Query psy8227
Match_columns 125
No_of_seqs 112 out of 148
Neff 2.6
Searched_HMMs 46136
Date Fri Aug 16 21:56:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8227.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8227hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3490|consensus 99.9 9.5E-26 2.1E-30 167.2 1.9 52 73-125 1-52 (111)
2 cd07973 Spt4 Transcription elo 99.8 5.6E-21 1.2E-25 137.5 2.1 48 78-125 1-48 (98)
3 PF06093 Spt4: Spt4/RpoE2 zinc 99.8 3.4E-20 7.4E-25 128.3 -0.2 45 80-125 1-45 (77)
4 COG5204 SPT4 Transcription elo 99.6 2.7E-16 5.8E-21 116.8 0.6 44 81-125 10-53 (112)
5 PRK06393 rpoE DNA-directed RNA 96.1 0.0025 5.4E-08 43.8 1.0 23 78-105 3-25 (64)
6 PRK08351 DNA-directed RNA poly 95.8 0.0039 8.5E-08 42.3 0.9 21 80-105 3-23 (61)
7 PRK12380 hydrogenase nickel in 87.1 1.6 3.4E-05 31.6 4.8 71 18-114 29-104 (113)
8 PF02591 DUF164: Putative zinc 85.8 0.43 9.4E-06 30.2 1.2 27 81-107 23-56 (56)
9 PF01155 HypA: Hydrogenase exp 73.5 4.3 9.3E-05 29.1 3.1 72 17-114 28-104 (113)
10 PRK06266 transcription initiat 73.5 1.4 3E-05 34.3 0.6 37 80-116 117-155 (178)
11 TIGR00373 conserved hypothetic 73.4 1.3 2.8E-05 33.6 0.4 37 80-116 109-147 (158)
12 PRK00398 rpoP DNA-directed RNA 71.8 1.3 2.7E-05 27.1 -0.0 36 81-116 4-40 (46)
13 smart00531 TFIIE Transcription 68.6 2.2 4.8E-05 31.6 0.7 37 80-116 99-142 (147)
14 COG0375 HybF Zn finger protein 64.6 3.6 7.8E-05 30.9 1.2 72 17-114 28-104 (115)
15 TIGR00100 hypA hydrogenase nic 63.5 18 0.00039 26.1 4.6 72 17-114 28-104 (115)
16 COG1579 Zn-ribbon protein, pos 61.5 4.6 9.9E-05 33.5 1.3 30 80-109 197-233 (239)
17 PF09845 DUF2072: Zn-ribbon co 61.1 3.6 7.7E-05 31.8 0.6 22 82-105 3-27 (131)
18 COG1645 Uncharacterized Zn-fin 61.0 3.5 7.5E-05 31.7 0.5 20 81-104 29-51 (131)
19 PF08916 Phe_ZIP: Phenylalanin 58.6 15 0.00032 24.9 3.2 35 3-37 15-49 (59)
20 COG3364 Zn-ribbon containing p 57.5 5.2 0.00011 30.5 0.9 24 82-105 4-28 (112)
21 PF07754 DUF1610: Domain of un 54.5 5.7 0.00012 22.7 0.6 22 83-104 1-23 (24)
22 TIGR00412 redox_disulf_2 small 51.7 5.1 0.00011 26.0 0.1 13 94-106 4-16 (76)
23 COG2093 DNA-directed RNA polym 51.3 5.7 0.00012 27.7 0.3 24 79-105 3-26 (64)
24 cd02973 TRX_GRX_like Thioredox 50.6 6.6 0.00014 23.9 0.5 14 94-107 5-18 (67)
25 PRK02935 hypothetical protein; 50.5 7.7 0.00017 29.4 0.9 29 82-112 72-101 (110)
26 PRK00481 NAD-dependent deacety 49.7 9.8 0.00021 29.9 1.4 39 68-107 111-152 (242)
27 PF13192 Thioredoxin_3: Thiore 47.0 9.4 0.0002 24.7 0.8 12 97-108 7-18 (76)
28 PRK15103 paraquat-inducible me 45.9 9.2 0.0002 33.3 0.8 31 77-107 7-40 (419)
29 PRK11788 tetratricopeptide rep 44.3 8.7 0.00019 30.0 0.4 24 81-107 355-378 (389)
30 PRK14890 putative Zn-ribbon RN 42.4 12 0.00025 25.6 0.7 29 78-106 5-34 (59)
31 TIGR00155 pqiA_fam integral me 41.8 11 0.00025 32.5 0.8 31 78-108 11-44 (403)
32 KOG1946|consensus 40.8 19 0.00042 29.8 1.9 17 2-18 119-136 (240)
33 cd00350 rubredoxin_like Rubred 39.9 13 0.00029 21.5 0.6 22 82-104 3-24 (33)
34 PRK03681 hypA hydrogenase nick 39.4 12 0.00027 27.0 0.5 72 18-114 29-105 (114)
35 PRK03824 hypA hydrogenase nick 39.4 13 0.00028 27.7 0.6 51 59-114 54-125 (135)
36 PF11023 DUF2614: Protein of u 38.2 14 0.00031 28.1 0.7 30 83-114 72-102 (114)
37 COG3880 Modulator of heat shoc 38.2 12 0.00026 30.4 0.3 28 78-107 72-102 (176)
38 PF02201 SWIB: SWIB/MDM2 domai 36.6 26 0.00055 23.4 1.7 15 4-18 22-37 (76)
39 PRK00564 hypA hydrogenase nick 35.8 15 0.00032 26.7 0.5 72 18-114 29-106 (117)
40 cd03026 AhpF_NTD_C TRX-GRX-lik 34.9 16 0.00035 24.8 0.5 18 92-109 16-33 (89)
41 PRK00420 hypothetical protein; 34.6 12 0.00025 28.0 -0.2 28 81-111 24-54 (112)
42 PF02150 RNA_POL_M_15KD: RNA p 34.6 10 0.00022 22.6 -0.5 22 100-121 4-25 (35)
43 PF12898 Stc1: Stc1 domain; I 34.5 20 0.00044 24.7 1.0 21 78-98 48-68 (84)
44 smart00661 RPOL9 RNA polymeras 33.9 25 0.00054 21.1 1.2 23 82-104 2-27 (52)
45 PRK03564 formate dehydrogenase 32.4 20 0.00044 30.6 0.8 21 82-105 214-234 (309)
46 PF09369 DUF1998: Domain of un 31.6 14 0.0003 24.5 -0.3 7 97-103 77-83 (84)
47 KOG2324|consensus 30.5 24 0.00053 32.2 1.0 28 78-105 225-255 (457)
48 PRK06580 putative monovalent c 29.7 1.2E+02 0.0026 22.0 4.4 56 36-91 6-65 (103)
49 cd01410 SIRT7 SIRT7: Eukaryoti 28.6 38 0.00083 26.4 1.7 38 69-107 85-130 (206)
50 PRK15103 paraquat-inducible me 28.5 29 0.00064 30.3 1.1 29 76-107 217-245 (419)
51 KOG3806|consensus 28.3 33 0.00071 27.8 1.3 29 1-29 100-128 (177)
52 PF00462 Glutaredoxin: Glutare 28.2 13 0.00029 22.5 -0.8 13 95-107 4-16 (60)
53 cd01659 TRX_superfamily Thiore 27.5 21 0.00046 18.6 0.1 14 95-108 4-17 (69)
54 PRK12654 putative monovalent c 26.5 1.2E+02 0.0025 23.7 4.0 42 38-79 3-46 (151)
55 cd03419 GRX_GRXh_1_2_like Glut 26.0 19 0.00042 22.3 -0.3 16 94-109 4-19 (82)
56 COG4357 Zinc finger domain con 25.8 30 0.00064 26.2 0.6 29 77-105 59-88 (105)
57 PF13842 Tnp_zf-ribbon_2: DDE_ 25.0 23 0.00051 20.8 -0.1 26 81-107 1-26 (32)
58 smart00151 SWIB SWI complex, B 24.9 52 0.0011 22.0 1.6 15 4-18 22-37 (77)
59 TIGR02183 GRXA Glutaredoxin, G 24.8 29 0.00064 22.9 0.4 15 95-109 5-19 (86)
60 PRK06279 putative monovalent c 24.2 1.4E+02 0.0029 21.3 3.7 42 38-79 5-46 (100)
61 TIGR00375 conserved hypothetic 23.9 29 0.00062 30.3 0.2 47 70-118 229-278 (374)
62 cd01407 SIR2-fam SIR2 family o 23.6 52 0.0011 25.4 1.6 38 69-107 99-143 (218)
63 TIGR02180 GRX_euk Glutaredoxin 23.3 30 0.00064 21.4 0.2 15 94-108 3-17 (84)
64 TIGR00515 accD acetyl-CoA carb 23.3 46 0.001 27.9 1.4 36 72-109 20-57 (285)
65 PF13719 zinc_ribbon_5: zinc-r 23.2 18 0.00038 21.5 -0.8 14 99-112 4-17 (37)
66 PF09626 DHC: Dihaem cytochrom 22.9 70 0.0015 23.8 2.1 19 2-20 39-57 (120)
67 PF10139 Virul_Fac: Putative b 22.9 1.1E+02 0.0023 29.9 3.8 59 2-64 169-244 (854)
68 CHL00174 accD acetyl-CoA carbo 22.6 59 0.0013 27.8 1.9 37 72-110 32-70 (296)
69 COG2888 Predicted Zn-ribbon RN 22.5 31 0.00068 23.8 0.2 26 80-105 9-35 (61)
70 cd02947 TRX_family TRX family; 22.4 31 0.00067 20.4 0.1 15 94-108 16-30 (93)
71 TIGR00411 redox_disulf_1 small 22.4 35 0.00076 20.9 0.4 14 95-108 6-19 (82)
72 PF14851 FAM176: FAM176 family 22.2 1.7E+02 0.0038 22.9 4.2 37 10-57 11-47 (153)
73 TIGR02949 anti_SigH_actin anti 21.8 1.7E+02 0.0036 19.9 3.7 35 4-45 10-46 (84)
74 PF07297 DPM2: Dolichol phosph 21.7 1.9E+02 0.0042 20.4 4.1 26 28-53 4-29 (78)
75 cd01411 SIR2H SIR2H: Uncharact 21.3 51 0.0011 25.9 1.1 39 68-107 107-146 (225)
76 PF05381 Peptidase_C21: Tymovi 21.2 1.2E+02 0.0026 22.7 3.0 32 8-46 19-58 (104)
77 COG2995 PqiA Uncharacterized p 20.8 80 0.0017 28.7 2.4 34 75-110 215-248 (418)
78 cd01408 SIRT1 SIRT1: Eukaryoti 20.7 65 0.0014 25.5 1.6 38 69-107 106-150 (235)
79 COG0846 SIR2 NAD-dependent pro 20.3 50 0.0011 27.2 1.0 36 69-105 112-154 (250)
80 TIGR02196 GlrX_YruB Glutaredox 20.1 38 0.00082 19.8 0.2 13 95-107 5-17 (74)
No 1
>KOG3490|consensus
Probab=99.91 E-value=9.5e-26 Score=167.19 Aligned_cols=52 Identities=54% Similarity=1.025 Sum_probs=50.5
Q ss_pred cccccccccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227 73 LAKYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125 (125)
Q Consensus 73 VP~~~R~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd 125 (125)
+|+++|+|||||+||||||.+||+++|||||+ +|+|+||.|+|+||||||||
T Consensus 1 ~~~~~~~lRACllCs~Vkt~~~F~~dGC~Nc~-~l~mkgn~e~V~ecTS~nF~ 52 (111)
T KOG3490|consen 1 VPKDLRKLRACLLCSIVKTLNGFRKDGCENCP-MLNMKGNVENVYECTSPNFD 52 (111)
T ss_pred CcchhhhhhhhhhhhhhhhhhhhhhcCCCCch-hhhhccCcceeEEecCCCcc
Confidence 58889999999999999999999999999999 99999999999999999997
No 2
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=99.81 E-value=5.6e-21 Score=137.51 Aligned_cols=48 Identities=60% Similarity=1.097 Sum_probs=46.6
Q ss_pred ccccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227 78 RQARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125 (125)
Q Consensus 78 R~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd 125 (125)
|++|||+.|++|+|.+||..+|||||+.+|+|+||+++|+||||++|+
T Consensus 1 r~lrAC~~C~~I~~~~qf~~~gCpnC~~~l~~~g~~~~v~~~tT~~f~ 48 (98)
T cd07973 1 RGLRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFE 48 (98)
T ss_pred CCCchhccCCcccccccccCCCCCCCcchhccCCCccccccccCCCcc
Confidence 689999999999999999999999999999999999999999999996
No 3
>PF06093 Spt4: Spt4/RpoE2 zinc finger; InterPro: IPR022800 This entry consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 []. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles []. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in []. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. ; PDB: 2EXU_A 3H7H_A 3LPE_F 3P8B_A 1RYQ_A 3QQC_E.
