Query 011315
Match_columns 488
No_of_seqs 228 out of 454
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 23:58:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011315.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011315hhsearch_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-113 3E-118 881.4 24.0 396 1-478 102-500 (500)
2 PF03835 Rad4: Rad4 transgluta 99.9 2.1E-22 4.7E-27 182.2 7.7 101 147-258 33-144 (145)
3 TIGR00605 rad4 DNA repair prot 99.8 8.8E-20 1.9E-24 200.9 8.1 186 116-320 255-530 (713)
4 PF01841 Transglut_core: Trans 99.5 4.6E-14 1E-18 118.7 6.7 79 89-168 18-113 (113)
5 smart00460 TGc Transglutaminas 99.4 4.7E-13 1E-17 104.2 6.2 53 115-169 1-67 (68)
6 COG1305 Transglutaminase-like 99.3 9.9E-12 2.1E-16 119.4 7.8 73 111-184 185-275 (319)
7 KOG2179 Nucleotide excision re 99.1 7.5E-11 1.6E-15 128.9 4.1 114 120-234 263-413 (669)
8 COG5535 RAD4 DNA repair protei 98.1 1.6E-07 3.5E-12 101.8 -4.1 123 115-237 242-399 (650)
9 PF04473 DUF553: Transglutamin 97.1 0.0019 4.1E-08 60.5 8.2 67 104-172 59-130 (153)
10 COG5279 CYK3 Uncharacterized p 94.3 0.11 2.3E-06 57.0 7.0 63 105-169 190-268 (521)
11 PF13369 Transglut_core2: Tran 93.3 0.27 5.8E-06 45.2 7.0 58 109-170 53-110 (152)
12 PF14381 EDR1: Ethylene-respon 92.0 0.26 5.7E-06 48.3 5.3 54 115-169 137-196 (204)
13 PF14402 7TM_transglut: 7 tran 90.2 0.27 5.9E-06 51.1 3.5 48 129-178 2-58 (313)
14 PF13471 Transglut_core3: Tran 88.9 0.69 1.5E-05 40.5 4.7 37 119-155 54-97 (117)
15 PF12760 Zn_Tnp_IS1595: Transp 87.6 0.44 9.5E-06 35.9 2.3 34 56-102 12-45 (46)
16 COG1571 Predicted DNA-binding 87.2 0.31 6.8E-06 52.5 1.7 35 61-110 349-383 (421)
17 COG2816 NPY1 NTP pyrophosphohy 82.7 1.6 3.5E-05 45.0 4.4 54 45-121 100-154 (279)
18 PRK10941 hypothetical protein; 79.6 14 0.0003 37.8 9.8 60 112-173 87-146 (269)
19 TIGR03655 anti_R_Lar restricti 72.5 3.9 8.4E-05 31.7 2.9 36 64-106 3-38 (53)
20 PF13453 zf-TFIIB: Transcripti 72.2 2.9 6.4E-05 30.7 2.0 28 64-103 1-28 (41)
21 PRK09710 lar restriction allev 69.7 4.1 9E-05 33.6 2.6 32 62-104 6-37 (64)
22 PF06035 Peptidase_C93: Bacter 69.0 4.3 9.4E-05 39.1 2.9 24 117-140 74-97 (170)
23 PRK00241 nudC NADH pyrophospha 68.5 7.4 0.00016 39.2 4.7 47 45-112 88-134 (256)
24 PRK00464 nrdR transcriptional 65.1 5 0.00011 38.0 2.5 33 64-102 2-36 (154)
25 PF00797 Acetyltransf_2: N-ace 61.3 7.9 0.00017 37.4 3.2 68 113-182 38-120 (240)
26 PHA02998 RNA polymerase subuni 58.6 7.8 0.00017 38.0 2.6 45 63-112 144-189 (195)
27 PRK03564 formate dehydrogenase 57.4 41 0.00088 35.4 7.7 50 59-125 184-234 (309)
28 PF14353 CpXC: CpXC protein 57.1 6.5 0.00014 35.0 1.7 41 63-104 2-48 (128)
29 PRK06556 vitamin B12-dependent 56.9 6.4 0.00014 46.8 2.1 31 58-104 920-950 (953)
30 PF14354 Lar_restr_allev: Rest 55.9 14 0.0003 28.8 3.1 13 63-75 4-16 (61)
31 PRK15047 N-hydroxyarylamine O- 55.8 42 0.00092 34.4 7.5 65 114-180 59-137 (281)
32 PF09862 DUF2089: Protein of u 54.5 11 0.00023 34.3 2.6 27 186-212 38-66 (113)
33 TIGR00686 phnA alkylphosphonat 52.2 9.5 0.00021 34.5 1.9 26 62-102 2-27 (109)
34 PF08274 PhnA_Zn_Ribbon: PhnA 52.0 5.1 0.00011 28.4 0.2 27 62-103 2-28 (30)
35 PRK10220 hypothetical protein; 49.0 12 0.00027 33.9 2.1 29 61-104 2-30 (111)
36 PF06397 Desulfoferrod_N: Desu 48.8 9.8 0.00021 28.1 1.2 14 91-104 3-16 (36)
37 COG3672 Predicted transglutami 46.4 52 0.0011 32.6 6.0 23 118-140 105-127 (191)
38 PF03811 Zn_Tnp_IS1: InsA N-te 45.7 20 0.00044 26.3 2.4 29 63-101 6-36 (36)
39 PF11023 DUF2614: Protein of u 44.8 10 0.00022 34.6 0.9 44 49-108 54-99 (114)
40 COG1656 Uncharacterized conser 44.6 39 0.00085 32.7 4.8 108 2-138 35-158 (165)
41 COG2162 NhoA Arylamine N-acety 43.6 49 0.0011 34.4 5.7 64 115-180 62-139 (275)
42 PHA00626 hypothetical protein 42.2 15 0.00031 30.0 1.3 29 64-102 2-31 (59)
43 PF04981 NMD3: NMD3 family ; 40.7 1.1E+02 0.0023 30.4 7.5 135 65-218 1-143 (236)
44 smart00440 ZnF_C2C2 C2C2 Zinc 40.3 26 0.00057 25.9 2.4 35 64-103 2-37 (40)
45 COG2888 Predicted Zn-ribbon RN 40.0 17 0.00037 29.8 1.5 10 62-71 9-18 (61)
46 PRK02935 hypothetical protein; 39.8 20 0.00044 32.5 2.0 44 48-107 54-99 (110)
47 PF13005 zf-IS66: zinc-finger 39.8 21 0.00046 26.4 1.9 38 63-101 3-47 (47)
48 cd00886 MogA_MoaB MogA_MoaB fa 39.1 40 0.00086 31.0 3.9 50 377-426 91-150 (152)
49 TIGR01562 FdhE formate dehydro 38.4 35 0.00076 35.8 3.8 14 91-104 249-262 (305)
50 PF01927 Mut7-C: Mut7-C RNAse 38.3 50 0.0011 30.4 4.5 54 44-103 72-133 (147)
51 PF14726 RTTN_N: Rotatin, an a 38.2 39 0.00084 29.9 3.5 17 42-65 28-44 (98)
52 PF14803 Nudix_N_2: Nudix N-te 38.1 17 0.00037 26.4 1.0 29 65-103 3-31 (34)
53 PF01096 TFIIS_C: Transcriptio 37.5 21 0.00045 26.3 1.5 35 64-103 2-37 (39)
54 PF14169 YdjO: Cold-inducible 37.1 17 0.00037 29.7 1.0 24 51-74 28-51 (59)
55 COG1997 RPL43A Ribosomal prote 36.9 24 0.00052 31.0 1.9 30 61-104 34-63 (89)
56 TIGR02667 moaB_proteo molybden 36.8 26 0.00056 32.9 2.4 71 360-431 73-159 (163)
57 PF07754 DUF1610: Domain of un 36.6 28 0.00061 23.7 1.8 9 94-102 16-24 (24)
58 COG1998 RPS31 Ribosomal protei 35.4 23 0.0005 28.1 1.5 29 61-103 18-46 (51)
59 COG3809 Uncharacterized protei 35.3 21 0.00045 31.0 1.3 28 64-103 3-30 (88)
60 TIGR01385 TFSII transcription 34.9 30 0.00065 36.1 2.6 44 58-106 254-298 (299)
61 PF04216 FdhE: Protein involve 34.7 17 0.00036 37.0 0.8 44 58-110 169-213 (290)
62 COG1594 RPB9 DNA-directed RNA 33.8 34 0.00074 30.8 2.5 40 62-106 72-112 (113)
63 PF12386 Peptidase_C71: Pseudo 33.6 40 0.00087 31.5 2.9 41 117-157 51-99 (142)
64 TIGR00319 desulf_FeS4 desulfof 32.6 25 0.00054 24.8 1.2 14 91-104 4-17 (34)
65 KOG4477 RING1 interactor RYBP 31.8 18 0.00038 35.8 0.4 35 77-111 15-59 (228)
66 TIGR02159 PA_CoA_Oxy4 phenylac 30.6 25 0.00053 33.0 1.1 34 62-103 105-139 (146)
67 TIGR00244 transcriptional regu 30.6 25 0.00054 33.4 1.2 43 64-112 2-44 (147)
68 TIGR00311 aIF-2beta translatio 30.5 72 0.0016 29.6 4.1 45 43-104 83-128 (133)
69 cd01675 RNR_III Class III ribo 30.1 44 0.00096 37.4 3.2 42 44-103 495-541 (555)
70 COG2912 Uncharacterized conser 29.6 95 0.0021 32.2 5.2 63 107-172 83-145 (269)
71 COG4332 Uncharacterized protei 29.6 33 0.00072 33.9 1.8 44 65-110 20-65 (203)
72 TIGR01562 FdhE formate dehydro 29.6 46 0.00099 34.9 3.0 49 60-125 182-232 (305)
73 TIGR03696 Rhs_assc_core RHS re 29.5 57 0.0012 26.8 3.0 39 150-189 32-70 (76)
74 cd04476 RPA1_DBD_C RPA1_DBD_C: 29.3 29 0.00063 32.1 1.3 61 58-166 31-96 (166)
75 TIGR00340 zpr1_rel ZPR1-relate 29.2 37 0.00081 32.5 2.1 34 65-103 1-37 (163)
76 PF09297 zf-NADH-PPase: NADH p 29.0 35 0.00075 23.8 1.4 13 63-75 4-16 (32)
77 PF14690 zf-ISL3: zinc-finger 28.9 40 0.00087 24.7 1.8 11 63-73 3-13 (47)
78 PF04216 FdhE: Protein involve 28.8 39 0.00084 34.4 2.3 42 57-104 205-248 (290)
79 PF04721 DUF750: Domain of unk 28.0 0.9 2E-05 37.1 -7.7 54 311-366 3-56 (62)
80 PRK03564 formate dehydrogenase 28.0 44 0.00095 35.1 2.5 42 57-104 220-262 (309)
81 PRK00432 30S ribosomal protein 27.9 33 0.00072 26.7 1.2 40 49-103 5-46 (50)
82 PRK00398 rpoP DNA-directed RNA 27.3 38 0.00083 25.3 1.5 26 64-103 5-30 (46)
83 TIGR01384 TFS_arch transcripti 27.1 57 0.0012 28.0 2.7 36 63-103 63-99 (104)
84 cd00974 DSRD Desulforedoxin (D 26.8 33 0.00073 24.2 1.0 13 92-104 2-14 (34)
85 PF11781 RRN7: RNA polymerase 26.8 49 0.0011 24.2 1.9 31 59-104 3-35 (36)
86 PF06044 DRP: Dam-replacing fa 26.2 32 0.00069 35.3 1.1 54 191-248 154-213 (254)
87 smart00661 RPOL9 RNA polymeras 25.9 50 0.0011 24.6 1.9 14 93-106 19-32 (52)
88 PF11672 DUF3268: Protein of u 25.9 59 0.0013 29.1 2.6 44 63-112 3-50 (102)
89 PRK03988 translation initiatio 24.8 1.3E+02 0.0028 28.1 4.7 46 43-105 88-134 (138)
90 COG1327 Predicted transcriptio 24.6 39 0.00084 32.4 1.3 25 215-239 75-99 (156)
91 PF08271 TF_Zn_Ribbon: TFIIB z 24.2 37 0.00081 25.1 0.9 29 64-105 2-30 (43)
92 TIGR00310 ZPR1_znf ZPR1 zinc f 23.9 59 0.0013 31.9 2.4 34 64-102 2-38 (192)
93 PF06827 zf-FPG_IleRS: Zinc fi 23.9 41 0.00089 23.0 1.0 27 64-102 3-29 (30)
94 smart00709 Zpr1 Duplicated dom 23.5 63 0.0014 30.8 2.5 34 64-102 2-37 (160)
95 PRK12336 translation initiatio 23.4 1.1E+02 0.0024 30.0 4.2 45 43-104 84-129 (201)
96 COG3877 Uncharacterized protei 22.9 70 0.0015 29.3 2.5 26 62-105 6-31 (122)
97 PHA02942 putative transposase; 22.8 58 0.0013 34.8 2.4 27 63-104 326-352 (383)
98 COG1571 Predicted DNA-binding 22.4 60 0.0013 35.6 2.4 62 352-413 48-111 (421)
99 PF12390 Se-cys_synth_N: Selen 22.1 53 0.0012 24.1 1.4 36 377-428 4-39 (40)
100 COG2051 RPS27A Ribosomal prote 22.1 52 0.0011 27.6 1.4 33 63-108 20-52 (67)
101 PF07282 OrfB_Zn_ribbon: Putat 21.9 64 0.0014 25.6 1.9 29 61-103 27-55 (69)
102 PRK03954 ribonuclease P protei 21.9 45 0.00098 30.6 1.1 17 91-108 91-107 (121)
103 PF13240 zinc_ribbon_2: zinc-r 21.7 56 0.0012 21.7 1.2 8 65-72 2-9 (23)
104 TIGR01206 lysW lysine biosynth 21.6 63 0.0014 25.8 1.7 31 63-105 3-33 (54)
105 PF05053 Menin: Menin; InterP 21.4 2E+02 0.0043 33.0 6.1 48 107-155 138-186 (618)
106 PRK15312 antimicrobial resista 20.9 3.1E+02 0.0068 29.0 7.0 80 114-193 174-276 (298)
107 PF01921 tRNA-synt_1f: tRNA sy 20.8 26 0.00056 37.5 -0.7 54 45-107 153-212 (360)
108 PF08646 Rep_fac-A_C: Replicat 20.8 27 0.00058 31.7 -0.6 25 145-169 61-85 (146)
109 COG0675 Transposase and inacti 20.6 60 0.0013 31.8 1.8 40 45-103 284-331 (364)
110 TIGR00280 L37a ribosomal prote 20.1 89 0.0019 27.6 2.5 27 63-103 36-62 (91)
No 1
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.4e-113 Score=881.39 Aligned_cols=396 Identities=43% Similarity=0.748 Sum_probs=365.6
Q ss_pred CCCCHHHHHHHhccCChHHHHHHHHHHHHHcCCCCCCCchhHHHHHHHHHHHhhcc-CeeecCCCCCCCCCCc-cccCCC
Q 011315 1 MYEDPIRQEAAKKTVPVERLEEKSLVSLAREGNFKPSKTEQDHAFLLQLLFWFKQT-FRWVNAPPCDGCSNET-VGQGMG 78 (488)
Q Consensus 1 ~YEd~~lq~~Al~~IPl~~L~~~a~~~l~~~g~~~~~~~~~~~~~l~~LL~wFK~~-F~wv~~P~C~~Cg~~t-~~~g~~ 78 (488)
+||||.||++||++||||+|+++|++.+++ +.+++.+.|..+..+||+|||++ |+|||+|||+.||++| ...|.+
T Consensus 102 vYEDP~lq~~Als~iPvdEL~~kA~ekla~---~eg~ki~kdy~i~leLL~WFKq~FF~WvN~PpC~~CG~et~~~l~~~ 178 (500)
T KOG0909|consen 102 VYEDPVLQAKALSTIPVDELKEKASEKLAK---AEGEKIYKDYLIKLELLNWFKQDFFKWVNNPPCNKCGGETSSGLGNQ 178 (500)
T ss_pred eecCHHHHHHHHhcCCHHHHHHHHHHhhcc---cchhhhhcchHHHHHHHHHHHHhhheecCCCCcccccccccccccCC
Confidence 699999999999999999999999998876 23445565555557999999998 7999999999999999 567888
Q ss_pred CCChhhhhcCCceEEEeecCCCCcccccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeCCCeEEEEEEeC
Q 011315 79 TPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQ 158 (488)
Q Consensus 79 ~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~~~dHvW~EVy~~ 158 (488)
+|+.+|.++||++||+|+|+.||+.+||||||||.+||+||+|||||||||||++|||+|++||||||.+||||+|||++
T Consensus 179 ~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPRYNdp~kLLeTRkGRCGEWANCFTllcralg~daR~i~d~tDHVWtEvYS~ 258 (500)
T KOG0909|consen 179 PPNEEEKKFGAGRVEIYKCNRCGTETRFPRYNDPIKLLETRKGRCGEWANCFTLLCRALGLDARYIWDRTDHVWTEVYSN 258 (500)
T ss_pred CCchhHhhcCCceEEEEEecCCCCcccCcccCCHHHHHhhccCccchHHHHHHHHHHHcCCcceEEeecCcchhHHhhhh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeEEeccCCCcCCCCeeeecCccCccceEEeecCCcceechhhhccChHHhhhhcccccHHHHHHHHHHHHHHHHcc
Q 011315 159 SLGRWMHLDPCEGIYDRPLLYEKGWNKKLNYVIAISKDGVFDVTKRYTRKWHEVLSRRNIATEQTVSAVLAKMTRECRRS 238 (488)
Q Consensus 159 ~~~rWIhVDP~e~~iD~Pllye~gwgKklsYVIAFs~DGv~DVTrRYt~~~~~~~~RR~rv~E~wl~~~L~~l~~~~r~~ 238 (488)
.++|||||||||+++|+|+||+.||||+|+|||||++|||+||||||+.+|.+++.+|+.|.|+.|+.+|+.||+++|.+
T Consensus 259 ~qqRW~HvDpcE~v~D~PllYe~GW~KklsY~iafgkD~VvDVT~RYi~~h~e~~~~R~~~~E~~l~~~l~~in~~rr~~ 338 (500)
T KOG0909|consen 259 AQQRWVHVDPCENVFDKPLLYEIGWGKKLSYCIAFGKDGVVDVTWRYILDHKENLLPRDLCKESVLQQTLQFINKRRRYS 338 (500)
T ss_pred hhheeEeecccccccccceeeecccCcccceEEEeccCceEeeehhhhccchhhccchhhcchHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHhhhhhhccHHHHHHHHhhccCCCCCCCCCCCCccccHHHHHhhcCCCCCCCCCcCCCCCCceeecccceeeEeec
Q 011315 239 FASETLSTLEDRDKCEREAMERDLYSTDDAPVSLPGRQSGDKEWRISRSEIGSDDNCSLSCSSCPVRVCIDEHVTTIYNA 318 (488)
Q Consensus 239 ls~ee~~~Le~Rd~~E~~EL~~~~~~~~~~~~~l~GRqSGs~eWr~aRGE~G~~~~~s~~~s~cp~~~c~d~hv~~iY~a 318 (488)
+++++++.|++||.+|+.||.+...+.+++..+||||||||.+||.+|||+|. |++ ||+.
