Query 021649
Match_columns 309
No_of_seqs 73 out of 75
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 04:37:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021649.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021649hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08097 ligB NAD-dependent DN 95.0 0.026 5.7E-07 58.4 4.4 49 125-173 8-69 (562)
2 cd00114 LIGANc NAD+ dependent 94.8 0.029 6.3E-07 53.7 3.9 28 147-174 11-39 (307)
3 PF01653 DNA_ligase_aden: NAD- 94.2 0.055 1.2E-06 52.0 4.1 26 148-173 16-42 (315)
4 smart00532 LIGANc Ligase N fam 93.4 0.08 1.7E-06 53.2 3.9 26 148-173 14-40 (441)
5 PRK07956 ligA NAD-dependent DN 93.2 0.09 2E-06 55.3 4.0 27 148-174 18-45 (665)
6 TIGR00575 dnlj DNA ligase, NAD 93.1 0.1 2.2E-06 54.8 4.2 29 146-174 5-34 (652)
7 cd00114 LIGANc NAD+ dependent 90.6 0.31 6.8E-06 46.8 4.2 35 96-130 4-38 (307)
8 PRK14351 ligA NAD-dependent DN 90.5 0.27 5.9E-06 52.1 4.0 27 148-174 45-72 (689)
9 PF01653 DNA_ligase_aden: NAD- 88.7 0.57 1.2E-05 45.1 4.3 35 95-129 7-41 (315)
10 smart00532 LIGANc Ligase N fam 88.6 0.47 1E-05 47.9 3.8 36 95-130 5-40 (441)
11 PRK14350 ligA NAD-dependent DN 88.1 0.53 1.1E-05 49.9 4.0 25 149-173 19-44 (669)
12 PRK08097 ligB NAD-dependent DN 86.9 0.62 1.4E-05 48.6 3.6 36 95-130 34-69 (562)
13 TIGR01206 lysW lysine biosynth 86.2 0.53 1.2E-05 35.3 2.0 29 274-302 24-52 (54)
14 PRK07956 ligA NAD-dependent DN 85.9 0.89 1.9E-05 48.0 4.2 36 95-130 9-44 (665)
15 PRK14351 ligA NAD-dependent DN 85.7 0.76 1.7E-05 48.8 3.6 36 95-130 36-71 (689)
16 TIGR00575 dnlj DNA ligase, NAD 82.3 1.2 2.7E-05 46.8 3.5 27 104-130 7-33 (652)
17 PRK14350 ligA NAD-dependent DN 80.9 1.4 3E-05 46.8 3.3 36 95-130 9-44 (669)
18 COG0272 Lig NAD-dependent DNA 80.5 1.8 3.8E-05 46.4 3.8 25 150-174 22-47 (667)
19 PF07754 DUF1610: Domain of un 78.9 0.86 1.9E-05 29.5 0.6 11 270-280 14-24 (24)
20 PF11023 DUF2614: Protein of u 77.9 2.5 5.5E-05 36.4 3.3 42 241-282 36-79 (114)
21 PF09851 SHOCT: Short C-termin 74.9 4.5 9.8E-05 26.8 3.2 25 147-173 5-30 (31)
22 COG5349 Uncharacterized protei 74.8 1.3 2.8E-05 38.7 0.8 17 271-287 20-39 (126)
23 COG2888 Predicted Zn-ribbon RN 74.0 1.5 3.3E-05 34.2 0.9 14 268-281 23-36 (61)
24 PF06170 DUF983: Protein of un 69.3 2.1 4.6E-05 34.6 0.8 32 266-297 2-34 (86)
25 smart00778 Prim_Zn_Ribbon Zinc 69.0 2.1 4.7E-05 30.0 0.7 13 272-284 3-17 (37)
26 PF09851 SHOCT: Short C-termin 67.5 7.4 0.00016 25.8 3.0 26 103-130 5-30 (31)
27 PF06906 DUF1272: Protein of u 66.8 2.4 5.2E-05 32.7 0.6 13 270-282 39-51 (57)
28 TIGR00340 zpr1_rel ZPR1-relate 66.1 5.5 0.00012 35.6 2.8 36 261-296 16-55 (163)
29 PRK05978 hypothetical protein; 65.0 3 6.5E-05 36.9 1.0 31 264-294 44-75 (148)
30 PF03367 zf-ZPR1: ZPR1 zinc-fi 62.1 7.1 0.00015 34.5 2.8 34 264-297 22-60 (161)
31 TIGR03831 YgiT_finger YgiT-typ 62.0 4.7 0.0001 27.1 1.3 16 267-282 23-42 (46)
32 smart00709 Zpr1 Duplicated dom 61.7 7.8 0.00017 34.4 2.9 33 264-296 21-58 (160)
33 PF08273 Prim_Zn_Ribbon: Zinc- 61.1 3.5 7.6E-05 29.3 0.6 12 272-283 3-16 (40)
34 TIGR00310 ZPR1_znf ZPR1 zinc f 61.0 7.9 0.00017 35.4 2.9 31 264-294 22-55 (192)
35 COG0272 Lig NAD-dependent DNA 59.4 11 0.00023 40.7 4.0 38 93-130 9-46 (667)
36 TIGR02098 MJ0042_CXXC MJ0042 f 57.7 5.5 0.00012 26.6 1.0 13 272-284 2-14 (38)
37 TIGR00097 HMP-P_kinase phospho 54.8 47 0.001 29.9 6.8 57 120-184 115-172 (254)
38 PF07508 Recombinase: Recombin 52.1 12 0.00027 28.6 2.3 20 155-174 82-101 (102)
39 PF09845 DUF2072: Zn-ribbon co 52.1 7.7 0.00017 34.1 1.3 23 269-292 17-40 (131)
40 PF11746 DUF3303: Protein of u 51.4 11 0.00025 30.3 2.1 70 96-165 11-89 (91)
41 PRK00420 hypothetical protein; 50.7 11 0.00025 32.0 2.1 28 257-284 8-36 (112)
42 PF13240 zinc_ribbon_2: zinc-r 50.5 6.6 0.00014 24.7 0.5 7 275-281 2-8 (23)
43 COG3813 Uncharacterized protei 50.1 6.8 0.00015 32.0 0.6 13 270-282 39-51 (84)
44 PF07503 zf-HYPF: HypF finger; 49.6 6.9 0.00015 27.1 0.5 12 274-285 23-34 (35)
45 PRK14890 putative Zn-ribbon RN 48.3 8.1 0.00018 29.9 0.7 12 270-281 23-34 (59)
46 PRK00398 rpoP DNA-directed RNA 46.0 11 0.00023 26.5 1.0 14 274-287 5-18 (46)
47 PRK08176 pdxK pyridoxal-pyrido 44.1 61 0.0013 30.0 5.9 53 123-183 143-196 (281)
48 PRK02935 hypothetical protein; 44.1 49 0.0011 28.6 4.8 42 245-286 41-84 (110)
49 PRK05978 hypothetical protein; 44.0 7.5 0.00016 34.5 -0.0 18 271-288 32-52 (148)
50 PF04216 FdhE: Protein involve 43.7 18 0.00038 34.0 2.4 40 251-290 151-192 (290)
51 PF13248 zf-ribbon_3: zinc-rib 41.6 11 0.00024 23.9 0.5 9 273-281 3-11 (26)
52 PF13717 zinc_ribbon_4: zinc-r 41.3 13 0.00029 25.4 0.9 13 272-284 2-14 (36)
53 PLN02919 haloacid dehalogenase 40.6 2.2E+02 0.0048 32.1 10.4 36 85-123 78-114 (1057)
54 COG3364 Zn-ribbon containing p 39.6 14 0.00031 31.7 1.0 22 267-289 16-38 (112)
55 PRK09710 lar restriction allev 38.8 18 0.0004 28.4 1.4 14 273-286 7-20 (64)
56 PF13719 zinc_ribbon_5: zinc-r 38.6 16 0.00034 25.0 0.9 13 272-284 2-14 (37)
57 PLN00049 carboxyl-terminal pro 37.9 66 0.0014 31.6 5.4 71 95-172 2-80 (389)
58 PRK12412 pyridoxal kinase; Rev 37.6 1.2E+02 0.0026 27.7 6.7 57 119-183 119-176 (268)
59 PF13005 zf-IS66: zinc-finger 36.3 26 0.00056 24.1 1.7 15 274-288 4-18 (47)
60 PRK13130 H/ACA RNA-protein com 35.9 16 0.00034 27.8 0.6 12 270-281 15-26 (56)
61 TIGR03829 YokU_near_AblA uncha 35.9 16 0.00035 30.2 0.7 10 274-283 37-46 (89)
62 PF02829 3H: 3H domain; Inter 35.5 82 0.0018 26.1 4.8 32 144-176 50-95 (98)
63 cd01169 HMPP_kinase 4-amino-5- 35.4 1.7E+02 0.0037 25.6 7.1 53 123-183 119-172 (242)
64 PF09538 FYDLN_acid: Protein o 35.1 16 0.00035 30.7 0.6 14 271-284 8-22 (108)
65 PF12677 DUF3797: Domain of un 34.6 18 0.00038 27.3 0.7 10 272-281 13-22 (49)
66 COG4443 Uncharacterized protei 34.5 24 0.00053 28.3 1.5 18 113-130 52-70 (72)
67 PF13913 zf-C2HC_2: zinc-finge 34.2 20 0.00043 22.7 0.8 10 273-282 3-12 (25)
68 smart00531 TFIIE Transcription 33.2 18 0.00039 31.0 0.6 14 272-285 99-112 (147)
69 PF08274 PhnA_Zn_Ribbon: PhnA 33.1 21 0.00046 24.1 0.8 14 273-286 3-16 (30)
70 cd07110 ALDH_F10_BADH Arabidop 33.0 1.3E+02 0.0029 29.6 6.6 70 116-185 238-334 (456)
71 PF14353 CpXC: CpXC protein 31.8 22 0.00047 29.3 0.9 15 267-281 33-47 (128)
72 PF04380 BMFP: Membrane fusoge 31.6 77 0.0017 25.0 3.9 36 94-130 25-60 (79)
73 PF04475 DUF555: Protein of un 31.2 24 0.00052 30.1 1.0 19 270-288 45-65 (102)
74 PF12767 SAGA-Tad1: Transcript 31.0 50 0.0011 30.5 3.2 36 92-130 19-55 (252)
75 PF04280 Tim44: Tim44-like dom 30.9 32 0.00069 28.2 1.7 37 139-175 21-62 (147)
76 PF05416 Peptidase_C37: Southa 30.8 16 0.00036 38.1 0.0 43 117-167 253-298 (535)
77 PF10571 UPF0547: Uncharacteri 30.8 22 0.00048 23.1 0.6 8 274-281 16-23 (26)
78 KOG4021 Mitochondrial ribosoma 30.4 23 0.0005 33.7 0.9 31 264-294 100-130 (239)
79 PRK03922 hypothetical protein; 30.4 25 0.00055 30.4 1.0 19 270-288 47-67 (113)
80 PF15616 TerY-C: TerY-C metal 29.3 22 0.00049 31.1 0.6 21 267-287 72-92 (131)
81 PF11793 FANCL_C: FANCL C-term 29.1 24 0.00052 27.0 0.6 18 266-283 49-66 (70)
82 PF03317 ELF: ELF protein; In 28.4 1.1E+02 0.0023 29.6 4.9 106 50-177 144-255 (284)
83 PF14255 Cys_rich_CPXG: Cystei 28.2 30 0.00066 25.8 1.0 12 274-285 2-13 (52)
84 PF05191 ADK_lid: Adenylate ki 28.0 22 0.00047 24.6 0.2 10 274-283 3-12 (36)
85 TIGR00686 phnA alkylphosphonat 27.9 32 0.00069 29.6 1.2 16 273-288 3-18 (109)
86 PF07295 DUF1451: Protein of u 27.8 29 0.00062 30.6 1.0 11 273-283 131-142 (146)
87 PF09930 DUF2162: Predicted tr 27.7 46 0.001 31.3 2.4 41 240-280 66-113 (224)
88 PRK11032 hypothetical protein; 27.2 35 0.00076 30.7 1.4 13 273-285 143-156 (160)
89 PF03884 DUF329: Domain of unk 27.2 32 0.00069 26.3 1.0 14 271-284 1-14 (57)
90 TIGR02300 FYDLN_acid conserved 26.9 27 0.00059 30.8 0.7 11 271-281 8-18 (129)
91 PF09863 DUF2090: Uncharacteri 26.6 1.7E+02 0.0036 29.3 6.0 56 94-149 188-254 (311)
92 PRK06427 bifunctional hydroxy- 26.3 2.5E+02 0.0054 25.2 6.7 54 123-184 124-179 (266)
93 COG1998 RPS31 Ribosomal protei 26.1 35 0.00076 25.9 1.0 13 268-280 15-27 (51)
94 PF01096 TFIIS_C: Transcriptio 26.1 34 0.00073 23.7 0.9 8 274-281 2-9 (39)
95 PRK12380 hydrogenase nickel in 25.8 35 0.00077 28.4 1.1 16 273-288 87-103 (113)
96 PF05193 Peptidase_M16_C: Pept 25.8 1.1E+02 0.0024 24.0 3.9 33 94-129 152-184 (184)
97 COG1885 Uncharacterized protei 25.4 37 0.0008 29.4 1.2 19 270-288 47-67 (115)
98 PRK03681 hypA hydrogenase nick 25.1 36 0.00079 28.4 1.1 17 273-289 88-105 (114)
99 PRK06266 transcription initiat 24.8 31 0.00067 30.9 0.7 30 257-286 102-131 (178)
100 PF10609 ParA: ParA/MinD ATPas 24.8 34 0.00074 27.6 0.8 14 273-286 66-79 (81)
101 PRK15398 aldehyde dehydrogenas 24.8 1.6E+02 0.0034 29.9 5.6 59 116-176 247-316 (465)
102 PF04423 Rad50_zn_hook: Rad50 24.6 28 0.00061 25.1 0.3 16 266-281 14-29 (54)
103 PRK10220 hypothetical protein; 24.5 37 0.00079 29.3 1.0 16 273-288 4-19 (111)
104 smart00834 CxxC_CXXC_SSSS Puta 24.3 41 0.00089 22.2 1.0 14 274-287 7-20 (41)
105 TIGR00777 ahpD alkylhydroperox 24.0 36 0.00078 31.2 0.9 27 149-175 78-105 (177)
106 PF14485 DUF4431: Domain of un 23.9 65 0.0014 23.6 2.1 22 159-183 5-26 (48)
107 PRK01103 formamidopyrimidine/5 23.8 53 0.0011 30.8 2.0 22 266-287 235-262 (274)
108 PRK12413 phosphomethylpyrimidi 23.5 3.2E+02 0.0068 24.4 6.8 45 132-183 128-173 (253)
109 PF10825 DUF2752: Protein of u 23.2 36 0.00078 24.9 0.6 15 274-288 11-28 (52)
110 PLN02898 HMP-P kinase/thiamin- 23.2 2.8E+02 0.0061 28.1 7.0 59 120-185 126-185 (502)
111 TIGR00373 conserved hypothetic 23.2 34 0.00075 29.9 0.6 14 272-285 109-122 (158)
112 PF04328 DUF466: Protein of un 22.6 1.6E+02 0.0035 22.7 4.1 34 144-177 26-59 (65)
113 PF14206 Cys_rich_CPCC: Cystei 22.4 38 0.00081 27.3 0.6 10 272-281 1-10 (78)
114 PF04267 SoxD: Sarcosine oxida 22.3 32 0.00068 28.2 0.2 14 274-287 3-20 (84)
115 PF08209 Sgf11: Sgf11 (transcr 22.3 43 0.00094 23.0 0.8 8 274-281 6-13 (33)
116 PF13058 DUF3920: Protein of u 22.0 39 0.00085 29.6 0.7 46 84-129 30-80 (126)
117 PF14803 Nudix_N_2: Nudix N-te 21.8 48 0.001 22.8 1.0 17 275-291 3-21 (34)
118 KOG3716 Carnitine O-acyltransf 21.8 52 0.0011 36.1 1.7 14 157-170 184-197 (764)
119 PF10711 DUF2513: Hypothetical 21.7 88 0.0019 25.3 2.7 36 125-179 65-100 (102)
120 PF02591 DUF164: Putative zinc 21.7 39 0.00084 24.5 0.5 7 274-280 48-54 (56)
121 PF01155 HypA: Hydrogenase exp 21.4 51 0.0011 27.3 1.2 15 275-289 89-104 (113)
122 PF06897 DUF1269: Protein of u 21.3 2.4E+02 0.0052 23.4 5.2 56 117-173 40-100 (102)
123 KOG3457 Sec61 protein transloc 21.1 46 0.00099 27.8 0.9 30 218-247 46-75 (88)
124 PF06044 DRP: Dam-replacing fa 21.0 33 0.00071 33.3 0.1 31 257-291 20-51 (254)
125 TIGR01031 rpmF_bact ribosomal 20.9 42 0.00092 25.1 0.6 9 273-281 27-35 (55)
126 cd07078 ALDH NAD(P)+ dependent 20.9 2.3E+02 0.0051 27.2 5.8 68 117-184 215-309 (432)
127 PF08278 DnaG_DnaB_bind: DNA p 20.9 1.8E+02 0.0039 23.5 4.3 47 94-149 79-125 (127)
128 KOG1372 GDP-mannose 4,6 dehydr 20.9 51 0.0011 32.9 1.3 39 99-137 257-309 (376)
129 PF01783 Ribosomal_L32p: Ribos 20.9 43 0.00093 24.8 0.6 9 273-281 27-35 (56)
130 smart00440 ZnF_C2C2 C2C2 Zinc 20.7 53 0.0012 22.8 1.1 8 274-281 2-9 (40)
131 PRK08351 DNA-directed RNA poly 20.7 42 0.00091 26.1 0.6 7 274-280 17-23 (61)
132 KOG4517 Uncharacterized conser 20.5 42 0.00091 29.2 0.6 12 272-283 106-117 (117)
133 cd00350 rubredoxin_like Rubred 20.5 37 0.00079 22.6 0.2 13 273-285 18-31 (33)
134 PRK12286 rpmF 50S ribosomal pr 20.5 44 0.00095 25.3 0.6 9 273-281 28-36 (57)
135 PRK00762 hypA hydrogenase nick 20.1 52 0.0011 27.8 1.1 19 272-290 92-111 (124)
136 PF08271 TF_Zn_Ribbon: TFIIB z 20.1 48 0.001 22.9 0.7 9 274-282 2-10 (43)
137 PF09889 DUF2116: Uncharacteri 20.1 44 0.00096 25.7 0.6 9 273-281 4-12 (59)
No 1
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=95.01 E-value=0.026 Score=58.42 Aligned_cols=49 Identities=35% Similarity=0.497 Sum_probs=33.9
Q ss_pred hHhhhhhcCCe---eEEeChhh--H--HHH-----HHHHhhhc-CCCccChHHHHHHHHHHh
Q 021649 125 LKEELMWEGSS---VVMLSSAE--Q--KFL-----EASMAYVA-GKPIMSDEEYDKLKQKLK 173 (309)
Q Consensus 125 LkEeL~WeGSs---vv~L~~~E--Q--~FL-----EA~~AY~~-GkPimsDeEFD~LK~kLk 173 (309)
|-.-|.|..|- |.+++..| + +.| ++-.+||. |+|+|||+|||+|..+|+
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~ 69 (562)
T PRK08097 8 LISLLLWSSSAWAVCPDWSPARAQEEIAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLT 69 (562)
T ss_pred HHHHHHhcccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 33457788876 55566554 1 112 22346775 999999999999999997
No 2
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=94.82 E-value=0.029 Score=53.69 Aligned_cols=28 Identities=32% Similarity=0.583 Sum_probs=23.5
Q ss_pred HHHHHhhhc-CCCccChHHHHHHHHHHhh
Q 021649 147 LEASMAYVA-GKPIMSDEEYDKLKQKLKM 174 (309)
Q Consensus 147 LEA~~AY~~-GkPimsDeEFD~LK~kLk~ 174 (309)
-++-.+||. |+|+|||+|||.|.++|+.
