Query 033496
Match_columns 118
No_of_seqs 89 out of 112
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 02:57:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033496.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033496hhsearch_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 2.4E-15 5.2E-20 88.5 2.4 30 25-54 1-30 (31)
2 TIGR01053 LSD1 zinc finger dom 99.5 6.8E-15 1.5E-19 86.6 2.1 31 64-94 1-31 (31)
3 PF06943 zf-LSD1: LSD1 zinc fi 99.5 1E-14 2.2E-19 82.8 2.5 25 28-52 1-25 (25)
4 PF06943 zf-LSD1: LSD1 zinc fi 99.5 2E-14 4.4E-19 81.6 2.3 25 67-91 1-25 (25)
5 PF10122 Mu-like_Com: Mu-like 95.1 0.01 2.2E-07 38.9 1.2 33 64-96 4-38 (51)
6 PF10122 Mu-like_Com: Mu-like 95.1 0.011 2.4E-07 38.7 1.3 36 22-57 1-38 (51)
7 PF09788 Tmemb_55A: Transmembr 94.4 0.062 1.3E-06 44.7 4.4 38 60-97 153-192 (256)
8 PF11331 DUF3133: Protein of u 92.1 0.17 3.7E-06 32.3 2.7 39 39-77 2-44 (46)
9 PLN00209 ribosomal protein S27 91.6 0.16 3.5E-06 36.3 2.5 40 43-84 36-75 (86)
10 PTZ00083 40S ribosomal protein 91.1 0.2 4.4E-06 35.7 2.5 39 43-83 35-73 (85)
11 PRK00398 rpoP DNA-directed RNA 91.0 0.33 7.1E-06 29.5 3.1 28 64-91 3-30 (46)
12 PF01667 Ribosomal_S27e: Ribos 90.5 0.21 4.7E-06 32.8 2.1 38 43-82 7-44 (55)
13 PRK00398 rpoP DNA-directed RNA 90.2 0.46 1E-05 28.9 3.3 28 24-51 2-29 (46)
14 PRK14890 putative Zn-ribbon RN 90.1 0.27 5.8E-06 33.0 2.3 53 22-91 4-57 (59)
15 PRK00415 rps27e 30S ribosomal 89.7 0.2 4.3E-06 33.5 1.4 35 44-80 12-46 (59)
16 TIGR02098 MJ0042_CXXC MJ0042 f 89.5 0.31 6.8E-06 28.2 2.0 31 44-74 3-35 (38)
17 PF13719 zinc_ribbon_5: zinc-r 88.1 0.54 1.2E-05 27.9 2.4 14 44-57 3-16 (37)
18 PF09788 Tmemb_55A: Transmembr 87.6 0.95 2.1E-05 37.8 4.4 37 20-56 152-190 (256)
19 COG2051 RPS27A Ribosomal prote 87.5 0.61 1.3E-05 32.1 2.7 38 43-82 19-56 (67)
20 PF13719 zinc_ribbon_5: zinc-r 83.6 1.2 2.5E-05 26.4 2.3 27 65-91 3-34 (37)
21 PF12773 DZR: Double zinc ribb 81.5 0.76 1.6E-05 27.8 1.0 40 46-93 1-40 (50)
22 TIGR02098 MJ0042_CXXC MJ0042 f 81.1 3 6.5E-05 24.0 3.4 28 64-91 2-34 (38)
23 KOG1779 40s ribosomal protein 79.7 2.8 6.2E-05 29.9 3.5 40 43-84 34-73 (84)
24 KOG1546 Metacaspase involved i 79.1 0.89 1.9E-05 39.7 1.0 30 65-96 5-34 (362)
25 PF04810 zf-Sec23_Sec24: Sec23 77.6 1.5 3.3E-05 26.3 1.4 17 39-55 20-36 (40)
26 PF13717 zinc_ribbon_4: zinc-r 76.4 2.6 5.5E-05 25.0 2.1 14 44-57 3-16 (36)
27 PF07754 DUF1610: Domain of un 75.1 2.4 5.2E-05 23.8 1.7 22 67-89 1-23 (24)
28 COG4357 Zinc finger domain con 74.3 0.67 1.5E-05 34.2 -0.9 27 26-52 63-89 (105)
29 PTZ00083 40S ribosomal protein 73.9 6.6 0.00014 28.1 4.0 47 56-103 27-74 (85)
30 PRK00415 rps27e 30S ribosomal 70.5 14 0.0003 24.8 4.7 43 57-100 4-47 (59)
31 PLN00209 ribosomal protein S27 69.5 9.6 0.00021 27.3 4.1 46 56-102 28-74 (86)
32 COG2888 Predicted Zn-ribbon RN 69.4 5 0.00011 27.2 2.5 50 26-91 10-59 (61)
33 smart00661 RPOL9 RNA polymeras 67.3 5.5 0.00012 23.9 2.2 28 67-94 3-32 (52)
34 PF04690 YABBY: YABBY protein; 65.3 5.2 0.00011 31.5 2.2 39 43-81 12-53 (170)
35 PF05129 Elf1: Transcription e 61.2 8.3 0.00018 26.5 2.4 40 42-81 21-63 (81)
36 PF01667 Ribosomal_S27e: Ribos 60.5 14 0.0003 24.3 3.3 38 62-100 5-43 (55)
37 PRK14714 DNA polymerase II lar 59.2 7.9 0.00017 38.9 2.7 57 22-93 664-720 (1337)
38 PRK14890 putative Zn-ribbon RN 58.9 7.6 0.00017 26.1 1.8 32 62-94 5-37 (59)
39 COG1096 Predicted RNA-binding 58.6 9.3 0.0002 30.7 2.6 28 62-91 147-174 (188)
40 PF02591 DUF164: Putative zinc 57.3 8.5 0.00018 24.1 1.8 28 25-52 22-55 (56)
41 PRK05580 primosome assembly pr 56.3 22 0.00047 32.5 4.8 50 32-93 368-419 (679)
42 KOG1546 Metacaspase involved i 54.9 5.4 0.00012 34.9 0.8 27 27-55 6-32 (362)
43 COG4416 Com Mu-like prophage p 54.6 3.3 7.1E-05 27.9 -0.5 31 64-94 4-36 (60)
44 COG4416 Com Mu-like prophage p 51.9 3.7 8E-05 27.7 -0.5 34 22-55 1-36 (60)
45 COG2051 RPS27A Ribosomal prote 51.4 19 0.00042 24.8 2.9 40 59-99 14-54 (67)
46 KOG1779 40s ribosomal protein 49.7 25 0.00055 25.2 3.4 30 62-91 32-62 (84)
47 PF05495 zf-CHY: CHY zinc fing 48.4 21 0.00046 23.7 2.7 16 25-40 41-56 (71)
48 smart00659 RPOLCX RNA polymera 47.0 23 0.00049 21.9 2.5 28 45-76 4-31 (44)
49 PF14634 zf-RING_5: zinc-RING 46.2 2.1 4.6E-05 25.5 -2.2 25 62-90 20-44 (44)
50 TIGR00595 priA primosomal prot 45.6 30 0.00066 30.4 4.0 43 39-93 208-251 (505)
51 PRK14873 primosome assembly pr 44.6 40 0.00086 31.2 4.7 49 29-90 368-418 (665)
52 COG1579 Zn-ribbon protein, pos 44.3 10 0.00022 31.2 0.8 26 27-52 199-230 (239)
53 smart00731 SprT SprT homologue 43.0 33 0.00071 25.0 3.2 33 44-76 113-145 (146)
54 PF12172 DUF35_N: Rubredoxin-l 42.0 19 0.0004 20.7 1.5 21 27-51 13-33 (37)
55 COG1096 Predicted RNA-binding 39.4 27 0.00059 28.1 2.5 26 26-53 150-175 (188)
56 PF11023 DUF2614: Protein of u 39.3 14 0.00029 27.8 0.7 33 40-77 66-98 (114)
57 PF09297 zf-NADH-PPase: NADH p 39.3 31 0.00067 19.4 2.1 24 67-90 6-29 (32)
58 PF13901 DUF4206: Domain of un 38.6 17 0.00037 28.3 1.2 28 66-93 154-183 (202)
59 TIGR01384 TFS_arch transcripti 38.2 21 0.00046 24.4 1.5 27 66-94 2-28 (104)
60 PF04690 YABBY: YABBY protein; 37.2 55 0.0012 25.8 3.8 33 59-91 7-45 (170)
61 KOG2907 RNA polymerase I trans 36.4 12 0.00026 28.2 0.0 33 64-96 7-39 (116)
62 PF03604 DNA_RNApol_7kD: DNA d 36.1 21 0.00046 20.9 1.1 7 83-89 18-24 (32)
63 PF02150 RNA_POL_M_15KD: RNA p 35.6 21 0.00047 20.9 1.0 27 67-93 4-31 (35)
64 PRK14892 putative transcriptio 35.2 37 0.00081 24.4 2.4 14 79-92 39-52 (99)
65 smart00647 IBR In Between Ring 34.8 51 0.0011 19.8 2.7 24 27-50 20-47 (64)
66 PF14369 zf-RING_3: zinc-finge 34.8 36 0.00079 20.0 2.0 24 27-50 4-28 (35)
67 PF08271 TF_Zn_Ribbon: TFIIB z 34.7 47 0.001 19.7 2.5 12 63-74 18-29 (43)
68 PRK11827 hypothetical protein; 34.6 44 0.00095 22.2 2.5 25 26-50 9-33 (60)
69 TIGR00155 pqiA_fam integral me 33.9 53 0.0012 28.4 3.6 9 46-54 16-24 (403)
70 PRK10996 thioredoxin 2; Provis 33.6 29 0.00063 24.8 1.7 32 43-75 2-33 (139)
71 TIGR00100 hypA hydrogenase nic 32.7 43 0.00093 24.0 2.4 33 63-97 69-101 (115)
72 PF07295 DUF1451: Protein of u 32.5 45 0.00098 25.4 2.6 35 62-96 110-144 (146)
73 PRK03681 hypA hydrogenase nick 31.9 45 0.00097 23.9 2.4 33 63-97 69-102 (114)
74 COG1996 RPC10 DNA-directed RNA 31.3 56 0.0012 21.1 2.5 36 62-97 4-39 (49)
75 PF05180 zf-DNL: DNL zinc fing 31.1 14 0.00031 25.0 -0.2 31 25-55 4-41 (66)
76 KOG3002 Zn finger protein [Gen 31.0 22 0.00047 30.0 0.8 40 44-90 49-88 (299)
77 smart00109 C1 Protein kinase C 30.9 21 0.00047 20.3 0.5 24 66-91 13-36 (49)
78 cd00029 C1 Protein kinase C co 30.7 29 0.00062 20.1 1.0 25 27-52 13-37 (50)
79 PRK12380 hydrogenase nickel in 30.7 48 0.001 23.7 2.4 31 63-95 69-99 (113)
80 COG4888 Uncharacterized Zn rib 30.6 37 0.00079 25.2 1.8 32 42-73 21-55 (104)
81 PLN00162 transport protein sec 29.8 61 0.0013 30.3 3.5 34 24-57 52-89 (761)
82 PF09082 DUF1922: Domain of un 29.5 65 0.0014 22.2 2.7 30 65-96 4-33 (68)
83 PF14599 zinc_ribbon_6: Zinc-r 29.5 84 0.0018 20.8 3.2 33 60-92 26-58 (61)
84 TIGR00155 pqiA_fam integral me 29.4 54 0.0012 28.3 2.9 27 65-91 14-42 (403)
85 COG1198 PriA Primosomal protei 28.5 86 0.0019 29.7 4.2 56 32-99 422-479 (730)
86 KOG4684 Uncharacterized conser 28.2 51 0.0011 27.8 2.4 35 62-96 168-203 (275)
87 PRK04351 hypothetical protein; 27.9 50 0.0011 25.0 2.2 16 62-77 130-145 (149)
88 PRK14559 putative protein seri 27.8 37 0.0008 31.5 1.7 37 45-94 3-39 (645)
89 PF00130 C1_1: Phorbol esters/ 26.9 57 0.0012 19.4 1.9 26 26-52 12-37 (53)
90 PRK02935 hypothetical protein; 26.0 53 0.0011 24.6 1.9 34 39-77 66-99 (110)
91 KOG4684 Uncharacterized conser 25.6 67 0.0015 27.1 2.7 47 39-86 76-125 (275)
92 PF10058 DUF2296: Predicted in 25.4 77 0.0017 20.3 2.4 9 46-54 25-33 (54)
93 COG2995 PqiA Uncharacterized p 25.2 41 0.00089 30.1 1.5 35 19-56 214-248 (418)
94 PRK04023 DNA polymerase II lar 25.1 47 0.001 33.1 1.9 55 22-96 623-677 (1121)
95 PRK11827 hypothetical protein; 24.7 95 0.0021 20.6 2.8 31 64-94 8-38 (60)
96 PF07295 DUF1451: Protein of u 24.6 76 0.0016 24.1 2.6 36 21-56 108-143 (146)
97 PF01753 zf-MYND: MYND finger; 24.5 35 0.00076 19.5 0.6 21 84-104 11-31 (37)
98 PF13248 zf-ribbon_3: zinc-rib 24.0 29 0.00063 18.9 0.2 23 44-73 3-25 (26)
