Query 032369
Match_columns 142
No_of_seqs 98 out of 119
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 13:12:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032369.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032369hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01053 LSD1 zinc finger dom 99.5 1E-14 2.2E-19 88.2 2.6 31 25-55 1-31 (31)
2 PF06943 zf-LSD1: LSD1 zinc fi 99.4 3.7E-14 7.9E-19 82.6 2.2 25 28-52 1-25 (25)
3 TIGR01053 LSD1 zinc finger dom 99.4 5E-14 1.1E-18 85.2 2.1 30 64-93 1-30 (31)
4 PF06943 zf-LSD1: LSD1 zinc fi 99.4 1.2E-13 2.6E-18 80.5 2.1 25 67-91 1-25 (25)
5 PF09788 Tmemb_55A: Transmembr 97.7 0.00034 7.3E-09 59.7 9.7 111 23-134 63-191 (256)
6 PF10122 Mu-like_Com: Mu-like 95.1 0.01 2.2E-07 39.9 1.1 34 63-96 3-38 (51)
7 PF10122 Mu-like_Com: Mu-like 94.4 0.013 2.9E-07 39.4 0.4 36 101-136 3-40 (51)
8 PRK14890 putative Zn-ribbon RN 93.6 0.049 1.1E-06 37.6 2.0 53 61-129 4-57 (59)
9 PF01667 Ribosomal_S27e: Ribos 92.0 0.15 3.3E-06 34.5 2.6 43 82-125 7-49 (55)
10 PLN00209 ribosomal protein S27 91.0 0.36 7.8E-06 35.6 3.9 46 82-128 36-81 (86)
11 TIGR02098 MJ0042_CXXC MJ0042 f 90.9 0.21 4.5E-06 29.9 2.1 30 83-112 3-35 (38)
12 PF11331 DUF3133: Protein of u 90.9 0.26 5.7E-06 32.3 2.7 38 40-77 3-44 (46)
13 PTZ00083 40S ribosomal protein 90.7 0.41 8.8E-06 35.2 3.9 44 82-126 35-78 (85)
14 PF11331 DUF3133: Protein of u 89.9 0.41 8.8E-06 31.4 3.0 37 79-115 3-44 (46)
15 PF13719 zinc_ribbon_5: zinc-r 89.8 0.31 6.8E-06 29.8 2.3 11 84-94 4-14 (37)
16 PF09788 Tmemb_55A: Transmembr 89.5 0.55 1.2E-05 40.4 4.3 66 31-96 111-191 (256)
17 PRK00415 rps27e 30S ribosomal 89.0 0.26 5.6E-06 33.9 1.7 38 82-120 11-48 (59)
18 PLN00209 ribosomal protein S27 89.0 0.35 7.5E-06 35.6 2.4 40 43-84 36-75 (86)
19 PRK00398 rpoP DNA-directed RNA 88.6 0.58 1.3E-05 29.3 2.9 25 65-89 4-28 (46)
20 PTZ00083 40S ribosomal protein 88.5 0.4 8.6E-06 35.3 2.4 39 43-83 35-73 (85)
21 PF01667 Ribosomal_S27e: Ribos 87.9 0.47 1E-05 32.1 2.3 38 43-82 7-44 (55)
22 COG2051 RPS27A Ribosomal prote 86.7 0.8 1.7E-05 32.4 3.0 39 82-121 19-57 (67)
23 PRK00415 rps27e 30S ribosomal 86.6 0.4 8.8E-06 33.0 1.4 34 44-79 12-45 (59)
24 PF13719 zinc_ribbon_5: zinc-r 85.9 0.85 1.8E-05 27.8 2.5 28 103-130 3-35 (37)
25 TIGR02098 MJ0042_CXXC MJ0042 f 85.0 0.78 1.7E-05 27.3 2.0 31 44-74 3-35 (38)
26 PRK00398 rpoP DNA-directed RNA 84.3 1.6 3.5E-05 27.3 3.3 30 83-114 4-33 (46)
27 KOG1779 40s ribosomal protein 83.6 2.3 5.1E-05 31.2 4.3 43 83-126 35-77 (84)
28 KOG4684 Uncharacterized conser 83.1 1.2 2.5E-05 38.4 3.0 95 39-134 76-203 (275)
29 PF13717 zinc_ribbon_4: zinc-r 81.9 1.5 3.2E-05 26.8 2.3 11 84-94 4-14 (36)
30 COG2888 Predicted Zn-ribbon RN 81.3 1.3 2.8E-05 30.9 2.2 50 65-129 10-59 (61)
31 COG2051 RPS27A Ribosomal prote 81.1 1.8 3.9E-05 30.7 2.8 38 43-82 19-56 (67)
32 KOG1779 40s ribosomal protein 77.9 3.7 8E-05 30.2 3.7 42 43-86 34-75 (84)
33 PRK14890 putative Zn-ribbon RN 77.3 2.4 5.3E-05 29.3 2.5 53 22-91 4-57 (59)
34 PF12773 DZR: Double zinc ribb 70.1 1.9 4.2E-05 26.8 0.6 29 64-93 12-40 (50)
35 PF05129 Elf1: Transcription e 64.9 10 0.00023 26.9 3.5 39 81-119 21-63 (81)
36 PF04690 YABBY: YABBY protein; 64.7 5.6 0.00012 32.3 2.4 40 43-82 12-54 (170)
37 PF04810 zf-Sec23_Sec24: Sec23 64.6 6.3 0.00014 24.3 2.1 19 116-134 20-38 (40)
38 KOG4684 Uncharacterized conser 61.8 6.9 0.00015 33.8 2.5 48 78-125 76-126 (275)
39 PF07754 DUF1610: Domain of un 60.8 6.1 0.00013 22.8 1.4 19 69-88 3-22 (24)
40 PRK05580 primosome assembly pr 60.5 15 0.00032 34.6 4.6 66 33-117 369-436 (679)
41 PF05495 zf-CHY: CHY zinc fing 59.9 15 0.00032 25.2 3.5 30 99-128 38-69 (71)
42 COG4416 Com Mu-like prophage p 56.6 2.7 5.9E-05 29.1 -0.6 32 63-94 3-36 (60)
43 KOG1546 Metacaspase involved i 55.0 4.8 0.0001 36.3 0.5 28 66-95 6-33 (362)
44 smart00661 RPOL9 RNA polymeras 53.9 13 0.00029 22.9 2.3 29 105-133 3-33 (52)
45 PRK14714 DNA polymerase II lar 53.8 9.7 0.00021 39.4 2.4 54 61-128 664-717 (1337)
46 PF11023 DUF2614: Protein of u 53.1 6.8 0.00015 30.3 1.0 32 80-115 67-98 (114)
47 COG4357 Zinc finger domain con 51.5 3.2 6.9E-05 31.6 -1.0 26 65-90 63-88 (105)
48 COG4357 Zinc finger domain con 51.5 3.7 8.1E-05 31.3 -0.7 27 25-51 62-88 (105)
49 PF08271 TF_Zn_Ribbon: TFIIB z 50.2 8.9 0.00019 23.6 1.0 6 103-108 20-25 (43)
50 TIGR00595 priA primosomal prot 50.0 24 0.00053 32.0 4.2 61 38-117 207-268 (505)
51 PF04690 YABBY: YABBY protein; 49.3 30 0.00065 28.1 4.2 45 59-117 7-51 (170)
52 TIGR01384 TFS_arch transcripti 47.0 16 0.00034 25.9 2.0 12 120-131 16-27 (104)
53 PRK14714 DNA polymerase II lar 44.9 15 0.00032 38.2 2.1 56 22-92 664-719 (1337)
54 KOG1546 Metacaspase involved i 43.4 12 0.00025 33.9 1.1 26 28-55 7-32 (362)
55 COG1096 Predicted RNA-binding 42.5 22 0.00048 29.5 2.5 31 60-92 143-175 (188)
56 TIGR00595 priA primosomal prot 41.6 30 0.00066 31.4 3.4 43 80-133 211-253 (505)
57 PF02150 RNA_POL_M_15KD: RNA p 41.2 17 0.00037 22.0 1.3 29 105-133 4-33 (35)
58 PRK14873 primosome assembly pr 39.7 32 0.0007 32.8 3.4 68 29-117 368-437 (665)
59 PRK05580 primosome assembly pr 39.3 31 0.00066 32.5 3.2 51 72-133 369-421 (679)
60 PF14634 zf-RING_5: zinc-RING 36.3 4.6 9.9E-05 24.8 -1.9 24 62-89 20-43 (44)
61 PF05458 Siva: Cd27 binding pr 35.3 13 0.00028 29.9 0.0 63 37-110 105-172 (175)
62 smart00731 SprT SprT homologue 33.6 48 0.001 25.0 2.9 12 63-74 132-143 (146)
63 PRK14873 primosome assembly pr 33.6 43 0.00093 31.9 3.2 50 68-129 368-419 (665)
64 PF12172 DUF35_N: Rubredoxin-l 33.4 28 0.00061 20.6 1.3 21 27-51 13-33 (37)
65 PF02591 DUF164: Putative zinc 32.2 34 0.00074 22.0 1.7 28 25-52 22-55 (56)
66 PRK02935 hypothetical protein; 32.1 29 0.00063 26.7 1.5 32 80-115 68-99 (110)
67 PRK04351 hypothetical protein; 31.0 42 0.00091 26.2 2.3 33 83-115 113-145 (149)
68 PF10058 DUF2296: Predicted in 30.7 49 0.0011 21.9 2.3 8 46-53 25-32 (54)
69 PF00130 C1_1: Phorbol esters/ 30.5 35 0.00077 21.0 1.5 27 103-130 12-38 (53)
70 TIGR00155 pqiA_fam integral me 30.4 39 0.00086 30.1 2.3 30 83-112 14-43 (403)
71 COG1198 PriA Primosomal protei 29.2 67 0.0014 31.3 3.7 60 33-111 423-484 (730)
72 PF14599 zinc_ribbon_6: Zinc-r 29.2 78 0.0017 21.6 3.1 34 60-93 26-59 (61)
73 PRK14559 putative protein seri 28.8 27 0.00059 33.3 1.1 50 44-112 2-51 (645)
74 COG1096 Predicted RNA-binding 28.7 81 0.0018 26.2 3.7 29 99-129 146-174 (188)
75 PF02318 FYVE_2: FYVE-type zin 28.6 6.5 0.00014 29.0 -2.5 62 62-139 52-113 (118)
76 cd00029 C1 Protein kinase C co 28.5 26 0.00057 20.9 0.6 25 104-129 13-37 (50)
77 PF13901 DUF4206: Domain of un 28.4 26 0.00057 28.2 0.8 27 104-130 154-182 (202)
78 PF09082 DUF1922: Domain of un 27.8 88 0.0019 22.2 3.2 30 103-134 4-33 (68)
79 PF09297 zf-NADH-PPase: NADH p 27.2 64 0.0014 18.6 2.1 22 67-88 6-27 (32)
80 smart00109 C1 Protein kinase C 26.8 24 0.00051 20.8 0.2 24 104-129 13-36 (49)
81 PF07295 DUF1451: Protein of u 26.8 58 0.0013 25.5 2.4 34 62-95 110-143 (146)
82 smart00659 RPOLCX RNA polymera 26.1 1.4E+02 0.0031 18.9 3.7 31 83-116 3-33 (44)
83 COG1198 PriA Primosomal protei 25.4 1.2E+02 0.0027 29.6 4.8 43 80-133 433-475 (730)
84 PF14369 zf-RING_3: zinc-finge 24.8 57 0.0012 19.8 1.6 23 67-89 5-28 (35)
85 PF07282 OrfB_Zn_ribbon: Putat 24.6 90 0.0019 20.3 2.7 13 81-93 27-39 (69)
86 PF04032 Rpr2: RNAse P Rpr2/Rp 24.3 51 0.0011 22.1 1.5 20 22-41 43-62 (85)
87 PF13909 zf-H2C2_5: C2H2-type 23.6 52 0.0011 17.3 1.2 11 121-131 1-11 (24)
88 PRK04023 DNA polymerase II lar 23.2 59 0.0013 33.4 2.3 54 61-133 623-676 (1121)
89 PF05180 zf-DNL: DNL zinc fing 22.1 32 0.0007 24.0 0.2 21 35-55 21-41 (66)
90 PRK14892 putative transcriptio 22.1 87 0.0019 23.3 2.5 10 100-109 40-49 (99)
91 KOG2907 RNA polymerase I trans 21.9 36 0.00078 26.4 0.4 30 26-55 8-37 (116)
92 TIGR01206 lysW lysine biosynth 21.7 89 0.0019 20.9 2.2 7 84-90 4-10 (54)
93 smart00647 IBR In Between Ring 21.4 98 0.0021 19.2 2.3 23 28-50 21-47 (64)
94 cd00069 GHB Glycoprotein hormo 21.4 72 0.0016 24.0 1.9 33 21-54 42-90 (102)
95 PHA00626 hypothetical protein 21.0 76 0.0016 22.1 1.8 31 84-129 2-32 (59)
