Query 031832
Match_columns 152
No_of_seqs 82 out of 84
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 05:58:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031832.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031832hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4118 Uncharacterized conser 99.7 5.3E-18 1.1E-22 121.6 -0.1 46 35-82 28-73 (74)
2 PF12907 zf-met2: Zinc-binding 98.9 2.7E-10 5.8E-15 73.5 0.3 31 46-76 1-34 (40)
3 PF12874 zf-met: Zinc-finger o 96.8 0.00028 6.2E-09 38.8 -0.1 23 47-69 1-23 (25)
4 PF13894 zf-C2H2_4: C2H2-type 95.6 0.0037 7.9E-08 32.7 0.3 24 47-70 1-24 (24)
5 PF09237 GAGA: GAGA factor; I 94.2 0.017 3.7E-07 40.0 0.6 29 46-74 24-52 (54)
6 PF00096 zf-C2H2: Zinc finger, 93.2 0.02 4.3E-07 30.7 -0.4 22 47-68 1-22 (23)
7 PF05605 zf-Di19: Drought indu 92.1 0.09 2E-06 34.0 1.5 28 46-74 2-29 (54)
8 PF12171 zf-C2H2_jaz: Zinc-fin 91.5 0.051 1.1E-06 30.8 -0.2 24 46-69 1-24 (27)
9 smart00451 ZnF_U1 U1-like zinc 89.8 0.15 3.2E-06 29.5 0.8 26 46-71 3-28 (35)
10 smart00355 ZnF_C2H2 zinc finge 89.5 0.15 3.3E-06 26.3 0.6 24 47-71 1-24 (26)
11 PF13912 zf-C2H2_6: C2H2-type 88.4 0.18 3.9E-06 27.9 0.4 26 46-71 1-26 (27)
12 PF13909 zf-H2C2_5: C2H2-type 87.1 0.15 3.2E-06 27.9 -0.4 24 47-71 1-24 (24)
13 PF12756 zf-C2H2_2: C2H2 type 80.9 0.89 1.9E-05 30.1 1.2 30 46-75 50-80 (100)
14 PF04988 AKAP95: A-kinase anch 80.0 0.73 1.6E-05 37.9 0.7 26 47-72 1-26 (165)
15 smart00734 ZnF_Rad18 Rad18-lik 76.8 1.4 2.9E-05 25.7 1.0 20 47-67 2-21 (26)
16 PF05605 zf-Di19: Drought indu 75.7 1.2 2.6E-05 28.8 0.6 23 46-70 31-53 (54)
17 KOG1842 FYVE finger-containing 75.0 1.1 2.3E-05 42.2 0.3 29 46-74 15-43 (505)
18 COG2879 Uncharacterized small 74.6 1.7 3.6E-05 31.3 1.2 23 53-75 19-41 (65)
19 PF12756 zf-C2H2_2: C2H2 type 73.6 1.1 2.3E-05 29.7 0.0 36 48-83 1-36 (100)
20 PF06783 UPF0239: Uncharacteri 65.3 8.6 0.00019 28.8 3.2 21 116-137 18-38 (85)
21 PF12013 DUF3505: Protein of u 64.3 3.1 6.6E-05 29.9 0.7 25 46-70 80-108 (109)
22 smart00614 ZnF_BED BED zinc fi 59.0 6.5 0.00014 25.0 1.5 29 45-73 17-50 (50)
23 PHA00616 hypothetical protein 56.2 3.5 7.6E-05 27.2 -0.1 32 47-78 2-33 (44)
24 PF04328 DUF466: Protein of un 54.8 5.5 0.00012 27.7 0.7 25 54-78 20-44 (65)
25 PF02892 zf-BED: BED zinc fing 51.9 5.7 0.00012 24.1 0.3 29 43-71 13-45 (45)
26 cd02970 PRX_like2 Peroxiredoxi 49.1 2.7 5.8E-05 29.4 -1.6 21 48-68 35-55 (149)
27 PF04780 DUF629: Protein of un 48.2 9 0.00019 35.7 1.1 29 46-74 57-85 (466)
28 PTZ00448 hypothetical protein; 47.3 8.9 0.00019 35.0 1.0 26 45-70 313-338 (373)
29 PRK09697 protein secretion pro 46.0 13 0.00027 29.9 1.5 25 54-78 68-92 (139)
30 cd03000 PDI_a_TMX3 PDIa family 44.3 5.7 0.00012 27.2 -0.6 21 48-68 26-46 (104)
31 PHA02768 hypothetical protein; 44.0 12 0.00026 25.7 1.0 27 45-72 4-30 (55)
32 PF10146 zf-C4H2: Zinc finger- 43.6 12 0.00025 31.6 1.0 17 48-74 210-226 (230)
33 PF05968 Bacillus_PapR: Bacill 42.9 19 0.00041 24.6 1.8 19 116-134 1-19 (48)
34 cd03017 PRX_BCP Peroxiredoxin 41.6 5.1 0.00011 28.1 -1.2 20 49-68 36-55 (140)
35 PHA00732 hypothetical protein 40.6 21 0.00045 25.4 1.8 25 47-71 2-26 (79)
36 KOG1280 Uncharacterized conser 40.0 18 0.00039 33.3 1.7 29 46-74 79-107 (381)
37 cd03005 PDI_a_ERp46 PDIa famil 39.5 5.4 0.00012 26.3 -1.2 25 48-72 27-51 (102)
38 cd02967 mauD Methylamine utili 38.3 7.3 0.00016 26.4 -0.8 19 48-66 32-50 (114)
39 KOG1146 Homeobox protein [Gene 38.1 17 0.00037 38.2 1.4 63 45-114 464-526 (1406)
40 PF00578 AhpC-TSA: AhpC/TSA fa 37.7 3.3 7.2E-05 28.2 -2.6 22 48-69 37-58 (124)
41 TIGR02738 TrbB type-F conjugat 37.4 5.2 0.00011 31.0 -1.8 41 21-66 36-79 (153)
42 PF10929 DUF2811: Protein of u 36.5 32 0.0007 24.0 2.2 25 102-127 13-37 (57)
43 PHA00733 hypothetical protein 36.4 19 0.00041 27.4 1.1 23 45-67 72-94 (128)
44 cd03012 TlpA_like_DipZ_like Tl 35.8 7.2 0.00016 27.5 -1.2 22 47-68 33-54 (126)
45 COG4049 Uncharacterized protei 35.2 12 0.00026 26.8 -0.1 28 43-70 14-41 (65)
46 PF06622 SepQ: SepQ protein; 34.2 25 0.00053 31.4 1.6 28 117-144 82-109 (305)
47 COG4416 Com Mu-like prophage p 34.0 29 0.00062 24.7 1.6 26 42-67 20-49 (60)
48 KOG2785 C2H2-type Zn-finger pr 33.9 22 0.00048 32.8 1.3 52 11-72 43-94 (390)
49 PTZ00256 glutathione peroxidas 33.5 8.4 0.00018 29.6 -1.2 21 49-69 53-73 (183)
50 TIGR03655 anti_R_Lar restricti 33.3 46 0.001 21.5 2.4 20 40-59 20-39 (53)
51 smart00504 Ubox Modified RING 32.5 23 0.00051 22.2 0.9 15 47-61 2-16 (63)
52 PRK09381 trxA thioredoxin; Pro 30.9 8.9 0.00019 26.1 -1.3 22 48-69 32-53 (109)
53 cd03011 TlpA_like_ScsD_MtbDsbE 30.7 12 0.00025 25.7 -0.8 18 48-65 31-48 (123)
54 cd03009 TryX_like_TryX_NRX Try 30.3 12 0.00025 26.4 -0.8 22 48-69 29-50 (131)
55 PF13913 zf-C2HC_2: zinc-finge 30.3 24 0.00052 20.1 0.6 20 47-67 3-22 (25)
56 COG5540 RING-finger-containing 29.9 25 0.00054 32.2 1.0 15 45-59 360-374 (374)
57 cd03018 PRX_AhpE_like Peroxire 29.6 9.7 0.00021 27.0 -1.3 20 49-68 41-60 (149)
58 PLN02748 tRNA dimethylallyltra 29.6 25 0.00055 32.4 1.0 26 44-69 416-442 (468)
59 cd02996 PDI_a_ERp44 PDIa famil 29.3 12 0.00026 25.6 -0.9 25 48-72 29-53 (108)
60 cd02985 TRX_CDSP32 TRX family, 29.1 8.6 0.00019 26.7 -1.7 41 10-66 1-44 (103)
61 PF10886 DUF2685: Protein of u 28.9 19 0.00041 25.0 0.1 17 48-64 3-19 (54)
62 cd00340 GSH_Peroxidase Glutath 27.9 12 0.00026 27.5 -1.1 21 47-68 32-52 (152)
63 cd02999 PDI_a_ERp44_like PDIa 26.9 12 0.00026 26.2 -1.3 19 49-67 30-48 (100)
64 cd02964 TryX_like_family Trypa 26.9 12 0.00027 26.6 -1.2 22 48-69 28-49 (132)
65 PF08534 Redoxin: Redoxin; In 26.7 6.8 0.00015 27.9 -2.6 21 48-68 40-60 (146)
66 TIGR02540 gpx7 putative glutat 26.6 15 0.00033 26.9 -0.8 22 48-69 33-54 (153)
67 TIGR00373 conserved hypothetic 25.2 26 0.00057 27.4 0.2 15 44-58 126-140 (158)
68 cd02971 PRX_family Peroxiredox 25.2 15 0.00032 25.6 -1.1 21 48-68 34-54 (140)
