Query psy3003
Match_columns 106
No_of_seqs 104 out of 439
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 23:01:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3003.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3003hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3165|consensus 100.0 8.7E-37 1.9E-41 217.5 9.2 103 3-105 91-193 (195)
2 PF04900 Fcf1: Fcf1; InterPro 100.0 2.7E-35 6E-40 194.9 9.4 95 2-98 3-101 (101)
3 KOG3164|consensus 100.0 5.4E-33 1.2E-37 205.4 8.2 99 3-103 53-154 (236)
4 COG1412 Uncharacterized protei 99.9 8.1E-28 1.8E-32 167.6 7.2 95 4-100 39-136 (136)
5 PRK13764 ATPase; Provisional 97.9 2E-05 4.3E-10 66.4 5.9 91 6-98 26-139 (602)
6 PF13638 PIN_4: PIN domain; PD 97.1 0.0013 2.8E-08 44.2 5.4 84 5-89 19-133 (133)
7 smart00670 PINc Large family o 96.8 0.0022 4.8E-08 41.2 4.0 70 6-75 24-111 (111)
8 PRK00124 hypothetical protein; 95.3 0.025 5.5E-07 40.2 3.8 79 13-94 9-98 (151)
9 COG4956 Integral membrane prot 93.3 0.15 3.3E-06 40.4 4.5 80 8-89 187-281 (356)
10 PF02639 DUF188: Uncharacteriz 93.3 0.11 2.4E-06 35.9 3.4 58 37-97 28-85 (130)
11 PF05991 NYN_YacP: YacP-like N 92.8 0.33 7.1E-06 34.5 5.4 39 47-86 76-118 (166)
12 PRK12496 hypothetical protein; 89.1 1.4 3E-05 31.5 5.6 80 8-91 21-118 (164)
13 smart00500 SFM Splicing Factor 87.3 0.44 9.6E-06 27.2 1.7 21 68-89 1-21 (44)
14 COG1656 Uncharacterized conser 83.8 2.6 5.6E-05 30.5 4.6 50 37-92 26-75 (165)
15 PF13344 Hydrolase_6: Haloacid 82.8 3.4 7.4E-05 26.7 4.5 36 49-85 18-58 (101)
16 COG1855 ATPase (PilT family) [ 78.4 21 0.00045 30.4 8.6 82 7-90 31-133 (604)
17 PF00462 Glutaredoxin: Glutare 77.1 2.2 4.8E-05 24.5 2.0 29 64-92 28-59 (60)
18 COG1671 Uncharacterized protei 77.1 3.1 6.7E-05 29.7 3.1 45 49-96 55-99 (150)
19 COG1911 RPL30 Ribosomal protei 77.0 2.7 5.8E-05 28.0 2.5 46 50-95 24-74 (100)
20 COG0069 GltB Glutamate synthas 76.4 1.4 3.1E-05 36.7 1.4 14 64-77 425-438 (485)
21 COG4634 Uncharacterized protei 75.7 6.2 0.00014 26.8 4.1 39 49-89 35-75 (113)
22 PF01927 Mut7-C: Mut7-C RNAse 75.6 8.4 0.00018 26.7 4.9 39 49-90 29-67 (147)
23 TIGR00305 probable toxin-antit 75.1 13 0.00028 24.1 5.5 71 3-74 27-112 (114)
24 COG0117 RibD Pyrimidine deamin 74.5 2.6 5.6E-05 29.9 2.1 46 39-86 74-126 (146)
25 PF02739 5_3_exonuc_N: 5'-3' e 72.9 2.9 6.2E-05 29.8 2.1 50 37-90 99-152 (169)
26 cd00008 53EXOc 5'-3' exonuclea 65.2 7.2 0.00016 29.2 2.9 39 38-78 99-141 (240)
27 TIGR02181 GRX_bact Glutaredoxi 64.9 13 0.00027 22.2 3.6 31 63-93 27-60 (79)
28 cd03418 GRX_GRXb_1_3_like Glut 64.1 8.4 0.00018 22.6 2.6 30 64-93 29-62 (75)
29 PF02254 TrkA_N: TrkA-N domain 63.6 25 0.00055 22.2 5.0 39 50-89 10-48 (116)
30 cd01543 PBP1_XylR Ligand-bindi 62.4 34 0.00073 24.5 6.0 61 27-91 18-80 (265)
31 COG0695 GrxC Glutaredoxin and 57.8 20 0.00044 22.2 3.6 30 63-92 29-63 (80)
32 PRK09482 flap endonuclease-lik 55.0 12 0.00025 28.7 2.5 39 46-86 104-146 (256)
33 TIGR02194 GlrX_NrdH Glutaredox 53.7 20 0.00044 21.2 3.0 28 64-91 28-57 (72)
34 cd06309 PBP1_YtfQ_like Peripla 53.1 71 0.0015 22.9 6.4 63 28-91 20-89 (273)
35 PF02348 CTP_transf_3: Cytidyl 52.3 26 0.00056 24.8 3.9 27 63-90 42-68 (217)
36 KOG3460|consensus 49.9 43 0.00094 21.7 4.2 20 81-100 69-88 (91)
37 TIGR00028 Mtu_PIN_fam Mycobact 49.7 15 0.00033 23.9 2.2 33 49-86 105-137 (142)
38 TIGR03875 RNA_lig_partner RNA 49.6 45 0.00099 25.0 4.8 37 49-87 158-194 (206)
39 TIGR01457 HAD-SF-IIA-hyp2 HAD- 49.5 27 0.00059 25.8 3.8 37 49-86 21-62 (249)
40 cd02066 GRX_family Glutaredoxi 49.3 20 0.00043 20.0 2.4 25 68-92 33-60 (72)
41 PRK04358 hypothetical protein; 48.9 30 0.00066 26.1 3.8 37 49-87 162-198 (217)
42 cd06301 PBP1_rhizopine_binding 48.8 96 0.0021 22.1 6.6 63 28-91 20-90 (272)
43 COG1439 Predicted nucleic acid 48.4 71 0.0015 23.3 5.6 78 9-90 29-128 (177)
44 PF11977 RNase_Zc3h12a: Zc3h12 48.3 16 0.00035 25.3 2.2 46 49-97 89-143 (155)
45 COG1875 NYN ribonuclease and A 48.2 24 0.00052 29.1 3.4 78 7-85 25-142 (436)
46 smart00475 53EXOc 5'-3' exonuc 47.9 20 0.00043 27.3 2.8 33 47-79 105-141 (259)
47 KOG1475|consensus 47.5 11 0.00024 30.0 1.4 33 63-95 206-239 (363)
48 TIGR02634 xylF D-xylose ABC tr 47.1 1.1E+02 0.0023 22.8 6.7 62 28-90 19-87 (302)
49 KOG3964|consensus 46.4 18 0.00039 30.0 2.4 17 63-79 416-432 (469)
50 PRK14976 5'-3' exonuclease; Pr 46.4 21 0.00046 27.5 2.8 49 38-90 104-156 (281)
51 cd03028 GRX_PICOT_like Glutare 45.8 23 0.00051 22.1 2.5 29 64-92 42-73 (90)
52 PF05716 AKAP_110: A-kinase an 45.7 18 0.0004 31.1 2.5 24 68-91 600-627 (685)
53 PTZ00062 glutaredoxin; Provisi 45.5 22 0.00047 26.2 2.6 29 65-93 148-179 (204)
54 PF08712 Nfu_N: Scaffold prote 43.1 65 0.0014 20.4 4.3 33 68-100 34-66 (87)
55 KOG0399|consensus 42.8 11 0.00024 35.6 0.8 19 64-82 1220-1238(2142)
56 TIGR00411 redox_disulf_1 small 42.4 47 0.001 19.4 3.4 30 67-98 39-68 (82)
57 cd03419 GRX_GRXh_1_2_like Glut 42.3 29 0.00062 20.5 2.4 22 71-92 39-63 (82)
58 cd03031 GRX_GRX_like Glutaredo 42.0 27 0.0006 24.4 2.6 26 67-92 38-70 (147)
59 cd03027 GRX_DEP Glutaredoxin ( 40.1 41 0.0009 19.7 2.9 29 64-92 30-61 (73)
60 PRK10824 glutaredoxin-4; Provi 38.4 72 0.0016 21.4 4.1 31 63-93 48-81 (115)
61 cd08556 GDPD Glycerophosphodie 38.1 1.3E+02 0.0027 20.4 6.9 43 50-92 77-123 (189)
62 TIGR00365 monothiol glutaredox 37.9 36 0.00079 21.7 2.5 26 67-92 49-77 (97)
63 smart00540 LEM in nuclear memb 37.4 20 0.00043 20.3 1.1 16 69-85 7-22 (44)
64 PF12226 Astro_capsid_p: Turke 37.4 31 0.00067 25.5 2.3 24 66-89 108-132 (230)
65 TIGR02180 GRX_euk Glutaredoxin 37.3 39 0.00085 19.8 2.5 22 71-92 40-64 (84)
66 cd03030 GRX_SH3BGR Glutaredoxi 36.9 42 0.00092 21.5 2.7 28 64-91 35-69 (92)
67 PF08745 UPF0278: UPF0278 fami 36.0 47 0.001 24.9 3.1 38 50-89 156-193 (205)
68 cd02973 TRX_GRX_like Thioredox 36.0 47 0.001 18.9 2.6 24 68-92 39-62 (67)
69 cd04888 ACT_PheB-BS C-terminal 35.4 89 0.0019 18.0 3.9 26 63-88 44-74 (76)
70 PHA00439 exonuclease 35.1 37 0.00079 26.6 2.5 30 47-76 118-152 (286)
71 COG1609 PurR Transcriptional r 34.5 2E+02 0.0043 22.2 6.6 64 28-92 79-147 (333)
72 TIGR02200 GlrX_actino Glutared 34.5 61 0.0013 18.6 3.0 35 64-99 29-67 (77)
73 PRK11440 putative hydrolase; P 34.3 40 0.00087 23.7 2.5 19 71-90 38-56 (188)
74 PRK09468 ompR osmolarity respo 33.4 66 0.0014 22.5 3.5 29 72-100 208-238 (239)
75 PRK10355 xylF D-xylose transpo 32.3 2E+02 0.0044 21.9 6.3 63 27-90 45-114 (330)
76 PHA03050 glutaredoxin; Provisi 32.0 54 0.0012 21.5 2.7 24 70-93 54-80 (108)
77 cd01141 TroA_d Periplasmic bin 31.8 42 0.00091 23.1 2.2 26 64-90 72-100 (186)
78 PF03407 Nucleotid_trans: Nucl 31.8 79 0.0017 22.3 3.7 28 63-91 5-32 (212)
79 PLN02645 phosphoglycolate phos 31.6 1.2E+02 0.0025 23.3 4.8 36 49-85 48-88 (311)
80 cd06292 PBP1_LacI_like_10 Liga 31.4 1.9E+02 0.0042 20.5 6.4 64 27-91 19-92 (273)
81 cd01540 PBP1_arabinose_binding 31.4 1.8E+02 0.0038 20.9 5.6 60 31-91 23-88 (289)
82 cd01541 PBP1_AraR Ligand-bindi 31.3 1.9E+02 0.0042 20.5 6.9 64 27-91 19-92 (273)
83 COG1654 BirA Biotin operon rep 31.2 40 0.00086 21.3 1.8 27 73-100 39-65 (79)
84 PF13407 Peripla_BP_4: Peripla 30.6 1.1E+02 0.0024 21.7 4.3 41 50-91 44-89 (257)
85 COG2002 AbrB Regulators of sta 30.6 1.2E+02 0.0026 19.1 4.0 32 70-101 19-53 (89)
86 PF01850 PIN: PIN domain; Int 30.5 66 0.0014 19.9 2.9 69 7-77 29-119 (121)
87 PF00875 DNA_photolyase: DNA p 30.0 60 0.0013 22.2 2.8 19 72-91 57-75 (165)
88 PHA02567 rnh RnaseH; Provision 29.7 48 0.001 26.2 2.4 38 47-85 128-169 (304)
89 COG3688 Predicted RNA-binding 29.3 63 0.0014 23.5 2.8 26 47-72 80-110 (173)
90 COG0278 Glutaredoxin-related p 29.2 1E+02 0.0022 20.7 3.5 38 54-91 39-80 (105)
91 KOG1752|consensus 29.1 68 0.0015 21.2 2.7 23 71-93 53-78 (104)
92 PF12813 XPG_I_2: XPG domain c 28.0 28 0.00062 26.2 0.9 30 40-73 23-52 (246)
93 PF08799 PRP4: pre-mRNA proces 27.9 18 0.0004 18.8 -0.1 16 73-89 1-16 (30)
94 COG1358 RPL8A Ribosomal protei 27.9 1.9E+02 0.004 19.5 4.8 42 50-91 32-79 (116)
95 cd06300 PBP1_ABC_sugar_binding 27.5 1.5E+02 0.0034 21.0 4.7 42 49-91 48-94 (272)
96 PF01202 SKI: Shikimate kinase 27.2 1.5E+02 0.0032 20.1 4.3 37 51-90 52-93 (158)
97 PRK10444 UMP phosphatase; Prov 27.1 92 0.002 23.2 3.5 35 49-84 21-60 (248)
98 cd08568 GDPD_TmGDE_like Glycer 27.1 2.4E+02 0.0052 20.2 7.5 79 10-90 60-148 (226)
99 PRK13010 purU formyltetrahydro 27.1 83 0.0018 24.4 3.3 40 51-91 107-150 (289)
100 TIGR02196 GlrX_YruB Glutaredox 27.0 1.1E+02 0.0024 16.9 3.2 23 68-90 33-58 (74)
101 PRK05647 purN phosphoribosylgl 26.6 1.8E+02 0.0038 21.1 4.8 47 43-90 8-59 (200)
102 cd02976 NrdH NrdH-redoxin (Nrd 26.5 1.2E+02 0.0026 16.8 3.3 24 68-91 33-59 (73)
103 TIGR03614 RutB pyrimidine util 26.4 64 0.0014 23.6 2.5 19 71-90 52-70 (226)
104 PRK04280 arginine repressor; P 26.4 46 0.00099 23.3 1.6 7 73-79 40-46 (148)
105 cd00128 XPG Xeroderma pigmento 26.2 55 0.0012 25.1 2.2 35 49-88 150-184 (316)
106 COG2908 Uncharacterized protei 25.7 62 0.0013 24.7 2.3 11 82-92 67-77 (237)
107 TIGR01458 HAD-SF-IIA-hyp3 HAD- 25.6 1.5E+02 0.0033 22.0 4.5 36 49-85 25-65 (257)
108 PF03020 LEM: LEM domain; Int 25.4 11 0.00024 21.3 -1.3 18 69-87 7-24 (43)
109 COG0773 MurC UDP-N-acetylmuram 25.3 1.2E+02 0.0026 25.4 4.1 46 53-98 200-251 (459)
110 PRK10329 glutaredoxin-like pro 25.3 1E+02 0.0022 18.9 3.0 28 64-91 30-59 (81)
111 cd06318 PBP1_ABC_sugar_binding 25.2 2.6E+02 0.0056 19.9 6.8 53 37-90 29-88 (282)
112 TIGR02765 crypto_DASH cryptoch 24.9 1.6E+02 0.0034 23.6 4.6 45 49-94 83-137 (429)
113 cd06321 PBP1_ABC_sugar_binding 24.7 2.6E+02 0.0056 19.8 6.5 54 37-91 31-91 (271)
114 TIGR02183 GRXA Glutaredoxin, G 24.7 61 0.0013 19.9 1.8 21 72-92 46-67 (86)
115 cd01539 PBP1_GGBP Periplasmic 24.6 1.7E+02 0.0038 21.6 4.6 39 52-91 48-91 (303)
116 PF07085 DRTGG: DRTGG domain; 24.4 1.3E+02 0.0028 19.0 3.4 40 51-91 51-94 (105)
117 cd08567 GDPD_SpGDE_like Glycer 24.3 2.8E+02 0.0061 20.1 6.3 39 52-90 151-193 (263)
118 TIGR03584 PseF pseudaminic aci 24.1 1.1E+02 0.0024 22.3 3.4 27 62-89 41-67 (222)
119 PF13241 NAD_binding_7: Putati 23.9 61 0.0013 20.6 1.8 25 63-87 63-90 (103)
120 PRK06027 purU formyltetrahydro 23.8 3E+02 0.0064 21.2 5.8 76 13-91 64-146 (286)
121 TIGR01452 PGP_euk phosphoglyco 23.6 1.3E+02 0.0028 22.5 3.8 35 49-84 22-61 (279)
122 cd08565 GDPD_pAtGDE_like Glyce 23.0 2.4E+02 0.0052 20.6 5.0 79 11-90 60-157 (235)
123 cd01542 PBP1_TreR_like Ligand- 22.8 2.8E+02 0.006 19.4 5.9 39 51-90 45-86 (259)
124 PRK15408 autoinducer 2-binding 22.3 2.2E+02 0.0049 21.9 5.0 39 52-91 71-114 (336)
125 COG0647 NagD Predicted sugar p 22.3 90 0.0019 24.1 2.7 35 49-83 28-67 (269)
126 TIGR02189 GlrX-like_plant Glut 22.2 1.7E+02 0.0036 18.6 3.6 29 64-92 37-71 (99)
127 cd06281 PBP1_LacI_like_5 Ligan 22.1 3E+02 0.0064 19.5 6.7 64 27-91 19-88 (269)
128 cd06278 PBP1_LacI_like_2 Ligan 22.0 2.9E+02 0.0062 19.3 5.7 42 49-91 42-86 (266)
129 cd06267 PBP1_LacI_sugar_bindin 21.8 2.8E+02 0.006 19.1 5.8 41 50-91 44-87 (264)
130 PF04392 ABC_sub_bind: ABC tra 21.5 1.8E+02 0.0038 21.8 4.2 40 50-89 48-88 (294)
131 PF10281 Ish1: Putative stress 21.5 51 0.0011 17.5 0.9 15 70-85 6-20 (38)
132 PF03927 NapD: NapD protein; 21.2 2.2E+02 0.0047 17.6 4.1 28 72-99 19-49 (79)
133 PRK13237 tyrosine phenol-lyase 21.2 84 0.0018 26.2 2.4 17 64-80 268-284 (460)
134 COG0258 Exo 5'-3' exonuclease 20.7 74 0.0016 24.5 2.0 44 47-92 117-164 (310)
135 cd06293 PBP1_LacI_like_11 Liga 20.3 3.2E+02 0.007 19.3 6.3 62 28-91 20-87 (269)
136 COG0244 RplJ Ribosomal protein 20.3 47 0.001 23.8 0.7 38 53-91 14-58 (175)
137 cd03282 ABC_MSH4_euk MutS4 hom 20.3 3.2E+02 0.0069 19.7 5.1 34 56-89 136-169 (204)
138 cd08358 Glo_EDI_BRP_like_21 Th 20.3 2.2E+02 0.0048 19.1 4.0 35 63-98 83-117 (127)
No 1
>KOG3165|consensus
Probab=100.00 E-value=8.7e-37 Score=217.49 Aligned_cols=103 Identities=72% Similarity=1.246 Sum_probs=99.5
Q ss_pred ccccceeeecHHHHHHHHhhCcchHHHHhhccCCceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCC
Q psy3003 3 QLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPG 82 (106)
Q Consensus 3 l~g~~~~~vt~cVl~EL~~Lg~~~~~al~~ak~~~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~G 82 (106)
|++++.|++|.||+.|||+||..|+.||.+|+||+|++++|.|+|++|||||++.+..|++|||||||++|++|+|+|||
T Consensus 91 l~Ak~~pcitDCVmaELEkLg~kyrvALri~kDpr~eRL~C~HKGTYADDClv~RV~qHkCYIVAT~D~dLK~RIrkIPG 170 (195)
T KOG3165|consen 91 LYAKCIPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATNDRDLKQRIRKIPG 170 (195)
T ss_pred HHhccccchhHHHHHHHHHhcchhhhhhhhhcCCcccccccccCCcchhhHHHHHHhhcceEEEEeccHHHHHHHhcCCC
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccEEEEecceEEEeeCCCCCCCC
Q psy3003 83 VPIMYISQHRYTIERMPDAYGAP 105 (106)
Q Consensus 83 VPviy~~~~~l~lE~~s~as~~~ 105 (106)
||+||+.+.++.+|.+++|+-.+
T Consensus 171 VPim~v~~hk~~IEr~pda~~g~ 193 (195)
T KOG3165|consen 171 VPIMYVANHKYSIERLPDATLGG 193 (195)
T ss_pred CceEEEecceeeeeeCCcccccC
Confidence 99999999999999999996554
No 2
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=100.00 E-value=2.7e-35 Score=194.94 Aligned_cols=95 Identities=49% Similarity=0.817 Sum_probs=89.6
Q ss_pred cccccceeeecHHHHHHHHhhCcchHHHHhhccCCc--eEEEecCCCCC--CHHHHHHHhhhcCCeEEEEecCHHHHHHH
Q psy3003 2 EQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPR--FERIPCMHKGT--YADDCIVNRVTQHKCYIVATCDKDLKRRI 77 (106)
Q Consensus 2 ~l~g~~~~~vt~cVl~EL~~Lg~~~~~al~~ak~~~--~~~~~c~h~~~--~ad~ci~~~~~~~~~~iVaTqD~~Lr~~L 77 (106)
.|+|+++++||+||++||++||++++++..+|+ + +++++|+|.+. ++||||++++++++.|+|||||++||++|
T Consensus 3 ~L~~~~~~~vt~cVl~EL~~L~~~~~~~~~~a~--~~~~~~~~c~h~~~~~~addci~~~~~~~~~~~VaT~D~~Lr~~l 80 (101)
T PF04900_consen 3 LLGGKVKPYVTQCVLEELESLGKKFKGALRIAK--RKALERRKCNHKETPGSADDCILDLAGKNNKYIVATQDKELRRRL 80 (101)
T ss_pred cccCccEEEecHHHHHHHHHhcccccchhhhhh--chhhHhhcCCCCCCCcCHHHHHHHHhccCCeEEEEecCHHHHHHH
Confidence 478999999999999999999999999999999 7 99999999964 89999999998875699999999999999
Q ss_pred hcCCCccEEEEecceEEEeeC
Q psy3003 78 RKVPGVPIMYISQHRYTIERM 98 (106)
Q Consensus 78 r~i~GVPviy~~~~~l~lE~~ 98 (106)
|++||||+||+++++++||+|
T Consensus 81 r~~~GvPvi~l~~~~~~le~p 101 (101)
T PF04900_consen 81 RKIPGVPVIYLRRNVLILEPP 101 (101)
T ss_pred hcCCCCCEEEEECCEEEecCC
Confidence 988999999999999999997
No 3
>KOG3164|consensus
Probab=99.98 E-value=5.4e-33 Score=205.44 Aligned_cols=99 Identities=32% Similarity=0.560 Sum_probs=93.3
Q ss_pred ccccceeeecHHHHHHHHhhCcchHHHHhhccCCceEEEecCCCCC-CHHHHHHHhhhc--CCeEEEEecCHHHHHHHhc
Q psy3003 3 QLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGT-YADDCIVNRVTQ--HKCYIVATCDKDLKRRIRK 79 (106)
Q Consensus 3 l~g~~~~~vt~cVl~EL~~Lg~~~~~al~~ak~~~~~~~~c~h~~~-~ad~ci~~~~~~--~~~~iVaTqD~~Lr~~Lr~ 79 (106)
|.|.+++|||+|||.||+.+|+++.+|+.+|+ +|++++|+|+.. +|++||.++++. ..||+|||||.+||+.||.
