Query 033829
Match_columns 110
No_of_seqs 81 out of 83
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 06:46:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033829.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033829hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4118 Uncharacterized conser 99.7 2.3E-18 4.9E-23 118.3 -0.6 46 35-82 28-73 (74)
2 PF12907 zf-met2: Zinc-binding 99.0 8.2E-11 1.8E-15 72.6 0.4 31 46-76 1-34 (40)
3 PF12874 zf-met: Zinc-finger o 97.1 0.0001 2.2E-09 38.7 -0.1 23 47-69 1-23 (25)
4 PF13894 zf-C2H2_4: C2H2-type 96.2 0.0017 3.7E-08 32.4 0.4 24 47-70 1-24 (24)
5 PF09237 GAGA: GAGA factor; I 95.0 0.0091 2E-07 39.5 0.7 29 46-74 24-52 (54)
6 PF00096 zf-C2H2: Zinc finger, 94.4 0.0092 2E-07 30.6 -0.3 22 47-68 1-22 (23)
7 PF12171 zf-C2H2_jaz: Zinc-fin 93.2 0.022 4.7E-07 30.8 -0.2 24 46-69 1-24 (27)
8 PF05605 zf-Di19: Drought indu 93.0 0.06 1.3E-06 33.2 1.5 28 46-74 2-29 (54)
9 smart00451 ZnF_U1 U1-like zinc 92.1 0.07 1.5E-06 29.4 0.8 25 46-70 3-27 (35)
10 smart00355 ZnF_C2H2 zinc finge 91.5 0.082 1.8E-06 26.0 0.6 24 47-71 1-24 (26)
11 PF13912 zf-C2H2_6: C2H2-type 90.8 0.092 2E-06 27.7 0.5 26 46-71 1-26 (27)
12 PF13909 zf-H2C2_5: C2H2-type 89.3 0.093 2E-06 27.3 -0.3 24 47-71 1-24 (24)
13 PF12756 zf-C2H2_2: C2H2 type 86.1 0.34 7.3E-06 30.6 0.8 30 46-75 50-80 (100)
14 PF04988 AKAP95: A-kinase anch 86.1 0.31 6.6E-06 38.2 0.7 26 47-72 1-26 (165)
15 smart00734 ZnF_Rad18 Rad18-lik 84.0 0.57 1.2E-05 26.0 1.0 20 47-67 2-21 (26)
16 PF05605 zf-Di19: Drought indu 82.8 0.54 1.2E-05 28.9 0.6 23 46-70 31-53 (54)
17 KOG1842 FYVE finger-containing 81.8 0.52 1.1E-05 42.2 0.4 29 46-74 15-43 (505)
18 PF12756 zf-C2H2_2: C2H2 type 80.4 0.53 1.2E-05 29.7 0.0 37 48-84 1-37 (100)
19 COG2879 Uncharacterized small 75.9 1.6 3.4E-05 29.9 1.3 28 53-80 19-47 (65)
20 PF12013 DUF3505: Protein of u 74.2 1.5 3.2E-05 30.0 0.8 25 46-70 80-108 (109)
21 smart00614 ZnF_BED BED zinc fi 68.4 3.6 7.9E-05 24.9 1.5 29 45-73 17-50 (50)
22 PHA00616 hypothetical protein 63.8 2.2 4.7E-05 26.9 -0.1 32 47-78 2-33 (44)
23 PF02892 zf-BED: BED zinc fing 63.7 2.7 5.9E-05 24.3 0.3 29 43-71 13-45 (45)
24 cd02970 PRX_like2 Peroxiredoxi 62.2 1.2 2.7E-05 29.7 -1.5 21 48-68 35-55 (149)
25 PF04780 DUF629: Protein of un 59.5 4.9 0.00011 35.6 1.3 30 45-74 56-85 (466)
26 PTZ00448 hypothetical protein; 58.8 4.7 0.0001 35.1 1.0 39 45-83 313-361 (373)
27 cd03000 PDI_a_TMX3 PDIa family 56.1 3 6.5E-05 27.2 -0.5 21 48-68 26-46 (104)
28 cd03017 PRX_BCP Peroxiredoxin 54.6 2.4 5.3E-05 28.3 -1.1 20 49-68 36-55 (140)
29 PHA02768 hypothetical protein; 54.2 7 0.00015 25.6 1.0 28 44-72 3-30 (55)
30 KOG2785 C2H2-type Zn-finger pr 54.2 7 0.00015 34.3 1.3 53 11-73 43-95 (390)
31 PF04328 DUF466: Protein of un 52.7 6.2 0.00013 26.1 0.6 25 54-78 20-44 (65)
32 PF00578 AhpC-TSA: AhpC/TSA fa 51.5 1.5 3.4E-05 28.4 -2.4 43 25-69 12-58 (124)
33 TIGR03655 anti_R_Lar restricti 50.6 21 0.00047 21.9 2.8 21 39-59 19-39 (53)
34 TIGR02738 TrbB type-F conjugat 50.2 2.5 5.4E-05 31.1 -1.7 41 21-66 36-79 (153)
35 PHA00732 hypothetical protein 50.0 13 0.00027 25.2 1.8 25 47-71 2-26 (79)
36 cd02967 mauD Methylamine utili 49.7 3.8 8.3E-05 26.4 -0.7 19 48-66 32-50 (114)
37 cd03012 TlpA_like_DipZ_like Tl 49.3 3.3 7.2E-05 27.9 -1.1 22 47-68 33-54 (126)
38 cd03005 PDI_a_ERp46 PDIa famil 48.6 3.4 7.3E-05 26.0 -1.1 24 49-72 28-51 (102)
39 KOG1280 Uncharacterized conser 47.8 12 0.00026 32.8 1.8 29 46-74 79-107 (381)
40 PF10146 zf-C4H2: Zinc finger- 47.4 8.9 0.00019 30.7 0.9 17 48-74 210-226 (230)
41 PHA00733 hypothetical protein 47.0 11 0.00023 27.3 1.2 22 46-67 73-94 (128)
42 PTZ00256 glutathione peroxidas 45.9 4.1 9E-05 29.8 -1.1 21 49-69 53-73 (183)
43 smart00504 Ubox Modified RING 44.0 12 0.00025 22.4 0.9 14 47-60 2-15 (63)
44 cd03011 TlpA_like_ScsD_MtbDsbE 43.4 5.6 0.00012 26.0 -0.7 17 49-65 32-48 (123)
45 cd03018 PRX_AhpE_like Peroxire 42.4 4.7 0.0001 27.3 -1.2 40 28-68 17-60 (149)
46 cd02985 TRX_CDSP32 TRX family, 42.1 4 8.8E-05 26.9 -1.5 41 10-66 1-44 (103)
47 PRK09381 trxA thioredoxin; Pro 41.9 4.7 0.0001 26.2 -1.2 21 48-68 32-52 (109)
48 cd03009 TryX_like_TryX_NRX Try 41.6 6.2 0.00013 26.5 -0.7 22 48-69 29-50 (131)
49 PLN02748 tRNA dimethylallyltra 41.2 13 0.00028 32.6 1.0 25 45-69 417-442 (468)
50 COG4416 Com Mu-like prophage p 40.5 12 0.00026 25.2 0.6 25 42-66 20-48 (60)
51 PF13913 zf-C2HC_2: zinc-finge 40.1 14 0.0003 20.0 0.7 20 47-67 3-22 (25)
52 KOG1146 Homeobox protein [Gene 39.8 9.9 0.00021 38.0 0.1 31 45-75 464-494 (1406)
53 cd00340 GSH_Peroxidase Glutath 39.1 6.2 0.00013 27.7 -1.1 21 47-68 32-52 (152)
54 COG4049 Uncharacterized protei 38.6 11 0.00024 25.7 0.2 33 33-70 9-41 (65)
55 TIGR02540 gpx7 putative glutat 38.5 7.4 0.00016 27.2 -0.7 22 48-69 33-54 (153)
56 cd02964 TryX_like_family Trypa 38.0 6.4 0.00014 26.7 -1.1 22 48-69 28-49 (132)
57 PF08534 Redoxin: Redoxin; In 38.0 3.5 7.6E-05 28.0 -2.4 43 25-69 15-61 (146)
58 cd02996 PDI_a_ERp44 PDIa famil 37.6 7.6 0.00017 25.3 -0.8 25 48-72 29-53 (108)
59 cd02971 PRX_family Peroxiredox 37.2 7 0.00015 25.9 -1.0 21 48-68 34-54 (140)
60 cd02999 PDI_a_ERp44_like PDIa 37.2 6.5 0.00014 26.1 -1.1 19 49-67 30-48 (100)
61 TIGR00373 conserved hypothetic 35.2 14 0.00029 27.5 0.2 16 44-59 126-141 (158)
62 COG5540 RING-finger-containing 35.1 18 0.00039 31.6 0.9 15 45-59 360-374 (374)
63 cd02969 PRX_like1 Peroxiredoxi 34.9 7.6 0.00017 27.4 -1.2 22 48-69 36-57 (171)
64 cd03016 PRX_1cys Peroxiredoxin 34.8 8.3 0.00018 28.8 -1.0 21 49-69 38-58 (203)
65 PRK09697 protein secretion pro 34.7 20 0.00043 27.5 1.0 25 54-78 68-92 (139)
66 PRK11088 rrmA 23S rRNA methylt 34.7 16 0.00034 28.2 0.4 12 46-57 2-13 (272)
67 TIGR02661 MauD methylamine deh 33.6 7.2 0.00016 28.8 -1.5 17 48-64 85-101 (189)
68 KOG0823 Predicted E3 ubiquitin 33.4 26 0.00057 28.7 1.6 31 23-59 30-60 (230)
69 PRK15000 peroxidase; Provision 33.0 9.3 0.0002 28.9 -1.0 22 48-69 46-67 (200)
70 cd03014 PRX_Atyp2cys Peroxired 32.4 7.6 0.00016 26.3 -1.5 39 26-66 14-56 (143)
71 cd02956 ybbN ybbN protein fami 32.4 7.6 0.00016 24.4 -1.4 21 48-68 23-43 (96)
72 TIGR03137 AhpC peroxiredoxin. 32.4 9.3 0.0002 28.1 -1.1 27 42-68 33-63 (187)
73 PF10886 DUF2685: Protein of u 32.1 15 0.00033 24.2 0.0 16 48-63 3-18 (54)
74 COG0526 TrxA Thiol-disulfide i 31.7 14 0.0003 21.5 -0.2 23 46-68 41-63 (127)
75 PRK06266 transcription initiat 31.4 20 0.00044 27.3 0.6 15 45-59 135-149 (178)
76 PRK10954 periplasmic protein d 31.2 17 0.00038 27.0 0.2 24 44-67 44-70 (207)
77 cd03010 TlpA_like_DsbE TlpA-li 31.2 5.9 0.00013 26.3 -2.1 17 48-64 36-52 (127)
78 PTZ00056 glutathione peroxidas 30.7 10 0.00022 28.5 -1.1 22 48-69 50-71 (199)
79 PRK13599 putative peroxiredoxi 30.5 11 0.00024 29.0 -1.0 22 48-69 40-61 (215)
80 PRK10382 alkyl hydroperoxide r 30.5 11 0.00023 28.6 -1.1 26 43-68 34-63 (187)
81 cd02966 TlpA_like_family TlpA- 30.1 12 0.00026 22.7 -0.7 20 48-67 30-49 (116)
82 PRK13728 conjugal transfer pro 29.6 9.5 0.00021 29.5 -1.5 18 49-66 81-98 (181)
83 PF04564 U-box: U-box domain; 29.4 22 0.00049 22.8 0.5 33 46-78 4-47 (73)
84 KOG3608 Zn finger proteins [Ge 27.0 36 0.00077 30.5 1.4 28 46-73 263-290 (467)
85 smart00746 TRASH metallochaper 26.1 38 0.00081 16.5 0.9 10 49-58 1-10 (39)
86 TIGR01206 lysW lysine biosynth 26.0 23 0.00051 22.8 0.1 11 46-56 2-12 (54)
87 PRK15412 thiol:disulfide inter 25.9 9.2 0.0002 28.0 -2.1 16 48-63 79-94 (185)
88 PF09986 DUF2225: Uncharacteri 25.7 31 0.00066 26.8 0.7 16 46-61 5-20 (214)
89 PRK13190 putative peroxiredoxi 25.4 15 0.00033 27.5 -1.0 21 49-69 40-60 (202)
90 PF13465 zf-H2C2_2: Zinc-finge 25.1 29 0.00062 18.5 0.3 10 45-54 13-22 (26)
91 PRK09437 bcp thioredoxin-depen 24.6 15 0.00033 25.3 -1.1 42 25-68 17-62 (154)
92 cd02948 TRX_NDPK TRX domain, T 24.4 13 0.00027 24.4 -1.4 20 48-67 28-47 (102)
93 PF15227 zf-C3HC4_4: zinc fing 24.2 26 0.00056 20.7 0.0 15 49-63 1-15 (42)
94 PF13453 zf-TFIIB: Transcripti 24.1 31 0.00067 20.1 0.4 13 48-60 1-13 (41)
95 PLN02412 probable glutathione 24.1 19 0.00042 26.0 -0.7 23 47-69 39-61 (167)
96 TIGR00385 dsbE periplasmic pro 23.9 11 0.00025 27.0 -1.9 16 48-63 74-89 (173)
97 PF09654 DUF2396: Protein of u 23.8 28 0.00061 27.4 0.2 15 46-60 6-20 (161)
98 cd02968 SCO SCO (an acronym fo 23.6 14 0.00031 24.6 -1.3 21 48-68 33-54 (142)
99 TIGR02652 conserved hypothetic 23.1 29 0.00063 27.3 0.1 15 46-60 9-23 (163)
100 cd03023 DsbA_Com1_like DsbA fa 22.9 15 0.00033 24.2 -1.3 19 45-63 13-31 (154)
101 cd03004 PDI_a_ERdj5_C PDIa fam 22.7 14 0.0003 23.6 -1.5 20 48-67 30-49 (104)
102 PF14357 DUF4404: Domain of un 22.6 43 0.00094 22.8 0.9 17 61-77 57-73 (85)
103 PF14169 YdjO: Cold-inducible 22.6 36 0.00079 22.6 0.5 13 46-58 39-51 (59)
104 cd02997 PDI_a_PDIR PDIa family 22.6 19 0.0004 22.5 -0.9 21 48-68 28-48 (104)
105 smart00531 TFIIE Transcription 22.5 35 0.00076 24.8 0.4 10 47-56 124-133 (147)
106 PF09889 DUF2116: Uncharacteri 22.5 43 0.00092 22.0 0.8 14 48-61 5-18 (59)
107 PF03811 Zn_Tnp_IS1: InsA N-te 22.5 61 0.0013 19.2 1.4 20 34-53 17-36 (36)
108 cd03003 PDI_a_ERdj5_N PDIa fam 22.4 15 0.00033 23.5 -1.3 21 48-68 29-49 (101)
109 cd03019 DsbA_DsbA DsbA family, 22.3 22 0.00047 24.5 -0.6 19 45-63 23-41 (178)
110 cd03008 TryX_like_RdCVF Trypar 22.1 17 0.00036 26.9 -1.3 23 48-70 36-58 (146)
111 PF08271 TF_Zn_Ribbon: TFIIB z 22.0 41 0.00088 19.7 0.6 9 47-55 1-9 (43)
112 cd03002 PDI_a_MPD1_like PDI fa 21.9 24 0.00052 22.5 -0.5 20 48-67 29-48 (109)
113 PF14353 CpXC: CpXC protein 21.5 36 0.00079 23.6 0.4 36 43-78 35-70 (128)
114 PF00301 Rubredoxin: Rubredoxi 21.2 39 0.00084 21.1 0.4 10 46-55 34-43 (47)
115 PLN00219 predicted protein; Pr 21.1 40 0.00086 22.9 0.5 24 54-77 34-57 (65)
116 COG1592 Rubrerythrin [Energy p 21.1 36 0.00079 26.4 0.3 21 32-56 124-144 (166)
117 cd00730 rubredoxin Rubredoxin; 21.0 38 0.00083 21.4 0.3 10 45-54 33-42 (50)
118 KOG3576 Ovo and related transc 20.9 56 0.0012 27.4 1.4 32 45-76 211-242 (267)
119 COG5246 PRP11 Splicing factor 20.7 46 0.001 27.3 0.8 35 41-75 48-82 (222)
120 PF04423 Rad50_zn_hook: Rad50 20.6 31 0.00066 21.1 -0.2 13 48-60 22-34 (54)
