Query 042199
Match_columns 220
No_of_seqs 14 out of 16
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 03:48:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042199hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2841 Structure-specific end 98.4 3E-06 6.5E-11 75.7 10.0 173 26-211 75-250 (254)
2 PF12826 HHH_2: Helix-hairpin- 98.1 1.4E-06 3.1E-11 61.0 1.1 53 160-212 7-59 (64)
3 PF14520 HHH_5: Helix-hairpin- 97.9 4.1E-06 8.9E-11 57.2 1.7 53 158-210 7-60 (60)
4 COG1948 MUS81 ERCC4-type nucle 97.1 0.0053 1.1E-07 54.8 10.6 133 62-211 86-237 (254)
5 PRK12766 50S ribosomal protein 97.1 0.00051 1.1E-08 60.7 3.6 56 157-212 4-60 (232)
6 PRK13766 Hef nuclease; Provisi 96.7 0.0093 2E-07 56.7 9.2 147 61-212 620-771 (773)
7 TIGR00596 rad1 DNA repair prot 96.5 0.0029 6.3E-08 63.3 4.6 146 60-211 643-811 (814)
8 PRK14351 ligA NAD-dependent DN 95.9 0.0065 1.4E-07 59.8 3.4 53 160-212 532-584 (689)
9 TIGR00575 dnlj DNA ligase, NAD 95.8 0.0079 1.7E-07 58.6 3.7 55 158-212 500-554 (652)
10 TIGR02236 recomb_radA DNA repa 95.4 0.011 2.5E-07 50.3 2.8 52 158-209 1-53 (310)
11 PRK00558 uvrC excinuclease ABC 95.3 0.015 3.3E-07 56.0 3.4 56 155-210 542-597 (598)
12 PRK07956 ligA NAD-dependent DN 95.0 0.021 4.5E-07 55.9 3.4 54 159-212 514-567 (665)
13 PRK00254 ski2-like helicase; P 94.8 0.067 1.5E-06 51.4 6.3 78 134-211 623-701 (720)
14 PRK14669 uvrC excinuclease ABC 94.3 0.035 7.7E-07 54.4 3.1 93 106-212 513-606 (624)
15 PRK14667 uvrC excinuclease ABC 94.3 0.087 1.9E-06 51.1 5.7 92 105-209 474-566 (567)
16 PRK14666 uvrC excinuclease ABC 94.1 0.12 2.5E-06 51.8 6.2 94 105-209 597-690 (694)
17 PRK13482 DNA integrity scannin 93.9 0.037 7.9E-07 51.5 2.3 53 156-208 287-339 (352)
18 PRK14670 uvrC excinuclease ABC 93.5 0.078 1.7E-06 51.6 3.8 92 105-210 476-568 (574)
19 PRK04301 radA DNA repair and r 92.5 0.097 2.1E-06 45.3 2.6 54 157-210 7-61 (317)
20 PRK14668 uvrC excinuclease ABC 92.5 0.11 2.4E-06 50.4 3.2 90 105-208 487-577 (577)
21 PF13905 Thioredoxin_8: Thiore 91.6 1.7 3.7E-05 30.0 7.6 65 47-115 4-70 (95)
22 PTZ00035 Rad51 protein; Provis 90.1 0.26 5.7E-06 44.1 3.0 52 158-209 23-77 (337)
23 smart00611 SEC63 Domain of unk 89.6 0.81 1.7E-05 38.8 5.4 66 144-209 139-205 (312)
24 cd02982 PDI_b'_family Protein 89.2 2.1 4.4E-05 29.8 6.3 65 44-113 12-77 (103)
25 PRK14671 uvrC excinuclease ABC 89.2 0.31 6.7E-06 47.7 2.9 52 156-209 569-620 (621)
26 PRK14350 ligA NAD-dependent DN 88.5 0.38 8.2E-06 47.7 3.0 53 160-212 506-565 (669)
27 PRK14672 uvrC excinuclease ABC 87.2 1 2.2E-05 45.4 5.2 51 156-206 608-658 (691)
28 TIGR00597 rad10 DNA repair pro 86.9 4.1 8.9E-05 32.8 7.5 60 7-76 8-68 (112)
29 TIGR02238 recomb_DMC1 meiotic 86.9 0.59 1.3E-05 41.6 3.0 48 162-209 7-55 (313)
30 COG0322 UvrC Nuclease subunit 85.4 7.5 0.00016 38.4 9.9 137 34-208 443-581 (581)
31 COG0272 Lig NAD-dependent DNA 85.3 0.73 1.6E-05 46.4 3.0 53 160-212 515-567 (667)
32 smart00839 ELFV_dehydrog Gluta 85.1 0.77 1.7E-05 34.9 2.5 45 30-77 47-95 (102)
33 PRK00116 ruvA Holliday junctio 82.9 1.3 2.7E-05 36.9 3.1 53 158-210 75-130 (192)
34 COG5241 RAD10 Nucleotide excis 82.8 1.5 3.2E-05 39.3 3.6 64 148-211 159-222 (224)
35 PLN03187 meiotic recombination 82.5 1.2 2.6E-05 40.7 3.0 52 155-206 28-82 (344)
36 PRK01172 ski2-like helicase; P 80.1 2 4.3E-05 40.9 3.7 75 134-208 590-665 (674)
37 PF06113 BRE: Brain and reprod 78.6 1.6 3.4E-05 40.8 2.5 45 32-76 78-126 (333)
38 PLN03186 DNA repair protein RA 77.3 2.2 4.9E-05 38.8 3.0 51 158-208 28-81 (342)
39 PF15162 DUF4580: Domain of un 77.1 15 0.00031 31.9 7.6 104 17-128 19-126 (162)
40 smart00478 ENDO3c endonuclease 74.6 3.6 7.9E-05 31.5 3.1 40 170-209 15-57 (149)
41 PRK08097 ligB NAD-dependent DN 73.5 2 4.2E-05 42.2 1.7 50 160-212 495-544 (562)
42 cd02966 TlpA_like_family TlpA- 72.0 14 0.0003 24.5 5.1 49 47-96 22-75 (116)
43 cd02956 ybbN ybbN protein fami 70.8 25 0.00055 24.2 6.4 68 41-114 9-76 (96)
44 PRK02362 ski2-like helicase; P 70.6 5.6 0.00012 38.6 4.1 71 139-211 635-706 (737)
45 cd01075 NAD_bind_Leu_Phe_Val_D 69.3 3.7 8E-05 34.0 2.2 44 31-77 132-175 (200)
46 cd02961 PDI_a_family Protein D 69.0 27 0.00059 22.9 6.0 67 41-114 13-81 (101)
47 cd03012 TlpA_like_DipZ_like Tl 66.9 22 0.00047 26.2 5.7 41 44-85 23-64 (126)
48 TIGR01954 nusA_Cterm_rpt trans 66.5 5.5 0.00012 25.4 2.2 39 169-207 6-45 (50)
49 TIGR02239 recomb_RAD51 DNA rep 66.2 4.9 0.00011 35.8 2.5 48 162-209 7-55 (316)
50 cd02998 PDI_a_ERp38 PDIa famil 64.2 29 0.00064 23.6 5.6 71 39-114 13-85 (105)
51 PF13848 Thioredoxin_6: Thiore 63.8 39 0.00084 25.5 6.6 91 14-110 63-157 (184)
52 KOG0907 Thioredoxin [Posttrans 62.1 30 0.00064 26.6 5.8 63 44-113 21-83 (106)
53 PF01408 GFO_IDH_MocA: Oxidore 61.1 20 0.00043 25.6 4.4 48 78-130 65-114 (120)
54 PF00730 HhH-GPD: HhH-GPD supe 60.7 9.7 0.00021 27.5 2.8 39 170-208 19-62 (108)
55 PF02889 Sec63: Sec63 Brl doma 60.6 16 0.00036 30.8 4.6 66 144-209 136-202 (314)
56 cd00502 DHQase_I Type I 3-dehy 60.0 26 0.00057 29.0 5.6 70 52-126 32-110 (225)
57 cd01076 NAD_bind_1_Glu_DH NAD( 60.0 1.6 3.4E-05 37.3 -1.7 44 31-77 152-202 (227)
58 PLN02477 glutamate dehydrogena 57.7 3.9 8.4E-05 38.5 0.4 45 31-78 327-378 (410)
59 TIGR00411 redox_disulf_1 small 55.4 58 0.0013 21.5 5.9 54 50-109 5-58 (82)
60 PLN02412 probable glutathione 52.7 89 0.0019 24.8 7.3 39 47-86 32-71 (167)
61 cd03002 PDI_a_MPD1_like PDI fa 52.6 49 0.0011 23.1 5.2 68 41-115 15-85 (109)
62 cd03010 TlpA_like_DsbE TlpA-li 52.1 70 0.0015 23.2 6.1 44 44-90 25-68 (127)
63 PF03834 Rad10: Binding domain 52.0 10 0.00023 28.3 1.8 48 26-76 20-69 (69)
64 cd02997 PDI_a_PDIR PDIa family 51.4 52 0.0011 22.5 5.1 66 41-114 15-85 (104)
65 cd02993 PDI_a_APS_reductase PD 50.4 76 0.0017 23.0 6.1 65 43-113 20-87 (109)
66 PF02371 Transposase_20: Trans 49.7 6.2 0.00013 28.6 0.3 28 156-183 2-29 (87)
67 cd02953 DsbDgamma DsbD gamma f 48.3 95 0.002 21.9 6.6 64 44-112 11-80 (104)
68 cd04168 TetM_like Tet(M)-like 47.2 55 0.0012 27.6 5.6 54 43-98 115-187 (237)
69 PLN02399 phospholipid hydroper 47.0 53 0.0011 28.7 5.6 41 44-85 99-140 (236)
70 PTZ00056 glutathione peroxidas 46.4 62 0.0013 26.8 5.7 38 47-85 42-80 (199)
71 KOG0190 Protein disulfide isom 46.0 1.2E+02 0.0026 29.9 8.4 95 18-117 227-324 (493)
72 TIGR00194 uvrC excinuclease AB 45.9 9.9 0.00021 37.2 1.1 72 105-188 501-573 (574)
73 cd03023 DsbA_Com1_like DsbA fa 45.6 1.1E+02 0.0025 22.0 10.1 39 46-84 6-45 (154)
74 TIGR01068 thioredoxin thioredo 45.4 78 0.0017 21.1 5.1 66 42-113 12-77 (101)
75 cd02985 TRX_CDSP32 TRX family, 45.2 1.1E+02 0.0025 22.0 6.9 66 44-115 15-82 (103)
76 cd03014 PRX_Atyp2cys Peroxired 45.0 66 0.0014 23.8 5.1 40 46-86 28-67 (143)
77 PF00578 AhpC-TSA: AhpC/TSA fa 43.8 1.1E+02 0.0023 21.6 5.8 46 50-96 32-80 (124)
78 cd03017 PRX_BCP Peroxiredoxin 41.9 91 0.002 22.6 5.4 49 47-95 26-77 (140)
79 PRK03980 flap endonuclease-1; 41.1 28 0.0006 31.2 3.1 71 131-213 163-238 (292)
80 cd00056 ENDO3c endonuclease II 40.6 20 0.00043 27.6 1.8 37 172-209 25-65 (158)
81 PRK00522 tpx lipid hydroperoxi 40.6 1.2E+02 0.0026 24.0 6.3 70 46-123 46-118 (167)
82 cd02968 SCO SCO (an acronym fo 40.3 1.1E+02 0.0025 22.2 5.7 40 46-86 24-68 (142)
83 PRK00024 hypothetical protein; 40.3 44 0.00096 28.8 4.1 43 163-205 37-83 (224)
84 PF01487 DHquinase_I: Type I 3 39.9 98 0.0021 25.5 5.9 64 52-120 31-101 (224)
85 TIGR02540 gpx7 putative glutat 39.7 1E+02 0.0023 23.5 5.7 38 47-85 25-63 (153)
86 PRK03147 thiol-disulfide oxido 39.5 1.3E+02 0.0028 22.8 6.0 44 47-91 64-108 (173)
87 cd02191 FtsZ FtsZ is a GTPase 36.5 1.5E+02 0.0033 26.5 6.9 152 36-210 85-273 (303)
88 TIGR00262 trpA tryptophan synt 36.0 2.3E+02 0.0051 24.6 7.9 103 58-165 69-176 (256)
89 KOG0910 Thioredoxin-like prote 34.7 93 0.002 26.4 5.0 57 39-96 56-112 (150)
90 PF05563 SpvD: Salmonella plas 34.5 59 0.0013 28.7 4.0 63 127-211 3-65 (216)
91 PRK15250 virulence protein Spv 34.5 59 0.0013 28.7 4.0 63 127-211 3-65 (216)
92 PRK10996 thioredoxin 2; Provis 34.4 2.1E+02 0.0046 22.0 6.7 66 43-114 51-116 (139)
93 PF08358 Flexi_CP_N: Carlaviru 34.3 14 0.00031 26.4 0.2 17 98-114 20-36 (52)
94 PTZ00256 glutathione peroxidas 33.8 97 0.0021 24.9 4.8 33 52-85 49-82 (183)
95 cd02983 P5_C P5 family, C-term 33.4 2.2E+02 0.0047 22.3 6.6 84 42-135 17-106 (130)
96 cd02967 mauD Methylamine utili 33.4 1.7E+02 0.0037 20.5 5.6 50 44-95 21-73 (114)
97 TIGR03470 HpnH hopanoid biosyn 33.0 46 0.00099 29.4 3.1 102 100-211 77-190 (318)
98 TIGR00608 radc DNA repair prot 32.4 73 0.0016 27.6 4.2 37 168-204 33-76 (218)
99 PF10397 ADSL_C: Adenylosuccin 32.1 22 0.00047 25.7 0.8 52 163-216 17-71 (81)
100 cd02950 TxlA TRX-like protein 31.4 2.1E+02 0.0045 22.3 6.2 64 39-111 16-83 (142)
101 PRK09414 glutamate dehydrogena 31.4 33 0.00072 32.9 2.1 19 32-50 361-379 (445)
102 PRK09381 trxA thioredoxin; Pro 31.2 1.9E+02 0.0041 20.4 6.0 64 44-113 21-84 (109)
103 cd03001 PDI_a_P5 PDIa family, 31.0 1.7E+02 0.0038 19.9 5.8 62 43-112 17-80 (103)
104 COG1623 Predicted nucleic-acid 30.8 39 0.00084 32.3 2.4 50 156-205 293-342 (349)
105 PRK13758 anaerobic sulfatase-m 30.2 86 0.0019 27.4 4.3 107 100-212 62-185 (370)
106 cd02948 TRX_NDPK TRX domain, T 29.9 2.1E+02 0.0046 20.5 6.2 65 40-114 14-81 (102)
107 TIGR02661 MauD methylamine deh 29.5 1.6E+02 0.0035 23.8 5.5 48 48-96 78-125 (189)
108 KOG0442 Structure-specific end 29.2 55 0.0012 34.7 3.3 53 156-209 821-873 (892)
109 PF06200 tify: tify domain; I 28.7 43 0.00093 22.3 1.7 15 194-208 20-34 (36)
110 PF14229 DUF4332: Domain of un 28.4 35 0.00077 26.7 1.5 34 160-193 57-91 (122)
111 cd03011 TlpA_like_ScsD_MtbDsbE 28.3 1.5E+02 0.0032 21.1 4.6 50 44-95 20-70 (123)
112 PF14947 HTH_45: Winged helix- 27.9 34 0.00075 24.5 1.2 36 183-218 18-61 (77)
113 cd02995 PDI_a_PDI_a'_C PDIa fa 27.8 2E+02 0.0043 19.5 5.8 63 44-113 18-82 (104)
114 cd07412 MPP_YhcR_N Bacillus su 27.7 1.3E+02 0.0028 26.1 4.9 62 21-82 121-199 (288)
115 TIGR02284 conserved hypothetic 27.6 1.5E+02 0.0032 23.6 4.9 94 112-208 13-125 (139)
116 TIGR01083 nth endonuclease III 27.3 78 0.0017 25.9 3.4 34 174-207 53-89 (191)
117 PF10975 DUF2802: Protein of u 26.9 50 0.0011 24.2 2.0 40 168-209 30-69 (70)
118 cd03026 AhpF_NTD_C TRX-GRX-lik 26.9 2.5E+02 0.0055 20.5 5.7 53 49-109 17-70 (89)
119 cd02951 SoxW SoxW family; SoxW 26.8 1.3E+02 0.0028 22.0 4.1 41 46-86 16-58 (125)
120 cd07381 MPP_CapA CapA and rela 26.7 2.5E+02 0.0055 23.1 6.3 45 35-80 121-180 (239)
121 cd03020 DsbA_DsbC_DsbG DsbA fa 26.2 1.3E+02 0.0029 24.1 4.4 39 35-73 67-105 (197)
122 PTZ00335 tubulin alpha chain; 25.8 76 0.0017 30.0 3.4 46 45-104 371-416 (448)
123 PRK09437 bcp thioredoxin-depen 25.4 2.1E+02 0.0046 21.5 5.2 39 47-85 33-72 (154)
124 KOG0384 Chromodomain-helicase 25.2 92 0.002 34.5 4.2 55 33-88 748-815 (1373)
125 PF06238 Borrelia_lipo_2: Borr 25.1 95 0.0021 25.6 3.4 34 117-150 67-100 (111)
126 KOG1210 Predicted 3-ketosphing 23.9 33 0.00071 32.5 0.7 27 28-54 105-131 (331)
127 PRK09492 treR trehalose repres 23.6 2.1E+02 0.0045 23.4 5.1 82 116-209 34-115 (315)
128 cd02186 alpha_tubulin The tubu 23.4 88 0.0019 29.3 3.3 37 58-103 378-414 (434)
129 KOG1636 DNA polymerase delta p 23.2 29 0.00062 32.0 0.1 9 212-220 248-256 (260)
130 PRK00125 pyrF orotidine 5'-pho 23.2 3.7E+02 0.008 24.2 7.0 67 150-219 141-220 (278)
131 cd07410 MPP_CpdB_N Escherichia 23.2 1.6E+02 0.0035 24.8 4.6 48 35-82 128-191 (277)
132 PF06596 PsbX: Photosystem II 23.1 38 0.00083 23.3 0.7 15 11-25 2-16 (39)
133 PF04321 RmlD_sub_bind: RmlD s 22.9 33 0.00073 29.2 0.5 14 33-46 49-62 (286)
134 PRK13660 hypothetical protein; 22.7 71 0.0015 27.3 2.4 30 65-94 60-89 (182)
135 smart00854 PGA_cap Bacterial c 22.6 2.8E+02 0.0061 23.0 5.9 41 36-77 118-175 (239)
136 PRK04140 hypothetical protein; 22.5 6.2E+02 0.014 23.4 11.7 167 14-211 5-181 (317)
137 cd05313 NAD_bind_2_Glu_DH NAD( 22.4 37 0.00079 30.2 0.6 18 32-49 171-188 (254)
138 PRK06423 phosphoribosylformylg 21.9 47 0.001 23.8 1.0 52 158-212 7-64 (73)
139 cd02189 delta_tubulin The tubu 21.6 94 0.002 29.2 3.1 36 59-103 392-427 (446)
140 PRK02412 aroD 3-dehydroquinate 21.4 3.7E+02 0.0079 23.2 6.5 69 61-129 59-135 (253)
141 PRK00507 deoxyribose-phosphate 21.4 1.1E+02 0.0024 26.3 3.4 68 142-209 78-146 (221)
142 cd05211 NAD_bind_Glu_Leu_Phe_V 21.0 49 0.0011 28.2 1.1 42 32-76 144-192 (217)
143 TIGR00433 bioB biotin syntheta 20.9 1.7E+02 0.0037 24.6 4.3 47 61-109 97-148 (296)
144 PTZ00134 40S ribosomal protein 20.6 1E+02 0.0022 25.9 2.9 53 156-217 30-82 (154)
145 PF09587 PGA_cap: Bacterial ca 20.5 2.6E+02 0.0056 23.4 5.3 45 38-84 122-192 (250)
146 TIGR00237 xseA exodeoxyribonuc 20.4 1.2E+02 0.0025 28.5 3.5 116 63-188 5-181 (432)
No 1
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=98.36 E-value=3e-06 Score=75.67 Aligned_cols=173 Identities=21% Similarity=0.340 Sum_probs=123.7
Q ss_pred cceeeee-eeCCceeeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccccC
Q 042199 26 SFRLNFV-LVAPDFIFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMELG 104 (220)
Q Consensus 26 S~RLnF~-~iaPDfIfn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g 104 (220)
.-++-|. .|-|||.++++ .+|-|+-.+.-.|.+ .-|.+||++|-.-|++--+++-+..+|++..-.+ -|+.-| ++
T Consensus 75 nv~w~f~ddi~PDf~lg~~-~cvLyLSl~yH~l~p-dYi~~Ri~~l~k~yk~~VLl~~vd~~e~~~~l~e-l~k~~~-l~ 150 (254)
T KOG2841|consen 75 NVKWEFGDDIIPDFVLGRG-CCVLYLSLKYHKLHP-DYIYRRIRKLGKNYKLRVLLVHVDMEEPYKPLLE-LTKTCD-LN 150 (254)
T ss_pred cCCeEecCCCCcceEecCc-eEEEEeehHhhhcCc-HHHHHHHHHhcccccceEEEEEecCcchHHHHHH-HHHHHH-hh
Confidence 6788899 99999998774 556666666655555 4588999999888999999999999999877544 445433 33
Q ss_pred cceeeecCCcchhHHHHHHHHHhhhhhhhhhhHHHHHHHHHh--hhhccceeEEeeeccCCCCccChhHHHHhhhhHHHH
Q 042199 105 RPTFVPVQDREMGFEKIIKIAHSRGVCKRQDAISKLKAERRR--AVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAI 182 (220)
Q Consensus 105 ~PtfvpV~d~eMgfEkivkIAh~~gvcKqQ~i~s~lk~ERkq--~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAI 182 (220)
-=|++=.-+.|-. -|+-.---.. ++--.++..||+. .++ .-++++|+|||+++-||-.|-|-.||+++|
T Consensus 151 ~~Tl~lA~s~Eea----aryIE~~k~~--ek~p~dli~~~~~~d~ls---~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~ 221 (254)
T KOG2841|consen 151 DVTLVLAWSMEEA----ARYIETYKEY--EKKPIDLIMERKDRDLLS---SLLGFLTTIPGVNKTDAQLLLQKFGSLQQI 221 (254)
T ss_pred ceeeeeeccHHHH----HHHHHHHHHh--hcCCchhhhhcccccHHH---HHHHHHHhCCCCCcccHHHHHHhcccHHHH
Confidence 3355444333322 2221111111 1112233333321 111 356889999999999999999999999999
Q ss_pred HhhhhhhhhhccCCChhhHHHHHHHhcCC
Q 042199 183 AKASKTYILENTDLSAEKAEMIVRFFRDP 211 (220)
Q Consensus 183 akaSke~IlenTDLS~dkAE~i~rffrDp 211 (220)
.-||.+++-.--.|-.-||+.+-+||.-|
T Consensus 222 ~~AS~~ele~~~G~G~~kak~l~~~l~~p 250 (254)
T KOG2841|consen 222 SNASEGELEQCPGLGPAKAKRLHKFLHQP 250 (254)
T ss_pred HhcCHhHHHhCcCcCHHHHHHHHHHHhcc
Confidence 99999999999999999999999999877
No 2
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=98.05 E-value=1.4e-06 Score=61.03 Aligned_cols=53 Identities=30% Similarity=0.479 Sum_probs=44.6
Q ss_pred ccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 160 SIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 160 SIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
+||||-...|..|++..||+|+|..|+.|++.+--|+....|++|..||+||+
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~ 59 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPE 59 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HH
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHH
Confidence 79999999999999999999999999999999999999999999999999984
No 3
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=97.94 E-value=4.1e-06 Score=57.22 Aligned_cols=53 Identities=30% Similarity=0.385 Sum_probs=50.3
Q ss_pred eeccCCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcC
Q 042199 158 VTSIPLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRD 210 (220)
Q Consensus 158 vTSIP~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~rffrD 210 (220)
+.+||||....|..|.++ ++++++|+.|+.+.+.+-..++..+|+.|.+.+||
T Consensus 7 L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 7 LLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAARE 60 (60)
T ss_dssp HHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHHH
T ss_pred hccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHhC
Confidence 468999999999999999 99999999999999999999999999999998874
No 4
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=97.13 E-value=0.0053 Score=54.84 Aligned_cols=133 Identities=26% Similarity=0.349 Sum_probs=98.9
Q ss_pred HHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHh-----------hhccccCcceeeecCCcchhHHHHHHHHHhhh-
Q 042199 62 VVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYF-----------KYGMELGRPTFVPVQDREMGFEKIIKIAHSRG- 129 (220)
Q Consensus 62 ~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYF-----------k~gm~~g~PtfvpV~d~eMgfEkivkIAh~~g- 129 (220)
-+|+-.++|+..+..--++|--. ++|.+-+| ..-.++|-| .+...|++-.-+.|-.||...-
T Consensus 86 RlfeQ~~rL~~~y~rpvliVegd-----~~~~~~~~i~~~av~~al~s~~vdfg~~-vi~t~~~~~Ta~~i~~la~req~ 159 (254)
T COG1948 86 RLFEQAKRLKKSYERPVLIVEGD-----DSFSRRPKIHPNAVRGALASLAVDFGLP-VIWTRSPEETAELIHELARREQE 159 (254)
T ss_pred hHHHHHHHHHhcCCccEEEEEcc-----cccccccccCHHHHHHHHHHHHhhcCce-EEEeCCHHHHHHHHHHHHHHHHH
Confidence 56889999999998766666433 44444331 112355633 4566788888888888887654
Q ss_pred hhhhhhhH-------HHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHH
Q 042199 130 VCKRQDAI-------SKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAE 202 (220)
Q Consensus 130 vcKqQ~i~-------s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE 202 (220)
.||+- +. ..++..+. ..|.|||||..+.|--|-+-.||++.+..||.+.++.--+.+.++|+
T Consensus 160 e~~r~-v~~~~~~~~~t~~e~q~----------~il~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~ 228 (254)
T COG1948 160 ERKRS-VNPHGKKKAKTLKELQL----------YILESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAR 228 (254)
T ss_pred hcccc-ccccccccccchHHHHH----------HHHHcCCCccHHHHHHHHHHhcCHHHHhhcCHHHHHHhcCccHHHHH
Confidence 55554 22 22222233 35789999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCC
Q 042199 203 MIVRFFRDP 211 (220)
Q Consensus 203 ~i~rffrDp 211 (220)
.|-+||+-|
T Consensus 229 ~I~~~~~t~ 237 (254)
T COG1948 229 EIYRFLRTE 237 (254)
T ss_pred HHHHHHhch
Confidence 999999866
No 5
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=97.07 E-value=0.00051 Score=60.67 Aligned_cols=56 Identities=20% Similarity=0.186 Sum_probs=52.8
Q ss_pred eeeccCCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 157 VVTSIPLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 157 vvTSIP~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
.+..||||---.|..|.++ +||+++|++||.+.|.+-..++..+|+.|..+|.++.