T Consensus 11 ~~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 39 (307)
T cd00114 11 NKHDYRYYVLDEPSVSDAEYDRLYRELRA 39 (307)
T ss_pred HHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 344567887 9999999999999999974
No 3
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=94.15 E-value=0.055 Score=51.96 Aligned_cols=26 Identities=50% Similarity=0.847 Sum_probs=22.1
Q ss_pred HHHHhhhc-CCCccChHHHHHHHHHHh
Q 021649 148 EASMAYVA-GKPIMSDEEYDKLKQKLK 173 (309)
Q Consensus 148 EA~~AY~~-GkPimsDeEFD~LK~kLk 173 (309)
++..+||. |+|+|||+|||.|..+|+
T Consensus 16 ~~~~~YY~~~~p~isD~eYD~l~~~L~ 42 (315)
T PF01653_consen 16 RHNYAYYNLGEPIISDAEYDQLFRELK 42 (315)
T ss_dssp HHHHHHHTTSSSSSSHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 34557777 899999999999999986
No 4
>smart00532 LIGANc Ligase N family.
Probab=93.40 E-value=0.08 Score=53.25 Aligned_cols=26 Identities=42% Similarity=0.755 Sum_probs=22.5
Q ss_pred HHHHhhhc-CCCccChHHHHHHHHHHh
Q 021649 148 EASMAYVA-GKPIMSDEEYDKLKQKLK 173 (309)
Q Consensus 148 EA~~AY~~-GkPimsDeEFD~LK~kLk 173 (309)
++..+||. |+|+|||+|||+|..+|+
T Consensus 14 ~~~~~YY~~~~p~IsD~eYD~L~~eL~ 40 (441)
T smart00532 14 KHDYRYYVLDAPIISDAEYDRLMRELK 40 (441)
T ss_pred HHHHHHHhcCCCCCChHHHHHHHHHHH
Confidence 34556876 999999999999999997
No 5
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=93.16 E-value=0.09 Score=55.26 Aligned_cols=27 Identities=37% Similarity=0.597 Sum_probs=23.5
Q ss_pred HHHHhhh-cCCCccChHHHHHHHHHHhh
Q 021649 148 EASMAYV-AGKPIMSDEEYDKLKQKLKM 174 (309)
Q Consensus 148 EA~~AY~-~GkPimsDeEFD~LK~kLk~ 174 (309)
++-.+|| .|+|+|||+|||.|.++|+.
T Consensus 18 ~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 45 (665)
T PRK07956 18 HHAYAYYVLDAPSISDAEYDRLYRELVA 45 (665)
T ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 4456788 99999999999999999973
No 6
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=93.11 E-value=0.1 Score=54.78 Aligned_cols=29 Identities=31% Similarity=0.556 Sum_probs=24.5
Q ss_pred HHHHHHhhhc-CCCccChHHHHHHHHHHhh
Q 021649 146 FLEASMAYVA-GKPIMSDEEYDKLKQKLKM 174 (309)
Q Consensus 146 FLEA~~AY~~-GkPimsDeEFD~LK~kLk~ 174 (309)
.-++..+||. |+|+|||+|||.|.++|+.
T Consensus 5 l~~~~~~YY~~~~p~IsD~eYD~L~~~L~~ 34 (652)
T TIGR00575 5 IRHHDYRYYVLDEPSISDAEYDRLYRELQE 34 (652)
T ss_pred HHHHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 3455667886 9999999999999999974
No 7
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=90.60 E-value=0.31 Score=46.77 Aligned_cols=35 Identities=26% Similarity=0.366 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 96 GELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 96 ge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
-++...--.+=..||..+.+++||+|||.|.++|.
T Consensus 4 ~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~ 38 (307)
T cd00114 4 AELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELR 38 (307)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 34555555556678888999999999999999984
No 8
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=90.52 E-value=0.27 Score=52.11 Aligned_cols=27 Identities=30% Similarity=0.600 Sum_probs=22.7
Q ss_pred HHHHhhh-cCCCccChHHHHHHHHHHhh
Q 021649 148 EASMAYV-AGKPIMSDEEYDKLKQKLKM 174 (309)
Q Consensus 148 EA~~AY~-~GkPimsDeEFD~LK~kLk~ 174 (309)
++-.+|| .|+|+|||+|||.|.++|+.
T Consensus 45 ~~~~~YY~~~~p~IsD~eYD~L~~eL~~ 72 (689)
T PRK14351 45 EHDHRYYVEADPVIADRAYDALFARLQA 72 (689)
T ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHHH
Confidence 4455777 57999999999999999973
No 9
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=88.68 E-value=0.57 Score=45.10 Aligned_cols=35 Identities=34% Similarity=0.582 Sum_probs=27.7
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 021649 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL 129 (309)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL 129 (309)
+-++...--.+=..||..+.++|||+|||.|.++|
T Consensus 7 i~~L~~~i~~~~~~YY~~~~p~isD~eYD~l~~~L 41 (315)
T PF01653_consen 7 IEELRKEINRHNYAYYNLGEPIISDAEYDQLFREL 41 (315)
T ss_dssp HHHHHHHHHHHHHHHHTTSSSSSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence 34455555566678999999999999999999885
No 10
>smart00532 LIGANc Ligase N family.
Probab=88.58 E-value=0.47 Score=47.87 Aligned_cols=36 Identities=25% Similarity=0.420 Sum_probs=28.6
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
+-++...-..+-..||..+.+++||+|||.|.+||.
T Consensus 5 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~ 40 (441)
T smart00532 5 ISELRKLLNKHDYRYYVLDAPIISDAEYDRLMRELK 40 (441)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHHH
Confidence 444555555566678889999999999999999985
No 11
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=88.06 E-value=0.53 Score=49.89 Aligned_cols=25 Identities=28% Similarity=0.397 Sum_probs=21.3
Q ss_pred HHHhhh-cCCCccChHHHHHHHHHHh
Q 021649 149 ASMAYV-AGKPIMSDEEYDKLKQKLK 173 (309)
Q Consensus 149 A~~AY~-~GkPimsDeEFD~LK~kLk 173 (309)
.-.+|| .|+|+|||++||.|..+|+
T Consensus 19 ~~~~YY~~~~p~IsD~~YD~L~~eL~ 44 (669)
T PRK14350 19 WDKEYYVDSSPSVEDFTYDKALLRLQ 44 (669)
T ss_pred HHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 345677 5799999999999999996
No 12
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=86.90 E-value=0.62 Score=48.58 Aligned_cols=36 Identities=28% Similarity=0.535 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
+-++...--.+=..||..+.|++||+|||.|.+||.
T Consensus 34 i~~L~~~l~~~~~~YY~~~~p~IsD~eYD~L~~eL~ 69 (562)
T PRK08097 34 IAALQQQLAQWDDAYWRQGKSEVDDEVYDQLRARLT 69 (562)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 444444555556679999999999999999999984
No 13
>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=86.24 E-value=0.53 Score=35.34 Aligned_cols=29 Identities=17% Similarity=0.291 Sum_probs=26.0
Q ss_pred cCCCCccceeecccCCCceeeeeeeCCCc
Q 021649 274 MFLSLGPYYQFLVVEPPTLLTAQIVEPPW 302 (309)
Q Consensus 274 pCPNCGee~aFv~~~~p~~~~~~~~~~~~ 302 (309)
.||+||.++.-+..++++|-.|.-++--|
T Consensus 24 ~Cp~CGaeleVv~~~p~~L~~ap~~~eDw 52 (54)
T TIGR01206 24 ICDECGAELEVVSLDPLRLEAAPEEAEDW 52 (54)
T ss_pred eCCCCCCEEEEEeCCCCEEEeCccccccc
Confidence 79999999888999999999888887777
No 14
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=85.86 E-value=0.89 Score=48.02 Aligned_cols=36 Identities=31% Similarity=0.504 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
+-++...--.+=..||..+.+++||+|||.|.++|.
T Consensus 9 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~~L~ 44 (665)
T PRK07956 9 IEELREELNHHAYAYYVLDAPSISDAEYDRLYRELV 44 (665)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 344444455555678889999999999999999986
No 15
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=85.71 E-value=0.76 Score=48.83 Aligned_cols=36 Identities=19% Similarity=0.390 Sum_probs=30.1
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
+-++...--.+=..||..+.+++||+|||.|.+||.
T Consensus 36 i~~L~~~i~~~~~~YY~~~~p~IsD~eYD~L~~eL~ 71 (689)
T PRK14351 36 AEQLREAIREHDHRYYVEADPVIADRAYDALFARLQ 71 (689)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 556666666666789999999999999999999996
No 16
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=82.33 E-value=1.2 Score=46.81 Aligned_cols=27 Identities=26% Similarity=0.411 Sum_probs=23.0
Q ss_pred HHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 104 QALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 104 ~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
.+-..||..+.|++||+|||.|.+||.
T Consensus 7 ~~~~~YY~~~~p~IsD~eYD~L~~~L~ 33 (652)
T TIGR00575 7 HHDYRYYVLDEPSISDAEYDRLYRELQ 33 (652)
T ss_pred HHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 344568888999999999999999985
No 17
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=80.89 E-value=1.4 Score=46.79 Aligned_cols=36 Identities=11% Similarity=0.200 Sum_probs=27.0
Q ss_pred hhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 95 LGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 95 lge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
+-++...--..=..||..+.|++||+|||.|.+||.
T Consensus 9 i~~L~~~i~~~~~~YY~~~~p~IsD~~YD~L~~eL~ 44 (669)
T PRK14350 9 ILDLKKLIRKWDKEYYVDSSPSVEDFTYDKALLRLQ 44 (669)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence 444444444445568889999999999999999984
No 18
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=80.51 E-value=1.8 Score=46.39 Aligned_cols=25 Identities=36% Similarity=0.616 Sum_probs=21.5
Q ss_pred HHhhhc-CCCccChHHHHHHHHHHhh
Q 021649 150 SMAYVA-GKPIMSDEEYDKLKQKLKM 174 (309)
Q Consensus 150 ~~AY~~-GkPimsDeEFD~LK~kLk~ 174 (309)
..+||- ++|+|+|+|||+|.++|..
T Consensus 22 ~~~Yyv~d~P~VsD~eYD~L~reL~~ 47 (667)
T COG0272 22 DYRYYVLDAPSVSDAEYDQLYRELQE 47 (667)
T ss_pred HHHHhccCCCCCChHHHHHHHHHHHH
Confidence 456666 9999999999999999975
No 19
>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=78.86 E-value=0.86 Score=29.52 Aligned_cols=11 Identities=9% Similarity=-0.182 Sum_probs=8.3
Q ss_pred eeeccCCCCcc
Q 021649 270 ILKRMFLSLGP 280 (309)
Q Consensus 270 iLKGpCPNCGe 280 (309)
...=.|||||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 44568999995
No 20
>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=77.90 E-value=2.5 Score=36.37 Aligned_cols=42 Identities=12% Similarity=0.155 Sum_probs=24.4
Q ss_pred hhhhhHHhhhhHHHHHHHHHHHhhhc--cceeeeccCCCCccce
Q 021649 241 SFIFTWFAAVPLIVYLSQSLTKLIVR--ESLILKRMFLSLGPYY 282 (309)
Q Consensus 241 gfi~tw~~~~P~i~~~a~~Lt~l~~~--D~liLKGpCPNCGee~ 282 (309)
.++.+.|+.+.++..++....=.|.+ -.-+.--.|||||.+.