99 PF01485 IBR: IBR domain; Int 23.9 48 0.001 19.9 1.2 25 27-51 20-48 (64)
100 PRK08351 DNA-directed RNA poly 23.7 38 0.00082 22.7 0.8 24 26-55 4-27 (61)
101 PF08792 A2L_zn_ribbon: A2L zi 23.2 1E+02 0.0022 18.0 2.4 8 63-70 20-27 (33)
102 PRK00564 hypA hydrogenase nick 23.2 52 0.0011 23.7 1.5 30 63-94 70-100 (117)
103 TIGR00595 priA primosomal prot 22.6 1.2E+02 0.0026 26.7 3.9 22 64-90 240-261 (505)
104 PRK11032 hypothetical protein; 22.2 1E+02 0.0022 24.0 3.0 35 62-96 122-156 (160)
105 cd02340 ZZ_NBR1_like Zinc fing 22.0 71 0.0015 19.3 1.7 22 66-91 2-23 (43)
106 PF11781 RRN7: RNA polymerase 21.7 86 0.0019 18.6 2.0 24 67-91 11-34 (36)
107 PF04032 Rpr2: RNAse P Rpr2/Rp 21.3 50 0.0011 21.4 1.0 20 22-41 43-62 (85)
108 PRK15103 paraquat-inducible me 21.0 81 0.0018 27.5 2.4 12 44-55 11-22 (419)
109 PRK05580 primosome assembly pr 20.9 1.3E+02 0.0028 27.5 3.8 27 28-54 393-419 (679)
110 PF10571 UPF0547: Uncharacteri 20.4 48 0.001 18.5 0.6 12 80-91 12-23 (26)
111 KOG2907 RNA polymerase I trans 20.1 38 0.00081 25.6 0.2 33 24-56 6-38 (116)
112 PF14835 zf-RING_6: zf-RING of 20.0 58 0.0013 22.2 1.1 42 45-92 9-50 (65)
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=99.54 E-value=2.4e-15 Score=88.55 Aligned_cols=30 Identities=60% Similarity=1.247 Sum_probs=19.9
Q ss_pred eEecCCCCeeEeecCCCCeEecCCCCcCcc
Q 033496 25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTA 54 (118)
Q Consensus 25 QlvC~GCr~lL~YprGA~sVrC~~C~tVn~ 54 (118)
|++|++||++|+||+||++|||+.|++||.
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 566666666666666666666666666664
No 2
>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=99.51 E-value=6.8e-15 Score=86.63 Aligned_cols=31 Identities=71% Similarity=1.338 Sum_probs=29.5
Q ss_pred EEEeCCcCceeeeecCCCeEeCCCCCccccc
Q 033496 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNLA 94 (118)
Q Consensus 64 ql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v 94 (118)
|++|++||++|+||+||.+|||+.|++||.+
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 6899999999999999999999999999875
No 3
>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=99.50 E-value=1e-14 Score=82.79 Aligned_cols=25 Identities=64% Similarity=1.364 Sum_probs=14.8
Q ss_pred cCCCCeeEeecCCCCeEecCCCCcC
Q 033496 28 CSGCRNLLLYPVGATSVCCAVCNAV 52 (118)
Q Consensus 28 C~GCr~lL~YprGA~sVrC~~C~tV 52 (118)
|+|||++|+||+||+||||+.|++|
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 5556666666666666666666554
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=99.47 E-value=2e-14 Score=81.60 Aligned_cols=25 Identities=80% Similarity=1.666 Sum_probs=24.4
Q ss_pred eCCcCceeeeecCCCeEeCCCCCcc
Q 033496 67 CGGCHTLLMYIRGATSVQCSCCHTV 91 (118)
Q Consensus 67 CGgCrtlLmYP~GA~sVrCs~C~tV 91 (118)
||+||++||||+||+||||+.|++|
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 8999999999999999999999987
No 5
>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=95.13 E-value=0.01 Score=38.86 Aligned_cols=33 Identities=27% Similarity=0.613 Sum_probs=24.5
Q ss_pred EEEeCCcCceeeee--cCCCeEeCCCCCccccccc
Q 033496 64 QLVCGGCHTLLMYI--RGATSVQCSCCHTVNLALE 96 (118)
Q Consensus 64 ql~CGgCrtlLmYP--~GA~sVrCs~C~tVt~v~e 96 (118)
.+.|++|+.+|+.- ..-..+||+.|.++|.+..
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 57788888888875 3445788888888887653
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=95.11 E-value=0.011 Score=38.70 Aligned_cols=36 Identities=19% Similarity=0.488 Sum_probs=30.2
Q ss_pred CceeEecCCCCeeEeecCCCC--eEecCCCCcCccCCC
Q 033496 22 AQSQLVCSGCRNLLLYPVGAT--SVCCAVCNAVTAVPP 57 (118)
Q Consensus 22 ~~sQlvC~GCr~lL~YprGA~--sVrC~~C~tVn~vp~ 57 (118)
|.-++.|+.|..||...-++. .+.|+.|.++|-+.+
T Consensus 1 m~~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 1 MLKEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred CCcceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 345789999999999975665 889999999998764
No 7
>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=94.43 E-value=0.062 Score=44.74 Aligned_cols=38 Identities=18% Similarity=0.495 Sum_probs=32.7
Q ss_pred CceeEEEeCCcCceeeeecCC--CeEeCCCCCcccccccc
Q 033496 60 TEMAQLVCGGCHTLLMYIRGA--TSVQCSCCHTVNLALEG 97 (118)
Q Consensus 60 ~~~aql~CGgCrtlLmYP~GA--~sVrCs~C~tVt~v~e~ 97 (118)
..+.-++||.|+...+|+.=. .-.||+.|+.|..|..+
T Consensus 153 p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~~ 192 (256)
T PF09788_consen 153 PGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGPR 192 (256)
T ss_pred CCceeEECCCCCCcEeccCCCCCccccCCCCceeccccch
Confidence 357889999999999999755 56799999999999863
No 8
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=92.11 E-value=0.17 Score=32.28 Aligned_cols=39 Identities=28% Similarity=0.646 Sum_probs=29.3
Q ss_pred CCCCeEecCCCCcCccCCCC----CCceeEEEeCCcCceeeee
Q 033496 39 VGATSVCCAVCNAVTAVPPP----GTEMAQLVCGGCHTLLMYI 77 (118)
Q Consensus 39 rGA~sVrC~~C~tVn~vp~~----~~~~aql~CGgCrtlLmYP 77 (118)
.||+-|-|..|..+-.+|.. .....++.||.|..+|.|-
T Consensus 2 GGAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 2 GGAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred CCCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence 47788888888777666542 2337899999999999874
No 9
>PLN00209 ribosomal protein S27; Provisional
Probab=91.60 E-value=0.16 Score=36.30 Aligned_cols=40 Identities=30% Similarity=0.546 Sum_probs=30.4
Q ss_pred eEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEe
Q 033496 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ 84 (118)
Q Consensus 43 sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVr 84 (118)
.|+|+.|..++.+= ++....+.|.+|.++|..|.|-....
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 48888888888764 34457788888888888888876543
No 10
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=91.08 E-value=0.2 Score=35.74 Aligned_cols=39 Identities=28% Similarity=0.603 Sum_probs=28.7
Q ss_pred eEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeE
Q 033496 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV 83 (118)
Q Consensus 43 sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sV 83 (118)
.|+|+.|..++.+= .+....+.|.+|.++|..|.|-...
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 3445778888888888888886544
No 11
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=91.03 E-value=0.33 Score=29.53 Aligned_cols=28 Identities=21% Similarity=0.434 Sum_probs=21.1
Q ss_pred EEEeCCcCceeeeecCCCeEeCCCCCcc
Q 033496 64 QLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (118)
Q Consensus 64 ql~CGgCrtlLmYP~GA~sVrCs~C~tV 91 (118)
...|.+|...+.+..+...++|+-|++-
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 4578888888888777777888888764
No 12
>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=90.48 E-value=0.21 Score=32.84 Aligned_cols=38 Identities=24% Similarity=0.417 Sum_probs=23.9
Q ss_pred eEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCe
Q 033496 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS 82 (118)
Q Consensus 43 sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~s 82 (118)
.|+|+.|..++.+= .+....+.|.+|.++|..|.|-..
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 47888888888763 344567888888888888888654
No 13
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.21 E-value=0.46 Score=28.88 Aligned_cols=28 Identities=21% Similarity=0.455 Sum_probs=20.9
Q ss_pred eeEecCCCCeeEeecCCCCeEecCCCCc
Q 033496 24 SQLVCSGCRNLLLYPVGATSVCCAVCNA 51 (118)
Q Consensus 24 sQlvC~GCr~lL~YprGA~sVrC~~C~t 51 (118)
-...|..|...+.+..+...++|+.|.+
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCC
Confidence 3467888888888877777778887775
No 14
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.12 E-value=0.27 Score=33.01 Aligned_cols=53 Identities=21% Similarity=0.477 Sum_probs=40.9
Q ss_pred CceeEecCCCCeeEeecCC-CCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCcc
Q 033496 22 AQSQLVCSGCRNLLLYPVG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (118)
Q Consensus 22 ~~sQlvC~GCr~lL~YprG-A~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tV 91 (118)
++.-.+|.+|...| .+++ ++.+-|+.|..+... .|..||.+ +...+|+.|++.
