Query psy13254
Match_columns 132
No_of_seqs 105 out of 1032
Neff 6.9
Searched_HMMs 46136
Date Sat Aug 17 00:03:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13254.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13254hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01070 mutS1 DNA mismatch r 100.0 2.7E-35 5.9E-40 261.0 12.5 113 2-132 56-168 (840)
2 PRK05399 DNA mismatch repair p 100.0 5.4E-34 1.2E-38 253.2 12.6 112 2-132 63-174 (854)
3 COG0249 MutS Mismatch repair A 100.0 1E-30 2.2E-35 231.4 13.0 112 2-132 56-168 (843)
4 KOG0217|consensus 100.0 6.9E-31 1.5E-35 231.2 1.4 126 2-132 297-429 (1125)
5 KOG0218|consensus 99.8 1.5E-21 3.2E-26 168.6 5.6 125 2-132 212-349 (1070)
6 PF01624 MutS_I: MutS domain I 99.8 2.6E-20 5.7E-25 129.6 6.6 57 3-71 56-112 (113)
7 PF05188 MutS_II: MutS domain 99.2 3.1E-11 6.6E-16 84.6 6.1 47 83-132 1-49 (137)
8 KOG0219|consensus 86.3 1.9 4E-05 39.5 5.7 105 6-132 77-190 (902)
9 KOG0220|consensus 82.1 2.1 4.5E-05 38.8 4.2 78 53-130 74-155 (867)
10 PF14359 DUF4406: Domain of un 75.3 2.4 5.3E-05 28.3 2.1 25 4-28 6-33 (92)
11 PF09339 HTH_IclR: IclR helix- 66.2 2.6 5.7E-05 24.6 0.6 20 6-25 28-47 (52)
12 PF13412 HTH_24: Winged helix- 63.5 3.2 6.9E-05 23.7 0.6 20 6-25 27-46 (48)
13 PF08497 Radical_SAM_N: Radica 62.4 6.7 0.00015 31.9 2.4 18 17-34 38-56 (302)
14 PF14947 HTH_45: Winged helix- 59.0 4.6 0.0001 25.7 0.8 22 5-26 28-49 (77)
15 PF03652 UPF0081: Uncharacteri 54.8 51 0.0011 23.3 5.7 48 84-131 2-53 (135)
16 PF08774 VRR_NUC: VRR-NUC doma 54.7 17 0.00036 23.9 3.0 22 10-31 76-97 (100)
17 PF01978 TrmB: Sugar-specific 53.1 6.4 0.00014 24.1 0.7 21 5-25 31-51 (68)
18 PF12840 HTH_20: Helix-turn-he 52.0 6.5 0.00014 23.6 0.6 20 6-25 34-53 (61)
19 TIGR03604 docking_ocin bacteri 52.0 23 0.00051 29.1 4.1 44 11-69 295-338 (377)
20 COG5561 Predicted metal-bindin 49.3 20 0.00043 24.3 2.6 23 7-29 72-95 (101)
21 PF02624 YcaO: YcaO-like famil 46.0 29 0.00064 27.4 3.7 40 10-67 291-330 (332)
22 KOG0839|consensus 45.0 16 0.00035 35.0 2.2 37 3-39 1379-1415(1477)
23 PF13730 HTH_36: Helix-turn-he 44.8 9.7 0.00021 22.1 0.6 20 6-25 35-54 (55)
24 cd07233 Glyoxalase_I Glyoxalas 44.7 40 0.00086 21.7 3.7 26 3-28 71-96 (121)
25 PF01022 HTH_5: Bacterial regu 43.7 12 0.00027 21.3 0.9 20 6-25 25-44 (47)
26 COG0223 Fmt Methionyl-tRNA for 42.8 12 0.00026 30.5 1.0 78 4-89 5-87 (307)
27 smart00419 HTH_CRP helix_turn_ 41.2 12 0.00026 20.7 0.5 22 5-26 17-38 (48)
28 PRK01254 hypothetical protein; 41.1 22 0.00047 32.2 2.4 18 17-34 61-79 (707)
29 PRK00109 Holliday junction res 40.7 93 0.002 22.0 5.2 48 84-131 5-56 (138)
30 PF09456 RcsC: RcsC Alpha-Beta 40.7 19 0.00041 24.3 1.5 22 10-31 8-30 (92)
31 COG2044 Predicted peroxiredoxi 40.1 44 0.00096 23.6 3.4 26 9-34 60-85 (120)
32 PF13450 NAD_binding_8: NAD(P) 39.8 36 0.00078 20.9 2.7 21 17-37 12-32 (68)
33 smart00346 HTH_ICLR helix_turn 39.3 17 0.00036 23.1 1.1 22 6-27 30-51 (91)
34 COG1763 MobB Molybdopterin-gua 38.5 36 0.00078 25.0 2.9 20 13-32 19-38 (161)
35 cd01427 HAD_like Haloacid deha 38.3 48 0.001 21.3 3.3 25 8-32 24-48 (139)
36 PF12681 Glyoxalase_2: Glyoxal 37.8 48 0.001 20.9 3.2 26 3-28 57-82 (108)
37 PF13601 HTH_34: Winged helix 37.1 17 0.00038 23.3 0.9 23 6-29 24-46 (80)
38 PRK04968 SecY interacting prot 36.5 51 0.0011 24.9 3.4 38 94-131 138-178 (181)
39 cd07254 Glo_EDI_BRP_like_20 Th 36.2 57 0.0012 21.2 3.4 26 3-28 59-87 (120)
40 cd00090 HTH_ARSR Arsenical Res 34.4 28 0.0006 20.3 1.5 23 6-28 30-52 (78)
41 TIGR03309 matur_yqeB selenium- 34.0 51 0.0011 26.3 3.3 18 16-33 13-30 (256)
42 cd03413 CbiK_C Anaerobic cobal 33.8 52 0.0011 22.1 2.9 24 8-31 76-99 (103)
43 PF08645 PNK3P: Polynucleotide 33.7 47 0.001 24.0 2.8 21 12-32 33-54 (159)
44 cd00529 RuvC_resolvase Hollida 33.6 1.3E+02 0.0028 21.5 5.1 47 85-131 2-61 (154)
45 PF12646 DUF3783: Domain of un 33.3 28 0.00062 21.0 1.4 25 3-27 4-28 (58)
46 PRK14489 putative bifunctional 33.3 1E+02 0.0022 25.3 5.1 29 4-32 209-241 (366)
47 cd07377 WHTH_GntR Winged helix 33.2 19 0.00042 21.0 0.6 21 5-25 34-54 (66)
48 PF02075 RuvC: Crossover junct 33.1 1.1E+02 0.0023 21.9 4.6 47 85-131 1-60 (149)
49 TIGR00620 sporelyase spore pho 33.0 38 0.00082 25.9 2.3 15 16-30 76-90 (199)
50 PF08820 DUF1803: Domain of un 32.2 35 0.00077 23.0 1.8 19 8-26 38-57 (93)
51 TIGR01261 hisB_Nterm histidino 31.9 60 0.0013 23.4 3.2 23 9-31 30-52 (161)
52 cd00092 HTH_CRP helix_turn_hel 31.6 21 0.00046 21.1 0.6 22 5-26 34-55 (67)
53 TIGR00250 RNAse_H_YqgF RNAse H 31.4 1.1E+02 0.0024 21.4 4.3 44 87-131 2-50 (130)
54 COG1233 Phytoene dehydrogenase 31.4 44 0.00096 28.4 2.7 21 17-37 19-39 (487)
55 COG2403 Predicted GTPase [Gene 31.2 43 0.00094 28.5 2.5 25 7-31 137-162 (449)
56 PF01946 Thi4: Thi4 family; PD 31.0 40 0.00086 26.5 2.1 20 17-36 33-52 (230)
57 cd01709 RT_like_1 RT_like_1: A 31.0 43 0.00092 27.9 2.4 36 92-127 178-213 (346)
58 PRK00955 hypothetical protein; 30.8 44 0.00096 29.9 2.6 20 15-34 33-53 (620)
59 cd08352 Glo_EDI_BRP_like_1 Thi 30.3 65 0.0014 20.6 2.9 26 4-29 74-99 (125)
60 TIGR01664 DNA-3'-Pase DNA 3'-p 29.8 74 0.0016 23.0 3.3 23 9-31 43-65 (166)
61 smart00732 YqgFc Likely ribonu 29.7 1.5E+02 0.0032 18.7 5.0 45 85-130 3-52 (99)
62 smart00252 SH2 Src homology 2 29.3 1.4E+02 0.0031 18.4 4.6 56 65-128 22-78 (84)
63 PRK08382 putative monovalent c 28.7 92 0.002 23.8 3.8 10 62-71 150-159 (201)
64 smart00753 PAM PCI/PINT associ 28.7 49 0.0011 20.8 2.0 30 6-35 34-63 (88)
65 smart00088 PINT motif in prote 28.7 49 0.0011 20.8 2.0 30 6-35 34-63 (88)
66 cd08362 BphC5-RrK37_N_like N-t 28.4 59 0.0013 21.0 2.4 26 3-28 59-87 (120)
67 PF05222 AlaDh_PNT_N: Alanine 27.4 55 0.0012 23.1 2.2 17 14-30 17-33 (136)
68 PF10614 CsgF: Type VIII secre 27.3 2.5E+02 0.0053 20.4 6.0 38 64-112 100-137 (142)
69 TIGR00213 GmhB_yaeD D,D-heptos 27.3 81 0.0017 22.6 3.2 22 10-31 28-49 (176)
70 COG1635 THI4 Ribulose 1,5-bisp 27.0 61 0.0013 25.8 2.6 20 17-36 46-65 (262)
71 cd03412 CbiK_N Anaerobic cobal 26.8 88 0.0019 21.7 3.2 24 7-30 52-75 (127)
72 PRK10749 lysophospholipase L2; 26.8 67 0.0015 25.4 2.9 28 7-34 62-91 (330)
73 PF01399 PCI: PCI domain; Int 26.7 39 0.00085 21.5 1.3 30 5-34 69-98 (105)
74 PF12146 Hydrolase_4: Putative 26.6 73 0.0016 20.2 2.5 24 12-35 31-54 (79)
75 smart00420 HTH_DEOR helix_turn 26.4 42 0.0009 18.5 1.2 20 6-25 24-43 (53)
76 PF03205 MobB: Molybdopterin g 26.2 76 0.0017 22.3 2.8 18 14-31 18-35 (140)
77 PF07879 PHB_acc_N: PHB/PHA ac 26.1 80 0.0017 19.9 2.5 18 15-32 23-40 (64)
78 PF02635 DrsE: DsrE/DsrF-like 25.9 75 0.0016 20.6 2.6 24 10-33 60-84 (122)
79 COG1703 ArgK Putative periplas 25.7 75 0.0016 26.2 2.9 20 12-31 67-86 (323)
80 PRK06279 putative monovalent c 25.7 61 0.0013 21.9 2.1 10 62-71 58-67 (100)
81 PF13076 DUF3940: Protein of u 25.5 61 0.0013 18.2 1.7 12 14-25 4-15 (38)
82 PTZ00445 p36-lilke protein; Pr 25.4 56 0.0012 25.4 2.1 27 9-35 27-53 (219)
83 COG1087 GalE UDP-glucose 4-epi 25.3 63 0.0014 26.7 2.5 22 16-37 16-37 (329)
84 PF03428 RP-C: Replication pro 25.3 40 0.00087 25.2 1.3 20 7-26 82-101 (177)
85 cd08584 PI-PLCc_GDPD_SF_unchar 25.2 64 0.0014 24.5 2.3 16 16-31 141-156 (192)
86 TIGR01509 HAD-SF-IA-v3 haloaci 25.1 1E+02 0.0022 21.5 3.3 25 9-33 86-110 (183)
87 PF06163 DUF977: Bacterial pro 25.1 31 0.00068 24.6 0.6 21 5-25 35-55 (127)
88 PF07348 Syd: Syd protein (SUK 24.9 34 0.00075 25.7 0.8 36 95-130 138-176 (176)
89 PF11372 DUF3173: Domain of un 24.9 46 0.001 20.6 1.3 21 7-27 13-37 (59)
90 TIGR01607 PST-A Plasmodium sub 24.8 70 0.0015 25.6 2.6 21 14-34 64-84 (332)
91 PTZ00445 p36-lilke protein; Pr 24.7 83 0.0018 24.5 2.9 23 12-34 79-101 (219)
92 PF01011 PQQ: PQQ enzyme repea 24.7 99 0.0021 16.5 2.5 18 96-113 11-28 (38)
93 PF09012 FeoC: FeoC like trans 24.6 30 0.00065 21.3 0.4 26 6-31 24-49 (69)
94 COG3019 Predicted metal-bindin 24.5 89 0.0019 22.9 2.8 25 13-37 39-63 (149)
95 PF12802 MarR_2: MarR family; 24.4 34 0.00074 19.9 0.6 21 6-26 31-51 (62)
96 cd04882 ACT_Bt0572_2 C-termina 24.1 1.4E+02 0.003 17.1 3.3 21 7-27 44-64 (65)
97 PF02082 Rrf2: Transcriptional 23.9 40 0.00086 21.4 0.9 20 6-25 35-54 (83)
98 PF07082 DUF1350: Protein of u 23.9 57 0.0012 25.9 1.9 25 6-30 29-53 (250)
99 PF04273 DUF442: Putative phos 23.8 70 0.0015 21.9 2.1 18 15-32 18-35 (110)
100 PF00201 UDPGT: UDP-glucoronos 23.7 37 0.0008 28.4 0.9 31 3-33 6-36 (500)
101 TIGR02467 CbiE precorrin-6y C5 23.5 96 0.0021 22.9 3.1 27 11-37 150-180 (204)
102 smart00418 HTH_ARSR helix_turn 23.5 53 0.0011 18.5 1.3 22 6-27 20-41 (66)
103 KOG1502|consensus 23.5 1.2E+02 0.0026 25.0 3.8 19 17-35 23-42 (327)
104 PF01726 LexA_DNA_bind: LexA D 23.5 31 0.00068 21.4 0.3 19 7-25 36-55 (65)
105 cd07247 SgaA_N_like N-terminal 23.4 1.5E+02 0.0033 18.7 3.7 25 4-28 63-87 (114)
106 smart00550 Zalpha Z-DNA-bindin 22.8 50 0.0011 20.4 1.2 20 6-25 32-51 (68)
107 COG1378 Predicted transcriptio 22.6 57 0.0012 25.5 1.7 25 5-29 39-63 (247)
108 PF00567 TUDOR: Tudor domain; 22.4 1.7E+02 0.0036 18.7 3.8 32 95-127 8-39 (121)
109 cd07238 Glo_EDI_BRP_like_5 Thi 22.1 1.2E+02 0.0026 19.3 3.0 25 4-28 59-83 (112)
110 PRK08383 putative monovalent c 22.1 1.7E+02 0.0036 21.7 4.0 10 62-71 118-127 (168)
111 TIGR01662 HAD-SF-IIIA HAD-supe 21.9 1.3E+02 0.0028 20.2 3.2 22 10-31 27-48 (132)
112 TIGR00338 serB phosphoserine p 21.9 1.2E+02 0.0027 22.1 3.4 23 9-31 86-108 (219)
113 PF04016 DUF364: Domain of unk 21.9 61 0.0013 23.2 1.6 72 2-81 13-86 (147)
114 PHA02540 61 DNA primase; Provi 21.6 92 0.002 25.7 2.8 28 12-39 271-302 (337)
115 TIGR01681 HAD-SF-IIIC HAD-supe 21.5 78 0.0017 21.7 2.1 24 9-32 30-53 (128)
116 PF01656 CbiA: CobQ/CobB/MinD/ 21.4 90 0.002 22.1 2.5 18 15-32 17-35 (195)
117 PF13477 Glyco_trans_4_2: Glyc 21.4 95 0.0021 20.7 2.5 24 9-32 9-32 (139)
118 PF12695 Abhydrolase_5: Alpha/ 21.4 76 0.0017 21.0 2.0 26 9-34 11-36 (145)
119 cd00851 MTH1175 This uncharact 21.3 63 0.0014 20.8 1.5 33 7-39 46-78 (103)
120 TIGR01656 Histidinol-ppas hist 21.1 1.3E+02 0.0027 20.9 3.1 23 9-31 28-50 (147)
121 PF08040 NADH_oxidored: MNLL s 21.1 32 0.00069 21.3 -0.0 46 7-59 3-50 (59)
122 TIGR02734 crtI_fam phytoene de 21.0 77 0.0017 26.6 2.3 21 17-37 14-34 (502)
123 COG1832 Predicted CoA-binding 20.9 1E+02 0.0022 22.4 2.6 24 9-32 28-51 (140)
124 PF01266 DAO: FAD dependent ox 20.8 92 0.002 23.9 2.6 15 19-33 17-31 (358)
125 PF09981 DUF2218: Uncharacteri 20.7 1E+02 0.0023 20.2 2.4 26 6-31 3-29 (89)
126 COG1341 Predicted GTPase or GT 20.6 79 0.0017 26.8 2.2 20 12-31 88-108 (398)
127 PF00707 IF3_C: Translation in 20.6 88 0.0019 20.3 2.1 18 16-33 24-41 (88)
128 PF05240 APOBEC_C: APOBEC-like 20.5 99 0.0021 18.8 2.1 17 15-31 6-22 (55)
129 PF14574 DUF4445: Domain of un 20.5 1.7E+02 0.0036 24.9 4.2 30 83-112 1-30 (412)
130 cd02040 NifH NifH gene encodes 20.4 93 0.002 23.6 2.5 14 18-31 23-36 (270)
131 PF06863 DUF1254: Protein of u 20.3 1E+02 0.0022 21.4 2.4 20 92-111 24-43 (128)
132 TIGR02253 CTE7 HAD superfamily 20.2 1.4E+02 0.0031 21.7 3.4 25 9-33 95-119 (221)
133 COG0278 Glutaredoxin-related p 20.1 1.5E+02 0.0033 20.4 3.2 33 2-38 26-59 (105)
No 1
>TIGR01070 mutS1 DNA mismatch repair protein MutS.