T Consensus 36 ~~im~ifmllG~L~~l~S~~VYfwIGmlStkav~V~CP~C~K~T 79 (114)
T PF11023_consen 36 PIIMVIFMLLGLLAILASTAVYFWIGMLSTKAVQVECPNCGKQT 79 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcccceeeECCCCCChH
Confidence 34555566666666665555554442 2233444599999874
No 21
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=74.85 E-value=4.5 Score=26.83 Aligned_cols=25 Identities=40% Similarity=0.590 Sum_probs=19.7
Q ss_pred HHHHHh-hhcCCCccChHHHHHHHHHHh
Q 021649 147 LEASMA-YVAGKPIMSDEEYDKLKQKLK 173 (309)
Q Consensus 147 LEA~~A-Y~~GkPimsDeEFD~LK~kLk 173 (309)
|+.+.. |-+| +||++||++.|.+|.
T Consensus 5 L~~L~~l~~~G--~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 5 LEKLKELYDKG--EISEEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHHcC--CCCHHHHHHHHHHHh
Confidence 455555 7777 799999999999884
No 22
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.82 E-value=1.3 Score=38.66 Aligned_cols=17 Identities=29% Similarity=0.221 Sum_probs=12.6
Q ss_pred eeccCCCCccc---eeeccc
Q 021649 271 LKRMFLSLGPY---YQFLVV 287 (309)
Q Consensus 271 LKGpCPNCGee---~aFv~~ 287 (309)
|+|.||+|||= -.|+++
T Consensus 20 l~grCP~CGeGrLF~gFLK~ 39 (126)
T COG5349 20 LRGRCPRCGEGRLFRGFLKV 39 (126)
T ss_pred hcCCCCCCCCchhhhhhccc
Confidence 68889999873 567765
No 23
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=73.99 E-value=1.5 Score=34.16 Aligned_cols=14 Identities=14% Similarity=-0.026 Sum_probs=10.9
Q ss_pred ceeeeccCCCCccc
Q 021649 268 SLILKRMFLSLGPY 281 (309)
Q Consensus 268 ~liLKGpCPNCGee 281 (309)
--.++=+||||||+
T Consensus 23 e~~v~F~CPnCGe~ 36 (61)
T COG2888 23 ETAVKFPCPNCGEV 36 (61)
T ss_pred CceeEeeCCCCCce
Confidence 34678899999964
No 24
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=69.29 E-value=2.1 Score=34.55 Aligned_cols=32 Identities=19% Similarity=0.180 Sum_probs=22.5
Q ss_pred ccceeeeccCCCCccceeeccc-CCCceeeeee
Q 021649 266 RESLILKRMFLSLGPYYQFLVV-EPPTLLTAQI 297 (309)
Q Consensus 266 ~D~liLKGpCPNCGee~aFv~~-~~p~~~~~~~ 297 (309)
+.++-+.-.|++||+.|.+... +-|+-++--|
T Consensus 2 ~g~Lk~~~~C~~CG~d~~~~~adDgPA~fvi~i 34 (86)
T PF06170_consen 2 RGYLKVAPRCPHCGLDYSHARADDGPAYFVILI 34 (86)
T ss_pred CccccCCCcccccCCccccCCcCccchhHHHHH
Confidence 4456788899999999888764 3466554433
No 25
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=69.04 E-value=2.1 Score=29.98 Aligned_cols=13 Identities=15% Similarity=0.263 Sum_probs=10.2
Q ss_pred eccCCCCccc--eee
Q 021649 272 KRMFLSLGPY--YQF 284 (309)
Q Consensus 272 KGpCPNCGee--~aF 284 (309)
++|||+||-. |.|
T Consensus 3 ~~pCP~CGG~DrFr~ 17 (37)
T smart00778 3 HGPCPNCGGSDRFRF 17 (37)
T ss_pred ccCCCCCCCcccccc
Confidence 5899999953 764
No 26
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=67.46 E-value=7.4 Score=25.79 Aligned_cols=26 Identities=35% Similarity=0.684 Sum_probs=21.4
Q ss_pred HHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 103 LQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 103 l~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
+..|...|..| .+|+|||...|.+|.
T Consensus 5 L~~L~~l~~~G--~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 5 LEKLKELYDKG--EISEEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHHcC--CCCHHHHHHHHHHHh
Confidence 46677888777 699999999999874
No 27
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=66.81 E-value=2.4 Score=32.66 Aligned_cols=13 Identities=15% Similarity=0.169 Sum_probs=10.3
Q ss_pred eeeccCCCCccce
Q 021649 270 ILKRMFLSLGPYY 282 (309)
Q Consensus 270 iLKGpCPNCGee~ 282 (309)
.|.|-|||||-++
T Consensus 39 ~l~~~CPNCgGel 51 (57)
T PF06906_consen 39 MLNGVCPNCGGEL 51 (57)
T ss_pred HhcCcCcCCCCcc
Confidence 3589999999763
No 28
>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=66.05 E-value=5.5 Score=35.56 Aligned_cols=36 Identities=8% Similarity=0.004 Sum_probs=27.3
Q ss_pred HHh-hhccceeeeccCCCCcc---ceeecccCCCceeeee
Q 021649 261 TKL-IVRESLILKRMFLSLGP---YYQFLVVEPPTLLTAQ 296 (309)
Q Consensus 261 t~l-~~~D~liLKGpCPNCGe---e~aFv~~~~p~~~~~~ 296 (309)
++. -|++.+|+...||+||- +.++.+..+|..+|-.
T Consensus 16 ~~IP~F~evii~sf~C~~CGyr~~ev~~~~~~~p~r~~l~ 55 (163)
T TIGR00340 16 YDIPYFGKIMLSTYICEKCGYRSTDVYQLEEKEPVRYIIK 55 (163)
T ss_pred ccCCCcceEEEEEEECCCCCCchhheeEcCCcCCEEEEEE
Confidence 444 58999999999999993 5788777777555543
No 29
>PRK05978 hypothetical protein; Provisional
Probab=65.04 E-value=3 Score=36.95 Aligned_cols=31 Identities=16% Similarity=0.140 Sum_probs=19.7
Q ss_pred hhccceeeeccCCCCccceeecc-cCCCceee
Q 021649 264 IVRESLILKRMFLSLGPYYQFLV-VEPPTLLT 294 (309)
Q Consensus 264 ~~~D~liLKGpCPNCGee~aFv~-~~~p~~~~ 294 (309)
+++-++-+.-.||+||+.|.+-+ .+-|+-++
T Consensus 44 LF~g~Lkv~~~C~~CG~~~~~~~a~DgpAy~~ 75 (148)
T PRK05978 44 LFRAFLKPVDHCAACGEDFTHHRADDLPAYLV 75 (148)
T ss_pred ccccccccCCCccccCCccccCCccccCcchh
Confidence 34555677777777777777763 35566544
No 30
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=62.05 E-value=7.1 Score=34.47 Aligned_cols=34 Identities=15% Similarity=0.045 Sum_probs=23.5
Q ss_pred hhccceeeeccCCCCcc---ceeecccCCCc--eeeeee
Q 021649 264 IVRESLILKRMFLSLGP---YYQFLVVEPPT--LLTAQI 297 (309)
Q Consensus 264 ~~~D~liLKGpCPNCGe---e~aFv~~~~p~--~~~~~~ 297 (309)
.|++.+|+...|++||- +.++.+.-+|. -+|-.+
T Consensus 22 ~F~evii~sf~C~~CGyk~~ev~~~~~~~~~G~r~tl~V 60 (161)
T PF03367_consen 22 YFKEVIIMSFECEHCGYKNNEVKSGGQIQPKGVRITLKV 60 (161)
T ss_dssp TTEEEEEEEEE-TTT--EEEEEEEECSS-SSEEEEEEEE
T ss_pred CCceEEEEEeECCCCCCEeeeEEECccCCCCceEEEEEE
Confidence 47999999999999993 57877777777 555443
No 31
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=61.99 E-value=4.7 Score=27.13 Aligned_cols=16 Identities=19% Similarity=0.337 Sum_probs=10.6
Q ss_pred cceeeec-c---CCCCccce
Q 021649 267 ESLILKR-M---FLSLGPYY 282 (309)
Q Consensus 267 D~liLKG-p---CPNCGee~ 282 (309)
..+++++ | ||+|||++
T Consensus 23 ~~~~i~~vp~~~C~~CGE~~ 42 (46)
T TIGR03831 23 ELIVIENVPALVCPQCGEEY 42 (46)
T ss_pred EEEEEeCCCccccccCCCEe
Confidence 3455544 4 99999873
No 32
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=61.71 E-value=7.8 Score=34.37 Aligned_cols=33 Identities=18% Similarity=0.049 Sum_probs=25.9
Q ss_pred hhccceeeeccCCCCcc---ceeecccCCCc--eeeee
Q 021649 264 IVRESLILKRMFLSLGP---YYQFLVVEPPT--LLTAQ 296 (309)
Q Consensus 264 ~~~D~liLKGpCPNCGe---e~aFv~~~~p~--~~~~~ 296 (309)
-|++.+|+...||+||- +.++.+.-+|. .+|-.
T Consensus 21 ~F~evii~sf~C~~CGyk~~ev~~~~~~~p~G~r~~l~ 58 (160)
T smart00709 21 YFREVIIMSFECEHCGYRNNEVKSGGAIEPKGTRITLK 58 (160)
T ss_pred CcceEEEEEEECCCCCCccceEEECcccCCCceEEEEE
Confidence 47999999999999993 68887777777 44443
No 33
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=61.15 E-value=3.5 Score=29.33 Aligned_cols=12 Identities=8% Similarity=0.011 Sum_probs=7.1
Q ss_pred eccCCCCccc--ee
Q 021649 272 KRMFLSLGPY--YQ 283 (309)
Q Consensus 272 KGpCPNCGee--~a 283 (309)
.+|||+||-. |.
T Consensus 3 h~pCP~CGG~DrFr 16 (40)
T PF08273_consen 3 HGPCPICGGKDRFR 16 (40)
T ss_dssp EE--TTTT-TTTEE
T ss_pred CCCCCCCcCccccc
Confidence 5899999954 66
No 34
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=60.98 E-value=7.9 Score=35.38 Aligned_cols=31 Identities=16% Similarity=0.039 Sum_probs=24.0
Q ss_pred hhccceeeeccCCCCcc---ceeecccCCCceee
Q 021649 264 IVRESLILKRMFLSLGP---YYQFLVVEPPTLLT 294 (309)
Q Consensus 264 ~~~D~liLKGpCPNCGe---e~aFv~~~~p~~~~ 294 (309)
.|++.+|+...||+||- +.++.+..+|..++
T Consensus 22 ~F~evii~sf~C~~CGyr~~ev~~~g~~~p~r~~ 55 (192)
T TIGR00310 22 YFGEVLETSTICEHCGYRSNDVKTLGAKEPKRYI 55 (192)
T ss_pred CcceEEEEEEECCCCCCccceeEECCCCCCEEEE
Confidence 47999999999999993 57777666666444
No 35
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=59.38 E-value=11 Score=40.70 Aligned_cols=38 Identities=24% Similarity=0.358 Sum_probs=30.5
Q ss_pred cchhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 93 KSLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 93 ~slge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
+-+.++.+.--..-.+||..+.|.++|.|||.|..||.
T Consensus 9 ~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~ 46 (667)
T COG0272 9 EEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQ 46 (667)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCCChHHHHHHHHHHH
Confidence 34566666666667789999999999999999988773
No 36
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=57.67 E-value=5.5 Score=26.58 Aligned_cols=13 Identities=0% Similarity=-0.013 Sum_probs=9.0
Q ss_pred eccCCCCccceee
Q 021649 272 KRMFLSLGPYYQF 284 (309)
Q Consensus 272 KGpCPNCGee~aF 284 (309)
+-.||+||+.|..
T Consensus 2 ~~~CP~C~~~~~v 14 (38)
T TIGR02098 2 RIQCPNCKTSFRV 14 (38)
T ss_pred EEECCCCCCEEEe
Confidence 4468888886554
No 37
>TIGR00097 HMP-P_kinase phosphomethylpyrimidine kinase. This model represents phosphomethylpyrimidine kinase, the ThiD protein of thiamine biosynthesis. The protein is commonly observed within operons containing other thiamine biosynthesis genes. Numerous examples are fusion proteins with other thiamine-biosynthetic domains. Saccaromyces has three recent paralogs, two of which are isofunctional and score above the trusted cutoff. The third shows a longer branch length in a phylogenetic tree and scores below the trusted cutoff, as do putative second copies in a number of species.
Probab=54.83 E-value=47 Score=29.90 Aligned_cols=57 Identities=21% Similarity=0.388 Sum_probs=40.4
Q ss_pred HHHhhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCCc-eeeecC
Q 021649 120 EEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSE-IVVEGP 184 (309)
Q Consensus 120 eefd~LkEeL~WeGSsvv~L~~~EQ~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eGS~-VVvk~P 184 (309)
+..+.++++| .....+++.+..|-+.| .|.++-+.++..+.-.+|...|-+ |++++-
T Consensus 115 ~~~~~~~~~l-l~~~dvitpN~~Ea~~L-------~g~~~~~~~~~~~~a~~l~~~g~~~Vvvt~G 172 (254)
T TIGR00097 115 EAIEALRKRL-LPLATLITPNLPEAEAL-------LGTKIRTEQDMIKAAKKLRELGPKAVLIKGG 172 (254)
T ss_pred HHHHHHHHhc-cccccEecCCHHHHHHH-------hCCCCCCHHHHHHHHHHHHhcCCCEEEEeCC
Confidence 3445566655 35667999999998877 356666777777778888877865 777764
No 38
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=52.11 E-value=12 Score=28.61 Aligned_cols=20 Identities=35% Similarity=0.717 Sum_probs=17.1
Q ss_pred cCCCccChHHHHHHHHHHhh
Q 021649 155 AGKPIMSDEEYDKLKQKLKM 174 (309)
Q Consensus 155 ~GkPimsDeEFD~LK~kLk~ 174 (309)
.-.||||+++|+++...|+.
T Consensus 82 ~~~~IIs~~~f~~vq~~l~~ 101 (102)
T PF07508_consen 82 YHPPIISEEEFERVQKKLDE 101 (102)
T ss_pred CCCCccCHHHHHHHHHHHhc
Confidence 34699999999999999863
No 39
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=52.11 E-value=7.7 Score=34.12 Aligned_cols=23 Identities=22% Similarity=0.203 Sum_probs=18.9
Q ss_pred eeeeccCCCCcc-ceeecccCCCce
Q 021649 269 LILKRMFLSLGP-YYQFLVVEPPTL 292 (309)
Q Consensus 269 liLKGpCPNCGe-e~aFv~~~~p~~ 292 (309)
.||+| ||+||- -|+|++.+....
T Consensus 17 eil~G-CP~CGg~kF~yv~~~~~~~ 40 (131)
T PF09845_consen 17 EILSG-CPECGGNKFQYVPEEKDAE 40 (131)
T ss_pred HHHcc-CcccCCcceEEcCCCcccc
Confidence 57777 999995 599999887665
No 40
>PF11746 DUF3303: Protein of unknown function (DUF3303); InterPro: IPR021734 Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature.