69 PF14353 CpXC: CpXC protein 24.8 14 0.00031 27.0 -1.3 37 42-78 34-70 (128)
70 PF04911 ATP-synt_J: ATP synth 24.7 1.2E+02 0.0025 21.2 3.3 26 116-141 10-35 (54)
71 cd02966 TlpA_like_family TlpA- 24.7 14 0.00031 23.5 -1.1 20 48-67 30-49 (116)
72 PRK10954 periplasmic protein d 24.6 27 0.00058 27.4 0.2 25 43-67 43-70 (207)
73 PRK11088 rrmA 23S rRNA methylt 24.3 31 0.00067 28.0 0.5 12 46-57 2-13 (272)
74 cd02969 PRX_like1 Peroxiredoxi 23.7 15 0.00033 27.2 -1.2 22 48-69 36-57 (171)
75 cd02956 ybbN ybbN protein fami 23.5 14 0.00029 24.5 -1.4 21 48-68 23-43 (96)
76 cd03016 PRX_1cys Peroxiredoxin 23.4 17 0.00037 28.5 -1.1 21 49-69 38-58 (203)
77 PRK15000 peroxidase; Provision 22.8 18 0.00039 28.8 -1.1 22 48-69 46-67 (200)
78 TIGR02661 MauD methylamine deh 22.6 15 0.00032 28.5 -1.6 16 48-63 85-100 (189)
79 PF10954 DUF2755: Protein of u 22.0 92 0.002 24.1 2.6 16 120-135 24-39 (100)
80 PRK06266 transcription initiat 22.0 39 0.00085 27.1 0.7 15 45-59 135-149 (178)
81 TIGR03137 AhpC peroxiredoxin. 21.8 19 0.0004 27.9 -1.2 25 44-68 35-63 (187)
82 cd03014 PRX_Atyp2cys Peroxired 21.7 15 0.00033 26.1 -1.6 18 49-66 39-56 (143)
83 COG0526 TrxA Thiol-disulfide i 21.5 26 0.00057 21.3 -0.3 23 46-68 41-63 (127)
84 smart00746 TRASH metallochaper 21.1 54 0.0012 16.7 0.9 10 49-58 1-10 (39)
85 PRK13599 putative peroxiredoxi 20.7 21 0.00046 28.9 -1.1 22 48-69 40-61 (215)
86 PRK10382 alkyl hydroperoxide r 20.7 21 0.00045 28.4 -1.1 25 44-68 35-63 (187)
87 KOG3608 Zn finger proteins [Ge 20.6 55 0.0012 30.8 1.4 28 46-73 263-290 (467)
88 PTZ00056 glutathione peroxidas 20.4 21 0.00045 28.3 -1.2 22 48-69 50-71 (199)
No 1
>KOG4118 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.67 E-value=5.3e-18 Score=121.65 Aligned_cols=46 Identities=30% Similarity=0.611 Sum_probs=41.2
Q ss_pred cccccccccceeeeCcccccCCCCcchhhhhhhhCCCCCCCChhHHhh
Q 031832 35 DRTGREKGGHAKYECPLCKVTAPDIKSMQIHHDARHPKLPFDEASLVN 82 (152)
Q Consensus 35 dR~g~~k~galK~~CpVCkaqmPD~Kt~k~HfESKHPK~plP~E~L~d 82 (152)
|.+- +..++|.|+|+||++|||||++|++|||+||||+|||+| |.+
T Consensus 28 DQK~-AA~~aL~~kCtVC~~~mpdpktfkqhfe~kHpk~~~P~e-L~~ 73 (74)
T KOG4118|consen 28 DQKA-AAMAALHHKCTVCMVQMPDPKTFKQHFENKHPKEPLPEE-LSE 73 (74)
T ss_pred cHHH-HHHHHHHhhhHhhHhhCCCCchHHHHHhhcCCCCCCCHh-hcc
Confidence 5553 467889999999999999999999999999999999999 765
No 2
>PF12907 zf-met2: Zinc-binding
Probab=98.90 E-value=2.7e-10 Score=73.53 Aligned_cols=31 Identities=23% Similarity=0.669 Sum_probs=28.1
Q ss_pred eeeCcccc---cCCCCcchhhhhhhhCCCCCCCC
Q 031832 46 KYECPLCK---VTAPDIKSMQIHHDARHPKLPFD 76 (152)
Q Consensus 46 K~~CpVCk---aqmPD~Kt~k~HfESKHPK~plP 76 (152)
+++|+||+ .++++++.|++||||||||.++.
T Consensus 1 ~i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~ 34 (40)
T PF12907_consen 1 NIICKICRQTFMQTTNEPQLKEHAENKHPKNTFE 34 (40)
T ss_pred CcCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHH
Confidence 47899999 89999999999999999997553
No 3
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.80 E-value=0.00028 Score=38.79 Aligned_cols=23 Identities=17% Similarity=0.537 Sum_probs=21.7
Q ss_pred eeCcccccCCCCcchhhhhhhhC
Q 031832 47 YECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfESK 69 (152)
|.|.+|..++.++.+|++|++++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999999985
No 4
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.62 E-value=0.0037 Score=32.66 Aligned_cols=24 Identities=21% Similarity=0.672 Sum_probs=20.4
Q ss_pred eeCcccccCCCCcchhhhhhhhCC
Q 031832 47 YECPLCKVTAPDIKSMQIHHDARH 70 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfESKH 70 (152)
|.|++|....++...|.+|....|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999998766
No 5
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=94.20 E-value=0.017 Score=40.04 Aligned_cols=29 Identities=28% Similarity=0.621 Sum_probs=22.4
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESKHPK~p 74 (152)
-.+||+|.+.++..+.++.|.|..|-+-|
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 46899999999999999999999997654
No 6
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=93.20 E-value=0.02 Score=30.74 Aligned_cols=22 Identities=23% Similarity=0.671 Sum_probs=20.7
Q ss_pred eeCcccccCCCCcchhhhhhhh
Q 031832 47 YECPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfES 68 (152)
|+|++|....++...|++|.+.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 7899999999999999999876
No 7
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=92.05 E-value=0.09 Score=34.05 Aligned_cols=28 Identities=21% Similarity=0.461 Sum_probs=25.3
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESKHPK~p 74 (152)
.|.||.|.. --|...|..|.+..|+.++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~ 29 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSES 29 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCC
Confidence 489999999 7999999999999999764
No 8
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=91.46 E-value=0.051 Score=30.79 Aligned_cols=24 Identities=13% Similarity=0.420 Sum_probs=21.6
Q ss_pred eeeCcccccCCCCcchhhhhhhhC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESK 69 (152)
.|.|.+|.-...|...+.+|..||
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCCcccCCCCcCCHHHHHHHHccC
Confidence 378999999999999999999875
No 9
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=89.78 E-value=0.15 Score=29.45 Aligned_cols=26 Identities=31% Similarity=0.566 Sum_probs=23.2
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDARHP 71 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESKHP 71 (152)
.|.|.+|....-|...+.+|+.+|.-
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H 28 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKH 28 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHH
Confidence 48899999999999999999988743
No 10
>smart00355 ZnF_C2H2 zinc finger.