121 PRK13191 putative peroxiredoxi 20.3 22 0.00048 27.3 -1.0 22 48-69 45-66 (215)
122 PF06974 DUF1298: Protein of u 20.2 69 0.0015 23.1 1.6 28 41-68 118-145 (153)
123 KOG2857 Predicted MYND Zn-fing 20.1 48 0.001 26.0 0.8 23 45-67 16-38 (157)
124 TIGR02098 MJ0042_CXXC MJ0042 f 20.1 55 0.0012 18.4 0.8 10 46-55 2-11 (38)
No 1
>KOG4118 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.69 E-value=2.3e-18 Score=118.26 Aligned_cols=46 Identities=30% Similarity=0.606 Sum_probs=40.6
Q ss_pred ccccccccceeeeeCcccccCCCCcchhhhhhhhCCCCCCCChHHHHH
Q 033829 35 DRTGREKGGHAKYECPLCKVTAPDIKSMQIHHDARHPKLPFDEASLVN 82 (110)
Q Consensus 35 dR~g~~k~galk~~C~VCkaqmPD~Kt~k~HfESKHPK~plp~E~l~d 82 (110)
|.+-. ..++|.|+|.||++||||+++|++|||+||||+|||+| |.+
T Consensus 28 DQK~A-A~~aL~~kCtVC~~~mpdpktfkqhfe~kHpk~~~P~e-L~~ 73 (74)
T KOG4118|consen 28 DQKAA-AMAALHHKCTVCMVQMPDPKTFKQHFENKHPKEPLPEE-LSE 73 (74)
T ss_pred cHHHH-HHHHHHhhhHhhHhhCCCCchHHHHHhhcCCCCCCCHh-hcc
Confidence 55433 56789999999999999999999999999999999999 765
No 2
>PF12907 zf-met2: Zinc-binding
Probab=98.99 E-value=8.2e-11 Score=72.58 Aligned_cols=31 Identities=23% Similarity=0.669 Sum_probs=28.1
Q ss_pred eeeCcccc---cCCCCcchhhhhhhhCCCCCCCC
Q 033829 46 KYECPLCK---VTAPDIKSMQIHHDARHPKLPFD 76 (110)
Q Consensus 46 k~~C~VCk---aqmPD~Kt~k~HfESKHPK~plp 76 (110)
+++|+||+ .++++++.|++||||||||.++.
T Consensus 1 ~i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~ 34 (40)
T PF12907_consen 1 NIICKICRQTFMQTTNEPQLKEHAENKHPKNTFE 34 (40)
T ss_pred CcCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHH
Confidence 47899999 89999999999999999997553
No 3
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.13 E-value=0.0001 Score=38.74 Aligned_cols=23 Identities=17% Similarity=0.537 Sum_probs=21.7
Q ss_pred eeCcccccCCCCcchhhhhhhhC
Q 033829 47 YECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfESK 69 (110)
|.|.+|..++.++.+|++|++++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999999985
No 4
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.15 E-value=0.0017 Score=32.41 Aligned_cols=24 Identities=21% Similarity=0.672 Sum_probs=20.4
Q ss_pred eeCcccccCCCCcchhhhhhhhCC
Q 033829 47 YECPLCKVTAPDIKSMQIHHDARH 70 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfESKH 70 (110)
|.|++|....++...|.+|....|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999998766
No 5
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.00 E-value=0.0091 Score=39.48 Aligned_cols=29 Identities=28% Similarity=0.621 Sum_probs=22.3
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCCC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESKHPK~p 74 (110)
-.+||+|.+.++..+.|+.|.|..|-+-|
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 46899999999999999999999997654
No 6
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=94.43 E-value=0.0092 Score=30.58 Aligned_cols=22 Identities=23% Similarity=0.671 Sum_probs=20.7
Q ss_pred eeCcccccCCCCcchhhhhhhh
Q 033829 47 YECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfES 68 (110)
|+|++|....++...|++|.+.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 7899999999999999999876
No 7
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=93.21 E-value=0.022 Score=30.82 Aligned_cols=24 Identities=13% Similarity=0.420 Sum_probs=21.6
Q ss_pred eeeCcccccCCCCcchhhhhhhhC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESK 69 (110)
.|.|.+|--.+.|...+.+|..||
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCCcccCCCCcCCHHHHHHHHccC
Confidence 378999999999999999999875
No 8
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=93.00 E-value=0.06 Score=33.23 Aligned_cols=28 Identities=21% Similarity=0.461 Sum_probs=25.3
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCCC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESKHPK~p 74 (110)
.|.||.|.. --|...|..|.+..|+.++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~ 29 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSES 29 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCC
Confidence 489999999 7899999999999999764
No 9
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.08 E-value=0.07 Score=29.40 Aligned_cols=25 Identities=32% Similarity=0.603 Sum_probs=22.7
Q ss_pred eeeCcccccCCCCcchhhhhhhhCC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDARH 70 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESKH 70 (110)
.|.|.+|...+-|...+.+|+.++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~ 27 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKK 27 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHH
Confidence 4889999999999999999998864
No 10
>smart00355 ZnF_C2H2 zinc finger.
Probab=91.46 E-value=0.082 Score=26.04 Aligned_cols=24 Identities=25% Similarity=0.595 Sum_probs=21.2
Q ss_pred eeCcccccCCCCcchhhhhhhhCCC
Q 033829 47 YECPLCKVTAPDIKSMQIHHDARHP 71 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfESKHP 71 (110)
|.|+.|....++..++..|.. .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 689999999999999999988 553
No 11
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=90.83 E-value=0.092 Score=27.71 Aligned_cols=26 Identities=19% Similarity=0.496 Sum_probs=23.2
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDARHP 71 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESKHP 71 (110)
.|+|.+|....++...|..|-..-|+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 38999999999999999999977665
No 12
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=89.32 E-value=0.093 Score=27.34 Aligned_cols=24 Identities=29% Similarity=0.808 Sum_probs=19.2
Q ss_pred eeCcccccCCCCcchhhhhhhhCCC
Q 033829 47 YECPLCKVTAPDIKSMQIHHDARHP 71 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfESKHP 71 (110)
|.|+.|-=... ...|..|.+..||
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 78999986666 8899999999887
No 13
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=86.09 E-value=0.34 Score=30.63 Aligned_cols=30 Identities=27% Similarity=0.542 Sum_probs=24.1
Q ss_pred eeeCcccccCCCCcchhhhhhhhC-CCCCCC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDAR-HPKLPF 75 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESK-HPK~pl 75 (110)
.+.|++|.....+...++.|..++ |.+...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 699999999999999999999987 555444
No 14
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=86.05 E-value=0.31 Score=38.18 Aligned_cols=26 Identities=23% Similarity=0.621 Sum_probs=24.1
Q ss_pred eeCcccccCCCCcchhhhhhhhCCCC
Q 033829 47 YECPLCKVTAPDIKSMQIHHDARHPK 72 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfESKHPK 72 (110)
|+|++|+-+.=+.+-+..|+||+==+
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~ 26 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHK 26 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHH
Confidence 78999999999999999999998666
No 15
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=84.03 E-value=0.57 Score=26.01 Aligned_cols=20 Identities=25% Similarity=0.554 Sum_probs=16.0
Q ss_pred eeCcccccCCCCcchhhhhhh
Q 033829 47 YECPLCKVTAPDIKSMQIHHD 67 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfE 67 (110)
+.||||-.++ ....+..|.+
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 5799999888 5577778876
No 16
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=82.80 E-value=0.54 Score=28.95 Aligned_cols=23 Identities=26% Similarity=0.715 Sum_probs=19.4
Q ss_pred eeeCcccccCCCCcchhhhhhhhCC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDARH 70 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESKH 70 (110)
.+.||||-....+ .|..|+...|
T Consensus 31 ~v~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 31 NVVCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred CccCCCchhhhhh--HHHHHHHHhc
Confidence 5899999987664 8999998877
No 17
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=81.82 E-value=0.52 Score=42.23 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=26.9
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCCC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESKHPK~p 74 (110)
.|.||+|+.-+|++-.|..||+.-|+-+.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 38999999999999999999999999765
No 18
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=80.36 E-value=0.53 Score=29.71 Aligned_cols=37 Identities=19% Similarity=0.337 Sum_probs=0.0
Q ss_pred eCcccccCCCCcchhhhhhhhCCCCCCCChHHHHHHH
Q 033829 48 ECPLCKVTAPDIKSMQIHHDARHPKLPFDEASLVNLH 84 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESKHPK~plp~E~l~d~h 84 (110)
+|.+|....+++..+.+|....|.-..-..+.|.+..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~ 37 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPN 37 (100)
T ss_dssp -------------------------------------
T ss_pred Ccccccccccccccccccccccccccccccccccccc
Confidence 5999999999999999999999976543344344433
No 19
>COG2879 Uncharacterized small protein [Function unknown]
Probab=75.91 E-value=1.6 Score=29.89 Aligned_cols=28 Identities=25% Similarity=0.377 Sum_probs=22.1
Q ss_pred ccCCCCcchhhhhhhhCCCCCCC-ChHHH
Q 033829 53 KVTAPDIKSMQIHHDARHPKLPF-DEASL 80 (110)
Q Consensus 53 kaqmPD~Kt~k~HfESKHPK~pl-p~E~l 80 (110)
++-+||+.+|..|...|||..|. ..|++
T Consensus 19 mvGvpdYdnYVehmr~~hPd~p~mT~~EF 47 (65)
T COG2879 19 MVGVPDYDNYVEHMRKKHPDKPPMTYEEF 47 (65)
T ss_pred HcCCCcHHHHHHHHHHhCcCCCcccHHHH
Confidence 46799999999999999997654 44433
No 20
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=74.20 E-value=1.5 Score=30.02 Aligned_cols=25 Identities=32% Similarity=0.672 Sum_probs=23.5
Q ss_pred eeeC----cccccCCCCcchhhhhhhhCC
Q 033829 46 KYEC----PLCKVTAPDIKSMQIHHDARH 70 (110)
Q Consensus 46 k~~C----~VCkaqmPD~Kt~k~HfESKH 70 (110)
=|.| +.|.--..+.++|..||..+|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 3899 999999999999999999998
No 21
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=68.41 E-value=3.6 Score=24.90 Aligned_cols=29 Identities=17% Similarity=0.439 Sum_probs=24.3
Q ss_pred eeeeCcccccCCCCc-----chhhhhhhhCCCCC
Q 033829 45 AKYECPLCKVTAPDI-----KSMQIHHDARHPKL 73 (110)
Q Consensus 45 lk~~C~VCkaqmPD~-----Kt~k~HfESKHPK~ 73 (110)
-...|..|...+.-. .+|..|..++||..