96 PF14835 zf-RING_6: zf-RING of 20.6 55 0.0012 23.0 1.1 43 45-93 9-51 (65)
97 PF13901 DUF4206: Domain of un 20.5 50 0.0011 26.6 1.0 29 66-94 154-184 (202)
98 KOG3002 Zn finger protein [Gen 20.4 39 0.00085 29.4 0.4 23 99-128 66-88 (299)
No 1
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=99.50 E-value=1e-14 Score=88.20 Aligned_cols=31 Identities=61% Similarity=1.243 Sum_probs=23.1
Q ss_pred eeeccCccceeecccCCCeEecCCCCccccC
Q 032369 25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTAV 55 (142)
Q Consensus 25 QlvC~gCr~lL~YprGA~~VrC~~C~tvn~v 55 (142)
|++|++||++|+||+||++|||+.|++||.+
T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~v 31 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTVNLV 31 (31)
T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeEecC
Confidence 6777777777777777777777777777753
No 2
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=99.45 E-value=3.7e-14 Score=82.63 Aligned_cols=25 Identities=64% Similarity=1.364 Sum_probs=15.9
Q ss_pred ccCccceeecccCCCeEecCCCCcc
Q 032369 28 CSGCRNLLLYPVGATSVCCAVCNAV 52 (142)
Q Consensus 28 C~gCr~lL~YprGA~~VrC~~C~tv 52 (142)
|+|||++|+||+||+||||+.|++|
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 5666666666666666666666654
No 3
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=99.43 E-value=5e-14 Score=85.17 Aligned_cols=30 Identities=73% Similarity=1.381 Sum_probs=19.7
Q ss_pred eEEeCCccceEEeecCCCeEECCCCccccc
Q 032369 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (142)
Q Consensus 64 ql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~ 93 (142)
|++|++||++|+||+||.+|||+.|++||.
T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~ 30 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTVNL 30 (31)
T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeEec
Confidence 456666666666666666666666666664
No 4
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=99.40 E-value=1.2e-13 Score=80.45 Aligned_cols=25 Identities=80% Similarity=1.666 Sum_probs=15.0
Q ss_pred eCCccceEEeecCCCeEECCCCccc
Q 032369 67 CGGCHTLLMYIRGATSVQCSCCHTV 91 (142)
Q Consensus 67 Cg~Cr~lLmYp~GA~sVrC~~C~tV 91 (142)
||+||++||||+||+||||+.|++|
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 5566666666666666666666554
No 5
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=97.70 E-value=0.00034 Score=59.66 Aligned_cols=111 Identities=23% Similarity=0.531 Sum_probs=85.2
Q ss_pred cceeeccCccceeeccc--CCCeEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCC--Cccc-ccccc-
Q 032369 23 QSQLVCSGCRNLLLYPV--GATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSC--CHTV-NLALE- 96 (142)
Q Consensus 23 ~sQlvC~gCr~lL~Ypr--GA~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~--C~tV-n~v~~- 96 (142)
+.-+.|.=|+.++--.. ----|+|..||-.|...++.....-++|- |.-||+=...++-+-|+. |..| |+.+.
T Consensus 63 ~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRCP-CNCLLICk~sS~rIaCPRp~CkRiI~L~~~~ 141 (256)
T PF09788_consen 63 APVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRCP-CNCLLICKSSSQRIACPRPNCKRIINLGPSH 141 (256)
T ss_pred CceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEecC-CceEEEeecccccccCCCCCCcceEEeCCcc
Confidence 35678999998876542 22348999999988865444556677774 788999999999999987 9876 44332
Q ss_pred ----------ccceeEEEcCCcceEEEeecCC--CeEeCCcCcceeeecc
Q 032369 97 ----------ANQVAHVNCGNCRMLLMYQYGA--RSVKCAVCNFVTAVGV 134 (142)
Q Consensus 97 ----------a~q~~~v~Cg~C~t~LmYP~GA--~sVkCa~C~~VT~i~~ 134 (142)
......++||+|+.+.+++.=. ...||+.|+.|..|+.
T Consensus 142 ~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~ 191 (256)
T PF09788_consen 142 QGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGP 191 (256)
T ss_pred CCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccccc
Confidence 2355789999999999999766 5669999999999985
No 6
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=95.07 E-value=0.01 Score=39.94 Aligned_cols=34 Identities=26% Similarity=0.637 Sum_probs=23.1
Q ss_pred eeEEeCCccceEEeecC--CCeEECCCCcccccccc
Q 032369 63 AQLVCGGCHTLLMYIRG--ATSVQCSCCHTVNLALE 96 (142)
Q Consensus 63 aql~Cg~Cr~lLmYp~G--A~sVrC~~C~tVn~v~~ 96 (142)
-.+.|++|+.+|+.--+ -..+||+.|.++|.+..
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 35677778777777433 34777888888877653
No 7
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=94.44 E-value=0.013 Score=39.36 Aligned_cols=36 Identities=25% Similarity=0.597 Sum_probs=30.3
Q ss_pred eEEEcCCcceEEEee--cCCCeEeCCcCcceeeecccc
Q 032369 101 AHVNCGNCRMLLMYQ--YGARSVKCAVCNFVTAVGVSN 136 (142)
Q Consensus 101 ~~v~Cg~C~t~LmYP--~GA~sVkCa~C~~VT~i~~~~ 136 (142)
..++|++|+-+|+-- +.....||+.|.+++.|+..+
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~ 40 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS 40 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence 358999999999995 555689999999999997654
No 8
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=93.61 E-value=0.049 Score=37.57 Aligned_cols=53 Identities=26% Similarity=0.590 Sum_probs=41.2
Q ss_pred ceeeEEeCCccceEEeecC-CCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcce
Q 032369 61 EMAQLVCGGCHTLLMYIRG-ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV 129 (142)
Q Consensus 61 ~~aql~Cg~Cr~lLmYp~G-A~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~V 129 (142)
++.-.+|.+|...| .|.+ +....|+.|..+.. .+|..||.+ +..++|+.|.|.
T Consensus 4 ~~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I---------~RC~~CRk~------~~~Y~CP~CGF~ 57 (59)
T PRK14890 4 MMEPPKCTSCGIEI-APREKAVKFLCPNCGEVII---------YRCEKCRKQ------SNPYTCPKCGFE 57 (59)
T ss_pred cccCccccCCCCcc-cCCCccCEeeCCCCCCeeE---------eechhHHhc------CCceECCCCCCc
Confidence 34455799999888 5666 99999999976554 469999976 467899999875
No 9
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=92.00 E-value=0.15 Score=34.49 Aligned_cols=43 Identities=19% Similarity=0.414 Sum_probs=28.3
Q ss_pred eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCc
Q 032369 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAV 125 (142)
Q Consensus 82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~ 125 (142)
.|||+.|..++.+= .+....+.|.+|.++|.-|.|-..-.=+.
T Consensus 7 ~VkCp~C~~~q~vF-Sha~t~V~C~~Cg~~L~~PtGGKa~l~~~ 49 (55)
T PF01667_consen 7 DVKCPGCYNIQTVF-SHAQTVVKCVVCGTVLAQPTGGKARLTEG 49 (55)
T ss_dssp EEE-TTT-SEEEEE-TT-SS-EE-SSSTSEEEEE-SSSEEESSS
T ss_pred EEECCCCCCeeEEE-ecCCeEEEcccCCCEecCCCCcCeEEeCC
Confidence 58999999888774 35567789999999999999976644333
No 10
>PLN00209 ribosomal protein S27; Provisional
Probab=91.03 E-value=0.36 Score=35.56 Aligned_cols=46 Identities=24% Similarity=0.631 Sum_probs=30.9
Q ss_pred eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcc
Q 032369 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNF 128 (142)
Q Consensus 82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~ 128 (142)
.|+|+.|..++.+= .+-...|.|..|.++|..|.|-....=..|.|
T Consensus 36 ~VkCp~C~n~q~VF-ShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~f 81 (86)
T PLN00209 36 DVKCQGCFNITTVF-SHSQTVVVCGSCQTVLCQPTGGKARLTEGCSF 81 (86)
T ss_pred EEECCCCCCeeEEE-ecCceEEEccccCCEeeccCCCCeEecCCceE
Confidence 46777777777654 34556778888888888888876654444443
No 11
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=90.86 E-value=0.21 Score=29.89 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=15.7
Q ss_pred EECCCCccccccccc---cceeEEEcCCcceEE
Q 032369 83 VQCSCCHTVNLALEA---NQVAHVNCGNCRMLL 112 (142)
Q Consensus 83 VrC~~C~tVn~v~~a---~q~~~v~Cg~C~t~L 112 (142)
++|+.|++.+.+.++ ..-..++|++|...+
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 556666665554421 112256666666554
No 12
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=90.86 E-value=0.26 Score=32.33 Aligned_cols=38 Identities=29% Similarity=0.691 Sum_probs=21.7
Q ss_pred CCCeEecCCCCccccCCCC----CCceeeEEeCCccceEEee
Q 032369 40 GATSVCCAVCNAVTAVPPP----GTEMAQLVCGGCHTLLMYI 77 (142)
Q Consensus 40 GA~~VrC~~C~tvn~vpp~----~~~~aql~Cg~Cr~lLmYp 77 (142)
||+-|-|..|..+=..|.. .....+|.||.|...|.|.