T Consensus 339 lt~~r~~~L~~rd~~e~~El~~~~~~~~~~~~~L~GR~SGs~eWr~~RGE~G~-------------------h~~-i~D~ 398 (500)
T KOG0909|consen 339 LTDDRKKELAQRDEREQIELIRGKTPETPTKSSLPGRQSGSVEWRAQRGEDGK-------------------HNT-IYDS 398 (500)
T ss_pred cChHHHHHHHhhhHHHHHHHHhccccCCCCCCCCCCcccccHHHHHhhccccc-------------------cce-ehhh
Confidence 99999999999999999999999999888999999999999999999999998 887 8877
Q ss_pred cchhhhccccCCCchhhHHHHHHHHHHHHhhccCCCcccccccccCCCCchhHHHHhh-hccHHHHHHhhccccccCCCC
Q 011315 319 FSSVLSHFVENNVPKSGAIELLKILKGILGDLKKSPYKTRRVSLNSVPNNGQKIVHQL-LPSIGHLLRVLSLKSELNTDG 397 (488)
Q Consensus 319 ~~~~ls~~~~~~~~~~~a~~~~~~~r~~~~dlk~~~f~~R~~~~~~~~~~~~~~~~~~-lps~~~ll~~lslk~~~~~~g 397 (488)
.- + |.++||++..|||+++.||||+ |++|.+--+-..++ +.| +-+.+.++.++||+.++.|.|
T Consensus 399 ~~-------~---~~~~~~e~~~i~r~ve~Dw~mt-ylaR~~~~s~~~is-----w~fd~~~~~~~~~~~~l~~~~qtf~ 462 (500)
T KOG0909|consen 399 YT-------E---WSAQAFELENIFRKVETDWKMT-YLARLEGDSPGNIS-----WHFDFKLKGLKVKSESLMAEIQTFG 462 (500)
T ss_pred hh-------h---HHHHHHHHHHHHHHHHhhHHHH-HHHHhcCCCCcccc-----chhhhhhcccHHHHHHHHhhhhhcC
Confidence 65 1 8999999999999999999999 99999865555544 444 338899999999999999998
Q ss_pred CeEEEecCCCccccchhhHhHHHHHHHHHhcccCcCCCCCcccccccccccccccceeccccccccceeeccccCCCccc
Q 011315 398 RVDIVLAGDPVKTSLSLPVVFKALDDMIHDLNNCDNFGKGSFCLPLLKLNRIHSGSVLASGEEFPFGIVTSAFDGIRPSK 477 (488)
Q Consensus 398 ~~~~~~~~~p~~tsl~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~a~~e~~p~g~~~~af~g~~~~k 477 (488)
+= ++||.+||.+.. .++++-.++. |+|.+|+|+.-.|
T Consensus 463 ~g-------------~~~v~~D~s~~s-ad~~~a~~l~-----------------------------i~t~~~~g~~~~~ 499 (500)
T KOG0909|consen 463 KG-------------CMRVTIDASALS-ADPSNATILK-----------------------------IRTELFSGKGDVK 499 (500)
T ss_pred CC-------------ceEeeechhccc-CCcccCceee-----------------------------eehhhcCCccccC
Confidence 74 888999999887 7777744331 9999999999999
Q ss_pred c
Q 011315 478 W 478 (488)
Q Consensus 478 w 478 (488)
|
T Consensus 500 w 500 (500)
T KOG0909|consen 500 W 500 (500)
T ss_pred C
Confidence 8
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=99.87 E-value=2.1e-22 Score=182.22 Aligned_cols=101 Identities=37% Similarity=0.569 Sum_probs=74.6
Q ss_pred CCCeEEEEEEeCCCCCeEEeccCCC-----cCCCCeeeecCccCccceEEeecCCc-ceechhhhccChHHhhhhccccc
Q 011315 147 FTDHVWTECFSQSLGRWMHLDPCEG-----IYDRPLLYEKGWNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSRRNIAT 220 (488)
Q Consensus 147 ~~dHvW~EVy~~~~~rWIhVDP~e~-----~iD~Pllye~gwgKklsYVIAFs~DG-v~DVTrRYt~~~~~~~~RR~rv~ 220 (488)
..+|+|+|||++.+++||||||+.+ .++.|+ ..+|+++|+|||||+.|| ++|||+||+.++.....+|.|+.
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 4789999999999999999999996 677777 778999999999996665 89999999998334556888998
Q ss_pred -----HHHHHHHHHHHHHHHHccCCHHHhhhhhhccHHHHHHH
Q 011315 221 -----EQTVSAVLAKMTRECRRSFASETLSTLEDRDKCEREAM 258 (488)
Q Consensus 221 -----E~wl~~~L~~l~~~~r~~ls~ee~~~Le~Rd~~E~~EL 258 (488)
++||..+|+.++...+... .||..|++||
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 9999999999885443321 5678888887
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=8.8e-20 Score=200.89 Aligned_cols=186 Identities=18% Similarity=0.275 Sum_probs=129.6
Q ss_pred HHhCCccchhhHHHHHHHHHHcCCCeEEEEe--------------C----------------------------------
Q 011315 116 VETKRGRCGEWANCFTLYCRAFGYESRLILD--------------F---------------------------------- 147 (488)
Q Consensus 116 L~tR~GrCgE~A~lF~~l~RalG~~aR~V~~--------------~---------------------------------- 147 (488)
-.++.|+.+=-|.+|++++|++|++||+|.+ .
T Consensus 255 a~~~~gsrd~~aql~~allr~~~~~~rlv~slqpl~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~s~~S~~~tsR~~l~ 334 (713)
T TIGR00605 255 SNRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHNDPEISSEGFVPKLSACNANQRLIMSCESADRTSRFRMK 334 (713)
T ss_pred hhccccccchhhhHHHHHHhhhcccccccccccccCcccCCCCcccccccccccccccccccccccccCCCCcccccccc
Confidence 3466788888999999999999999999841 0
Q ss_pred ----------------------------------CCeEEEEEEeCCCCCeEEeccCC-CcCCCCeeeecCccCccceEEe
Q 011315 148 ----------------------------------TDHVWTECFSQSLGRWMHLDPCE-GIYDRPLLYEKGWNKKLNYVIA 192 (488)
Q Consensus 148 ----------------------------------~dHvW~EVy~~~~~rWIhVDP~e-~~iD~Pllye~gwgKklsYVIA 192 (488)
.+++|+|||++.+++||||||+. +++|+|..|..+|+++|+||||
T Consensus 335 ~~l~~P~fs~~~~~~k~~~~~~~~~~~~~~~~~~~p~~W~Ev~~~~~~rWI~VD~~~~~~~~~~~~~~e~~~~~m~YVvA 414 (713)
T TIGR00605 335 KDPSLPGFSAYSDMDKSPIFTCEEGDKFIDRWITYVDFWVEVFIEQEEKWVCVDAVHSGVVPKGVTCFEPATLMMTYVFA 414 (713)
T ss_pred ccCCCCCccccccCCCCCccchhcccccccccCCCCeeEEEEeecccceeEEeccccccccCCchhhccCCCCceEEEEE
Confidence 03899999999999999999999 9999999999999999999999
Q ss_pred ecCCc-ceechhhhccChHHhhhhcccccHHHHHHH-HHHHHHHHHccCCHHHhhhhhhccHHHHHHHHhhccCCCCCCC
Q 011315 193 ISKDG-VFDVTKRYTRKWHEVLSRRNIATEQTVSAV-LAKMTRECRRSFASETLSTLEDRDKCEREAMERDLYSTDDAPV 270 (488)
Q Consensus 193 Fs~DG-v~DVTrRYt~~~~~~~~RR~rv~E~wl~~~-L~~l~~~~r~~ls~ee~~~Le~Rd~~E~~EL~~~~~~~~~~~~ 270 (488)
|+.|| ++|||+||+.+|+. ..|+.||+..||.++ ++.+...+.. .... +|..|+.||......+
T Consensus 415 f~~d~~~kDVT~RY~~~~~~-k~r~~Rv~~~w~~~~w~~~~~~~~~~-------r~~~-~d~~Ed~el~~~~~~e----- 480 (713)
T TIGR00605 415 YDRDGYVKDVTRRYCDQWST-KVRKRRVEKADFGETWFRPIFGALHK-------RKRT-IDDIEDQEFLRRHESE----- 480 (713)
T ss_pred EcCCCceeechhhHhhhhhh-hhheeeecccchHHHHHHHHhhhhcc-------Cccc-hhhhhhhHhhhhhccc-----
Confidence 99995 99999999999976 468888987777766 5554432211 1111 5567777776543221
Q ss_pred CCCCCccccHHHHHh---hcCCCCCCCCCcCC--CCCCceeecccceeeEeeccc
Q 011315 271 SLPGRQSGDKEWRIS---RSEIGSDDNCSLSC--SSCPVRVCIDEHVTTIYNAFS 320 (488)
Q Consensus 271 ~l~GRqSGs~eWr~a---RGE~G~~~~~s~~~--s~cp~~~c~d~hv~~iY~a~~ 320 (488)
.+| .| =.+.|.+ --|--...+.++.| ..++++.|..+. .||....
T Consensus 481 ~~P--~s-i~~fKnHP~YvLer~L~~~Evi~P~~~~~~~g~~~g~~--~VY~Rs~ 530 (713)
T TIGR00605 481 GIP--KS-IQDLKNHPLYVLERHLKKTQALKPGKKACTLGFVNGKA--GVYSRKD 530 (713)
T ss_pred CCC--hh-HHHhhcCceEEehhhcccceeeccCCCCCceeccCCCC--CccchhH
Confidence 122 00 1122221 11212223344444 456778887644 3777665
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=4.6e-14 Score=118.66 Aligned_cols=79 Identities=25% Similarity=0.532 Sum_probs=62.3
Q ss_pred CceEEEeecCCCCcc--cccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeC---------------CCeE
Q 011315 89 AARVELFRCKVCSKI--TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDF---------------TDHV 151 (488)
Q Consensus 89 a~rVE~y~C~~C~~~--~RFPRYn~p~~LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~~---------------~dHv 151 (488)
+..+-.|-.+++.-. ...+...+|..+|++++|.|.++|.+|++|||++|||||+|... ..|+
T Consensus 18 ~~~i~~~v~~~~~y~~~~~~~~~~~~~~~l~~~~G~C~~~a~l~~allr~~Gipar~v~g~~~~~~~~~~~~~~~~~~H~ 97 (113)
T PF01841_consen 18 AKAIYDWVRSNIRYDDPNYSPGPRDASEVLRSGRGDCEDYASLFVALLRALGIPARVVSGYVKGPDPDGDYSVDGNDNHA 97 (113)
T ss_dssp CCCCCCCCCCCCCEC-TCCCCCCTTHHHHHHCEEESHHHHHHHHHHHHHHHT--EEEEEEEEEECSSTTCTSTSSEEEEE
T ss_pred HHHHHHHHHhCcEEeCCCCCCCCCCHHHHHHcCCCccHHHHHHHHHHHhhCCCceEEEEEEcCCccccccccCCCCCCEE
Confidence 444444555554443 56778888999999999999999999999999999999999631 2399
Q ss_pred EEEEEeCCCCCeEEecc
Q 011315 152 WTECFSQSLGRWMHLDP 168 (488)
Q Consensus 152 W~EVy~~~~~rWIhVDP 168 (488)
|+|||++. ++|+++||
T Consensus 98 w~ev~~~~-~~W~~~Dp 113 (113)
T PF01841_consen 98 WVEVYLPG-GGWIPLDP 113 (113)
T ss_dssp EEEEEETT-TEEEEEET
T ss_pred EEEEEEcC-CcEEEcCC
Confidence 99999954 67999998
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=99.40 E-value=4.7e-13 Score=104.21 Aligned_cols=53 Identities=36% Similarity=0.853 Sum_probs=48.4
Q ss_pred HHHhCCccchhhHHHHHHHHHHcCCCeEEEEe--------------CCCeEEEEEEeCCCCCeEEeccC
Q 011315 115 LVETKRGRCGEWANCFTLYCRAFGYESRLILD--------------FTDHVWTECFSQSLGRWMHLDPC 169 (488)
Q Consensus 115 LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~--------------~~dHvW~EVy~~~~~rWIhVDP~ 169 (488)
+|++|.|.|.++|++|+.+||++|+|||+|.. ...|+|+|||.+ ++|+.+||+
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 47899999999999999999999999999953 467999999997 689999997
No 6
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=99.26 E-value=9.9e-12 Score=119.42 Aligned_cols=73 Identities=23% Similarity=0.542 Sum_probs=60.1
Q ss_pred CHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeC-----------------CCeEEEEEEeCCCCCeEEeccCCCcC
Q 011315 111 DPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDF-----------------TDHVWTECFSQSLGRWMHLDPCEGIY 173 (488)
Q Consensus 111 ~p~~LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~~-----------------~dHvW~EVy~~~~~rWIhVDP~e~~i 173 (488)
++...|++++|.|.++|++|++|||++|+|||+|.++ ..|+|+|+|.+.. +|+++||+.+..