T Consensus 53 l~~~vKL~tTqCvikele~~g~~l~ga~~iAK--~fe~~~C~H~~~~s~seCl~svv~~~Nk~~YvvATQD~el~~kLr~ 130 (236)
T KOG3164|consen 53 LQGEVKLMTTQCVIKELEELGKDLYGAKGIAK--QFEIRNCNHKDARSPSECLRSVVRISNKHHYVVATQDQELRRKLRK 130 (236)
T ss_pred hcCCCeeeehHHHHHHHHHhCcchhhhHHHHH--HHhHhcCCCCCCCCHHHHHHHHHhccCCceEEEecCCHHHHHHHhc
Confidence 67899999999999999999999999999999 999999999654 999999999985 2389999999999999999
Q ss_pred CCCccEEEEecceEEEeeCCCCCC
Q psy3003 80 VPGVPIMYISQHRYTIERMPDAYG 103 (106)
Q Consensus 80 i~GVPviy~~~~~l~lE~~s~as~ 103 (106)
+||||+||++++.++||+||.||.
T Consensus 131 ~pgvPli~~~r~t~vld~~S~at~ 154 (236)
T KOG3164|consen 131 EPGVPLIYLKRNTLVLDAPSQATA 154 (236)
T ss_pred CCCCceEEEecceEEecCcchhhH
Confidence 999999999999999999999983
No 4
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=99.95 E-value=8.1e-28 Score=167.56 Aligned_cols=95 Identities=43% Similarity=0.725 Sum_probs=82.0
Q ss_pred cccceeeecHHHHHHHHhhCcchHHHHh--hccCCceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCC
Q psy3003 4 LQMGIPYITDCVLGEIEKLGQKYKVALR--IIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVP 81 (106)
Q Consensus 4 ~g~~~~~vt~cVl~EL~~Lg~~~~~al~--~ak~~~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~ 81 (106)
+.+++++||+||++||++|++.++++.. ++.. .+++++|.|.+.++||||.+.+.++++|+|||||++||+|||+.
T Consensus 39 ~~~~~~~Ip~~Vi~EL~~l~~~~~~~~r~~ia~~-~~er~~~~~~~~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~- 116 (136)
T COG1412 39 GAKYKPAIPSCVIRELEKLKRKHRGKARIAIALK-YAERLECIHKGRYADECLLEAALKHGRYIVATNDKELKRRLREN- 116 (136)
T ss_pred cccccccchHHHHHHHHHHHHhcCchHHHHHHHH-HhhccCccccCCChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHc-
Confidence 3348999999999999999987666555 4541 36788999998899999999999988899999999999999997
Q ss_pred CccEEEEec-ceEEEeeCCC
Q psy3003 82 GVPIMYISQ-HRYTIERMPD 100 (106)
Q Consensus 82 GVPviy~~~-~~l~lE~~s~ 100 (106)
|||+||+++ +.+++|++++
T Consensus 117 GIPvi~lr~r~~~~ie~~~~ 136 (136)
T COG1412 117 GIPVITLRQRKLLIIERLSD 136 (136)
T ss_pred CCCEEEEeCCeEEEeeCCCC
Confidence 999999995 5599998763
No 5
>PRK13764 ATPase; Provisional
Probab=97.93 E-value=2e-05 Score=66.44 Aligned_cols=91 Identities=20% Similarity=0.211 Sum_probs=65.0
Q ss_pred cceeeecHHHHHHHHhhCcc----hHHHHhhccCC-------ceEEEecCCCC----------CCHHHHHHHhhhcCCeE
Q psy3003 6 MGIPYITDCVLGEIEKLGQK----YKVALRIIKDP-------RFERIPCMHKG----------TYADDCIVNRVTQHKCY 64 (106)
Q Consensus 6 ~~~~~vt~cVl~EL~~Lg~~----~~~al~~ak~~-------~~~~~~c~h~~----------~~ad~ci~~~~~~~~~~ 64 (106)
.-.++||.-|++||+.++.. -..|++.++.. .+++.-.++.. ...|+-|.+++.+.+ +
T Consensus 26 ~~~IiIP~~Vl~ELe~~A~~~r~~G~~gLeeL~~L~~l~~~g~i~ie~~~~~p~~~~~~~~~~gevD~~I~~~A~~~~-~ 104 (602)
T PRK13764 26 GGTIIIPEAVVAELEAQANQGREIGFSGLEELKKLRELAEEGLIELEFVGERPTLEQIKLAKGGEIDALIREVAKELG-A 104 (602)
T ss_pred CCEEEeehHHHHHHHHHhhccchhhHHHHHHHHHHHHhhccCceEEEEeccccchhhcccccCCCHHHHHHHHHHHcC-C
Confidence 35799999999999999754 23345555410 12121112111 368999999999875 9
Q ss_pred EEEecCHHHHHHHhcCCCccEEEEecce--EEEeeC
Q psy3003 65 IVATCDKDLKRRIRKVPGVPIMYISQHR--YTIERM 98 (106)
Q Consensus 65 iVaTqD~~Lr~~Lr~i~GVPviy~~~~~--l~lE~~ 98 (106)
++.|||..|++.++.. |||++|+++.. +.+|..
T Consensus 105 ~lvT~D~~l~~~A~~~-GI~V~~l~~~~~~L~ie~~ 139 (602)
T PRK13764 105 TLVTSDRVQAEVARAK-GIDVIYLKPEREPLEIEKF 139 (602)
T ss_pred EEEeCCHHHHHHHHHc-CCEEEEeCCCCCccchHHH
Confidence 9999999999999995 99999999643 666664
No 6
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=97.13 E-value=0.0013 Score=44.17 Aligned_cols=84 Identities=23% Similarity=0.298 Sum_probs=48.5
Q ss_pred ccceeeecHHHHHHHHhhCcc-----------hHHHHhhccCC---ceEEEecC--CC---------CCCHHHHHHHhhh
Q psy3003 5 QMGIPYITDCVLGEIEKLGQK-----------YKVALRIIKDP---RFERIPCM--HK---------GTYADDCIVNRVT 59 (106)
Q Consensus 5 g~~~~~vt~cVl~EL~~Lg~~-----------~~~al~~ak~~---~~~~~~c~--h~---------~~~ad~ci~~~~~ 59 (106)
++..++||.+|++||+++... ++.+..+.... ....+... +. ....|+.|++.+.
T Consensus 19 ~~~~ivIP~~Vl~ELd~lk~~~~~~~~~~~~~ar~~~~~l~~~~~~~~~~i~~q~~~~~~~~~~~~~~~~~D~~Il~~a~ 98 (133)
T PF13638_consen 19 EQNKIVIPLTVLEELDRLKKSSRDRDRELRKRAREAIRWLEKLLKRGSRSIRVQTSDEEIDEDLNLDAQRNDDRILNCAL 98 (133)
T ss_dssp SSSEEEEEHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCT-TTEEECTTTS-EES--S----HHHHHHHHHHH
T ss_pred ccCEEEechHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHhcCCCeEecchhhhhcchhhhccccccHHHHHHHHH
Confidence 467899999999999887542 33344443200 00011111 10 1257888888774
Q ss_pred c------CCeEEEEecCHHHHHHHhcCCCccEEEEe
Q psy3003 60 Q------HKCYIVATCDKDLKRRIRKVPGVPIMYIS 89 (106)
Q Consensus 60 ~------~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~ 89 (106)
. ....++.|+|..||.+.+.. |+|...++
T Consensus 99 ~~~~~~~~~~vvLvT~D~~l~~~A~~~-gi~~~~~~ 133 (133)
T PF13638_consen 99 YLQEENPGRKVVLVTNDKNLRLKARAE-GIPAVSYE 133 (133)
T ss_dssp HHHHHCGCEEEEEEE--HHHHHHHHHT-T--EE---
T ss_pred HHHHhcCCCeEEEEeCCHHHHHHHhhc-ccccccCC
Confidence 2 23589999999999999995 99988653
No 7
>smart00670 PINc Large family of predicted nucleotide-binding domains. From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Probab=96.77 E-value=0.0022 Score=41.24 Aligned_cols=70 Identities=26% Similarity=0.323 Sum_probs=42.3
Q ss_pred cceeeecHHHHHHHHhhCc--c---hHHHHh-------hccCCc-eEEEecCCCCC-----CHHHHHHHhhhcCCeEEEE
Q psy3003 6 MGIPYITDCVLGEIEKLGQ--K---YKVALR-------IIKDPR-FERIPCMHKGT-----YADDCIVNRVTQHKCYIVA 67 (106)
Q Consensus 6 ~~~~~vt~cVl~EL~~Lg~--~---~~~al~-------~ak~~~-~~~~~c~h~~~-----~ad~ci~~~~~~~~~~iVa 67 (106)
...+++|.+|+.||+.... . +..-.. ...+.. +....+.+.+. ..|.+|.+.+...+..+++
T Consensus 24 ~~~~~i~~~v~~El~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~~il~~a~~~~~~~lv 103 (111)
T smart00670 24 KGEVYIPPTVLEELEYLAKLRSLKKLEELALEGKIKLKVLKEERKLEEEILERLSLKLELLPNDALILATAKELGNVVLV 103 (111)
T ss_pred CCcEEECHHHHHHHHHHHHHHHHhhHHHHHHhcccccceeecCCCeEEEecccCChhhcCCCChHHHHHHHHHCCCCEEE
Confidence 4678999999999999762 1 111111 010000 22222322221 3688999999876458999
Q ss_pred ecCHHHHH
Q psy3003 68 TCDKDLKR 75 (106)
Q Consensus 68 TqD~~Lr~ 75 (106)
|+|.+|++
T Consensus 104 T~D~~l~~ 111 (111)
T smart00670 104 TNDRDLRR 111 (111)
T ss_pred eCCcccCC
Confidence 99998863
No 8
>PRK00124 hypothetical protein; Validated
Probab=95.34 E-value=0.025 Score=40.21 Aligned_cols=79 Identities=20% Similarity=0.194 Sum_probs=53.5
Q ss_pred HH-HHHHHHhhCcchHHHHhh-c------cCCc---eEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCC
Q psy3003 13 DC-VLGEIEKLGQKYKVALRI-I------KDPR---FERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVP 81 (106)
Q Consensus 13 ~c-Vl~EL~~Lg~~~~~al~~-a------k~~~---~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~ 81 (106)
.| |.+|+.+++.+++.-+-+ | ..+. .+.+-.+.....||+-|++.+.+. -+|.|||-.|-.++-..
T Consensus 9 ACPVk~~i~r~a~r~~i~v~~Vas~n~~~~~~~~~~v~~v~V~~g~D~AD~~Iv~~~~~g--DiVIT~Di~LAa~~l~K- 85 (151)
T PRK00124 9 ACPVKDIIIRVAERHGIPVTLVASFNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKG--DIVITQDYGLAALALEK- 85 (151)
T ss_pred CCcHHHHHHHHHHHHCCeEEEEEeCCcccCCCCCCceEEEEeCCCCChHHHHHHHhCCCC--CEEEeCCHHHHHHHHHC-
Confidence 35 899999998764332111 1 1111 122333222237999999999876 68899999999999995
Q ss_pred CccEEEEecceEE
Q psy3003 82 GVPIMYISQHRYT 94 (106)
Q Consensus 82 GVPviy~~~~~l~ 94 (106)
|.-+|.-++..+.
T Consensus 86 ga~vl~prG~~yt 98 (151)
T PRK00124 86 GAIVLNPRGYIYT 98 (151)
T ss_pred CCEEECCCCcCCC
Confidence 9999988876654
No 9
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=93.34 E-value=0.15 Score=40.44 Aligned_cols=80 Identities=20% Similarity=0.239 Sum_probs=56.5
Q ss_pred eeeecHHHHHHHHhhCcc--------hHHHHhhccC-----C-ceEEEecCCCC-CCHHHHHHHhhhcCCeEEEEecCHH
Q psy3003 8 IPYITDCVLGEIEKLGQK--------YKVALRIIKD-----P-RFERIPCMHKG-TYADDCIVNRVTQHKCYIVATCDKD 72 (106)
Q Consensus 8 ~~~vt~cVl~EL~~Lg~~--------~~~al~~ak~-----~-~~~~~~c~h~~-~~ad~ci~~~~~~~~~~iVaTqD~~ 72 (106)
.++||+-|+.||..++.. =+.+|++... + +.+++.-+-.+ ...|.=++.+++..+ ..|.|||-.
T Consensus 187 ~iiiP~FVL~ELQ~iADssD~lKR~RGRRGLdILn~iqk~~~~~v~I~~~Df~di~eVD~KLvklAk~~~-g~lvTND~N 265 (356)
T COG4956 187 TIIIPQFVLLELQHIADSSDDLKRNRGRRGLDILNEIQKEDPIQVEIYEGDFEDIPEVDSKLVKLAKVTG-GKLVTNDFN 265 (356)
T ss_pred eEeeeHHHHHHHHHHhhccchhhhhcccchhHHHHHHHhhCCCcEEEccCCccchhhHHHHHHHHHHHhC-CEEEeccCc
Confidence 579999999999999743 2456666641 0 23333332111 267889999998874 789999999
Q ss_pred HHHHHhcCCCccEEEEe
Q psy3003 73 LKRRIRKVPGVPIMYIS 89 (106)
Q Consensus 73 Lr~~Lr~i~GVPviy~~ 89 (106)
|-+-..- -|||++.++
T Consensus 266 LnKVae~-qgV~vLNIN 281 (356)
T COG4956 266 LNKVAEL-QGVQVLNIN 281 (356)
T ss_pred HHHHHhh-cCCceecHH
Confidence 9776654 599999877
No 10
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=93.29 E-value=0.11 Score=35.89 Aligned_cols=58 Identities=28% Similarity=0.157 Sum_probs=45.2
Q ss_pred ceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEEEecceEEEee
Q psy3003 37 RFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIER 97 (106)
Q Consensus 37 ~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~~l~lE~ 97 (106)
..+.+-++.....||.-|++.+.+. -+|.|||-.|-.++-.. |+.+|.-++..+.-|+
T Consensus 28 ~~~~i~Vd~g~DaaD~~I~~~~~~g--DiVITqDigLA~~~l~K-ga~vl~~rG~~yt~~n 85 (130)
T PF02639_consen 28 YVEMIVVDSGFDAADFYIVNHAKPG--DIVITQDIGLASLLLAK-GAYVLNPRGKEYTKEN 85 (130)
T ss_pred CeEEEEECCCCChHHHHHHHcCCCC--CEEEECCHHHHHHHHHC-CCEEECCCCCCCCHHH
Confidence 3455666543348999999999876 57889999999999995 9999988877665443
No 11
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=92.85 E-value=0.33 Score=34.54 Aligned_cols=39 Identities=31% Similarity=0.429 Sum_probs=31.8
Q ss_pred CCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHhcCCCccEE
Q psy3003 47 GTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIRKVPGVPIM 86 (106)
Q Consensus 47 ~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr~i~GVPvi 86 (106)
+.+||+.|.+++.. +....|+|.|..++...+.. |.-.+
T Consensus 76 ~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~~-GA~~i 118 (166)
T PF05991_consen 76 GETADDYIERLVRELKNRPRQVTVVTSDREIQRAARGR-GAKRI 118 (166)
T ss_pred CCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhhC-CCEEE
Confidence 35899999999964 34699999999999999985 65544
No 12
>PRK12496 hypothetical protein; Provisional
Probab=89.10 E-value=1.4 Score=31.45 Aligned_cols=80 Identities=14% Similarity=0.167 Sum_probs=50.5
Q ss_pred eeeecHHHHHHHHhhCcchHHHHhhccCC-ceEEEecCCC------------C-----CCHHHHHHHhhhcCCeEEEEec
Q psy3003 8 IPYITDCVLGEIEKLGQKYKVALRIIKDP-RFERIPCMHK------------G-----TYADDCIVNRVTQHKCYIVATC 69 (106)
Q Consensus 8 ~~~vt~cVl~EL~~Lg~~~~~al~~ak~~-~~~~~~c~h~------------~-----~~ad~ci~~~~~~~~~~iVaTq 69 (106)
+++||+-|++|+..-.. +..++.+... .+.+..=... | ..+|.-++.++...+ ..+.|.
T Consensus 21 ~i~tp~~V~~Ev~d~~~--~~~~~~l~~~~~i~v~~p~~~~i~~v~~~a~~tgd~~~Ls~~D~~~iaLA~el~-~~lvtD 97 (164)
T PRK12496 21 EHYTTPSVVEEVKDKES--RLILESAISAGKLKILEPSPESIEKVEEAAIKTGDLMRLSNTDIEVLALALELN-GTLYTD 97 (164)
T ss_pred CEEecHHHHHHHhCHHH--HHHHHHhcccCCeEEECCCHHHHHHHHHHHHhcCCccccchhhHHHHHHHHHhC-CcEECc
Confidence 57999999999987322 2222333200 1333321110 0 134555666666554 689999
Q ss_pred CHHHHHHHhcCCCccEEEEecc
Q psy3003 70 DKDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 70 D~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
|..+|+-++.. |++++-+++.
T Consensus 98 D~~~~~vA~~l-gi~v~~~~~~ 118 (164)
T PRK12496 98 DYGIQNVAKKL-NIKFENIKTK 118 (164)
T ss_pred HHHHHHHHHHc-CCeEeccccc
Confidence 99999999996 9999998843
No 13
>smart00500 SFM Splicing Factor Motif, present in Prp18 and Pr04.
Probab=87.33 E-value=0.44 Score=27.17 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=19.2
Q ss_pred ecCHHHHHHHhcCCCccEEEEe
Q psy3003 68 TCDKDLKRRIRKVPGVPIMYIS 89 (106)
Q Consensus 68 TqD~~Lr~~Lr~i~GVPviy~~ 89 (106)
|.|.+.+++||+. |=||.++-
T Consensus 1 ~~d~eV~~~LR~l-gePi~lFG 21 (44)
T smart00500 1 LPDSEVIRRLREL-GEPITLFG 21 (44)
T ss_pred CCHHHHHHHHHHc-CCCeeecC
Confidence 6899999999997 99999886
No 14
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=83.80 E-value=2.6 Score=30.48 Aligned_cols=50 Identities=22% Similarity=0.368 Sum_probs=39.5
Q ss_pred ceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEEEecce
Q psy3003 37 RFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHR 92 (106)
Q Consensus 37 ~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~~ 92 (106)
++..+-++ ...|+=|..++.+++ -|+-|-|.+|-+|. +. |++.||++.+.