T Consensus 3 GAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 3 GAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred CCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence 5666666666655555432 1225566677776666653
No 13
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=90.73 E-value=0.41 Score=35.21 Aligned_cols=44 Identities=23% Similarity=0.542 Sum_probs=29.0
Q ss_pred eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcC
Q 032369 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC 126 (142)
Q Consensus 82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C 126 (142)
.|+|+.|..++.+= .+-...|.|.+|.++|.-|.|-....=.-|
T Consensus 35 ~VkCp~C~n~q~VF-ShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc 78 (85)
T PTZ00083 35 DVKCPGCSQITTVF-SHAQTVVLCGGCSSQLCQPTGGKAKLTEGC 78 (85)
T ss_pred EEECCCCCCeeEEE-ecCceEEEccccCCEeeccCCCCeEecCCc
Confidence 46777777776654 244566788888888888887665443333
No 14
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=89.86 E-value=0.41 Score=31.43 Aligned_cols=37 Identities=27% Similarity=0.594 Sum_probs=25.7
Q ss_pred CCCeEECCCCcccccccc-----ccceeEEEcCCcceEEEee
Q 032369 79 GATSVQCSCCHTVNLALE-----ANQVAHVNCGNCRMLLMYQ 115 (142)
Q Consensus 79 GA~sVrC~~C~tVn~v~~-----a~q~~~v~Cg~C~t~LmYP 115 (142)
||+-|-|..|..+=..+. ...+.+++||.|...|.|-
T Consensus 3 GAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 3 GAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred CCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence 666666666665544432 2348899999999999874
No 15
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.78 E-value=0.31 Score=29.76 Aligned_cols=11 Identities=27% Similarity=0.549 Sum_probs=4.9
Q ss_pred ECCCCcccccc
Q 032369 84 QCSCCHTVNLA 94 (142)
Q Consensus 84 rC~~C~tVn~v 94 (142)
+|+.|++.-.+
T Consensus 4 ~CP~C~~~f~v 14 (37)
T PF13719_consen 4 TCPNCQTRFRV 14 (37)
T ss_pred ECCCCCceEEc
Confidence 44444444433
No 16
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=89.51 E-value=0.55 Score=40.40 Aligned_cols=66 Identities=21% Similarity=0.587 Sum_probs=45.0
Q ss_pred ccceeecccCCCeEecCC--CCcc-ccCCC---C-------CCceeeEEeCCccceEEeecCC--CeEECCCCccccccc
Q 032369 31 CRNLLLYPVGATSVCCAV--CNAV-TAVPP---P-------GTEMAQLVCGGCHTLLMYIRGA--TSVQCSCCHTVNLAL 95 (142)
Q Consensus 31 Cr~lL~YprGA~~VrC~~--C~tv-n~vpp---~-------~~~~aql~Cg~Cr~lLmYp~GA--~sVrC~~C~tVn~v~ 95 (142)
|.-||+=..-++-+-|++ |..| |+.|. + ...+..++||+|+...+++.=. +-.||+.|..|+.+.
T Consensus 111 CNCLLICk~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG 190 (256)
T PF09788_consen 111 CNCLLICKSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG 190 (256)
T ss_pred CceEEEeecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence 334555555555555555 7654 44432 1 2467889999999999999755 556999999999885
Q ss_pred c
Q 032369 96 E 96 (142)
Q Consensus 96 ~ 96 (142)
.
T Consensus 191 ~ 191 (256)
T PF09788_consen 191 P 191 (256)
T ss_pred c
Confidence 3
No 17
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=89.01 E-value=0.26 Score=33.95 Aligned_cols=38 Identities=21% Similarity=0.461 Sum_probs=24.1
Q ss_pred eEECCCCccccccccccceeEEEcCCcceEEEeecCCCe
Q 032369 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120 (142)
Q Consensus 82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~s 120 (142)
.|||+.|..++.+= .+-...+.|..|.++|.-|.|-..
T Consensus 11 ~VkCp~C~n~q~vF-sha~t~V~C~~Cg~~L~~PtGGKa 48 (59)
T PRK00415 11 KVKCPDCGNEQVVF-SHASTVVRCLVCGKTLAEPTGGKA 48 (59)
T ss_pred EEECCCCCCeEEEE-ecCCcEEECcccCCCcccCCCcce
Confidence 46666676666543 234456777777777777777543
No 18
>PLN00209 ribosomal protein S27; Provisional
Probab=88.95 E-value=0.35 Score=35.63 Aligned_cols=40 Identities=30% Similarity=0.546 Sum_probs=30.7
Q ss_pred eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEE
Q 032369 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ 84 (142)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVr 84 (142)
.|+|..|..++.+= ++....+.|.+|.++|..|.|--...
T Consensus 36 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa~l 75 (86)
T PLN00209 36 DVKCQGCFNITTVF--SHSQTVVVCGSCQTVLCQPTGGKARL 75 (86)
T ss_pred EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCeEe
Confidence 58888888888763 45677888888888888888866543
No 19
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=88.60 E-value=0.58 Score=29.32 Aligned_cols=25 Identities=24% Similarity=0.515 Sum_probs=11.0
Q ss_pred EEeCCccceEEeecCCCeEECCCCc
Q 032369 65 LVCGGCHTLLMYIRGATSVQCSCCH 89 (142)
Q Consensus 65 l~Cg~Cr~lLmYp~GA~sVrC~~C~ 89 (142)
..|.+|...+.+..+...++|+.|+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG 28 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCG 28 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCC
Confidence 3444444444444444444444443
No 20
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=88.48 E-value=0.4 Score=35.25 Aligned_cols=39 Identities=28% Similarity=0.603 Sum_probs=29.4
Q ss_pred eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeE
Q 032369 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV 83 (142)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sV 83 (142)
.|+|..|..++.+= ++....+.|.+|.++|..|.|--..
T Consensus 35 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa~ 73 (85)
T PTZ00083 35 DVKCPGCSQITTVF--SHAQTVVLCGGCSSQLCQPTGGKAK 73 (85)
T ss_pred EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCeE
Confidence 47888888888763 4557778888888888888886544
No 21
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=87.89 E-value=0.47 Score=32.14 Aligned_cols=38 Identities=24% Similarity=0.417 Sum_probs=23.9
Q ss_pred eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCe
Q 032369 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS 82 (142)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~s 82 (142)
.|+|..|..++.+= ++....+.|.+|.++|..|.|-..
T Consensus 7 ~VkCp~C~~~q~vF--Sha~t~V~C~~Cg~~L~~PtGGKa 44 (55)
T PF01667_consen 7 DVKCPGCYNIQTVF--SHAQTVVKCVVCGTVLAQPTGGKA 44 (55)
T ss_dssp EEE-TTT-SEEEEE--TT-SS-EE-SSSTSEEEEE-SSSE
T ss_pred EEECCCCCCeeEEE--ecCCeEEEcccCCCEecCCCCcCe
Confidence 47888888888762 455677888888888888887654
No 22
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=86.74 E-value=0.8 Score=32.42 Aligned_cols=39 Identities=21% Similarity=0.436 Sum_probs=27.5
Q ss_pred eEECCCCccccccccccceeEEEcCCcceEEEeecCCCeE
Q 032369 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSV 121 (142)
Q Consensus 82 sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sV 121 (142)
.|+|+.|...+.+- ++-...++|..|.++|..|.|-.+.
T Consensus 19 ~VkCpdC~N~q~vF-shast~V~C~~CG~~l~~PTGGka~ 57 (67)
T COG2051 19 RVKCPDCGNEQVVF-SHASTVVTCLICGTTLAEPTGGKAK 57 (67)
T ss_pred EEECCCCCCEEEEe-ccCceEEEecccccEEEecCCCeEE
Confidence 47777777766553 3445668888888888888886543
No 23
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=86.55 E-value=0.4 Score=33.01 Aligned_cols=34 Identities=24% Similarity=0.331 Sum_probs=15.6
Q ss_pred EecCCCCccccCCCCCCceeeEEeCCccceEEeecC
Q 032369 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRG 79 (142)
Q Consensus 44 VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~G 79 (142)
|+|+.|..++.+= ++....+.|..|.++|..|.|
T Consensus 12 VkCp~C~n~q~vF--sha~t~V~C~~Cg~~L~~PtG 45 (59)
T PRK00415 12 VKCPDCGNEQVVF--SHASTVVRCLVCGKTLAEPTG 45 (59)
T ss_pred EECCCCCCeEEEE--ecCCcEEECcccCCCcccCCC
Confidence 4555555544331 223344455555555555544
No 24
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.90 E-value=0.85 Score=27.83 Aligned_cols=28 Identities=32% Similarity=0.771 Sum_probs=19.1
Q ss_pred EEcCCcceEEEeec-----CCCeEeCCcCccee
Q 032369 103 VNCGNCRMLLMYQY-----GARSVKCAVCNFVT 130 (142)
Q Consensus 103 v~Cg~C~t~LmYP~-----GA~sVkCa~C~~VT 130 (142)
++|-+|.+..-.|. +...|||+.|+++=
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 56777777776554 45677777777653
No 25
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=85.05 E-value=0.78 Score=27.33 Aligned_cols=31 Identities=23% Similarity=0.592 Sum_probs=17.9
Q ss_pred EecCCCCccccCCCC--CCceeeEEeCCccceE
Q 032369 44 VCCAVCNAVTAVPPP--GTEMAQLVCGGCHTLL 74 (142)
Q Consensus 44 VrC~~C~tvn~vpp~--~~~~aql~Cg~Cr~lL 74 (142)
+.|+.|.+...++++ ..+-..+.|+.|...+
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 678888887766532 1122356666666554
No 26
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=84.26 E-value=1.6 Score=27.26 Aligned_cols=30 Identities=20% Similarity=0.445 Sum_probs=12.2
Q ss_pred EECCCCccccccccccceeEEEcCCcceEEEe
Q 032369 83 VQCSCCHTVNLALEANQVAHVNCGNCRMLLMY 114 (142)
Q Consensus 83 VrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmY 114 (142)
.+|+.|+......+..+ .++|-.|...++|
T Consensus 4 y~C~~CG~~~~~~~~~~--~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGT--GVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCC--ceECCCCCCeEEE
Confidence 34444444433322222 3444444444444
No 27
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=83.56 E-value=2.3 Score=31.23 Aligned_cols=43 Identities=21% Similarity=0.539 Sum_probs=23.4
Q ss_pred EECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcC
Q 032369 83 VQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC 126 (142)
Q Consensus 83 VrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C 126 (142)
|||+.|-.+|-+-+ +-+.-+.|++|.+.|.-|.|-..+.=..|
T Consensus 35 VkC~gc~~iT~vfS-HaqtvVvc~~c~~il~~~tggra~ls~~c 77 (84)
T KOG1779|consen 35 VKCPGCFKITTVFS-HAQTVVVCEGCSTILCQPTGGKAKLSEGC 77 (84)
T ss_pred EEcCCceEEEEEee-cCceEEEcCCCceEEEEecCCcEEecCCC
Confidence 44555544444332 23344667777777777776665544444
No 28
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=83.11 E-value=1.2 Score=38.43 Aligned_cols=95 Identities=24% Similarity=0.553 Sum_probs=62.9
Q ss_pred cCCCeEecCCCCccccCCCCCCceeeEEeCCccceE---EeecCCCeEECCC-------------------Ccc-ccccc
Q 032369 39 VGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLL---MYIRGATSVQCSC-------------------CHT-VNLAL 95 (142)
Q Consensus 39 rGA~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lL---mYp~GA~sVrC~~-------------------C~t-Vn~v~ 95 (142)
-+++-|-|..|+..-.+- --+|.-.+.|+.|..-- --|.|-..|||++ |.. ||+.+
T Consensus 76 g~~PmvtCRVCq~~i~~e-gk~~QHVVKC~~CnEATPIrnAPpGKKYVRCPCNCLLICK~sSqRIACPRpnCkRiInL~p 154 (275)
T KOG4684|consen 76 GQFPMVTCRVCQVAISLE-GKNQQHVVKCHSCNEATPIRNAPPGKKYVRCPCNCLLICKASSQRIACPRPNCKRIINLDP 154 (275)
T ss_pred CCCceEeehhhhHHhccc-cccceeeEeecccCccccCCCCCCCCceeecCCcEEEEEecccceeccCCCCcceeeecCC
Confidence 456678888887765542 23555666788886532 3567778888874 222 23221
Q ss_pred ---------cccceeEEEcCCcceEEEeec-CCCeEeCCcCcceeeecc
Q 032369 96 ---------EANQVAHVNCGNCRMLLMYQY-GARSVKCAVCNFVTAVGV 134 (142)
Q Consensus 96 ---------~a~q~~~v~Cg~C~t~LmYP~-GA~sVkCa~C~~VT~i~~ 134 (142)
.+...-.|+||.|+-+.+|-. --...+|+-|+.|..|+.