Probab=51.38 E-value=11 Score=30.29 Aligned_cols=70 Identities=27% Similarity=0.307 Sum_probs=49.6
Q ss_pred hHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhhh-cCCeeEEeChhhHHHHHHHHh-hhcC-------CCccChHHH
Q 021649 96 GELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMW-EGSSVVMLSSAEQKFLEASMA-YVAG-------KPIMSDEEY 165 (309)
Q Consensus 96 ge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~W-eGSsvv~L~~~EQ~FLEA~~A-Y~~G-------kPimsDeEF 165 (309)
++..+.--+++.+|+..|++...-|.|..|..=..= .|..++.+..+..+-|-+-.+ ..+. .|+|+|+|+
T Consensus 11 ~~~~~~~~~~~~~~~~~G~~~~~peG~~~l~rw~~~~~g~g~~i~eadd~~~l~~~~~~W~~~fg~~~ei~Pv~~d~e~ 89 (91)
T PF11746_consen 11 GESQQEAYKAFERFMESGAPGDPPEGFKVLGRWHDPGGGRGFAIVEADDAKALFKHFAPWRDLFGMEFEITPVMTDEEA 89 (91)
T ss_pred cccchhHHHHHHHHHhcCCCCCCCCCEEEEEEEEecCCCcEEEEEEeCCHHHHHHHHhhhhhccCceEEEEecccHHHh
Confidence 455566778999999999888777877777654333 566677776666666655444 4444 699999997
No 41
>PRK00420 hypothetical protein; Validated
Probab=50.72 E-value=11 Score=32.03 Aligned_cols=28 Identities=11% Similarity=0.276 Sum_probs=20.8
Q ss_pred HHHHHHhhhccceeeeccCCCCccc-eee
Q 021649 257 SQSLTKLIVRESLILKRMFLSLGPY-YQF 284 (309)
Q Consensus 257 a~~Lt~l~~~D~liLKGpCPNCGee-~aF 284 (309)
++.+..++++=...|...||.||.+ |.+
T Consensus 8 ~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~l 36 (112)
T PRK00420 8 VKKAAELLLKGAKMLSKHCPVCGLPLFEL 36 (112)
T ss_pred HHHHHHHHHhHHHHccCCCCCCCCcceec
Confidence 4566677777666788999999976 654
No 42
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=50.51 E-value=6.6 Score=24.70 Aligned_cols=7 Identities=14% Similarity=0.026 Sum_probs=5.9
Q ss_pred CCCCccc
Q 021649 275 FLSLGPY 281 (309)
Q Consensus 275 CPNCGee 281 (309)
||+||.+
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 8999965
No 43
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.08 E-value=6.8 Score=32.02 Aligned_cols=13 Identities=15% Similarity=0.069 Sum_probs=10.5
Q ss_pred eeeccCCCCccce
Q 021649 270 ILKRMFLSLGPYY 282 (309)
Q Consensus 270 iLKGpCPNCGee~ 282 (309)
.|.|-|||||-+.
T Consensus 39 ~l~g~CPnCGGel 51 (84)
T COG3813 39 RLHGLCPNCGGEL 51 (84)
T ss_pred hhcCcCCCCCchh
Confidence 4789999999663
No 44
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=49.57 E-value=6.9 Score=27.09 Aligned_cols=12 Identities=25% Similarity=0.559 Sum_probs=8.4
Q ss_pred cCCCCccceeec
Q 021649 274 MFLSLGPYYQFL 285 (309)
Q Consensus 274 pCPNCGee~aFv 285 (309)
.|++||..+.++
T Consensus 23 sC~~CGPr~~i~ 34 (35)
T PF07503_consen 23 SCTNCGPRYSII 34 (35)
T ss_dssp -BTTCC-SCCCE
T ss_pred cCCCCCCCEEEe
Confidence 699999988765
No 45
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=48.26 E-value=8.1 Score=29.94 Aligned_cols=12 Identities=17% Similarity=0.143 Sum_probs=9.4
Q ss_pred eeeccCCCCccc
Q 021649 270 ILKRMFLSLGPY 281 (309)
Q Consensus 270 iLKGpCPNCGee 281 (309)
..+=.|||||++
T Consensus 23 ~~~F~CPnCG~~ 34 (59)
T PRK14890 23 AVKFLCPNCGEV 34 (59)
T ss_pred cCEeeCCCCCCe
Confidence 456689999975
No 46
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=45.97 E-value=11 Score=26.45 Aligned_cols=14 Identities=7% Similarity=-0.152 Sum_probs=9.1
Q ss_pred cCCCCccceeeccc
Q 021649 274 MFLSLGPYYQFLVV 287 (309)
Q Consensus 274 pCPNCGee~aFv~~ 287 (309)
-|||||.++.|-..
T Consensus 5 ~C~~CG~~~~~~~~ 18 (46)
T PRK00398 5 KCARCGREVELDEY 18 (46)
T ss_pred ECCCCCCEEEECCC
Confidence 48888877665433
No 47
>PRK08176 pdxK pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase; Reviewed
Probab=44.13 E-value=61 Score=29.99 Aligned_cols=53 Identities=15% Similarity=0.142 Sum_probs=39.8
Q ss_pred hhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC-ceeeec
Q 021649 123 DNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS-EIVVEG 183 (309)
Q Consensus 123 d~LkEeL~WeGSsvv~L~~~EQ~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eGS-~VVvk~ 183 (309)
..+|++| .....+++.+..|.++| .|.++-++++..+.-.+|...|. .|++++
T Consensus 143 ~~~~~~L-l~~advitPN~~Ea~~L-------~g~~~~~~~~~~~~~~~l~~~g~~~VvIT~ 196 (281)
T PRK08176 143 EAYRQHL-LPLAQGLTPNIFELEIL-------TGKPCRTLDSAIAAAKSLLSDTLKWVVITS 196 (281)
T ss_pred HHHHHHh-HhhcCEeCCCHHHHHHH-------hCCCCCCHHHHHHHHHHHHhcCCCEEEEee
Confidence 4566655 47788999999998887 47777788877777777877785 466665
No 48
>PRK02935 hypothetical protein; Provisional
Probab=44.10 E-value=49 Score=28.57 Aligned_cols=42 Identities=10% Similarity=0.121 Sum_probs=21.2
Q ss_pred hHHhhhhHHHHHHHHHHHhhhc--cceeeeccCCCCccceeecc
Q 021649 245 TWFAAVPLIVYLSQSLTKLIVR--ESLILKRMFLSLGPYYQFLV 286 (309)
Q Consensus 245 tw~~~~P~i~~~a~~Lt~l~~~--D~liLKGpCPNCGee~aFv~ 286 (309)
+.|+.+=++..++....=.|.+ -.-+..-.||||+.+.--++
T Consensus 41 ~ifm~~G~l~~l~S~vvYFwiGmlStkavqV~CP~C~K~TKmLG 84 (110)
T PRK02935 41 TIFMLLGFLAVIASTVVYFWIGMLSTKAVQVICPSCEKPTKMLG 84 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcccceeeECCCCCchhhhcc
Confidence 3344344444444444333332 22445558999998744433
No 49
>PRK05978 hypothetical protein; Provisional
Probab=43.96 E-value=7.5 Score=34.48 Aligned_cols=18 Identities=17% Similarity=0.080 Sum_probs=13.4
Q ss_pred eeccCCCCccc---eeecccC
Q 021649 271 LKRMFLSLGPY---YQFLVVE 288 (309)
Q Consensus 271 LKGpCPNCGee---~aFv~~~ 288 (309)
|+|-||+||+- ..|+++.
T Consensus 32 l~grCP~CG~G~LF~g~Lkv~ 52 (148)
T PRK05978 32 FRGRCPACGEGKLFRAFLKPV 52 (148)
T ss_pred HcCcCCCCCCCcccccccccC
Confidence 68999999984 4566554
No 50
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=43.65 E-value=18 Score=34.01 Aligned_cols=40 Identities=13% Similarity=0.093 Sum_probs=17.9
Q ss_pred hHHHHHHHHHHHhhhccceeeeccCCCCccc--eeecccCCC
Q 021649 251 PLIVYLSQSLTKLIVRESLILKRMFLSLGPY--YQFLVVEPP 290 (309)
Q Consensus 251 P~i~~~a~~Lt~l~~~D~liLKGpCPNCGee--~aFv~~~~p 290 (309)
|+.-..+..+..-.....---+|-||.||.. ...|.++.+
T Consensus 151 ~~~~~~a~~l~~~~~~~~~w~~g~CPvCGs~P~~s~l~~~~~ 192 (290)
T PF04216_consen 151 PFLAALAAALDAALLPPEGWQRGYCPVCGSPPVLSVLRGGER 192 (290)
T ss_dssp HHHHHHHHT--TTSSS---TT-SS-TTT---EEEEEEE----
T ss_pred HHHHHHHHhccccccccCCccCCcCCCCCCcCceEEEecCCC
Confidence 6665666555544544444557999999964 777777654
No 51
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=41.56 E-value=11 Score=23.89 Aligned_cols=9 Identities=11% Similarity=0.017 Sum_probs=6.9
Q ss_pred ccCCCCccc
Q 021649 273 RMFLSLGPY 281 (309)
Q Consensus 273 GpCPNCGee 281 (309)
-.|||||.+
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 369999974
No 52
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=41.31 E-value=13 Score=25.38 Aligned_cols=13 Identities=8% Similarity=-0.026 Sum_probs=9.8
Q ss_pred eccCCCCccceee
Q 021649 272 KRMFLSLGPYYQF 284 (309)
Q Consensus 272 KGpCPNCGee~aF 284 (309)
+-.||||+..|..
T Consensus 2 ~i~Cp~C~~~y~i 14 (36)
T PF13717_consen 2 IITCPNCQAKYEI 14 (36)
T ss_pred EEECCCCCCEEeC
Confidence 3469999988765
No 53
>PLN02919 haloacid dehalogenase-like hydrolase family protein
Probab=40.62 E-value=2.2e+02 Score=32.06 Aligned_cols=36 Identities=22% Similarity=0.218 Sum_probs=18.4
Q ss_pred cccccccccchhHHHHHHHHHHHHhhhc-CccccChHHHh
Q 021649 85 CSIDKKEKKSLGELEQEFLQALQAFYYE-GKAVMSNEEFD 123 (309)
Q Consensus 85 CsiD~~~k~slge~E~~fl~Al~~fY~~-gk~~msneefd 123 (309)
+-.|=++ ||-+-|..+.+|++..+.+ |. .++.+++.
T Consensus 78 VIFDlDG--TLiDS~~~~~~a~~~~~~~~G~-~it~e~~~ 114 (1057)
T PLN02919 78 VLFDMDG--VLCNSEEPSRRAAVDVFAEMGV-EVTVEDFV 114 (1057)
T ss_pred EEECCCC--CeEeChHHHHHHHHHHHHHcCC-CCCHHHHH
Confidence 4455443 4555555666666555543 33 34555553
No 54
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=39.61 E-value=14 Score=31.73 Aligned_cols=22 Identities=18% Similarity=0.173 Sum_probs=18.1
Q ss_pred cceeeeccCCCCcc-ceeecccCC
Q 021649 267 ESLILKRMFLSLGP-YYQFLVVEP 289 (309)
Q Consensus 267 D~liLKGpCPNCGe-e~aFv~~~~ 289 (309)
|-.||.| ||+||- -|.+|+.|.
T Consensus 16 ~~~il~G-Cp~CG~nkF~yv~~e~ 38 (112)
T COG3364 16 SEEILSG-CPKCGCNKFLYVPEEK 38 (112)
T ss_pred cHHHHcc-CccccchheEeccccc
Confidence 4567776 999996 599999987
No 55
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=38.79 E-value=18 Score=28.42 Aligned_cols=14 Identities=7% Similarity=-0.287 Sum_probs=10.2
Q ss_pred ccCCCCccceeecc
Q 021649 273 RMFLSLGPYYQFLV 286 (309)
Q Consensus 273 GpCPNCGee~aFv~ 286 (309)
-|||.||.+..-++
T Consensus 7 KPCPFCG~~~~~v~ 20 (64)
T PRK09710 7 KPCPFCGCPSVTVK 20 (64)
T ss_pred cCCCCCCCceeEEE
Confidence 38999998755444
No 56
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=38.61 E-value=16 Score=25.01 Aligned_cols=13 Identities=0% Similarity=-0.120 Sum_probs=9.1
Q ss_pred eccCCCCccceee
Q 021649 272 KRMFLSLGPYYQF 284 (309)
Q Consensus 272 KGpCPNCGee~aF 284 (309)
+-.||||+..|.-
T Consensus 2 ~i~CP~C~~~f~v 14 (37)
T PF13719_consen 2 IITCPNCQTRFRV 14 (37)
T ss_pred EEECCCCCceEEc
Confidence 3469999987653
No 57
>PLN00049 carboxyl-terminal processing protease; Provisional
Probab=37.88 E-value=66 Score=31.62 Aligned_cols=71 Identities=17% Similarity=0.247 Sum_probs=45.9
Q ss_pred hhHHHHHHHHH---HHHhhhcCccccChHHHhhhHhhhhhcCCeeEEeChhhHHHHHHHH---h-hhcCCC-ccChHHHH
Q 021649 95 LGELEQEFLQA---LQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEASM---A-YVAGKP-IMSDEEYD 166 (309)
Q Consensus 95 lge~E~~fl~A---l~~fY~~gk~~msneefd~LkEeL~WeGSsvv~L~~~EQ~FLEA~~---A-Y~~GkP-imsDeEFD 166 (309)
+-|..|+|.+| ++.+||+.+ |...+|+.+||+.-|.- . +...+ ++..|+. + .-+.-- .++-++|.
T Consensus 2 ~~~~~~~f~e~w~~v~~~~~d~~--~~g~dW~~~~e~y~~~~-~---~~~~~-~~~~~i~~ml~~L~D~hs~y~~~~~~~ 74 (389)
T PLN00049 2 LTEENLLFLEAWRTVDRAYVDKT--FNGQSWFRYRENALKNE-P---MNTRE-ETYAAIRKMLATLDDPFTRFLEPEKFK 74 (389)
T ss_pred CccHHHHHHHHHHHHHHHHcCcc--ccccCHHHHHHHHhhcc-C---CCcHH-HHHHHHHHHHhhCCCCcccCcCHHHHH
Confidence 34678999998 667888875 89999999999999974 2 22222 3333422 2 111111 67788888
Q ss_pred HHHHHH
Q 021649 167 KLKQKL 172 (309)
Q Consensus 167 ~LK~kL 172 (309)
.+....
T Consensus 75 ~~~~~~ 80 (389)
T PLN00049 75 SLRSGT 80 (389)
T ss_pred HHHHhc
Confidence 776543
No 58
>PRK12412 pyridoxal kinase; Reviewed
Probab=37.64 E-value=1.2e+02 Score=27.75 Aligned_cols=57 Identities=26% Similarity=0.311 Sum_probs=42.3
Q ss_pred hHHHhhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC-ceeeec
Q 021649 119 NEEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS-EIVVEG 183 (309)
Q Consensus 119 neefd~LkEeL~WeGSsvv~L~~~EQ~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eGS-~VVvk~ 183 (309)
++..+.++++|. ....+++.+..|-+.| .|.++-+.++..+.-.+|...|- .|++++
T Consensus 119 ~~~~~~~~~~ll-~~advitpN~~Ea~~L-------~g~~~~~~~~~~~aa~~l~~~g~~~ViIt~ 176 (268)
T PRK12412 119 PETNDCLRDVLV-PKALVVTPNLFEAYQL-------SGVKINSLEDMKEAAKKIHALGAKYVLIKG 176 (268)
T ss_pred hHHHHHHHHhhh-ccceEEcCCHHHHHHH-------hCcCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence 345567787765 5678999999998877 47777777777777788887786 466664
No 59
>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=36.30 E-value=26 Score=24.14 Aligned_cols=15 Identities=13% Similarity=-0.080 Sum_probs=11.0
Q ss_pred cCCCCccceeecccC
Q 021649 274 MFLSLGPYYQFLVVE 288 (309)
Q Consensus 274 pCPNCGee~aFv~~~ 288 (309)
.||+||....-++.+
T Consensus 4 ~C~~Cg~~l~~ig~~ 18 (47)
T PF13005_consen 4 ACPDCGGELKEIGEE 18 (47)
T ss_pred cCCCCCceeeECCce
Confidence 699999987744443
No 60
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=35.88 E-value=16 Score=27.82 Aligned_cols=12 Identities=25% Similarity=0.191 Sum_probs=9.5
Q ss_pred eeeccCCCCccc
Q 021649 270 ILKRMFLSLGPY 281 (309)
Q Consensus 270 iLKGpCPNCGee 281 (309)
-||..||+||+.