T Consensus 26 Gydt~~~~---~~~d~~i~~i~~~e~-rIllTRDr~L~~r~-k~-g~~~i~i~~~s 75 (165)
T COG1656 26 GYDTVYSS---NESDDEIILIAKKEG-RILLTRDRELYKRA-KL-GIKAILIRSDS 75 (165)
T ss_pred CCceeeec---cCCcHHHHHHHhcCC-eEEEeccHHHHHHh-hc-cCceEEEeCCC
Confidence 45555453 256888888888875 88999999999999 64 99999999764
No 15
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=82.76 E-value=3.4 Score=26.74 Aligned_cols=36 Identities=17% Similarity=0.351 Sum_probs=29.2
Q ss_pred CHHHHHHHhhhcCCeEEEEecC-----HHHHHHHhcCCCccE
Q psy3003 49 YADDCIVNRVTQHKCYIVATCD-----KDLKRRIRKVPGVPI 85 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD-----~~Lr~~Lr~i~GVPv 85 (106)
.|.++|..+-..+.++++.||. .++.++|++. |+++
T Consensus 18 ga~e~l~~L~~~g~~~~~lTNns~~s~~~~~~~L~~~-Gi~~ 58 (101)
T PF13344_consen 18 GAVEALDALRERGKPVVFLTNNSSRSREEYAKKLKKL-GIPV 58 (101)
T ss_dssp THHHHHHHHHHTTSEEEEEES-SSS-HHHHHHHHHHT-TTT-
T ss_pred CHHHHHHHHHHcCCCEEEEeCCCCCCHHHHHHHHHhc-CcCC
Confidence 6889999888876689999999 4899999985 9984
No 16
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=78.43 E-value=21 Score=30.39 Aligned_cols=82 Identities=16% Similarity=0.189 Sum_probs=56.3
Q ss_pred ceeeecHHHHHHHHhhCcc-----------hHHHHhhccCCceEEEecCCCC----------CCHHHHHHHhhhcCCeEE
Q psy3003 7 GIPYITDCVLGEIEKLGQK-----------YKVALRIIKDPRFERIPCMHKG----------TYADDCIVNRVTQHKCYI 65 (106)
Q Consensus 7 ~~~~vt~cVl~EL~~Lg~~-----------~~~al~~ak~~~~~~~~c~h~~----------~~ad~ci~~~~~~~~~~i 65 (106)
...++|+.|+.||+..+.. ++.-.+++++-.+++.-.+..+ ...|.-|.+++...+ ++
T Consensus 31 ~~viipeAvvsele~qAn~Gr~~G~~gLeEL~kL~~l~~~g~i~~~~~gerp~~~~Ik~ak~GEid~miR~vA~e~~-a~ 109 (604)
T COG1855 31 ATVIIPEAVVSELEAQANRGREIGFAGLEELKKLRDLADEGKIELEFVGERPTLEEIKRAKSGEIDAMIREVALEYG-AT 109 (604)
T ss_pred cEEEeeHHHHHHHHHHhccchhhhhhHHHHHHHHHHHHhcCcEEEEEEeccCchhhhcccccccHHHHHHHHHHHhC-cE
Confidence 5789999999999998643 2333344432113333333211 246778888888886 99
Q ss_pred EEecCHHHHHHHhcCCCccEEEEec
Q psy3003 66 VATCDKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 66 VaTqD~~Lr~~Lr~i~GVPviy~~~ 90 (106)
..|.|+-=+.-.+. .|+-+.|+..
T Consensus 110 lVTsD~vQ~~va~a-~Giev~yl~p 133 (604)
T COG1855 110 LVTSDRVQRDVARA-KGIEVEYLEP 133 (604)
T ss_pred EEechHHHHHHHHh-cCceEEEeCC
Confidence 99999877777776 5999999976
No 17
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=77.15 E-value=2.2 Score=24.47 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=21.4
Q ss_pred EEEEecCHHHHHHHhcC---CCccEEEEecce
Q psy3003 64 YIVATCDKDLKRRIRKV---PGVPIMYISQHR 92 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr~i---~GVPviy~~~~~ 92 (106)
++=.+.|.+.++.|++. .++|.+++.+..
T Consensus 28 ~~dv~~~~~~~~~l~~~~g~~~~P~v~i~g~~ 59 (60)
T PF00462_consen 28 EVDVDEDEEAREELKELSGVRTVPQVFIDGKF 59 (60)
T ss_dssp EEEGGGSHHHHHHHHHHHSSSSSSEEEETTEE
T ss_pred EcccccchhHHHHHHHHcCCCccCEEEECCEE
Confidence 55567777888888653 799999996543
No 18
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=77.11 E-value=3.1 Score=29.65 Aligned_cols=45 Identities=31% Similarity=0.327 Sum_probs=36.7
Q ss_pred CHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEEEecceEEEe
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIE 96 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~~l~lE 96 (106)
.||+-|++++.+. -+|.|||-.|-.+|-.. |+-++.=++..+.-|
T Consensus 55 aaD~~Iv~~a~~g--DlVVT~Di~LA~~ll~k-g~~v~~prGr~y~~~ 99 (150)
T COG1671 55 AADDWIVNLAEKG--DLVVTADIPLASLLLDK-GAAVLNPRGRLYTEE 99 (150)
T ss_pred hHHHHHHHhCCCC--CEEEECchHHHHHHHhc-CCEEECCCCcccCHh
Confidence 6899999999876 58899999999999995 988887666555433
No 19
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=76.96 E-value=2.7 Score=27.99 Aligned_cols=46 Identities=11% Similarity=0.104 Sum_probs=32.6
Q ss_pred HHHHHHHhhh-cCCeEEEEecCHHHHHHHhc----CCCccEEEEecceEEE
Q psy3003 50 ADDCIVNRVT-QHKCYIVATCDKDLKRRIRK----VPGVPIMYISQHRYTI 95 (106)
Q Consensus 50 ad~ci~~~~~-~~~~~iVaTqD~~Lr~~Lr~----i~GVPviy~~~~~l~l 95 (106)
...-|+.+.. +.+..+||.|-++.+++--+ ..|+||+++.++.+.|
T Consensus 24 ~k~tiK~lk~gkaKliiiAsN~P~~~k~~ieyYAkLs~ipV~~y~Gt~~eL 74 (100)
T COG1911 24 SKRTIKSLKLGKAKLIIIASNCPKELKEDIEYYAKLSDIPVYVYEGTSVEL 74 (100)
T ss_pred hHHHHHHHHcCCCcEEEEecCCCHHHHHHHHHHHHHcCCcEEEecCCceeH
Confidence 3455555543 34568999998877666554 4599999999988765
No 20
>COG0069 GltB Glutamate synthase domain 2 [Amino acid transport and metabolism]
Probab=76.43 E-value=1.4 Score=36.75 Aligned_cols=14 Identities=36% Similarity=0.565 Sum_probs=13.0
Q ss_pred EEEEecCHHHHHHH
Q psy3003 64 YIVATCDKDLKRRI 77 (106)
Q Consensus 64 ~iVaTqD~~Lr~~L 77 (106)
.-|||||++||+||
T Consensus 425 ~GIaTqdp~Lrkrl 438 (485)
T COG0069 425 VGIATQDPELRKRL 438 (485)
T ss_pred ceeeecCHHHHhhc
Confidence 67999999999997
No 21
>COG4634 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.70 E-value=6.2 Score=26.82 Aligned_cols=39 Identities=23% Similarity=0.319 Sum_probs=32.2
Q ss_pred CHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCcc--EEEEe
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVP--IMYIS 89 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVP--viy~~ 89 (106)
..|.-|.+.++.++ +++.|+|.++-...... |.| ++.++
T Consensus 35 a~D~EI~a~A~~~~-~iivTkDsDF~~la~~~-G~Ppki~wLr 75 (113)
T COG4634 35 ATDIEIWAYARRNN-RIIVTKDSDFADLALTL-GSPPKIVWLR 75 (113)
T ss_pred CccHHHHHHHHhcC-cEEEEcCccHHHHHHHc-CCCCeEEEEE
Confidence 34788889998886 99999999998777775 888 77777
No 22
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=75.63 E-value=8.4 Score=26.67 Aligned_cols=39 Identities=31% Similarity=0.424 Sum_probs=31.1
Q ss_pred CHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEEEec
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~ 90 (106)
..|+-|++++.+.+ =++-|.|++|.++.....+ ++++..
T Consensus 29 ~~D~~il~~A~~e~-RillTrd~~l~~~~~~~~~--~~li~~ 67 (147)
T PF01927_consen 29 IDDDEILELAREEG-RILLTRDRDLLKRRRVSGG--VILIRS 67 (147)
T ss_pred CChHHHHHHhhhCC-eEEEECCHHHHHHhhccCC--EEEEcC
Confidence 46899999998876 6677999999999998645 666644
No 23
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=75.07 E-value=13 Score=24.15 Aligned_cols=71 Identities=17% Similarity=0.048 Sum_probs=41.8
Q ss_pred ccccceeeecHHHHHHH-HhhC-----cc-----hHHHHhhccCCceEEEecCCC----CCCHHHHHHHhhhcCCeEEEE
Q psy3003 3 QLQMGIPYITDCVLGEI-EKLG-----QK-----YKVALRIIKDPRFERIPCMHK----GTYADDCIVNRVTQHKCYIVA 67 (106)
Q Consensus 3 l~g~~~~~vt~cVl~EL-~~Lg-----~~-----~~~al~~ak~~~~~~~~c~h~----~~~ad~ci~~~~~~~~~~iVa 67 (106)
..|.+.++++..++.|+ +-+. +. .+..+..... .+++..-... ..+.|+.+.+.+...+--++.
T Consensus 27 ~~~~~~~~~s~~~l~E~~~~l~~~~~~~~~~~~~~~~~l~~l~~-~~~~~~~~~~~~~~~D~~D~~~l~~A~~~~ad~iV 105 (114)
T TIGR00305 27 IDNKIVNCTSVEILQEVEFVLLYPKLQKYFALETILEILLLLGE-KSTIINPNPEFDDCRDKKDNKFLNTAYASKANALI 105 (114)
T ss_pred HhCCEEEEECHHHHHHHHHHHhhHhhhhhcCHHHHHHHHHHHHH-hcEEecCCCCCCCCCCchhHHHHHHHHhcCCCEEE
Confidence 46788999999999999 4343 11 1222222221 3333332111 225678888888765444677
Q ss_pred ecCHHHH
Q psy3003 68 TCDKDLK 74 (106)
Q Consensus 68 TqD~~Lr 74 (106)
|.|++|-
T Consensus 106 T~Dkdll 112 (114)
T TIGR00305 106 TGDTDLL 112 (114)
T ss_pred ECCHHHh
Confidence 9999873
No 24
>COG0117 RibD Pyrimidine deaminase [Coenzyme metabolism]
Probab=74.52 E-value=2.6 Score=29.92 Aligned_cols=46 Identities=24% Similarity=0.402 Sum_probs=31.4
Q ss_pred EEEecCCCCCCHHHHHHHhhhc-CCeEEEEecCHHHH------HHHhcCCCccEE
Q psy3003 39 ERIPCMHKGTYADDCIVNRVTQ-HKCYIVATCDKDLK------RRIRKVPGVPIM 86 (106)
Q Consensus 39 ~~~~c~h~~~~ad~ci~~~~~~-~~~~iVaTqD~~Lr------~~Lr~i~GVPvi 86 (106)
..-.|+|.|. .--|-..++.. -.+.+||+.|++-+ .+|++ .||.|-
T Consensus 74 TLEPCsH~Gr-TPPC~~ali~agi~rVvva~~DPnp~Vag~G~~~L~~-aGi~V~ 126 (146)
T COG0117 74 TLEPCSHYGR-TPPCADALIKAGVARVVVAMLDPNPLVAGGGLARLRA-AGIEVE 126 (146)
T ss_pred EecCcccCCC-CcchHHHHHHhCCCEEEEEecCCCccccCchHHHHHH-cCCeEE
Confidence 4668999985 23355555543 23799999999943 67888 487654
No 25
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=72.87 E-value=2.9 Score=29.82 Aligned_cols=50 Identities=22% Similarity=0.280 Sum_probs=33.9
Q ss_pred ceEEEecCCCCCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHhcCCCccEEEEec
Q psy3003 37 RFERIPCMHKGTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 37 ~~~~~~c~h~~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~ 90 (106)
++..+.. .|-.|||+|-.++.. ....+|.|.|++|.+-+.+ ++-|..+..
T Consensus 99 gi~~~~~--~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~--~~~V~~~~~ 152 (169)
T PF02739_consen 99 GIPVLEV--PGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDE--NVNVYLLDP 152 (169)
T ss_dssp TSEEEEE--TTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS---TSEEEEET
T ss_pred CCCEecC--CCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCC--CceEEEeec
Confidence 4555554 345799999999874 2369999999999998887 355555553
No 26
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=65.19 E-value=7.2 Score=29.16 Aligned_cols=39 Identities=23% Similarity=0.262 Sum_probs=27.9
Q ss_pred eEEEecCCCCCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHh
Q psy3003 38 FERIPCMHKGTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIR 78 (106)
Q Consensus 38 ~~~~~c~h~~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr 78 (106)
+..+.. .+-.|||.|-.++.+ ...++|+|.|+++..-+.
T Consensus 99 i~~i~~--~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~ 141 (240)
T cd00008 99 IPVLEI--EGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVS 141 (240)
T ss_pred CCEEec--CCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCC
Confidence 444444 234799999988863 236899999999997663
No 27
>TIGR02181 GRX_bact Glutaredoxin, GrxC family. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulfides.
Probab=64.95 E-value=13 Score=22.25 Aligned_cols=31 Identities=19% Similarity=0.274 Sum_probs=23.1
Q ss_pred eEEEEecCHHHHHHHhc---CCCccEEEEecceE
Q psy3003 63 CYIVATCDKDLKRRIRK---VPGVPIMYISQHRY 93 (106)
Q Consensus 63 ~~iVaTqD~~Lr~~Lr~---i~GVPviy~~~~~l 93 (106)
..+=.++|.+.++.+.+ ..++|+|++.+..+
T Consensus 27 ~~~di~~~~~~~~~~~~~~g~~~vP~i~i~g~~i 60 (79)
T TIGR02181 27 TEIRVDGDPALRDEMMQRSGRRTVPQIFIGDVHV 60 (79)
T ss_pred EEEEecCCHHHHHHHHHHhCCCCcCEEEECCEEE
Confidence 35666788888888864 36899999987643
No 28
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=64.10 E-value=8.4 Score=22.60 Aligned_cols=30 Identities=20% Similarity=0.275 Sum_probs=21.6
Q ss_pred EEEEecCHHHHHHHhcC---C-CccEEEEecceE
Q psy3003 64 YIVATCDKDLKRRIRKV---P-GVPIMYISQHRY 93 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr~i---~-GVPviy~~~~~l 93 (106)
++-.++|.++++.+++. . +||.|++.++.+
T Consensus 29 ~i~i~~~~~~~~~~~~~~~~~~~vP~v~i~g~~i 62 (75)
T cd03418 29 EIDVDGDPALREEMINRSGGRRTVPQIFIGDVHI 62 (75)
T ss_pred EEECCCCHHHHHHHHHHhCCCCccCEEEECCEEE
Confidence 55667788888877532 2 899999987643
No 29
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=63.59 E-value=25 Score=22.25 Aligned_cols=39 Identities=15% Similarity=0.172 Sum_probs=28.1
Q ss_pred HHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEEEe
Q psy3003 50 ADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYIS 89 (106)
Q Consensus 50 ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~ 89 (106)
+...+..+......+++.+.|++.-+.+++. |++++|-.
T Consensus 10 ~~~i~~~L~~~~~~vvvid~d~~~~~~~~~~-~~~~i~gd 48 (116)
T PF02254_consen 10 GREIAEQLKEGGIDVVVIDRDPERVEELREE-GVEVIYGD 48 (116)
T ss_dssp HHHHHHHHHHTTSEEEEEESSHHHHHHHHHT-TSEEEES-
T ss_pred HHHHHHHHHhCCCEEEEEECCcHHHHHHHhc-cccccccc
Confidence 3444444444333699999999999999994 89988755
No 30
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=62.36 E-value=34 Score=24.55 Aligned_cols=61 Identities=11% Similarity=0.123 Sum_probs=37.3
Q ss_pred HHHHhhccC-CceEEEecCCCCCCHHHHHHHhhhcC-CeEEEEecCHHHHHHHhcCCCccEEEEecc
Q psy3003 27 KVALRIIKD-PRFERIPCMHKGTYADDCIVNRVTQH-KCYIVATCDKDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 27 ~~al~~ak~-~~~~~~~c~h~~~~ad~ci~~~~~~~-~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
++..+.+++ ..+..+-+... ..+++..+.... .-.|+.+.|.++...+.+ .|+|++++.+.
T Consensus 18 ~gi~~~~~~~~g~~~~~~~~~---~~~~~~~l~~~~vdGiI~~~~~~~~~~~l~~-~~~PvV~~~~~ 80 (265)
T cd01543 18 RGIARYAREHGPWSIYLEPRG---LQEPLRWLKDWQGDGIIARIDDPEMAEALQK-LGIPVVDVSGS 80 (265)
T ss_pred HHHHHHHHhcCCeEEEEeccc---chhhhhhccccccceEEEECCCHHHHHHHhh-CCCCEEEEeCc
Confidence 344444543 24555555432 256665555431 237777777788788888 49999999864
No 31
>COG0695 GrxC Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]
Probab=57.81 E-value=20 Score=22.15 Aligned_cols=30 Identities=17% Similarity=0.286 Sum_probs=23.4
Q ss_pred eEEEEecCH--HHHHHHhcC---CCccEEEEecce
Q psy3003 63 CYIVATCDK--DLKRRIRKV---PGVPIMYISQHR 92 (106)
Q Consensus 63 ~~iVaTqD~--~Lr~~Lr~i---~GVPviy~~~~~ 92 (106)
..+..+.|. +.+..+++. ..||+|++.++.
T Consensus 29 ~~i~~~~~~~~~~~~~~~~~~g~~tvP~I~i~~~~ 63 (80)
T COG0695 29 EEIDVDDDEPEEAREMVKRGKGQRTVPQIFIGGKH 63 (80)
T ss_pred EEEEecCCcHHHHHHHHHHhCCCCCcCEEEECCEE
Confidence 477778888 777777764 689999999764
No 32
>PRK09482 flap endonuclease-like protein; Provisional
Probab=55.00 E-value=12 Score=28.74 Aligned_cols=39 Identities=21% Similarity=0.241 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHhcCCCccEE
Q psy3003 46 KGTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIRKVPGVPIM 86 (106)
Q Consensus 46 ~~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr~i~GVPvi 86 (106)
.+-.|||.|-.++.+ +...+++|.|++|.+-+.. +|-+.
T Consensus 104 ~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~--~v~~~ 146 (256)
T PRK09482 104 DGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSP--TIQIR 146 (256)
T ss_pred CCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCC--CeEEE
Confidence 345799999988864 2358899999999776653 45444
No 33
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=53.67 E-value=20 Score=21.16 Aligned_cols=28 Identities=11% Similarity=0.115 Sum_probs=20.6
Q ss_pred EEEEecCHHHHHHHhcC--CCccEEEEecc
Q psy3003 64 YIVATCDKDLKRRIRKV--PGVPIMYISQH 91 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr~i--~GVPviy~~~~ 91 (106)
++=.++|.+.+..+++. .+||++++.++
T Consensus 28 ~~di~~~~~~~~~~~~~g~~~vP~v~~~g~ 57 (72)
T TIGR02194 28 EINIDEQPEAIDYVKAQGFRQVPVIVADGD 57 (72)
T ss_pred EEECCCCHHHHHHHHHcCCcccCEEEECCC
Confidence 44456788888888743 47999999765
No 34
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=53.09 E-value=71 Score=22.90 Aligned_cols=63 Identities=11% Similarity=0.156 Sum_probs=36.2
Q ss_pred HHHhhccCCceEEEecCCCCC--CHHHHHHHhhhcC-CeEEEEecC----HHHHHHHhcCCCccEEEEecc
Q psy3003 28 VALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQH-KCYIVATCD----KDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 28 ~al~~ak~~~~~~~~c~h~~~--~ad~ci~~~~~~~-~~~iVaTqD----~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
+..+.+++.++++.-++.... ...++|..++.++ .-.++.+.+ .+.-+.+.+. |+|++++.+.
T Consensus 20 ~~~~~a~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~i~~~~~~-~iPvV~~~~~ 89 (273)
T cd06309 20 SIKDAAEKRGFDLKFADAQQKQENQISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAA-GIPVILVDRG 89 (273)
T ss_pred HHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHHHcCCCEEEEcCCccccchHHHHHHHHC-CCCEEEEecC
Confidence 333444433566666654322 3446777777652 235554433 3444667774 9999999863
No 35
>PF02348 CTP_transf_3: Cytidylyltransferase; InterPro: IPR003329 Synonym(s): CMP-N-acetylneuraminic acid synthetase Acylneuraminate cytidylyltransferase (2.7.7.43 from EC) (CMP-NeuAc synthetase) catalyzes the reaction of CTP and NeuAc to form CMP-NeuAc, which is the nucleotide sugar donor used by sialyltransferases []. The outer membrane lipooligosaccharides of some microorganisms contain terminal sialic acid attached to N-acetyllactosamine and so this modification may be important in pathogenesis.; GO: 0009103 lipopolysaccharide biosynthetic process; PDB: 3K8D_C 1VH1_B 3K8E_C 1QWJ_A 3EWI_A 1VIC_B 3DUV_A 1VH3_C 3TQD_A 2Y6P_C ....
Probab=52.30 E-value=26 Score=24.75 Aligned_cols=27 Identities=19% Similarity=0.330 Sum_probs=21.8
Q ss_pred eEEEEecCHHHHHHHhcCCCccEEEEec
Q psy3003 63 CYIVATCDKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 63 ~~iVaTqD~~Lr~~Lr~i~GVPviy~~~ 90 (106)
+.+|+|.|.+...-+.+. |+.+++.+.