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~~~ 50 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHPAR 50 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCcCC
Confidence 578999999888655 59999999999963
No 22
>PHA00616 hypothetical protein
Probab=63.82 E-value=2.2 Score=26.86 Aligned_cols=32 Identities=19% Similarity=0.213 Sum_probs=28.3
Q ss_pred eeCcccccCCCCcchhhhhhhhCCCCCCCChH
Q 033829 47 YECPLCKVTAPDIKSMQIHHDARHPKLPFDEA 78 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfESKHPK~plp~E 78 (110)
|+|+-|.-..-+.+.|..|..+-|-..++.-|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 78999999999999999999998887776544
No 23
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=63.72 E-value=2.7 Score=24.34 Aligned_cols=29 Identities=21% Similarity=0.469 Sum_probs=21.0
Q ss_pred ceeeeeCcccccCCCC----cchhhhhhhhCCC
Q 033829 43 GHAKYECPLCKVTAPD----IKSMQIHHDARHP 71 (110)
Q Consensus 43 galk~~C~VCkaqmPD----~Kt~k~HfESKHP 71 (110)
+-...+|..|...+.- ...|..|...+||
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~hp 45 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKHP 45 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTTH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhCc
Confidence 3467899999987765 5789999999997
No 24
>cd02970 PRX_like2 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. TRXs alter the redox state of target proteins by catalyzing the reduction of their disulfide bonds via the CXXC motif using reducing equivalents derived from either NADPH or ferredoxins.
Probab=62.15 E-value=1.2 Score=29.66 Aligned_cols=21 Identities=24% Similarity=0.564 Sum_probs=18.1
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfES 68 (110)
-|+.|..+||+...+..-|..
T Consensus 35 ~Cp~C~~~~~~l~~~~~~~~~ 55 (149)
T cd02970 35 GCPFCREYLRALSKLLPELDA 55 (149)
T ss_pred CChhHHHHHHHHHHHHHHHHh
Confidence 699999999999888877763
No 25
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=59.49 E-value=4.9 Score=35.62 Aligned_cols=30 Identities=27% Similarity=0.441 Sum_probs=26.7
Q ss_pred eeeeCcccccCCCCcchhhhhhhhCCCCCC
Q 033829 45 AKYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (110)
Q Consensus 45 lk~~C~VCkaqmPD~Kt~k~HfESKHPK~p 74 (110)
-=..||.|-....|...+.+|.+++|+-.-
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 346899999999999999999999998753
No 26
>PTZ00448 hypothetical protein; Provisional
Probab=58.76 E-value=4.7 Score=35.06 Aligned_cols=39 Identities=18% Similarity=0.359 Sum_probs=30.4
Q ss_pred eeeeCcccccCCCCcchhhhhhhhCCC----------CCCCChHHHHHH
Q 033829 45 AKYECPLCKVTAPDIKSMQIHHDARHP----------KLPFDEASLVNL 83 (110)
Q Consensus 45 lk~~C~VCkaqmPD~Kt~k~HfESKHP----------K~plp~E~l~d~ 83 (110)
..|+|..|..+..|....+.||.|-+= -.|+.++.+..+
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~gLppvse~eF~~~ 361 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNARKMEPISEEEFLEL 361 (373)
T ss_pred CCccccccccccCCHHHHHHHhhhhHHHHHHHHHhcCCCCCCHHHHHHH
Confidence 368999999999999999999998653 345666655544
No 27
>cd03000 PDI_a_TMX3 PDIa family, TMX3 subfamily; composed of eukaryotic proteins similar to human TMX3, a TRX related transmembrane protein containing one redox active TRX domain at the N-terminus and a classical ER retrieval sequence for type I transmembrane proteins at the C-terminus. The TMX3 transcript is found in a variety of tissues with the highest levels detected in skeletal muscle and the heart. In vitro, TMX3 showed oxidase activity albeit slightly lower than that of protein disulfide isomerase.
Probab=56.07 E-value=3 Score=27.17 Aligned_cols=21 Identities=19% Similarity=0.306 Sum_probs=18.4
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfES 68 (110)
-|+.|+.++|-...+.++|+.
T Consensus 26 wC~~C~~~~p~l~~l~~~~~~ 46 (104)
T cd03000 26 WCGHCKKLEPVWNEVGAELKS 46 (104)
T ss_pred CCHHHHhhChHHHHHHHHHHh
Confidence 399999999999999988853
No 28
>cd03017 PRX_BCP Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The protein was named BCP based on its electrophoretic mobility before its function was known. BCP shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides. BCP contains the peroxidatic cysteine but appears not to possess a resolving cysteine (some sequences, not all, contain a second cysteine but its role is still unknown). Unlike other PRXs, BCP exists as a monomer. The plant homolog of BCP is PRX Q, which is expressed only in leaves and is cellularly localized in the chloroplasts and the guard cells of stomata. Also included in this subfamily is the fungal nuclear protein, Dot5p (for disrupter of telomere silencing protein 5), w
Probab=54.62 E-value=2.4 Score=28.26 Aligned_cols=20 Identities=25% Similarity=0.373 Sum_probs=17.3
Q ss_pred CcccccCCCCcchhhhhhhh
Q 033829 49 CPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 49 C~VCkaqmPD~Kt~k~HfES 68 (110)
||+|..++|....+.+-|+.
T Consensus 36 cp~C~~~~~~l~~~~~~~~~ 55 (140)
T cd03017 36 TPGCTKEACDFRDLYEEFKA 55 (140)
T ss_pred CCchHHHHHHHHHHHHHHHH
Confidence 99999999998888877764
No 29
>PHA02768 hypothetical protein; Provisional
Probab=54.23 E-value=7 Score=25.55 Aligned_cols=28 Identities=36% Similarity=0.549 Sum_probs=24.5
Q ss_pred eeeeeCcccccCCCCcchhhhhhhhCCCC
Q 033829 44 HAKYECPLCKVTAPDIKSMQIHHDARHPK 72 (110)
Q Consensus 44 alk~~C~VCkaqmPD~Kt~k~HfESKHPK 72 (110)
-|-|.|+.|--.......|..|... |.|
T Consensus 3 ~~~y~C~~CGK~Fs~~~~L~~H~r~-H~k 30 (55)
T PHA02768 3 LLGYECPICGEIYIKRKSMITHLRK-HNT 30 (55)
T ss_pred ccccCcchhCCeeccHHHHHHHHHh-cCC
Confidence 3679999999999999999999988 663
No 30
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=54.17 E-value=7 Score=34.27 Aligned_cols=53 Identities=17% Similarity=0.224 Sum_probs=37.5
Q ss_pred cHHHHHHHHHHHHhhCCCCcccccccccccccceeeeeCcccccCCCCcchhhhhhhhCCCCC
Q 033829 11 TAKEIAMKVDAATTNRGGGKAGMADRTGREKGGHAKYECPLCKVTAPDIKSMQIHHDARHPKL 73 (110)
Q Consensus 11 takeia~k~~aa~tN~GGGkaG~~dR~g~~k~galk~~C~VCkaqmPD~Kt~k~HfESKHPK~ 73 (110)
||.+++.|+.++..-. =... ..+-+.+.|.||.-..+.++-+.+|.-||-=++
T Consensus 43 taE~F~~k~~s~~~~~---------~~~~-e~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~ 95 (390)
T KOG2785|consen 43 TAEEFNEKVLSDDSEK---------EENL-EEAESVVYCEACNKSFASPKAHENHLKSKKHVE 95 (390)
T ss_pred CHHHHhHHHhhhhhhh---------hhhh-hhcccceehHHhhccccChhhHHHHHHHhhcch
Confidence 7889999984432100 0111 235588999999999999999999998875443
No 31
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=52.65 E-value=6.2 Score=26.10 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=20.4
Q ss_pred cCCCCcchhhhhhhhCCCCCCCChH
Q 033829 54 VTAPDIKSMQIHHDARHPKLPFDEA 78 (110)
Q Consensus 54 aqmPD~Kt~k~HfESKHPK~plp~E 78 (110)
+-.||+..|..|+...||-.|...+
T Consensus 20 ~G~~~Ye~Yv~H~~~~HP~~p~ms~ 44 (65)
T PF04328_consen 20 VGEPDYERYVEHMRRHHPDEPPMSE 44 (65)
T ss_pred cCcHHHHHHHHHHHHHCcCCCCCCH
Confidence 4479999999999999997765543
No 32
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=51.51 E-value=1.5 Score=28.41 Aligned_cols=43 Identities=19% Similarity=0.475 Sum_probs=28.5
Q ss_pred hCCCCcccccccccccccceeee----eCcccccCCCCcchhhhhhhhC
Q 033829 25 NRGGGKAGMADRTGREKGGHAKY----ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 25 N~GGGkaG~~dR~g~~k~galk~----~C~VCkaqmPD~Kt~k~HfESK 69 (110)
+.-|+.--|.|-.| +---+.| -|+.|..+++....+...|+.+
T Consensus 12 ~~~g~~~~l~~l~g--k~~vl~f~~~~~c~~c~~~l~~l~~~~~~~~~~ 58 (124)
T PF00578_consen 12 DSDGKTVSLSDLKG--KPVVLFFWPTAWCPFCQAELPELNELYKKYKDK 58 (124)
T ss_dssp TTTSEEEEGGGGTT--SEEEEEEESTTTSHHHHHHHHHHHHHHHHHHTT
T ss_pred CCCCCEEEHHHHCC--CcEEEEEeCccCccccccchhHHHHHhhhhccc
Confidence 33455555555543 2222222 5999999999999999888854
No 33
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=50.60 E-value=21 Score=21.91 Aligned_cols=21 Identities=19% Similarity=0.374 Sum_probs=16.5
Q ss_pred ccccceeeeeCcccccCCCCc
Q 033829 39 REKGGHAKYECPLCKVTAPDI 59 (110)
Q Consensus 39 ~~k~galk~~C~VCkaqmPD~ 59 (110)
.++.+...|.|+.|.+.+|..
T Consensus 19 ~~~~~~~~~~C~~Cga~~~~~ 39 (53)
T TIGR03655 19 DPLDLSHYFECSTCGASGPVE 39 (53)
T ss_pred CCCCCEEEEECCCCCCCcccc
Confidence 345666778999999999973
No 34
>TIGR02738 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. The protein is closely related to TraF (TIGR02739) which is somewhat longer, lacks the cysteine motif and is apparently not functional as a disulfide bond isomerase.
Probab=50.19 E-value=2.5 Score=31.14 Aligned_cols=41 Identities=29% Similarity=0.479 Sum_probs=28.2
Q ss_pred HHHhhCCCCcccccccccccccceeee---eCcccccCCCCcchhhhhh
Q 033829 21 AATTNRGGGKAGMADRTGREKGGHAKY---ECPLCKVTAPDIKSMQIHH 66 (110)
Q Consensus 21 aa~tN~GGGkaG~~dR~g~~k~galk~---~C~VCkaqmPD~Kt~k~Hf 66 (110)
++|.|+|-|+.-..... .-++| -|+.|+..||....+.+.|
T Consensus 36 ~~~~~~~~G~~~~l~~~-----~lvnFWAsWCppCr~e~P~L~~l~~~~ 79 (153)
T TIGR02738 36 AATDNAPQGRHANQDDY-----ALVFFYQSTCPYCHQFAPVLKRFSQQF 79 (153)
T ss_pred ccccccCcchhhhcCCC-----EEEEEECCCChhHHHHHHHHHHHHHHc
Confidence 45667777654333322 23444 4999999999999998876
No 35
>PHA00732 hypothetical protein
Probab=49.97 E-value=13 Score=25.21 Aligned_cols=25 Identities=24% Similarity=0.716 Sum_probs=19.2
Q ss_pred eeCcccccCCCCcchhhhhhhhCCC
Q 033829 47 YECPLCKVTAPDIKSMQIHHDARHP 71 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfESKHP 71 (110)
|.|+.|.....+..++++|....|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC
Confidence 6788888888888888888775454
No 36
>cd02967 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.