T Consensus 155 ~~~~p~~P~~~P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrKvSsvGs 203 (275)
T KOG4684|consen 155 LIEKPRDPGTAPTGCRVKCGHCNETFLFNTLTNALARCPHCRKVSSVGS 203 (275)
T ss_pred CCCCCCCCCCCCcceEEEecCccceeehhhHHHHHhcCCcccchhhhhh
Confidence 123456899999998888743 225679999999999975
No 29
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=81.91 E-value=1.5 Score=26.80 Aligned_cols=11 Identities=18% Similarity=0.507 Sum_probs=4.8
Q ss_pred ECCCCcccccc
Q 032369 84 QCSCCHTVNLA 94 (142)
Q Consensus 84 rC~~C~tVn~v 94 (142)
.|+.|++.-.+
T Consensus 4 ~Cp~C~~~y~i 14 (36)
T PF13717_consen 4 TCPNCQAKYEI 14 (36)
T ss_pred ECCCCCCEEeC
Confidence 44444444433
No 30
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=81.28 E-value=1.3 Score=30.86 Aligned_cols=50 Identities=28% Similarity=0.687 Sum_probs=39.6
Q ss_pred EEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcce
Q 032369 65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV 129 (142)
Q Consensus 65 l~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~V 129 (142)
-+|.+|...|.--.++.+..|+.|.-+.. .+|..||.+ ...++|+.|.|.
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~I---------~Rc~~CRk~------g~~Y~Cp~CGF~ 59 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEVEI---------YRCAKCRKL------GNPYRCPKCGFE 59 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCCceee---------ehhhhHHHc------CCceECCCcCcc
Confidence 58999999998888999999999985544 478888875 346788888875
No 31
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=81.08 E-value=1.8 Score=30.68 Aligned_cols=38 Identities=24% Similarity=0.337 Sum_probs=24.7
Q ss_pred eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCe
Q 032369 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS 82 (142)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~s 82 (142)
.|+|..|...+-+= ++....+.|..|.++|..|-|-..
T Consensus 19 ~VkCpdC~N~q~vF--shast~V~C~~CG~~l~~PTGGka 56 (67)
T COG2051 19 RVKCPDCGNEQVVF--SHASTVVTCLICGTTLAEPTGGKA 56 (67)
T ss_pred EEECCCCCCEEEEe--ccCceEEEecccccEEEecCCCeE
Confidence 47777777666552 334556777777777777777543
No 32
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=77.89 E-value=3.7 Score=30.21 Aligned_cols=42 Identities=29% Similarity=0.513 Sum_probs=30.6
Q ss_pred eEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECC
Q 032369 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCS 86 (142)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~ 86 (142)
.|+|+.|-.||.+= ++...-++|+||.+.|.-|.|-..+.=.
T Consensus 34 ~VkC~gc~~iT~vf--SHaqtvVvc~~c~~il~~~tggra~ls~ 75 (84)
T KOG1779|consen 34 DVKCPGCFKITTVF--SHAQTVVVCEGCSTILCQPTGGKAKLSE 75 (84)
T ss_pred EEEcCCceEEEEEe--ecCceEEEcCCCceEEEEecCCcEEecC
Confidence 47888888888763 4456668888888888888887665433
No 33
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.25 E-value=2.4 Score=29.27 Aligned_cols=53 Identities=21% Similarity=0.477 Sum_probs=40.2
Q ss_pred ccceeeccCccceeecccC-CCeEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCCCccc
Q 032369 22 AQSQLVCSGCRNLLLYPVG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (142)
Q Consensus 22 ~~sQlvC~gCr~lL~YprG-A~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tV 91 (142)
+++-.+|.+|...| .|++ |..--|+.|..+... +|..||++ +...+|+.|.+.
T Consensus 4 ~~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I~----------RC~~CRk~------~~~Y~CP~CGF~ 57 (59)
T PRK14890 4 MMEPPKCTSCGIEI-APREKAVKFLCPNCGEVIIY----------RCEKCRKQ------SNPYTCPKCGFE 57 (59)
T ss_pred cccCccccCCCCcc-cCCCccCEeeCCCCCCeeEe----------echhHHhc------CCceECCCCCCc
Confidence 45556899999887 5666 999999999876543 48889886 367788888764
No 34
>PF12773 DZR: Double zinc ribbon
Probab=70.10 E-value=1.9 Score=26.78 Aligned_cols=29 Identities=24% Similarity=0.380 Sum_probs=18.3
Q ss_pred eEEeCCccceEEeecCCCeEECCCCccccc
Q 032369 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (142)
Q Consensus 64 ql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~ 93 (142)
...|..|.+.|. ......+.|+.|.+.+.
T Consensus 12 ~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 12 AKFCPHCGTPLP-PPDQSKKICPNCGAENP 40 (50)
T ss_pred ccCChhhcCChh-hccCCCCCCcCCcCCCc
Confidence 566777777776 44455566777766543
No 35
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=64.89 E-value=10 Score=26.85 Aligned_cols=39 Identities=10% Similarity=0.312 Sum_probs=19.5
Q ss_pred CeEECCCCccccccc----cccceeEEEcCCcceEEEeecCCC
Q 032369 81 TSVQCSCCHTVNLAL----EANQVAHVNCGNCRMLLMYQYGAR 119 (142)
Q Consensus 81 ~sVrC~~C~tVn~v~----~a~q~~~v~Cg~C~t~LmYP~GA~ 119 (142)
....|+.|+.-+.+. ..+.++++.|+.|...-.+..+..
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L 63 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPL 63 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCcc
Confidence 456788888555442 357889999999977766665543
No 36
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=64.74 E-value=5.6 Score=32.28 Aligned_cols=40 Identities=33% Similarity=0.549 Sum_probs=27.1
Q ss_pred eEecCCCCccccCCCCC---CceeeEEeCCccceEEeecCCCe
Q 032369 43 SVCCAVCNAVTAVPPPG---TEMAQLVCGGCHTLLMYIRGATS 82 (142)
Q Consensus 43 ~VrC~~C~tvn~vpp~~---~~~aql~Cg~Cr~lLmYp~GA~s 82 (142)
.|+|.-|+||=+|--|. -++--++||+|-.+|..--++..
T Consensus 12 YVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~ 54 (170)
T PF04690_consen 12 YVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALL 54 (170)
T ss_pred EEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccc
Confidence 58888888888765432 34455678888888776666554
No 37
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=64.64 E-value=6.3 Score=24.27 Aligned_cols=19 Identities=16% Similarity=0.392 Sum_probs=10.4
Q ss_pred cCCCeEeCCcCcceeeecc
Q 032369 116 YGARSVKCAVCNFVTAVGV 134 (142)
Q Consensus 116 ~GA~sVkCa~C~~VT~i~~ 134 (142)
.+..+.+|..|.+.++++.
T Consensus 20 ~~~~~w~C~~C~~~N~lp~ 38 (40)
T PF04810_consen 20 DGGKTWICNFCGTKNPLPP 38 (40)
T ss_dssp TTTTEEEETTT--EEE--G
T ss_pred CCCCEEECcCCCCcCCCCC
Confidence 3666777777777777664
No 38
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=61.80 E-value=6.9 Score=33.82 Aligned_cols=48 Identities=23% Similarity=0.374 Sum_probs=35.1
Q ss_pred cCCCeEECCCCccccccccccceeEEEcCCcceEE---EeecCCCeEeCCc
Q 032369 78 RGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLL---MYQYGARSVKCAV 125 (142)
Q Consensus 78 ~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~L---mYP~GA~sVkCa~ 125 (142)
-+++.|.|.+|+..-.+-..+|+--|+|+.|+-.- =-|.|...|+|++
T Consensus 76 g~~PmvtCRVCq~~i~~egk~~QHVVKC~~CnEATPIrnAPpGKKYVRCPC 126 (275)
T KOG4684|consen 76 GQFPMVTCRVCQVAISLEGKNQQHVVKCHSCNEATPIRNAPPGKKYVRCPC 126 (275)
T ss_pred CCCceEeehhhhHHhccccccceeeEeecccCccccCCCCCCCCceeecCC
Confidence 35677888888877666667788888888887432 2477888888874
No 39
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=60.78 E-value=6.1 Score=22.82 Aligned_cols=19 Identities=26% Similarity=0.627 Sum_probs=8.9
Q ss_pred CccceEEeecC-CCeEECCCC
Q 032369 69 GCHTLLMYIRG-ATSVQCSCC 88 (142)
Q Consensus 69 ~Cr~lLmYp~G-A~sVrC~~C 88 (142)
.|...|. |++ +....|+.|
T Consensus 3 sC~~~i~-~r~~~v~f~CPnC 22 (24)
T PF07754_consen 3 SCGRPIA-PREQAVPFPCPNC 22 (24)
T ss_pred cCCCccc-CcccCceEeCCCC
Confidence 3433333 444 555555555
No 40
>PRK05580 primosome assembly protein PriA; Validated
Probab=60.52 E-value=15 Score=34.63 Aligned_cols=66 Identities=24% Similarity=0.440 Sum_probs=50.0
Q ss_pred ceeecc-cC-CCeEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcce
Q 032369 33 NLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRM 110 (142)
Q Consensus 33 ~lL~Yp-rG-A~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t 110 (142)
.||+-+ || |+.+.|..|..+- .|..|...|.|.......+|.-|......+. .|.+|.-
T Consensus 369 vll~~nrrGy~~~~~C~~Cg~~~------------~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~-------~Cp~Cg~ 429 (679)
T PRK05580 369 VLLFLNRRGYAPFLLCRDCGWVA------------ECPHCDASLTLHRFQRRLRCHHCGYQEPIPK-------ACPECGS 429 (679)
T ss_pred EEEEEcCCCCCCceEhhhCcCcc------------CCCCCCCceeEECCCCeEECCCCcCCCCCCC-------CCCCCcC
Confidence 455555 45 6789999998764 5889999999999999999999998766543 5888866
Q ss_pred EEEeecC
Q 032369 111 LLMYQYG 117 (142)
Q Consensus 111 ~LmYP~G 117 (142)
.-+.+.|
T Consensus 430 ~~l~~~g 436 (679)
T PRK05580 430 TDLVPVG 436 (679)
T ss_pred CeeEEee
Confidence 5555544
No 41
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=59.93 E-value=15 Score=25.17 Aligned_cols=30 Identities=27% Similarity=0.544 Sum_probs=15.4
Q ss_pred ceeEEEcCCcceEEEeecCCCe--EeCCcCcc
Q 032369 99 QVAHVNCGNCRMLLMYQYGARS--VKCAVCNF 128 (142)
Q Consensus 99 q~~~v~Cg~C~t~LmYP~GA~s--VkCa~C~~ 128 (142)
....|.||.|++.+.+-.-.-+ ..|+.|+.
