Query 032227
Match_columns 145
No_of_seqs 100 out of 132
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 11:17:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032227.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032227hhsearch_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 8.7E-15 1.9E-19 88.7 2.7 31 25-55 1-31 (31)
2 PF06943 zf-LSD1: LSD1 zinc fi 99.5 3E-14 6.6E-19 83.2 2.2 25 28-52 1-25 (25)
3 TIGR01053 LSD1 zinc finger dom 99.4 5.6E-14 1.2E-18 85.2 2.1 30 64-93 1-30 (31)
4 PF06943 zf-LSD1: LSD1 zinc fi 99.4 1.3E-13 2.9E-18 80.5 2.1 25 67-91 1-25 (25)
5 PF09788 Tmemb_55A: Transmembr 97.8 0.00023 5E-09 60.8 9.8 112 22-134 62-191 (256)
6 PF10122 Mu-like_Com: Mu-like 95.9 0.0029 6.2E-08 42.7 0.8 39 102-140 4-44 (51)
7 PF10122 Mu-like_Com: Mu-like 94.8 0.014 3.1E-07 39.3 1.2 34 63-96 3-38 (51)
8 PRK14890 putative Zn-ribbon RN 93.9 0.042 9.2E-07 38.0 2.0 53 61-129 4-57 (59)
9 PF01667 Ribosomal_S27e: Ribos 93.6 0.083 1.8E-06 35.9 3.0 42 82-124 7-48 (55)
10 PLN00209 ribosomal protein S27 92.8 0.19 4.1E-06 37.1 4.0 46 82-128 36-81 (86)
11 PTZ00083 40S ribosomal protein 92.6 0.21 4.5E-06 36.8 4.1 44 82-126 35-78 (85)
12 PRK00415 rps27e 30S ribosomal 91.9 0.12 2.5E-06 35.8 1.9 38 82-120 11-48 (59)
13 PF11331 DUF3133: Protein of u 91.5 0.2 4.4E-06 33.0 2.6 37 40-76 3-43 (46)
14 KOG1779 40s ribosomal protein 91.1 0.47 1E-05 35.0 4.5 45 82-127 34-78 (84)
15 TIGR02098 MJ0042_CXXC MJ0042 f 90.1 0.26 5.7E-06 29.5 2.1 30 83-112 3-35 (38)
16 COG2051 RPS27A Ribosomal prote 90.1 0.39 8.5E-06 34.1 3.2 39 82-121 19-57 (67)
17 PLN00209 ribosomal protein S27 89.5 0.29 6.3E-06 36.2 2.3 40 43-84 36-75 (86)
18 PF13719 zinc_ribbon_5: zinc-r 89.2 0.43 9.3E-06 29.2 2.6 12 118-129 23-34 (37)
19 PTZ00083 40S ribosomal protein 89.1 0.33 7.1E-06 35.8 2.3 39 43-83 35-73 (85)
20 PF09788 Tmemb_55A: Transmembr 88.9 0.64 1.4E-05 40.1 4.3 65 31-95 111-190 (256)
21 PF13719 zinc_ribbon_5: zinc-r 88.8 0.36 7.9E-06 29.6 2.1 9 102-110 25-33 (37)
22 PF01667 Ribosomal_S27e: Ribos 88.0 0.42 9.2E-06 32.5 2.1 38 43-82 7-44 (55)
23 PF11331 DUF3133: Protein of u 88.0 0.67 1.4E-05 30.5 3.0 37 79-115 3-44 (46)
24 PRK00398 rpoP DNA-directed RNA 87.5 0.74 1.6E-05 28.9 2.9 23 105-127 6-28 (46)
25 PRK00415 rps27e 30S ribosomal 87.2 0.35 7.5E-06 33.5 1.4 34 44-79 12-45 (59)
26 PRK00398 rpoP DNA-directed RNA 85.9 1.3 2.9E-05 27.8 3.5 26 65-90 4-29 (46)
27 PF13717 zinc_ribbon_4: zinc-r 83.3 1.8 3.9E-05 26.5 3.1 13 83-95 3-15 (36)
28 COG2888 Predicted Zn-ribbon RN 82.9 1.1 2.3E-05 31.4 2.2 50 65-129 10-59 (61)
29 COG2051 RPS27A Ribosomal prote 81.8 1.5 3.3E-05 31.1 2.7 38 43-82 19-56 (67)
30 PF13717 zinc_ribbon_4: zinc-r 80.1 1.9 4E-05 26.4 2.4 13 44-56 3-15 (36)