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 34555899999888 4566 999999999876543 48899986 367889999875
No 15
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=89.66 E-value=0.2 Score=33.53 Aligned_cols=35 Identities=23% Similarity=0.326 Sum_probs=16.1
Q ss_pred EecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCC
Q 033496 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGA 80 (118)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA 80 (118)
|+|+.|..++.+= ++....+.|..|.++|..|.|-
T Consensus 12 VkCp~C~n~q~vF--sha~t~V~C~~Cg~~L~~PtGG 46 (59)
T PRK00415 12 VKCPDCGNEQVVF--SHASTVVRCLVCGKTLAEPTGG 46 (59)
T ss_pred EECCCCCCeEEEE--ecCCcEEECcccCCCcccCCCc
Confidence 4555555554332 1222445555555555555543
No 16
>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=89.52 E-value=0.31 Score=28.23 Aligned_cols=31 Identities=23% Similarity=0.592 Sum_probs=17.8
Q ss_pred EecCCCCcCccCCCC--CCceeEEEeCCcCcee
Q 033496 44 VCCAVCNAVTAVPPP--GTEMAQLVCGGCHTLL 74 (118)
Q Consensus 44 VrC~~C~tVn~vp~~--~~~~aql~CGgCrtlL 74 (118)
+.|+.|.+.+.++.+ ..+...+.|+.|+..+
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 677778776666531 1122356666666655
No 17
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.14 E-value=0.54 Score=27.87 Aligned_cols=14 Identities=29% Similarity=0.726 Sum_probs=9.1
Q ss_pred EecCCCCcCccCCC
Q 033496 44 VCCAVCNAVTAVPP 57 (118)
Q Consensus 44 VrC~~C~tVn~vp~ 57 (118)
++|+.|++.-.++.
T Consensus 3 i~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 3 ITCPNCQTRFRVPD 16 (37)
T ss_pred EECCCCCceEEcCH
Confidence 56777777666653
No 18
>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=87.58 E-value=0.95 Score=37.82 Aligned_cols=37 Identities=24% Similarity=0.580 Sum_probs=31.1
Q ss_pred CCCceeEecCCCCeeEeecCCC--CeEecCCCCcCccCC
Q 033496 20 NGAQSQLVCSGCRNLLLYPVGA--TSVCCAVCNAVTAVP 56 (118)
Q Consensus 20 ~~~~sQlvC~GCr~lL~YprGA--~sVrC~~C~tVn~vp 56 (118)
...+-.++|+.|+...+++.=. +-.||+.|+.+.++-
T Consensus 152 ~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG 190 (256)
T PF09788_consen 152 QPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG 190 (256)
T ss_pred CCCceeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence 4468889999999999998644 667999999999874
No 19
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=87.52 E-value=0.61 Score=32.07 Aligned_cols=38 Identities=24% Similarity=0.337 Sum_probs=25.8
Q ss_pred eEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCe
Q 033496 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS 82 (118)
Q Consensus 43 sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~s 82 (118)
.|+|+.|...+.+= ++....+.|..|..+|..|.|-..
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 47788887776653 233466778888888888877543
No 20
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=83.63 E-value=1.2 Score=26.41 Aligned_cols=27 Identities=30% Similarity=0.699 Sum_probs=13.3
Q ss_pred EEeCCcCceeeeec-----CCCeEeCCCCCcc
Q 033496 65 LVCGGCHTLLMYIR-----GATSVQCSCCHTV 91 (118)
Q Consensus 65 l~CGgCrtlLmYP~-----GA~sVrCs~C~tV 91 (118)
+.|-+|.+....+. +...|||+.|+++
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 34555555554433 2455555555544
No 21
>PF12773 DZR: Double zinc ribbon
Probab=81.45 E-value=0.76 Score=27.79 Aligned_cols=40 Identities=23% Similarity=0.427 Sum_probs=24.6
Q ss_pred cCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCcccc
Q 033496 46 CAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (118)
Q Consensus 46 C~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~ 93 (118)
|+.|.+.+.. ....|..|.+.|. ......+.|+.|.+.+.
T Consensus 1 Cp~Cg~~~~~-------~~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 1 CPHCGTPNPD-------DAKFCPHCGTPLP-PPDQSKKICPNCGAENP 40 (50)
T ss_pred CCCcCCcCCc-------cccCChhhcCChh-hccCCCCCCcCCcCCCc
Confidence 5566665432 3566777777776 44555667777777643
No 22
>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=81.14 E-value=3 Score=24.02 Aligned_cols=28 Identities=25% Similarity=0.651 Sum_probs=19.4
Q ss_pred EEEeCCcCceeeeec-----CCCeEeCCCCCcc
Q 033496 64 QLVCGGCHTLLMYIR-----GATSVQCSCCHTV 91 (118)
Q Consensus 64 ql~CGgCrtlLmYP~-----GA~sVrCs~C~tV 91 (118)
.+.|-.|.+....+. +...|+|+.|+++
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 467788888777774 2336888888765
No 23
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=79.65 E-value=2.8 Score=29.94 Aligned_cols=40 Identities=30% Similarity=0.537 Sum_probs=26.7
Q ss_pred eEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEe
Q 033496 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ 84 (118)
Q Consensus 43 sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVr 84 (118)
.|+|+.|-.||.+=. +...-++|+||.+.|.-|.|-..+.
T Consensus 34 ~VkC~gc~~iT~vfS--HaqtvVvc~~c~~il~~~tggra~l 73 (84)
T KOG1779|consen 34 DVKCPGCFKITTVFS--HAQTVVVCEGCSTILCQPTGGKAKL 73 (84)
T ss_pred EEEcCCceEEEEEee--cCceEEEcCCCceEEEEecCCcEEe
Confidence 377777777776632 3335577888888888777766554
No 24
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=79.11 E-value=0.89 Score=39.65 Aligned_cols=30 Identities=30% Similarity=0.627 Sum_probs=24.0
Q ss_pred EEeCCcCceeeeecCCCeEeCCCCCccccccc
Q 033496 65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (118)
Q Consensus 65 l~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~e 96 (118)
+.|. |++-|+-|.||+. +|+.|++||.+.+
T Consensus 5 ~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~~ 34 (362)
T KOG1546|consen 5 VGCN-CQRPMAPPPGARY-QCAGCHAVTQIAQ 34 (362)
T ss_pred ccCC-CCCCCCCCCCCcc-cccccceeeeecc
Confidence 3455 8888888888888 8888888888763
No 25
>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=77.64 E-value=1.5 Score=26.25 Aligned_cols=17 Identities=18% Similarity=0.526 Sum_probs=6.7
Q ss_pred CCCCeEecCCCCcCccC
Q 033496 39 VGATSVCCAVCNAVTAV 55 (118)
Q Consensus 39 rGA~sVrC~~C~tVn~v 55 (118)
.+...-.|..|++.|.+
T Consensus 20 ~~~~~w~C~~C~~~N~l 36 (40)
T PF04810_consen 20 DGGKTWICNFCGTKNPL 36 (40)
T ss_dssp TTTTEEEETTT--EEE-
T ss_pred CCCCEEECcCCCCcCCC
Confidence 34444455555554444
No 26
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=76.37 E-value=2.6 Score=24.95 Aligned_cols=14 Identities=21% Similarity=0.593 Sum_probs=9.2
Q ss_pred EecCCCCcCccCCC
Q 033496 44 VCCAVCNAVTAVPP 57 (118)
Q Consensus 44 VrC~~C~tVn~vp~ 57 (118)
+.|+.|++.-.++.
T Consensus 3 i~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 3 ITCPNCQAKYEIDD 16 (36)
T ss_pred EECCCCCCEEeCCH
Confidence 56777777766653
No 27
>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=75.14 E-value=2.4 Score=23.80 Aligned_cols=22 Identities=27% Similarity=0.678 Sum_probs=12.3
Q ss_pred eCCcCceeeeecC-CCeEeCCCCC
Q 033496 67 CGGCHTLLMYIRG-ATSVQCSCCH 89 (118)
Q Consensus 67 CGgCrtlLmYP~G-A~sVrCs~C~ 89 (118)
|.+|...|. |++ +..+.|+.|.
T Consensus 1 C~sC~~~i~-~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIA-PREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCccc-CcccCceEeCCCCC
Confidence 344555444 555 6666666664
No 28
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=74.33 E-value=0.67 Score=34.25 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=24.7
Q ss_pred EecCCCCeeEeecCCCCeEecCCCCcC
Q 033496 26 LVCSGCRNLLLYPVGATSVCCAVCNAV 52 (118)
Q Consensus 26 lvC~GCr~lL~YprGA~sVrC~~C~tV 52 (118)
++||-||.+|.|..=-..++|+.|++-
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~sp 89 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSP 89 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCC
Confidence 899999999999988888899999874
No 29
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=73.88 E-value=6.6 Score=28.09 Aligned_cols=47 Identities=19% Similarity=0.425 Sum_probs=30.6
Q ss_pred CCCCCceeEEEeCCcC-ceeeeecCCCeEeCCCCCcccccccccccchh
Q 033496 56 PPPGTEMAQLVCGGCH-TLLMYIRGATSVQCSCCHTVNLALEGCTRQLW 103 (118)
Q Consensus 56 p~~~~~~aql~CGgCr-tlLmYP~GA~sVrCs~C~tVt~v~e~~~r~~~ 103 (118)
+.+..-...+.|.+|. ...+|-+-++-|.|..|+++ ++.+.+-+..+
T Consensus 27 ~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~-L~~PTGGKa~l 74 (85)
T PTZ00083 27 QGPNSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQ-LCQPTGGKAKL 74 (85)
T ss_pred cCCCCeEEEEECCCCCCeeEEEecCceEEEccccCCE-eeccCCCCeEe
Confidence 3445556677787775 45677777777888888877 55555544433
No 30
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=70.50 E-value=14 Score=24.77 Aligned_cols=43 Identities=21% Similarity=0.511 Sum_probs=29.4
Q ss_pred CCCCceeEEEeCCcCc-eeeeecCCCeEeCCCCCccccccccccc
Q 033496 57 PPGTEMAQLVCGGCHT-LLMYIRGATSVQCSCCHTVNLALEGCTR 100 (118)
Q Consensus 57 ~~~~~~aql~CGgCrt-lLmYP~GA~sVrCs~C~tVt~v~e~~~r 100 (118)
.+......+.|.+|.. ...|-+-++-|+|..|+++ ++.+.+-+
T Consensus 4 ~p~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~-L~~PtGGK 47 (59)
T PRK00415 4 QPRSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKT-LAEPTGGK 47 (59)
T ss_pred CCCCeEEEEECCCCCCeEEEEecCCcEEECcccCCC-cccCCCcc
Confidence 3455567788888864 4678888888888888887 44444443
No 31
>PLN00209 ribosomal protein S27; Provisional
Probab=69.54 E-value=9.6 Score=27.32 Aligned_cols=46 Identities=24% Similarity=0.517 Sum_probs=30.5
Q ss_pred CCCCCceeEEEeCCcC-ceeeeecCCCeEeCCCCCcccccccccccch
Q 033496 56 PPPGTEMAQLVCGGCH-TLLMYIRGATSVQCSCCHTVNLALEGCTRQL 102 (118)
Q Consensus 56 p~~~~~~aql~CGgCr-tlLmYP~GA~sVrCs~C~tVt~v~e~~~r~~ 102 (118)
+.+..-...+.|.+|. ...+|-+-++-|.|..|+++ ++.+.+-+..