Probab=100.00 E-value=2.7e-35 Score=260.96 Aligned_cols=113 Identities=24% Similarity=0.398 Sum_probs=101.3
Q ss_pred CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCCC
Q psy13254 2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVD 81 (132)
Q Consensus 2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~~ 81 (132)
++||||||+|+++.|++|||++|||||||||+|+|+.+ .++|+|+|++||||||++++.+ +++.+
T Consensus 56 ~~pm~GvP~ha~~~yl~kLv~~G~kVai~eQ~e~~~~~------------kg~v~Rev~ri~TpGT~~~~~~---l~~~~ 120 (840)
T TIGR01070 56 PIPMAGIPYHAVEAYLEKLVKQGESVAICEQIEDPKTA------------KGPVEREVVQLITPGTVSDEAL---LPERQ 120 (840)
T ss_pred CCCcccCCHHHHHHHHHHHHHCCCEEEEEEecCCchhc------------CCceeeEEEEEECCCccccccc---ccCCC
Confidence 58999999999999999999999999999999998753 2799999999999999998643 67889
Q ss_pred cceEEEEEecCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254 82 NKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR 132 (132)
Q Consensus 82 ~~yllai~~~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~ 132 (132)
+|||+||......||+||+|+|||+|++++|.|+ +.|.++|.+++|+|
T Consensus 121 ~nyl~ai~~~~~~~gla~~D~sTG~~~~~~~~d~---~~l~~~l~~~~P~E 168 (840)
T TIGR01070 121 DNLLAAIAQESNGFGLATLDLTTGEFKVTELADK---ETLYAELQRLNPAE 168 (840)
T ss_pred CceEEEEEeCCCeEEEEEEEccccEEEEEEecCH---HHHHHHHhccCCeE
Confidence 9999999743446999999999999999999875 36999999999986
No 2
>PRK05399 DNA mismatch repair protein MutS; Provisional
Probab=100.00 E-value=5.4e-34 Score=253.20 Aligned_cols=112 Identities=28% Similarity=0.481 Sum_probs=101.3
Q ss_pred CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCCC
Q psy13254 2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVD 81 (132)
Q Consensus 2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~~ 81 (132)
++||||||+|+++.|+++||++|||||||||+|+|+.+ .++|+|+|++||||||++++.+ +++..
T Consensus 63 ~~pm~GvP~h~~~~yl~kLv~~GyKVaI~EQ~e~~~~~------------k~~v~R~v~~i~TpGT~~~~~~---l~~~~ 127 (854)
T PRK05399 63 PIPMAGVPYHAAEGYLAKLVKKGYKVAICEQVEDPATA------------KGPVKREVVRIVTPGTVTDEAL---LDEKQ 127 (854)
T ss_pred CCCEecCcHHHHHHHHHHHHHCCCEEEEEEecCChhhc------------CCccceEEEEEECCCeeecccc---cCCCC
Confidence 57999999999999999999999999999999999754 1799999999999999998644 67889
Q ss_pred cceEEEEEecCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254 82 NKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR 132 (132)
Q Consensus 82 ~~yllai~~~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~ 132 (132)
++||+||......||+||+|+|||+|++++|. +++|+++|.+++|++
T Consensus 128 ~~yl~ai~~~~~~~Gia~~D~stg~~~~~~~~----~~~L~~~l~~~~P~E 174 (854)
T PRK05399 128 NNYLAAIAQDGGGYGLAYLDLSTGEFRVTELD----EEELLAELARLNPAE 174 (854)
T ss_pred CcEEEEEEECCCeEEEEEEECCCCeEEEEEEc----HHHHHHHHHhcCCcE
Confidence 99999998655679999999999999999993 468999999999985
No 3
>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=99.97 E-value=1e-30 Score=231.41 Aligned_cols=112 Identities=29% Similarity=0.505 Sum_probs=101.5
Q ss_pred CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCCC
Q psy13254 2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVD 81 (132)
Q Consensus 2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~~ 81 (132)
++||||||+|+++.|+.+||++|||||||||+|+|+.+ .++|+|+|+||+||||++|+.+ +.+..
T Consensus 56 ~~pm~gvP~h~~~~yl~~li~~g~kVAiceQ~e~~~~~------------k~~v~R~v~rv~TpGt~~d~~~---l~~~~ 120 (843)
T COG0249 56 NIPMAGVPYHALDYYLAKLIELGYKVAICEQLEDPAEA------------KGVVERKVVRVVTPGTLTDEAL---LSDRE 120 (843)
T ss_pred CCcCCCCccccHHHHHHHHHhCCCeEEEEEcccChhhh------------cCcceeEEEEEECCCeeecccc---ccccc
Confidence 37999999999999999999999999999999999875 2699999999999999999755 56779
Q ss_pred cceEEEEEecCC-EEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254 82 NKFLLGVTKEGD-RLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR 132 (132)
Q Consensus 82 ~~yllai~~~~~-~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~ 132 (132)
+|||+||..... .||+||+|+|||+|++.+|. +.+|.+.|.|++|++
T Consensus 121 ~n~l~a~~~~~~~~~gla~~dlstGef~~~~~~----~~~l~~~l~r~~p~E 168 (843)
T COG0249 121 NNYLAALAIDRDGKVGLAFIDLSTGEFFVSEFE----REKLLSELKRLQPKE 168 (843)
T ss_pred cceEEEEEecCCCEEEEEEEEcccCeEEEEEee----HHHHHHHHHhCCCcE
Confidence 999999985444 79999999999999999999 358999999999985
No 4
>KOG0217|consensus
Probab=99.96 E-value=6.9e-31 Score=231.20 Aligned_cols=126 Identities=43% Similarity=0.738 Sum_probs=114.4
Q ss_pred CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCCC
Q psy13254 2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVD 81 (132)
Q Consensus 2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~~ 81 (132)
++||+|||+++++.|+.+|+++|||||+|||+|++..+..|.++.+ +++++|+|||++|+|.||++|+.+ +.+..
T Consensus 297 N~~~~GfPE~sf~~~a~q~iq~GYkvarVEQtEt~l~~e~r~~~~~--~kdkvvrRev~~ilt~GT~td~~l---~~~~~ 371 (1125)
T KOG0217|consen 297 NMPHSGFPEGSFDYWADQFIQKGYKVARVEQTETPLGKEIRERKTG--KKDKVVRREVCRILTNGTLTDIAL---LTSDL 371 (1125)
T ss_pred ccccCCCCccchhhHHHHHHhccceeeeeccccChHHhhhhhcccc--cchhhHHHHHHHHhcCCcchhHHH---hccHH
Confidence 6899999999999999999999999999999999999999988776 457999999999999999998644 45566
Q ss_pred cceEEEEEec-------CCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254 82 NKFLLGVTKE-------GDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR 132 (132)
Q Consensus 82 ~~yllai~~~-------~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~ 132 (132)
+.|||||.+. ...+|+|++|.+||+|++++|+||..++.|.|+|++++|+|
T Consensus 372 akylmai~e~~~~~~~~~~s~gvc~iDtstge~~~~eF~DDr~~s~L~tlLs~~rp~E 429 (1125)
T KOG0217|consen 372 AKYLMAIKESEESYSTGEVSFGVCFIDTSTGEINIGEFCDDRHCSKLDTLLSQVRPVE 429 (1125)
T ss_pred HHHHHHHhhcCCCCCcCceeeeEEEEEcccceEEEEEeecchhhhHHHHHHHcccHHH
Confidence 8899999753 14799999999999999999999999999999999999975
No 5
>KOG0218|consensus
Probab=99.84 E-value=1.5e-21 Score=168.64 Aligned_cols=125 Identities=23% Similarity=0.307 Sum_probs=107.0
Q ss_pred CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeecccc--c--ccc
Q psy13254 2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIM--D--VDA 77 (132)
Q Consensus 2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~--~--~~l 77 (132)
+|+.|.||.++++.|++|||.+|||||||+|+||++.+ +.+.+ +.+++.|.++++||+||+.++.. . ...
T Consensus 212 nFmtaS~P~~Rl~vHleRLv~~g~KVaVVkQtETAAiK-----s~gas-RsslF~RklsavyTKaTl~eds~~~~r~e~~ 285 (1070)
T KOG0218|consen 212 NFMTASFPDVRLNVHLERLVHHGLKVAVVKQTETAAIK-----SHGAS-RSSLFERKLSAVYTKATLGEDSTFVLRGERI 285 (1070)
T ss_pred ceeeccCCcchhhHHHHHHHhcCceEEEEeehhhHHHH-----hcCCc-ccchHHHHHHHHhhhhhhccccccccchhhh
Confidence 58889999999999999999999999999999999875 33333 35899999999999999997642 0 012
Q ss_pred CCCCcceEEEEEec---------CCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254 78 NYVDNKFLLGVTKE---------GDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR 132 (132)
Q Consensus 78 ~~~~~~yllai~~~---------~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~ 132 (132)
-...++||+|+... ...+|+.-+.+|||++-+++|.|+..|++|++.|.+++|.+
T Consensus 286 ~~~~ssfllcv~dn~~ksk~ksg~v~vgligVqlstGevVydeFqdnf~rseLqtrisslqP~E 349 (1070)
T KOG0218|consen 286 LGDTSSFLLCVRDNVHKSKEKSGVVKVGLIGVQLSTGEVVYDEFQDNFARSELQTRISSLQPIE 349 (1070)
T ss_pred cCCcceEEEEEehhhhhhhhhcCceEEEEEEEecCCCcEehHhhhhhHHHHHHHHHHhccCcce
Confidence 34578999999751 25899999999999999999999999999999999999975
No 6
>PF01624 MutS_I: MutS domain I C-terminus.; InterPro: IPR007695 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the N-terminal domain of proteins in the MutS family of DNA mismatch repair proteins, as well as closely related proteins. The N-terminal domain of MutS is responsible for mismatch recognition and forms a 6-stranded mixed beta-sheet surrounded by three alpha-helices, which is similar to the structure of tRNA endonuclease. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 3THY_B 3THZ_B 3THW_B 3THX_B 2WTU_A 1OH7_A ....
Probab=99.82 E-value=2.6e-20 Score=129.63 Aligned_cols=57 Identities=30% Similarity=0.533 Sum_probs=47.2
Q ss_pred eeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeecc
Q psy13254 3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFS 71 (132)
Q Consensus 3 ~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~ 71 (132)
+||||||.++++.|+++|+++||+|+||||.|++... .++++|+|++|+||||++|+
T Consensus 56 ~~~~gfp~~~l~~~l~~Ll~~G~~V~i~~q~~~~~~~------------~~~~~R~v~~i~TpGt~~~~ 112 (113)
T PF01624_consen 56 VPMAGFPKSQLDKYLKKLLEAGYRVAIYEQVETPSET------------KGLIEREVTRIYTPGTLIDD 112 (113)
T ss_dssp EEEEEEEGGGHHHHHHHHHHTT-EEEEEEE-S-HHHH------------SSS--EEEEEEEBTTS-TST
T ss_pred ccEecccHHHHHHHHHHHHHcCCEEEEEEecCCcccc------------CCCccEEEEEEECcCeecCc
Confidence 7999999999999999999999999999999998764 26899999999999999874
No 7
>PF05188 MutS_II: MutS domain II; InterPro: IPR007860 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the connector domain (domain 2) found in proteins of the MutS family. The structure of the MutS connector domain consists of a parallel beta-sheet surrounded by four alpha helices, which is similar to the structure of the Holliday junction resolvase ruvC.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 2WTU_A ....
Probab=99.21 E-value=3.1e-11 Score=84.59 Aligned_cols=47 Identities=34% Similarity=0.693 Sum_probs=42.2
Q ss_pred ceEEEEEe--cCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254 83 KFLLGVTK--EGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR 132 (132)
Q Consensus 83 ~yllai~~--~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~ 132 (132)
|||+||.. ....+|+||+|+|||+|++++|.| +++|.+.|.+++|+|
T Consensus 1 Nyl~aI~~~~~~~~~gla~~D~sTGe~~~~~~~d---~~~L~~~L~~~~P~E 49 (137)
T PF05188_consen 1 NYLAAIYEKNDEDSYGLAYIDLSTGEFYVTEFED---YSELKSELARLSPRE 49 (137)
T ss_dssp -EEEEEEEETCSSEEEEEEEETTTTEEEEEEEEC---HHHHHHHHHHH-ESE
T ss_pred CEEEEEEEecCCCEEEEEEEECCCCEEEEEEeCC---HHHHHHHHHhcCCeE
Confidence 79999998 667899999999999999999998 689999999999986
No 8
>KOG0219|consensus
Probab=86.29 E-value=1.9 Score=39.47 Aligned_cols=105 Identities=21% Similarity=0.259 Sum_probs=69.7
Q ss_pred eeecCcCHHHHHHHHH-HcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccC--CCCc
Q psy13254 6 SGFPEISYGKFAQTLV-EKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDAN--YVDN 82 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv-~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~--~~~~ 82 (132)
+.+--..++..++.|+ ..+|+|-+.+=-|. ..++++| =+||-+.+- ++.+. .+.+
T Consensus 77 v~ls~~~~e~~vr~~l~~~~~~Ve~y~~~~~---------------~w~l~~~-----~sPGN~~~f--edll~~~~~v~ 134 (902)
T KOG0219|consen 77 VSLSKGNFEKVVRELLLVLRYRVEVYSSNQG---------------DWKLTKR-----GSPGNLVQF--EDLLFSNNDVP 134 (902)
T ss_pred EEecHHHHHHHHHHHHHHhccceEEeecCcc---------------ceeEEec-----CCCCcHHHH--HHHHcccccch
Confidence 3444456777777766 47999987762211 1234444 479987642 22121 1111
Q ss_pred ---ceEEEEEe---cCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254 83 ---KFLLGVTK---EGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR 132 (132)
Q Consensus 83 ---~yllai~~---~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~ 132 (132)
-|+...+. +..++|+|++|.+--.+++.+|.|+..++.|+..|.++.|.+
T Consensus 135 is~~~~~v~~~~~~~~~~vgv~~~d~~~~k~~~~ef~Dn~~~snle~~l~~lg~kE 190 (902)
T KOG0219|consen 135 ISIISLIVKHPGVDGQRRVGVAFVDTINVKIGLSEFVDDDSFSNLEALLIQLGPKE 190 (902)
T ss_pred hhhhheeEEeeccCCCceeEEEEechhheeeehhhhcCcHHHHHHHHHHHhcCCeE
Confidence 13333332 246899999999999999999999999999999999999974
No 9
>KOG0220|consensus
Probab=82.11 E-value=2.1 Score=38.80 Aligned_cols=78 Identities=14% Similarity=0.153 Sum_probs=50.9
Q ss_pred CeEEeeeeEEEccceeeccccccccCCCCcceEEEEEec----CCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccC
Q psy13254 53 RVVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKE----GDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHY 128 (132)
Q Consensus 53 ~~v~Rev~~I~TpGT~~~~~~~~~l~~~~~~yllai~~~----~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~ 128 (132)
+..+|...+--+|.-.........+.+....-++|+.+. ...+|+|.+|+-++|+++++|-|+..+.++.+-|.-+
T Consensus 74 ~~~qrs~~~~~a~sl~~sssn~s~~~~~~~~v~~~v~e~r~~~~~~Ig~~~~~~~~~q~~l~~f~dst~y~~v~~~l~i~ 153 (867)
T KOG0220|consen 74 GNPQRSGYKSWAPSLGYSSSNSSAISAHSPSVIVAVVEGRGLARGEIGMASIDLKNPQIILSQFADSTTYAKVITKLKIL 153 (867)
T ss_pred cccchhhhhhccchhhccccchhhhccCCCceEEEEEecCCcccceeEEEEecCCCCceehhhhhccchhHHHHhHhhcc
Confidence 456666665544433221111111233334456666653 3589999999999999999999998888888777666
Q ss_pred CC
Q psy13254 129 PP 130 (132)
Q Consensus 129 ~P 130 (132)
.|
T Consensus 154 s~ 155 (867)
T KOG0220|consen 154 SP 155 (867)
T ss_pred Ch
Confidence 65
No 10
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=75.32 E-value=2.4 Score=28.30 Aligned_cols=25 Identities=32% Similarity=0.675 Sum_probs=20.1
Q ss_pred eeeeecCc---CHHHHHHHHHHcCCeEE
Q psy13254 4 AHSGFPEI---SYGKFAQTLVEKGYKVA 28 (132)
Q Consensus 4 ~maGfP~~---~l~~y~~kLv~~G~kVa 28 (132)
||.|.|++ +++.-.++|.++||.|.
T Consensus 6 PmtG~~~~N~~~f~~~a~~L~~~G~~vv 33 (92)
T PF14359_consen 6 PMTGLPDYNRPAFNAAAKRLRAKGYEVV 33 (92)
T ss_pred CcCCCcchHHHHHHHHHHHHHHCCCEEe
Confidence 89999988 45566778888998775
No 11
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=66.21 E-value=2.6 Score=24.64 Aligned_cols=20 Identities=45% Similarity=0.796 Sum_probs=18.0
Q ss_pred eeecCcCHHHHHHHHHHcCC
Q psy13254 6 SGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~ 25 (132)
+|.|..+...+++.|++.||
T Consensus 28 ~gl~~stv~r~L~tL~~~g~ 47 (52)
T PF09339_consen 28 LGLPKSTVHRLLQTLVEEGY 47 (52)
T ss_dssp HTS-HHHHHHHHHHHHHTTS
T ss_pred HCcCHHHHHHHHHHHHHCcC
Confidence 68999999999999999998
No 12
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=63.55 E-value=3.2 Score=23.67 Aligned_cols=20 Identities=25% Similarity=0.484 Sum_probs=17.4
Q ss_pred eeecCcCHHHHHHHHHHcCC
Q psy13254 6 SGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~ 25 (132)
+|++..++..|+++|.++|+
T Consensus 27 ~~is~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 27 LGISRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp HTS-HHHHHHHHHHHHHTTS
T ss_pred hCCCHHHHHHHHHHHHHCcC
Confidence 68888999999999999997
No 13
>PF08497 Radical_SAM_N: Radical SAM N-terminal; InterPro: IPR013704 This domain tends to occur to the N terminus of PF04055 from PFAM radical SAM domain in hypothetical bacterial proteins. Proteins in this entry are radical SAM proteins, they catalyse diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [, ].
Probab=62.36 E-value=6.7 Score=31.86 Aligned_cols=18 Identities=22% Similarity=0.545 Sum_probs=14.3
Q ss_pred HHHHH-HcCCeEEEEeecc
Q psy13254 17 AQTLV-EKGYKVARVEQTE 34 (132)
Q Consensus 17 ~~kLv-~~G~kVaiveQ~e 34 (132)
+.|++ ++||||+|+-|-.
