Query psy2469
Match_columns 220
No_of_seqs 94 out of 109
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 17:03:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2469.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2469hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4397|consensus 100.0 8.3E-86 1.8E-90 563.6 10.6 211 1-218 1-213 (213)
2 PRK05417 glutathione-dependent 94.6 0.059 1.3E-06 47.0 4.9 44 87-130 92-139 (191)
3 COG3791 Uncharacterized conser 93.8 0.23 4.9E-06 40.3 6.5 86 30-118 7-99 (133)
4 TIGR02820 formald_GSH S-(hydro 90.6 0.35 7.7E-06 42.0 4.1 41 89-130 90-135 (182)
5 PF04828 GFA: Glutathione-depe 88.8 0.31 6.8E-06 35.0 2.1 33 87-119 47-79 (92)
6 PF04359 DUF493: Protein of un 66.6 6.3 0.00014 29.4 2.8 30 140-169 41-70 (85)
7 PRK02047 hypothetical protein; 66.1 6 0.00013 30.4 2.7 28 142-169 49-76 (91)
8 PRK00341 hypothetical protein; 61.4 7.8 0.00017 29.9 2.6 27 143-169 50-76 (91)
9 PF04502 DUF572: Family of unk 60.9 5.8 0.00013 36.7 2.1 32 86-118 75-107 (324)
10 PF06397 Desulfoferrod_N: Desu 60.8 7.3 0.00016 25.8 2.0 19 24-42 2-21 (36)
11 PF01641 SelR: SelR domain; I 59.0 45 0.00098 27.5 6.8 89 18-119 27-121 (124)
12 KOG2923|consensus 58.8 4.9 0.00011 30.1 1.0 27 19-45 13-39 (67)
13 PRK04998 hypothetical protein; 57.3 9.7 0.00021 28.9 2.4 28 142-169 46-73 (88)
14 PRK05550 bifunctional methioni 55.8 14 0.0003 34.3 3.6 87 19-120 27-118 (283)
15 PRK00907 hypothetical protein; 54.9 12 0.00027 29.1 2.7 29 141-169 49-77 (92)
16 TIGR00357 methionine-R-sulfoxi 54.8 34 0.00073 28.6 5.4 84 19-119 31-123 (134)
17 PF05207 zf-CSL: CSL zinc fing 52.8 10 0.00023 26.7 1.8 27 21-47 11-37 (55)
18 PF03226 Yippee-Mis18: Yippee 45.4 20 0.00043 27.0 2.5 67 28-102 2-71 (96)
19 PRK00222 methionine sulfoxide 45.0 49 0.0011 28.0 5.0 88 19-120 34-127 (142)
20 COG5216 Uncharacterized conser 42.3 22 0.00048 26.5 2.2 22 19-40 13-34 (67)
21 PRK05508 methionine sulfoxide 41.5 97 0.0021 25.5 6.0 83 19-119 24-114 (119)
22 COG5134 Uncharacterized conser 40.9 33 0.00071 31.5 3.5 41 87-127 78-118 (272)
23 PHA02107 hypothetical protein 40.5 14 0.00031 32.6 1.1 30 151-184 180-211 (216)
24 smart00834 CxxC_CXXC_SSSS Puta 38.8 55 0.0012 20.5 3.5 13 25-37 2-15 (41)
25 TIGR00319 desulf_FeS4 desulfof 38.8 27 0.00059 21.9 2.0 16 26-41 5-21 (34)
26 cd00974 DSRD Desulforedoxin (D 38.2 27 0.00058 21.9 1.9 16 26-41 2-18 (34)
27 PF11331 DUF3133: Protein of u 37.7 18 0.00039 25.2 1.1 17 85-101 28-44 (46)
28 TIGR01624 LRP1_Cterm LRP1 C-te 37.4 17 0.00037 25.9 0.9 19 148-166 8-27 (50)
29 TIGR02605 CxxC_CxxC_SSSS putat 36.6 22 0.00048 23.8 1.4 11 25-35 2-13 (52)
30 COG1645 Uncharacterized Zn-fin 31.4 20 0.00044 29.9 0.6 12 89-100 29-40 (131)
31 PF09723 Zn-ribbon_8: Zinc rib 30.9 68 0.0015 21.1 3.0 14 25-38 2-16 (42)
32 PF06429 Flg_bbr_C: Flagellar 30.6 67 0.0014 23.0 3.2 35 152-186 30-64 (74)
33 COG1998 RPS31 Ribosomal protei 27.2 28 0.00061 24.9 0.7 12 88-99 37-48 (51)
34 PRK12632 flgC flagellar basal 26.2 74 0.0016 25.5 3.0 34 153-186 84-117 (130)
35 PF05142 DUF702: Domain of unk 25.9 32 0.00069 29.6 0.9 21 147-167 109-129 (154)
36 COG2921 Uncharacterized conser 23.4 67 0.0015 25.4 2.2 25 145-169 51-75 (90)
37 PRK07191 flgK flagellar hook-a 23.2 64 0.0014 31.1 2.5 28 157-184 416-443 (456)
38 PF11648 RIG-I_C-RD: C-termina 22.9 34 0.00073 27.6 0.5 20 85-104 1-20 (123)
39 PRK06003 flgB flagellar basal 22.8 1.1E+02 0.0025 24.5 3.5 32 157-188 87-118 (126)
40 KOG3994|consensus 22.6 1.2E+02 0.0026 28.4 3.9 60 125-192 152-211 (291)
41 PF01529 zf-DHHC: DHHC palmito 22.2 39 0.00084 27.1 0.7 22 21-42 55-77 (174)
42 PF06170 DUF983: Protein of un 21.0 20 0.00042 27.6 -1.2 23 88-110 8-30 (86)
43 PRK00432 30S ribosomal protein 20.7 49 0.0011 23.0 0.9 13 87-99 36-48 (50)
44 PRK07521 flgK flagellar hook-a 20.5 74 0.0016 30.9 2.3 28 157-184 443-470 (483)
45 PF14090 HTH_39: Helix-turn-he 20.0 70 0.0015 23.0 1.6 25 167-193 19-43 (70)
46 PRK00398 rpoP DNA-directed RNA 20.0 64 0.0014 21.3 1.3 17 88-104 21-37 (46)
No 1
>KOG4397|consensus
Probab=100.00 E-value=8.3e-86 Score=563.61 Aligned_cols=211 Identities=57% Similarity=0.858 Sum_probs=192.7
Q ss_pred CCceeeeeeeecCccchhccCCCCceeEEEeccCCeeeeeecccccCCCCCCCCeeEecCCCceeeeeccCCceEEEeCC
Q psy2469 1 MPKVISRSIVCSDTKDKEEYGEEKPLHIYYCVCGQMTLILDCAVEKLPLRRRDGARVIDGPKHAHKLTCEPDEVFHLKRP 80 (220)