T Consensus 15 TLk~~CP~CG~~ 26 (56)
T PRK13130 15 TLKEICPVCGGK 26 (56)
T ss_pred EccccCcCCCCC
Confidence 358889999975
No 61
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=35.87 E-value=16 Score=30.17 Aligned_cols=10 Identities=30% Similarity=0.202 Sum_probs=8.2
Q ss_pred cCCCCcccee
Q 021649 274 MFLSLGPYYQ 283 (309)
Q Consensus 274 pCPNCGee~a 283 (309)
.|++||+.|.
T Consensus 37 ~C~~CGe~y~ 46 (89)
T TIGR03829 37 SCSHCGMEYQ 46 (89)
T ss_pred cccCCCcEee
Confidence 5999999764
No 62
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=35.52 E-value=82 Score=26.11 Aligned_cols=32 Identities=34% Similarity=0.618 Sum_probs=24.8
Q ss_pred HHHHHHHHhhhcCCCcc--------------ChHHHHHHHHHHhhhC
Q 021649 144 QKFLEASMAYVAGKPIM--------------SDEEYDKLKQKLKMEG 176 (309)
Q Consensus 144 Q~FLEA~~AY~~GkPim--------------sDeEFD~LK~kLk~eG 176 (309)
++|++.+..+ .++|+. +.+.+|+++++|+.+|
T Consensus 50 ~~Fi~~l~~~-~~~~Ls~LT~GvH~HtI~a~~~e~l~~I~~~L~~~G 95 (98)
T PF02829_consen 50 DKFIEKLEKS-KAKPLSSLTGGVHYHTIEAPDEEDLDKIEEALKKKG 95 (98)
T ss_dssp HHHHHHHHH---S--STTGGGGEEEEEEEESSHHHHHHHHHHHHHTT
T ss_pred HHHHHHHhcc-CCcchHHhcCCEeeEEEEECCHHHHHHHHHHHHHCC
Confidence 8999999888 788875 4689999999999998
No 63
>cd01169 HMPP_kinase 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction.
Probab=35.42 E-value=1.7e+02 Score=25.57 Aligned_cols=53 Identities=23% Similarity=0.394 Sum_probs=37.1
Q ss_pred hhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC-ceeeec
Q 021649 123 DNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS-EIVVEG 183 (309)
Q Consensus 123 d~LkEeL~WeGSsvv~L~~~EQ~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eGS-~VVvk~ 183 (309)
+.++++| +....+++.+..|-+.| .|.++-++++-.+...+|...|- .|++++
T Consensus 119 ~~~~~~l-l~~~dvitpN~~Ea~~L-------~g~~~~~~~~~~~~~~~l~~~g~~~Vvit~ 172 (242)
T cd01169 119 EALRELL-LPLATLITPNLPEAELL-------TGLEIATEEDMMKAAKALLALGAKAVLIKG 172 (242)
T ss_pred HHHHHHh-hccCeEEeCCHHHHHHH-------hCCCCCCHHHHHHHHHHHHhcCCCEEEEec
Confidence 4566655 67788999999998877 36666565555556677777775 466664
No 64
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=35.09 E-value=16 Score=30.71 Aligned_cols=14 Identities=36% Similarity=0.456 Sum_probs=8.8
Q ss_pred eeccCCCCccc-eee
Q 021649 271 LKRMFLSLGPY-YQF 284 (309)
Q Consensus 271 LKGpCPNCGee-~aF 284 (309)
.|--||+||.- |-.
T Consensus 8 tKR~Cp~CG~kFYDL 22 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDL 22 (108)
T ss_pred CcccCCCCcchhccC
Confidence 46677777765 443
No 65
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=34.60 E-value=18 Score=27.29 Aligned_cols=10 Identities=10% Similarity=-0.240 Sum_probs=8.8
Q ss_pred eccCCCCccc
Q 021649 272 KRMFLSLGPY 281 (309)
Q Consensus 272 KGpCPNCGee 281 (309)
++.||+||.+
T Consensus 13 Y~~Cp~CGN~ 22 (49)
T PF12677_consen 13 YCKCPKCGND 22 (49)
T ss_pred hccCcccCCc
Confidence 7899999975
No 66
>COG4443 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.54 E-value=24 Score=28.29 Aligned_cols=18 Identities=50% Similarity=0.772 Sum_probs=15.0
Q ss_pred Ccc-ccChHHHhhhHhhhh
Q 021649 113 GKA-VMSNEEFDNLKEELM 130 (309)
Q Consensus 113 gk~-~msneefd~LkEeL~ 130 (309)
||- +||||||..||+.|+
T Consensus 52 GKGiTLt~eE~~~l~d~l~ 70 (72)
T COG4443 52 GKGITLTNEEFKALKDLLN 70 (72)
T ss_pred cCceeecHHHHHHHHHHHh
Confidence 444 899999999999874
No 67
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=34.24 E-value=20 Score=22.73 Aligned_cols=10 Identities=10% Similarity=-0.067 Sum_probs=7.9
Q ss_pred ccCCCCccce
Q 021649 273 RMFLSLGPYY 282 (309)
Q Consensus 273 GpCPNCGee~ 282 (309)
-+||.||..|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 3799999754
No 68
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=33.15 E-value=18 Score=31.00 Aligned_cols=14 Identities=21% Similarity=0.171 Sum_probs=11.0
Q ss_pred eccCCCCccceeec
Q 021649 272 KRMFLSLGPYYQFL 285 (309)
Q Consensus 272 KGpCPNCGee~aFv 285 (309)
.=-||+||..|.|.
T Consensus 99 ~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 99 YYKCPNCQSKYTFL 112 (147)
T ss_pred EEECcCCCCEeeHH
Confidence 44599999888774
No 69
>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=33.05 E-value=21 Score=24.07 Aligned_cols=14 Identities=14% Similarity=0.062 Sum_probs=4.1
Q ss_pred ccCCCCccceeecc
Q 021649 273 RMFLSLGPYYQFLV 286 (309)
Q Consensus 273 GpCPNCGee~aFv~ 286 (309)
..||.||.+|++.-
T Consensus 3 p~Cp~C~se~~y~D 16 (30)
T PF08274_consen 3 PKCPLCGSEYTYED 16 (30)
T ss_dssp ---TTT-----EE-
T ss_pred CCCCCCCCcceecc
Confidence 47999999887743
No 70
>cd07110 ALDH_F10_BADH Arabidopsis betaine aldehyde dehydrogenase 1 and 2, ALDH family 10A8 and 10A9-like. Present in this CD are the Arabidopsis betaine aldehyde dehydrogenase (BADH) 1 (chloroplast) and 2 (mitochondria), also known as, aldehyde dehydrogenase family 10 member A8 and aldehyde dehydrogenase family 10 member A9, respectively, and are putative dehydration- and salt-inducible BADHs (EC 1.2.1.8) that catalyze the oxidation of betaine aldehyde to the compatible solute glycine betaine.
Probab=33.00 E-value=1.3e+02 Score=29.56 Aligned_cols=70 Identities=26% Similarity=0.493 Sum_probs=46.6
Q ss_pred ccChHHHhhhHhhhhhc-----CC-----eeEEeC-hhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHH
Q 021649 116 VMSNEEFDNLKEELMWE-----GS-----SVVMLS-SAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQK 171 (309)
Q Consensus 116 ~msneefd~LkEeL~We-----GS-----svv~L~-~~EQ~FLEA~~A----Y~~Gk---------PimsDeEFD~LK~k 171 (309)
++.|.+.|..-+.+.|. |. +.+.+- ..-.+|++++.+ +.-|. |+++.+.+++++.-
T Consensus 238 V~~dadl~~aa~~i~~~~~~~~GQ~C~a~~rv~V~~~i~d~f~~~l~~~~~~~~~g~p~~~~~~~Gpli~~~~~~~~~~~ 317 (456)
T cd07110 238 VFDDADLEKAVEWAMFGCFWNNGQICSATSRLLVHESIADAFLERLATAAEAIRVGDPLEEGVRLGPLVSQAQYEKVLSF 317 (456)
T ss_pred ECCCCCHHHHHHHHHHHHHhcCCCCCCCCceEEEcHHHHHHHHHHHHHHHHhcCCCCCCCCCCCcCCCCCHHHHHHHHHH
Confidence 45577888877777765 33 333343 335678887654 33343 68899999999988
Q ss_pred Hhh---hCCceeeecCc
Q 021649 172 LKM---EGSEIVVEGPR 185 (309)
Q Consensus 172 Lk~---eGS~VVvk~Pr 185 (309)
+++ +|.+++.-|.+
T Consensus 318 v~~a~~~Ga~~~~gg~~ 334 (456)
T cd07110 318 IARGKEEGARLLCGGRR 334 (456)
T ss_pred HHHHHhCCCEEEeCCCc
Confidence 765 68787775543
No 71
>PF14353 CpXC: CpXC protein
Probab=31.78 E-value=22 Score=29.30 Aligned_cols=15 Identities=13% Similarity=0.071 Sum_probs=11.0
Q ss_pred cceeeeccCCCCccc
Q 021649 267 ESLILKRMFLSLGPY 281 (309)
Q Consensus 267 D~liLKGpCPNCGee 281 (309)
|--+..-.||+||..
T Consensus 33 ~g~l~~~~CP~Cg~~ 47 (128)
T PF14353_consen 33 DGSLFSFTCPSCGHK 47 (128)
T ss_pred cCCcCEEECCCCCCc
Confidence 444556789999975
No 72
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=31.62 E-value=77 Score=24.98 Aligned_cols=36 Identities=28% Similarity=0.344 Sum_probs=30.2
Q ss_pred chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 94 slge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
...|.|..+-..+++.+.. ....|.||||.+++.|.
T Consensus 25 ~~~e~e~~~r~~l~~~l~k-ldlVtREEFd~q~~~L~ 60 (79)
T PF04380_consen 25 PREEIEKNIRARLQSALSK-LDLVTREEFDAQKAVLA 60 (79)
T ss_pred hHHHHHHHHHHHHHHHHHH-CCCCcHHHHHHHHHHHH
Confidence 4467899999999998865 77899999999998854
No 73
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=31.18 E-value=24 Score=30.08 Aligned_cols=19 Identities=16% Similarity=0.235 Sum_probs=13.3
Q ss_pred eeeccCCCCccc--eeecccC
Q 021649 270 ILKRMFLSLGPY--YQFLVVE 288 (309)
Q Consensus 270 iLKGpCPNCGee--~aFv~~~ 288 (309)
+=.-.||.||++ -+|+..+
T Consensus 45 vG~~~cP~Cge~~~~a~vva~ 65 (102)
T PF04475_consen 45 VGDTICPKCGEELDSAFVVAD 65 (102)
T ss_pred cCcccCCCCCCccCceEEEec
Confidence 334579999987 6676554
No 74
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=30.98 E-value=50 Score=30.52 Aligned_cols=36 Identities=31% Similarity=0.550 Sum_probs=30.8
Q ss_pred ccchh-HHHHHHHHHHHHhhhcCccccChHHHhhhHhhhh
Q 021649 92 KKSLG-ELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELM 130 (309)
Q Consensus 92 k~slg-e~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~ 130 (309)
.+.|| |....|.+.|..|+-.+ +|.+|||.+=..+.
T Consensus 19 ~~~LG~~~~~~Y~~~l~~fl~~k---lsk~Efd~~~~~~L 55 (252)
T PF12767_consen 19 QKRLGPDRWKKYFQSLKRFLSGK---LSKEEFDKECRRIL 55 (252)
T ss_pred HHHHChHHHHHHHHHHHHHHHhc---cCHHHHHHHHHHHh
Confidence 45789 99999999999999854 89999999877754
No 75
>PF04280 Tim44: Tim44-like domain; InterPro: IPR007379 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane []. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005744 mitochondrial inner membrane presequence translocase complex; PDB: 2CW9_A 2FXT_A 3QK9_A.
Probab=30.91 E-value=32 Score=28.25 Aligned_cols=37 Identities=30% Similarity=0.668 Sum_probs=30.0
Q ss_pred eChhhHHHHHHHHhhhcCC-----CccChHHHHHHHHHHhhh
Q 021649 139 LSSAEQKFLEASMAYVAGK-----PIMSDEEYDKLKQKLKME 175 (309)
Q Consensus 139 L~~~EQ~FLEA~~AY~~Gk-----PimsDeEFD~LK~kLk~e 175 (309)
+...++.|+....||.+|+ +.++++.|..++.++++.
T Consensus 21 ~~~ak~~f~~i~~A~~~~D~~~l~~~~t~~~~~~~~~~i~~~ 62 (147)
T PF04280_consen 21 LEEAKEAFLPIQEAWAKGDLEALRPLLTEELYERLQAEIKAR 62 (147)
T ss_dssp HHHHHHTHHHHHHHHHHT-HHHHHHHB-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHhCHHHHHHHHHHHHHH
Confidence 4456778888777899985 899999999999999988
No 76
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=30.82 E-value=16 Score=38.08 Aligned_cols=43 Identities=26% Similarity=0.382 Sum_probs=0.0
Q ss_pred cChHHHhh---hHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHH
Q 021649 117 MSNEEFDN---LKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDK 167 (309)
Q Consensus 117 msneefd~---LkEeL~WeGSsvv~L~~~EQ~FLEA~~AY~~GkPimsDeEFD~ 167 (309)
|||||||. +||| |.|.-- =|+|||.++-||+.-.+..-.++|-
T Consensus 253 LSDEEYDEyKkiREe--r~g~YS------IeEYLqdReRy~Eela~~~a~~~~~ 298 (535)
T PF05416_consen 253 LSDEEYDEYKKIREE--RGGKYS------IEEYLQDRERYEEELAEAQATEEDF 298 (535)
T ss_dssp ------------------------------------------------------
T ss_pred CChhHHHHHHHHHHH--hcCCcc------HHHHHHHHHHHHHHhhhhhhhhccc
Confidence 99999886 5666 665432 1899999999998877765544443
No 77
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=30.75 E-value=22 Score=23.10 Aligned_cols=8 Identities=13% Similarity=-0.102 Sum_probs=4.9
Q ss_pred cCCCCccc
Q 021649 274 MFLSLGPY 281 (309)
Q Consensus 274 pCPNCGee 281 (309)
.||+||-+
T Consensus 16 ~Cp~CG~~ 23 (26)
T PF10571_consen 16 FCPHCGYD 23 (26)
T ss_pred cCCCCCCC
Confidence 46777644
No 78
>KOG4021 consensus Mitochondrial ribosomal protein S18b [Translation, ribosomal structure and biogenesis]
Probab=30.41 E-value=23 Score=33.68 Aligned_cols=31 Identities=19% Similarity=0.195 Sum_probs=28.3
Q ss_pred hhccceeeeccCCCCccceeecccCCCceee
Q 021649 264 IVRESLILKRMFLSLGPYYQFLVVEPPTLLT 294 (309)
Q Consensus 264 ~~~D~liLKGpCPNCGee~aFv~~~~p~~~~ 294 (309)
|.+|-+-+--|||-|--||-.|--+||.||.