Probab=99.77 E-value=3.4e-20 Score=128.33 Aligned_cols=45 Identities=58% Similarity=1.069 Sum_probs=39.6
Q ss_pred ccccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227 80 ARACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125 (125)
Q Consensus 80 LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd 125 (125)
||||+.|++|+|.+||+++||||| ++|+|+||+|++.+|||++|+
T Consensus 1 lrAC~~C~~i~t~~qF~~~gCpnC-~~l~~~~~~~~~~~~tT~~f~ 45 (77)
T PF06093_consen 1 LRACLRCRLIKTEDQFRDEGCPNC-PFLQMKGDRDRVSDCTTPNFE 45 (77)
T ss_dssp EEEETTT-BEECCCHHHHH--TTT-HHHH-TCHCHHCHCCEESSEE
T ss_pred CcccccCCcccCHhHccCCCCCCC-ccccccCCcCcccccCCCCCc
Confidence 799999999999999999999999 699999999999999999995
No 4
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=99.58 E-value=2.7e-16 Score=116.82 Aligned_cols=44 Identities=52% Similarity=1.041 Sum_probs=42.9
Q ss_pred cccccCCcccchhhhhhcCCCChhhhhhccCCcccccccccCCCC
Q psy8227 81 RACLGCSQIKTFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFD 125 (125)
Q Consensus 81 RACLlCsLVKT~dQF~~dGCpNCe~~L~Mkgn~drV~dCTS~nFd 125 (125)
||||.||||||.+.|.++|||||+ .|.|+|+-+.|.+||||.|+
T Consensus 10 RACl~Cgiv~t~n~F~~dGCpNc~-~l~~~~gV~~ve~~TSp~Fe 53 (112)
T COG5204 10 RACLGCGIVKTLNGFRKDGCPNCP-MLNMKGGVTNVEECTSPKFE 53 (112)
T ss_pred hhhhhcceeeecccccccCCCCCc-ccccccCccceeeecCcchH
Confidence 999999999999999999999998 89999999999999999996
No 5
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=96.07 E-value=0.0025 Score=43.76 Aligned_cols=23 Identities=26% Similarity=0.517 Sum_probs=19.3
Q ss_pred ccccccccCCcccchhhhhhcCCCChhh
Q psy8227 78 RQARACLGCSQIKTFDQFEFDGCDNCDE 105 (125)
Q Consensus 78 R~LRACLlCsLVKT~dQF~~dGCpNCe~ 105 (125)
+.++||..|..|.+ .+.||||.+
T Consensus 3 ~~~~AC~~C~~i~~-----~~~Cp~Cgs 25 (64)
T PRK06393 3 VQYRACKKCKRLTP-----EKTCPVHGD 25 (64)
T ss_pred chhhhHhhCCcccC-----CCcCCCCCC
Confidence 46899999999995 448999984
No 6
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=95.78 E-value=0.0039 Score=42.32 Aligned_cols=21 Identities=38% Similarity=0.784 Sum_probs=17.6
Q ss_pred ccccccCCcccchhhhhhcCCCChhh
Q psy8227 80 ARACLGCSQIKTFDQFEFDGCDNCDE 105 (125)
Q Consensus 80 LRACLlCsLVKT~dQF~~dGCpNCe~ 105 (125)
++||..|+.|.+.+ .||||.+
T Consensus 3 ~kAC~~C~~i~~~~-----~CP~Cgs 23 (61)
T PRK08351 3 EKACRHCHYITTED-----RCPVCGS 23 (61)
T ss_pred hhhhhhCCcccCCC-----cCCCCcC
Confidence 46999999999655 5999985
No 7
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=87.05 E-value=1.6 Score=31.60 Aligned_cols=71 Identities=20% Similarity=0.427 Sum_probs=44.7
Q ss_pred heeeecCc----chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCccccccccccccccccccccccCCcccchh
Q psy8227 18 VHVQVGRM----PESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFD 93 (125)
Q Consensus 18 ~~~~~~~~----~~~~~~~~~~~~~~~c~~~~flw~~v~~~~m~h~~s~~~~~~~s~~~VP~~~R~LRACLlCsLVKT~d 93 (125)
|+++||.+ ||+|..-|. +..-||--+.++..-- .+|... -|..|+-.-..+
T Consensus 29 V~l~iG~ls~v~pe~L~f~f~--------------------~~~~~T~~egA~L~I~-~vp~~~----~C~~Cg~~~~~~ 83 (113)
T PRK12380 29 VWLEIGALSCVEESAVRFSFE--------------------IVCHGTVAQGCDLHIV-YKPAQA----WCWDCSQVVEIH 83 (113)
T ss_pred EEEEEcCccccCHHHHHHHHH--------------------HHhCCCccCCCEEEEE-eeCcEE----EcccCCCEEecC
Confidence 78999987 666654332 1345777777766543 666654 499999555555
Q ss_pred hhhhcCCCChhhh-hhccCCcc
Q psy8227 94 QFEFDGCDNCDEF-LHMKNSRD 114 (125)
Q Consensus 94 QF~~dGCpNCe~~-L~Mkgn~d 114 (125)
++... ||+|.+. +++.+.++
T Consensus 84 ~~~~~-CP~Cgs~~~~i~~G~E 104 (113)
T PRK12380 84 QHDAQ-CPHCHGERLRVDTGDS 104 (113)
T ss_pred CcCcc-CcCCCCCCcEEccCCe
Confidence 44443 9999864 35554444
No 8
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=85.80 E-value=0.43 Score=30.21 Aligned_cols=27 Identities=30% Similarity=0.712 Sum_probs=22.1
Q ss_pred cccccCCcccchhhhhh--cC-----CCChhhhh
Q psy8227 81 RACLGCSQIKTFDQFEF--DG-----CDNCDEFL 107 (125)
Q Consensus 81 RACLlCsLVKT~dQF~~--dG-----CpNCe~~L 107 (125)
.+|..|.+..+.+.+.+ .+ ||||..+|
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 59999999999988865 23 99998765
No 9
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=73.49 E-value=4.3 Score=29.11 Aligned_cols=72 Identities=22% Similarity=0.505 Sum_probs=41.9
Q ss_pred hheeeecCc----chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCccccccccccccccccccccccCCcccch
Q psy8227 17 HVHVQVGRM----PESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTF 92 (125)
Q Consensus 17 ~~~~~~~~~----~~~~~~~~~~~~~~~c~~~~flw~~v~~~~m~h~~s~~~~~~~s~~~VP~~~R~LRACLlCsLVKT~ 92 (125)
-|++.||.+ ||+|..-|. ++.-||--+.++.+- ..+|... .|..|+-.-+.