Probab=89.49 E-value=0.15 Score=26.28 Aligned_cols=24 Identities=25% Similarity=0.595 Sum_probs=21.3
Q ss_pred eeCcccccCCCCcchhhhhhhhCCC
Q 031832 47 YECPLCKVTAPDIKSMQIHHDARHP 71 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfESKHP 71 (152)
|.|+.|....++..++..|.+ .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 689999999999999999988 554
No 11
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=88.37 E-value=0.18 Score=27.92 Aligned_cols=26 Identities=19% Similarity=0.496 Sum_probs=23.3
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDARHP 71 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESKHP 71 (152)
.|+|.+|....++...|..|-..-|+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 38999999999999999999977765
No 12
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.07 E-value=0.15 Score=27.86 Aligned_cols=24 Identities=29% Similarity=0.808 Sum_probs=19.4
Q ss_pred eeCcccccCCCCcchhhhhhhhCCC
Q 031832 47 YECPLCKVTAPDIKSMQIHHDARHP 71 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfESKHP 71 (152)
|.|+.|-=... +..|..|.+..||
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 78999986666 8899999999887
No 13
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=80.87 E-value=0.89 Score=30.11 Aligned_cols=30 Identities=27% Similarity=0.542 Sum_probs=24.1
Q ss_pred eeeCcccccCCCCcchhhhhhhhC-CCCCCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDAR-HPKLPF 75 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESK-HPK~pl 75 (152)
.+.|++|...-.+...++.|..++ |.+...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 699999999999999999999987 555444
No 14
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=79.96 E-value=0.73 Score=37.86 Aligned_cols=26 Identities=23% Similarity=0.621 Sum_probs=24.3
Q ss_pred eeCcccccCCCCcchhhhhhhhCCCC
Q 031832 47 YECPLCKVTAPDIKSMQIHHDARHPK 72 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfESKHPK 72 (152)
|+|++||-+.-+.+-+..|+||+-=+
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~ 26 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHK 26 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHH
Confidence 78999999999999999999998766
No 15
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=76.80 E-value=1.4 Score=25.74 Aligned_cols=20 Identities=25% Similarity=0.554 Sum_probs=15.8
Q ss_pred eeCcccccCCCCcchhhhhhh
Q 031832 47 YECPLCKVTAPDIKSMQIHHD 67 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfE 67 (152)
+.||||-.++ .......|-+
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 5799999888 5567777766
No 16
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=75.69 E-value=1.2 Score=28.76 Aligned_cols=23 Identities=26% Similarity=0.715 Sum_probs=19.4
Q ss_pred eeeCcccccCCCCcchhhhhhhhCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDARH 70 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESKH 70 (152)
.+.||||-....+ .+..|....|
T Consensus 31 ~v~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 31 NVVCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred CccCCCchhhhhh--HHHHHHHHhc
Confidence 5899999987664 8999998877
No 17
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=74.99 E-value=1.1 Score=42.22 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=26.9
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESKHPK~p 74 (152)
.|.||+|+.-+|++-.+..||+.-||-+.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~ed 43 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEED 43 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhccccc
Confidence 38999999999999999999999999765
No 18
>COG2879 Uncharacterized small protein [Function unknown]
Probab=74.63 E-value=1.7 Score=31.27 Aligned_cols=23 Identities=30% Similarity=0.466 Sum_probs=20.1
Q ss_pred ccCCCCcchhhhhhhhCCCCCCC
Q 031832 53 KVTAPDIKSMQIHHDARHPKLPF 75 (152)
Q Consensus 53 kaqmPD~Kt~k~HfESKHPK~pl 75 (152)
++-+||+.+|..|.+.|||..|.
T Consensus 19 mvGvpdYdnYVehmr~~hPd~p~ 41 (65)
T COG2879 19 MVGVPDYDNYVEHMRKKHPDKPP 41 (65)
T ss_pred HcCCCcHHHHHHHHHHhCcCCCc
Confidence 46789999999999999997664
No 19
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=73.64 E-value=1.1 Score=29.73 Aligned_cols=36 Identities=19% Similarity=0.336 Sum_probs=0.0
Q ss_pred eCcccccCCCCcchhhhhhhhCCCCCCCChhHHhhH
Q 031832 48 ECPLCKVTAPDIKSMQIHHDARHPKLPFDEASLVNL 83 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESKHPK~plP~E~L~dv 83 (152)
+|.+|....+++..+.+|....|.-..-..+.+.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~ 36 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDP 36 (100)
T ss_dssp ------------------------------------
T ss_pred Cccccccccccccccccccccccccccccccccccc
Confidence 599999999999999999999997654334434433
No 20
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=65.32 E-value=8.6 Score=28.76 Aligned_cols=21 Identities=48% Similarity=0.820 Sum_probs=14.8
Q ss_pred HHHHhHHHHHHHHHHHHHHHHH
Q 031832 116 MLRLLDYGLFVLMMLWAVQCIL 137 (152)
Q Consensus 116 m~~~~~~gl~~~~~~~~~~~~~ 137 (152)
|+-||.|||||-.++= +-|||
T Consensus 18 ~e~llRYGLf~GAIFQ-liCil 38 (85)
T PF06783_consen 18 FENLLRYGLFVGAIFQ-LICIL 38 (85)
T ss_pred HHHHHHHHHHHHHHHH-HHHHH
Confidence 6789999999876542 33554
No 21
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=64.33 E-value=3.1 Score=29.92 Aligned_cols=25 Identities=32% Similarity=0.672 Sum_probs=23.6
Q ss_pred eeeC----cccccCCCCcchhhhhhhhCC
Q 031832 46 KYEC----PLCKVTAPDIKSMQIHHDARH 70 (152)
Q Consensus 46 K~~C----pVCkaqmPD~Kt~k~HfESKH 70 (152)
=|.| +.|.--..+.++|+.||..+|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 3899 999999999999999999998
No 22
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=59.05 E-value=6.5 Score=25.02 Aligned_cols=29 Identities=17% Similarity=0.439 Sum_probs=24.3
Q ss_pred eeeeCcccccCCCCc-----chhhhhhhhCCCCC
Q 031832 45 AKYECPLCKVTAPDI-----KSMQIHHDARHPKL 73 (152)
Q Consensus 45 lK~~CpVCkaqmPD~-----Kt~k~HfESKHPK~ 73 (152)
-.-.|..|...+.-. .+|..|..++||..
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~~~ 50 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHPAR 50 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCcCC
Confidence 578999999888655 59999999999963
No 23
>PHA00616 hypothetical protein
Probab=56.22 E-value=3.5 Score=27.24 Aligned_cols=32 Identities=19% Similarity=0.213 Sum_probs=28.2
Q ss_pred eeCcccccCCCCcchhhhhhhhCCCCCCCChh
Q 031832 47 YECPLCKVTAPDIKSMQIHHDARHPKLPFDEA 78 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfESKHPK~plP~E 78 (152)
|+|+-|.-.--+.+.|..|..+-|-..|+--|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 78999999999999999999998887776544
No 24
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=54.80 E-value=5.5 Score=27.68 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=20.9
Q ss_pred cCCCCcchhhhhhhhCCCCCCCChh
Q 031832 54 VTAPDIKSMQIHHDARHPKLPFDEA 78 (152)
Q Consensus 54 aqmPD~Kt~k~HfESKHPK~plP~E 78 (152)
+-.||+..|-.|+...||-.|...+
T Consensus 20 ~G~~~Ye~Yv~H~~~~HP~~p~ms~ 44 (65)
T PF04328_consen 20 VGEPDYERYVEHMRRHHPDEPPMSE 44 (65)
T ss_pred cCcHHHHHHHHHHHHHCcCCCCCCH
Confidence 3479999999999999998776554
No 25
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=51.94 E-value=5.7 Score=24.14 Aligned_cols=29 Identities=21% Similarity=0.469 Sum_probs=21.0
Q ss_pred cceeeeCcccccCCCC----cchhhhhhhhCCC
Q 031832 43 GHAKYECPLCKVTAPD----IKSMQIHHDARHP 71 (152)
Q Consensus 43 galK~~CpVCkaqmPD----~Kt~k~HfESKHP 71 (152)
+....+|..|...+.- ...|..|...+||
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~hp 45 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKHP 45 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTTH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhCc
Confidence 3467799999987765 5789999999997
No 26
>cd02970 PRX_like2 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. TRXs alter the redox state of target proteins by catalyzing the reduction of their disulfide bonds via the CXXC motif using reducing equivalents derived from either NADPH or ferredoxins.
Probab=49.08 E-value=2.7 Score=29.45 Aligned_cols=21 Identities=24% Similarity=0.564 Sum_probs=18.4
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 031832 48 ECPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfES 68 (152)
-||.|+.+||+...+..-|+.
T Consensus 35 ~Cp~C~~~~~~l~~~~~~~~~ 55 (149)
T cd02970 35 GCPFCREYLRALSKLLPELDA 55 (149)
T ss_pred CChhHHHHHHHHHHHHHHHHh
Confidence 699999999999988888863
No 27
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=48.16 E-value=9 Score=35.69 Aligned_cols=29 Identities=28% Similarity=0.463 Sum_probs=26.1
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESKHPK~p 74 (152)
=..||.|-..-+|...+.+|.+++||-.-
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 46899999999999999999999998753
No 28
>PTZ00448 hypothetical protein; Provisional
Probab=47.33 E-value=8.9 Score=35.03 Aligned_cols=26 Identities=15% Similarity=0.330 Sum_probs=23.6
Q ss_pred eeeeCcccccCCCCcchhhhhhhhCC
Q 031832 45 AKYECPLCKVTAPDIKSMQIHHDARH 70 (152)
Q Consensus 45 lK~~CpVCkaqmPD~Kt~k~HfESKH 70 (152)
..|+|..|..+..|...+++||.|-+
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KSDw 338 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRSEW 338 (373)
T ss_pred CCccccccccccCCHHHHHHHhhhhH
Confidence 36899999999999999999999865
No 29
>PRK09697 protein secretion protein GspB; Provisional
Probab=45.95 E-value=13 Score=29.95 Aligned_cols=25 Identities=24% Similarity=0.295 Sum_probs=22.5
Q ss_pred cCCCCcchhhhhhhhCCCCCCCChh
Q 031832 54 VTAPDIKSMQIHHDARHPKLPFDEA 78 (152)
Q Consensus 54 aqmPD~Kt~k~HfESKHPK~plP~E 78 (152)
...||+++.++||-=|-.-+|.|++
T Consensus 68 ~~tP~~~Qs~qH~~FKKqPLPV~E~ 92 (139)
T PRK09697 68 AETPAFKQSTQHYFFKKQPLPVVES 92 (139)
T ss_pred CCCcchhhhhhheeeecCCCCCccc
Confidence 5789999999999999888888887
No 30
>cd03000 PDI_a_TMX3 PDIa family, TMX3 subfamily; composed of eukaryotic proteins similar to human TMX3, a TRX related transmembrane protein containing one redox active TRX domain at the N-terminus and a classical ER retrieval sequence for type I transmembrane proteins at the C-terminus. The TMX3 transcript is found in a variety of tissues with the highest levels detected in skeletal muscle and the heart. In vitro, TMX3 showed oxidase activity albeit slightly lower than that of protein disulfide isomerase.