T Consensus 100 Irkn~~~~gnpCPICRDeyL~~DyRN~~LlE 130 (239)
T KOG4021|consen 100 IRKNGRFLGNPCPICRDEYLYFDYRNPGLLE 130 (239)
T ss_pred HhhcCeecCCCCCccccceEEEeccCHHHHH
Confidence 7788888999999999999999999999985
No 79
>PRK03922 hypothetical protein; Provisional
Probab=30.37 E-value=25 Score=30.41 Aligned_cols=19 Identities=16% Similarity=0.182 Sum_probs=13.6
Q ss_pred eeeccCCCCccc--eeecccC
Q 021649 270 ILKRMFLSLGPY--YQFLVVE 288 (309)
Q Consensus 270 iLKGpCPNCGee--~aFv~~~ 288 (309)
+=.-.||.||++ -+|+..+
T Consensus 47 vG~~~cP~cge~~~~afvvA~ 67 (113)
T PRK03922 47 VGLTICPKCGEPFDSAFVVAD 67 (113)
T ss_pred cCcccCCCCCCcCCcEEEEec
Confidence 344579999987 6776654
No 80
>PF15616 TerY-C: TerY-C metal binding domain
Probab=29.33 E-value=22 Score=31.08 Aligned_cols=21 Identities=29% Similarity=0.243 Sum_probs=16.4
Q ss_pred cceeeeccCCCCccceeeccc
Q 021649 267 ESLILKRMFLSLGPYYQFLVV 287 (309)
Q Consensus 267 D~liLKGpCPNCGee~aFv~~ 287 (309)
|-+|=..-||.||++++|+.-
T Consensus 72 seL~g~PgCP~CGn~~~fa~C 92 (131)
T PF15616_consen 72 SELIGAPGCPHCGNQYAFAVC 92 (131)
T ss_pred HHhcCCCCCCCCcChhcEEEe
Confidence 334555889999999999864
No 81
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=29.07 E-value=24 Score=27.03 Aligned_cols=18 Identities=0% Similarity=-0.250 Sum_probs=10.1
Q ss_pred ccceeeeccCCCCcccee
Q 021649 266 RESLILKRMFLSLGPYYQ 283 (309)
Q Consensus 266 ~D~liLKGpCPNCGee~a 283 (309)
+.+..+.|.||.|.++.+
T Consensus 49 ~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 49 QSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp -TTT--EEE-TTT-SEEE
T ss_pred eeecccccCCcCCCCeee
Confidence 456788999999997643
No 82
>PF03317 ELF: ELF protein; InterPro: IPR004990 This is a family of hypothetical proteins from cereal crops.
Probab=28.41 E-value=1.1e+02 Score=29.62 Aligned_cols=106 Identities=20% Similarity=0.248 Sum_probs=68.6
Q ss_pred ccccccccccCCcccccccCCccCccccccccccccccccccccchhHHHHHHHHHHHHhhhcCccccC----hHHHhhh
Q 021649 50 FTVRRRSFVLPSKATTDQQGQVEGDEVVDSKILQYCSIDKKEKKSLGELEQEFLQALQAFYYEGKAVMS----NEEFDNL 125 (309)
Q Consensus 50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~i~~yCsiD~~~k~slge~E~~fl~Al~~fY~~gk~~ms----neefd~L 125 (309)
++-|-|+|++..+-+.-.++-+||=-...+++++|--|..- .-.+|+++|-..=.++.+ ..-|..|
T Consensus 144 IPGRLrLFLMEE~~S~~R~DliQefvalY~r~g~~LPiEPY----------lleealrSYlD~i~atD~fsiLqAaYQdL 213 (284)
T PF03317_consen 144 IPGRLRLFLMEEKLSSMRQDLIQEFVALYQRSGPVLPIEPY----------LLEEALRSYLDHIHATDSFSILQAAYQDL 213 (284)
T ss_pred CcchhhhhhhHhHHHHHHHHHHHHHHHHHHccCCcccccHH----------HHHHHHHHHHHhhcccccHHHHHHHHHHH
Confidence 44566788887776665566666644456666666555321 223456666555333332 7889999
Q ss_pred HhhhhhcCCeeEEeChh--hHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC
Q 021649 126 KEELMWEGSSVVMLSSA--EQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS 177 (309)
Q Consensus 126 kEeL~WeGSsvv~L~~~--EQ~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eGS 177 (309)
+|+ +|-|+....-- .|.||||-.+- .-+-+++++.+|+|-
T Consensus 214 ren---e~GS~FF~~~VSHNrD~LeA~ss~---------Rr~~Eveqrirw~~I 255 (284)
T PF03317_consen 214 REN---EEGSVFFRDVVSHNRDFLEAESSA---------RRCLEVEQRIRWEEI 255 (284)
T ss_pred Hhc---CCCcEEeHhhhhccHhHHHHHhhh---------hHHHHHHHHhhhhhh
Confidence 998 77777665543 59999996543 346788899999873
No 83
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=28.19 E-value=30 Score=25.84 Aligned_cols=12 Identities=17% Similarity=0.044 Sum_probs=9.3
Q ss_pred cCCCCccceeec
Q 021649 274 MFLSLGPYYQFL 285 (309)
Q Consensus 274 pCPNCGee~aFv 285 (309)
.||.||+.+.++
T Consensus 2 ~CPyCge~~~~~ 13 (52)
T PF14255_consen 2 QCPYCGEPIEIL 13 (52)
T ss_pred CCCCCCCeeEEE
Confidence 599999976554
No 84
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=28.02 E-value=22 Score=24.58 Aligned_cols=10 Identities=20% Similarity=0.401 Sum_probs=8.0
Q ss_pred cCCCCcccee
Q 021649 274 MFLSLGPYYQ 283 (309)
Q Consensus 274 pCPNCGee~a 283 (309)
-||+||..|.
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 4999999754
No 85
>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=27.93 E-value=32 Score=29.62 Aligned_cols=16 Identities=6% Similarity=-0.101 Sum_probs=12.5
Q ss_pred ccCCCCccceeecccC
Q 021649 273 RMFLSLGPYYQFLVVE 288 (309)
Q Consensus 273 GpCPNCGee~aFv~~~ 288 (309)
-+||.|+.+|++--++
T Consensus 3 p~CP~C~seytY~dg~ 18 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT 18 (109)
T ss_pred CcCCcCCCcceEecCC
Confidence 4799999988876554
No 86
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=27.85 E-value=29 Score=30.63 Aligned_cols=11 Identities=9% Similarity=0.005 Sum_probs=8.4
Q ss_pred ccCCCCcc-cee
Q 021649 273 RMFLSLGP-YYQ 283 (309)
Q Consensus 273 GpCPNCGe-e~a 283 (309)
-|||+||. +|+
T Consensus 131 ~~Cp~C~~~~F~ 142 (146)
T PF07295_consen 131 PPCPKCGHTEFT 142 (146)
T ss_pred CCCCCCCCCeee
Confidence 58999995 454
No 87
>PF09930 DUF2162: Predicted transporter (DUF2162); InterPro: IPR017199 This group represents a predicted membrane transporter, MTH672 type.
Probab=27.75 E-value=46 Score=31.25 Aligned_cols=41 Identities=17% Similarity=0.058 Sum_probs=28.1
Q ss_pred chhhhhHHhhhhHHHHHHHHHHHh--h-----hccceeeeccCCCCcc
Q 021649 240 FSFIFTWFAAVPLIVYLSQSLTKL--I-----VRESLILKRMFLSLGP 280 (309)
Q Consensus 240 ~gfi~tw~~~~P~i~~~a~~Lt~l--~-----~~D~liLKGpCPNCGe 280 (309)
+|+.....+++=+++|.-..+-+- - .+.++++--|||+|-.
T Consensus 66 yg~~~h~imal~li~~Gi~ti~~W~~~~~~~s~~t~lal~~PCPvCl~ 113 (224)
T PF09930_consen 66 YGMVIHLIMALLLIYAGIYTIKKWKKSGKDSSRRTFLALSLPCPVCLT 113 (224)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHcccCCCCcccchhhhhcCchHHHH
Confidence 344545566777777777777443 1 3557999999999974
No 88
>PRK11032 hypothetical protein; Provisional
Probab=27.22 E-value=35 Score=30.72 Aligned_cols=13 Identities=15% Similarity=0.094 Sum_probs=9.0
Q ss_pred ccCCCCcc-ceeec
Q 021649 273 RMFLSLGP-YYQFL 285 (309)
Q Consensus 273 GpCPNCGe-e~aFv 285 (309)
-|||+||. +|+=.
T Consensus 143 ~pCp~C~~~~F~R~ 156 (160)
T PRK11032 143 PLCPKCGHDQFQRR 156 (160)
T ss_pred CCCCCCCCCeeeeC
Confidence 58999995 56533
No 89
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=27.20 E-value=32 Score=26.28 Aligned_cols=14 Identities=7% Similarity=0.007 Sum_probs=6.9
Q ss_pred eeccCCCCccceee
Q 021649 271 LKRMFLSLGPYYQF 284 (309)
Q Consensus 271 LKGpCPNCGee~aF 284 (309)
+|-.||.||....+
T Consensus 1 m~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 1 MTVKCPICGKPVEW 14 (57)
T ss_dssp -EEE-TTT--EEE-
T ss_pred CcccCCCCCCeecc
Confidence 46789999986554
No 90
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=26.87 E-value=27 Score=30.77 Aligned_cols=11 Identities=27% Similarity=0.320 Sum_probs=8.1
Q ss_pred eeccCCCCccc
Q 021649 271 LKRMFLSLGPY 281 (309)
Q Consensus 271 LKGpCPNCGee 281 (309)
.|--||+||..
T Consensus 8 tKr~Cp~cg~k 18 (129)
T TIGR02300 8 TKRICPNTGSK 18 (129)
T ss_pred ccccCCCcCcc
Confidence 46778888875
No 91
>PF09863 DUF2090: Uncharacterized protein conserved in bacteria (DUF2090); InterPro: IPR018659 This domain, found in various prokaryotic carbohydrate kinases, has no known function.
Probab=26.58 E-value=1.7e+02 Score=29.26 Aligned_cols=56 Identities=18% Similarity=0.274 Sum_probs=43.0
Q ss_pred chhHHHHHHHHHHHHhhhcCc-------cccChHHHhhhHhhhhhcCCe---eEEeChhh-HHHHHH
Q 021649 94 SLGELEQEFLQALQAFYYEGK-------AVMSNEEFDNLKEELMWEGSS---VVMLSSAE-QKFLEA 149 (309)
Q Consensus 94 slge~E~~fl~Al~~fY~~gk-------~~msneefd~LkEeL~WeGSs---vv~L~~~E-Q~FLEA 149 (309)
+....+.-|..+|+.||+-|- +-||.+.|.++-+-..=.++- ||+||.+- .+.|.+
T Consensus 188 ~~~~~~~~~~~ai~r~Y~lGI~PDWWKLep~s~~~W~~i~~~I~~~Dp~crGvVvLGLdAP~e~L~~ 254 (311)
T PF09863_consen 188 DMPVDDDTYARAIERFYNLGIKPDWWKLEPLSAAAWQAIEALIEERDPYCRGVVVLGLDAPEEELAA 254 (311)
T ss_pred CCCCChHHHHHHHHHHHHcCCCCCeeccCCCCHHHHHHHHHHHHHhCCCceeEEEecCCCCHHHHHH
Confidence 345568899999999999873 467999999999888777774 78998763 344444
No 92
>PRK06427 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed
Probab=26.25 E-value=2.5e+02 Score=25.18 Aligned_cols=54 Identities=22% Similarity=0.388 Sum_probs=36.4
Q ss_pred hhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHH-HHHHHHHHhhhCC-ceeeecC
Q 021649 123 DNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEE-YDKLKQKLKMEGS-EIVVEGP 184 (309)
Q Consensus 123 d~LkEeL~WeGSsvv~L~~~EQ~FLEA~~AY~~GkPimsDeE-FD~LK~kLk~eGS-~VVvk~P 184 (309)
+.++++| .....+++.+..|-+.| .|.++-++++ ..+.-.+|...|- .|++++-
T Consensus 124 ~~~~~~l-l~~~dvitpN~~Ea~~L-------~g~~~~~~~~~~~~~a~~l~~~g~~~Vvit~g 179 (266)
T PRK06427 124 AALRERL-LPLATLITPNLPEAEAL-------TGLPIADTEDEMKAAARALHALGCKAVLIKGG 179 (266)
T ss_pred HHHHHhh-hCcCeEEcCCHHHHHHH-------hCCCCCCcHHHHHHHHHHHHhcCCCEEEEcCC
Confidence 4566654 35577999999998877 3666655554 5566667777775 5666653
No 93
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=26.09 E-value=35 Score=25.93 Aligned_cols=13 Identities=23% Similarity=0.230 Sum_probs=10.0
Q ss_pred ceeeeccCCCCcc
Q 021649 268 SLILKRMFLSLGP 280 (309)
Q Consensus 268 ~liLKGpCPNCGe 280 (309)
+.-++--||+||+
T Consensus 15 v~rk~~~CPrCG~ 27 (51)
T COG1998 15 VKRKNRFCPRCGP 27 (51)
T ss_pred EEEccccCCCCCC
Confidence 3556778999996
No 94
>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=26.05 E-value=34 Score=23.67 Aligned_cols=8 Identities=13% Similarity=-0.072 Sum_probs=4.0
Q ss_pred cCCCCccc
Q 021649 274 MFLSLGPY 281 (309)
Q Consensus 274 pCPNCGee 281 (309)
.||+||..
T Consensus 2 ~Cp~Cg~~ 9 (39)
T PF01096_consen 2 KCPKCGHN 9 (39)
T ss_dssp --SSS-SS
T ss_pred CCcCCCCC
Confidence 69999953
No 95
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.82 E-value=35 Score=28.40 Aligned_cols=16 Identities=0% Similarity=-0.311 Sum_probs=10.6
Q ss_pred ccCCCCccc-eeecccC
Q 021649 273 RMFLSLGPY-YQFLVVE 288 (309)
Q Consensus 273 GpCPNCGee-~aFv~~~ 288 (309)
..||+||.. ...+.|+
T Consensus 87 ~~CP~Cgs~~~~i~~G~ 103 (113)
T PRK12380 87 AQCPHCHGERLRVDTGD 103 (113)
T ss_pred ccCcCCCCCCcEEccCC
Confidence 358888864 6666664
No 96
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=25.78 E-value=1.1e+02 Score=24.00 Aligned_cols=33 Identities=33% Similarity=0.493 Sum_probs=26.1
Q ss_pred chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhh
Q 021649 94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEEL 129 (309)
Q Consensus 94 slge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL 129 (309)
.+.+.+..+++-+...=..| ++++||++.|+.|
T Consensus 152 ~~~~~~~~~~~~l~~l~~~~---~s~~el~~~k~~L 184 (184)
T PF05193_consen 152 NLDEAIEAILQELKRLREGG---ISEEELERAKNQL 184 (184)
T ss_dssp GHHHHHHHHHHHHHHHHHHC---S-HHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHcC---CCHHHHHHHHhcC
Confidence 56777778888887777765 9999999999876
No 97
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.43 E-value=37 Score=29.42 Aligned_cols=19 Identities=16% Similarity=0.121 Sum_probs=13.8
Q ss_pred eeeccCCCCccc--eeecccC
Q 021649 270 ILKRMFLSLGPY--YQFLVVE 288 (309)
Q Consensus 270 iLKGpCPNCGee--~aFv~~~ 288 (309)
+=.-.||.||+. -+|+..+
T Consensus 47 ~G~t~CP~Cg~~~e~~fvva~ 67 (115)
T COG1885 47 VGSTSCPKCGEPFESAFVVAN 67 (115)
T ss_pred cccccCCCCCCccceeEEEec
Confidence 345689999985 6777654
No 98
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.07 E-value=36 Score=28.35 Aligned_cols=17 Identities=6% Similarity=-0.087 Sum_probs=11.9
Q ss_pred ccCCCCccc-eeecccCC
Q 021649 273 RMFLSLGPY-YQFLVVEP 289 (309)
Q Consensus 273 GpCPNCGee-~aFv~~~~ 289 (309)
-.||.||.. ...+.|+-
T Consensus 88 ~~CP~Cgs~~~~i~~G~E 105 (114)
T PRK03681 88 RRCPQCHGDMLRIVADDG 105 (114)
T ss_pred CcCcCcCCCCcEEccCCe
Confidence 469999965 67776653
No 99
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=24.84 E-value=31 Score=30.92 Aligned_cols=30 Identities=10% Similarity=-0.030 Sum_probs=17.2
Q ss_pred HHHHHHhhhccceeeeccCCCCccceeecc
Q 021649 257 SQSLTKLIVRESLILKRMFLSLGPYYQFLV 286 (309)
Q Consensus 257 a~~Lt~l~~~D~liLKGpCPNCGee~aFv~ 286 (309)
...|...+-.+.--.-=-|||||..|.|.-
T Consensus 102 ~~klk~~l~~e~~~~~Y~Cp~C~~rytf~e 131 (178)
T PRK06266 102 LKKLKEQLEEEENNMFFFCPNCHIRFTFDE 131 (178)
T ss_pred HHHHHHHhhhccCCCEEECCCCCcEEeHHH
Confidence 334444433333333445999999888763
No 100
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=24.77 E-value=34 Score=27.62 Aligned_cols=14 Identities=7% Similarity=-0.112 Sum_probs=7.7
Q ss_pred ccCCCCccceeecc
Q 021649 273 RMFLSLGPYYQFLV 286 (309)
Q Consensus 273 GpCPNCGee~aFv~ 286 (309)
-.||+||+.+..|+
T Consensus 66 ~~Cp~Cg~~~~iFg 79 (81)
T PF10609_consen 66 FVCPHCGERIYIFG 79 (81)
T ss_dssp EE-TTT--EEETTT
T ss_pred cCCCCCCCeecCCC
Confidence 47999999865554
No 101
>PRK15398 aldehyde dehydrogenase EutE; Provisional
Probab=24.76 E-value=1.6e+02 Score=29.93 Aligned_cols=59 Identities=14% Similarity=0.313 Sum_probs=44.3
Q ss_pred ccChHHHhhhHhhhhh-----cCCe------eEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhC
Q 021649 116 VMSNEEFDNLKEELMW-----EGSS------VVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEG 176 (309)
Q Consensus 116 ~msneefd~LkEeL~W-----eGSs------vv~L~~~EQ~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eG 176 (309)
++.|.+.|.--+.+.| .|.. +++=...-.+|++++.+. +.|+++.+++|+++.-+...|
T Consensus 247 V~~dADld~Aa~~i~~g~~~n~GQ~C~A~~rvlV~~si~d~f~~~l~~~--~~~li~~~~~~~v~~~l~~~~ 316 (465)
T PRK15398 247 VDETADIEKAARDIVKGASFDNNLPCIAEKEVIVVDSVADELMRLMEKN--GAVLLTAEQAEKLQKVVLKNG 316 (465)
T ss_pred EecCCCHHHHHHHHHHhcccCCCCcCCCCceEEEeHHHHHHHHHHHHHc--CCccCCHHHHHHHHHHHhhcc
Confidence 3457788888888888 4554 444444567899998887 789999999999998777554
No 102
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=24.59 E-value=28 Score=25.07 Aligned_cols=16 Identities=19% Similarity=-0.141 Sum_probs=7.9
Q ss_pred ccceeeeccCCCCccc
Q 021649 266 RESLILKRMFLSLGPY 281 (309)
Q Consensus 266 ~D~liLKGpCPNCGee 281 (309)
+.+--.+|.||-||..