T Consensus 38 IgR~Le~~GyrVgIiaQPd 56 (302)
T PF08497_consen 38 IGRVLEAHGYRVGIIAQPD 56 (302)
T ss_pred HHHHHHHcCCeEEEEeCCC
Confidence 44555 5899999999986
No 14
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=59.01 E-value=4.6 Score=25.75 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=18.2
Q ss_pred eeeecCcCHHHHHHHHHHcCCe
Q psy13254 5 HSGFPEISYGKFAQTLVEKGYK 26 (132)
Q Consensus 5 maGfP~~~l~~y~~kLv~~G~k 26 (132)
.|+.|..++..|+..|.++|+=
T Consensus 28 ~~~L~~~~~~~yL~~L~~~gLI 49 (77)
T PF14947_consen 28 KANLNYSTLKKYLKELEEKGLI 49 (77)
T ss_dssp TST--HHHHHHHHHHHHHTTSE
T ss_pred HhCcCHHHHHHHHHHHHHCcCe
Confidence 4789999999999999999993
No 15
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=54.84 E-value=51 Score=23.31 Aligned_cols=48 Identities=19% Similarity=0.245 Sum_probs=34.1
Q ss_pred eEEEEEecCCEEEEEEEECCcce-EEEEEEe---ChhhHHHHHHhhccCCCC
Q psy13254 84 FLLGVTKEGDRLGVCFIDTTIGE-FHVGEFE---DDKQFSRLSTLMSHYPPC 131 (132)
Q Consensus 84 yllai~~~~~~~Gi~~~D~sTg~-~~~~~~~---d~~~~~~L~t~l~~~~P~ 131 (132)
.+|||..+..++|+|+.|....- .-+..+. .......|..++.+++|.
T Consensus 2 riL~lD~G~kriGiAvsd~~~~~a~pl~~i~~~~~~~~~~~l~~li~~~~i~ 53 (135)
T PF03652_consen 2 RILGLDYGTKRIGIAVSDPLGIIASPLETIPRRNREKDIEELKKLIEEYQID 53 (135)
T ss_dssp EEEEEEECSSEEEEEEEETTTSSEEEEEEEEECCCCCCHHHHHHHHHHCCEC
T ss_pred eEEEEEeCCCeEEEEEecCCCCeEeeeEEEECCCCchHHHHHHHHHHHhCCC
Confidence 37888778889999999997653 2333333 234577899988887764
No 16
>PF08774 VRR_NUC: VRR-NUC domain; InterPro: IPR014883 This entry contains proteins with the VRR-NUC domain. It is associated with members of the PD-(D/E)XK nuclease superfamily, which include the type III restriction modification enzymes, for example StyLTI: (P40815 from SWISSPROT).; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=54.74 E-value=17 Score=23.94 Aligned_cols=22 Identities=23% Similarity=0.373 Sum_probs=18.5
Q ss_pred CcCHHHHHHHHHHcCCeEEEEe
Q psy13254 10 EISYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 10 ~~~l~~y~~kLv~~G~kVaive 31 (132)
-..-..|++.|.++|+.|+||.
T Consensus 76 s~~Q~~~~~~l~~~G~~v~V~~ 97 (100)
T PF08774_consen 76 SPNQKEWIDKLREAGFRVAVCR 97 (100)
T ss_pred CHHHHHHHHHHHHCCCEEEEEE
Confidence 3445689999999999999996
No 17
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=53.09 E-value=6.4 Score=24.09 Aligned_cols=21 Identities=24% Similarity=0.303 Sum_probs=19.2
Q ss_pred eeeecCcCHHHHHHHHHHcCC
Q psy13254 5 HSGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 5 maGfP~~~l~~y~~kLv~~G~ 25 (132)
.+|+|..++...+++|.++|+
T Consensus 31 ~l~i~~~~v~~~L~~L~~~Gl 51 (68)
T PF01978_consen 31 ELGISRSTVYRALKSLEEKGL 51 (68)
T ss_dssp HHTSSHHHHHHHHHHHHHTTS
T ss_pred HHCcCHHHHHHHHHHHHHCCC
Confidence 368999999999999999997
No 18
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=52.04 E-value=6.5 Score=23.64 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=17.8
Q ss_pred eeecCcCHHHHHHHHHHcCC
Q psy13254 6 SGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~ 25 (132)
.|+|..++..|+++|.++|+
T Consensus 34 l~~~~~t~s~hL~~L~~aGl 53 (61)
T PF12840_consen 34 LGISQSTVSYHLKKLEEAGL 53 (61)
T ss_dssp HTS-HHHHHHHHHHHHHTTS
T ss_pred HCCCHHHHHHHHHHHHHCCC
Confidence 58899999999999999998
No 19
>TIGR03604 docking_ocin bacteriocin biosynthesis docking scaffold, SagD family. prokaryotic systems for making a general class of heterocycle-containing bacteriocins.
Probab=52.02 E-value=23 Score=29.09 Aligned_cols=44 Identities=11% Similarity=0.116 Sum_probs=32.8
Q ss_pred cCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceee
Q psy13254 11 ISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQT 69 (132)
Q Consensus 11 ~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~ 69 (132)
..+...+++|-.+|+.|.+||++- ++... .-=-|++++-||...
T Consensus 295 ~~l~~l~~~L~~~G~~v~~vDlT~-pdi~~--------------~gl~vVrvivPgl~~ 338 (377)
T TIGR03604 295 DDLKELLDRLKAAGLEAIVVDITP-PDIRA--------------AGLYVVRVIIPGLLP 338 (377)
T ss_pred hhHHHHHHHHHhcCCcEEEEeCCC-HhHHh--------------cCCeEEEEecCCccc
Confidence 456788899999999999999964 43320 123589999999775
No 20
>COG5561 Predicted metal-binding protein [Function unknown]
Probab=49.31 E-value=20 Score=24.33 Aligned_cols=23 Identities=30% Similarity=0.306 Sum_probs=20.2
Q ss_pred eecCcCHHHHHHHHHH-cCCeEEE
Q psy13254 7 GFPEISYGKFAQTLVE-KGYKVAR 29 (132)
Q Consensus 7 GfP~~~l~~y~~kLv~-~G~kVai 29 (132)
+.|+-++|.|++++++ .|-+|+.
T Consensus 72 kCpy~~~eei~Kk~ie~~~i~Vv~ 95 (101)
T COG5561 72 KCPYASAEEIAKKEIEKMGIKVVM 95 (101)
T ss_pred CCCccCHHHHHHHHHHHhCCcEEe
Confidence 6799999999999998 6999874
No 21
>PF02624 YcaO: YcaO-like family; InterPro: IPR003776 This domain comprises the whole of a protein in Methanocaldococcus jannaschii (Methanococcus jannaschii) and Methanobacterium thermoautotrophicum, all but the N-terminal 60 residues from a protein of Mycobacterium tuberculosis, and all but the C-terminal 180 residues from a protein in Haemophilus influenzae and Escherichia coli, among proteins from published complete genomes.
Probab=46.01 E-value=29 Score=27.36 Aligned_cols=40 Identities=20% Similarity=0.263 Sum_probs=30.9
Q ss_pred CcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccce
Q psy13254 10 EISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGA 67 (132)
Q Consensus 10 ~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT 67 (132)
...+...+++|-++|+.|.++|.+ ... .-=.|++|+-||.
T Consensus 291 ~~~l~~l~~~l~~~g~~v~~~d~t--~~~----------------~g~~vvkvivPgl 330 (332)
T PF02624_consen 291 EEDLRSLLDRLKKAGIDVYVVDLT--VRE----------------LGLPVVKVIVPGL 330 (332)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEee--ccc----------------cCeEEEEEECCCc
Confidence 456777888899999999999998 111 2246899999985
No 22
>KOG0839|consensus
Probab=44.97 E-value=16 Score=35.01 Aligned_cols=37 Identities=19% Similarity=0.254 Sum_probs=33.5
Q ss_pred eeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhh
Q psy13254 3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQM 39 (132)
Q Consensus 3 ~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~ 39 (132)
+||.+||..++-.|+++.-..||+|.=+||+-..-..
T Consensus 1379 ~pieeVk~~~L~~fLq~kK~EGyTiIglEQTakSV~L 1415 (1477)
T KOG0839|consen 1379 MPIEEVKLDELASFLQEKKKEGYTIIGLEQTAKSVKL 1415 (1477)
T ss_pred cchhccChHHHHHHHHHhhhcCcEEEeehhccccccc
Confidence 7999999999999999999999999999998765443
No 23
>PF13730 HTH_36: Helix-turn-helix domain
Probab=44.76 E-value=9.7 Score=22.12 Aligned_cols=20 Identities=25% Similarity=0.316 Sum_probs=17.2
Q ss_pred eeecCcCHHHHHHHHHHcCC
Q psy13254 6 SGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~ 25 (132)
+|+=..++..+++.|+++||
T Consensus 35 ~g~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 35 LGVSRRTVQRAIKELEEKGL 54 (55)
T ss_pred HCcCHHHHHHHHHHHHHCcC
Confidence 56667889999999999997
No 24
>cd07233 Glyoxalase_I Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione. Glyoxalase I (also known as lactoylglutathione lyase; EC 4.4.1.5) is part of the glyoxalase system, a two-step system for detoxifying methylglyoxal, a side product of glycolysis. This system is responsible for the conversion of reactive, acyclic alpha-oxoaldehydes into the corresponding alpha-hydroxyacids and involves 2 enzymes, glyoxalase I and II. Glyoxalase I catalyses an intramolecular redox reaction of the hemithioacetal (formed from methylglyoxal and glutathione) to form the thioester, S-D-lactoylglutathione. This reaction involves the transfer of two hydrogen atoms from C1 to C2 of the methylglyoxal, and proceeds via an ene-diol intermediate. Glyoxalase I has a requirement for bound metal ions for catalysis. Eukaryotic glyoxalase I prefers the divalent cation zinc as cofactor, whereas Escherichia coil and other prokaryotic gly
Probab=44.68 E-value=40 Score=21.72 Aligned_cols=26 Identities=23% Similarity=0.275 Sum_probs=20.9
Q ss_pred eeeeeecCcCHHHHHHHHHHcCCeEE
Q psy13254 3 YAHSGFPEISYGKFAQTLVEKGYKVA 28 (132)
Q Consensus 3 ~~maGfP~~~l~~y~~kLv~~G~kVa 28 (132)
..+.+|-...++...++|.++|.++.
T Consensus 71 ~~~i~~~v~did~~~~~l~~~G~~~~ 96 (121)
T cd07233 71 FGHLAFAVDDVYAACERLEEMGVEVT 96 (121)
T ss_pred eEEEEEEeCCHHHHHHHHHHCCCEEe
Confidence 34667777788999999999999885
No 25
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=43.68 E-value=12 Score=21.26 Aligned_cols=20 Identities=20% Similarity=0.340 Sum_probs=17.0
Q ss_pred eeecCcCHHHHHHHHHHcCC
Q psy13254 6 SGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~ 25 (132)
.|++..++..|+++|.+.|+
T Consensus 25 l~~s~~~vs~hL~~L~~~gl 44 (47)
T PF01022_consen 25 LGLSQSTVSHHLKKLREAGL 44 (47)
T ss_dssp HTS-HHHHHHHHHHHHHTTS
T ss_pred ccccchHHHHHHHHHHHCcC
Confidence 57788899999999999996
No 26
>COG0223 Fmt Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]
Probab=42.84 E-value=12 Score=30.48 Aligned_cols=78 Identities=18% Similarity=0.171 Sum_probs=47.8
Q ss_pred eeeeecCcCHHHHHHHHHHcCCeE-EEEeeccChhhhhhhhccCCCCCCCCeEEeeeeE----EEccceeeccccccccC
Q psy13254 4 AHSGFPEISYGKFAQTLVEKGYKV-ARVEQTESAEQMDIRTKRDKVPQKQRVVRREICK----ITCRGAQTFSIMDVDAN 78 (132)
Q Consensus 4 ~maGfP~~~l~~y~~kLv~~G~kV-aiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~----I~TpGT~~~~~~~~~l~ 78 (132)
-.+|-|+.+. .-++.|+++||.| +|+-|.+.+... +++.. ...|++.--+ ||+|..+.++.+...+.
T Consensus 5 vF~GTp~fa~-~~L~~L~~~~~eivaV~Tqpdkp~gR---~~~l~----~spVk~~A~~~~ipv~qP~~l~~~e~~~~l~ 76 (307)
T COG0223 5 VFFGTPEFAV-PSLEALIEAGHEIVAVVTQPDKPAGR---GKKLT----PSPVKRLALELGIPVFQPEKLNDPEFLEELA 76 (307)
T ss_pred EEEcCchhhH-HHHHHHHhCCCceEEEEeCCCCccCC---CCcCC----CChHHHHHHHcCCceeccccCCcHHHHHHHh
Confidence 4567777765 4589999999998 788988776542 22211 2345555554 89998888653322333
Q ss_pred CCCcceEEEEE
Q psy13254 79 YVDNKFLLGVT 89 (132)
Q Consensus 79 ~~~~~yllai~ 89 (132)
.-....++++.
T Consensus 77 ~l~~D~ivvva 87 (307)
T COG0223 77 ALDPDLIVVVA 87 (307)
T ss_pred ccCCCEEEEEe
Confidence 33444455443
No 27
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=41.19 E-value=12 Score=20.67 Aligned_cols=22 Identities=14% Similarity=0.196 Sum_probs=18.5
Q ss_pred eeeecCcCHHHHHHHHHHcCCe
Q psy13254 5 HSGFPEISYGKFAQTLVEKGYK 26 (132)
Q Consensus 5 maGfP~~~l~~y~~kLv~~G~k 26 (132)
+.|++..++..++++|.+.|+=
T Consensus 17 ~l~~s~~tv~~~l~~L~~~g~l 38 (48)
T smart00419 17 LLGLTRETVSRTLKRLEKEGLI 38 (48)
T ss_pred HHCCCHHHHHHHHHHHHHCCCE
Confidence 4678888899999999998874
No 28
>PRK01254 hypothetical protein; Provisional
Probab=41.13 E-value=22 Score=32.25 Aligned_cols=18 Identities=17% Similarity=0.530 Sum_probs=14.3
Q ss_pred HHHHH-HcCCeEEEEeecc
Q psy13254 17 AQTLV-EKGYKVARVEQTE 34 (132)
Q Consensus 17 ~~kLv-~~G~kVaiveQ~e 34 (132)
+.|++ .+||||+|+-|-.
T Consensus 61 igR~Le~~G~rVgIiaQPd 79 (707)
T PRK01254 61 IGRMLEAQGFRVGIIAQPD 79 (707)
T ss_pred HHHHHHHcCCeEEEEeCCC
Confidence 45555 4899999999985
No 29
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=40.69 E-value=93 Score=22.03 Aligned_cols=48 Identities=23% Similarity=0.441 Sum_probs=30.6
Q ss_pred eEEEEEecCCEEEEEEEECCcceEE-EEEE--eC-hhhHHHHHHhhccCCCC
Q psy13254 84 FLLGVTKEGDRLGVCFIDTTIGEFH-VGEF--ED-DKQFSRLSTLMSHYPPC 131 (132)
Q Consensus 84 yllai~~~~~~~Gi~~~D~sTg~~~-~~~~--~d-~~~~~~L~t~l~~~~P~ 131 (132)
-++||..+..++|+|+.|....--. +..+ .+ ......|..++...+|.
T Consensus 5 ~iLalD~G~kriGvAv~d~~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~i~ 56 (138)
T PRK00109 5 RILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPD 56 (138)
T ss_pred cEEEEEeCCCEEEEEEecCCCCEEcCEEEEEcCCCchHHHHHHHHHHHhCCC
Confidence 3889987888999999997432211 1111 22 22356788888877764
No 30
>PF09456 RcsC: RcsC Alpha-Beta-Loop (ABL); InterPro: IPR019017 This domain is found in the C terminus of the signal transduction response regulator (phospho-relay) kinase RcsC, between the ATP-binding region (IPR003594 from INTERPRO) and the receiver region (IPR001789 from INTERPRO). This domain forms a discrete alpha/beta/loop structure []. The Rcs signalling pathway controls a variety of physiological functions like capsule synthesis, cell division or motility in prokaryotes. The Rcs regulation cascade, involving a multi-step phosphorelay between the two membrane-bound hybrid sensor kinases RcsC and RcsD and the global regulator RcsB, is, up to now, one of the most complicated regulatory systems in bacteria []. ; GO: 0004673 protein histidine kinase activity, 0004871 signal transducer activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent, 0018106 peptidyl-histidine phosphorylation, 0005886 plasma membrane, 0016021 integral to membrane; PDB: 2AYY_A 2AYX_A.
Probab=40.68 E-value=19 Score=24.26 Aligned_cols=22 Identities=27% Similarity=0.517 Sum_probs=18.2
Q ss_pred CcCHHHHHHHHHH-cCCeEEEEe
Q psy13254 10 EISYGKFAQTLVE-KGYKVARVE 31 (132)
Q Consensus 10 ~~~l~~y~~kLv~-~G~kVaive 31 (132)
..+|+.|+.+|+. +|..|..++
T Consensus 8 Na~Le~yL~~lL~~~G~~v~~y~ 30 (92)
T PF09456_consen 8 NAYLESYLQRLLSYHGFQVQRYE 30 (92)
T ss_dssp -HHHHHHHHHHHCTTTEEEEE-S
T ss_pred hHHHHHHHHHHHHHCCcEEEEec
Confidence 4578999999997 799999998
No 31
>COG2044 Predicted peroxiredoxins [General function prediction only]
Probab=40.13 E-value=44 Score=23.60 Aligned_cols=26 Identities=19% Similarity=0.179 Sum_probs=23.1
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEeecc
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVEQTE 34 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaiveQ~e 34 (132)
|...+..+++..+++|-|.-+|||--
T Consensus 60 ~~~~l~~~~~~a~e~GVk~yvCe~s~ 85 (120)
T COG2044 60 NFPPLEELIKQAIEAGVKIYVCEQSL 85 (120)
T ss_pred CCCCHHHHHHHHHHcCCEEEEEcchh
Confidence 44789999999999999999999853
No 32
>PF13450 NAD_binding_8: NAD(P)-binding Rossmann-like domain; PDB: 3KA7_A 1V0J_D 3INR_B 3KYB_B 3GF4_A 2BI8_A 3INT_B 1WAM_A 2BI7_A 3MJ4_G ....
Probab=39.80 E-value=36 Score=20.88 Aligned_cols=21 Identities=29% Similarity=0.461 Sum_probs=16.3
Q ss_pred HHHHHHcCCeEEEEeeccChh
Q psy13254 17 AQTLVEKGYKVARVEQTESAE 37 (132)
Q Consensus 17 ~~kLv~~G~kVaiveQ~e~~~ 37 (132)
+..|-++|++|.|.|+-..+-
T Consensus 12 A~~L~~~g~~v~v~E~~~~~G 32 (68)
T PF13450_consen 12 AYYLAKAGYRVTVFEKNDRLG 32 (68)
T ss_dssp HHHHHHTTSEEEEEESSSSSS
T ss_pred HHHHHHCCCcEEEEecCcccC
Confidence 446667899999999877653
No 33
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=39.28 E-value=17 Score=23.05 Aligned_cols=22 Identities=27% Similarity=0.391 Sum_probs=19.9
Q ss_pred eeecCcCHHHHHHHHHHcCCeE
Q psy13254 6 SGFPEISYGKFAQTLVEKGYKV 27 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~kV 27 (132)
.|+|..++..++..|.+.||=.
