4 transgluta 99.9 2.8E-22 6.2E-27 183.0 7.9 101 182-293 33-144 (145)
3 TIGR00605 rad4 DNA repair prot 99.8 7.7E-20 1.7E-24 203.0 8.1 104 185-297 371-477 (713)
4 PF01841 Transglut_core: Trans 99.5 4.7E-14 1E-18 119.8 6.7 80 123-203 17-113 (113)
5 smart00460 TGc Transglutaminas 99.4 5.8E-13 1.3E-17 104.6 6.2 53 150-204 1-67 (68)
6 COG1305 Transglutaminase-like 99.3 3.9E-12 8.4E-17 123.4 10.3 99 78-219 159-275 (319)
7 KOG2179 Nucleotide excision re 99.1 5.5E-11 1.2E-15 131.0 4.4 174 155-357 263-484 (669)
8 COG5535 RAD4 DNA repair protei 98.2 6.6E-08 1.4E-12 105.6 -4.0 122 151-272 243-399 (650)
9 PF04473 DUF553: Transglutamin 97.0 0.0029 6.2E-08 59.9 8.3 66 139-206 59-129 (153)
10 COG5279 CYK3 Uncharacterized p 94.6 0.08 1.7E-06 58.5 7.1 64 139-204 189-268 (521)
11 PF13369 Transglut_core2: Tran 93.7 0.21 4.6E-06 46.3 7.1 59 143-205 52-110 (152)
12 PF14381 EDR1: Ethylene-respon 91.9 0.28 6.1E-06 48.6 5.3 54 150-204 137-196 (204)
13 TIGR01385 TFSII transcription 90.3 1 2.2E-05 47.1 7.9 127 3-141 167-298 (299)
14 PF14402 7TM_transglut: 7 tran 90.0 0.28 6.2E-06 51.4 3.6 48 164-213 2-58 (313)
15 PF13471 Transglut_core3: Tran 87.1 1 2.2E-05 39.9 4.6 37 154-190 54-97 (117)
16 COG1571 Predicted DNA-binding 85.5 0.45 9.8E-06 51.8 1.9 35 96-145 349-383 (421)
17 PF12760 Zn_Tnp_IS1595: Transp 85.2 0.94 2E-05 34.5 3.0 34 91-137 12-45 (46)
18 PRK10941 hypothetical protein; 80.8 16 0.00034 37.7 10.7 60 147-208 87-146 (269)
19 COG2816 NPY1 NTP pyrophosphohy 79.3 2.5 5.3E-05 44.1 4.4 54 80-156 100-154 (279)
20 TIGR03655 anti_R_Lar restricti 75.4 4.9 0.00011 31.4 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 PRK09710 lar restriction allev 69.1 4.3 9.3E-05 33.9 2.5 34 97-141 6-39 (64)
23 PRK00464 nrdR transcriptional 68.5 3.8 8.2E-05 39.2 2.5 34 99-137 2-36 (154)
24 PRK03564 formate dehydrogenase 68.4 38 0.00083 35.9 10.0 112 23-145 103-228 (309)
25 PF00797 Acetyltransf_2: N-ace 66.5 5.4 0.00012 38.9 3.2 68 148-217 38-120 (240)
26 PF06035 Peptidase_C93: Bacter 66.3 3.6 7.8E-05 40.0 1.9 24 152-175 74-97 (170)
27 PRK06556 vitamin B12-dependent 65.0 3.8 8.2E-05 49.1 2.1 31 93-139 920-950 (953)
28 PRK15047 N-hydroxyarylamine O- 64.8 19 0.00042 37.3 6.9 67 148-216 58-138 (281)
29 PF08274 PhnA_Zn_Ribbon: PhnA 63.8 2.6 5.6E-05 30.2 0.3 27 97-138 2-28 (30)
30 PRK00241 nudC NADH pyrophospha 63.0 11 0.00023 38.4 4.6 47 80-147 88-134 (256)
31 PF14353 CpXC: CpXC protein 62.8 4.7 0.0001 36.3 1.8 42 98-140 2-49 (128)
32 PF14354 Lar_restr_allev: Rest 61.8 9.9 0.00021 29.9 3.3 33 98-137 4-37 (61)
33 TIGR00686 phnA alkylphosphonat 61.1 5.5 0.00012 36.4 1.9 26 97-137 2-27 (109)
34 PF09862 DUF2089: Protein of u 59.3 7.7 0.00017 35.5 2.5 27 221-247 38-66 (113)
35 PRK10220 hypothetical protein; 58.6 7 0.00015 35.8 2.1 28 96-138 2-29 (111)
36 PHA02998 RNA polymerase subuni 53.0 11 0.00023 37.4 2.5 45 98-147 144-189 (195)
37 PF14803 Nudix_N_2: Nudix N-te 48.0 11 0.00025 27.5 1.4 29 100-138 3-31 (34)
38 COG1997 RPL43A Ribosomal prote 46.3 17 0.00036 32.2 2.4 31 96-140 34-64 (89)
39 PF06397 Desulfoferrod_N: Desu 45.5 12 0.00025 28.0 1.2 14 126-139 3-16 (36)
40 PRK02935 hypothetical protein; 44.3 16 0.00034 33.5 2.0 31 97-143 70-100 (110)
41 PF03811 Zn_Tnp_IS1: InsA N-te 43.9 21 0.00046 26.4 2.3 31 98-136 6-36 (36)
42 PF04216 FdhE: Protein involve 43.6 11 0.00023 38.7 1.0 44 93-145 169-213 (290)
43 PHA00626 hypothetical protein 43.1 16 0.00034 30.1 1.7 29 99-137 2-31 (59)
44 PF13005 zf-IS66: zinc-finger 40.3 22 0.00047 26.6 2.0 38 98-136 3-47 (47)
45 PF04981 NMD3: NMD3 family ; 39.7 1E+02 0.0022 30.9 7.1 135 100-253 1-143 (236)
46 KOG1105 Transcription elongati 39.3 1E+02 0.0022 32.8 7.2 126 4-141 165-295 (296)
47 cd00886 MogA_MoaB MogA_MoaB fa 37.5 43 0.00093 31.0 3.9 50 412-461 91-150 (152)
48 COG2912 Uncharacterized conser 37.5 60 0.0013 34.0 5.2 63 142-207 83-145 (269)
49 TIGR01562 FdhE formate dehydro 37.3 29 0.00063 36.7 3.0 49 95-160 182-232 (305)
50 PF06044 DRP: Dam-replacing fa 36.7 16 0.00035 37.6 1.1 54 226-283 154-213 (254)
51 COG1656 Uncharacterized conser 36.6 46 0.001 32.5 4.0 90 36-138 34-139 (165)
52 COG2162 NhoA Arylamine N-acety 36.6 72 0.0016 33.5 5.6 66 148-215 59-139 (275)
53 TIGR00340 zpr1_rel ZPR1-relate 36.6 27 0.00058 33.8 2.4 34 100-137 1-36 (163)
54 smart00440 ZnF_C2C2 C2C2 Zinc 35.9 35 0.00075 25.5 2.4 35 99-138 2-37 (40)
55 COG1594 RPB9 DNA-directed RNA 35.9 31 0.00066 31.4 2.6 41 97-141 72-112 (113)
56 PF09297 zf-NADH-PPase: NADH p 35.8 24 0.00052 24.8 1.5 14 97-110 3-16 (32)
57 PF11023 DUF2614: Protein of u 35.6 18 0.00038 33.4 1.0 32 96-143 68-99 (114)
58 PF11781 RRN7: RNA polymerase 35.2 28 0.00061 25.7 1.8 31 94-139 3-35 (36)
59 PF14169 YdjO: Cold-inducible 34.3 20 0.00043 29.6 1.0 23 86-108 28-50 (59)
60 PF01096 TFIIS_C: Transcriptio 33.8 28 0.0006 25.9 1.6 35 99-138 2-37 (39)
61 TIGR02159 PA_CoA_Oxy4 phenylac 33.2 19 0.00042 34.0 0.9 66 53-138 73-139 (146)
62 TIGR02667 moaB_proteo molybden 33.2 32 0.00069 32.6 2.4 56 411-466 92-159 (163)
63 COG4332 Uncharacterized protei 32.6 29 0.00063 34.6 2.0 44 100-145 20-65 (203)
64 COG3672 Predicted transglutami 31.8 1E+02 0.0022 30.9 5.6 23 153-175 105-127 (191)
65 TIGR00319 desulf_FeS4 desulfof 31.4 26 0.00056 25.0 1.1 14 126-139 4-17 (34)
66 PF01927 Mut7-C: Mut7-C RNAse 30.8 79 0.0017 29.4 4.5 54 79-138 72-133 (147)
67 PF12386 Peptidase_C71: Pseudo 30.7 48 0.001 31.3 3.0 29 152-180 51-79 (142)
68 PF14690 zf-ISL3: zinc-finger 29.6 38 0.00082 25.1 1.8 11 98-108 3-13 (47)
69 PF13240 zinc_ribbon_2: zinc-r 29.5 28 0.0006 23.3 0.9 8 100-107 2-9 (23)
70 PF04216 FdhE: Protein involve 29.2 38 0.00082 34.8 2.3 42 92-139 205-248 (290)
71 TIGR00310 ZPR1_znf ZPR1 zinc f 29.2 35 0.00077 33.7 2.0 34 99-137 2-38 (192)
72 PF14726 RTTN_N: Rotatin, an a 29.0 66 0.0014 28.7 3.5 17 77-100 28-44 (98)
73 cd04476 RPA1_DBD_C RPA1_DBD_C: 28.6 30 0.00066 32.3 1.4 61 93-201 31-96 (166)
74 KOG4477 RING1 interactor RYBP 28.2 23 0.00051 35.3 0.5 35 112-146 15-59 (228)
75 COG1998 RPS31 Ribosomal protei 27.9 38 0.00082 27.2 1.5 28 96-137 18-45 (51)
76 PF11672 DUF3268: Protein of u 27.6 56 0.0012 29.5 2.8 74 98-177 3-97 (102)
77 COG3877 Uncharacterized protei 27.4 51 0.0011 30.4 2.5 26 97-140 6-31 (122)
78 smart00709 Zpr1 Duplicated dom 26.7 43 0.00093 32.2 2.0 34 99-137 2-37 (160)
79 PRK00398 rpoP DNA-directed RNA 26.6 40 0.00086 25.5 1.4 11 129-139 21-31 (46)
80 cd01675 RNR_III Class III ribo 26.5 64 0.0014 36.5 3.6 41 80-138 496-541 (555)
81 COG3809 Uncharacterized protei 26.5 35 0.00077 29.9 1.3 27 99-137 3-29 (88)
82 TIGR00244 transcriptional regu 25.9 30 0.00065 33.2 0.8 42 99-146 2-43 (147)
83 cd00974 DSRD Desulforedoxin (D 25.3 36 0.00079 24.3 1.0 13 127-139 2-14 (34)
84 PF01921 tRNA-synt_1f: tRNA sy 25.3 19 0.00042 38.9 -0.7 54 81-143 154-213 (360)
85 TIGR03696 Rhs_assc_core RHS re 25.3 74 0.0016 26.4 3.0 39 185-224 32-70 (76)
86 PF04721 DUF750: Domain of unk 24.9 1.1 2.5E-05 36.9 -7.7 54 346-401 3-56 (62)
87 PRK03564 formate dehydrogenase 24.6 56 0.0012 34.7 2.6 42 92-139 220-262 (309)
88 TIGR03830 CxxCG_CxxCG_HTH puta 24.0 45 0.00097 29.3 1.5 38 100-138 1-40 (127)
89 TIGR00311 aIF-2beta translatio 23.8 58 0.0012 30.6 2.2 45 78-138 83-127 (133)
90 PRK15312 antimicrobial resista 23.7 2.2E+02 0.0049 30.3 6.7 82 148-229 173-277 (298)
91 PRK10445 endonuclease VIII; Pr 23.4 47 0.001 33.9 1.7 26 98-137 236-263 (263)
92 TIGR01384 TFS_arch transcripti 23.1 76 0.0016 27.5 2.7 36 98-138 63-99 (104)
93 COG1327 Predicted transcriptio 23.1 43 0.00093 32.4 1.3 25 250-274 75-99 (156)
94 PF08271 TF_Zn_Ribbon: TFIIB z 22.8 43 0.00094 25.0 1.0 30 99-141 2-31 (43)
95 PRK00432 30S ribosomal protein 22.8 57 0.0012 25.7 1.7 28 96-138 19-46 (50)
96 PF07282 OrfB_Zn_ribbon: Putat 22.5 61 0.0013 26.0 1.9 29 96-138 27-55 (69)
97 PF01780 Ribosomal_L37ae: Ribo 22.3 52 0.0011 29.2 1.6 26 99-138 37-62 (90)
98 PRK00420 hypothetical protein; 22.2 65 0.0014 29.6 2.2 41 80-138 7-49 (112)
99 PRK03954 ribonuclease P protei 22.2 43 0.00094 31.1 1.1 17 126-143 91-107 (121)
100 COG0675 Transposase and inacti 22.0 53 0.0011 32.5 1.8 40 80-138 284-331 (364)
101 PF12390 Se-cys_synth_N: Selen 21.9 54 0.0012 24.3 1.3 37 411-463 3-39 (40)
102 COG1779 C4-type Zn-finger prot 21.9 58 0.0013 32.8 2.0 37 97-137 14-51 (201)
103 PF08421 Methyltransf_13: Puta 21.8 59 0.0013 26.3 1.7 19 120-138 31-49 (62)
104 smart00661 RPOL9 RNA polymeras 21.8 65 0.0014 24.3 1.8 14 128-141 19-32 (52)
105 cd00674 LysRS_core_class_I cat 21.6 46 0.001 35.7 1.3 45 97-150 169-213 (353)
106 PLN02678 seryl-tRNA synthetase 21.6 1.6E+02 0.0035 32.8 5.5 47 163-209 310-364 (448)
107 PF09855 DUF2082: Nucleic-acid 21.3 83 0.0018 26.2 2.4 41 99-139 2-46 (64)