T Consensus 42 ~IvVaTd~~~i~~~~~~~-g~~v~~~~~ 68 (217)
T PF02348_consen 42 EIVVATDDEEIDDIAEEY-GAKVIFRRG 68 (217)
T ss_dssp EEEEEESSHHHHHHHHHT-TSEEEE--T
T ss_pred eEEEeCCCHHHHHHHHHc-CCeeEEcCh
Confidence 699999999999999996 887766654
No 36
>KOG3460|consensus
Probab=49.86 E-value=43 Score=21.69 Aligned_cols=20 Identities=10% Similarity=0.215 Sum_probs=15.7
Q ss_pred CCccEEEEecceEEEeeCCC
Q psy3003 81 PGVPIMYISQHRYTIERMPD 100 (106)
Q Consensus 81 ~GVPviy~~~~~l~lE~~s~ 100 (106)
..+|.+|+|+..++|-.|+.
T Consensus 69 r~~emlFvRGd~Vilvspp~ 88 (91)
T KOG3460|consen 69 RTVEMLFVRGDGVILVSPPL 88 (91)
T ss_pred cceeEEEEeCCeEEEEcCcc
Confidence 36999999998877766654
No 37
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
Probab=49.69 E-value=15 Score=23.91 Aligned_cols=33 Identities=15% Similarity=0.259 Sum_probs=21.4
Q ss_pred CHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEE
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIM 86 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPvi 86 (106)
.+|..|...+..++ ..+.|.|+++ +..+|+.++
T Consensus 105 ~~D~~i~a~A~~~~-~~lvT~D~~f----~~~~~~~i~ 137 (142)
T TIGR00028 105 VTDAHLAALAREHG-AELVTFDRGF----ARFAGIRWR 137 (142)
T ss_pred chHHHHHHHHHHcC-CEEEecCCCc----cccCCCeee
Confidence 34555567777776 5666999865 455677664
No 38
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=49.58 E-value=45 Score=24.95 Aligned_cols=37 Identities=11% Similarity=0.200 Sum_probs=30.3
Q ss_pred CHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEE
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMY 87 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy 87 (106)
.+|--++.++..-+ ..|.|.|..+++.+.+. |+.++-
T Consensus 158 ~~DidvlaLA~ELd-a~lvTdD~giqn~A~~L-gi~~~~ 194 (206)
T TIGR03875 158 AEDLDVLLLAKELD-AAVVSADEGIRKWAERL-GLRFVD 194 (206)
T ss_pred hhhHHHHHHHHHcC-cEEEeCcHHHHHHHHHc-CCeeec
Confidence 46666777777764 89999999999999997 988764
No 39
>TIGR01457 HAD-SF-IIA-hyp2 HAD-superfamily subfamily IIA hydrolase, TIGR01457. This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram positive (low-GC) bacteria. Sequences found in this model are annotated variously as related to NagD or 4-nitrophenyl phosphatase, and this hypothetical equivalog, of all of those within the Class IIA subfamily, is most closely related to the E. coli NagD enzyme and the PGP_euk equivalog (TIGR01452). However, there is presently no evidence that this hypothetical equivalog has the same function of either those.
Probab=49.51 E-value=27 Score=25.85 Aligned_cols=37 Identities=11% Similarity=0.192 Sum_probs=28.1
Q ss_pred CHHHHHHHhhhcCCeEEEEec-----CHHHHHHHhcCCCccEE
Q psy3003 49 YADDCIVNRVTQHKCYIVATC-----DKDLKRRIRKVPGVPIM 86 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTq-----D~~Lr~~Lr~i~GVPvi 86 (106)
.+.++|..+..++.+++++|| -..+..+|++. |+++-
T Consensus 21 ~a~~~l~~l~~~g~~~~~~Tnn~~r~~~~~~~~l~~~-g~~~~ 62 (249)
T TIGR01457 21 EAETFVHELQKRDIPYLFVTNNSTRTPESVAEMLASF-DIPAT 62 (249)
T ss_pred CHHHHHHHHHHCCCeEEEEeCCCCCCHHHHHHHHHHc-CCCCC
Confidence 577888888777667999998 56678888885 77753
No 40
>cd02066 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which
Probab=49.35 E-value=20 Score=20.00 Aligned_cols=25 Identities=24% Similarity=0.506 Sum_probs=17.2
Q ss_pred ecCHHHHHHHhc---CCCccEEEEecce
Q psy3003 68 TCDKDLKRRIRK---VPGVPIMYISQHR 92 (106)
Q Consensus 68 TqD~~Lr~~Lr~---i~GVPviy~~~~~ 92 (106)
.+|.++++.+.+ .+.+|++|+++..
T Consensus 33 ~~~~~~~~~l~~~~~~~~~P~~~~~~~~ 60 (72)
T cd02066 33 LEDGELREELKELSGWPTVPQIFINGEF 60 (72)
T ss_pred CCCHHHHHHHHHHhCCCCcCEEEECCEE
Confidence 556667777764 2579999886543
No 41
>PRK04358 hypothetical protein; Provisional
Probab=48.94 E-value=30 Score=26.08 Aligned_cols=37 Identities=11% Similarity=0.200 Sum_probs=29.0
Q ss_pred CHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEE
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMY 87 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy 87 (106)
.+|--++.++..-+ ..|.|.|..+++.+.+. |+.++-
T Consensus 162 ~~DidvlaLA~ELd-a~lvTdD~giqn~A~~L-GI~~~~ 198 (217)
T PRK04358 162 AEDLDVLLLAKELD-AAVVSADEGIRKWAERL-GLRFVD 198 (217)
T ss_pred hhhHHHHHHHHHhC-CEEEeCCHHHHHHHHHc-CCeeec
Confidence 34555666666664 89999999999999997 998764
No 42
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=48.83 E-value=96 Score=22.08 Aligned_cols=63 Identities=17% Similarity=0.179 Sum_probs=35.7
Q ss_pred HHHhhccC-CceEEEecCCCCC--CHHHHHHHhhhcC-CeEEEEecC----HHHHHHHhcCCCccEEEEecc
Q psy3003 28 VALRIIKD-PRFERIPCMHKGT--YADDCIVNRVTQH-KCYIVATCD----KDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 28 ~al~~ak~-~~~~~~~c~h~~~--~ad~ci~~~~~~~-~~~iVaTqD----~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
+..+.+++ .++.++-++.... ...++|..++... .-.+|+..| .++...+.+ .|+|++.+.+.
T Consensus 20 gi~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiii~~~~~~~~~~~~~~l~~-~~iPvv~~~~~ 90 (272)
T cd06301 20 AMKEHAKVLGGVELQFEDAKNDVATQLSQVENFIAQGVDAIIVVPVDTAATAPIVKAANA-AGIPLVYVNRR 90 (272)
T ss_pred HHHHHHHHcCCcEEEEeCCCCCHHHHHHHHHHHHHcCCCEEEEecCchhhhHHHHHHHHH-CCCeEEEecCC
Confidence 33444443 3566666654322 3446777766542 235555443 455566666 59999998753
No 43
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=48.40 E-value=71 Score=23.35 Aligned_cols=78 Identities=17% Similarity=0.110 Sum_probs=52.4
Q ss_pred eeecHHHHHHHHhhCcc--hHHHHhhccCCceEEEecCCCC-----------------CCHHHHHHHhhhcC---CeEEE
Q psy3003 9 PYITDCVLGEIEKLGQK--YKVALRIIKDPRFERIPCMHKG-----------------TYADDCIVNRVTQH---KCYIV 66 (106)
Q Consensus 9 ~~vt~cVl~EL~~Lg~~--~~~al~~ak~~~~~~~~c~h~~-----------------~~ad~ci~~~~~~~---~~~iV 66 (106)
.++|.-|++|++.-.+. +..++.-. ++.+..+++.. ..+|--++.++-.. .+..+
T Consensus 29 ~yttp~Vv~Eikd~~s~~~~e~~~~~~---~~kv~~P~~e~vk~V~e~a~~tgd~~~LS~tDi~VlalAlel~~~~~v~l 105 (177)
T COG1439 29 LYTTPSVVEEIKDRESRSLLELLLESG---KVKVAEPSTEYVKEVREAAKKTGDLGNLSPTDIEVLALALELGEEVQVAL 105 (177)
T ss_pred ccccHHHHHHHhchhhhHHHHHHhhhc---CeeEecCCHHHHHHHHHHHHhhCcccccChhhHHHHHHHHhhccccceeE
Confidence 58889999999886544 23333333 36677777521 13454444554332 34799
Q ss_pred EecCHHHHHHHhcCCCccEEEEec
Q psy3003 67 ATCDKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 67 aTqD~~Lr~~Lr~i~GVPviy~~~ 90 (106)
+|-|-.+++-+.+. |+-+.++..
T Consensus 106 ~TdDysvQNVa~~L-gi~~~~~~~ 128 (177)
T COG1439 106 ATDDYSVQNVALQL-GLNVRSISY 128 (177)
T ss_pred EecchHHHHHHHHh-CceEEeeec
Confidence 99999999999997 999987553
No 44
>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes []. It has been suggested that this domain belongs to the PIN domain superfamily []. ; PDB: 3V33_A 3V34_B 3V32_B.
Probab=48.29 E-value=16 Score=25.34 Aligned_cols=46 Identities=15% Similarity=0.316 Sum_probs=23.8
Q ss_pred CHHHHHHHhhhcCCeEEEEecCH---------HHHHHHhcCCCccEEEEecceEEEee
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDK---------DLKRRIRKVPGVPIMYISQHRYTIER 97 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~---------~Lr~~Lr~i~GVPviy~~~~~l~lE~ 97 (106)
+.|..|+++|.+.+ .+|.|||+ ++++.++.. =|+ ..+.++.+.+.+
T Consensus 89 ydD~~il~~A~~~~-a~IVSND~frD~~~~~~~~~~~~~~~-~i~-~tf~~~~~~~~~ 143 (155)
T PF11977_consen 89 YDDRYILYYAEEKD-AVIVSNDRFRDHIFENPELRRWIERR-LIR-FTFVGDEFMPPP 143 (155)
T ss_dssp -HHHHHHHHHHHTT--EEE-S---HHHHHH-HHHHHHHHHH-EE---EEETTEEE--S
T ss_pred cchHHHHHHHHHcC-CEEEeCchHHHHhhcchHHHHHHHHe-eee-EEEECCEEEcCC
Confidence 58899999999885 67779996 366666431 133 233355544443
No 45
>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]
Probab=48.17 E-value=24 Score=29.12 Aligned_cols=78 Identities=15% Similarity=0.218 Sum_probs=49.3
Q ss_pred ceeeecHHHHHHHHhhCc-------chHHHHhhccCC-----------------ceEEEecCCCC----------CCHHH
Q psy3003 7 GIPYITDCVLGEIEKLGQ-------KYKVALRIIKDP-----------------RFERIPCMHKG----------TYADD 52 (106)
Q Consensus 7 ~~~~vt~cVl~EL~~Lg~-------~~~~al~~ak~~-----------------~~~~~~c~h~~----------~~ad~ 52 (106)
-..++|--|++||+++++ .++.|+...... ..-++.-+|.. ...|.
T Consensus 25 h~VvIP~~VlEELd~~Kr~~~evgrnAR~a~r~ld~L~~~~~~l~~giPl~~~G~~l~iel~~~~~~~~~~~~~~~~~Dn 104 (436)
T COG1875 25 HDVVIPMVVIEELDATKRGHSEIGRNARQASRLLDELRNEHGRLKAGIPLGNKGGTLHVELNHQNSTKLPNGFREGVNDN 104 (436)
T ss_pred cceEeeehHHHHHHhhcccchhhHHHHHHHHHHHHHHHhhcCCccCCcccCCCCCeEEEEEeccCccccccccccccchH
Confidence 357899999999999754 355554443210 11123333421 15677
Q ss_pred HHHHhhh----c--CCeEEEEecCHHHHHHHhcCCCccE
Q psy3003 53 CIVNRVT----Q--HKCYIVATCDKDLKRRIRKVPGVPI 85 (106)
Q Consensus 53 ci~~~~~----~--~~~~iVaTqD~~Lr~~Lr~i~GVPv 85 (106)
-|++++. . ..+.+..|-|-.+|-+.+.. |++.
T Consensus 105 rIL~~~~~L~~~~~~~~VvLVSKDi~~RvkA~a~-Gl~A 142 (436)
T COG1875 105 RILAVVLNLQEEEPGRRVVLVSKDINLRVKASAL-GLAA 142 (436)
T ss_pred HHHHHHHHHHhcCCCCcEEEEECCccceeehhhc-CccH
Confidence 7777664 2 23689999999999888885 8874
No 46
>smart00475 53EXOc 5'-3' exonuclease.
Probab=47.93 E-value=20 Score=27.29 Aligned_cols=33 Identities=27% Similarity=0.282 Sum_probs=25.6
Q ss_pred CCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHhc
Q psy3003 47 GTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIRK 79 (106)
Q Consensus 47 ~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr~ 79 (106)
+-.|||.|-.++.+ ....+|+|.|+++.+-+..
T Consensus 105 g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~ 141 (259)
T smart00475 105 GYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSD 141 (259)
T ss_pred CcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCC
Confidence 34799999888864 2358999999999887653
No 47
>KOG1475|consensus
Probab=47.45 E-value=11 Score=30.04 Aligned_cols=33 Identities=21% Similarity=0.472 Sum_probs=27.8
Q ss_pred eEEEEecCHHHHHHHhcCCCccEEEEec-ceEEE
Q psy3003 63 CYIVATCDKDLKRRIRKVPGVPIMYISQ-HRYTI 95 (106)
Q Consensus 63 ~~iVaTqD~~Lr~~Lr~i~GVPviy~~~-~~l~l 95 (106)
-++|-++|.+.-+.+|.+|||-++.+.+ |-+.|
T Consensus 206 PlVVy~Ed~~ivkAFRNIpGV~~~nV~~LnlLkL 239 (363)
T KOG1475|consen 206 PLVVYNEDNGIVKAFRNIPGVELMNVERLNLLKL 239 (363)
T ss_pred CEEEEecCcchhhhhcCCCcceeechhhhhhhhc
Confidence 3899999999999999999999999875 33443
No 48
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=47.13 E-value=1.1e+02 Score=22.83 Aligned_cols=62 Identities=6% Similarity=0.101 Sum_probs=37.0
Q ss_pred HHHhhccCCceEEEecCCCCC--CHHHHHHHhhhcC-CeEEEEecCH----HHHHHHhcCCCccEEEEec
Q psy3003 28 VALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQH-KCYIVATCDK----DLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 28 ~al~~ak~~~~~~~~c~h~~~--~ad~ci~~~~~~~-~~~iVaTqD~----~Lr~~Lr~i~GVPviy~~~ 90 (106)
+..+.|++..+.+.-+++... .-.+.|..++.+. .-.+++..|. +.-+++++ .|+|++++.+
T Consensus 19 ~i~~~a~~~g~~v~~~~~~~~~~~q~~~i~~l~~~~vDgIIi~~~~~~~~~~~l~~~~~-~~iPvV~~d~ 87 (302)
T TIGR02634 19 IFVAAAESLGAKVFVQSANGNEAKQISQIENLIARGVDVLVIIPQNGQVLSNAVQEAKD-EGIKVVAYDR 87 (302)
T ss_pred HHHHHHHhcCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhHHHHHHHHHHH-CCCeEEEecC
Confidence 334455533567777766432 2336666666552 3477776553 34455666 5999999975
No 49
>KOG3964|consensus
Probab=46.40 E-value=18 Score=29.99 Aligned_cols=17 Identities=18% Similarity=0.473 Sum_probs=15.7
Q ss_pred eEEEEecCHHHHHHHhc
Q psy3003 63 CYIVATCDKDLKRRIRK 79 (106)
Q Consensus 63 ~~iVaTqD~~Lr~~Lr~ 79 (106)
.+.|.|+|.+|++||+.
T Consensus 416 n~livT~nqel~qrl~a 432 (469)
T KOG3964|consen 416 NILIVTENQELQQRLHA 432 (469)
T ss_pred ceEEEecCHHHHHHHHH
Confidence 59999999999999985
No 50
>PRK14976 5'-3' exonuclease; Provisional
Probab=46.36 E-value=21 Score=27.45 Aligned_cols=49 Identities=18% Similarity=0.234 Sum_probs=33.6
Q ss_pred eEEEecCCCCCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHhcCCCccEEEEec
Q psy3003 38 FERIPCMHKGTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 38 ~~~~~c~h~~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~ 90 (106)
+..+.. .+-.|||.|-.++.+ ....+|+|.|+++.+-+.. +|.+.+..+
T Consensus 104 i~~~~~--~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~--~v~~~~~~~ 156 (281)
T PRK14976 104 IKWEEQ--PGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNE--NTDVLLKKK 156 (281)
T ss_pred CCEEec--CCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCC--CeEEEEecC
Confidence 444444 234799999988864 2358899999999987654 566665443
No 51
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=45.84 E-value=23 Score=22.07 Aligned_cols=29 Identities=14% Similarity=0.397 Sum_probs=21.5
Q ss_pred EEEEecCHHHHHHHhcC---CCccEEEEecce
Q psy3003 64 YIVATCDKDLKRRIRKV---PGVPIMYISQHR 92 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr~i---~GVPviy~~~~~ 92 (106)
++=..+|.++++.|.+. ..+|.||+.+..
T Consensus 42 ~idv~~~~~~~~~l~~~~g~~tvP~vfi~g~~ 73 (90)
T cd03028 42 TFDILEDEEVRQGLKEYSNWPTFPQLYVNGEL 73 (90)
T ss_pred EEEcCCCHHHHHHHHHHhCCCCCCEEEECCEE
Confidence 44446789999998864 568999998654
No 52
>PF05716 AKAP_110: A-kinase anchor protein 110 kDa (AKAP 110); InterPro: IPR018292 This family consists of several mammalian protein kinase A anchoring protein 3 (PRKA3) or A-kinase anchor protein 110 kDa (AKAP 110) sequences. Agents that increase intracellular cAMP are potent stimulators of sperm motility. Anchoring inhibitor peptides, designed to disrupt the interaction of the cAMP-dependent protein kinase A (PKA) with A kinase-anchoring proteins (AKAPs), are potent inhibitors of sperm motility. PKA anchoring is a key biochemical mechanism controlling motility. AKAP110 shares compartments with both RI and RII isoforms of PKA and may function as a regulator of both motility- and head-associated functions such as capacitation and the acrosome reaction []. This entry represents a sub group of the A-kinase anschor 110kDa protein.
Probab=45.75 E-value=18 Score=31.14 Aligned_cols=24 Identities=25% Similarity=0.527 Sum_probs=19.1
Q ss_pred ecCHHHHHHHh----cCCCccEEEEecc
Q psy3003 68 TCDKDLKRRIR----KVPGVPIMYISQH 91 (106)
Q Consensus 68 TqD~~Lr~~Lr----~i~GVPviy~~~~ 91 (106)
++|++||--|. ...|||++||++.
T Consensus 600 v~d~QLrAVLQWIAASEl~VP~LYF~~~ 627 (685)
T PF05716_consen 600 VQDKQLRAVLQWIAASELNVPMLYFRKD 627 (685)
T ss_pred CCcHHHHHHHHHHHHhhcCCceEEEecC
Confidence 46789998776 4579999999964
No 53
>PTZ00062 glutaredoxin; Provisional
Probab=45.46 E-value=22 Score=26.25 Aligned_cols=29 Identities=21% Similarity=0.372 Sum_probs=21.9
Q ss_pred EEEecCHHHHHHHhcC---CCccEEEEecceE
Q psy3003 65 IVATCDKDLKRRIRKV---PGVPIMYISQHRY 93 (106)
Q Consensus 65 iVaTqD~~Lr~~Lr~i---~GVPviy~~~~~l 93 (106)
+=..+|.+.|+.|.+. +.||.||+++..+
T Consensus 148 ~DI~~d~~~~~~l~~~sg~~TvPqVfI~G~~I 179 (204)
T PTZ00062 148 YNIFEDPDLREELKVYSNWPTYPQLYVNGELI 179 (204)
T ss_pred EEcCCCHHHHHHHHHHhCCCCCCeEEECCEEE
Confidence 3345788999988754 7899999997643
No 54
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=43.08 E-value=65 Score=20.40 Aligned_cols=33 Identities=27% Similarity=0.542 Sum_probs=27.2
Q ss_pred ecCHHHHHHHhcCCCccEEEEecceEEEeeCCC
Q psy3003 68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPD 100 (106)
Q Consensus 68 TqD~~Lr~~Lr~i~GVPviy~~~~~l~lE~~s~ 100 (106)
+.+..|-++|-.++||-=+|+-.+-+.+++-+.