T Consensus 30 l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 30 LGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred hCCCHHHHHHHHHHHHHCCCee
Confidence 5899999999999999999864
No 34
>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]
Probab=38.53 E-value=36 Score=25.05 Aligned_cols=20 Identities=35% Similarity=0.649 Sum_probs=16.2
Q ss_pred HHHHHHHHHHcCCeEEEEee
Q psy13254 13 YGKFAQTLVEKGYKVARVEQ 32 (132)
Q Consensus 13 l~~y~~kLv~~G~kVaiveQ 32 (132)
++.-+++|-+.||||+++.=
T Consensus 19 ie~lv~~L~~~G~rVa~iKH 38 (161)
T COG1763 19 IEKLVRKLKARGYRVATVKH 38 (161)
T ss_pred HHHHHHHHHhCCcEEEEEEe
Confidence 45667888889999999963
No 35
>cd01427 HAD_like Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
Probab=38.27 E-value=48 Score=21.32 Aligned_cols=25 Identities=24% Similarity=0.092 Sum_probs=20.7
Q ss_pred ecCcCHHHHHHHHHHcCCeEEEEee
Q psy13254 8 FPEISYGKFAQTLVEKGYKVARVEQ 32 (132)
Q Consensus 8 fP~~~l~~y~~kLv~~G~kVaiveQ 32 (132)
-|...+...+++|-++|++++||--
T Consensus 24 ~~~~~~~~~l~~l~~~g~~i~ivS~ 48 (139)
T cd01427 24 ELYPGVKEALKELKEKGIKLALATN 48 (139)
T ss_pred CcCcCHHHHHHHHHHCCCeEEEEeC
Confidence 3556678899999999999999963
No 36
>PF12681 Glyoxalase_2: Glyoxalase-like domain; PDB: 3G12_B 1JIF_B 1JIE_B 1QTO_A 3OXH_A 2PJS_A 2RBB_A 3SK1_B 3SK2_B 3RRI_A ....
Probab=37.80 E-value=48 Score=20.88 Aligned_cols=26 Identities=19% Similarity=0.137 Sum_probs=22.3
Q ss_pred eeeeeecCcCHHHHHHHHHHcCCeEE
Q psy13254 3 YAHSGFPEISYGKFAQTLVEKGYKVA 28 (132)
Q Consensus 3 ~~maGfP~~~l~~y~~kLv~~G~kVa 28 (132)
..+..|....++...++|.++|.++.
T Consensus 57 ~~~~~~~v~dv~~~~~~l~~~G~~~~ 82 (108)
T PF12681_consen 57 GFHLCFEVEDVDALYERLKELGAEIV 82 (108)
T ss_dssp EEEEEEEESHHHHHHHHHHHTTSEEE
T ss_pred eeEEEEEEcCHHHHHHHHHHCCCeEe
Confidence 56778888999999999999998873
No 37
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=37.10 E-value=17 Score=23.33 Aligned_cols=23 Identities=30% Similarity=0.446 Sum_probs=18.1
Q ss_pred eeecCcCHHHHHHHHHHcCCeEEE
Q psy13254 6 SGFPEISYGKFAQTLVEKGYKVAR 29 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~kVai 29 (132)
.|++..++..++++|.++|| |-+
T Consensus 24 l~lt~g~Ls~hL~~Le~~Gy-V~~ 46 (80)
T PF13601_consen 24 LGLTDGNLSKHLKKLEEAGY-VEV 46 (80)
T ss_dssp TT--HHHHHHHHHHHHHTTS-EEE
T ss_pred hCcCHHHHHHHHHHHHHCCC-EEE
Confidence 57788899999999999999 444
No 38
>PRK04968 SecY interacting protein Syd; Provisional
Probab=36.50 E-value=51 Score=24.91 Aligned_cols=38 Identities=13% Similarity=0.128 Sum_probs=29.6
Q ss_pred EEEEEEEECCcceEEEEEEeCh---hhHHHHHHhhccCCCC
Q psy13254 94 RLGVCFIDTTIGEFHVGEFEDD---KQFSRLSTLMSHYPPC 131 (132)
Q Consensus 94 ~~Gi~~~D~sTg~~~~~~~~d~---~~~~~L~t~l~~~~P~ 131 (132)
..-+..+|..||++.+-.+... ..-..|...|.++.|+
T Consensus 138 e~~~isv~N~sGeV~lE~~G~~~r~vLA~sL~eFL~~L~P~ 178 (181)
T PRK04968 138 EDEVISVCNLSGEVILETLGTRKRTVLAPSLAEFLNQLEPL 178 (181)
T ss_pred CCeEEEEECCCCeEEEEeCCCCcceehhhCHHHHHHhCCcc
Confidence 3557789999999999988743 2345788999999985
No 39
>cd07254 Glo_EDI_BRP_like_20 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and types I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=36.16 E-value=57 Score=21.19 Aligned_cols=26 Identities=15% Similarity=0.057 Sum_probs=20.6
Q ss_pred eeeeeecCcC---HHHHHHHHHHcCCeEE
Q psy13254 3 YAHSGFPEIS---YGKFAQTLVEKGYKVA 28 (132)
Q Consensus 3 ~~maGfP~~~---l~~y~~kLv~~G~kVa 28 (132)
..|.+|.... ++.+.++|.++|+++.
T Consensus 59 ~~h~~f~v~~~~dl~~~~~~l~~~G~~~~ 87 (120)
T cd07254 59 LNHLGVQVDSAEEVAEAKARAEAAGLPTF 87 (120)
T ss_pred eeEEEEEeCCHHHHHHHHHHHHHcCCeEE
Confidence 4467777776 7889999999998874
No 40
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=34.38 E-value=28 Score=20.33 Aligned_cols=23 Identities=17% Similarity=0.291 Sum_probs=19.3
Q ss_pred eeecCcCHHHHHHHHHHcCCeEE
Q psy13254 6 SGFPEISYGKFAQTLVEKGYKVA 28 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~kVa 28 (132)
.|+|..++..++++|.+.|+=..
T Consensus 30 ~~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 30 LGLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred HCcCHhHHHHHHHHHHHCCCeEE
Confidence 47899999999999999986543
No 41
>TIGR03309 matur_yqeB selenium-dependent molybdenum hydroxylase system protein, YqeB family. Members of this protein family are probable accessory proteins for the biosynthesis of enzymes with labile selenium-containing centers, different from selenocysteine-containing proteins.
Probab=34.04 E-value=51 Score=26.25 Aligned_cols=18 Identities=33% Similarity=0.462 Sum_probs=14.9
Q ss_pred HHHHHHHcCCeEEEEeec
Q psy13254 16 FAQTLVEKGYKVARVEQT 33 (132)
Q Consensus 16 y~~kLv~~G~kVaiveQ~ 33 (132)
-+.+|-++||+|++.|.-
T Consensus 13 va~~L~~aGf~Vv~~e~~ 30 (256)
T TIGR03309 13 VAHRLHRSGFKVLMTETE 30 (256)
T ss_pred HHHHHHhCCCEEEEccCC
Confidence 467899999999998853
No 42
>cd03413 CbiK_C Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases, and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=33.76 E-value=52 Score=22.10 Aligned_cols=24 Identities=21% Similarity=0.169 Sum_probs=18.5
Q ss_pred ecCcCHHHHHHHHHHcCCeEEEEe
Q psy13254 8 FPEISYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 8 fP~~~l~~y~~kLv~~G~kVaive 31 (132)
+|...-+.|-.+|-++||+|..+.
T Consensus 76 ipge~~~SW~~~l~~~g~~v~~~~ 99 (103)
T cd03413 76 MAGDEPDSWKSILEAAGIKVETVL 99 (103)
T ss_pred CCCCCchhHHHHHHHCCCeeEEEe
Confidence 355566789999999999987654
No 43
>PF08645 PNK3P: Polynucleotide kinase 3 phosphatase; InterPro: IPR013954 Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin []. ; PDB: 2FPW_A 2FPR_A 2FPX_A 2FPS_A 2FPU_B 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B 3U7G_A ....
Probab=33.73 E-value=47 Score=23.99 Aligned_cols=21 Identities=33% Similarity=0.455 Sum_probs=17.1
Q ss_pred CHHHHHHHHHHcCCeEEEE-ee
Q psy13254 12 SYGKFAQTLVEKGYKVARV-EQ 32 (132)
Q Consensus 12 ~l~~y~~kLv~~G~kVaiv-eQ 32 (132)
.+-..|++|.++||+++|+ .|
T Consensus 33 ~v~~~L~~l~~~Gy~IvIvTNQ 54 (159)
T PF08645_consen 33 GVPEALRELHKKGYKIVIVTNQ 54 (159)
T ss_dssp THHHHHHHHHHTTEEEEEEEE-
T ss_pred hHHHHHHHHHhcCCeEEEEeCc
Confidence 3667889999999999999 45
No 44
>cd00529 RuvC_resolvase Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes only the bacterial and mitochondrial HJR's. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the E.coli HJR. RuvC and its orthologs are homodimers and are structurely similar to RNase H and Hsp70.
Probab=33.59 E-value=1.3e+02 Score=21.50 Aligned_cols=47 Identities=13% Similarity=0.280 Sum_probs=30.1
Q ss_pred EEEEEecCCEEEEEEEECCcceEEEEE---EeCh----------hhHHHHHHhhccCCCC
Q psy13254 85 LLGVTKEGDRLGVCFIDTTIGEFHVGE---FEDD----------KQFSRLSTLMSHYPPC 131 (132)
Q Consensus 85 llai~~~~~~~Gi~~~D~sTg~~~~~~---~~d~----------~~~~~L~t~l~~~~P~ 131 (132)
+++|..+-..+|++++|...+.+.+.. +..+ ..+++|..+|..++|.
T Consensus 2 ILGIDPGl~~~G~av~~~~~~~~~~~~~g~i~t~~~~~~~~rl~~I~~~l~~~i~~~~Pd 61 (154)
T cd00529 2 ILGIDPGSRNTGYGVIEQEGRKLIYLASGVIRTSSDAPLPSRLKTIYDGLNEVIDQFQPD 61 (154)
T ss_pred EEEEccCcCceEEEEEEeeCCeEEEEEeeEEECCCCCCHHHHHHHHHHHHHHHHHHhCCC
Confidence 456655545789999988777764432 2211 2356788888888774
No 45
>PF12646 DUF3783: Domain of unknown function (DUF3783); InterPro: IPR016621 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=33.29 E-value=28 Score=20.99 Aligned_cols=25 Identities=28% Similarity=0.446 Sum_probs=20.7
Q ss_pred eeeeeecCcCHHHHHHHHHHcCCeE
Q psy13254 3 YAHSGFPEISYGKFAQTLVEKGYKV 27 (132)
Q Consensus 3 ~~maGfP~~~l~~y~~kLv~~G~kV 27 (132)
+-|+||+...++..+..+=++|.++
T Consensus 4 ll~~g~~~~el~~~l~~~r~~~~~~ 28 (58)
T PF12646_consen 4 LLFSGFSGEELDKFLDALRKAGIPI 28 (58)
T ss_pred EEECCCCHHHHHHHHHHHHHcCCCc
Confidence 3579999999999999888887755
No 46
>PRK14489 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional
Probab=33.28 E-value=1e+02 Score=25.26 Aligned_cols=29 Identities=14% Similarity=0.483 Sum_probs=20.3
Q ss_pred eeeeecCcCHHHHHHHHH----HcCCeEEEEee
Q psy13254 4 AHSGFPEISYGKFAQTLV----EKGYKVARVEQ 32 (132)
Q Consensus 4 ~maGfP~~~l~~y~~kLv----~~G~kVaiveQ 32 (132)
..+|.|-.---..+.+|+ +.||+|+++..
T Consensus 209 ~~~g~~~~GKtt~~~~l~~~l~~~g~~v~~iKh 241 (366)
T PRK14489 209 GVVGYSGTGKTTLLEKLIPELIARGYRIGLIKH 241 (366)
T ss_pred EEecCCCCCHHHHHHHHHHHHHHcCCEEEEEEE
Confidence 346777766555555555 57999999983
No 47
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=33.20 E-value=19 Score=20.98 Aligned_cols=21 Identities=14% Similarity=0.218 Sum_probs=18.9
Q ss_pred eeeecCcCHHHHHHHHHHcCC
Q psy13254 5 HSGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 5 maGfP~~~l~~y~~kLv~~G~ 25 (132)
+.|++..++...+++|.+.|+
T Consensus 34 ~~~is~~~v~~~l~~L~~~G~ 54 (66)
T cd07377 34 ELGVSRTTVREALRELEAEGL 54 (66)
T ss_pred HHCCCHHHHHHHHHHHHHCCC
Confidence 468888999999999999998
No 48
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=33.15 E-value=1.1e+02 Score=21.94 Aligned_cols=47 Identities=19% Similarity=0.438 Sum_probs=28.9
Q ss_pred EEEEEecCCEEEEEEEECCcceEEEEEEe-----Ch--------hhHHHHHHhhccCCCC
Q psy13254 85 LLGVTKEGDRLGVCFIDTTIGEFHVGEFE-----DD--------KQFSRLSTLMSHYPPC 131 (132)
Q Consensus 85 llai~~~~~~~Gi~~~D~sTg~~~~~~~~-----d~--------~~~~~L~t~l~~~~P~ 131 (132)
+|+|..+-...|.+++|...+++.+..+. .+ ..+++|..+|..++|.
T Consensus 1 ILGIDPgl~~tG~avi~~~~~~~~~i~~G~I~t~~~~~~~~Rl~~I~~~l~~li~~~~P~ 60 (149)
T PF02075_consen 1 ILGIDPGLSNTGYAVIEEDGGKLRLIDYGTIKTSSKDSLPERLKEIYEELEELIEEYNPD 60 (149)
T ss_dssp EEEEE--SSEEEEEEEEEETTEEEEEEEEEEE---S--HHHHHHHHHHHHHHHHHHH--S
T ss_pred CEEECCCCCCeeEEEEEeeCCEEEEEEeCeEECCCCCCHHHHHHHHHHHHHHHHHhhCCC
Confidence 45665555678999999988787655442 11 1256788888888885
No 49
>TIGR00620 sporelyase spore photoproduct lyase. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.02 E-value=38 Score=25.92 Aligned_cols=15 Identities=20% Similarity=0.388 Sum_probs=13.0
Q ss_pred HHHHHHHcCCeEEEE
Q psy13254 16 FAQTLVEKGYKVARV 30 (132)
Q Consensus 16 y~~kLv~~G~kVaiv 30 (132)
-+++++++||+|++|
T Consensus 76 Aa~k~a~aGy~Vg~~ 90 (199)
T TIGR00620 76 AAVKVAKAGYPLGFI 90 (199)
T ss_pred HHHHHHHcCCeEEEE
Confidence 468899999999887
No 50
>PF08820 DUF1803: Domain of unknown function (DUF1803); InterPro: IPR014924 This small protein is found in one or two copies in bacteria. The function of this is unknown.
Probab=32.21 E-value=35 Score=23.00 Aligned_cols=19 Identities=32% Similarity=0.684 Sum_probs=16.4
Q ss_pred ec-CcCHHHHHHHHHHcCCe
Q psy13254 8 FP-EISYGKFAQTLVEKGYK 26 (132)
Q Consensus 8 fP-~~~l~~y~~kLv~~G~k 26 (132)
|| ..++|.++..||.+||=
T Consensus 38 f~~qk~~D~fie~li~~GYI 57 (93)
T PF08820_consen 38 FPKQKRLDIFIEALIKLGYI 57 (93)
T ss_pred hccccchhHHHHHHHHcCCe
Confidence 56 78899999999999993
No 51
>TIGR01261 hisB_Nterm histidinol-phosphatase. This model describes histidinol phosphatase. All known examples in the scope of this model are bifunctional proteins with a histidinol phosphatase domain followed by an imidazoleglycerol-phosphate dehydratase domain. These enzymatic domains catalyze the ninth and seventh steps, respectively, of histidine biosynthesis.
Probab=31.88 E-value=60 Score=23.42 Aligned_cols=23 Identities=26% Similarity=0.138 Sum_probs=18.8
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEe
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaive 31 (132)
|.......+++|-++||+++|+-
T Consensus 30 ~~pgv~e~L~~L~~~g~~l~IvS 52 (161)
T TIGR01261 30 FEKGVIPALLKLKKAGYKFVMVT 52 (161)
T ss_pred ECCCHHHHHHHHHHCCCeEEEEe
Confidence 44556778999999999999985
No 52
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=31.64 E-value=21 Score=21.08 Aligned_cols=22 Identities=18% Similarity=0.229 Sum_probs=18.0
Q ss_pred eeeecCcCHHHHHHHHHHcCCe
Q psy13254 5 HSGFPEISYGKFAQTLVEKGYK 26 (132)
Q Consensus 5 maGfP~~~l~~y~~kLv~~G~k 26 (132)
+.|++..++..++++|.+.|+=
T Consensus 34 ~~g~s~~tv~r~l~~L~~~g~i 55 (67)
T cd00092 34 YLGLTRETVSRTLKELEEEGLI 55 (67)
T ss_pred HHCCCHHHHHHHHHHHHHCCCE
Confidence 4678888889999999998873
No 53
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=31.42 E-value=1.1e+02 Score=21.43 Aligned_cols=44 Identities=20% Similarity=0.369 Sum_probs=27.3
Q ss_pred EEEecCCEEEEEEEECCcceEE--EEEEe---ChhhHHHHHHhhccCCCC
Q psy13254 87 GVTKEGDRLGVCFIDTTIGEFH--VGEFE---DDKQFSRLSTLMSHYPPC 131 (132)
Q Consensus 87 ai~~~~~~~Gi~~~D~sTg~~~--~~~~~---d~~~~~~L~t~l~~~~P~ 131 (132)
||..+..++|+|..|. +|.+. +..+. .......|..++.+++|.