Probab=44.28 E-value=5.7 Score=27.17 Aligned_cols=21 Identities=19% Similarity=0.306 Sum_probs=18.4
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 031832 48 ECPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfES 68 (152)
-|+.|+.++|-...+.++|+.
T Consensus 26 wC~~C~~~~p~l~~l~~~~~~ 46 (104)
T cd03000 26 WCGHCKKLEPVWNEVGAELKS 46 (104)
T ss_pred CCHHHHhhChHHHHHHHHHHh
Confidence 399999999999999888853
No 31
>PHA02768 hypothetical protein; Provisional
Probab=43.96 E-value=12 Score=25.68 Aligned_cols=27 Identities=37% Similarity=0.593 Sum_probs=24.1
Q ss_pred eeeeCcccccCCCCcchhhhhhhhCCCC
Q 031832 45 AKYECPLCKVTAPDIKSMQIHHDARHPK 72 (152)
Q Consensus 45 lK~~CpVCkaqmPD~Kt~k~HfESKHPK 72 (152)
+-|.|+.|.-.......|..|... |.|
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~-H~k 30 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRK-HNT 30 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHh-cCC
Confidence 569999999999999999999988 664
No 32
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=43.65 E-value=12 Score=31.57 Aligned_cols=17 Identities=53% Similarity=1.138 Sum_probs=12.2
Q ss_pred eCcccccCCCCcchhhhhhhhCCCCCC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDARHPKLP 74 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESKHPK~p 74 (152)
+||.||+- .+|||||-|
T Consensus 210 iCPlCK~K----------sRSrnpKk~ 226 (230)
T PF10146_consen 210 ICPLCKAK----------SRSRNPKKP 226 (230)
T ss_pred CCcccccc----------cccCCCCCc
Confidence 57888753 478888865
No 33
>PF05968 Bacillus_PapR: Bacillus PapR protein; InterPro: IPR009239 This family consists of the Bacillus species-specific PapR protein. The papR gene belongs to the PlcR regulon and is located 70 bp downstream from plcR. It encodes a 48-amino-acid peptide. Disruption of the papR gene abolishes expression of the PlcR regulon, resulting in a large decrease in haemolysis and virulence in insect larvae. A processed form of PapR activates the PlcR regulon by allowing PlcR to bind to its DNA target. This activating mechanism is strain specific [].
Probab=42.92 E-value=19 Score=24.62 Aligned_cols=19 Identities=37% Similarity=0.630 Sum_probs=16.5
Q ss_pred HHHHhHHHHHHHHHHHHHH
Q 031832 116 MLRLLDYGLFVLMMLWAVQ 134 (152)
Q Consensus 116 m~~~~~~gl~~~~~~~~~~ 134 (152)
|.++|.-+|..+.|+|.+.
T Consensus 1 mkkll~~slltlam~~gis 19 (48)
T PF05968_consen 1 MKKLLIGSLLTLAMAWGIS 19 (48)
T ss_pred CchHHHhHHHHHHHHhhhh
Confidence 5688999999999999864
No 34
>cd03017 PRX_BCP Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The protein was named BCP based on its electrophoretic mobility before its function was known. BCP shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides. BCP contains the peroxidatic cysteine but appears not to possess a resolving cysteine (some sequences, not all, contain a second cysteine but its role is still unknown). Unlike other PRXs, BCP exists as a monomer. The plant homolog of BCP is PRX Q, which is expressed only in leaves and is cellularly localized in the chloroplasts and the guard cells of stomata. Also included in this subfamily is the fungal nuclear protein, Dot5p (for disrupter of telomere silencing protein 5), w
Probab=41.56 E-value=5.1 Score=28.07 Aligned_cols=20 Identities=25% Similarity=0.373 Sum_probs=17.1
Q ss_pred CcccccCCCCcchhhhhhhh
Q 031832 49 CPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 49 CpVCkaqmPD~Kt~k~HfES 68 (152)
||+|..++|....+.+-|+.
T Consensus 36 cp~C~~~~~~l~~~~~~~~~ 55 (140)
T cd03017 36 TPGCTKEACDFRDLYEEFKA 55 (140)
T ss_pred CCchHHHHHHHHHHHHHHHH
Confidence 99999999998888777764
No 35
>PHA00732 hypothetical protein
Probab=40.58 E-value=21 Score=25.41 Aligned_cols=25 Identities=24% Similarity=0.716 Sum_probs=20.5
Q ss_pred eeCcccccCCCCcchhhhhhhhCCC
Q 031832 47 YECPLCKVTAPDIKSMQIHHDARHP 71 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfESKHP 71 (152)
|.|+.|....++..++++|....|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC
Confidence 6799998888888889988876554
No 36
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=40.01 E-value=18 Score=33.29 Aligned_cols=29 Identities=21% Similarity=0.582 Sum_probs=27.8
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDARHPKLP 74 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESKHPK~p 74 (152)
-|+||.|+.+==...+|..|--+-||-.+
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~ 107 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEAS 107 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccC
Confidence 69999999999999999999999999987
No 37
>cd03005 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.
Probab=39.48 E-value=5.4 Score=26.30 Aligned_cols=25 Identities=24% Similarity=0.493 Sum_probs=20.7
Q ss_pred eCcccccCCCCcchhhhhhhhCCCC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDARHPK 72 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESKHPK 72 (152)
-|+.|+..+|....+...++...|+
T Consensus 27 wC~~C~~~~p~~~~~~~~~~~~~~~ 51 (102)
T cd03005 27 WCGHCKRLAPTWEQLAKKFNNENPS 51 (102)
T ss_pred CCHHHHHhCHHHHHHHHHHhccCCc
Confidence 3999999999999998888764444
No 38
>cd02967 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.
Probab=38.31 E-value=7.3 Score=26.41 Aligned_cols=19 Identities=37% Similarity=0.779 Sum_probs=14.7
Q ss_pred eCcccccCCCCcchhhhhh
Q 031832 48 ECPLCKVTAPDIKSMQIHH 66 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~Hf 66 (152)
-|+.|+.++|..+.+.+-|
T Consensus 32 wC~~C~~~~p~l~~~~~~~ 50 (114)
T cd02967 32 TCPVCKKLLPVIRSIARAE 50 (114)
T ss_pred CCcchHhHhHHHHHHHHHh
Confidence 5999999999887764433
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=38.07 E-value=17 Score=38.21 Aligned_cols=63 Identities=19% Similarity=0.339 Sum_probs=41.5
Q ss_pred eeeeCcccccCCCCcchhhhhhhhCCCCCCCChhHHhhHHhhhcccccCCCCCceeeccchhhhhhccch
Q 031832 45 AKYECPLCKVTAPDIKSMQIHHDARHPKLPFDEASLVNLHAARVDAESSKPKPGIRVVRKDFQCLKACNL 114 (152)
Q Consensus 45 lK~~CpVCkaqmPD~Kt~k~HfESKHPK~plP~E~L~dvha~~~~~~~~~~~~~VrGs~kk~~~~~~~~~ 114 (152)
-.++||.|...-++..++..|.++|||-.---- +.-.+ ....--.+..-++..+.+.|. +||.
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~--c~~gq----~~~~~arg~~~~~~~~p~~C~-~C~~ 526 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAY--CKAGQ----NHPRLARGEVYRCPGKPYPCR-ACNY 526 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhH--hHhcc----ccccccccccccCCCCcccce-eeee
Confidence 458999999999999999999999999776611 11111 111122234455666777776 5554
No 40
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=37.65 E-value=3.3 Score=28.20 Aligned_cols=22 Identities=18% Similarity=0.652 Sum_probs=19.6
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESK 69 (152)
-||.|..++|....+...|+.+
T Consensus 37 ~c~~c~~~l~~l~~~~~~~~~~ 58 (124)
T PF00578_consen 37 WCPFCQAELPELNELYKKYKDK 58 (124)
T ss_dssp TSHHHHHHHHHHHHHHHHHHTT
T ss_pred CccccccchhHHHHHhhhhccc
Confidence 5999999999999999888855
No 41
>TIGR02738 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. The protein is closely related to TraF (TIGR02739) which is somewhat longer, lacks the cysteine motif and is apparently not functional as a disulfide bond isomerase.