T Consensus 38 ~~~~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 38 PVKRVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp T--EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred cccCeECCCCCCccChhhhhcCCCccCcCcCC
Confidence 3347777777777766543333 67777764
No 42
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=56.64 E-value=2.7 Score=29.11 Aligned_cols=32 Identities=28% Similarity=0.598 Sum_probs=20.8
Q ss_pred eeEEeCCccceEEeecCC--CeEECCCCcccccc
Q 032369 63 AQLVCGGCHTLLMYIRGA--TSVQCSCCHTVNLA 94 (142)
Q Consensus 63 aql~Cg~Cr~lLmYp~GA--~sVrC~~C~tVn~v 94 (142)
.-++|..|..+|.=..|- .-++|+.|..||..
T Consensus 3 ~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 3 QTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred eeeehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 345666666666554443 45788888888864
No 43
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=55.04 E-value=4.8 Score=36.30 Aligned_cols=28 Identities=32% Similarity=0.630 Sum_probs=23.2
Q ss_pred EeCCccceEEeecCCCeEECCCCccccccc
Q 032369 66 VCGGCHTLLMYIRGATSVQCSCCHTVNLAL 95 (142)
Q Consensus 66 ~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~ 95 (142)
.|. |++.++-|.||.+ +|+.||+++...
T Consensus 6 ~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~ 33 (362)
T KOG1546|consen 6 GCN-CQRPMAPPPGARY-QCAGCHAVTQIA 33 (362)
T ss_pred cCC-CCCCCCCCCCCcc-cccccceeeeec
Confidence 355 8888999999999 999999998764
No 44
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=53.86 E-value=13 Score=22.88 Aligned_cols=29 Identities=24% Similarity=0.689 Sum_probs=14.7
Q ss_pred cCCcceEEEeecCC--CeEeCCcCcceeeec
Q 032369 105 CGNCRMLLMYQYGA--RSVKCAVCNFVTAVG 133 (142)
Q Consensus 105 Cg~C~t~LmYP~GA--~sVkCa~C~~VT~i~ 133 (142)
|..|..+|....+. ..+.|+.|.++-.++
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeEECC
Confidence 44454444333332 245677777666554
No 45
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.80 E-value=9.7 Score=39.41 Aligned_cols=54 Identities=22% Similarity=0.450 Sum_probs=31.5
Q ss_pred ceeeEEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcc
Q 032369 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNF 128 (142)
Q Consensus 61 ~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~ 128 (142)
|+++..|-.|.+.... .+|+.|.+-+.. ...|.+|+..+-..... +.+|+-|..
T Consensus 664 EV~~rkCPkCG~~t~~------~fCP~CGs~te~-------vy~CPsCGaev~~des~-a~~CP~CGt 717 (1337)
T PRK14714 664 EVGRRRCPSCGTETYE------NRCPDCGTHTEP-------VYVCPDCGAEVPPDESG-RVECPRCDV 717 (1337)
T ss_pred EEEEEECCCCCCcccc------ccCcccCCcCCC-------ceeCccCCCccCCCccc-cccCCCCCC
Confidence 5566677777665321 277777766532 23677777765543322 667777764
No 46
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=53.13 E-value=6.8 Score=30.26 Aligned_cols=32 Identities=25% Similarity=0.468 Sum_probs=21.0
Q ss_pred CCeEECCCCccccccccccceeEEEcCCcceEEEee
Q 032369 80 ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQ 115 (142)
Q Consensus 80 A~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP 115 (142)
|..|+|+.|+-.|...-.. -.|-.|++.|-..
T Consensus 67 av~V~CP~C~K~TKmLGr~----D~CM~C~~pLTLd 98 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGRV----DACMHCKEPLTLD 98 (114)
T ss_pred ceeeECCCCCChHhhhchh----hccCcCCCcCccC
Confidence 5667888888888664322 2677777776543
No 47
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=51.53 E-value=3.2 Score=31.62 Aligned_cols=26 Identities=27% Similarity=0.726 Sum_probs=21.5
Q ss_pred EEeCCccceEEeecCCCeEECCCCcc
Q 032369 65 LVCGGCHTLLMYIRGATSVQCSCCHT 90 (142)
Q Consensus 65 l~Cg~Cr~lLmYp~GA~sVrC~~C~t 90 (142)
++||-||.+|-+..=-..+.|+.|++
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 88999999888887777778888875
No 48
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=51.50 E-value=3.7 Score=31.27 Aligned_cols=27 Identities=26% Similarity=0.635 Sum_probs=24.2
Q ss_pred eeeccCccceeecccCCCeEecCCCCc
Q 032369 25 QLVCSGCRNLLLYPVGATSVCCAVCNA 51 (142)
Q Consensus 25 QlvC~gCr~lL~YprGA~~VrC~~C~t 51 (142)
-++||-||.+|.+..=-..++|+.|+.
T Consensus 62 ~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 62 AIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred cEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 389999999999998888889999986
No 49
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=50.24 E-value=8.9 Score=23.58 Aligned_cols=6 Identities=50% Similarity=1.375 Sum_probs=2.4
Q ss_pred EEcCCc
Q 032369 103 VNCGNC 108 (142)
Q Consensus 103 v~Cg~C 108 (142)
+.|.+|
T Consensus 20 ~vC~~C 25 (43)
T PF08271_consen 20 LVCPNC 25 (43)
T ss_dssp EEETTT
T ss_pred EECCCC
Confidence 334443
No 50
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.02 E-value=24 Score=32.04 Aligned_cols=61 Identities=20% Similarity=0.507 Sum_probs=44.8
Q ss_pred ccC-CCeEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcceEEEeec
Q 032369 38 PVG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQY 116 (142)
Q Consensus 38 prG-A~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~ 116 (142)
.|| |+.+.|..|..+- .|..|...|.|-......+|.-|......+. .|-+|.-.-+-+.
T Consensus 207 rrGya~~~~C~~Cg~~~------------~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~-------~Cp~C~s~~l~~~ 267 (505)
T TIGR00595 207 RRGYSKNLLCRSCGYIL------------CCPNCDVSLTYHKKEGKLRCHYCGYQEPIPK-------TCPQCGSEDLVYK 267 (505)
T ss_pred CCcCCCeeEhhhCcCcc------------CCCCCCCceEEecCCCeEEcCCCcCcCCCCC-------CCCCCCCCeeEee
Confidence 455 5678999998764 5788999999988888888988887766542 6777766544444
Q ss_pred C
Q 032369 117 G 117 (142)
Q Consensus 117 G 117 (142)
|
T Consensus 268 g 268 (505)
T TIGR00595 268 G 268 (505)
T ss_pred c
Confidence 4
No 51
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=49.27 E-value=30 Score=28.10 Aligned_cols=45 Identities=31% Similarity=0.628 Sum_probs=22.4
Q ss_pred CCceeeEEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcceEEEeecC
Q 032369 59 GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYG 117 (142)
Q Consensus 59 ~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~G 117 (142)
..+.-.+.|+-|.|.|. .+|-|+. --.+--|+||.|.-+|..=-+
T Consensus 7 sE~lCYVhCnFC~TiLa-----VsVP~ss---------L~~~VTVRCGHCtNLLSVNm~ 51 (170)
T PF04690_consen 7 SEQLCYVHCNFCNTILA-----VSVPCSS---------LLKTVTVRCGHCTNLLSVNMR 51 (170)
T ss_pred CCcEEEEEcCCcCeEEE-----Eecchhh---------hhhhhceeccCccceeeeecc
Confidence 34555555555555554 2333332 113334667777666654333
No 52
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=46.99 E-value=16 Score=25.93 Aligned_cols=12 Identities=17% Similarity=0.617 Sum_probs=5.3
Q ss_pred eEeCCcCcceee
Q 032369 120 SVKCAVCNFVTA 131 (142)
Q Consensus 120 sVkCa~C~~VT~ 131 (142)
.++|..|.+...
T Consensus 16 ~~~C~~C~~~~~ 27 (104)
T TIGR01384 16 VYVCPSCGYEKE 27 (104)
T ss_pred eEECcCCCCccc
Confidence 344444444433
No 53
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=44.94 E-value=15 Score=38.17 Aligned_cols=56 Identities=20% Similarity=0.380 Sum_probs=34.7
Q ss_pred ccceeeccCccceeecccCCCeEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCCCcccc
Q 032369 22 AQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVN 92 (142)
Q Consensus 22 ~~sQlvC~gCr~lL~YprGA~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn 92 (142)
+.++..|..|.+.... .+|+.|.+.+.. ...|.+|+..+-..... +.+|+-|.+-.
T Consensus 664 EV~~rkCPkCG~~t~~------~fCP~CGs~te~--------vy~CPsCGaev~~des~-a~~CP~CGtpl 719 (1337)
T PRK14714 664 EVGRRRCPSCGTETYE------NRCPDCGTHTEP--------VYVCPDCGAEVPPDESG-RVECPRCDVEL 719 (1337)
T ss_pred EEEEEECCCCCCcccc------ccCcccCCcCCC--------ceeCccCCCccCCCccc-cccCCCCCCcc
Confidence 4455778888875422 288888877632 23777777766543322 66777777544
No 54
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=43.44 E-value=12 Score=33.89 Aligned_cols=26 Identities=42% Similarity=0.855 Sum_probs=23.6
Q ss_pred ccCccceeecccCCCeEecCCCCccccC
Q 032369 28 CSGCRNLLLYPVGATSVCCAVCNAVTAV 55 (142)
Q Consensus 28 C~gCr~lL~YprGA~~VrC~~C~tvn~v 55 (142)
|+ ||+-++-|-||.. ||+.|++++..
T Consensus 7 ~~-~~~p~~~pp~ar~-q~~~~~~~~~~ 32 (362)
T KOG1546|consen 7 CN-CQRPMAPPPGARY-QCAGCHAVTQI 32 (362)
T ss_pred CC-CCCCCCCCCCCcc-cccccceeeee
Confidence 55 9999999999999 99999999864
No 55
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=42.49 E-value=22 Score=29.47 Aligned_cols=31 Identities=16% Similarity=0.538 Sum_probs=24.4
Q ss_pred Cceee--EEeCCccceEEeecCCCeEECCCCcccc
Q 032369 60 TEMAQ--LVCGGCHTLLMYIRGATSVQCSCCHTVN 92 (142)
Q Consensus 60 ~~~aq--l~Cg~Cr~lLmYp~GA~sVrC~~C~tVn 92 (142)
++++- -.|..||..|++ .-...+|+.|..+-
T Consensus 143 ~dlGVI~A~CsrC~~~L~~--~~~~l~Cp~Cg~tE 175 (188)
T COG1096 143 NDLGVIYARCSRCRAPLVK--KGNMLKCPNCGNTE 175 (188)
T ss_pred CcceEEEEEccCCCcceEE--cCcEEECCCCCCEE
Confidence 45554 479999999999 77889999998753
No 56
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.60 E-value=30 Score=31.43 Aligned_cols=43 Identities=21% Similarity=0.690 Sum_probs=33.5
Q ss_pred CCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcceeeec
Q 032369 80 ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVG 133 (142)
Q Consensus 80 A~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~VT~i~ 133 (142)
|+.+.|..|..+ ..|.+|...|-|=......+|.-|.+...++
T Consensus 211 a~~~~C~~Cg~~-----------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~ 253 (505)
T TIGR00595 211 SKNLLCRSCGYI-----------LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIP 253 (505)
T ss_pred CCeeEhhhCcCc-----------cCCCCCCCceEEecCCCeEEcCCCcCcCCCC
Confidence 577889988875 3588888888888888888888888776654
No 57
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=41.21 E-value=17 Score=22.01 Aligned_cols=29 Identities=24% Similarity=0.638 Sum_probs=13.1
Q ss_pred cCCcceEEEeecCCCe-EeCCcCcceeeec
Q 032369 105 CGNCRMLLMYQYGARS-VKCAVCNFVTAVG 133 (142)
Q Consensus 105 Cg~C~t~LmYP~GA~s-VkCa~C~~VT~i~ 133 (142)
|..|..+|....+... +.|..|.|+-+|.