Q Consensus 1 mPkvvSRsiv~sdt~d~eey~~e~~L~vYyClCG~~~Li~d~~Le~LP~RktD~A~Vld~~kh~~Kl~~~~~~~v~IrR~ 80 (220)
|||||||||||||++|+||| +.+|||+|||+||+|+||+||+|++||+|++|+|+|||...|++|++..+++.+||||+
T Consensus 1 mp~vvsrsvv~sdt~d~eeY-~~kpl~~yYClc~~m~li~DtqLekmPkRe~DrsrVid~~~h~akl~~~eg~~VylKR~ 79 (213)
T KOG4397|consen 1 MPKVVSRSVVCSDTDDREEY-GIKPLYLYYCLCGNMALILDTQLEKMPKRERDRSRVIDAKTHAAKLNVSEGETVYLKRG 79 (213)
T ss_pred CCcceecceeccccccHHHh-CCccceEEEEeeccchhhhhhHHHhccCcccccccccchhhhHHHhccCCCCeEEEecC
Confidence 99999999999999999999 44999999999999999999999999999999999999999999999999999999999
Q ss_pred C-cchhhhcccCCccceeeEEeeCC-CCCEEEEEcCceeeccCCCCchhhhhhhhhcCCeeEEEEeeeeccCceeeeEee
Q psy2469 81 E-GIERQHRFKCKKCGLFLYYKHDP-SSNIIFIVQGAVVKSSGEMPKMDIYNQVAVAKPKKIMVTKHTKNMGKFSSVTVS 158 (220)
Q Consensus 81 ~-GiEkQ~R~~C~rCgLpl~Y~~~~-~~~~~YIl~GALv~~~g~~~~~~~~~~~a~~~~kkvm~tk~tk~~GkfssvTvs 158 (220)
+ |||+|||.+|.+|+|||||||+| ..+++||+.+||..-|+++ .+.++++. ..|||||||+||||||||||||||
T Consensus 80 e~giErQyR~~C~~C~Lpl~Yr~~~~~~~~TFI~~~al~~~q~~~-~~~~~~~~--Q~~kkv~~~r~~k~~gk~ssvtvs 156 (213)
T KOG4397|consen 80 EGGIERQYRKKCIKCSLPLFYRHEPNLETVTFIYIVALALGQEVG-GFSINNEE--QRPKKVIMTRNTKNMGKFSSVTVS 156 (213)
T ss_pred CccHHHHHHHhhhcCCceeEEecCCCCCceEEEEEchhhhhhhcC-CCCCCChh--hccchheeeeeeecccccceeeec
Confidence 8 69999999999999999999999 8899999999999965544 34444432 357999999999999999999999
Q ss_pred cccchhhHHHHHHHHHHhhhhHHHHHHHHHhcCCCCcccCcccCCCCCCcccCCCccccc
Q psy2469 159 TIDEEEDEIEAREIADSYANNARIIEKQLERKGMNKRKSDSTTLNTGETEVKKPVRGTLI 218 (220)
Q Consensus 159 TideeEdEieareiadsYa~NAriiekql~rkg~~~~~~~~~~~~~~~~~~~~k~rGTLi 218 (220)
|||||||||||||+|||||+||||||+||+|||+++...+.. .+.++++||+|||||
T Consensus 157 t~dEeeeeieare~adsy~~narii~~qL~rkg~s~~~~~~~---a~~e~p~kk~rgtll 213 (213)
T KOG4397|consen 157 TIDEEEEEIEARETADSYAMNARIIEKQLKRKGSSSSSSAAA---AESETPVKKKRGTLL 213 (213)
T ss_pred chhHHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhHhh---hcccCchhhhccccC
Confidence 999999999999999999999999999999999998887662 222366788899997
No 2
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=94.60 E-value=0.059 Score=47.01 Aligned_cols=44 Identities=18% Similarity=0.421 Sum_probs=29.6
Q ss_pred hcccCCccceeeEEeeCC----CCCEEEEEcCceeeccCCCCchhhhh
Q psy2469 87 HRFKCKKCGLFLYYKHDP----SSNIIFIVQGAVVKSSGEMPKMDIYN 130 (220)
Q Consensus 87 ~R~~C~rCgLpl~Y~~~~----~~~~~YIl~GALv~~~g~~~~~~~~~ 130 (220)
.|.-|+.||-+|+++.+. -...+||--|.|-......|...+|.
T Consensus 92 ~R~FC~~CGS~L~~~~e~~~~~~pgl~fV~~gllDd~~~~~P~~~ifv 139 (191)
T PRK05417 92 QRHACKECGVHMYGRIENKDHPFYGLDFVHTELSQEQGWSAPGFAAFV 139 (191)
T ss_pred EeeeCCCCCCccccccccccCCCCCeEEEehhhcCCCCCCCceEEeee
Confidence 345699999999999872 33566777776666544445555553
No 3
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=93.80 E-value=0.23 Score=40.29 Aligned_cols=86 Identities=14% Similarity=0.207 Sum_probs=53.0
Q ss_pred EeccCCeeeeeecccccCC-------CCCCCCeeEecCCCceeeeeccCCceEEEeCCCcchhhhcccCCccceeeEEee
Q psy2469 30 YCVCGQMTLILDCAVEKLP-------LRRRDGARVIDGPKHAHKLTCEPDEVFHLKRPEGIERQHRFKCKKCGLFLYYKH 102 (220)
Q Consensus 30 yClCG~~~Li~d~~Le~LP-------~RktD~A~Vld~~kh~~Kl~~~~~~~v~IrR~~GiEkQ~R~~C~rCgLpl~Y~~ 102 (220)
.|+||..-+-.+-++..+= +|.+..+...-..-....+.-..+.+.+-......++. -|+.||-+|+|+.
T Consensus 7 ~C~CGaVrf~v~~~~~~~~~ChCs~Crk~~G~~~~~~~~~~~~~~~~~~g~~~~~~~s~~~~r~---FC~~CGs~l~~~~ 83 (133)
T COG3791 7 GCLCGAVRFEVEGDPGHVSACHCSDCRKASGAAFAAYAVVPRDALRGTRGLPTYYFSSGSAGRG---FCPTCGSPLFWRG 83 (133)
T ss_pred ceeeceEEEEEecCCCCceeeCchHhhhhhCCceeeeeecccceeeecCCCceEEeecCCCCCe---ecccCCCceEEec
Confidence 4777777776666665533 22233333333322233334444555555444445555 7999999999998
Q ss_pred CCCCCEEEEEcCceee
Q psy2469 103 DPSSNIIFIVQGAVVK 118 (220)
Q Consensus 103 ~~~~~~~YIl~GALv~ 118 (220)
....+++.|.-|+|-.
T Consensus 84 ~~~~~~~~v~~~~ld~ 99 (133)
T COG3791 84 PDEDPFVGVNAGALDD 99 (133)
T ss_pred CCCCceEEEEEeeecC
Confidence 7744899999888873
No 4
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=90.61 E-value=0.35 Score=41.97 Aligned_cols=41 Identities=22% Similarity=0.470 Sum_probs=26.1
Q ss_pred ccCCccceeeEEeeCC-CCCEE---EEEcCceeeccCC-CCchhhhh
Q psy2469 89 FKCKKCGLFLYYKHDP-SSNII---FIVQGAVVKSSGE-MPKMDIYN 130 (220)
Q Consensus 89 ~~C~rCgLpl~Y~~~~-~~~~~---YIl~GALv~~~g~-~~~~~~~~ 130 (220)
.-|+.||-+|+++... +.++. ||--|.|-.. +. .|...||.