Probab=37.39 E-value=5.2 Score=30.98 Aligned_cols=41 Identities=29% Similarity=0.479 Sum_probs=27.1
Q ss_pred hhhhcCCCCccCcccccccccccceee---eCcccccCCCCcchhhhhh
Q 031832 21 AATTNRGGGKAGMADRTGREKGGHAKY---ECPLCKVTAPDIKSMQIHH 66 (152)
Q Consensus 21 aattNkGGGKaGl~dR~g~~k~galK~---~CpVCkaqmPD~Kt~k~Hf 66 (152)
++|.|+|-|+.-..... .-++| -|+.|+..||+...+.+.|
T Consensus 36 ~~~~~~~~G~~~~l~~~-----~lvnFWAsWCppCr~e~P~L~~l~~~~ 79 (153)
T TIGR02738 36 AATDNAPQGRHANQDDY-----ALVFFYQSTCPYCHQFAPVLKRFSQQF 79 (153)
T ss_pred ccccccCcchhhhcCCC-----EEEEEECCCChhHHHHHHHHHHHHHHc
Confidence 35567776544333221 23333 4999999999999988776
No 42
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=36.46 E-value=32 Score=24.04 Aligned_cols=25 Identities=28% Similarity=0.246 Sum_probs=20.2
Q ss_pred ccchhhhhhccchhHHHHhHHHHHHH
Q 031832 102 VRKDFQCLKACNLEMLRLLDYGLFVL 127 (152)
Q Consensus 102 s~kk~~~~~~~~~~m~~~~~~gl~~~ 127 (152)
++++|-.. .||||-+||+.+-|-..
T Consensus 13 ~m~~fie~-hP~WDQ~Rl~~aALa~F 37 (57)
T PF10929_consen 13 AMKDFIET-HPNWDQYRLFQAALAGF 37 (57)
T ss_pred HHHHHHHc-CCCchHHHHHHHHHHHH
Confidence 56777777 99999999999877543
No 43
>PHA00733 hypothetical protein
Probab=36.39 E-value=19 Score=27.35 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=15.3
Q ss_pred eeeeCcccccCCCCcchhhhhhh
Q 031832 45 AKYECPLCKVTAPDIKSMQIHHD 67 (152)
Q Consensus 45 lK~~CpVCkaqmPD~Kt~k~HfE 67 (152)
-.|+|+.|....++..++++|.+
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHh
Confidence 34677777766777666666665
No 44
>cd03012 TlpA_like_DipZ_like TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3.
Probab=35.78 E-value=7.2 Score=27.55 Aligned_cols=22 Identities=23% Similarity=0.437 Sum_probs=18.4
Q ss_pred eeCcccccCCCCcchhhhhhhh
Q 031832 47 YECPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfES 68 (152)
.-|+.|..++|..+.+.+-|..
T Consensus 33 ~~C~~C~~~~p~l~~l~~~~~~ 54 (126)
T cd03012 33 YCCINCLHTLPYLTDLEQKYKD 54 (126)
T ss_pred CCCccHHHHHHHHHHHHHHcCc
Confidence 4699999999999888887753
No 45
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=35.20 E-value=12 Score=26.82 Aligned_cols=28 Identities=25% Similarity=0.447 Sum_probs=23.4
Q ss_pred cceeeeCcccccCCCCcchhhhhhhhCC
Q 031832 43 GHAKYECPLCKVTAPDIKSMQIHHDARH 70 (152)
Q Consensus 43 galK~~CpVCkaqmPD~Kt~k~HfESKH 70 (152)
|..-+.||-|-+..-+.|+|..|-.--|
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 3478999999999999999999965444
No 46
>PF06622 SepQ: SepQ protein; InterPro: IPR009532 This family consists of several enterobacterial SepQ proteins from Escherichia coli and Citrobacter rodentium. The function of this family is unclear.
Probab=34.25 E-value=25 Score=31.43 Aligned_cols=28 Identities=43% Similarity=0.573 Sum_probs=22.6
Q ss_pred HHHhHHHHHHHHHHHHHHHHHhhccccc
Q 031832 117 LRLLDYGLFVLMMLWAVQCILLNSTVKN 144 (152)
Q Consensus 117 ~~~~~~gl~~~~~~~~~~~~~~~~~~~~ 144 (152)
-+|+..-|+++|.+|+.|-.|--+.|.+
T Consensus 82 p~ll~~Dli~~M~~W~iq~~Lp~~dvS~ 109 (305)
T PF06622_consen 82 PRLLPEDLIKLMSLWAIQPVLPEDDVSV 109 (305)
T ss_pred cccChHHHHHHHHHHHHHhcCCcccccc
Confidence 3678889999999999998886665544
No 47
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=33.96 E-value=29 Score=24.66 Aligned_cols=26 Identities=27% Similarity=0.501 Sum_probs=17.5
Q ss_pred ccceeeeCcccccC----CCCcchhhhhhh
Q 031832 42 GGHAKYECPLCKVT----APDIKSMQIHHD 67 (152)
Q Consensus 42 ~galK~~CpVCkaq----mPD~Kt~k~HfE 67 (152)
+|.+..+||-||.. .|..-+.++|-.
T Consensus 20 ~~yle~KCPrCK~vN~~~~~~e~~t~~~ks 49 (60)
T COG4416 20 QAYLEKKCPRCKEVNEFYIKEEATTQIHKS 49 (60)
T ss_pred ceeeeecCCccceeeeeecccccchhhhhc
Confidence 68999999999953 444444444433
No 48
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=33.88 E-value=22 Score=32.81 Aligned_cols=52 Identities=17% Similarity=0.239 Sum_probs=37.3
Q ss_pred cHHHHHHHHHhhhhcCCCCccCcccccccccccceeeeCcccccCCCCcchhhhhhhhCCCC
Q 031832 11 TAKEIAMKVDAATTNRGGGKAGMADRTGREKGGHAKYECPLCKVTAPDIKSMQIHHDARHPK 72 (152)
Q Consensus 11 TAkEiaaK~~aattNkGGGKaGl~dR~g~~k~galK~~CpVCkaqmPD~Kt~k~HfESKHPK 72 (152)
||.+++.|+.+....+ -++ ...+...+.|++|.-..+.++-+.+|-.||-=+
T Consensus 43 taE~F~~k~~s~~~~~--~~~--------~e~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~ 94 (390)
T KOG2785|consen 43 TAEEFNEKVLSDDSEK--EEN--------LEEAESVVYCEACNKSFASPKAHENHLKSKKHV 94 (390)
T ss_pred CHHHHhHHHhhhhhhh--hhh--------hhhcccceehHHhhccccChhhHHHHHHHhhcc
Confidence 7888888886552111 011 124568899999999999999999999886443
No 49
>PTZ00256 glutathione peroxidase; Provisional
Probab=33.46 E-value=8.4 Score=29.65 Aligned_cols=21 Identities=10% Similarity=0.184 Sum_probs=17.9
Q ss_pred CcccccCCCCcchhhhhhhhC
Q 031832 49 CPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 49 CpVCkaqmPD~Kt~k~HfESK 69 (152)
||.|+..||....+.+-|+++
T Consensus 53 Cp~C~~e~p~l~~l~~~~~~~ 73 (183)
T PTZ00256 53 CGLTSDHYTQLVELYKQYKSQ 73 (183)
T ss_pred CCchHHHHHHHHHHHHHHhhC
Confidence 999999999998887777654
No 50
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=33.32 E-value=46 Score=21.50 Aligned_cols=20 Identities=20% Similarity=0.398 Sum_probs=15.6
Q ss_pred ccccceeeeCcccccCCCCc
Q 031832 40 EKGGHAKYECPLCKVTAPDI 59 (152)
Q Consensus 40 ~k~galK~~CpVCkaqmPD~ 59 (152)
.+.+.-.|.|+.|.+.+|..
T Consensus 20 ~~~~~~~~~C~~Cga~~~~~ 39 (53)
T TIGR03655 20 PLDLSHYFECSTCGASGPVE 39 (53)
T ss_pred CCCCEEEEECCCCCCCcccc
Confidence 34556677999999999973
No 51
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=32.53 E-value=23 Score=22.18 Aligned_cols=15 Identities=20% Similarity=0.392 Sum_probs=12.2
Q ss_pred eeCcccccCCCCcch
Q 031832 47 YECPLCKVTAPDIKS 61 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt 61 (152)
+.||+|+..|-||=.
T Consensus 2 ~~Cpi~~~~~~~Pv~ 16 (63)
T smart00504 2 FLCPISLEVMKDPVI 16 (63)
T ss_pred cCCcCCCCcCCCCEE
Confidence 679999999888743
No 52
>PRK09381 trxA thioredoxin; Provisional
Probab=30.88 E-value=8.9 Score=26.14 Aligned_cols=22 Identities=23% Similarity=0.448 Sum_probs=18.7
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESK 69 (152)
-|+.|+.++|..+.+...|..+
T Consensus 32 ~C~~C~~~~p~~~~l~~~~~~~ 53 (109)
T PRK09381 32 WCGPCKMIAPILDEIADEYQGK 53 (109)
T ss_pred CCHHHHHHhHHHHHHHHHhCCC
Confidence 3999999999999988887643
No 53
>cd03011 TlpA_like_ScsD_MtbDsbE TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif. The Salmonella typhimurium ScsD is a thioredoxin-like protein which confers copper tolerance to copper-sensitive mutants of E. coli. MtbDsbE has been characterized as an oxidase in vitro, catalyzing the disulfide bond formation of substrates like hirudin. The reduced form of MtbDsbE is more stable than its oxidized form, consistent with an oxidase function. This is in contrast to the function of DsbE from gram-negative bacteria which is a specific reductase of apocytochrome c.