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~~ 60 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLE 60 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhcccc
Confidence 4678999999999999999 9999999999999999999999999999999998664
No 6
>PRK13766 Hef nuclease; Provisional
Probab=96.72 E-value=0.0093 Score=56.65 Aligned_cols=147 Identities=18% Similarity=0.276 Sum_probs=93.7
Q ss_pred HHHHHHHHHHHHhhcceEEEEEec--Ccc--chhhHHHhHhhhccccCcceeeecCCcchhHHHHHHHHHhhhhhhhhhh
Q 042199 61 AVVFSRIKKLKEQFAHFYVVLALP--TRE--QNDSFVRSYFKYGMELGRPTFVPVQDREMGFEKIIKIAHSRGVCKRQDA 136 (220)
Q Consensus 61 a~ifsRV~kLK~qF~~lYVVvtl~--t~e--q~dsF~~sYFk~gm~~g~PtfvpV~d~eMgfEkivkIAh~~gvcKqQ~i 136 (220)
.-+|.++.+|++.+.+-.++|.-. +.. ..++....--.+-...|-|. +...|++..-+-+..++...- ...+-
T Consensus 620 ~r~~~q~~~l~~~~~~~~lliE~~~~~~~~~~~~~i~~~l~~l~~~~~~~i-i~~~~~~eta~~l~~l~~~~~--~~~~~ 696 (773)
T PRK13766 620 RRLFEQVKDLKRAYERPVLIIEGDLYTIRNIHPNAIRGALASIAVDFGIPI-LFTRDEEETADLLKVIAKREQ--EEEKR 696 (773)
T ss_pred CcHHHHHHHHHhcCCCcEEEEEcCchhhcccCHHHHHHHHHHHHHHcCceE-EEeCCHHHHHHHHHHHHhhcc--ccCCC
Confidence 568889999999998888888663 111 11233333334455666664 445677766555555543210 00000
Q ss_pred HHHHHHHHHhhh-hccceeEEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 137 ISKLKAERRRAV-QTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 137 ~s~lk~ERkq~V-Q~md~flrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
.-.+..+++..- ..+..+ .+++||||..+.|..|.+..||+++|..||.+.+.+--.+...+|+.|..||..|.
T Consensus 697 ~~~~~~~~~~~~~~~~~~~--~L~~ipgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~~~ 771 (773)
T PRK13766 697 EVSVHGEKKAMTLKEQQEY--IVESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVTSEY 771 (773)
T ss_pred CcccccCCCCCCHHHHHHH--HHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhhhh
Confidence 000000000000 000011 38999999999999999999999999999999988877899999999999998763
No 7
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=96.52 E-value=0.0029 Score=63.32 Aligned_cols=146 Identities=15% Similarity=0.182 Sum_probs=93.9
Q ss_pred hHHHHHHHHHHHHhhcceEEEEEecCccchhhHH-HhHh---------------h---hccccCcceeeecCCcchhHHH
Q 042199 60 TAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFV-RSYF---------------K---YGMELGRPTFVPVQDREMGFEK 120 (220)
Q Consensus 60 ~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~-~sYF---------------k---~gm~~g~PtfvpV~d~eMgfEk 120 (220)
-.-+|+.+++|++.|++-.++|... +.++|. ++++ + .=+.+-+--++...|++..-+=
T Consensus 643 ~gRL~~Q~~~m~~~Y~~PvLLIE~d---~~~~f~l~~~~~~~~~~~~~~~~i~~~L~~L~l~fP~l~IiwS~s~~~TA~i 719 (814)
T TIGR00596 643 NGRLYNQCEKMLRYYAYPVLLIEFD---QNKSFSLEPRNDLSQEISSVNNDIQQKLALLTLHFPKLRIIWSSSPYATAEI 719 (814)
T ss_pred cchHHHHHHHHHHhcCCcEEEEEec---CCcccccccccccccccCccHHHHHHHHHHHHHhcCCceEEecCCHHHHHHH
Confidence 3458999999999999988888773 444443 1111 1 1223423445667777777777
Q ss_pred HHHHHHhhhhhhhhhhHHHHH----HHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCC
Q 042199 121 IIKIAHSRGVCKRQDAISKLK----AERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDL 196 (220)
Q Consensus 121 ivkIAh~~gvcKqQ~i~s~lk----~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDL 196 (220)
+..+|..... +..+..-.+. ...|. ...-..-..++.|||||..+.|..|-.-.||+++|+.||.+.+.+--.
T Consensus 720 ~~~Lk~~e~e-pd~~~~v~i~~~~~~~~k~-~~~~~~~q~~L~~lPgI~~~~a~~ll~~f~si~~l~~as~eeL~~~iG- 796 (814)
T TIGR00596 720 FEELKLGKEE-PDPATAAALGSDENTTAEG-LKFNDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIG- 796 (814)
T ss_pred HHHHHhcCCC-CCcccceecCccccccccc-ccccHHHHHHHHHCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHHhC-
Confidence 7777665332 1111111111 00000 000001123466999999999999999999999999999999988533
Q ss_pred ChhhHHHHHHHhcCC
Q 042199 197 SAEKAEMIVRFFRDP 211 (220)
Q Consensus 197 S~dkAE~i~rffrDp 211 (220)
+.++|+.|.+||+-+
T Consensus 797 ~~~~A~~i~~fl~~~ 811 (814)
T TIGR00596 797 DEEAAKRLYDFLRTE 811 (814)
T ss_pred CHHHHHHHHHHhccc
Confidence 488999999999976
No 8
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.89 E-value=0.0065 Score=59.79 Aligned_cols=53 Identities=28% Similarity=0.423 Sum_probs=51.3
Q ss_pred ccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 160 SIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 160 SIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
+||||-..-|..|.+..||+++|..||.+.+.+-.++....|+.|..||+||.
T Consensus 532 gIpgIG~~~ak~L~~~F~si~~L~~As~eeL~~i~GIG~k~A~sI~~ff~~~~ 584 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPTVAEEIREFFDSER 584 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhH
Confidence 69999999999999999999999999999999999999999999999999986
No 9
>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=95.84 E-value=0.0079 Score=58.57 Aligned_cols=55 Identities=27% Similarity=0.440 Sum_probs=52.4
Q ss_pred eeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 158 VTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 158 vTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
.-.||||-...|..|.+..||+++|..||.+.+.+-.++....|+.|..||++|.
T Consensus 500 aLgIpgVG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff~~~~ 554 (652)
T TIGR00575 500 ALGIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPN 554 (652)
T ss_pred hccCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHhhhh
Confidence 3489999999999999999999999999999999999999999999999999986
No 10
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=95.45 E-value=0.011 Score=50.34 Aligned_cols=52 Identities=29% Similarity=0.330 Sum_probs=48.7
Q ss_pred eeccCCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 158 VTSIPLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 158 vTSIP~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~rffr 209 (220)
+..||||....|..|..+ |.|++.+++|+.+.+.+-.+++.++|+.+.+..+
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAAR 53 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence 467999999999999999 9999999999999999999999999999988776
No 11
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=95.29 E-value=0.015 Score=56.01 Aligned_cols=56 Identities=27% Similarity=0.304 Sum_probs=52.1
Q ss_pred EEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcC
Q 042199 155 LRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRD 210 (220)
Q Consensus 155 lrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrD 210 (220)
.-.+++||||-.--+..|.+..||+++|..||.+.|.+-.+++...|+.|..||++
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~~ 597 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEALHK 597 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhcc
Confidence 34578999999999999999999999999999999988779999999999999986
No 12
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.99 E-value=0.021 Score=55.92 Aligned_cols=54 Identities=28% Similarity=0.358 Sum_probs=51.8
Q ss_pred eccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 159 TSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 159 TSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
-.||||-...|..|++..||+++|..||.+++.+-.++....|+.|..||+||.
T Consensus 514 lgi~~IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~ 567 (665)
T PRK07956 514 LGIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAVEE 567 (665)
T ss_pred hhccCcCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhh
Confidence 379999999999999999999999999999999999999999999999999986
No 13
>PRK00254 ski2-like helicase; Provisional
Probab=94.82 E-value=0.067 Score=51.37 Aligned_cols=78 Identities=24% Similarity=0.286 Sum_probs=68.2
Q ss_pred hhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCC
Q 042199 134 QDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDP 211 (220)
Q Consensus 134 Q~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp 211 (220)
.+....|..=+.+++||+-.-+=-+..|||+..--|..|.++ +||+++|++|+.+.|.+-..+....|+.|.++++.+
T Consensus 623 ~~~~~~l~~l~~rl~~g~~~~~~~L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~~ 701 (720)
T PRK00254 623 QEVLDYLETLHLRVKHGVREELLELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGVE 701 (720)
T ss_pred hhHHHHHHHHHHHHHcCCCHHHhhhhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhccc
Confidence 444555554488889998777777889999999999999999 999999999999999999999999999999999844
No 14
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=94.29 E-value=0.035 Score=54.36 Aligned_cols=93 Identities=20% Similarity=0.254 Sum_probs=66.3
Q ss_pred ceeeecCCcchhH-HHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHh
Q 042199 106 PTFVPVQDREMGF-EKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAK 184 (220)
Q Consensus 106 PtfvpV~d~eMgf-EkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIak 184 (220)
|...|-.++.+-| -+|=.-|| |=.|...=+.-+|+... -.+.+||||-.-=+.+|-.-.||+++|.+
T Consensus 513 ~~~l~~~s~~l~lLq~iRDEaH------RFAIt~hRk~R~k~~~~------S~L~~IpGIG~kr~~~LL~~FgSi~~I~~ 580 (624)
T PRK14669 513 PIVLDRFSPVLHLVQSIRDEAH------RFAITFHRKRRETRDRT------SELLEIPGVGAKTVQRLLKHFGSLERVRA 580 (624)
T ss_pred eeecCCCCHHHHHHHHHHHHHH------HHHHHHhHHHhhHHHHH------HHHhcCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 5556666665533 23333344 33343333333333333 35779999999999999999999999999
Q ss_pred hhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 185 ASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 185 aSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
||.|.|.+- ++...|+.|..+|+.+.
T Consensus 581 As~eeL~~v--i~~k~A~~I~~~l~~~~ 606 (624)
T PRK14669 581 ATETQLAAV--VGRAAAEAIIAHFTTEE 606 (624)
T ss_pred CCHHHHHHH--hCHHHHHHHHHHhcCcC
Confidence 999999775 99999999999998653
No 15
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=94.26 E-value=0.087 Score=51.10 Aligned_cols=92 Identities=9% Similarity=0.069 Sum_probs=67.4
Q ss_pred cceeeecCCcchhH-HHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHH
Q 042199 105 RPTFVPVQDREMGF-EKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIA 183 (220)
Q Consensus 105 ~PtfvpV~d~eMgf-EkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIa 183 (220)
.|..+|-.++.+-| .+|=.-||.-+ |..-=+.-.|+. +--.+..||||-..=..+|-+..||+++|.
T Consensus 474 ~~~~l~~~s~~l~lLq~irDEaHRFA------i~~hR~~r~k~~------~~S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik 541 (567)
T PRK14667 474 KEIPLKENPILYKVFGLIRDEAHRFA------LSYNRKLREKEG------LKDILDKIKGIGEVKKEIIYRNFKTLYDFL 541 (567)
T ss_pred ceeeCCCCCHHHHHHHHHHHHHHHHH------HHHHHHHhhccc------ccCccccCCCCCHHHHHHHHHHhCCHHHHH
Confidence 37767766766643 34444455443 332222222222 224577999999999999999999999999
Q ss_pred hhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 184 KASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 184 kaSke~IlenTDLS~dkAE~i~rffr 209 (220)
+||-|.|.+- .++...|+.|..+|+
T Consensus 542 ~As~eeL~~v-gi~~~~A~~I~~~l~ 566 (567)
T PRK14667 542 KADDEELKKL-GIPPSVKQEVKKYLS 566 (567)
T ss_pred hCCHHHHHHc-CCCHHHHHHHHHHhc
Confidence 9999999998 999999999999885
No 16
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=94.05 E-value=0.12 Score=51.85 Aligned_cols=94 Identities=17% Similarity=0.209 Sum_probs=71.3
Q ss_pred cceeeecCCcchhHHHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHh
Q 042199 105 RPTFVPVQDREMGFEKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAK 184 (220)
Q Consensus 105 ~PtfvpV~d~eMgfEkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIak 184 (220)
.|...|..++++-| +.|.|-+.-|--|...=+.-.|+...+ .+..||||-...+..|.+..||+|+|..
T Consensus 597 ~p~~L~~~~~~l~~-----Lq~iRDEaHRfAi~~hR~~r~k~~~~s------~L~~IPGIGpkr~k~LL~~FGSle~I~~ 665 (694)
T PRK14666 597 NPLPLRAGAPELLF-----LQHVRDTVHDYAIGRHRRARAGAALTG------ELQRVEGIGPATARLLWERFGSLQAMAA 665 (694)
T ss_pred ceeecCCCCHHHHH-----HHHHHHHHHHHHHHHHHHHHHhhhhHh------HHhhCCCCCHHHHHHHHHHhCCHHHHHh
Confidence 57777888877665 233344444444444444444444443 5789999999999999999999999999
Q ss_pred hhhhhhhhccCCChhhHHHHHHHhc
Q 042199 185 ASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 185 aSke~IlenTDLS~dkAE~i~rffr 209 (220)
||.+.|-+-..++...|+.|.++|+
T Consensus 666 AS~eELa~V~Gig~k~Ae~I~~~L~ 690 (694)
T PRK14666 666 AGEEGLAAVPGIGPARAAALHEHLK 690 (694)
T ss_pred cCHHHHHhcCCcCHHHHHHHHHHHH
Confidence 9999988888999999999998874
No 17
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=93.93 E-value=0.037 Score=51.50 Aligned_cols=53 Identities=21% Similarity=0.267 Sum_probs=49.4
Q ss_pred EeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHh
Q 042199 156 RVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFF 208 (220)
Q Consensus 156 rvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rff 208 (220)
|++++||+|+...|..|....||++.|..||.+.+.+--.+...+|..|...+
T Consensus 287 RiLs~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l 339 (352)
T PRK13482 287 RLLSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGL 339 (352)
T ss_pred HHHhcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHH
Confidence 89999999999999999999999999999999999998899999998876554
No 18
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=93.45 E-value=0.078 Score=51.56 Aligned_cols=92 Identities=17% Similarity=0.207 Sum_probs=68.8
Q ss_pred cceeeecCCcchhH-HHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHH
Q 042199 105 RPTFVPVQDREMGF-EKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIA 183 (220)
Q Consensus 105 ~PtfvpV~d~eMgf-EkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIa 183 (220)
.|.-.|-.++.+-| .+|=.-||.-+. .. -+.-|.+ .. -.+..||||-..=..+|-...||++.|.
T Consensus 476 ~~~~l~~~s~~l~lLq~iRDEaHRFAi------t~-hRk~R~k-~~------s~L~~I~GiG~kr~~~LL~~Fgs~~~I~ 541 (574)
T PRK14670 476 QGIKLPKGNPALRILQNVRDEAHRKAN------GF-NKKLREN-IK------LNYTKIKGIGEKKAKKILKSLGTYKDIL 541 (574)
T ss_pred ceeecCCCCHHHHHHHHHHHHHHHHHH------HH-HHHhhcc-cc------cccccCCCCCHHHHHHHHHHhCCHHHHH
Confidence 46666666665543 344444554443 22 2222333 22 2678999999999999999999999999
Q ss_pred hhhhhhhhhccCCChhhHHHHHHHhcC
Q 042199 184 KASKTYILENTDLSAEKAEMIVRFFRD 210 (220)
Q Consensus 184 kaSke~IlenTDLS~dkAE~i~rffrD 210 (220)
+||-|.|.+-..++...|+.|-.+|+.
T Consensus 542 ~As~eeL~~v~gi~~~~A~~I~~~l~~ 568 (574)
T PRK14670 542 LLNEDEIAEKMKINIKMAKKIKKFAEK 568 (574)
T ss_pred hCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 999999999999999999999999964
No 19
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=92.47 E-value=0.097 Score=45.33 Aligned_cols=54 Identities=26% Similarity=0.333 Sum_probs=49.0
Q ss_pred eeeccCCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcC
Q 042199 157 VVTSIPLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRD 210 (220)
Q Consensus 157 vvTSIP~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~rffrD 210 (220)
-++++|||+.--|..|... |.+++.++.++.+.+.+-.+++.++|+.+.+--+.
T Consensus 7 ~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 7 DLEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAARE 61 (317)
T ss_pred cHhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 3689999999999999987 99999999999999999999999999988876543
No 20
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=92.45 E-value=0.11 Score=50.37 Aligned_cols=90 Identities=20% Similarity=0.242 Sum_probs=64.8
Q ss_pred cceeeecCCcchhH-HHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHH
Q 042199 105 RPTFVPVQDREMGF-EKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIA 183 (220)
Q Consensus 105 ~PtfvpV~d~eMgf-EkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIa 183 (220)
.|...|-.++.+-| .+|=.-||.-+.--.... |+. +--.+++||||-.--+..|-+..||+++|-
T Consensus 487 ~~~~l~~~~~~l~lL~~irDEaHRFAi~~hR~~-------r~~-------~~~~L~~IpGIG~kr~~~LL~~FGS~~~I~ 552 (577)
T PRK14668 487 RTYDWPDDAPQLHLLQRVRDEAHRFAVQYHQTL-------RDD-------VSTVLDDVPGVGPETRKRLLRRFGSVEGVR 552 (577)
T ss_pred CeeecCCCCHHHHHHHHHHHHHHHHHhhHHHHH-------HHH-------HHhHHhcCCCCCHHHHHHHHHHcCCHHHHH
Confidence 45445666665533 445555665544322211 211 224578999999999999999999999999
Q ss_pred hhhhhhhhhccCCChhhHHHHHHHh
Q 042199 184 KASKTYILENTDLSAEKAEMIVRFF 208 (220)
Q Consensus 184 kaSke~IlenTDLS~dkAE~i~rff 208 (220)
.||.+.|.+-..++...|+.|..++
T Consensus 553 ~As~eeL~~vpGi~~~~A~~I~~~~ 577 (577)
T PRK14668 553 EASVEDLRDVPGVGEKTAETIRERL 577 (577)
T ss_pred hCCHHHHHhCCCCCHHHHHHHHHhC
Confidence 9999999888899999999998763
No 21
>PF13905 Thioredoxin_8: Thioredoxin-like; PDB: 1FG4_A 1I5G_A 1OC8_B 1O6J_A 1OC9_B 1O81_A 3FKF_A 1O85_A 1O7U_A 1O8W_A ....
Probab=91.62 E-value=1.7 Score=30.00 Aligned_cols=65 Identities=15% Similarity=0.307 Sum_probs=45.9
Q ss_pred EEEEEeeccCCCchHHHHHHHHHHHHhhc--ceEEEEEecCccchhhHHHhHhhhccccCcceeeecCCcc
Q 042199 47 ISFVFITNWDCHNTAVVFSRIKKLKEQFA--HFYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQDRE 115 (220)
Q Consensus 47 vAFifvt~wdc~n~a~ifsRV~kLK~qF~--~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d~e 115 (220)
+...|-+.| |..+...+..+++|..+++ .=..+|.++..++.+.+.+..=++++ ....+|+.+..
T Consensus 4 ~ll~fwa~~-c~~c~~~~~~l~~l~~~~~~~~~v~~v~Vs~d~~~~~~~~~~~~~~~---~~~~~~~~~~~ 70 (95)
T PF13905_consen 4 VLLYFWASW-CPPCKKELPKLKELYKKYKKKDDVEFVFVSLDEDEEEWKKFLKKNNF---PWYNVPFDDDN 70 (95)
T ss_dssp EEEEEE-TT-SHHHHHHHHHHHHHHHHHTTTTTEEEEEEE-SSSHHHHHHHHHTCTT---SSEEEETTTHH
T ss_pred EEEEEECCC-CHHHHHHHHHHHHHHHHhCCCCCEEEEEEEeCCCHHHHHHHHHhcCC---CceEEeeCcch
Confidence 445555665 7889999999999999999 77788889888777766655555533 35566766544
No 22
>PTZ00035 Rad51 protein; Provisional
Probab=90.06 E-value=0.26 Score=44.14 Aligned_cols=52 Identities=25% Similarity=0.304 Sum_probs=46.2
Q ss_pred eecc--CCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 158 VTSI--PLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 158 vTSI--P~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~rffr 209 (220)
+..+ |||.-.|++.|..| |-+++.++.+++..+.+-++||.++|+.|.+--|
T Consensus 23 ~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~ 77 (337)
T PTZ00035 23 IEKLQSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAAS 77 (337)
T ss_pred HHHHhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHH
Confidence 4445 88999999999876 9999999999999999999999999999986544
No 23
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=89.62 E-value=0.81 Score=38.76 Aligned_cols=66 Identities=12% Similarity=0.091 Sum_probs=55.3
Q ss_pred HHhhhhccceeEEeeeccCCCCccChhHHHH-hhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 144 RRRAVQTMDVFLRVVTSIPLIDNHDANALNQ-AIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 144 Rkq~VQ~md~flrvvTSIP~id~HDAn~L~Q-aIGSieAIakaSke~IlenTDLS~dkAE~i~rffr 209 (220)
.+.++|++-...--+..+|+++.+-+..|.. .|.|++.+...+.+.+-+=..+....++.|.++.+
T Consensus 139 ~q~i~q~~w~~~~~L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~ 205 (312)
T smart00611 139 SQMIIQALWPTDSPLLQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLS 205 (312)
T ss_pred HHHHHHhhCCCCCccccCCCCCHHHHHHHHhCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHH
Confidence 6778888887777788999999999999998 48899999999887777666777788888888764
No 24
>cd02982 PDI_b'_family Protein Disulfide Isomerase (PDIb') family, redox inactive TRX-like domain b'; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI, calsequestrin and other PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5 and PDIR. PDI, ERp57, ERp72, P5 and PDIR are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and one or more redox inactive TRX-like (b) domains. The molecular structure of PDI is abb'a'. Also included in this family is the PDI-related protein ERp27, w
Probab=89.17 E-value=2.1 Score=29.80 Aligned_cols=65 Identities=11% Similarity=0.228 Sum_probs=46.1
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccc-cCcceeeecCC
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGME-LGRPTFVPVQD 113 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~-~g~PtfvpV~d 113 (220)
|..+.+.|.+.| |..+..+-..++++-++|..-..++.+...+ +..+.+. ||.. .+-|+++=..+
T Consensus 12 ~~~~~~~f~~~~-~~~~~~~~~~~~~vA~~~~~~v~f~~vd~~~-~~~~~~~---~~i~~~~~P~~~~~~~ 77 (103)
T cd02982 12 GKPLLVLFYNKD-DSESEELRERFKEVAKKFKGKLLFVVVDADD-FGRHLEY---FGLKEEDLPVIAIINL 77 (103)
T ss_pred CCCEEEEEEcCC-hhhHHHHHHHHHHHHHHhCCeEEEEEEchHh-hHHHHHH---cCCChhhCCEEEEEec
Confidence 567888888888 5566677777788888887766777777665 3445553 4664 58999887766
No 25
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=89.15 E-value=0.31 Score=47.67 Aligned_cols=52 Identities=31% Similarity=0.395 Sum_probs=47.6
Q ss_pred EeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 156 RVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 156 rvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffr 209 (220)
..+.+||||-..=|.+|.+..||+++|..||.+.|.+- +....|+.|..||.
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~Fgs~~~i~~As~eeL~~v--ig~k~A~~I~~~~~ 620 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHFGSVEKVAKASLEELAAV--AGPKTAETIYRYYH 620 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhC
Confidence 35689999999999999999999999999999998776 88999999999984
No 26
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=88.50 E-value=0.38 Score=47.67 Aligned_cols=53 Identities=17% Similarity=0.197 Sum_probs=48.7
Q ss_pred ccCCCCccChhHHH-HhhhhHHHHHh------hhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 160 SIPLIDNHDANALN-QAIGSIEAIAK------ASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 160 SIP~id~HDAn~L~-QaIGSieAIak------aSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
.||++-.+-|..|+ +..++++++.. ++.|++++=.|+....|++|..||+||.
T Consensus 506 GI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff~~~~ 565 (669)
T PRK14350 506 GIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAFNDKI 565 (669)
T ss_pred CCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHHcCHH
Confidence 38999999999999 89999999976 5788999999999999999999999985
No 27
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=87.24 E-value=1 Score=45.44 Aligned_cols=51 Identities=18% Similarity=0.260 Sum_probs=47.6
Q ss_pred EeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHH
Q 042199 156 RVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVR 206 (220)
Q Consensus 156 rvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~r 206 (220)
-.+..||||-..=+.+|-+-.||+++|.+||-+.|.+-..++...|++|..
T Consensus 608 s~L~~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~ 658 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFGSFRSLQSATPQDIATAIHIPLTQAHTILH 658 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHH
Confidence 356799999999999999999999999999999999999999999999854
No 28
>TIGR00597 rad10 DNA repair protein rad10. All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.94 E-value=4.1 Score=32.85 Aligned_cols=60 Identities=17% Similarity=0.459 Sum_probs=42.7
Q ss_pred ccccCCchHHHHHHHHhcccceeeeeeeCCceeeeCCCceEEEEEee-ccCCCchHHHHHHHHHHHHhhcc
Q 042199 7 RDEQHPSFINFISSFLSANSFRLNFVLVAPDFIFNCGGMSISFVFIT-NWDCHNTAVVFSRIKKLKEQFAH 76 (220)
Q Consensus 7 rd~q~ps~infis~fL~AnS~RLnF~~iaPDfIfn~gglSvAFifvt-~wdc~n~a~ifsRV~kLK~qF~~ 76 (220)
||+..| ++++| .. -+..|..|.|||+++.. .+.+|.| ..-.-+..-|.+|+++|++.|..