T Consensus 28 ~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~-L~~PTGGKa~ 74 (86)
T PLN00209 28 QSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTV-LCQPTGGKAR 74 (86)
T ss_pred cCCCCEEEEEECCCCCCeeEEEecCceEEEccccCCE-eeccCCCCeE
Confidence 3445556677888885 45677777777888888877 5555554443
No 32
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=69.40 E-value=5 Score=27.22 Aligned_cols=50 Identities=24% Similarity=0.547 Sum_probs=38.2
Q ss_pred EecCCCCeeEeecCCCCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCcc
Q 033496 26 LVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (118)
Q Consensus 26 lvC~GCr~lL~YprGA~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tV 91 (118)
-+|.+|...|.--.+|+.+-|++|.-+.. ..|..||.+ ....+|+-|.+.
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 58999999998889999999999975443 357788875 334678888765
No 33
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=67.35 E-value=5.5 Score=23.90 Aligned_cols=28 Identities=21% Similarity=0.489 Sum_probs=15.2
Q ss_pred eCCcCceeeeecCCC--eEeCCCCCccccc
Q 033496 67 CGGCHTLLMYIRGAT--SVQCSCCHTVNLA 94 (118)
Q Consensus 67 CGgCrtlLmYP~GA~--sVrCs~C~tVt~v 94 (118)
|..|..+|....+.. ...|+.|+++-.+
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 555655544443332 5667777776444
No 34
>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=65.30 E-value=5.2 Score=31.49 Aligned_cols=39 Identities=33% Similarity=0.581 Sum_probs=23.4
Q ss_pred eEecCCCCcCccCCCCC---CceeEEEeCCcCceeeeecCCC
Q 033496 43 SVCCAVCNAVTAVPPPG---TEMAQLVCGGCHTLLMYIRGAT 81 (118)
Q Consensus 43 sVrC~~C~tVn~vp~~~---~~~aql~CGgCrtlLmYP~GA~ 81 (118)
.|+|.-|+||-+|.-|. -.+--+.||.|-.||..--++.
T Consensus 12 YVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~ 53 (170)
T PF04690_consen 12 YVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRAL 53 (170)
T ss_pred EEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeecccc
Confidence 47777777777765432 3344566777777766444433
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=61.18 E-value=8.3 Score=26.55 Aligned_cols=40 Identities=18% Similarity=0.287 Sum_probs=21.1
Q ss_pred CeEecCCCCcCccCCC---CCCceeEEEeCCcCceeeeecCCC
Q 033496 42 TSVCCAVCNAVTAVPP---PGTEMAQLVCGGCHTLLMYIRGAT 81 (118)
Q Consensus 42 ~sVrC~~C~tVn~vp~---~~~~~aql~CGgCrtlLmYP~GA~ 81 (118)
+.+.|+.|++-+++-- .....+.+.|+.|...-.+..+..
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 5688999998777632 246789999999987776665544
No 36
>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=60.51 E-value=14 Score=24.28 Aligned_cols=38 Identities=29% Similarity=0.587 Sum_probs=19.6
Q ss_pred eeEEEeCCcCc-eeeeecCCCeEeCCCCCccccccccccc
Q 033496 62 MAQLVCGGCHT-LLMYIRGATSVQCSCCHTVNLALEGCTR 100 (118)
Q Consensus 62 ~aql~CGgCrt-lLmYP~GA~sVrCs~C~tVt~v~e~~~r 100 (118)
...+.|.+|.. ..+|-+-++.|+|..|+++ ++.+.+-+
T Consensus 5 Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~-L~~PtGGK 43 (55)
T PF01667_consen 5 FMDVKCPGCYNIQTVFSHAQTVVKCVVCGTV-LAQPTGGK 43 (55)
T ss_dssp EEEEE-TTT-SEEEEETT-SS-EE-SSSTSE-EEEE-SSS
T ss_pred EEEEECCCCCCeeEEEecCCeEEEcccCCCE-ecCCCCcC
Confidence 34566777753 4567777777777777776 44444433
No 37
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=59.16 E-value=7.9 Score=38.86 Aligned_cols=57 Identities=19% Similarity=0.366 Sum_probs=42.6
Q ss_pred CceeEecCCCCeeEeecCCCCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCcccc
Q 033496 22 AQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (118)
Q Consensus 22 ~~sQlvC~GCr~lL~YprGA~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~ 93 (118)
+.++..|-.|.+.... .+|+.|.+.+.. ...|.+|+..+-.-... +.+|+-|++-..
T Consensus 664 EV~~rkCPkCG~~t~~------~fCP~CGs~te~--------vy~CPsCGaev~~des~-a~~CP~CGtplv 720 (1337)
T PRK14714 664 EVGRRRCPSCGTETYE------NRCPDCGTHTEP--------VYVCPDCGAEVPPDESG-RVECPRCDVELT 720 (1337)
T ss_pred EEEEEECCCCCCcccc------ccCcccCCcCCC--------ceeCccCCCccCCCccc-cccCCCCCCccc
Confidence 4567899999996432 299999998742 24899999987755433 789999997543
No 38
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=58.90 E-value=7.6 Score=26.06 Aligned_cols=32 Identities=25% Similarity=0.436 Sum_probs=24.0
Q ss_pred eeEEEeCCcCceeeeecC-CCeEeCCCCCccccc
Q 033496 62 MAQLVCGGCHTLLMYIRG-ATSVQCSCCHTVNLA 94 (118)
Q Consensus 62 ~aql~CGgCrtlLmYP~G-A~sVrCs~C~tVt~v 94 (118)
+...+|.+|...| .|.+ +..+.|+.|..+...
T Consensus 5 ~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I~ 37 (59)
T PRK14890 5 MEPPKCTSCGIEI-APREKAVKFLCPNCGEVIIY 37 (59)
T ss_pred ccCccccCCCCcc-cCCCccCEeeCCCCCCeeEe
Confidence 3445799999888 5666 899999999876443
No 39
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=58.60 E-value=9.3 Score=30.73 Aligned_cols=28 Identities=18% Similarity=0.515 Sum_probs=23.7
Q ss_pred eeEEEeCCcCceeeeecCCCeEeCCCCCcc
Q 033496 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (118)
Q Consensus 62 ~aql~CGgCrtlLmYP~GA~sVrCs~C~tV 91 (118)
+-.-.|..||..|++ .-...+|+.|+.+
T Consensus 147 VI~A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 147 VIYARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEEEEccCCCcceEE--cCcEEECCCCCCE
Confidence 345689999999999 7788999999976
No 40
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=57.30 E-value=8.5 Score=24.08 Aligned_cols=28 Identities=32% Similarity=0.592 Sum_probs=18.0
Q ss_pred eEecCCCCeeEeec------CCCCeEecCCCCcC
Q 033496 25 QLVCSGCRNLLLYP------VGATSVCCAVCNAV 52 (118)
Q Consensus 25 QlvC~GCr~lL~Yp------rGA~sVrC~~C~tV 52 (118)
.-+|+||++.|.-- +|..-+.|+.|+.|
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 34788888877532 44566777777654
No 41
>PRK05580 primosome assembly protein PriA; Validated
Probab=56.25 E-value=22 Score=32.47 Aligned_cols=50 Identities=26% Similarity=0.461 Sum_probs=35.5
Q ss_pred CeeEeec-CC-CCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCcccc
Q 033496 32 RNLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (118)
Q Consensus 32 r~lL~Yp-rG-A~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~ 93 (118)
++||..+ || |+.+.|..|..+- .|..|...|.|.......+|.-|++...
T Consensus 368 qvll~~nrrGy~~~~~C~~Cg~~~------------~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 368 QVLLFLNRRGYAPFLLCRDCGWVA------------ECPHCDASLTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred eEEEEEcCCCCCCceEhhhCcCcc------------CCCCCCCceeEECCCCeEECCCCcCCCC
Confidence 4556665 45 6789999998653 4777888888877777777777776644
No 42
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=54.90 E-value=5.4 Score=34.94 Aligned_cols=27 Identities=41% Similarity=0.783 Sum_probs=24.0
Q ss_pred ecCCCCeeEeecCCCCeEecCCCCcCccC
Q 033496 27 VCSGCRNLLLYPVGATSVCCAVCNAVTAV 55 (118)
Q Consensus 27 vC~GCr~lL~YprGA~sVrC~~C~tVn~v 55 (118)
-|. ||+-|+-|.||.. ||+.|++++..
T Consensus 6 ~~~-~~~p~~~pp~ar~-q~~~~~~~~~~ 32 (362)
T KOG1546|consen 6 GCN-CQRPMAPPPGARY-QCAGCHAVTQI 32 (362)
T ss_pred cCC-CCCCCCCCCCCcc-cccccceeeee
Confidence 355 9999999999999 99999999864
No 43
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=54.55 E-value=3.3 Score=27.94 Aligned_cols=31 Identities=29% Similarity=0.620 Sum_probs=19.0
Q ss_pred EEEeCCcCceeeeecCC--CeEeCCCCCccccc
Q 033496 64 QLVCGGCHTLLMYIRGA--TSVQCSCCHTVNLA 94 (118)
Q Consensus 64 ql~CGgCrtlLmYP~GA--~sVrCs~C~tVt~v 94 (118)
-+.|..|.-+|.=-.|. ..++|+.|..||..
T Consensus 4 tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred eeehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 35555555555544333 45788888888764
No 44
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=51.93 E-value=3.7 Score=27.68 Aligned_cols=34 Identities=24% Similarity=0.518 Sum_probs=26.9
Q ss_pred CceeEecCCCCeeEeecCCC--CeEecCCCCcCccC
Q 033496 22 AQSQLVCSGCRNLLLYPVGA--TSVCCAVCNAVTAV 55 (118)
Q Consensus 22 ~~sQlvC~GCr~lL~YprGA--~sVrC~~C~tVn~v 55 (118)
+|--|.|..|..||.=..|. -.+.|+.|.+||..