Probab=30.73 E-value=12 Score=25.73 Aligned_cols=18 Identities=28% Similarity=0.896 Sum_probs=15.2
Q ss_pred eCcccccCCCCcchhhhh
Q 031832 48 ECPLCKVTAPDIKSMQIH 65 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~H 65 (152)
-|+.|+.++|....+.+.
T Consensus 31 ~C~~C~~~~~~l~~~~~~ 48 (123)
T cd03011 31 WCPVCRFTSPTVNQLAAD 48 (123)
T ss_pred cChhhhhhChHHHHHHhh
Confidence 399999999998877665
No 54
>cd03009 TryX_like_TryX_NRX Tryparedoxin (TryX)-like family, TryX and nucleoredoxin (NRX) subfamily; TryX and NRX are thioredoxin (TRX)-like protein disulfide oxidoreductases that alter the redox state of target proteins via the reversible oxidation of an active center CXXC motif. TryX is involved in the regulation of oxidative stress in parasitic trypanosomatids by reducing TryX peroxidase, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. TryX derives reducing equivalents from reduced trypanothione, a polyamine peptide conjugate unique to trypanosomatids, which is regenerated by the NADPH-dependent flavoprotein trypanothione reductase. Vertebrate NRX is a 400-amino acid nuclear protein with one redox active TRX domain containing a CPPC active site motif followed by one redox inactive TRX-like domain. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. Plant NRX, longer than the
Probab=30.35 E-value=12 Score=26.41 Aligned_cols=22 Identities=18% Similarity=0.468 Sum_probs=17.3
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESK 69 (152)
-|+.|+.++|....+...+..+
T Consensus 29 wC~~C~~~~p~l~~~~~~~~~~ 50 (131)
T cd03009 29 WCPPCRAFTPKLVEFYEKLKES 50 (131)
T ss_pred CChHHHHHhHHHHHHHHHHHhc
Confidence 4999999999887776666543
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=30.33 E-value=24 Score=20.10 Aligned_cols=20 Identities=20% Similarity=0.595 Sum_probs=15.8
Q ss_pred eeCcccccCCCCcchhhhhhh
Q 031832 47 YECPLCKVTAPDIKSMQIHHD 67 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfE 67 (152)
..||+|.-.. .+..+..|..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 4799998877 7888888853
No 56
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.86 E-value=25 Score=32.23 Aligned_cols=15 Identities=27% Similarity=0.820 Sum_probs=11.3
Q ss_pred eeeeCcccccCCCCc
Q 031832 45 AKYECPLCKVTAPDI 59 (152)
Q Consensus 45 lK~~CpVCkaqmPD~ 59 (152)
-+++||||++..|-+
T Consensus 360 y~~~CPvCrt~iPPp 374 (374)
T COG5540 360 YSNKCPVCRTAIPPP 374 (374)
T ss_pred hcccCCccCCCCCCC
Confidence 357899998888753
No 57
>cd03018 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.
Probab=29.64 E-value=9.7 Score=27.00 Aligned_cols=20 Identities=15% Similarity=0.293 Sum_probs=16.3
Q ss_pred CcccccCCCCcchhhhhhhh
Q 031832 49 CPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 49 CpVCkaqmPD~Kt~k~HfES 68 (152)
|+.|..++|..+.+..-|..
T Consensus 41 c~~C~~~~~~l~~~~~~~~~ 60 (149)
T cd03018 41 TPVCTKELCALRDSLELFEA 60 (149)
T ss_pred CccHHHHHHHHHHHHHHHHh
Confidence 99999999988877666653
No 58
>PLN02748 tRNA dimethylallyltransferase
Probab=29.63 E-value=25 Score=32.40 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=22.9
Q ss_pred ceeeeCccccc-CCCCcchhhhhhhhC
Q 031832 44 HAKYECPLCKV-TAPDIKSMQIHHDAR 69 (152)
Q Consensus 44 alK~~CpVCka-qmPD~Kt~k~HfESK 69 (152)
--+|+|.+|.. .|-......+|..|+
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcch
Confidence 36789999997 799999999999886
No 59
>cd02996 PDI_a_ERp44 PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain, similar to that of PDIa, with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. The CXFS motif in the N-terminal domain allows ERp44 to form stable reversible mixed disulfides with its substrates. Through this activity, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. It also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol.
Probab=29.28 E-value=12 Score=25.61 Aligned_cols=25 Identities=12% Similarity=0.284 Sum_probs=21.0
Q ss_pred eCcccccCCCCcchhhhhhhhCCCC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDARHPK 72 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESKHPK 72 (152)
-|+.|+...|....+...+++.+|.
T Consensus 29 wC~~C~~~~p~~~~~a~~~~~~~~~ 53 (108)
T cd02996 29 WCRFSQMLHPIFEEAAAKIKEEFPD 53 (108)
T ss_pred CCHHHHhhHHHHHHHHHHHhhccCC
Confidence 3999999999998888888776664
No 60
>cd02985 TRX_CDSP32 TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif. CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form.
Probab=29.13 E-value=8.6 Score=26.66 Aligned_cols=41 Identities=12% Similarity=0.238 Sum_probs=28.9
Q ss_pred ccHHHHHHHHHhhhhcCCCCccCcccccccccccceee---eCcccccCCCCcchhhhhh
Q 031832 10 HTAKEIAMKVDAATTNRGGGKAGMADRTGREKGGHAKY---ECPLCKVTAPDIKSMQIHH 66 (152)
Q Consensus 10 HTAkEiaaK~~aattNkGGGKaGl~dR~g~~k~galK~---~CpVCkaqmPD~Kt~k~Hf 66 (152)
||+.|+.+.+..+ + |+-=+ +.| -|+.|+.++|....+.+.|
T Consensus 1 ~~~~~~~~~i~~~---~--~k~vv-----------v~F~a~wC~~C~~~~p~l~~la~~~ 44 (103)
T cd02985 1 HSVEELDEALKKA---K--GRLVV-----------LEFALKHSGPSVKIYPTMVKLSRTC 44 (103)
T ss_pred CCHHHHHHHHHHc---C--CCEEE-----------EEEECCCCHhHHHHhHHHHHHHHHC
Confidence 7888888888543 1 22211 333 3999999999999888777
No 61
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=28.94 E-value=19 Score=24.96 Aligned_cols=17 Identities=24% Similarity=0.473 Sum_probs=13.2
Q ss_pred eCcccccCCCCcchhhh
Q 031832 48 ECPLCKVTAPDIKSMQI 64 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~ 64 (152)
+|.|||..+++--....
T Consensus 3 ~CvVCKqpi~~a~~v~T 19 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVET 19 (54)
T ss_pred eeeeeCCccCcceEEEc
Confidence 69999999998655443
No 62
>cd00340 GSH_Peroxidase Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes.
Probab=27.85 E-value=12 Score=27.49 Aligned_cols=21 Identities=5% Similarity=0.101 Sum_probs=16.1
Q ss_pred eeCcccccCCCCcchhhhhhhh
Q 031832 47 YECPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 47 ~~CpVCkaqmPD~Kt~k~HfES 68 (152)
..|| |..+||+...+.+-|+.
T Consensus 32 twC~-C~~e~p~l~~l~~~~~~ 52 (152)
T cd00340 32 SKCG-FTPQYEGLEALYEKYKD 52 (152)
T ss_pred CCCC-chHHHHHHHHHHHHhcC
Confidence 4699 99999987777666654
No 63
>cd02999 PDI_a_ERp44_like PDIa family, endoplasmic reticulum protein 44 (ERp44)-like subfamily; composed of uncharacterized PDI-like eukaryotic proteins containing only one redox active TRX (a) domain with a CXXS motif, similar to ERp44. CXXS is still a redox active motif; however, the mixed disulfide formed with the substrate is more stable than those formed by CXXC motif proteins. PDI-related proteins are usually involved in the oxidative protein folding in the ER by acting as catalysts and folding assistants. ERp44 is involved in thiol-mediated retention in the ER.
Probab=26.90 E-value=12 Score=26.16 Aligned_cols=19 Identities=16% Similarity=0.474 Sum_probs=17.1
Q ss_pred CcccccCCCCcchhhhhhh
Q 031832 49 CPLCKVTAPDIKSMQIHHD 67 (152)
Q Consensus 49 CpVCkaqmPD~Kt~k~HfE 67 (152)
|+.|+.++|....+...|.