T Consensus 8 ~QkgNP-lL~~i----~n--v~wey~di~~Dy~~g~~---~~vLFLSLkYH~L~peYi~~Ri~~L~~~~~l 68 (112)
T TIGR00597 8 RQKGNP-LLKHV----RN--VPWEYGDVIPDYVLGQG---TCALFLSLRYHNLHPDYIHRRLQSLGKNFNL 68 (112)
T ss_pred cccCCh-HHHHH----hc--CCeEecCcCCCEEEcCc---cEEEEEEhhhhccCHHHHHHHHHHhccccce
Confidence 577777 55543 33 34556699999999765 4445554 55566778899999999998876
No 29
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=86.88 E-value=0.59 Score=41.64 Aligned_cols=48 Identities=19% Similarity=0.218 Sum_probs=43.4
Q ss_pred CCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 162 PLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 162 P~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~rffr 209 (220)
+||.-.|++.|..+ |.+++.++.++++.+++-++||-++|+.|.+-.+
T Consensus 7 ~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~ 55 (313)
T TIGR02238 7 HGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAAS 55 (313)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 56999999999765 9999999999999999999999999999987544
No 30
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=85.44 E-value=7.5 Score=38.42 Aligned_cols=137 Identities=22% Similarity=0.257 Sum_probs=85.6
Q ss_pred eCCceeeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhcc-ccCcceeeecC
Q 042199 34 VAPDFIFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGM-ELGRPTFVPVQ 112 (220)
Q Consensus 34 iaPDfIfn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm-~~g~PtfvpV~ 112 (220)
--||.|+-.||-+ -++.++..-..+.---.||.|.-.+. ..=+ ..+.|.-.|-.
T Consensus 443 ~~Pdli~iDGGkg----------------Ql~~a~~vl~~l~~~~~viglaK~~~---------~~~~~~~~~~~~l~~~ 497 (581)
T COG0322 443 ELPDLILIDGGKG----------------QLNAAKEVLKELGLDIPVIGLAKGEE---------ELLLPGPGEEFDLPPN 497 (581)
T ss_pred CCCCEEEEeCCHH----------------HHHHHHHHHHHcCCCccEEEEEecCc---------eeEecCCCceecCCCC
Confidence 3579999999853 23333333333332233666655544 1111 12234444555
Q ss_pred CcchhH-HHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhh
Q 042199 113 DREMGF-EKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYIL 191 (220)
Q Consensus 113 d~eMgf-EkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~Il 191 (220)
++.+-| .+|=.-||.- .|..--+.--|..+|+ .+-.||||-.+=..+|-.-.||+++|.+||-|+|.
T Consensus 498 ~p~l~~lq~irDEaHrf------Ai~~hR~~R~k~~~~s------~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~ 565 (581)
T COG0322 498 SPALYLLQRIRDEAHRF------AITYHRKKRSKAMLQS------SLDDIPGIGPKRRKALLKHFGSLKGIKSASVEELA 565 (581)
T ss_pred CHHHHHHHHHHHHHHHH------HHHHHHHHhhhhhhcC------ccccCCCcCHHHHHHHHHHhhCHHHHHhcCHHHHH
Confidence 555544 2333344443 3333333223334443 46689999999999999999999999999999999
Q ss_pred hccCCChhhHHHHHHHh
Q 042199 192 ENTDLSAEKAEMIVRFF 208 (220)
Q Consensus 192 enTDLS~dkAE~i~rff 208 (220)
+- .++..-||+|...+
T Consensus 566 ~v-gi~~~~a~~i~~~~ 581 (581)
T COG0322 566 KV-GISKKLAEKIYEAL 581 (581)
T ss_pred Hc-CCCHHHHHHHHhhC
Confidence 99 99999999997653
No 31
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=85.27 E-value=0.73 Score=46.37 Aligned_cols=53 Identities=23% Similarity=0.380 Sum_probs=50.8
Q ss_pred ccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 160 SIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 160 SIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
.||.+-.--|-.|++..||+|++.+||.+.+.+--|+-..-|+.|+.||++|.
T Consensus 515 GIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~si~~ff~~~~ 567 (667)
T COG0272 515 GIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVARSIIEFFANEE 567 (667)
T ss_pred CCchhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccchhHHHHHHHHHHHcCHH
Confidence 68999999999999999999999999999999999999999999999999985
No 32
>smart00839 ELFV_dehydrog Glutamate/Leucine/Phenylalanine/Valine dehydrogenase. Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction.
Probab=85.13 E-value=0.77 Score=34.93 Aligned_cols=45 Identities=27% Similarity=0.348 Sum_probs=29.4
Q ss_pred eeeeeCCceeeeCCCceEEEEEeeccCCC---chHHHH-HHHHHHHHhhcce
Q 042199 30 NFVLVAPDFIFNCGGMSISFVFITNWDCH---NTAVVF-SRIKKLKEQFAHF 77 (220)
Q Consensus 30 nF~~iaPDfIfn~gglSvAFifvt~wdc~---n~a~if-sRV~kLK~qF~~l 77 (220)
+=+.+.||++.|.||+-+...- |.-+ ....++ ....+|++.+.++
T Consensus 47 rGi~~~PD~~~NaGGvi~s~~E---~~~~~~~~~e~v~~~~~~~i~~~~~~v 95 (102)
T smart00839 47 RGVLYAPDFAANAGGVIVSALE---MLQNLARTAEEVFTDLSEIMRNALEEI 95 (102)
T ss_pred CCCEEcCcceecCCCEEeehhh---hhcccCCCHHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999885543 4333 444566 4455666666543
No 33
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=82.92 E-value=1.3 Score=36.93 Aligned_cols=53 Identities=21% Similarity=0.245 Sum_probs=34.0
Q ss_pred eeccCCCCccChhHHHHhhhh---HHHHHhhhhhhhhhccCCChhhHHHHHHHhcC
Q 042199 158 VTSIPLIDNHDANALNQAIGS---IEAIAKASKTYILENTDLSAEKAEMIVRFFRD 210 (220)
Q Consensus 158 vTSIP~id~HDAn~L~QaIGS---ieAIakaSke~IlenTDLS~dkAE~i~rffrD 210 (220)
+.+||||-.-=|-.+....|+ ++||.+++.+.+.+-..++..+|+.|...+++
T Consensus 75 L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 75 LISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 345666666666666666666 66666666666666666666666666666654
No 34
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=82.78 E-value=1.5 Score=39.30 Aligned_cols=64 Identities=19% Similarity=0.228 Sum_probs=54.0
Q ss_pred hhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCC
Q 042199 148 VQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDP 211 (220)
Q Consensus 148 VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp 211 (220)
.|+.|-=--++++||++|+-|+..+---||+++-.--||++..---..+-.+||+.+.++++-|
T Consensus 159 ~~s~d~s~~fl~~i~~Vnksds~~~L~d~g~L~rf~gaSrdE~e~l~g~g~~ka~~~ieyln~p 222 (224)
T COG5241 159 MQSLDRSNEFLILIFIVNKSDSEDTLNDIGKLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLP 222 (224)
T ss_pred cCCCcccccceEEEEeeccccHHHHHHHHHHHHHHhccchhHHHHHHccCHHHHHHHHHHhccc
Confidence 3555533457899999999999999999999999999999876666678899999999988765
No 35
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=82.45 E-value=1.2 Score=40.67 Aligned_cols=52 Identities=19% Similarity=0.251 Sum_probs=45.5
Q ss_pred EEeeecc--CCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHH
Q 042199 155 LRVVTSI--PLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVR 206 (220)
Q Consensus 155 lrvvTSI--P~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~r 206 (220)
..-+..+ +||.-.|++.|..| |-++++++.++++.+++-++||-++|+.|.+
T Consensus 28 ~~~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~ 82 (344)
T PLN03187 28 FESIDKLISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICE 82 (344)
T ss_pred ccCHHHHhhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHH
Confidence 3445666 77999999999876 9999999999999999999999999998764
No 36
>PRK01172 ski2-like helicase; Provisional
Probab=80.14 E-value=2 Score=40.92 Aligned_cols=75 Identities=21% Similarity=0.169 Sum_probs=60.5
Q ss_pred hhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHH-hhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHh
Q 042199 134 QDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQ-AIGSIEAIAKASKTYILENTDLSAEKAEMIVRFF 208 (220)
Q Consensus 134 Q~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~Q-aIGSieAIakaSke~IlenTDLS~dkAE~i~rff 208 (220)
-++..+|..=++|++||+-.=+=-+..|||++..-|..|.+ +|-|+++|+.++-+.+.+=-.++..+|+.|..-.
T Consensus 590 ~~~~~~l~~~~~rl~~gv~~~~~~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~ 665 (674)
T PRK01172 590 PEMRRKLEILNIRIKEGIREDLIDLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRA 665 (674)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHhhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHH
Confidence 34556666668889998866666667899999999999987 6899999999988887666678889998887643
No 37
>PF06113 BRE: Brain and reproductive organ-expressed protein (BRE); InterPro: IPR010358 This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene. Compared to normal cells, immortalised human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms. It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities [].
Probab=78.64 E-value=1.6 Score=40.85 Aligned_cols=45 Identities=22% Similarity=0.467 Sum_probs=32.2
Q ss_pred eeeCCceeee-CCCce---EEEEEeeccCCCchHHHHHHHHHHHHhhcc
Q 042199 32 VLVAPDFIFN-CGGMS---ISFVFITNWDCHNTAVVFSRIKKLKEQFAH 76 (220)
Q Consensus 32 ~~iaPDfIfn-~gglS---vAFifvt~wdc~n~a~ifsRV~kLK~qF~~ 76 (220)
-..+|||||+ ....- -..=..++||++|.-..++=|..|..+|+.
T Consensus 78 p~~pPDfiF~eD~~F~pd~s~l~~L~~Wd~~dp~~Ll~li~EL~~~Y~~ 126 (333)
T PF06113_consen 78 PEFPPDFIFGEDDNFLPDPSKLPSLVNWDPSDPNCLLNLISELRQLYKE 126 (333)
T ss_pred CCCCCCEEeCCCcCcCCChhhcchhhcCCCCCchHHHHHHHHHHHHHHH
Confidence 3579999997 21100 011236899999999999999999988763
No 38
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=77.29 E-value=2.2 Score=38.78 Aligned_cols=51 Identities=25% Similarity=0.330 Sum_probs=44.2
Q ss_pred eecc--CCCCccChhHHHH-hhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHh
Q 042199 158 VTSI--PLIDNHDANALNQ-AIGSIEAIAKASKTYILENTDLSAEKAEMIVRFF 208 (220)
Q Consensus 158 vTSI--P~id~HDAn~L~Q-aIGSieAIakaSke~IlenTDLS~dkAE~i~rff 208 (220)
++.+ +||.-.|++.|.. +|.++++++.+++..+.+-++||.++|+.+.+--
T Consensus 28 ~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~ 81 (342)
T PLN03186 28 IEQLQASGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAA 81 (342)
T ss_pred HHHHHhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHH
Confidence 5556 6799999999965 4999999999999999999999999998776544
No 39
>PF15162 DUF4580: Domain of unknown function (DUF4580)
Probab=77.14 E-value=15 Score=31.87 Aligned_cols=104 Identities=20% Similarity=0.384 Sum_probs=76.3
Q ss_pred HHHHHHhcccceeeee-eeCCc-eeeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCc--cchhhH
Q 042199 17 FISSFLSANSFRLNFV-LVAPD-FIFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTR--EQNDSF 92 (220)
Q Consensus 17 fis~fL~AnS~RLnF~-~iaPD-fIfn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~--eq~dsF 92 (220)
=|++.|+.-+||.+++ ++.++ +||.=.| |||..++.=||- +-+.||.|.-.-+.|.|+|+..+-- ++.+.-
T Consensus 19 ei~~~L~~~~hkiR~S~sve~~svIFpLSG--vAFLL~d~~~~~---~~l~ki~kF~~ihrNsflvL~aalhg~~ew~~m 93 (162)
T PF15162_consen 19 EIATILSNQSHKIRYSDSVEPGSVIFPLSG--VAFLLMDAQECF---MFLAKIEKFIDIHRNSFLVLSAALHGPEEWKLM 93 (162)
T ss_pred HHHHHHhcccceEEecccccCCeEEEEccc--ceeeEeccHHHh---hHHHHHHHHHhccCCceEEeehhhcCHHHHHHH
Confidence 3788999999999997 45555 5666554 799999995554 4899999999999999999865533 333222
Q ss_pred HHhHhhhccccCcceeeecCCcchhHHHHHHHHHhh
Q 042199 93 VRSYFKYGMELGRPTFVPVQDREMGFEKIIKIAHSR 128 (220)
Q Consensus 93 ~~sYFk~gm~~g~PtfvpV~d~eMgfEkivkIAh~~ 128 (220)
.+= --+=+.+--++||..+--.-+=|.-||...
T Consensus 94 ~~i---qRFLG~nl~ilpvhn~~~~v~~M~tiAK~t 126 (162)
T PF15162_consen 94 FRI---QRFLGSNLRILPVHNPANCVKLMCTIAKTT 126 (162)
T ss_pred HHH---HHHhcCCceEEecCCHHHHHHHHHHHHHHh
Confidence 111 111225678999999999999999998754
No 40
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=74.64 E-value=3.6 Score=31.46 Aligned_cols=40 Identities=18% Similarity=0.262 Sum_probs=31.3
Q ss_pred hHHHHhhhhHHHHHhhhhhhh---hhccCCChhhHHHHHHHhc
Q 042199 170 NALNQAIGSIEAIAKASKTYI---LENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 170 n~L~QaIGSieAIakaSke~I---lenTDLS~dkAE~i~rffr 209 (220)
+.|.+..|++|+|++++.+.| +....++..||+.|.+.-+
T Consensus 15 ~~l~~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~ 57 (149)
T smart00478 15 ERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELAR 57 (149)
T ss_pred HHHHHHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence 345666789999999999877 4567899999999976543
No 41
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=73.50 E-value=2 Score=42.22 Aligned_cols=50 Identities=22% Similarity=0.329 Sum_probs=42.5
Q ss_pred ccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCCc
Q 042199 160 SIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 160 SIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp~ 212 (220)
.||+|-.. +..+ ..++++++..|+.|++++=-|+....|+.|..||.||.
T Consensus 495 GI~~vG~~-~ak~--~~~~i~~l~~a~~e~l~~i~gIG~~~a~si~~~f~~~~ 544 (562)
T PRK08097 495 GIPLPQAA-LNAL--DDRSWQQLLSRSEQQWQQLPGIGEGRARQLIAFLQHPE 544 (562)
T ss_pred CCccHHHH-HHHH--hcCCHHHHHcCCHHHHhcCCCchHHHHHHHHHHHcCHH
Confidence 47777653 2233 77999999999999999999999999999999999975
No 42
>cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.
Probab=72.01 E-value=14 Score=24.50 Aligned_cols=49 Identities=14% Similarity=0.420 Sum_probs=32.2
Q ss_pred EEEEEeeccCCCchHHHHHHHHHHHHhhc--ce-EEEEEecC--ccchhhHHHhH
Q 042199 47 ISFVFITNWDCHNTAVVFSRIKKLKEQFA--HF-YVVLALPT--REQNDSFVRSY 96 (220)
Q Consensus 47 vAFifvt~wdc~n~a~ifsRV~kLK~qF~--~l-YVVvtl~t--~eq~dsF~~sY 96 (220)
+-+.|...| |.-+.....+++++..+++ ++ .+.|...+ .|....|.+.+
T Consensus 22 ~ll~f~~~~-C~~C~~~~~~l~~~~~~~~~~~~~~~~v~~d~~~~~~~~~~~~~~ 75 (116)
T cd02966 22 VLVNFWASW-CPPCRAEMPELEALAKEYKDDGVEVVGVNVDDDDPAAVKAFLKKY 75 (116)
T ss_pred EEEEeeccc-ChhHHHHhHHHHHHHHHhCCCCeEEEEEECCCCCHHHHHHHHHHc
Confidence 445555667 8888888889999999994 32 33344433 56666666654
No 43
>cd02956 ybbN ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.
Probab=70.81 E-value=25 Score=24.15 Aligned_cols=68 Identities=10% Similarity=0.230 Sum_probs=44.0
Q ss_pred eCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccccCcceeeecCCc
Q 042199 41 NCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQDR 114 (220)
Q Consensus 41 n~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d~ 114 (220)
++.|-.+-..|-+.| |..+...-..++++..+|++-+.++.+-..+ ...+.+. ||. .|-||++=..+.
T Consensus 9 ~~~~~~vlv~f~a~w-C~~C~~~~~~~~~~~~~~~~~~~~~~vd~~~-~~~l~~~---~~i-~~~Pt~~~~~~g 76 (96)
T cd02956 9 ESTQVPVVVDFWAPR-SPPSKELLPLLERLAEEYQGQFVLAKVNCDA-QPQIAQQ---FGV-QALPTVYLFAAG 76 (96)
T ss_pred hcCCCeEEEEEECCC-ChHHHHHHHHHHHHHHHhCCcEEEEEEeccC-CHHHHHH---cCC-CCCCEEEEEeCC
Confidence 344666777788888 5555555666777888888767677776544 3444443 343 478998866554
No 44
>PRK02362 ski2-like helicase; Provisional
Probab=70.62 E-value=5.6 Score=38.64 Aligned_cols=71 Identities=20% Similarity=0.126 Sum_probs=58.9
Q ss_pred HHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCC
Q 042199 139 KLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDP 211 (220)
Q Consensus 139 ~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp 211 (220)
.+..=+++++||+-.=+--+..||||...-|..|.++ |-|+++|+.|+.+.|.+- +...-|+.|.+-.++.
T Consensus 635 ~~~~l~~~l~~gv~~~~~~L~~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~~~~ 706 (737)
T PRK02362 635 AARELEKRVEYGVREELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENILEQAGRR 706 (737)
T ss_pred HHHHHHHHHHhCCCHHHHHHhCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHhCcc
Confidence 3333477888888776667778999999999999774 889999999998888887 9999999999988843
No 45
>cd01075 NAD_bind_Leu_Phe_Val_DH NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino acids to the corresponding 2-oxoacid derivative. Amino acid DH -like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily inc
Probab=69.31 E-value=3.7 Score=33.95 Aligned_cols=44 Identities=23% Similarity=0.381 Sum_probs=31.1
Q ss_pred eeeeCCceeeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcce
Q 042199 31 FVLVAPDFIFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHF 77 (220)
Q Consensus 31 F~~iaPDfIfn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~l 77 (220)
=+.+.|||+.|.||+-+.+. -|.-+....++.|++++...++..
T Consensus 132 Gi~~~Pd~~~NaGGv~~~~~---e~~~~~~~~~~~~~~~~~~~~~~v 175 (200)
T cd01075 132 GILYAPDYVVNAGGLINVAD---ELYGGNEARVLAKVEAIYDTLLEI 175 (200)
T ss_pred CCEEeCceeeeCcCceeehh---HHhCCcHHHHHHHHHHHHHHHHHH
Confidence 35678999999999987433 233333556888888887777654
No 46
>cd02961 PDI_a_family Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies
Probab=68.97 E-value=27 Score=22.89 Aligned_cols=67 Identities=19% Similarity=0.372 Sum_probs=41.5
Q ss_pred eCCCceEEEEEeeccCCCchHHHHHHHHHHHHhh--cceEEEEEecCccchhhHHHhHhhhccccCcceeeecCCc
Q 042199 41 NCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQF--AHFYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQDR 114 (220)
Q Consensus 41 n~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF--~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d~ 114 (220)
..++ .+...|.++| |..+......++++..++ ..-+.++.+...+ +..+.+. ||. -+-||++=..+.
T Consensus 13 ~~~~-~~~v~f~~~~-C~~C~~~~~~~~~~~~~~~~~~~~~~~~v~~~~-~~~~~~~---~~i-~~~Pt~~~~~~~ 81 (101)
T cd02961 13 KDSK-DVLVEFYAPW-CGHCKALAPEYEKLAKELKGDGKVVVAKVDCTA-NNDLCSE---YGV-RGYPTIKLFPNG 81 (101)
T ss_pred hCCC-cEEEEEECCC-CHHHHhhhHHHHHHHHHhccCCceEEEEeeccc-hHHHHHh---CCC-CCCCEEEEEcCC
Confidence 4445 5666777888 777776666677777777 3455566665554 3344333 344 478988766554
No 47
>cd03012 TlpA_like_DipZ_like TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3.
Probab=66.85 E-value=22 Score=26.17 Aligned_cols=41 Identities=20% Similarity=0.361 Sum_probs=27.1
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhcce-EEEEEecC
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLALPT 85 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl~t 85 (220)
|=-+.+.|-+.| |..+.....++++|..+|++. ..|+.+++
T Consensus 23 gk~vvl~F~a~~-C~~C~~~~p~l~~l~~~~~~~~~~vi~i~~ 64 (126)
T cd03012 23 GKVVLLDFWTYC-CINCLHTLPYLTDLEQKYKDDGLVVIGVHS 64 (126)
T ss_pred CCEEEEEEECCC-CccHHHHHHHHHHHHHHcCcCCeEEEEecc
Confidence 444555665664 777777788888999999742 34455543
No 48
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=66.51 E-value=5.5 Score=25.42 Aligned_cols=39 Identities=18% Similarity=0.237 Sum_probs=32.5
Q ss_pred hhHHH-HhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHH
Q 042199 169 ANALN-QAIGSIEAIAKASKTYILENTDLSAEKAEMIVRF 207 (220)
Q Consensus 169 An~L~-QaIGSieAIakaSke~IlenTDLS~dkAE~i~rf 207 (220)
|..|. .++.|+|.+|.++.+.+.+-..++.++|+.+..=
T Consensus 6 ~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~ 45 (50)
T TIGR01954 6 AQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINR 45 (50)
T ss_pred HHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHH
Confidence 44443 5789999999999999999999999999987643
No 49
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=66.22 E-value=4.9 Score=35.81 Aligned_cols=48 Identities=27% Similarity=0.304 Sum_probs=41.6
Q ss_pred CCCCccChhHHH-HhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 162 PLIDNHDANALN-QAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 162 P~id~HDAn~L~-QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffr 209 (220)
+||.-.+++.|. .+|.+++.++.++++.+++-++||.++++.+.+-.+
T Consensus 7 ~~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~ 55 (316)
T TIGR02239 7 NGITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEAA 55 (316)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 348888888885 579999999999999999999999999998876443
No 50
>cd02998 PDI_a_ERp38 PDIa family, endoplasmic reticulum protein 38 (ERp38) subfamily; composed of proteins similar to the P5-like protein first isolated from alfalfa, which contains two redox active TRX (a) domains at the N-terminus, like human P5, and a C-terminal domain with homology to the C-terminal domain of ERp29, unlike human P5. The cDNA clone of this protein (named G1) was isolated from an alfalfa cDNA library by screening with human protein disulfide isomerase (PDI) cDNA. The G1 protein is constitutively expressed in all major organs of the plant and its expression is induced by treatment with tunicamycin, indicating that it may be a glucose-regulated protein. The G1 homolog in the eukaryotic social amoeba Dictyostelium discoideum is also described as a P5-like protein, which is located in the endoplasmic reticulum (ER) despite the absence of an ER-retrieval signal. G1 homologs from Aspergillus niger and Neurospora crassa have also been characterized, and are named TIGA and ER
Probab=64.16 E-value=29 Score=23.57 Aligned_cols=71 Identities=21% Similarity=0.373 Sum_probs=42.7
Q ss_pred eeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhc--ceEEEEEecCccchhhHHHhHhhhccccCcceeeecCCc
Q 042199 39 IFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFA--HFYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQDR 114 (220)
Q Consensus 39 Ifn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~--~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d~ 114 (220)
+++..|-.+...|.+.| |..+...-..+..+..+++ .-++++.+...+.+..+.+. ||. -|-||++=..+.
T Consensus 13 ~~~~~~~~~~v~f~a~~-C~~C~~~~~~~~~~~~~~~~~~~~~~~~id~~~~~~~~~~~---~~i-~~~P~~~~~~~~ 85 (105)
T cd02998 13 VVGDDKKDVLVEFYAPW-CGHCKNLAPEYEKLAAVFANEDDVVIAKVDADEANKDLAKK---YGV-SGFPTLKFFPKG 85 (105)
T ss_pred HhcCCCCcEEEEEECCC-CHHHHhhChHHHHHHHHhCCCCCEEEEEEECCCcchhhHHh---CCC-CCcCEEEEEeCC
Confidence 44555655555666666 7777666666777777776 33666677655523444443 343 578988765544
No 51
>PF13848 Thioredoxin_6: Thioredoxin-like domain; PDB: 3EC3_B 3BOA_A 2B5E_A 1BJX_A 2K18_A 3UEM_A 3BJ5_A 2BJX_A 2R2J_A 2L4C_A ....
Probab=63.79 E-value=39 Score=25.46 Aligned_cols=91 Identities=16% Similarity=0.288 Sum_probs=64.2
Q ss_pred hHHHHHHHHhcccceeeeeeeCCcee--eeCCCce-EEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchh
Q 042199 14 FINFISSFLSANSFRLNFVLVAPDFI--FNCGGMS-ISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQND 90 (220)
Q Consensus 14 ~infis~fL~AnS~RLnF~~iaPDfI--fn~gglS-vAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~d 90 (220)
=.+-|..|+..|++-| +..+.++-. +..+|.. +.++|. +=+......+...++.+-..+++-++++.+-.. ...