T Consensus 1 ~~~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 1 MMQTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred CceeeehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 35568899999999877665 46889999999874
No 45
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=51.40 E-value=19 Score=24.77 Aligned_cols=40 Identities=23% Similarity=0.459 Sum_probs=30.7
Q ss_pred CCceeEEEeCCcC-ceeeeecCCCeEeCCCCCcccccccccc
Q 033496 59 GTEMAQLVCGGCH-TLLMYIRGATSVQCSCCHTVNLALEGCT 99 (118)
Q Consensus 59 ~~~~aql~CGgCr-tlLmYP~GA~sVrCs~C~tVt~v~e~~~ 99 (118)
..-...+.|.+|. ....|-+-++.|+|..|.++ .+.+.+-
T Consensus 14 ~s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~-l~~PTGG 54 (67)
T COG2051 14 RSRFLRVKCPDCGNEQVVFSHASTVVTCLICGTT-LAEPTGG 54 (67)
T ss_pred CceEEEEECCCCCCEEEEeccCceEEEecccccE-EEecCCC
Confidence 3456788999996 46789999999999999988 4444443
No 46
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=49.71 E-value=25 Score=25.16 Aligned_cols=30 Identities=27% Similarity=0.694 Sum_probs=16.5
Q ss_pred eeEEEeCCcC-ceeeeecCCCeEeCCCCCcc
Q 033496 62 MAQLVCGGCH-TLLMYIRGATSVQCSCCHTV 91 (118)
Q Consensus 62 ~aql~CGgCr-tlLmYP~GA~sVrCs~C~tV 91 (118)
...+.|+||+ ++..|.+--..|-|..|.+|
T Consensus 32 Fm~VkC~gc~~iT~vfSHaqtvVvc~~c~~i 62 (84)
T KOG1779|consen 32 FMDVKCPGCFKITTVFSHAQTVVVCEGCSTI 62 (84)
T ss_pred EEEEEcCCceEEEEEeecCceEEEcCCCceE
Confidence 3445565543 44455555555666666665
No 47
>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=48.42 E-value=21 Score=23.65 Aligned_cols=16 Identities=19% Similarity=0.416 Sum_probs=8.9
Q ss_pred eEecCCCCeeEeecCC
Q 033496 25 QLVCSGCRNLLLYPVG 40 (118)
Q Consensus 25 QlvC~GCr~lL~YprG 40 (118)
+++||-|++.+.+..-
T Consensus 41 ~v~Cg~C~~~~~~~~~ 56 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEY 56 (71)
T ss_dssp EEEETTT--EEES-SB
T ss_pred CeECCCCCCccChhhh
Confidence 7777777777766543
No 48
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.04 E-value=23 Score=21.91 Aligned_cols=28 Identities=18% Similarity=0.564 Sum_probs=12.3
Q ss_pred ecCCCCcCccCCCCCCceeEEEeCCcCceeee
Q 033496 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMY 76 (118)
Q Consensus 45 rC~~C~tVn~vp~~~~~~aql~CGgCrtlLmY 76 (118)
.|..|.+.+... ....+.|-.|.--++|
T Consensus 4 ~C~~Cg~~~~~~----~~~~irC~~CG~rIly 31 (44)
T smart00659 4 ICGECGRENEIK----SKDVVRCRECGYRILY 31 (44)
T ss_pred ECCCCCCEeecC----CCCceECCCCCceEEE
Confidence 455555543321 1244555555444444
No 49
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=46.24 E-value=2.1 Score=25.49 Aligned_cols=25 Identities=28% Similarity=0.723 Sum_probs=19.3
Q ss_pred eeEEEeCCcCceeeeecCCCeEeCCCCCc
Q 033496 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHT 90 (118)
Q Consensus 62 ~aql~CGgCrtlLmYP~GA~sVrCs~C~t 90 (118)
=+|+.|..|-..++ ...++|+.|+.
T Consensus 20 CgH~~C~~C~~~~~----~~~~~CP~C~k 44 (44)
T PF14634_consen 20 CGHIFCEKCLKKLK----GKSVKCPICRK 44 (44)
T ss_pred cCCHHHHHHHHhhc----CCCCCCcCCCC
Confidence 46777778888887 77888888863
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=45.61 E-value=30 Score=30.44 Aligned_cols=43 Identities=21% Similarity=0.601 Sum_probs=27.1
Q ss_pred CC-CCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCcccc
Q 033496 39 VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (118)
Q Consensus 39 rG-A~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~ 93 (118)
|| |+.+.|..|..+- .|..|..-|-|=......+|.-|++...
T Consensus 208 rGya~~~~C~~Cg~~~------------~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 208 RGYSKNLLCRSCGYIL------------CCPNCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CcCCCeeEhhhCcCcc------------CCCCCCCceEEecCCCeEEcCCCcCcCC
Confidence 45 4667888887653 3666666666666666666666665543
No 51
>PRK14873 primosome assembly protein PriA; Provisional
Probab=44.62 E-value=40 Score=31.17 Aligned_cols=49 Identities=27% Similarity=0.547 Sum_probs=31.9
Q ss_pred CCCCeeEeec-CC-CCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCc
Q 033496 29 SGCRNLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHT 90 (118)
Q Consensus 29 ~GCr~lL~Yp-rG-A~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~t 90 (118)
.| ++||+-+ || |+.+.|..|..+- .|..|...|-|..+....+|.-|++
T Consensus 368 ~g-qvll~lnRrGyap~l~C~~Cg~~~------------~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 368 HG-PVLVQVPRRGYVPSLACARCRTPA------------RCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred cC-cEEEEecCCCCCCeeEhhhCcCee------------ECCCCCCceeEecCCCeeECCCCcC
Confidence 36 7777765 45 4566888887643 4666666666666666666666665
No 52
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=44.35 E-value=10 Score=31.22 Aligned_cols=26 Identities=31% Similarity=0.658 Sum_probs=13.9
Q ss_pred ecCCCCeeEee------cCCCCeEecCCCCcC
Q 033496 27 VCSGCRNLLLY------PVGATSVCCAVCNAV 52 (118)
Q Consensus 27 vC~GCr~lL~Y------prGA~sVrC~~C~tV 52 (118)
+||||+..|-= ..+=.-|.|+.|..|
T Consensus 199 ~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred cccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 68888776621 123444555555544
No 53
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=42.99 E-value=33 Score=25.03 Aligned_cols=33 Identities=18% Similarity=0.414 Sum_probs=20.4
Q ss_pred EecCCCCcCccCCCCCCceeEEEeCCcCceeee
Q 033496 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMY 76 (118)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmY 76 (118)
-+|..|+......--.+...+..|+.|+-.|.+
T Consensus 113 y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l~~ 145 (146)
T smart00731 113 YRCTGCGQRYLRVRRSNNVSRYRCGKCGGKLIL 145 (146)
T ss_pred EECCCCCCCCceEccccCcceEEcCCCCCEEEe
Confidence 356666655442222234488899999888764
No 54
>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=41.95 E-value=19 Score=20.73 Aligned_cols=21 Identities=24% Similarity=0.729 Sum_probs=9.2
Q ss_pred ecCCCCeeEeecCCCCeEecCCCCc
Q 033496 27 VCSGCRNLLLYPVGATSVCCAVCNA 51 (118)
Q Consensus 27 vC~GCr~lL~YprGA~sVrC~~C~t 51 (118)
.|..|..+..||+ ..|+.|..
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 4667777766666 34566653
No 55
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=39.43 E-value=27 Score=28.11 Aligned_cols=26 Identities=27% Similarity=0.583 Sum_probs=21.0
Q ss_pred EecCCCCeeEeecCCCCeEecCCCCcCc
Q 033496 26 LVCSGCRNLLLYPVGATSVCCAVCNAVT 53 (118)
Q Consensus 26 lvC~GCr~lL~YprGA~sVrC~~C~tVn 53 (118)
-+|..||..|++ .-....|+.|..+-
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~tE 175 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGNTE 175 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCCEE
Confidence 479999999999 55778899997653
No 56
>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=39.29 E-value=14 Score=27.80 Aligned_cols=33 Identities=24% Similarity=0.317 Sum_probs=23.6
Q ss_pred CCCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeee
Q 033496 40 GATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYI 77 (118)
Q Consensus 40 GA~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP 77 (118)
-|..|.|+.|+-.|-.-- -.-.|-.|++.|-..
T Consensus 66 kav~V~CP~C~K~TKmLG-----r~D~CM~C~~pLTLd 98 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLG-----RVDACMHCKEPLTLD 98 (114)
T ss_pred cceeeECCCCCChHhhhc-----hhhccCcCCCcCccC
Confidence 468899999999997542 123788888877543
No 57
>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=39.28 E-value=31 Score=19.39 Aligned_cols=24 Identities=25% Similarity=0.612 Sum_probs=9.1
Q ss_pred eCCcCceeeeecCCCeEeCCCCCc
Q 033496 67 CGGCHTLLMYIRGATSVQCSCCHT 90 (118)
Q Consensus 67 CGgCrtlLmYP~GA~sVrCs~C~t 90 (118)
|+.|...+..-.+-..-+|+.|+.
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSSS-
T ss_pred cCcCCccccCCCCcCEeECCCCcC
Confidence 455555555444545555555543
No 58
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=38.58 E-value=17 Score=28.34 Aligned_cols=28 Identities=25% Similarity=0.605 Sum_probs=24.1
Q ss_pred EeCCcC-ceeeeecCC-CeEeCCCCCcccc
Q 033496 66 VCGGCH-TLLMYIRGA-TSVQCSCCHTVNL 93 (118)
Q Consensus 66 ~CGgCr-tlLmYP~GA-~sVrCs~C~tVt~ 93 (118)
+|.-|+ ..++||... ..++|..|.+|-.
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~H 183 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVFH 183 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCccccc
Confidence 677787 589999999 9999999999854
No 59
>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=38.25 E-value=21 Score=24.42 Aligned_cols=27 Identities=19% Similarity=0.459 Sum_probs=18.9
Q ss_pred EeCCcCceeeeecCCCeEeCCCCCccccc
Q 033496 66 VCGGCHTLLMYIRGATSVQCSCCHTVNLA 94 (118)
Q Consensus 66 ~CGgCrtlLmYP~GA~sVrCs~C~tVt~v 94 (118)
.|..|..+| ++.+ ..++|..|.+....
T Consensus 2 fC~~Cg~~l-~~~~-~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLM-TPKN-GVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCccc-ccCC-CeEECcCCCCcccc
Confidence 477888877 4544 36889999887543
No 60
>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=37.24 E-value=55 Score=25.80 Aligned_cols=33 Identities=21% Similarity=0.571 Sum_probs=27.7
Q ss_pred CCceeEEEeCCcCceeeeec------CCCeEeCCCCCcc
Q 033496 59 GTEMAQLVCGGCHTLLMYIR------GATSVQCSCCHTV 91 (118)
Q Consensus 59 ~~~~aql~CGgCrtlLmYP~------GA~sVrCs~C~tV 91 (118)
..+.-++.|+-|.|.|+.-. ..-+|||..|..+
T Consensus 7 sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNL 45 (170)
T PF04690_consen 7 SEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNL 45 (170)
T ss_pred CCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccce
Confidence 56889999999999998643 5678999999865
No 61
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=36.45 E-value=12 Score=28.20 Aligned_cols=33 Identities=21% Similarity=0.373 Sum_probs=27.0
Q ss_pred EEEeCCcCceeeeecCCCeEeCCCCCccccccc
Q 033496 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (118)
Q Consensus 64 ql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~e 96 (118)
-+-|+.|..+|+-|.-...|-|..|..+..+..
T Consensus 7 ~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~ 39 (116)
T KOG2907|consen 7 LDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQ 39 (116)
T ss_pred cchhhhhhhhcccccccCceEeccccccCCHHH
Confidence 356888999999998888899999988877653
No 62
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=36.08 E-value=21 Score=20.90 Aligned_cols=7 Identities=29% Similarity=1.122 Sum_probs=2.9
Q ss_pred EeCCCCC
Q 033496 83 VQCSCCH 89 (118)
Q Consensus 83 VrCs~C~ 89 (118)
|+|.-|+
T Consensus 18 irC~~CG 24 (32)
T PF03604_consen 18 IRCPECG 24 (32)
T ss_dssp SSBSSSS
T ss_pred EECCcCC
Confidence 3444443
No 63
>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=35.56 E-value=21 Score=20.92 Aligned_cols=27 Identities=26% Similarity=0.511 Sum_probs=14.7
Q ss_pred eCCcCceeeeecCCCe-EeCCCCCcccc
Q 033496 67 CGGCHTLLMYIRGATS-VQCSCCHTVNL 93 (118)
Q Consensus 67 CGgCrtlLmYP~GA~s-VrCs~C~tVt~ 93 (118)
|..|..+|....+... +.|..|.++-.
T Consensus 4 Cp~C~nlL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp ETTTTSBEEEEEETTTTEEESSSS-EEE
T ss_pred CCCCCccceEcCCCccCcCCCCCCCccC
Confidence 6667766644443333 34777777643
No 64
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=35.22 E-value=37 Score=24.43 Aligned_cols=14 Identities=14% Similarity=0.472 Sum_probs=9.6
Q ss_pred CCCeEeCCCCCccc
Q 033496 79 GATSVQCSCCHTVN 92 (118)
Q Consensus 79 GA~sVrCs~C~tVt 92 (118)
|-.++.|+.|++-.