T Consensus 30 C~~C~~~~p~l~~la~~~~ 48 (100)
T cd02999 30 CPFSASFRPHFNALSSMFP 48 (100)
T ss_pred CHHHHhHhHHHHHHHHHhc
Confidence 9999999999999888774
No 64
>cd02964 TryX_like_family Tryparedoxin (TryX)-like family; composed of TryX and related proteins including nucleoredoxin (NRX), rod-derived cone viability factor (RdCVF) and the nematode homolog described as a 16-kD class of TRX. Most members of this family, except RdCVF, are protein disulfide oxidoreductases containing an active site CXXC motif, similar to TRX.
Probab=26.88 E-value=12 Score=26.63 Aligned_cols=22 Identities=18% Similarity=0.477 Sum_probs=17.3
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESK 69 (152)
-|+.|+.+||....+.+.+..+
T Consensus 28 wC~~C~~~~p~l~~l~~~~~~~ 49 (132)
T cd02964 28 WCPPCRAFTPKLVEFYEKLKEE 49 (132)
T ss_pred CCchHHHHHHHHHHHHHHHhhc
Confidence 5999999999887776666544
No 65
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=26.69 E-value=6.8 Score=27.90 Aligned_cols=21 Identities=24% Similarity=0.536 Sum_probs=15.3
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 031832 48 ECPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfES 68 (152)
-||.|..+||..+.+..-|..
T Consensus 40 ~Cp~C~~~~p~l~~l~~~~~~ 60 (146)
T PF08534_consen 40 WCPPCRKELPYLNELQEKYKD 60 (146)
T ss_dssp TSHHHHHHHHHHHHHHHHHHT
T ss_pred CCCcchhhhhhHHhhhhhhcc
Confidence 599999999966666544443
No 66
>TIGR02540 gpx7 putative glutathione peroxidase Gpx7. This model represents one of several families of known and probable glutathione peroxidases. This family is restricted to animals and designated GPX7.
Probab=26.56 E-value=15 Score=26.93 Aligned_cols=22 Identities=9% Similarity=0.243 Sum_probs=17.5
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESK 69 (152)
-||.|+..||+...+..-|..+
T Consensus 33 ~C~~c~~~~~~l~~l~~~~~~~ 54 (153)
T TIGR02540 33 ECGFTDQNYRALQELHRELGPS 54 (153)
T ss_pred CCCchhhhHHHHHHHHHHHhhC
Confidence 4999999999888877777654
No 67
>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=25.19 E-value=26 Score=27.37 Aligned_cols=15 Identities=20% Similarity=0.603 Sum_probs=11.6
Q ss_pred ceeeeCcccccCCCC
Q 031832 44 HAKYECPLCKVTAPD 58 (152)
Q Consensus 44 alK~~CpVCkaqmPD 58 (152)
...|+||+|..++-.
T Consensus 126 ~~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 126 ELNFTCPRCGAMLDY 140 (158)
T ss_pred HcCCcCCCCCCEeee
Confidence 357999999988643
No 68
>cd02971 PRX_family Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. They confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either TRX, glutathione, trypanothione and AhpF. They are distinct from other peroxidases in that they have no cofactors such as metals or prosthetic groups. The first step of catalysis, common to all PRXs, is the nucleophilic attack by the catalytic cysteine (also known as the peroxidatic cysteine) on the peroxide leading to cleavage of the oxygen-oxygen bond and the formation of a
Probab=25.17 E-value=15 Score=25.64 Aligned_cols=21 Identities=10% Similarity=0.249 Sum_probs=17.1
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 031832 48 ECPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfES 68 (152)
-|+.|..++|..+.+.+-|+.
T Consensus 34 ~c~~C~~~~~~l~~~~~~~~~ 54 (140)
T cd02971 34 FTPVCTTELCAFRDLAEEFAK 54 (140)
T ss_pred CCCcCHHHHHHHHHHHHHHHH
Confidence 399999999998888777743
No 69
>PF14353 CpXC: CpXC protein
Probab=24.82 E-value=14 Score=27.04 Aligned_cols=37 Identities=14% Similarity=0.232 Sum_probs=26.0
Q ss_pred ccceeeeCcccccCCCCcchhhhhhhhCCCCCCCChh
Q 031832 42 GGHAKYECPLCKVTAPDIKSMQIHHDARHPKLPFDEA 78 (152)
Q Consensus 42 ~galK~~CpVCkaqmPD~Kt~k~HfESKHPK~plP~E 78 (152)
+--+.|+||.|.....=.-.+--|...++--.-+.|+
T Consensus 34 g~l~~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred CCcCEEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 3457899999998877666666777777655544444
No 70
>PF04911 ATP-synt_J: ATP synthase j chain; InterPro: IPR006995 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit J found in the F0 complex of F-ATPases from fungal mitochondria. This subunit does not appear to display sequence similarity with subunits of F-ATPases found in other organisms []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o)
Probab=24.71 E-value=1.2e+02 Score=21.16 Aligned_cols=26 Identities=23% Similarity=0.257 Sum_probs=22.7
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHhhcc
Q 031832 116 MLRLLDYGLFVLMMLWAVQCILLNST 141 (152)
Q Consensus 116 m~~~~~~gl~~~~~~~~~~~~~~~~~ 141 (152)
|--.|..|+|++..++..|-...||.
T Consensus 10 ~wPFf~ag~iv~ygv~k~~~a~~ns~ 35 (54)
T PF04911_consen 10 MWPFFAAGAIVYYGVNKAQNAMMNSD 35 (54)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhcCH
Confidence 44578999999999999999999884
No 71
>cd02966 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases.
Probab=24.68 E-value=14 Score=23.46 Aligned_cols=20 Identities=20% Similarity=0.677 Sum_probs=17.6
Q ss_pred eCcccccCCCCcchhhhhhh
Q 031832 48 ECPLCKVTAPDIKSMQIHHD 67 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfE 67 (152)
.|+.|..++|..+.+.+-|+
T Consensus 30 ~C~~C~~~~~~l~~~~~~~~ 49 (116)
T cd02966 30 WCPPCRAEMPELEALAKEYK 49 (116)
T ss_pred cChhHHHHhHHHHHHHHHhC
Confidence 79999999999999887775
No 72
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=24.56 E-value=27 Score=27.39 Aligned_cols=25 Identities=12% Similarity=0.248 Sum_probs=17.4
Q ss_pred cceeeeCcccccCCCCc---chhhhhhh
Q 031832 43 GHAKYECPLCKVTAPDI---KSMQIHHD 67 (152)
Q Consensus 43 galK~~CpVCkaqmPD~---Kt~k~HfE 67 (152)
--+-|.||+|...-|.. +.++.++.
T Consensus 43 Effdy~CphC~~~~~~l~~~~~~~~~~~ 70 (207)
T PRK10954 43 EFFSFYCPHCYQFEEVYHVSDNVKKKLP 70 (207)
T ss_pred EEeCCCCccHHHhcccccchHHHHHhCC
Confidence 34678999999877754 55566544
No 73
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=24.34 E-value=31 Score=27.96 Aligned_cols=12 Identities=42% Similarity=1.173 Sum_probs=10.0
Q ss_pred eeeCcccccCCC
Q 031832 46 KYECPLCKVTAP 57 (152)
Q Consensus 46 K~~CpVCkaqmP 57 (152)
.|.||+|...+.
T Consensus 2 ~~~CP~C~~~l~ 13 (272)
T PRK11088 2 SYQCPLCHQPLT 13 (272)
T ss_pred cccCCCCCcchh
Confidence 378999998884
No 74
>cd02969 PRX_like1 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF.
Probab=23.70 E-value=15 Score=27.21 Aligned_cols=22 Identities=18% Similarity=0.433 Sum_probs=19.6
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESK 69 (152)
-||.|..++|....+..+|+.+
T Consensus 36 ~Cp~c~~~~~~l~~l~~~~~~~ 57 (171)
T cd02969 36 HCPYVKAIEDRLNRLAKEYGAK 57 (171)
T ss_pred CCccHHHHHHHHHHHHHHHhhC
Confidence 6999999999999999999754
No 75
>cd02956 ybbN ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.
Probab=23.51 E-value=14 Score=24.48 Aligned_cols=21 Identities=14% Similarity=0.186 Sum_probs=17.6
Q ss_pred eCcccccCCCCcchhhhhhhh
Q 031832 48 ECPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfES 68 (152)
-|+.|+.++|....+...|..