T Consensus 14 ~~l~~~~~~CPlC~r~ 29 (54)
T PF04423_consen 14 EELKEAKGCCPLCGRP 29 (54)
T ss_dssp HHHTT-SEE-TTT--E
T ss_pred HHHhcCCCcCCCCCCC
Confidence 3344456799999954
No 103
>PRK10220 hypothetical protein; Provisional
Probab=24.50 E-value=37 Score=29.35 Aligned_cols=16 Identities=6% Similarity=-0.089 Sum_probs=12.1
Q ss_pred ccCCCCccceeecccC
Q 021649 273 RMFLSLGPYYQFLVVE 288 (309)
Q Consensus 273 GpCPNCGee~aFv~~~ 288 (309)
-+||.|+.+|++--++
T Consensus 4 P~CP~C~seytY~d~~ 19 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG 19 (111)
T ss_pred CcCCCCCCcceEcCCC
Confidence 4799999988875543
No 104
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=24.35 E-value=41 Score=22.22 Aligned_cols=14 Identities=14% Similarity=0.121 Sum_probs=10.3
Q ss_pred cCCCCccceeeccc
Q 021649 274 MFLSLGPYYQFLVV 287 (309)
Q Consensus 274 pCPNCGee~aFv~~ 287 (309)
.||+||.+|..+..
T Consensus 7 ~C~~Cg~~fe~~~~ 20 (41)
T smart00834 7 RCEDCGHTFEVLQK 20 (41)
T ss_pred EcCCCCCEEEEEEe
Confidence 69999987665543
No 105
>TIGR00777 ahpD alkylhydroperoxidase, AhpD family. Members of this family are alkylhydroperoxidases, which catalyze the reduction of peroxides to their corresponding alcohols via oxidation of cysteine residues. In these alkylhydroperoxidases, the cysteines are located in a conserved -CXXC- motif located towards the COOH terminus. In Mycobacterium tuberculosis, two non-homologous alkylhydroperoxidases, AhpD and AhpC, are found in the same operon.
Probab=24.01 E-value=36 Score=31.20 Aligned_cols=27 Identities=26% Similarity=0.577 Sum_probs=23.4
Q ss_pred HHHh-hhcCCCccChHHHHHHHHHHhhh
Q 021649 149 ASMA-YVAGKPIMSDEEYDKLKQKLKME 175 (309)
Q Consensus 149 A~~A-Y~~GkPimsDeEFD~LK~kLk~e 175 (309)
||.- ||+...+++|++|+.++.+||..
T Consensus 78 amnNv~Yr~~hl~~~~~y~~~pa~lrmn 105 (177)
T TIGR00777 78 AMNNVFYRGRHLLEGARYDDLRPGLRMN 105 (177)
T ss_pred hhhhHHHHhHhhcccchhhcCCccchhH
Confidence 3444 99999999999999999999876
No 106
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=23.92 E-value=65 Score=23.56 Aligned_cols=22 Identities=41% Similarity=0.768 Sum_probs=18.2
Q ss_pred ccChHHHHHHHHHHhhhCCceeeec
Q 021649 159 IMSDEEYDKLKQKLKMEGSEIVVEG 183 (309)
Q Consensus 159 imsDeEFD~LK~kLk~eGS~VVvk~ 183 (309)
++++++|+.++. ..|..|.|.|
T Consensus 5 ~l~~~~~~~~~~---~~Gk~V~V~G 26 (48)
T PF14485_consen 5 ILSEEDYSYLKS---LLGKRVSVTG 26 (48)
T ss_pred EeChhhhHHHHH---hcCCeEEEEE
Confidence 458999999887 6899998876
No 107
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=23.81 E-value=53 Score=30.81 Aligned_cols=22 Identities=14% Similarity=-0.191 Sum_probs=13.6
Q ss_pred ccceeeec----cCCCCccc--eeeccc
Q 021649 266 RESLILKR----MFLSLGPY--YQFLVV 287 (309)
Q Consensus 266 ~D~liLKG----pCPNCGee--~aFv~~ 287 (309)
++.+-++| |||.||.. ...+.+
T Consensus 235 ~~~l~Vy~R~g~pC~~Cg~~I~~~~~~g 262 (274)
T PRK01103 235 QQSLQVYGREGEPCRRCGTPIEKIKQGG 262 (274)
T ss_pred cceeEEcCCCCCCCCCCCCeeEEEEECC
Confidence 34455554 89999975 444443
No 108
>PRK12413 phosphomethylpyrimidine kinase; Provisional
Probab=23.45 E-value=3.2e+02 Score=24.36 Aligned_cols=45 Identities=27% Similarity=0.393 Sum_probs=33.6
Q ss_pred cCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCCc-eeeec
Q 021649 132 EGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSE-IVVEG 183 (309)
Q Consensus 132 eGSsvv~L~~~EQ~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eGS~-VVvk~ 183 (309)
....+++.+..|-+.| .|.++-+.++..+.-.+|...|.+ |++++
T Consensus 128 ~~~dli~pN~~E~~~L-------~g~~~~~~~~~~~~a~~l~~~g~~~Vvvt~ 173 (253)
T PRK12413 128 PYVTVITPNLVEAELL-------SGKEIKTLEDMKEAAKKLYDLGAKAVVIKG 173 (253)
T ss_pred ccCcEECCCHHHHHHH-------hCcCCCCHHHHHHHHHHHHHcCCCEEEEeC
Confidence 4457999999998777 478887778787877788878875 55553
No 109
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=23.23 E-value=36 Score=24.94 Aligned_cols=15 Identities=13% Similarity=0.117 Sum_probs=11.0
Q ss_pred cCCCCcc---ceeecccC
Q 021649 274 MFLSLGP---YYQFLVVE 288 (309)
Q Consensus 274 pCPNCGe---e~aFv~~~ 288 (309)
+||.||- ..+++.++
T Consensus 11 ~CPgCG~tRa~~~ll~gd 28 (52)
T PF10825_consen 11 PCPGCGMTRAFIALLHGD 28 (52)
T ss_pred CCCCCcHHHHHHHHHCCC
Confidence 7999994 26666665
No 110
>PLN02898 HMP-P kinase/thiamin-monophosphate pyrophosphorylase
Probab=23.21 E-value=2.8e+02 Score=28.06 Aligned_cols=59 Identities=22% Similarity=0.348 Sum_probs=40.1
Q ss_pred HHHhhhHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC-ceeeecCc
Q 021649 120 EEFDNLKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS-EIVVEGPR 185 (309)
Q Consensus 120 eefd~LkEeL~WeGSsvv~L~~~EQ~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eGS-~VVvk~Pr 185 (309)
+-.+.+|++|. .-..+++.+..|-+.|- .+.++-+.++..+.-.+|...|. .|++++..
T Consensus 126 ~~~~~l~~~Ll-~~adiitPN~~Ea~~L~------g~~~~~~~~~~~~~a~~l~~~G~~~VvItgg~ 185 (502)
T PLN02898 126 SILSALREELL-PLATIVTPNVKEASALL------GGDPLETVADMRSAAKELHKLGPRYVLVKGGH 185 (502)
T ss_pred HHHHHHHHhhh-ccCeEEcCCHHHHHHHh------CCCCCCCHHHHHHHHHHHHhcCCCEEEEcCCC
Confidence 44456776664 55679999999988772 12334455667777788888884 67777643
No 111
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=23.18 E-value=34 Score=29.92 Aligned_cols=14 Identities=7% Similarity=0.005 Sum_probs=10.8
Q ss_pred eccCCCCccceeec
Q 021649 272 KRMFLSLGPYYQFL 285 (309)
Q Consensus 272 KGpCPNCGee~aFv 285 (309)
-=-||||+..|.|.
T Consensus 109 ~Y~Cp~c~~r~tf~ 122 (158)
T TIGR00373 109 FFICPNMCVRFTFN 122 (158)
T ss_pred eEECCCCCcEeeHH
Confidence 34599999888775
No 112
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=22.65 E-value=1.6e+02 Score=22.74 Aligned_cols=34 Identities=18% Similarity=0.332 Sum_probs=28.2
Q ss_pred HHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCC
Q 021649 144 QKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGS 177 (309)
Q Consensus 144 Q~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eGS 177 (309)
..||+=..+--.|+|+||-+||-+-..+=++.|-
T Consensus 26 e~Yv~H~~~~HP~~p~ms~~eF~r~r~~~r~~~~ 59 (65)
T PF04328_consen 26 ERYVEHMRRHHPDEPPMSEREFFRERQDARYGNP 59 (65)
T ss_pred HHHHHHHHHHCcCCCCCCHHHHHHHHHHHHhcCC
Confidence 5688888888899999999999988777766553
No 113
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=22.36 E-value=38 Score=27.32 Aligned_cols=10 Identities=30% Similarity=0.195 Sum_probs=7.3
Q ss_pred eccCCCCccc
Q 021649 272 KRMFLSLGPY 281 (309)
Q Consensus 272 KGpCPNCGee 281 (309)
|-+||+||..
T Consensus 1 K~~CPCCg~~ 10 (78)
T PF14206_consen 1 KYPCPCCGYY 10 (78)
T ss_pred CccCCCCCcE
Confidence 4579999853
No 114
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=22.32 E-value=32 Score=28.17 Aligned_cols=14 Identities=14% Similarity=0.119 Sum_probs=10.0
Q ss_pred cCCCCcc----ceeeccc
Q 021649 274 MFLSLGP----YYQFLVV 287 (309)
Q Consensus 274 pCPNCGe----e~aFv~~ 287 (309)
+||.||+ ||.+.+-
T Consensus 3 ~CP~CG~R~~~EF~y~G~ 20 (84)
T PF04267_consen 3 PCPHCGPRDESEFTYGGE 20 (84)
T ss_dssp EETTTEEEEGGGSEEEEE
T ss_pred cCCCCCccchhheecCcE
Confidence 7999995 4666553
No 115
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=22.30 E-value=43 Score=23.05 Aligned_cols=8 Identities=13% Similarity=-0.126 Sum_probs=5.7
Q ss_pred cCCCCccc
Q 021649 274 MFLSLGPY 281 (309)
Q Consensus 274 pCPNCGee 281 (309)
.||||+-.
T Consensus 6 ~C~nC~R~ 13 (33)
T PF08209_consen 6 ECPNCGRP 13 (33)
T ss_dssp E-TTTSSE
T ss_pred ECCCCcCC
Confidence 69999964
No 116
>PF13058 DUF3920: Protein of unknown function (DUF3920)
Probab=22.02 E-value=39 Score=29.62 Aligned_cols=46 Identities=33% Similarity=0.523 Sum_probs=35.0
Q ss_pred cccccccc--ccchhHHHHHHHHHHHHhhhcCccc---cChHHHhhhHhhh
Q 021649 84 YCSIDKKE--KKSLGELEQEFLQALQAFYYEGKAV---MSNEEFDNLKEEL 129 (309)
Q Consensus 84 yCsiD~~~--k~slge~E~~fl~Al~~fY~~gk~~---msneefd~LkEeL 129 (309)
+|..=+.. -.+|||.|-+||..+..||-..|.+ .-=|||+.+-+.|
T Consensus 30 FcdTc~an~vl~~LgeeeeefLf~~~g~y~kek~~iFv~~we~y~qvlktl 80 (126)
T PF13058_consen 30 FCDTCDANKVLLSLGEEEEEFLFPAGGFYHKEKQLIFVCMWEEYEQVLKTL 80 (126)
T ss_pred EecccchhHHHHHhccchhhhccccchhhhccccEEEEEehHHHHHHHHHH
Confidence 55444443 3389999999999999999998873 3478888877665
No 117
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.80 E-value=48 Score=22.81 Aligned_cols=17 Identities=6% Similarity=-0.160 Sum_probs=6.7
Q ss_pred CCCCccc--eeecccCCCc
Q 021649 275 FLSLGPY--YQFLVVEPPT 291 (309)
Q Consensus 275 CPNCGee--~aFv~~~~p~ 291 (309)
||+||.. .....+++..