T Consensus 34 a~~spLA~~Lf~i~gV~~Vf~~~dfItVtK~~~ 66 (87)
T PF08712_consen 34 ASDSPLAQALFAIPGVKSVFIGDDFITVTKNPD 66 (87)
T ss_dssp TTS-HHHHHHHTSTTEEEEEEETTEEEEEE-TT
T ss_pred cccCHHHHHhcCCCCEeEEEEECCEEEEeeCCC
Confidence 345779999999999999999999999988554
No 55
>KOG0399|consensus
Probab=42.79 E-value=11 Score=35.55 Aligned_cols=19 Identities=26% Similarity=0.351 Sum_probs=15.2
Q ss_pred EEEEecCHHHHHHHhcCCC
Q psy3003 64 YIVATCDKDLKRRIRKVPG 82 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr~i~G 82 (106)
.-|||||++||.++.-.|+
T Consensus 1220 VGiAtQdp~LRakF~G~Pe 1238 (2142)
T KOG0399|consen 1220 VGIATQDPELRAKFPGQPE 1238 (2142)
T ss_pred cccccCCHHHHhhCCCCcH
Confidence 6799999999998854443
No 56
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=42.39 E-value=47 Score=19.37 Aligned_cols=30 Identities=10% Similarity=0.057 Sum_probs=20.2
Q ss_pred EecCHHHHHHHhcCCCccEEEEecceEEEeeC
Q psy3003 67 ATCDKDLKRRIRKVPGVPIMYISQHRYTIERM 98 (106)
Q Consensus 67 aTqD~~Lr~~Lr~i~GVPviy~~~~~l~lE~~ 98 (106)
..+|+++-++.. +.|+|.++++ +...+.+.
T Consensus 39 ~~~~~~~~~~~~-v~~vPt~~~~-g~~~~~G~ 68 (82)
T TIGR00411 39 VMENPQKAMEYG-IMAVPAIVIN-GDVEFIGA 68 (82)
T ss_pred CccCHHHHHHcC-CccCCEEEEC-CEEEEecC
Confidence 346777777754 4699999984 44555553
No 57
>cd03419 GRX_GRXh_1_2_like Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes
Probab=42.31 E-value=29 Score=20.47 Aligned_cols=22 Identities=14% Similarity=0.345 Sum_probs=15.0
Q ss_pred HHHHHHHhc---CCCccEEEEecce
Q psy3003 71 KDLKRRIRK---VPGVPIMYISQHR 92 (106)
Q Consensus 71 ~~Lr~~Lr~---i~GVPviy~~~~~ 92 (106)
.+++..+.+ .+++|.+|+.+..
T Consensus 39 ~~~~~~~~~~~g~~~~P~v~~~g~~ 63 (82)
T cd03419 39 SEIQDYLQELTGQRTVPNVFIGGKF 63 (82)
T ss_pred HHHHHHHHHHhCCCCCCeEEECCEE
Confidence 455555543 4789999988654
No 58
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=42.01 E-value=27 Score=24.41 Aligned_cols=26 Identities=12% Similarity=0.453 Sum_probs=17.8
Q ss_pred EecCHHHHHHHhcC-------CCccEEEEecce
Q psy3003 67 ATCDKDLKRRIRKV-------PGVPIMYISQHR 92 (106)
Q Consensus 67 aTqD~~Lr~~Lr~i-------~GVPviy~~~~~ 92 (106)
...|.+.++.|++. +.+|.||+++..
T Consensus 38 Vs~~~~~~~EL~~~~g~~~~~~tvPqVFI~G~~ 70 (147)
T cd03031 38 VSMDSGFREELRELLGAELKAVSLPRVFVDGRY 70 (147)
T ss_pred CCCCHHHHHHHHHHhCCCCCCCCCCEEEECCEE
Confidence 34566666666543 689999999754
No 59
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=40.13 E-value=41 Score=19.71 Aligned_cols=29 Identities=14% Similarity=0.172 Sum_probs=19.3
Q ss_pred EEEEecCHHHHHHHhc---CCCccEEEEecce
Q psy3003 64 YIVATCDKDLKRRIRK---VPGVPIMYISQHR 92 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr~---i~GVPviy~~~~~ 92 (106)
++=...|.+.+..+.+ ..++|++++++..
T Consensus 30 ~~di~~~~~~~~el~~~~g~~~vP~v~i~~~~ 61 (73)
T cd03027 30 EINIDIFPERKAELEERTGSSVVPQIFFNEKL 61 (73)
T ss_pred EEECCCCHHHHHHHHHHhCCCCcCEEEECCEE
Confidence 4555666666666653 2589999998754
No 60
>PRK10824 glutaredoxin-4; Provisional
Probab=38.41 E-value=72 Score=21.38 Aligned_cols=31 Identities=16% Similarity=0.415 Sum_probs=24.3
Q ss_pred eEEEEecCHHHHHHHhcC---CCccEEEEecceE
Q psy3003 63 CYIVATCDKDLKRRIRKV---PGVPIMYISQHRY 93 (106)
Q Consensus 63 ~~iVaTqD~~Lr~~Lr~i---~GVPviy~~~~~l 93 (106)
.++-..+|.++|..|.+. +-||-||+++..+
T Consensus 48 ~~idi~~d~~~~~~l~~~sg~~TVPQIFI~G~~I 81 (115)
T PRK10824 48 AYVDILQNPDIRAELPKYANWPTFPQLWVDGELV 81 (115)
T ss_pred eEEEecCCHHHHHHHHHHhCCCCCCeEEECCEEE
Confidence 366667899999998864 6799999997543
No 61
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=38.13 E-value=1.3e+02 Score=20.41 Aligned_cols=43 Identities=14% Similarity=0.339 Sum_probs=33.8
Q ss_pred HHHHHHHhhhc---CCeEEEEecCHHHHHHHhcC-CCccEEEEecce
Q psy3003 50 ADDCIVNRVTQ---HKCYIVATCDKDLKRRIRKV-PGVPIMYISQHR 92 (106)
Q Consensus 50 ad~ci~~~~~~---~~~~iVaTqD~~Lr~~Lr~i-~GVPviy~~~~~ 92 (106)
..+.+.+++.+ .++.++.+=|.+..+++++. |++|+.++..+.
T Consensus 77 ~~~~l~~~i~~~~~~~~v~i~s~~~~~l~~~~~~~p~~~~~~~~~~~ 123 (189)
T cd08556 77 LEAKVAELLREYGLEERVVVSSFDHEALRALKELDPEVPTGLLVDKP 123 (189)
T ss_pred HHHHHHHHHHHcCCcCCEEEEeCCHHHHHHHHHhCCCCcEEEEeecC
Confidence 45667777765 35799999999999999974 999999887654
No 62
>TIGR00365 monothiol glutaredoxin, Grx4 family. The gene for the member of this glutaredoxin family in E. coli, originally designated ydhD, is now designated grxD. Its protein, Grx4, is a monothiol glutaredoxin similar to Grx5 of yeast, which is involved in iron-sulfur cluster formation.
Probab=37.94 E-value=36 Score=21.68 Aligned_cols=26 Identities=19% Similarity=0.503 Sum_probs=19.7
Q ss_pred EecCHHHHHHHhc---CCCccEEEEecce
Q psy3003 67 ATCDKDLKRRIRK---VPGVPIMYISQHR 92 (106)
Q Consensus 67 aTqD~~Lr~~Lr~---i~GVPviy~~~~~ 92 (106)
..+|.++++.|.+ .+.||.||+++..
T Consensus 49 i~~~~~~~~~l~~~tg~~tvP~vfi~g~~ 77 (97)
T TIGR00365 49 VLEDPEIRQGIKEYSNWPTIPQLYVKGEF 77 (97)
T ss_pred CCCCHHHHHHHHHHhCCCCCCEEEECCEE
Confidence 3577888888864 3689999998764
No 63
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=37.37 E-value=20 Score=20.29 Aligned_cols=16 Identities=25% Similarity=0.686 Sum_probs=12.3
Q ss_pred cCHHHHHHHhcCCCccE
Q psy3003 69 CDKDLKRRIRKVPGVPI 85 (106)
Q Consensus 69 qD~~Lr~~Lr~i~GVPv 85 (106)
.|.+||..|++. |+|.
T Consensus 7 Sd~eL~~~L~~~-G~~~ 22 (44)
T smart00540 7 SDAELRAELKQY-GLPP 22 (44)
T ss_pred CHHHHHHHHHHc-CCCC
Confidence 588999999983 5554
No 64
>PF12226 Astro_capsid_p: Turkey astrovirus capsid protein; InterPro: IPR022027 This family of proteins is found in viruses. Proteins in this family are typically between 241 and 261 amino acids in length. These proteins are capsid proteins from various astrovirus strains. ; PDB: 3TS3_D.
Probab=37.35 E-value=31 Score=25.54 Aligned_cols=24 Identities=29% Similarity=0.488 Sum_probs=15.2
Q ss_pred EEec-CHHHHHHHhcCCCccEEEEe
Q psy3003 66 VATC-DKDLKRRIRKVPGVPIMYIS 89 (106)
Q Consensus 66 VaTq-D~~Lr~~Lr~i~GVPviy~~ 89 (106)
=-|| |..|+.||.-..|=|||.+-
T Consensus 108 ~TTnld~~lK~RlnL~EgDPViS~G 132 (230)
T PF12226_consen 108 GTTNLDQQLKDRLNLTEGDPVISMG 132 (230)
T ss_dssp GG--S-HHHHHHHT--TT-EEEEEE
T ss_pred CCccHHHHHHHhhccccCCceeeec
Confidence 3466 99999999977899999764
No 65
>TIGR02180 GRX_euk Glutaredoxin. This model represents eukaryotic glutaredoxins and includes sequences from fungi, plants and metazoans as well as viruses.
Probab=37.28 E-value=39 Score=19.82 Aligned_cols=22 Identities=14% Similarity=0.350 Sum_probs=14.4
Q ss_pred HHHHHHHhc---CCCccEEEEecce
Q psy3003 71 KDLKRRIRK---VPGVPIMYISQHR 92 (106)
Q Consensus 71 ~~Lr~~Lr~---i~GVPviy~~~~~ 92 (106)
.++++.+.+ +.++|.+|+.+..
T Consensus 40 ~~~~~~l~~~~g~~~vP~v~i~g~~ 64 (84)
T TIGR02180 40 SEIQDYLEEITGQRTVPNIFINGKF 64 (84)
T ss_pred HHHHHHHHHHhCCCCCCeEEECCEE
Confidence 445555543 4689999988654
No 66
>cd03030 GRX_SH3BGR Glutaredoxin (GRX) family, SH3BGR (SH3 domain binding glutamic acid-rich protein) subfamily; a recently-identified subfamily composed of SH3BGR and similar proteins possessing significant sequence similarity to GRX, but without a redox active CXXC motif. The SH3BGR gene was cloned in an effort to identify genes mapping to chromosome 21, which could be involved in the pathogenesis of congenital heart disease affecting Down syndrome newborns. Several human SH3BGR-like (SH3BGRL) genes have been identified since, mapping to different locations in the chromosome. Of these, SH3BGRL3 was identified as a tumor necrosis factor (TNF) alpha inhibitory protein and was also named TIP-B1. Upregulation of expression of SH3BGRL3 is associated with differentiation. It has been suggested that it functions as a regulator of differentiation-related signal transduction pathways.
Probab=36.94 E-value=42 Score=21.50 Aligned_cols=28 Identities=11% Similarity=0.273 Sum_probs=19.9
Q ss_pred EEEEecCHHHHHHHhcC-------CCccEEEEecc
Q psy3003 64 YIVATCDKDLKRRIRKV-------PGVPIMYISQH 91 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr~i-------~GVPviy~~~~ 91 (106)
-+=.+.|++.|+.+++. +.+|-||+.+.
T Consensus 35 eiDI~~d~~~r~em~~~~~~~~g~~tvPQIFi~~~ 69 (92)
T cd03030 35 EVDISMNEENRQWMRENVPNENGKPLPPQIFNGDE 69 (92)
T ss_pred EEecCCCHHHHHHHHHhcCCCCCCCCCCEEEECCE
Confidence 34455688888888754 45899998754
No 67
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=36.01 E-value=47 Score=24.87 Aligned_cols=38 Identities=13% Similarity=0.155 Sum_probs=20.1
Q ss_pred HHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEEEe
Q psy3003 50 ADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYIS 89 (106)
Q Consensus 50 ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~ 89 (106)
+|=-++-++..-+ ..|.|+|..+++...+. |+-+|--+
T Consensus 156 ~D~dvl~LA~El~-a~lvt~D~gi~~~A~~l-Gi~~i~~~ 193 (205)
T PF08745_consen 156 EDIDVLLLALELD-AVLVTDDYGIQNWAEKL-GIRFIDAR 193 (205)
T ss_dssp HHHHHHHHHHHHT---EE---HHHHHHHHHT-T--EE---
T ss_pred HhHHHHHHHHHcC-CEEEeCCHhHHHHHHHC-CCEEEecc
Confidence 3444455555554 88999999999999997 98776544
No 68
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=35.97 E-value=47 Score=18.86 Aligned_cols=24 Identities=21% Similarity=0.135 Sum_probs=17.2
Q ss_pred ecCHHHHHHHhcCCCccEEEEecce
Q psy3003 68 TCDKDLKRRIRKVPGVPIMYISQHR 92 (106)
Q Consensus 68 TqD~~Lr~~Lr~i~GVPviy~~~~~ 92 (106)
..+++|.+++.- .++|.+++.+..
T Consensus 39 ~~~~~l~~~~~i-~~vPti~i~~~~ 62 (67)
T cd02973 39 AEFPDLADEYGV-MSVPAIVINGKV 62 (67)
T ss_pred ccCHhHHHHcCC-cccCEEEECCEE
Confidence 445677777665 599999987643
No 69
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=35.36 E-value=89 Score=18.03 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=19.8
Q ss_pred eEEEEecCHH-----HHHHHhcCCCccEEEE
Q psy3003 63 CYIVATCDKD-----LKRRIRKVPGVPIMYI 88 (106)
Q Consensus 63 ~~iVaTqD~~-----Lr~~Lr~i~GVPviy~ 88 (106)
.|.|.+.|.+ +.++|+++|||.=+++
T Consensus 44 ~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 44 TISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 4667777775 7788999999877665
No 70
>PHA00439 exonuclease
Probab=35.10 E-value=37 Score=26.57 Aligned_cols=30 Identities=30% Similarity=0.372 Sum_probs=23.2
Q ss_pred CCCHHHHHHHhhhc---CC--eEEEEecCHHHHHH
Q psy3003 47 GTYADDCIVNRVTQ---HK--CYIVATCDKDLKRR 76 (106)
Q Consensus 47 ~~~ad~ci~~~~~~---~~--~~iVaTqD~~Lr~~ 76 (106)
|-.|||+|-.++.+ .+ ..+|+|.|++|.+-
T Consensus 118 G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QL 152 (286)
T PHA00439 118 GLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTI 152 (286)
T ss_pred CccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhc
Confidence 45799999888863 21 47999999998875
No 71
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=34.48 E-value=2e+02 Score=22.23 Aligned_cols=64 Identities=8% Similarity=0.167 Sum_probs=38.9
Q ss_pred HHHhhccCCceEEEecCCCCC--CHHHHHHHhhhcC-CeEEEEe--cCHHHHHHHhcCCCccEEEEecce
Q psy3003 28 VALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQH-KCYIVAT--CDKDLKRRIRKVPGVPIMYISQHR 92 (106)
Q Consensus 28 ~al~~ak~~~~~~~~c~h~~~--~ad~ci~~~~~~~-~~~iVaT--qD~~Lr~~Lr~i~GVPviy~~~~~ 92 (106)
+.-+.++..++.++-|+.... ...+++..+..+. .-.|++. .+..+.+.+.+. |+|++.+.+..
T Consensus 79 gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~~~~~~~~~~~l~~~-~~P~V~i~~~~ 147 (333)
T COG1609 79 GIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDGLILLGERPNDSLLELLAAA-GIPVVVIDRSP 147 (333)
T ss_pred HHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEecCCCCHHHHHHHHhc-CCCEEEEeCCC
Confidence 333444433677777765432 2345555555541 2366665 566778888885 99999999743
No 72
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=34.46 E-value=61 Score=18.56 Aligned_cols=35 Identities=11% Similarity=0.201 Sum_probs=21.3
Q ss_pred EEEEecCHHHHHHHh----cCCCccEEEEecceEEEeeCC
Q psy3003 64 YIVATCDKDLKRRIR----KVPGVPIMYISQHRYTIERMP 99 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr----~i~GVPviy~~~~~l~lE~~s 99 (106)
++=..+|.+....++ ...+||++.+.++.. +..|+
T Consensus 29 ~idi~~~~~~~~~~~~~~~~~~~vP~i~~~~g~~-l~~~~ 67 (77)
T TIGR02200 29 WVDIEEDEGAADRVVSVNNGNMTVPTVKFADGSF-LTNPS 67 (77)
T ss_pred EEeCcCCHhHHHHHHHHhCCCceeCEEEECCCeE-ecCCC
Confidence 333456777766663 345899998776654 44444
No 73
>PRK11440 putative hydrolase; Provisional
Probab=34.28 E-value=40 Score=23.69 Aligned_cols=19 Identities=21% Similarity=0.527 Sum_probs=14.6
Q ss_pred HHHHHHHhcCCCccEEEEec
Q psy3003 71 KDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 71 ~~Lr~~Lr~i~GVPviy~~~ 90 (106)
..|.+..|+ .|+||||++.
T Consensus 38 ~~l~~~ar~-~g~pVi~~~~ 56 (188)
T PRK11440 38 ARLAAKFRA-SGSPVVLVRV 56 (188)
T ss_pred HHHHHHHHH-cCCcEEEEec
Confidence 346677888 4999999873
No 74
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=33.42 E-value=66 Score=22.51 Aligned_cols=29 Identities=21% Similarity=0.148 Sum_probs=20.3
Q ss_pred HHHHHHhcCCCc--cEEEEecceEEEeeCCC
Q psy3003 72 DLKRRIRKVPGV--PIMYISQHRYTIERMPD 100 (106)
Q Consensus 72 ~Lr~~Lr~i~GV--Pviy~~~~~l~lE~~s~ 100 (106)
.||++|...++. .|-.+++..+.+++++.
T Consensus 208 ~LR~kl~~~~~~~~~I~tv~g~GY~~~~~~~ 238 (239)
T PRK09468 208 RLRRLIEEDPAHPRYIQTVWGLGYVFVPDGA 238 (239)
T ss_pred HHHHHhccCCCCCCeEEEeCCCCeEEccCCC
Confidence 477777654443 48888888899987654
No 75
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=32.32 E-value=2e+02 Score=21.87 Aligned_cols=63 Identities=6% Similarity=0.165 Sum_probs=36.3
Q ss_pred HHHHhhccCCceEEEecCCCCC--CHHHHHHHhhhc-CCeEEEEecC----HHHHHHHhcCCCccEEEEec
Q psy3003 27 KVALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQ-HKCYIVATCD----KDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 27 ~~al~~ak~~~~~~~~c~h~~~--~ad~ci~~~~~~-~~~~iVaTqD----~~Lr~~Lr~i~GVPviy~~~ 90 (106)
++.-+.+++.++...-|+.... ...+.|..++.. -.-.++...+ .+..+++.+ .|+|++.+.+
T Consensus 45 ~gi~~~a~~~g~~l~i~~~~~~~~~~~~~i~~l~~~~vDGiIi~~~~~~~~~~~l~~~~~-~~iPvV~id~ 114 (330)
T PRK10355 45 DIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVIKEAKQ-EGIKVLAYDR 114 (330)
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEeCCChhhHHHHHHHHHH-CCCeEEEECC
Confidence 4444455433666666765432 245667777654 2235565544 244466666 4999999965
No 76
>PHA03050 glutaredoxin; Provisional
Probab=32.04 E-value=54 Score=21.49 Aligned_cols=24 Identities=13% Similarity=0.455 Sum_probs=17.7
Q ss_pred CHHHHHHHhcC---CCccEEEEecceE
Q psy3003 70 DKDLKRRIRKV---PGVPIMYISQHRY 93 (106)
Q Consensus 70 D~~Lr~~Lr~i---~GVPviy~~~~~l 93 (106)
+.++++.+.+. ..||.||+.+..+
T Consensus 54 ~~~~~~~l~~~tG~~tVP~IfI~g~~i 80 (108)
T PHA03050 54 ENELRDYFEQITGGRTVPRIFFGKTSI 80 (108)
T ss_pred CHHHHHHHHHHcCCCCcCEEEECCEEE
Confidence 46778877753 5789999987653
No 77
>cd01141 TroA_d Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=31.83 E-value=42 Score=23.14 Aligned_cols=26 Identities=12% Similarity=0.623 Sum_probs=19.5
Q ss_pred EEEEec---CHHHHHHHhcCCCccEEEEec
Q psy3003 64 YIVATC---DKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 64 ~iVaTq---D~~Lr~~Lr~i~GVPviy~~~ 90 (106)
.++++. +.++...|.++ |||++++..
T Consensus 72 lii~~~~~~~~~~~~~l~~~-gIpvv~i~~ 100 (186)
T cd01141 72 LVILYGGFQAQTILDKLEQL-GIPVLYVNE 100 (186)
T ss_pred EEEEecCCCchhHHHHHHHc-CCCEEEeCC
Confidence 555543 33699999996 999999963
No 78
>PF03407 Nucleotid_trans: Nucleotide-diphospho-sugar transferase; InterPro: IPR005069 Proteins in this family have been been predicted to be nucleotide-diphospho-sugar transferases [].
Probab=31.80 E-value=79 Score=22.35 Aligned_cols=28 Identities=18% Similarity=0.500 Sum_probs=25.2
Q ss_pred eEEEEecCHHHHHHHhcCCCccEEEEecc
Q psy3003 63 CYIVATCDKDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 63 ~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
+++|++-|.+-.+.+++. |.|++++...