108 PF05876 Terminase_GpA: Phage 21.2 72 0.0016 36.1 2.8 28 450-477 468-495 (557)
109 PRK01103 formamidopyrimidine/5 21.0 57 0.0012 33.4 1.8 32 94-137 239-273 (274)
110 PF08646 Rep_fac-A_C: Replicat 20.8 28 0.0006 31.9 -0.5 25 180-204 61-85 (146)
111 PHA02942 putative transposase; 20.4 73 0.0016 34.4 2.5 44 80-138 300-351 (383)
112 COG5525 Bacteriophage tail ass 20.4 63 0.0014 37.2 2.1 55 84-141 214-271 (611)
113 TIGR01562 FdhE formate dehydro 20.3 76 0.0016 33.6 2.5 44 92-139 218-262 (305)
114 PRK05978 hypothetical protein; 20.3 73 0.0016 30.5 2.2 41 80-141 24-64 (148)
115 PTZ00326 phenylalanyl-tRNA syn 20.2 1.1E+02 0.0024 34.6 3.9 103 137-241 373-489 (494)
No 1
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-117 Score=918.07 Aligned_cols=419 Identities=42% Similarity=0.725 Sum_probs=384.3
Q ss_pred HhhccCchhhHHHHHhhhhhhchhcCCHHHHHHHhccCChHHHHHHHHHHHHHcCCCCCCCchhHHHHHHHHHHHHhhc-
Q 009800 13 QHAVGENSGQFEETVHPYISKVLMYEDPIRQEAAKKTVPVERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLLFWFKQT- 91 (525)
Q Consensus 13 q~~~~~~~~~f~~~l~s~~~~v~~YEd~~lq~~Al~~IPl~~L~~~a~~~l~~~g~~~~~~~~~~~~~l~~LL~WFK~~- 91 (525)
+.++...+++|++.|.+|++||++||||.||++||++||+|+|+++|++++++ ..+++.+.|..+..+||+|||++
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 22344555555556999999998
Q ss_pred CeeecCCCCCCCCCCc-cccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHHHHhcCccchhhHHHHHHHHH
Q 009800 92 FRWVNAPPCDGCSNET-VGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCR 170 (525)
Q Consensus 92 F~wv~~P~C~~Cg~~t-~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~Ll~tR~GrCgE~A~~F~~l~R 170 (525)
|+|||+|||+.||++| ...|.++|+.+|.++||++||+|+|+.||+.+||||||+|.+||+||+|||||||||||++||
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 577888899999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCCCcCCCCeeeecCccCccceEEeecCCcceechhhhccChHHhhhh
Q 009800 171 AFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSR 250 (525)
Q Consensus 171 AlG~~aR~V~d~~dHvW~EVy~~~~~rWI~VDP~e~~~D~PllYe~gwgKklsYVIAFs~dgv~DVTrRYt~~~~~~~~R 250 (525)
|+|++||||||.+||||+|||++.++|||||||||+++|+|+||+.||||+|+|||||++|||+||||||+.+|.+++.+
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 cccccHHHHHHHHHHHHHHHHccCCHHHhhhhhhhcHHHHHHHHhhccCCCCCCCCCCCCccccHHHHHhhcCCCCCCCC
Q 009800 251 RNIATEQTVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAMERDLYSTDDAPVSLPGRQSGDKEWRISRSEIGSDDNC 330 (525)
Q Consensus 251 R~rv~E~wl~~~L~~l~~~~r~~ls~~e~~~Le~Rd~~E~~EL~~~~~~~~~~~~~l~GRqSGS~eWr~aRGE~G~~~~~ 330 (525)
|+.|.|+.|+.+|..||+++|.++++++++.|++||++|+.||.+...+.+++..+||||||||++||.+|||+|.
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 9999999999999999999999999999999999999999999999998888999999999999999999999998
Q ss_pred CcCCCCCCceeecccceeeEeeccchhhhccccCCCchhhHHHHHHHHHHHHhhccCCCcccccccccCCCCchhHHHHh
Q 009800 331 SLSCSSCPVRVCIDEHVTTIYNAFSSVLSHFVENNVPKSGAIELLKILKGILGDLKKSPYKTRRVSLNSVPNNGQKIVHQ 410 (525)
Q Consensus 331 s~~~s~cp~r~c~d~hv~~iY~a~~~~ls~~~~~~~~~~~a~~~~~~~r~~~~dlk~~~f~~R~~~~~~~~~~~~~~~~~ 410 (525)
|++ ||+..- + |.+++|++..|||+++.||||+ |++|.+--+-..++ +.
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 009800 411 L-LPSIGHLLRVLSLKSELNTDGRVDIVLAGDPVKTSLSLPVVFKALDDMIHDLNNCDNFGKGSFCLPLLKLNRIHSGSV 489 (525)
Q Consensus 411 ~-lps~~~ll~~lslk~~~~~~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 489 (525)
| +-+.+.++.++||+.++.|.|+= ++||.+||.+.. .++++-.++.
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 44889999999999999999874 888999999887 7777744331
Q ss_pred eccccccccceeeccccCCCcccc
Q 009800 490 LASGEEFPFGIVTSAFDGIRPSKW 513 (525)
Q Consensus 490 ~a~~e~~p~g~~~~af~g~~~~kw 513 (525)
|+|.+|+|+.-.||
T Consensus 487 ----------i~t~~~~g~~~~~w 500 (500)
T KOG0909|consen 487 ----------IRTELFSGKGDVKW 500 (500)
T ss_pred ----------eehhhcCCccccCC
Confidence 99999999999998
No 2
>PF03835 Rad4: Rad4 transglutaminase-like domain; InterPro: IPR018325 RAD4/Xp-C proteins contain an ancient transglutaminase fold that is also found in peptide-N-glycanases (PNGases), which remove glycans from glycoproteins during their degradation. The PNGases retain the catalytic triad that is typical of this fold and are predicted to have a reaction mechanism similar to that involved in transglutamination. In contrast, the RAD4/Xp-C proteins are predicted to be inactive and are likely to only possess the interaction function in DNA repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A 1X3W_A 1X3Z_A 3ESW_A.
Probab=99.86 E-value=2.8e-22 Score=183.03 Aligned_cols=101 Identities=37% Similarity=0.569 Sum_probs=74.6
Q ss_pred CCCeeEEEEEeCCCCCeEEeccCCC-----cCCCCeeeecCccCccceEEeecCCc-ceechhhhccChHHhhhhccccc
Q 009800 182 FTDHVWTECFSQSLGRWMHLDPCEG-----IYDRPLLYEKGWNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSRRNIAT 255 (525)
Q Consensus 182 ~~dHvW~EVy~~~~~rWI~VDP~e~-----~~D~PllYe~gwgKklsYVIAFs~dg-v~DVTrRYt~~~~~~~~RR~rv~ 255 (525)
..+|+|+|||++.+++||||||+.+ .++.|+ ..+|+++|+|||||+.|| |+|||+||+.++.....+|.|+.
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 3679999999999999999999996 677888 778999999999996665 99999999998334456888888
Q ss_pred -----HHHHHHHHHHHHHHHHccCCHHHhhhhhhhcHHHHHHH
Q 009800 256 -----EQTVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAM 293 (525)
Q Consensus 256 -----E~wl~~~L~~l~~~~r~~ls~~e~~~Le~Rd~~E~~EL 293 (525)
+.||..+|+.++...+... .||..|+.||
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 9999999999885443221 5788888887
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=99.79 E-value=7.7e-20 Score=202.99 Aligned_cols=104 Identities=21% Similarity=0.404 Sum_probs=82.6
Q ss_pred eeEEEEEeCCCCCeEEeccCC-CcCCCCeeeecCccCccceEEeecCCc-ceechhhhccChHHhhhhcccccHHHHHHH
Q 009800 185 HVWTECFSQSLGRWMHLDPCE-GIYDRPLLYEKGWNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSRRNIATEQTVSAV 262 (525)
Q Consensus 185 HvW~EVy~~~~~rWI~VDP~e-~~~D~PllYe~gwgKklsYVIAFs~dg-v~DVTrRYt~~~~~~~~RR~rv~E~wl~~~ 262 (525)
++|+|||++.+++||||||++ +++|+|..|..+|+++|+|||||+.|| |+|||+||+.+|+. ..|+.||+..||.++
T Consensus 371 ~~W~Ev~~~~~~rWI~VD~~~~~~~~~~~~~~e~~~~~m~YVvAf~~d~~~kDVT~RY~~~~~~-k~r~~Rv~~~w~~~~ 449 (713)
T TIGR00605 371 DFWVEVFIEQEEKWVCVDAVHSGVVPKGVTCFEPATLMMTYVFAYDRDGYVKDVTRRYCDQWST-KVRKRRVEKADFGET 449 (713)
T ss_pred eeEEEEeecccceeEEeccccccccCCchhhccCCCCceEEEEEEcCCCceeechhhHhhhhhh-hhheeeecccchHHH
Confidence 899999999999999999999 999999999999999999999999996 99999999999976 358888876666665
Q ss_pred -HHHHHHHHHccCCHHHhhhhhhhcHHHHHHHHhhc
Q 009800 263 -LAKMTRECRRSFASETLSTLEDRDKCEREAMERDL 297 (525)
Q Consensus 263 -L~~l~~~~r~~ls~~e~~~Le~Rd~~E~~EL~~~~ 297 (525)
++.+-..... + ... +|..|+.||....
T Consensus 450 w~~~~~~~~~~------r-~~~-~d~~Ed~el~~~~ 477 (713)
T TIGR00605 450 WFRPIFGALHK------R-KRT-IDDIEDQEFLRRH 477 (713)
T ss_pred HHHHHhhhhcc------C-ccc-hhhhhhhHhhhhh
Confidence 5554332211 1 111 5667777776543
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=99.49 E-value=4.7e-14 Score=119.75 Aligned_cols=80 Identities=25% Similarity=0.520 Sum_probs=62.9
Q ss_pred CCceEEEeeeCCCCcc--cccCCCCCHHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeC---------------CCe
Q 009800 123 GAARVELFRCKVCSKI--TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDF---------------TDH 185 (525)
Q Consensus 123 ga~rVE~y~C~~C~~~--~RFPRYn~p~~Ll~tR~GrCgE~A~~F~~l~RAlG~~aR~V~d~---------------~dH 185 (525)
.+..+-.|..+++.-. ...+...+|..+|.+++|.|.++|.+|++|||++|||||+|+.. ..|
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 3444555555555444 57778888999999999999999999999999999999999531 239
Q ss_pred eEEEEEeCCCCCeEEecc
Q 009800 186 VWTECFSQSLGRWMHLDP 203 (525)
Q Consensus 186 vW~EVy~~~~~rWI~VDP 203 (525)
+|+|||+++ ++|+++||
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
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=99.39 E-value=5.8e-13 Score=104.62 Aligned_cols=53 Identities=36% Similarity=0.853 Sum_probs=48.1
Q ss_pred HHHhcCccchhhHHHHHHHHHHcCCCeEEEEe--------------CCCeeEEEEEeCCCCCeEEeccC
Q 009800 150 LVETKRGRCGEWANCFTLYCRAFGYESRLILD--------------FTDHVWTECFSQSLGRWMHLDPC 204 (525)
Q Consensus 150 Ll~tR~GrCgE~A~~F~~l~RAlG~~aR~V~d--------------~~dHvW~EVy~~~~~rWI~VDP~ 204 (525)
+|++|.|.|.++|++|+++||++|||||+|.. ...|+|+|||.+ ++|+.+||+
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 47899999999999999999999999999952 467999999998 689999997
No 6
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=99.35 E-value=3.9e-12 Score=123.39 Aligned_cols=99 Identities=20% Similarity=0.407 Sum_probs=77.2
Q ss_pred HHHHHHHHHHHhhcCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHHHHhcCcc
Q 009800 78 HAFLLQLLFWFKQTFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGR 157 (525)
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 (525)
...+..+..|+...|.|...+.+ . ..++...|.+++|.