T Consensus 28 ~V~l~iG~ls~V~pe~L~f~f~--------------------~~~~~T~~e~a~L~I-e~~p~~~----~C~~Cg~~~~~ 82 (113)
T PF01155_consen 28 KVRLEIGELSGVEPEALRFAFE--------------------VLAEGTILEGAELEI-EEVPARA----RCRDCGHEFEP 82 (113)
T ss_dssp EEEEEEETTS---HHHHHHHHH--------------------HHHCCSTTTT-EEEE-EEE--EE----EETTTS-EEEC
T ss_pred EEEEEECCcccCCHHHHHHHHH--------------------HHhCCCCccCCEEEE-EecCCcE----ECCCCCCEEec
Confidence 478999987 555543222 233566666665543 3566554 59999988888
Q ss_pred hhhhhcCCCChhhh-hhccCCcc
Q psy8227 93 DQFEFDGCDNCDEF-LHMKNSRD 114 (125)
Q Consensus 93 dQF~~dGCpNCe~~-L~Mkgn~d 114 (125)
+++. .-||+|.+. +++.+.++
T Consensus 83 ~~~~-~~CP~Cgs~~~~i~~G~e 104 (113)
T PF01155_consen 83 DEFD-FSCPRCGSPDVEIISGRE 104 (113)
T ss_dssp HHCC-HH-SSSSSS-EEEEESS-
T ss_pred CCCC-CCCcCCcCCCcEEccCCe
Confidence 8887 449999864 24444443
No 10
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=73.48 E-value=1.4 Score=34.28 Aligned_cols=37 Identities=27% Similarity=0.463 Sum_probs=29.7
Q ss_pred ccccccCCcccchhhhhhcC--CCChhhhhhccCCcccc
Q psy8227 80 ARACLGCSQIKTFDQFEFDG--CDNCDEFLHMKNSRDNV 116 (125)
Q Consensus 80 LRACLlCsLVKT~dQF~~dG--CpNCe~~L~Mkgn~drV 116 (125)
-=-|..|+.--|+++=...| ||+|.+.|....|.+.+
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~dn~~~~ 155 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEYDNSELI 155 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCCCCCeecccHHHH
Confidence 34599999888888866665 99999999887777654
No 11
>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=73.42 E-value=1.3 Score=33.57 Aligned_cols=37 Identities=16% Similarity=0.287 Sum_probs=29.7
Q ss_pred ccccccCCcccchhhhhhcC--CCChhhhhhccCCcccc
Q psy8227 80 ARACLGCSQIKTFDQFEFDG--CDNCDEFLHMKNSRDNV 116 (125)
Q Consensus 80 LRACLlCsLVKT~dQF~~dG--CpNCe~~L~Mkgn~drV 116 (125)
-=-|..|+.--|+++=...| ||+|...|....|.+.|
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~~dn~~~i 147 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAMELNFTCPRCGAMLDYLDNSEAI 147 (158)
T ss_pred eEECCCCCcEeeHHHHHHcCCcCCCCCCEeeeccCHHHH
Confidence 34599999888888876666 99999999888877654
No 12
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=71.76 E-value=1.3 Score=27.13 Aligned_cols=36 Identities=19% Similarity=0.378 Sum_probs=27.3
Q ss_pred cccccCCcccchhhhh-hcCCCChhhhhhccCCcccc
Q psy8227 81 RACLGCSQIKTFDQFE-FDGCDNCDEFLHMKNSRDNV 116 (125)
Q Consensus 81 RACLlCsLVKT~dQF~-~dGCpNCe~~L~Mkgn~drV 116 (125)
-.|..|+-..+.++.. .--||+|..-+.++.++..|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~~~v 40 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKERPPVV 40 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccCCCcc
Confidence 3588999888777776 46799999877777766644
No 13
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=68.63 E-value=2.2 Score=31.57 Aligned_cols=37 Identities=22% Similarity=0.369 Sum_probs=27.8
Q ss_pred ccccccCCcccchhhhhhcC-------CCChhhhhhccCCcccc
Q psy8227 80 ARACLGCSQIKTFDQFEFDG-------CDNCDEFLHMKNSRDNV 116 (125)
Q Consensus 80 LRACLlCsLVKT~dQF~~dG-------CpNCe~~L~Mkgn~drV 116 (125)
.=-|..|+..=|.+.....+ ||+|..-|....|.+.+
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~~~~ 142 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNSEPI 142 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCchhhH
Confidence 34589999777777665443 99999999888777654
No 14
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=64.60 E-value=3.6 Score=30.93 Aligned_cols=72 Identities=22% Similarity=0.544 Sum_probs=52.7
Q ss_pred hheeeecCc----chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCccccccccccccccccccccccCCcccch
Q psy8227 17 HVHVQVGRM----PESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTF 92 (125)
Q Consensus 17 ~~~~~~~~~----~~~~~~~~~~~~~~~c~~~~flw~~v~~~~m~h~~s~~~~~~~s~~~VP~~~R~LRACLlCsLVKT~ 92 (125)
.|+|.+|++ |+.|..-|. +.-.||..+.++.. ...+|...+ |+.|+-.-+.
T Consensus 28 ~V~l~IG~ls~v~~~~l~FaFe--------------------v~~egT~aega~l~-Ie~~p~~~~----C~~C~~~~~~ 82 (115)
T COG0375 28 AVWLEIGELSCVEPEALRFAFE--------------------VVAEGTIAEGAELH-IEEEPAECW----CLDCGQEVEL 82 (115)
T ss_pred EEEEEEcceeccCHHHHHHHHH--------------------HHhccCcccCCEEE-EEEeccEEE----eccCCCeecc
Confidence 467888875 666653332 23489999999988 778888765 9999888888
Q ss_pred hhhhhcCCCChh-hhhhccCCcc
Q psy8227 93 DQFEFDGCDNCD-EFLHMKNSRD 114 (125)
Q Consensus 93 dQF~~dGCpNCe-~~L~Mkgn~d 114 (125)
+.+... ||.|. ..++..+.++
T Consensus 83 e~~~~~-CP~C~s~~~~i~~G~e 104 (115)
T COG0375 83 EELDYR-CPKCGSINLRIIGGDE 104 (115)
T ss_pred hhheeE-CCCCCCCceEEecCCe
Confidence 887777 99998 4456555554
No 15
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=63.45 E-value=18 Score=26.11 Aligned_cols=72 Identities=21% Similarity=0.448 Sum_probs=42.9
Q ss_pred hheeeecCc----chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCccccccccccccccccccccccCCcccch
Q psy8227 17 HVHVQVGRM----PESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTF 92 (125)
Q Consensus 17 ~~~~~~~~~----~~~~~~~~~~~~~~~c~~~~flw~~v~~~~m~h~~s~~~~~~~s~~~VP~~~R~LRACLlCsLVKT~ 92 (125)
-|+++||++ |++|..-|.. ..=||--+.++.+ ...+|... -|..|+-.-+.
T Consensus 28 ~V~l~iG~ls~V~p~~L~faf~~--------------------~~~~t~~ega~L~-I~~~p~~~----~C~~Cg~~~~~ 82 (115)
T TIGR00100 28 RVTLEIGELSCVNPSQLQFAFEV--------------------VREGTVAEGAKLN-IEDEPVEC----ECEDCSEEVSP 82 (115)
T ss_pred EEEEEEccccccCHHHHHHHHHH--------------------HhCCCccCCCEEE-EEeeCcEE----EcccCCCEEec
Confidence 388999986 6776544431 1235555555443 34666554 49999965555
Q ss_pred hhhhhcCCCChhhh-hhccCCcc
Q psy8227 93 DQFEFDGCDNCDEF-LHMKNSRD 114 (125)
Q Consensus 93 dQF~~dGCpNCe~~-L~Mkgn~d 114 (125)
+++. .-||+|... +++.+.++
T Consensus 83 ~~~~-~~CP~Cgs~~~~i~~G~E 104 (115)
T TIGR00100 83 EIDL-YRCPKCHGIMLQVRAGKE 104 (115)
T ss_pred CCcC-ccCcCCcCCCcEEecCCe
Confidence 5543 349999864 24444443
No 16
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=61.47 E-value=4.6 Score=33.50 Aligned_cols=30 Identities=23% Similarity=0.464 Sum_probs=21.6
Q ss_pred ccccccCCcccchhhh---hhc----CCCChhhhhhc
Q psy8227 80 ARACLGCSQIKTFDQF---EFD----GCDNCDEFLHM 109 (125)
Q Consensus 80 LRACLlCsLVKT~dQF---~~d----GCpNCe~~L~M 109 (125)
-++|-+|.++.+..-- ..+ -||+|..||=.
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy~ 233 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILYY 233 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccchHHHh
Confidence 5799999998765433 222 49999998843
No 17
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=61.06 E-value=3.6 Score=31.76 Aligned_cols=22 Identities=27% Similarity=0.895 Sum_probs=14.6
Q ss_pred ccccCCcccchhh---hhhcCCCChhh
Q psy8227 82 ACLGCSQIKTFDQ---FEFDGCDNCDE 105 (125)
Q Consensus 82 ACLlCsLVKT~dQ---F~~dGCpNCe~ 105 (125)
-|..|+ +.++. =..+|||+|..
T Consensus 3 ~Ct~Cg--~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 3 QCTKCG--RVFEDGSKEILSGCPECGG 27 (131)
T ss_pred ccCcCC--CCcCCCcHHHHccCcccCC
Confidence 388898 33332 24579999974
No 18
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=60.96 E-value=3.5 Score=31.75 Aligned_cols=20 Identities=35% Similarity=0.879 Sum_probs=16.5
Q ss_pred cccccCCcccchhhhhhcC---CCChh
Q psy8227 81 RACLGCSQIKTFDQFEFDG---CDNCD 104 (125)
Q Consensus 81 RACLlCsLVKT~dQF~~dG---CpNCe 104 (125)
-.|..|+..+ |+++| ||+|+
T Consensus 29 ~hCp~Cg~PL----F~KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPL----FRKDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCcc----eeeCCeEECCCCC
Confidence 3699999654 88999 99998
No 19
>PF08916 Phe_ZIP: Phenylalanine zipper; InterPro: IPR015012 The phenylalanine zipper consists of aromatic side chains from ten phenylalanine residues that are stacked within a hydrophobic core. This zipper mediates dimerisation of various proteins, such as APS, SH2-B and Lnk []. ; GO: 0004871 signal transducer activity, 0035556 intracellular signal transduction; PDB: 1Q2H_B.
Probab=58.58 E-value=15 Score=24.95 Aligned_cols=35 Identities=17% Similarity=0.210 Sum_probs=24.4
Q ss_pred chHHHHHHHHHHHhhheeeecCcchHHHHHHHHHH
Q psy8227 3 ARDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHV 37 (125)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 (125)
|+|=..+-|.|+++|-|+.-.--+++...||+++.