Probab=49.66 E-value=3.8 Score=26.44 Aligned_cols=19 Identities=37% Similarity=0.779 Sum_probs=15.4
Q ss_pred eCcccccCCCCcchhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHH 66 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~Hf 66 (110)
-|+.|+.++|..+.+.+-|
T Consensus 32 wC~~C~~~~p~l~~~~~~~ 50 (114)
T cd02967 32 TCPVCKKLLPVIRSIARAE 50 (114)
T ss_pred CCcchHhHhHHHHHHHHHh
Confidence 5999999999988765544
No 37
>cd03012 TlpA_like_DipZ_like TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3.
Probab=49.32 E-value=3.3 Score=27.85 Aligned_cols=22 Identities=23% Similarity=0.437 Sum_probs=18.6
Q ss_pred eeCcccccCCCCcchhhhhhhh
Q 033829 47 YECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfES 68 (110)
.-|+.|..+||..+.+.+-|..
T Consensus 33 ~~C~~C~~~~p~l~~l~~~~~~ 54 (126)
T cd03012 33 YCCINCLHTLPYLTDLEQKYKD 54 (126)
T ss_pred CCCccHHHHHHHHHHHHHHcCc
Confidence 3699999999999988887764
No 38
>cd03005 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.
Probab=48.60 E-value=3.4 Score=26.00 Aligned_cols=24 Identities=25% Similarity=0.573 Sum_probs=20.1
Q ss_pred CcccccCCCCcchhhhhhhhCCCC
Q 033829 49 CPLCKVTAPDIKSMQIHHDARHPK 72 (110)
Q Consensus 49 C~VCkaqmPD~Kt~k~HfESKHPK 72 (110)
|+.|+.++|....+...++...++
T Consensus 28 C~~C~~~~p~~~~~~~~~~~~~~~ 51 (102)
T cd03005 28 CGHCKRLAPTWEQLAKKFNNENPS 51 (102)
T ss_pred CHHHHHhCHHHHHHHHHHhccCCc
Confidence 999999999999998888764443
No 39
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=47.83 E-value=12 Score=32.81 Aligned_cols=29 Identities=21% Similarity=0.582 Sum_probs=27.6
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCCC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESKHPK~p 74 (110)
-|+||.|+.+==...+|..|--+-||-.+
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~ 107 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEAS 107 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccC
Confidence 69999999999999999999999999887
No 40
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=47.41 E-value=8.9 Score=30.68 Aligned_cols=17 Identities=53% Similarity=1.138 Sum_probs=12.3
Q ss_pred eCcccccCCCCcchhhhhhhhCCCCCC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDARHPKLP 74 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESKHPK~p 74 (110)
+||.||+- .+|||||-|
T Consensus 210 iCPlCK~K----------sRSrnpKk~ 226 (230)
T PF10146_consen 210 ICPLCKAK----------SRSRNPKKP 226 (230)
T ss_pred CCcccccc----------cccCCCCCc
Confidence 68888763 478888865
No 41
>PHA00733 hypothetical protein
Probab=47.05 E-value=11 Score=27.31 Aligned_cols=22 Identities=32% Similarity=0.647 Sum_probs=13.5
Q ss_pred eeeCcccccCCCCcchhhhhhh
Q 033829 46 KYECPLCKVTAPDIKSMQIHHD 67 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfE 67 (110)
.|.|+.|....++..++++|.+
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHh
Confidence 4666666666666666666654
No 42
>PTZ00256 glutathione peroxidase; Provisional
Probab=45.86 E-value=4.1 Score=29.81 Aligned_cols=21 Identities=10% Similarity=0.184 Sum_probs=18.2
Q ss_pred CcccccCCCCcchhhhhhhhC
Q 033829 49 CPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 49 C~VCkaqmPD~Kt~k~HfESK 69 (110)
|+.|+..||....+.+-|.++
T Consensus 53 Cp~C~~e~p~l~~l~~~~~~~ 73 (183)
T PTZ00256 53 CGLTSDHYTQLVELYKQYKSQ 73 (183)
T ss_pred CCchHHHHHHHHHHHHHHhhC
Confidence 999999999999888877654
No 43
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=44.00 E-value=12 Score=22.40 Aligned_cols=14 Identities=21% Similarity=0.463 Sum_probs=11.4
Q ss_pred eeCcccccCCCCcc
Q 033829 47 YECPLCKVTAPDIK 60 (110)
Q Consensus 47 ~~C~VCkaqmPD~K 60 (110)
+.||||+..|-||=
T Consensus 2 ~~Cpi~~~~~~~Pv 15 (63)
T smart00504 2 FLCPISLEVMKDPV 15 (63)
T ss_pred cCCcCCCCcCCCCE
Confidence 67999998887763
No 44
>cd03011 TlpA_like_ScsD_MtbDsbE TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif. The Salmonella typhimurium ScsD is a thioredoxin-like protein which confers copper tolerance to copper-sensitive mutants of E. coli. MtbDsbE has been characterized as an oxidase in vitro, catalyzing the disulfide bond formation of substrates like hirudin. The reduced form of MtbDsbE is more stable than its oxidized form, consistent with an oxidase function. This is in contrast to the function of DsbE from gram-negative bacteria which is a specific reductase of apocytochrome c.
Probab=43.44 E-value=5.6 Score=26.01 Aligned_cols=17 Identities=29% Similarity=1.032 Sum_probs=14.9
Q ss_pred CcccccCCCCcchhhhh
Q 033829 49 CPLCKVTAPDIKSMQIH 65 (110)
Q Consensus 49 C~VCkaqmPD~Kt~k~H 65 (110)
|+.|+.++|....+...
T Consensus 32 C~~C~~~~~~l~~~~~~ 48 (123)
T cd03011 32 CPVCRFTSPTVNQLAAD 48 (123)
T ss_pred ChhhhhhChHHHHHHhh
Confidence 99999999999887665
No 45
>cd03018 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.
Probab=42.42 E-value=4.7 Score=27.26 Aligned_cols=40 Identities=18% Similarity=0.272 Sum_probs=25.9
Q ss_pred CCcccccccccccccceeeee----CcccccCCCCcchhhhhhhh
Q 033829 28 GGKAGMADRTGREKGGHAKYE----CPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 28 GGkaG~~dR~g~~k~galk~~----C~VCkaqmPD~Kt~k~HfES 68 (110)
|..--+.|-.|. +--.+.|- |++|..++|....+..-|..
T Consensus 17 g~~v~l~~~~g~-k~~vl~f~~~~~c~~C~~~~~~l~~~~~~~~~ 60 (149)
T cd03018 17 GQEVRLSEFRGR-KPVVLVFFPLAFTPVCTKELCALRDSLELFEA 60 (149)
T ss_pred CCEEeHHHHcCC-CeEEEEEeCCCCCccHHHHHHHHHHHHHHHHh
Confidence 444555554441 33345554 99999999988887766654
No 46
>cd02985 TRX_CDSP32 TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif. CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form.
Probab=42.11 E-value=4 Score=26.94 Aligned_cols=41 Identities=12% Similarity=0.207 Sum_probs=28.3
Q ss_pred ccHHHHHHHHHHHHhhCCCCcccccccccccccceeee---eCcccccCCCCcchhhhhh
Q 033829 10 HTAKEIAMKVDAATTNRGGGKAGMADRTGREKGGHAKY---ECPLCKVTAPDIKSMQIHH 66 (110)
Q Consensus 10 Htakeia~k~~aa~tN~GGGkaG~~dR~g~~k~galk~---~C~VCkaqmPD~Kt~k~Hf 66 (110)
||..|+..-+..+ +|+.=+ +.| -|+.|+.++|....+.+.|
T Consensus 1 ~~~~~~~~~i~~~-----~~k~vv-----------v~F~a~wC~~C~~~~p~l~~la~~~ 44 (103)
T cd02985 1 HSVEELDEALKKA-----KGRLVV-----------LEFALKHSGPSVKIYPTMVKLSRTC 44 (103)
T ss_pred CCHHHHHHHHHHc-----CCCEEE-----------EEEECCCCHhHHHHhHHHHHHHHHC
Confidence 7888888777433 122211 333 3999999999999888877
No 47
>PRK09381 trxA thioredoxin; Provisional
Probab=41.90 E-value=4.7 Score=26.17 Aligned_cols=21 Identities=24% Similarity=0.427 Sum_probs=18.2
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfES 68 (110)
-|+.|+.++|..+.+...|..
T Consensus 32 ~C~~C~~~~p~~~~l~~~~~~ 52 (109)
T PRK09381 32 WCGPCKMIAPILDEIADEYQG 52 (109)
T ss_pred CCHHHHHHhHHHHHHHHHhCC
Confidence 399999999999998887754
No 48
>cd03009 TryX_like_TryX_NRX Tryparedoxin (TryX)-like family, TryX and nucleoredoxin (NRX) subfamily; TryX and NRX are thioredoxin (TRX)-like protein disulfide oxidoreductases that alter the redox state of target proteins via the reversible oxidation of an active center CXXC motif. TryX is involved in the regulation of oxidative stress in parasitic trypanosomatids by reducing TryX peroxidase, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. TryX derives reducing equivalents from reduced trypanothione, a polyamine peptide conjugate unique to trypanosomatids, which is regenerated by the NADPH-dependent flavoprotein trypanothione reductase. Vertebrate NRX is a 400-amino acid nuclear protein with one redox active TRX domain containing a CPPC active site motif followed by one redox inactive TRX-like domain. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. Plant NRX, longer than the
Probab=41.59 E-value=6.2 Score=26.46 Aligned_cols=22 Identities=18% Similarity=0.468 Sum_probs=17.4
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESK 69 (110)
-|+.|+.++|....+...+..+
T Consensus 29 wC~~C~~~~p~l~~~~~~~~~~ 50 (131)
T cd03009 29 WCPPCRAFTPKLVEFYEKLKES 50 (131)
T ss_pred CChHHHHHhHHHHHHHHHHHhc
Confidence 4999999999988776666543
No 49
>PLN02748 tRNA dimethylallyltransferase
Probab=41.23 E-value=13 Score=32.60 Aligned_cols=25 Identities=20% Similarity=0.474 Sum_probs=22.6
Q ss_pred eeeeCccccc-CCCCcchhhhhhhhC
Q 033829 45 AKYECPLCKV-TAPDIKSMQIHHDAR 69 (110)
Q Consensus 45 lk~~C~VCka-qmPD~Kt~k~HfESK 69 (110)
-.|+|.+|.. .|-......+|..|+
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcch
Confidence 6789999998 799999999999886
No 50
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=40.52 E-value=12 Score=25.24 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=17.3
Q ss_pred cceeeeeCcccccC----CCCcchhhhhh
Q 033829 42 GGHAKYECPLCKVT----APDIKSMQIHH 66 (110)
Q Consensus 42 ~galk~~C~VCkaq----mPD~Kt~k~Hf 66 (110)
.|.|..+||-|+.. .|..-+.++|-
T Consensus 20 ~~yle~KCPrCK~vN~~~~~~e~~t~~~k 48 (60)
T COG4416 20 QAYLEKKCPRCKEVNEFYIKEEATTQIHK 48 (60)
T ss_pred ceeeeecCCccceeeeeecccccchhhhh
Confidence 68999999999953 44444444443
No 51
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=40.14 E-value=14 Score=20.05 Aligned_cols=20 Identities=20% Similarity=0.595 Sum_probs=16.0
Q ss_pred eeCcccccCCCCcchhhhhhh
Q 033829 47 YECPLCKVTAPDIKSMQIHHD 67 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfE 67 (110)
..|++|.-.. .+..+..|..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4799998887 7888888853
No 52
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=39.77 E-value=9.9 Score=38.03 Aligned_cols=31 Identities=19% Similarity=0.490 Sum_probs=28.3
Q ss_pred eeeeCcccccCCCCcchhhhhhhhCCCCCCC
Q 033829 45 AKYECPLCKVTAPDIKSMQIHHDARHPKLPF 75 (110)
Q Consensus 45 lk~~C~VCkaqmPD~Kt~k~HfESKHPK~pl 75 (110)
-.|+||.|...-++..++..|.++|||-.--
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~ 494 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQS 494 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccch
Confidence 3589999999999999999999999997765
No 53
>cd00340 GSH_Peroxidase Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes.