T Consensus 2 aiD~G~kriGvA~~d~-~~~~a~pl~~i~~~~~~~~~~~l~~~i~~~~~~ 50 (130)
T TIGR00250 2 GLDFGTKSIGVAGQDI-TGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPD 50 (130)
T ss_pred eEccCCCeEEEEEECC-CCCEEeceEEEEecCCcHHHHHHHHHHHHcCCC
Confidence 5555567899999988 33332 11221 223367788888888774
No 54
>COG1233 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=31.36 E-value=44 Score=28.44 Aligned_cols=21 Identities=29% Similarity=0.414 Sum_probs=16.8
Q ss_pred HHHHHHcCCeEEEEeeccChh
Q psy13254 17 AQTLVEKGYKVARVEQTESAE 37 (132)
Q Consensus 17 ~~kLv~~G~kVaiveQ~e~~~ 37 (132)
+..|-++||+|.|+|+-+.+-
T Consensus 19 Aa~LA~~G~~V~VlE~~~~~G 39 (487)
T COG1233 19 AALLARAGLKVTVLEKNDRVG 39 (487)
T ss_pred HHHHHhCCCEEEEEEecCCCC
Confidence 456778999999999877653
No 55
>COG2403 Predicted GTPase [General function prediction only]
Probab=31.23 E-value=43 Score=28.52 Aligned_cols=25 Identities=24% Similarity=0.589 Sum_probs=21.2
Q ss_pred eecCcCHHHHHHHHHH-cCCeEEEEe
Q psy13254 7 GFPEISYGKFAQTLVE-KGYKVARVE 31 (132)
Q Consensus 7 GfP~~~l~~y~~kLv~-~G~kVaive 31 (132)
|+-..+...|+.|+++ .||||++|-
T Consensus 137 g~GKsaVS~~v~r~l~ergyrv~vVr 162 (449)
T COG2403 137 GVGKSAVSRYVARLLRERGYRVCVVR 162 (449)
T ss_pred ccchhHHHHHHHHHHHHcCCceEEEe
Confidence 5566788999999997 799999984
No 56
>PF01946 Thi4: Thi4 family; PDB: 1RP0_A 3FPZ_B 3JSK_K.
Probab=31.02 E-value=40 Score=26.46 Aligned_cols=20 Identities=40% Similarity=0.423 Sum_probs=14.1
Q ss_pred HHHHHHcCCeEEEEeeccCh
Q psy13254 17 AQTLVEKGYKVARVEQTESA 36 (132)
Q Consensus 17 ~~kLv~~G~kVaiveQ~e~~ 36 (132)
+..|-++|+||+++|+--.+
T Consensus 33 A~~La~~g~kV~v~E~~~~~ 52 (230)
T PF01946_consen 33 AYYLAKAGLKVAVIERKLSP 52 (230)
T ss_dssp HHHHHHHTS-EEEEESSSS-
T ss_pred HHHHHHCCCeEEEEecCCCC
Confidence 34677789999999986554
No 57
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=30.97 E-value=43 Score=27.86 Aligned_cols=36 Identities=17% Similarity=0.303 Sum_probs=28.9
Q ss_pred CCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhcc
Q psy13254 92 GDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSH 127 (132)
Q Consensus 92 ~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~ 127 (132)
+.+||+-.+|.+||.|.+++-.-|..-++|+.-|..
T Consensus 178 ~i~wgfL~Ld~~~G~~~Idq~~Vd~hi~el~~QL~~ 213 (346)
T cd01709 178 PVRWGFLKLDPKTGRWEIDQSQVDAHIDELRKQLDA 213 (346)
T ss_pred CceeeeEEecCCCCcEEeeHHHHHHHHHHHHHHhhc
Confidence 468999999999999999997766656677766643
No 58
>PRK00955 hypothetical protein; Provisional
Probab=30.76 E-value=44 Score=29.90 Aligned_cols=20 Identities=20% Similarity=0.496 Sum_probs=15.6
Q ss_pred HHHHHHHH-cCCeEEEEeecc
Q psy13254 15 KFAQTLVE-KGYKVARVEQTE 34 (132)
Q Consensus 15 ~y~~kLv~-~G~kVaiveQ~e 34 (132)
.++.++++ +||+|+|+.|-.
T Consensus 33 a~i~r~L~~~G~~v~ii~qp~ 53 (620)
T PRK00955 33 AIIGRVLEAEGFRVGIIAQPN 53 (620)
T ss_pred HHHHHHHHHCCCEEEEecCCC
Confidence 45666665 899999999863
No 59
>cd08352 Glo_EDI_BRP_like_1 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=30.31 E-value=65 Score=20.57 Aligned_cols=26 Identities=23% Similarity=0.244 Sum_probs=20.0
Q ss_pred eeeeecCcCHHHHHHHHHHcCCeEEE
Q psy13254 4 AHSGFPEISYGKFAQTLVEKGYKVAR 29 (132)
Q Consensus 4 ~maGfP~~~l~~y~~kLv~~G~kVai 29 (132)
.+.+|-...++...++|.++|.++..
T Consensus 74 ~h~~~~v~d~~~~~~~l~~~G~~~~~ 99 (125)
T cd08352 74 RHLAFSVEDIEAAVKHLKAKGVEVEP 99 (125)
T ss_pred eEEEEEeCCHHHHHHHHHHcCCcccc
Confidence 46677777788888888888888653
No 60
>TIGR01664 DNA-3'-Pase DNA 3'-phosphatase. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region.
Probab=29.76 E-value=74 Score=22.99 Aligned_cols=23 Identities=22% Similarity=0.167 Sum_probs=18.9
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEe
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaive 31 (132)
|..-+...+++|-++||+++|+-
T Consensus 43 ~~pgv~e~L~~Lk~~G~~l~I~T 65 (166)
T TIGR01664 43 LYPEIPAKLQELDDEGYKIVIFT 65 (166)
T ss_pred ecCCHHHHHHHHHHCCCEEEEEe
Confidence 34557778999999999999994
No 61
>smart00732 YqgFc Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.
Probab=29.71 E-value=1.5e+02 Score=18.69 Aligned_cols=45 Identities=27% Similarity=0.515 Sum_probs=27.8
Q ss_pred EEEEEecCCEEEEEEEECCcceEE-EEEEe----ChhhHHHHHHhhccCCC
Q psy13254 85 LLGVTKEGDRLGVCFIDTTIGEFH-VGEFE----DDKQFSRLSTLMSHYPP 130 (132)
Q Consensus 85 llai~~~~~~~Gi~~~D~sTg~~~-~~~~~----d~~~~~~L~t~l~~~~P 130 (132)
+++|..+...++++++|. .|++. ...+. .+...+.|..++.+++|
T Consensus 3 ilgiD~Ggt~i~~a~~d~-~g~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~ 52 (99)
T smart00732 3 VLGLDPGRKGIGVAVVDE-TGKLADPLEVIPRTNKEADAARLKKLIKKYQP 52 (99)
T ss_pred EEEEccCCCeEEEEEECC-CCCEecCEEEEEecCcchHHHHHHHHHHHhCC
Confidence 567766777899999986 44443 22221 12335677777777665
No 62
>smart00252 SH2 Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
Probab=29.26 E-value=1.4e+02 Score=18.35 Aligned_cols=56 Identities=23% Similarity=0.422 Sum_probs=30.2
Q ss_pred cceeeccccccccCCCCcceEEEEEecCCEEEEEEEEC-CcceEEEEEEeChhhHHHHHHhhccC
Q psy13254 65 RGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDT-TIGEFHVGEFEDDKQFSRLSTLMSHY 128 (132)
Q Consensus 65 pGT~~~~~~~~~l~~~~~~yllai~~~~~~~Gi~~~D~-sTg~~~~~~~~d~~~~~~L~t~l~~~ 128 (132)
+||++-- ........|.+++...+ .+-=..+.. .+|.+.+.. ...+..|..+|.++
T Consensus 22 ~G~FLvR----~s~~~~~~~~Lsv~~~~-~~~h~~I~~~~~~~~~l~~---~~~F~sl~eLI~~y 78 (84)
T smart00252 22 DGDFLVR----DSESEPGDYVLSVRVKG-KVKHYRIRRNEDGKFYLDG---GRKFPSLVELVEHY 78 (84)
T ss_pred CcEEEEE----cCCCCCCCEEEEEEECC-EEEEEEEEECCCCcEEECC---CCccCCHHHHHHHH
Confidence 6887621 11223466889887543 233333333 337666654 33456677777655
No 63
>PRK08382 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=28.71 E-value=92 Score=23.80 Aligned_cols=10 Identities=20% Similarity=0.245 Sum_probs=7.1
Q ss_pred EEccceeecc
Q psy13254 62 ITCRGAQTFS 71 (132)
Q Consensus 62 I~TpGT~~~~ 71 (132)
-+||||++-|
T Consensus 150 TLTPGTltvd 159 (201)
T PRK08382 150 TLTPGTLTLD 159 (201)
T ss_pred hcCCCeEEEE
Confidence 4788888743
No 64
>smart00753 PAM PCI/PINT associated module.
Probab=28.68 E-value=49 Score=20.83 Aligned_cols=30 Identities=17% Similarity=0.277 Sum_probs=25.8
Q ss_pred eeecCcCHHHHHHHHHHcCCeEEEEeeccC
Q psy13254 6 SGFPEISYGKFAQTLVEKGYKVARVEQTES 35 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~kVaiveQ~e~ 35 (132)
.++|..-++.++.+++..|.=-|.+||...
T Consensus 34 ~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~ 63 (88)
T smart00753 34 LGLSVPEVEKLVSKAIRDGEISAKIDQVNG 63 (88)
T ss_pred hCcCHHHHHHHHHHHHHCCCeEEEEcCcCC
Confidence 477777899999999999988899998764
No 65
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=28.68 E-value=49 Score=20.83 Aligned_cols=30 Identities=17% Similarity=0.277 Sum_probs=25.8
Q ss_pred eeecCcCHHHHHHHHHHcCCeEEEEeeccC
Q psy13254 6 SGFPEISYGKFAQTLVEKGYKVARVEQTES 35 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~kVaiveQ~e~ 35 (132)
.++|..-++.++.+++..|.=-|.+||...
T Consensus 34 ~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~ 63 (88)
T smart00088 34 LGLSVPEVEKLVSKAIRDGEISAKIDQVNG 63 (88)
T ss_pred hCcCHHHHHHHHHHHHHCCCeEEEEcCcCC
Confidence 477777899999999999988899998764
No 66
>cd08362 BphC5-RrK37_N_like N-terminal, non-catalytic, domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Rhodococcus rhodochrous K37, and similar proteins. 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). The enzyme contains a N-terminal and a C-terminal domain of similar structure fold, resulting from an ancient gene duplication. BphC belongs to the type I extradiol dioxygenase family, which requires a metal in the active site for its catalytic activity. Polychlorinated biphenyl degrading bacteria demonstrate multiplicity of BphCs. Bacterium Rhodococcus rhodochrous K37 has eight genes encoding BphC enzymes. This family includes the N-terminal domain of BphC5-RrK37. The crystal structure of the protein from Novosphingobium aromaticivorans has a Mn(II)in the active site, although most proteins of type I extradiol dioxyge
Probab=28.44 E-value=59 Score=20.96 Aligned_cols=26 Identities=15% Similarity=0.211 Sum_probs=17.7
Q ss_pred eeeeeecC---cCHHHHHHHHHHcCCeEE
Q psy13254 3 YAHSGFPE---ISYGKFAQTLVEKGYKVA 28 (132)
Q Consensus 3 ~~maGfP~---~~l~~y~~kLv~~G~kVa 28 (132)
..|.+|.. ..++.+.++|.++|.++.
T Consensus 59 ~~~~~~~v~~~~~l~~~~~~l~~~G~~~~ 87 (120)
T cd08362 59 LDVVSFSVASRADVDALARQVAARGGTVL 87 (120)
T ss_pred CceEEEEeCCHHHHHHHHHHHHHcCCcee
Confidence 34556655 467788888888888753
No 67
>PF05222 AlaDh_PNT_N: Alanine dehydrogenase/PNT, N-terminal domain; InterPro: IPR007886 Alanine dehydrogenases (1.4.1.1 from EC) and pyridine nucleotide transhydrogenase (1.6.1.1 from EC) have been shown to share regions of similarity []. Alanine dehydrogenase catalyzes the NAD-dependent reversible reductive amination of pyruvate into alanine. Pyridine nucleotide transhydrogenase catalyzes the reduction of NADP+ to NADPH with the concomitant oxidation of NADH to NAD+. This enzyme is located in the plasma membrane of prokaryotes and in the inner membrane of the mitochondria of eukaryotes. The transhydrogenation between NADH and NADP is coupled with the translocation of a proton across the membrane. In prokaryotes the enzyme is composed of two different subunits, an alpha chain (gene pntA) and a beta chain (gene pntB), while in eukaryotes it is a single chain protein. The sequence of alanine dehydrogenase from several bacterial species are related with those of the alpha subunit of bacterial pyridine nucleotide transhydrogenase and of the N-terminal half of the eukaryotic enzyme. The two most conserved regions correspond respectively to the N-terminal extremity of these proteins, represented in this entry, and to a central glycine-rich region which is part of the NAD(H)-binding site.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1X15_A 2BRU_A 1X14_B 1X13_A 2EEZ_F 2VOE_F 2VHV_B 2VHY_A 2VHX_A 2VHW_A ....
Probab=27.41 E-value=55 Score=23.11 Aligned_cols=17 Identities=24% Similarity=0.143 Sum_probs=14.3
Q ss_pred HHHHHHHHHcCCeEEEE
Q psy13254 14 GKFAQTLVEKGYKVARV 30 (132)
Q Consensus 14 ~~y~~kLv~~G~kVaiv 30 (132)
-..+++|+++|++|.|=
T Consensus 17 P~~v~~L~~~G~~V~VE 33 (136)
T PF05222_consen 17 PEDVKKLVKLGHEVLVE 33 (136)
T ss_dssp HHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHhCCCEEEEE
Confidence 35789999999999874
No 68
>PF10614 CsgF: Type VIII secretion system (T8SS), CsgF protein; InterPro: IPR018893 Fimbriae are cell-surface protein polymers, of e.g. Escherichia coli and Salmonella spp, that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), that differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae (Tafi) are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp. and the controlling operon termed agf; however subsequent isolation of the homologous operon in E. coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix []. CsgF is one of three putative curli assembly factors appearing to act as a nucleator protein. Unlike eukaryotic amyloid formation, curli biogenesis is a productive pathway requiring a specific assembly machinery [].
Probab=27.34 E-value=2.5e+02 Score=20.41 Aligned_cols=38 Identities=24% Similarity=0.262 Sum_probs=28.8
Q ss_pred ccceeeccccccccCCCCcceEEEEEecCCEEEEEEEECCcceEEEEEE
Q psy13254 64 CRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEF 112 (132)
Q Consensus 64 TpGT~~~~~~~~~l~~~~~~yllai~~~~~~~Gi~~~D~sTg~~~~~~~ 112 (132)
.+||+.-+ .|.+.|......+-|-+.|..|||....++
T Consensus 100 ~~Gt~~~g-----------df~I~i~~~~g~l~v~I~D~~TGe~T~I~V 137 (142)
T PF10614_consen 100 KPGTFTTG-----------DFTIEIVNSDGGLVVNITDKNTGEVTTIEV 137 (142)
T ss_pred CCceEEEC-----------CEEEEEEeCCCeEEEEEEeCCCccEEEEEe
Confidence 56777632 467777766678999999999999876654
No 69
>TIGR00213 GmhB_yaeD D,D-heptose 1,7-bisphosphate phosphatase. This family of proteins formerly designated yaeD resembles the histidinol phosphatase domain of the bifunctional protein HisB. The member from E. coli has been characterized as D,D-heptose 1,7-bisphosphate phosphatase, GmhB, involved in inner core LPS assembly (PubMed:11751812).
Probab=27.33 E-value=81 Score=22.63 Aligned_cols=22 Identities=18% Similarity=0.090 Sum_probs=18.2
Q ss_pred CcCHHHHHHHHHHcCCeEEEEe
Q psy13254 10 EISYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 10 ~~~l~~y~~kLv~~G~kVaive 31 (132)
..-+...+++|-++||+++|+-
T Consensus 28 ~pgv~e~L~~Lk~~G~~l~i~T 49 (176)
T TIGR00213 28 IDGVIDALRELKKMGYALVLVT 49 (176)
T ss_pred CCCHHHHHHHHHHCCCEEEEEe
Confidence 3456778999999999999995
No 70
>COG1635 THI4 Ribulose 1,5-bisphosphate synthetase, converts PRPP to RuBP, flavoprotein [Carbohydrate transport and metabolism]
Probab=27.01 E-value=61 Score=25.79 Aligned_cols=20 Identities=40% Similarity=0.323 Sum_probs=15.6
Q ss_pred HHHHHHcCCeEEEEeeccCh
Q psy13254 17 AQTLVEKGYKVARVEQTESA 36 (132)
Q Consensus 17 ~~kLv~~G~kVaiveQ~e~~ 36 (132)
+..|-++|.||+|+||.=.+
T Consensus 46 AyyLAk~g~kV~i~E~~ls~ 65 (262)
T COG1635 46 AYYLAKAGLKVAIFERKLSF 65 (262)
T ss_pred HHHHHhCCceEEEEEeeccc
Confidence 44677889999999986544
No 71
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=26.84 E-value=88 Score=21.67 Aligned_cols=24 Identities=21% Similarity=0.209 Sum_probs=20.6
Q ss_pred eecCcCHHHHHHHHHHcCCeEEEE
Q psy13254 7 GFPEISYGKFAQTLVEKGYKVARV 30 (132)
Q Consensus 7 GfP~~~l~~y~~kLv~~G~kVaiv 30 (132)
|+...++...+.+|.+.||+=++|
T Consensus 52 ~~~~p~~~eaL~~l~~~G~~~V~V 75 (127)
T cd03412 52 GIEVDTPEEALAKLAADGYTEVIV 75 (127)
T ss_pred CCCCCCHHHHHHHHHHCCCCEEEE
Confidence 566789999999999999988777
No 72
>PRK10749 lysophospholipase L2; Provisional
Probab=26.81 E-value=67 Score=25.41 Aligned_cols=28 Identities=29% Similarity=0.430 Sum_probs=21.9
Q ss_pred eecCcC--HHHHHHHHHHcCCeEEEEeecc
Q psy13254 7 GFPEIS--YGKFAQTLVEKGYKVARVEQTE 34 (132)
Q Consensus 7 GfP~~~--l~~y~~kLv~~G~kVaiveQ~e 34 (132)
|+..|. ...++..|.++||.|..+|.--
T Consensus 62 G~~~~~~~y~~~~~~l~~~g~~v~~~D~~G 91 (330)
T PRK10749 62 GRIESYVKYAELAYDLFHLGYDVLIIDHRG 91 (330)
T ss_pred CccchHHHHHHHHHHHHHCCCeEEEEcCCC
Confidence 777665 4556667889999999999864
No 73
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=26.67 E-value=39 Score=21.52 Aligned_cols=30 Identities=17% Similarity=0.236 Sum_probs=26.3
Q ss_pred eeeecCcCHHHHHHHHHHcCCeEEEEeecc
Q psy13254 5 HSGFPEISYGKFAQTLVEKGYKVARVEQTE 34 (132)
Q Consensus 5 maGfP~~~l~~y~~kLv~~G~kVaiveQ~e 34 (132)
++++|...++.++.+++..|.==|.+||..