T Consensus 39 ~~~h~~C~~CG~y~ 52 (99)
T PRK14892 39 NIAIITCGNCGLYT 52 (99)
T ss_pred CcceEECCCCCCcc
Confidence 56677777777663
No 65
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=34.84 E-value=51 Score=19.81 Aligned_cols=24 Identities=25% Similarity=0.753 Sum_probs=15.4
Q ss_pred ecC--CCCeeEeecC--CCCeEecCCCC
Q 033496 27 VCS--GCRNLLLYPV--GATSVCCAVCN 50 (118)
Q Consensus 27 vC~--GCr~lL~Ypr--GA~sVrC~~C~ 50 (118)
-|- +|..++.... |...|.|..|+
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~ 47 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCG 47 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCC
Confidence 366 6777666654 66667776665
No 66
>PF14369 zf-RING_3: zinc-finger
Probab=34.82 E-value=36 Score=20.02 Aligned_cols=24 Identities=21% Similarity=0.646 Sum_probs=13.4
Q ss_pred ecCCCCeeEeec-CCCCeEecCCCC
Q 033496 27 VCSGCRNLLLYP-VGATSVCCAVCN 50 (118)
Q Consensus 27 vC~GCr~lL~Yp-rGA~sVrC~~C~ 50 (118)
-|..|++.+.-. .+...+.|+.|+
T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~ 28 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCH 28 (35)
T ss_pred eCccCCCEeEeCcCCCCCcCCcCCC
Confidence 466666655553 344444566665
No 67
>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=34.65 E-value=47 Score=19.67 Aligned_cols=12 Identities=42% Similarity=0.958 Sum_probs=5.4
Q ss_pred eEEEeCCcCcee
Q 033496 63 AQLVCGGCHTLL 74 (118)
Q Consensus 63 aql~CGgCrtlL 74 (118)
+.++|..|..+|
T Consensus 18 g~~vC~~CG~Vl 29 (43)
T PF08271_consen 18 GELVCPNCGLVL 29 (43)
T ss_dssp TEEEETTT-BBE
T ss_pred CeEECCCCCCEe
Confidence 445555554444
No 68
>PRK11827 hypothetical protein; Provisional
Probab=34.61 E-value=44 Score=22.24 Aligned_cols=25 Identities=24% Similarity=0.581 Sum_probs=13.5
Q ss_pred EecCCCCeeEeecCCCCeEecCCCC
Q 033496 26 LVCSGCRNLLLYPVGATSVCCAVCN 50 (118)
Q Consensus 26 lvC~GCr~lL~YprGA~sVrC~~C~ 50 (118)
|+|-.|+.-|.|-.++....|..|+
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~ 33 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDN 33 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccC
Confidence 5566666666665554444444444
No 69
>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=33.92 E-value=53 Score=28.39 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=3.8
Q ss_pred cCCCCcCcc
Q 033496 46 CAVCNAVTA 54 (118)
Q Consensus 46 C~~C~tVn~ 54 (118)
|..|+.+..
T Consensus 16 C~~Cd~l~~ 24 (403)
T TIGR00155 16 CSQCDMLVA 24 (403)
T ss_pred CCCCCCccc
Confidence 444444443
No 70
>PRK10996 thioredoxin 2; Provisional
Probab=33.57 E-value=29 Score=24.84 Aligned_cols=32 Identities=25% Similarity=0.618 Sum_probs=24.0
Q ss_pred eEecCCCCcCccCCCCCCceeEEEeCCcCceee
Q 033496 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLM 75 (118)
Q Consensus 43 sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLm 75 (118)
+-.|..|+.+|..|++.. -.+..||+|-..+.
T Consensus 2 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 33 (139)
T PRK10996 2 NTVCTSCQAINRLPDERI-EDAAKCGRCGHDLF 33 (139)
T ss_pred eEECCCCCCcCCCCCccc-cCCCcCCCCCCccC
Confidence 457999999999876443 34567999887765
No 71
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=32.73 E-value=43 Score=24.01 Aligned_cols=33 Identities=18% Similarity=0.448 Sum_probs=22.5
Q ss_pred eEEEeCCcCceeeeecCCCeEeCCCCCcccccccc
Q 033496 63 AQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEG 97 (118)
Q Consensus 63 aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~e~ 97 (118)
+...|..|.. .|+.....+.|+.|+.-+.-...
T Consensus 69 ~~~~C~~Cg~--~~~~~~~~~~CP~Cgs~~~~i~~ 101 (115)
T TIGR00100 69 VECECEDCSE--EVSPEIDLYRCPKCHGIMLQVRA 101 (115)
T ss_pred cEEEcccCCC--EEecCCcCccCcCCcCCCcEEec
Confidence 5678888883 45555557889999987644333
No 72
>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=32.51 E-value=45 Score=25.36 Aligned_cols=35 Identities=17% Similarity=0.376 Sum_probs=24.5
Q ss_pred eeEEEeCCcCceeeeecCCCeEeCCCCCccccccc
Q 033496 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (118)
Q Consensus 62 ~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~e 96 (118)
.+.++|-+|.-.+.|-.-..--.|+.|+.....++
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R~ 144 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERLPPCPKCGHTEFTRQ 144 (146)
T ss_pred CceEecccCCCEEEecCCCcCCCCCCCCCCeeeeC
Confidence 46777777777777776666667777777665443
No 73
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=31.94 E-value=45 Score=23.93 Aligned_cols=33 Identities=21% Similarity=0.398 Sum_probs=23.3
Q ss_pred eEEEeCCcCceeeeecCCCe-EeCCCCCcccccccc
Q 033496 63 AQLVCGGCHTLLMYIRGATS-VQCSCCHTVNLALEG 97 (118)
Q Consensus 63 aql~CGgCrtlLmYP~GA~s-VrCs~C~tVt~v~e~ 97 (118)
+...|..|.. .|+..... .+|+.|+..+.-...
T Consensus 69 ~~~~C~~Cg~--~~~~~~~~~~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 69 AECWCETCQQ--YVTLLTQRVRRCPQCHGDMLRIVA 102 (114)
T ss_pred cEEEcccCCC--eeecCCccCCcCcCcCCCCcEEcc
Confidence 6788999985 56665554 789999987544433
No 74
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.26 E-value=56 Score=21.08 Aligned_cols=36 Identities=19% Similarity=0.433 Sum_probs=24.2
Q ss_pred eeEEEeCCcCceeeeecCCCeEeCCCCCcccccccc
Q 033496 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEG 97 (118)
Q Consensus 62 ~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~e~ 97 (118)
+..-.|..|...+--.....-++|+-|++=-++-+.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~R 39 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSRILVKER 39 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcEEEEecc
Confidence 455567777777766667777888888765444443
No 75
>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=31.06 E-value=14 Score=24.99 Aligned_cols=31 Identities=23% Similarity=0.542 Sum_probs=17.9
Q ss_pred eEecCCCCee-------EeecCCCCeEecCCCCcCccC
Q 033496 25 QLVCSGCRNL-------LLYPVGATSVCCAVCNAVTAV 55 (118)
Q Consensus 25 QlvC~GCr~l-------L~YprGA~sVrC~~C~tVn~v 55 (118)
+..|..|.+- .+|-+|...|+|+.|+..-..
T Consensus 4 ~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred EEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeee
Confidence 3456666543 357788888888888765543
No 76
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=31.01 E-value=22 Score=29.98 Aligned_cols=40 Identities=28% Similarity=0.620 Sum_probs=26.5
Q ss_pred EecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCc
Q 033496 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHT 90 (118)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~t 90 (118)
.-|+.|---=.-|---=+.+||.|..||+ -.+.+|+.|+-
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~-------~~~~~CP~Cr~ 88 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRT-------KVSNKCPTCRL 88 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhh-------hhcccCCcccc
Confidence 45777643322221124579999999998 45789999974
No 77
>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=30.91 E-value=21 Score=20.29 Aligned_cols=24 Identities=21% Similarity=0.476 Sum_probs=15.7
Q ss_pred EeCCcCceeeeecCCCeEeCCCCCcc
Q 033496 66 VCGGCHTLLMYIRGATSVQCSCCHTV 91 (118)
Q Consensus 66 ~CGgCrtlLmYP~GA~sVrCs~C~tV 91 (118)
.|..|+..|.... ..++|+.|+.+
T Consensus 13 ~C~~C~~~i~~~~--~~~~C~~C~~~ 36 (49)
T smart00109 13 KCCVCRKSIWGSF--QGLRCSWCKVK 36 (49)
T ss_pred CccccccccCcCC--CCcCCCCCCch
Confidence 4777777765433 46777777655
No 78
>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=30.74 E-value=29 Score=20.05 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=17.6
Q ss_pred ecCCCCeeEeecCCCCeEecCCCCcC
Q 033496 27 VCSGCRNLLLYPVGATSVCCAVCNAV 52 (118)
Q Consensus 27 vC~GCr~lL~YprGA~sVrC~~C~tV 52 (118)
.|..|+.+|... +....+|+.|+.+
T Consensus 13 ~C~~C~~~i~~~-~~~~~~C~~C~~~ 37 (50)
T cd00029 13 FCDVCRKSIWGL-FKQGLRCSWCKVK 37 (50)
T ss_pred Chhhcchhhhcc-ccceeEcCCCCCc
Confidence 477888877653 5677788888643
No 79
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.74 E-value=48 Score=23.73 Aligned_cols=31 Identities=29% Similarity=0.513 Sum_probs=21.9
Q ss_pred eEEEeCCcCceeeeecCCCeEeCCCCCcccccc
Q 033496 63 AQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAL 95 (118)
Q Consensus 63 aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~ 95 (118)
+...|..|.. .|+.......|+.|+..+.-.