31 PRK14890 putative Zn-ribbon RN 79.1 2 4.3E-05 29.8 2.5 53 22-91 4-57 (59)
32 KOG1779 40s ribosomal protein 79.1 3 6.5E-05 30.8 3.6 40 43-84 34-73 (84)
33 TIGR02098 MJ0042_CXXC MJ0042 f 78.9 4.9 0.00011 23.9 3.9 29 102-130 2-35 (38)
34 PF12773 DZR: Double zinc ribb 77.9 1.1 2.3E-05 28.1 0.8 28 64-92 12-39 (50)
35 PF04690 YABBY: YABBY protein; 69.8 3.7 8.1E-05 33.4 2.3 40 43-82 12-54 (170)
36 PF05495 zf-CHY: CHY zinc fing 67.7 8.3 0.00018 26.5 3.4 29 100-128 39-69 (71)
37 PF04810 zf-Sec23_Sec24: Sec23 67.4 4.3 9.2E-05 25.1 1.7 19 116-134 20-38 (40)
38 smart00661 RPOL9 RNA polymeras 66.4 6.3 0.00014 24.5 2.4 31 105-135 3-35 (52)
39 KOG4684 Uncharacterized conser 66.3 5.1 0.00011 34.7 2.5 75 38-132 75-152 (275)
40 PRK05580 primosome assembly pr 64.5 13 0.00027 35.2 5.0 68 32-118 368-437 (679)
41 KOG4684 Uncharacterized conser 63.3 23 0.0005 30.8 5.9 109 25-134 80-203 (275)
42 PRK14714 DNA polymerase II lar 62.8 5.2 0.00011 41.4 2.3 54 61-128 664-717 (1337)
43 PF07754 DUF1610: Domain of un 61.6 6.2 0.00014 22.8 1.6 9 80-88 14-22 (24)
44 TIGR00595 priA primosomal prot 60.7 10 0.00022 34.6 3.5 28 104-131 224-251 (505)
45 PRK05580 primosome assembly pr 60.3 9.2 0.0002 36.1 3.3 51 72-133 369-421 (679)
46 PF05129 Elf1: Transcription e 60.0 14 0.0003 26.3 3.5 39 81-119 21-63 (81)
47 PRK14873 primosome assembly pr 55.8 14 0.0003 35.3 3.6 68 29-117 368-437 (665)
48 COG4357 Zinc finger domain con 55.7 3 6.5E-05 31.9 -0.6 27 25-51 62-88 (105)
49 PF02150 RNA_POL_M_15KD: RNA p 54.5 9.1 0.0002 23.3 1.5 31 104-134 3-34 (35)
50 KOG1546 Metacaspase involved i 53.9 5.2 0.00011 36.2 0.5 28 66-95 6-33 (362)
51 PF04690 YABBY: YABBY protein; 53.1 28 0.00061 28.4 4.6 48 59-120 7-54 (170)
52 TIGR00595 priA primosomal prot 52.4 19 0.00041 32.8 3.9 61 38-117 207-268 (505)
53 PF08271 TF_Zn_Ribbon: TFIIB z 52.3 6.9 0.00015 24.2 0.8 17 113-129 12-28 (43)
54 TIGR01384 TFS_arch transcripti 51.4 11 0.00025 26.7 1.9 26 105-132 3-28 (104)
55 PF11023 DUF2614: Protein of u 50.9 7.9 0.00017 30.0 1.0 32 80-115 67-98 (114)
56 COG4416 Com Mu-like prophage p 50.6 4.3 9.4E-05 28.2 -0.4 30 65-94 5-36 (60)
57 PRK14714 DNA polymerase II lar 50.0 12 0.00026 38.9 2.4 55 22-91 664-718 (1337)
58 COG1198 PriA Primosomal protei 47.5 24 0.00053 34.4 3.9 41 42-94 434-474 (730)
59 PRK14873 primosome assembly pr 47.2 22 0.00047 34.0 3.5 48 71-129 370-419 (665)
60 PF09082 DUF1922: Domain of un 47.1 29 0.00062 24.7 3.3 33 102-136 3-35 (68)
61 COG1096 Predicted RNA-binding 46.7 31 0.00068 28.7 4.0 29 99-129 146-174 (188)
62 COG4357 Zinc finger domain con 45.4 4.7 0.0001 30.8 -0.9 28 64-91 62-89 (105)