Probab=39.09 E-value=6.2 Score=27.65 Aligned_cols=21 Identities=5% Similarity=0.101 Sum_probs=16.7
Q ss_pred eeCcccccCCCCcchhhhhhhh
Q 033829 47 YECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfES 68 (110)
..|+ |..+||+...+.+-|..
T Consensus 32 twC~-C~~e~p~l~~l~~~~~~ 52 (152)
T cd00340 32 SKCG-FTPQYEGLEALYEKYKD 52 (152)
T ss_pred CCCC-chHHHHHHHHHHHHhcC
Confidence 3699 99999988877776654
No 54
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=38.65 E-value=11 Score=25.71 Aligned_cols=33 Identities=27% Similarity=0.485 Sum_probs=26.9
Q ss_pred ccccccccccceeeeeCcccccCCCCcchhhhhhhhCC
Q 033829 33 MADRTGREKGGHAKYECPLCKVTAPDIKSMQIHHDARH 70 (110)
Q Consensus 33 ~~dR~g~~k~galk~~C~VCkaqmPD~Kt~k~HfESKH 70 (110)
+.||-|. .-+.||-|-+..-+.|+|..|-.--|
T Consensus 9 v~~RDGE-----~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 9 VRDRDGE-----EFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eeccCCc-----eeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 3566654 78999999999999999999976555
No 55
>TIGR02540 gpx7 putative glutathione peroxidase Gpx7. This model represents one of several families of known and probable glutathione peroxidases. This family is restricted to animals and designated GPX7.
Probab=38.45 E-value=7.4 Score=27.18 Aligned_cols=22 Identities=9% Similarity=0.243 Sum_probs=17.6
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESK 69 (110)
-||.|+..||+...+..-|..+
T Consensus 33 ~C~~c~~~~~~l~~l~~~~~~~ 54 (153)
T TIGR02540 33 ECGFTDQNYRALQELHRELGPS 54 (153)
T ss_pred CCCchhhhHHHHHHHHHHHhhC
Confidence 4999999999888887777653
No 56
>cd02964 TryX_like_family Tryparedoxin (TryX)-like family; composed of TryX and related proteins including nucleoredoxin (NRX), rod-derived cone viability factor (RdCVF) and the nematode homolog described as a 16-kD class of TRX. Most members of this family, except RdCVF, are protein disulfide oxidoreductases containing an active site CXXC motif, similar to TRX.
Probab=38.05 E-value=6.4 Score=26.75 Aligned_cols=22 Identities=18% Similarity=0.477 Sum_probs=17.5
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESK 69 (110)
-|+.|+.+||....+.+.+..+
T Consensus 28 wC~~C~~~~p~l~~l~~~~~~~ 49 (132)
T cd02964 28 WCPPCRAFTPKLVEFYEKLKEE 49 (132)
T ss_pred CCchHHHHHHHHHHHHHHHhhc
Confidence 5999999999888776666544
No 57
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=37.96 E-value=3.5 Score=27.96 Aligned_cols=43 Identities=19% Similarity=0.434 Sum_probs=25.6
Q ss_pred hCCCCcccccccccccccceeee----eCcccccCCCCcchhhhhhhhC
Q 033829 25 NRGGGKAGMADRTGREKGGHAKY----ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 25 N~GGGkaG~~dR~g~~k~galk~----~C~VCkaqmPD~Kt~k~HfESK 69 (110)
+.-|..--|.+-.|. ---+.| -||.|..+||..+.+..-|..+
T Consensus 15 ~~~g~~~~l~~~~gk--~~vv~f~~~~~Cp~C~~~~p~l~~l~~~~~~~ 61 (146)
T PF08534_consen 15 DLDGKPVSLSDFKGK--PVVVNFWASAWCPPCRKELPYLNELQEKYKDK 61 (146)
T ss_dssp ETTSEEEEGGGGTTS--EEEEEEESTTTSHHHHHHHHHHHHHHHHHHTT
T ss_pred cCCCCEecHHHhCCC--eEEEEEEccCCCCcchhhhhhHHhhhhhhccC
Confidence 355666666664442 222222 5999999999776665544433
No 58
>cd02996 PDI_a_ERp44 PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain, similar to that of PDIa, with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. The CXFS motif in the N-terminal domain allows ERp44 to form stable reversible mixed disulfides with its substrates. Through this activity, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. It also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol.
Probab=37.56 E-value=7.6 Score=25.32 Aligned_cols=25 Identities=12% Similarity=0.284 Sum_probs=20.8
Q ss_pred eCcccccCCCCcchhhhhhhhCCCC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDARHPK 72 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESKHPK 72 (110)
-|+.|+..+|....+...+++.+|.
T Consensus 29 wC~~C~~~~p~~~~~a~~~~~~~~~ 53 (108)
T cd02996 29 WCRFSQMLHPIFEEAAAKIKEEFPD 53 (108)
T ss_pred CCHHHHhhHHHHHHHHHHHhhccCC
Confidence 3999999999998888888766654
No 59
>cd02971 PRX_family Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. They confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either TRX, glutathione, trypanothione and AhpF. They are distinct from other peroxidases in that they have no cofactors such as metals or prosthetic groups. The first step of catalysis, common to all PRXs, is the nucleophilic attack by the catalytic cysteine (also known as the peroxidatic cysteine) on the peroxide leading to cleavage of the oxygen-oxygen bond and the formation of a
Probab=37.18 E-value=7 Score=25.94 Aligned_cols=21 Identities=10% Similarity=0.249 Sum_probs=17.1
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfES 68 (110)
-|+.|..++|..+.+.+-|+.
T Consensus 34 ~c~~C~~~~~~l~~~~~~~~~ 54 (140)
T cd02971 34 FTPVCTTELCAFRDLAEEFAK 54 (140)
T ss_pred CCCcCHHHHHHHHHHHHHHHH
Confidence 399999999999888777643
No 60
>cd02999 PDI_a_ERp44_like PDIa family, endoplasmic reticulum protein 44 (ERp44)-like subfamily; composed of uncharacterized PDI-like eukaryotic proteins containing only one redox active TRX (a) domain with a CXXS motif, similar to ERp44. CXXS is still a redox active motif; however, the mixed disulfide formed with the substrate is more stable than those formed by CXXC motif proteins. PDI-related proteins are usually involved in the oxidative protein folding in the ER by acting as catalysts and folding assistants. ERp44 is involved in thiol-mediated retention in the ER.
Probab=37.17 E-value=6.5 Score=26.13 Aligned_cols=19 Identities=16% Similarity=0.474 Sum_probs=17.1
Q ss_pred CcccccCCCCcchhhhhhh
Q 033829 49 CPLCKVTAPDIKSMQIHHD 67 (110)
Q Consensus 49 C~VCkaqmPD~Kt~k~HfE 67 (110)
|+.|+.++|....+...|.
T Consensus 30 C~~C~~~~p~l~~la~~~~ 48 (100)
T cd02999 30 CPFSASFRPHFNALSSMFP 48 (100)
T ss_pred CHHHHhHhHHHHHHHHHhc
Confidence 9999999999999888774
No 61
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=35.16 E-value=14 Score=27.54 Aligned_cols=16 Identities=19% Similarity=0.623 Sum_probs=12.0
Q ss_pred eeeeeCcccccCCCCc
Q 033829 44 HAKYECPLCKVTAPDI 59 (110)
Q Consensus 44 alk~~C~VCkaqmPD~ 59 (110)
...|+||+|..++-..
T Consensus 126 ~~~F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 126 ELNFTCPRCGAMLDYL 141 (158)
T ss_pred HcCCcCCCCCCEeeec
Confidence 3579999999886443
No 62
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.09 E-value=18 Score=31.58 Aligned_cols=15 Identities=27% Similarity=0.820 Sum_probs=11.5
Q ss_pred eeeeCcccccCCCCc
Q 033829 45 AKYECPLCKVTAPDI 59 (110)
Q Consensus 45 lk~~C~VCkaqmPD~ 59 (110)
-+++||||++..|-+
T Consensus 360 y~~~CPvCrt~iPPp 374 (374)
T COG5540 360 YSNKCPVCRTAIPPP 374 (374)
T ss_pred hcccCCccCCCCCCC
Confidence 357899999888853
No 63
>cd02969 PRX_like1 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF.
Probab=34.93 E-value=7.6 Score=27.45 Aligned_cols=22 Identities=18% Similarity=0.433 Sum_probs=19.7
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESK 69 (110)
-||.|..++|....+..+|+.+
T Consensus 36 ~Cp~c~~~~~~l~~l~~~~~~~ 57 (171)
T cd02969 36 HCPYVKAIEDRLNRLAKEYGAK 57 (171)
T ss_pred CCccHHHHHHHHHHHHHHHhhC
Confidence 5999999999999999999754
No 64
>cd03016 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes an
Probab=34.81 E-value=8.3 Score=28.82 Aligned_cols=21 Identities=14% Similarity=0.368 Sum_probs=18.5
Q ss_pred CcccccCCCCcchhhhhhhhC
Q 033829 49 CPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 49 C~VCkaqmPD~Kt~k~HfESK 69 (110)
||+|.++||....+.+.|+.+
T Consensus 38 cp~C~~el~~l~~~~~~f~~~ 58 (203)
T cd03016 38 TPVCTTELGAFAKLAPEFKKR 58 (203)
T ss_pred CCcCHHHHHHHHHHHHHHHHc
Confidence 999999999999888888754
No 65
>PRK09697 protein secretion protein GspB; Provisional
Probab=34.74 E-value=20 Score=27.48 Aligned_cols=25 Identities=24% Similarity=0.295 Sum_probs=22.4
Q ss_pred cCCCCcchhhhhhhhCCCCCCCChH
Q 033829 54 VTAPDIKSMQIHHDARHPKLPFDEA 78 (110)
Q Consensus 54 aqmPD~Kt~k~HfESKHPK~plp~E 78 (110)
...||.++.++||-=|-.-+|.|++
T Consensus 68 ~~tP~~~Qs~qH~~FKKqPLPV~E~ 92 (139)
T PRK09697 68 AETPAFKQSTQHYFFKKQPLPVVES 92 (139)
T ss_pred CCCcchhhhhhheeeecCCCCCccc
Confidence 5689999999999999888888887
No 66
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=34.68 E-value=16 Score=28.19 Aligned_cols=12 Identities=42% Similarity=1.173 Sum_probs=10.0
Q ss_pred eeeCcccccCCC
Q 033829 46 KYECPLCKVTAP 57 (110)
Q Consensus 46 k~~C~VCkaqmP 57 (110)
.|.||+|...|.
T Consensus 2 ~~~CP~C~~~l~ 13 (272)
T PRK11088 2 SYQCPLCHQPLT 13 (272)
T ss_pred cccCCCCCcchh
Confidence 378999998884
No 67
>TIGR02661 MauD methylamine dehydrogenase accessory protein MauD. This protein, MauD, appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulfide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulfide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded.
Probab=33.61 E-value=7.2 Score=28.78 Aligned_cols=17 Identities=41% Similarity=0.802 Sum_probs=13.8
Q ss_pred eCcccccCCCCcchhhh
Q 033829 48 ECPLCKVTAPDIKSMQI 64 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~ 64 (110)
-||.|+.++|+...+..