T Consensus 63 ~~~~l~~fI~~~~~P~-v~~~t~~n~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~a~~~~~~~~f~~~d~~-~~~ 139 (184)
T PF13848_consen 63 TPEELKKFIKKNSFPL-VPELTPENFEKLFSSPKPPVLILFD-NKDNESTEAFKKELQDIAKKFKGKINFVYVDAD-DFP 139 (184)
T ss_dssp SHHHHHHHHHHHSSTS-CEEESTTHHHHHHSTSSEEEEEEEE-TTTHHHHHHHHHHHHHHHHCTTTTSEEEEEETT-TTH
T ss_pred CHHHHHHHHHHhcccc-ccccchhhHHHHhcCCCceEEEEEE-cCCchhHHHHHHHHHHHHHhcCCeEEEEEeehH-HhH
Confidence 3678999999999999 899998632 3456766 555553 324566677888888888888887677776666 555
Q ss_pred hHHHhHhhhccc-cCcceeee
Q 042199 91 SFVRSYFKYGME-LGRPTFVP 110 (220)
Q Consensus 91 sF~~sYFk~gm~-~g~Ptfvp 110 (220)
.+.+ | +|++ -..|+++=
T Consensus 140 ~~~~-~--~~i~~~~~P~~vi 157 (184)
T PF13848_consen 140 RLLK-Y--FGIDEDDLPALVI 157 (184)
T ss_dssp HHHH-H--TTTTTSSSSEEEE
T ss_pred HHHH-H--cCCCCccCCEEEE
Confidence 5655 3 3775 56788773
No 52
>KOG0907 consensus Thioredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=62.13 E-value=30 Score=26.63 Aligned_cols=63 Identities=21% Similarity=0.410 Sum_probs=49.6
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccccCcceeeecCC
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQD 113 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d 113 (220)
+-.|-.=|-+.| |.-+-++.-.+.+|-.++++ -+.+.+...| +.++.+.|=-- +-|||+=..+
T Consensus 21 ~kliVvdF~a~w-CgPCk~i~P~~~~La~~y~~-v~Flkvdvde-~~~~~~~~~V~----~~PTf~f~k~ 83 (106)
T KOG0907|consen 21 DKLVVVDFYATW-CGPCKAIAPKFEKLAEKYPD-VVFLKVDVDE-LEEVAKEFNVK----AMPTFVFYKG 83 (106)
T ss_pred CCeEEEEEECCC-CcchhhhhhHHHHHHHHCCC-CEEEEEeccc-CHhHHHhcCce----EeeEEEEEEC
Confidence 455556667777 89999999999999999999 8888999999 88888876433 3488876543
No 53
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=61.12 E-value=20 Score=25.63 Aligned_cols=48 Identities=25% Similarity=0.383 Sum_probs=36.9
Q ss_pred EEEEEecCccchhhHHHhHhhhccccCcceee--ecCCcchhHHHHHHHHHhhhh
Q 042199 78 YVVLALPTREQNDSFVRSYFKYGMELGRPTFV--PVQDREMGFEKIIKIAHSRGV 130 (220)
Q Consensus 78 YVVvtl~t~eq~dsF~~sYFk~gm~~g~Ptfv--pV~d~eMgfEkivkIAh~~gv 130 (220)
.|+|+.|+.. -..+.+.-++.|+|.++ |+..-.-..++|++.|..+|+
T Consensus 65 ~V~I~tp~~~-----h~~~~~~~l~~g~~v~~EKP~~~~~~~~~~l~~~a~~~~~ 114 (120)
T PF01408_consen 65 AVIIATPPSS-----HAEIAKKALEAGKHVLVEKPLALTLEEAEELVEAAKEKGV 114 (120)
T ss_dssp EEEEESSGGG-----HHHHHHHHHHTTSEEEEESSSSSSHHHHHHHHHHHHHHTS
T ss_pred EEEEecCCcc-----hHHHHHHHHHcCCEEEEEcCCcCCHHHHHHHHHHHHHhCC
Confidence 5677777744 44567778899999887 566677788999999998875
No 54
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=60.69 E-value=9.7 Score=27.50 Aligned_cols=39 Identities=31% Similarity=0.341 Sum_probs=32.0
Q ss_pred hHHHHhhh--hHHHHHhhhhhhhhhc---cCCChhhHHHHHHHh
Q 042199 170 NALNQAIG--SIEAIAKASKTYILEN---TDLSAEKAEMIVRFF 208 (220)
Q Consensus 170 n~L~QaIG--SieAIakaSke~Ilen---TDLS~dkAE~i~rff 208 (220)
+.|.+..| ++|+|+.++-+.|-+- ..++.-||+.|.+.-
T Consensus 19 ~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a 62 (108)
T PF00730_consen 19 RRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELA 62 (108)
T ss_dssp HHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHH
Confidence 45778888 9999999998887443 699999999998764
No 55
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=60.62 E-value=16 Score=30.77 Aligned_cols=66 Identities=14% Similarity=0.104 Sum_probs=47.6
Q ss_pred HHhhhhccceeEEeeeccCCCCccChhHHHHh-hhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 144 RRRAVQTMDVFLRVVTSIPLIDNHDANALNQA-IGSIEAIAKASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 144 Rkq~VQ~md~flrvvTSIP~id~HDAn~L~Qa-IGSieAIakaSke~IlenTDLS~dkAE~i~rffr 209 (220)
.+-++|++--.--.+..+|||+...+..|.+. |-+++.+.+.+.+.+-+=...+.+.++.|.++.+
T Consensus 136 ~q~i~q~~w~~~~~L~Qlp~i~~~~~~~l~~~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~ 202 (314)
T PF02889_consen 136 SQCIVQALWDSDSPLLQLPHIGEESLKKLEKRGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVAS 202 (314)
T ss_dssp HHHHHHTS-TTS-GGGGSTT--HHHHHHHHHTT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHC
T ss_pred HHHHHhhcCCCCChhhcCCCCCHHHHHHHhccCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHH
Confidence 45677777655677889999999999999985 4589999999988887777767799999988876
No 56
>cd00502 DHQase_I Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyzes the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate to produce dehydroshikimate. Dehydroquinase is the third enzyme in the shikimate pathway, which is involved in the biosynthesis of aromatic amino acids. Type I DHQase exists as a homodimer. Type II 3-dehydroquinase also catalyzes the same overall reaction, but is unrelated in terms of sequence and structure, and utilizes a completely different reaction mechanism.
Probab=59.99 E-value=26 Score=29.01 Aligned_cols=70 Identities=17% Similarity=0.323 Sum_probs=43.7
Q ss_pred eeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhH------HHhHhhhccccCcceeeecCCcchh---HHHHH
Q 042199 52 ITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSF------VRSYFKYGMELGRPTFVPVQDREMG---FEKII 122 (220)
Q Consensus 52 vt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF------~~sYFk~gm~~g~PtfvpV~d~eMg---fEkiv 122 (220)
++-|.......+-.-+.+|++... +=+++|+.+++|-..| -..+++.++++| | ...|.|+. +++++
T Consensus 32 ~D~~~~~~~~~~~~~~~~lr~~~~-~piI~T~R~~~eGG~~~~~~~~~~~ll~~~~~~~-~---d~vDiEl~~~~~~~~~ 106 (225)
T cd00502 32 VDLLEDPSIDDVAEQLSLLRELTP-LPIIFTVRTKSEGGNFEGSEEEYLELLEEALKLG-P---DYVDIELDSALLEELI 106 (225)
T ss_pred EeeccccchHHHHHHHHHHHHhCC-CCEEEEEcccccCCCcCCCHHHHHHHHHHHHHHC-C---CEEEEEecchHHHHHH
Confidence 344444333344455666666554 7899999999875433 233455577888 4 44566776 77788
Q ss_pred HHHH
Q 042199 123 KIAH 126 (220)
Q Consensus 123 kIAh 126 (220)
+.+|
T Consensus 107 ~~~~ 110 (225)
T cd00502 107 NSRK 110 (225)
T ss_pred HHHH
Confidence 7776
No 57
>cd01076 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids
Probab=59.97 E-value=1.6 Score=37.27 Aligned_cols=44 Identities=39% Similarity=0.682 Sum_probs=30.7
Q ss_pred eeeeCCceeeeCCCceEEEEEee------ccCCCchHHHHHHHH-HHHHhhcce
Q 042199 31 FVLVAPDFIFNCGGMSISFVFIT------NWDCHNTAVVFSRIK-KLKEQFAHF 77 (220)
Q Consensus 31 F~~iaPDfIfn~gglSvAFifvt------~wdc~n~a~ifsRV~-kLK~qF~~l 77 (220)
=+.+.||++.|.||+=++..=.. .|+ ...+.+|+. +|+..+.++
T Consensus 152 Gi~~~PD~~aNaGGvi~s~~E~~~~~~~~~~~---~~~v~~~l~~~i~~~~~~v 202 (227)
T cd01076 152 GVLVVPDILANAGGVTVSYFEWVQNLQGFYWD---EEEVNSRLETKMREAFEAV 202 (227)
T ss_pred CCEEEChHHhcCcchhhhHHHHhhhhccCcCC---HHHHHHHHHHHHHHHHHHH
Confidence 46789999999999876332221 343 456778888 888877663
No 58
>PLN02477 glutamate dehydrogenase
Probab=57.69 E-value=3.9 Score=38.48 Aligned_cols=45 Identities=24% Similarity=0.475 Sum_probs=32.3
Q ss_pred eeeeCCceeeeCCCceEEEEEee----c--cCCCchHHHHHHHH-HHHHhhcceE
Q 042199 31 FVLVAPDFIFNCGGMSISFVFIT----N--WDCHNTAVVFSRIK-KLKEQFAHFY 78 (220)
Q Consensus 31 F~~iaPDfIfn~gglSvAFifvt----~--wdc~n~a~ifsRV~-kLK~qF~~lY 78 (220)
=+.+.||++.|.||+-+...=.. . | +...+.+|++ +|+..|.++|
T Consensus 327 GI~~~PD~~aNaGGVivs~~E~~qn~~~~~w---~~~~v~~~l~~~m~~~~~~v~ 378 (410)
T PLN02477 327 GVVVLPDIYANSGGVTVSYFEWVQNIQGFMW---EEEKVNRELDRYMTDAFKALK 378 (410)
T ss_pred CcEEEChHHhCCCCeeeeHHHhhhccccCCC---CHHHHHHHHHHHHHHHHHHHH
Confidence 37789999999999977543221 1 4 3456778988 8888887753
No 59
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=55.40 E-value=58 Score=21.52 Aligned_cols=54 Identities=15% Similarity=0.281 Sum_probs=28.1
Q ss_pred EEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccccCcceee
Q 042199 50 VFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMELGRPTFV 109 (220)
Q Consensus 50 ifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~Ptfv 109 (220)
+|...| |..+.....-+.+|...+..-+-++.+.-.++-+... +||.. |-||++
T Consensus 5 ~f~~~~-C~~C~~~~~~l~~l~~~~~~~~~~~~vd~~~~~~~~~----~~~v~-~vPt~~ 58 (82)
T TIGR00411 5 LFTSPT-CPYCPAAKRVVEEVAKEMGDAVEVEYINVMENPQKAM----EYGIM-AVPAIV 58 (82)
T ss_pred EEECCC-CcchHHHHHHHHHHHHHhcCceEEEEEeCccCHHHHH----HcCCc-cCCEEE
Confidence 455555 5555555555555555554323334444333333332 35644 679998
No 60
>PLN02412 probable glutathione peroxidase
Probab=52.74 E-value=89 Score=24.78 Aligned_cols=39 Identities=21% Similarity=0.414 Sum_probs=31.3
Q ss_pred EEEEEeeccCCCchHHHHHHHHHHHHhhcce-EEEEEecCc
Q 042199 47 ISFVFITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLALPTR 86 (220)
Q Consensus 47 vAFifvt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl~t~ 86 (220)
|-..|...| |.-+.....+++.|..+|+.. +.|+.+++.
T Consensus 32 vlv~f~a~~-C~~c~~e~~~l~~l~~~~~~~g~~vvgv~~~ 71 (167)
T PLN02412 32 LLIVNVASK-CGLTDSNYKELNVLYEKYKEQGFEILAFPCN 71 (167)
T ss_pred EEEEEeCCC-CCChHHHHHHHHHHHHHHhhCCcEEEEeccc
Confidence 444455676 998888899999999999976 888999863
No 61
>cd03002 PDI_a_MPD1_like PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces cerevisiae MPD1 protein, which contains a single redox active TRX domain located at the N-terminus, and an ER retention signal at the C-terminus indicative of an ER-resident protein. MPD1 has been shown to suppress the maturation defect of carboxypeptidase Y caused by deletion of the yeast PDI1 gene. Other characterized members of this subfamily include the Aspergillus niger prpA protein and Giardia PDI-1. PrpA is non-essential to strain viability, however, its transcript level is induced by heterologous protein expression suggesting a possible role in oxidative protein folding during high protein production. Giardia PDI-1 has the ability to refold scrambled RNase and exhibits transglutaminase activity.
Probab=52.61 E-value=49 Score=23.09 Aligned_cols=68 Identities=19% Similarity=0.374 Sum_probs=40.8
Q ss_pred eCCCceEEEEEeeccC--CCchHHHHHHHHHHHHhhcceEEEEEecCccc-hhhHHHhHhhhccccCcceeeecCCcc
Q 042199 41 NCGGMSISFVFITNWD--CHNTAVVFSRIKKLKEQFAHFYVVLALPTREQ-NDSFVRSYFKYGMELGRPTFVPVQDRE 115 (220)
Q Consensus 41 n~gglSvAFifvt~wd--c~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq-~dsF~~sYFk~gm~~g~PtfvpV~d~e 115 (220)
.+.|-.+-..|.+.|. |....+.|..+ ..++.+-..++.+...++ +..+.+. ||. -|-||++=..+..
T Consensus 15 ~~~~~~~lv~f~a~wC~~C~~~~~~~~~~---a~~~~~~~~~~~v~~~~~~~~~~~~~---~~i-~~~Pt~~~~~~~~ 85 (109)
T cd03002 15 HNTNYTTLVEFYAPWCGHCKNLKPEYAKA---AKELDGLVQVAAVDCDEDKNKPLCGK---YGV-QGFPTLKVFRPPK 85 (109)
T ss_pred hcCCCeEEEEEECCCCHHHHhhChHHHHH---HHHhcCCceEEEEecCccccHHHHHH---cCC-CcCCEEEEEeCCC
Confidence 4556667788889985 66666766655 445555455555554432 3444443 343 4679887666554
No 62
>cd03010 TlpA_like_DsbE TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c maturation (Ccm) factor with a redox active CXXC motif. Assembly of cytochrome c requires the ligation of heme to reduced thiols of the apocytochrome. In bacteria, this assembly occurs in the periplasm. The reductase activity of DsbE in the oxidizing environment of the periplasm is crucial in the maturation of cytochrome c.
Probab=52.12 E-value=70 Score=23.20 Aligned_cols=44 Identities=11% Similarity=0.231 Sum_probs=29.1
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchh
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQND 90 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~d 90 (220)
|--+...|...| |..+......+++|+..+. +.||.++..+..+
T Consensus 25 gk~vvv~F~a~~-C~~C~~~~~~l~~l~~~~~--~~vv~v~~~~~~~ 68 (127)
T cd03010 25 GKPYLLNVWASW-CAPCREEHPVLMALARQGR--VPIYGINYKDNPE 68 (127)
T ss_pred CCEEEEEEEcCc-CHHHHHHHHHHHHHHHhcC--cEEEEEECCCCHH
Confidence 444666777888 7777777777777877763 6667776443333
No 63
>PF03834 Rad10: Binding domain of DNA repair protein Ercc1 (rad10/Swi10); InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. In yeast, Rad10 works as a heterodimer with Rad1, and is involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts or cross-linking agents. The complex forms an endonuclease which specifically degrades single-stranded DNA. Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA inter-strand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex [].; GO: 0003684 damaged DNA binding, 0004519 endonuclease activity, 0006281 DNA repair, 0005634 nucleus; PDB: 2JNW_A 2JPD_A 2A1I_A.
Probab=52.05 E-value=10 Score=28.33 Aligned_cols=48 Identities=17% Similarity=0.443 Sum_probs=31.0
Q ss_pred cceeee-eeeCCceeeeCCCceEEEEEee-ccCCCchHHHHHHHHHHHHhhcc
Q 042199 26 SFRLNF-VLVAPDFIFNCGGMSISFVFIT-NWDCHNTAVVFSRIKKLKEQFAH 76 (220)
Q Consensus 26 S~RLnF-~~iaPDfIfn~gglSvAFifvt-~wdc~n~a~ifsRV~kLK~qF~~ 76 (220)
..+..| ..|.|||+++-. .+.+|.+ .+-.-+-.-|..|+++|++.|.+
T Consensus 20 nv~we~~~~i~~Dy~vg~~---~~vLFLSLkYH~L~P~YI~~Ri~~L~~~~~~ 69 (69)
T PF03834_consen 20 NVPWEYDSDIVPDYVVGST---TCVLFLSLKYHRLHPEYIHERIKKLGKNYNL 69 (69)
T ss_dssp SS-EEE----SSSEEEETT---EEEEEEEHHHHHHSTCHHHHHHHHHTTSSS-
T ss_pred cCCeEecCCCCCCEEECCe---EEEEEEeeeeecCCHHHHHHHHHHhhhhcCC
Confidence 456778 789999999544 4455554 44445566799999999998753
No 64
>cd02997 PDI_a_PDIR PDIa family, PDIR subfamily; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity.
Probab=51.35 E-value=52 Score=22.47 Aligned_cols=66 Identities=18% Similarity=0.357 Sum_probs=34.9
Q ss_pred eCCCceEEEEEeeccC--CCchHHHHHHHHHHHHhhc--ceEEEEEecCccc-hhhHHHhHhhhccccCcceeeecCCc
Q 042199 41 NCGGMSISFVFITNWD--CHNTAVVFSRIKKLKEQFA--HFYVVLALPTREQ-NDSFVRSYFKYGMELGRPTFVPVQDR 114 (220)
Q Consensus 41 n~gglSvAFifvt~wd--c~n~a~ifsRV~kLK~qF~--~lYVVvtl~t~eq-~dsF~~sYFk~gm~~g~PtfvpV~d~ 114 (220)
+.+. .+-..|.++|. |....+.+.++. ..|+ .-.+++.+...++ +..+.+. ||. -|-||++=..+.
T Consensus 15 ~~~~-~~~v~f~a~wC~~C~~~~~~~~~~~---~~~~~~~~~~~~~id~~~~~~~~~~~~---~~i-~~~Pt~~~~~~g 85 (104)
T cd02997 15 KKEK-HVLVMFYAPWCGHCKKMKPEFTKAA---TELKEDGKGVLAAVDCTKPEHDALKEE---YNV-KGFPTFKYFENG 85 (104)
T ss_pred hhCC-CEEEEEECCCCHHHHHhCHHHHHHH---HHHhhCCceEEEEEECCCCccHHHHHh---CCC-ccccEEEEEeCC
Confidence 3444 55567777874 556666666554 3443 2223444544442 4444443 343 377888655543
No 65
>cd02993 PDI_a_APS_reductase PDIa family, 5'-Adenylylsulfate (APS) reductase subfamily; composed of plant-type APS reductases containing a C-terminal redox active TRX domain and an N-terminal reductase domain which is part of a superfamily that includes N type ATP PPases. APS reductase catalyzes the reduction of activated sulfate to sulfite, a key step in the biosynthesis of sulfur-containing metabolites. Sulfate is first activated by ATP sulfurylase, forming APS, which can be phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Depending on the organism, either APS or PAPS can be used for sulfate reduction. Prokaryotes and fungi use PAPS, whereas plants use both APS and PAPS. Since plant-type APS reductase uses glutathione (GSH) as its electron donor, the C-terminal domain may function like glutaredoxin, a GSH-dependent member of the TRX superfamily. The flow of reducing equivalents goes from GSH - C-terminal TRX domain - N-terminal reductase domain - APS. Plant-type APS red
Probab=50.36 E-value=76 Score=22.95 Aligned_cols=65 Identities=17% Similarity=0.256 Sum_probs=37.0
Q ss_pred CCceEEEEEeecc--CCCchHHHHHHHHHHHHhhcce-EEEEEecCccchhhHHHhHhhhccccCcceeeecCC
Q 042199 43 GGMSISFVFITNW--DCHNTAVVFSRIKKLKEQFAHF-YVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQD 113 (220)
Q Consensus 43 gglSvAFifvt~w--dc~n~a~ifsRV~kLK~qF~~l-YVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d 113 (220)
.|-.+-..|.+.| .|....++|.. |...++.- .+++.+...++...+.+.+| | .-+-||++=..+
T Consensus 20 ~~k~vlv~f~a~wC~~C~~~~~~~~~---la~~~~~~~~~~~~vd~d~~~~~~~~~~~--~-v~~~Pti~~f~~ 87 (109)
T cd02993 20 RNQSTLVVLYAPWCPFCQAMEASYEE---LAEKLAGSNVKVAKFNADGEQREFAKEEL--Q-LKSFPTILFFPK 87 (109)
T ss_pred cCCCEEEEEECCCCHHHHHHhHHHHH---HHHHhccCCeEEEEEECCccchhhHHhhc--C-CCcCCEEEEEcC
Confidence 3556777888999 24455566554 44555542 55566665554444544433 2 357888764433
No 66
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=49.72 E-value=6.2 Score=28.64 Aligned_cols=28 Identities=36% Similarity=0.426 Sum_probs=23.8
Q ss_pred EeeeccCCCCccChhHHHHhhhhHHHHH
Q 042199 156 RVVTSIPLIDNHDANALNQAIGSIEAIA 183 (220)
Q Consensus 156 rvvTSIP~id~HDAn~L~QaIGSieAIa 183 (220)
+.++|||||...=|-.|.-.||.++...
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~ 29 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFK 29 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcc
Confidence 4689999999999999988888887654
No 67
>cd02953 DsbDgamma DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD alpha). DsbD beta, a transmembrane domain comprising of eight helices, acquires its reducing potential from the cytoplasmic thioredoxin. DsbD alpha transfers the acquired reducing potential from DsbD gamma to target proteins such as the periplasmic protein disulphide isomerases, DsbC and DsbG. This flow of reducing potential from the cytoplasm through DsbD allows DsbC and DsbG to act as isomerases in the oxidizing environment of the bacterial periplasm. DsbD also transfers reducing potential from the cytoplasm to specific reductases in the periplasm which are involved in the maturation of cytochromes.
Probab=48.34 E-value=95 Score=21.87 Aligned_cols=64 Identities=17% Similarity=0.397 Sum_probs=37.3
Q ss_pred CceEEEEEeeccCCCchHHHHHHH---HHHHHhhcceEEEEEecCccc---hhhHHHhHhhhccccCcceeeecC
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRI---KKLKEQFAHFYVVLALPTREQ---NDSFVRSYFKYGMELGRPTFVPVQ 112 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV---~kLK~qF~~lYVVvtl~t~eq---~dsF~~sYFk~gm~~g~PtfvpV~ 112 (220)
|-.|-..|-++| |..+-..-..+ .+++.++..-++++.+...+. +..+.+.| |. -|-||++=..
T Consensus 11 ~k~vlv~f~a~w-C~~C~~~~~~~~~~~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~~---~i-~~~Pti~~~~ 80 (104)
T cd02953 11 GKPVFVDFTADW-CVTCKVNEKVVFSDPEVQAALKKDVVLLRADWTKNDPEITALLKRF---GV-FGPPTYLFYG 80 (104)
T ss_pred CCeEEEEEEcch-hHHHHHHHHHhcCCHHHHHHHhCCeEEEEEecCCCCHHHHHHHHHc---CC-CCCCEEEEEC
Confidence 345666788888 55555444333 466777764455556654332 44555543 44 4789887665
No 68
>cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=47.16 E-value=55 Score=27.65 Aligned_cols=54 Identities=15% Similarity=0.262 Sum_probs=41.6
Q ss_pred CCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecC-------------------ccchhhHHHhHhh
Q 042199 43 GGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPT-------------------REQNDSFVRSYFK 98 (220)
Q Consensus 43 gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t-------------------~eq~dsF~~sYFk 98 (220)
-|+.+ +||++++|..+. ..-.+++.|+.+|..--|.+.+|. .|..|..++.||.
T Consensus 115 ~~~P~-iivvNK~D~~~a-~~~~~~~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~l~e~vae~dd~l~e~yl~ 187 (237)
T cd04168 115 LNIPT-IIFVNKIDRAGA-DLEKVYQEIKEKLSSDIVPMQKVGLAPNICETNEIDDEFWETLAEGDDELLEKYLE 187 (237)
T ss_pred cCCCE-EEEEECccccCC-CHHHHHHHHHHHHCCCeEEEECCcEeeeeeeeeeccHHHHHHHhcCCHHHHHHHhC
Confidence 36665 689999997753 446778889999998888888876 5667788888886
No 69
>PLN02399 phospholipid hydroperoxide glutathione peroxidase
Probab=46.98 E-value=53 Score=28.71 Aligned_cols=41 Identities=24% Similarity=0.461 Sum_probs=32.2
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhcce-EEEEEecC
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLALPT 85 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl~t 85 (220)
|=.|-..|.+.| |..+...+.++++|..+|+.- ..||.++.
T Consensus 99 GK~vvl~FwAsw-Cp~c~~e~p~L~~L~~~~~~~Gv~VIgV~~ 140 (236)
T PLN02399 99 GKVLLIVNVASK-CGLTSSNYSELSHLYEKYKTQGFEILAFPC 140 (236)
T ss_pred CCeEEEEEEcCC-CcchHHHHHHHHHHHHHHhcCCcEEEEEec
Confidence 444666777887 899999999999999999864 67777774
No 70
>PTZ00056 glutathione peroxidase; Provisional
Probab=46.43 E-value=62 Score=26.77 Aligned_cols=38 Identities=21% Similarity=0.350 Sum_probs=28.0
Q ss_pred EEEEEeeccCCCchHHHHHHHHHHHHhhcce-EEEEEecC
Q 042199 47 ISFVFITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLALPT 85 (220)
Q Consensus 47 vAFifvt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl~t 85 (220)
|-..|...| |..+......+++|..+|+.- ++||.++.