T Consensus 185 ~~~~~l~~~~G~C~d~a~l~val~Ra~GIpAR~V~Gy~~~~~~~~~~~~~~~~~~~Haw~ev~~~~~-gW~~~Dpt~~~~ 263 (319)
T COG1305 185 SASDALRLGRGVCRDFAHLLVALLRAAGIPARYVSGYLGAEVEPLSGRPLVRNDDAHAWAEVYLPGR-GWVPLDPTNGLL 263 (319)
T ss_pred CHHHHHHhCCcccccHHHHHHHHHHHcCCcceeeeccccCCCCcccccccccCcccceeeeeecCCC-ccEeecCCCCCc
Confidence 4679999999999999999999999999999999642 3599999999975 799999998755
Q ss_pred CCCee-eecCcc
Q 011315 174 DRPLL-YEKGWN 184 (488)
Q Consensus 174 D~Pll-ye~gwg 184 (488)
-.... +..+|+
T Consensus 264 ~~~~~~~~~~~~ 275 (319)
T COG1305 264 AGGRYSILAAWG 275 (319)
T ss_pred cCcccccccccc
Confidence 44433 344554
No 7
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=99.07 E-value=7.5e-11 Score=128.93 Aligned_cols=114 Identities=25% Similarity=0.403 Sum_probs=91.3
Q ss_pred CccchhhHHHHHHHHHHcCCCeEEEEe-----------------------------CCCeEEEEEEeCCCCCeEEecc--
Q 011315 120 RGRCGEWANCFTLYCRAFGYESRLILD-----------------------------FTDHVWTECFSQSLGRWMHLDP-- 168 (488)
Q Consensus 120 ~GrCgE~A~lF~~l~RalG~~aR~V~~-----------------------------~~dHvW~EVy~~~~~rWIhVDP-- 168 (488)
+|+-.--+..|.+++|..+ ++|...+ ..+..|+|||+..++.||||||
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 7787778899999999998 5554410 1347899999999999999996
Q ss_pred CCCcCCCCeeeecCc---cCccceEEeecCCc-ceechhhhccChHHhhhhc--ccccHHHHHHHHHHHHHH
Q 011315 169 CEGIYDRPLLYEKGW---NKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSRR--NIATEQTVSAVLAKMTRE 234 (488)
Q Consensus 169 ~e~~iD~Pllye~gw---gKklsYVIAFs~DG-v~DVTrRYt~~~~~~~~RR--~rv~E~wl~~~L~~l~~~ 234 (488)
..+.++.++...... +..|.|||||+.+| ++|||+||+..|+.....| .+++..||..+++.++..
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 356666666655433 45999999999998 9999999999998765433 567899999999999865
No 8
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=98.11 E-value=1.6e-07 Score=101.79 Aligned_cols=123 Identities=21% Similarity=0.250 Sum_probs=91.5
Q ss_pred HHHhCCccchhhHHHHHHHHHHcCCCeEEEEe--------------------------CCCeEEEEEEeCCCCCeEEecc
Q 011315 115 LVETKRGRCGEWANCFTLYCRAFGYESRLILD--------------------------FTDHVWTECFSQSLGRWMHLDP 168 (488)
Q Consensus 115 LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~--------------------------~~dHvW~EVy~~~~~rWIhVDP 168 (488)
-+-...|+-.--+.+|++++|++.+++|++.+ .....|+|||....+.||+|||
T Consensus 242 ~~~~~~~~~D~~vrgf~a~~r~~~v~~Rli~~l~~P~Fs~~~~~~~~~e~~~~~iD~l~~p~fw~ev~~~~~~kwv~vdp 321 (650)
T COG5535 242 PLKSADGRRDADVRGFEAEHRILNVFARLIASLIQPVFSNNSDLDVLSEGLLEYIDSLEYPGFWGEVVDKFEKKWVFVDP 321 (650)
T ss_pred hHhhccCCCcchhHHHHHHHHHhccchhhhccccCcccccccccccCccccceeccchhcchHHHHHHHHHHhceEeccc
Confidence 34566777777788999999999999999842 0346799999999999999999
Q ss_pred CC--CcCCC-Ceeeec---CccCccceEEeecCCc-ceechhhhccChHHhhhh--cccccHHHHHHHHHHHHHHHHc
Q 011315 169 CE--GIYDR-PLLYEK---GWNKKLNYVIAISKDG-VFDVTKRYTRKWHEVLSR--RNIATEQTVSAVLAKMTRECRR 237 (488)
Q Consensus 169 ~e--~~iD~-Pllye~---gwgKklsYVIAFs~DG-v~DVTrRYt~~~~~~~~R--R~rv~E~wl~~~L~~l~~~~r~ 237 (488)
.. .++.. -.-+|. --.+.|.||+|++.++ ++|||.||+......+.| +...++.|+...+.-+++..+.
T Consensus 322 ~~l~~v~~~l~~kfepa~~~~~n~~~~V~ayd~~~y~~DVt~RY~d~~~s~~kritk~~fs~qy~~r~~~~l~~~k~~ 399 (650)
T COG5535 322 VRLYIVYSELKCKFEPAASIHLNIMEYVGAYDACVYVKDVTLRYRDQSYSFLKRITKHLFSVQYFVRQFPGLGKCKEA 399 (650)
T ss_pred chhhhhhhhhhheechhHHHHHHHHHHhhhhccCccchhHHHHHHHHHhhhhhhhhccchHHHHHHHHhcccCccccc
Confidence 84 33331 111222 1356899999999875 899999999976554432 2345889999999998876553
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=97.13 E-value=0.0019 Score=60.53 Aligned_cols=67 Identities=22% Similarity=0.352 Sum_probs=56.4
Q ss_pred cccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEe--CC---CeEEEEEEeCCCCCeEEeccCCCc
Q 011315 104 TRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILD--FT---DHVWTECFSQSLGRWMHLDPCEGI 172 (488)
Q Consensus 104 ~RFPRYn~p~~LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~--~~---dHvW~EVy~~~~~rWIhVDP~e~~ 172 (488)
...+++++|..+|..|+|.|++||.+..++|-.+|+..=+|+. .. .|+|+-|-.. +.|-.+|..--.
T Consensus 59 ~~~~~i~tp~etl~~k~GiC~DYA~Lta~lLl~~g~~~~yi~~~~~~~~~~Haa~aV~in--g~~yvlDq~~p~ 130 (153)
T PF04473_consen 59 KNSTYIQTPYETLKYKKGICGDYAILTAALLLNMGYSPVYILHIEFDNDPGHAAVAVKIN--GKYYVLDQHLPP 130 (153)
T ss_pred cccccccCHHHHHHcCCeeeHHHHHHHHHHHHHCCCCceEEEEEecCCCCCeEEEEEEEC--CEEEEEeCCCCC
Confidence 3456788999999999999999999999999999998877753 33 5999999987 479999987443
No 10
>COG5279 CYK3 Uncharacterized protein involved in cytokinesis, contains TGc (transglutaminase/protease-like) domain [Cell division and chromosome partitioning]
Probab=94.26 E-value=0.11 Score=57.03 Aligned_cols=63 Identities=24% Similarity=0.523 Sum_probs=53.4
Q ss_pred ccCCCCCHH----HHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeC------------CCeEEEEEEeCCCCCeEEecc
Q 011315 105 RFPRYNDPL----KLVETKRGRCGEWANCFTLYCRAFGYESRLILDF------------TDHVWTECFSQSLGRWMHLDP 168 (488)
Q Consensus 105 RFPRYn~p~----~LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~~------------~dHvW~EVy~~~~~rWIhVDP 168 (488)
+-|||.... -.+..+++.|--||.+|-+||.++|++|=+|.++ -.|+|.-|-..+ .|--||.
T Consensus 190 ~d~~ytt~l~~~r~~~I~heavCtgYa~lfK~lcn~lgIp~~iIegf~k~~~~~~~~~~iNHaWN~VkiD~--~yy~VDt 267 (521)
T COG5279 190 QDPRYTTVLAQMRSVLINHEAVCTGYAELFKELCNALGIPCEIIEGFLKSPIYYTRDININHAWNIVKIDN--EYYLVDT 267 (521)
T ss_pred CcchhhhhhhhhhhhhhhcccccchHHHHHHHHHHhcCCceEEEeecccccccccCCccccceeeEEEECC--eEEEEee
Confidence 447776544 2356789999999999999999999999999875 469999999986 6999999
Q ss_pred C
Q 011315 169 C 169 (488)
Q Consensus 169 ~ 169 (488)
+
T Consensus 268 T 268 (521)
T COG5279 268 T 268 (521)
T ss_pred e
Confidence 8
No 11
>PF13369 Transglut_core2: Transglutaminase-like superfamily
Probab=93.33 E-value=0.27 Score=45.21 Aligned_cols=58 Identities=22% Similarity=0.284 Sum_probs=48.4
Q ss_pred CCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeCCCeEEEEEEeCCCCCeEEeccCC
Q 011315 109 YNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCE 170 (488)
Q Consensus 109 Yn~p~~LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~~~dHvW~EVy~~~~~rWIhVDP~e 170 (488)
.....++|++|+|-|.--|.+|..++|.+|+++..| ++..|+.+-+-. + + -+=|||..
T Consensus 53 n~~l~~vL~~r~G~Pi~L~ily~~va~rlGl~~~~v-~~Pgh~l~r~~~-~-~-~~~iDpf~ 110 (152)
T PF13369_consen 53 NSFLHKVLERRRGIPISLAILYLEVARRLGLPAEPV-NFPGHFLVRVRS-D-G-EFYIDPFN 110 (152)
T ss_pred hhhHHHHHhcCCCCcHHHHHHHHHHHHHcCCeEEEE-ecCCEEEEEEec-C-C-cEEEccCC
Confidence 445689999999999999999999999999999876 477888777774 2 2 36899986
No 12
>PF14381 EDR1: Ethylene-responsive protein kinase Le-CTR1
Probab=92.03 E-value=0.26 Score=48.33 Aligned_cols=54 Identities=19% Similarity=0.221 Sum_probs=44.2
Q ss_pred HHHhCCccchhhHHHHHHHHHHcCCCeEEEEe-----C-CCeEEEEEEeCCCCCeEEeccC
Q 011315 115 LVETKRGRCGEWANCFTLYCRAFGYESRLILD-----F-TDHVWTECFSQSLGRWMHLDPC 169 (488)
Q Consensus 115 LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~-----~-~dHvW~EVy~~~~~rWIhVDP~ 169 (488)
|=.-+.|.|.|-|.||-.+|-++|+|+|+|-. + .+++|+.|-..+...+ =||-+
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 55678999999999999999999999999964 3 6789999988764444 35544
No 13
>PF14402 7TM_transglut: 7 transmembrane helices usually fused to an inactive transglutaminase
Probab=90.17 E-value=0.27 Score=51.11 Aligned_cols=48 Identities=21% Similarity=0.405 Sum_probs=39.9
Q ss_pred HHHHHHHHcCCCeEEEEe---------CCCeEEEEEEeCCCCCeEEeccCCCcCCCCee
Q 011315 129 CFTLYCRAFGYESRLILD---------FTDHVWTECFSQSLGRWMHLDPCEGIYDRPLL 178 (488)
Q Consensus 129 lF~~l~RalG~~aR~V~~---------~~dHvW~EVy~~~~~rWIhVDP~e~~iD~Pll 178 (488)
++..+++..|+|||.|.. ...+-|.|||+. ++|+.+||..+....|.-
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 356889999987 579999999988877743
No 14
>PF13471 Transglut_core3: Transglutaminase-like superfamily
Probab=88.88 E-value=0.69 Score=40.52 Aligned_cols=37 Identities=30% Similarity=0.608 Sum_probs=32.5
Q ss_pred CCccchhhHHHHHHHHHHcCCCeEEEEe-------CCCeEEEEE
Q 011315 119 KRGRCGEWANCFTLYCRAFGYESRLILD-------FTDHVWTEC 155 (488)
Q Consensus 119 R~GrCgE~A~lF~~l~RalG~~aR~V~~-------~~dHvW~EV 155 (488)
.+..|-+.|.....+||..|+++.+|+. +..|+|+|+
T Consensus 54 ~~~~CL~~ala~~~~L~~~gi~~~l~iGv~~~~~~~~aHAWve~ 97 (117)
T PF13471_consen 54 WRSKCLPRALALQRLLRRRGIPATLVIGVRKDDDPFAAHAWVEC 97 (117)
T ss_pred CCCChHHHHHHHHHHHHhcCCCcEEEEEEeeCCCCceEEEEEEE
Confidence 3569999999999999999999999974 467999993
No 15
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=87.57 E-value=0.44 Score=35.90 Aligned_cols=34 Identities=26% Similarity=0.607 Sum_probs=25.3
Q ss_pred cCeeecCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCc
Q 011315 56 TFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 102 (488)
Q Consensus 56 ~F~wv~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~ 102 (488)
+++|-+.+.|+.||+.....- ...-.|+|..|+.