T Consensus 69 ~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~ 98 (105)
T PF01399_consen 69 ALQLSEEEVESILIDLISNGLIKAKIDQVN 98 (105)
T ss_dssp HHTCCHHHHHHHHHHHHHTTSSEEEEETTT
T ss_pred HhccchHHHHHHHHHHHHCCCEEEEEECCC
Confidence 367888899999999999999889999864
No 74
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=26.60 E-value=73 Score=20.21 Aligned_cols=24 Identities=29% Similarity=0.527 Sum_probs=19.7
Q ss_pred CHHHHHHHHHHcCCeEEEEeeccC
Q psy13254 12 SYGKFAQTLVEKGYKVARVEQTES 35 (132)
Q Consensus 12 ~l~~y~~kLv~~G~kVaiveQ~e~ 35 (132)
.+...++.|.++||.|...|+---
T Consensus 31 ry~~~a~~L~~~G~~V~~~D~rGh 54 (79)
T PF12146_consen 31 RYAHLAEFLAEQGYAVFAYDHRGH 54 (79)
T ss_pred HHHHHHHHHHhCCCEEEEECCCcC
Confidence 356678899999999999998643
No 75
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=26.41 E-value=42 Score=18.47 Aligned_cols=20 Identities=25% Similarity=0.376 Sum_probs=17.9
Q ss_pred eeecCcCHHHHHHHHHHcCC
Q psy13254 6 SGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~ 25 (132)
.|++..++..+++.|.++|+
T Consensus 24 l~~s~~tv~~~l~~L~~~g~ 43 (53)
T smart00420 24 LGVSEMTIRRDLNKLEEQGL 43 (53)
T ss_pred HCCCHHHHHHHHHHHHHCCC
Confidence 47888899999999999988
No 76
>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A.
Probab=26.18 E-value=76 Score=22.34 Aligned_cols=18 Identities=33% Similarity=0.641 Sum_probs=11.0
Q ss_pred HHHHHHHHHcCCeEEEEe
Q psy13254 14 GKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 14 ~~y~~kLv~~G~kVaive 31 (132)
..-++.|.+.||+|+++-
T Consensus 18 ~~Li~~l~~~g~~v~~ik 35 (140)
T PF03205_consen 18 RKLINELKRRGYRVAVIK 35 (140)
T ss_dssp HHHHHHHHHTT--EEEEE
T ss_pred HHHHHHHhHcCCceEEEE
Confidence 344566777999999664
No 77
>PF07879 PHB_acc_N: PHB/PHA accumulation regulator DNA-binding domain; InterPro: IPR012909 This domain is found at the N terminus of the polyhydroxyalkanoate (PHA) synthesis regulators. These regulators have been shown to directly bind DNA and PHA []. The invariant nature of this domain compared to the C-terminal IPR007897 from INTERPRO domain(s) suggests that it contains the DNA-binding function.
Probab=26.09 E-value=80 Score=19.88 Aligned_cols=18 Identities=22% Similarity=0.237 Sum_probs=15.6
Q ss_pred HHHHHHHHcCCeEEEEee
Q psy13254 15 KFAQTLVEKGYKVARVEQ 32 (132)
Q Consensus 15 ~y~~kLv~~G~kVaiveQ 32 (132)
.-++.||..|..|.|+|=
T Consensus 23 ~di~~lV~~g~~~~V~D~ 40 (64)
T PF07879_consen 23 EDIAQLVREGEDFKVVDA 40 (64)
T ss_pred HHHHHHHHCCCeEEEEEC
Confidence 357899999999999984
No 78
>PF02635 DrsE: DsrE/DsrF-like family; InterPro: IPR003787 Four small, soluble proteins (DsrE, DsrF, DsrH and DsrC) are encoded in the dsr gene region of the phototrophic sulphur bacterium Chromatium vinosum D. The dsrAB genes encoding dissimilatory sulphite reductase are part of the gene cluster, dsrABEFHCMK. The remaining proteins that are encoded are a transmembrane protein (DsrM) with similarity to haem-b-binding polypeptides and a soluble protein (DsrK) resembling [4Fe-4S]-cluster-containing heterodisulphide reductase from methanogenic archaea. DsrE is a small soluble protein involved in intracellular sulphur reduction [].; PDB: 1L1S_A 2HYB_B 2HY5_B 2PD2_B 3MC3_A 2D1P_H 1JX7_B 2FB6_A.
Probab=25.91 E-value=75 Score=20.61 Aligned_cols=24 Identities=21% Similarity=0.267 Sum_probs=19.7
Q ss_pred CcCHHHHHHHHHHcC-CeEEEEeec
Q psy13254 10 EISYGKFAQTLVEKG-YKVARVEQT 33 (132)
Q Consensus 10 ~~~l~~y~~kLv~~G-~kVaiveQ~ 33 (132)
...+..+++.|.++| -++.+|+..
T Consensus 60 ~~~~~~~l~~l~~~g~v~i~~C~~~ 84 (122)
T PF02635_consen 60 DPPLQELLKELKEAGGVKIYVCETC 84 (122)
T ss_dssp SHCHHHHHHHHHHTTT-EEEEEHHH
T ss_pred cccHHHHHHHHHhcCCcEEEEcHHH
Confidence 456889999999997 999999853
No 79
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=25.72 E-value=75 Score=26.17 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=16.2
Q ss_pred CHHHHHHHHHHcCCeEEEEe
Q psy13254 12 SYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 12 ~l~~y~~kLv~~G~kVaive 31 (132)
-++.....|.+.|+||||.-
T Consensus 67 li~~L~~~l~~~G~rVaVlA 86 (323)
T COG1703 67 LIEALGRELRERGHRVAVLA 86 (323)
T ss_pred HHHHHHHHHHHCCcEEEEEE
Confidence 45777788888999999973
No 80
>PRK06279 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=25.72 E-value=61 Score=21.86 Aligned_cols=10 Identities=20% Similarity=0.212 Sum_probs=7.6
Q ss_pred EEccceeecc
Q psy13254 62 ITCRGAQTFS 71 (132)
Q Consensus 62 I~TpGT~~~~ 71 (132)
-+||||+.-+
T Consensus 58 TLTPGTltvd 67 (100)
T PRK06279 58 TLTPGTLTID 67 (100)
T ss_pred hCCCCeEEEE
Confidence 4799999843
No 81
>PF13076 DUF3940: Protein of unknown function (DUF3940)
Probab=25.47 E-value=61 Score=18.18 Aligned_cols=12 Identities=17% Similarity=0.407 Sum_probs=9.8
Q ss_pred HHHHHHHHHcCC
Q psy13254 14 GKFAQTLVEKGY 25 (132)
Q Consensus 14 ~~y~~kLv~~G~ 25 (132)
+.++.+|++.|+
T Consensus 4 ~~lI~~Li~~Gi 15 (38)
T PF13076_consen 4 DFLIEKLIQSGI 15 (38)
T ss_pred HHHHHHHHHcCC
Confidence 578899999884
No 82
>PTZ00445 p36-lilke protein; Provisional
Probab=25.38 E-value=56 Score=25.44 Aligned_cols=27 Identities=33% Similarity=0.332 Sum_probs=21.8
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEeeccC
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVEQTES 35 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaiveQ~e~ 35 (132)
|..+.+.+++.|-+.|.|++++|=--|
T Consensus 27 ~~~~~~~~v~~L~~~GIk~Va~D~DnT 53 (219)
T PTZ00445 27 PHESADKFVDLLNECGIKVIASDFDLT 53 (219)
T ss_pred HHHHHHHHHHHHHHcCCeEEEecchhh
Confidence 456778899999999999999984333
No 83
>COG1087 GalE UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]
Probab=25.34 E-value=63 Score=26.66 Aligned_cols=22 Identities=14% Similarity=0.297 Sum_probs=18.3
Q ss_pred HHHHHHHcCCeEEEEeeccChh
Q psy13254 16 FAQTLVEKGYKVARVEQTESAE 37 (132)
Q Consensus 16 y~~kLv~~G~kVaiveQ~e~~~ 37 (132)
-+..|+++||.|+|+|-..+..
T Consensus 16 tv~~Ll~~G~~vvV~DNL~~g~ 37 (329)
T COG1087 16 TVRQLLKTGHEVVVLDNLSNGH 37 (329)
T ss_pred HHHHHHHCCCeEEEEecCCCCC
Confidence 3578999999999999887654
No 84
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=25.32 E-value=40 Score=25.22 Aligned_cols=20 Identities=30% Similarity=0.441 Sum_probs=18.7
Q ss_pred eecCcCHHHHHHHHHHcCCe
Q psy13254 7 GFPEISYGKFAQTLVEKGYK 26 (132)
Q Consensus 7 GfP~~~l~~y~~kLv~~G~k 26 (132)
|+++.++..++..|+++|.=
T Consensus 82 G~s~~tlrR~l~~LveaGLI 101 (177)
T PF03428_consen 82 GMSERTLRRHLARLVEAGLI 101 (177)
T ss_pred CCCHHHHHHHHHHHHHCCCe
Confidence 99999999999999999973
No 85
>cd08584 PI-PLCc_GDPD_SF_unchar2 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=25.18 E-value=64 Score=24.54 Aligned_cols=16 Identities=25% Similarity=0.397 Sum_probs=13.9
Q ss_pred HHHHHHHcCCeEEEEe
Q psy13254 16 FAQTLVEKGYKVARVE 31 (132)
Q Consensus 16 y~~kLv~~G~kVaive 31 (132)
-+++|+++|+||.+|-
T Consensus 141 ~~~~~~~~~~~~c~VS 156 (192)
T cd08584 141 LILKLLKAGKKICLVS 156 (192)
T ss_pred HHHHHHHCCcEEEEEC
Confidence 3679999999999994
No 86
>TIGR01509 HAD-SF-IA-v3 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED. HAD subfamilies caused by an overly broad single model.
Probab=25.10 E-value=1e+02 Score=21.52 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=20.0
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEeec
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVEQT 33 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaiveQ~ 33 (132)
|..-+...+++|-++|++++|+--.
T Consensus 86 ~~~g~~~~l~~l~~~g~~~~i~Tn~ 110 (183)
T TIGR01509 86 PLPGVEPLLEALRARGKKLALLTNS 110 (183)
T ss_pred cCcCHHHHHHHHHHCCCeEEEEeCC
Confidence 4456778899999999999999643
No 87
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.07 E-value=31 Score=24.62 Aligned_cols=21 Identities=19% Similarity=0.408 Sum_probs=18.8
Q ss_pred eeeecCcCHHHHHHHHHHcCC
Q psy13254 5 HSGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 5 maGfP~~~l~~y~~kLv~~G~ 25 (132)
+.|.+.+++..|+..||+.|.
T Consensus 35 ~TGasR~Tvk~~lreLVa~G~ 55 (127)
T PF06163_consen 35 KTGASRNTVKRYLRELVARGD 55 (127)
T ss_pred HHCCCHHHHHHHHHHHHHcCC
Confidence 568999999999999999875
No 88
>PF07348 Syd: Syd protein (SUKH-2); InterPro: IPR009948 This family contains a number of bacterial Syd proteins approximately 180 residues long. It has been suggested that Syd is loosely associated with the cytoplasmic surface of the cytoplasmic membrane, and that interaction with SecY may be involved in this membrane association [].; GO: 0009898 internal side of plasma membrane; PDB: 3FFV_B.
Probab=24.92 E-value=34 Score=25.66 Aligned_cols=36 Identities=19% Similarity=0.282 Sum_probs=23.6
Q ss_pred EEEEEEECCcceEEEEEEeChh---hHHHHHHhhccCCC
Q psy13254 95 LGVCFIDTTIGEFHVGEFEDDK---QFSRLSTLMSHYPP 130 (132)
Q Consensus 95 ~Gi~~~D~sTg~~~~~~~~d~~---~~~~L~t~l~~~~P 130 (132)
--+..+|..||++.+-.+.... .-..|.+.|.++.|
T Consensus 138 ~~lisv~N~sGeV~LE~~G~~~~~~LA~sL~eFL~~L~P 176 (176)
T PF07348_consen 138 DMLISVDNESGEVILEQFGTKPREVLAPSLAEFLSQLEP 176 (176)
T ss_dssp TEEEEEETTT--EEEEETTSS-EEEEESSHHHHHHH-EE
T ss_pred CcEEEEECCCCeEEEEeCCCCcceehhhhHHHHHHhcCC
Confidence 4477889999999998886432 13358888888776
No 89
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=24.88 E-value=46 Score=20.57 Aligned_cols=21 Identities=33% Similarity=0.623 Sum_probs=15.4
Q ss_pred eecCcCHHHHHH----HHHHcCCeE
Q psy13254 7 GFPEISYGKFAQ----TLVEKGYKV 27 (132)
Q Consensus 7 GfP~~~l~~y~~----kLv~~G~kV 27 (132)
|||.|+...-++ .||++||..
T Consensus 13 Gf~~~tA~~IIrqAK~~lV~~G~~~ 37 (59)
T PF11372_consen 13 GFSESTARDIIRQAKALLVQKGFSF 37 (59)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 889888877665 477788753
No 90
>TIGR01607 PST-A Plasmodium subtelomeric family (PST-A). These genes are preferentially located in the subtelomeric regions of the chromosomes of both P. falciparum and P. yoelii.
Probab=24.81 E-value=70 Score=25.59 Aligned_cols=21 Identities=14% Similarity=0.379 Sum_probs=17.9
Q ss_pred HHHHHHHHHcCCeEEEEeecc
Q psy13254 14 GKFAQTLVEKGYKVARVEQTE 34 (132)
Q Consensus 14 ~~y~~kLv~~G~kVaiveQ~e 34 (132)
+.+++.|.++||.|..+|+.-
T Consensus 64 ~~~~~~l~~~G~~V~~~D~rG 84 (332)
T TIGR01607 64 DSWIENFNKNGYSVYGLDLQG 84 (332)
T ss_pred HHHHHHHHHCCCcEEEecccc
Confidence 356899999999999999864
No 91
>PTZ00445 p36-lilke protein; Provisional
Probab=24.75 E-value=83 Score=24.51 Aligned_cols=23 Identities=13% Similarity=0.284 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHcCCeEEEEeecc
Q psy13254 12 SYGKFAQTLVEKGYKVARVEQTE 34 (132)
Q Consensus 12 ~l~~y~~kLv~~G~kVaiveQ~e 34 (132)
-+..|+++|-++|.+|+||-...
T Consensus 79 efk~~~~~l~~~~I~v~VVTfSd 101 (219)
T PTZ00445 79 DFKILGKRLKNSNIKISVVTFSD 101 (219)
T ss_pred HHHHHHHHHHHCCCeEEEEEccc
Confidence 37889999999999999996543
No 92
>PF01011 PQQ: PQQ enzyme repeat family.; InterPro: IPR002372 Pyrrolo-quinoline quinone (PQQ) is a redox coenzyme, which serves as a cofactor for a number of enzymes (quinoproteins) and particularly for some bacterial dehydrogenases [, ]. A number of bacterial quinoproteins belong to this family. Enzymes in this group have repeats of a beta propeller.; PDB: 1H4I_C 1H4J_E 1W6S_A 2YH3_A 3PRW_A 3P1L_A 3Q7M_A 3Q7O_A 3Q7N_A 1G72_A ....
Probab=24.65 E-value=99 Score=16.49 Aligned_cols=18 Identities=11% Similarity=-0.029 Sum_probs=13.1
Q ss_pred EEEEEECCcceEEEEEEe
Q psy13254 96 GVCFIDTTIGEFHVGEFE 113 (132)
Q Consensus 96 Gi~~~D~sTg~~~~~~~~ 113 (132)
.|..+|..||++....-.
T Consensus 11 ~l~AlD~~TG~~~W~~~~ 28 (38)
T PF01011_consen 11 YLYALDAKTGKVLWKFQT 28 (38)
T ss_dssp EEEEEETTTTSEEEEEES
T ss_pred EEEEEECCCCCEEEeeeC
Confidence 356679999999766543
No 93
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=24.61 E-value=30 Score=21.29 Aligned_cols=26 Identities=19% Similarity=0.215 Sum_probs=19.0
Q ss_pred eeecCcCHHHHHHHHHHcCCeEEEEe
Q psy13254 6 SGFPEISYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~kVaive 31 (132)
.|.|...++..+..|+++||=.-+..
T Consensus 24 ~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 24 FGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp TT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 46788889999999999998554443
No 94
>COG3019 Predicted metal-binding protein [General function prediction only]
Probab=24.48 E-value=89 Score=22.87 Aligned_cols=25 Identities=24% Similarity=0.411 Sum_probs=20.3
Q ss_pred HHHHHHHHHHcCCeEEEEeeccChh
Q psy13254 13 YGKFAQTLVEKGYKVARVEQTESAE 37 (132)
Q Consensus 13 l~~y~~kLv~~G~kVaiveQ~e~~~ 37 (132)
=+.|++.|-.+||+|-+++-.+-.+
T Consensus 39 C~~w~~~mk~~Gf~Vk~~~~~d~~a 63 (149)
T COG3019 39 CDEWAQHMKANGFEVKVVETDDFLA 63 (149)
T ss_pred HHHHHHHHHhCCcEEEEeecCcHHH
Confidence 4789999999999999998655433
No 95
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=24.41 E-value=34 Score=19.93 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=17.1
Q ss_pred eeecCcCHHHHHHHHHHcCCe
Q psy13254 6 SGFPEISYGKFAQTLVEKGYK 26 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~k 26 (132)
.|++..++..-+++|.++||=
T Consensus 31 l~~~~~~vs~~v~~L~~~Glv 51 (62)
T PF12802_consen 31 LGISKSTVSRIVKRLEKKGLV 51 (62)
T ss_dssp HTS-HHHHHHHHHHHHHTTSE
T ss_pred HCcCHHHHHHHHHHHHHCCCE
Confidence 567788889999999999984
No 96
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.08 E-value=1.4e+02 Score=17.06 Aligned_cols=21 Identities=24% Similarity=0.270 Sum_probs=12.3
Q ss_pred eecCcCHHHHHHHHHHcCCeE
Q psy13254 7 GFPEISYGKFAQTLVEKGYKV 27 (132)
Q Consensus 7 GfP~~~l~~y~~kLv~~G~kV 27 (132)
-|.....+.-.+.|-++||+|
T Consensus 44 ~~~ve~~~~~~~~L~~~G~~v 64 (65)
T cd04882 44 IFRTEDIEKAIEVLQERGVEL 64 (65)
T ss_pred EEEeCCHHHHHHHHHHCCceE
Confidence 344444566666666677765
No 97
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=23.92 E-value=40 Score=21.41 Aligned_cols=20 Identities=25% Similarity=0.272 Sum_probs=17.6
Q ss_pred eeecCcCHHHHHHHHHHcCC
Q psy13254 6 SGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~ 25 (132)
.|+|...+...+++|.++|+
T Consensus 35 ~~i~~~~l~kil~~L~~~Gl 54 (83)
T PF02082_consen 35 LGISPSYLRKILQKLKKAGL 54 (83)
T ss_dssp HTS-HHHHHHHHHHHHHTTS
T ss_pred HCcCHHHHHHHHHHHhhCCe
Confidence 57899999999999999998
No 98
>PF07082 DUF1350: Protein of unknown function (DUF1350); InterPro: IPR010765 This family consists of several hypothetical proteins from both cyanobacteria and plants. Members of this family are typically around 250 residues in length. The function of this family is unknown but the species distribution indicates that the family may be involved in photosynthesis.