T Consensus 42 vlv~fwAsw-C~~C~~e~p~L~~l~~~~~~~g~~vvgv~~ 80 (199)
T PTZ00056 42 LMITNSASK-CGLTKKHVDQMNRLHSVFNPLGLEILAFPT 80 (199)
T ss_pred EEEEEECCC-CCChHHHHHHHHHHHHHHhcCceEEEEecc
Confidence 444555666 777777788888898888754 78889874
No 71
>KOG0190 consensus Protein disulfide isomerase (prolyl 4-hydroxylase beta subunit) [Posttranslational modification, protein turnover, chaperones]
Probab=45.97 E-value=1.2e+02 Score=29.91 Aligned_cols=95 Identities=15% Similarity=0.294 Sum_probs=69.6
Q ss_pred HHHHHhcccceeee--eeeCCceeeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHh
Q 042199 18 ISSFLSANSFRLNF--VLVAPDFIFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRS 95 (220)
Q Consensus 18 is~fL~AnS~RLnF--~~iaPDfIfn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~s 95 (220)
|.-||+.|+..|=. -.=.-+.|++. ++--..+|..+-.|+...-+-+++..+-..|+..+..|.+ +.++|-+-
T Consensus 227 l~~Fi~~~~~plv~~ft~~~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~~~vAk~f~~~l~Fi~~----d~e~~~~~ 301 (493)
T KOG0190|consen 227 LKKFIQENSLPLVTEFTVANNAKIYSS-FVKLGLDFFVFFKCNRFEELRKKFEEVAKKFKGKLRFILI----DPESFARV 301 (493)
T ss_pred HHHHHHHhcccccceecccccceeecc-ccccceeEEeccccccHHHHHHHHHHHHHhcccceEEEEE----ChHHhhHH
Confidence 78899999988732 22233445544 7777888999999999999999999999999999888888 55566663
Q ss_pred Hhhhccc-cCcceeeecCCcchh
Q 042199 96 YFKYGME-LGRPTFVPVQDREMG 117 (220)
Q Consensus 96 YFk~gm~-~g~PtfvpV~d~eMg 117 (220)
-=-|||+ .+.|..+=.++.+|+
T Consensus 302 ~~~~Gl~~~~~~~~~v~~~~~~~ 324 (493)
T KOG0190|consen 302 LEFFGLEEEQLPIRAVILNEDGS 324 (493)
T ss_pred HHhcCcccccCCeeEEeeccccc
Confidence 3346997 777745545555544
No 72
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=45.87 E-value=9.9 Score=37.25 Aligned_cols=72 Identities=19% Similarity=0.225 Sum_probs=49.1
Q ss_pred cceeeecCCcchhH-HHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHH
Q 042199 105 RPTFVPVQDREMGF-EKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIA 183 (220)
Q Consensus 105 ~PtfvpV~d~eMgf-EkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIa 183 (220)
.|...|..++.+-| -+|=.-||.-+ |...=+.-+|.... -.+..||||-..=..+|-.-.||+++|.
T Consensus 501 ~~i~l~~~s~~l~lLq~irDEaHRFA------i~~hR~~r~k~~~~------S~Ld~I~GIG~kr~~~LL~~Fgs~~~i~ 568 (574)
T TIGR00194 501 QGINIDLNSPALQLLQHIRDEAHRFA------ISFHRKKRLKASLQ------SPLLKIPGVGEKRVQKLLKYFGSLKGIK 568 (574)
T ss_pred ceeecCCCCHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHH------HHHhcCCCCCHHHHHHHHHHcCCHHHHH
Confidence 57777777776644 34444555444 33222222233333 2467899999999999999999999999
Q ss_pred hhhhh
Q 042199 184 KASKT 188 (220)
Q Consensus 184 kaSke 188 (220)
+||-|
T Consensus 569 ~As~e 573 (574)
T TIGR00194 569 KASVE 573 (574)
T ss_pred hCCcc
Confidence 99976
No 73
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=45.55 E-value=1.1e+02 Score=21.98 Aligned_cols=39 Identities=15% Similarity=0.322 Sum_probs=30.1
Q ss_pred eEEEEEeeccCCCchHHHHHHHHHHHHhhcce-EEEEEec
Q 042199 46 SISFVFITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLALP 84 (220)
Q Consensus 46 SvAFifvt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl~ 84 (220)
.+-.+..+|+.|.-+......++++..+..++ +++..+|
T Consensus 6 ~~~i~~f~D~~Cp~C~~~~~~l~~~~~~~~~~~~~~~~~p 45 (154)
T cd03023 6 DVTIVEFFDYNCGYCKKLAPELEKLLKEDPDVRVVFKEFP 45 (154)
T ss_pred CEEEEEEECCCChhHHHhhHHHHHHHHHCCCceEEEEeCC
Confidence 45567888999999999999999988887775 3333444
No 74
>TIGR01068 thioredoxin thioredoxin. Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model.
Probab=45.42 E-value=78 Score=21.13 Aligned_cols=66 Identities=15% Similarity=0.320 Sum_probs=33.5
Q ss_pred CCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccccCcceeeecCC
Q 042199 42 CGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQD 113 (220)
Q Consensus 42 ~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d 113 (220)
+.+-.+.+.|-+.|. ..+......++++..++.+-..++.+-..+ ++.+.+. ||.. +-||++=..+
T Consensus 12 ~~~~~vvi~f~~~~C-~~C~~~~~~l~~~~~~~~~~~~~~~vd~~~-~~~~~~~---~~v~-~~P~~~~~~~ 77 (101)
T TIGR01068 12 SSDKPVLVDFWAPWC-GPCKMIAPILEELAKEYEGKVKFVKLNVDE-NPDIAAK---YGIR-SIPTLLLFKN 77 (101)
T ss_pred hcCCcEEEEEECCCC-HHHHHhCHHHHHHHHHhcCCeEEEEEECCC-CHHHHHH---cCCC-cCCEEEEEeC
Confidence 345556677778874 444444444556666776433344444332 2333332 2332 5677665443
No 75
>cd02985 TRX_CDSP32 TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif. CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form.
Probab=45.23 E-value=1.1e+02 Score=21.95 Aligned_cols=66 Identities=18% Similarity=0.263 Sum_probs=41.1
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccc--hhhHHHhHhhhccccCcceeeecCCcc
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQ--NDSFVRSYFKYGMELGRPTFVPVQDRE 115 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq--~dsF~~sYFk~gm~~g~PtfvpV~d~e 115 (220)
|=.|-.-|-..| |..+......+.+|..++.++ +++.+...++ ...+.+.| | .-|-|||+=..|.+
T Consensus 15 ~k~vvv~F~a~w-C~~C~~~~p~l~~la~~~~~v-~~~~vd~d~~~~~~~l~~~~---~-V~~~Pt~~~~~~G~ 82 (103)
T cd02985 15 GRLVVLEFALKH-SGPSVKIYPTMVKLSRTCNDV-VFLLVNGDENDSTMELCRRE---K-IIEVPHFLFYKDGE 82 (103)
T ss_pred CCEEEEEEECCC-CHhHHHHhHHHHHHHHHCCCC-EEEEEECCCChHHHHHHHHc---C-CCcCCEEEEEeCCe
Confidence 445666677777 666766666777788888654 4455554443 23555554 3 46789987665543
No 76
>cd03014 PRX_Atyp2cys Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial periplasmic peroxidase which differs from other PRXs in that it shows substrate specificity toward alkyl hydroperoxides over hydrogen peroxide. As with all other PRXs, the peroxidatic cysteine (N-terminal) of Tpx is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Tpx is able to resolve this intermediate by forming an intramolecular disulfide bond with a conserved C-terminal cysteine (the resolving cysteine), which can then be reduced by thioredoxin. This differs from the typical 2-cys PRX which resolves the oxidized cysteine by forming an intermolecular disulfide bond with the resolving cysteine from the other subunit of the homodimer. Atypical 2-cys PRX homodimers have a loop-based
Probab=45.02 E-value=66 Score=23.81 Aligned_cols=40 Identities=18% Similarity=0.160 Sum_probs=32.2
Q ss_pred eEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCc
Q 042199 46 SISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTR 86 (220)
Q Consensus 46 SvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~ 86 (220)
-+-+.|...|.|..+.....++.++..+|+++ .||+++..
T Consensus 28 ~vvl~f~~~~~c~~C~~e~~~l~~~~~~~~~~-~vi~Is~d 67 (143)
T cd03014 28 VKVISVFPSIDTPVCATQTKRFNKEAAKLDNT-VVLTISAD 67 (143)
T ss_pred eEEEEEEcCCCCCcCHHHHHHHHHHHHhcCCC-EEEEEECC
Confidence 46677888999998888899999999999874 67777653
No 77
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=43.83 E-value=1.1e+02 Score=21.64 Aligned_cols=46 Identities=17% Similarity=0.450 Sum_probs=27.2
Q ss_pred EEeeccCCCchHHHHHHHHHHHHhhcce-EEEEEe--cCccchhhHHHhH
Q 042199 50 VFITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLAL--PTREQNDSFVRSY 96 (220)
Q Consensus 50 ifvt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl--~t~eq~dsF~~sY 96 (220)
.+-+.| |.-+......++++..+|+.. +-|+.+ .+.++...|.+.|
T Consensus 32 f~~~~~-c~~c~~~l~~l~~~~~~~~~~~~~vi~is~d~~~~~~~~~~~~ 80 (124)
T PF00578_consen 32 FWPTAW-CPFCQAELPELNELYKKYKDKGVQVIGISTDDPEEIKQFLEEY 80 (124)
T ss_dssp EESTTT-SHHHHHHHHHHHHHHHHHHTTTEEEEEEESSSHHHHHHHHHHH
T ss_pred EeCccC-ccccccchhHHHHHhhhhccceEEeeecccccccchhhhhhhh
Confidence 333334 777778888888888888843 233333 4444445555544
No 78
>cd03017 PRX_BCP Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The protein was named BCP based on its electrophoretic mobility before its function was known. BCP shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides. BCP contains the peroxidatic cysteine but appears not to possess a resolving cysteine (some sequences, not all, contain a second cysteine but its role is still unknown). Unlike other PRXs, BCP exists as a monomer. The plant homolog of BCP is PRX Q, which is expressed only in leaves and is cellularly localized in the chloroplasts and the guard cells of stomata. Also included in this subfamily is the fungal nuclear protein, Dot5p (for disrupter of telomere silencing protein 5), w
Probab=41.90 E-value=91 Score=22.63 Aligned_cols=49 Identities=18% Similarity=0.250 Sum_probs=29.2
Q ss_pred EEEEEeeccCCCchHHHHHHHHHHHHhhcc-eEEEEEec--CccchhhHHHh
Q 042199 47 ISFVFITNWDCHNTAVVFSRIKKLKEQFAH-FYVVLALP--TREQNDSFVRS 95 (220)
Q Consensus 47 vAFifvt~wdc~n~a~ifsRV~kLK~qF~~-lYVVvtl~--t~eq~dsF~~s 95 (220)
+-..|...|.|.-+..-...++++..+|+. =+.||+++ +.+....|.+.
T Consensus 26 ~ll~f~~~~~cp~C~~~~~~l~~~~~~~~~~~~~vv~is~d~~~~~~~~~~~ 77 (140)
T cd03017 26 VVLYFYPKDDTPGCTKEACDFRDLYEEFKALGAVVIGVSPDSVESHAKFAEK 77 (140)
T ss_pred EEEEEeCCCCCCchHHHHHHHHHHHHHHHHCCCEEEEEcCCCHHHHHHHHHH
Confidence 334444457777777777778888888753 23455554 44444555554
No 79
>PRK03980 flap endonuclease-1; Provisional
Probab=41.11 E-value=28 Score=31.19 Aligned_cols=71 Identities=20% Similarity=0.314 Sum_probs=51.9
Q ss_pred hhhhhhHHHHHHHHHhhhh-----ccceeEEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHH
Q 042199 131 CKRQDAISKLKAERRRAVQ-----TMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIV 205 (220)
Q Consensus 131 cKqQ~i~s~lk~ERkq~VQ-----~md~flrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~ 205 (220)
...+++.+++...|+|++. |.|. ..+||||---=|-.|.+.-||||.|-+ +.+...+.-+.+-
T Consensus 163 ~~~~~vl~~lgl~~~q~id~~iL~G~Dy----~~GI~GIG~ktA~kLi~~~~sle~i~~--------~~~~~~~~~~~~r 230 (292)
T PRK03980 163 IELEEVLKELGITREQLIDIAILVGTDY----NPGIKGIGPKTALKLIKKHGDLEKVLE--------ERGFEIENYDEIR 230 (292)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHhcCCCC----CCCCCCccHHHHHHHHHHCCCHHHHHH--------hccCCCCCHHHHH
Confidence 3456677788888888753 5554 348999999999999999999999876 2333444556777
Q ss_pred HHhcCCcc
Q 042199 206 RFFRDPKL 213 (220)
Q Consensus 206 rffrDp~~ 213 (220)
.+|.+|.-
T Consensus 231 ~~f~~p~v 238 (292)
T PRK03980 231 EFFLNPPV 238 (292)
T ss_pred HHhcCCCC
Confidence 77777653
No 80
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=40.59 E-value=20 Score=27.59 Aligned_cols=37 Identities=24% Similarity=0.200 Sum_probs=24.2
Q ss_pred HHHhh-hhHHHHHhhhhhhhhhccCCC---hhhHHHHHHHhc
Q 042199 172 LNQAI-GSIEAIAKASKTYILENTDLS---AEKAEMIVRFFR 209 (220)
Q Consensus 172 L~QaI-GSieAIakaSke~IlenTDLS---~dkAE~i~rffr 209 (220)
|.+.. -++|+|++++-+.+ ++.-.+ ..||+.|.+.-+
T Consensus 25 l~~~~gpt~~~l~~~~~~~l-~~~~~~~G~~~kA~~i~~~a~ 65 (158)
T cd00056 25 LFERYGPTPEALAAADEEEL-RELIRSLGYRRKAKYLKELAR 65 (158)
T ss_pred HHHHhCCCHHHHHCCCHHHH-HHHHHhcChHHHHHHHHHHHH
Confidence 44444 48888888887663 444455 578888876543
No 81
>PRK00522 tpx lipid hydroperoxide peroxidase; Provisional
Probab=40.58 E-value=1.2e+02 Score=24.00 Aligned_cols=70 Identities=16% Similarity=0.237 Sum_probs=40.1
Q ss_pred eEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCcc--chhhHHHhHhhhccccCcceeeecCC-cchhHHHHH
Q 042199 46 SISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTRE--QNDSFVRSYFKYGMELGRPTFVPVQD-REMGFEKII 122 (220)
Q Consensus 46 SvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~e--q~dsF~~sYFk~gm~~g~PtfvpV~d-~eMgfEkiv 122 (220)
-+-..|...|+|.-+..-...+.++...|.+ ..||.++... ....|.+. .|-|.+.-+.| ....+-|..
T Consensus 46 ~vvl~f~~s~~cp~C~~e~~~l~~~~~~~~~-~~vv~vs~D~~~~~~~f~~~-------~~~~~~~~lsD~~~~~~~~~~ 117 (167)
T PRK00522 46 RKVLNIFPSIDTGVCATSVRKFNQEAAELDN-TVVLCISADLPFAQKRFCGA-------EGLENVITLSDFRDHSFGKAY 117 (167)
T ss_pred EEEEEEEcCCCCCccHHHHHHHHHHHHHcCC-cEEEEEeCCCHHHHHHHHHh-------CCCCCceEeecCCccHHHHHh
Confidence 3567788889877666666677778888865 4555555432 23334443 23333444556 344555544
Q ss_pred H
Q 042199 123 K 123 (220)
Q Consensus 123 k 123 (220)
.
T Consensus 118 g 118 (167)
T PRK00522 118 G 118 (167)
T ss_pred C
Confidence 4
No 82
>cd02968 SCO SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properti
Probab=40.33 E-value=1.1e+02 Score=22.18 Aligned_cols=40 Identities=10% Similarity=0.180 Sum_probs=28.5
Q ss_pred eEEEEEeeccCCCc-hHHHHHHHHHHHHhhcce----EEEEEecCc
Q 042199 46 SISFVFITNWDCHN-TAVVFSRIKKLKEQFAHF----YVVLALPTR 86 (220)
Q Consensus 46 SvAFifvt~wdc~n-~a~ifsRV~kLK~qF~~l----YVVvtl~t~ 86 (220)
-+-.+|...| |.. +......++++..+|+.- ..+|.++..
T Consensus 24 ~~vl~f~~~~-C~~~C~~~l~~l~~~~~~~~~~~~~~v~~v~vs~d 68 (142)
T cd02968 24 PVLVYFGYTH-CPDVCPTTLANLAQALKQLGADGGDDVQVVFISVD 68 (142)
T ss_pred EEEEEEEcCC-CcccCHHHHHHHHHHHHHhhHhhcCceEEEEEEEC
Confidence 3556677777 775 777888888888888764 566777653
No 83
>PRK00024 hypothetical protein; Reviewed
Probab=40.25 E-value=44 Score=28.76 Aligned_cols=43 Identities=19% Similarity=0.180 Sum_probs=34.0
Q ss_pred CCCccChhHHH----HhhhhHHHHHhhhhhhhhhccCCChhhHHHHH
Q 042199 163 LIDNHDANALN----QAIGSIEAIAKASKTYILENTDLSAEKAEMIV 205 (220)
Q Consensus 163 ~id~HDAn~L~----QaIGSieAIakaSke~IlenTDLS~dkAE~i~ 205 (220)
|+...|++.|+ +-.||+.++..||.+...+-..+...||.++.
T Consensus 37 g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~ 83 (224)
T PRK00024 37 GTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLK 83 (224)
T ss_pred CCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHH
Confidence 45557777777 45689999999999998888888888886653
No 84
>PF01487 DHquinase_I: Type I 3-dehydroquinase; InterPro: IPR001381 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. The best studied type I enzyme is from Escherichia coli (gene aroD) and related bacteria where it is a homodimeric protein. In fungi, dehydroquinase is part of a multifunctional enzyme which catalyzes five consecutive steps in the shikimate pathway. A histidine [] is involved in the catalytic mechanism.; GO: 0003855 3-dehydroquinate dehydratase activity; PDB: 2O7Q_A 2GPT_A 2O7S_A 1SFL_A 2OCZ_A 2OX1_C 1GQN_A 1QFE_B 1L9W_D 3L9C_A ....
Probab=39.89 E-value=98 Score=25.47 Aligned_cols=64 Identities=17% Similarity=0.502 Sum_probs=44.1
Q ss_pred eeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHH---HhH---hhhccccCcceeeecCCcchh-HHH
Q 042199 52 ITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFV---RSY---FKYGMELGRPTFVPVQDREMG-FEK 120 (220)
Q Consensus 52 vt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~---~sY---Fk~gm~~g~PtfvpV~d~eMg-fEk 120 (220)
++-|.+.+...+-.-+..|+... ++-+++|+.+++|-..|. ..| ++...++| |..| |.|+. +++
T Consensus 31 lD~l~~~~~~~~~~~l~~lr~~~-~~piI~T~R~~~eGG~~~~~~~~~~~ll~~~~~~~-~d~i---DiE~~~~~~ 101 (224)
T PF01487_consen 31 LDYLENDSAEDISEQLAELRRSL-DLPIIFTVRTKEEGGRFQGSEEEYLELLERAIRLG-PDYI---DIELDLFPD 101 (224)
T ss_dssp GGGSTTTSHHHHHHHHHHHHHHC-TSEEEEE--BGGGTSSBSS-HHHHHHHHHHHHHHT-SSEE---EEEGGCCHH
T ss_pred eccccccChHHHHHHHHHHHHhC-CCCEEEEecccccCCCCcCCHHHHHHHHHHHHHcC-CCEE---EEEcccchh
Confidence 34455577888889999999988 999999999997765542 344 44577888 6655 55666 443
No 85
>TIGR02540 gpx7 putative glutathione peroxidase Gpx7. This model represents one of several families of known and probable glutathione peroxidases. This family is restricted to animals and designated GPX7.
Probab=39.73 E-value=1e+02 Score=23.49 Aligned_cols=38 Identities=21% Similarity=0.369 Sum_probs=29.4
Q ss_pred EEEEEeeccCCCchHHHHHHHHHHHHhhcc-eEEEEEecC
Q 042199 47 ISFVFITNWDCHNTAVVFSRIKKLKEQFAH-FYVVLALPT 85 (220)
Q Consensus 47 vAFifvt~wdc~n~a~ifsRV~kLK~qF~~-lYVVvtl~t 85 (220)
+-.+|.+.| |.-+...+.++++|-.+|+. =..|+.++.
T Consensus 25 vvv~~~as~-C~~c~~~~~~l~~l~~~~~~~~~~v~~i~~ 63 (153)
T TIGR02540 25 SLVVNVASE-CGFTDQNYRALQELHRELGPSHFNVLAFPC 63 (153)
T ss_pred EEEEEeCCC-CCchhhhHHHHHHHHHHHhhCCeEEEEEec
Confidence 334477888 99999999999999999975 356777763
No 86
>PRK03147 thiol-disulfide oxidoreductase; Provisional
Probab=39.51 E-value=1.3e+02 Score=22.78 Aligned_cols=44 Identities=14% Similarity=0.326 Sum_probs=29.0
Q ss_pred EEEEEeeccCCCchHHHHHHHHHHHHhhcce-EEEEEecCccchhh
Q 042199 47 ISFVFITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLALPTREQNDS 91 (220)
Q Consensus 47 vAFifvt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl~t~eq~ds 91 (220)
+...|...| |..+.....+++++-.+|+.- ..|+.++..+..+.
T Consensus 64 ~~l~f~a~~-C~~C~~~~~~l~~~~~~~~~~~~~vi~i~~d~~~~~ 108 (173)
T PRK03147 64 VFLNFWGTW-CKPCEKEMPYMNELYPKYKEKGVEIIAVNVDETELA 108 (173)
T ss_pred EEEEEECCc-CHHHHHHHHHHHHHHHHhhcCCeEEEEEEcCCCHHH
Confidence 455666666 777888888888888888653 34556655444333
No 87
>cd02191 FtsZ FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
Probab=36.54 E-value=1.5e+02 Score=26.49 Aligned_cols=152 Identities=20% Similarity=0.238 Sum_probs=84.1
Q ss_pred CceeeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhh-hcc---ccCcceeeec
Q 042199 36 PDFIFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFK-YGM---ELGRPTFVPV 111 (220)
Q Consensus 36 PDfIfn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk-~gm---~~g~PtfvpV 111 (220)
.|.+|-++||+=+ |. .-.+|++- +.+|+.+...|.||++|...+. =.+.|=- +|+ .--..+.+.+
T Consensus 85 ~D~v~i~aglGGG----TG---SG~ap~ia--~~~ke~~~~~~~vvt~Pf~~Eg--~~~~~NA~~~l~~L~~~~D~~iv~ 153 (303)
T cd02191 85 VDMVFITAGLGGG----TG---TGGAPVVA--EHLKRIGTLTVAVVTLPFSDEG--GIRMLNAAEGFQTLVREVDNLMVI 153 (303)
T ss_pred CCEEEEEeccCCc----cc---hhHHHHHH--HHHHHhCCCEEEEEeCCcccCC--ccchhhHHHHHHHHHHhCCEEEEE
Confidence 5667777666543 22 44566664 5678889999999999975432 1121111 011 0011233333
Q ss_pred CCcchhHHHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhh--------------
Q 042199 112 QDREMGFEKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIG-------------- 177 (220)
Q Consensus 112 ~d~eMgfEkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIG-------------- 177 (220)
.. +++.+++...+. +..-+.+...=.|.+.+.= ..+ ..||.=|-|.+.+.+.+.
T Consensus 154 dN-----~~L~~~~~~~~~---~~af~~~N~~ia~~i~~it---~~i-~~~g~invD~~dv~~~l~~~G~a~ig~g~~~g 221 (303)
T cd02191 154 PN-----EKLRQIGEKASL---EGAFDHADEVLVRAVGGLF---GAI-EIEGEINVDFADVKNVMDGGGVAMVGYGSEDV 221 (303)
T ss_pred eh-----HHHHHHhhcCCh---HHHHHHHHHHHHHHHHHHH---Hhh-ccCCcccCCHHHHHHHhccCCeEEEEEEEecC
Confidence 22 455555432221 2233344444344444432 222 268888888888876541
Q ss_pred ---hHHHHHhhhhhhhhhcc----------------CCChhhHHHHHHHhcC
Q 042199 178 ---SIEAIAKASKTYILENT----------------DLSAEKAEMIVRFFRD 210 (220)
Q Consensus 178 ---SieAIakaSke~IlenT----------------DLS~dkAE~i~rffrD 210 (220)
-.+|+.+|-+..+|+.. ||+.+..+.++++.++
T Consensus 222 ~~~~~~a~~~Al~~pll~~~~~~~A~~~Lv~i~g~~~l~~~e~~~~~~~i~~ 273 (303)
T cd02191 222 TNRATEAVRKAALGPLLLPCEIEGAEGALLVMAGPPDLNLKEIERVRKWLEE 273 (303)
T ss_pred chHHHHHHHHHHhCCCCCCCCcccCCEEEEEEECCCCCCHHHHHHHHHHHHH
Confidence 25688888888878765 4666677777776654
No 88
>TIGR00262 trpA tryptophan synthase, alpha subunit. Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. The alpha chain is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. In bacteria and plants each domain is found on a separate subunit (alpha and beta chains), while in fungi the two domains are fused together on a single multifunctional protein. The signature pattern for trpA contains three conserved acidic residues. [LIVM]-E-[LIVM]-G-x(2)-[FYC]-[ST]-[DE]-[PA]-[LIVMY]-[AGLI]-[DE]-G and this is located between residues 43-58 of the model. The Sulfolobus solfataricus trpA is known to be quite divergent from other known trpA sequences.
Probab=35.99 E-value=2.3e+02 Score=24.64 Aligned_cols=103 Identities=15% Similarity=0.172 Sum_probs=50.3
Q ss_pred CchHHHHHHHHHHHHhhcceEEE-EEecCc---cchhhHHHhHhhhccccCcceeeecCCcchhHHHHHHHHHhhhhhhh
Q 042199 58 HNTAVVFSRIKKLKEQFAHFYVV-LALPTR---EQNDSFVRSYFKYGMELGRPTFVPVQDREMGFEKIIKIAHSRGVCKR 133 (220)
Q Consensus 58 ~n~a~ifsRV~kLK~qF~~lYVV-vtl~t~---eq~dsF~~sYFk~gm~~g~PtfvpV~d~eMgfEkivkIAh~~gvcKq 133 (220)
-+...+|+-|+++|+...+.-++ .+.-.. --.+.|.+.+-+.|.+. ..+|-...|- .+.+++.++.+|.+-=
T Consensus 69 ~~~~~~~~~v~~ir~~~~~~plv~m~Y~Npi~~~G~e~f~~~~~~aGvdg---viipDlp~ee-~~~~~~~~~~~gl~~i 144 (256)
T TIGR00262 69 MTPEKCFELLKKVRQKHPNIPIGLLTYYNLIFRKGVEEFYAKCKEVGVDG---VLVADLPLEE-SGDLVEAAKKHGVKPI 144 (256)
T ss_pred CCHHHHHHHHHHHHhcCCCCCEEEEEeccHHhhhhHHHHHHHHHHcCCCE---EEECCCChHH-HHHHHHHHHHCCCcEE
Confidence 45667888899998764343322 222111 01255666666666532 2333322222 3456666666654322
Q ss_pred hhhHHHHHHHH-HhhhhccceeEEeeeccCCCC
Q 042199 134 QDAISKLKAER-RRAVQTMDVFLRVVTSIPLID 165 (220)
Q Consensus 134 Q~i~s~lk~ER-kq~VQ~md~flrvvTSIP~id 165 (220)
.=+.-.-..|| +.+....|-|+=+||+- |..