T Consensus 5 ~~lv~a~D~~t~~~l~~~-~~~~~~~~~~ 32 (212)
T PF03407_consen 5 NFLVVALDEETYDALEEL-GPPCFYFPSD 32 (212)
T ss_pred cEEEEEECHHHHHHHHhc-CCCeEEEecc
Confidence 699999999999999985 9999988765
No 79
>PLN02645 phosphoglycolate phosphatase
Probab=31.60 E-value=1.2e+02 Score=23.28 Aligned_cols=36 Identities=8% Similarity=0.150 Sum_probs=26.1
Q ss_pred CHHHHHHHhhhcCCeEEEEecCH-----HHHHHHhcCCCccE
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDK-----DLKRRIRKVPGVPI 85 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~-----~Lr~~Lr~i~GVPv 85 (106)
.+.+.|..+-.++.+++++||.. ++-++|++. |+++
T Consensus 48 ga~e~l~~lr~~g~~~~~~TN~~~~~~~~~~~~l~~l-Gi~~ 88 (311)
T PLN02645 48 GVPETLDMLRSMGKKLVFVTNNSTKSRAQYGKKFESL-GLNV 88 (311)
T ss_pred CHHHHHHHHHHCCCEEEEEeCCCCCCHHHHHHHHHHC-CCCC
Confidence 57788887776666799999954 455677775 7763
No 80
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=31.38 E-value=1.9e+02 Score=20.48 Aligned_cols=64 Identities=9% Similarity=0.244 Sum_probs=34.4
Q ss_pred HHHHhhccCCceEEEecCCCCC--CHHHHHHHhhhcC-CeEEEEe---cCHH----HHHHHhcCCCccEEEEecc
Q psy3003 27 KVALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQH-KCYIVAT---CDKD----LKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 27 ~~al~~ak~~~~~~~~c~h~~~--~ad~ci~~~~~~~-~~~iVaT---qD~~----Lr~~Lr~i~GVPviy~~~~ 91 (106)
++..+.++..++...-+..... ...+.+..+...+ .-.|+.. +|.. .-+.+.+ .|+|++++.+.
T Consensus 19 ~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~~~~i~~~~~-~~ipvV~i~~~ 92 (273)
T cd06292 19 EAIEAALAQYGYTVLLCNTYRGGVSEADYVEDLLARGVRGVVFISSLHADTHADHSHYERLAE-RGLPVVLVNGR 92 (273)
T ss_pred HHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHcCCCEEEEeCCCCCcccchhHHHHHHHh-CCCCEEEEcCC
Confidence 3444444433555555554321 3446677777652 2255542 3333 2355666 49999999764
No 81
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=31.36 E-value=1.8e+02 Score=20.95 Aligned_cols=60 Identities=12% Similarity=0.145 Sum_probs=32.5
Q ss_pred hhccCCceEEEecCCCCC-CHHHHHHHhhhcC-CeEEEEecC----HHHHHHHhcCCCccEEEEecc
Q psy3003 31 RIIKDPRFERIPCMHKGT-YADDCIVNRVTQH-KCYIVATCD----KDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 31 ~~ak~~~~~~~~c~h~~~-~ad~ci~~~~~~~-~~~iVaTqD----~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
+.++..++.+.-++.... ...+.+..++..+ .-.+|...| .++.+.+++ .|+|++.+.+.
T Consensus 23 ~~~~~~g~~~~~~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~~~~-~~iPvV~~~~~ 88 (289)
T cd01540 23 KAAKEKGFTVVKIDVPDGEKVLSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAKA-YNMKVVAVDDR 88 (289)
T ss_pred HHHHHcCCEEEEccCCCHHHHHHHHHHHHHcCCCEEEEccCchhhhHHHHHHHHh-CCCeEEEecCC
Confidence 333322556565654311 2235555555442 236666554 344566777 59999998653
No 82
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=31.30 E-value=1.9e+02 Score=20.51 Aligned_cols=64 Identities=16% Similarity=0.356 Sum_probs=34.2
Q ss_pred HHHHhhccCCceEEEecCCCCC--CHHHHHHHhhhcC-CeEEEEec-------CHHHHHHHhcCCCccEEEEecc
Q psy3003 27 KVALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQH-KCYIVATC-------DKDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 27 ~~al~~ak~~~~~~~~c~h~~~--~ad~ci~~~~~~~-~~~iVaTq-------D~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
.+..+.+++.++...-+..... ...+.+..++... .-.+++.- |.+..+.+++ .|+|++.+.+.
T Consensus 19 ~gi~~~~~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~~~~~-~~ipvV~~~~~ 92 (273)
T cd01541 19 RGIESVLSEKGYSLLLASTNNDPERERKCLENMLSQGIDGLIIEPTKSALPNPNIDLYLKLEK-LGIPYVFINAS 92 (273)
T ss_pred HHHHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHHcCCCEEEEeccccccccccHHHHHHHHH-CCCCEEEEecC
Confidence 3344445533455555543221 2446676766542 22444321 3345566766 49999999864
No 83
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=31.23 E-value=40 Score=21.31 Aligned_cols=27 Identities=26% Similarity=0.521 Sum_probs=21.7
Q ss_pred HHHHHhcCCCccEEEEecceEEEeeCCC
Q psy3003 73 LKRRIRKVPGVPIMYISQHRYTIERMPD 100 (106)
Q Consensus 73 Lr~~Lr~i~GVPviy~~~~~l~lE~~s~ 100 (106)
.-++||+. |++|...+++.+.|..++.
T Consensus 39 ~Iq~Lr~~-G~~I~s~~~kGY~L~~~~~ 65 (79)
T COG1654 39 HIQQLREE-GVDIESVRGKGYLLPQLPD 65 (79)
T ss_pred HHHHHHHh-CCceEecCCCceeccCccc
Confidence 35778885 9999999998888877665
No 84
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=30.65 E-value=1.1e+02 Score=21.68 Aligned_cols=41 Identities=17% Similarity=0.353 Sum_probs=27.8
Q ss_pred HHHHHHHhhhcC-CeEEEEecCH----HHHHHHhcCCCccEEEEecc
Q psy3003 50 ADDCIVNRVTQH-KCYIVATCDK----DLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 50 ad~ci~~~~~~~-~~~iVaTqD~----~Lr~~Lr~i~GVPviy~~~~ 91 (106)
-.++|..++.++ .-.+|.+.|. ++-+++++ .||||+.+.+.
T Consensus 44 q~~~i~~~i~~~~d~Iiv~~~~~~~~~~~l~~~~~-~gIpvv~~d~~ 89 (257)
T PF13407_consen 44 QIEQIEQAISQGVDGIIVSPVDPDSLAPFLEKAKA-AGIPVVTVDSD 89 (257)
T ss_dssp HHHHHHHHHHTTESEEEEESSSTTTTHHHHHHHHH-TTSEEEEESST
T ss_pred HHHHHHHHHHhcCCEEEecCCCHHHHHHHHHHHhh-cCceEEEEecc
Confidence 456777777653 3366665664 45566777 49999998876
No 85
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=30.59 E-value=1.2e+02 Score=19.08 Aligned_cols=32 Identities=16% Similarity=0.253 Sum_probs=25.9
Q ss_pred CHHHHHHHhcCCCccEEEEec---ceEEEeeCCCC
Q psy3003 70 DKDLKRRIRKVPGVPIMYISQ---HRYTIERMPDA 101 (106)
Q Consensus 70 D~~Lr~~Lr~i~GVPviy~~~---~~l~lE~~s~a 101 (106)
=.++|++|.=.+|-++.++.. +.++|++..++
T Consensus 19 PkeiR~~lgi~~Gd~lei~~~~~~~~ivl~k~~~~ 53 (89)
T COG2002 19 PKEIREALGIKEGDVLEIIVDGDGGRIVLKKYKPA 53 (89)
T ss_pred cHHHHHHhCCCCCCEEEEEEeCCCCEEEEEECCcc
Confidence 468999999668999988885 45999997764
No 86
>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids. The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....
Probab=30.55 E-value=66 Score=19.92 Aligned_cols=69 Identities=19% Similarity=0.231 Sum_probs=39.9
Q ss_pred ceeeecHHHHHHHHhhCcc---------hHHHHhhccCCceEEEecCCCC------------CCHHHHHH-HhhhcCCeE
Q psy3003 7 GIPYITDCVLGEIEKLGQK---------YKVALRIIKDPRFERIPCMHKG------------TYADDCIV-NRVTQHKCY 64 (106)
Q Consensus 7 ~~~~vt~cVl~EL~~Lg~~---------~~~al~~ak~~~~~~~~c~h~~------------~~ad~ci~-~~~~~~~~~ 64 (106)
..++++.-++.|+-..-.. ......... .+.+...+... .+..||+. ..+..++.-
T Consensus 29 ~~~~is~~~~~E~~~~~~~~~~~~~~~~~~~~~~~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~Da~~~a~A~~~~~~ 106 (121)
T PF01850_consen 29 IEIVISSLVLAELLYVLRRRSKQQKAIALLELLILLS--NFNILPITSEVFERAAELMRKYGLDFADALIAATAKENGAP 106 (121)
T ss_dssp SEEEEEHHHHHHHHHHHHHSHCHHHHHHHHHHHHHHC--TSEEEEBCHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHT-E
T ss_pred CCEEEcHHHHHHHHHHhhhccccchhhhHHHHHHHHh--hhccccchhHHHHHHHHHHHhccCChhHHHHHHHHHHcCCE
Confidence 5788999999998655332 111122223 56677654210 24555554 555556545
Q ss_pred EEEecCHHHHHHH
Q psy3003 65 IVATCDKDLKRRI 77 (106)
Q Consensus 65 iVaTqD~~Lr~~L 77 (106)
.|.|.|+.+++--
T Consensus 107 ~v~T~D~~f~~~a 119 (121)
T PF01850_consen 107 LVVTFDKDFRKVA 119 (121)
T ss_dssp EE-ESSHHHHHHH
T ss_pred EEEECCcCHHhcc
Confidence 6669999988754
No 87
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=30.02 E-value=60 Score=22.18 Aligned_cols=19 Identities=32% Similarity=0.819 Sum_probs=12.0
Q ss_pred HHHHHHhcCCCccEEEEecc
Q psy3003 72 DLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 72 ~Lr~~Lr~i~GVPviy~~~~ 91 (106)
+|++.|++. |+|++.+.++
T Consensus 57 ~L~~~L~~~-g~~L~v~~g~ 75 (165)
T PF00875_consen 57 DLQESLRKL-GIPLLVLRGD 75 (165)
T ss_dssp HHHHHHHHT-TS-EEEEESS
T ss_pred HHHHHHHhc-CcceEEEecc
Confidence 467777775 7777776654
No 88
>PHA02567 rnh RnaseH; Provisional
Probab=29.70 E-value=48 Score=26.19 Aligned_cols=38 Identities=24% Similarity=0.323 Sum_probs=28.2
Q ss_pred CCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHhcCCCccE
Q psy3003 47 GTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIRKVPGVPI 85 (106)
Q Consensus 47 ~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr~i~GVPv 85 (106)
+-.|||.|-.++++ ....+|+|.|++|.+=+.. +||-+
T Consensus 128 g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~-~~v~~ 169 (304)
T PHA02567 128 KAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHKY-PGVKQ 169 (304)
T ss_pred CccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhccCC-CCeEE
Confidence 44799999888864 2358999999999887753 35543
No 89
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=29.33 E-value=63 Score=23.50 Aligned_cols=26 Identities=38% Similarity=0.437 Sum_probs=20.3
Q ss_pred CCCHHHHHHHhhhc-----CCeEEEEecCHH
Q psy3003 47 GTYADDCIVNRVTQ-----HKCYIVATCDKD 72 (106)
Q Consensus 47 ~~~ad~ci~~~~~~-----~~~~iVaTqD~~ 72 (106)
+..||.-|..++.+ ..+.+|||.|..
T Consensus 80 ~ETADs~IEr~~~el~~~~t~~V~VaTSD~~ 110 (173)
T COG3688 80 GETADSFIERYVAELRNAATHQVIVATSDRA 110 (173)
T ss_pred CccHHHHHHHHHHHHhccccceEEEEeCchh
Confidence 44799999988864 227999999975
No 90
>COG0278 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=29.15 E-value=1e+02 Score=20.73 Aligned_cols=38 Identities=16% Similarity=0.428 Sum_probs=28.4
Q ss_pred HHHhhh-cCCeEEEEecCHHHHHHHhc---CCCccEEEEecc
Q psy3003 54 IVNRVT-QHKCYIVATCDKDLKRRIRK---VPGVPIMYISQH 91 (106)
Q Consensus 54 i~~~~~-~~~~~iVaTqD~~Lr~~Lr~---i~GVPviy~~~~ 91 (106)
|++..+ -+-.|+=.-+|.++|+-|.+ =|-+|-+|+++.
T Consensus 39 iL~~~g~v~~~~vnVL~d~eiR~~lk~~s~WPT~PQLyi~GE 80 (105)
T COG0278 39 ILSACGVVDFAYVDVLQDPEIRQGLKEYSNWPTFPQLYVNGE 80 (105)
T ss_pred HHHHcCCcceeEEeeccCHHHHhccHhhcCCCCCceeeECCE
Confidence 444445 23357778899999999996 478999999864
No 91
>KOG1752|consensus
Probab=29.14 E-value=68 Score=21.20 Aligned_cols=23 Identities=17% Similarity=0.475 Sum_probs=17.6
Q ss_pred HHHHHHHhcC---CCccEEEEecceE
Q psy3003 71 KDLKRRIRKV---PGVPIMYISQHRY 93 (106)
Q Consensus 71 ~~Lr~~Lr~i---~GVPviy~~~~~l 93 (106)
.++.+.|.++ ..||.||+.++.+
T Consensus 53 ~eiq~~l~~~tg~~tvP~vFI~Gk~i 78 (104)
T KOG1752|consen 53 SEIQKALKKLTGQRTVPNVFIGGKFI 78 (104)
T ss_pred HHHHHHHHHhcCCCCCCEEEECCEEE
Confidence 3788888854 3799999998654
No 92
>PF12813 XPG_I_2: XPG domain containing
Probab=27.95 E-value=28 Score=26.22 Aligned_cols=30 Identities=23% Similarity=0.191 Sum_probs=23.9
Q ss_pred EEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHH
Q psy3003 40 RIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDL 73 (106)
Q Consensus 40 ~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~L 73 (106)
++.|.. .||.=+..++++.+ +.|.|||.+|
T Consensus 23 ~~~~~~---EAD~~~A~~A~~~~-~~VLt~DSDf 52 (246)
T PF12813_consen 23 VVQCPG---EADRECAALARKWG-CPVLTNDSDF 52 (246)
T ss_pred EEEcCc---cchHHHHHHHHHcC-CeEEccCCCE
Confidence 445633 68999999999886 6899999985
No 93
>PF08799 PRP4: pre-mRNA processing factor 4 (PRP4) like; InterPro: IPR014906 This small protein is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing. ; PDB: 1MZW_B 2DK4_A.
Probab=27.93 E-value=18 Score=18.84 Aligned_cols=16 Identities=38% Similarity=0.864 Sum_probs=10.6
Q ss_pred HHHHHhcCCCccEEEEe
Q psy3003 73 LKRRIRKVPGVPIMYIS 89 (106)
Q Consensus 73 Lr~~Lr~i~GVPviy~~ 89 (106)
.+++||+. |=||.+|-
T Consensus 1 V~~~LR~l-gePi~lFG 16 (30)
T PF08799_consen 1 VRRRLREL-GEPITLFG 16 (30)
T ss_dssp HHHHHHHC-T--SCETT
T ss_pred ChHHHHhc-CCChhhhC
Confidence 36889996 99988764
No 94
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=27.87 E-value=1.9e+02 Score=19.53 Aligned_cols=42 Identities=14% Similarity=0.257 Sum_probs=26.6
Q ss_pred HHHHHHHhhhcCCeEEEEecCHH---HHHHHh---cCCCccEEEEecc
Q psy3003 50 ADDCIVNRVTQHKCYIVATCDKD---LKRRIR---KVPGVPIMYISQH 91 (106)
Q Consensus 50 ad~ci~~~~~~~~~~iVaTqD~~---Lr~~Lr---~i~GVPviy~~~~ 91 (106)
..++...+-+..-+++|-++|-+ +-+.|- +-.|||++|+.+.
T Consensus 32 ~~e~~Kai~~g~a~LVviA~Dv~P~~~~~~l~~lc~~~~vpyv~V~sk 79 (116)
T COG1358 32 TNEVTKAIERGKAKLVVIAEDVSPEELVKHLPALCEEKNVPYVYVGSK 79 (116)
T ss_pred HHHHHHHHHcCCCcEEEEecCCCHHHHHHHHHHHHHhcCCCEEEeCCH
Confidence 45555555544446888888876 333332 3369999999753
No 95
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=27.50 E-value=1.5e+02 Score=21.02 Aligned_cols=42 Identities=14% Similarity=0.205 Sum_probs=25.8
Q ss_pred CHHHHHHHhhhcC-CeEEEEecCH----HHHHHHhcCCCccEEEEecc
Q psy3003 49 YADDCIVNRVTQH-KCYIVATCDK----DLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 49 ~ad~ci~~~~~~~-~~~iVaTqD~----~Lr~~Lr~i~GVPviy~~~~ 91 (106)
...+.+..++... .-.++...|. +.-..+++ .|+|++.+.+.
T Consensus 48 ~~~~~~~~~~~~~vdgiIi~~~~~~~~~~~l~~~~~-~~iPvv~~~~~ 94 (272)
T cd06300 48 QQIADIRNLIAQGVDAIIINPASPTALNPVIEEACE-AGIPVVSFDGT 94 (272)
T ss_pred HHHHHHHHHHHcCCCEEEEeCCChhhhHHHHHHHHH-CCCeEEEEecC
Confidence 3457777766642 2355555553 34456777 49999999853
No 96
>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2.7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....
Probab=27.22 E-value=1.5e+02 Score=20.14 Aligned_cols=37 Identities=5% Similarity=0.295 Sum_probs=20.7
Q ss_pred HHHHHHhhhcCCeEEEEe-----cCHHHHHHHhcCCCccEEEEec
Q psy3003 51 DDCIVNRVTQHKCYIVAT-----CDKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 51 d~ci~~~~~~~~~~iVaT-----qD~~Lr~~Lr~i~GVPviy~~~ 90 (106)
.+++.+++..+ ..+|+| .+++.++.|++ ..++||+..
T Consensus 52 ~~~l~~l~~~~-~~VIa~GGG~~~~~~~~~~L~~--~g~vI~L~~ 93 (158)
T PF01202_consen 52 SEALRELLKEN-NCVIACGGGIVLKEENRELLKE--NGLVIYLDA 93 (158)
T ss_dssp HHHHHHHHCSS-SEEEEE-TTGGGSHHHHHHHHH--HSEEEEEE-
T ss_pred HHHHHHHhccC-cEEEeCCCCCcCcHHHHHHHHh--CCEEEEEeC
Confidence 34455555444 366666 55666666664 455777654
No 97
>PRK10444 UMP phosphatase; Provisional
Probab=27.10 E-value=92 Score=23.23 Aligned_cols=35 Identities=17% Similarity=0.149 Sum_probs=24.5
Q ss_pred CHHHHHHHhhhcCCeEEEEecCHH-----HHHHHhcCCCcc
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDKD-----LKRRIRKVPGVP 84 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~~-----Lr~~Lr~i~GVP 84 (106)
.+.++|..+......++++||... +.++|+.. |++
T Consensus 21 ~a~~~l~~L~~~g~~~~~~Tn~~~~~~~~~~~~l~~~-G~~ 60 (248)
T PRK10444 21 GAAEFLHRILDKGLPLVLLTNYPSQTGQDLANRFATA-GVD 60 (248)
T ss_pred cHHHHHHHHHHCCCeEEEEeCCCCCCHHHHHHHHHHc-CCC
Confidence 567777777666557888888754 67777774 765
No 98
>cd08568 GDPD_TmGDE_like Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. TmGDE exists as a monomer that might be the biologically relevant form.
Probab=27.10 E-value=2.4e+02 Score=20.24 Aligned_cols=79 Identities=18% Similarity=0.214 Sum_probs=52.7
Q ss_pred eecHHHHHHHHhhC------cchHHHHhhccCCceEEEecCCCCCCHHHHHHHhhhc---CCeEEEEecCHHHHHHHhc-
Q psy3003 10 YITDCVLGEIEKLG------QKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQ---HKCYIVATCDKDLKRRIRK- 79 (106)
Q Consensus 10 ~vt~cVl~EL~~Lg------~~~~~al~~ak~~~~~~~~c~h~~~~ad~ci~~~~~~---~~~~iVaTqD~~Lr~~Lr~- 79 (106)
.|.+.-++||+.+. +.+...++.+.+ +. .+...-+.....+-+.+++++ .++.+|.+-|.+.-+++++
T Consensus 60 ~v~~~t~~eL~~l~~~g~~iPtL~evl~~~~~-~~-~l~iEiK~~~~~~~~~~~l~~~~~~~~v~i~SF~~~~l~~~~~~ 137 (226)
T cd08568 60 KVKELTYKELKKLHPGGELIPTLEEVFRALPN-DA-IINVEIKDIDAVEPVLEIVEKFNALDRVIFSSFNHDALRELRKL 137 (226)
T ss_pred eeecCCHHHHhhCCCCCCcCCCHHHHHHhcCC-Cc-EEEEEECCccHHHHHHHHHHHcCCCCcEEEEECCHHHHHHHHHh
Confidence 35566678888873 236777777762 11 233333333344566677665 2479999999999999996
Q ss_pred CCCccEEEEec
Q psy3003 80 VPGVPIMYISQ 90 (106)
Q Consensus 80 i~GVPviy~~~ 90 (106)
.|.+|+.++-.