T Consensus 4 Cp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEKRVACRTCGYEEPIS 33 (35)
T ss_dssp ETTTTSBEEEEEETTTTEEESSSS-EEE-S
T ss_pred CCCCCccceEcCCCccCcCCCCCCCccCCC
Confidence 5555555433322222 2477777666654
No 58
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.69 E-value=32 Score=32.76 Aligned_cols=68 Identities=22% Similarity=0.432 Sum_probs=49.4
Q ss_pred cCccceeecc-cC-CCeEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcC
Q 032369 29 SGCRNLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCG 106 (142)
Q Consensus 29 ~gCr~lL~Yp-rG-A~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg 106 (142)
.| +.||+-+ || |+.+.|..|..+- .|.+|...|-|..+....+|.-|...- . .-.|.
T Consensus 368 ~g-qvll~lnRrGyap~l~C~~Cg~~~------------~C~~C~~~L~~h~~~~~l~Ch~CG~~~-~-------p~~Cp 426 (665)
T PRK14873 368 HG-PVLVQVPRRGYVPSLACARCRTPA------------RCRHCTGPLGLPSAGGTPRCRWCGRAA-P-------DWRCP 426 (665)
T ss_pred cC-cEEEEecCCCCCCeeEhhhCcCee------------ECCCCCCceeEecCCCeeECCCCcCCC-c-------CccCC
Confidence 57 7777766 56 4677999998754 688999999998888889999998732 1 23788
Q ss_pred CcceEEEeecC
Q 032369 107 NCRMLLMYQYG 117 (142)
Q Consensus 107 ~C~t~LmYP~G 117 (142)
+|.-.-+-+.|
T Consensus 427 ~Cgs~~l~~~g 437 (665)
T PRK14873 427 RCGSDRLRAVV 437 (665)
T ss_pred CCcCCcceeee
Confidence 88765444444
No 59
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.30 E-value=31 Score=32.54 Aligned_cols=51 Identities=27% Similarity=0.582 Sum_probs=39.3
Q ss_pred ceEEeec-C-CCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcceeeec
Q 032369 72 TLLMYIR-G-ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVG 133 (142)
Q Consensus 72 ~lLmYp~-G-A~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~VT~i~ 133 (142)
++|..++ | |+.+.|..|..+ .+|.+|...|-|.......+|.-|.+...++
T Consensus 369 vll~~nrrGy~~~~~C~~Cg~~-----------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~ 421 (679)
T PRK05580 369 VLLFLNRRGYAPFLLCRDCGWV-----------AECPHCDASLTLHRFQRRLRCHHCGYQEPIP 421 (679)
T ss_pred EEEEEcCCCCCCceEhhhCcCc-----------cCCCCCCCceeEECCCCeEECCCCcCCCCCC
Confidence 3455553 4 678999999875 4689999999999888888888888876653
No 60
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=36.27 E-value=4.6 Score=24.77 Aligned_cols=24 Identities=29% Similarity=0.751 Sum_probs=15.8
Q ss_pred eeeEEeCCccceEEeecCCCeEECCCCc
Q 032369 62 MAQLVCGGCHTLLMYIRGATSVQCSCCH 89 (142)
Q Consensus 62 ~aql~Cg~Cr~lLmYp~GA~sVrC~~C~ 89 (142)
=+|+.|..|-..++ ...++|+.|+
T Consensus 20 CgH~~C~~C~~~~~----~~~~~CP~C~ 43 (44)
T PF14634_consen 20 CGHIFCEKCLKKLK----GKSVKCPICR 43 (44)
T ss_pred cCCHHHHHHHHhhc----CCCCCCcCCC
Confidence 45666666777776 6667777665
No 61
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=35.31 E-value=13 Score=29.94 Aligned_cols=63 Identities=35% Similarity=0.675 Sum_probs=36.6
Q ss_pred cccCCCeEecCCCCccccCCCCCCceeeEEeCCccceEEe-----ecCCCeEECCCCccccccccccceeEEEcCCcce
Q 032369 37 YPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMY-----IRGATSVQCSCCHTVNLALEANQVAHVNCGNCRM 110 (142)
Q Consensus 37 YprGA~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmY-----p~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t 110 (142)
-+.|+....|+.|..-.. .+.+|+.|...|=- ..+=..+-|+.|.++|.. .+..++-|-+|.+
T Consensus 105 ~~~~~~~~aCs~C~r~~~--------~~~~C~~Cdr~lC~~C~~~C~~C~~~~Cs~Cs~~~y~---~~~e~~lC~~C~m 172 (175)
T PF05458_consen 105 DPSGPASRACSVCQRTQR--------IKSVCSQCDRALCESCIRSCSSCSEVFCSLCSTVNYS---DQYERVLCLSCSM 172 (175)
T ss_pred CCCCCcCccCcCCcCCCC--------CCccccccCcHHHHHHHhhhhchhhhhhcCccccccC---CcccccccCCCCC
Confidence 345656667888963332 23356665554422 455566777777777664 2445666666654
No 62
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=33.64 E-value=48 Score=24.96 Aligned_cols=12 Identities=33% Similarity=0.791 Sum_probs=5.6
Q ss_pred eeEEeCCccceE
Q 032369 63 AQLVCGGCHTLL 74 (142)
Q Consensus 63 aql~Cg~Cr~lL 74 (142)
.+..|+.|+-.|
T Consensus 132 ~~y~C~~C~g~l 143 (146)
T smart00731 132 SRYRCGKCGGKL 143 (146)
T ss_pred ceEEcCCCCCEE
Confidence 444444444444
No 63
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.62 E-value=43 Score=31.94 Aligned_cols=50 Identities=26% Similarity=0.529 Sum_probs=35.4
Q ss_pred CCccceEEeec-C-CCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcce
Q 032369 68 GGCHTLLMYIR-G-ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV 129 (142)
Q Consensus 68 g~Cr~lLmYp~-G-A~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~V 129 (142)
.| .++|+-++ | |+.+.|..|..+ .+|.+|...|-|..+....+|.-|.+.
T Consensus 368 ~g-qvll~lnRrGyap~l~C~~Cg~~-----------~~C~~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 368 HG-PVLVQVPRRGYVPSLACARCRTP-----------ARCRHCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred cC-cEEEEecCCCCCCeeEhhhCcCe-----------eECCCCCCceeEecCCCeeECCCCcCC
Confidence 35 66666663 4 467788888765 457888888888777777778777763
No 64
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=33.37 E-value=28 Score=20.60 Aligned_cols=21 Identities=24% Similarity=0.729 Sum_probs=9.5
Q ss_pred eccCccceeecccCCCeEecCCCCc
Q 032369 27 VCSGCRNLLLYPVGATSVCCAVCNA 51 (142)
Q Consensus 27 vC~gCr~lL~YprGA~~VrC~~C~t 51 (142)
.|..|.++..||| ..|+.|..
T Consensus 13 rC~~Cg~~~~pPr----~~Cp~C~s 33 (37)
T PF12172_consen 13 RCRDCGRVQFPPR----PVCPHCGS 33 (37)
T ss_dssp E-TTT--EEES------SEETTTT-
T ss_pred EcCCCCCEecCCC----cCCCCcCc
Confidence 4777777777776 34566653
No 65
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=32.20 E-value=34 Score=21.98 Aligned_cols=28 Identities=32% Similarity=0.592 Sum_probs=16.9
Q ss_pred eeeccCccceeecc------cCCCeEecCCCCcc
Q 032369 25 QLVCSGCRNLLLYP------VGATSVCCAVCNAV 52 (142)
Q Consensus 25 QlvC~gCr~lL~Yp------rGA~~VrC~~C~tv 52 (142)
+-+|+||+.-|.-- ++...+.|..|+.|
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 34788888766432 34456666666543
No 66
>PRK02935 hypothetical protein; Provisional
Probab=32.12 E-value=29 Score=26.74 Aligned_cols=32 Identities=25% Similarity=0.451 Sum_probs=18.9
Q ss_pred CCeEECCCCccccccccccceeEEEcCCcceEEEee
Q 032369 80 ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQ 115 (142)
Q Consensus 80 A~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP 115 (142)
|..|.|+.|+-.|...-.. -.|-.|++.|-..
T Consensus 68 avqV~CP~C~K~TKmLGrv----D~CM~C~~PLTLd 99 (110)
T PRK02935 68 AVQVICPSCEKPTKMLGRV----DACMHCNQPLTLD 99 (110)
T ss_pred ceeeECCCCCchhhhccce----eecCcCCCcCCcC
Confidence 5567777777777654211 2566666666443
No 67
>PRK04351 hypothetical protein; Provisional
Probab=31.01 E-value=42 Score=26.24 Aligned_cols=33 Identities=24% Similarity=0.488 Sum_probs=18.5
Q ss_pred EECCCCccccccccccceeEEEcCCcceEEEee
Q 032369 83 VQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQ 115 (142)
Q Consensus 83 VrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP 115 (142)
.+|..|+.+-.-.-......-+||.|+..|.+-
T Consensus 113 Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 113 YECQSCGQQYLRKRRINTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EECCCCCCEeeeeeecCCCcEEeCCCCcEeeec
Confidence 345555543321112234677889998888764
No 68
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=30.67 E-value=49 Score=21.89 Aligned_cols=8 Identities=25% Similarity=0.787 Sum_probs=3.6
Q ss_pred cCCCCccc
Q 032369 46 CAVCNAVT 53 (142)
Q Consensus 46 C~~C~tvn 53 (142)
|+.|+..|
T Consensus 25 C~~C~~hN 32 (54)
T PF10058_consen 25 CSKCFSHN 32 (54)
T ss_pred Ccccchhh
Confidence 44444444
No 69
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=30.48 E-value=35 Score=21.04 Aligned_cols=27 Identities=22% Similarity=0.759 Sum_probs=16.5
Q ss_pred EEcCCcceEEEeecCCCeEeCCcCccee
Q 032369 103 VNCGNCRMLLMYQYGARSVKCAVCNFVT 130 (142)
Q Consensus 103 v~Cg~C~t~LmYP~GA~sVkCa~C~~VT 130 (142)
..|..|+..| .-.+.+.++|+.|..+-
T Consensus 12 ~~C~~C~~~i-~g~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 12 TYCDVCGKFI-WGLGKQGYRCSWCGLVC 38 (53)
T ss_dssp EB-TTSSSBE-CSSSSCEEEETTTT-EE
T ss_pred CCCcccCccc-CCCCCCeEEECCCCChH
Confidence 3577777776 33667777777777653
No 70
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=30.44 E-value=39 Score=30.13 Aligned_cols=30 Identities=20% Similarity=0.439 Sum_probs=14.1
Q ss_pred EECCCCccccccccccceeEEEcCCcceEE
Q 032369 83 VQCSCCHTVNLALEANQVAHVNCGNCRMLL 112 (142)
Q Consensus 83 VrC~~C~tVn~v~~a~q~~~v~Cg~C~t~L 112 (142)
+.|+.|+.+...++-..-..-.|..|...|
T Consensus 14 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 14 ILCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eeCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 445555555544432222234455555555
No 71
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=29.24 E-value=67 Score=31.35 Aligned_cols=60 Identities=22% Similarity=0.501 Sum_probs=46.5
Q ss_pred ceeecc-cC-CCeEecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcce
Q 032369 33 NLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRM 110 (142)
Q Consensus 33 ~lL~Yp-rG-A~~VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t 110 (142)
.||+-+ || ++.+.|..|..+- .|-+|...|.|-.....-+|--|..-..++ ..|.+|..