T Consensus 85 wCp~C~~~lp~l~~~~~ 101 (189)
T TIGR02661 85 SCPVCDKLFPIIKSIAR 101 (189)
T ss_pred CChhHHHHHHHHHHHHH
Confidence 59999999998876543
No 68
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.41 E-value=26 Score=28.74 Aligned_cols=31 Identities=29% Similarity=0.537 Sum_probs=21.4
Q ss_pred HhhCCCCcccccccccccccceeeeeCcccccCCCCc
Q 033829 23 TTNRGGGKAGMADRTGREKGGHAKYECPLCKVTAPDI 59 (110)
Q Consensus 23 ~tN~GGGkaG~~dR~g~~k~galk~~C~VCkaqmPD~ 59 (110)
..|.|++..|--+|-| -.|.|.||..++=|+
T Consensus 30 ~~~~~~~~~~~~~~~~------~~FdCNICLd~akdP 60 (230)
T KOG0823|consen 30 KENNGTIEVGGRNRDG------GFFDCNICLDLAKDP 60 (230)
T ss_pred ccccccccccCccCCC------CceeeeeeccccCCC
Confidence 3466666666555555 478999998888776
No 69
>PRK15000 peroxidase; Provisional
Probab=32.96 E-value=9.3 Score=28.88 Aligned_cols=22 Identities=9% Similarity=0.007 Sum_probs=18.7
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESK 69 (110)
-|++|.++||....+.+-|+.+
T Consensus 46 ~t~vC~~El~~l~~~~~~f~~~ 67 (200)
T PRK15000 46 FTFVCPSELIAFDKRYEEFQKR 67 (200)
T ss_pred CCCCCHHHHHHHHHHHHHHHHC
Confidence 3899999999999888888754
No 70
>cd03014 PRX_Atyp2cys Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial periplasmic peroxidase which differs from other PRXs in that it shows substrate specificity toward alkyl hydroperoxides over hydrogen peroxide. As with all other PRXs, the peroxidatic cysteine (N-terminal) of Tpx is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Tpx is able to resolve this intermediate by forming an intramolecular disulfide bond with a conserved C-terminal cysteine (the resolving cysteine), which can then be reduced by thioredoxin. This differs from the typical 2-cys PRX which resolves the oxidized cysteine by forming an intermolecular disulfide bond with the resolving cysteine from the other subunit of the homodimer. Atypical 2-cys PRX homodimers have a loop-based
Probab=32.42 E-value=7.6 Score=26.32 Aligned_cols=39 Identities=15% Similarity=0.228 Sum_probs=23.4
Q ss_pred CCCCcccccccccccccceeee----eCcccccCCCCcchhhhhh
Q 033829 26 RGGGKAGMADRTGREKGGHAKY----ECPLCKVTAPDIKSMQIHH 66 (110)
Q Consensus 26 ~GGGkaG~~dR~g~~k~galk~----~C~VCkaqmPD~Kt~k~Hf 66 (110)
.-|..--|.|-.| +---+.| -|+.|+.+||....+.+-|
T Consensus 14 ~~g~~~~l~~~~g--k~vvl~f~~~~~c~~C~~e~~~l~~~~~~~ 56 (143)
T cd03014 14 SDLSEVSLADFAG--KVKVISVFPSIDTPVCATQTKRFNKEAAKL 56 (143)
T ss_pred CCCcEEeHHHhCC--CeEEEEEEcCCCCCcCHHHHHHHHHHHHhc
Confidence 3344555555443 2333443 2899999999877665554
No 71
>cd02956 ybbN ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.
Probab=32.38 E-value=7.6 Score=24.45 Aligned_cols=21 Identities=14% Similarity=0.186 Sum_probs=17.4
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfES 68 (110)
-|+.|+.++|....+...|..
T Consensus 23 wC~~C~~~~~~~~~~~~~~~~ 43 (96)
T cd02956 23 RSPPSKELLPLLERLAEEYQG 43 (96)
T ss_pred CChHHHHHHHHHHHHHHHhCC
Confidence 399999999998888877753
No 72
>TIGR03137 AhpC peroxiredoxin. This gene contains two invariant cysteine residues, one near the N-terminus and one near the C-terminus, each followed immediately by a proline residue.
Probab=32.35 E-value=9.3 Score=28.12 Aligned_cols=27 Identities=7% Similarity=0.004 Sum_probs=20.7
Q ss_pred cceeeee----CcccccCCCCcchhhhhhhh
Q 033829 42 GGHAKYE----CPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 42 ~galk~~----C~VCkaqmPD~Kt~k~HfES 68 (110)
.--+.|- |++|..+||....+..-|+.
T Consensus 33 ~vvl~F~p~~~cp~C~~el~~l~~~~~~~~~ 63 (187)
T TIGR03137 33 WSVFFFYPADFTFVCPTELEDLADKYAELKK 63 (187)
T ss_pred EEEEEEECCCcCCcCHHHHHHHHHHHHHHHh
Confidence 3446663 99999999999887777754
No 73
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=32.06 E-value=15 Score=24.19 Aligned_cols=16 Identities=25% Similarity=0.515 Sum_probs=12.5
Q ss_pred eCcccccCCCCcchhh
Q 033829 48 ECPLCKVTAPDIKSMQ 63 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k 63 (110)
+|.|||..+++--...
T Consensus 3 ~CvVCKqpi~~a~~v~ 18 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVE 18 (54)
T ss_pred eeeeeCCccCcceEEE
Confidence 6999999999864443
No 74
>COG0526 TrxA Thiol-disulfide isomerase and thioredoxins [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]
Probab=31.65 E-value=14 Score=21.46 Aligned_cols=23 Identities=22% Similarity=0.466 Sum_probs=19.4
Q ss_pred eeeCcccccCCCCcchhhhhhhh
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfES 68 (110)
..-|+.|+..+|....+..-+..
T Consensus 41 ~~~C~~C~~~~~~l~~~~~~~~~ 63 (127)
T COG0526 41 APWCPPCRAEAPLLEELAEEYGG 63 (127)
T ss_pred cCcCHHHHhhchhHHHHHHHhcC
Confidence 46799999999999888877765
No 75
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=31.45 E-value=20 Score=27.29 Aligned_cols=15 Identities=20% Similarity=0.620 Sum_probs=12.0
Q ss_pred eeeeCcccccCCCCc
Q 033829 45 AKYECPLCKVTAPDI 59 (110)
Q Consensus 45 lk~~C~VCkaqmPD~ 59 (110)
..|.||+|..++--.
T Consensus 135 ~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 135 YGFRCPQCGEMLEEY 149 (178)
T ss_pred cCCcCCCCCCCCeec
Confidence 479999999888653
No 76
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=31.20 E-value=17 Score=27.04 Aligned_cols=24 Identities=13% Similarity=0.270 Sum_probs=16.8
Q ss_pred eeeeeCcccccCCCCc---chhhhhhh
Q 033829 44 HAKYECPLCKVTAPDI---KSMQIHHD 67 (110)
Q Consensus 44 alk~~C~VCkaqmPD~---Kt~k~HfE 67 (110)
-+-|.||+|...-|.. +.++.++.
T Consensus 44 ffdy~CphC~~~~~~l~~~~~~~~~~~ 70 (207)
T PRK10954 44 FFSFYCPHCYQFEEVYHVSDNVKKKLP 70 (207)
T ss_pred EeCCCCccHHHhcccccchHHHHHhCC
Confidence 4668999999877654 55565543
No 77
>cd03010 TlpA_like_DsbE TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c maturation (Ccm) factor with a redox active CXXC motif. Assembly of cytochrome c requires the ligation of heme to reduced thiols of the apocytochrome. In bacteria, this assembly occurs in the periplasm. The reductase activity of DsbE in the oxidizing environment of the periplasm is crucial in the maturation of cytochrome c.
Probab=31.20 E-value=5.9 Score=26.31 Aligned_cols=17 Identities=18% Similarity=0.472 Sum_probs=13.8
Q ss_pred eCcccccCCCCcchhhh
Q 033829 48 ECPLCKVTAPDIKSMQI 64 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~ 64 (110)
-|+.|+.++|....+.+
T Consensus 36 ~C~~C~~~~~~l~~l~~ 52 (127)
T cd03010 36 WCAPCREEHPVLMALAR 52 (127)
T ss_pred cCHHHHHHHHHHHHHHH
Confidence 59999999998877643
No 78
>PTZ00056 glutathione peroxidase; Provisional
Probab=30.74 E-value=10 Score=28.53 Aligned_cols=22 Identities=14% Similarity=0.298 Sum_probs=19.1
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESK 69 (110)
-|+.|+..||....+...|..+
T Consensus 50 wC~~C~~e~p~L~~l~~~~~~~ 71 (199)
T PTZ00056 50 KCGLTKKHVDQMNRLHSVFNPL 71 (199)
T ss_pred CCCChHHHHHHHHHHHHHHhcC
Confidence 4999999999999998888764
No 79
>PRK13599 putative peroxiredoxin; Provisional
Probab=30.50 E-value=11 Score=29.04 Aligned_cols=22 Identities=9% Similarity=0.149 Sum_probs=18.5
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESK 69 (110)
=||+|.++||....+..-|+.+
T Consensus 40 ~tpvCt~El~~l~~~~~~f~~~ 61 (215)
T PRK13599 40 FTPVCTTEFVEFARKANDFKEL 61 (215)
T ss_pred CCCcCHHHHHHHHHHHHHHHHC
Confidence 3999999999988888877654
No 80
>PRK10382 alkyl hydroperoxide reductase subunit C; Provisional
Probab=30.49 E-value=11 Score=28.56 Aligned_cols=26 Identities=8% Similarity=0.027 Sum_probs=21.1
Q ss_pred ceeeee----CcccccCCCCcchhhhhhhh
Q 033829 43 GHAKYE----CPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 43 galk~~----C~VCkaqmPD~Kt~k~HfES 68 (110)
--|.|- |++|..+||....+.+.|+.
T Consensus 34 vvL~F~P~~~~p~C~~el~~l~~~~~~f~~ 63 (187)
T PRK10382 34 SVFFFYPADFTFVCPTELGDVADHYEELQK 63 (187)
T ss_pred EEEEEECCCCCCcCHHHHHHHHHHHHHHHh
Confidence 346655 99999999999988888864
No 81
>cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.
Probab=30.07 E-value=12 Score=22.69 Aligned_cols=20 Identities=20% Similarity=0.677 Sum_probs=17.6
Q ss_pred eCcccccCCCCcchhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHD 67 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfE 67 (110)
-|+.|..++|..+.+.+-|+
T Consensus 30 ~C~~C~~~~~~l~~~~~~~~ 49 (116)
T cd02966 30 WCPPCRAEMPELEALAKEYK 49 (116)
T ss_pred cChhHHHHhHHHHHHHHHhC
Confidence 69999999999999887775
No 82
>PRK13728 conjugal transfer protein TrbB; Provisional
Probab=29.57 E-value=9.5 Score=29.51 Aligned_cols=18 Identities=28% Similarity=0.700 Sum_probs=16.3
Q ss_pred CcccccCCCCcchhhhhh
Q 033829 49 CPLCKVTAPDIKSMQIHH 66 (110)
Q Consensus 49 C~VCkaqmPD~Kt~k~Hf 66 (110)
||.|+..||..+.+.+-|
T Consensus 81 Cp~C~~e~P~L~~l~~~~ 98 (181)
T PRK13728 81 CPYCHQFDPVLKQLAQQY 98 (181)
T ss_pred CHhHHHHHHHHHHHHHHc
Confidence 999999999999987775
No 83
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=29.43 E-value=22 Score=22.84 Aligned_cols=33 Identities=15% Similarity=0.308 Sum_probs=19.1
Q ss_pred eeeCcccccCCCCcc-----------hhhhhhhhCCCCCCCChH
Q 033829 46 KYECPLCKVTAPDIK-----------SMQIHHDARHPKLPFDEA 78 (110)
Q Consensus 46 k~~C~VCkaqmPD~K-----------t~k~HfESKHPK~plp~E 78 (110)
-|.||+|...|-||= ++.++++..+...|+.-+
T Consensus 4 ~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~ 47 (73)
T PF04564_consen 4 EFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQ 47 (73)
T ss_dssp GGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-S
T ss_pred ccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCC
Confidence 378999999998873 334455555666666543
No 84
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=27.04 E-value=36 Score=30.51 Aligned_cols=28 Identities=39% Similarity=0.739 Sum_probs=26.3
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCC
Q 033829 46 KYECPLCKVTAPDIKSMQIHHDARHPKL 73 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt~k~HfESKHPK~ 73 (110)
-|+||.|-...|.+.+|..|..-+|.+.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~d 290 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKD 290 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccC
Confidence 4899999999999999999999999984
No 85
>smart00746 TRASH metallochaperone-like domain.
Probab=26.11 E-value=38 Score=16.46 Aligned_cols=10 Identities=20% Similarity=0.697 Sum_probs=7.9
Q ss_pred CcccccCCCC
Q 033829 49 CPLCKVTAPD 58 (110)
Q Consensus 49 C~VCkaqmPD 58 (110)
|++|...+.+
T Consensus 1 c~~C~~~~~~ 10 (39)
T smart00746 1 CSFCGKDIYN 10 (39)
T ss_pred CCCCCCCccC
Confidence 8899888854
No 86
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=26.03 E-value=23 Score=22.81 Aligned_cols=11 Identities=36% Similarity=1.056 Sum_probs=8.4
Q ss_pred eeeCcccccCC
Q 033829 46 KYECPLCKVTA 56 (110)
Q Consensus 46 k~~C~VCkaqm 56 (110)
.|+||+|.+.+
T Consensus 2 ~~~CP~CG~~i 12 (54)
T TIGR01206 2 QFECPDCGAEI 12 (54)
T ss_pred ccCCCCCCCEE
Confidence 57899998754
No 87
>PRK15412 thiol:disulfide interchange protein DsbE; Provisional
Probab=25.85 E-value=9.2 Score=27.97 Aligned_cols=16 Identities=19% Similarity=0.640 Sum_probs=13.8
Q ss_pred eCcccccCCCCcchhh
Q 033829 48 ECPLCKVTAPDIKSMQ 63 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k 63 (110)
-|+.|+.+||..+.+.