T Consensus 12 ~~RW~~g~~CP~Cg~~~~~~~-------------~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 12 EIRWPDGFVCPHCGSTKHYRL-------------KTRGRYRCKACRK 45 (46)
T ss_pred HhcCCCCCCCCCCCCeeeEEe-------------CCCCeEECCCCCC
Confidence 468999999999999743321 1145799999985
No 16
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=87.16 E-value=0.31 Score=52.54 Aligned_cols=35 Identities=29% Similarity=0.549 Sum_probs=27.9
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccccCCCC
Q 011315 61 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 110 (488)
Q Consensus 61 ~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPRYn 110 (488)
.+|.|+.||..|.+.|. + -|+|++||...+-.++-
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 56999999999999873 2 59999999876655544
No 17
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=82.74 E-value=1.6 Score=45.00 Aligned_cols=54 Identities=31% Similarity=0.655 Sum_probs=39.1
Q ss_pred HHHHHHHHhhcc-CeeecCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccccCCCCCHHHHHHhCCc
Q 011315 45 FLLQLLFWFKQT-FRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRG 121 (488)
Q Consensus 45 ~l~~LL~wFK~~-F~wv~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~G 121 (488)
.-.+|++|.++. | |..||++|..... +. ...|++||+.. |||.. |.-+.-+++|
T Consensus 100 ~a~~l~~w~~~~RF-------Cg~CG~~~~~~~~------------g~--~~~C~~cg~~~-fPR~d-P~vIv~v~~~ 154 (279)
T COG2816 100 RAVQLLEWYRSHRF-------CGRCGTKTYPREG------------GW--ARVCPKCGHEH-FPRID-PCVIVAVIRG 154 (279)
T ss_pred HHHHHHHHHhhCcC-------CCCCCCcCccccC------------ce--eeeCCCCCCcc-CCCCC-CeEEEEEecC
Confidence 457899999864 5 9999999876521 11 35799999866 99975 5566666665
No 18
>PRK10941 hypothetical protein; Provisional
Probab=79.62 E-value=14 Score=37.79 Aligned_cols=60 Identities=12% Similarity=0.135 Sum_probs=46.7
Q ss_pred HHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeCCCeEEEEEEeCCCCCeEEeccCCCcC
Q 011315 112 PLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIY 173 (488)
Q Consensus 112 p~~LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~~~dHvW~EVy~~~~~rWIhVDP~e~~i 173 (488)
..++|++|+|-=.--|.+|+.++|.+|+|+.-| ++..|.=+-+=.+..+.| =+||++|.+
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 368999999999999999999999999999765 566666666543433345 589997654
No 19
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=72.49 E-value=3.9 Score=31.67 Aligned_cols=36 Identities=22% Similarity=0.400 Sum_probs=22.5
Q ss_pred CCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCccccc
Q 011315 64 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 106 (488)
Q Consensus 64 ~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RF 106 (488)
||+.||+....+..+. ..-+....|.|..||....+
T Consensus 3 PCPfCGg~~~~~~~~~-------~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGF-------DPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEecc-------CCCCCEEEEECCCCCCCccc
Confidence 6999999766332110 01133445699999998765
No 20
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=72.15 E-value=2.9 Score=30.68 Aligned_cols=28 Identities=29% Similarity=0.583 Sum_probs=20.2
Q ss_pred CCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 64 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 64 ~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
.||.|+........ +.|+++.|.+|+-.
T Consensus 1 ~CP~C~~~l~~~~~------------~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRL------------GDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEE------------CCEEEEECCCCCeE
Confidence 48899886543321 45999999999864
No 21
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=69.74 E-value=4.1 Score=33.64 Aligned_cols=32 Identities=22% Similarity=0.391 Sum_probs=23.8
Q ss_pred CCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 62 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 62 ~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
--|||.||.++..+.. .+..+...|.+|+...
T Consensus 6 lKPCPFCG~~~~~v~~-----------~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 6 VKPCPFCGCPSVTVKA-----------ISGYYRAKCNGCESRT 37 (64)
T ss_pred ccCCCCCCCceeEEEe-----------cCceEEEEcCCCCcCc
Confidence 3469999998776652 1446678899999865
No 22
>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=68.96 E-value=4.3 Score=39.13 Aligned_cols=24 Identities=17% Similarity=0.299 Sum_probs=19.6
Q ss_pred HhCCccchhhHHHHHHHHHHcCCC
Q 011315 117 ETKRGRCGEWANCFTLYCRAFGYE 140 (488)
Q Consensus 117 ~tR~GrCgE~A~lF~~l~RalG~~ 140 (488)
.++.|.|.+||.+=.+.|+++|++
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 23
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=68.52 E-value=7.4 Score=39.20 Aligned_cols=47 Identities=19% Similarity=0.451 Sum_probs=31.9
Q ss_pred HHHHHHHHhhccCeeecCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccccCCCCCH
Q 011315 45 FLLQLLFWFKQTFRWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 112 (488)
Q Consensus 45 ~l~~LL~wFK~~F~wv~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPRYn~p 112 (488)
...+|++|.++. ++ |+.||+++.... +... -.|..|+. .-|||....
T Consensus 88 ~a~~l~~w~~~~-~f-----C~~CG~~~~~~~-------------~~~~-~~C~~c~~-~~yp~~~pa 134 (256)
T PRK00241 88 RAVQLAEFYRSH-RF-----CGYCGHPMHPSK-------------TEWA-MLCPHCRE-RYYPRIAPC 134 (256)
T ss_pred HHHHHHHHhhcC-cc-----ccccCCCCeecC-------------Ccee-EECCCCCC-EECCCCCCE
Confidence 457889998763 22 999999876531 1222 46999985 569997654
No 24
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=65.06 E-value=5 Score=37.99 Aligned_cols=33 Identities=21% Similarity=0.432 Sum_probs=20.1
Q ss_pred CCCCCCCCc-cccCCCCCChhhhhcCCceE-EEeecCCCCc
Q 011315 64 PCDGCSNET-VGQGMGTPLPSEIQYGAARV-ELFRCKVCSK 102 (488)
Q Consensus 64 ~C~~Cg~~t-~~~g~~~Pt~eE~~~ga~rV-E~y~C~~C~~ 102 (488)
.||.||++. ..... .+. ..| ..| ..|+|+.||.
T Consensus 2 ~cp~c~~~~~~~~~s-~~~----~~~-~~~~~~~~c~~c~~ 36 (154)
T PRK00464 2 RCPFCGHPDTRVIDS-RPA----EDG-NAIRRRRECLACGK 36 (154)
T ss_pred cCCCCCCCCCEeEec-ccc----CCC-CceeeeeeccccCC
Confidence 599999975 43321 111 112 234 4699999997
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=61.31 E-value=7.9 Score=37.41 Aligned_cols=68 Identities=25% Similarity=0.319 Sum_probs=44.4
Q ss_pred HHHH-HhCCccchhhHHHHHHHHHHcCCCeEEEEe------------CCCeEEEEEEeCCCCCeEEeccCCCc--CCCCe
Q 011315 113 LKLV-ETKRGRCGEWANCFTLYCRAFGYESRLILD------------FTDHVWTECFSQSLGRWMHLDPCEGI--YDRPL 177 (488)
Q Consensus 113 ~~LL-~tR~GrCgE~A~lF~~l~RalG~~aR~V~~------------~~dHvW~EVy~~~~~rWIhVDP~e~~--iD~Pl 177 (488)
.+++ +.|-|.|-|-..+|..+++++|++++++.. ...|.=.=|-.++ ++| =||+.-|. .-.|+
T Consensus 38 ~kiv~~~rGG~C~elN~lf~~lL~~lGf~v~~~~arv~~~~~~~~~~~~~H~~liV~~~~-~~y-lvDvGfG~~~~~~Pl 115 (240)
T PF00797_consen 38 DKIVRRGRGGYCFELNGLFYWLLRELGFDVTLVSARVYSPGGPDYWPPRTHLVLIVTLDG-ERY-LVDVGFGGPSPREPL 115 (240)
T ss_dssp HHHTTTT--B-HHHHHHHHHHHHHHCT-EEEEEEEEEETTTTTCCSSSEEEEEEEEEETT-EEE-EE-SSSTTC--SS-E
T ss_pred HHHHhcCCCeEhHHHHHHHHHHHHHCCCeEEEEEEEEEeCCCCCCCCCCceEEEEEEECC-EEE-EEeccCCCcCcccce
Confidence 3555 667789999999999999999999998841 1257766677765 357 68887654 35666
Q ss_pred eeecC
Q 011315 178 LYEKG 182 (488)
Q Consensus 178 lye~g 182 (488)
....+
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
>PHA02998 RNA polymerase subunit; Provisional
Probab=58.56 E-value=7.8 Score=38.00 Aligned_cols=45 Identities=22% Similarity=0.520 Sum_probs=30.3
Q ss_pred CCCCCCCCCcc-ccCCCCCChhhhhcCCceEEEeecCCCCcccccCCCCCH
Q 011315 63 PPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 112 (488)
Q Consensus 63 P~C~~Cg~~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPRYn~p 112 (488)
-+|+.||+... ..-...=++|| ...=-|+|..||...+=|||-+.
T Consensus 144 v~CPkCg~~~A~f~qlQTRSADE-----PmT~FYkC~~CG~~wkppkf~~~ 189 (195)
T PHA02998 144 TPCPNCKSKNTTPMMIQTRAADE-----PPLVRHACRDCKKHFKPPKFRDK 189 (195)
T ss_pred CCCCCCCCCceEEEEEeeccCCC-----CceEEEEcCCCCCccCCcccccc
Confidence 56999998632 22222223333 34557999999999999998765
No 27
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=57.41 E-value=41 Score=35.37 Aligned_cols=50 Identities=16% Similarity=0.269 Sum_probs=32.9
Q ss_pred eecCCCCCCCCCCcc-ccCCCCCChhhhhcCCceEEEeecCCCCcccccCCCCCHHHHHHhCCccchh
Q 011315 59 WVNAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGE 125 (488)
Q Consensus 59 wv~~P~C~~Cg~~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~GrCgE 125 (488)
|-+..-|+.||+.-. .+-. ..+....--..|..|++.-+|+|. +.-.||+
T Consensus 184 ~~~~~~CPvCGs~P~~s~v~--------~~~~~G~RyL~CslC~teW~~~R~---------~C~~Cg~ 234 (309)
T PRK03564 184 GEQRQFCPVCGSMPVSSVVQ--------IGTTQGLRYLHCNLCESEWHVVRV---------KCSNCEQ 234 (309)
T ss_pred ccCCCCCCCCCCcchhheee--------ccCCCCceEEEcCCCCCcccccCc---------cCCCCCC
Confidence 457788999999643 2100 011233456789999999999984 4566764
No 28
>PF14353 CpXC: CpXC protein
Probab=57.05 E-value=6.5 Score=35.01 Aligned_cols=41 Identities=20% Similarity=0.262 Sum_probs=24.9
Q ss_pred CCCCCCCCCccc-----c-CCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 63 PPCDGCSNETVG-----Q-GMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 63 P~C~~Cg~~t~~-----~-g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
-.|+.||.+... + ....|-.-|.-- .+..=.|.|++||+..
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il-~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKIL-DGSLFSFTCPSCGHKF 48 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHH-cCCcCEEECCCCCCce
Confidence 369999987431 1 222332233222 4566789999999876
No 29
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=56.95 E-value=6.4 Score=46.77 Aligned_cols=31 Identities=26% Similarity=0.664 Sum_probs=25.1
Q ss_pred eeecCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 58 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 58 ~wv~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
.-++.|+|+.||+.+...|. -|.|..||..+
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 45799999999987777664 38999999864
No 30
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=55.90 E-value=14 Score=28.80 Aligned_cols=13 Identities=31% Similarity=0.577 Sum_probs=9.7
Q ss_pred CCCCCCCCCcccc
Q 011315 63 PPCDGCSNETVGQ 75 (488)
Q Consensus 63 P~C~~Cg~~t~~~ 75 (488)
.||+.||......
T Consensus 4 kPCPFCG~~~~~~ 16 (61)
T PF14354_consen 4 KPCPFCGSADVLI 16 (61)
T ss_pred cCCCCCCCcceEe
Confidence 4699998876644
No 31
>PRK15047 N-hydroxyarylamine O-acetyltransferase; Provisional
Probab=55.81 E-value=42 Score=34.44 Aligned_cols=65 Identities=25% Similarity=0.338 Sum_probs=45.9
Q ss_pred HHH-HhCCccchhhHHHHHHHHHHcCCCeEEE-----Ee------CCCeEEEEEEeCCCCCeEEeccCCC--cCCCCeee
Q 011315 114 KLV-ETKRGRCGEWANCFTLYCRAFGYESRLI-----LD------FTDHVWTECFSQSLGRWMHLDPCEG--IYDRPLLY 179 (488)
Q Consensus 114 ~LL-~tR~GrCgE~A~lF~~l~RalG~~aR~V-----~~------~~dHvW~EVy~~~~~rWIhVDP~e~--~iD~Plly 179 (488)
||+ +.|-|.|-|-..+|..++|++||+++.+ ++ ...|.=.=|..++ ++| =||.--| ..-.|+..
T Consensus 59 KlV~~~RGGyCfE~N~Lf~~~L~~LGF~v~~~~arV~~~~~~~~~~~tH~~l~V~i~~-~~y-LvDVGFG~~~~~~Pl~L 136 (281)
T PRK15047 59 KLVIARRGGYCFEQNGLFERVLRELGFNVRSLLGRVVLSNPPALPPRTHRLLLVELEG-EKW-IADVGFGGQTLTAPIRL 136 (281)
T ss_pred HHhcCCCCEEcHhHHHHHHHHHHHcCCcEEEEEEEEEecCCCCCCCcCcEEEEEEECC-eeE-EEEecCCCCCCCccEEC
Confidence 555 4577899999999999999999997765 22 1247777777765 457 5777655 34566655
Q ss_pred e
Q 011315 180 E 180 (488)
Q Consensus 180 e 180 (488)
+
T Consensus 137 ~ 137 (281)
T PRK15047 137 V 137 (281)
T ss_pred C
Confidence 4
No 32
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=54.47 E-value=11 Score=34.31 Aligned_cols=27 Identities=19% Similarity=0.393 Sum_probs=17.6
Q ss_pred ccceEEeecCC-c-ceechhhhccChHHh
Q 011315 186 KLNYVIAISKD-G-VFDVTKRYTRKWHEV 212 (488)
Q Consensus 186 klsYVIAFs~D-G-v~DVTrRYt~~~~~~ 212 (488)
.+.+|..|=.. | ++||.+-|--.|..+
T Consensus 38 ~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTv 66 (113)
T PF09862_consen 38 QLEFIKLFIKNRGNLKEMEKELGISYPTV 66 (113)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHCCCcHHH
Confidence 34555566432 3 788888888888754
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=52.20 E-value=9.5 Score=34.52 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=20.0
Q ss_pred CCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCc
Q 011315 62 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 102 (488)
Q Consensus 62 ~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~ 102 (488)
-|+|+.|+++-.+... ++|-|+.|++
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 3689999987
No 34
>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=51.98 E-value=5.1 Score=28.41 Aligned_cols=27 Identities=33% Similarity=0.710 Sum_probs=12.9
Q ss_pred CCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 62 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 62 ~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
-|+|+.|+++..... | ++|-|+.|+..
T Consensus 2 ~p~Cp~C~se~~y~D-----------~----~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYTYED-----------G----ELLVCPECGHE 28 (30)
T ss_dssp S---TTT-----EE------------S----SSEEETTTTEE
T ss_pred CCCCCCCCCcceecc-----------C----CEEeCCccccc
Confidence 389999999876642 1 25889999864
No 35
>PRK10220 hypothetical protein; Provisional
Probab=48.98 E-value=12 Score=33.89 Aligned_cols=29 Identities=21% Similarity=0.543 Sum_probs=21.5
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 61 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 61 ~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
+-|+|+.|+++-.+... ++|-|+.|++.-
T Consensus 2 ~lP~CP~C~seytY~d~---------------~~~vCpeC~hEW 30 (111)
T PRK10220 2 SLPHCPKCNSEYTYEDN---------------GMYICPECAHEW 30 (111)
T ss_pred CCCcCCCCCCcceEcCC---------------CeEECCcccCcC
Confidence 56999999998665421 268999999743
No 36
>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=48.85 E-value=9.8 Score=28.13 Aligned_cols=14 Identities=29% Similarity=0.956 Sum_probs=9.0
Q ss_pred eEEEeecCCCCccc
Q 011315 91 RVELFRCKVCSKIT 104 (488)
Q Consensus 91 rVE~y~C~~C~~~~ 104 (488)
.-|.|+|..||.++
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 45899999999876
No 37
>COG3672 Predicted transglutaminase-like cysteine proteinase [General function prediction only]
Probab=46.39 E-value=52 Score=32.57 Aligned_cols=23 Identities=22% Similarity=0.200 Sum_probs=21.5
Q ss_pred hCCccchhhHHHHHHHHHHcCCC
Q 011315 118 TKRGRCGEWANCFTLYCRAFGYE 140 (488)
Q Consensus 118 tR~GrCgE~A~lF~~l~RalG~~ 140 (488)
+..|.|++||..=-.-+..+|++
T Consensus 105 ~~~GDCEDyal~KRr~L~~~G~s 127 (191)
T COG3672 105 TGAGDCEDYALEKRRRLMEAGVS 127 (191)
T ss_pred CCcccHHHHHHHHHHHHHHcCCC
Confidence 89999999999988889999987
No 38
>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=45.69 E-value=20 Score=26.29 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=20.6
Q ss_pred CCCCCCCCCccc--cCCCCCChhhhhcCCceEEEeecCCCC
Q 011315 63 PPCDGCSNETVG--QGMGTPLPSEIQYGAARVELFRCKVCS 101 (488)
Q Consensus 63 P~C~~Cg~~t~~--~g~~~Pt~eE~~~ga~rVE~y~C~~C~ 101 (488)
..|+.|++.... .|. +...-..|+|..|.