T Consensus 159 ~~~~~~~~~~~~~~~~y~~~~~~---------~---------------------------------~~~~~~~l~~~~G~ 196 (319)
T COG1305 159 REKAAALFDYVNSKIRYSPGPTP---------V---------------------------------TGSASDALRLGRGV 196 (319)
T ss_pred HHHHHHHHHHHhhcceeecCCCC---------C---------------------------------CCCHHHHHHhCCcc
Confidence 35788999999966888766543 1 12458999999999
Q ss_pred chhhHHHHHHHHHHcCCCeEEEEe-----------------CCCeeEEEEEeCCCCCeEEeccCCCcCCCCee-eecCcc
Q 009800 158 CGEWANCFTLYCRAFGYESRLILD-----------------FTDHVWTECFSQSLGRWMHLDPCEGIYDRPLL-YEKGWN 219 (525)
Q Consensus 158 CgE~A~~F~~l~RAlG~~aR~V~d-----------------~~dHvW~EVy~~~~~rWI~VDP~e~~~D~Pll-Ye~gwg 219 (525)
|.++|++|+++||++|||||+|.+ ...|+|+|||.++. +|+++||+.+..-.... +..+|+
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 999999999999999999999953 13599999999976 79999999765533332 334453
No 7
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=99.09 E-value=5.5e-11 Score=131.03 Aligned_cols=174 Identities=24% Similarity=0.341 Sum_probs=120.2
Q ss_pred CccchhhHHHHHHHHHHcCCCeEEEEe-----------------------------CCCeeEEEEEeCCCCCeEEecc--
Q 009800 155 RGRCGEWANCFTLYCRAFGYESRLILD-----------------------------FTDHVWTECFSQSLGRWMHLDP-- 203 (525)
Q Consensus 155 ~GrCgE~A~~F~~l~RAlG~~aR~V~d-----------------------------~~dHvW~EVy~~~~~rWI~VDP-- 203 (525)
+|+-.--+..|.+++|..| ++|...+ .....|+|||+..++.||+|||
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 7777778999999999998 5554410 1247899999999999999995
Q ss_pred CCCcCCCCeeeecC---ccCccceEEeecCCc-ceechhhhccChHHhhhhc--ccccHHHHHHHHHHHHHHHHccCCHH
Q 009800 204 CEGIYDRPLLYEKG---WNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSRR--NIATEQTVSAVLAKMTRECRRSFASE 277 (525)
Q Consensus 204 ~e~~~D~PllYe~g---wgKklsYVIAFs~dg-v~DVTrRYt~~~~~~~~RR--~rv~E~wl~~~L~~l~~~~r~~ls~~ 277 (525)
..+.++.++....- -+..|.|||||+.+| ++|||+||+..|+.....| .+++..||..+++.+...
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 45667766665543 456999999999998 9999999999998776534 467899999999999864
Q ss_pred HhhhhhhhcHHHHHHHHhhccCCCCCCCCCCCCccccHHHHHhhcCCCCCC----------CCCcCC-CCCCceeecccc
Q 009800 278 TLSTLEDRDKCEREAMERDLYSTDDAPVSLPGRQSGDKEWRISRSEIGSDD----------NCSLSC-SSCPVRVCIDEH 346 (525)
Q Consensus 278 e~~~Le~Rd~~E~~EL~~~~~~~~~~~~~l~GRqSGS~eWr~aRGE~G~~~----------~~s~~~-s~cp~r~c~d~h 346 (525)
...|+..|..++...... ..+|-=+ ++.-.+. +..+.| ..|-++.|...
T Consensus 414 ----~~~~e~~ed~~~~~~~~~-----~~lP~sv----------~~~K~Hp~fvler~Lkk~q~l~P~k~p~~g~~kG~- 473 (669)
T KOG2179|consen 414 ----RKDREDTEDIELLRRHTS-----EGLPTSV----------QDLKNHPLFVLERHLKKNQALKPCKKPTLGFTKGD- 473 (669)
T ss_pred ----cchHHHHHHHHHHHHhcc-----CCCCchH----------HHhccCchhhhHHHHhhcccccccccceeeeecCC-
Confidence 134555566655443221 1222100 1111111 222344 67778888886
Q ss_pred eeeEeeccchh
Q 009800 347 VTTIYNAFSSV 357 (525)
Q Consensus 347 v~~iY~a~~~~ 357 (525)
|..||...-.+
T Consensus 474 ~E~VY~R~~V~ 484 (669)
T KOG2179|consen 474 VEAVYLRRDVV 484 (669)
T ss_pred ceeeeehhhHH
Confidence 78899876533
No 8
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=98.23 E-value=6.6e-08 Score=105.57 Aligned_cols=122 Identities=21% Similarity=0.269 Sum_probs=90.9
Q ss_pred HHhcCccchhhHHHHHHHHHHcCCCeEEEEe-------------C-------------CCeeEEEEEeCCCCCeEEeccC
Q 009800 151 VETKRGRCGEWANCFTLYCRAFGYESRLILD-------------F-------------TDHVWTECFSQSLGRWMHLDPC 204 (525)
Q Consensus 151 l~tR~GrCgE~A~~F~~l~RAlG~~aR~V~d-------------~-------------~dHvW~EVy~~~~~rWI~VDP~ 204 (525)
+-...|+-.--+.||+++||++.+++|++.+ + ..-.|+|||...++.||.|||.
T Consensus 243 ~~~~~~~~D~~vrgf~a~~r~~~v~~Rli~~l~~P~Fs~~~~~~~~~e~~~~~iD~l~~p~fw~ev~~~~~~kwv~vdp~ 322 (650)
T COG5535 243 LKSADGRRDADVRGFEAEHRILNVFARLIASLIQPVFSNNSDLDVLSEGLLEYIDSLEYPGFWGEVVDKFEKKWVFVDPV 322 (650)
T ss_pred HhhccCCCcchhHHHHHHHHHhccchhhhccccCcccccccccccCccccceeccchhcchHHHHHHHHHHhceEecccc
Confidence 4456777777889999999999999999842 0 2367999999999999999998
Q ss_pred C--CcCCC-Ceeeec---CccCccceEEeecCCc-ceechhhhccChHHhhhh--cccccHHHHHHHHHHHHHHHHc
Q 009800 205 E--GIYDR-PLLYEK---GWNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSR--RNIATEQTVSAVLAKMTRECRR 272 (525)
Q Consensus 205 e--~~~D~-PllYe~---gwgKklsYVIAFs~dg-v~DVTrRYt~~~~~~~~R--R~rv~E~wl~~~L~~l~~~~r~ 272 (525)
. .++.. ---+|. --.+.|.||+|++.++ ++|||.||+......+.| +...++.|+...+..++...+.
T Consensus 323 ~l~~v~~~l~~kfepa~~~~~n~~~~V~ayd~~~y~~DVt~RY~d~~~s~~kritk~~fs~qy~~r~~~~l~~~k~~ 399 (650)
T COG5535 323 RLYIVYSELKCKFEPAASIHLNIMEYVGAYDACVYVKDVTLRYRDQSYSFLKRITKHLFSVQYFVRQFPGLGKCKEA 399 (650)
T ss_pred hhhhhhhhhhheechhHHHHHHHHHHhhhhccCccchhHHHHHHHHHhhhhhhhhccchHHHHHHHHhcccCccccc
Confidence 4 23331 011111 1357899999999875 899999999987655432 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=97.01 E-value=0.0029 Score=59.87 Aligned_cols=66 Identities=21% Similarity=0.350 Sum_probs=55.9
Q ss_pred cccCCCCCHHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEE--eCC---CeeEEEEEeCCCCCeEEeccCCC
Q 009800 139 TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLIL--DFT---DHVWTECFSQSLGRWMHLDPCEG 206 (525)
Q Consensus 139 ~RFPRYn~p~~Ll~tR~GrCgE~A~~F~~l~RAlG~~aR~V~--d~~---dHvW~EVy~~~~~rWI~VDP~e~ 206 (525)
...+++++|..++..|+|.|++||.+..++|-.+|+..=||+ +.. .|+|+-|-..+ .|-.+|..--
T Consensus 59 ~~~~~i~tp~etl~~k~GiC~DYA~Lta~lLl~~g~~~~yi~~~~~~~~~~Haa~aV~ing--~~yvlDq~~p 129 (153)
T PF04473_consen 59 KNSTYIQTPYETLKYKKGICGDYAILTAALLLNMGYSPVYILHIEFDNDPGHAAVAVKING--KYYVLDQHLP 129 (153)
T ss_pred cccccccCHHHHHHcCCeeeHHHHHHHHHHHHHCCCCceEEEEEecCCCCCeEEEEEEECC--EEEEEeCCCC
Confidence 345667799999999999999999999999999999887774 333 59999999985 6999998743
No 10
>COG5279 CYK3 Uncharacterized protein involved in cytokinesis, contains TGc (transglutaminase/protease-like) domain [Cell division and chromosome partitioning]
Probab=94.63 E-value=0.08 Score=58.48 Aligned_cols=64 Identities=23% Similarity=0.512 Sum_probs=54.1
Q ss_pred cccCCCCCHH----HHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeC------------CCeeEEEEEeCCCCCeEEec
Q 009800 139 TRFPRYNDPL----KLVETKRGRCGEWANCFTLYCRAFGYESRLILDF------------TDHVWTECFSQSLGRWMHLD 202 (525)
Q Consensus 139 ~RFPRYn~p~----~Ll~tR~GrCgE~A~~F~~l~RAlG~~aR~V~d~------------~dHvW~EVy~~~~~rWI~VD 202 (525)
++-|||.... ..+-.+++.|.-||.+|-+||.++||||=+|-++ -+|+|.-|-..+ .|--||
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 4457887554 2466789999999999999999999999999764 369999999987 599999
Q ss_pred cC
Q 009800 203 PC 204 (525)
Q Consensus 203 P~ 204 (525)
.+
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=93.75 E-value=0.21 Score=46.35 Aligned_cols=59 Identities=20% Similarity=0.190 Sum_probs=49.0
Q ss_pred CCCCHHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCC
Q 009800 143 RYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCE 205 (525)
Q Consensus 143 RYn~p~~Ll~tR~GrCgE~A~~F~~l~RAlG~~aR~V~d~~dHvW~EVy~~~~~rWI~VDP~e 205 (525)
......++|++|+|-|.-.|.+|..+||.+|+++..|- +..|+.+-+-. +. .+=|||.+
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-DG--EFYIDPFN 110 (152)
T ss_pred HhhhHHHHHhcCCCCcHHHHHHHHHHHHHcCCeEEEEe-cCCEEEEEEec-CC--cEEEccCC
Confidence 34567999999999999999999999999999998764 67788777774 32 36789986
No 12
>PF14381 EDR1: Ethylene-responsive protein kinase Le-CTR1
Probab=91.85 E-value=0.28 Score=48.60 Aligned_cols=54 Identities=19% Similarity=0.221 Sum_probs=43.9
Q ss_pred HHHhcCccchhhHHHHHHHHHHcCCCeEEEEe-----C-CCeeEEEEEeCCCCCeEEeccC
Q 009800 150 LVETKRGRCGEWANCFTLYCRAFGYESRLILD-----F-TDHVWTECFSQSLGRWMHLDPC 204 (525)
Q Consensus 150 Ll~tR~GrCgE~A~~F~~l~RAlG~~aR~V~d-----~-~dHvW~EVy~~~~~rWI~VDP~ 204 (525)
|=.-+.|.|.|-|.+|-.+|-++|+|+|+|-. + .+++|+.|-..+...+ =||-+
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 45568999999999999999999999999942 4 6899999998775445 35544
No 13
>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=90.29 E-value=1 Score=47.06 Aligned_cols=127 Identities=13% Similarity=0.195 Sum_probs=74.8
Q ss_pred hHHHHHHHHHHhhccCchhhHHHHHhhhhhhchhcCCHHHHHHHhcc-CChHHHHHHHHHHHHHcCCCCCCCchhHHHHH
Q 009800 3 QAEEEALLFQQHAVGENSGQFEETVHPYISKVLMYEDPIRQEAAKKT-VPVERLEEKSLVSLAREGNFKPSKTEQDHAFL 81 (525)
Q Consensus 3 q~e~~~~~~qq~~~~~~~~~f~~~l~s~~~~v~~YEd~~lq~~Al~~-IPl~~L~~~a~~~l~~~g~~~~~~~~~~~~~l 81 (525)
-+|+|..++..+.. +...+..++++.+..+--=.||.|....+.- |+.++|-......++.+ +.......+.
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 4456888998888877777899998888775 88888854433323210 0001111233
Q ss_pred HHHHHHHh---hcCeeecCCCCCCCCCC-ccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009800 82 LQLLFWFK---QTFRWVNAPPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (525)
Q Consensus 82 ~~LL~WFK---~~F~wv~~P~C~~Cg~~-t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (525)
++-|+==. ..-+=++..+|+.||+. +.+.-...=++|| ...=.|.|..||+.-+|
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 14
>PF14402 7TM_transglut: 7 transmembrane helices usually fused to an inactive transglutaminase
Probab=90.02 E-value=0.28 Score=51.40 Aligned_cols=48 Identities=21% Similarity=0.405 Sum_probs=39.5
Q ss_pred HHHHHHHHcCCCeEEEEe---------CCCeeEEEEEeCCCCCeEEeccCCCcCCCCee
Q 009800 164 CFTLYCRAFGYESRLILD---------FTDHVWTECFSQSLGRWMHLDPCEGIYDRPLL 213 (525)
Q Consensus 164 ~F~~l~RAlG~~aR~V~d---------~~dHvW~EVy~~~~~rWI~VDP~e~~~D~Pll 213 (525)
++..+++..|+|||.|.. ..-+-|.|||+. ++|+.+||..+....|.-
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 LIVKLLAMAGIPARVVHGLKLEDGRRRQSLEPWLEVFNG--GKWVLFNPRTGEQGLPEN 58 (313)
T ss_pred HHHHHHHhCCCCccEeeeEEecCCccccCcHhHHheeeC--CeEEEECCCCCCcCCCCC
Confidence 567899999999999952 345789999997 469999999988877743
No 15
>PF13471 Transglut_core3: Transglutaminase-like superfamily
Probab=87.12 E-value=1 Score=39.89 Aligned_cols=37 Identities=30% Similarity=0.608 Sum_probs=32.2
Q ss_pred cCccchhhHHHHHHHHHHcCCCeEEEEe-------CCCeeEEEE
Q 009800 154 KRGRCGEWANCFTLYCRAFGYESRLILD-------FTDHVWTEC 190 (525)
Q Consensus 154 R~GrCgE~A~~F~~l~RAlG~~aR~V~d-------~~dHvW~EV 190 (525)
.+..|-+.|.....+||..|+++.+|+. +..|+|+|+
T Consensus 54 ~~~~CL~~ala~~~~L~~~gi~~~l~iGv~~~~~~~~aHAWve~ 97 (117)
T PF13471_consen 54 WRSKCLPRALALQRLLRRRGIPATLVIGVRKDDDPFAAHAWVEC 97 (117)
T ss_pred CCCChHHHHHHHHHHHHhcCCCcEEEEEEeeCCCCceEEEEEEE
Confidence 3568999999999999999999999964 457999993
No 16
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=85.54 E-value=0.45 Score=51.82 Aligned_cols=35 Identities=29% Similarity=0.549 Sum_probs=28.0
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCC
Q 009800 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 145 (525)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn 145 (525)
.+|.|+.||..|.+.|. + -|+|++||...+-.++-
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 46999999999988873 1 49999999877666554
No 17
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=85.18 E-value=0.94 Score=34.45 Aligned_cols=34 Identities=26% Similarity=0.598 Sum_probs=25.1
Q ss_pred cCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009800 91 TFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 91 ~F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
+++|-+.+.|+.||+.....-. ..-.|+|..|+.