T Consensus 79 wC~~C~~e~p~l~~l~ 94 (185)
T PRK15412 79 WCPTCRAEHQYLNQLS 94 (185)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 5999999999987764
No 88
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=25.72 E-value=31 Score=26.76 Aligned_cols=16 Identities=31% Similarity=0.607 Sum_probs=11.4
Q ss_pred eeeCcccccCCCCcch
Q 033829 46 KYECPLCKVTAPDIKS 61 (110)
Q Consensus 46 k~~C~VCkaqmPD~Kt 61 (110)
+++||||.....-.+.
T Consensus 5 ~~~CPvC~~~F~~~~v 20 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKV 20 (214)
T ss_pred ceECCCCCCeeeeeEE
Confidence 6899999876555443
No 89
>PRK13190 putative peroxiredoxin; Provisional
Probab=25.37 E-value=15 Score=27.54 Aligned_cols=21 Identities=10% Similarity=0.132 Sum_probs=17.1
Q ss_pred CcccccCCCCcchhhhhhhhC
Q 033829 49 CPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 49 C~VCkaqmPD~Kt~k~HfESK 69 (110)
||+|..+||....+..-|+.+
T Consensus 40 cp~C~~El~~l~~~~~~f~~~ 60 (202)
T PRK13190 40 TPVCTTEFIAFSRRYEDFKKL 60 (202)
T ss_pred CCCCHHHHHHHHHHHHHHHHC
Confidence 999999999888777666644
No 90
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=25.11 E-value=29 Score=18.53 Aligned_cols=10 Identities=40% Similarity=1.192 Sum_probs=7.9
Q ss_pred eeeeCccccc
Q 033829 45 AKYECPLCKV 54 (110)
Q Consensus 45 lk~~C~VCka 54 (110)
-.|.|++|.-
T Consensus 13 k~~~C~~C~k 22 (26)
T PF13465_consen 13 KPYKCPYCGK 22 (26)
T ss_dssp SSEEESSSSE
T ss_pred CCCCCCCCcC
Confidence 4599999953
No 91
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=24.56 E-value=15 Score=25.30 Aligned_cols=42 Identities=17% Similarity=0.273 Sum_probs=25.7
Q ss_pred hCCCCcccccccccccccceeee----eCcccccCCCCcchhhhhhhh
Q 033829 25 NRGGGKAGMADRTGREKGGHAKY----ECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 25 N~GGGkaG~~dR~g~~k~galk~----~C~VCkaqmPD~Kt~k~HfES 68 (110)
+.-|..--|.+=.| +.--+.| -|++|..+++....+.+.|..
T Consensus 17 ~~~G~~~~l~~~~g--k~~ll~f~~~~~~p~C~~~~~~l~~~~~~~~~ 62 (154)
T PRK09437 17 DQDGEQVSLTDFQG--QRVLVYFYPKAMTPGCTVQACGLRDNMDELKK 62 (154)
T ss_pred CCCCCEEeHHHhCC--CCEEEEEECCCCCCchHHHHHHHHHHHHHHHH
Confidence 33444444444333 3344555 399999999887777777654
No 92
>cd02948 TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which
Probab=24.40 E-value=13 Score=24.45 Aligned_cols=20 Identities=20% Similarity=0.313 Sum_probs=16.8
Q ss_pred eCcccccCCCCcchhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHD 67 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfE 67 (110)
-|+.|+.++|-...+...|.
T Consensus 28 wC~~Ck~~~p~l~~~~~~~~ 47 (102)
T cd02948 28 WCGPCKAVVSLFKKIKNELG 47 (102)
T ss_pred cCHhHHHHhHHHHHHHHHcC
Confidence 49999999998888777664
No 93
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=24.24 E-value=26 Score=20.75 Aligned_cols=15 Identities=33% Similarity=0.654 Sum_probs=10.7
Q ss_pred CcccccCCCCcchhh
Q 033829 49 CPLCKVTAPDIKSMQ 63 (110)
Q Consensus 49 C~VCkaqmPD~Kt~k 63 (110)
||||...+-||-++.
T Consensus 1 CpiC~~~~~~Pv~l~ 15 (42)
T PF15227_consen 1 CPICLDLFKDPVSLP 15 (42)
T ss_dssp ETTTTSB-SSEEE-S
T ss_pred CCccchhhCCccccC
Confidence 889998888887763
No 94
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=24.11 E-value=31 Score=20.12 Aligned_cols=13 Identities=23% Similarity=0.815 Sum_probs=9.4
Q ss_pred eCcccccCCCCcc
Q 033829 48 ECPLCKVTAPDIK 60 (110)
Q Consensus 48 ~C~VCkaqmPD~K 60 (110)
+||.|...|-...
T Consensus 1 ~CP~C~~~l~~~~ 13 (41)
T PF13453_consen 1 KCPRCGTELEPVR 13 (41)
T ss_pred CcCCCCcccceEE
Confidence 5999988776443
No 95
>PLN02412 probable glutathione peroxidase
Probab=24.07 E-value=19 Score=26.01 Aligned_cols=23 Identities=9% Similarity=0.205 Sum_probs=19.9
Q ss_pred eeCcccccCCCCcchhhhhhhhC
Q 033829 47 YECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 47 ~~C~VCkaqmPD~Kt~k~HfESK 69 (110)
..|+.|..+||..+.+.+-|..+
T Consensus 39 ~~C~~c~~e~~~l~~l~~~~~~~ 61 (167)
T PLN02412 39 SKCGLTDSNYKELNVLYEKYKEQ 61 (167)
T ss_pred CCCCChHHHHHHHHHHHHHHhhC
Confidence 36999999999999998888865
No 96
>TIGR00385 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily. Involved in the biogenesis of c-type cytochromes as well as in disulfide bond formation in some periplasmic proteins.
Probab=23.95 E-value=11 Score=27.02 Aligned_cols=16 Identities=25% Similarity=0.773 Sum_probs=13.1
Q ss_pred eCcccccCCCCcchhh
Q 033829 48 ECPLCKVTAPDIKSMQ 63 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k 63 (110)
-|+.|+.++|....+.
T Consensus 74 wC~~C~~~~p~l~~l~ 89 (173)
T TIGR00385 74 WCPPCRAEHPYLNELA 89 (173)
T ss_pred cCHHHHHHHHHHHHHH
Confidence 5999999999876654
No 97
>PF09654 DUF2396: Protein of unknown function (DUF2396); InterPro: IPR013472 These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N terminus.
Probab=23.77 E-value=28 Score=27.38 Aligned_cols=15 Identities=33% Similarity=0.977 Sum_probs=12.1
Q ss_pred eeeCcccccCCCCcc
Q 033829 46 KYECPLCKVTAPDIK 60 (110)
Q Consensus 46 k~~C~VCkaqmPD~K 60 (110)
-..||+|+.++|-.-
T Consensus 6 ei~CPhCRq~ipALt 20 (161)
T PF09654_consen 6 EIQCPHCRQTIPALT 20 (161)
T ss_pred cCcCchhhcccchhe
Confidence 467999999998654
No 98
>cd02968 SCO SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properti
Probab=23.58 E-value=14 Score=24.59 Aligned_cols=21 Identities=24% Similarity=0.572 Sum_probs=16.1
Q ss_pred eCc-ccccCCCCcchhhhhhhh
Q 033829 48 ECP-LCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 48 ~C~-VCkaqmPD~Kt~k~HfES 68 (110)
-|+ +|..++|..+.+.+-|..
T Consensus 33 ~C~~~C~~~l~~l~~~~~~~~~ 54 (142)
T cd02968 33 HCPDVCPTTLANLAQALKQLGA 54 (142)
T ss_pred CCcccCHHHHHHHHHHHHHhhH
Confidence 698 599999988887766644
No 99
>TIGR02652 conserved hypothetical protein TIGR02652, cyanobacterial. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end.
Probab=23.12 E-value=29 Score=27.34 Aligned_cols=15 Identities=27% Similarity=0.904 Sum_probs=12.1
Q ss_pred eeeCcccccCCCCcc
Q 033829 46 KYECPLCKVTAPDIK 60 (110)
Q Consensus 46 k~~C~VCkaqmPD~K 60 (110)
-..||+|+.++|-.-
T Consensus 9 ei~CPhCRQ~ipALt 23 (163)
T TIGR02652 9 EIRCPHCRQNIPALT 23 (163)
T ss_pred cCcCchhhcccchhe
Confidence 467999999998654
No 100
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=22.85 E-value=15 Score=24.25 Aligned_cols=19 Identities=32% Similarity=0.815 Sum_probs=14.2
Q ss_pred eeeeCcccccCCCCcchhh
Q 033829 45 AKYECPLCKVTAPDIKSMQ 63 (110)
Q Consensus 45 lk~~C~VCkaqmPD~Kt~k 63 (110)
.-|.||.|+...|..+.+.
T Consensus 13 ~D~~Cp~C~~~~~~l~~~~ 31 (154)
T cd03023 13 FDYNCGYCKKLAPELEKLL 31 (154)
T ss_pred ECCCChhHHHhhHHHHHHH
Confidence 3578999998887766643
No 101
>cd03004 PDI_a_ERdj5_C PDIa family, C-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains. This subfamily is composed of the three TRX domains located at the C-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation. Also included in the alignment is the single complete TRX domain of an uncharacterized protein from Tetraodon nigroviridis, which also contains a DnaJ domain at its N-terminus.
Probab=22.70 E-value=14 Score=23.65 Aligned_cols=20 Identities=15% Similarity=0.406 Sum_probs=17.5
Q ss_pred eCcccccCCCCcchhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHD 67 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfE 67 (110)
-|+.|+..+|....+...|.
T Consensus 30 wC~~C~~~~p~~~~~~~~~~ 49 (104)
T cd03004 30 WCGPCQALLPELRKAARALK 49 (104)
T ss_pred CCHHHHHHHHHHHHHHHHhc
Confidence 39999999999999988873
No 102
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=22.65 E-value=43 Score=22.82 Aligned_cols=17 Identities=29% Similarity=0.198 Sum_probs=13.2
Q ss_pred hhhhhhhhCCCCCCCCh
Q 033829 61 SMQIHHDARHPKLPFDE 77 (110)
Q Consensus 61 t~k~HfESKHPK~plp~ 77 (110)
....|||..||+...--
T Consensus 57 ~av~~FE~~HP~l~~~l 73 (85)
T PF14357_consen 57 EAVERFEASHPKLAGIL 73 (85)
T ss_pred HHHHHHHHhCCcHHHHH
Confidence 46789999999976443
No 103
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=22.64 E-value=36 Score=22.61 Aligned_cols=13 Identities=38% Similarity=0.797 Sum_probs=10.1
Q ss_pred eeeCcccccCCCC
Q 033829 46 KYECPLCKVTAPD 58 (110)
Q Consensus 46 k~~C~VCkaqmPD 58 (110)
.-.||.|.+.|-.
T Consensus 39 ~p~CPlC~s~M~~ 51 (59)
T PF14169_consen 39 EPVCPLCKSPMVS 51 (59)
T ss_pred CccCCCcCCcccc
Confidence 4589999988753
No 104
>cd02997 PDI_a_PDIR PDIa family, PDIR subfamily; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity.
Probab=22.63 E-value=19 Score=22.54 Aligned_cols=21 Identities=19% Similarity=0.393 Sum_probs=18.3
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfES 68 (110)
-|+.|+...|....+...+..
T Consensus 28 wC~~C~~~~~~~~~~~~~~~~ 48 (104)
T cd02997 28 WCGHCKKMKPEFTKAATELKE 48 (104)
T ss_pred CCHHHHHhCHHHHHHHHHHhh
Confidence 399999999999999888764
No 105
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.52 E-value=35 Score=24.76 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=8.7
Q ss_pred eeCcccccCC
Q 033829 47 YECPLCKVTA 56 (110)
Q Consensus 47 ~~C~VCkaqm 56 (110)
|.||.|..++
T Consensus 124 f~Cp~Cg~~l 133 (147)
T smart00531 124 FTCPRCGEEL 133 (147)
T ss_pred EECCCCCCEE
Confidence 9999998776
No 106
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=22.51 E-value=43 Score=22.04 Aligned_cols=14 Identities=36% Similarity=0.852 Sum_probs=11.4
Q ss_pred eCcccccCCCCcch
Q 033829 48 ECPLCKVTAPDIKS 61 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt 61 (110)
.|++|...+|..+.