T Consensus 6 v~CP~C~s~~~v~k~G~----------~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTEGVKKNGK----------SPSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCCcceeCCC----------CCCCCEeEecCcCC
Confidence 569999997632 343 24667889999994
No 39
>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=44.79 E-value=10 Score=34.61 Aligned_cols=44 Identities=20% Similarity=0.332 Sum_probs=28.8
Q ss_pred HHHHhhccC--eeecCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccccCC
Q 011315 49 LLFWFKQTF--RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 108 (488)
Q Consensus 49 LL~wFK~~F--~wv~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPR 108 (488)
..-||-=.+ +-.-.-.||.|+..|...| ++ ..|-.|++.....|
T Consensus 54 ~~VYfwIGmlStkav~V~CP~C~K~TKmLG--------------r~--D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 54 TAVYFWIGMLSTKAVQVECPNCGKQTKMLG--------------RV--DACMHCKEPLTLDP 99 (114)
T ss_pred HHHHHHhhhhcccceeeECCCCCChHhhhc--------------hh--hccCcCCCcCccCc
Confidence 334554332 2233456999999999997 33 38999998764443
No 40
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=44.57 E-value=39 Score=32.69 Aligned_cols=108 Identities=20% Similarity=0.238 Sum_probs=56.6
Q ss_pred CCCHHHHHHHhc--cCChHH---HHHHHHHHHHHcCCC---CCCCchhHHHHHHHHHHHhhccCeeec--CCCCCCCCCC
Q 011315 2 YEDPIRQEAAKK--TVPVER---LEEKSLVSLAREGNF---KPSKTEQDHAFLLQLLFWFKQTFRWVN--APPCDGCSNE 71 (488)
Q Consensus 2 YEd~~lq~~Al~--~IPl~~---L~~~a~~~l~~~g~~---~~~~~~~~~~~l~~LL~wFK~~F~wv~--~P~C~~Cg~~ 71 (488)
++|+..+..|.. .|=|.+ |+.++ + .|-. -++.. ....+.+++.-|.-.+ |+. .-.|+.|+++
T Consensus 35 ~~d~~i~~i~~~e~rIllTRDr~L~~r~-k----~g~~~i~i~~~s--~~~Ql~e~~~~~~l~~-~~~~e~~RCp~CN~~ 106 (165)
T COG1656 35 ESDDEIILIAKKEGRILLTRDRELYKRA-K----LGIKAILIRSDS--IEEQLAEFLARLGLKP-RLFPEFSRCPECNGE 106 (165)
T ss_pred CCcHHHHHHHhcCCeEEEeccHHHHHHh-h----ccCceEEEeCCC--HHHHHHHHHHHhccch-hcccccccCcccCCE
Confidence 567777777777 443433 44444 2 2211 01111 1123555555454443 432 3469999986
Q ss_pred ccccCCCCCChhhhh------cCCceEEEeecCCCCcccccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcC
Q 011315 72 TVGQGMGTPLPSEIQ------YGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFG 138 (488)
Q Consensus 72 t~~~g~~~Pt~eE~~------~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~GrCgE~A~lF~~l~RalG 138 (488)
-..+ +.+|.. .--.--|.|+|+.||+.- =+| +||.+.--.+.+++.
T Consensus 107 L~~v-----s~eev~~~Vp~~~~~~~~~f~~C~~CgkiY--------------W~G--sHw~~m~~~~~~~~~ 158 (165)
T COG1656 107 LEKV-----SREEVKEKVPEKVYRNYEEFYRCPKCGKIY--------------WKG--SHWRRMVERIVENLR 158 (165)
T ss_pred eccC-----cHHHHhhccchhhhhcccceeECCCCcccc--------------cCc--hHHHHHHHHHHHHhc
Confidence 4332 112211 112345789999999864 234 377777666666554
No 41
>COG2162 NhoA Arylamine N-acetyltransferase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=43.61 E-value=49 Score=34.36 Aligned_cols=64 Identities=20% Similarity=0.367 Sum_probs=43.9
Q ss_pred HHHhCCccchhhHHHHHHHHHHcCCCeE-----EEEeC-------CCeEEEEEEeCCCCCeEEeccCCC--cCCCCeeee
Q 011315 115 LVETKRGRCGEWANCFTLYCRAFGYESR-----LILDF-------TDHVWTECFSQSLGRWMHLDPCEG--IYDRPLLYE 180 (488)
Q Consensus 115 LL~tR~GrCgE~A~lF~~l~RalG~~aR-----~V~~~-------~dHvW~EVy~~~~~rWIhVDP~e~--~iD~Pllye 180 (488)
++..|-|.|-|--.+|..+++++||++| ++|.. ..|.=.-|..++. -|+ +|.-.| ..-.|+-.+
T Consensus 62 v~~rRGGyCfElNglf~~vL~~lGF~v~~l~arV~~g~~~~a~~~~tH~~L~v~~~~~-~~l-~DvGFGg~~l~APlrL~ 139 (275)
T COG2162 62 VLARRGGYCFELNGLFGRVLRELGFNVRLLLARVVWGLAPDALPPRTHRLLLVELEGE-TWL-ADVGFGGQTLTAPIRLE 139 (275)
T ss_pred HhccccceehhhhhHHHHHHHHcCCcceeeEEEEEecCCCCCCCcccceEEEEEecCc-eeE-EecCCCCCCcCCCcccC
Confidence 3456778999999999999999999854 55643 3687777777764 473 565544 333355544
No 42
>PHA00626 hypothetical protein
Probab=42.23 E-value=15 Score=29.98 Aligned_cols=29 Identities=14% Similarity=0.433 Sum_probs=18.7
Q ss_pred CCCCCCCCcccc-CCCCCChhhhhcCCceEEEeecCCCCc
Q 011315 64 PCDGCSNETVGQ-GMGTPLPSEIQYGAARVELFRCKVCSK 102 (488)
Q Consensus 64 ~C~~Cg~~t~~~-g~~~Pt~eE~~~ga~rVE~y~C~~C~~ 102 (488)
.||.||+.++.. |... ...-.|.|+.||-
T Consensus 2 ~CP~CGS~~Ivrcg~cr----------~~snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR----------GWSDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCceeeeeceec----------ccCcceEcCCCCC
Confidence 499999965532 3210 1134699999995
No 43
>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=40.70 E-value=1.1e+02 Score=30.38 Aligned_cols=135 Identities=18% Similarity=0.260 Sum_probs=66.3
Q ss_pred CCCCCCCcccc--CCCCC---ChhhhhcCCceEEEeecCCCCcccccCCCCCHHHHHHhCCccchhhHHHHHHHHHHcCC
Q 011315 65 CDGCSNETVGQ--GMGTP---LPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAFGY 139 (488)
Q Consensus 65 C~~Cg~~t~~~--g~~~P---t~eE~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~GrCgE~A~lF~~l~RalG~ 139 (488)
|+.||.++... |+... ..-++..=...+++..|+.||+.-.=-++.++ +.+ ..-+.|+-.+-+.+.-
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 43211 00011112356899999999985432366655 110 1112222222222221
Q ss_pred CeEEEEeCCCeEEEEEEeCCCCCeEEeccCCCcCC-CCeeeecCccCccceEEeecC--CcceechhhhccChHHhhhhc
Q 011315 140 ESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYD-RPLLYEKGWNKKLNYVIAISK--DGVFDVTKRYTRKWHEVLSRR 216 (488)
Q Consensus 140 ~aR~V~~~~dHvW~EVy~~~~~rWIhVDP~e~~iD-~Pllye~gwgKklsYVIAFs~--DGv~DVTrRYt~~~~~~~~RR 216 (488)
...+......+|+|..+. .-.++|.-...+.+ .|+ ..+|.+-|.- .-+-|=+++....|..+++-|
T Consensus 73 -~~~~~~d~~~v~~e~~~~--r~~v~v~v~~~v~~~~~~--------~~~~~v~~~v~~~~C~~C~r~~~~~~eaiVQvR 141 (236)
T PF04981_consen 73 -NIKVHVDAEFVWTEPHSK--RIKVKVTVQGEVHGGTPV--------EQEYEVEVRVKRQQCPDCSRIAGGYYEAIVQVR 141 (236)
T ss_pred -hhcccccccEEEEEeeCC--EEEEEEEEEEEEcccceE--------EEEEEEEEEEEcCCChhHHhhhCCCccEEEEEE
Confidence 111233455678888332 23555554433333 333 2345555553 335577777766777777777
Q ss_pred cc
Q 011315 217 NI 218 (488)
Q Consensus 217 ~r 218 (488)
..
T Consensus 142 ~~ 143 (236)
T PF04981_consen 142 QR 143 (236)
T ss_pred ec
Confidence 55
No 44
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=40.32 E-value=26 Score=25.93 Aligned_cols=35 Identities=23% Similarity=0.497 Sum_probs=21.1
Q ss_pred CCCCCCCCcc-ccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 64 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 64 ~C~~Cg~~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
+|+.||+... ..-...=++|| ...=-|.|..|+..
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 22211112333 44567999999974
No 45
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.96 E-value=17 Score=29.81 Aligned_cols=10 Identities=40% Similarity=1.125 Sum_probs=7.2
Q ss_pred CCCCCCCCCC
Q 011315 62 APPCDGCSNE 71 (488)
Q Consensus 62 ~P~C~~Cg~~ 71 (488)
.|.|.+||..
T Consensus 9 ~~~CtSCg~~ 18 (61)
T COG2888 9 PPVCTSCGRE 18 (61)
T ss_pred CceeccCCCE
Confidence 5678888765
No 46
>PRK02935 hypothetical protein; Provisional
Probab=39.84 E-value=20 Score=32.45 Aligned_cols=44 Identities=20% Similarity=0.394 Sum_probs=28.7
Q ss_pred HHHHHhhcc-C-eeecCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccccC
Q 011315 48 QLLFWFKQT-F-RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFP 107 (488)
Q Consensus 48 ~LL~wFK~~-F-~wv~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFP 107 (488)
...-||--- . +-.-+-.||.|+..|...| ||+ .|-.|++...-+
T Consensus 54 S~vvYFwiGmlStkavqV~CP~C~K~TKmLG--------------rvD--~CM~C~~PLTLd 99 (110)
T PRK02935 54 STVVYFWIGMLSTKAVQVICPSCEKPTKMLG--------------RVD--ACMHCNQPLTLD 99 (110)
T ss_pred HHHHHHHHhhhcccceeeECCCCCchhhhcc--------------cee--ecCcCCCcCCcC
Confidence 344455432 1 2233456999999999997 343 799999876543
No 47
>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=39.76 E-value=21 Score=26.37 Aligned_cols=38 Identities=16% Similarity=0.407 Sum_probs=22.1
Q ss_pred CCCCCCCCCccccCCCCCChhhhhc-------CCceEEEeecCCCC
Q 011315 63 PPCDGCSNETVGQGMGTPLPSEIQY-------GAARVELFRCKVCS 101 (488)
Q Consensus 63 P~C~~Cg~~t~~~g~~~Pt~eE~~~-------ga~rVE~y~C~~C~ 101 (488)
.-|+.||+....+|.. ...+++.. --.+...|.|..|+
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 4599999987655532 01222221 12455678899886
No 48
>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=39.06 E-value=40 Score=30.96 Aligned_cols=50 Identities=28% Similarity=0.489 Sum_probs=38.3
Q ss_pred hccHHHHHHhhccccccCC----------CCCeEEEecCCCccccchhhHhHHHHHHHHH
Q 011315 377 LPSIGHLLRVLSLKSELNT----------DGRVDIVLAGDPVKTSLSLPVVFKALDDMIH 426 (488)
Q Consensus 377 lps~~~ll~~lslk~~~~~----------~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~ 426 (488)
||-++..+..+++|.--.. +|+..++|-|+|+.+..++=+++++|+.++.
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 4556778888888864322 6889999999999887777678888877765
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=38.37 E-value=35 Score=35.75 Aligned_cols=14 Identities=14% Similarity=0.365 Sum_probs=9.8
Q ss_pred eEEEeecCCCCccc
Q 011315 91 RVELFRCKVCSKIT 104 (488)
Q Consensus 91 rVE~y~C~~C~~~~ 104 (488)
.+.++.|..|+...
T Consensus 249 ~~r~e~C~~C~~Yl 262 (305)
T TIGR01562 249 VLKAETCDSCQGYL 262 (305)
T ss_pred ceEEeeccccccch
Confidence 45556788888765
No 50
>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=38.34 E-value=50 Score=30.40 Aligned_cols=54 Identities=22% Similarity=0.362 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhccCeeec--CCCCCCCCCCcccc------CCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 44 AFLLQLLFWFKQTFRWVN--APPCDGCSNETVGQ------GMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 44 ~~l~~LL~wFK~~F~wv~--~P~C~~Cg~~t~~~------g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
..|.++++-|.=.+ +.+ --.|+.|++.-..+ +..+|..- ...-+-|+|+.||++
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 45778888775333 222 23799999864322 22222211 123358999999985
No 51
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=38.24 E-value=39 Score=29.86 Aligned_cols=17 Identities=53% Similarity=0.993 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHhhccCeeecCCCC
Q 011315 42 DHAFLLQLLFWFKQTFRWVNAPPC 65 (488)
Q Consensus 42 ~~~~l~~LL~wFK~~F~wv~~P~C 65 (488)
...++++||+|| |-|++
T Consensus 28 ~~~Ll~~LleWF-------nf~~~ 44 (98)
T PF14726_consen 28 ERLLLKQLLEWF-------NFPPV 44 (98)
T ss_pred HHHHHHHHHHHh-------CCCCC
Confidence 456899999999 55665
No 52
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=38.12 E-value=17 Score=26.39 Aligned_cols=29 Identities=24% Similarity=0.505 Sum_probs=14.4
Q ss_pred CCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 65 CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 65 C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
|+.||++.... -|.. +.-|.+.|+.||.+
T Consensus 3 C~~CG~~l~~~---ip~g-------d~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERR---IPEG-------DDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE-----TT--------SS-EEEETTTTEE
T ss_pred cccccChhhhh---cCCC-------CCccceECCCCCCE
Confidence 89999985432 0111 33477899999975
No 53
>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=37.53 E-value=21 Score=26.27 Aligned_cols=35 Identities=17% Similarity=0.356 Sum_probs=18.6
Q ss_pred CCCCCCCCcc-ccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 64 PCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 64 ~C~~Cg~~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
+|+.||+... ..-...=.+|| ...=.|.|..||+.
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 22111112233 45667999999974
No 54
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=37.13 E-value=17 Score=29.66 Aligned_cols=24 Identities=25% Similarity=0.715 Sum_probs=20.1
Q ss_pred HHhhccCeeecCCCCCCCCCCccc
Q 011315 51 FWFKQTFRWVNAPPCDGCSNETVG 74 (488)
Q Consensus 51 ~wFK~~F~wv~~P~C~~Cg~~t~~ 74 (488)
-|-+.+|+.-..|.|+-|++++..