T Consensus 145 ~lv~P~T~~eri~~i~~~~~gfiy~vs~~-G~T 176 (256)
T TIGR00262 145 FLVAPNADDERLKQIAEKSQGFVYLVSRA-GVT 176 (256)
T ss_pred EEECCCCCHHHHHHHHHhCCCCEEEEECC-CCC
Confidence 22222233455 34444455577777653 444
No 89
>KOG0910 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=34.71 E-value=93 Score=26.39 Aligned_cols=57 Identities=12% Similarity=0.205 Sum_probs=50.2
Q ss_pred eeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhH
Q 042199 39 IFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSY 96 (220)
Q Consensus 39 Ifn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sY 96 (220)
-+.|.+..|-.-|-+.| |.-+-++=-|+++|-+.+++-....++-|.|..+-=.+.+
T Consensus 56 ~Vi~S~~PVlVdF~A~W-CgPCk~l~P~l~~~~~~~~g~~k~~kvdtD~~~ela~~Y~ 112 (150)
T KOG0910|consen 56 KVINSDVPVLVDFHAEW-CGPCKMLGPILEELVSEYAGKFKLYKVDTDEHPELAEDYE 112 (150)
T ss_pred HHHccCCCEEEEEecCc-CccHhHhhHHHHHHHHhhcCeEEEEEEccccccchHhhcc
Confidence 35789999999999999 8999999999999999999999999999998877655544
No 90
>PF05563 SpvD: Salmonella plasmid virulence protein SpvD; InterPro: IPR008834 This family consists of several SpvD plasmid virulence proteins from different Salmonella species.
Probab=34.53 E-value=59 Score=28.71 Aligned_cols=63 Identities=27% Similarity=0.440 Sum_probs=49.5
Q ss_pred hhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHH
Q 042199 127 SRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVR 206 (220)
Q Consensus 127 ~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~r 206 (220)
..|....|||+|++.. .+|+|.|.|..... -.|+---|||.||--..||.|.-....|
T Consensus 3 vsgsassqdiisrins-------------------kninnndsnevkri---kdalcieskerilypqnlsrdnlkqmar 60 (216)
T PF05563_consen 3 VSGSASSQDIISRINS-------------------KNINNNDSNEVKRI---KDALCIESKERILYPQNLSRDNLKQMAR 60 (216)
T ss_pred cccccchhHHHHHhcc-------------------ccCCCCchHHHHHh---hhhhhhcchhheecccccChhHHHHHHH
Confidence 3566778888887532 47899999976542 2466667999999999999999999999
Q ss_pred HhcCC
Q 042199 207 FFRDP 211 (220)
Q Consensus 207 ffrDp 211 (220)
+.++.
T Consensus 61 yvnnt 65 (216)
T PF05563_consen 61 YVNNT 65 (216)
T ss_pred HhcCc
Confidence 98764
No 91
>PRK15250 virulence protein SpvD; Provisional
Probab=34.50 E-value=59 Score=28.71 Aligned_cols=63 Identities=27% Similarity=0.440 Sum_probs=49.5
Q ss_pred hhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHH
Q 042199 127 SRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVR 206 (220)
Q Consensus 127 ~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~r 206 (220)
..|....|||+|++.. .+|+|.|.|..... -.|+---|||.||--..||.|.-....|
T Consensus 3 vsgsassqdiisrins-------------------kninnndsnevkri---kdalcieskerilypqnlsrdnlkqmar 60 (216)
T PRK15250 3 VSGSASSQDIISRINS-------------------KNINNNDSNEVKRI---KDALCIESKERILYPQNLSRDNLKQMAR 60 (216)
T ss_pred cccccchHHHHHHhcc-------------------ccCCCCchHHHHHh---hhhhhhcchhheecccccChhHHHHHHH
Confidence 3566778888887532 47899999976542 2466667999999999999999999999
Q ss_pred HhcCC
Q 042199 207 FFRDP 211 (220)
Q Consensus 207 ffrDp 211 (220)
+.++.
T Consensus 61 yvnnt 65 (216)
T PRK15250 61 YVNNT 65 (216)
T ss_pred HhcCc
Confidence 98764
No 92
>PRK10996 thioredoxin 2; Provisional
Probab=34.42 E-value=2.1e+02 Score=22.04 Aligned_cols=66 Identities=9% Similarity=0.228 Sum_probs=39.3
Q ss_pred CCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccccCcceeeecCCc
Q 042199 43 GGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQDR 114 (220)
Q Consensus 43 gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d~ 114 (220)
.|-.+...|-++| |...-..-..++++..++..-++++.+...+ +..+.+ +||. -|-||++=..+.
T Consensus 51 ~~k~vvv~F~a~w-C~~C~~~~~~l~~l~~~~~~~v~~~~vd~~~-~~~l~~---~~~V-~~~Ptlii~~~G 116 (139)
T PRK10996 51 DDLPVVIDFWAPW-CGPCRNFAPIFEDVAAERSGKVRFVKVNTEA-ERELSA---RFRI-RSIPTIMIFKNG 116 (139)
T ss_pred CCCeEEEEEECCC-CHHHHHHHHHHHHHHHHhCCCeEEEEEeCCC-CHHHHH---hcCC-CccCEEEEEECC
Confidence 3556778888899 6665544445555666666546666665544 334443 3343 578888755443
No 93
>PF08358 Flexi_CP_N: Carlavirus coat; InterPro: IPR013569 This domain is found together with the viral coat protein domain (IPR000052 from INTERPRO) in coat/capsid proteins of the plant infecting Carlavirus. It is required for genome encapsidation by forming ribonucleoprotein complexes along with TGB1 helicase and viral RNA. The N- and the C terminus of this coat protein can be exposed on the surface of the virus particle. The central core sequence may be important in maintaining correct tertiary structure of the coat protein and/or play a role in the interaction with the viral RNA. Coat proteins are often used to distinguish between Carlavirus isolates. In the coat protein amino acid sequences of definitive and tentative species of carlaviruses, there is a region of seven amino acids (GLGVPTE) that are conserved []. The complete coat protein (CP) sequences of 29 Indian Chrysanthemum virus B (CVB) isolates were highly heterogeneous, sharing nucleotide sequence identities of 74-98% [, ].
Probab=34.26 E-value=14 Score=26.36 Aligned_cols=17 Identities=41% Similarity=0.821 Sum_probs=14.1
Q ss_pred hhccccCcceeeecCCc
Q 042199 98 KYGMELGRPTFVPVQDR 114 (220)
Q Consensus 98 k~gm~~g~PtfvpV~d~ 114 (220)
..|||.|+|..-|+.+.
T Consensus 20 N~~fE~GRP~l~~~~~m 36 (52)
T PF08358_consen 20 NPGFEIGRPKLEPSDDM 36 (52)
T ss_pred ccccccCCcCCcCchhh
Confidence 46999999999888764
No 94
>PTZ00256 glutathione peroxidase; Provisional
Probab=33.76 E-value=97 Score=24.86 Aligned_cols=33 Identities=21% Similarity=0.395 Sum_probs=21.2
Q ss_pred eeccCCCchHHHHHHHHHHHHhhcce-EEEEEecC
Q 042199 52 ITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLALPT 85 (220)
Q Consensus 52 vt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl~t 85 (220)
...| |..+..-.-.+++|..+|++. ..||.++.
T Consensus 49 ~atw-Cp~C~~e~p~l~~l~~~~~~~gv~vv~vs~ 82 (183)
T PTZ00256 49 VACK-CGLTSDHYTQLVELYKQYKSQGLEILAFPC 82 (183)
T ss_pred ECCC-CCchHHHHHHHHHHHHHHhhCCcEEEEEec
Confidence 4444 555666666677777777654 66777774
No 95
>cd02983 P5_C P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. The C-terminal domain is likely involved in substrate binding, similar to the b and b' domains of PDI.
Probab=33.44 E-value=2.2e+02 Score=22.29 Aligned_cols=84 Identities=20% Similarity=0.364 Sum_probs=53.5
Q ss_pred CCCceEEEE--EeeccCCCch--HHHHHHHHHHHHhhcce-EEEEEecCccchhhHHHhHhhhcc-ccCcceeeecCCcc
Q 042199 42 CGGMSISFV--FITNWDCHNT--AVVFSRIKKLKEQFAHF-YVVLALPTREQNDSFVRSYFKYGM-ELGRPTFVPVQDRE 115 (220)
Q Consensus 42 ~gglSvAFi--fvt~wdc~n~--a~ifsRV~kLK~qF~~l-YVVvtl~t~eq~dsF~~sYFk~gm-~~g~PtfvpV~d~e 115 (220)
|++-.+-+| +-..-||+.. ..+..+++++-..|+.- +..|.+...+|.. ...|| |+ +-|.|+++=+...
T Consensus 17 C~~~~~C~i~~l~~~~d~~~e~~~~~~~~l~~vAk~~kgk~i~Fv~vd~~~~~~--~~~~f--gl~~~~~P~v~i~~~~- 91 (130)
T cd02983 17 CEEKQLCIIAFLPHILDCQASCRNKYLEILKSVAEKFKKKPWGWLWTEAGAQLD--LEEAL--NIGGFGYPAMVAINFR- 91 (130)
T ss_pred ccCCCeEEEEEcCccccCCHHHHHHHHHHHHHHHHHhcCCcEEEEEEeCcccHH--HHHHc--CCCccCCCEEEEEecc-
Confidence 654433333 3333466654 47889999999999888 8888888888766 55666 54 3389998866542
Q ss_pred hhHHHHHHHHHhhhhhhhhh
Q 042199 116 MGFEKIIKIAHSRGVCKRQD 135 (220)
Q Consensus 116 MgfEkivkIAh~~gvcKqQ~ 135 (220)
++ |.++-+|.-....
T Consensus 92 ----~~-KY~~~~~~~t~e~ 106 (130)
T cd02983 92 ----KM-KFATLKGSFSEDG 106 (130)
T ss_pred ----cC-ccccccCccCHHH
Confidence 33 5554445433333
No 96
>cd02967 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.
Probab=33.38 E-value=1.7e+02 Score=20.50 Aligned_cols=50 Identities=16% Similarity=0.323 Sum_probs=24.6
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhc-ceEEEEEec--CccchhhHHHh
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFA-HFYVVLALP--TREQNDSFVRS 95 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~-~lYVVvtl~--t~eq~dsF~~s 95 (220)
|=-+-..|-+.| |..+......++++...++ ++-|+ .++ +.++...|.+.
T Consensus 21 gk~vvl~F~~~w-C~~C~~~~p~l~~~~~~~~~~~~vi-~v~~~~~~~~~~~~~~ 73 (114)
T cd02967 21 GRPTLLFFLSPT-CPVCKKLLPVIRSIARAEADWLDVV-LASDGEKAEHQRFLKK 73 (114)
T ss_pred CCeEEEEEECCC-CcchHhHhHHHHHHHHHhcCCcEEE-EEeCCCHHHHHHHHHH
Confidence 434555677777 4444444444555555553 33333 332 33444445554
No 97
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=33.02 E-value=46 Score=29.41 Aligned_cols=102 Identities=15% Similarity=0.252 Sum_probs=53.4
Q ss_pred ccccCcceeeecCCcchhHHHHHHHHHhhhhhhhhhhHH---HHHHHHHhhhhccceeEEeeeccCCC-CccChh-----
Q 042199 100 GMELGRPTFVPVQDREMGFEKIIKIAHSRGVCKRQDAIS---KLKAERRRAVQTMDVFLRVVTSIPLI-DNHDAN----- 170 (220)
Q Consensus 100 gm~~g~PtfvpV~d~eMgfEkivkIAh~~gvcKqQ~i~s---~lk~ERkq~VQ~md~flrvvTSIP~i-d~HDAn----- 170 (220)
.+.+|-|+.-| .+..|++.++++|. .-.+.+ .|..+-.+ +...+ +..+--|+-|. +.||+.
T Consensus 77 ~i~GGEPLL~p------dl~eiv~~~~~~g~--~v~l~TNG~ll~~~~~~-l~~~~-~~~i~VSLDG~~e~hd~~~~~~g 146 (318)
T TIGR03470 77 SIPGGEPLLHP------EIDEIVRGLVARKK--FVYLCTNALLLEKKLDK-FEPSP-YLTFSVHLDGLREHHDASVCREG 146 (318)
T ss_pred EEeCccccccc------cHHHHHHHHHHcCC--eEEEecCceehHHHHHH-HHhCC-CcEEEEEEecCchhhchhhcCCC
Confidence 45679999875 37899999998873 222211 12111111 21112 23455588886 458763
Q ss_pred HHHHhhhhHHHHHhhhhhhhhhc---cCCChhhHHHHHHHhcCC
Q 042199 171 ALNQAIGSIEAIAKASKTYILEN---TDLSAEKAEMIVRFFRDP 211 (220)
Q Consensus 171 ~L~QaIGSieAIakaSke~Ilen---TDLS~dkAE~i~rffrDp 211 (220)
+..+++-.|++..++-..--+.. +..+.+..+.+.+++++-
T Consensus 147 ~f~~~l~~I~~l~~~G~~v~v~~tv~~~~n~~ei~~~~~~~~~l 190 (318)
T TIGR03470 147 VFDRAVEAIREAKARGFRVTTNTTLFNDTDPEEVAEFFDYLTDL 190 (318)
T ss_pred cHHHHHHHHHHHHHCCCcEEEEEEEeCCCCHHHHHHHHHHHHHc
Confidence 33444434443333321111111 235667888888888764
No 98
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.44 E-value=73 Score=27.59 Aligned_cols=37 Identities=16% Similarity=0.193 Sum_probs=25.6
Q ss_pred ChhHHH----Hhh---hhHHHHHhhhhhhhhhccCCChhhHHHH
Q 042199 168 DANALN----QAI---GSIEAIAKASKTYILENTDLSAEKAEMI 204 (220)
Q Consensus 168 DAn~L~----QaI---GSieAIakaSke~IlenTDLS~dkAE~i 204 (220)
|+..|+ +.. ||+.++..||.+...+-..+...||-+|
T Consensus 33 ~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l 76 (218)
T TIGR00608 33 DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQL 76 (218)
T ss_pred CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHH
Confidence 666666 455 7777777777777777777777777655
No 99
>PF10397 ADSL_C: Adenylosuccinate lyase C-terminus; InterPro: IPR019468 Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP) []. This entry represents the C-terminal, seven alpha-helical, domain of adenylosuccinate lyase [].; PDB: 1YIS_A 1C3U_B 1C3C_A 3C8T_A 2PFM_B 1RE5_D 1Q5N_A 2VD6_D 2J91_B 2X75_A.
Probab=32.06 E-value=22 Score=25.66 Aligned_cols=52 Identities=23% Similarity=0.411 Sum_probs=26.9
Q ss_pred CCCccChhHHHHhhhhHHHHHh--hhhhhhhhccCCC-hhhHHHHHHHhcCCccccC
Q 042199 163 LIDNHDANALNQAIGSIEAIAK--ASKTYILENTDLS-AEKAEMIVRFFRDPKLYLS 216 (220)
Q Consensus 163 ~id~HDAn~L~QaIGSieAIak--aSke~IlenTDLS-~dkAE~i~rffrDp~~yls 216 (220)
|+...+|+.+.|.+ +.+|.+. .=++-++++.+++ .=.++.|.+.| ||.+|+.
T Consensus 17 G~gR~~Ah~lv~~~-a~~a~~~~~~l~e~l~~d~~i~~~ls~~el~~l~-dp~~ylg 71 (81)
T PF10397_consen 17 GLGRQEAHELVQEA-AMEAWENGRDLREVLLADPEIAAYLSEEELEELF-DPESYLG 71 (81)
T ss_dssp TH-HHHHHHHHHHH-HHHHHHTTS-HHHHHCTTHHHHTTSHHHHHHHHT--GGGGCT
T ss_pred ccCHHHHHHHHHHH-HHHHHHHCCCHHHHHHCCHHHHhHCCHHHHHhhc-CHHHHHh
Confidence 57777888887754 2233221 1233444444443 11245577777 9999985
No 100
>cd02950 TxlA TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport.
Probab=31.45 E-value=2.1e+02 Score=22.31 Aligned_cols=64 Identities=23% Similarity=0.447 Sum_probs=33.0
Q ss_pred eeeCCCceEEEEEeecc--CCCchHHHHHHHHHHHHhhcce--EEEEEecCccchhhHHHhHhhhccccCcceeeec
Q 042199 39 IFNCGGMSISFVFITNW--DCHNTAVVFSRIKKLKEQFAHF--YVVLALPTREQNDSFVRSYFKYGMELGRPTFVPV 111 (220)
Q Consensus 39 Ifn~gglSvAFifvt~w--dc~n~a~ifsRV~kLK~qF~~l--YVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV 111 (220)
....|. .+-..|-+.| .|....+.|. +|..+|..- ++.|.+... ......+ +||. -|-||++=+
T Consensus 16 a~~~gk-~vvV~F~A~WC~~C~~~~p~l~---~l~~~~~~~~~~v~v~vd~~-~~~~~~~---~~~V-~~iPt~v~~ 83 (142)
T cd02950 16 ALSNGK-PTLVEFYADWCTVCQEMAPDVA---KLKQKYGDQVNFVMLNVDNP-KWLPEID---RYRV-DGIPHFVFL 83 (142)
T ss_pred HHhCCC-EEEEEEECCcCHHHHHhHHHHH---HHHHHhccCeeEEEEEcCCc-ccHHHHH---HcCC-CCCCEEEEE
Confidence 334444 4666777888 2455555555 555666532 233333321 1222333 4454 378998876
No 101
>PRK09414 glutamate dehydrogenase; Provisional
Probab=31.40 E-value=33 Score=32.85 Aligned_cols=19 Identities=42% Similarity=0.520 Sum_probs=16.3
Q ss_pred eeeCCceeeeCCCceEEEE
Q 042199 32 VLVAPDFIFNCGGMSISFV 50 (220)
Q Consensus 32 ~~iaPDfIfn~gglSvAFi 50 (220)
+.+.||++-|.||+-++..
T Consensus 361 I~~vPD~laNaGGVivs~~ 379 (445)
T PRK09414 361 VLFAPGKAANAGGVATSGL 379 (445)
T ss_pred cEEECchhhcCCCeeeeeh
Confidence 6788999999999988553
No 102
>PRK09381 trxA thioredoxin; Provisional
Probab=31.24 E-value=1.9e+02 Score=20.40 Aligned_cols=64 Identities=19% Similarity=0.410 Sum_probs=39.0
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccccCcceeeecCC
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQD 113 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d 113 (220)
+-.+...|-+.| |..+...-..+++|..++..-+.+..+...++ ..+.+ +||. -+-||++=..+
T Consensus 21 ~~~vvv~f~~~~-C~~C~~~~p~~~~l~~~~~~~~~~~~vd~~~~-~~~~~---~~~v-~~~Pt~~~~~~ 84 (109)
T PRK09381 21 DGAILVDFWAEW-CGPCKMIAPILDEIADEYQGKLTVAKLNIDQN-PGTAP---KYGI-RGIPTLLLFKN 84 (109)
T ss_pred CCeEEEEEECCC-CHHHHHHhHHHHHHHHHhCCCcEEEEEECCCC-hhHHH---hCCC-CcCCEEEEEeC
Confidence 334555555665 77788777788888888876555666655443 33322 3443 46788765544
No 103
>cd03001 PDI_a_P5 PDIa family, P5 subfamily; composed of eukaryotic proteins similar to human P5, a PDI-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. Some members of this subfamily are P5-like proteins containing only one redox active TRX domain.
Probab=31.04 E-value=1.7e+02 Score=19.89 Aligned_cols=62 Identities=21% Similarity=0.326 Sum_probs=34.2
Q ss_pred CCceEEEEEeeccC--CCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccccCcceeeecC
Q 042199 43 GGMSISFVFITNWD--CHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQ 112 (220)
Q Consensus 43 gglSvAFifvt~wd--c~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~ 112 (220)
.+--+...|-+.|. |....+.|.++ ..+++.-+.++.+-.. ++..+.+ +||. -|-||++=..
T Consensus 17 ~~~~vlv~f~a~~C~~C~~~~~~~~~~---~~~~~~~~~~~~id~~-~~~~~~~---~~~i-~~~P~~~~~~ 80 (103)
T cd03001 17 SDDVWLVEFYAPWCGHCKNLAPEWKKA---AKALKGIVKVGAVDAD-VHQSLAQ---QYGV-RGFPTIKVFG 80 (103)
T ss_pred CCCcEEEEEECCCCHHHHHHhHHHHHH---HHHhcCCceEEEEECc-chHHHHH---HCCC-CccCEEEEEC
Confidence 34445666777875 55666666665 4455554555555433 3444544 3354 4678775443
No 104
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=30.79 E-value=39 Score=32.28 Aligned_cols=50 Identities=22% Similarity=0.311 Sum_probs=43.5
Q ss_pred EeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHH
Q 042199 156 RVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIV 205 (220)
Q Consensus 156 rvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~ 205 (220)
|++..||+|...+..-|..+.|.+.+|-+||-|+.=+-...+.-+|..|.
T Consensus 293 R~l~kIpRlp~~iv~nlV~~F~~l~~il~As~edL~~VeGIGe~rAr~i~ 342 (349)
T COG1623 293 RLLNKIPRLPFAIVENLVRAFGTLDGILEASAEDLDAVEGIGEARARAIK 342 (349)
T ss_pred HHHhcCcCccHHHHHHHHHHHhhHHHHHHhcHhHHhhhcchhHHHHHHHH
Confidence 78899999999999999999999999999999987766666666676654
No 105
>PRK13758 anaerobic sulfatase-maturase; Provisional
Probab=30.24 E-value=86 Score=27.41 Aligned_cols=107 Identities=15% Similarity=0.213 Sum_probs=58.2
Q ss_pred ccccCcceeeecCCcchhHHHHHHHHHhhhhhhh---hhhH---HHHHHHHHhhhhccceeEEeeeccCCCCc-cChh--
Q 042199 100 GMELGRPTFVPVQDREMGFEKIIKIAHSRGVCKR---QDAI---SKLKAERRRAVQTMDVFLRVVTSIPLIDN-HDAN-- 170 (220)
Q Consensus 100 gm~~g~PtfvpV~d~eMgfEkivkIAh~~gvcKq---Q~i~---s~lk~ERkq~VQ~md~flrvvTSIP~id~-HDAn-- 170 (220)
.+-+|-|+.-| .+ -++.|+++|...|.... -.|. ..+..|.-+.+..... .|--|+.|.+. ||+.
T Consensus 62 ~~~GGEPll~~---~~-~~~~~~~~~~~~~~~~~~~~~~i~TNG~ll~~~~~~~l~~~~~--~v~iSlDg~~~~hd~~R~ 135 (370)
T PRK13758 62 AFQGGEPTLAG---LE-FFEELMELQRKHNYKNLKIYNSLQTNGTLIDESWAKFLSENKF--LVGLSMDGPKEIHNLNRK 135 (370)
T ss_pred EEECCccccCC---hH-HHHHHHHHHHHhccCCCeEEEEEEecCEecCHHHHHHHHHcCc--eEEEeecCCHHHhccccC
Confidence 45679999987 11 36789999988874321 1121 1233344444443332 56669999754 7764
Q ss_pred ------HHHHhhhhHHHHHhhhhhhhhhc--cCCChhhHHHHHHHhcCCc
Q 042199 171 ------ALNQAIGSIEAIAKASKTYILEN--TDLSAEKAEMIVRFFRDPK 212 (220)
Q Consensus 171 ------~L~QaIGSieAIakaSke~Ilen--TDLS~dkAE~i~rffrDp~ 212 (220)
+..+.+-.|+.+.+...+..+.. |..+.+.-+.+.+|+++-.
T Consensus 136 ~~~g~~~f~~v~~~i~~l~~~~~~~~i~~~v~~~n~~~l~~i~~~~~~~g 185 (370)
T PRK13758 136 DCCGLDTFSKVERAAELFKKYKVEFNILCVVTSNTARHVNKIYKYFKEKD 185 (370)
T ss_pred CCCCCccHHHHHHHHHHHHHhCCCceEEEEeccccccCHHHHHHHHHHcC
Confidence 45555555655555432211111 2223445567777776543
No 106
>cd02948 TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which
Probab=29.91 E-value=2.1e+02 Score=20.47 Aligned_cols=65 Identities=15% Similarity=0.337 Sum_probs=36.9
Q ss_pred eeCCCceEEEEEeecc--CCCchHHHHHHHHHHHHhhcc-eEEEEEecCccchhhHHHhHhhhccccCcceeeecCCc
Q 042199 40 FNCGGMSISFVFITNW--DCHNTAVVFSRIKKLKEQFAH-FYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQDR 114 (220)
Q Consensus 40 fn~gglSvAFifvt~w--dc~n~a~ifsRV~kLK~qF~~-lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d~ 114 (220)
+++++ .+...|-+.| .|...+++|.++ ..+++. ...++.+... .....+.| + .-+-|||+=..+.
T Consensus 14 i~~~~-~vvv~F~a~wC~~Ck~~~p~l~~~---~~~~~~~~~~~~~vd~d--~~~~~~~~---~-v~~~Pt~~~~~~g 81 (102)
T cd02948 14 LSNKG-LTVVDVYQEWCGPCKAVVSLFKKI---KNELGDDLLHFATAEAD--TIDTLKRY---R-GKCEPTFLFYKNG 81 (102)
T ss_pred HccCC-eEEEEEECCcCHhHHHHhHHHHHH---HHHcCCCcEEEEEEeCC--CHHHHHHc---C-CCcCcEEEEEECC
Confidence 34555 4667888888 356666666554 455652 3455556555 23334443 3 3456887766554
No 107
>TIGR02661 MauD methylamine dehydrogenase accessory protein MauD. This protein, MauD, appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulfide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulfide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded.