T Consensus 5 HC~~CG~~Ip~~~~ 18 (59)
T PF09889_consen 5 HCPVCGKPIPPDES 18 (59)
T ss_pred cCCcCCCcCCcchh
Confidence 59999999997543
No 107
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=22.49 E-value=61 Score=19.22 Aligned_cols=20 Identities=30% Similarity=0.958 Sum_probs=16.6
Q ss_pred cccccccccceeeeeCcccc
Q 033829 34 ADRTGREKGGHAKYECPLCK 53 (110)
Q Consensus 34 ~dR~g~~k~galk~~C~VCk 53 (110)
.-|-|....|+-.|-|..|+
T Consensus 17 v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 17 VKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred ceeCCCCCCCCEeEecCcCC
Confidence 34777778999999999995
No 108
>cd03003 PDI_a_ERdj5_N PDIa family, N-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains. This subfamily is comprised of the first TRX domain of ERdj5 located after the DnaJ domain at the N-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation.
Probab=22.45 E-value=15 Score=23.54 Aligned_cols=21 Identities=24% Similarity=0.525 Sum_probs=18.2
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfES 68 (110)
-|+.|+.++|....+...++.
T Consensus 29 wC~~C~~~~p~~~~~a~~~~~ 49 (101)
T cd03003 29 RCSHCHDLAPTWREFAKEMDG 49 (101)
T ss_pred CChHHHHhHHHHHHHHHHhcC
Confidence 499999999999999888753
No 109
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=22.29 E-value=22 Score=24.51 Aligned_cols=19 Identities=26% Similarity=0.586 Sum_probs=13.9
Q ss_pred eeeeCcccccCCCCcchhh
Q 033829 45 AKYECPLCKVTAPDIKSMQ 63 (110)
Q Consensus 45 lk~~C~VCkaqmPD~Kt~k 63 (110)
.-|.||.|+..-+....+.
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~ 41 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWV 41 (178)
T ss_pred ECCCCcchhhhhHHHHHHH
Confidence 4588999998777665443
No 110
>cd03008 TryX_like_RdCVF Tryparedoxin (TryX)-like family, Rod-derived cone viability factor (RdCVF) subfamily; RdCVF is a thioredoxin (TRX)-like protein specifically expressed in photoreceptors. RdCVF was isolated and identified as a factor that supports cone survival in retinal cultures. Cone photoreceptor loss is responsible for the visual handicap resulting from the inherited disease, retinitis pigmentosa. RdCVF shows 33% similarity to TRX but does not exhibit any detectable thiol oxidoreductase activity.
Probab=22.09 E-value=17 Score=26.88 Aligned_cols=23 Identities=22% Similarity=0.502 Sum_probs=17.2
Q ss_pred eCcccccCCCCcchhhhhhhhCC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDARH 70 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESKH 70 (110)
-|+.|+..||....+..=+..++
T Consensus 36 WCppCr~e~P~L~~ly~~~~~~~ 58 (146)
T cd03008 36 VSPQCQLFAPKLKDFFVRLTDEF 58 (146)
T ss_pred CChhHHHHHHHHHHHHHHHHhhc
Confidence 49999999999987655444444
No 111
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=22.00 E-value=41 Score=19.74 Aligned_cols=9 Identities=33% Similarity=0.984 Sum_probs=6.5
Q ss_pred eeCcccccC
Q 033829 47 YECPLCKVT 55 (110)
Q Consensus 47 ~~C~VCkaq 55 (110)
|+||.|...
T Consensus 1 m~Cp~Cg~~ 9 (43)
T PF08271_consen 1 MKCPNCGSK 9 (43)
T ss_dssp ESBTTTSSS
T ss_pred CCCcCCcCC
Confidence 578888764
No 112
>cd03002 PDI_a_MPD1_like PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces cerevisiae MPD1 protein, which contains a single redox active TRX domain located at the N-terminus, and an ER retention signal at the C-terminus indicative of an ER-resident protein. MPD1 has been shown to suppress the maturation defect of carboxypeptidase Y caused by deletion of the yeast PDI1 gene. Other characterized members of this subfamily include the Aspergillus niger prpA protein and Giardia PDI-1. PrpA is non-essential to strain viability, however, its transcript level is induced by heterologous protein expression suggesting a possible role in oxidative protein folding during high protein production. Giardia PDI-1 has the ability to refold scrambled RNase and exhibits transglutaminase activity.
Probab=21.89 E-value=24 Score=22.48 Aligned_cols=20 Identities=25% Similarity=0.401 Sum_probs=16.8
Q ss_pred eCcccccCCCCcchhhhhhh
Q 033829 48 ECPLCKVTAPDIKSMQIHHD 67 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfE 67 (110)
-|+.|+..+|....+..-+.
T Consensus 29 wC~~C~~~~~~~~~~a~~~~ 48 (109)
T cd03002 29 WCGHCKNLKPEYAKAAKELD 48 (109)
T ss_pred CCHHHHhhChHHHHHHHHhc
Confidence 39999999999888877665
No 113
>PF14353 CpXC: CpXC protein
Probab=21.51 E-value=36 Score=23.64 Aligned_cols=36 Identities=11% Similarity=0.178 Sum_probs=25.1
Q ss_pred ceeeeeCcccccCCCCcchhhhhhhhCCCCCCCChH
Q 033829 43 GHAKYECPLCKVTAPDIKSMQIHHDARHPKLPFDEA 78 (110)
Q Consensus 43 galk~~C~VCkaqmPD~Kt~k~HfESKHPK~plp~E 78 (110)
--+.|+||.|.....=.=.+--|...++--.-+.|+
T Consensus 35 ~l~~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 35 SLFSFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred CcCEEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 447899999998776666666677776655544444
No 114
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=21.16 E-value=39 Score=21.13 Aligned_cols=10 Identities=30% Similarity=1.139 Sum_probs=6.1
Q ss_pred eeeCcccccC
Q 033829 46 KYECPLCKVT 55 (110)
Q Consensus 46 k~~C~VCkaq 55 (110)
.+.||+|.+.
T Consensus 34 ~w~CP~C~a~ 43 (47)
T PF00301_consen 34 DWVCPVCGAP 43 (47)
T ss_dssp T-B-TTTSSB
T ss_pred CCcCcCCCCc
Confidence 5899999763
No 115
>PLN00219 predicted protein; Provisional
Probab=21.14 E-value=40 Score=22.86 Aligned_cols=24 Identities=29% Similarity=0.480 Sum_probs=18.9
Q ss_pred cCCCCcchhhhhhhhCCCCCCCCh
Q 033829 54 VTAPDIKSMQIHHDARHPKLPFDE 77 (110)
Q Consensus 54 aqmPD~Kt~k~HfESKHPK~plp~ 77 (110)
+.|||.|.-..-+-|.||.+.|+.
T Consensus 34 trmpdskerskthlsqhpeesldq 57 (65)
T PLN00219 34 TRMPDSKERSKTHLSQHPEESLDQ 57 (65)
T ss_pred hhCCchhhhhhhhhhhCchhhhhh
Confidence 679999888777788898776653
No 116
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=21.10 E-value=36 Score=26.36 Aligned_cols=21 Identities=33% Similarity=0.773 Sum_probs=13.5
Q ss_pred cccccccccccceeeeeCcccccCC
Q 033829 32 GMADRTGREKGGHAKYECPLCKVTA 56 (110)
Q Consensus 32 G~~dR~g~~k~galk~~C~VCkaqm 56 (110)
++.||....+ .|.|+||.-..
T Consensus 124 ~~Le~~~~~~----~~vC~vCGy~~ 144 (166)
T COG1592 124 GLLERLEEGK----VWVCPVCGYTH 144 (166)
T ss_pred HHHHhhhcCC----EEEcCCCCCcc
Confidence 4556664322 99999997544
No 117
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=21.02 E-value=38 Score=21.36 Aligned_cols=10 Identities=30% Similarity=1.125 Sum_probs=8.0
Q ss_pred eeeeCccccc
Q 033829 45 AKYECPLCKV 54 (110)
Q Consensus 45 lk~~C~VCka 54 (110)
..+.||+|.+
T Consensus 33 ~~w~CP~C~a 42 (50)
T cd00730 33 DDWVCPVCGA 42 (50)
T ss_pred CCCCCCCCCC
Confidence 3689999975
No 118
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=20.85 E-value=56 Score=27.42 Aligned_cols=32 Identities=25% Similarity=0.361 Sum_probs=29.0
Q ss_pred eeeeCcccccCCCCcchhhhhhhhCCCCCCCC
Q 033829 45 AKYECPLCKVTAPDIKSMQIHHDARHPKLPFD 76 (110)
Q Consensus 45 lk~~C~VCkaqmPD~Kt~k~HfESKHPK~plp 76 (110)
-.|.|.-|.-+.+.+..|-+|...-||-+|+=
T Consensus 211 kl~vcedcg~t~~~~e~~~~h~~~~hp~Spal 242 (267)
T KOG3576|consen 211 KLYVCEDCGYTSERPEVYYLHLKLHHPFSPAL 242 (267)
T ss_pred heeeecccCCCCCChhHHHHHHHhcCCCCHHH
Confidence 56999999999999999999999999987753
No 119
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=20.65 E-value=46 Score=27.30 Aligned_cols=35 Identities=29% Similarity=0.376 Sum_probs=27.7
Q ss_pred ccceeeeeCcccccCCCCcchhhhhhhhCCCCCCC
Q 033829 41 KGGHAKYECPLCKVTAPDIKSMQIHHDARHPKLPF 75 (110)
Q Consensus 41 k~galk~~C~VCkaqmPD~Kt~k~HfESKHPK~pl 75 (110)
|--.-+|.|-.|+++-.+..+|..|-+-|--++-+
T Consensus 48 knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~ 82 (222)
T COG5246 48 KNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENS 82 (222)
T ss_pred hcCCCcEEeeeeccccccHHHHHHhhccchhhhhH
Confidence 33445899999999999999999999876554443
No 120
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=20.55 E-value=31 Score=21.10 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=6.5
Q ss_pred eCcccccCCCCcc
Q 033829 48 ECPLCKVTAPDIK 60 (110)
Q Consensus 48 ~C~VCkaqmPD~K 60 (110)
.||||...+.+.+
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999987766543
No 121
>PRK13191 putative peroxiredoxin; Provisional
Probab=20.31 E-value=22 Score=27.29 Aligned_cols=22 Identities=9% Similarity=0.073 Sum_probs=18.3
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 033829 48 ECPLCKVTAPDIKSMQIHHDAR 69 (110)
Q Consensus 48 ~C~VCkaqmPD~Kt~k~HfESK 69 (110)
=|++|.+.||....+...|+.+
T Consensus 45 ftpvC~tEl~~l~~~~~ef~~~ 66 (215)
T PRK13191 45 FTPVCTTEFYSFAKKYEEFKKL 66 (215)
T ss_pred CCCcCHHHHHHHHHHHHHHHHC
Confidence 4999999999988888887643
No 122
>PF06974 DUF1298: Protein of unknown function (DUF1298); InterPro: IPR009721 This entry represents the C terminus (approximately 170 residues) of a number of hypothetical plant proteins. O-acyltransferase WSD1 is a bifunctional wax ester synthase/diacylglycerol acyltransferase, which is involved in cuticular wax biosynthesis [].; GO: 0004144 diacylglycerol O-acyltransferase activity
Probab=20.18 E-value=69 Score=23.06 Aligned_cols=28 Identities=11% Similarity=0.163 Sum_probs=24.3
Q ss_pred ccceeeeeCcccccCCCCcchhhhhhhh
Q 033829 41 KGGHAKYECPLCKVTAPDIKSMQIHHDA 68 (110)
Q Consensus 41 k~galk~~C~VCkaqmPD~Kt~k~HfES 68 (110)
-+|.+.+-...|...+||+..+-.+||.
T Consensus 118 Y~g~l~~gi~ad~~~vpD~~~l~~~~~~ 145 (153)
T PF06974_consen 118 YAGKLDFGIVADRDAVPDPQRLADCFEE 145 (153)
T ss_pred eCCEEEEEEEEccccCCCHHHHHHHHHH
Confidence 3577888999999999999999999873
No 123
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=20.15 E-value=48 Score=26.03 Aligned_cols=23 Identities=35% Similarity=0.800 Sum_probs=20.6
Q ss_pred eeeeCcccccCCCCcchhhhhhh
Q 033829 45 AKYECPLCKVTAPDIKSMQIHHD 67 (110)
Q Consensus 45 lk~~C~VCkaqmPD~Kt~k~HfE 67 (110)
.||+||-|...-=+.--+++|-+
T Consensus 16 ~KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 16 IKYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hhccCCCCCCccccchhhhhccC
Confidence 48999999999888888999987
No 124
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=20.06 E-value=55 Score=18.38 Aligned_cols=10 Identities=40% Similarity=1.198 Sum_probs=7.5
Q ss_pred eeeCcccccC
Q 033829 46 KYECPLCKVT 55 (110)
Q Consensus 46 k~~C~VCkaq 55 (110)
++.||.|.++
T Consensus 2 ~~~CP~C~~~ 11 (38)
T TIGR02098 2 RIQCPNCKTS 11 (38)
T ss_pred EEECCCCCCE
Confidence 5788888764
Done!