T Consensus 28 gWmR~nFs~~~~p~CPlC~s~M~~ 51 (59)
T PF14169_consen 28 GWMRDNFSFEEEPVCPLCKSPMVS 51 (59)
T ss_pred cccccccccCCCccCCCcCCcccc
Confidence 477777999999999999998763
No 55
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=36.92 E-value=24 Score=30.98 Aligned_cols=30 Identities=20% Similarity=0.523 Sum_probs=21.4
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 61 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 61 ~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
..+.|+.|+..++.- ..+-+.+|.+||...
T Consensus 34 ~~~~Cp~C~~~~VkR--------------~a~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRTTVKR--------------IATGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCcceee--------------eccCeEEcCCCCCee
Confidence 567899999985532 122378999999754
No 56
>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=36.77 E-value=26 Score=32.88 Aligned_cols=71 Identities=17% Similarity=0.236 Sum_probs=50.4
Q ss_pred ccccCCCCchhHHHHhh----hccHHHHHHhhcccc-c---------cC-CCCCeEEEecCCCccccchh-hHhHHHHHH
Q 011315 360 VSLNSVPNNGQKIVHQL----LPSIGHLLRVLSLKS-E---------LN-TDGRVDIVLAGDPVKTSLSL-PVVFKALDD 423 (488)
Q Consensus 360 ~~~~~~~~~~~~~~~~~----lps~~~ll~~lslk~-~---------~~-~~g~~~~~~~~~p~~tsl~l-~~~~~~~~~ 423 (488)
++....+-+ .+++.++ +|-++.++..+++|. - ++ .+|..-++|-|+|+....++ -.+..+|+.
T Consensus 73 tg~g~~D~t-~eal~~l~~~~l~G~~~~~~~i~~~p~G~~~~lsr~~~g~~~~~~v~~LPG~P~aa~~~~~~~v~P~l~~ 151 (163)
T TIGR02667 73 TGFTGRDVT-PEALEPLFDKTVEGFGELFRQLSYEEIGTSTIQSRALAGLANGTFVFCLPGSTGACRTAWDKIIAAQLDA 151 (163)
T ss_pred cCCCCCCCc-HHHHHHHHCCcCCcHHHHHHHHhhcccCHHHHHhhhhheeeCCeEEEECCCCHHHHHHHHHHHHHHHHHH
Confidence 444444434 2344444 777889999999986 2 22 25679999999999998888 568888888
Q ss_pred HHHhcccC
Q 011315 424 MIHDLNNC 431 (488)
Q Consensus 424 ~~~~~~~~ 431 (488)
+++..++-
T Consensus 152 ~~~~~~~~ 159 (163)
T TIGR02667 152 RHRPCNFV 159 (163)
T ss_pred Hhcccccc
Confidence 87777663
No 57
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=36.64 E-value=28 Score=23.71 Aligned_cols=9 Identities=33% Similarity=0.781 Sum_probs=7.3
Q ss_pred EeecCCCCc
Q 011315 94 LFRCKVCSK 102 (488)
Q Consensus 94 ~y~C~~C~~ 102 (488)
.|.|++||.
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 499999983
No 58
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=35.36 E-value=23 Score=28.15 Aligned_cols=29 Identities=14% Similarity=0.371 Sum_probs=20.4
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 61 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 61 ~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
.++.|++||..+.+. .--+.|.|..||-.
T Consensus 18 k~~~CPrCG~gvfmA--------------~H~dR~~CGkCgyT 46 (51)
T COG1998 18 KNRFCPRCGPGVFMA--------------DHKDRWACGKCGYT 46 (51)
T ss_pred ccccCCCCCCcchhh--------------hcCceeEeccccce
Confidence 457799999866554 22347889999853
No 59
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.27 E-value=21 Score=30.98 Aligned_cols=28 Identities=29% Similarity=0.453 Sum_probs=22.5
Q ss_pred CCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 64 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 64 ~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
-|+.|+.+..+.. -+.||+=.|+.|+.+
T Consensus 3 lCP~C~v~l~~~~------------rs~vEiD~CPrCrGV 30 (88)
T COG3809 3 LCPICGVELVMSV------------RSGVEIDYCPRCRGV 30 (88)
T ss_pred ccCcCCceeeeee------------ecCceeeeCCccccE
Confidence 4999999877653 378999999999864
No 60
>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=34.90 E-value=30 Score=36.08 Aligned_cols=44 Identities=16% Similarity=0.337 Sum_probs=28.1
Q ss_pred eeecCCCCCCCCCC-ccccCCCCCChhhhhcCCceEEEeecCCCCccccc
Q 011315 58 RWVNAPPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRF 106 (488)
Q Consensus 58 ~wv~~P~C~~Cg~~-t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RF 106 (488)
+=++.-+|+.||+. +.+.-...=++|| ...=-|.|..||+.-+|
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDE-----pmT~f~~C~~Cg~~w~f 298 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADE-----PMTTFVTCEECGNRWKF 298 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCC-----CCeEEEEcCCCCCeeee
Confidence 44677899999985 3332222223333 33447899999998777
No 61
>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=34.66 E-value=17 Score=36.97 Aligned_cols=44 Identities=23% Similarity=0.497 Sum_probs=19.2
Q ss_pred eeecCCCCCCCCCCccccCCCCCChhhhhcCC-ceEEEeecCCCCcccccCCCC
Q 011315 58 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGA-ARVELFRCKVCSKITRFPRYN 110 (488)
Q Consensus 58 ~wv~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga-~rVE~y~C~~C~~~~RFPRYn 110 (488)
.| +..-|+.||+.-...- +..+. ..---..|..|++.-+|+|..
T Consensus 169 ~w-~~g~CPvCGs~P~~s~--------l~~~~~~G~R~L~Cs~C~t~W~~~R~~ 213 (290)
T PF04216_consen 169 GW-QRGYCPVCGSPPVLSV--------LRGGEREGKRYLHCSLCGTEWRFVRIK 213 (290)
T ss_dssp -T-T-SS-TTT---EEEEE--------EE------EEEEEETTT--EEE--TTS
T ss_pred Cc-cCCcCCCCCCcCceEE--------EecCCCCccEEEEcCCCCCeeeecCCC
Confidence 45 4578999999643211 00111 123567899999999999954
No 62
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=33.82 E-value=34 Score=30.75 Aligned_cols=40 Identities=18% Similarity=0.379 Sum_probs=25.8
Q ss_pred CCCCCCCCCCcccc-CCCCCChhhhhcCCceEEEeecCCCCccccc
Q 011315 62 APPCDGCSNETVGQ-GMGTPLPSEIQYGAARVELFRCKVCSKITRF 106 (488)
Q Consensus 62 ~P~C~~Cg~~t~~~-g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RF 106 (488)
...|+.||+..... -...=.+ +-.-+.-|+|..||..-||
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsa-----DEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSA-----DEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEeeehhcc-----CCCceEEEEecccCCEeec
Confidence 45699999975422 1111122 2367788999999987665
No 63
>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=33.60 E-value=40 Score=31.53 Aligned_cols=41 Identities=15% Similarity=0.225 Sum_probs=30.6
Q ss_pred HhCCccchhhHHHHHHHHHHcCCCeEEEE------e--CCCeEEEEEEe
Q 011315 117 ETKRGRCGEWANCFTLYCRAFGYESRLIL------D--FTDHVWTECFS 157 (488)
Q Consensus 117 ~tR~GrCgE~A~lF~~l~RalG~~aR~V~------~--~~dHvW~EVy~ 157 (488)
.|.---|-+|+++|.-++.+||+.+|++. | |..|+-.-+=.
T Consensus 51 ~~~GiNCtD~~Qlf~~v~~~lGY~Vq~~HVk~rc~~g~wygH~~LRv~~ 99 (142)
T PF12386_consen 51 RTSGINCTDACQLFYRVIESLGYDVQFEHVKCRCNSGKWYGHYRLRVKH 99 (142)
T ss_pred HhcCCCchhHHHHHHHHHHhcCceEEEEEEEEEecCCceeeEEEEEecc
Confidence 34334599999999999999999999984 2 34666655543
No 64
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=32.64 E-value=25 Score=24.81 Aligned_cols=14 Identities=29% Similarity=0.980 Sum_probs=11.7
Q ss_pred eEEEeecCCCCccc
Q 011315 91 RVELFRCKVCSKIT 104 (488)
Q Consensus 91 rVE~y~C~~C~~~~ 104 (488)
+.+.|+|..||...
T Consensus 4 ~~~~ykC~~Cgniv 17 (34)
T TIGR00319 4 EGQVYKCEVCGNIV 17 (34)
T ss_pred cCcEEEcCCCCcEE
Confidence 46799999999865
No 65
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=31.84 E-value=18 Score=35.82 Aligned_cols=35 Identities=34% Similarity=0.594 Sum_probs=25.9
Q ss_pred CCCCChhhhhcCCc------eEEEeecCCCC----cccccCCCCC
Q 011315 77 MGTPLPSEIQYGAA------RVELFRCKVCS----KITRFPRYND 111 (488)
Q Consensus 77 ~~~Pt~eE~~~ga~------rVE~y~C~~C~----~~~RFPRYn~ 111 (488)
.+-|+.||-.|.|+ +.|-|+|..|+ +.+|=||.|+
T Consensus 15 ~akp~~Deg~WdCsvCTFrNsAeAfkC~vCdvRKGTSTRkpr~ns 59 (228)
T KOG4477|consen 15 DAKPNDDEGKWDCSVCTFRNSAEAFKCFVCDVRKGTSTRKPRCNS 59 (228)
T ss_pred cCCCccccCceeeeeeeecchhhhhheeeecccccccccCCcchH
Confidence 45577777777664 67999999997 4677777774
No 66
>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=30.58 E-value=25 Score=33.00 Aligned_cols=34 Identities=24% Similarity=0.613 Sum_probs=21.1
Q ss_pred CCCCCCCCCC-ccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 62 APPCDGCSNE-TVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 62 ~P~C~~Cg~~-t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
...|++||+. |.....-.||+=- -+|+|..|...
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~ck--------a~~~c~~c~ep 139 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACK--------ALYRCRACKEP 139 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhH--------HHhhhhhhCCc
Confidence 4789999995 4433222233321 37999999763
No 67
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=30.55 E-value=25 Score=33.38 Aligned_cols=43 Identities=16% Similarity=0.318 Sum_probs=24.8
Q ss_pred CCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccccCCCCCH
Q 011315 64 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDP 112 (488)
Q Consensus 64 ~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPRYn~p 112 (488)
.||.||.+...+=...|+. .|...=-.=.|..||. ||--|...
T Consensus 2 ~CP~C~~~dtkViDSR~~~----dg~~IRRRReC~~C~~--RFTTyErv 44 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVE----DGQSIRRRRECLECHE--RFTTFERA 44 (147)
T ss_pred CCCCCCCCCCEeeeccccC----CCCeeeecccCCccCC--ccceeeec
Confidence 5999999644332222332 2333334467999995 66666544
No 68
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=30.46 E-value=72 Score=29.64 Aligned_cols=45 Identities=22% Similarity=0.502 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhhccCeeecCCCCCCCCCCcc-ccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 43 HAFLLQLLFWFKQTFRWVNAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 43 ~~~l~~LL~wFK~~F~wv~~P~C~~Cg~~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
...+.++|+=|=. .||. |+.|+++.+ ..- -+++-.-+|..||+..
T Consensus 83 ~~~i~~~L~~yI~--~yVl---C~~C~sPdT~l~k------------~~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 83 HFLLNERIEDYVR--KYVI---CRECNRPDTRIIK------------EGRVSLLKCEACGAKA 128 (133)
T ss_pred HHHHHHHHHHHHh--heEE---CCCCCCCCcEEEE------------eCCeEEEecccCCCCC
Confidence 3457777766543 4455 999999744 332 1567777999999853
No 69
>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=30.10 E-value=44 Score=37.40 Aligned_cols=42 Identities=26% Similarity=0.415 Sum_probs=27.4
Q ss_pred HHHHHHHHH-hhcc--CeeecCCC--CCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 44 AFLLQLLFW-FKQT--FRWVNAPP--CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 44 ~~l~~LL~w-FK~~--F~wv~~P~--C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
.-+++|++. |++. +-|++.|. |..||.... -+.+.|+.||..
T Consensus 495 ~al~~lv~~a~~~~~~y~~~~~p~~~C~~CG~~~~------------------~~~~~CP~CGs~ 541 (555)
T cd01675 495 EALEALVKKAAKRGVIYFGINTPIDICNDCGYIGE------------------GEGFKCPKCGSE 541 (555)
T ss_pred HHHHHHHHHHHHcCCceEEEecCCccCCCCCCCCc------------------CCCCCCcCCCCc
Confidence 356677776 6663 45666665 888886322 234899999964
No 70
>COG2912 Uncharacterized conserved protein [Function unknown]
Probab=29.61 E-value=95 Score=32.19 Aligned_cols=63 Identities=14% Similarity=0.151 Sum_probs=52.4
Q ss_pred CCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCCeEEEEeCCCeEEEEEEeCCCCCeEEeccCCCc
Q 011315 107 PRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGI 172 (488)
Q Consensus 107 PRYn~p~~LL~tR~GrCgE~A~lF~~l~RalG~~aR~V~~~~dHvW~EVy~~~~~rWIhVDP~e~~ 172 (488)
||----..++++|+|.=..-|..++.+++++|+|- +=+|+.+|.=.-+..+. +-| -+||+++-
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 44444579999999999999999999999999998 55688899988888887 445 89999764
No 71
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.59 E-value=33 Score=33.87 Aligned_cols=44 Identities=11% Similarity=0.241 Sum_probs=27.5
Q ss_pred CCCCCCCccc--cCCCCCChhhhhcCCceEEEeecCCCCcccccCCCC
Q 011315 65 CDGCSNETVG--QGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYN 110 (488)
Q Consensus 65 C~~Cg~~t~~--~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPRYn 110 (488)
|..||..+.+ .|+-.-++.-. --+.==+|+|.+|+..--||-|.