Probab=23.88 E-value=57 Score=25.91 Aligned_cols=25 Identities=28% Similarity=0.612 Sum_probs=21.3
Q ss_pred eeecCcCHHHHHHHHHHcCCeEEEE
Q psy13254 6 SGFPEISYGKFAQTLVEKGYKVARV 30 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~kVaiv 30 (132)
.-+|.-++...++.|.++||.|.-.
T Consensus 29 ga~P~itYr~lLe~La~~Gy~ViAt 53 (250)
T PF07082_consen 29 GAAPQITYRYLLERLADRGYAVIAT 53 (250)
T ss_pred ccCcHHHHHHHHHHHHhCCcEEEEE
Confidence 4589999999999999999977543
No 99
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=23.78 E-value=70 Score=21.87 Aligned_cols=18 Identities=17% Similarity=0.187 Sum_probs=12.5
Q ss_pred HHHHHHHHcCCeEEEEee
Q psy13254 15 KFAQTLVEKGYKVARVEQ 32 (132)
Q Consensus 15 ~y~~kLv~~G~kVaiveQ 32 (132)
.-++.|.++|||.+||--
T Consensus 18 ~d~~~la~~GfktVInlR 35 (110)
T PF04273_consen 18 EDLAQLAAQGFKTVINLR 35 (110)
T ss_dssp HHHHHHHHCT--EEEE-S
T ss_pred HHHHHHHHCCCcEEEECC
Confidence 456799999999999954
No 100
>PF00201 UDPGT: UDP-glucoronosyl and UDP-glucosyl transferase; InterPro: IPR002213 UDP glycosyltransferases (UGT) are a superfamily of enzymes that catalyzes the addition of the glycosyl group from a UTP-sugar to a small hydrophobic molecule. This family currently consist of: Mammalian UDP-glucuronosyl transferases (2.4.1.17 from EC) (UDPGT) []. A large family of membrane-bound microsomal enzymes which catalyze the transfer of glucuronic acid to a wide variety of exogenous and endogenous lipophilic substrates. These enzymes are of major importance in the detoxification and subsequent elimination of xenobiotics such as drugs and carcinogens. A large number of putative UDPGT from Caenorhabditis elegans. Mammalian 2-hydroxyacylsphingosine 1-beta-galactosyltransferase [] (2.4.1.45 from EC) (also known as UDP-galactose-ceramide galactosyltransferase). This enzyme catalyzes the transfer of galactose to ceramide, a key enzymatic step in the biosynthesis of galactocerebrosides, which are abundant sphingolipids of the myelin membrane of the central nervous system and peripheral nervous system. Plants flavonol O(3)-glucosyltransferase (2.4.1.91 from EC). An enzyme [] that catalyzes the transfer of glucose from UDP-glucose to a flavanol. This reaction is essential and one of the last steps in anthocyanin pigment biosynthesis. Baculoviruses ecdysteroid UDP-glucosyltransferase (2.4.1 from EC) [] (egt). This enzyme catalyzes the transfer of glucose from UDP-glucose to ectysteroids which are insect molting hormones. The expression of egt in the insect host interferes with the normal insect development by blocking the molting process. Prokaryotic zeaxanthin glucosyltransferase (2.4.1 from EC) (gene crtX), an enzyme involved in carotenoid biosynthesis and that catalyses the glycosylation reaction which converts zeaxanthin to zeaxanthin-beta-diglucoside. Streptomyces macrolide glycosyltransferases (2.4.1 from EC) []. These enzymes specifically inactivates macrolide anitibiotics via 2'-O-glycosylation using UDP-glucose. These enzymes share a conserved domain of about 50 amino acid residues located in their C-terminal section.; GO: 0016758 transferase activity, transferring hexosyl groups, 0008152 metabolic process; PDB: 3HBJ_A 3HBF_A 2PQ6_A 3IA7_B 3RSC_A 3IAA_B 2IYA_A 2IYF_B 2O6L_A 2VCH_A ....
Probab=23.66 E-value=37 Score=28.40 Aligned_cols=31 Identities=19% Similarity=0.210 Sum_probs=20.4
Q ss_pred eeeeeecCcCHHHHHHHHHHcCCeEEEEeec
Q psy13254 3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQT 33 (132)
Q Consensus 3 ~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~ 33 (132)
+||++=....+..+++.|+++|+.|.+.-..
T Consensus 6 ~p~~~SH~~~~~~l~~~L~~rGH~VTvl~~~ 36 (500)
T PF00201_consen 6 FPMAYSHFIFMRPLAEELAERGHNVTVLTPS 36 (500)
T ss_dssp ------SHHHHHHHHHHHHHH-TTSEEEHHH
T ss_pred eCCCcCHHHHHHHHHHHHHhcCCceEEEEee
Confidence 4666666667889999999999999998543
No 101
>TIGR02467 CbiE precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit. This model recognizes the CbiE methylase which is responsible, in part (along with CbiT), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiT subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL.
Probab=23.55 E-value=96 Score=22.93 Aligned_cols=27 Identities=19% Similarity=0.209 Sum_probs=17.7
Q ss_pred cCHHHHHHHHHHcCC----eEEEEeeccChh
Q psy13254 11 ISYGKFAQTLVEKGY----KVARVEQTESAE 37 (132)
Q Consensus 11 ~~l~~y~~kLv~~G~----kVaiveQ~e~~~ 37 (132)
..+..-++.|.+.|+ +|+++++...+.
T Consensus 150 ~~~~~i~~~L~~~g~~~~~~v~v~~~l~~~~ 180 (204)
T TIGR02467 150 NGPAEIARELIELGIGGSYELTVGENLGYED 180 (204)
T ss_pred CCHHHHHHHHHHCCCCCCeEEEEEcccCCCC
Confidence 456666666777766 677777666553
No 102
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=23.51 E-value=53 Score=18.49 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=17.7
Q ss_pred eeecCcCHHHHHHHHHHcCCeE
Q psy13254 6 SGFPEISYGKFAQTLVEKGYKV 27 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~kV 27 (132)
.|++..++..++++|.+.|+=.
T Consensus 20 l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 20 LGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred HCCCHHHHHHHHHHHHHCCCee
Confidence 3677788899999999988753
No 103
>KOG1502|consensus
Probab=23.51 E-value=1.2e+02 Score=24.99 Aligned_cols=19 Identities=32% Similarity=0.634 Sum_probs=14.3
Q ss_pred HHHHHHcCCeE-EEEeeccC
Q psy13254 17 AQTLVEKGYKV-ARVEQTES 35 (132)
Q Consensus 17 ~~kLv~~G~kV-aiveQ~e~ 35 (132)
+++|+.+||+| +-|.=.|+
T Consensus 23 vk~LL~rGY~V~gtVR~~~~ 42 (327)
T KOG1502|consen 23 VKLLLSRGYTVRGTVRDPED 42 (327)
T ss_pred HHHHHhCCCEEEEEEcCcch
Confidence 67899999999 66654444
No 104
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=23.50 E-value=31 Score=21.37 Aligned_cols=19 Identities=26% Similarity=0.511 Sum_probs=15.3
Q ss_pred eec-CcCHHHHHHHHHHcCC
Q psy13254 7 GFP-EISYGKFAQTLVEKGY 25 (132)
Q Consensus 7 GfP-~~~l~~y~~kLv~~G~ 25 (132)
|+- -.++..|++.|.++||
T Consensus 36 g~~S~~tv~~~L~~Le~kG~ 55 (65)
T PF01726_consen 36 GLKSTSTVQRHLKALERKGY 55 (65)
T ss_dssp TSSSHHHHHHHHHHHHHTTS
T ss_pred CCCChHHHHHHHHHHHHCcC
Confidence 444 4578899999999998
No 105
>cd07247 SgaA_N_like N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains. SgaA suppresses the growth disturbances caused by high osmolarity and a high concentration of A-factor, a microbial hormone, during the early growth phase in Streptomyces griseus. A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) controls morphological differentiation and secondary metabolism in Streptomyces griseus. It is a chemical signaling molecule that at a very low concentration acts as a switch for yellow pigment production, aerial mycelium formation, streptomycin production, and streptomycin resistance. The structure and amino acid sequence of SgaA are closely related to a group of antibiotics resistance proteins, including bleomycin resistance protein, mitomycin resistance protein, and fosfomycin resistance proteins. SgaA might also function as a strep
Probab=23.38 E-value=1.5e+02 Score=18.73 Aligned_cols=25 Identities=20% Similarity=-0.032 Sum_probs=17.7
Q ss_pred eeeeecCcCHHHHHHHHHHcCCeEE
Q psy13254 4 AHSGFPEISYGKFAQTLVEKGYKVA 28 (132)
Q Consensus 4 ~maGfP~~~l~~y~~kLv~~G~kVa 28 (132)
.+..|-...++.+.++|.++|.++.
T Consensus 63 ~~~~f~v~di~~~~~~l~~~g~~~~ 87 (114)
T cd07247 63 WLVYFAVDDVDAAAARVEAAGGKVL 87 (114)
T ss_pred EEEEEEeCCHHHHHHHHHHCCCEEE
Confidence 3556666777888888888887655
No 106
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=22.82 E-value=50 Score=20.37 Aligned_cols=20 Identities=25% Similarity=0.419 Sum_probs=18.7
Q ss_pred eeecCcCHHHHHHHHHHcCC
Q psy13254 6 SGFPEISYGKFAQTLVEKGY 25 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~G~ 25 (132)
.|+|-.+...++.+|.+.|+
T Consensus 32 lgl~~~~v~r~L~~L~~~G~ 51 (68)
T smart00550 32 LGLPKKEVNRVLYSLEKKGK 51 (68)
T ss_pred HCCCHHHHHHHHHHHHHCCC
Confidence 68899999999999999999
No 107
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=22.62 E-value=57 Score=25.53 Aligned_cols=25 Identities=24% Similarity=0.243 Sum_probs=22.1
Q ss_pred eeeecCcCHHHHHHHHHHcCCeEEE
Q psy13254 5 HSGFPEISYGKFAQTLVEKGYKVAR 29 (132)
Q Consensus 5 maGfP~~~l~~y~~kLv~~G~kVai 29 (132)
++|+|...+...++.|..+|+=-++
T Consensus 39 ~sgvP~~kvY~vl~sLe~kG~v~~~ 63 (247)
T COG1378 39 ASGVPRPKVYDVLRSLEKKGLVEVI 63 (247)
T ss_pred HcCCCchhHHHHHHHHHHCCCEEee
Confidence 4799999999999999999995554
No 108
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=22.37 E-value=1.7e+02 Score=18.68 Aligned_cols=32 Identities=25% Similarity=0.415 Sum_probs=22.6
Q ss_pred EEEEEEECCcceEEEEEEeChhhHHHHHHhhcc
Q psy13254 95 LGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSH 127 (132)
Q Consensus 95 ~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~ 127 (132)
+-|..++ +.++|++.....+..+.+|...|..
T Consensus 8 v~It~v~-~~~~~~v~~~~~~~~~~~l~~~l~~ 39 (121)
T PF00567_consen 8 VYITHVD-SPGEFYVQPDSADKAYEKLQEELQD 39 (121)
T ss_dssp EEEEEEC-TTSEEEEEECCCHHHHHHHHHHHHH
T ss_pred EEEEEEe-cCCEEEEEEcCCHHHHHHHHHHHHH
Confidence 4566677 8899999666666667777776654
No 109
>cd07238 Glo_EDI_BRP_like_5 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The structure of this family is a that of a strand-swapped dimer.
Probab=22.11 E-value=1.2e+02 Score=19.26 Aligned_cols=25 Identities=8% Similarity=0.073 Sum_probs=16.7
Q ss_pred eeeeecCcCHHHHHHHHHHcCCeEE
Q psy13254 4 AHSGFPEISYGKFAQTLVEKGYKVA 28 (132)
Q Consensus 4 ~maGfP~~~l~~y~~kLv~~G~kVa 28 (132)
++.+|-...++...++|.++|.++.
T Consensus 59 ~~i~~~v~d~~~~~~~l~~~G~~~~ 83 (112)
T cd07238 59 PDLSIEVDDVDAALARAVAAGFAIV 83 (112)
T ss_pred CEEEEEeCCHHHHHHHHHhcCCeEe
Confidence 4555666667777777777777653
No 110
>PRK08383 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=22.05 E-value=1.7e+02 Score=21.70 Aligned_cols=10 Identities=20% Similarity=0.202 Sum_probs=7.5
Q ss_pred EEccceeecc
Q psy13254 62 ITCRGAQTFS 71 (132)
Q Consensus 62 I~TpGT~~~~ 71 (132)
-.||||++-+
T Consensus 118 TLTPGTl~vd 127 (168)
T PRK08383 118 TLTPGTLTIE 127 (168)
T ss_pred hcCCCeEEEE
Confidence 3789999843
No 111
>TIGR01662 HAD-SF-IIIA HAD-superfamily hydrolase, subfamily IIIA. In the case of histidinol phosphatase and PNK-3'-phosphatase, this model represents a domain of a bifunctional system. In the histidinol phosphatase HisB, a C-terminal domain is an imidazoleglycerol-phosphate dehydratase which catalyzes a related step in histidine biosynthesis. In PNK-3'-phosphatase, N- and C-terminal domains constitute the polynucleotide kinase and DNA-binding components of the enzyme.
Probab=21.91 E-value=1.3e+02 Score=20.15 Aligned_cols=22 Identities=32% Similarity=0.250 Sum_probs=17.9
Q ss_pred CcCHHHHHHHHHHcCCeEEEEe
Q psy13254 10 EISYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 10 ~~~l~~y~~kLv~~G~kVaive 31 (132)
..-+...++.|-++|++++++-
T Consensus 27 ~~~v~~~l~~L~~~g~~l~i~S 48 (132)
T TIGR01662 27 YPEVPDALAELKEAGYKVVIVT 48 (132)
T ss_pred CCCHHHHHHHHHHCCCEEEEEE
Confidence 4455668899999999999994
No 112
>TIGR00338 serB phosphoserine phosphatase SerB. Phosphoserine phosphatase catalyzes the reaction 3-phospho-serine + H2O = L-serine + phosphate. It catalyzes the last of three steps in the biosynthesis of serine from D-3-phosphoglycerate. Note that this enzyme acts on free phosphoserine, not on phosphoserine residues of phosphoproteins.
Probab=21.91 E-value=1.2e+02 Score=22.06 Aligned_cols=23 Identities=39% Similarity=0.485 Sum_probs=19.4
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEe
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaive 31 (132)
|...+...++.|-++|++++|+-
T Consensus 86 ~~~g~~~~l~~l~~~g~~~~IvS 108 (219)
T TIGR00338 86 LTEGAEELVKTLKEKGYKVAVIS 108 (219)
T ss_pred cCCCHHHHHHHHHHCCCEEEEEC
Confidence 55667788999999999999985
No 113
>PF04016 DUF364: Domain of unknown function (DUF364); InterPro: IPR007161 This is a entry represents of bacterial and archaeal proteins of unknown function.; PDB: 3L5O_B 3NPG_A.
Probab=21.88 E-value=61 Score=23.17 Aligned_cols=72 Identities=11% Similarity=0.070 Sum_probs=38.7
Q ss_pred Ceeeee-ecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhcc-CCCCCCCCeEEeeeeEEEccceeeccccccccCC
Q psy13254 2 EYAHSG-FPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICKITCRGAQTFSIMDVDANY 79 (132)
Q Consensus 2 ~~~maG-fP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~-~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~ 79 (132)
++.|.| || .++++|.+.|++|-|+|=-.+.... .+. -+......++.+.=.=++|-.|++....+..|+.
T Consensus 13 ~V~~VG~f~-----P~~~~l~~~~~~v~v~d~~~~~~~~---~~~~~~~~~~~~~l~~aD~viiTGsTlvN~Ti~~iL~~ 84 (147)
T PF04016_consen 13 KVGMVGYFQ-----PLVEKLKERGAEVRVFDLNPDNIGE---EPGDVPDEDAEEILPWADVVIITGSTLVNGTIDDILEL 84 (147)
T ss_dssp EEEEES--H-----CCHHHHCCCCSEEEEEESSGGG--S---SCT-EEGGGHHHHGGG-SEEEEECHHCCTTTHHHHHHH
T ss_pred EEEEEcCcH-----HHHHHHhcCCCCEEEEECCCCCCCC---CCCcCCHHHHHHHHccCCEEEEEeeeeecCCHHHHHHh
Confidence 356788 51 2678888899999999843321110 000 0000011344444456889999987765554443
Q ss_pred CC
Q psy13254 80 VD 81 (132)
Q Consensus 80 ~~ 81 (132)
..
T Consensus 85 ~~ 86 (147)
T PF04016_consen 85 AR 86 (147)
T ss_dssp TT
T ss_pred Cc
Confidence 33
No 114
>PHA02540 61 DNA primase; Provisional
Probab=21.62 E-value=92 Score=25.73 Aligned_cols=28 Identities=21% Similarity=0.232 Sum_probs=22.4
Q ss_pred CHHHHHHHHHHcCCeEEEEeec----cChhhh
Q psy13254 12 SYGKFAQTLVEKGYKVARVEQT----ESAEQM 39 (132)
Q Consensus 12 ~l~~y~~kLv~~G~kVaiveQ~----e~~~~~ 39 (132)
+.-.-+++|+++|.+|+|...- ++|++.
T Consensus 271 at~r~~~~l~~~g~~v~v~~~~~~~~kDpde~ 302 (337)
T PHA02540 271 DTIKRISKLIDAGEKVVIWDKCPWPSKDINDM 302 (337)
T ss_pred HHHHHHHHHHHCCCeEEEecCCCCCCcCHHHH
Confidence 3445588999999999999876 788765
No 115
>TIGR01681 HAD-SF-IIIC HAD-superfamily phosphatase, subfamily IIIC. No member of this subfamily is characterized with respect to function, however the MDP-1 protein is a characterized phosphatase. All of the characterized enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases are present in subfamily IIIC.