T Consensus 23 wC~~C~~~~~~~~~~~~~~~~ 43 (96)
T cd02956 23 RSPPSKELLPLLERLAEEYQG 43 (96)
T ss_pred CChHHHHHHHHHHHHHHHhCC
Confidence 499999999998888877753
No 76
>cd03016 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes an
Probab=23.41 E-value=17 Score=28.54 Aligned_cols=21 Identities=14% Similarity=0.368 Sum_probs=18.2
Q ss_pred CcccccCCCCcchhhhhhhhC
Q 031832 49 CPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 49 CpVCkaqmPD~Kt~k~HfESK 69 (152)
||+|.+++|....+.+.|+.+
T Consensus 38 cp~C~~el~~l~~~~~~f~~~ 58 (203)
T cd03016 38 TPVCTTELGAFAKLAPEFKKR 58 (203)
T ss_pred CCcCHHHHHHHHHHHHHHHHc
Confidence 999999999988888888654
No 77
>PRK15000 peroxidase; Provisional
Probab=22.82 E-value=18 Score=28.75 Aligned_cols=22 Identities=9% Similarity=0.007 Sum_probs=18.0
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESK 69 (152)
-|++|.+++|....+.+-|+.+
T Consensus 46 ~t~vC~~El~~l~~~~~~f~~~ 67 (200)
T PRK15000 46 FTFVCPSELIAFDKRYEEFQKR 67 (200)
T ss_pred CCCCCHHHHHHHHHHHHHHHHC
Confidence 3899999999988887777643
No 78
>TIGR02661 MauD methylamine dehydrogenase accessory protein MauD. This protein, MauD, appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulfide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulfide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded.
Probab=22.64 E-value=15 Score=28.51 Aligned_cols=16 Identities=44% Similarity=0.901 Sum_probs=13.2
Q ss_pred eCcccccCCCCcchhh
Q 031832 48 ECPLCKVTAPDIKSMQ 63 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k 63 (152)
.||.|+.++|+...+.
T Consensus 85 wCp~C~~~lp~l~~~~ 100 (189)
T TIGR02661 85 SCPVCDKLFPIIKSIA 100 (189)
T ss_pred CChhHHHHHHHHHHHH
Confidence 5999999999876654
No 79
>PF10954 DUF2755: Protein of unknown function (DUF2755); InterPro: IPR020513 This entry contains membrane proteins with no known function.; GO: 0016021 integral to membrane
Probab=22.00 E-value=92 Score=24.05 Aligned_cols=16 Identities=44% Similarity=0.887 Sum_probs=13.8
Q ss_pred hHHHHHHHHHHHHHHH
Q 031832 120 LDYGLFVLMMLWAVQC 135 (152)
Q Consensus 120 ~~~gl~~~~~~~~~~~ 135 (152)
++|.||||.-.||---
T Consensus 24 iAYAlFVLfcfWaGaQ 39 (100)
T PF10954_consen 24 IAYALFVLFCFWAGAQ 39 (100)
T ss_pred hHHHHHHHHHHHhhHH
Confidence 6899999999998543
No 80
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.96 E-value=39 Score=27.08 Aligned_cols=15 Identities=20% Similarity=0.620 Sum_probs=12.0
Q ss_pred eeeeCcccccCCCCc
Q 031832 45 AKYECPLCKVTAPDI 59 (152)
Q Consensus 45 lK~~CpVCkaqmPD~ 59 (152)
..|.||+|..++-..
T Consensus 135 ~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 135 YGFRCPQCGEMLEEY 149 (178)
T ss_pred cCCcCCCCCCCCeec
Confidence 479999999887653
No 81
>TIGR03137 AhpC peroxiredoxin. This gene contains two invariant cysteine residues, one near the N-terminus and one near the C-terminus, each followed immediately by a proline residue.
Probab=21.80 E-value=19 Score=27.90 Aligned_cols=25 Identities=8% Similarity=0.052 Sum_probs=19.3
Q ss_pred ceeee----CcccccCCCCcchhhhhhhh
Q 031832 44 HAKYE----CPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 44 alK~~----CpVCkaqmPD~Kt~k~HfES 68 (152)
-+.|- ||+|..+||....+..-|+.
T Consensus 35 vl~F~p~~~cp~C~~el~~l~~~~~~~~~ 63 (187)
T TIGR03137 35 VFFFYPADFTFVCPTELEDLADKYAELKK 63 (187)
T ss_pred EEEEECCCcCCcCHHHHHHHHHHHHHHHh
Confidence 35663 99999999998877766653
No 82
>cd03014 PRX_Atyp2cys Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial periplasmic peroxidase which differs from other PRXs in that it shows substrate specificity toward alkyl hydroperoxides over hydrogen peroxide. As with all other PRXs, the peroxidatic cysteine (N-terminal) of Tpx is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Tpx is able to resolve this intermediate by forming an intramolecular disulfide bond with a conserved C-terminal cysteine (the resolving cysteine), which can then be reduced by thioredoxin. This differs from the typical 2-cys PRX which resolves the oxidized cysteine by forming an intermolecular disulfide bond with the resolving cysteine from the other subunit of the homodimer. Atypical 2-cys PRX homodimers have a loop-based
Probab=21.71 E-value=15 Score=26.09 Aligned_cols=18 Identities=11% Similarity=0.322 Sum_probs=13.9
Q ss_pred CcccccCCCCcchhhhhh
Q 031832 49 CPLCKVTAPDIKSMQIHH 66 (152)
Q Consensus 49 CpVCkaqmPD~Kt~k~Hf 66 (152)
||.|+.+||....+.+-|
T Consensus 39 c~~C~~e~~~l~~~~~~~ 56 (143)
T cd03014 39 TPVCATQTKRFNKEAAKL 56 (143)
T ss_pred CCcCHHHHHHHHHHHHhc
Confidence 899999999876655443
No 83
>COG0526 TrxA Thiol-disulfide isomerase and thioredoxins [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]
Probab=21.55 E-value=26 Score=21.30 Aligned_cols=23 Identities=22% Similarity=0.466 Sum_probs=19.4
Q ss_pred eeeCcccccCCCCcchhhhhhhh
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfES 68 (152)
..-|+.|+..+|....+..-+..
T Consensus 41 ~~~C~~C~~~~~~l~~~~~~~~~ 63 (127)
T COG0526 41 APWCPPCRAEAPLLEELAEEYGG 63 (127)
T ss_pred cCcCHHHHhhchhHHHHHHHhcC
Confidence 46799999999998888877765
No 84
>smart00746 TRASH metallochaperone-like domain.
Probab=21.14 E-value=54 Score=16.69 Aligned_cols=10 Identities=20% Similarity=0.697 Sum_probs=7.4
Q ss_pred CcccccCCCC
Q 031832 49 CPLCKVTAPD 58 (152)
Q Consensus 49 CpVCkaqmPD 58 (152)
|++|...+++
T Consensus 1 c~~C~~~~~~ 10 (39)
T smart00746 1 CSFCGKDIYN 10 (39)
T ss_pred CCCCCCCccC
Confidence 7888877753
No 85
>PRK13599 putative peroxiredoxin; Provisional
Probab=20.74 E-value=21 Score=28.88 Aligned_cols=22 Identities=9% Similarity=0.149 Sum_probs=18.1
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESK 69 (152)
-||+|.++||....+..-|+.+
T Consensus 40 ~tpvCt~El~~l~~~~~~f~~~ 61 (215)
T PRK13599 40 FTPVCTTEFVEFARKANDFKEL 61 (215)
T ss_pred CCCcCHHHHHHHHHHHHHHHHC
Confidence 4999999999888887777654
No 86
>PRK10382 alkyl hydroperoxide reductase subunit C; Provisional
Probab=20.70 E-value=21 Score=28.39 Aligned_cols=25 Identities=8% Similarity=0.022 Sum_probs=20.2
Q ss_pred ceeee----CcccccCCCCcchhhhhhhh
Q 031832 44 HAKYE----CPLCKVTAPDIKSMQIHHDA 68 (152)
Q Consensus 44 alK~~----CpVCkaqmPD~Kt~k~HfES 68 (152)
-+.|- ||+|..+||....+.+.|+.
T Consensus 35 vL~F~P~~~~p~C~~el~~l~~~~~~f~~ 63 (187)
T PRK10382 35 VFFFYPADFTFVCPTELGDVADHYEELQK 63 (187)
T ss_pred EEEEECCCCCCcCHHHHHHHHHHHHHHHh
Confidence 35554 99999999999888888864
No 87
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=20.57 E-value=55 Score=30.81 Aligned_cols=28 Identities=39% Similarity=0.739 Sum_probs=26.3
Q ss_pred eeeCcccccCCCCcchhhhhhhhCCCCC
Q 031832 46 KYECPLCKVTAPDIKSMQIHHDARHPKL 73 (152)
Q Consensus 46 K~~CpVCkaqmPD~Kt~k~HfESKHPK~ 73 (152)
-|+||.|-...|.+.++..|..-||.+.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~d 290 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSKD 290 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhccC
Confidence 4899999999999999999999999984
No 88
>PTZ00056 glutathione peroxidase; Provisional
Probab=20.44 E-value=21 Score=28.28 Aligned_cols=22 Identities=14% Similarity=0.298 Sum_probs=19.0
Q ss_pred eCcccccCCCCcchhhhhhhhC
Q 031832 48 ECPLCKVTAPDIKSMQIHHDAR 69 (152)
Q Consensus 48 ~CpVCkaqmPD~Kt~k~HfESK 69 (152)
-|+.|+..||....+.+.|..+
T Consensus 50 wC~~C~~e~p~L~~l~~~~~~~ 71 (199)
T PTZ00056 50 KCGLTKKHVDQMNRLHSVFNPL 71 (199)
T ss_pred CCCChHHHHHHHHHHHHHHhcC
Confidence 4999999999999998888764
Done!