T Consensus 90 ~FC~~CGS~L~~~~~~~~~~~~g~v~I~aGtLDd~-~~~~P~~hIft 135 (182)
T TIGR02820 90 HACKGCGTHMYGRIENKDHPFYGLDFIHTELSAED-GWSAPGFAAFV 135 (182)
T ss_pred ecCCCCCCcccccccccCCCccceeEEEEeecCCC-CcCCCeEEEEE
Confidence 3699999999999852 33333 7777776542 32 35555553
No 5
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=88.84 E-value=0.31 Score=34.98 Aligned_cols=33 Identities=18% Similarity=0.528 Sum_probs=24.5
Q ss_pred hcccCCccceeeEEeeCCCCCEEEEEcCceeec
Q psy2469 87 HRFKCKKCGLFLYYKHDPSSNIIFIVQGAVVKS 119 (220)
Q Consensus 87 ~R~~C~rCgLpl~Y~~~~~~~~~YIl~GALv~~ 119 (220)
.|.-|+.||-+|++.....+.+++|--|.|-..
T Consensus 47 ~r~FC~~CGs~l~~~~~~~~~~~~V~~g~ld~~ 79 (92)
T PF04828_consen 47 ERYFCPTCGSPLFSEDERDPDLVGVNAGTLDDP 79 (92)
T ss_dssp EEEEETTT--EEEEEESSTTTEEEEEGGGBTT-
T ss_pred cCcccCCCCCeeecccCCCCCEEEEEeEeeCCC
Confidence 347899999999999767788888888877665
No 6
>PF04359 DUF493: Protein of unknown function (DUF493); InterPro: IPR007454 This family includes several proteins of uncharacterised function.; PDB: 1RWU_A 2JOQ_A 2H9Z_A.
Probab=66.65 E-value=6.3 Score=29.35 Aligned_cols=30 Identities=33% Similarity=0.464 Sum_probs=24.0
Q ss_pred EEEEeeeeccCceeeeEeecccchhhHHHH
Q psy2469 140 IMVTKHTKNMGKFSSVTVSTIDEEEDEIEA 169 (220)
Q Consensus 140 vm~tk~tk~~GkfssvTvsTideeEdEiea 169 (220)
..++-+.-.-|||-||||+..=+.+|++.|
T Consensus 41 ~~~~~k~S~~GkY~Svtv~v~v~s~eq~~~ 70 (85)
T PF04359_consen 41 EKVSSKPSSKGKYVSVTVSVTVESAEQVDA 70 (85)
T ss_dssp EEEEECCSTTSSEEEEEEEEEESSHHHHHH
T ss_pred CceEEecCCCCeEEEEEEEEEECCHHHHHH
Confidence 345556888899999999888888888765
No 7
>PRK02047 hypothetical protein; Provisional
Probab=66.07 E-value=6 Score=30.43 Aligned_cols=28 Identities=7% Similarity=0.395 Sum_probs=23.5
Q ss_pred EEeeeeccCceeeeEeecccchhhHHHH
Q psy2469 142 VTKHTKNMGKFSSVTVSTIDEEEDEIEA 169 (220)
Q Consensus 142 ~tk~tk~~GkfssvTvsTideeEdEiea 169 (220)
++-+.-..|||-||||+..=+.+|+++|
T Consensus 49 i~~k~Ss~GkY~Svtv~v~v~s~eq~~~ 76 (91)
T PRK02047 49 IEERPSSGGNYTGLTITVRATSREQLDN 76 (91)
T ss_pred eEEccCCCCeEEEEEEEEEECCHHHHHH
Confidence 4557788899999999888888888876
No 8
>PRK00341 hypothetical protein; Provisional
Probab=61.43 E-value=7.8 Score=29.92 Aligned_cols=27 Identities=19% Similarity=0.533 Sum_probs=23.2
Q ss_pred EeeeeccCceeeeEeecccchhhHHHH
Q psy2469 143 TKHTKNMGKFSSVTVSTIDEEEDEIEA 169 (220)
Q Consensus 143 tk~tk~~GkfssvTvsTideeEdEiea 169 (220)
+-+.-..|||-||||+-.=+.+|+++|
T Consensus 50 ~~k~Ss~GkY~S~tv~i~~~s~~q~~~ 76 (91)
T PRK00341 50 AERQSSNGKYTTVQLHIVATDEDQLQD 76 (91)
T ss_pred eeccCCCCEEEEEEEEEEECCHHHHHH
Confidence 447778899999999999989998876
No 9
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=60.86 E-value=5.8 Score=36.73 Aligned_cols=32 Identities=25% Similarity=0.594 Sum_probs=25.4
Q ss_pred hhcccCCccceeeEEeeCC-CCCEEEEEcCceee
Q psy2469 86 QHRFKCKKCGLFLYYKHDP-SSNIIFIVQGAVVK 118 (220)
Q Consensus 86 Q~R~~C~rCgLpl~Y~~~~-~~~~~YIl~GALv~ 118 (220)
+|+++|..|+=.|-.++|| +..|+ +..||--.
T Consensus 75 rF~~kC~~C~~~i~~kTDPkn~dY~-~~~Ga~R~ 107 (324)
T PF04502_consen 75 RFYIKCPRCSNEIEFKTDPKNTDYV-VESGARRN 107 (324)
T ss_pred EEEEEcCCCCCEEeeecCCCCCCee-eecCeeec
Confidence 4889999999999999999 66665 44566553
No 10
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=60.76 E-value=7.3 Score=25.81 Aligned_cols=19 Identities=26% Similarity=0.621 Sum_probs=11.8
Q ss_pred CceeEEEe-ccCCeeeeeec
Q psy2469 24 KPLHIYYC-VCGQMTLILDC 42 (220)
Q Consensus 24 ~~L~vYyC-lCG~~~Li~d~ 42 (220)
+.+.+|.| +||..+.+++.