Probab=29.52 E-value=1.6e+02 Score=23.80 Aligned_cols=48 Identities=17% Similarity=0.238 Sum_probs=26.9
Q ss_pred EEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhH
Q 042199 48 SFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSY 96 (220)
Q Consensus 48 AFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sY 96 (220)
-..|.+.| |..+...+..++++..+..-=.+.|+..+.++...|.+.+
T Consensus 78 vl~F~atw-Cp~C~~~lp~l~~~~~~~~~~vv~Is~~~~~~~~~~~~~~ 125 (189)
T TIGR02661 78 LLMFTAPS-CPVCDKLFPIIKSIARAEETDVVMISDGTPAEHRRFLKDH 125 (189)
T ss_pred EEEEECCC-ChhHHHHHHHHHHHHHhcCCcEEEEeCCCHHHHHHHHHhc
Confidence 34566777 4444444445555554433224555666667777777765
No 108
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=29.21 E-value=55 Score=34.67 Aligned_cols=53 Identities=19% Similarity=0.313 Sum_probs=46.7
Q ss_pred EeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 156 RVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 156 rvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffr 209 (220)
.++-++|||.--++..|.--++|+...|..|-+.|-|--.. .++|+.|-+||+
T Consensus 821 ~fll~lPgVs~~n~~~l~~k~ks~~~La~sS~~el~el~~~-~~~a~~LYdFi~ 873 (892)
T KOG0442|consen 821 DFLLSLPGVSYINYRNLRHKFKSLKELANSSQEELSELLGV-HENAKLLYDFIH 873 (892)
T ss_pred HHHhcCCCccHHHHHHHHHHhhHHHHHHhCcHHHHHHHhcc-hHHHHHHHHHHH
Confidence 45568999999999999988999999999999988776666 899999999997
No 109
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=28.71 E-value=43 Score=22.32 Aligned_cols=15 Identities=27% Similarity=0.408 Sum_probs=12.6
Q ss_pred cCCChhhHHHHHHHh
Q 042199 194 TDLSAEKAEMIVRFF 208 (220)
Q Consensus 194 TDLS~dkAE~i~rff 208 (220)
-|.+.|||+.|+++.
T Consensus 20 d~v~~~Ka~~im~lA 34 (36)
T PF06200_consen 20 DDVPPDKAQEIMLLA 34 (36)
T ss_pred CCCCHHHHHHHHHHh
Confidence 368999999999874
No 110
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=28.35 E-value=35 Score=26.68 Aligned_cols=34 Identities=24% Similarity=0.384 Sum_probs=29.1
Q ss_pred ccCCCCccChhHHHHh-hhhHHHHHhhhhhhhhhc
Q 042199 160 SIPLIDNHDANALNQA-IGSIEAIAKASKTYILEN 193 (220)
Q Consensus 160 SIP~id~HDAn~L~Qa-IGSieAIakaSke~Ilen 193 (220)
.||||.-++|.-|..| |.|++++|.++-+.+.+.
T Consensus 57 ri~gi~~~~a~LL~~AGv~Tv~~LA~~~p~~L~~~ 91 (122)
T PF14229_consen 57 RIPGIGPQYAELLEHAGVDTVEELAQRNPQNLHQK 91 (122)
T ss_pred hcCCCCHHHHHHHHHhCcCcHHHHHhCCHHHHHHH
Confidence 7999999999998774 889999999988777653
No 111
>cd03011 TlpA_like_ScsD_MtbDsbE TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif. The Salmonella typhimurium ScsD is a thioredoxin-like protein which confers copper tolerance to copper-sensitive mutants of E. coli. MtbDsbE has been characterized as an oxidase in vitro, catalyzing the disulfide bond formation of substrates like hirudin. The reduced form of MtbDsbE is more stable than its oxidized form, consistent with an oxidase function. This is in contrast to the function of DsbE from gram-negative bacteria which is a specific reductase of apocytochrome c.
Probab=28.31 E-value=1.5e+02 Score=21.10 Aligned_cols=50 Identities=14% Similarity=0.331 Sum_probs=28.4
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEec-CccchhhHHHh
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALP-TREQNDSFVRS 95 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~-t~eq~dsF~~s 95 (220)
|-.+-..|.+.| |..+-.....+.+|.+.++ +.+|.+-+ +.++...|.+.
T Consensus 20 ~k~~vl~F~~~~-C~~C~~~~~~l~~~~~~~~-~i~i~~~~~~~~~~~~~~~~ 70 (123)
T cd03011 20 GKPVLVYFWATW-CPVCRFTSPTVNQLAADYP-VVSVALRSGDDGAVARFMQK 70 (123)
T ss_pred CCEEEEEEECCc-ChhhhhhChHHHHHHhhCC-EEEEEccCCCHHHHHHHHHH
Confidence 334566667888 7777777777777777743 22222222 24555555554
No 112
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=27.87 E-value=34 Score=24.45 Aligned_cols=36 Identities=25% Similarity=0.272 Sum_probs=24.3
Q ss_pred HhhhhhhhhhccCCChhhHHHHHHHhc--------CCccccCCC
Q 042199 183 AKASKTYILENTDLSAEKAEMIVRFFR--------DPKLYLSPK 218 (220)
Q Consensus 183 akaSke~IlenTDLS~dkAE~i~rffr--------Dp~~ylsPk 218 (220)
..++++.|+..++||...+....+.+. +-.|.++||
T Consensus 18 ~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~~~~~Y~lTek 61 (77)
T PF14947_consen 18 GGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKKKDGKYRLTEK 61 (77)
T ss_dssp T-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEEETTEEEE-HH
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeCCCCEEEECcc
Confidence 456789999999999999999888875 445555554
No 113
>cd02995 PDI_a_PDI_a'_C PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. PDI and ERp57 have the abb'a' domain structure (where a and a' are redox active TRX domains while b and b' are redox inactive TRX-like domains). PDI also contains an acidic region (c domain) after the a' domain that is absent in ERp57. ERp72 has an additional a domain at the N-terminus (a"abb'a' domain structure). ERp57 interacts with the lectin chaperones, calnexin and calreticu
Probab=27.76 E-value=2e+02 Score=19.49 Aligned_cols=63 Identities=16% Similarity=0.301 Sum_probs=37.0
Q ss_pred CceEEEEEeeccCCCchHHHHHHHHHHHHhhcc--eEEEEEecCccchhhHHHhHhhhccccCcceeeecCC
Q 042199 44 GMSISFVFITNWDCHNTAVVFSRIKKLKEQFAH--FYVVLALPTREQNDSFVRSYFKYGMELGRPTFVPVQD 113 (220)
Q Consensus 44 glSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~--lYVVvtl~t~eq~dsF~~sYFk~gm~~g~PtfvpV~d 113 (220)
|-.+-..|-+.| |..+...-..+.++...+++ -..++.+-..++ + ... +++. -|-||++=..+
T Consensus 18 ~~~~~v~f~~~~-C~~C~~~~~~~~~~~~~~~~~~~~~~~~id~~~~-~-~~~---~~~~-~~~Pt~~~~~~ 82 (104)
T cd02995 18 DKDVLVEFYAPW-CGHCKALAPIYEELAEKLKGDDNVVIAKMDATAN-D-VPS---EFVV-DGFPTILFFPA 82 (104)
T ss_pred CCcEEEEEECCC-CHHHHHHhhHHHHHHHHhcCCCCEEEEEEeCcch-h-hhh---hccC-CCCCEEEEEcC
Confidence 344556677787 77777666777777777766 234444554432 2 222 2344 57888875544
No 114
>cd07412 MPP_YhcR_N Bacillus subtilis YhcR endonuclease and related proteins, N-terminal metallophosphatase domain. YhcR is a Bacillus subtilis sugar-nonspecific endonuclease. It cleaves endonucleolytically to yield nucleotide 3'-monophosphate products, similar to Staphylococcus aureus micrococcal nuclease. YhcR appears to be located in the cell wall, and is thought to be a substrate for a Bacillus subtilis sortase. YhcR is the major calcium-activated nuclease of B. subtilis. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated wi
Probab=27.68 E-value=1.3e+02 Score=26.07 Aligned_cols=62 Identities=23% Similarity=0.313 Sum_probs=36.2
Q ss_pred HHhcccceee--eeeeCCceeeeCCCceEEEEEeec--------------cCCCchHHHHHH-HHHHHHhhcceEEEEE
Q 042199 21 FLSANSFRLN--FVLVAPDFIFNCGGMSISFVFITN--------------WDCHNTAVVFSR-IKKLKEQFAHFYVVLA 82 (220)
Q Consensus 21 fL~AnS~RLn--F~~iaPDfIfn~gglSvAFifvt~--------------wdc~n~a~ifsR-V~kLK~qF~~lYVVvt 82 (220)
+|+||-+.-+ -..+.|--|+.-+|+.||||=+|. |.-.+......+ +++||.+=+++-||++
T Consensus 121 ~l~aNv~~~~~~~~~~~py~i~~~~G~kIgviGl~~~~~~~~~~~~~~~g~~f~d~~e~~~~~v~~lr~~~~D~IIvL~ 199 (288)
T cd07412 121 YLAANVYDKGTGTPALPPYTIKDVGGVKVGFIGAVTKDTPNLVSPDGVAGLEFTDEVEAINAVAPELKAGGVDAIVVLA 199 (288)
T ss_pred EEEEeEEecCCCCcccCCEEEEEECCEEEEEEeecCCCccceeccccccCceEcCHHHHHHHHHHHHHHCCCCEEEEEe
Confidence 5666654321 112456677888999999998852 222233333333 6778876566665553
No 115
>TIGR02284 conserved hypothetical protein. Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.
Probab=27.59 E-value=1.5e+02 Score=23.62 Aligned_cols=94 Identities=16% Similarity=0.219 Sum_probs=62.2
Q ss_pred CCcchhHHHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCC-------------------CCccChhHH
Q 042199 112 QDREMGFEKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPL-------------------IDNHDANAL 172 (220)
Q Consensus 112 ~d~eMgfEkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~-------------------id~HDAn~L 172 (220)
.|.+-||++.+.-+..-.. ......+..||++.+.-....++-.-.-|- +..+|..+.
T Consensus 13 ~D~~~gY~~aae~v~~~~l---k~~f~~~~~~~~~~~~eL~~~v~~lGg~p~~~gs~~g~lhr~w~~lks~~~~~~d~ai 89 (139)
T TIGR02284 13 IDGKDGFEESAEEVKDPEL---ATLFRRIAGEKSAIVSELQQVVASLGGKPEDHGSMVGSLHQFWGKIRATLTPNDDYVV 89 (139)
T ss_pred ccHHHHHHHHHHHCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHcCCChHHH
Confidence 4778899998887754333 456677888898888777776666555453 222444445
Q ss_pred HHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHh
Q 042199 173 NQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFF 208 (220)
Q Consensus 173 ~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rff 208 (220)
..++=.-|.-+..-=+..|+..||+.+--..|.|=.
T Consensus 90 L~~~e~gEd~~~~~y~~aL~~~~l~~~~r~~l~~q~ 125 (139)
T TIGR02284 90 LEEAERGEDRAKKAYDETLADQDTPAAARDVALRQY 125 (139)
T ss_pred HHHHHHhHHHHHHHHHHHHhcCCCChHHHHHHHHHH
Confidence 555555555555666778888889988777776643
No 116
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=27.30 E-value=78 Score=25.95 Aligned_cols=34 Identities=21% Similarity=0.239 Sum_probs=24.6
Q ss_pred HhhhhHHHHHhhhhhhhh---hccCCChhhHHHHHHH
Q 042199 174 QAIGSIEAIAKASKTYIL---ENTDLSAEKAEMIVRF 207 (220)
Q Consensus 174 QaIGSieAIakaSke~Il---enTDLS~dkAE~i~rf 207 (220)
+...++|+|++++-+.+. .-..++.-||+.|.+.
T Consensus 53 ~~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~ 89 (191)
T TIGR01083 53 EVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIAL 89 (191)
T ss_pred HHCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHH
Confidence 345678888888887763 4567888888887654
No 117
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=26.91 E-value=50 Score=24.19 Aligned_cols=40 Identities=30% Similarity=0.410 Sum_probs=28.8
Q ss_pred ChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhc
Q 042199 168 DANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 168 DAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffr 209 (220)
|...-.||+==++ .-||-+.|.++.+||-..||-++++-+
T Consensus 30 ~~~~Y~~A~klv~--~Ga~~~el~~~CgL~~aEAeLl~~Lh~ 69 (70)
T PF10975_consen 30 DSPLYSQAIKLVR--QGASVEELMEECGLSRAEAELLLSLHR 69 (70)
T ss_pred CcchHHHHHHHHH--cCCCHHHHHHHcCCCHHHHHHHHHHhc
Confidence 3344566653333 237888999999999999999998743
No 118
>cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain.
Probab=26.89 E-value=2.5e+02 Score=20.46 Aligned_cols=53 Identities=13% Similarity=0.180 Sum_probs=33.2
Q ss_pred EEEeeccCCCchHHHHHHHHHHHHhhcce-EEEEEecCccchhhHHHhHhhhccccCcceee
Q 042199 49 FVFITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLALPTREQNDSFVRSYFKYGMELGRPTFV 109 (220)
Q Consensus 49 Fifvt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl~t~eq~dsF~~sYFk~gm~~g~Ptfv 109 (220)
.+|++.| |..+-.+-.-+++|..++.++ |.++.+ +.+.+---+||.. +-||++
T Consensus 17 ~~F~~~~-C~~C~~~~~~~~~l~~~~~~i~~~~vd~------~~~~e~a~~~~V~-~vPt~v 70 (89)
T cd03026 17 ETYVSLS-CHNCPDVVQALNLMAVLNPNIEHEMIDG------ALFQDEVEERGIM-SVPAIF 70 (89)
T ss_pred EEEECCC-CCCcHHHHHHHHHHHHHCCCceEEEEEh------HhCHHHHHHcCCc-cCCEEE
Confidence 4677777 888777777778888888643 333332 2222233366654 689997
No 119
>cd02951 SoxW SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide fixation during autotrophic growth and the respiratory electron transport chain. It is unclear what the role of SoxW is, since it has been found to be dispensable in the oxidation of thiosulfate to sulfate. SoxW is specifically kept in the reduced state by SoxV, which is essential in thiosulfate oxidation.
Probab=26.80 E-value=1.3e+02 Score=21.96 Aligned_cols=41 Identities=10% Similarity=0.166 Sum_probs=20.3
Q ss_pred eEEEEEeeccC--CCchHHHHHHHHHHHHhhcceEEEEEecCc
Q 042199 46 SISFVFITNWD--CHNTAVVFSRIKKLKEQFAHFYVVLALPTR 86 (220)
Q Consensus 46 SvAFifvt~wd--c~n~a~ifsRV~kLK~qF~~lYVVvtl~t~ 86 (220)
.|...|.+.|- |....+.+.....++..+..=|+++.+...
T Consensus 16 ~vlv~f~a~wC~~C~~~~~~~~~~~~~~~~~~~~~~~~~i~~d 58 (125)
T cd02951 16 PLLLLFSQPGCPYCDKLKRDYLNDPAVQAYIRAHFVVVYINID 58 (125)
T ss_pred cEEEEEeCCCCHHHHHHHHHhcCcHHHHHHHHhheEEEEEEcc
Confidence 45566777773 444444443223444444344555555443
No 120
>cd07381 MPP_CapA CapA and related proteins, metallophosphatase domain. CapA is one of three membrane-associated enzymes in Bacillus anthracis that is required for synthesis of gamma-polyglutamic acid (PGA), a major component of the bacterial capsule. The YwtB and PgsA proteins of Bacillus subtilis are closely related to CapA and are also included in this alignment model. CapA belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal
Probab=26.75 E-value=2.5e+02 Score=23.10 Aligned_cols=45 Identities=18% Similarity=0.225 Sum_probs=32.6
Q ss_pred CCceeeeCCCceEEEEEeeccCCCc---------------hHHHHHHHHHHHHhhcceEEE
Q 042199 35 APDFIFNCGGMSISFVFITNWDCHN---------------TAVVFSRIKKLKEQFAHFYVV 80 (220)
Q Consensus 35 aPDfIfn~gglSvAFifvt~wdc~n---------------~a~ifsRV~kLK~qF~~lYVV 80 (220)
.|-.|+.-.|+.||||=+|.+.-.. ...+-..|++||.+ +.+-||
T Consensus 121 ~~~~i~~~~g~kVg~ig~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lr~~-~D~vIv 180 (239)
T cd07381 121 RRPAILEVNGIKVAFLAYTYGTNGIPLAAGARPGGVNPLDLERIAADIAEAKKK-ADIVIV 180 (239)
T ss_pred cCcEEEEECCEEEEEEEEECCCCCCcCcccCCccccCccCHHHHHHHHHHHhhc-CCEEEE
Confidence 3456788889999999998765432 35577889999998 554333
No 121
>cd03020 DsbA_DsbC_DsbG DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins. DsbC and DsbG are kept in their reduced state by the cytoplasmic membrane protein DsbD, which utilizes the TRX/TRX reductase system in the cytosol as a source of reducing equivalents. DsbG differ from DsbC in that it has a more limited substrate specificity, and it may preferentially act later in the folding process to catalyze disulfide rearrangements in folded or partially folded proteins. Also included in the alignment is the predicted protein TrbB, whose gene was sequenced from the enterohemorrhagic E. coli type IV pilus gene cluster, which is required for efficient plasmid transfer.
Probab=26.20 E-value=1.3e+02 Score=24.06 Aligned_cols=39 Identities=13% Similarity=0.160 Sum_probs=32.2
Q ss_pred CCceeeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHh
Q 042199 35 APDFIFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQ 73 (220)
Q Consensus 35 aPDfIfn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~q 73 (220)
.-.+.+.++.-...+++.||.+|.-+......+.++.+.
T Consensus 67 ~~~i~~g~~~~~~~i~~f~D~~Cp~C~~~~~~l~~~~~~ 105 (197)
T cd03020 67 DDAIVYGKGNGKRVVYVFTDPDCPYCRKLEKELKPNADG 105 (197)
T ss_pred ccCeEEcCCCCCEEEEEEECCCCccHHHHHHHHhhccCc
Confidence 345778888889999999999999999999988874333
No 122
>PTZ00335 tubulin alpha chain; Provisional
Probab=25.81 E-value=76 Score=29.99 Aligned_cols=46 Identities=24% Similarity=0.489 Sum_probs=32.2
Q ss_pred ceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhccccC
Q 042199 45 MSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMELG 104 (220)
Q Consensus 45 lSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~g 104 (220)
...+-.+++| .-.|-+-.+++..||..+| .-..|.+-|-++|||-+
T Consensus 371 ~~~s~~~lsN-----stsI~~~f~~i~~~f~~mf---------~rkAflh~Y~~eGmee~ 416 (448)
T PTZ00335 371 VQRAVCMISN-----STAIAEVFSRIDHKFDLMY---------AKRAFVHWYVGEGMEEG 416 (448)
T ss_pred cceEEEEecC-----CcHHHHHHHHHHHHHHHHH---------hhcchhhhhhccCCchH
Confidence 3444445544 4556666667778998888 45689999999999643
No 123
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=25.42 E-value=2.1e+02 Score=21.51 Aligned_cols=39 Identities=15% Similarity=0.173 Sum_probs=24.5
Q ss_pred EEEEEeeccCCCchHHHHHHHHHHHHhhcce-EEEEEecC
Q 042199 47 ISFVFITNWDCHNTAVVFSRIKKLKEQFAHF-YVVLALPT 85 (220)
Q Consensus 47 vAFifvt~wdc~n~a~ifsRV~kLK~qF~~l-YVVvtl~t 85 (220)
+-..|...|.|..+..-..+++++..+|+.- ..||+++.
T Consensus 33 ~ll~f~~~~~~p~C~~~~~~l~~~~~~~~~~~v~vi~Is~ 72 (154)
T PRK09437 33 VLVYFYPKAMTPGCTVQACGLRDNMDELKKAGVVVLGIST 72 (154)
T ss_pred EEEEEECCCCCCchHHHHHHHHHHHHHHHHCCCEEEEEcC
Confidence 3334555577777777777788888887642 34555554
No 124
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=25.22 E-value=92 Score=34.47 Aligned_cols=55 Identities=25% Similarity=0.506 Sum_probs=44.3
Q ss_pred eeCCceeee----CCCceEE-------EEEeeccCCCchHHHHHHHHHHHHhhc--ceEEEEEecCccc
Q 042199 33 LVAPDFIFN----CGGMSIS-------FVFITNWDCHNTAVVFSRIKKLKEQFA--HFYVVLALPTREQ 88 (220)
Q Consensus 33 ~iaPDfIfn----~gglSvA-------Fifvt~wdc~n~a~ifsRV~kLK~qF~--~lYVVvtl~t~eq 88 (220)
|=|+||+|- -|||+|- .||=.+|..+|-.---.|-.++ ||=+ |.|=.||=-|.|.
T Consensus 748 p~SddFvFLLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRI-GQkk~VnVYRLVTk~TvEe 815 (1373)
T KOG0384|consen 748 PDSDDFVFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRI-GQKKHVNVYRLVTKNTVEE 815 (1373)
T ss_pred CCCCceEEEEecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhh-cccceEEEEEEecCCchHH
Confidence 557899986 6999984 7999999999999888898887 4443 6788888777764
No 125
>PF06238 Borrelia_lipo_2: Borrelia burgdorferi BBR25 lipoprotein; InterPro: IPR009358 This entry consists of a number of lipoproteins conserved in Borrelia species [].
Probab=25.08 E-value=95 Score=25.64 Aligned_cols=34 Identities=26% Similarity=0.290 Sum_probs=28.4
Q ss_pred hHHHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhc
Q 042199 117 GFEKIIKIAHSRGVCKRQDAISKLKAERRRAVQT 150 (220)
Q Consensus 117 gfEkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~ 150 (220)
=..+.++|-.+-..-|..+|+|-||++|-.++|.
T Consensus 67 Ilk~nieiIeai~~~k~~~iIs~LkakRNkiMke 100 (111)
T PF06238_consen 67 ILKYNIEIIEAISTDKNKRIISSLKAKRNKIMKE 100 (111)
T ss_pred HHHHHHHHHHHHccchhhhHHHHHHHHHHHHHHH
Confidence 3456677788888888999999999999999885
No 126
>KOG1210 consensus Predicted 3-ketosphinganine reductase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=23.93 E-value=33 Score=32.46 Aligned_cols=27 Identities=22% Similarity=0.321 Sum_probs=23.5
Q ss_pred eeeeeeeCCceeeeCCCceEEEEEeec
Q 042199 28 RLNFVLVAPDFIFNCGGMSISFVFITN 54 (220)
Q Consensus 28 RLnF~~iaPDfIfn~gglSvAFifvt~ 54 (220)
+|.++-..||-+|+|||+.|.=.|+.+
T Consensus 105 ~l~~~~~~~d~l~~cAG~~v~g~f~~~ 131 (331)
T KOG1210|consen 105 ELRDLEGPIDNLFCCAGVAVPGLFEDL 131 (331)
T ss_pred hhhhccCCcceEEEecCcccccccccC
Confidence 466777889999999999999999865
No 127
>PRK09492 treR trehalose repressor; Provisional
Probab=23.57 E-value=2.1e+02 Score=23.45 Aligned_cols=82 Identities=11% Similarity=0.208 Sum_probs=42.5
Q ss_pred hhHHHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccC
Q 042199 116 MGFEKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTD 195 (220)
Q Consensus 116 MgfEkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTD 195 (220)
-.=||+.++|...|- +.......|+..|. .-+-++ +|.+++.-.+.+.++|- ++..+.--.-++-+++
T Consensus 34 ~tr~rV~~~a~elgY-~pn~~a~~l~~~~~-------~~Ig~i--~~~~~~~~~~~~~~~i~--~~~~~~gy~~~~~~~~ 101 (315)
T PRK09492 34 ETRERVEAVINQHGF-SPSKSARAMRGQSD-------KVVGII--VSRLDSLSENQAVRTML--PAFYEQGYDPIIMESQ 101 (315)
T ss_pred HHHHHHHHHHHHHCC-CcCHHHHHhhcCCC-------CeEEEE--ecCCcCcccHHHHHHHH--HHHHHcCCeEEEEecC
Confidence 346788888888884 44333333332221 224444 46676655555555442 2333333344555666
Q ss_pred CChhhHHHHHHHhc
Q 042199 196 LSAEKAEMIVRFFR 209 (220)
Q Consensus 196 LS~dkAE~i~rffr 209 (220)
.+.++.+...+-+.