T Consensus 15 A~dfAk~~~~f~~~nP~~a~~~~~~~F~~kF~d~F 49 (59)
T PF08916_consen 15 ARDFAKAFRRFINENPQYARPLSHRSFSRKFADLF 49 (59)
T ss_dssp HHHHHHHHHHHHHH-GGG-STTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcCccccCCCCHHHHHHHHHHHH
Confidence 45666678999999988744445677888888763
No 20
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=57.48 E-value=5.2 Score=30.45 Aligned_cols=24 Identities=21% Similarity=0.595 Sum_probs=17.7
Q ss_pred ccccCCcccch-hhhhhcCCCChhh
Q psy8227 82 ACLGCSQIKTF-DQFEFDGCDNCDE 105 (125)
Q Consensus 82 ACLlCsLVKT~-dQF~~dGCpNCe~ 105 (125)
-|..|+-|-.- +.-...|||+|..
T Consensus 4 ~CtrCG~vf~~g~~~il~GCp~CG~ 28 (112)
T COG3364 4 QCTRCGEVFDDGSEEILSGCPKCGC 28 (112)
T ss_pred eecccccccccccHHHHccCccccc
Confidence 48999966544 5566689999974
No 21
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=54.52 E-value=5.7 Score=22.75 Aligned_cols=22 Identities=27% Similarity=0.510 Sum_probs=14.7
Q ss_pred cccCCcccch-hhhhhcCCCChh
Q psy8227 83 CLGCSQIKTF-DQFEFDGCDNCD 104 (125)
Q Consensus 83 CLlCsLVKT~-dQF~~dGCpNCe 104 (125)
|..|+..... +|...--||||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 6677655443 346777899996
No 22
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=51.70 E-value=5.1 Score=26.04 Aligned_cols=13 Identities=38% Similarity=0.657 Sum_probs=10.4
Q ss_pred hhhhcCCCChhhh
Q psy8227 94 QFEFDGCDNCDEF 106 (125)
Q Consensus 94 QF~~dGCpNCe~~ 106 (125)
+|..+|||+|+..
T Consensus 4 ~~~a~~C~~C~~~ 16 (76)
T TIGR00412 4 QIYGTGCANCQMT 16 (76)
T ss_pred EEECCCCcCHHHH
Confidence 4667999999865
No 23
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=51.30 E-value=5.7 Score=27.67 Aligned_cols=24 Identities=25% Similarity=0.700 Sum_probs=17.8
Q ss_pred cccccccCCcccchhhhhhcCCCChhh
Q psy8227 79 QARACLGCSQIKTFDQFEFDGCDNCDE 105 (125)
Q Consensus 79 ~LRACLlCsLVKT~dQF~~dGCpNCe~ 105 (125)
+.+||..|.-+.+.|+ +-||+|.+
T Consensus 3 ~~kAC~~Ck~l~~~d~---e~CP~Cgs 26 (64)
T COG2093 3 TEKACKNCKRLTPEDT---EICPVCGS 26 (64)
T ss_pred hhHHHhhccccCCCCC---ccCCCCCC
Confidence 4689999987666543 45999963
No 24
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=50.59 E-value=6.6 Score=23.91 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=11.0
Q ss_pred hhhhcCCCChhhhh
Q psy8227 94 QFEFDGCDNCDEFL 107 (125)
Q Consensus 94 QF~~dGCpNCe~~L 107 (125)
-|...|||.|....
T Consensus 5 ~f~~~~C~~C~~~~ 18 (67)
T cd02973 5 VFVSPTCPYCPDAV 18 (67)
T ss_pred EEECCCCCCcHHHH
Confidence 47788999998654
No 25
>PRK02935 hypothetical protein; Provisional
Probab=50.48 E-value=7.7 Score=29.44 Aligned_cols=29 Identities=28% Similarity=0.671 Sum_probs=13.4
Q ss_pred ccccCCcccchhhhh-hcCCCChhhhhhccCC
Q psy8227 82 ACLGCSQIKTFDQFE-FDGCDNCDEFLHMKNS 112 (125)
Q Consensus 82 ACLlCsLVKT~dQF~-~dGCpNCe~~L~Mkgn 112 (125)
-|..|. |...--- .|.|..|.+-|.++.+
T Consensus 72 ~CP~C~--K~TKmLGrvD~CM~C~~PLTLd~~ 101 (110)
T PRK02935 72 ICPSCE--KPTKMLGRVDACMHCNQPLTLDRS 101 (110)
T ss_pred ECCCCC--chhhhccceeecCcCCCcCCcCcc
Confidence 355554 3333332 2455555555555443
No 26
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=49.75 E-value=9.8 Score=29.90 Aligned_cols=39 Identities=26% Similarity=0.544 Sum_probs=28.4
Q ss_pred ccccccccccccccccccCCcccchhhhhhc---CCCChhhhh
Q psy8227 68 DDFNNLAKYFRQARACLGCSQIKTFDQFEFD---GCDNCDEFL 107 (125)
Q Consensus 68 ~s~~~VP~~~R~LRACLlCsLVKT~dQF~~d---GCpNCe~~L 107 (125)
+....+-.++..++ |+.|+-.-..+..... -||+|...|
T Consensus 111 ~~v~elHG~~~~~~-C~~C~~~~~~~~~~~~~~p~C~~Cgg~l 152 (242)
T PRK00481 111 KNVIELHGSLLRAR-CTKCGQTYDLDEYLKPEPPRCPKCGGIL 152 (242)
T ss_pred CceeeccCCcCcee-eCCCCCCcChhhhccCCCCCCCCCCCcc
Confidence 45566778888888 9999977666666543 399997654
No 27
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=47.03 E-value=9.4 Score=24.68 Aligned_cols=12 Identities=33% Similarity=0.886 Sum_probs=9.1
Q ss_pred hcCCCChhhhhh
Q psy8227 97 FDGCDNCDEFLH 108 (125)
Q Consensus 97 ~dGCpNCe~~L~ 108 (125)
..|||||+...+
T Consensus 7 ~~~C~~C~~~~~ 18 (76)
T PF13192_consen 7 SPGCPYCPELVQ 18 (76)
T ss_dssp CSSCTTHHHHHH
T ss_pred CCCCCCcHHHHH
Confidence 468999996554
No 28
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=45.92 E-value=9.2 Score=33.34 Aligned_cols=31 Identities=19% Similarity=0.505 Sum_probs=24.8
Q ss_pred cccccccccCCcccchhhhhhcC---CCChhhhh
Q psy8227 77 FRQARACLGCSQIKTFDQFEFDG---CDNCDEFL 107 (125)
Q Consensus 77 ~R~LRACLlCsLVKT~dQF~~dG---CpNCe~~L 107 (125)
..++.+|-.|+++.....-...+ ||+|...|
T Consensus 7 ~~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 7 AAKHILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred CCCcccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 35678999999998777665554 99999877
No 29
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=44.27 E-value=8.7 Score=29.96 Aligned_cols=24 Identities=17% Similarity=0.501 Sum_probs=17.4
Q ss_pred cccccCCcccchhhhhhcCCCChhhhh
Q psy8227 81 RACLGCSQIKTFDQFEFDGCDNCDEFL 107 (125)
Q Consensus 81 RACLlCsLVKT~dQF~~dGCpNCe~~L 107 (125)
-+|..||.+-+.=++. ||||+.+=
T Consensus 355 ~~c~~cg~~~~~~~~~---c~~c~~~~ 378 (389)
T PRK11788 355 YRCRNCGFTARTLYWH---CPSCKAWE 378 (389)
T ss_pred EECCCCCCCCccceeE---CcCCCCcc
Confidence 4599999776654444 99999753
No 30
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=42.36 E-value=12 Score=25.59 Aligned_cols=29 Identities=21% Similarity=0.306 Sum_probs=21.4
Q ss_pred ccccccccCCcccchhh-hhhcCCCChhhh
Q psy8227 78 RQARACLGCSQIKTFDQ-FEFDGCDNCDEF 106 (125)
Q Consensus 78 R~LRACLlCsLVKT~dQ-F~~dGCpNCe~~ 106 (125)
.+...|..|+....... ...-.||||.+.
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCe
Confidence 44567999998777544 777789999753
No 31
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=41.83 E-value=11 Score=32.54 Aligned_cols=31 Identities=19% Similarity=0.489 Sum_probs=24.9
Q ss_pred ccccccccCCcccchhhhhhcC---CCChhhhhh
Q psy8227 78 RQARACLGCSQIKTFDQFEFDG---CDNCDEFLH 108 (125)
Q Consensus 78 R~LRACLlCsLVKT~dQF~~dG---CpNCe~~L~ 108 (125)
+++.+|-.|.++.........+ ||+|...|.
T Consensus 11 ~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 11 AKHILCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred CCeeeCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 4578999999998877666554 999998774
No 32
>KOG1946|consensus
Probab=40.84 E-value=19 Score=29.81 Aligned_cols=17 Identities=35% Similarity=1.034 Sum_probs=12.6
Q ss_pred cchHH-HHHHHHHHHhhh
Q psy8227 2 IARDE-VAQLWAYVRSHV 18 (125)
Q Consensus 2 ~~~~~-~~~~~~~~~~~~ 18 (125)
|.|-| |..+|||+|.|=
T Consensus 119 lsR~~vvk~iw~YIke~n 136 (240)
T KOG1946|consen 119 LSRTDVVKKIWAYIKEHN 136 (240)
T ss_pred ccHHHHHHHHHHHHHHhc
Confidence 44544 578999999983
No 33
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=39.94 E-value=13 Score=21.49 Aligned_cols=22 Identities=23% Similarity=0.383 Sum_probs=15.7
Q ss_pred ccccCCcccchhhhhhcCCCChh
Q psy8227 82 ACLGCSQIKTFDQFEFDGCDNCD 104 (125)
Q Consensus 82 ACLlCsLVKT~dQF~~dGCpNCe 104 (125)
-|..|+.+-..+. ...-||.|.
T Consensus 3 ~C~~CGy~y~~~~-~~~~CP~Cg 24 (33)
T cd00350 3 VCPVCGYIYDGEE-APWVCPVCG 24 (33)
T ss_pred ECCCCCCEECCCc-CCCcCcCCC
Confidence 4889998865543 445699996
No 34
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=39.42 E-value=12 Score=27.01 Aligned_cols=72 Identities=22% Similarity=0.327 Sum_probs=45.0
Q ss_pred heeeecCc----chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCccccccccccccccccccccccCCcccchh
Q psy8227 18 VHVQVGRM----PESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFD 93 (125)
Q Consensus 18 ~~~~~~~~----~~~~~~~~~~~~~~~c~~~~flw~~v~~~~m~h~~s~~~~~~~s~~~VP~~~R~LRACLlCsLVKT~d 93 (125)
|++++|++ |++|.--|. ...-||--+.++..-- .+|...+ |..|+-.-+..