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 4789999999999997332211 145799999985
No 18
>PRK10941 hypothetical protein; Provisional
Probab=80.76 E-value=16 Score=37.72 Aligned_cols=60 Identities=12% Similarity=0.135 Sum_probs=46.1
Q ss_pred HHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCCCcC
Q 009800 147 PLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIY 208 (525)
Q Consensus 147 p~~Ll~tR~GrCgE~A~~F~~l~RAlG~~aR~V~d~~dHvW~EVy~~~~~rWI~VDP~e~~~ 208 (525)
..++|++|+|-=.-.|.+|..++|.+|+|+.=| ++..|+=.-+=.++...| =+||++|-+
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 478999999999999999999999999998764 556666555533333334 589987654
No 19
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=79.34 E-value=2.5 Score=44.06 Aligned_cols=54 Identities=33% Similarity=0.698 Sum_probs=39.0
Q ss_pred HHHHHHHHHhhc-CeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHHHHhcCc
Q 009800 80 FLLQLLFWFKQT-FRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRG 156 (525)
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 (525)
.-.+|++|.++. | |..||++|.....+ -...|++||. .-|||.. |.-+..+++|
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 457899999764 5 99999998755211 1468999987 4699975 6666666666
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=75.40 E-value=4.9 Score=31.44 Aligned_cols=36 Identities=22% Similarity=0.400 Sum_probs=22.6
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009800 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (525)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (525)
|||.||+.......+. ..-+....|.|..||....+
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=69.73 E-value=3.6 Score=30.54 Aligned_cols=27 Identities=26% Similarity=0.506 Sum_probs=19.4
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009800 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
.||.|+....... .+.|+++.|++|+-
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
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=69.15 E-value=4.3 Score=33.87 Aligned_cols=34 Identities=21% Similarity=0.408 Sum_probs=24.3
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009800 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (525)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (525)
--|||.||.+...+.. .+..+...|.+|++..-|
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 23
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=68.53 E-value=3.8 Score=39.16 Aligned_cols=34 Identities=21% Similarity=0.409 Sum_probs=20.0
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceE-EEeeeCCCCc
Q 009800 99 PCDGCSNETVGQGMGTPLPSEIQYGAARV-ELFRCKVCSK 137 (525)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rV-E~y~C~~C~~ 137 (525)
.||.||++.+.+-...+. ..| ..| ..|+|+.||.
T Consensus 2 ~cp~c~~~~~~~~~s~~~----~~~-~~~~~~~~c~~c~~ 36 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPA----EDG-NAIRRRRECLACGK 36 (154)
T ss_pred cCCCCCCCCCEeEecccc----CCC-CceeeeeeccccCC
Confidence 599999975433211111 112 234 4699999986
No 24
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=68.45 E-value=38 Score=35.91 Aligned_cols=112 Identities=13% Similarity=0.233 Sum_probs=57.9
Q ss_pred HHHHHhhhhhhchhcCCHHHHHHH--hccCChHHHHHHHHHHHHHcCCCCCCCchhHHHHHH-HHHHHHhh---cC----
Q 009800 23 FEETVHPYISKVLMYEDPIRQEAA--KKTVPVERLEEKSLVSLAREGNFKPSKTEQDHAFLL-QLLFWFKQ---TF---- 92 (525)
Q Consensus 23 f~~~l~s~~~~v~~YEd~~lq~~A--l~~IPl~~L~~~a~~~l~~~g~~~~~~~~~~~~~l~-~LL~WFK~---~F---- 92 (525)
....|..+.+.+.-+-.+.++... +...+-++|+..|..-+. |.+....... .-+|- +|--||.+ .+
T Consensus 103 w~~~L~~Ll~~l~~~~~~~~~~~l~~L~~~~~~~l~~~A~~Ll~--~~~~~v~~~~-a~Fi~AALqv~wa~~a~~l~~~~ 179 (309)
T PRK03564 103 WQKLLMALIAELKPEASGPALAVIENLEKASTQELEDMASALLA--SDFSSVSSDK-APFIWAALSLYWAQMAQQIPGKA 179 (309)
T ss_pred HHHHHHHHHHHhcccCCHHHHHHHHHHHhCCHHHHHHHHHHHhc--CCccccchhH-HHHHHHHHHHHHHHHHhhCCccc
Confidence 445555555555444444443322 222445566666665443 3322211112 22444 44445543 13
Q ss_pred ---eeecCCCCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCC
Q 009800 93 ---RWVNAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 145 (525)
Q Consensus 93 ---~wv~~P~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn 145 (525)
.|-+..-|+.||+.-. .+-. ..+....--..|.-|++.-+|+|..
T Consensus 180 ~~~~~~~~~~CPvCGs~P~~s~v~--------~~~~~G~RyL~CslC~teW~~~R~~ 228 (309)
T PRK03564 180 RAEYGEQRQFCPVCGSMPVSSVVQ--------IGTTQGLRYLHCNLCESEWHVVRVK 228 (309)
T ss_pred ccccccCCCCCCCCCCcchhheee--------ccCCCCceEEEcCCCCCcccccCcc
Confidence 2446788999999643 2110 0112344567899999999999954
No 25
>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=66.52 E-value=5.4 Score=38.92 Aligned_cols=68 Identities=25% Similarity=0.309 Sum_probs=45.0
Q ss_pred HHHH-HhcCccchhhHHHHHHHHHHcCCCeEEEEe------------CCCeeEEEEEeCCCCCeEEeccCCCc--CCCCe
Q 009800 148 LKLV-ETKRGRCGEWANCFTLYCRAFGYESRLILD------------FTDHVWTECFSQSLGRWMHLDPCEGI--YDRPL 212 (525)
Q Consensus 148 ~~Ll-~tR~GrCgE~A~~F~~l~RAlG~~aR~V~d------------~~dHvW~EVy~~~~~rWI~VDP~e~~--~D~Pl 212 (525)
.+++ +.|-|.|-|...+|..+|+++|++++++.. ..+|.=.=|-.++. +| =||+.-|. .-.|+
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 677899999999999999999999999841 12577777777664 67 58887655 46666
Q ss_pred eeecC
Q 009800 213 LYEKG 217 (525)
Q Consensus 213 lYe~g 217 (525)
....+
T Consensus 116 ~l~~~ 120 (240)
T PF00797_consen 116 PLEDG 120 (240)
T ss_dssp ESSST
T ss_pred EccCC
Confidence 66554
No 26
>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=66.32 E-value=3.6 Score=40.04 Aligned_cols=24 Identities=17% Similarity=0.299 Sum_probs=19.8
Q ss_pred HhcCccchhhHHHHHHHHHHcCCC
Q 009800 152 ETKRGRCGEWANCFTLYCRAFGYE 175 (525)
Q Consensus 152 ~tR~GrCgE~A~~F~~l~RAlG~~ 175 (525)
.++.|-|.|||..=-..|+++|+|
T Consensus 74 ~~g~GDCEDyai~K~~~L~~~G~p 97 (170)
T PF06035_consen 74 ARGAGDCEDYAIAKRFALIELGVP 97 (170)
T ss_dssp HHTEE-HHHHHHHHHHHHHHHT--
T ss_pred CCCcCCcHhHHHHHHHHHHHcCCC
Confidence 478999999999999999999998
No 27
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=65.02 E-value=3.8 Score=49.06 Aligned_cols=31 Identities=26% Similarity=0.664 Sum_probs=25.6
Q ss_pred eeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009800 93 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (525)
Q Consensus 93 ~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (525)
.-++.|+|+.||+.+...|. -|.|..||..+
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 45799999999988777775 49999999864
No 28
>PRK15047 N-hydroxyarylamine O-acetyltransferase; Provisional
Probab=64.77 E-value=19 Score=37.25 Aligned_cols=67 Identities=24% Similarity=0.302 Sum_probs=48.3
Q ss_pred HHHH-HhcCccchhhHHHHHHHHHHcCCCeEEE-----Ee------CCCeeEEEEEeCCCCCeEEeccCCC--cCCCCee
Q 009800 148 LKLV-ETKRGRCGEWANCFTLYCRAFGYESRLI-----LD------FTDHVWTECFSQSLGRWMHLDPCEG--IYDRPLL 213 (525)
Q Consensus 148 ~~Ll-~tR~GrCgE~A~~F~~l~RAlG~~aR~V-----~d------~~dHvW~EVy~~~~~rWI~VDP~e~--~~D~Pll 213 (525)
.|++ +-|-|.|-|...+|..++|++|++++.+ +. .-.|.=.=|..+++ +| =||+--| ..-.|+.
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 4677899999999999999999997766 21 12477777777764 68 5787755 3567776
Q ss_pred eec
Q 009800 214 YEK 216 (525)
Q Consensus 214 Ye~ 216 (525)
.+.
T Consensus 136 L~~ 138 (281)
T PRK15047 136 LVA 138 (281)
T ss_pred CCC
Confidence 543
No 29
>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=63.77 E-value=2.6 Score=30.19 Aligned_cols=27 Identities=30% Similarity=0.586 Sum_probs=13.2
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
-|+|+.|+++...... ++|-|+.|+..
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 36899999864
No 30
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=62.96 E-value=11 Score=38.45 Aligned_cols=47 Identities=19% Similarity=0.440 Sum_probs=31.7
Q ss_pred HHHHHHHHHhhcCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCH
Q 009800 80 FLLQLLFWFKQTFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 147 (525)
Q Consensus 80 ~l~~LL~WFK~~F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p 147 (525)
...+|++|-++. ++ |+.||+++.... .. . .-.|..|+. .-|||....
T Consensus 88 ~a~~l~~w~~~~-~f-----C~~CG~~~~~~~------------~~-~-~~~C~~c~~-~~yp~~~pa 134 (256)
T PRK00241 88 RAVQLAEFYRSH-RF-----CGYCGHPMHPSK------------TE-W-AMLCPHCRE-RYYPRIAPC 134 (256)
T ss_pred HHHHHHHHhhcC-cc-----ccccCCCCeecC------------Cc-e-eEECCCCCC-EECCCCCCE
Confidence 346788888653 22 999999876431 11 2 246999984 789997654
No 31
>PF14353 CpXC: CpXC protein
Probab=62.82 E-value=4.7 Score=36.28 Aligned_cols=42 Identities=21% Similarity=0.293 Sum_probs=25.6
Q ss_pred CCCCCCCCCccc-----c-CCCCCChhhhccCCceEEEeeeCCCCcccc
Q 009800 98 PPCDGCSNETVG-----Q-GMGTPLPSEIQYGAARVELFRCKVCSKITR 140 (525)
Q Consensus 98 P~C~~Cg~~t~~-----~-g~~~P~~~E~~~ga~rVE~y~C~~C~~~~R 140 (525)
..|+.||.+... + ....|..-|.-- .+..=.|.|++||+..+
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 32
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=61.80 E-value=9.9 Score=29.90 Aligned_cols=33 Identities=27% Similarity=0.480 Sum_probs=18.1
Q ss_pred CCCCCCCCCccccCCCCCChhhhccCC-ceEEEeeeCCCCc
Q 009800 98 PPCDGCSNETVGQGMGTPLPSEIQYGA-ARVELFRCKVCSK 137 (525)
Q Consensus 98 P~C~~Cg~~t~~~g~~~P~~~E~~~ga-~rVE~y~C~~C~~ 137 (525)
.|||.||.+............ +. ..|+ |..||.
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 469999877654432111100 01 3333 999998
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=61.10 E-value=5.5 Score=36.35 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=20.2
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009800 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
-|+|+.|+++-.+... ++|-|+.|++
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
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=59.32 E-value=7.7 Score=35.55 Aligned_cols=27 Identities=19% Similarity=0.362 Sum_probs=18.2
Q ss_pred ccceEEeecC-Cc-ceechhhhccChHHh
Q 009800 221 KLNYVIAISK-DG-VFDVTKRYTRKWHEV 247 (525)
Q Consensus 221 klsYVIAFs~-dg-v~DVTrRYt~~~~~~ 247 (525)
.+.+|..|=. .| ++||.+-|--.|..+
T Consensus 38 ~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTv 66 (113)
T PF09862_consen 38 QLEFIKLFIKNRGNLKEMEKELGISYPTV 66 (113)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHCCCcHHH
Confidence 3456666653 34 888888888888754
No 35
>PRK10220 hypothetical protein; Provisional
Probab=58.62 E-value=7 Score=35.77 Aligned_cols=28 Identities=21% Similarity=0.604 Sum_probs=21.3
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
+-|+|+.|+++-.+... ++|-|+.|++.