T Consensus 138 ~p~~~~~~l~~ 148 (226)
T cd08568 138 DPDAKVGLLIG 148 (226)
T ss_pred CCCCcEEEEee
Confidence 58999988864
No 99
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=27.09 E-value=83 Score=24.37 Aligned_cols=40 Identities=10% Similarity=0.059 Sum_probs=29.0
Q ss_pred HHHHHHhhhcC----CeEEEEecCHHHHHHHhcCCCccEEEEecc
Q psy3003 51 DDCIVNRVTQH----KCYIVATCDKDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 51 d~ci~~~~~~~----~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
...|++.+..+ +-..|.||.+++..+.++. |||+.++..+
T Consensus 107 l~al~~~~~~~~l~~~i~~visn~~~~~~~A~~~-gIp~~~~~~~ 150 (289)
T PRK13010 107 LNDLLYRWRMGELDMDIVGIISNHPDLQPLAVQH-DIPFHHLPVT 150 (289)
T ss_pred HHHHHHHHHCCCCCcEEEEEEECChhHHHHHHHc-CCCEEEeCCC
Confidence 44455544431 2478889999999999985 9999998754
No 100
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
Probab=27.03 E-value=1.1e+02 Score=16.91 Aligned_cols=23 Identities=22% Similarity=0.421 Sum_probs=14.3
Q ss_pred ecCHHHHHHH---hcCCCccEEEEec
Q psy3003 68 TCDKDLKRRI---RKVPGVPIMYISQ 90 (106)
Q Consensus 68 TqD~~Lr~~L---r~i~GVPviy~~~ 90 (106)
++|.+.++.+ ..+.++|++.+.+
T Consensus 33 ~~~~~~~~~~~~~~~~~~vP~~~~~~ 58 (74)
T TIGR02196 33 EKDSAAREEVLKVLGQRGVPVIVIGH 58 (74)
T ss_pred cCCHHHHHHHHHHhCCCcccEEEECC
Confidence 4455544433 2346899999974
No 101
>PRK05647 purN phosphoribosylglycinamide formyltransferase; Reviewed
Probab=26.60 E-value=1.8e+02 Score=21.12 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=27.6
Q ss_pred cCCCCCCHHHHHHHhhhcC---CeEEEEec--CHHHHHHHhcCCCccEEEEec
Q psy3003 43 CMHKGTYADDCIVNRVTQH---KCYIVATC--DKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 43 c~h~~~~ad~ci~~~~~~~---~~~iVaTq--D~~Lr~~Lr~i~GVPviy~~~ 90 (106)
|++.|..+..++..+..++ .-.+|.|| |...+.+.++. |||++.+..
T Consensus 8 ~sg~gs~~~~ll~~~~~~~~~~~I~~vvs~~~~~~~~~~a~~~-gIp~~~~~~ 59 (200)
T PRK05647 8 ASGNGSNLQAIIDACAAGQLPAEIVAVISDRPDAYGLERAEAA-GIPTFVLDH 59 (200)
T ss_pred EcCCChhHHHHHHHHHcCCCCcEEEEEEecCccchHHHHHHHc-CCCEEEECc
Confidence 5555556666666655442 12333466 44677777774 999887653
No 102
>cd02976 NrdH NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase activity that is dependent on TRX reductase, not glutathione (GSH). It is part of the NrdHIEF operon, where NrdEF codes for class Ib ribonucleotide reductase (RNR-Ib), an efficient enzyme at low oxygen levels. Under these conditions when GSH is mostly conjugated to spermidine, NrdH can still function and act as a hydrogen donor for RNR-Ib. It has been suggested that the NrdHEF system may be the oldest RNR reducing system, capable of functioning in a microaerophilic environment, where GSH was not yet available. NrdH from Corynebacterium ammoniagenes can form domain-swapped dimers, although it is unknown if this happens in vivo. Domain-swapped dimerization, which results in the blocking of the TRX reductase binding site, cou
Probab=26.54 E-value=1.2e+02 Score=16.76 Aligned_cols=24 Identities=21% Similarity=0.400 Sum_probs=16.5
Q ss_pred ecCHHHHHHHhc---CCCccEEEEecc
Q psy3003 68 TCDKDLKRRIRK---VPGVPIMYISQH 91 (106)
Q Consensus 68 TqD~~Lr~~Lr~---i~GVPviy~~~~ 91 (106)
..|.+.+..+++ ..++|++++.+.
T Consensus 33 ~~~~~~~~~~~~~~~~~~vP~i~~~~~ 59 (73)
T cd02976 33 DEDPEALEELKKLNGYRSVPVVVIGDE 59 (73)
T ss_pred CCCHHHHHHHHHHcCCcccCEEEECCE
Confidence 346667777763 468999998653
No 103
>TIGR03614 RutB pyrimidine utilization protein B. RL Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9. Epub 2006 Mar 15.
Probab=26.40 E-value=64 Score=23.58 Aligned_cols=19 Identities=21% Similarity=0.499 Sum_probs=14.6
Q ss_pred HHHHHHHhcCCCccEEEEec
Q psy3003 71 KDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 71 ~~Lr~~Lr~i~GVPviy~~~ 90 (106)
..|.+..|+. |+||||++.
T Consensus 52 ~~l~~~aR~~-g~pVI~~~~ 70 (226)
T TIGR03614 52 KKAVTAARAA-GIQVIYFQN 70 (226)
T ss_pred HHHHHHHHHc-CCEEEEEec
Confidence 3567778884 999999874
No 104
>PRK04280 arginine repressor; Provisional
Probab=26.38 E-value=46 Score=23.31 Aligned_cols=7 Identities=29% Similarity=0.676 Sum_probs=3.2
Q ss_pred HHHHHhc
Q psy3003 73 LKRRIRK 79 (106)
Q Consensus 73 Lr~~Lr~ 79 (106)
+-+.|++
T Consensus 40 iSRDike 46 (148)
T PRK04280 40 VSRDIKE 46 (148)
T ss_pred HHHHHHH
Confidence 4444444
No 105
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=26.17 E-value=55 Score=25.14 Aligned_cols=35 Identities=23% Similarity=0.190 Sum_probs=26.8
Q ss_pred CHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEEE
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYI 88 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~ 88 (106)
.||+.+..+.++...+.|+|+|.++-. . |.|.++.
T Consensus 150 EAdaq~a~l~~~g~v~~i~S~DsD~l~----f-g~~~vi~ 184 (316)
T cd00128 150 EAEAQCAYLAKKGLVDAIITEDSDLLL----F-GAPRVYR 184 (316)
T ss_pred CHHHHHHHHHhCCCeeEEEecCCCeee----e-cCceEEE
Confidence 689998888887656789999999654 2 6676664
No 106
>COG2908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.72 E-value=62 Score=24.70 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=8.0
Q ss_pred CccEEEEecce
Q psy3003 82 GVPIMYISQHR 92 (106)
Q Consensus 82 GVPviy~~~~~ 92 (106)
|+|++|+.+|.
T Consensus 67 G~~v~~i~GN~ 77 (237)
T COG2908 67 GTRVYYIHGNH 77 (237)
T ss_pred CCeEEEecCch
Confidence 77777777664
No 107
>TIGR01458 HAD-SF-IIA-hyp3 HAD-superfamily subfamily IIA hydrolase, TIGR01458. This hypothetical equivalog is a member of the IIA subfamily (TIGR01460) of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. One sequence (GP|10716807) has been annotated as a "phospholysine phosphohistidine inorganic pyrophosphatase," probably in reference to studies on similarly described (but unsequenced) enzymes from bovine and rat tissues. However, the supporting information for this annotation has never been published.
Probab=25.59 E-value=1.5e+02 Score=21.96 Aligned_cols=36 Identities=17% Similarity=0.207 Sum_probs=25.8
Q ss_pred CHHHHHHHhhhcCCeEEEEecC-----HHHHHHHhcCCCccE
Q psy3003 49 YADDCIVNRVTQHKCYIVATCD-----KDLKRRIRKVPGVPI 85 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD-----~~Lr~~Lr~i~GVPv 85 (106)
.+.++|..+-....+++++||. .++.++|++. |+++
T Consensus 25 ~a~~al~~l~~~G~~~~~~Tn~~~~~~~~~~~~l~~~-g~~~ 65 (257)
T TIGR01458 25 GSQEAVKRLRGASVKVRFVTNTTKESKQDLLERLQRL-GFDI 65 (257)
T ss_pred CHHHHHHHHHHCCCeEEEEECCCCCCHHHHHHHHHHc-CCCC
Confidence 6778888877665578899973 2567777775 7764
No 108
>PF03020 LEM: LEM domain; InterPro: IPR003887 The LEM domain is found in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin []. Defects in the emerin gene are a cause of Emery-Dreifuss muscular dystrophy, an X-linked disorder characterised by early contractures, muscle wasting, weakness and cardiomyopathy.; GO: 0005635 nuclear envelope; PDB: 2ODG_C 2ODC_I 1JEI_A 1H9F_A 1GJJ_A.
Probab=25.42 E-value=11 Score=21.30 Aligned_cols=18 Identities=28% Similarity=0.499 Sum_probs=11.2
Q ss_pred cCHHHHHHHhcCCCccEEE
Q psy3003 69 CDKDLKRRIRKVPGVPIMY 87 (106)
Q Consensus 69 qD~~Lr~~Lr~i~GVPviy 87 (106)
.|.|||..|++. |++.-=
T Consensus 7 Sd~ELr~~L~~~-G~~~GP 24 (43)
T PF03020_consen 7 SDEELREELREY-GEPPGP 24 (43)
T ss_dssp -CCCCHHCCCCC-T-S---
T ss_pred CHHHHHHHHHHc-CCCCCC
Confidence 488999999984 776543
No 109
>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]
Probab=25.34 E-value=1.2e+02 Score=25.39 Aligned_cols=46 Identities=13% Similarity=0.137 Sum_probs=33.0
Q ss_pred HHHHhhhc---CCeEEEEecCHHHHHHHhcCCCccEEEEecc---eEEEeeC
Q psy3003 53 CIVNRVTQ---HKCYIVATCDKDLKRRIRKVPGVPIMYISQH---RYTIERM 98 (106)
Q Consensus 53 ci~~~~~~---~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~---~l~lE~~ 98 (106)
...+++.. .+..++|..|+.||+-+..+...|++++-.+ -+.++..
T Consensus 200 ~F~~f~~~vp~~G~~v~~~dd~~l~~l~~~~~~~~v~tyG~~~~ad~~a~ni 251 (459)
T COG0773 200 AFHHFVRNVPFYGRAVVCGDDPNLRELLSRGCWSPVVTYGFDDEADWRAENI 251 (459)
T ss_pred HHHHHHHhCCccceEEEECCCHHHHHHHhcccCCcEEeecCCCcCcEEEEEe
Confidence 33444443 3457999999999999998789999999644 3555543
No 110
>PRK10329 glutaredoxin-like protein; Provisional
Probab=25.33 E-value=1e+02 Score=18.86 Aligned_cols=28 Identities=11% Similarity=0.157 Sum_probs=19.9
Q ss_pred EEEEecCHHHHHHHhcC--CCccEEEEecc
Q psy3003 64 YIVATCDKDLKRRIRKV--PGVPIMYISQH 91 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr~i--~GVPviy~~~~ 91 (106)
.+=.++|++.+..++.. -.||++.+.+.
T Consensus 30 ~idi~~~~~~~~~~~~~g~~~vPvv~i~~~ 59 (81)
T PRK10329 30 MINVDRVPEAAETLRAQGFRQLPVVIAGDL 59 (81)
T ss_pred EEECCCCHHHHHHHHHcCCCCcCEEEECCE
Confidence 56667888877777642 37899988653
No 111
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=25.23 E-value=2.6e+02 Score=19.93 Aligned_cols=53 Identities=17% Similarity=0.275 Sum_probs=30.0
Q ss_pred ceEEEecCCCCC--CHHHHHHHhhhcC-CeEEEEecCH----HHHHHHhcCCCccEEEEec
Q psy3003 37 RFERIPCMHKGT--YADDCIVNRVTQH-KCYIVATCDK----DLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 37 ~~~~~~c~h~~~--~ad~ci~~~~~~~-~~~iVaTqD~----~Lr~~Lr~i~GVPviy~~~ 90 (106)
++++.-++..+. ...+.|..++... .-.++.+.|. ++-+++.+ .|+|++++.+
T Consensus 29 g~~v~~~~~~~~~~~~~~~i~~~~~~~~Dgiii~~~~~~~~~~~i~~~~~-~~iPvV~~~~ 88 (282)
T cd06318 29 GYELISTDAQGDLTKQIADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKA-AGVPVVVVDS 88 (282)
T ss_pred CCEEEEEcCCCCHHHHHHHHHHHHHcCCCEEEEecCCccchHHHHHHHHH-CCCCEEEecC
Confidence 555555543222 1234555555442 2366666553 34567777 4999999975
No 112
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=24.86 E-value=1.6e+02 Score=23.57 Aligned_cols=45 Identities=9% Similarity=0.128 Sum_probs=33.4
Q ss_pred CHHHHHHHhhhcCCeEEEEec----------CHHHHHHHhcCCCccEEEEecceEE
Q psy3003 49 YADDCIVNRVTQHKCYIVATC----------DKDLKRRIRKVPGVPIMYISQHRYT 94 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTq----------D~~Lr~~Lr~i~GVPviy~~~~~l~ 94 (106)
.+.+.|.+++.+.+---|.+| |..+++.+.+. ||++..+..+.+.
T Consensus 83 ~~~~vl~~L~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~-~i~~~~~~~~~l~ 137 (429)
T TIGR02765 83 KPEDVLPELIKELGVRTVFLHQEVGSEEKSVERLLQQALARL-GIHVEQHWGSTLY 137 (429)
T ss_pred CHHHHHHHHHHHhCCCEEEEeccCCHHHHHHHHHHHHHHHhc-CceEEEecCCEeE
Confidence 578899999986443445555 78888889885 9998877776653
No 113
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=24.66 E-value=2.6e+02 Score=19.81 Aligned_cols=54 Identities=9% Similarity=0.083 Sum_probs=29.7
Q ss_pred ceEEEecCCCCC--CHHHHHHHhhhcC-CeEEEEecCH----HHHHHHhcCCCccEEEEecc
Q psy3003 37 RFERIPCMHKGT--YADDCIVNRVTQH-KCYIVATCDK----DLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 37 ~~~~~~c~h~~~--~ad~ci~~~~~~~-~~~iVaTqD~----~Lr~~Lr~i~GVPviy~~~~ 91 (106)
++..+-+...+. ...+++..++... .-.++.+.|. +.-+++++ .|+|+|.+.+.
T Consensus 31 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~~~-~~ipvv~~~~~ 91 (271)
T cd06321 31 GVKVTVVSADYDLNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRAQA-AGIVVVAVDVA 91 (271)
T ss_pred CeEEEEccCCCCHHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHHHH-CCCeEEEecCC
Confidence 455555543222 2335666655532 2255555443 33456666 49999999763
No 114
>TIGR02183 GRXA Glutaredoxin, GrxA family. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase.
Probab=24.65 E-value=61 Score=19.92 Aligned_cols=21 Identities=29% Similarity=0.678 Sum_probs=13.6
Q ss_pred HHHHHHhc-CCCccEEEEecce
Q psy3003 72 DLKRRIRK-VPGVPIMYISQHR 92 (106)
Q Consensus 72 ~Lr~~Lr~-i~GVPviy~~~~~ 92 (106)
+|..+... ...||+|++.+..
T Consensus 46 ~l~~~~g~~~~tVP~ifi~g~~ 67 (86)
T TIGR02183 46 DLEKTVGKPVETVPQIFVDEKH 67 (86)
T ss_pred HHHHHhCCCCCCcCeEEECCEE
Confidence 55555443 2489999997654
No 115
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=24.56 E-value=1.7e+02 Score=21.60 Aligned_cols=39 Identities=10% Similarity=0.335 Sum_probs=23.9
Q ss_pred HHHHHhhhcC-CeEEEEecCH----HHHHHHhcCCCccEEEEecc
Q psy3003 52 DCIVNRVTQH-KCYIVATCDK----DLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 52 ~ci~~~~~~~-~~~iVaTqD~----~Lr~~Lr~i~GVPviy~~~~ 91 (106)
+.|..++... .-++|+..|. +..+++++ .|+|+|.+.+.
T Consensus 48 ~~i~~l~~~~vdgiii~~~~~~~~~~~~~~~~~-~giPvV~~~~~ 91 (303)
T cd01539 48 EQIDTALAKGVDLLAVNLVDPTAAQTVINKAKQ-KNIPVIFFNRE 91 (303)
T ss_pred HHHHHHHHcCCCEEEEecCchhhHHHHHHHHHH-CCCCEEEeCCC
Confidence 4555555542 2366665553 35566666 49999999754
No 116
>PF07085 DRTGG: DRTGG domain; InterPro: IPR010766 This presumed domain is about 120 amino acids in length. It is found associated with CBS domains IPR000644 from INTERPRO, as well as the CbiA domain IPR002586 from INTERPRO. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea. ; PDB: 3L31_B 3L2B_A 2IOJ_A.
Probab=24.39 E-value=1.3e+02 Score=19.05 Aligned_cols=40 Identities=13% Similarity=0.312 Sum_probs=22.1
Q ss_pred HHHHHHhhhcCCeEEEEecC----HHHHHHHhcCCCccEEEEecc
Q psy3003 51 DDCIVNRVTQHKCYIVATCD----KDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 51 d~ci~~~~~~~~~~iVaTqD----~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
.|.+...+...-..+|-|.+ +++.+.+++. |+||++...+
T Consensus 51 ~di~~~a~~~~i~~iIltg~~~~~~~v~~la~~~-~i~vi~t~~d 94 (105)
T PF07085_consen 51 EDIQLAAIEAGIACIILTGGLEPSEEVLELAKEL-GIPVISTPYD 94 (105)
T ss_dssp HHHHHHHCCTTECEEEEETT----HHHHHHHHHH-T-EEEE-SS-
T ss_pred HHHHHHHHHhCCCEEEEeCCCCCCHHHHHHHHHC-CCEEEEECCC
Confidence 45555555444347777774 4455566663 7888876544
No 117
>cd08567 GDPD_SpGDE_like Glycerophosphodiester phosphodiesterase domain of putative Silicibacter pomeroyi glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and similar proteins. The prototype of this CD is a putative GP-GDE from Silicibacter pomeroyi (SpGDE). It shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=24.31 E-value=2.8e+02 Score=20.09 Aligned_cols=39 Identities=13% Similarity=0.415 Sum_probs=28.8
Q ss_pred HHHHHhhhc---CCeEEEEecCHHHHHHHhc-CCCccEEEEec
Q psy3003 52 DCIVNRVTQ---HKCYIVATCDKDLKRRIRK-VPGVPIMYISQ 90 (106)
Q Consensus 52 ~ci~~~~~~---~~~~iVaTqD~~Lr~~Lr~-i~GVPviy~~~ 90 (106)
+-+++++.+ .++.++.+-|.+.-+++++ .|.+|+.|+..
T Consensus 151 ~~v~~~l~~~~~~~~v~~~Sf~~~~l~~~~~~~p~~~~~~l~~ 193 (263)
T cd08567 151 DAVLAVIRKAGLEDRVVLQSFDWRTLQEVRRLAPDIPTVALTE 193 (263)
T ss_pred HHHHHHHHHcCCCCceEEEeCCHHHHHHHHHHCCCccEEEEec
Confidence 455566554 2468899999888888884 68899998874
No 118
>TIGR03584 PseF pseudaminic acid CMP-transferase. The sequences in this family include the pfam02348 (cytidyltransferase) domain and are homologous to the NeuA protein responsible for the transfer of CMP to neuraminic acid. According to, this gene is responsible for the transfer of CMP to the structurally related sugar, pseudaminic acid which is observed as a component of sugar modifications of flagellin in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci.
Probab=24.12 E-value=1.1e+02 Score=22.26 Aligned_cols=27 Identities=15% Similarity=0.363 Sum_probs=21.6
Q ss_pred CeEEEEecCHHHHHHHhcCCCccEEEEe
Q psy3003 62 KCYIVATCDKDLKRRIRKVPGVPIMYIS 89 (106)
Q Consensus 62 ~~~iVaTqD~~Lr~~Lr~i~GVPviy~~ 89 (106)
+..+|.|+|.++.+..++. |+.+++.|
T Consensus 41 d~IvVstd~~~i~~~a~~~-g~~v~~~r 67 (222)
T TIGR03584 41 DKVVVSTDDEEIAEVAKSY-GASVPFLR 67 (222)
T ss_pred CEEEEeCCCHHHHHHHHHc-CCEeEEeC
Confidence 3688999999999988874 87776654
No 119
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=23.85 E-value=61 Score=20.64 Aligned_cols=25 Identities=24% Similarity=0.266 Sum_probs=16.3
Q ss_pred eEEEEecCHHHHHHHhc---CCCccEEE
Q psy3003 63 CYIVATCDKDLKRRIRK---VPGVPIMY 87 (106)
Q Consensus 63 ~~iVaTqD~~Lr~~Lr~---i~GVPviy 87 (106)
-.++||+|+++-+++.+ ..|+|+-.