T Consensus 29 V~l~iG~ls~V~p~~L~f~f~--------------------~~~~~t~~egA~L~i~-~~p~~~~----C~~Cg~~~~~~ 83 (114)
T PRK03681 29 VWLKIGAFSCVETSSLAFCFD--------------------LVCRGTVAEGCKLHLE-EQEAECW----CETCQQYVTLL 83 (114)
T ss_pred EEEEEcCccccCHHHHHHHHH--------------------HHhCCCccCCCEEEEE-eeCcEEE----cccCCCeeecC
Confidence 78999987 666543221 1235776677766543 6666654 99999555554
Q ss_pred hhhhcCCCChhhh-hhccCCcc
Q psy8227 94 QFEFDGCDNCDEF-LHMKNSRD 114 (125)
Q Consensus 94 QF~~dGCpNCe~~-L~Mkgn~d 114 (125)
++...-||.|.+. +++.+.++
T Consensus 84 ~~~~~~CP~Cgs~~~~i~~G~E 105 (114)
T PRK03681 84 TQRVRRCPQCHGDMLRIVADDG 105 (114)
T ss_pred CccCCcCcCcCCCCcEEccCCe
Confidence 4444559999864 45555554
No 35
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.40 E-value=13 Score=27.65 Aligned_cols=51 Identities=22% Similarity=0.397 Sum_probs=30.3
Q ss_pred cccCCccccccccccccccccccccccCCcccchhh--h------------------hhcCCCChhhh-hhccCCcc
Q psy8227 59 GTSNNNAKIDDFNNLAKYFRQARACLGCSQIKTFDQ--F------------------EFDGCDNCDEF-LHMKNSRD 114 (125)
Q Consensus 59 ~~s~~~~~~~s~~~VP~~~R~LRACLlCsLVKT~dQ--F------------------~~dGCpNCe~~-L~Mkgn~d 114 (125)
|+-.+.++.. ...+|.. --|..|+-.-+.++ + ...-||+|.+. +++.+.++
T Consensus 54 gt~~ega~L~-i~~~p~~----~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~e 125 (135)
T PRK03824 54 GTILEGAEII-FEEEEAV----LKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGRG 125 (135)
T ss_pred CCcccCCEEE-EEecceE----EECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCce
Confidence 5555555433 3355544 45999997777652 1 22349999864 56555554
No 36
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=38.22 E-value=14 Score=28.08 Aligned_cols=30 Identities=30% Similarity=0.617 Sum_probs=21.1
Q ss_pred cccCCcccchhhhhh-cCCCChhhhhhccCCcc
Q psy8227 83 CLGCSQIKTFDQFEF-DGCDNCDEFLHMKNSRD 114 (125)
Q Consensus 83 CLlCsLVKT~dQF~~-dGCpNCe~~L~Mkgn~d 114 (125)
|..|+ |...-.-+ |.|.+|.+-|.++.+.+
T Consensus 72 CP~C~--K~TKmLGr~D~CM~C~~pLTLd~~le 102 (114)
T PF11023_consen 72 CPNCG--KQTKMLGRVDACMHCKEPLTLDPSLE 102 (114)
T ss_pred CCCCC--ChHhhhchhhccCcCCCcCccCchhh
Confidence 88888 55555533 78999988887765543
No 37
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=38.21 E-value=12 Score=30.39 Aligned_cols=28 Identities=29% Similarity=0.738 Sum_probs=23.0
Q ss_pred ccccccccCCcccchhhhhhc---CCCChhhhh
Q psy8227 78 RQARACLGCSQIKTFDQFEFD---GCDNCDEFL 107 (125)
Q Consensus 78 R~LRACLlCsLVKT~dQF~~d---GCpNCe~~L 107 (125)
..+-+|-.|+ .|+++|... ||-+|-..+
T Consensus 72 ~e~l~C~~C~--~Tfk~f~~~g~fGCaeCY~tf 102 (176)
T COG3880 72 EELLGCHNCG--MTFKEFIQSGLFGCAECYKTF 102 (176)
T ss_pred HHHhcCcccc--ccHHHHHHhcccchHHHHHHH
Confidence 4478999999 899999884 899996543
No 38
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=36.55 E-value=26 Score=23.40 Aligned_cols=15 Identities=40% Similarity=0.979 Sum_probs=11.2
Q ss_pred hHH-HHHHHHHHHhhh
Q psy8227 4 RDE-VAQLWAYVRSHV 18 (125)
Q Consensus 4 ~~~-~~~~~~~~~~~~ 18 (125)
|.| +..+|+|++.|-
T Consensus 22 r~~v~~~lw~YIk~~~ 37 (76)
T PF02201_consen 22 RSEVVKRLWQYIKENN 37 (76)
T ss_dssp HHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHhc
Confidence 444 457999999884
No 39
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.79 E-value=15 Score=26.69 Aligned_cols=72 Identities=15% Similarity=0.384 Sum_probs=44.0
Q ss_pred heeeecCc----chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-cCCccccccccccccccccccccccCCcccch
Q psy8227 18 VHVQVGRM----PESLAAKFTQHVGILCYCLWFLWTLVHSATMVHGT-SNNNAKIDDFNNLAKYFRQARACLGCSQIKTF 92 (125)
Q Consensus 18 ~~~~~~~~----~~~~~~~~~~~~~~~c~~~~flw~~v~~~~m~h~~-s~~~~~~~s~~~VP~~~R~LRACLlCsLVKT~ 92 (125)
|++.||++ |++|..-|.. ..-|| --+.++.. ...+|... -|..|+-.-+.
T Consensus 29 V~l~IG~ls~V~pe~L~faf~~--------------------~~~~T~~~ega~L~-Ie~vp~~~----~C~~Cg~~~~~ 83 (117)
T PRK00564 29 VVVGIGERSGMDKSLFVSAFET--------------------FREESLVCKDAILD-IVDEKVEL----ECKDCSHVFKP 83 (117)
T ss_pred EEEEEccccCcCHHHHHHHHHH--------------------HhcCCcccCCCEEE-EEecCCEE----EhhhCCCcccc
Confidence 78999986 6666533321 23456 34555544 34666654 49999966666
Q ss_pred hhhhhcCCCChhhh-hhccCCcc
Q psy8227 93 DQFEFDGCDNCDEF-LHMKNSRD 114 (125)
Q Consensus 93 dQF~~dGCpNCe~~-L~Mkgn~d 114 (125)
+++...-||.|... +++.+.++
T Consensus 84 ~~~~~~~CP~Cgs~~~~i~~G~E 106 (117)
T PRK00564 84 NALDYGVCEKCHSKNVIITQGNE 106 (117)
T ss_pred CCccCCcCcCCCCCceEEecCCE
Confidence 65544459999864 45554444
No 40
>cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain.
Probab=34.86 E-value=16 Score=24.78 Aligned_cols=18 Identities=22% Similarity=0.706 Sum_probs=13.6
Q ss_pred hhhhhhcCCCChhhhhhc
Q psy8227 92 FDQFEFDGCDNCDEFLHM 109 (125)
Q Consensus 92 ~dQF~~dGCpNCe~~L~M 109 (125)
..-|...|||+|+...++
T Consensus 16 i~~F~~~~C~~C~~~~~~ 33 (89)
T cd03026 16 FETYVSLSCHNCPDVVQA 33 (89)
T ss_pred EEEEECCCCCCcHHHHHH
Confidence 455888999999975544
No 41
>PRK00420 hypothetical protein; Validated
Probab=34.62 E-value=12 Score=27.96 Aligned_cols=28 Identities=21% Similarity=0.352 Sum_probs=19.2
Q ss_pred cccccCCcccchhhhhhcC---CCChhhhhhccC
Q psy8227 81 RACLGCSQIKTFDQFEFDG---CDNCDEFLHMKN 111 (125)
Q Consensus 81 RACLlCsLVKT~dQF~~dG---CpNCe~~L~Mkg 111 (125)
..|..|+..... + ++| ||||..++.-++
T Consensus 24 ~~CP~Cg~pLf~--l-k~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 24 KHCPVCGLPLFE--L-KDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCCCCCCccee--c-CCCceECCCCCCeeeecc
Confidence 679999954432 2 455 999998766544
No 42
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=34.56 E-value=10 Score=22.63 Aligned_cols=22 Identities=23% Similarity=0.694 Sum_probs=12.3
Q ss_pred CCChhhhhhccCCccccccccc
Q psy8227 100 CDNCDEFLHMKNSRDNVYNCTS 121 (125)
Q Consensus 100 CpNCe~~L~Mkgn~drV~dCTS 121 (125)
||.|...|.-+.+.+....|.+
T Consensus 4 Cp~C~nlL~p~~~~~~~~~C~~ 25 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEKRVACRT 25 (35)
T ss_dssp ETTTTSBEEEEEETTTTEEESS
T ss_pred CCCCCccceEcCCCccCcCCCC
Confidence 6666666665555554334543
No 43
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=34.45 E-value=20 Score=24.75 Aligned_cols=21 Identities=24% Similarity=0.529 Sum_probs=16.7
Q ss_pred ccccccccCCcccchhhhhhc
Q psy8227 78 RQARACLGCSQIKTFDQFEFD 98 (125)
Q Consensus 78 R~LRACLlCsLVKT~dQF~~d 98 (125)
....-|..|+.+|++|+|-++
T Consensus 48 ~~El~C~~C~~~k~ld~FSK~ 68 (84)
T PF12898_consen 48 VVELTCSPCGKTKPLDEFSKN 68 (84)
T ss_pred cCcCEeccCCCCcCHHHHhHH
Confidence 334468899999999999764
No 44
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.94 E-value=25 Score=21.08 Aligned_cols=23 Identities=17% Similarity=0.366 Sum_probs=13.7
Q ss_pred ccccCCcccchhhhh---hcCCCChh
Q psy8227 82 ACLGCSQIKTFDQFE---FDGCDNCD 104 (125)
Q Consensus 82 ACLlCsLVKT~dQF~---~dGCpNCe 104 (125)
-|..||=+...++.. ..=||.|+
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg 27 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCG 27 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCC
Confidence 467777666555432 23488887
No 45
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=32.35 E-value=20 Score=30.61 Aligned_cols=21 Identities=24% Similarity=0.498 Sum_probs=15.4
Q ss_pred ccccCCcccchhhhhhcCCCChhh
Q psy8227 82 ACLGCSQIKTFDQFEFDGCDNCDE 105 (125)
Q Consensus 82 ACLlCsLVKT~dQF~~dGCpNCe~ 105 (125)
-|..|+ |.=.|.+-+||||++
T Consensus 214 ~CslC~---teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 214 HCNLCE---SEWHVVRVKCSNCEQ 234 (309)
T ss_pred EcCCCC---CcccccCccCCCCCC
Confidence 355554 777778889999985
No 46
>PF09369 DUF1998: Domain of unknown function (DUF1998); InterPro: IPR018973 This entry represents a family of DEAD/DEAH-box-containing family of helicases. It includes Hrq1 from Saccharomyces, a putative RecQ helicase []. RecQ helicases are involved in maintaining genomic integrity.