T Consensus 3 C~~CG~~l~~~ip~gd~r~ 21 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRE 21 (34)
T ss_dssp -TTT--B-EEE--TT-SS-
T ss_pred cccccChhhhhcCCCCCcc
Confidence 9999975 5555556543
No 118
>KOG3716 consensus Carnitine O-acyltransferase CPTI [Lipid transport and metabolism]
Probab=21.78 E-value=52 Score=36.12 Aligned_cols=14 Identities=57% Similarity=1.168 Sum_probs=0.0
Q ss_pred CCccChHHHHHHHH
Q 021649 157 KPIMSDEEYDKLKQ 170 (309)
Q Consensus 157 kPimsDeEFD~LK~ 170 (309)
|||||||||++|.+
T Consensus 184 kpilseEe~~~l~~ 197 (764)
T KOG3716|consen 184 KPILSEEEFDRLEE 197 (764)
T ss_pred ccccCHHHHHHHHH
No 119
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=21.75 E-value=88 Score=25.26 Aligned_cols=36 Identities=31% Similarity=0.650 Sum_probs=27.8
Q ss_pred hHhhhhhcCCeeEEeChhhHHHHHHHHhhhcCCCccChHHHHHHHHHHhhhCCce
Q 021649 125 LKEELMWEGSSVVMLSSAEQKFLEASMAYVAGKPIMSDEEYDKLKQKLKMEGSEI 179 (309)
Q Consensus 125 LkEeL~WeGSsvv~L~~~EQ~FLEA~~AY~~GkPimsDeEFD~LK~kLk~eGS~V 179 (309)
.=..|+|+| .+||+++. +|+-|.+.|.+++..|..+
T Consensus 65 ~i~~LT~~G----------HdFLd~IR---------d~~vW~k~K~~i~~k~~s~ 100 (102)
T PF10711_consen 65 IIKRLTWSG----------HDFLDAIR---------DDTVWNKTKDKIASKGGSF 100 (102)
T ss_pred hhcccChhH----------HHHHHHhc---------CchHHHHHHHHHHHhcCCC
Confidence 334566666 79999864 6899999999998877665
No 120
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.66 E-value=39 Score=24.51 Aligned_cols=7 Identities=14% Similarity=0.173 Sum_probs=4.5
Q ss_pred cCCCCcc
Q 021649 274 MFLSLGP 280 (309)
Q Consensus 274 pCPNCGe 280 (309)
.|||||.
T Consensus 48 ~Cp~CgR 54 (56)
T PF02591_consen 48 FCPNCGR 54 (56)
T ss_pred ECcCCCc
Confidence 4777764
No 121
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=21.37 E-value=51 Score=27.30 Aligned_cols=15 Identities=7% Similarity=-0.018 Sum_probs=9.1
Q ss_pred CCCCccc-eeecccCC
Q 021649 275 FLSLGPY-YQFLVVEP 289 (309)
Q Consensus 275 CPNCGee-~aFv~~~~ 289 (309)
||+||.. ...+.|+.
T Consensus 89 CP~Cgs~~~~i~~G~e 104 (113)
T PF01155_consen 89 CPRCGSPDVEIISGRE 104 (113)
T ss_dssp -SSSSSS-EEEEESS-
T ss_pred CcCCcCCCcEEccCCe
Confidence 8888865 56666653
No 122
>PF06897 DUF1269: Protein of unknown function (DUF1269); InterPro: IPR009200 There are currently no experimental data for members of this group or their homologues. However, these proteins are predicted to contain two or more transmembrane segments.
Probab=21.26 E-value=2.4e+02 Score=23.36 Aligned_cols=56 Identities=27% Similarity=0.484 Sum_probs=39.3
Q ss_pred cChHHHhhhHhhhhhcCCe--eEEeChhhHHHHHHHHhhhcCCCc---cChHHHHHHHHHHh
Q 021649 117 MSNEEFDNLKEELMWEGSS--VVMLSSAEQKFLEASMAYVAGKPI---MSDEEYDKLKQKLK 173 (309)
Q Consensus 117 msneefd~LkEeL~WeGSs--vv~L~~~EQ~FLEA~~AY~~GkPi---msDeEFD~LK~kLk 173 (309)
++|+.-+.+.+.|. .|++ ++.+.+...+.+.+..+-|.|+=+ +|.++=++|++-|.
T Consensus 40 I~d~~~~ev~~~L~-~GssAl~~lv~~~~~d~v~~~l~~~gg~v~~t~ls~~~e~~L~~al~ 100 (102)
T PF06897_consen 40 IDDEFIKEVGEALK-PGSSALFLLVDEATEDKVDAALRKFGGKVLRTSLSEEDEDELQEALD 100 (102)
T ss_pred CCHHHHHHHHhhcC-CCceEEEEEeccCCHHHHHHHHHhcCCEEEeccCCHHHHHHHHHHHh
Confidence 56777888888877 6888 444555556667777777777766 77777777776653
No 123
>KOG3457 consensus Sec61 protein translocation complex, beta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=21.07 E-value=46 Score=27.78 Aligned_cols=30 Identities=30% Similarity=0.527 Sum_probs=20.8
Q ss_pred hhhccccccceeeeecccCCCCchhhhhHH
Q 021649 218 LFFFLDDITGFEITYLLELPEPFSFIFTWF 247 (309)
Q Consensus 218 ~~~~ldd~~GfeIt~~~~lpeP~gfi~tw~ 247 (309)
+.|+-||+.|+.|.....+-=-++||+.+|
T Consensus 46 lkfYTDda~GlKV~PvvVLvmSvgFIasV~ 75 (88)
T KOG3457|consen 46 LKFYTDDAPGLKVDPVVVLVMSVGFIASVF 75 (88)
T ss_pred eEEeecCCCCceeCCeeehhhhHHHHHHHH
Confidence 456779999998776655544567776554
No 124
>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=21.01 E-value=33 Score=33.26 Aligned_cols=31 Identities=16% Similarity=0.065 Sum_probs=10.5
Q ss_pred HHHHHHhhhccceeeeccCCCCccc-eeecccCCCc
Q 021649 257 SQSLTKLIVRESLILKRMFLSLGPY-YQFLVVEPPT 291 (309)
Q Consensus 257 a~~Lt~l~~~D~liLKGpCPNCGee-~aFv~~~~p~ 291 (309)
|..||..|+ .=.+.|||||.. ..=+.-+.|.
T Consensus 20 aRVltE~Wv----~~n~yCP~Cg~~~L~~f~NN~PV 51 (254)
T PF06044_consen 20 ARVLTEDWV----AENMYCPNCGSKPLSKFENNRPV 51 (254)
T ss_dssp HHHHHHHHH----HHH---TTT--SS-EE-------
T ss_pred hHHHHHHHH----HHCCcCCCCCChhHhhccCCCcc
Confidence 455555554 445789999965 4444555553
No 125
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=20.94 E-value=42 Score=25.08 Aligned_cols=9 Identities=11% Similarity=0.264 Sum_probs=7.0
Q ss_pred ccCCCCccc
Q 021649 273 RMFLSLGPY 281 (309)
Q Consensus 273 GpCPNCGee 281 (309)
..||+||+.
T Consensus 27 ~~C~~cG~~ 35 (55)
T TIGR01031 27 VVCPNCGEF 35 (55)
T ss_pred eECCCCCCc
Confidence 359999984
No 126
>cd07078 ALDH NAD(P)+ dependent aldehyde dehydrogenase family. The aldehyde dehydrogenase family (ALDH) of NAD(P)+ dependent enzymes, in general, oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or as osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer
Probab=20.92 E-value=2.3e+02 Score=27.24 Aligned_cols=68 Identities=18% Similarity=0.391 Sum_probs=43.3
Q ss_pred cChHHHhhhHhhhh-----hcCCe------eEEeChhhHHHHHHHHh----hhcCC---------CccChHHHHHHHHHH
Q 021649 117 MSNEEFDNLKEELM-----WEGSS------VVMLSSAEQKFLEASMA----YVAGK---------PIMSDEEYDKLKQKL 172 (309)
Q Consensus 117 msneefd~LkEeL~-----WeGSs------vv~L~~~EQ~FLEA~~A----Y~~Gk---------PimsDeEFD~LK~kL 172 (309)
+.+.+++..-+.+. +.|-. +++.+....+|++++.. +.-|. |+++.+.+++++..+
T Consensus 215 ~~~ad~~~aa~~i~~~~~~~~Gq~C~a~~~i~v~~~~~~~~~~~L~~~l~~~~~g~p~~~~~~~~~~~~~~~~~~~~~~i 294 (432)
T cd07078 215 FDDADLDAAVKGAVFGAFGNAGQVCTAASRLLVHESIYDEFVERLVERVKALKVGNPLDPDTDMGPLISAAQLDRVLAYI 294 (432)
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCccCCceEEEcHHHHHHHHHHHHHHHHccCcCCCCCCCCCCCCCCCHHHHHHHHHHH
Confidence 55666666555544 34532 33444444678887543 55454 488999999999888
Q ss_pred hh---hCCceeeecC
Q 021649 173 KM---EGSEIVVEGP 184 (309)
Q Consensus 173 k~---eGS~VVvk~P 184 (309)
.. .|.+++.-|+
T Consensus 295 ~~~~~~g~~~~~gg~ 309 (432)
T cd07078 295 EDAKAEGAKLLCGGK 309 (432)
T ss_pred HHHHhCCCEEEeCCc
Confidence 76 5777776443
No 127
>PF08278 DnaG_DnaB_bind: DNA primase DnaG DnaB-binding ; InterPro: IPR013173 Eubacterial DnaG primases interact with several factors to form the replisome. One of these factors is DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB []. This domain has a multi-helical structure that forms an orthogonal bundle [].; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 2HAJ_A 1T3W_B.
Probab=20.92 E-value=1.8e+02 Score=23.47 Aligned_cols=47 Identities=26% Similarity=0.351 Sum_probs=32.4
Q ss_pred chhHHHHHHHHHHHHhhhcCccccChHHHhhhHhhhhhcCCeeEEeChhhHHHHHH
Q 021649 94 SLGELEQEFLQALQAFYYEGKAVMSNEEFDNLKEELMWEGSSVVMLSSAEQKFLEA 149 (309)
Q Consensus 94 slge~E~~fl~Al~~fY~~gk~~msneefd~LkEeL~WeGSsvv~L~~~EQ~FLEA 149 (309)
+-.+.|++|.+++....... -+.+++.||....=+| ++..|++.|-.
T Consensus 79 ~~~~~~~ef~d~l~~L~~~~----~~~~i~~L~~k~~~~~-----Lt~eEk~el~~ 125 (127)
T PF08278_consen 79 DEEDIEQEFQDALARLQEQA----LERRIEELKAKPRRGG-----LTDEEKQELRR 125 (127)
T ss_dssp HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHTTT--------HHHHHHHHH
T ss_pred CchhHHHHHHHHHHHHHHHH----HHHHHHHHHHhhccCC-----cCHHHHHHHHH
Confidence 66789999999999988765 5678888887744322 67777666544
No 128
>KOG1372 consensus GDP-mannose 4,6 dehydratase [Carbohydrate transport and metabolism]
Probab=20.88 E-value=51 Score=32.92 Aligned_cols=39 Identities=28% Similarity=0.444 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhhcCccc---------cChHHHhh-----hHhhhhhcCCeeE
Q 021649 99 EQEFLQALQAFYYEGKAV---------MSNEEFDN-----LKEELMWEGSSVV 137 (309)
Q Consensus 99 E~~fl~Al~~fY~~gk~~---------msneefd~-----LkEeL~WeGSsvv 137 (309)
-.+|.+|||.--...+|. -|-+||++ +-|+|+|+|..|=
T Consensus 257 A~dYVEAMW~mLQ~d~PdDfViATge~hsVrEF~~~aF~~ig~~l~Weg~gv~ 309 (376)
T KOG1372|consen 257 AGDYVEAMWLMLQQDSPDDFVIATGEQHSVREFCNLAFAEIGEVLNWEGEGVD 309 (376)
T ss_pred hHHHHHHHHHHHhcCCCCceEEecCCcccHHHHHHHHHHhhCcEEeecccccc
Confidence 358999999988777662 24556665 5799999987653
No 129
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=20.86 E-value=43 Score=24.81 Aligned_cols=9 Identities=11% Similarity=-0.149 Sum_probs=7.3
Q ss_pred ccCCCCccc
Q 021649 273 RMFLSLGPY 281 (309)
Q Consensus 273 GpCPNCGee 281 (309)
..||+||+.
T Consensus 27 ~~c~~cg~~ 35 (56)
T PF01783_consen 27 VKCPNCGEP 35 (56)
T ss_dssp EESSSSSSE
T ss_pred eeeccCCCE
Confidence 579999974
No 130
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=20.73 E-value=53 Score=22.85 Aligned_cols=8 Identities=13% Similarity=-0.122 Sum_probs=6.6
Q ss_pred cCCCCccc
Q 021649 274 MFLSLGPY 281 (309)
Q Consensus 274 pCPNCGee 281 (309)
.||+||..
T Consensus 2 ~Cp~C~~~ 9 (40)
T smart00440 2 PCPKCGNR 9 (40)
T ss_pred cCCCCCCC
Confidence 69999964
No 131
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=20.70 E-value=42 Score=26.05 Aligned_cols=7 Identities=14% Similarity=-0.012 Sum_probs=6.1
Q ss_pred cCCCCcc
Q 021649 274 MFLSLGP 280 (309)
Q Consensus 274 pCPNCGe 280 (309)
.|||||.
T Consensus 17 ~CP~Cgs 23 (61)
T PRK08351 17 RCPVCGS 23 (61)
T ss_pred cCCCCcC
Confidence 5999995
No 132
>KOG4517 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.51 E-value=42 Score=29.20 Aligned_cols=12 Identities=33% Similarity=0.548 Sum_probs=9.8
Q ss_pred eccCCCCcccee
Q 021649 272 KRMFLSLGPYYQ 283 (309)
Q Consensus 272 KGpCPNCGee~a 283 (309)
|--|||||+.++
T Consensus 106 ~rrc~ncg~~f~ 117 (117)
T KOG4517|consen 106 KRRCPNCGPTFA 117 (117)
T ss_pred hccCCCcccccC
Confidence 568999998764
No 133
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.51 E-value=37 Score=22.57 Aligned_cols=13 Identities=15% Similarity=0.031 Sum_probs=9.0
Q ss_pred ccCCCCccc-eeec
Q 021649 273 RMFLSLGPY-YQFL 285 (309)
Q Consensus 273 GpCPNCGee-~aFv 285 (309)
-.||.||.. .+|.
T Consensus 18 ~~CP~Cg~~~~~F~ 31 (33)
T cd00350 18 WVCPVCGAPKDKFE 31 (33)
T ss_pred CcCcCCCCcHHHcE
Confidence 379999974 5554
No 134
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=20.47 E-value=44 Score=25.27 Aligned_cols=9 Identities=11% Similarity=-0.171 Sum_probs=6.9
Q ss_pred ccCCCCccc
Q 021649 273 RMFLSLGPY 281 (309)
Q Consensus 273 GpCPNCGee 281 (309)
-.||+||+.
T Consensus 28 ~~C~~CG~~ 36 (57)
T PRK12286 28 VECPNCGEP 36 (57)
T ss_pred eECCCCCCc
Confidence 359999974
No 135
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.15 E-value=52 Score=27.82 Aligned_cols=19 Identities=11% Similarity=-0.241 Sum_probs=13.5
Q ss_pred eccCCCCccc-eeecccCCC
Q 021649 272 KRMFLSLGPY-YQFLVVEPP 290 (309)
Q Consensus 272 KGpCPNCGee-~aFv~~~~p 290 (309)
...||+||.. ..-+.|+-=
T Consensus 92 ~~~CP~Cgs~~~~i~~G~El 111 (124)
T PRK00762 92 VIECPVCGNKRAHILGGREC 111 (124)
T ss_pred CCcCcCCCCCCCEEecCCeE
Confidence 4679999964 777776543
No 136
>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=20.08 E-value=48 Score=22.92 Aligned_cols=9 Identities=11% Similarity=-0.105 Sum_probs=6.3
Q ss_pred cCCCCccce
Q 021649 274 MFLSLGPYY 282 (309)
Q Consensus 274 pCPNCGee~ 282 (309)
-||+||...
T Consensus 2 ~Cp~Cg~~~ 10 (43)
T PF08271_consen 2 KCPNCGSKE 10 (43)
T ss_dssp SBTTTSSSE
T ss_pred CCcCCcCCc
Confidence 388888643
No 137
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=20.07 E-value=44 Score=25.65 Aligned_cols=9 Identities=11% Similarity=-0.046 Sum_probs=7.0
Q ss_pred ccCCCCccc
Q 021649 273 RMFLSLGPY 281 (309)
Q Consensus 273 GpCPNCGee 281 (309)
.-||+||+.
T Consensus 4 kHC~~CG~~ 12 (59)
T PF09889_consen 4 KHCPVCGKP 12 (59)
T ss_pred CcCCcCCCc
Confidence 469999963
Done!