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=53.00 E-value=11 Score=37.41 Aligned_cols=45 Identities=22% Similarity=0.520 Sum_probs=29.7
Q ss_pred CCCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCH
Q 009800 98 PPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 147 (525)
Q Consensus 98 P~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p 147 (525)
.+|+.||+... ..-...=++|| ...=-|+|..||...+=||+-+.
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 56999998633 22111122333 33456999999999999998765
No 37
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=48.05 E-value=11 Score=27.55 Aligned_cols=29 Identities=24% Similarity=0.515 Sum_probs=14.3
Q ss_pred CCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 100 CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 100 C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
|+.||++.... -|..| .-|.+.|+.||.+
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 38
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=46.30 E-value=17 Score=32.23 Aligned_cols=31 Identities=19% Similarity=0.500 Sum_probs=21.7
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccc
Q 009800 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR 140 (525)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~R 140 (525)
..+.|+.|+.++..- ..+-+++|.+||...-
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 567899999985521 1123799999997643
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=45.51 E-value=12 Score=28.01 Aligned_cols=14 Identities=29% Similarity=0.956 Sum_probs=8.8
Q ss_pred eEEEeeeCCCCccc
Q 009800 126 RVELFRCKVCSKIT 139 (525)
Q Consensus 126 rVE~y~C~~C~~~~ 139 (525)
.-|+|+|..||..+
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
>PRK02935 hypothetical protein; Provisional
Probab=44.26 E-value=16 Score=33.46 Aligned_cols=31 Identities=23% Similarity=0.429 Sum_probs=24.0
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCC
Q 009800 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 143 (525)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPR 143 (525)
+-.||.|+.+|...|. +..|-.|+++..-++
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 348999998765443
No 41
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=43.91 E-value=21 Score=26.43 Aligned_cols=31 Identities=23% Similarity=0.502 Sum_probs=20.5
Q ss_pred CCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCC
Q 009800 98 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCS 136 (525)
Q Consensus 98 P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~ 136 (525)
..|+.|++.......| .+...-..|+|..|.
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 124566789999984
No 42
>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=43.55 E-value=11 Score=38.74 Aligned_cols=44 Identities=23% Similarity=0.508 Sum_probs=19.3
Q ss_pred eeecCCCCCCCCCCccccCCCCCChhhhccCC-ceEEEeeeCCCCcccccCCCC
Q 009800 93 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGA-ARVELFRCKVCSKITRFPRYN 145 (525)
Q Consensus 93 ~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga-~rVE~y~C~~C~~~~RFPRYn 145 (525)
.| +..-||.||+.-... .+..+. ..---..|.-|++.-+|+|..
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 43
>PHA00626 hypothetical protein
Probab=43.14 E-value=16 Score=30.05 Aligned_cols=29 Identities=14% Similarity=0.433 Sum_probs=18.3
Q ss_pred CCCCCCCCcccc-CCCCCChhhhccCCceEEEeeeCCCCc
Q 009800 99 PCDGCSNETVGQ-GMGTPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 99 ~C~~Cg~~t~~~-g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
.||.||+.++.. |... ...-.|+|+.||-
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 44
>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=40.26 E-value=22 Score=26.59 Aligned_cols=38 Identities=16% Similarity=0.407 Sum_probs=22.3
Q ss_pred CCCCCCCCCccccCCCCCChhhhcc-------CCceEEEeeeCCCC
Q 009800 98 PPCDGCSNETVGQGMGTPLPSEIQY-------GAARVELFRCKVCS 136 (525)
Q Consensus 98 P~C~~Cg~~t~~~g~~~P~~~E~~~-------ga~rVE~y~C~~C~ 136 (525)
.-|+.||+....+|.. ...+++.. --.+...|.|..|+
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 12455678999986
No 45
>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=39.73 E-value=1e+02 Score=30.94 Aligned_cols=135 Identities=18% Similarity=0.272 Sum_probs=66.3
Q ss_pred CCCCCCCcccc--CCCCC---ChhhhccCCceEEEeeeCCCCcccccCCCCCHHHHHHhcCccchhhHHHHHHHHHHcCC
Q 009800 100 CDGCSNETVGQ--GMGTP---LPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGY 174 (525)
Q Consensus 100 C~~Cg~~t~~~--g~~~P---~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~Ll~tR~GrCgE~A~~F~~l~RAlG~ 174 (525)
|+.||.++... |+... ..-+...=...+++..|+.||+.-.=-++.++ +.+ ..-+.|+-.+-+.+.-
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~~W~~~----~~~----el~~~~lk~v~~~l~~ 72 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGGRWVDP----ESR----ELEELCLKKVERGLKK 72 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCEECCCEeeec----Ccc----cHHHHHHHHHHHHHHH
Confidence 78888765422 33211 00011112356899999999985433466665 111 1112222222122221
Q ss_pred CeEEEEeCCCeeEEEEEeCCCCCeEEeccCCCcCC-CCeeeecCccCccceEEeec--CCcceechhhhccChHHhhhhc
Q 009800 175 ESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYD-RPLLYEKGWNKKLNYVIAIS--KDGVFDVTKRYTRKWHEVLSRR 251 (525)
Q Consensus 175 ~aR~V~d~~dHvW~EVy~~~~~rWI~VDP~e~~~D-~PllYe~gwgKklsYVIAFs--~dgv~DVTrRYt~~~~~~~~RR 251 (525)
.. .+......+|+|..+. .-.+.|.....+.+ .|+ ..+|.+-|. ..-+-|=+++....|..+++-|
T Consensus 73 ~~-~~~~d~~~v~~e~~~~--r~~v~v~v~~~v~~~~~~--------~~~~~v~~~v~~~~C~~C~r~~~~~~eaiVQvR 141 (236)
T PF04981_consen 73 NI-KVHVDAEFVWTEPHSK--RIKVKVTVQGEVHGGTPV--------EQEYEVEVRVKRQQCPDCSRIAGGYYEAIVQVR 141 (236)
T ss_pred hh-cccccccEEEEEeeCC--EEEEEEEEEEEEcccceE--------EEEEEEEEEEEcCCChhHHhhhCCCccEEEEEE
Confidence 11 1223344678888332 23555554433333 333 234555555 3335677777777787777777
Q ss_pred cc
Q 009800 252 NI 253 (525)
Q Consensus 252 ~r 253 (525)
..
T Consensus 142 ~~ 143 (236)
T PF04981_consen 142 QR 143 (236)
T ss_pred ec
Confidence 54
No 46
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=39.30 E-value=1e+02 Score=32.79 Aligned_cols=126 Identities=16% Similarity=0.233 Sum_probs=74.3
Q ss_pred HHHHHHHHHHhhccCchhhHHHHHhhhhhhchhcCCHHHHHHHhcc-CChHHHHHHHHHHHHHcCCCCCCCchhHHHHHH
Q 009800 4 AEEEALLFQQHAVGENSGQFEETVHPYISKVLMYEDPIRQEAAKKT-VPVERLEEKSLVSLAREGNFKPSKTEQDHAFLL 82 (525)
Q Consensus 4 ~e~~~~~~qq~~~~~~~~~f~~~l~s~~~~v~~YEd~~lq~~Al~~-IPl~~L~~~a~~~l~~~g~~~~~~~~~~~~~l~ 82 (525)
.++|.+|++. ...+......++++-+..+--=.||.|+..++.- |+-++|-....+.++.+ +.-+....+++
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 3445566778888888788888999999998876 66677743322222110 11122334565
Q ss_pred HHHHHH-hh--cCeeecCCCCCCCCCC-ccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009800 83 QLLFWF-KQ--TFRWVNAPPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (525)
Q Consensus 83 ~LL~WF-K~--~F~wv~~P~C~~Cg~~-t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (525)
+-|+.= -. +=+=+|...|..|+.. ....-...+++||- -..-| .|+.||..-.|
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 555432 11 1244567789999985 33444455666653 12333 59999986654
No 47
>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=37.48 E-value=43 Score=31.05 Aligned_cols=50 Identities=28% Similarity=0.484 Sum_probs=38.0
Q ss_pred cccHHHHHHhhccccccC----------CCCCeEEEecCCCccccchhhHhHHHHHHHHH
Q 009800 412 LPSIGHLLRVLSLKSELN----------TDGRVDIVLAGDPVKTSLSLPVVFKALDDMIH 461 (525)
Q Consensus 412 lps~~~ll~~lslk~~~~----------~~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~ 461 (525)
||-++.++..+++|.--. .+|+..++|-|+|+.+..++=+++++|+.++.
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 48
>COG2912 Uncharacterized conserved protein [Function unknown]
Probab=37.46 E-value=60 Score=33.96 Aligned_cols=63 Identities=14% Similarity=0.151 Sum_probs=52.6
Q ss_pred CCCCCHHHHHHhcCccchhhHHHHHHHHHHcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCCCc
Q 009800 142 PRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGI 207 (525)
Q Consensus 142 PRYn~p~~Ll~tR~GrCgE~A~~F~~l~RAlG~~aR~V~d~~dHvW~EVy~~~~~rWI~VDP~e~~ 207 (525)
||--.-..++++|+|.=-..|..++.+++++|+|- +=+|+.+|.=.-+..+. +-| -+||+++-
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 44445589999999999999999999999999998 44688899988888887 445 89999763
No 49
>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=37.26 E-value=29 Score=36.67 Aligned_cols=49 Identities=20% Similarity=0.497 Sum_probs=32.7
Q ss_pred ecCCCCCCCCCCccccCCCCCChhhhcc--CCceEEEeeeCCCCcccccCCCCCHHHHHHhcCccchh
Q 009800 95 VNAPPCDGCSNETVGQGMGTPLPSEIQY--GAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGE 160 (525)
Q Consensus 95 v~~P~C~~Cg~~t~~~g~~~P~~~E~~~--ga~rVE~y~C~~C~~~~RFPRYn~p~~Ll~tR~GrCgE 160 (525)
-+..-|+.||+.-. ...... +..+.-...|.-|++.-+|+|. +.-.||+
T Consensus 182 ~~~~~CPvCGs~P~--------~s~~~~~~~~~G~RyL~CslC~teW~~~R~---------~C~~Cg~ 232 (305)
T TIGR01562 182 ESRTLCPACGSPPV--------ASMVRQGGKETGLRYLSCSLCATEWHYVRV---------KCSHCEE 232 (305)
T ss_pred CCCCcCCCCCChhh--------hhhhcccCCCCCceEEEcCCCCCcccccCc---------cCCCCCC
Confidence 45678999999532 111111 1345567799999999999995 4556665
No 50
>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=36.74 E-value=16 Score=37.65 Aligned_cols=54 Identities=17% Similarity=0.334 Sum_probs=29.5
Q ss_pred EeecCCcc----eechhhhccChHHhhhhccc--ccHHHHHHHHHHHHHHHHccCCHHHhhhhh
Q 009800 226 IAISKDGV----FDVTKRYTRKWHEVLSRRNI--ATEQTVSAVLAKMTRECRRSFASETLSTLE 283 (525)
Q Consensus 226 IAFs~dgv----~DVTrRYt~~~~~~~~RR~r--v~E~wl~~~L~~l~~~~r~~ls~~e~~~Le 283 (525)
|-+=+||. ..|+.. |.+.+.-|+. -+-.|+..+|.-+...-...++-++...++
T Consensus 154 I~lv~~~~~~~~~~V~~~----~~~tlfLr~~~~~~rGWlldi~~cid~i~~~~FtL~diY~Fe 213 (254)
T PF06044_consen 154 IFLVKNGQIIPPEEVLEQ----WQKTLFLRTQNIESRGWLLDIMKCIDKIPKNEFTLDDIYAFE 213 (254)
T ss_dssp EEEEETTEE--HHHHHHH----HHHGGGGGGS-HHHHHHHHHHHHHHHHS-SSEEEHHHHHTTH
T ss_pred EEEEeCCeEcCHHHHHHH----HHHHHHHHhccccccchHHHHHHHHHhcCccceeHHHHHHHH
Confidence 44445663 245544 4444444433 245899999998874443455555555443
No 51
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=36.65 E-value=46 Score=32.53 Aligned_cols=90 Identities=21% Similarity=0.169 Sum_probs=47.5
Q ss_pred hcCCHHHHHHHhc--cCChHH---HHHHHHHHHHHcCCC---CCCCchhHHHHHHHHHHHHhhcCeeec--CCCCCCCCC
Q 009800 36 MYEDPIRQEAAKK--TVPVER---LEEKSLVSLAREGNF---KPSKTEQDHAFLLQLLFWFKQTFRWVN--APPCDGCSN 105 (525)
Q Consensus 36 ~YEd~~lq~~Al~--~IPl~~---L~~~a~~~l~~~g~~---~~~~~~~~~~~l~~LL~WFK~~F~wv~--~P~C~~Cg~ 105 (525)
.++|+..+..|.. -|=+.+ |+.++ + .|-. -++.. ....+.+++.-|.-.+ |+. .-.|+.|++
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 44544 2 2211 01111 1123555555454433 433 246999998
Q ss_pred Ccccc------CCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 106 ETVGQ------GMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 106 ~t~~~------g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
+-..+ +..+|- .--.--|.|+|++||..