T Consensus 69 ~~~~C~~Cg~--~~~~~~~~~~CP~Cgs~~~~i 99 (113)
T PRK12380 69 AQAWCWDCSQ--VVEIHQHDAQCPHCHGERLRV 99 (113)
T ss_pred cEEEcccCCC--EEecCCcCccCcCCCCCCcEE
Confidence 6788888883 455555667799999765433
No 80
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=30.62 E-value=37 Score=25.20 Aligned_cols=32 Identities=19% Similarity=0.509 Sum_probs=23.6
Q ss_pred CeEecCCCCcCccCC---CCCCceeEEEeCCcCce
Q 033496 42 TSVCCAVCNAVTAVP---PPGTEMAQLVCGGCHTL 73 (118)
Q Consensus 42 ~sVrC~~C~tVn~vp---~~~~~~aql~CGgCrtl 73 (118)
..+-|+.|++.+.+. --....+-++||.|..-
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred ceEecCccCCeeeeEEEEEecCceeEEEcccCcce
Confidence 357799999998762 12456789999999753
No 81
>PLN00162 transport protein sec23; Provisional
Probab=29.79 E-value=61 Score=30.29 Aligned_cols=34 Identities=29% Similarity=0.583 Sum_probs=28.3
Q ss_pred eeEecCCCCeeE----eecCCCCeEecCCCCcCccCCC
Q 033496 24 SQLVCSGCRNLL----LYPVGATSVCCAVCNAVTAVPP 57 (118)
Q Consensus 24 sQlvC~GCr~lL----~YprGA~sVrC~~C~tVn~vp~ 57 (118)
.-++|..||..| ..-.|...-+|..|+..|..|+
T Consensus 52 ~pvRC~~CraylNPf~~~d~~~~~W~C~~C~~~N~~P~ 89 (761)
T PLN00162 52 DPLRCRTCRAVLNPYCRVDFQAKIWICPFCFQRNHFPP 89 (761)
T ss_pred CCCccCCCcCEECCceEEecCCCEEEccCCCCCCCCch
Confidence 458899999988 3456788999999999999875
No 82
>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=29.51 E-value=65 Score=22.15 Aligned_cols=30 Identities=27% Similarity=0.556 Sum_probs=21.0
Q ss_pred EEeCCcCceeeeecCCCeEeCCCCCccccccc
Q 033496 65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (118)
Q Consensus 65 l~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~e 96 (118)
..| .|+..|.-..|+..-+| .|+....+-+
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 578 79999999999999999 8988766543
No 83
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=29.51 E-value=84 Score=20.82 Aligned_cols=33 Identities=18% Similarity=0.366 Sum_probs=17.0
Q ss_pred CceeEEEeCCcCceeeeecCCCeEeCCCCCccc
Q 033496 60 TEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVN 92 (118)
Q Consensus 60 ~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt 92 (118)
+.+.++.|..|+..=--++--.-.||+.|+.-|
T Consensus 26 ~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYN 58 (61)
T PF14599_consen 26 NKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYN 58 (61)
T ss_dssp --EEEEEESSS--EEEEE--TT----TTTS---
T ss_pred CCEEEEECCCCCCccceeeeHhhhcCCCCCCcc
Confidence 557888888888888888888888888888765
No 84
>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=29.37 E-value=54 Score=28.34 Aligned_cols=27 Identities=26% Similarity=0.706 Sum_probs=13.6
Q ss_pred EEeCCcCceeeeec--CCCeEeCCCCCcc
Q 033496 65 LVCGGCHTLLMYIR--GATSVQCSCCHTV 91 (118)
Q Consensus 65 l~CGgCrtlLmYP~--GA~sVrCs~C~tV 91 (118)
+.|-.|..+.-.|. .....+|+.|+++
T Consensus 14 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 42 (403)
T TIGR00155 14 ILCSQCDMLVALPRIESGQKAACPRCGTT 42 (403)
T ss_pred eeCCCCCCcccccCCCCCCeeECCCCCCC
Confidence 34555555555553 2233445555555
No 85
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.52 E-value=86 Score=29.69 Aligned_cols=56 Identities=21% Similarity=0.529 Sum_probs=41.1
Q ss_pred CeeEeec-CC-CCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCcccccccccc
Q 033496 32 RNLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEGCT 99 (118)
Q Consensus 32 r~lL~Yp-rG-A~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~e~~~ 99 (118)
++||+-+ || ++.+.|..|..+- .|-+|...|-|-.....-+|--|++-..+...+-
T Consensus 422 Q~llflnRRGys~~l~C~~Cg~v~------------~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp 479 (730)
T COG1198 422 QVLLFLNRRGYAPLLLCRDCGYIA------------ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCP 479 (730)
T ss_pred eEEEEEccCCccceeecccCCCcc------------cCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCC
Confidence 3455544 45 4588999998764 4778888888888888888888888866665553
No 86
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=28.21 E-value=51 Score=27.84 Aligned_cols=35 Identities=17% Similarity=0.487 Sum_probs=16.3
Q ss_pred eeEEEeCCcCceeeee-cCCCeEeCCCCCccccccc
Q 033496 62 MAQLVCGGCHTLLMYI-RGATSVQCSCCHTVNLALE 96 (118)
Q Consensus 62 ~aql~CGgCrtlLmYP-~GA~sVrCs~C~tVt~v~e 96 (118)
+-.++||.|..+.+|- .--...+|+.|+.|..+..
T Consensus 168 gcRV~CgHC~~tFLfnt~tnaLArCPHCrKvSsvGs 203 (275)
T KOG4684|consen 168 GCRVKCGHCNETFLFNTLTNALARCPHCRKVSSVGS 203 (275)
T ss_pred ceEEEecCccceeehhhHHHHHhcCCcccchhhhhh
Confidence 3444444444443332 1113445666666665554
No 87
>PRK04351 hypothetical protein; Provisional
Probab=27.87 E-value=50 Score=25.00 Aligned_cols=16 Identities=31% Similarity=0.646 Sum_probs=12.0
Q ss_pred eeEEEeCCcCceeeee
Q 033496 62 MAQLVCGGCHTLLMYI 77 (118)
Q Consensus 62 ~aql~CGgCrtlLmYP 77 (118)
..+-.||.|+..|.+-
T Consensus 130 ~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 130 TKRYRCGKCRGKLKLI 145 (149)
T ss_pred CCcEEeCCCCcEeeec
Confidence 4678888888888753
No 88
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.80 E-value=37 Score=31.47 Aligned_cols=37 Identities=24% Similarity=0.461 Sum_probs=21.4
Q ss_pred ecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCccccc
Q 033496 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLA 94 (118)
Q Consensus 45 rC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v 94 (118)
.|+.|++.|.. ..-.|..|.+.|- .-.|+.|++-+..
T Consensus 3 ~Cp~Cg~~n~~-------~akFC~~CG~~l~------~~~Cp~CG~~~~~ 39 (645)
T PRK14559 3 ICPQCQFENPN-------NNRFCQKCGTSLT------HKPCPQCGTEVPV 39 (645)
T ss_pred cCCCCCCcCCC-------CCccccccCCCCC------CCcCCCCCCCCCc
Confidence 57777777642 3346777766662 1246666666443
No 89
>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=26.86 E-value=57 Score=19.43 Aligned_cols=26 Identities=23% Similarity=0.632 Sum_probs=16.6
Q ss_pred EecCCCCeeEeecCCCCeEecCCCCcC
Q 033496 26 LVCSGCRNLLLYPVGATSVCCAVCNAV 52 (118)
Q Consensus 26 lvC~GCr~lL~YprGA~sVrC~~C~tV 52 (118)
..|.-|+.+|. ..+....+|+.|+.+
T Consensus 12 ~~C~~C~~~i~-g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 12 TYCDVCGKFIW-GLGKQGYRCSWCGLV 37 (53)
T ss_dssp EB-TTSSSBEC-SSSSCEEEETTTT-E
T ss_pred CCCcccCcccC-CCCCCeEEECCCCCh
Confidence 36777888773 366777788887753
No 90
>PRK02935 hypothetical protein; Provisional
Probab=25.98 E-value=53 Score=24.58 Aligned_cols=34 Identities=24% Similarity=0.346 Sum_probs=23.3
Q ss_pred CCCCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeee
Q 033496 39 VGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYI 77 (118)
Q Consensus 39 rGA~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP 77 (118)
.-|..|.|+.|+-.|-.-- -.-.|-.|++.|-..
T Consensus 66 tkavqV~CP~C~K~TKmLG-----rvD~CM~C~~PLTLd 99 (110)
T PRK02935 66 TKAVQVICPSCEKPTKMLG-----RVDACMHCNQPLTLD 99 (110)
T ss_pred ccceeeECCCCCchhhhcc-----ceeecCcCCCcCCcC
Confidence 4578899999999887642 223577777766443
No 91
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=25.61 E-value=67 Score=27.15 Aligned_cols=47 Identities=19% Similarity=0.376 Sum_probs=26.1
Q ss_pred CCCCeEecCCCCcCccCCCCCCceeEEEeCCcCce---eeeecCCCeEeCC
Q 033496 39 VGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTL---LMYIRGATSVQCS 86 (118)
Q Consensus 39 rGA~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtl---LmYP~GA~sVrCs 86 (118)
-+++-|-|..|+..-.+- --+|.--+.|+.|..- ---|.|...|||+
T Consensus 76 g~~PmvtCRVCq~~i~~e-gk~~QHVVKC~~CnEATPIrnAPpGKKYVRCP 125 (275)
T KOG4684|consen 76 GQFPMVTCRVCQVAISLE-GKNQQHVVKCHSCNEATPIRNAPPGKKYVRCP 125 (275)
T ss_pred CCCceEeehhhhHHhccc-cccceeeEeecccCccccCCCCCCCCceeecC
Confidence 355566777776544331 1244444567766542 2356677777777
No 92
>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=25.43 E-value=77 Score=20.31 Aligned_cols=9 Identities=22% Similarity=0.719 Sum_probs=3.8
Q ss_pred cCCCCcCcc
Q 033496 46 CAVCNAVTA 54 (118)
Q Consensus 46 C~~C~tVn~ 54 (118)
|+.|++.|-
T Consensus 25 C~~C~~hNG 33 (54)
T PF10058_consen 25 CSKCFSHNG 33 (54)
T ss_pred Ccccchhhc
Confidence 444444443
No 93
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=25.20 E-value=41 Score=30.13 Aligned_cols=35 Identities=17% Similarity=0.333 Sum_probs=26.4
Q ss_pred CCCCceeEecCCCCeeEeecCCCCeEecCCCCcCccCC
Q 033496 19 ANGAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVP 56 (118)
Q Consensus 19 ~~~~~sQlvC~GCr~lL~YprGA~sVrC~~C~tVn~vp 56 (118)
.+.+++...|.+|..+..-. ...+|+.|++--.+.
T Consensus 214 ~~~~~~~~~C~~C~~~~~~~---~~~~CpRC~~~Ly~r 248 (418)
T COG2995 214 TGAREGLRSCLCCHYILPHD---AEPRCPRCGSKLYVR 248 (418)
T ss_pred CCCcccceecccccccCCHh---hCCCCCCCCChhhcc
Confidence 67788889999998776544 677888888765543
No 94
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.07 E-value=47 Score=33.12 Aligned_cols=55 Identities=16% Similarity=0.356 Sum_probs=39.9
Q ss_pred CceeEecCCCCeeEeecCCCCeEecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCccccccc
Q 033496 22 AQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (118)
Q Consensus 22 ~~sQlvC~GCr~lL~YprGA~sVrC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~e 96 (118)
+.+.-.|..|...+ ...+|+.|.+.|. ....|..|++..- ...|+.|.+.+....
T Consensus 623 EVg~RfCpsCG~~t------~~frCP~CG~~Te--------~i~fCP~CG~~~~------~y~CPKCG~El~~~s 677 (1121)
T PRK04023 623 EIGRRKCPSCGKET------FYRRCPFCGTHTE--------PVYRCPRCGIEVE------EDECEKCGREPTPYS 677 (1121)
T ss_pred cccCccCCCCCCcC------CcccCCCCCCCCC--------cceeCccccCcCC------CCcCCCCCCCCCccc
Confidence 34555899999984 5689999999853 2358999977643 145999999866443
No 95
>PRK11827 hypothetical protein; Provisional
Probab=24.73 E-value=95 Score=20.63 Aligned_cols=31 Identities=16% Similarity=0.279 Sum_probs=23.4
Q ss_pred EEEeCCcCceeeeecCCCeEeCCCCCccccc
Q 033496 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNLA 94 (118)
Q Consensus 64 ql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v 94 (118)
-+.|-.|+.-|.|=.++....|..|+-.-.+
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYPI 38 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFPL 38 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeeccc
Confidence 4678888888888777777888888766544
No 96
>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=24.58 E-value=76 Score=24.13 Aligned_cols=36 Identities=17% Similarity=0.298 Sum_probs=30.1
Q ss_pred CCceeEecCCCCeeEeecCCCCeEecCCCCcCccCC
Q 033496 21 GAQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVP 56 (118)
Q Consensus 21 ~~~sQlvC~GCr~lL~YprGA~sVrC~~C~tVn~vp 56 (118)
.-.+.++|-.|...+.|..-..--.|+.|+......