Probab=21.49 E-value=78 Score=21.67 Aligned_cols=24 Identities=21% Similarity=0.134 Sum_probs=19.3
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEee
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVEQ 32 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaiveQ 32 (132)
|...+...++.|-++|++++|+-=
T Consensus 30 ~~~gv~e~L~~Lk~~g~~l~i~Sn 53 (128)
T TIGR01681 30 TIKEIRDKLQTLKKNGFLLALASY 53 (128)
T ss_pred HHHHHHHHHHHHHHCCeEEEEEeC
Confidence 455677788888889999999953
No 116
>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....
Probab=21.43 E-value=90 Score=22.06 Aligned_cols=18 Identities=28% Similarity=0.274 Sum_probs=11.8
Q ss_pred HHHHH-HHHcCCeEEEEee
Q psy13254 15 KFAQT-LVEKGYKVARVEQ 32 (132)
Q Consensus 15 ~y~~k-Lv~~G~kVaiveQ 32 (132)
..+.. |-++|+||+++|-
T Consensus 17 ~~la~~la~~g~~VlliD~ 35 (195)
T PF01656_consen 17 ANLAQALARKGKKVLLIDL 35 (195)
T ss_dssp HHHHHHHHHTTS-EEEEEE
T ss_pred HHHHhcccccccccccccc
Confidence 33444 4457999999996
No 117
>PF13477 Glyco_trans_4_2: Glycosyl transferase 4-like
Probab=21.43 E-value=95 Score=20.68 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=19.4
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEee
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVEQ 32 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaiveQ 32 (132)
|+.-.-.+++.|.+.||.|-++-.
T Consensus 9 ~~~~~~~~~~~L~~~g~~V~ii~~ 32 (139)
T PF13477_consen 9 PSTFIYNLAKELKKRGYDVHIITP 32 (139)
T ss_pred cHHHHHHHHHHHHHCCCEEEEEEc
Confidence 444566889999999999998876
No 118
>PF12695 Abhydrolase_5: Alpha/beta hydrolase family; PDB: 3D0K_B 2I3D_B 3DOH_B 3DOI_B 3PFB_A 3S2Z_B 3PFC_A 3QM1_A 3PF8_B 3PF9_A ....
Probab=21.38 E-value=76 Score=20.95 Aligned_cols=26 Identities=27% Similarity=0.492 Sum_probs=21.0
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEeecc
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVEQTE 34 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaiveQ~e 34 (132)
....+..+++.|.++||-|+.++.-.
T Consensus 11 ~~~~~~~~~~~l~~~G~~v~~~~~~~ 36 (145)
T PF12695_consen 11 SRRDYQPLAEALAEQGYAVVAFDYPG 36 (145)
T ss_dssp TTHHHHHHHHHHHHTTEEEEEESCTT
T ss_pred CHHHHHHHHHHHHHCCCEEEEEecCC
Confidence 34557789999999999999998543
No 119
>cd00851 MTH1175 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).
Probab=21.33 E-value=63 Score=20.75 Aligned_cols=33 Identities=21% Similarity=0.092 Sum_probs=24.7
Q ss_pred eecCcCHHHHHHHHHHcCCeEEEEeeccChhhh
Q psy13254 7 GFPEISYGKFAQTLVEKGYKVARVEQTESAEQM 39 (132)
Q Consensus 7 GfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~ 39 (132)
+.+.+.-...++.|...|-.++||-++......
T Consensus 46 ~~~~~~~~~~~~~l~~~~v~~vi~~~iG~~~~~ 78 (103)
T cd00851 46 HATGGAGGKAAEFLADEGVDVVIVGGIGPRALN 78 (103)
T ss_pred cccCCCchHHHHHHHHcCCCEEEeCCCCcCHHH
Confidence 333445577888888899999999998766544
No 120
>TIGR01656 Histidinol-ppas histidinol-phosphate phosphatase family domain. This domain is a member of the haloacid-dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. This superfamily is distinguished by the presence of three motifs: an N-terminal motif containing the nucleophilic aspartate, a central motif containing an conserved serine or threonine, and a C-terminal motif containing a conserved lysine (or arginine) and conserved aspartates. More specifically, the domian modelled here is a member of subfamily III of the HAD-superfamily by virtue of lacking a "capping" domain in either of the two common positions, between motifs 1 and 2, or between motifs 2 and 3.
Probab=21.08 E-value=1.3e+02 Score=20.92 Aligned_cols=23 Identities=26% Similarity=0.120 Sum_probs=18.4
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEe
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVE 31 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaive 31 (132)
|..-+...++.|-++||+++|+-
T Consensus 28 ~~~g~~~~l~~Lk~~g~~~~I~S 50 (147)
T TIGR01656 28 LRPGAVPALLTLRAAGYTVVVVT 50 (147)
T ss_pred EcCChHHHHHHHHHCCCEEEEEe
Confidence 34455678899999999999995
No 121
>PF08040 NADH_oxidored: MNLL subunit; InterPro: IPR012575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of the MNLL subunits of NADH:ubiquinone oxidoreductase complex []. MNLL subunit is one of the many subunits found in the complex and it contains a mitochondrial import sequence. However, the role of MNLL subunit is unclear [].; GO: 0003954 NADH dehydrogenase activity, 0005739 mitochondrion
Probab=21.06 E-value=32 Score=21.31 Aligned_cols=46 Identities=20% Similarity=0.335 Sum_probs=31.9
Q ss_pred eecCcCHHHHHHHHHHcCCeEEEE-eeccChhhhhhhhccCCCCCCCCeEE-eee
Q psy13254 7 GFPEISYGKFAQTLVEKGYKVARV-EQTESAEQMDIRTKRDKVPQKQRVVR-REI 59 (132)
Q Consensus 7 GfP~~~l~~y~~kLv~~G~kVaiv-eQ~e~~~~~~~r~k~~~~~~~~~~v~-Rev 59 (132)
+|=.-.-+.|+..++-.||=|+.. |-.|+......|+| +.+.. ||+
T Consensus 3 n~~~~vr~~~~~~~vPlgf~iG~yLDr~~~erlT~FR~K-------SaLygrRel 50 (59)
T PF08040_consen 3 NLIQIVRDHWVWILVPLGFVIGCYLDRKETERLTAFRNK-------SALYGRREL 50 (59)
T ss_pred cHHHHHHHHHHHHHHhhHhhheeeecccchHHHHhhcch-------hhhccCCCC
Confidence 333334578999999899988776 66677777777776 25666 454
No 122
>TIGR02734 crtI_fam phytoene desaturase. Phytoene is converted to lycopene by desaturation at four (two symmetrical pairs of) sites. This is achieved by two enzymes (crtP and crtQ) in cyanobacteria (Gloeobacter being an exception) and plants, but by a single enzyme in most other bacteria and in fungi. This single enzyme is called the bacterial-type phytoene desaturase, or CrtI. Most members of this family, part of the larger Pfam family pfam01593, which also contains amino oxidases, are CrtI itself; it is likely that all members act on either phytoene or on related compounds such as dehydrosqualene, for carotenoid biosynthesis.
Probab=20.95 E-value=77 Score=26.63 Aligned_cols=21 Identities=33% Similarity=0.368 Sum_probs=16.5
Q ss_pred HHHHHHcCCeEEEEeeccChh
Q psy13254 17 AQTLVEKGYKVARVEQTESAE 37 (132)
Q Consensus 17 ~~kLv~~G~kVaiveQ~e~~~ 37 (132)
+..|-++|++|.|+|+-..+-
T Consensus 14 A~~La~~G~~V~VlE~~~~~G 34 (502)
T TIGR02734 14 AIRLAAAGIPVTVVEQRDKPG 34 (502)
T ss_pred HHHHHhCCCcEEEEECCCCCc
Confidence 446677999999999877653
No 123
>COG1832 Predicted CoA-binding protein [General function prediction only]
Probab=20.87 E-value=1e+02 Score=22.36 Aligned_cols=24 Identities=33% Similarity=0.522 Sum_probs=20.0
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEee
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVEQ 32 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaiveQ 32 (132)
|......-.+-|.++||+|.=|.-
T Consensus 28 P~r~sy~V~kyL~~~GY~ViPVNP 51 (140)
T COG1832 28 PDRPSYRVAKYLQQKGYRVIPVNP 51 (140)
T ss_pred CCccHHHHHHHHHHCCCEEEeeCc
Confidence 677777778889999999998874
No 124
>PF01266 DAO: FAD dependent oxidoreductase; InterPro: IPR006076 This entry includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase (1.1.99.5 from EC), Sarcosine oxidase beta subunit (1.5.3.1 from EC), D-alanine oxidase (1.4.99.1 from EC), D-aspartate oxidase (1.4.3.1 from EC). D-amino acid oxidase (1.4.3.3 from EC) (DAMOX or DAO) is an FAD flavoenzyme that catalyzes the oxidation of neutral and basic D-amino acids into their corresponding keto acids. DAOs have been characterised and sequenced in fungi and vertebrates where they are known to be located in the peroxisomes. D-aspartate oxidase (1.4.3.1 from EC) (DASOX) [] is an enzyme, structurally related to DAO, which catalyzes the same reaction but is active only toward dicarboxylic D-amino acids. In DAO, a conserved histidine has been shown [] to be important for the enzyme's catalytic activity.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2RGO_A 3NYE_A 3NYF_A 3NYC_A 3SM8_A 3SGL_A 3PVC_A 3DME_A 2GAH_B 3NLC_A ....
Probab=20.79 E-value=92 Score=23.92 Aligned_cols=15 Identities=27% Similarity=0.428 Sum_probs=11.3
Q ss_pred HHHHcCCeEEEEeec
Q psy13254 19 TLVEKGYKVARVEQT 33 (132)
Q Consensus 19 kLv~~G~kVaiveQ~ 33 (132)
.|.+.|++|.++|+-
T Consensus 17 ~La~~G~~V~l~e~~ 31 (358)
T PF01266_consen 17 ELARRGHSVTLLERG 31 (358)
T ss_dssp HHHHTTSEEEEEESS
T ss_pred HHHHCCCeEEEEeec
Confidence 455588888888876
No 125
>PF09981 DUF2218: Uncharacterized protein conserved in bacteria (DUF2218); InterPro: IPR014543 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2JPI_A.
Probab=20.74 E-value=1e+02 Score=20.19 Aligned_cols=26 Identities=8% Similarity=0.056 Sum_probs=20.0
Q ss_pred eeecCcCHHHHHHHHHHc-CCeEEEEe
Q psy13254 6 SGFPEISYGKFAQTLVEK-GYKVARVE 31 (132)
Q Consensus 6 aGfP~~~l~~y~~kLv~~-G~kVaive 31 (132)
+-||-.+...|+++|.++ ++|+-+-.
T Consensus 3 a~v~T~~~~ryl~qLc~Hf~hk~~v~~ 29 (89)
T PF09981_consen 3 ARVATPNASRYLKQLCKHFAHKFEVEW 29 (89)
T ss_dssp EEE--SSHHHHHHHHHHHTTTSSEEEE
T ss_pred eEEECCCHHHHHHHHHHHhcCCCceEE
Confidence 567888899999999995 99987654
No 126
>COG1341 Predicted GTPase or GTP-binding protein [General function prediction only]
Probab=20.62 E-value=79 Score=26.82 Aligned_cols=20 Identities=30% Similarity=0.576 Sum_probs=14.8
Q ss_pred CHHHH-HHHHHHcCCeEEEEe
Q psy13254 12 SYGKF-AQTLVEKGYKVARVE 31 (132)
Q Consensus 12 ~l~~y-~~kLv~~G~kVaive 31 (132)
+|-.| +.+|++.||||+|+|
T Consensus 88 TLt~~LaN~~l~rG~~v~iiD 108 (398)
T COG1341 88 TLTTYLANKLLARGRKVAIID 108 (398)
T ss_pred HHHHHHHHHHhhcCceEEEEe
Confidence 34444 467888899999998
No 127
>PF00707 IF3_C: Translation initiation factor IF-3, C-terminal domain; InterPro: IPR019815 Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit []. The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 []. ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2IFE_A 1TIG_A 2CRQ_A.
Probab=20.60 E-value=88 Score=20.27 Aligned_cols=18 Identities=39% Similarity=0.383 Sum_probs=13.8
Q ss_pred HHHHHHHcCCeEEEEeec
Q psy13254 16 FAQTLVEKGYKVARVEQT 33 (132)
Q Consensus 16 y~~kLv~~G~kVaiveQ~ 33 (132)
-+.+++++||+|=|+=+.
T Consensus 24 ~~~~fL~kG~~Vkv~i~~ 41 (88)
T PF00707_consen 24 QAKKFLEKGHKVKVVIRF 41 (88)
T ss_dssp HHHHHHHTTEEEEEEEE-
T ss_pred HHHHHHHCCCEEEEEEEe
Confidence 477899999999776544
No 128
>PF05240 APOBEC_C: APOBEC-like C-terminal domain; InterPro: IPR007904 This domain is found at the C terminus of the Apolipoprotein B mRNA editing enzyme. Apobec-1 catalyzes C to U editing of apolipoprotein B (apoB) mRNA in the mammalian intestine. C to U RNA editing of mammalian apolipoprotein B (apoB) RNA is a site-specific posttranscriptional modification in which a single cytidine is enzymatically deaminated to uridine, thereby generating a UAA stop codon in the edited mRNA. The function of this domain is currently unknown.; GO: 0008270 zinc ion binding, 0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines; PDB: 2NYT_D.
Probab=20.54 E-value=99 Score=18.79 Aligned_cols=17 Identities=18% Similarity=0.216 Sum_probs=11.9
Q ss_pred HHHHHHHHcCCeEEEEe
Q psy13254 15 KFAQTLVEKGYKVARVE 31 (132)
Q Consensus 15 ~y~~kLv~~G~kVaive 31 (132)
.=|.+|.++|-+|.|-.
T Consensus 6 egLr~L~~aG~~v~iM~ 22 (55)
T PF05240_consen 6 EGLRRLCQAGAQVSIMT 22 (55)
T ss_dssp HHHHHHHHTT-EEEE--
T ss_pred HHHHHHHHCCCeEEecC
Confidence 34789999999999875
No 129
>PF14574 DUF4445: Domain of unknown function (DUF4445); PDB: 3ZYY_X.
Probab=20.46 E-value=1.7e+02 Score=24.87 Aligned_cols=30 Identities=13% Similarity=0.216 Sum_probs=21.4
Q ss_pred ceEEEEEecCCEEEEEEEECCcceEEEEEE
Q psy13254 83 KFLLGVTKEGDRLGVCFIDTTIGEFHVGEF 112 (132)
Q Consensus 83 ~yllai~~~~~~~Gi~~~D~sTg~~~~~~~ 112 (132)
+|-+||.....++..+++|+.||++.-...
T Consensus 1 ~~GiAvDiGTTti~~~L~dl~~G~~l~~~s 30 (412)
T PF14574_consen 1 NYGIAVDIGTTTIAAYLVDLETGEVLATAS 30 (412)
T ss_dssp -EEEEEEE-SSEEEEEEEETTT--EEEEEE
T ss_pred CEEEEEEcchhheeeEEEECCCCCEEEeec
Confidence 467788777889999999999999865544
No 130
>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.
Probab=20.42 E-value=93 Score=23.57 Aligned_cols=14 Identities=43% Similarity=0.413 Sum_probs=11.3
Q ss_pred HHHHHcCCeEEEEe
Q psy13254 18 QTLVEKGYKVARVE 31 (132)
Q Consensus 18 ~kLv~~G~kVaive 31 (132)
..|.+.|+||+++|
T Consensus 23 ~~La~~G~kVlliD 36 (270)
T cd02040 23 AALAEMGKKVMIVG 36 (270)
T ss_pred HHHHhCCCeEEEEE
Confidence 34556999999997
No 131
>PF06863 DUF1254: Protein of unknown function (DUF1254); InterPro: IPR010679 This entry represents an immunoglobulin-like beta-sandwich domain found in a group of hypothetical proteins of unknown function.; PDB: 3VB9_D 2P3Y_A 3U07_A.
Probab=20.31 E-value=1e+02 Score=21.35 Aligned_cols=20 Identities=10% Similarity=0.184 Sum_probs=14.0
Q ss_pred CCEEEEEEEECCcceEEEEE
Q psy13254 92 GDRLGVCFIDTTIGEFHVGE 111 (132)
Q Consensus 92 ~~~~Gi~~~D~sTg~~~~~~ 111 (132)
+.-|+.||+|++.|-+.+.-
T Consensus 24 DtlYs~a~~DL~~gPvvi~v 43 (128)
T PF06863_consen 24 DTLYSSAWLDLSNGPVVIEV 43 (128)
T ss_dssp SCEEEEEEEEHCCSSEEEEE
T ss_pred CceeEEEEEEcCCCCEEEEe
Confidence 34688888999888554443
No 132
>TIGR02253 CTE7 HAD superfamily (subfamily IA) hydrolase, TIGR02253. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549).
Probab=20.19 E-value=1.4e+02 Score=21.66 Aligned_cols=25 Identities=16% Similarity=0.171 Sum_probs=20.5
Q ss_pred cCcCHHHHHHHHHHcCCeEEEEeec
Q psy13254 9 PEISYGKFAQTLVEKGYKVARVEQT 33 (132)
Q Consensus 9 P~~~l~~y~~kLv~~G~kVaiveQ~ 33 (132)
|..-+...++.|-++|++++|+--.
T Consensus 95 ~~~g~~~~L~~L~~~g~~~~i~Tn~ 119 (221)
T TIGR02253 95 VYPGVRDTLMELRESGYRLGIITDG 119 (221)
T ss_pred CCCCHHHHHHHHHHCCCEEEEEeCC
Confidence 5566778899999999999999644
No 133
>COG0278 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.07 E-value=1.5e+02 Score=20.40 Aligned_cols=33 Identities=27% Similarity=0.406 Sum_probs=24.9
Q ss_pred CeeeeeecCcCHHHHHHHHHHcC-CeEEEEeeccChhh
Q psy13254 2 EYAHSGFPEISYGKFAQTLVEKG-YKVARVEQTESAEQ 38 (132)
Q Consensus 2 ~~~maGfP~~~l~~y~~kLv~~G-~kVaiveQ~e~~~~ 38 (132)
.+|+|||...+ ++.|-..| -..+-++=.++++-
T Consensus 26 ~~P~CGFS~~~----vqiL~~~g~v~~~~vnVL~d~ei 59 (105)
T COG0278 26 EFPQCGFSAQA----VQILSACGVVDFAYVDVLQDPEI 59 (105)
T ss_pred CCCCCCccHHH----HHHHHHcCCcceeEEeeccCHHH
Confidence 47999998644 55677789 67888888888654
Done!