T Consensus 102 ~~~~~~~~~~~~l~ 115 (315)
T PRK09492 102 FSPEKVNEHLGVLK 115 (315)
T ss_pred CChHHHHHHHHHHH
Confidence 66666555444443
No 128
>cd02186 alpha_tubulin The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. The alpha/beta-tubulin heterodimer is the structural subunit of microtubules. The alpha- and beta-tubulins share 40% amino-acid sequence identity, exist in several isotype forms, and undergo a variety of posttranslational modifications. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three regions based on function: the amino
Probab=23.41 E-value=88 Score=29.28 Aligned_cols=37 Identities=30% Similarity=0.488 Sum_probs=29.6
Q ss_pred CchHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhcccc
Q 042199 58 HNTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMEL 103 (220)
Q Consensus 58 ~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~ 103 (220)
.|.-.|-.-.+++..+|..+| .-..|.+-|-++|||-
T Consensus 378 ~Nst~i~~~f~~i~~~f~~mf---------~rkAflh~Y~~~Gmee 414 (434)
T cd02186 378 SNTTAIAEAWSRLDHKFDLMY---------SKRAFVHWYVGEGMEE 414 (434)
T ss_pred cCchHHHHHHHHHHHHHHHHH---------hhcchhhhhcCcCCch
Confidence 456667777777888999888 4578999999999964
No 129
>KOG1636 consensus DNA polymerase delta processivity factor (proliferating cell nuclear antigen) [Replication, recombination and repair]
Probab=23.21 E-value=29 Score=32.01 Aligned_cols=9 Identities=56% Similarity=1.158 Sum_probs=7.7
Q ss_pred ccccCCCCC
Q 042199 212 KLYLSPKIN 220 (220)
Q Consensus 212 ~~ylsPkin 220 (220)
+|||.||||
T Consensus 248 r~YLAPKie 256 (260)
T KOG1636|consen 248 RYYLAPKIE 256 (260)
T ss_pred EEEEccccC
Confidence 689999986
No 130
>PRK00125 pyrF orotidine 5'-phosphate decarboxylase; Reviewed
Probab=23.18 E-value=3.7e+02 Score=24.22 Aligned_cols=67 Identities=19% Similarity=0.157 Sum_probs=33.9
Q ss_pred ccceeEEeeeccCC-CCcc-----ChhHHHHhhhhHHHHHhhhhhh--hhhccC---CC--hhhHHHHHHHhcCCccccC
Q 042199 150 TMDVFLRVVTSIPL-IDNH-----DANALNQAIGSIEAIAKASKTY--ILENTD---LS--AEKAEMIVRFFRDPKLYLS 216 (220)
Q Consensus 150 ~md~flrvvTSIP~-id~H-----DAn~L~QaIGSieAIakaSke~--IlenTD---LS--~dkAE~i~rffrDp~~yls 216 (220)
+..+|+=|.||.|| =|.- |...|.|.+... +.++.+++ -..+.. =| .+.+..|.+.+-+ -..|+
T Consensus 141 ~k~vfVlvlTSnp~s~~lq~~~~~~~~~l~~~V~~~--a~~~~~~~~~~~g~~G~VVgaT~p~e~~~iR~~~~~-~~iL~ 217 (278)
T PRK00125 141 GKGVFVLCRTSNPGGSDLQFLRTADGRPLYQHVADL--AAALNNLGNCGYGSIGLVVGATFPPELAAVRKILGG-MPLLI 217 (278)
T ss_pred CCEEEEEEeCCCCCHHHHHhhhccCCCcHHHHHHHH--HHHHhccccCCCCCCEEEECCCCHHHHHHHHHhCCC-CeEEe
Confidence 45789999999998 2211 222344444321 11111100 011111 12 5667788777755 45777
Q ss_pred CCC
Q 042199 217 PKI 219 (220)
Q Consensus 217 Pki 219 (220)
|=|
T Consensus 218 PGi 220 (278)
T PRK00125 218 PGI 220 (278)
T ss_pred CCc
Confidence 744
No 131
>cd07410 MPP_CpdB_N Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain. CpdB is a bacterial periplasmic protein with an N-terminal metallophosphatase domain and a C-terminal 3'-nucleotidase domain. This alignment model represents the N-terminal metallophosphatase domain, which has 2',3'-cyclic phosphodiesterase activity, hydrolyzing the 2',3'-cyclic phosphates of adenosine, guanosine, cytosine and uridine to yield nucleoside and phosphate. CpdB also hydrolyzes the chromogenic substrates p-nitrophenyl phosphate (PNPP), bis(PNPP) and p-nitrophenyl phosphorylcholine (NPPC). CpdB is thought to play a scavenging role during RNA hydrolysis by converting the non-transportable nucleotides produced by RNaseI to nucleosides which can easily enter a cell for use as a carbon source. This family also includes YfkN, a Bacillus subtilis nucleotide phosphoesterase with two copies of each of the metallophosphatase and 3'-nucleotidase domains. The N-terminal metallophos
Probab=23.16 E-value=1.6e+02 Score=24.80 Aligned_cols=48 Identities=25% Similarity=0.407 Sum_probs=32.0
Q ss_pred CCceeeeCC-CceEEEEEeec-----cCC----------CchHHHHHHHHHHHHhhcceEEEEE
Q 042199 35 APDFIFNCG-GMSISFVFITN-----WDC----------HNTAVVFSRIKKLKEQFAHFYVVLA 82 (220)
Q Consensus 35 aPDfIfn~g-glSvAFifvt~-----wdc----------~n~a~ifsRV~kLK~qF~~lYVVvt 82 (220)
.|=.|+.-+ |+.||||=+|. |.- +....+=.-+++||.+=+.+.|+++
T Consensus 128 ~~~~i~~~~~g~kVgviG~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~v~~lr~~~~D~IIvl~ 191 (277)
T cd07410 128 KPYVILERDVGVKVGIIGLTTPQIPNWEKPNLIGGLKFTDPVETAKKYVPKLRAEGADVVVVLA 191 (277)
T ss_pred CCEEEEEecCCCEEEEEecCCcccccccCcccCCCcEEcCHHHHHHHHHHHHHHcCCCEEEEEe
Confidence 466788888 99999998873 321 1122344557888886677666654
No 132
>PF06596 PsbX: Photosystem II reaction centre X protein (PsbX); InterPro: IPR009518 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII [], and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) site [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0016020 membrane; PDB: 3ARC_x 3A0H_X 3A0B_X 3PRR_X 1S5L_x 4FBY_j 3PRQ_X 3KZI_X 3BZ2_X 3BZ1_X.
Probab=23.08 E-value=38 Score=23.30 Aligned_cols=15 Identities=33% Similarity=0.634 Sum_probs=12.3
Q ss_pred CCchHHHHHHHHhcc
Q 042199 11 HPSFINFISSFLSAN 25 (220)
Q Consensus 11 ~ps~infis~fL~An 25 (220)
.||+-|||.++++..
T Consensus 2 TpSL~nfl~Sl~aG~ 16 (39)
T PF06596_consen 2 TPSLSNFLLSLVAGA 16 (39)
T ss_dssp -HHHHHHHHHHHHHH
T ss_pred CHhHHHHHHHHHhhh
Confidence 489999999998764
No 133
>PF04321 RmlD_sub_bind: RmlD substrate binding domain; InterPro: IPR005913 dTDP-4-dehydrorhamnose reductase (1.1.1.133 from EC) catalyzes the last of 4 steps in making dTDP-rhamnose, a precursor of LPS molecules such as core antigen and O-antigen. dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + NADPH ; GO: 0008831 dTDP-4-dehydrorhamnose reductase activity, 0045226 extracellular polysaccharide biosynthetic process; PDB: 2YDX_D 2YDY_A 3SC6_C 1VL0_B 2GGS_A 1KBZ_A 1KC3_A 1KC1_A 1N2S_A.
Probab=22.89 E-value=33 Score=29.24 Aligned_cols=14 Identities=29% Similarity=0.776 Sum_probs=5.9
Q ss_pred eeCCceeeeCCCce
Q 042199 33 LVAPDFIFNCGGMS 46 (220)
Q Consensus 33 ~iaPDfIfn~gglS 46 (220)
.+.||.|+||||++
T Consensus 49 ~~~pd~Vin~aa~~ 62 (286)
T PF04321_consen 49 AFKPDVVINCAAYT 62 (286)
T ss_dssp HH--SEEEE-----
T ss_pred HhCCCeEeccceee
Confidence 35799999999874
No 134
>PRK13660 hypothetical protein; Provisional
Probab=22.68 E-value=71 Score=27.29 Aligned_cols=30 Identities=17% Similarity=0.408 Sum_probs=27.0
Q ss_pred HHHHHHHHhhcceEEEEEecCccchhhHHH
Q 042199 65 SRIKKLKEQFAHFYVVLALPTREQNDSFVR 94 (220)
Q Consensus 65 sRV~kLK~qF~~lYVVvtl~t~eq~dsF~~ 94 (220)
.=|..||.+++++=+++.+|=++|.+.++.
T Consensus 60 Evvl~LK~~yp~lkL~~~~PF~~q~~~W~e 89 (182)
T PRK13660 60 EVVLELKEEYPDLKLAVITPFEEHGENWNE 89 (182)
T ss_pred HHHHHHHhhCCCeEEEEEeCccchhhcCCH
Confidence 558899999999999999999999987765
No 135
>smart00854 PGA_cap Bacterial capsule synthesis protein PGA_cap. This protein is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein.
Probab=22.60 E-value=2.8e+02 Score=23.02 Aligned_cols=41 Identities=15% Similarity=0.258 Sum_probs=29.4
Q ss_pred CceeeeCCCceEEEEEeeccCCC-----------------chHHHHHHHHHHHHhhcce
Q 042199 36 PDFIFNCGGMSISFVFITNWDCH-----------------NTAVVFSRIKKLKEQFAHF 77 (220)
Q Consensus 36 PDfIfn~gglSvAFifvt~wdc~-----------------n~a~ifsRV~kLK~qF~~l 77 (220)
|=.|+.-+|+.||||=+|.++-. ....+-..|++||.+ +.+
T Consensus 118 ~~~i~~~~g~kIg~ig~t~~~~~~~~~~~~~~g~~~~~~~~~~~i~~~i~~lr~~-~D~ 175 (239)
T smart00854 118 KPAIVEVKGIKIALLAYTYGTNNGWAASKDRPGVALLPDLDREKILADIARARKK-ADV 175 (239)
T ss_pred CcEEEEECCEEEEEEEEEcCCCCCcccCCCCCCeeecCcCCHHHHHHHHHHHhcc-CCE
Confidence 34688889999999998864311 145677889999985 444
No 136
>PRK04140 hypothetical protein; Provisional
Probab=22.54 E-value=6.2e+02 Score=23.42 Aligned_cols=167 Identities=17% Similarity=0.221 Sum_probs=104.7
Q ss_pred hHHHHHHHHhcccceee----eeeeCCceeeeCCCceEEEEEeeccCCCchHHHHHHHHHHHHhhcceEEEEEecCccch
Q 042199 14 FINFISSFLSANSFRLN----FVLVAPDFIFNCGGMSISFVFITNWDCHNTAVVFSRIKKLKEQFAHFYVVLALPTREQN 89 (220)
Q Consensus 14 ~infis~fL~AnS~RLn----F~~iaPDfIfn~gglSvAFifvt~wdc~n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~ 89 (220)
+++-+...|..+.|... +-|=+.|.|-.-++.=+-.=+..|=|--+. ..-+=+++|-.-|.-.=+||...++.+.
T Consensus 5 li~~v~~~L~~~gf~vs~~~~~~~~~fdi~a~~~~~~~~~Kv~~n~d~~~~-~~~~~l~~~~~~~~a~p~ivg~~~~~~~ 83 (317)
T PRK04140 5 LISEVIALLEDAGFKVSDRCPIRPSCFDLVARRGDLLLLLKILYNIDSLSE-EQAEELKRLAKYLKASPLIIGLRTRNEE 83 (317)
T ss_pred HHHHHHHHHHHCCCEEEeeccCCCceEEEEEecCCcEEEEEEEeccccCCH-HHHHHHHHHHHHhCCccEEEEEecCCCc
Confidence 67888899999999877 567788988776665443334456554443 3345678888888889999999987653
Q ss_pred hhHHHhHhhhccccCcceeeecCCcchhHHHHHH-----HHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCCC
Q 042199 90 DSFVRSYFKYGMELGRPTFVPVQDREMGFEKIIK-----IAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPLI 164 (220)
Q Consensus 90 dsF~~sYFk~gm~~g~PtfvpV~d~eMgfEkivk-----IAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~i 164 (220)
--=-==|++|| ||+.+++--|+.+++ +-.++|-.-=.=...+|+.-|++.
T Consensus 84 le~gvvy~r~g--------i~~~~~~tl~~~~~~g~~p~v~~~~Gg~~v~i~GerLk~lRe~~----------------- 138 (317)
T PRK04140 84 LEDGVVYERHG--------IPALSPDTLYDDFVEGEPPLIYAAPGGFYVKIDGDVLREAREEL----------------- 138 (317)
T ss_pred cCCCcEEEecC--------ceeecHHHHHHHHhCCCCceEEEcCCCeeehhhHHHHHHHHHHc-----------------
Confidence 21111266666 566677766776664 222344332222335565555542
Q ss_pred CccChhHHHHhhh-hHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCC
Q 042199 165 DNHDANALNQAIG-SIEAIAKASKTYILENTDLSAEKAEMIVRFFRDP 211 (220)
Q Consensus 165 d~HDAn~L~QaIG-SieAIakaSke~IlenTDLS~dkAE~i~rffrDp 211 (220)
+.-...|++.+| |-.+|++--++ .++.+.+.|..+.++|.-|
T Consensus 139 -GlSq~eLA~~lGVSr~tIskyE~G----~~~Ps~e~~~kLa~~Lgv~ 181 (317)
T PRK04140 139 -GLSLGELASELGVSRRTISKYENG----GMNASIEVAIKLEEILDVP 181 (317)
T ss_pred -CCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCCC
Confidence 122467777777 55555543221 3667888888888888765
No 137
>cd05313 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids t
Probab=22.42 E-value=37 Score=30.23 Aligned_cols=18 Identities=44% Similarity=0.584 Sum_probs=15.5
Q ss_pred eeeCCceeeeCCCceEEE
Q 042199 32 VLVAPDFIFNCGGMSISF 49 (220)
Q Consensus 32 ~~iaPDfIfn~gglSvAF 49 (220)
+.+.||++-|.||+-+..
T Consensus 171 I~vvPD~laNaGGVivs~ 188 (254)
T cd05313 171 VLFAPGKAANAGGVAVSG 188 (254)
T ss_pred cEEECchhhcCCCeeeeH
Confidence 678899999999998754
No 138
>PRK06423 phosphoribosylformylglycinamidine synthase; Provisional
Probab=21.94 E-value=47 Score=23.83 Aligned_cols=52 Identities=21% Similarity=0.335 Sum_probs=40.9
Q ss_pred eeccCCCCccChhHHHHhhhh-----HHHHHhhhhhhhhhccCCChhhHHHHHH-HhcCCc
Q 042199 158 VTSIPLIDNHDANALNQAIGS-----IEAIAKASKTYILENTDLSAEKAEMIVR-FFRDPK 212 (220)
Q Consensus 158 vTSIP~id~HDAn~L~QaIGS-----ieAIakaSke~IlenTDLS~dkAE~i~r-ffrDp~ 212 (220)
|+--||+.+=-+.++.+++.. +++ .+.+|.+.++- ++.+.++.+.+ ++-||.
T Consensus 7 V~~k~gv~Dp~G~ti~~~l~~lg~~~v~~-Vr~~k~~~l~~--~~~~~~~~i~~~lL~Npv 64 (73)
T PRK06423 7 VTYKPGVEDPEALTILKNLNILGYNGIKG-VSISKVYYFDA--DSYNEVDEIAGKILTNPV 64 (73)
T ss_pred EEECCCCcChHHHHHHHHHHHcCCCCcce-EEEEEEEEEec--CCHHHHHHHHHHhcCCce
Confidence 556799988888888888764 344 68889998866 88899999975 888884
No 139
>cd02189 delta_tubulin The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. Delta-tubulin plays an essential role in forming the triplet microtubules of centrioles and basal bodies.
Probab=21.63 E-value=94 Score=29.20 Aligned_cols=36 Identities=19% Similarity=0.514 Sum_probs=26.3
Q ss_pred chHHHHHHHHHHHHhhcceEEEEEecCccchhhHHHhHhhhcccc
Q 042199 59 NTAVVFSRIKKLKEQFAHFYVVLALPTREQNDSFVRSYFKYGMEL 103 (220)
Q Consensus 59 n~a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~~sYFk~gm~~ 103 (220)
|.-.|-.-++++..+|..+| .-..|.+-|-++|||-
T Consensus 392 Nst~i~~~l~~i~~~f~~mf---------~~rAflH~Y~~~Gmee 427 (446)
T cd02189 392 NSQTIIDPLDNILEKAWNMF---------ASGAYLHQYEKYGLEE 427 (446)
T ss_pred CCchHHHHHHHHHHHHHHHH---------hcCcchhhhhccCCcH
Confidence 34445555566778888887 3467999999999983
No 140
>PRK02412 aroD 3-dehydroquinate dehydratase; Provisional
Probab=21.44 E-value=3.7e+02 Score=23.23 Aligned_cols=69 Identities=19% Similarity=0.373 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHhhcceEEEEEecCccchhhHH---HhH---hhhccccCcceeeecCC--cchhHHHHHHHHHhhh
Q 042199 61 AVVFSRIKKLKEQFAHFYVVLALPTREQNDSFV---RSY---FKYGMELGRPTFVPVQD--REMGFEKIIKIAHSRG 129 (220)
Q Consensus 61 a~ifsRV~kLK~qF~~lYVVvtl~t~eq~dsF~---~sY---Fk~gm~~g~PtfvpV~d--~eMgfEkivkIAh~~g 129 (220)
..+-.-+.+|+..+.++=+++|+.+++|--.|. +.| ++-++++|.|.+|=+-- .+--+..+++.||..|
T Consensus 59 ~~~~~~~~~l~~~~~~~PiI~T~R~~~eGG~~~~~~~~~~~ll~~~~~~~~~d~vDiEl~~~~~~~~~l~~~~~~~~ 135 (253)
T PRK02412 59 ESVLAAAPAIREKFAGKPLLFTFRTAKEGGEIALSDEEYLALIKAVIKSGLPDYIDVELFSGKDVVKEMVAFAHEHG 135 (253)
T ss_pred HHHHHHHHHHHHhcCCCcEEEEECChhhCCCCCCCHHHHHHHHHHHHhcCCCCEEEEeccCChHHHHHHHHHHHHcC
Confidence 445555667778888888999999998643332 334 44477888787775531 1123556667776544
No 141
>PRK00507 deoxyribose-phosphate aldolase; Provisional
Probab=21.36 E-value=1.1e+02 Score=26.33 Aligned_cols=68 Identities=19% Similarity=0.177 Sum_probs=46.6
Q ss_pred HHHHhhhhccceeEEeeeccCCCCccChhHHHHhhhhHHHHHh-hhhhhhhhccCCChhhHHHHHHHhc
Q 042199 142 AERRRAVQTMDVFLRVVTSIPLIDNHDANALNQAIGSIEAIAK-ASKTYILENTDLSAEKAEMIVRFFR 209 (220)
Q Consensus 142 ~ERkq~VQ~md~flrvvTSIP~id~HDAn~L~QaIGSieAIak-aSke~IlenTDLS~dkAE~i~rffr 209 (220)
.|=+++++.-=--+.+|-.+.-+..+|.+.+.|.|-.+-..+. .-=.-|||+.+|+.|.-+.+.+--.
T Consensus 78 ~e~~~Ai~~GA~EiD~Vin~~~~~~g~~~~v~~ei~~v~~~~~~~~lKvIlEt~~L~~e~i~~a~~~~~ 146 (221)
T PRK00507 78 FEAKDAIANGADEIDMVINIGALKSGDWDAVEADIRAVVEAAGGAVLKVIIETCLLTDEEKVKACEIAK 146 (221)
T ss_pred HHHHHHHHcCCceEeeeccHHHhcCCCHHHHHHHHHHHHHhcCCceEEEEeecCcCCHHHHHHHHHHHH
Confidence 4545555543334558888888889999999998877666431 1234689999999887777666543
No 142
>cd05211 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parral
Probab=20.99 E-value=49 Score=28.18 Aligned_cols=42 Identities=24% Similarity=0.444 Sum_probs=26.2
Q ss_pred eeeCCceeeeCCCceEEEEEeeccCCCch------HHHH-HHHHHHHHhhcc
Q 042199 32 VLVAPDFIFNCGGMSISFVFITNWDCHNT------AVVF-SRIKKLKEQFAH 76 (220)
Q Consensus 32 ~~iaPDfIfn~gglSvAFifvt~wdc~n~------a~if-sRV~kLK~qF~~ 76 (220)
+.+.||++.|.||+-+.+. .|.-++. ..+. .+..+|++.|..
T Consensus 144 i~v~Pd~~~NaGGvi~s~~---E~~q~~~~~~w~~~~v~~~l~~~m~~~~~~ 192 (217)
T cd05211 144 IVVAPDIVANAGGVIVSYF---EWVQNLQRLSWDAEEVRSKLEQVMTDIHNG 192 (217)
T ss_pred cEEEChHHhcCCCeEeEHH---HhcCCccccCCCHHHHHHHHHHHHHHHHHH
Confidence 7899999999999977543 3433332 4444 333455555544
No 143
>TIGR00433 bioB biotin synthetase. Catalyzes the last step of the biotin biosynthesis pathway.
Probab=20.94 E-value=1.7e+02 Score=24.57 Aligned_cols=47 Identities=13% Similarity=0.244 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhhcceEEEEE--ecCccchhhHHHh---HhhhccccCcceee
Q 042199 61 AVVFSRIKKLKEQFAHFYVVLA--LPTREQNDSFVRS---YFKYGMELGRPTFV 109 (220)
Q Consensus 61 a~ifsRV~kLK~qF~~lYVVvt--l~t~eq~dsF~~s---YFk~gm~~g~Ptfv 109 (220)
..++..+.+++... ++.+.++ +.++|+.+.+.+. ....|.| +.|...
T Consensus 97 ~~~~~~i~~~~~~~-~i~~~~~~g~~~~e~l~~Lk~aG~~~v~i~~E-~~~~~~ 148 (296)
T TIGR00433 97 MEYVEAMVQIVEEM-GLKTCATLGLLDPEQAKRLKDAGLDYYNHNLD-TSQEFY 148 (296)
T ss_pred HHHHHHHHHHHHhC-CCeEEecCCCCCHHHHHHHHHcCCCEEEEccc-CCHHHH
Confidence 34555555554442 4555444 3566666666554 3334556 555433
No 144
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=20.59 E-value=1e+02 Score=25.94 Aligned_cols=53 Identities=26% Similarity=0.314 Sum_probs=38.3
Q ss_pred EeeeccCCCCccChhHHHHhhhhHHHHHhhhhhhhhhccCCChhhHHHHHHHhcCCccccCC
Q 042199 156 RVVTSIPLIDNHDANALNQAIGSIEAIAKASKTYILENTDLSAEKAEMIVRFFRDPKLYLSP 217 (220)
Q Consensus 156 rvvTSIP~id~HDAn~L~QaIGSieAIakaSke~IlenTDLS~dkAE~i~rffrDp~~ylsP 217 (220)
--+|+|-||-.+=|..++-..| |. .=.---||+.+..+.|..+..+|..|.-|
T Consensus 30 ~aLt~I~GIG~~~A~~I~~~lg----i~-----~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP 82 (154)
T PTZ00134 30 YALTAIKGIGRRFAYLVCKKAG----ID-----VTKRAGELTAEEIEKIVEIIANPLQFKIP 82 (154)
T ss_pred EeecccccccHHHHHHHHHHcC----cC-----cCCCcccCCHHHHHHHHHHHhccccCCCC
Confidence 3469999999888888877776 10 01112489999999999999998655433
No 145
>PF09587 PGA_cap: Bacterial capsule synthesis protein PGA_cap; InterPro: IPR019079 CapA is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein [].
Probab=20.50 E-value=2.6e+02 Score=23.40 Aligned_cols=45 Identities=22% Similarity=0.288 Sum_probs=32.1
Q ss_pred eeeeCCCceEEEEEeeccCC----Cc----------------------hHHHHHHHHHHHHhhcceEEEEEec
Q 042199 38 FIFNCGGMSISFVFITNWDC----HN----------------------TAVVFSRIKKLKEQFAHFYVVLALP 84 (220)
Q Consensus 38 fIfn~gglSvAFifvt~wdc----~n----------------------~a~ifsRV~kLK~qF~~lYVVvtl~ 84 (220)
.|+.-+|+.|||+-.|.+.- .. ...+-+.|+++| +-+ =+|||.+-
T Consensus 122 ~i~~~~g~kia~l~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~r-~~~-D~vIv~~H 192 (250)
T PF09587_consen 122 AIIEVNGVKIAFLGYTDGENGYSSANGNRPYGFSYRPDKAGLNPNRPGIERIKEDIREAR-KKA-DVVIVSLH 192 (250)
T ss_pred EEEEECCEEEEEEEEEcCCCCCccccccccccccccccccccccccchHHHHHHHHHHHh-cCC-CEEEEEec
Confidence 78888999999999998751 11 166888999999 323 34565553
No 146
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=20.37 E-value=1.2e+02 Score=28.45 Aligned_cols=116 Identities=17% Similarity=0.241 Sum_probs=74.0
Q ss_pred HHHHHHH-HHHhhcceEEEEEecCccchhhHHHhHhhh-------------------------cc---ccCcceeeecCC
Q 042199 63 VFSRIKK-LKEQFAHFYVVLALPTREQNDSFVRSYFKY-------------------------GM---ELGRPTFVPVQD 113 (220)
Q Consensus 63 ifsRV~k-LK~qF~~lYVVvtl~t~eq~dsF~~sYFk~-------------------------gm---~~g~PtfvpV~d 113 (220)
+=.+|+. |++.|+++||.=.++.--...| -+-||.+ || -.|+.+|+|..-
T Consensus 5 l~~~ik~~le~~~~~v~V~GEisn~~~~~s-GH~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~~~G 83 (432)
T TIGR00237 5 LNAQIKALLEATFLQVWIQGEISNFTQPVS-GHWYFTLKDENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYEPRG 83 (432)
T ss_pred HHHHHHHHHHhhCCcEEEEEEecCCeeCCC-ceEEEEEEcCCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEECCCC
Confidence 3345554 4445999998877765432222 2445544 66 357888877542
Q ss_pred ----------------cchhHHHHHHHHHhhhhhhhhhhHHHHHHHHHhhhhccceeEEeeeccCC--------------
Q 042199 114 ----------------REMGFEKIIKIAHSRGVCKRQDAISKLKAERRRAVQTMDVFLRVVTSIPL-------------- 163 (220)
Q Consensus 114 ----------------~eMgfEkivkIAh~~gvcKqQ~i~s~lk~ERkq~VQ~md~flrvvTSIP~-------------- 163 (220)
....||++.+-..+.|. .+.|||+-+=..=-.+.||||-.|
T Consensus 84 ~~ql~v~~i~~~G~G~l~~~~~~lk~~L~~eGl---------fd~~~k~~lP~~p~~i~vits~~~aa~~D~~~~~~~r~ 154 (432)
T TIGR00237 84 DYQIICFEMQPAGEGLLQLAYEQLKEKLAAEGL---------FDQEYKKPLPHFPKRVGVITSQTGAALADILHILKRRD 154 (432)
T ss_pred cEEEEEEEeccCChHHHHHHHHHHHHHHHHCCC---------CCchhcCCCCCCCCEEEEEeCCccHHHHHHHHHHHhhC
Confidence 33446666655555543 456788888777778899998655
Q ss_pred --CCccChhHHHHhhhhHHHHHhhhhh
Q 042199 164 --IDNHDANALNQAIGSIEAIAKASKT 188 (220)
Q Consensus 164 --id~HDAn~L~QaIGSieAIakaSke 188 (220)
++-.-..+.+|+-+..+.|++|=+.
T Consensus 155 p~~~~~~~~~~vQG~~a~~~i~~al~~ 181 (432)
T TIGR00237 155 PSLKVVIYPTLVQGEGAVQSIVESIEL 181 (432)
T ss_pred CCceEEEecccccCccHHHHHHHHHHH
Confidence 4444456788998888877777543
Done!