T Consensus 2 ~~~~~YkC~~CGniVev~~~ 21 (36)
T PF06397_consen 2 KKGEFYKCEHCGNIVEVVHD 21 (36)
T ss_dssp -TTEEEE-TTT--EEEEEE-
T ss_pred CcccEEEccCCCCEEEEEEC
Confidence 35678999 89999988764
No 11
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=58.99 E-value=45 Score=27.47 Aligned_cols=89 Identities=20% Similarity=0.292 Sum_probs=49.6
Q ss_pred hccCCCCceeEEEe-ccCCeeeeeecccccCCCCCCCCeeEecCCCceeeeeccCCceEEEeCCCc-chhhhcccCCccc
Q psy2469 18 EEYGEEKPLHIYYC-VCGQMTLILDCAVEKLPLRRRDGARVIDGPKHAHKLTCEPDEVFHLKRPEG-IERQHRFKCKKCG 95 (220)
Q Consensus 18 eey~~e~~L~vYyC-lCG~~~Li~d~~Le~LP~RktD~A~Vld~~kh~~Kl~~~~~~~v~IrR~~G-iEkQ~R~~C~rCg 95 (220)
.+|.....--+|+| .||.-+.-++...++=-== -.|. ...+++.|..++... .-.+--..|.+|+
T Consensus 27 g~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GW------------PSF~-~~i~~~~v~~~~D~s~g~~R~Ev~C~~Cg 93 (124)
T PF01641_consen 27 GEYWDHKEEGIYVCAVCGTPLFSSDTKFDSGCGW------------PSFW-QPIPGDAVKEREDFSHGMVRTEVRCARCG 93 (124)
T ss_dssp SGGCCTTSSEEEEETTTS-EEEEGGGEETSSSSS------------SEES-SCSSTTSEEEEEEECTSSEEEEEEETTTC
T ss_pred cCCcCCCCCEEEEcCCCCCccccCcccccCCcCC------------cccc-CcCChHHEEEeccccCCceEEEEEecCCC
Confidence 35667778889999 7998888887766521100 0000 011222222222211 1233446899999
Q ss_pred eeeEEeeCC--C--CCEEEEEcCceeec
Q psy2469 96 LFLYYKHDP--S--SNIIFIVQGAVVKS 119 (220)
Q Consensus 96 Lpl~Y~~~~--~--~~~~YIl~GALv~~ 119 (220)
-.||+.-++ . ..--|-|+++-+.+
T Consensus 94 ~HLGHVF~DGp~~~tg~RyCINS~sL~F 121 (124)
T PF01641_consen 94 SHLGHVFDDGPPPPTGLRYCINSASLKF 121 (124)
T ss_dssp CEEEEEESTSSTTCTSCEEEE-GGGEEE
T ss_pred CccccEeCCCCCCCCCcEEEeeeeeEEE
Confidence 999999875 1 23567777776654
No 12
>KOG2923|consensus
Probab=58.85 E-value=4.9 Score=30.11 Aligned_cols=27 Identities=33% Similarity=0.508 Sum_probs=20.7
Q ss_pred ccCCCCceeEEEeccCCeeeeeecccc
Q psy2469 19 EYGEEKPLHIYYCVCGQMTLILDCAVE 45 (220)
Q Consensus 19 ey~~e~~L~vYyClCG~~~Li~d~~Le 45 (220)
+|+.++..+.|=|.||...-|+--+|+
T Consensus 13 e~~~e~~~y~yPCpCGDrf~It~edL~ 39 (67)
T KOG2923|consen 13 EFDEENQTYYYPCPCGDRFQITLEDLE 39 (67)
T ss_pred eeccCCCeEEcCCCCCCeeeecHHHHh
Confidence 457889999999999988766654443
No 13
>PRK04998 hypothetical protein; Provisional
Probab=57.30 E-value=9.7 Score=28.91 Aligned_cols=28 Identities=18% Similarity=0.369 Sum_probs=22.7
Q ss_pred EEeeeeccCceeeeEeecccchhhHHHH
Q psy2469 142 VTKHTKNMGKFSSVTVSTIDEEEDEIEA 169 (220)
Q Consensus 142 ~tk~tk~~GkfssvTvsTideeEdEiea 169 (220)
++-|.-..|||-||||+..=+.+|++.|
T Consensus 46 ~~~r~S~~GkY~Svtv~v~v~s~eq~~~ 73 (88)
T PRK04998 46 PTVKPSSKGNYHSVSITITATSIEQVET 73 (88)
T ss_pred ceEccCCCCEEEEEEEEEEECCHHHHHH
Confidence 3446678899999999988888888765
No 14
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=55.78 E-value=14 Score=34.27 Aligned_cols=87 Identities=20% Similarity=0.261 Sum_probs=50.9
Q ss_pred ccCCCCceeEEEe-ccCCeeeeeecccccCCCCCCCCeeEecCCCceeeeeccCCceEEEeCCCcchhhhcccCCcccee
Q psy2469 19 EYGEEKPLHIYYC-VCGQMTLILDCAVEKLPLRRRDGARVIDGPKHAHKLTCEPDEVFHLKRPEGIERQHRFKCKKCGLF 97 (220)
Q Consensus 19 ey~~e~~L~vYyC-lCG~~~Li~d~~Le~LP~RktD~A~Vld~~kh~~Kl~~~~~~~v~IrR~~GiEkQ~R~~C~rCgLp 97 (220)
+|.....--+|+| .||.-+.-++...++= + ..-.| ....++..+.++-..|+ +--.+|.+|+-.
T Consensus 27 ~~~~~~~~G~y~c~~c~~~LF~s~~Kf~sg----~--------GWPsF-~~~~~~~~~~~~d~~~~--R~Ev~c~~c~~H 91 (283)
T PRK05550 27 EYYDHDEKGVYLCRRCGAPLFRSEDKFNSG----C--------GWPSF-DDEIPGAVKRLPDADGR--RTEIVCANCGAH 91 (283)
T ss_pred cCcCCCCCcEEEcCCCCchhcCChhhccCC----C--------CCcCc-CcccCCccEEEEcCCCc--eEEEEecCCCCc
Confidence 4556677789999 6998777776655530 0 00000 01112222222222343 455899999999
Q ss_pred eEEeeCCCC----CEEEEEcCceeecc
Q psy2469 98 LYYKHDPSS----NIIFIVQGAVVKSS 120 (220)
Q Consensus 98 l~Y~~~~~~----~~~YIl~GALv~~~ 120 (220)
||+--+.++ ..-|-++++...+.
T Consensus 92 LGHvF~ddgp~ptg~RyCiNs~sL~f~ 118 (283)
T PRK05550 92 LGHVFEGEGLTPKNTRHCVNSASLDFV 118 (283)
T ss_pred cCcccCCCCCCCCCccccccccccccC
Confidence 999876332 24577888777653
No 15
>PRK00907 hypothetical protein; Provisional
Probab=54.93 E-value=12 Score=29.12 Aligned_cols=29 Identities=21% Similarity=0.349 Sum_probs=24.5
Q ss_pred EEEeeeeccCceeeeEeecccchhhHHHH
Q psy2469 141 MVTKHTKNMGKFSSVTVSTIDEEEDEIEA 169 (220)
Q Consensus 141 m~tk~tk~~GkfssvTvsTideeEdEiea 169 (220)
-++-|.-..|||-||||+-.=+.+|+++|
T Consensus 49 ~i~~r~Ss~GkY~Svtv~i~ats~eQld~ 77 (92)
T PRK00907 49 RISWKHSSSGKYVSVRIGFRAESREQYDA 77 (92)
T ss_pred cEEeccCCCCEEEEEEEEEEECCHHHHHH
Confidence 34557788999999999988899999886
No 16
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=54.80 E-value=34 Score=28.64 Aligned_cols=84 Identities=23% Similarity=0.384 Sum_probs=49.8
Q ss_pred ccCCCCceeEEEe-ccCCeeeeeeccccc---CCCCCCCCeeEecCCCceeeeeccCCceEEEeCCC--cchhhhcccCC
Q psy2469 19 EYGEEKPLHIYYC-VCGQMTLILDCAVEK---LPLRRRDGARVIDGPKHAHKLTCEPDEVFHLKRPE--GIERQHRFKCK 92 (220)
Q Consensus 19 ey~~e~~L~vYyC-lCG~~~Li~d~~Le~---LP~RktD~A~Vld~~kh~~Kl~~~~~~~v~IrR~~--GiEkQ~R~~C~ 92 (220)
+|.....--+|+| .||.-+.-++...++ .|-= + ...+.+.|-.+... |+ .+--..|.