Probab=31.55 E-value=14 Score=24.48 Aligned_cols=7 Identities=57% Similarity=1.426 Sum_probs=6.1
Q ss_pred hcCCCCh
Q psy8227 97 FDGCDNC 103 (125)
Q Consensus 97 ~dGCpNC 103 (125)
++|||+|
T Consensus 77 ~~gC~~C 83 (84)
T PF09369_consen 77 DDGCPSC 83 (84)
T ss_pred cccCccc
Confidence 7899998
No 47
>KOG2324|consensus
Probab=30.52 E-value=24 Score=32.15 Aligned_cols=28 Identities=21% Similarity=0.660 Sum_probs=24.7
Q ss_pred ccccccccCCcccchhhhhhcC---CCChhh
Q psy8227 78 RQARACLGCSQIKTFDQFEFDG---CDNCDE 105 (125)
Q Consensus 78 R~LRACLlCsLVKT~dQF~~dG---CpNCe~ 105 (125)
..+--|..|++-+..+.|.-.+ ||+|.+
T Consensus 225 D~l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~ 255 (457)
T KOG2324|consen 225 DTLMSCPSCGYSKNSEDLDLSKIASCPKCNE 255 (457)
T ss_pred cceeecCcCCccCchhhhcCCccccCCcccC
Confidence 5678899999999999998865 999986
No 48
>PRK06580 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=29.73 E-value=1.2e+02 Score=22.04 Aligned_cols=56 Identities=18% Similarity=0.092 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH--hcccCCccccccccccccccccc--cccccCCcccc
Q psy8227 36 HVGILCYCLWFLWTLVHSATMV--HGTSNNNAKIDDFNNLAKYFRQA--RACLGCSQIKT 91 (125)
Q Consensus 36 ~~~~~c~~~~flw~~v~~~~m~--h~~s~~~~~~~s~~~VP~~~R~L--RACLlCsLVKT 91 (125)
.+..+.|++||+|-.+.+.+-| .-.+...-....+-.+|.++++. ++=+.+++-.|
T Consensus 6 ~i~~~~y~~~~~~eiv~sni~Va~~vl~p~~~i~P~ii~vp~~l~t~~~~~~LAnsITLT 65 (103)
T PRK06580 6 KIKFILYFPWLLLEIWKSAFSVIKIIWQRKIGIEPVFEWVDAEGLEEIGEIIYGNSITLT 65 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCcEEEEeCCCCChHHHHHHHHHHhCC
Confidence 4667889999999999987665 22222222345556678777532 33344444333
No 49
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=28.63 E-value=38 Score=26.38 Aligned_cols=38 Identities=18% Similarity=0.343 Sum_probs=26.2
Q ss_pred cccccccccccccccccCCcccchhhhhh--------cCCCChhhhh
Q psy8227 69 DFNNLAKYFRQARACLGCSQIKTFDQFEF--------DGCDNCDEFL 107 (125)
Q Consensus 69 s~~~VP~~~R~LRACLlCsLVKT~dQF~~--------dGCpNCe~~L 107 (125)
+...+-.+++.++ |+.|+-.-+.+++.. .-||+|...|
T Consensus 85 ~vielHG~~~~~~-C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~l 130 (206)
T cd01410 85 KLSELHGNMFIEV-CKSCGPEYVRDDVVETRGDKETGRRCHACGGIL 130 (206)
T ss_pred cEEEecCCcCccc-CCCCCCccchHHHHHHhhcCCCCCcCCCCcCcc
Confidence 3556677888887 999997666555431 2399997654
No 50
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=28.53 E-value=29 Score=30.29 Aligned_cols=29 Identities=21% Similarity=0.382 Sum_probs=22.3
Q ss_pred ccccccccccCCcccchhhhhhcCCCChhhhh
Q psy8227 76 YFRQARACLGCSQIKTFDQFEFDGCDNCDEFL 107 (125)
Q Consensus 76 ~~R~LRACLlCsLVKT~dQF~~dGCpNCe~~L 107 (125)
..+++.+|-.|.++... ++.-||+|...|
T Consensus 217 ~~~~l~~C~~Cd~l~~~---~~a~CpRC~~~L 245 (419)
T PRK15103 217 LRQGLRSCSCCTAILPA---DQPVCPRCHTKG 245 (419)
T ss_pred cccCCCcCCCCCCCCCC---CCCCCCCCCCcC
Confidence 34689999999998543 234699999877
No 51
>KOG3806|consensus
Probab=28.33 E-value=33 Score=27.75 Aligned_cols=29 Identities=24% Similarity=0.588 Sum_probs=16.9
Q ss_pred CcchHHHHHHHHHHHhhheeeecCcchHH
Q psy8227 1 MIARDEVAQLWAYVRSHVHVQVGRMPESL 29 (125)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 29 (125)
|+..||||+||---..--..---.|..+|
T Consensus 100 l~dp~eVArlWG~rK~kp~MNYdKLSRaL 128 (177)
T KOG3806|consen 100 LVDPDEVARLWGARKNKPNMNYDKLSRAL 128 (177)
T ss_pred ecCHHHHHHHHhhhhCCCCCCHHHHHHHH
Confidence 56789999999754443333333333333
No 52
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=28.16 E-value=13 Score=22.45 Aligned_cols=13 Identities=23% Similarity=0.662 Sum_probs=9.7
Q ss_pred hhhcCCCChhhhh
Q psy8227 95 FEFDGCDNCDEFL 107 (125)
Q Consensus 95 F~~dGCpNCe~~L 107 (125)
|-..|||.|....
T Consensus 4 y~~~~C~~C~~~~ 16 (60)
T PF00462_consen 4 YTKPGCPYCKKAK 16 (60)
T ss_dssp EESTTSHHHHHHH
T ss_pred EEcCCCcCHHHHH
Confidence 4568999998654
No 53
>cd01659 TRX_superfamily Thioredoxin (TRX) superfamily; a large, diverse group of proteins containing a TRX-fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include TRX, protein disulfide isomerase (PDI), tlpA-like, glutaredoxin, NrdH redoxin, and the bacterial Dsb (DsbA, DsbC, DsbG, DsbE, DsbDgamma) protein families. Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins and glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others.
Probab=27.50 E-value=21 Score=18.61 Aligned_cols=14 Identities=21% Similarity=0.384 Sum_probs=10.4
Q ss_pred hhhcCCCChhhhhh
Q psy8227 95 FEFDGCDNCDEFLH 108 (125)
Q Consensus 95 F~~dGCpNCe~~L~ 108 (125)
|..++|+.|.....
T Consensus 4 ~~~~~c~~c~~~~~ 17 (69)
T cd01659 4 FYAPWCPFCQALRP 17 (69)
T ss_pred EECCCChhHHhhhh
Confidence 56678999987663
No 54
>PRK12654 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=26.51 E-value=1.2e+02 Score=23.74 Aligned_cols=42 Identities=7% Similarity=0.073 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH--hcccCCcccccccccccccccc
Q psy8227 38 GILCYCLWFLWTLVHSATMV--HGTSNNNAKIDDFNNLAKYFRQ 79 (125)
Q Consensus 38 ~~~c~~~~flw~~v~~~~m~--h~~s~~~~~~~s~~~VP~~~R~ 79 (125)
..+.|++||+|-.+.+.+-| .-.+...-..-.+-.+|.++++
T Consensus 3 ~~l~y~~~~l~eiv~Sni~Va~~vl~p~~~i~P~iV~vpl~l~t 46 (151)
T PRK12654 3 HALKYAPWLIGQIFVAGFSLIKDAFKGDKNFNPVVVRYPLRVTK 46 (151)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCeEEEEeccCCC
Confidence 35789999999999997666 2222222244555567776654
No 55
>cd03419 GRX_GRXh_1_2_like Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes
Probab=26.01 E-value=19 Score=22.32 Aligned_cols=16 Identities=19% Similarity=0.395 Sum_probs=12.1
Q ss_pred hhhhcCCCChhhhhhc
Q psy8227 94 QFEFDGCDNCDEFLHM 109 (125)
Q Consensus 94 QF~~dGCpNCe~~L~M 109 (125)
.|..+|||.|...-++
T Consensus 4 ~y~~~~Cp~C~~~~~~ 19 (82)
T cd03419 4 VFSKSYCPYCKRAKSL 19 (82)
T ss_pred EEEcCCCHHHHHHHHH
Confidence 4677899999876544
No 56
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=25.78 E-value=30 Score=26.17 Aligned_cols=29 Identities=21% Similarity=0.496 Sum_probs=23.9
Q ss_pred cccccccccCCcccchhhhhh-cCCCChhh
Q psy8227 77 FRQARACLGCSQIKTFDQFEF-DGCDNCDE 105 (125)
Q Consensus 77 ~R~LRACLlCsLVKT~dQF~~-dGCpNCe~ 105 (125)
..+.--|-+|.=..|.+++.. .-||||.+
T Consensus 59 ~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 59 NPKAIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred CCccEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 356677999999999999986 56999975
No 57
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=24.98 E-value=23 Score=20.77 Aligned_cols=26 Identities=35% Similarity=0.512 Sum_probs=18.1
Q ss_pred cccccCCcccchhhhhhcCCCChhhhh
Q psy8227 81 RACLGCSQIKTFDQFEFDGCDNCDEFL 107 (125)
Q Consensus 81 RACLlCsLVKT~dQF~~dGCpNCe~~L 107 (125)
|.|..|.. +...+.-.-.|..|+-.|
T Consensus 1 rrC~vC~~-~k~rk~T~~~C~~C~v~l 26 (32)
T PF13842_consen 1 RRCKVCSK-KKRRKDTRYMCSKCDVPL 26 (32)
T ss_pred CCCeECCc-CCccceeEEEccCCCCcc
Confidence 67888987 444455667899997444
No 58
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=24.90 E-value=52 Score=21.96 Aligned_cols=15 Identities=40% Similarity=1.072 Sum_probs=10.6
Q ss_pred hHH-HHHHHHHHHhhh
Q psy8227 4 RDE-VAQLWAYVRSHV 18 (125)
Q Consensus 4 ~~~-~~~~~~~~~~~~ 18 (125)
|-| +.-+|+|++.|=
T Consensus 22 r~ev~~~lw~YIk~n~ 37 (77)
T smart00151 22 RTEIIKRLWEYIKEHN 37 (77)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 444 456899999873
No 59
>TIGR02183 GRXA Glutaredoxin, GrxA family. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase.