T Consensus 108 ~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVELTHPERLPPCPKCGHTEFTR 143 (146)
T ss_pred ecCceEecccCCCEEEecCCCcCCCCCCCCCCeeee
Confidence 456889999999999988877788999999887654
No 97
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=24.53 E-value=35 Score=19.49 Aligned_cols=21 Identities=38% Similarity=0.880 Sum_probs=15.3
Q ss_pred eCCCCCcccccccccccchhh
Q 033496 84 QCSCCHTVNLALEGCTRQLWE 104 (118)
Q Consensus 84 rCs~C~tVt~v~e~~~r~~~~ 104 (118)
+|+.|..|-.-.++..+.-|.
T Consensus 11 ~C~~C~~~~YCs~~Cq~~~w~ 31 (37)
T PF01753_consen 11 RCSRCKSVYYCSEECQRADWP 31 (37)
T ss_dssp EETTTSSSEESSHHHHHHHHH
T ss_pred cCCCCCCEEecCHHHHHHHHH
Confidence 777787777777777776663
No 98
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.00 E-value=29 Score=18.87 Aligned_cols=23 Identities=22% Similarity=0.530 Sum_probs=13.3
Q ss_pred EecCCCCcCccCCCCCCceeEEEeCCcCce
Q 033496 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTL 73 (118)
Q Consensus 44 VrC~~C~tVn~vp~~~~~~aql~CGgCrtl 73 (118)
+.|+.|.+.+.. ..-.|..|..-
T Consensus 3 ~~Cp~Cg~~~~~-------~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP-------DAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc-------ccccChhhCCC
Confidence 467777775431 34566666554
No 99
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=23.93 E-value=48 Score=19.89 Aligned_cols=25 Identities=28% Similarity=0.711 Sum_probs=12.4
Q ss_pred ecCC--CCeeEeecCCCCe--EecCCCCc
Q 033496 27 VCSG--CRNLLLYPVGATS--VCCAVCNA 51 (118)
Q Consensus 27 vC~G--Cr~lL~YprGA~s--VrC~~C~t 51 (118)
.|-+ |..++....|... |+|..|++
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 48 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGT 48 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCS
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCC
Confidence 5644 7777777777666 77776654
No 100
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=23.75 E-value=38 Score=22.66 Aligned_cols=24 Identities=21% Similarity=0.527 Sum_probs=14.6
Q ss_pred EecCCCCeeEeecCCCCeEecCCCCcCccC
Q 033496 26 LVCSGCRNLLLYPVGATSVCCAVCNAVTAV 55 (118)
Q Consensus 26 lvC~GCr~lL~YprGA~sVrC~~C~tVn~v 55 (118)
..|..|+.|+. .-+|+.|...+.+
T Consensus 4 kAC~~C~~i~~------~~~CP~Cgs~~~T 27 (61)
T PRK08351 4 KACRHCHYITT------EDRCPVCGSRDLS 27 (61)
T ss_pred hhhhhCCcccC------CCcCCCCcCCccc
Confidence 46777777762 1157777776643
No 101
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=23.24 E-value=1e+02 Score=18.01 Aligned_cols=8 Identities=38% Similarity=0.496 Sum_probs=3.3
Q ss_pred eEEEeCCc
Q 033496 63 AQLVCGGC 70 (118)
Q Consensus 63 aql~CGgC 70 (118)
++++|..|
T Consensus 20 ~~~~C~~C 27 (33)
T PF08792_consen 20 DYEVCIFC 27 (33)
T ss_pred CeEEcccC
Confidence 34444444
No 102
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.20 E-value=52 Score=23.71 Aligned_cols=30 Identities=27% Similarity=0.639 Sum_probs=19.5
Q ss_pred eEEEeCCcCceeeeecCCCe-EeCCCCCccccc
Q 033496 63 AQLVCGGCHTLLMYIRGATS-VQCSCCHTVNLA 94 (118)
Q Consensus 63 aql~CGgCrtlLmYP~GA~s-VrCs~C~tVt~v 94 (118)
+...|..|... |+..... .+|+.|+.-+.-
T Consensus 70 ~~~~C~~Cg~~--~~~~~~~~~~CP~Cgs~~~~ 100 (117)
T PRK00564 70 VELECKDCSHV--FKPNALDYGVCEKCHSKNVI 100 (117)
T ss_pred CEEEhhhCCCc--cccCCccCCcCcCCCCCceE
Confidence 67788888833 4444333 459999986543
No 103
>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=22.64 E-value=1.2e+02 Score=26.75 Aligned_cols=22 Identities=23% Similarity=0.478 Sum_probs=10.8
Q ss_pred EEEeCCcCceeeeecCCCeEeCCCCCc
Q 033496 64 QLVCGGCHTLLMYIRGATSVQCSCCHT 90 (118)
Q Consensus 64 ql~CGgCrtlLmYP~GA~sVrCs~C~t 90 (118)
.+.|.-|.-..-+|. +|+.|+.
T Consensus 240 ~l~Ch~Cg~~~~~~~-----~Cp~C~s 261 (505)
T TIGR00595 240 KLRCHYCGYQEPIPK-----TCPQCGS 261 (505)
T ss_pred eEEcCCCcCcCCCCC-----CCCCCCC
Confidence 455555554333332 5666654
No 104
>PRK11032 hypothetical protein; Provisional
Probab=22.21 E-value=1e+02 Score=23.98 Aligned_cols=35 Identities=23% Similarity=0.509 Sum_probs=25.6
Q ss_pred eeEEEeCCcCceeeeecCCCeEeCCCCCccccccc
Q 033496 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALE 96 (118)
Q Consensus 62 ~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt~v~e 96 (118)
.+.|+|-+|.-.+-|-.-..--.|+-|+.....++
T Consensus 122 ~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F~R~ 156 (160)
T PRK11032 122 LGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQRR 156 (160)
T ss_pred cceEEecCCCCEEEecCCCcCCCCCCCCCCeeeeC
Confidence 46788888888887777777777888877766544
No 105
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=22.03 E-value=71 Score=19.34 Aligned_cols=22 Identities=27% Similarity=0.862 Sum_probs=11.2
Q ss_pred EeCCcCceeeeecCCCeEeCCCCCcc
Q 033496 66 VCGGCHTLLMYIRGATSVQCSCCHTV 91 (118)
Q Consensus 66 ~CGgCrtlLmYP~GA~sVrCs~C~tV 91 (118)
.|.+|+..+ .| ...+|..|...
T Consensus 2 ~Cd~C~~~i---~G-~ry~C~~C~d~ 23 (43)
T cd02340 2 ICDGCQGPI---VG-VRYKCLVCPDY 23 (43)
T ss_pred CCCCCCCcC---cC-CeEECCCCCCc
Confidence 456666511 33 45666666543
No 106
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=21.71 E-value=86 Score=18.55 Aligned_cols=24 Identities=17% Similarity=0.423 Sum_probs=12.0
Q ss_pred eCCcCceeeeecCCCeEeCCCCCcc
Q 033496 67 CGGCHTLLMYIRGATSVQCSCCHTV 91 (118)
Q Consensus 67 CGgCrtlLmYP~GA~sVrCs~C~tV 91 (118)
|+.|+.. .|-...-..-|..|+++
T Consensus 11 C~~C~~~-~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 11 CPVCGSR-WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCCCCe-EeEccCCEEEhhhCceE
Confidence 5555555 44444445555555544
No 107
>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=21.27 E-value=50 Score=21.43 Aligned_cols=20 Identities=25% Similarity=0.564 Sum_probs=11.4
Q ss_pred CceeEecCCCCeeEeecCCC
Q 033496 22 AQSQLVCSGCRNLLLYPVGA 41 (118)
Q Consensus 22 ~~sQlvC~GCr~lL~YprGA 41 (118)
+..+.+|.+|.++|..-..+
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 46788999999999876654
No 108
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=20.99 E-value=81 Score=27.50 Aligned_cols=12 Identities=25% Similarity=0.858 Sum_probs=5.4
Q ss_pred EecCCCCcCccC
Q 033496 44 VCCAVCNAVTAV 55 (118)
Q Consensus 44 VrC~~C~tVn~v 55 (118)
+.|..|+.+...
T Consensus 11 ~~C~~Cd~l~~~ 22 (419)
T PRK15103 11 ILCPQCDMLVAL 22 (419)
T ss_pred ccCCCCCceeec
Confidence 334444444443
No 109
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.89 E-value=1.3e+02 Score=27.55 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=15.0
Q ss_pred cCCCCeeEeecCCCCeEecCCCCcCcc
Q 033496 28 CSGCRNLLLYPVGATSVCCAVCNAVTA 54 (118)
Q Consensus 28 C~GCr~lL~YprGA~sVrC~~C~tVn~ 54 (118)
|..|..-|.|...-....|..|.....
T Consensus 393 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 393 CPHCDASLTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred CCCCCCceeEECCCCeEECCCCcCCCC
Confidence 444555556655555556666665443
No 110
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=20.35 E-value=48 Score=18.48 Aligned_cols=12 Identities=17% Similarity=0.396 Sum_probs=6.8
Q ss_pred CCeEeCCCCCcc
Q 033496 80 ATSVQCSCCHTV 91 (118)
Q Consensus 80 A~sVrCs~C~tV 91 (118)
....+|+.|+++
T Consensus 12 ~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 12 ESAKFCPHCGYD 23 (26)
T ss_pred hhcCcCCCCCCC
Confidence 344566666654
No 111
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=20.07 E-value=38 Score=25.57 Aligned_cols=33 Identities=30% Similarity=0.556 Sum_probs=29.5
Q ss_pred eeEecCCCCeeEeecCCCCeEecCCCCcCccCC
Q 033496 24 SQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVP 56 (118)
Q Consensus 24 sQlvC~GCr~lL~YprGA~sVrC~~C~tVn~vp 56 (118)
+-+-|+.|..||.-+.-...|-|..|.....+.
T Consensus 6 ~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~ 38 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVS 38 (116)
T ss_pred CcchhhhhhhhcccccccCceEeccccccCCHH
Confidence 456799999999999999999999999998765
No 112
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=20.02 E-value=58 Score=22.24 Aligned_cols=42 Identities=24% Similarity=0.586 Sum_probs=14.7
Q ss_pred ecCCCCcCccCCCCCCceeEEEeCCcCceeeeecCCCeEeCCCCCccc
Q 033496 45 CCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVN 92 (118)
Q Consensus 45 rC~~C~tVn~vp~~~~~~aql~CGgCrtlLmYP~GA~sVrCs~C~tVt 92 (118)
||+.|..+-..|---..=.|+-|..|-.- -.|. .|++|++=.
T Consensus 9 rCs~C~~~l~~pv~l~~CeH~fCs~Ci~~---~~~~---~CPvC~~Pa 50 (65)
T PF14835_consen 9 RCSICFDILKEPVCLGGCEHIFCSSCIRD---CIGS---ECPVCHTPA 50 (65)
T ss_dssp S-SSS-S--SS-B---SSS--B-TTTGGG---GTTT---B-SSS--B-
T ss_pred CCcHHHHHhcCCceeccCccHHHHHHhHH---hcCC---CCCCcCChH
Confidence 67777776544321123457777777533 1222 488888643
Done!