T Consensus 31 ~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF--~--------------~~i~~~~V~~~~D~s~gm-~RtEv~C~ 93 (134)
T TIGR00357 31 EYWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSF--Y--------------KPISEEVVAYERDESHGM-IRTEVRCR 93 (134)
T ss_pred CCCCCCCCeEEEccCCCCccccccchhcCCCCCcCc--C--------------cccCCCceEEeecCCCCc-EEEEEEec
Confidence 4666778889999 799877777665543 1110 0 00111111111111 32 22457899
Q ss_pred ccceeeEEeeCC---CCCEEEEEcCceeec
Q psy2469 93 KCGLFLYYKHDP---SSNIIFIVQGAVVKS 119 (220)
Q Consensus 93 rCgLpl~Y~~~~---~~~~~YIl~GALv~~ 119 (220)
+|+-.||+--+. ....-|=++++-+.+
T Consensus 94 ~Cg~HLGHVF~DGP~ptg~RyCINs~sL~F 123 (134)
T TIGR00357 94 NCDAHLGHVFDDGPEPTGLRYCINSAALKF 123 (134)
T ss_pred CCCCccCcccCCCCCCCCceEeecceeEec
Confidence 999999997654 233568888888777
No 17
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=52.79 E-value=10 Score=26.68 Aligned_cols=27 Identities=30% Similarity=0.402 Sum_probs=21.7
Q ss_pred CCCCceeEEEeccCCeeeeeecccccC
Q psy2469 21 GEEKPLHIYYCVCGQMTLILDCAVEKL 47 (220)
Q Consensus 21 ~~e~~L~vYyClCG~~~Li~d~~Le~L 47 (220)
+.+...++|-|-||....|+...|+.-
T Consensus 11 ~~~~~~~~y~CRCG~~f~i~e~~l~~~ 37 (55)
T PF05207_consen 11 DEEEGVYSYPCRCGGEFEISEEDLEEG 37 (55)
T ss_dssp ETTTTEEEEEETTSSEEEEEHHHHHCT
T ss_pred cCCCCEEEEcCCCCCEEEEcchhccCc
Confidence 456667999999999988888887643
No 18
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=45.41 E-value=20 Score=26.97 Aligned_cols=67 Identities=18% Similarity=0.295 Sum_probs=35.8
Q ss_pred EEEe-ccCCeeeeeecccccCCCCCCCCeeEecCCCceeee-eccCCceEEEeCCCcchhhhc-ccCCccceeeEEee
Q psy2469 28 IYYC-VCGQMTLILDCAVEKLPLRRRDGARVIDGPKHAHKL-TCEPDEVFHLKRPEGIERQHR-FKCKKCGLFLYYKH 102 (220)
Q Consensus 28 vYyC-lCG~~~Li~d~~Le~LP~RktD~A~Vld~~kh~~Kl-~~~~~~~v~IrR~~GiEkQ~R-~~C~rCgLpl~Y~~ 102 (220)
+|.| .|..++--++--+. +..+.-+|+++. ++ +..+.+..+.....|.+=-|+ +.|..|+..||..-
T Consensus 2 vf~C~~C~t~l~ds~~lvs--~~g~~~~a~l~~------~v~~~~~~~~~~~t~~~~~~~~~~~l~C~~C~~~lGwkY 71 (96)
T PF03226_consen 2 VFQCKNCKTILADSNELVS--FHGREGKAYLFN------NVSNGVPVDRELMTGETGGDHTVRDLFCSGCNTILGWKY 71 (96)
T ss_pred EEECCCCCCCcCCHHHhee--cCCCCccEEEEe------eeeecccccceEEEeeCCCCEEEEEeEcccCChhHCcEE
Confidence 6778 57655433333333 222334666664 22 333333333333334443333 89999999999664
No 19
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=45.04 E-value=49 Score=27.95 Aligned_cols=88 Identities=20% Similarity=0.328 Sum_probs=49.3
Q ss_pred ccCCCCceeEEEe-ccCCeeeeeecccccCCCCCCCCeeEecCCCceeeeeccCCceEEEeCC--CcchhhhcccCCccc
Q psy2469 19 EYGEEKPLHIYYC-VCGQMTLILDCAVEKLPLRRRDGARVIDGPKHAHKLTCEPDEVFHLKRP--EGIERQHRFKCKKCG 95 (220)
Q Consensus 19 ey~~e~~L~vYyC-lCG~~~Li~d~~Le~LP~RktD~A~Vld~~kh~~Kl~~~~~~~v~IrR~--~GiEkQ~R~~C~rCg 95 (220)
+|.....--+|+| .||.-+.-++...++= ...-.|- ...+.+.|-.+.. -|+. +--..|.+|+
T Consensus 34 ~~~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg------------~GWPSF~-~~i~~~~V~~~~D~s~gm~-RtEv~C~~Cg 99 (142)
T PRK00222 34 EYLDNKEKGIYVCIVCGEPLFSSDTKFDSG------------CGWPSFT-KPIDEEAIRELRDTSHGMV-RTEVRCANCD 99 (142)
T ss_pred CCCCCCCCeEEEecCCCchhcCCcccccCC------------CCCcCcC-cccCCCceEEeeccCCCce-EEEEEeCCCC
Confidence 4566777889999 7997777665544320 0000000 0111112222221 2322 2447899999
Q ss_pred eeeEEeeCC---CCCEEEEEcCceeecc
Q psy2469 96 LFLYYKHDP---SSNIIFIVQGAVVKSS 120 (220)
Q Consensus 96 Lpl~Y~~~~---~~~~~YIl~GALv~~~ 120 (220)
-.||+.-+. ....-|-+++|.+.+.