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 222211 11244568999999974
No 52
>COG2162 NhoA Arylamine N-acetyltransferase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=36.61 E-value=72 Score=33.52 Aligned_cols=66 Identities=24% Similarity=0.374 Sum_probs=45.1
Q ss_pred HHH-HHhcCccchhhHHHHHHHHHHcCCCeEE-----EEeC-------CCeeEEEEEeCCCCCeEEeccCCC--cCCCCe
Q 009800 148 LKL-VETKRGRCGEWANCFTLYCRAFGYESRL-----ILDF-------TDHVWTECFSQSLGRWMHLDPCEG--IYDRPL 212 (525)
Q Consensus 148 ~~L-l~tR~GrCgE~A~~F~~l~RAlG~~aR~-----V~d~-------~dHvW~EVy~~~~~rWI~VDP~e~--~~D~Pl 212 (525)
.|| +..|-|.|-|.--+|..+++++|+++|. +|.. -.|.=.-|..++. -|+ +|.--| +.-.|+
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 344 4467789999999999999999998655 4542 3587777777764 584 566544 333365
Q ss_pred eee
Q 009800 213 LYE 215 (525)
Q Consensus 213 lYe 215 (525)
..+
T Consensus 137 rL~ 139 (275)
T COG2162 137 RLE 139 (275)
T ss_pred ccC
Confidence 544
No 53
>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=36.56 E-value=27 Score=33.76 Aligned_cols=34 Identities=21% Similarity=0.590 Sum_probs=22.1
Q ss_pred CCCCCCCcccc-CCCCCChhhhc-cCCceEEEeeeCCCCc
Q 009800 100 CDGCSNETVGQ-GMGTPLPSEIQ-YGAARVELFRCKVCSK 137 (525)
Q Consensus 100 C~~Cg~~t~~~-g~~~P~~~E~~-~ga~rVE~y~C~~C~~ 137 (525)
|+.||+++... ... .++. ++--.+--|.|++||-
T Consensus 1 CP~Cg~~~~~~~~~~----~~IP~F~evii~sf~C~~CGy 36 (163)
T TIGR00340 1 CPVCGSRTLKAVTYD----YDIPYFGKIMLSTYICEKCGY 36 (163)
T ss_pred CCCCCCcceEeeeEe----ccCCCcceEEEEEEECCCCCC
Confidence 99999874322 111 1222 3567788999999996
No 54
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=35.91 E-value=35 Score=25.55 Aligned_cols=35 Identities=23% Similarity=0.497 Sum_probs=20.6
Q ss_pred CCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 99 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 99 ~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
+|+.||+... ..-...=++|| ...=.|.|..||..
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 55
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=35.89 E-value=31 Score=31.35 Aligned_cols=41 Identities=15% Similarity=0.271 Sum_probs=25.7
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009800 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (525)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (525)
...|+.||+.....-. ...+..+-.-+.-|+|..||..-||
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 4679999997542210 0111122356778999999997765
No 56
>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=35.84 E-value=24 Score=24.84 Aligned_cols=14 Identities=21% Similarity=0.363 Sum_probs=7.4
Q ss_pred CCCCCCCCCCcccc
Q 009800 97 APPCDGCSNETVGQ 110 (525)
Q Consensus 97 ~P~C~~Cg~~t~~~ 110 (525)
..-|+.||++|...
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 57
>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=35.62 E-value=18 Score=33.41 Aligned_cols=32 Identities=22% Similarity=0.387 Sum_probs=24.4
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCC
Q 009800 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 143 (525)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPR 143 (525)
-.-.||.|+..|...|. + ..|-.|+++....|
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 34569999999999873 3 48999998765544
No 58
>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=35.21 E-value=28 Score=25.68 Aligned_cols=31 Identities=23% Similarity=0.730 Sum_probs=19.5
Q ss_pred eecCCC--CCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009800 94 WVNAPP--CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (525)
Q Consensus 94 wv~~P~--C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (525)
|+-.|. |+.|++.......| .|-|..||+.+
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 99999972222111 58899999764
No 59
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=34.33 E-value=20 Score=29.58 Aligned_cols=23 Identities=26% Similarity=0.741 Sum_probs=19.8
Q ss_pred HHHhhcCeeecCCCCCCCCCCcc
Q 009800 86 FWFKQTFRWVNAPPCDGCSNETV 108 (525)
Q Consensus 86 ~WFK~~F~wv~~P~C~~Cg~~t~ 108 (525)
-|-+..|+.-..|.|+-|++++.
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 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=33.83 E-value=28 Score=25.86 Aligned_cols=35 Identities=17% Similarity=0.356 Sum_probs=18.2
Q ss_pred CCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 99 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 99 ~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
+|+.||++.. ..-...=.+|| ...=.|.|..||+.
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
>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=33.22 E-value=19 Score=34.03 Aligned_cols=66 Identities=18% Similarity=0.308 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHcCCCCCCCchhHHHHHHHHHHHHhhcCeeecCCCCCCCCCC-ccccCCCCCChhhhccCCceEEEee
Q 009800 53 ERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLLFWFKQTFRWVNAPPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFR 131 (525)
Q Consensus 53 ~~L~~~a~~~l~~~g~~~~~~~~~~~~~l~~LL~WFK~~F~wv~~P~C~~Cg~~-t~~~g~~~P~~~E~~~ga~rVE~y~ 131 (525)
|.|.+.+..+|..-|-.-|....... . ..+.| ...|++||+. |.....-.||+=- -+|+
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 66777777767655543333221111 0 12344 5789999995 4433222233322 3799
Q ss_pred eCCCCcc
Q 009800 132 CKVCSKI 138 (525)
Q Consensus 132 C~~C~~~ 138 (525)
|..|...
T Consensus 133 c~~c~ep 139 (146)
T TIGR02159 133 CRACKEP 139 (146)
T ss_pred hhhhCCc
Confidence 9999764
No 62
>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=33.17 E-value=32 Score=32.60 Aligned_cols=56 Identities=20% Similarity=0.261 Sum_probs=44.0
Q ss_pred hcccHHHHHHhhcccc-c---------cC-CCCCeEEEecCCCccccchh-hHhHHHHHHHHHhcccC
Q 009800 411 LLPSIGHLLRVLSLKS-E---------LN-TDGRVDIVLAGDPVKTSLSL-PVVFKALDDMIHDLNNC 466 (525)
Q Consensus 411 ~lps~~~ll~~lslk~-~---------~~-~~g~~~~~~~~~p~~tsl~l-~~~~~~~~~~~~~~~~~ 466 (525)
-+|-++.++..+++|. - ++ .+|..-++|-|+|+....++ -.+..+|+.+++..++-
T Consensus 92 ~l~G~~~~~~~i~~~p~G~~~~lsr~~~g~~~~~~v~~LPG~P~aa~~~~~~~v~P~l~~~~~~~~~~ 159 (163)
T TIGR02667 92 TVEGFGELFRQLSYEEIGTSTIQSRALAGLANGTFVFCLPGSTGACRTAWDKIIAAQLDARHRPCNFV 159 (163)
T ss_pred cCCcHHHHHHHHhhcccCHHHHHhhhhheeeCCeEEEECCCCHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3777888999999986 2 22 25679999999999998888 56888888887777663
No 63
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.57 E-value=29 Score=34.56 Aligned_cols=44 Identities=11% Similarity=0.241 Sum_probs=27.6
Q ss_pred CCCCCCCccc--cCCCCCChhhhccCCceEEEeeeCCCCcccccCCCC
Q 009800 100 CDGCSNETVG--QGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 145 (525)
Q Consensus 100 C~~Cg~~t~~--~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn 145 (525)
|+.||..+.+ .|+-.-++.- ---+.==+|+|.+|...-.||-|.
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 012445689999999876666553
No 64
>COG3672 Predicted transglutaminase-like cysteine proteinase [General function prediction only]
Probab=31.76 E-value=1e+02 Score=30.87 Aligned_cols=23 Identities=22% Similarity=0.200 Sum_probs=21.8
Q ss_pred hcCccchhhHHHHHHHHHHcCCC
Q 009800 153 TKRGRCGEWANCFTLYCRAFGYE 175 (525)
Q Consensus 153 tR~GrCgE~A~~F~~l~RAlG~~ 175 (525)
+..|-|.|||..=-.-|..+|++
T Consensus 105 ~~~GDCEDyal~KRr~L~~~G~s 127 (191)
T COG3672 105 TGAGDCEDYALEKRRRLMEAGVS 127 (191)
T ss_pred CCcccHHHHHHHHHHHHHHcCCC
Confidence 89999999999999999999997
No 65
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=31.43 E-value=26 Score=24.96 Aligned_cols=14 Identities=29% Similarity=0.980 Sum_probs=11.4
Q ss_pred eEEEeeeCCCCccc
Q 009800 126 RVELFRCKVCSKIT 139 (525)
Q Consensus 126 rVE~y~C~~C~~~~ 139 (525)
+.+.|+|..||...
T Consensus 4 ~~~~ykC~~Cgniv 17 (34)
T TIGR00319 4 EGQVYKCEVCGNIV 17 (34)
T ss_pred cCcEEEcCCCCcEE
Confidence 46799999999754
No 66
>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=29.41 Aligned_cols=54 Identities=22% Similarity=0.362 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhhcCeeec--CCCCCCCCCCcccc------CCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 79 AFLLQLLFWFKQTFRWVN--APPCDGCSNETVGQ------GMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 79 ~~l~~LL~WFK~~F~wv~--~P~C~~Cg~~t~~~------g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
..|.++++-|.=.+ +.+ ---|+.|++.-..+ +..+|..- ...-+.|+|+.||+.
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 13699999864322 22222211 123358999999974
No 67
>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=30.65 E-value=48 Score=31.30 Aligned_cols=29 Identities=17% Similarity=0.303 Sum_probs=24.5
Q ss_pred HhcCccchhhHHHHHHHHHHcCCCeEEEE
Q 009800 152 ETKRGRCGEWANCFTLYCRAFGYESRLIL 180 (525)
Q Consensus 152 ~tR~GrCgE~A~~F~~l~RAlG~~aR~V~ 180 (525)
.|.---|-||+++|--++.+||+++|++.
T Consensus 51 ~~~GiNCtD~~Qlf~~v~~~lGY~Vq~~H 79 (142)
T PF12386_consen 51 RTSGINCTDACQLFYRVIESLGYDVQFEH 79 (142)
T ss_pred HhcCCCchhHHHHHHHHHHhcCceEEEEE
Confidence 34334599999999999999999999983
No 68
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=29.61 E-value=38 Score=25.11 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=8.9
Q ss_pred CCCCCCCCCcc
Q 009800 98 PPCDGCSNETV 108 (525)
Q Consensus 98 P~C~~Cg~~t~ 108 (525)
+.|+.||+.+.
T Consensus 3 ~~Cp~Cg~~~~ 13 (47)
T PF14690_consen 3 PRCPHCGSPSV 13 (47)
T ss_pred ccCCCcCCCce
Confidence 56999999874
No 69
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=29.48 E-value=28 Score=23.33 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=5.8
Q ss_pred CCCCCCCc
Q 009800 100 CDGCSNET 107 (525)
Q Consensus 100 C~~Cg~~t 107 (525)
|+.||.+.
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 78888743
No 70
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=29.19 E-value=38 Score=34.77 Aligned_cols=42 Identities=19% Similarity=0.315 Sum_probs=19.5
Q ss_pred Cee-ecCCCCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009800 92 FRW-VNAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (525)
Q Consensus 92 F~w-v~~P~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (525)
+.| +....|+.||+... ....-. ..+...+.++.|..|+..+
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 71
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=29.18 E-value=35 Score=33.73 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=21.9
Q ss_pred CCCCCCCCcc--ccCCC-CCChhhhccCCceEEEeeeCCCCc
Q 009800 99 PCDGCSNETV--GQGMG-TPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 99 ~C~~Cg~~t~--~~g~~-~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
+|+.||.+.. ..-.. -|- ++--.+--+.|++||-
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 121 4567778999999986
No 72
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=28.99 E-value=66 Score=28.70 Aligned_cols=17 Identities=53% Similarity=0.993 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHhhcCeeecCCCC
Q 009800 77 DHAFLLQLLFWFKQTFRWVNAPPC 100 (525)
Q Consensus 77 ~~~~l~~LL~WFK~~F~wv~~P~C 100 (525)
...++++||+|| |-|++
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 73
>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=28.64 E-value=30 Score=32.27 Aligned_cols=61 Identities=31% Similarity=0.695 Sum_probs=40.0
Q ss_pred eeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHHHHhcCccchhhHHHHHHHHHHc
Q 009800 93 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAF 172 (525)
Q Consensus 93 ~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~Ll~tR~GrCgE~A~~F~~l~RAl 172 (525)
.|+. +-|+.|+.+....+. ..|+|..|+...-=|
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 4655 669999886543321 579999999864212
Q ss_pred CCCeEEE-----EeCCCeeEEEEEeCCCCCeEEe
Q 009800 173 GYESRLI-----LDFTDHVWTECFSQSLGRWMHL 201 (525)
Q Consensus 173 G~~aR~V-----~d~~dHvW~EVy~~~~~rWI~V 201 (525)
..||. .|.++.+|+=+|.+....=++.