Probab=24.76 E-value=29 Score=22.92 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=10.9
Q ss_pred hhhcCCCChhhhhhc
Q psy8227 95 FEFDGCDNCDEFLHM 109 (125)
Q Consensus 95 F~~dGCpNCe~~L~M 109 (125)
|-++|||.|....++
T Consensus 5 ys~~~Cp~C~~ak~~ 19 (86)
T TIGR02183 5 FGRPGCPYCVRAKQL 19 (86)
T ss_pred EeCCCCccHHHHHHH
Confidence 456899999865544
No 60
>PRK06279 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=24.22 E-value=1.4e+02 Score=21.34 Aligned_cols=42 Identities=10% Similarity=0.013 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccCCcccccccccccccccc
Q psy8227 38 GILCYCLWFLWTLVHSATMVHGTSNNNAKIDDFNNLAKYFRQ 79 (125)
Q Consensus 38 ~~~c~~~~flw~~v~~~~m~h~~s~~~~~~~s~~~VP~~~R~ 79 (125)
..+-|+.||+|-.+.+.+-|=-.-..+-....+-.+|.++++
T Consensus 5 ~~~~~~~~~l~eiv~ani~Va~~vl~~~i~P~ii~~p~~l~~ 46 (100)
T PRK06279 5 YGIGYLIVLIKAIIEAWIDVVKRSLNGKIDPEVIEIETEINR 46 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCCCCceEEEEeccCCC
Confidence 345699999999998866551111112234455566766644
No 61
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=23.92 E-value=29 Score=30.35 Aligned_cols=47 Identities=17% Similarity=0.287 Sum_probs=31.3
Q ss_pred ccccccccc-cccccccCCcccchhhhhhc--CCCChhhhhhccCCcccccc
Q psy8227 70 FNNLAKYFR-QARACLGCSQIKTFDQFEFD--GCDNCDEFLHMKNSRDNVYN 118 (125)
Q Consensus 70 ~~~VP~~~R-~LRACLlCsLVKT~dQF~~d--GCpNCe~~L~Mkgn~drV~d 118 (125)
...-|..-| ++-+|..|....+.++=... -|| |..- =.+|-.+||.+
T Consensus 229 ~g~~P~~GKYh~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~-i~~GV~~Rv~e 278 (374)
T TIGR00375 229 YGLDPLLGKYHQTACEACGEPAVSEDAETACANCP-CGGR-IKKGVSDRLRE 278 (374)
T ss_pred eeECcCCCccchhhhcccCCcCCchhhhhcCCCCC-CCCc-ceechHHHHHH
Confidence 334455544 45699999998888875542 399 9865 45566666654
No 62
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=23.63 E-value=52 Score=25.38 Aligned_cols=38 Identities=24% Similarity=0.504 Sum_probs=26.2
Q ss_pred cccccccccccccccccCCcccchhhh-------hhcCCCChhhhh
Q psy8227 69 DFNNLAKYFRQARACLGCSQIKTFDQF-------EFDGCDNCDEFL 107 (125)
Q Consensus 69 s~~~VP~~~R~LRACLlCsLVKT~dQF-------~~dGCpNCe~~L 107 (125)
....+-.++..++ |+.|+-....+.+ .-.-||+|...|
T Consensus 99 ~v~elHG~~~~~~-C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~l 143 (218)
T cd01407 99 KVIELHGSLFRVR-CTKCGKEYPRDELQADIDREEVPRCPKCGGLL 143 (218)
T ss_pred CEEECcCCcCcce-eCCCcCCCcHHHHhHhhccCCCCcCCCCCCcc
Confidence 4556677788887 9999976665543 113499998764
No 63
>TIGR02180 GRX_euk Glutaredoxin. This model represents eukaryotic glutaredoxins and includes sequences from fungi, plants and metazoans as well as viruses.
Probab=23.35 E-value=30 Score=21.39 Aligned_cols=15 Identities=20% Similarity=0.390 Sum_probs=11.7
Q ss_pred hhhhcCCCChhhhhh
Q psy8227 94 QFEFDGCDNCDEFLH 108 (125)
Q Consensus 94 QF~~dGCpNCe~~L~ 108 (125)
.|..+|||-|.....
T Consensus 3 ~f~~~~Cp~C~~~~~ 17 (84)
T TIGR02180 3 VFSKSYCPYCKKAKE 17 (84)
T ss_pred EEECCCChhHHHHHH
Confidence 467899999987654
No 64
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=23.35 E-value=46 Score=27.90 Aligned_cols=36 Identities=22% Similarity=0.510 Sum_probs=28.8
Q ss_pred ccccccccccccccCCcccchhhhhhc--CCCChhhhhhc
Q psy8227 72 NLAKYFRQARACLGCSQIKTFDQFEFD--GCDNCDEFLHM 109 (125)
Q Consensus 72 ~VP~~~R~LRACLlCsLVKT~dQF~~d--GCpNCe~~L~M 109 (125)
.+|..+ -..|-.|+-+...++++++ =||+|...+.|
T Consensus 20 ~~~~~~--~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 20 EVPEGV--WTKCPKCGQVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred CCCCCC--eeECCCCcchhhHHHHHhhCCCCCCCCCcCcC
Confidence 567654 6779999999999988775 59999977665
No 65
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.16 E-value=18 Score=21.53 Aligned_cols=14 Identities=21% Similarity=0.688 Sum_probs=10.4
Q ss_pred CCCChhhhhhccCC
Q psy8227 99 GCDNCDEFLHMKNS 112 (125)
Q Consensus 99 GCpNCe~~L~Mkgn 112 (125)
-||||...+++..+
T Consensus 4 ~CP~C~~~f~v~~~ 17 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD 17 (37)
T ss_pred ECCCCCceEEcCHH
Confidence 49999987766554
No 66
>PF09626 DHC: Dihaem cytochrome c; InterPro: IPR018588 Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway. DHC acts as the physiological electron donor for SHP during phototrophic growth []. In certain species DHC is found upstream of IPR011577 from INTERPRO. ; PDB: 2FWT_A 2FW5_A.
Probab=22.91 E-value=70 Score=23.84 Aligned_cols=19 Identities=21% Similarity=0.580 Sum_probs=14.3
Q ss_pred cchHHHHHHHHHHHhhhee
Q psy8227 2 IARDEVAQLWAYVRSHVHV 20 (125)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~ 20 (125)
+..++.+.+|+|+++|-=-
T Consensus 39 Ld~~~~~~I~~YL~~nAa~ 57 (120)
T PF09626_consen 39 LDPATQAEIWAYLQANAAD 57 (120)
T ss_dssp --HHHHHHHHHHHHHTSTT
T ss_pred CCHHHHHHHHHHHHHcccc
Confidence 4568899999999998643
No 67
>PF10139 Virul_Fac: Putative bacterial virulence factor; InterPro: IPR017030 This group represents a virulence effector protein, SrfC type.
Probab=22.90 E-value=1.1e+02 Score=29.86 Aligned_cols=59 Identities=20% Similarity=0.445 Sum_probs=36.7
Q ss_pred cchHHHHHHHHHHHhhheeeecCcchHHHHHHHHHHHHHH---------HHHHHHH--------HHHHHHHHHhcccCCc
Q psy8227 2 IARDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGILC---------YCLWFLW--------TLVHSATMVHGTSNNN 64 (125)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c---------~~~~flw--------~~v~~~~m~h~~s~~~ 64 (125)
|..|||..||.|++.|+ |.....|...|-...+.+- =.+-.|| ...+.+-.+|..++..
T Consensus 169 l~~ddv~~L~dy~~~~~----~~~~~~l~~~fW~~a~~LaP~L~~~dRa~lfslLWge~~~lT~~y~~la~~L~~Lg~a~ 244 (854)
T PF10139_consen 169 LTEDDVVDLWDYLQRHF----PKRQQQLEDHFWPQAAELAPYLSIDDRARLFSLLWGEQPELTQLYRQLAHTLQQLGHAE 244 (854)
T ss_pred CCHHHHHHHHHHHHHhc----hhhHHHHHHhhHHHHHHHhCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCCch
Confidence 56899999999999985 4445566666655544332 1234455 3344466667666544
No 68
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=22.59 E-value=59 Score=27.80 Aligned_cols=37 Identities=19% Similarity=0.332 Sum_probs=28.9
Q ss_pred ccccccccccccccCCcccchhhhhhc--CCCChhhhhhcc
Q psy8227 72 NLAKYFRQARACLGCSQIKTFDQFEFD--GCDNCDEFLHMK 110 (125)
Q Consensus 72 ~VP~~~R~LRACLlCsLVKT~dQF~~d--GCpNCe~~L~Mk 110 (125)
.+|..+ -..|-.|+-+...++++++ =||+|...+.|.