T Consensus 100 ~HLGHVF~DGP~ptg~RyCINs~sL~F~ 127 (142)
T PRK00222 100 SHLGHVFPDGPKPTGLRYCINSASLKFI 127 (142)
T ss_pred CccCcccCCCCCCCCCEeeeceeeEEee
Confidence 999997654 3335688888887773
No 20
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=42.29 E-value=22 Score=26.50 Aligned_cols=22 Identities=27% Similarity=0.555 Sum_probs=17.7
Q ss_pred ccCCCCceeEEEeccCCeeeee
Q psy2469 19 EYGEEKPLHIYYCVCGQMTLIL 40 (220)
Q Consensus 19 ey~~e~~L~vYyClCG~~~Li~ 40 (220)
+|+.++.+++|-|.||.-.=|+
T Consensus 13 tf~~e~~~ftyPCPCGDRFeIs 34 (67)
T COG5216 13 TFSREEKTFTYPCPCGDRFEIS 34 (67)
T ss_pred EEcCCCceEEecCCCCCEeEEE
Confidence 4589999999999999665443
No 21
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=41.49 E-value=97 Score=25.54 Aligned_cols=83 Identities=19% Similarity=0.217 Sum_probs=50.2
Q ss_pred ccCCCCceeEEEe-ccCCeeeeeeccccc---CCCCCCCCeeEecCCCceeeeeccCCceEEEeCCCcchhhhcccCCcc
Q psy2469 19 EYGEEKPLHIYYC-VCGQMTLILDCAVEK---LPLRRRDGARVIDGPKHAHKLTCEPDEVFHLKRPEGIERQHRFKCKKC 94 (220)
Q Consensus 19 ey~~e~~L~vYyC-lCG~~~Li~d~~Le~---LP~RktD~A~Vld~~kh~~Kl~~~~~~~v~IrR~~GiEkQ~R~~C~rC 94 (220)
+|.....--+|+| .||.-+.-++...++ .|-= +. ..++ .|........ .|.-.+|.+|
T Consensus 24 ~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF--~~--------------~i~~-~v~~~~D~~~-~RtEv~C~~C 85 (119)
T PRK05508 24 EYNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSF--DD--------------EIKG-AVKRIPDADG-RRTEIVCANC 85 (119)
T ss_pred CCcCcCCCeEEEecCCCCccccccccccCCCCCccc--Cc--------------cccc-ceEEEecCCC-cEEEEEeCCC
Confidence 5666778889999 799877777766543 1100 00 0111 1111111111 3556899999
Q ss_pred ceeeEEeeCCCC----CEEEEEcCceeec
Q psy2469 95 GLFLYYKHDPSS----NIIFIVQGAVVKS 119 (220)
Q Consensus 95 gLpl~Y~~~~~~----~~~YIl~GALv~~ 119 (220)
+-.||+--+.++ ..-|=+++|-..+
T Consensus 86 ~~HLGHVF~d~gp~ptg~RyCINS~sL~F 114 (119)
T PRK05508 86 GGHLGHVFEGEGFTPKNTRHCVNSISLKF 114 (119)
T ss_pred CCccCcccCCCCCCCCCCEEeecceeEEe
Confidence 999999766332 3568888887776
No 22
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=40.91 E-value=33 Score=31.48 Aligned_cols=41 Identities=20% Similarity=0.285 Sum_probs=26.8
Q ss_pred hcccCCccceeeEEeeCCCCCEEEEEcCceeeccCCCCchh
Q psy2469 87 HRFKCKKCGLFLYYKHDPSSNIIFIVQGAVVKSSGEMPKMD 127 (220)
Q Consensus 87 ~R~~C~rCgLpl~Y~~~~~~~~~YIl~GALv~~~g~~~~~~ 127 (220)
|-..|.+|+-+|+.+.||.+...-+=-|..-..-.|.+.-|
T Consensus 78 f~I~C~~C~n~i~~RTDPkN~~YV~EsGg~R~i~pq~~n~D 118 (272)
T COG5134 78 FSIKCHLCSNPIDVRTDPKNTEYVVESGGRRKIEPQDINED 118 (272)
T ss_pred EEEEccCCCCceeeecCCCCceEEEecCceeecCccccccC
Confidence 44799999999999999955542233344443444555544
No 23
>PHA02107 hypothetical protein
Probab=40.54 E-value=14 Score=32.62 Aligned_cols=30 Identities=53% Similarity=0.773 Sum_probs=24.3
Q ss_pred ceeeeEeecccchhhHHHHH--HHHHHhhhhHHHHH
Q psy2469 151 KFSSVTVSTIDEEEDEIEAR--EIADSYANNARIIE 184 (220)
Q Consensus 151 kfssvTvsTideeEdEiear--eiadsYa~NAriie 184 (220)
-|+||.+|-||+|=-|+.|| ||.| |-++|-
T Consensus 180 ~F~S~Ri~EID~EI~~LQA~RKEiED----N~K~IK 211 (216)
T PHA02107 180 HFASVRISEIDEEIKELQARRKEIED----NIKSIK 211 (216)
T ss_pred hhhhhhHhHHhHHHHHHHHHHHHHHH----HHHHHH
Confidence 48899999999999999996 5655 666664
No 24
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=38.82 E-value=55 Score=20.49 Aligned_cols=13 Identities=38% Similarity=0.937 Sum_probs=10.9
Q ss_pred ceeEEEe-ccCCee
Q psy2469 25 PLHIYYC-VCGQMT 37 (220)
Q Consensus 25 ~L~vYyC-lCG~~~ 37 (220)
|+|.|.| -||+..
T Consensus 2 p~Y~y~C~~Cg~~f 15 (41)
T smart00834 2 PIYEYRCEDCGHTF 15 (41)
T ss_pred CCEEEEcCCCCCEE
Confidence 7899999 699944
No 25
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=38.79 E-value=27 Score=21.87 Aligned_cols=16 Identities=38% Similarity=0.968 Sum_probs=14.2
Q ss_pred eeEEEe-ccCCeeeeee
Q psy2469 26 LHIYYC-VCGQMTLILD 41 (220)
Q Consensus 26 L~vYyC-lCG~~~Li~d 41 (220)
+.+|.| .||..+.+++
T Consensus 5 ~~~ykC~~Cgniv~v~~ 21 (34)
T TIGR00319 5 GQVYKCEVCGNIVEVLH 21 (34)
T ss_pred CcEEEcCCCCcEEEEEE
Confidence 678999 8999999886
No 26
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=38.21 E-value=27 Score=21.95 Aligned_cols=16 Identities=38% Similarity=1.157 Sum_probs=13.7
Q ss_pred eeEEEe-ccCCeeeeee
Q psy2469 26 LHIYYC-VCGQMTLILD 41 (220)
Q Consensus 26 L~vYyC-lCG~~~Li~d 41 (220)
+.+|.| .||..+.+++
T Consensus 2 ~~~ykC~~CGniv~v~~ 18 (34)
T cd00974 2 LEVYKCEICGNIVEVLN 18 (34)
T ss_pred CcEEEcCCCCcEEEEEE
Confidence 458999 8999999886
No 27
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=37.68 E-value=18 Score=25.18 Aligned_cols=17 Identities=24% Similarity=0.747 Sum_probs=14.8
Q ss_pred hhhcccCCccceeeEEe
Q psy2469 85 RQHRFKCKKCGLFLYYK 101 (220)
Q Consensus 85 kQ~R~~C~rCgLpl~Y~ 101 (220)
+|++++|+.|.=.|-|.
T Consensus 28 ~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 28 NQQKLRCGACSEVLSFS 44 (46)
T ss_pred ceeEEeCCCCceeEEEe
Confidence 48999999999988875
No 28
>TIGR01624 LRP1_Cterm LRP1 C-terminal domain. This model represents a tightly conserved small domain found in LRP1 and related plant proteins. This family also contains a well-conserved putative zinc finger domain (TIGR01623). The rest of the sequence of most members consists of highly divergent, low-complexity sequence.