T Consensus 423 ~llflnRRGys~~l~C~~Cg~v~------------~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p-------~~Cp~Cgs 483 (730)
T COG1198 423 VLLFLNRRGYAPLLLCRDCGYIA------------ECPNCDSPLTLHKATGQLRCHYCGYQEPIP-------QSCPECGS 483 (730)
T ss_pred EEEEEccCCccceeecccCCCcc------------cCCCCCcceEEecCCCeeEeCCCCCCCCCC-------CCCCCCCC
Confidence 445544 55 4589999998874 499999999999999999999998886654 36777776
Q ss_pred E
Q 032369 111 L 111 (142)
Q Consensus 111 ~ 111 (142)
.
T Consensus 484 ~ 484 (730)
T COG1198 484 E 484 (730)
T ss_pred C
Confidence 6
No 72
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=29.19 E-value=78 Score=21.63 Aligned_cols=34 Identities=18% Similarity=0.342 Sum_probs=17.7
Q ss_pred CceeeEEeCCccceEEeecCCCeEECCCCccccc
Q 032369 60 TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (142)
Q Consensus 60 ~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~ 93 (142)
....++.|..|+..=-.+.--.-.||+.|.+-|-
T Consensus 26 ~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT 59 (61)
T PF14599_consen 26 NKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNT 59 (61)
T ss_dssp --EEEEEESSS--EEEEE--TT----TTTS---E
T ss_pred CCEEEEECCCCCCccceeeeHhhhcCCCCCCccc
Confidence 4578888999998888888888889998887663
No 73
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=28.76 E-value=27 Score=33.31 Aligned_cols=50 Identities=24% Similarity=0.492 Sum_probs=33.5
Q ss_pred EecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcceEE
Q 032369 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLL 112 (142)
Q Consensus 44 VrC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~L 112 (142)
..|+.|++.|. .+.-.|..|.+.|- .-.|+.|.+.+.. ..-.|.+|.+.+
T Consensus 2 ~~Cp~Cg~~n~-------~~akFC~~CG~~l~------~~~Cp~CG~~~~~------~~~fC~~CG~~~ 51 (645)
T PRK14559 2 LICPQCQFENP-------NNNRFCQKCGTSLT------HKPCPQCGTEVPV------DEAHCPNCGAET 51 (645)
T ss_pred CcCCCCCCcCC-------CCCccccccCCCCC------CCcCCCCCCCCCc------ccccccccCCcc
Confidence 36888888873 23347888988773 2368888887654 234677776643
No 74
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=28.74 E-value=81 Score=26.21 Aligned_cols=29 Identities=28% Similarity=0.580 Sum_probs=24.8
Q ss_pred ceeEEEcCCcceEEEeecCCCeEeCCcCcce
Q 032369 99 QVAHVNCGNCRMLLMYQYGARSVKCAVCNFV 129 (142)
Q Consensus 99 q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~V 129 (142)
-+-.-.|-+|+..|++ .-...+|+.|..+
T Consensus 146 GVI~A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 146 GVIYARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred eEEEEEccCCCcceEE--cCcEEECCCCCCE
Confidence 4556689999999999 7789999999875
No 75
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=28.63 E-value=6.5 Score=28.99 Aligned_cols=62 Identities=16% Similarity=0.386 Sum_probs=38.2
Q ss_pred eeeEEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcceeeecccceEE
Q 032369 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGVSNHIF 139 (142)
Q Consensus 62 ~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~VT~i~~~~~~~ 139 (142)
++.-.|.-|.+.+-+-. .....|..|+ +-.|..|+.- -.+.....|..|+.-.++...++-.
T Consensus 52 ~~~~~C~~C~~~fg~l~-~~~~~C~~C~------------~~VC~~C~~~---~~~~~~WlC~vC~k~rel~~~sG~W 113 (118)
T PF02318_consen 52 YGERHCARCGKPFGFLF-NRGRVCVDCK------------HRVCKKCGVY---SKKEPIWLCKVCQKQRELKKKSGEW 113 (118)
T ss_dssp HCCSB-TTTS-BCSCTS-TTCEEETTTT------------EEEETTSEEE---TSSSCCEEEHHHHHHHHHHHHCSHH
T ss_pred cCCcchhhhCCcccccC-CCCCcCCcCC------------ccccCccCCc---CCCCCCEEChhhHHHHHHHHHhhhH
Confidence 34446666666554332 2236677664 5678888876 4467788899988877776555533
No 76
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=28.47 E-value=26 Score=20.88 Aligned_cols=25 Identities=20% Similarity=0.490 Sum_probs=15.3
Q ss_pred EcCCcceEEEeecCCCeEeCCcCcce
Q 032369 104 NCGNCRMLLMYQYGARSVKCAVCNFV 129 (142)
Q Consensus 104 ~Cg~C~t~LmYP~GA~sVkCa~C~~V 129 (142)
.|-.|+..|... +.+..+|+.|..+
T Consensus 13 ~C~~C~~~i~~~-~~~~~~C~~C~~~ 37 (50)
T cd00029 13 FCDVCRKSIWGL-FKQGLRCSWCKVK 37 (50)
T ss_pred Chhhcchhhhcc-ccceeEcCCCCCc
Confidence 466666665543 4677777777654
No 77
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=28.39 E-value=26 Score=28.18 Aligned_cols=27 Identities=22% Similarity=0.637 Sum_probs=20.7
Q ss_pred EcCCcc-eEEEeecCC-CeEeCCcCccee
Q 032369 104 NCGNCR-MLLMYQYGA-RSVKCAVCNFVT 130 (142)
Q Consensus 104 ~Cg~C~-t~LmYP~GA-~sVkCa~C~~VT 130 (142)
.|.-|+ ..++||... .+++|+.|..|-
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~ 182 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVF 182 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCcccc
Confidence 477777 478888888 888888887764
No 78
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=27.78 E-value=88 Score=22.15 Aligned_cols=30 Identities=33% Similarity=0.669 Sum_probs=18.6
Q ss_pred EEcCCcceEEEeecCCCeEeCCcCcceeeecc
Q 032369 103 VNCGNCRMLLMYQYGARSVKCAVCNFVTAVGV 134 (142)
Q Consensus 103 v~Cg~C~t~LmYP~GA~sVkCa~C~~VT~i~~ 134 (142)
.+| .|.-.|.-..|+.+-|| .|.+..+|..
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~ 33 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKE 33 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEEEE--S
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCeeeeee
Confidence 467 57777777778888888 7877777754
No 79
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=27.17 E-value=64 Score=18.64 Aligned_cols=22 Identities=27% Similarity=0.693 Sum_probs=6.5
Q ss_pred eCCccceEEeecCCCeEECCCC
Q 032369 67 CGGCHTLLMYIRGATSVQCSCC 88 (142)
Q Consensus 67 Cg~Cr~lLmYp~GA~sVrC~~C 88 (142)
|+.|...+..-.+-..-+|+.|
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~C 27 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSC 27 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSS
T ss_pred cCcCCccccCCCCcCEeECCCC
Confidence 3333333333333333334333
No 80
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=26.83 E-value=24 Score=20.77 Aligned_cols=24 Identities=21% Similarity=0.708 Sum_probs=13.8
Q ss_pred EcCCcceEEEeecCCCeEeCCcCcce
Q 032369 104 NCGNCRMLLMYQYGARSVKCAVCNFV 129 (142)
Q Consensus 104 ~Cg~C~t~LmYP~GA~sVkCa~C~~V 129 (142)
.|..|+..|.... +.++|+.|..+
T Consensus 13 ~C~~C~~~i~~~~--~~~~C~~C~~~ 36 (49)
T smart00109 13 KCCVCRKSIWGSF--QGLRCSWCKVK 36 (49)
T ss_pred CccccccccCcCC--CCcCCCCCCch
Confidence 4666666655432 46677766554
No 81
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=26.81 E-value=58 Score=25.54 Aligned_cols=34 Identities=18% Similarity=0.371 Sum_probs=22.8
Q ss_pred eeeEEeCCccceEEeecCCCeEECCCCccccccc
Q 032369 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAL 95 (142)
Q Consensus 62 ~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~ 95 (142)
.+.++|-+|...+.|-.-..--.|+.|+...+.+
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERLPPCPKCGHTEFTR 143 (146)
T ss_pred CceEecccCCCEEEecCCCcCCCCCCCCCCeeee
Confidence 4667777777777766656666777777666554
No 82
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=26.06 E-value=1.4e+02 Score=18.89 Aligned_cols=31 Identities=23% Similarity=0.476 Sum_probs=16.4
Q ss_pred EECCCCccccccccccceeEEEcCCcceEEEeec
Q 032369 83 VQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQY 116 (142)
Q Consensus 83 VrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~ 116 (142)
.+|..|...+... ....++|..|.--++|-.
T Consensus 3 Y~C~~Cg~~~~~~---~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 3 YICGECGRENEIK---SKDVVRCRECGYRILYKK 33 (44)
T ss_pred EECCCCCCEeecC---CCCceECCCCCceEEEEe
Confidence 3555565554432 334566666665555543
No 83
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.40 E-value=1.2e+02 Score=29.60 Aligned_cols=43 Identities=21% Similarity=0.589 Sum_probs=29.6
Q ss_pred CCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcceeeec
Q 032369 80 ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVG 133 (142)
Q Consensus 80 A~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~VT~i~ 133 (142)
++.+.|..|.++- .|-+|...|-|-.....-+|--|.+...++
T Consensus 433 s~~l~C~~Cg~v~-----------~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p 475 (730)
T COG1198 433 APLLLCRDCGYIA-----------ECPNCDSPLTLHKATGQLRCHYCGYQEPIP 475 (730)
T ss_pred cceeecccCCCcc-----------cCCCCCcceEEecCCCeeEeCCCCCCCCCC
Confidence 4467777777653 377777777777777777777777766554
No 84
>PF14369 zf-RING_3: zinc-finger
Probab=24.85 E-value=57 Score=19.79 Aligned_cols=23 Identities=26% Similarity=0.761 Sum_probs=10.4
Q ss_pred eCCccceEEee-cCCCeEECCCCc
Q 032369 67 CGGCHTLLMYI-RGATSVQCSCCH 89 (142)
Q Consensus 67 Cg~Cr~lLmYp-~GA~sVrC~~C~ 89 (142)
|..|+..+.-. .+...+.|+.|+
T Consensus 5 Ch~C~~~V~~~~~~~~~~~CP~C~ 28 (35)
T PF14369_consen 5 CHQCNRFVRIAPSPDSDVACPRCH 28 (35)
T ss_pred CccCCCEeEeCcCCCCCcCCcCCC
Confidence 44555444442 233333455555
No 85
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=24.62 E-value=90 Score=20.29 Aligned_cols=13 Identities=38% Similarity=0.575 Sum_probs=7.0
Q ss_pred CeEECCCCccccc
Q 032369 81 TSVQCSCCHTVNL 93 (142)
Q Consensus 81 ~sVrC~~C~tVn~ 93 (142)
+|-.|+.|..++.