T Consensus 32 ~~p~~l--w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 32 QKYKHL--WVQCENCYGLNYKKFLKSKMNICEQCGYHLKMS 70 (296)
T ss_pred CCCCCC--eeECCCccchhhHHHHHHcCCCCCCCCCCcCCC
Confidence 366553 5679999999999999885 599998766554
No 69
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=22.55 E-value=31 Score=23.83 Aligned_cols=26 Identities=23% Similarity=0.418 Sum_probs=19.9
Q ss_pred ccccccCCccc-chhhhhhcCCCChhh
Q psy8227 80 ARACLGCSQIK-TFDQFEFDGCDNCDE 105 (125)
Q Consensus 80 LRACLlCsLVK-T~dQF~~dGCpNCe~ 105 (125)
..-|..|+.+. ..+.+..-=||||.+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe 35 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGE 35 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCc
Confidence 45799999888 555666667999984
No 70
>cd02947 TRX_family TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functio
Probab=22.43 E-value=31 Score=20.38 Aligned_cols=15 Identities=20% Similarity=0.401 Sum_probs=11.0
Q ss_pred hhhhcCCCChhhhhh
Q psy8227 94 QFEFDGCDNCDEFLH 108 (125)
Q Consensus 94 QF~~dGCpNCe~~L~ 108 (125)
.|...+|+.|..+..
T Consensus 16 ~~~~~~C~~C~~~~~ 30 (93)
T cd02947 16 DFWAPWCGPCKAIAP 30 (93)
T ss_pred EEECCCChhHHHhhH
Confidence 366678999987653
No 71
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=22.38 E-value=35 Score=20.94 Aligned_cols=14 Identities=21% Similarity=0.446 Sum_probs=10.7
Q ss_pred hhhcCCCChhhhhh
Q psy8227 95 FEFDGCDNCDEFLH 108 (125)
Q Consensus 95 F~~dGCpNCe~~L~ 108 (125)
|...+||.|.....
T Consensus 6 f~~~~C~~C~~~~~ 19 (82)
T TIGR00411 6 FTSPTCPYCPAAKR 19 (82)
T ss_pred EECCCCcchHHHHH
Confidence 66789999986553
No 72
>PF14851 FAM176: FAM176 family
Probab=22.15 E-value=1.7e+02 Score=22.87 Aligned_cols=37 Identities=27% Similarity=0.382 Sum_probs=26.1
Q ss_pred HHHHHHhhheeeecCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8227 10 LWAYVRSHVHVQVGRMPESLAAKFTQHVGILCYCLWFLWTLVHSATMV 57 (125)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~flw~~v~~~~m~ 57 (125)
..||+|.| ||+.|--| |.+.|+-|.++-|++-.-+..
T Consensus 11 aya~I~~~--------PE~~aLYF---v~gVC~GLlLtLcllV~risc 47 (153)
T PF14851_consen 11 AYAHIRDN--------PERFALYF---VSGVCAGLLLTLCLLVIRISC 47 (153)
T ss_pred HHHHHHhC--------hHHHHHHH---HHHHHHHHHHHHHHHHhhhee
Confidence 45677765 99999888 467788888777776554433
No 73
>TIGR02949 anti_SigH_actin anti-sigma factor, TIGR02949 family. This group of anti-sigma factors are associated in an apparent operon with a family of sigma-70 family sigma factors (TIGR02947). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria.
Probab=21.84 E-value=1.7e+02 Score=19.94 Aligned_cols=35 Identities=17% Similarity=0.420 Sum_probs=27.1
Q ss_pred hHHHHHHHHHHHhhheeeecCcchHHHHHHHHHHHH--HHHHHH
Q psy8227 4 RDEVAQLWAYVRSHVHVQVGRMPESLAAKFTQHVGI--LCYCLW 45 (125)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~c~~~~ 45 (125)
+|-+.+|.+|+- |.+++.-+++|.+|++. .|.-..
T Consensus 10 ~e~~~~l~~ylD-------geL~~~e~~~~e~HL~~C~~C~~e~ 46 (84)
T TIGR02949 10 DEVIDHLYEFLD-------GEMGPSDREQLRRHLEACPECLEEY 46 (84)
T ss_pred HHHHHHHHHHHc-------CCCCHHHHHHHHHHHHhCHHHHHHH
Confidence 345678888874 88999999999999986 454443
No 74
>PF07297 DPM2: Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2); InterPro: IPR009914 This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2 [].; GO: 0009059 macromolecule biosynthetic process, 0030176 integral to endoplasmic reticulum membrane
Probab=21.73 E-value=1.9e+02 Score=20.43 Aligned_cols=26 Identities=15% Similarity=0.433 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8227 28 SLAAKFTQHVGILCYCLWFLWTLVHS 53 (125)
Q Consensus 28 ~~~~~~~~~~~~~c~~~~flw~~v~~ 53 (125)
.+..+.---++.+.|.|..+|.+++.
T Consensus 4 r~vG~~~l~~a~~vF~YYt~WvlllP 29 (78)
T PF07297_consen 4 RLVGLLMLAVALSVFTYYTIWVLLLP 29 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34444445567889999999998764
No 75
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=21.26 E-value=51 Score=25.92 Aligned_cols=39 Identities=8% Similarity=0.275 Sum_probs=27.3
Q ss_pred ccccccccccccccccccCCcccchhhhhh-cCCCChhhhh
Q psy8227 68 DDFNNLAKYFRQARACLGCSQIKTFDQFEF-DGCDNCDEFL 107 (125)
Q Consensus 68 ~s~~~VP~~~R~LRACLlCsLVKT~dQF~~-dGCpNCe~~L 107 (125)
++...+-.++..++ |+.|+-.-..+.+.. .-||+|...|
T Consensus 107 ~~v~elHG~~~~~~-C~~C~~~~~~~~~~~~p~C~~Cgg~l 146 (225)
T cd01411 107 KNVVEFHGSLYRIY-CTVCGKTVDWEEYLKSPYHAKCGGVI 146 (225)
T ss_pred CcEEEeCCCcCeeE-eCCCCCccchhhcCCCCCCCCCCCEe
Confidence 44566778888887 889986655555543 4699997654
No 76
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=21.17 E-value=1.2e+02 Score=22.71 Aligned_cols=32 Identities=34% Similarity=0.641 Sum_probs=25.1
Q ss_pred HHHHHHHHhhheeeecCcchHHH-----HHH---HHHHHHHHHHHHH
Q psy8227 8 AQLWAYVRSHVHVQVGRMPESLA-----AKF---TQHVGILCYCLWF 46 (125)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~-----~~~---~~~~~~~c~~~~f 46 (125)
.+||+++.+. +|.||- +++ |.|...+||.|=|
T Consensus 19 ~~LW~~L~~~-------lPDSlL~n~ei~~~GLSTDhltaLa~~~~~ 58 (104)
T PF05381_consen 19 ETLWATLCEI-------LPDSLLDNPEIRTLGLSTDHLTALAYRYHF 58 (104)
T ss_pred HHHHHHHHHh-------CchhhcCchhhhhcCCcHHHHHHHHHHHhe
Confidence 5799999864 788886 333 8899999998755
No 77
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=20.83 E-value=80 Score=28.71 Aligned_cols=34 Identities=26% Similarity=0.465 Sum_probs=27.1
Q ss_pred cccccccccccCCcccchhhhhhcCCCChhhhhhcc
Q psy8227 75 KYFRQARACLGCSQIKTFDQFEFDGCDNCDEFLHMK 110 (125)
Q Consensus 75 ~~~R~LRACLlCsLVKT~dQF~~dGCpNCe~~L~Mk 110 (125)
..-.++|+|..|..+...+ .+--||-|..-|+..
T Consensus 215 ~~~~~~~~C~~C~~~~~~~--~~~~CpRC~~~Ly~r 248 (418)
T COG2995 215 GAREGLRSCLCCHYILPHD--AEPRCPRCGSKLYVR 248 (418)
T ss_pred CCcccceecccccccCCHh--hCCCCCCCCChhhcc
Confidence 4457899999999999988 556699998766543
No 78
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=20.67 E-value=65 Score=25.54 Aligned_cols=38 Identities=18% Similarity=0.386 Sum_probs=25.7
Q ss_pred cccccccccccccccccCCcccchhhhhh-------cCCCChhhhh
Q psy8227 69 DFNNLAKYFRQARACLGCSQIKTFDQFEF-------DGCDNCDEFL 107 (125)
Q Consensus 69 s~~~VP~~~R~LRACLlCsLVKT~dQF~~-------dGCpNCe~~L 107 (125)
....+-.+++.+| |..|+-.-..+.+.. .-||+|...|
T Consensus 106 ~V~elHG~l~~~~-C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~l 150 (235)
T cd01408 106 RIIEAHGSFATAH-CIKCKHKYPGDWMREDIFNQEVPKCPRCGGLV 150 (235)
T ss_pred CEEEeCcCCCccc-cccCCCcCCHHHHHHHHhCCCCccCCCCCCCc
Confidence 4556677888887 999997555443321 2499998665
No 79
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=20.30 E-value=50 Score=27.23 Aligned_cols=36 Identities=25% Similarity=0.554 Sum_probs=25.0
Q ss_pred cccccccccccccccccCCcccchhh---hhhcC----CCChhh
Q psy8227 69 DFNNLAKYFRQARACLGCSQIKTFDQ---FEFDG----CDNCDE 105 (125)
Q Consensus 69 s~~~VP~~~R~LRACLlCsLVKT~dQ---F~~dG----CpNCe~ 105 (125)
....+-.++...| |..|+-....+. +.+++ ||.|..
T Consensus 112 ~Vi~lHGsl~~~~-C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~ 154 (250)
T COG0846 112 NVIELHGSLKRVR-CSKCGNQYYDEDVIKFIEDGLIPRCPKCGG 154 (250)
T ss_pred cEEEeccceeeeE-eCCCcCccchhhhhhhcccCCCCcCccCCC
Confidence 4444556677776 999986665444 55577 999997
No 80
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
Probab=20.09 E-value=38 Score=19.79 Aligned_cols=13 Identities=15% Similarity=0.432 Sum_probs=10.3
Q ss_pred hhhcCCCChhhhh
Q psy8227 95 FEFDGCDNCDEFL 107 (125)
Q Consensus 95 F~~dGCpNCe~~L 107 (125)
|...+||.|....
T Consensus 5 f~~~~C~~C~~~~ 17 (74)
T TIGR02196 5 YTTPWCPPCKKAK 17 (74)
T ss_pred EcCCCChhHHHHH
Confidence 6678999998653
Done!