Probab=37.43 E-value=17 Score=25.92 Aligned_cols=19 Identities=37% Similarity=0.539 Sum_probs=15.4
Q ss_pred ccCceeeeEeecccchhh-H
Q psy2469 148 NMGKFSSVTVSTIDEEED-E 166 (220)
Q Consensus 148 ~~GkfssvTvsTideeEd-E 166 (220)
..--|..|.||.|||.|+ |
T Consensus 8 s~AvFrcvRvs~idd~~~~e 27 (50)
T TIGR01624 8 APAVFKCVRVTAIDDGEQAE 27 (50)
T ss_pred cceEEEEEEEeccCCCCCce
Confidence 345688999999999887 5
No 29
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=36.57 E-value=22 Score=23.80 Aligned_cols=11 Identities=45% Similarity=1.283 Sum_probs=9.9
Q ss_pred ceeEEEe-ccCC
Q psy2469 25 PLHIYYC-VCGQ 35 (220)
Q Consensus 25 ~L~vYyC-lCG~ 35 (220)
|+|.|.| -||+
T Consensus 2 P~Yey~C~~Cg~ 13 (52)
T TIGR02605 2 PIYEYRCTACGH 13 (52)
T ss_pred CCEEEEeCCCCC
Confidence 7899999 6998
No 30
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=31.45 E-value=20 Score=29.94 Aligned_cols=12 Identities=42% Similarity=0.880 Sum_probs=10.6
Q ss_pred ccCCccceeeEE
Q psy2469 89 FKCKKCGLFLYY 100 (220)
Q Consensus 89 ~~C~rCgLpl~Y 100 (220)
.-|+.||.|||=
T Consensus 29 ~hCp~Cg~PLF~ 40 (131)
T COG1645 29 KHCPKCGTPLFR 40 (131)
T ss_pred hhCcccCCccee
Confidence 469999999997
No 31
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=30.85 E-value=68 Score=21.12 Aligned_cols=14 Identities=36% Similarity=0.795 Sum_probs=10.9
Q ss_pred ceeEEEe-ccCCeee
Q psy2469 25 PLHIYYC-VCGQMTL 38 (220)
Q Consensus 25 ~L~vYyC-lCG~~~L 38 (220)
|+|.|.| -||+..=
T Consensus 2 P~Yey~C~~Cg~~fe 16 (42)
T PF09723_consen 2 PIYEYRCEECGHEFE 16 (42)
T ss_pred CCEEEEeCCCCCEEE
Confidence 7899999 6995443
No 32
>PF06429 Flg_bbr_C: Flagellar basal body rod FlgEFG protein C-terminal; InterPro: IPR010930 This entry consists of a number of C-terminal domains of unknown function. This domain seems to be specific to flagellar basal-body rod and flagellar hook proteins in which IPR001444 from INTERPRO is often present at the extreme N terminus.; GO: 0019861 flagellum; PDB: 2D4Y_A 2BGY_A 1WLG_B 2BGZ_A 3A69_A.
Probab=30.58 E-value=67 Score=22.95 Aligned_cols=35 Identities=23% Similarity=0.379 Sum_probs=25.1
Q ss_pred eeeeEeecccchhhHHHHHHHHHHhhhhHHHHHHH
Q psy2469 152 FSSVTVSTIDEEEDEIEAREIADSYANNARIIEKQ 186 (220)
Q Consensus 152 fssvTvsTideeEdEieareiadsYa~NAriiekq 186 (220)
-+.+-.|-+|-.+|=.+--++.-+|.+|+|+|.-.
T Consensus 30 ~g~le~SnVd~~~Em~~li~~qr~y~a~~kvi~~~ 64 (74)
T PF06429_consen 30 QGYLEGSNVDLDEEMVDLIEAQRAYEANAKVIQTA 64 (74)
T ss_dssp CCCCEE-----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hcchhcCCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34578899998888888899999999999999754
No 33
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.16 E-value=28 Score=24.92 Aligned_cols=12 Identities=42% Similarity=1.101 Sum_probs=8.6
Q ss_pred cccCCccceeeE
Q psy2469 88 RFKCKKCGLFLY 99 (220)
Q Consensus 88 R~~C~rCgLpl~ 99 (220)
||-|++||..-+
T Consensus 37 R~~CGkCgyTe~ 48 (51)
T COG1998 37 RWACGKCGYTEF 48 (51)
T ss_pred eeEeccccceEe
Confidence 788888886543
No 34
>PRK12632 flgC flagellar basal body rod protein FlgC; Provisional
Probab=26.24 E-value=74 Score=25.54 Aligned_cols=34 Identities=26% Similarity=0.333 Sum_probs=30.3
Q ss_pred eeeEeecccchhhHHHHHHHHHHhhhhHHHHHHH
Q psy2469 153 SSVTVSTIDEEEDEIEAREIADSYANNARIIEKQ 186 (220)
Q Consensus 153 ssvTvsTideeEdEieareiadsYa~NAriiekq 186 (220)
+.+-.|.+|-++|=.+.-+..-+|..|+++|+.+
T Consensus 84 g~~e~snVdl~~Em~~~~~~~r~y~a~~~~~~~~ 117 (130)
T PRK12632 84 GYYDGSNVDLVVEIADAREAQRSYEANLRMFDQA 117 (130)
T ss_pred ccccCCCcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3678899998999899999999999999999874
No 35
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function.
Probab=25.85 E-value=32 Score=29.57 Aligned_cols=21 Identities=43% Similarity=0.578 Sum_probs=17.3
Q ss_pred eccCceeeeEeecccchhhHH
Q psy2469 147 KNMGKFSSVTVSTIDEEEDEI 167 (220)
Q Consensus 147 k~~GkfssvTvsTideeEdEi 167 (220)
-.+--|--|-||-|||.|||+
T Consensus 109 ~spAvFRCVRVssiDdgedE~ 129 (154)
T PF05142_consen 109 SSPAVFRCVRVSSIDDGEDEY 129 (154)
T ss_pred cccceEEEEEEecccCcccce
Confidence 445568889999999999984
No 36
>COG2921 Uncharacterized conserved protein [Function unknown]
Probab=23.45 E-value=67 Score=25.43 Aligned_cols=25 Identities=20% Similarity=0.411 Sum_probs=21.4
Q ss_pred eeeccCceeeeEeecccchhhHHHH
Q psy2469 145 HTKNMGKFSSVTVSTIDEEEDEIEA 169 (220)
Q Consensus 145 ~tk~~GkfssvTvsTideeEdEiea 169 (220)
+--+.|+|-||+|+-+-+.=|.+||
T Consensus 51 k~SSkGnY~svsI~i~A~~~EQ~e~ 75 (90)
T COG2921 51 KPSSKGNYLSVSITIRATNIEQVEA 75 (90)
T ss_pred ccCCCCceEEEEEEEEECCHHHHHH
Confidence 3467899999999999988888886
No 37
>PRK07191 flgK flagellar hook-associated protein FlgK; Validated
Probab=23.22 E-value=64 Score=31.09 Aligned_cols=28 Identities=21% Similarity=0.499 Sum_probs=22.1
Q ss_pred eecccchhhHHHHHHHHHHhhhhHHHHH
Q psy2469 157 VSTIDEEEDEIEAREIADSYANNARIIE 184 (220)
Q Consensus 157 vsTideeEdEieareiadsYa~NAriie 184 (220)
||-++-+||=..==..--+|..|||||-
T Consensus 416 vSGVslDEE~~nLi~~QqaY~A~AkvIt 443 (456)
T PRK07191 416 FSGVNNDEEAMNLMEYQRAYQSNMKVIA 443 (456)
T ss_pred hcCcCHHHHHHHHHHHHHHHHHHhhHHH
Confidence 6777766666666677789999999995
No 38
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=22.90 E-value=34 Score=27.62 Aligned_cols=20 Identities=25% Similarity=0.527 Sum_probs=17.7
Q ss_pred hhhcccCCccceeeEEeeCC
Q psy2469 85 RQHRFKCKKCGLFLYYKHDP 104 (220)
Q Consensus 85 kQ~R~~C~rCgLpl~Y~~~~ 104 (220)
++|++.|+.|...++|-.|-
T Consensus 1 ~~v~llC~kC~~~~C~~~DI 20 (123)
T PF11648_consen 1 ENVKLLCRKCKKFACSGSDI 20 (123)
T ss_dssp CGEEEEETTTTCEEEEGGGE
T ss_pred CceEEECCCCCceeEchhhe
Confidence 46899999999999998776
No 39
>PRK06003 flgB flagellar basal body rod protein FlgB; Reviewed
Probab=22.80 E-value=1.1e+02 Score=24.47 Aligned_cols=32 Identities=22% Similarity=0.336 Sum_probs=28.3
Q ss_pred eecccchhhHHHHHHHHHHhhhhHHHHHHHHH
Q psy2469 157 VSTIDEEEDEIEAREIADSYANNARIIEKQLE 188 (220)
Q Consensus 157 vsTideeEdEieareiadsYa~NAriiekql~ 188 (220)
=+++|-|+|=.+.-+.+-.|..|+.+|.+++.