T Consensus 20 C~~Cg~kr~f~cSg~fRvNAq~K--~LDvWlIYkC~~Cd~tWN~~Ife 65 (203)
T COG4332 20 CNSCGVKRAFTCSGKFRVNAQGK--VLDVWLIYKCTHCDYTWNISIFE 65 (203)
T ss_pred CcccCCcceeeecCcEEEcCCCc--EEEEEEEEEeeccCCccchhhhh
Confidence 9999997653 35433333211 12445689999999876665543
No 72
>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=29.59 E-value=46 Score=34.91 Aligned_cols=49 Identities=20% Similarity=0.498 Sum_probs=32.4
Q ss_pred ecCCCCCCCCCCccccCCCCCChhhhhc--CCceEEEeecCCCCcccccCCCCCHHHHHHhCCccchh
Q 011315 60 VNAPPCDGCSNETVGQGMGTPLPSEIQY--GAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGE 125 (488)
Q Consensus 60 v~~P~C~~Cg~~t~~~g~~~Pt~eE~~~--ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~GrCgE 125 (488)
-+..-|+.||+.-.. ..... +..+.--..|..|++.-+|+|. +.-.||+
T Consensus 182 ~~~~~CPvCGs~P~~--------s~~~~~~~~~G~RyL~CslC~teW~~~R~---------~C~~Cg~ 232 (305)
T TIGR01562 182 ESRTLCPACGSPPVA--------SMVRQGGKETGLRYLSCSLCATEWHYVRV---------KCSHCEE 232 (305)
T ss_pred CCCCcCCCCCChhhh--------hhhcccCCCCCceEEEcCCCCCcccccCc---------cCCCCCC
Confidence 456789999996431 11111 1244556789999999999884 4666765
No 73
>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=29.48 E-value=57 Score=26.84 Aligned_cols=39 Identities=23% Similarity=0.309 Sum_probs=26.4
Q ss_pred eEEEEEEeCCCCCeEEeccCCCcCCCCeeeecCccCccce
Q 011315 150 HVWTECFSQSLGRWMHLDPCEGIYDRPLLYEKGWNKKLNY 189 (488)
Q Consensus 150 HvW~EVy~~~~~rWIhVDP~e~~iD~Pllye~gwgKklsY 189 (488)
+...-.|++..+||+..||.. ..+..-.|.=..+.++++
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 456678999999999999974 334344454445556554
No 74
>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=29.28 E-value=29 Score=32.07 Aligned_cols=61 Identities=30% Similarity=0.637 Sum_probs=40.1
Q ss_pred eeecCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccccCCCCCHHHHHHhCCccchhhHHHHHHHHHHc
Q 011315 58 RWVNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPRYNDPLKLVETKRGRCGEWANCFTLYCRAF 137 (488)
Q Consensus 58 ~wv~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPRYn~p~~LL~tR~GrCgE~A~lF~~l~Ral 137 (488)
.|+. +-|+.|..+....+. ..|+|..|+...--
T Consensus 31 ~~~Y-~aC~~C~kkv~~~~~---------------~~~~C~~C~~~~~~------------------------------- 63 (166)
T cd04476 31 NWWY-PACPGCNKKVVEEGN---------------GTYRCEKCNKSVPN------------------------------- 63 (166)
T ss_pred CeEE-ccccccCcccEeCCC---------------CcEECCCCCCcCCC-------------------------------
Confidence 4554 679999886543321 57999999986411
Q ss_pred CCCeEEE-----EeCCCeEEEEEEeCCCCCeEEe
Q 011315 138 GYESRLI-----LDFTDHVWTECFSQSLGRWMHL 166 (488)
Q Consensus 138 G~~aR~V-----~~~~dHvW~EVy~~~~~rWIhV 166 (488)
...||. .|.++.+|+-+|.+....=+..
T Consensus 64 -~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~l~G~ 96 (166)
T cd04476 64 -PEYRYILSLNVADHTGEAWLTLFDEVAEQIFGK 96 (166)
T ss_pred -ccEEEEEEEEEEeCCCCEEEEEehHHHHHHhCC
Confidence 122333 3788999999998765555554
No 75
>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=29.18 E-value=37 Score=32.45 Aligned_cols=34 Identities=21% Similarity=0.590 Sum_probs=22.0
Q ss_pred CCCCCCCcccc-C--CCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 65 CDGCSNETVGQ-G--MGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 65 C~~Cg~~t~~~-g--~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
|+.||+++... . ..-|- ++--.+--+.|++||-.
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~-----F~evii~sf~C~~CGyr 37 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPY-----FGKIMLSTYICEKCGYR 37 (163)
T ss_pred CCCCCCcceEeeeEeccCCC-----cceEEEEEEECCCCCCc
Confidence 89999874322 1 11222 34567789999999973
No 76
>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=29.00 E-value=35 Score=23.80 Aligned_cols=13 Identities=23% Similarity=0.411 Sum_probs=7.1
Q ss_pred CCCCCCCCCcccc
Q 011315 63 PPCDGCSNETVGQ 75 (488)
Q Consensus 63 P~C~~Cg~~t~~~ 75 (488)
.-|+.||++|...
T Consensus 4 rfC~~CG~~t~~~ 16 (32)
T PF09297_consen 4 RFCGRCGAPTKPA 16 (32)
T ss_dssp SB-TTT--BEEE-
T ss_pred cccCcCCccccCC
Confidence 4599999998865
No 77
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=28.93 E-value=40 Score=24.71 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=9.0
Q ss_pred CCCCCCCCCcc
Q 011315 63 PPCDGCSNETV 73 (488)
Q Consensus 63 P~C~~Cg~~t~ 73 (488)
+.|+.||+.+.
T Consensus 3 ~~Cp~Cg~~~~ 13 (47)
T PF14690_consen 3 PRCPHCGSPSV 13 (47)
T ss_pred ccCCCcCCCce
Confidence 56999999874
No 78
>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=28.84 E-value=39 Score=34.35 Aligned_cols=42 Identities=19% Similarity=0.315 Sum_probs=19.5
Q ss_pred Cee-ecCCCCCCCCCCcc-ccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 57 FRW-VNAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 57 F~w-v~~P~C~~Cg~~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
+.| +..-.|+.||+... ....-. ..+...+.++.|..|+..+
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 478 67788999998643 222210 1122456666899999865
No 79
>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=28.00 E-value=0.9 Score=37.07 Aligned_cols=54 Identities=19% Similarity=0.155 Sum_probs=34.9
Q ss_pred ceeeEeeccchhhhccccCCCchhhHHHHHHHHHHHHhhccCCCcccccccccCCC
Q 011315 311 HVTTIYNAFSSVLSHFVENNVPKSGAIELLKILKGILGDLKKSPYKTRRVSLNSVP 366 (488)
Q Consensus 311 hv~~iY~a~~~~ls~~~~~~~~~~~a~~~~~~~r~~~~dlk~~~f~~R~~~~~~~~ 366 (488)
+|..-|+-..-.-||-.++ .|...++.+..|.|+++.||+|+ |.+|+...+...
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 999988765543
No 80
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=27.99 E-value=44 Score=35.14 Aligned_cols=42 Identities=19% Similarity=0.298 Sum_probs=24.7
Q ss_pred Cee-ecCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 57 FRW-VNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 57 F~w-v~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
..| +..-.|+.||+. ..+++- +.++ +...+.++.|..|+...
T Consensus 220 teW~~~R~~C~~Cg~~-~~l~y~--~~~~---~~~~~r~e~C~~C~~Yl 262 (309)
T PRK03564 220 SEWHVVRVKCSNCEQS-GKLHYW--SLDS---EQAAVKAESCGDCGTYL 262 (309)
T ss_pred CcccccCccCCCCCCC-Cceeee--eecC---CCcceEeeecccccccc
Confidence 366 667788888873 222221 1111 11246667899999876
No 81
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.88 E-value=33 Score=26.73 Aligned_cols=40 Identities=10% Similarity=0.269 Sum_probs=23.9
Q ss_pred HHHHhhcc-Cee-ecCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 49 LLFWFKQT-FRW-VNAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 49 LL~wFK~~-F~w-v~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
.|.||+=+ .+= .+..-||.||+. .... .-..+.|..||-.
T Consensus 5 ~~~~y~v~~~~v~~~~~fCP~Cg~~-~m~~--------------~~~r~~C~~Cgyt 46 (50)
T PRK00432 5 KREYYEVDGGKVKRKNKFCPRCGSG-FMAE--------------HLDRWHCGKCGYT 46 (50)
T ss_pred eeeeEEECCCEEEEccCcCcCCCcc-hhec--------------cCCcEECCCcCCE
Confidence 45566543 320 245679999986 3321 1147889999854
No 82
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=27.25 E-value=38 Score=25.29 Aligned_cols=26 Identities=23% Similarity=0.427 Sum_probs=15.7
Q ss_pred CCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 64 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 64 ~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
.|+.||........ ....+|+.||..
T Consensus 5 ~C~~CG~~~~~~~~--------------~~~~~Cp~CG~~ 30 (46)
T PRK00398 5 KCARCGREVELDEY--------------GTGVRCPYCGYR 30 (46)
T ss_pred ECCCCCCEEEECCC--------------CCceECCCCCCe
Confidence 48888875443311 115688888874
No 83
>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=27.09 E-value=57 Score=28.04 Aligned_cols=36 Identities=17% Similarity=0.463 Sum_probs=23.1
Q ss_pred CCCCCCCCCcc-ccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 63 PPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 63 P~C~~Cg~~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
-+|+.||+... ..-+..-++|| ...=.|.|..|+..
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 57999998743 32222223444 45568999999974
No 84
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=26.79 E-value=33 Score=24.19 Aligned_cols=13 Identities=31% Similarity=1.216 Sum_probs=10.7
Q ss_pred EEEeecCCCCccc
Q 011315 92 VELFRCKVCSKIT 104 (488)
Q Consensus 92 VE~y~C~~C~~~~ 104 (488)
.+.|+|..||...
T Consensus 2 ~~~ykC~~CGniv 14 (34)
T cd00974 2 LEVYKCEICGNIV 14 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4689999999865
No 85
>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=26.77 E-value=49 Score=24.18 Aligned_cols=31 Identities=19% Similarity=0.665 Sum_probs=19.3
Q ss_pred eecCCC--CCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 59 WVNAPP--CDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 59 wv~~P~--C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
|+-.|. |+.|++....... + .|-|..||+..
T Consensus 3 ~~~~~~~~C~~C~~~~~~~~d------------G---~~yC~~cG~~~ 35 (36)
T PF11781_consen 3 WMRGPNEPCPVCGSRWFYSDD------------G---FYYCDRCGHQS 35 (36)
T ss_pred ccccCCCcCCCCCCeEeEccC------------C---EEEhhhCceEc
Confidence 444444 9999997222211 1 58899999764
No 86
>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=26.16 E-value=32 Score=35.28 Aligned_cols=54 Identities=15% Similarity=0.270 Sum_probs=29.0
Q ss_pred EeecCCcc----eechhhhccChHHhhhhcccc--cHHHHHHHHHHHHHHHHccCCHHHhhhhh
Q 011315 191 IAISKDGV----FDVTKRYTRKWHEVLSRRNIA--TEQTVSAVLAKMTRECRRSFASETLSTLE 248 (488)
Q Consensus 191 IAFs~DGv----~DVTrRYt~~~~~~~~RR~rv--~E~wl~~~L~~l~~~~r~~ls~ee~~~Le 248 (488)
|-+=+||. ..|+..| .+.+.-|+.- +-.|+..+|.-+...-...++-++.+..+
T Consensus 154 I~lv~~~~~~~~~~V~~~~----~~tlfLr~~~~~~rGWlldi~~cid~i~~~~FtL~diY~Fe 213 (254)
T PF06044_consen 154 IFLVKNGQIIPPEEVLEQW----QKTLFLRTQNIESRGWLLDIMKCIDKIPKNEFTLDDIYAFE 213 (254)
T ss_dssp EEEEETTEE--HHHHHHHH----HHGGGGGGS-HHHHHHHHHHHHHHHHS-SSEEEHHHHHTTH
T ss_pred EEEEeCCeEcCHHHHHHHH----HHHHHHHhccccccchHHHHHHHHHhcCccceeHHHHHHHH
Confidence 33445663 3555544 4333444322 44899999998875443555555555443
No 87
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=25.89 E-value=50 Score=24.64 Aligned_cols=14 Identities=21% Similarity=0.543 Sum_probs=10.7
Q ss_pred EEeecCCCCccccc
Q 011315 93 ELFRCKVCSKITRF 106 (488)
Q Consensus 93 E~y~C~~C~~~~RF 106 (488)
..|.|+.||...+-
T Consensus 19 ~~~vC~~Cg~~~~~ 32 (52)
T smart00661 19 RRFVCRKCGYEEPI 32 (52)
T ss_pred CEEECCcCCCeEEC
Confidence 37899999976543
No 88
>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=25.87 E-value=59 Score=29.08 Aligned_cols=44 Identities=27% Similarity=0.439 Sum_probs=25.2
Q ss_pred CCCCCCCCCccccCCCCCChhhhhcCC---ceEEEeecCCCCcccc-cCCCCCH
Q 011315 63 PPCDGCSNETVGQGMGTPLPSEIQYGA---ARVELFRCKVCSKITR-FPRYNDP 112 (488)
Q Consensus 63 P~C~~Cg~~t~~~g~~~Pt~eE~~~ga---~rVE~y~C~~C~~~~R-FPRYn~p 112 (488)
..|+.||++...... ++. ++- ..=-+|.|..|++.+- +|.=+-|
T Consensus 3 ~~CpYCg~~~~l~~~-----~~i-Yg~~~~~~~~~y~C~~C~AyVG~H~~t~~P 50 (102)
T PF11672_consen 3 IICPYCGGPAELVDG-----SEI-YGHRYDDGPYLYVCTPCDAYVGCHPGTDIP 50 (102)
T ss_pred cccCCCCCeeEEccc-----chh-cCccCCCCceeEECCCCCceeeeeCCCCCc
Confidence 359999998765421 111 221 1123599999998654 4543333
No 89
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=24.75 E-value=1.3e+02 Score=28.11 Aligned_cols=46 Identities=15% Similarity=0.382 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhccCeeecCCCCCCCCCCcc-ccCCCCCChhhhhcCCceEEEeecCCCCcccc
Q 011315 43 HAFLLQLLFWFKQTFRWVNAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITR 105 (488)
Q Consensus 43 ~~~l~~LL~wFK~~F~wv~~P~C~~Cg~~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~R 105 (488)
...+.++|+=|=.+ ||. |+.|+++.+ ..- -+++-.-+|..||+..-
T Consensus 88 ~~~i~~~L~~yI~~--yVl---C~~C~spdT~l~k------------~~r~~~l~C~ACGa~~~ 134 (138)
T PRK03988 88 PRVINEKIDRYVKE--YVI---CPECGSPDTKLIK------------EGRIWVLKCEACGAETP 134 (138)
T ss_pred HHHHHHHHHHHHHh--cEE---CCCCCCCCcEEEE------------cCCeEEEEcccCCCCCc
Confidence 34577777666444 444 999999744 332 16788889999998653
No 90
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=24.64 E-value=39 Score=32.42 Aligned_cols=25 Identities=12% Similarity=0.268 Sum_probs=21.0
Q ss_pred hcccccHHHHHHHHHHHHHHHHccC
Q 011315 215 RRNIATEQTVSAVLAKMTRECRRSF 239 (488)
Q Consensus 215 RR~rv~E~wl~~~L~~l~~~~r~~l 239 (488)
++..|+.+.++.+++.+..++|+.-
T Consensus 75 ~KRpVs~e~ie~~v~~ie~~Lr~~g 99 (156)
T COG1327 75 EKRPVSSEQIEEAVSHIERQLRSSG 99 (156)
T ss_pred hcCCCCHHHHHHHHHHHHHHHHhcC
Confidence 5568999999999999999888653
No 91
>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=24.20 E-value=37 Score=25.05 Aligned_cols=29 Identities=21% Similarity=0.550 Sum_probs=17.1
Q ss_pred CCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccc
Q 011315 64 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR 105 (488)
Q Consensus 64 ~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~R 105 (488)
.|+.||+...... ..+=| +-|..||.+..
T Consensus 2 ~Cp~Cg~~~~~~D------------~~~g~-~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSKEIVFD------------PERGE-LVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSSEEEEE------------TTTTE-EEETTT-BBEE
T ss_pred CCcCCcCCceEEc------------CCCCe-EECCCCCCEee
Confidence 4899999763221 11122 48999998764
No 92
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=23.94 E-value=59 Score=31.90 Aligned_cols=34 Identities=21% Similarity=0.504 Sum_probs=21.9
Q ss_pred CCCCCCCCcc--ccCCC-CCChhhhhcCCceEEEeecCCCCc
Q 011315 64 PCDGCSNETV--GQGMG-TPLPSEIQYGAARVELFRCKVCSK 102 (488)
Q Consensus 64 ~C~~Cg~~t~--~~g~~-~Pt~eE~~~ga~rVE~y~C~~C~~ 102 (488)
+|+.||.+.. ..-.. -|- ++--.+--+.|++||-
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 6999997522 22111 222 3456778999999996
No 93
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=23.92 E-value=41 Score=22.96 Aligned_cols=27 Identities=26% Similarity=0.563 Sum_probs=14.5
Q ss_pred CCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCc
Q 011315 64 PCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSK 102 (488)
Q Consensus 64 ~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~ 102 (488)
+|+.|++....++. +.-..|-|..|..