T Consensus 27 TSq~C~~CG~~~~ 39 (69)
T PF07282_consen 27 TSQTCPRCGHRNK 39 (69)
T ss_pred CccCccCcccccc
Confidence 4555555555554
No 86
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=24.30 E-value=51 Score=22.10 Aligned_cols=20 Identities=25% Similarity=0.564 Sum_probs=11.8
Q ss_pred ccceeeccCccceeecccCC
Q 032369 22 AQSQLVCSGCRNLLLYPVGA 41 (142)
Q Consensus 22 ~~sQlvC~gCr~lL~YprGA 41 (142)
+..+.+|.+|.++|..-..+
T Consensus 43 ~~kr~~Ck~C~~~liPG~~~ 62 (85)
T PF04032_consen 43 EIKRTICKKCGSLLIPGVNC 62 (85)
T ss_dssp TCCCTB-TTT--B--CTTTE
T ss_pred HHhcccccCCCCEEeCCCcc
Confidence 46788999999999987654
No 87
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=23.55 E-value=52 Score=17.33 Aligned_cols=11 Identities=36% Similarity=0.969 Sum_probs=7.3
Q ss_pred EeCCcCcceee
Q 032369 121 VKCAVCNFVTA 131 (142)
Q Consensus 121 VkCa~C~~VT~ 131 (142)
++|+.|.|.+.
T Consensus 1 y~C~~C~y~t~ 11 (24)
T PF13909_consen 1 YKCPHCSYSTS 11 (24)
T ss_dssp EE-SSSS-EES
T ss_pred CCCCCCCCcCC
Confidence 58999998885
No 88
>PRK04023 DNA polymerase II large subunit; Validated
Probab=23.18 E-value=59 Score=33.40 Aligned_cols=54 Identities=19% Similarity=0.391 Sum_probs=37.2
Q ss_pred ceeeEEeCCccceEEeecCCCeEECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcceeeec
Q 032369 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVG 133 (142)
Q Consensus 61 ~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~VT~i~ 133 (142)
+.+.-.|..|.+.. ...+|+.|...|.. ..+|..|++..- ...|+.|.+.+.-.
T Consensus 623 EVg~RfCpsCG~~t------~~frCP~CG~~Te~-------i~fCP~CG~~~~------~y~CPKCG~El~~~ 676 (1121)
T PRK04023 623 EIGRRKCPSCGKET------FYRRCPFCGTHTEP-------VYRCPRCGIEVE------EDECEKCGREPTPY 676 (1121)
T ss_pred cccCccCCCCCCcC------CcccCCCCCCCCCc-------ceeCccccCcCC------CCcCCCCCCCCCcc
Confidence 45666788888774 55789999888542 348888865432 24699998877654
No 89
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=22.15 E-value=32 Score=24.02 Aligned_cols=21 Identities=24% Similarity=0.449 Sum_probs=14.3
Q ss_pred eecccCCCeEecCCCCccccC
Q 032369 35 LLYPVGATSVCCAVCNAVTAV 55 (142)
Q Consensus 35 L~YprGA~~VrC~~C~tvn~v 55 (142)
..|-+|.-.|||+.|+..-..
T Consensus 21 ~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 21 QAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp HHHHTSEEEEE-TTS--EEES
T ss_pred HHHhCCeEEEECCCCcceeee
Confidence 568899999999999876554
No 90
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.12 E-value=87 Score=23.26 Aligned_cols=10 Identities=50% Similarity=1.308 Sum_probs=5.0
Q ss_pred eeEEEcCCcc
Q 032369 100 VAHVNCGNCR 109 (142)
Q Consensus 100 ~~~v~Cg~C~ 109 (142)
.+|+.|..|.
T Consensus 40 ~~h~~C~~CG 49 (99)
T PRK14892 40 IAIITCGNCG 49 (99)
T ss_pred cceEECCCCC
Confidence 4455555554
No 91
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=21.92 E-value=36 Score=26.42 Aligned_cols=30 Identities=33% Similarity=0.619 Sum_probs=0.0
Q ss_pred eeccCccceeecccCCCeEecCCCCccccC
Q 032369 26 LVCSGCRNLLLYPVGATSVCCAVCNAVTAV 55 (142)
Q Consensus 26 lvC~gCr~lL~YprGA~~VrC~~C~tvn~v 55 (142)
+.|+.|.+||.=|.-+..|-|..|.....+
T Consensus 8 ~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v 37 (116)
T KOG2907|consen 8 DFCSDCGSLLEEPSAQSTVLCIRCKIEYPV 37 (116)
T ss_pred chhhhhhhhcccccccCceEeccccccCCH
No 92
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=21.73 E-value=89 Score=20.88 Aligned_cols=7 Identities=29% Similarity=1.004 Sum_probs=3.3
Q ss_pred ECCCCcc
Q 032369 84 QCSCCHT 90 (142)
Q Consensus 84 rC~~C~t 90 (142)
+|+.|..
T Consensus 4 ~CP~CG~ 10 (54)
T TIGR01206 4 ECPDCGA 10 (54)
T ss_pred CCCCCCC
Confidence 4444544
No 93
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=21.37 E-value=98 Score=19.16 Aligned_cols=23 Identities=26% Similarity=0.823 Sum_probs=13.9
Q ss_pred cc--Cccceeeccc--CCCeEecCCCC
Q 032369 28 CS--GCRNLLLYPV--GATSVCCAVCN 50 (142)
Q Consensus 28 C~--gCr~lL~Ypr--GA~~VrC~~C~ 50 (142)
|- +|..++.... |...|.|..|+
T Consensus 21 CP~~~C~~~~~~~~~~~~~~v~C~~C~ 47 (64)
T smart00647 21 CPAPDCSAAIIVTEEEGCNRVTCPKCG 47 (64)
T ss_pred CCCCCCcceEEecCCCCCCeeECCCCC
Confidence 65 6666666653 56666665554
No 94
>cd00069 GHB Glycoprotein hormone beta chain homologues. Gonadotropins; reproductive hormones consisting of two glycosylated chains (alpha and beta) of similar topology with Cysteine-knot motifs.
Probab=21.35 E-value=72 Score=24.02 Aligned_cols=33 Identities=42% Similarity=0.768 Sum_probs=24.3
Q ss_pred cccceeecc------------Cccc----eeecccCCCeEecCCCCcccc
Q 032369 21 GAQSQLVCS------------GCRN----LLLYPVGATSVCCAVCNAVTA 54 (142)
Q Consensus 21 ~~~sQlvC~------------gCr~----lL~YprGA~~VrC~~C~tvn~ 54 (142)
....|-||. ||.- ...||- |.|.+|+.|++-|.
T Consensus 42 ~~~~Q~vCtY~~~~Y~tv~lpgCp~gvdp~~tYPV-AlsC~C~~C~t~~t 90 (102)
T cd00069 42 SPLPQRVCTYRELSYETVRLPGCPPGVDPGVTYPV-ALSCHCGKCNTDTT 90 (102)
T ss_pred CCcccCcccCCcEEEEEEECCCCcCCCCCCEEeee-ecccccCCcCCCCc
Confidence 446788885 6776 778884 88888888887653
No 95
>PHA00626 hypothetical protein
Probab=20.97 E-value=76 Score=22.06 Aligned_cols=31 Identities=19% Similarity=0.469 Sum_probs=19.9
Q ss_pred ECCCCccccccccccceeEEEcCCcceEEEeecCCCeEeCCcCcce
Q 032369 84 QCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV 129 (142)
Q Consensus 84 rC~~C~tVn~v~~a~q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~V 129 (142)
.||.|...+. ++||.||.. ...++|..|.|-
T Consensus 2 ~CP~CGS~~I---------vrcg~cr~~------snrYkCkdCGY~ 32 (59)
T PHA00626 2 SCPKCGSGNI---------AKEKTMRGW------SDDYVCCDCGYN 32 (59)
T ss_pred CCCCCCCcee---------eeeceeccc------CcceEcCCCCCe
Confidence 4666765544 367777642 567788888774
No 96
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=20.62 E-value=55 Score=23.04 Aligned_cols=43 Identities=23% Similarity=0.567 Sum_probs=14.4
Q ss_pred ecCCCCccccCCCCCCceeeEEeCCccceEEeecCCCeEECCCCccccc
Q 032369 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (142)
Q Consensus 45 rC~~C~tvn~vpp~~~~~aql~Cg~Cr~lLmYp~GA~sVrC~~C~tVn~ 93 (142)
||+.|..+=..|---..=.|+-|..|-.- -.|. +|+.|++=.-
T Consensus 9 rCs~C~~~l~~pv~l~~CeH~fCs~Ci~~---~~~~---~CPvC~~Paw 51 (65)
T PF14835_consen 9 RCSICFDILKEPVCLGGCEHIFCSSCIRD---CIGS---ECPVCHTPAW 51 (65)
T ss_dssp S-SSS-S--SS-B---SSS--B-TTTGGG---GTTT---B-SSS--B-S
T ss_pred CCcHHHHHhcCCceeccCccHHHHHHhHH---hcCC---CCCCcCChHH
Confidence 56777666544322233456666666533 1221 4788876543
No 97
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=20.48 E-value=50 Score=26.59 Aligned_cols=29 Identities=24% Similarity=0.580 Sum_probs=24.0
Q ss_pred EeCCcc-ceEEeecCC-CeEECCCCcccccc
Q 032369 66 VCGGCH-TLLMYIRGA-TSVQCSCCHTVNLA 94 (142)
Q Consensus 66 ~Cg~Cr-~lLmYp~GA-~sVrC~~C~tVn~v 94 (142)
+|--|+ ..++||... ..++|+.|.+|-..
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~ 184 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVFHK 184 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCccccch
Confidence 566777 489999999 99999999988653
No 98
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=20.37 E-value=39 Score=29.36 Aligned_cols=23 Identities=35% Similarity=0.891 Sum_probs=16.4
Q ss_pred ceeEEEcCCcceEEEeecCCCeEeCCcCcc
Q 032369 99 QVAHVNCGNCRMLLMYQYGARSVKCAVCNF 128 (142)
Q Consensus 99 q~~~v~Cg~C~t~LmYP~GA~sVkCa~C~~ 128 (142)
+.+|+.|..|++ -.+.||+.|+.
T Consensus 66 ~nGHlaCssC~~-------~~~~~CP~Cr~ 88 (299)
T KOG3002|consen 66 DNGHLACSSCRT-------KVSNKCPTCRL 88 (299)
T ss_pred CCCcEehhhhhh-------hhcccCCcccc
Confidence 567788888877 45677777763
Done!