T Consensus 87 GN~Vdl~~Em~~~~~n~~~Y~a~~~~~~~~~~ 118 (126)
T PRK06003 87 GNSVSLEQEMMKAGEIKRQYSLNTAIVKSFHR 118 (126)
T ss_pred CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36788888888999999999999999999876
No 40
>KOG3994|consensus
Probab=22.57 E-value=1.2e+02 Score=28.36 Aligned_cols=60 Identities=28% Similarity=0.285 Sum_probs=43.1
Q ss_pred chhhhhhhhhcCCeeEEEEeeeeccCceeeeEeecccchhhHHHHHHHHHHhhhhHHHHHHHHHhcCC
Q psy2469 125 KMDIYNQVAVAKPKKIMVTKHTKNMGKFSSVTVSTIDEEEDEIEAREIADSYANNARIIEKQLERKGM 192 (220)
Q Consensus 125 ~~~~~~~~a~~~~kkvm~tk~tk~~GkfssvTvsTideeEdEieareiadsYa~NAriiekql~rkg~ 192 (220)
+.++|-+.+..+-.=+-+|..+++.=+--| ||-|||---+|.++-+-||-|=..|.+-|+
T Consensus 152 ~~~lFP~~~~~k~t~~niTQKsefDM~vwS--------ee~eiErekL~akFI~~A~eiC~~L~~~GY 211 (291)
T KOG3994|consen 152 LLELFPVPVVAKQTCINITQKSEFDMLVWS--------EEGEIEREKLAAKFILAAREICDRLLSYGY 211 (291)
T ss_pred HHHhCchhccceeEEEEeecccccchhhhh--------hhHHHHHHHHHHHHHHHHHHHHHHHHhcch
Confidence 455554443332223345666666655666 888888888999999999999999999986
No 41
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=22.16 E-value=39 Score=27.12 Aligned_cols=22 Identities=32% Similarity=0.467 Sum_probs=17.2
Q ss_pred CCCCceeEEEe-ccCCeeeeeec
Q psy2469 21 GEEKPLHIYYC-VCGQMTLILDC 42 (220)
Q Consensus 21 ~~e~~L~vYyC-lCG~~~Li~d~ 42 (220)
...+|.+++|| .||.-++--|+
T Consensus 55 ~~~kp~Rs~HC~~C~~CV~~~DH 77 (174)
T PF01529_consen 55 KIIKPPRSHHCRVCNRCVLRFDH 77 (174)
T ss_pred CCcCCCcceeccccccccccccc
Confidence 55789999999 79977766554
No 42
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=21.05 E-value=20 Score=27.61 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=18.3
Q ss_pred cccCCccceeeEEeeCCCCCEEE
Q psy2469 88 RFKCKKCGLFLYYKHDPSSNIIF 110 (220)
Q Consensus 88 R~~C~rCgLpl~Y~~~~~~~~~Y 110 (220)
+-+|..||+.++.....|+|-.|
T Consensus 8 ~~~C~~CG~d~~~~~adDgPA~f 30 (86)
T PF06170_consen 8 APRCPHCGLDYSHARADDGPAYF 30 (86)
T ss_pred CCcccccCCccccCCcCccchhH
Confidence 46899999999888877777444
No 43
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.68 E-value=49 Score=22.97 Aligned_cols=13 Identities=38% Similarity=1.053 Sum_probs=10.3
Q ss_pred hcccCCccceeeE
Q psy2469 87 HRFKCKKCGLFLY 99 (220)
Q Consensus 87 ~R~~C~rCgLpl~ 99 (220)
-|+.|++||+..+
T Consensus 36 ~r~~C~~Cgyt~~ 48 (50)
T PRK00432 36 DRWHCGKCGYTEF 48 (50)
T ss_pred CcEECCCcCCEEe
Confidence 4889999998654
No 44
>PRK07521 flgK flagellar hook-associated protein FlgK; Validated
Probab=20.53 E-value=74 Score=30.94 Aligned_cols=28 Identities=21% Similarity=0.467 Sum_probs=19.9
Q ss_pred eecccchhhHHHHHHHHHHhhhhHHHHH
Q psy2469 157 VSTIDEEEDEIEAREIADSYANNARIIE 184 (220)
Q Consensus 157 vsTideeEdEieareiadsYa~NAriie 184 (220)
||=++-+||=..=-..--+|+.|||||-
T Consensus 443 vsGVnlDEE~~nLi~~QqaY~AsArvIt 470 (483)
T PRK07521 443 ATGVDTDDEMALLLDLEQSYAASAKVIS 470 (483)
T ss_pred ccCCCHHHHHHHHHHHHHHHHhhhhhhh
Confidence 4555555555555667789999999984
No 45
>PF14090 HTH_39: Helix-turn-helix domain
Probab=20.05 E-value=70 Score=22.98 Aligned_cols=25 Identities=40% Similarity=0.440 Sum_probs=22.7
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHhcCCC
Q psy2469 167 IEAREIADSYANNARIIEKQLERKGMN 193 (220)
Q Consensus 167 ieareiadsYa~NAriiekql~rkg~~ 193 (220)
+||++..+.|.-.|||-| |+++|+.
T Consensus 19 ~ea~~~~gi~~~~aRI~e--LR~~G~~ 43 (70)
T PF14090_consen 19 LEARRELGIMRLAARISE--LRKKGYP 43 (70)
T ss_pred HHHHHHcCCCCHHHHHHH--HHHcCCe
Confidence 689999999999999977 9999984
No 46
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=20.04 E-value=64 Score=21.34 Aligned_cols=17 Identities=29% Similarity=0.868 Sum_probs=13.0
Q ss_pred cccCCccceeeEEeeCC
Q psy2469 88 RFKCKKCGLFLYYKHDP 104 (220)
Q Consensus 88 R~~C~rCgLpl~Y~~~~ 104 (220)
-+.|+.||-++.|...+
T Consensus 21 ~~~Cp~CG~~~~~~~~~ 37 (46)
T PRK00398 21 GVRCPYCGYRILFKERP 37 (46)
T ss_pred ceECCCCCCeEEEccCC
Confidence 46799999888887544
Done!