T Consensus 63 lV~~at~d~~~n~~i~~~a~~~~i~vn~ 90 (103)
T PF13241_consen 63 LVFAATDDPELNEAIYADARARGILVNV 90 (103)
T ss_dssp EEEE-SS-HHHHHHHHHHHHHTTSEEEE
T ss_pred EEEecCCCHHHHHHHHHHHhhCCEEEEE
Confidence 58889999998877763 24777644
No 120
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=23.77 E-value=3e+02 Score=21.16 Aligned_cols=76 Identities=12% Similarity=0.186 Sum_probs=43.1
Q ss_pred HHHHHHHHhhCcchHH--HHhhccCC-ceEEEecCCCCCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHhcCCCccE
Q psy3003 13 DCVLGEIEKLGQKYKV--ALRIIKDP-RFERIPCMHKGTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIRKVPGVPI 85 (106)
Q Consensus 13 ~cVl~EL~~Lg~~~~~--al~~ak~~-~~~~~~c~h~~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr~i~GVPv 85 (106)
..+-++|+.++.++.. .+.--+.+ +.-++-. +.| +--+.|.+.+.. .+-..|.||-+++....++ .|||+
T Consensus 64 ~~L~~~L~~l~~~l~l~i~l~~~~~~~ri~vl~S-g~g-snl~al~~~~~~~~~~~~i~~visn~~~~~~lA~~-~gIp~ 140 (286)
T PRK06027 64 ETLRADFAALAEEFEMDWRLLDSAERKRVVILVS-KED-HCLGDLLWRWRSGELPVEIAAVISNHDDLRSLVER-FGIPF 140 (286)
T ss_pred HHHHHHHHHHHHHhCCEEEEcccccCcEEEEEEc-CCC-CCHHHHHHHHHcCCCCcEEEEEEEcChhHHHHHHH-hCCCE
Confidence 4556667777765322 12222111 2222222 222 445566655543 2347788999999988888 59999
Q ss_pred EEEecc
Q psy3003 86 MYISQH 91 (106)
Q Consensus 86 iy~~~~ 91 (106)
+++..+
T Consensus 141 ~~~~~~ 146 (286)
T PRK06027 141 HHVPVT 146 (286)
T ss_pred EEeccC
Confidence 998754
No 121
>TIGR01452 PGP_euk phosphoglycolate/pyridoxal phosphate phosphatase family. This model is closely related to a family of bacterial sequences including the E. coli NagD and B. subtilus AraL genes which are characterized by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The chlamydomonas PGPase does not catalyze this reaction and so presumably these two groups have different functions and substrate specificities. Many of the genes in this alignment have been annotated as pNPPases due to this association.
Probab=23.61 E-value=1.3e+02 Score=22.48 Aligned_cols=35 Identities=11% Similarity=0.156 Sum_probs=23.5
Q ss_pred CHHHHHHHhhhcCCeEEEEecCH-----HHHHHHhcCCCcc
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDK-----DLKRRIRKVPGVP 84 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~-----~Lr~~Lr~i~GVP 84 (106)
.+.+.|..+-.++.+++++||.. ++..+|++. |++
T Consensus 22 ga~e~l~~L~~~g~~~~~~Tnns~~~~~~~~~~l~~~-G~~ 61 (279)
T TIGR01452 22 GAPELLDRLARAGKAALFVTNNSTKSRAEYALKFARL-GFN 61 (279)
T ss_pred CHHHHHHHHHHCCCeEEEEeCCCCCCHHHHHHHHHHc-CCC
Confidence 46677766665555788899842 455677775 765
No 122
>cd08565 GDPD_pAtGDE_like Glycerophosphodiester phosphodiesterase domain of putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (pAtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=23.02 E-value=2.4e+02 Score=20.63 Aligned_cols=79 Identities=18% Similarity=0.222 Sum_probs=49.6
Q ss_pred ecHHHHHHHHhhC------c---chHHHHhhccCCceEEEecCCCC----C---CHHHHHHHhhhc---CCeEEEEecCH
Q psy3003 11 ITDCVLGEIEKLG------Q---KYKVALRIIKDPRFERIPCMHKG----T---YADDCIVNRVTQ---HKCYIVATCDK 71 (106)
Q Consensus 11 vt~cVl~EL~~Lg------~---~~~~al~~ak~~~~~~~~c~h~~----~---~ad~ci~~~~~~---~~~~iVaTqD~ 71 (106)
|.+.-++||++|. . .+...++++++.+. .+....+. . ...+-+.+++++ .++.++.+-|.
T Consensus 60 v~~~t~~el~~l~~~~~~~~~iptL~evl~~~~~~~~-~l~iEiK~~~~~~~~~~~~~~v~~~i~~~~~~~~v~~~Sf~~ 138 (235)
T cd08565 60 VRDLTLAERKALRLRDSFGEKIPTLEEVLALFAPSGL-ELHVEIKTDADGTPYPGAAALAAATLRRHGLLERSVLTSFDP 138 (235)
T ss_pred eeeccHHHHhcCCCCCCCCCCCCCHHHHHHHhhccCc-EEEEEECCCCCCCccHHHHHHHHHHHHhCCCcCCEEEEECCH
Confidence 4556678888873 1 26777777753221 11121121 1 123455666654 23689999999
Q ss_pred HHHHHHhcCCCccEEEEec
Q psy3003 72 DLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 72 ~Lr~~Lr~i~GVPviy~~~ 90 (106)
+.-+++|+.|.+|+.++-.
T Consensus 139 ~~l~~~~~~p~~~~~~l~~ 157 (235)
T cd08565 139 AVLTEVRKHPGVRTLGSVD 157 (235)
T ss_pred HHHHHHHhCCCCcEEEEec
Confidence 9999999879999988764
No 123
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=22.81 E-value=2.8e+02 Score=19.42 Aligned_cols=39 Identities=18% Similarity=0.322 Sum_probs=24.0
Q ss_pred HHHHHHhhhcC-CeEEEEec--CHHHHHHHhcCCCccEEEEec
Q psy3003 51 DDCIVNRVTQH-KCYIVATC--DKDLKRRIRKVPGVPIMYISQ 90 (106)
Q Consensus 51 d~ci~~~~~~~-~~~iVaTq--D~~Lr~~Lr~i~GVPviy~~~ 90 (106)
.+.|.+++... .-.++... +..+.+.+++. |+|++++.+
T Consensus 45 ~~~i~~l~~~~~dgii~~~~~~~~~~~~~~~~~-~ipvv~~~~ 86 (259)
T cd01542 45 IEALELLARQKVDGIILLATTITDEHREAIKKL-NVPVVVVGQ 86 (259)
T ss_pred HHHHHHHHhcCCCEEEEeCCCCCHHHHHHHhcC-CCCEEEEec
Confidence 35566666542 22344333 45666778874 999999965
No 124
>PRK15408 autoinducer 2-binding protein lsrB; Provisional
Probab=22.32 E-value=2.2e+02 Score=21.92 Aligned_cols=39 Identities=23% Similarity=0.246 Sum_probs=24.9
Q ss_pred HHHHHhhhcC-CeEEEEecC----HHHHHHHhcCCCccEEEEecc
Q psy3003 52 DCIVNRVTQH-KCYIVATCD----KDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 52 ~ci~~~~~~~-~~~iVaTqD----~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
+.|.+++.++ .-.+|+.+| ...-+++++ .|||+|.+.+.
T Consensus 71 ~~i~~li~~~vdgIiv~~~d~~al~~~l~~a~~-~gIpVV~~d~~ 114 (336)
T PRK15408 71 QLINNFVNQGYNAIIVSAVSPDGLCPALKRAMQ-RGVKVLTWDSD 114 (336)
T ss_pred HHHHHHHHcCCCEEEEecCCHHHHHHHHHHHHH-CCCeEEEeCCC
Confidence 4555666542 236666667 345556667 49999999864
No 125
>COG0647 NagD Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]
Probab=22.31 E-value=90 Score=24.06 Aligned_cols=35 Identities=20% Similarity=0.203 Sum_probs=22.3
Q ss_pred CHHHHHHHhhhcCCeEEEEecCHH-----HHHHHhcCCCc
Q psy3003 49 YADDCIVNRVTQHKCYIVATCDKD-----LKRRIRKVPGV 83 (106)
Q Consensus 49 ~ad~ci~~~~~~~~~~iVaTqD~~-----Lr~~Lr~i~GV 83 (106)
.|.+-|..+-.++..|+..||... +.++|++.-|+
T Consensus 28 ga~e~l~~L~~~g~~~iflTNn~~~s~~~~~~~L~~~~~~ 67 (269)
T COG0647 28 GAAEALKRLKAAGKPVIFLTNNSTRSREVVAARLSSLGGV 67 (269)
T ss_pred hHHHHHHHHHHcCCeEEEEeCCCCCCHHHHHHHHHhhcCC
Confidence 456666666555556888888885 56666664344
No 126
>TIGR02189 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa.
Probab=22.24 E-value=1.7e+02 Score=18.59 Aligned_cols=29 Identities=14% Similarity=0.368 Sum_probs=19.5
Q ss_pred EEEEecCH---HHHHHHhc---CCCccEEEEecce
Q psy3003 64 YIVATCDK---DLKRRIRK---VPGVPIMYISQHR 92 (106)
Q Consensus 64 ~iVaTqD~---~Lr~~Lr~---i~GVPviy~~~~~ 92 (106)
++-..+|+ ++++.+.+ ...||.||+.+..
T Consensus 37 ~vdid~~~~~~~~~~~l~~~tg~~tvP~Vfi~g~~ 71 (99)
T TIGR02189 37 VHEIDKEPAGKDIENALSRLGCSPAVPAVFVGGKL 71 (99)
T ss_pred EEEcCCCccHHHHHHHHHHhcCCCCcCeEEECCEE
Confidence 55566664 36666663 3689999998754
No 127
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=22.13 E-value=3e+02 Score=19.53 Aligned_cols=64 Identities=9% Similarity=0.113 Sum_probs=34.0
Q ss_pred HHHHhhccCCceEEEecCCCCC--CHHHHHHHhhhcC-CeEEEEec--C-HHHHHHHhcCCCccEEEEecc
Q psy3003 27 KVALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQH-KCYIVATC--D-KDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 27 ~~al~~ak~~~~~~~~c~h~~~--~ad~ci~~~~~~~-~~~iVaTq--D-~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
++..+.+++.++..+-+..... ...++|..+.... .-.++... | ..+.+.+++ .|+|++++.+.
T Consensus 19 ~~i~~~a~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgii~~~~~~~~~~~~~~~~~-~~ipvV~i~~~ 88 (269)
T cd06281 19 SGAEDRLRAAGYSLLIANSLNDPERELEILRSFEQRRMDGIIIAPGDERDPELVDALAS-LDLPIVLLDRD 88 (269)
T ss_pred HHHHHHHHHcCCEEEEEeCCCChHHHHHHHHHHHHcCCCEEEEecCCCCcHHHHHHHHh-CCCCEEEEecc
Confidence 3344455433455444433221 2446666666542 22444432 2 456677777 49999999753
No 128
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=22.00 E-value=2.9e+02 Score=19.32 Aligned_cols=42 Identities=19% Similarity=0.359 Sum_probs=24.7
Q ss_pred CHHHHHHHhhhcC-CeEEEEec--CHHHHHHHhcCCCccEEEEecc
Q psy3003 49 YADDCIVNRVTQH-KCYIVATC--DKDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 49 ~ad~ci~~~~~~~-~~~iVaTq--D~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
...+.|..++.+. .-.++... +...-+.+.+ .|+|++++.+.
T Consensus 42 ~~~~~i~~~~~~~vdgiii~~~~~~~~~~~~~~~-~~ipvV~~~~~ 86 (266)
T cd06278 42 DLDAALRQLLQYRVDGVIVTSGTLSSELAEECRR-NGIPVVLINRY 86 (266)
T ss_pred HHHHHHHHHHHcCCCEEEEecCCCCHHHHHHHhh-cCCCEEEECCc
Confidence 3456676666542 22444322 3445556667 49999999753
No 129
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=21.81 E-value=2.8e+02 Score=19.09 Aligned_cols=41 Identities=10% Similarity=0.210 Sum_probs=23.6
Q ss_pred HHHHHHHhhhcCCeEEEEecC--HHH-HHHHhcCCCccEEEEecc
Q psy3003 50 ADDCIVNRVTQHKCYIVATCD--KDL-KRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 50 ad~ci~~~~~~~~~~iVaTqD--~~L-r~~Lr~i~GVPviy~~~~ 91 (106)
..+.+..++...-..+|.... ..+ .+++.+ .|+|++.+...
T Consensus 44 ~~~~~~~~~~~~~d~iii~~~~~~~~~~~~~~~-~~ipvv~~~~~ 87 (264)
T cd06267 44 EREALELLLSRRVDGIILAPSRLDDELLEELAA-LGIPVVLVDRP 87 (264)
T ss_pred HHHHHHHHHHcCcCEEEEecCCcchHHHHHHHH-cCCCEEEeccc
Confidence 346666666543234444433 233 344555 59999999754
No 130
>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.; PDB: 3LFT_A 3LKV_A.
Probab=21.54 E-value=1.8e+02 Score=21.80 Aligned_cols=40 Identities=10% Similarity=0.165 Sum_probs=25.3
Q ss_pred HHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCC-ccEEEEe
Q psy3003 50 ADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPG-VPIMYIS 89 (106)
Q Consensus 50 ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~G-VPviy~~ 89 (106)
....+.++...+-..++++-+...+.-.+...+ +||+|.-
T Consensus 48 ~~~~~~~l~~~~~DlIi~~gt~aa~~~~~~~~~~iPVVf~~ 88 (294)
T PF04392_consen 48 LRQIARKLKAQKPDLIIAIGTPAAQALAKHLKDDIPVVFCG 88 (294)
T ss_dssp HHHHHHHHCCTS-SEEEEESHHHHHHHHHH-SS-S-EEEEC
T ss_pred HHHHHHHHhcCCCCEEEEeCcHHHHHHHHhcCCCcEEEEEe
Confidence 334444444333348888888888887777778 9999976
No 131
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=21.52 E-value=51 Score=17.46 Aligned_cols=15 Identities=40% Similarity=0.864 Sum_probs=11.8
Q ss_pred CHHHHHHHhcCCCccE
Q psy3003 70 DKDLKRRIRKVPGVPI 85 (106)
Q Consensus 70 D~~Lr~~Lr~i~GVPv 85 (106)
|.+||..|.+. |||+
T Consensus 6 ~~~L~~wL~~~-gi~~ 20 (38)
T PF10281_consen 6 DSDLKSWLKSH-GIPV 20 (38)
T ss_pred HHHHHHHHHHc-CCCC
Confidence 57899999984 8774
No 132
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=21.23 E-value=2.2e+02 Score=17.60 Aligned_cols=28 Identities=21% Similarity=0.464 Sum_probs=17.0
Q ss_pred HHHHHHhcCCCccEEEEec-ce--EEEeeCC
Q psy3003 72 DLKRRIRKVPGVPIMYISQ-HR--YTIERMP 99 (106)
Q Consensus 72 ~Lr~~Lr~i~GVPviy~~~-~~--l~lE~~s 99 (106)
++++.|..+||+=|-.... ++ ++||..+
T Consensus 19 ~v~~~l~~~~gvEVh~~~~~GKiVVtiE~~~ 49 (79)
T PF03927_consen 19 EVAEALAAIPGVEVHAVDEDGKIVVTIEAES 49 (79)
T ss_dssp HHHHHHCCSTTEEEEEEETTTEEEEEEEESS
T ss_pred HHHHHHHcCCCcEEEeeCCCCeEEEEEEeCC
Confidence 4666666777776655554 44 5566654
No 133
>PRK13237 tyrosine phenol-lyase; Provisional
Probab=21.17 E-value=84 Score=26.21 Aligned_cols=17 Identities=18% Similarity=0.259 Sum_probs=15.7
Q ss_pred EEEEecCHHHHHHHhcC
Q psy3003 64 YIVATCDKDLKRRIRKV 80 (106)
Q Consensus 64 ~iVaTqD~~Lr~~Lr~i 80 (106)
-+|+|+|.+|-+++|..
T Consensus 268 G~i~t~D~eL~~~~r~~ 284 (460)
T PRK13237 268 GFLAMNDEELFDEAKEL 284 (460)
T ss_pred eEEEECCHHHHHHHHHh
Confidence 78999999999999975
No 134
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=20.72 E-value=74 Score=24.48 Aligned_cols=44 Identities=23% Similarity=0.243 Sum_probs=31.3
Q ss_pred CCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHhcCCCccEEEEecce
Q psy3003 47 GTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIRKVPGVPIMYISQHR 92 (106)
Q Consensus 47 ~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~~ 92 (106)
|-.|||+|-.++.. ...+.|+|+|+++-+-.... +=+++.+++.
T Consensus 117 G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~~~~--~~~~~~~~~~ 164 (310)
T COG0258 117 GIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLVSPN--VLVINGKKGE 164 (310)
T ss_pred CCCcchhHHHHHHHHHhcCCeEEEEeCCcchhhhcCCC--cEEEeccCCC
Confidence 44689999887762 34799999999998776653 5555555544
No 135
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=20.34 E-value=3.2e+02 Score=19.28 Aligned_cols=62 Identities=13% Similarity=0.064 Sum_probs=29.9
Q ss_pred HHHhhccCCceEEEecCCCCC--CHHHHHHHhhhc-CCeEEEEe---cCHHHHHHHhcCCCccEEEEecc
Q psy3003 28 VALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQ-HKCYIVAT---CDKDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 28 ~al~~ak~~~~~~~~c~h~~~--~ad~ci~~~~~~-~~~~iVaT---qD~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
+..+.+++.++.+.-+..... ...+.+..+... -.-.++.. +|..++..+ + .|+|++++.+.
T Consensus 20 gi~~~~~~~gy~v~~~~~~~~~~~~~~~i~~~~~~~~dgiii~~~~~~~~~~~~~~-~-~~~pvV~i~~~ 87 (269)
T cd06293 20 AVEEEADARGLSLVLCATRNRPERELTYLRWLDTNHVDGLIFVTNRPDDGALAKLI-N-SYGNIVLVDED 87 (269)
T ss_pred HHHHHHHHCCCEEEEEeCCCCHHHHHHHHHHHHHCCCCEEEEeCCCCCHHHHHHHH-h-cCCCEEEECCC
Confidence 334444433455444433221 223444444443 22355543 344454444 4 38999999853
No 136
>COG0244 RplJ Ribosomal protein L10 [Translation, ribosomal structure and biogenesis]
Probab=20.32 E-value=47 Score=23.83 Aligned_cols=38 Identities=8% Similarity=0.301 Sum_probs=24.0
Q ss_pred HHHHhhhcCCeEEE-------EecCHHHHHHHhcCCCccEEEEecc
Q psy3003 53 CIVNRVTQHKCYIV-------ATCDKDLKRRIRKVPGVPIMYISQH 91 (106)
Q Consensus 53 ci~~~~~~~~~~iV-------aTqD~~Lr~~Lr~i~GVPviy~~~~ 91 (106)
-|.+++++...++| ++|..+||++||+. |+.+.-++++
T Consensus 14 el~e~~~~s~~~~i~dy~Gl~~~ql~~lR~~lr~~-g~~lkV~KNt 58 (175)
T COG0244 14 ELKELIKESPSVVIVDYRGLTVAQLTELRKKLREA-GAKLKVVKNT 58 (175)
T ss_pred HHHHHHhhCCEEEEEEeCCCcHHHHHHHHHHHHhC-CcEEEEEhhH
Confidence 34455554433333 57889999999984 7776655543
No 137
>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=20.31 E-value=3.2e+02 Score=19.68 Aligned_cols=34 Identities=12% Similarity=0.086 Sum_probs=25.6
Q ss_pred HhhhcCCeEEEEecCHHHHHHHhcCCCccEEEEe
Q psy3003 56 NRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYIS 89 (106)
Q Consensus 56 ~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~ 89 (106)
.+...+...+++|-|.++-+.+...+++-..++.
T Consensus 136 ~l~~~~~~~i~~TH~~~l~~~~~~~~~v~~~~~~ 169 (204)
T cd03282 136 CLIKKESTVFFATHFRDIAAILGNKSCVVHLHMK 169 (204)
T ss_pred HHHhcCCEEEEECChHHHHHHhhcCCCeEEEEEE
Confidence 3333445799999999999999876777666664
No 138
>cd08358 Glo_EDI_BRP_like_21 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.
Probab=20.29 E-value=2.2e+02 Score=19.07 Aligned_cols=35 Identities=11% Similarity=0.158 Sum_probs=23.3
Q ss_pred eEEEEecCHHHHHHHhcCCCccEEEEecceEEEeeC
Q psy3003 63 CYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIERM 98 (106)
Q Consensus 63 ~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~~l~lE~~ 98 (106)
+.-+|..|.++.++|++. |+|+.-...+...++.|
T Consensus 83 ~~hlav~~~d~~~~l~~~-Gv~~~~~~~~~~fi~DP 117 (127)
T cd08358 83 FLGITIHSKQAVSNAKKH-NWPVTEVEDGVYEVKAP 117 (127)
T ss_pred EEEEEEECHHHHHHHHHC-CCceecCCCCEEEEECC
Confidence 456666777888999995 98776544334454444
Done!