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 12333 3688899999998765555555
No 74
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=28.16 E-value=23 Score=35.32 Aligned_cols=35 Identities=34% Similarity=0.594 Sum_probs=26.7
Q ss_pred CCCCChhhhccCCc------eEEEeeeCCCC----cccccCCCCC
Q 009800 112 MGTPLPSEIQYGAA------RVELFRCKVCS----KITRFPRYND 146 (525)
Q Consensus 112 ~~~P~~~E~~~ga~------rVE~y~C~~C~----~~~RFPRYn~ 146 (525)
.+-|+.||-.|.|+ +.|-|+|..|+ ..+|=||.|+
T Consensus 15 ~akp~~Deg~WdCsvCTFrNsAeAfkC~vCdvRKGTSTRkpr~ns 59 (228)
T KOG4477|consen 15 DAKPNDDEGKWDCSVCTFRNSAEAFKCFVCDVRKGTSTRKPRCNS 59 (228)
T ss_pred cCCCccccCceeeeeeeecchhhhhheeeecccccccccCCcchH
Confidence 45578888777764 57999999997 5678888774
No 75
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.92 E-value=38 Score=27.25 Aligned_cols=28 Identities=14% Similarity=0.396 Sum_probs=19.5
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009800 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
.++.||+||..+.+.. --+.|.|..||-
T Consensus 18 k~~~CPrCG~gvfmA~--------------H~dR~~CGkCgy 45 (51)
T COG1998 18 KNRFCPRCGPGVFMAD--------------HKDRWACGKCGY 45 (51)
T ss_pred ccccCCCCCCcchhhh--------------cCceeEeccccc
Confidence 4577999997655442 223788999985
No 76
>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=27.62 E-value=56 Score=29.53 Aligned_cols=74 Identities=20% Similarity=0.359 Sum_probs=38.8
Q ss_pred CCCCCCCCCccccCCCCCChhhhccCC---ceEEEeeeCCCCcccc-cCCCCCHHHHHHh---c--C------------c
Q 009800 98 PPCDGCSNETVGQGMGTPLPSEIQYGA---ARVELFRCKVCSKITR-FPRYNDPLKLVET---K--R------------G 156 (525)
Q Consensus 98 P~C~~Cg~~t~~~g~~~P~~~E~~~ga---~rVE~y~C~~C~~~~R-FPRYn~p~~Ll~t---R--~------------G 156 (525)
..|+.||++...+.. ++. ++- ..=-+|.|..|++.+- +|.=+-|.=.|.. | | -
T Consensus 3 ~~CpYCg~~~~l~~~-----~~i-Yg~~~~~~~~~y~C~~C~AyVG~H~~t~~PlGtLAd~~lR~~R~~ah~~fd~lw~~ 76 (102)
T PF11672_consen 3 IICPYCGGPAELVDG-----SEI-YGHRYDDGPYLYVCTPCDAYVGCHPGTDIPLGTLADAELRRARKAAHRAFDPLWQS 76 (102)
T ss_pred cccCCCCCeeEEccc-----chh-cCccCCCCceeEECCCCCceeeeeCCCCCcCcccCCHHHHHHHHHHHHHHHHHHHh
Confidence 459999998765421 111 221 1123599999998653 5544333221110 0 0 0
Q ss_pred cchhhHHHHHHHHHHcCCCeE
Q 009800 157 RCGEWANCFTLYCRAFGYESR 177 (525)
Q Consensus 157 rCgE~A~~F~~l~RAlG~~aR 177 (525)
.-.+-...+.-+++.||++.+
T Consensus 77 ~~~~R~~aY~wLA~~lgi~~~ 97 (102)
T PF11672_consen 77 GHMSRSDAYRWLAKKLGIPVE 97 (102)
T ss_pred CcccHHHHHHHHHHHcCCChH
Confidence 012245566777788887654
No 77
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.38 E-value=51 Score=30.42 Aligned_cols=26 Identities=19% Similarity=0.563 Sum_probs=18.5
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccc
Q 009800 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR 140 (525)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~R 140 (525)
-|+|+.||.+... ---+|+.|++.+|
T Consensus 6 ~~~cPvcg~~~iV------------------TeL~c~~~etTVr 31 (122)
T COG3877 6 INRCPVCGRKLIV------------------TELKCSNCETTVR 31 (122)
T ss_pred CCCCCccccccee------------------EEEecCCCCceEe
Confidence 4789999984433 3357999988765
No 78
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=26.72 E-value=43 Score=32.18 Aligned_cols=34 Identities=18% Similarity=0.477 Sum_probs=21.9
Q ss_pred CCCCCCCCcc--ccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009800 99 PCDGCSNETV--GQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 99 ~C~~Cg~~t~--~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
.|+.||.+.. ..-..-|- ++--.+-.|.|++||-
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 3556778999999996
No 79
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=26.57 E-value=40 Score=25.48 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=8.0
Q ss_pred EeeeCCCCccc
Q 009800 129 LFRCKVCSKIT 139 (525)
Q Consensus 129 ~y~C~~C~~~~ 139 (525)
..+|+.||...
T Consensus 21 ~~~Cp~CG~~~ 31 (46)
T PRK00398 21 GVRCPYCGYRI 31 (46)
T ss_pred ceECCCCCCeE
Confidence 56888888743
No 80
>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=26.46 E-value=64 Score=36.53 Aligned_cols=41 Identities=27% Similarity=0.425 Sum_probs=26.6
Q ss_pred HHHHHHHH-Hhhc--CeeecCCC--CCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 80 FLLQLLFW-FKQT--FRWVNAPP--CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 80 ~l~~LL~W-FK~~--F~wv~~P~--C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
-+++|++. |++. +-|++.|. |..||.... -+.+.|+.||..
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 81
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.46 E-value=35 Score=29.88 Aligned_cols=27 Identities=30% Similarity=0.432 Sum_probs=21.3
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009800 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
-|+.|+-+..+.. -+.||+=.|+.|+.
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 4999998766552 36799999999975
No 82
>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=25.86 E-value=30 Score=33.17 Aligned_cols=42 Identities=17% Similarity=0.350 Sum_probs=24.5
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCC
Q 009800 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYND 146 (525)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~ 146 (525)
.||.||.+.+.+=...|+.+ |...=-.=.|..||. ||-=|..
T Consensus 2 ~CP~C~~~dtkViDSR~~~d----g~~IRRRReC~~C~~--RFTTyEr 43 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVED----GQSIRRRRECLECHE--RFTTFER 43 (147)
T ss_pred CCCCCCCCCCEeeeccccCC----CCeeeecccCCccCC--ccceeee
Confidence 59999996543322233322 333334467999995 5555553
No 83
>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=25.32 E-value=36 Score=24.27 Aligned_cols=13 Identities=31% Similarity=1.216 Sum_probs=10.4
Q ss_pred EEEeeeCCCCccc
Q 009800 127 VELFRCKVCSKIT 139 (525)
Q Consensus 127 VE~y~C~~C~~~~ 139 (525)
.+.|+|..||...
T Consensus 2 ~~~ykC~~CGniv 14 (34)
T cd00974 2 LEVYKCEICGNIV 14 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4689999999754
No 84
>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=25.29 E-value=19 Score=38.87 Aligned_cols=54 Identities=17% Similarity=0.396 Sum_probs=27.1
Q ss_pred HHHHHHHHh-hc-C-ee-ecCCCCCCCCC-Ccc-ccCCCCCChhhhccCCceEEEeeeCCCCcccccCC
Q 009800 81 LLQLLFWFK-QT-F-RW-VNAPPCDGCSN-ETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 143 (525)
Q Consensus 81 l~~LL~WFK-~~-F-~w-v~~P~C~~Cg~-~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPR 143 (525)
+.++|.=+. +. - +| --.|.|+.||. .|+ .... ..+...|+ |+|..||+....+-
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 455554443 33 2 55 33588999999 444 3321 11356676 99999999665553
No 85
>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=25.27 E-value=74 Score=26.42 Aligned_cols=39 Identities=23% Similarity=0.309 Sum_probs=26.1
Q ss_pred eeEEEEEeCCCCCeEEeccCCCcCCCCeeeecCccCccce
Q 009800 185 HVWTECFSQSLGRWMHLDPCEGIYDRPLLYEKGWNKKLNY 224 (525)
Q Consensus 185 HvW~EVy~~~~~rWI~VDP~e~~~D~PllYe~gwgKklsY 224 (525)
+...-.|++..+||+..||.. ..+..-.|.=..+.+++|
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 456778999999999999973 334334444344555554
No 86
>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=24.94 E-value=1.1 Score=36.86 Aligned_cols=54 Identities=19% Similarity=0.155 Sum_probs=34.8
Q ss_pred ceeeEeeccchhhhccccCCCchhhHHHHHHHHHHHHhhccCCCcccccccccCCC
Q 009800 346 HVTTIYNAFSSVLSHFVENNVPKSGAIELLKILKGILGDLKKSPYKTRRVSLNSVP 401 (525)
Q Consensus 346 hv~~iY~a~~~~ls~~~~~~~~~~~a~~~~~~~r~~~~dlk~~~f~~R~~~~~~~~ 401 (525)
+|..-|+-..-.-|+-.++ .|...++.+..|.|+++.||+|+ |.+|+...+...
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 999987765543
No 87
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.55 E-value=56 Score=34.72 Aligned_cols=42 Identities=19% Similarity=0.290 Sum_probs=25.7
Q ss_pred Cee-ecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009800 92 FRW-VNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (525)
Q Consensus 92 F~w-v~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (525)
..| +....|+.||+. ...++ -+.++ +...+.++.|..|+...
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 22222 11121 11346777999999864
No 88
>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=23.97 E-value=45 Score=29.28 Aligned_cols=38 Identities=13% Similarity=0.277 Sum_probs=20.1
Q ss_pred CCCCCCCccccCCCCCChhhhccCC--ceEEEeeeCCCCcc
Q 009800 100 CDGCSNETVGQGMGTPLPSEIQYGA--ARVELFRCKVCSKI 138 (525)
Q Consensus 100 C~~Cg~~t~~~g~~~P~~~E~~~ga--~rVE~y~C~~C~~~ 138 (525)
|+.||+.+...+...=+-+ ..+.. -.|..+.|+.||..
T Consensus 1 C~~C~~~~~~~~~~~~~~~-~~G~~~~v~~~~~~C~~CGe~ 40 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYT-YKGESITIGVPGWYCPACGEE 40 (127)
T ss_pred CCCCCCccceeeeecceEE-EcCEEEEEeeeeeECCCCCCE
Confidence 8899865433322111111 11111 25678999999974
No 89
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=23.78 E-value=58 Score=30.56 Aligned_cols=45 Identities=22% Similarity=0.487 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHhhcCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 78 HAFLLQLLFWFKQTFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 78 ~~~l~~LL~WFK~~F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
...+.++|+=|=. .||. |+.|+++.+..-. -+++-.-+|..||+.
T Consensus 83 ~~~i~~~L~~yI~--~yVl---C~~C~sPdT~l~k-----------~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 83 HFLLNERIEDYVR--KYVI---CRECNRPDTRIIK-----------EGRVSLLKCEACGAK 127 (133)
T ss_pred HHHHHHHHHHHHh--heEE---CCCCCCCCcEEEE-----------eCCeEEEecccCCCC
Confidence 3457777766544 4555 9999996443211 156777799999974
No 90
>PRK15312 antimicrobial resistance protein Mig-14; Provisional
Probab=23.71 E-value=2.2e+02 Score=30.30 Aligned_cols=82 Identities=17% Similarity=0.165 Sum_probs=52.9
Q ss_pred HHHHHhcCccch---hhHHH--HHHHHHHcCCCeEEEEeCCCeeEEEEEeCCCCCeEEeccCCCcCCCCee-eecC----
Q 009800 148 LKLVETKRGRCG---EWANC--FTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDRPLL-YEKG---- 217 (525)
Q Consensus 148 ~~Ll~tR~GrCg---E~A~~--F~~l~RAlG~~aR~V~d~~dHvW~EVy~~~~~rWI~VDP~e~~~D~Pll-Ye~g---- 217 (525)
..|++.|.|.+. +.+++ |...+|-+=+-.=+-+|-.+.+=.=|+--....||.+|-.++-+|.-.. +..|
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 567888888543 33332 2223343333322336777777777887777899999999999986643 3333
Q ss_pred -------------ccCccceEEeec
Q 009800 218 -------------WNKKLNYVIAIS 229 (525)
Q Consensus 218 -------------wgKklsYVIAFs 229 (525)
-+|+|.|-||..
T Consensus 253 WlNi~~A~~~~~~~~K~lrfSfG~~ 277 (298)
T PRK15312 253 WLNISRARHYCQERQKKLIFSIGIL 277 (298)
T ss_pred EecHHHHHHHHHhcCCcEEEEecCC
Confidence 289999999843
No 91
>PRK10445 endonuclease VIII; Provisional
Probab=23.36 E-value=47 Score=33.92 Aligned_cols=26 Identities=19% Similarity=0.538 Sum_probs=17.6
Q ss_pred CCCCCCCCCcc--ccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009800 98 PPCDGCSNETV--GQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 98 P~C~~Cg~~t~--~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
-+|+.||++-. .+|. =-.|.|+.|+.
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 2221 12599999974
No 92
>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=23.14 E-value=76 Score=27.55 Aligned_cols=36 Identities=17% Similarity=0.463 Sum_probs=22.5
Q ss_pred CCCCCCCCCcc-ccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 98 PPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 98 P~C~~Cg~~t~-~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
-+|+.||+... ..-...-++|| ...=.|.|.+||..
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 93
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=23.11 E-value=43 Score=32.44 Aligned_cols=25 Identities=12% Similarity=0.268 Sum_probs=20.7
Q ss_pred hcccccHHHHHHHHHHHHHHHHccC
Q 009800 250 RRNIATEQTVSAVLAKMTRECRRSF 274 (525)
Q Consensus 250 RR~rv~E~wl~~~L~~l~~~~r~~l 274 (525)
++..|+.+.++.+++.+-.++|..-
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 94
>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=22.78 E-value=43 Score=24.97 Aligned_cols=30 Identities=20% Similarity=0.489 Sum_probs=17.1
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009800 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (525)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (525)
.|+.||+...... ..+=| +.|..||.....
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 95
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.77 E-value=57 Score=25.71 Aligned_cols=28 Identities=14% Similarity=0.437 Sum_probs=18.5
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
+..-||.||+. ..... -..+.|..||-.