T Consensus 3 ~C~rC~~~~~~~~~------------~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGI------------NGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEE------------TTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEe------------cCCCCeECcCCcC
Confidence 69999986554432 2334688999875
No 94
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=23.51 E-value=63 Score=30.76 Aligned_cols=34 Identities=18% Similarity=0.458 Sum_probs=22.0
Q ss_pred CCCCCCCCc--cccCCCCCChhhhhcCCceEEEeecCCCCc
Q 011315 64 PCDGCSNET--VGQGMGTPLPSEIQYGAARVELFRCKVCSK 102 (488)
Q Consensus 64 ~C~~Cg~~t--~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~ 102 (488)
.|+.||.+. ...-..-|- ++--.+--+.|++||-
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 599999753 222222232 3446777999999996
No 95
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=23.43 E-value=1.1e+02 Score=30.04 Aligned_cols=45 Identities=18% Similarity=0.343 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhccCeeecCCCCCCCCCCcc-ccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 43 HAFLLQLLFWFKQTFRWVNAPPCDGCSNETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 43 ~~~l~~LL~wFK~~F~wv~~P~C~~Cg~~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
...+.++|+=|-. .||. |+.|+++.+ ..-. +++-.-+|..||+..
T Consensus 84 ~~~i~~~l~~yi~--~yV~---C~~C~~pdT~l~k~------------~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 84 EEDIQAAIDAYVD--EYVI---CSECGLPDTRLVKE------------DRVLMLRCDACGAHR 129 (201)
T ss_pred HHHHHHHHHHHHH--heEE---CCCCCCCCcEEEEc------------CCeEEEEcccCCCCc
Confidence 3457777766544 4455 999999744 3321 467778999999854
No 96
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.89 E-value=70 Score=29.26 Aligned_cols=26 Identities=23% Similarity=0.649 Sum_probs=18.2
Q ss_pred CCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccc
Q 011315 62 APPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR 105 (488)
Q Consensus 62 ~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~R 105 (488)
-|+|+.||.+.. |-.-+|+.|+..+|
T Consensus 6 ~~~cPvcg~~~i------------------VTeL~c~~~etTVr 31 (122)
T COG3877 6 INRCPVCGRKLI------------------VTELKCSNCETTVR 31 (122)
T ss_pred CCCCCcccccce------------------eEEEecCCCCceEe
Confidence 478999987433 33357888887765
No 97
>PHA02942 putative transposase; Provisional
Probab=22.81 E-value=58 Score=34.81 Aligned_cols=27 Identities=30% Similarity=0.668 Sum_probs=18.1
Q ss_pred CCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCccc
Q 011315 63 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKIT 104 (488)
Q Consensus 63 P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~ 104 (488)
-.|+.||..+... ..| .|.|..||...
T Consensus 326 q~Cs~CG~~~~~l-------------~~r--~f~C~~CG~~~ 352 (383)
T PHA02942 326 VSCPKCGHKMVEI-------------AHR--YFHCPSCGYEN 352 (383)
T ss_pred ccCCCCCCccCcC-------------CCC--EEECCCCCCEe
Confidence 4599999854211 122 69999999853
No 98
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.40 E-value=60 Score=35.60 Aligned_cols=62 Identities=19% Similarity=0.142 Sum_probs=40.8
Q ss_pred CCCccccccc-ccCCCCchhHHHHhhhccHHHHHHhhccccccCCCCCeEEEec-CCCccccch
Q 011315 352 KSPYKTRRVS-LNSVPNNGQKIVHQLLPSIGHLLRVLSLKSELNTDGRVDIVLA-GDPVKTSLS 413 (488)
Q Consensus 352 ~~~f~~R~~~-~~~~~~~~~~~~~~~lps~~~ll~~lslk~~~~~~g~~~~~~~-~~p~~tsl~ 413 (488)
+.|||+|... +.-.......-...++--.-.+...++++...+|+|.+.|+.. ++++.+|++
T Consensus 48 ~ipyKTRGN~av~l~~~~~~~d~~~~~~~~~~~ve~~~~~~~~~t~PG~vv~~~~~~ev~~~~~ 111 (421)
T COG1571 48 NIPYKTRGNAAVLLLVARRRGDANDIFYLAREGVEKLALKDSENTNPGEVVAVGELPEVLRSFY 111 (421)
T ss_pred CCceeccCCceeEEEeecCccchHHHHHHHHHHHHHhhccccccCCCcEEEEecCCcHHHHHHH
Confidence 5799999988 2111111000001223334678889999999999999999999 777766554
No 99
>PF12390 Se-cys_synth_N: Selenocysteine synthase N terminal
Probab=22.13 E-value=53 Score=24.10 Aligned_cols=36 Identities=31% Similarity=0.634 Sum_probs=27.0
Q ss_pred hccHHHHHHhhccccccCCCCCeEEEecCCCccccchhhHhHHHHHHHHHhc
Q 011315 377 LPSIGHLLRVLSLKSELNTDGRVDIVLAGDPVKTSLSLPVVFKALDDMIHDL 428 (488)
Q Consensus 377 lps~~~ll~~lslk~~~~~~g~~~~~~~~~p~~tsl~l~~~~~~~~~~~~~~ 428 (488)
|||.+.+|....++.-+..-|+ +++.+++.+++..+
T Consensus 4 LPsVD~lL~~~~~~~l~~~~~r----------------~~v~~~vR~~ld~~ 39 (40)
T PF12390_consen 4 LPSVDELLQEPEIQDLIERYGR----------------PLVVDAVREVLDEL 39 (40)
T ss_pred CchHHHHHhChhhHHHHHHcCH----------------HHHHHHHHHHHHHh
Confidence 8999999999888877666554 56777777776543
No 100
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=22.07 E-value=52 Score=27.60 Aligned_cols=33 Identities=24% Similarity=0.506 Sum_probs=22.6
Q ss_pred CCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccccCC
Q 011315 63 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITRFPR 108 (488)
Q Consensus 63 P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFPR 108 (488)
-.|+.|++++...+.. +.. -+|..||...--|.
T Consensus 20 VkCpdC~N~q~vFsha----------st~---V~C~~CG~~l~~PT 52 (67)
T COG2051 20 VKCPDCGNEQVVFSHA----------STV---VTCLICGTTLAEPT 52 (67)
T ss_pred EECCCCCCEEEEeccC----------ceE---EEecccccEEEecC
Confidence 4599999988776531 232 36999998765553
No 101
>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=21.94 E-value=64 Score=25.57 Aligned_cols=29 Identities=17% Similarity=0.501 Sum_probs=19.8
Q ss_pred cCCCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 61 NAPPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 61 ~~P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
-.-.|+.||...... ..-..|.|+.||..
T Consensus 27 TSq~C~~CG~~~~~~--------------~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKR--------------RSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccc--------------cccceEEcCCCCCE
Confidence 344599999854441 23457999999975
No 102
>PRK03954 ribonuclease P protein component 4; Validated
Probab=21.94 E-value=45 Score=30.64 Aligned_cols=17 Identities=35% Similarity=0.893 Sum_probs=14.9
Q ss_pred eEEEeecCCCCcccccCC
Q 011315 91 RVELFRCKVCSKITRFPR 108 (488)
Q Consensus 91 rVE~y~C~~C~~~~RFPR 108 (488)
.| ++.|..||...|||=
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 103
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=21.69 E-value=56 Score=21.65 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=5.7
Q ss_pred CCCCCCCc
Q 011315 65 CDGCSNET 72 (488)
Q Consensus 65 C~~Cg~~t 72 (488)
|+.||.+.
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 77888753
No 104
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=21.64 E-value=63 Score=25.80 Aligned_cols=31 Identities=23% Similarity=0.350 Sum_probs=19.1
Q ss_pred CCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcccc
Q 011315 63 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKITR 105 (488)
Q Consensus 63 P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~R 105 (488)
..|+.||.+-..-+. .+=|+..|..||...+
T Consensus 3 ~~CP~CG~~iev~~~------------~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIELENP------------ELGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEecCCC------------ccCCEEeCCCCCCEEE
Confidence 469999995432211 1123568999998654
No 105
>PF05053 Menin: Menin; InterPro: IPR007747 MEN1, the gene responsible for multiple endocrine neoplasia type 1, is a tumour suppressor gene that encodes a protein called Menin which may be an atypical GTPase stimulated by nm23 [].; GO: 0005634 nucleus; PDB: 3RE2_A 3U84_B 3U86_A 3U88_B 3U85_A.
Probab=21.37 E-value=2e+02 Score=33.05 Aligned_cols=48 Identities=21% Similarity=0.410 Sum_probs=34.0
Q ss_pred CCCCCHHHHHHhCCccchhhHHHHHHHHHHcCCC-eEEEEeCCCeEEEEE
Q 011315 107 PRYNDPLKLVETKRGRCGEWANCFTLYCRAFGYE-SRLILDFTDHVWTEC 155 (488)
Q Consensus 107 PRYn~p~~LL~tR~GrCgE~A~lF~~l~RalG~~-aR~V~~~~dHvW~EV 155 (488)
+-.++.-..|..++=.|---|..-++.|.+||+. ++++++ +||+|+..
T Consensus 138 aH~QslyS~ltg~kLDcfGvAfavva~cq~Lg~~dvhLalS-eDHawv~f 186 (618)
T PF05053_consen 138 AHLQSLYSYLTGNKLDCFGVAFAVVAACQVLGYKDVHLALS-EDHAWVVF 186 (618)
T ss_dssp TT-SSHHHHHHCSB--HHHHHHHHHHHHHHCT-TT-EEEE--SS-EEEEE
T ss_pred HHHHHHHHHHhcCCCCccchHHHHHHHHhhhCcchheeeec-CCceEEEe
Confidence 4566677778888888999999999999999995 787775 89999854
No 106
>PRK15312 antimicrobial resistance protein Mig-14; Provisional
Probab=20.85 E-value=3.1e+02 Score=28.98 Aligned_cols=80 Identities=18% Similarity=0.166 Sum_probs=50.9
Q ss_pred HHHHhCCccch---hhHHH--HHHHHHHcCCCeEEEEeCCCeEEEEEEeCCCCCeEEeccCCCcCCCCee-eecC-----
Q 011315 114 KLVETKRGRCG---EWANC--FTLYCRAFGYESRLILDFTDHVWTECFSQSLGRWMHLDPCEGIYDRPLL-YEKG----- 182 (488)
Q Consensus 114 ~LL~tR~GrCg---E~A~l--F~~l~RalG~~aR~V~~~~dHvW~EVy~~~~~rWIhVDP~e~~iD~Pll-ye~g----- 182 (488)
.|++.|-|.+. +.+.+ |...+|-+=+-.=+.+|..+.+=.=|+-.....||.+|-.++-+|.-.. +..|
T Consensus 174 ~Lf~~Rwg~~~~~~~~~~l~e~f~~Lr~l~fG~VLfl~~~PcA~qlv~k~eSp~wi~~D~iNgG~Dpe~~~~spGSIL~W 253 (298)
T PRK15312 174 ELFRSRFGNTLSCYPADNLANFFSQLRHLLFGHILYIEGIPCAFDIVLKSESQMNVYFDVPNGAVKNECMPLSPGSILMW 253 (298)
T ss_pred HHHHHHhCCCCCcccHHHHHHHHHHhHHhheeeEEEECCcceEEEEEEEecCCCcEEEecccCccCcccccCCCccEEEE
Confidence 46666666433 33333 2222333333322336788888888888778899999999998986533 3333
Q ss_pred ------------ccCccceEEee
Q 011315 183 ------------WNKKLNYVIAI 193 (488)
Q Consensus 183 ------------wgKklsYVIAF 193 (488)
-+|+|.|-||.
T Consensus 254 lNi~~A~~~~~~~~K~lrfSfG~ 276 (298)
T PRK15312 254 LNISRARHYCQERQKKLIFSIGI 276 (298)
T ss_pred ecHHHHHHHHHhcCCcEEEEecC
Confidence 37889998884
No 107
>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=20.84 E-value=26 Score=37.53 Aligned_cols=54 Identities=17% Similarity=0.363 Sum_probs=26.5
Q ss_pred HHHHHHHHh-hcc-C-ee-ecCCCCCCCCC-Ccc-ccCCCCCChhhhhcCCceEEEeecCCCCcccccC
Q 011315 45 FLLQLLFWF-KQT-F-RW-VNAPPCDGCSN-ETV-GQGMGTPLPSEIQYGAARVELFRCKVCSKITRFP 107 (488)
Q Consensus 45 ~l~~LL~wF-K~~-F-~w-v~~P~C~~Cg~-~t~-~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~~RFP 107 (488)
.|.++|.=+ .+. - +| --.|.|+.||. .|+ .... .-+...|+ |+|..||+....+
T Consensus 153 ~I~~Il~~~~~~~~~~~y~Pf~piC~~cGri~tt~v~~~--------d~~~~~v~-Y~c~~cG~~g~~~ 212 (360)
T PF01921_consen 153 EIREILNEYRGRERPETYSPFLPICEKCGRIDTTEVTEY--------DPEGGTVT-YRCEECGHEGEVD 212 (360)
T ss_dssp HHHHHHHHHHHHT--TT--SEEEEETTTEE--EEEEEEE----------SSSEEE-EE--TTS---EEE
T ss_pred HHHHHHHHhcCcCCCCCeeeeeeeccccCCcccceeeEe--------ecCCCEEE-EEecCCCCEEEEe
Confidence 345554444 333 2 55 34688999998 443 3332 11246666 9999999865433
No 108
>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=20.80 E-value=27 Score=31.68 Aligned_cols=25 Identities=16% Similarity=0.341 Sum_probs=19.0
Q ss_pred EeCCCeEEEEEEeCCCCCeEEeccC
Q 011315 145 LDFTDHVWTECFSQSLGRWMHLDPC 169 (488)
Q Consensus 145 ~~~~dHvW~EVy~~~~~rWIhVDP~ 169 (488)
.|.++..|+-+|.+...+-+..+..
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 4789999999998766666666554
No 109
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.65 E-value=60 Score=31.80 Aligned_cols=40 Identities=23% Similarity=0.368 Sum_probs=24.5
Q ss_pred HHHHHHHHhhcc---CeeecC-----CCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 45 FLLQLLFWFKQT---FRWVNA-----PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 45 ~l~~LL~wFK~~---F~wv~~-----P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
.+++.|.|.-.. +..++. --|+.||. -....|.|+.||..
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 355666665542 333332 34888887 12567999999974
No 110
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=20.10 E-value=89 Score=27.58 Aligned_cols=27 Identities=22% Similarity=0.599 Sum_probs=19.0
Q ss_pred CCCCCCCCCccccCCCCCChhhhhcCCceEEEeecCCCCcc
Q 011315 63 PPCDGCSNETVGQGMGTPLPSEIQYGAARVELFRCKVCSKI 103 (488)
Q Consensus 63 P~C~~Cg~~t~~~g~~~Pt~eE~~~ga~rVE~y~C~~C~~~ 103 (488)
-.|+.||.....- ..|-+.+|.+|+..
T Consensus 36 y~CpfCgk~~vkR--------------~a~GIW~C~~C~~~ 62 (91)
T TIGR00280 36 YVCPFCGKKTVKR--------------GSTGIWTCRKCGAK 62 (91)
T ss_pred ccCCCCCCCceEE--------------EeeEEEEcCCCCCE
Confidence 3599999754321 45668999999964
Done!