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 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=22.54 E-value=61 Score=25.96 Aligned_cols=29 Identities=17% Similarity=0.477 Sum_probs=19.7
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 96 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 96 ~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
-+-.|+.||..... ...-..|.|+.||..
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 44569999985443 123357999999975
No 97
>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=22.31 E-value=52 Score=29.21 Aligned_cols=26 Identities=27% Similarity=0.736 Sum_probs=17.0
Q ss_pred CCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 99 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
.|+.||.....- ..+=+++|.+|+..
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 499999975311 01116999999964
No 98
>PRK00420 hypothetical protein; Validated
Probab=22.18 E-value=65 Score=29.57 Aligned_cols=41 Identities=15% Similarity=0.227 Sum_probs=24.6
Q ss_pred HHHHHHHHHhhcCeeecCCCCCCCCCCccc--cCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 80 FLLQLLFWFKQTFRWVNAPPCDGCSNETVG--QGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 80 ~l~~LL~WFK~~F~wv~~P~C~~Cg~~t~~--~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
.++.+-.+..+-.+- ..-.||.||.+... .| ...|+.||..
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 344444444433222 44779999997653 33 2579999974
No 99
>PRK03954 ribonuclease P protein component 4; Validated
Probab=22.17 E-value=43 Score=31.06 Aligned_cols=17 Identities=35% Similarity=0.893 Sum_probs=15.0
Q ss_pred eEEEeeeCCCCcccccCC
Q 009800 126 RVELFRCKVCSKITRFPR 143 (525)
Q Consensus 126 rVE~y~C~~C~~~~RFPR 143 (525)
.| ++.|..||...|||=
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 100
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.03 E-value=53 Score=32.52 Aligned_cols=40 Identities=23% Similarity=0.375 Sum_probs=24.6
Q ss_pred HHHHHHHHHhhc---Ceeec-----CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 80 FLLQLLFWFKQT---FRWVN-----APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 80 ~l~~LL~WFK~~---F~wv~-----~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
.+++.|.|.-.. +..++ +-.|+.||. -....|.|+.||..
T Consensus 284 ~~~~~l~yka~~~~~~v~~~~~~~tS~~C~~cg~-------------------~~~r~~~C~~cg~~ 331 (364)
T COG0675 284 ELRRQLEYKAEWGGIVVKVVPPYYTSKTCPCCGH-------------------LSGRLFKCPRCGFV 331 (364)
T ss_pred HHHHHHHHHHHhCCeEEEECCCCCCcccccccCC-------------------ccceeEECCCCCCe
Confidence 466666666543 22222 245888888 12467999999973
No 101
>PF12390 Se-cys_synth_N: Selenocysteine synthase N terminal
Probab=21.93 E-value=54 Score=24.34 Aligned_cols=37 Identities=30% Similarity=0.602 Sum_probs=27.0
Q ss_pred hcccHHHHHHhhccccccCCCCCeEEEecCCCccccchhhHhHHHHHHHHHhc
Q 009800 411 LLPSIGHLLRVLSLKSELNTDGRVDIVLAGDPVKTSLSLPVVFKALDDMIHDL 463 (525)
Q Consensus 411 ~lps~~~ll~~lslk~~~~~~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~~~ 463 (525)
-|||.+.+|....++.-+..-|+ +++.+++.+++..+
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
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=21.86 E-value=58 Score=32.75 Aligned_cols=37 Identities=16% Similarity=0.325 Sum_probs=23.8
Q ss_pred CCCCCCCCCCccccCCCCCChhhhc-cCCceEEEeeeCCCCc
Q 009800 97 APPCDGCSNETVGQGMGTPLPSEIQ-YGAARVELFRCKVCSK 137 (525)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~-~ga~rVE~y~C~~C~~ 137 (525)
...||.||+........ .+.. +|--.+=.+.|.+||-
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 1222 3566777899999985
No 103
>PF08421 Methyltransf_13: Putative zinc binding domain; InterPro: IPR013630 This domain is found at the N terminus of bacterial methyltransferases. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=21.79 E-value=59 Score=26.28 Aligned_cols=19 Identities=16% Similarity=0.412 Sum_probs=11.8
Q ss_pred hccCCceEEEeeeCCCCcc
Q 009800 120 IQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 120 ~~~ga~rVE~y~C~~C~~~ 138 (525)
...-.-..++|.|..|+..
T Consensus 31 ~~e~~~pL~l~~C~~Cglv 49 (62)
T PF08421_consen 31 EPEPRYPLDLYVCEDCGLV 49 (62)
T ss_dssp S---EEEEEEEEETTT--E
T ss_pred CCceEECCEEEECCCCCch
Confidence 3345678999999999963
No 104
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.76 E-value=65 Score=24.30 Aligned_cols=14 Identities=21% Similarity=0.543 Sum_probs=10.5
Q ss_pred EEeeeCCCCccccc
Q 009800 128 ELFRCKVCSKITRF 141 (525)
Q Consensus 128 E~y~C~~C~~~~RF 141 (525)
..|.|+.||...+-
T Consensus 19 ~~~vC~~Cg~~~~~ 32 (52)
T smart00661 19 RRFVCRKCGYEEPI 32 (52)
T ss_pred CEEECCcCCCeEEC
Confidence 37899999975443
No 105
>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=21.64 E-value=46 Score=35.74 Aligned_cols=45 Identities=22% Similarity=0.445 Sum_probs=0.0
Q ss_pred CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcccccCCCCCHHHH
Q 009800 97 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKL 150 (525)
Q Consensus 97 ~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~L 150 (525)
.|.|+.||.-++.+ .+....+..|+ |+| .||+...-+-.+.-.||
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 106
>PLN02678 seryl-tRNA synthetase
Probab=21.57 E-value=1.6e+02 Score=32.76 Aligned_cols=47 Identities=11% Similarity=0.182 Sum_probs=35.4
Q ss_pred HHHHHHHHHcCCCeEEEE----eC----CCeeEEEEEeCCCCCeEEeccCCCcCC
Q 009800 163 NCFTLYCRAFGYESRLIL----DF----TDHVWTECFSQSLGRWMHLDPCEGIYD 209 (525)
Q Consensus 163 ~~F~~l~RAlG~~aR~V~----d~----~dHvW~EVy~~~~~rWI~VDP~e~~~D 209 (525)
..-.-++..||+|.|.|. |. .-.+=.|||.|++++|.-|-.|.+.-|
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 21 123348999999999999999977655
No 107
>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=21.29 E-value=83 Score=26.19 Aligned_cols=41 Identities=20% Similarity=0.380 Sum_probs=22.7
Q ss_pred CCCCCCCCccccCCCCCChhh---h-ccCCceEEEeeeCCCCccc
Q 009800 99 PCDGCSNETVGQGMGTPLPSE---I-QYGAARVELFRCKVCSKIT 139 (525)
Q Consensus 99 ~C~~Cg~~t~~~g~~~P~~~E---~-~~ga~rVE~y~C~~C~~~~ 139 (525)
.|+.||++.--.+....+-.- . ..+-.+--..-|+.||-..
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE 46 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTE 46 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEE
Confidence 599999975433322111111 1 1123456678899999753
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=21.17 E-value=72 Score=36.09 Aligned_cols=28 Identities=21% Similarity=0.173 Sum_probs=18.5
Q ss_pred hHhHHHHHHHHHhcccCcCCCCCccccc
Q 009800 450 PVVFKALDDMIHDLNNCDNFGKGSFCLP 477 (525)
Q Consensus 450 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 477 (525)
+|=.|.++++++.-=+-...+.|.++||
T Consensus 468 ~vgt~~~K~~l~~rL~~~~~~~g~~hfp 495 (557)
T PF05876_consen 468 LVGTDAAKDTLYGRLRREEPGPGYVHFP 495 (557)
T ss_pred EEccHHHHHHHHHhhcccCCCCceEEcC
Confidence 4456888888875444344566778888
No 109
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=21.05 E-value=57 Score=33.37 Aligned_cols=32 Identities=31% Similarity=0.622 Sum_probs=19.5
Q ss_pred eecC---CCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCc
Q 009800 94 WVNA---PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 137 (525)
Q Consensus 94 wv~~---P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~ 137 (525)
||.. -||+.||.+-.....+ +| -.|.|+.|+.
T Consensus 239 ~Vy~R~g~pC~~Cg~~I~~~~~~-----------gR-~t~~CP~CQ~ 273 (274)
T PRK01103 239 QVYGREGEPCRRCGTPIEKIKQG-----------GR-STFFCPRCQK 273 (274)
T ss_pred EEcCCCCCCCCCCCCeeEEEEEC-----------CC-CcEECcCCCC
Confidence 5553 4799999864322110 11 2599999985
No 110
>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=20.75 E-value=28 Score=31.92 Aligned_cols=25 Identities=16% Similarity=0.341 Sum_probs=18.6
Q ss_pred EeCCCeeEEEEEeCCCCCeEEeccC
Q 009800 180 LDFTDHVWTECFSQSLGRWMHLDPC 204 (525)
Q Consensus 180 ~d~~dHvW~EVy~~~~~rWI~VDP~ 204 (525)
.|.++..|+-+|.+...+-++.+..
T Consensus 61 ~D~tg~~~~~~F~~~a~~l~G~~a~ 85 (146)
T PF08646_consen 61 SDGTGSIWVTLFDEEAEQLLGMSAD 85 (146)
T ss_dssp EETTEEEEEEEEHHHHHHHHCCHHC
T ss_pred EeCCCeEEEEEEhHHHHHHhCCCHH
Confidence 4789999999998765556666554
No 111
>PHA02942 putative transposase; Provisional
Probab=20.44 E-value=73 Score=34.43 Aligned_cols=44 Identities=25% Similarity=0.556 Sum_probs=25.9
Q ss_pred HHHHHHHHHhhc----Ceeec----CCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCcc
Q 009800 80 FLLQLLFWFKQT----FRWVN----APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 138 (525)
Q Consensus 80 ~l~~LL~WFK~~----F~wv~----~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~ 138 (525)
.|.+.|.|=... +..|| +-.|+.||..+... ..| .|.|..||..
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 455666665431 33333 34599999854211 122 6999999985
No 112
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=20.42 E-value=63 Score=37.25 Aligned_cols=55 Identities=18% Similarity=0.378 Sum_probs=29.3
Q ss_pred HHHHHhh-cCeeecCCCCCCCCCCcccc--CCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009800 84 LLFWFKQ-TFRWVNAPPCDGCSNETVGQ--GMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (525)
Q Consensus 84 LL~WFK~-~F~wv~~P~C~~Cg~~t~~~--g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (525)
+++=|.. +|+|..- +|+.||...... .+..| .-..+-+.--=.|+|++|+..++-
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 3334444 4755553 599999864421 11111 111111222235799999999987
No 113
>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=20.33 E-value=76 Score=33.63 Aligned_cols=44 Identities=14% Similarity=0.258 Sum_probs=26.0
Q ss_pred Cee-ecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccc
Q 009800 92 FRW-VNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 139 (525)
Q Consensus 92 F~w-v~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~ 139 (525)
..| +....|+.||+.. ..++- +.++ ..+...+.++.|..|+...
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 0122457777999999853
No 114
>PRK05978 hypothetical protein; Provisional
Probab=20.32 E-value=73 Score=30.52 Aligned_cols=41 Identities=15% Similarity=0.343 Sum_probs=25.3
Q ss_pred HHHHHHHHHhhcCeeecCCCCCCCCCCccccCCCCCChhhhccCCceEEEeeeCCCCccccc
Q 009800 80 FLLQLLFWFKQTFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 141 (525)
Q Consensus 80 ~l~~LL~WFK~~F~wv~~P~C~~Cg~~t~~~g~~~P~~~E~~~ga~rVE~y~C~~C~~~~RF 141 (525)
..+.+++=++ -.|++||......|.-...+ +|+.||..-.+
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 46999999766555432222 59999975443
No 115
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=20.16 E-value=1.1e+02 Score=34.55 Aligned_cols=103 Identities=17% Similarity=0.333 Sum_probs=59.8
Q ss_pred cccccCCCCCHHHHHHhcCccchhhHHHHHHHHHHcCC-CeEEE--EeC--CCeeEEEEEeCCCCCeEEeccCCCcCCCC
Q 009800 137 KITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGY-ESRLI--LDF--TDHVWTECFSQSLGRWMHLDPCEGIYDRP 211 (525)
Q Consensus 137 ~~~RFPRYn~p~~Ll~tR~GrCgE~A~~F~~l~RAlG~-~aR~V--~d~--~dHvW~EVy~~~~~rWI~VDP~e~~~D~P 211 (525)
..+++|-|+..+-++--+.-.-+|.-.++..+++++|+ ..||. |.. ++-+=.++|.+..++||-|=-| |++..-
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 44555555544433322222334555666788899998 68888 443 3333345555666679999888 777655
Q ss_pred eeeecCccCccceEEeec---------CCcceechhhhc
Q 009800 212 LLYEKGWNKKLNYVIAIS---------KDGVFDVTKRYT 241 (525)
Q Consensus 212 llYe~gwgKklsYVIAFs---------~dgv~DVTrRYt 241 (525)
.+-..|-..+.+ |+||+ +.|+.|+--=|.
T Consensus 452 vL~~~Gi~~~~~-~~A~GlGleRlaMi~ygi~DIR~l~~ 489 (494)
T PTZ00326 452 MLRPMGFPEDVT-VIAWGLSLERPTMIKYGIKNIRDLFG 489 (494)
T ss_pred HHHhcCCCCcce-EEEEEecHHHHHHHHhCCcHHHHHhc
Confidence 444334433332 66665 366666654444
Done!