63 KOG1546 Metacaspase involved i 43.9 11 0.00024 34.1 1.1 26 28-55 7-32 (362)
64 TIGR00155 pqiA_fam integral me 37.8 25 0.00054 31.5 2.3 31 82-112 13-43 (403)
65 COG1096 Predicted RNA-binding 36.0 32 0.00069 28.6 2.5 30 60-91 143-174 (188)
66 PF12172 DUF35_N: Rubredoxin-l 35.5 25 0.00055 20.9 1.4 21 27-51 13-33 (37)
67 PRK14559 putative protein seri 35.2 20 0.00044 34.2 1.4 50 44-112 2-51 (645)
68 PF14634 zf-RING_5: zinc-RING 34.8 5.5 0.00012 24.5 -1.7 24 62-89 20-43 (44)
69 PF09297 zf-NADH-PPase: NADH p 33.4 48 0.001 19.2 2.3 23 105-127 6-28 (32)
70 PRK04023 DNA polymerase II lar 33.2 26 0.00056 35.9 1.8 56 61-135 623-678 (1121)
71 PF02591 DUF164: Putative zinc 31.9 36 0.00078 21.9 1.8 29 24-52 21-55 (56)
72 smart00731 SprT SprT homologue 30.4 56 0.0012 24.6 2.9 13 101-113 132-144 (146)
73 PF13901 DUF4206: Domain of un 30.1 24 0.00052 28.5 0.8 28 104-131 154-183 (202)
74 PF05458 Siva: Cd27 binding pr 30.0 19 0.00041 29.1 0.2 63 37-110 105-172 (175)
75 smart00659 RPOLCX RNA polymera 29.7 1.1E+02 0.0025 19.4 3.8 32 83-117 3-34 (44)
76 PRK02935 hypothetical protein; 29.1 37 0.00081 26.2 1.7 32 79-114 67-98 (110)
77 cd00029 C1 Protein kinase C co 28.6 26 0.00057 21.0 0.6 26 104-130 13-38 (50)
78 PF07282 OrfB_Zn_ribbon: Putat 28.2 74 0.0016 20.8 2.8 14 81-94 27-40 (69)
79 PF00130 C1_1: Phorbol esters/ 28.2 41 0.00088 20.8 1.5 28 103-131 12-39 (53)
80 PRK04351 hypothetical protein; 27.8 51 0.0011 25.8 2.3 15 101-115 131-145 (149)
81 COG1198 PriA Primosomal protei 27.7 94 0.002 30.5 4.4 52 72-134 423-476 (730)
82 smart00109 C1 Protein kinase C 27.1 24 0.00051 20.8 0.2 24 104-129 13-36 (49)
83 PF02318 FYVE_2: FYVE-type zin 25.7 14 0.0003 27.3 -1.1 59 62-136 52-110 (118)
84 KOG2907 RNA polymerase I trans 25.6 22 0.00047 27.7 -0.2 36 102-137 7-42 (116)
85 smart00647 IBR In Between Ring 25.2 87 0.0019 19.5 2.6 25 104-128 20-48 (64)
86 TIGR01206 lysW lysine biosynth 25.1 73 0.0016 21.4 2.3 7 84-90 4-10 (54)
87 PRK15103 paraquat-inducible me 24.7 44 0.00095 30.1 1.6 30 83-112 11-40 (419)
88 PF04032 Rpr2: RNAse P Rpr2/Rp 24.5 48 0.001 22.3 1.4 20 22-41 43-62 (85)
89 PF11781 RRN7: RNA polymerase 24.2 76 0.0016 19.4 2.1 24 105-129 11-34 (36)
90 smart00782 PhnA_Zn_Ribbon PhnA 24.0 32 0.0007 22.5 0.5 27 4-33 18-44 (47)
91 PRK11827 hypothetical protein; 23.7 1E+02 0.0022 21.2 2.9 32 102-133 8-39 (60)
92 KOG2907 RNA polymerase I trans 23.3 32 0.00069 26.8 0.4 33 24-56 6-38 (116)
93 PF10571 UPF0547: Uncharacteri 23.2 34 0.00074 19.8 0.4 21 105-129 3-23 (26)
94 PF05180 zf-DNL: DNL zinc fing 23.0 30 0.00065 24.3 0.2 30 26-55 5-41 (66)
95 PF14369 zf-RING_3: zinc-finge 22.8 65 0.0014 19.6 1.6 23 67-89 5-28 (35)
96 PF10058 DUF2296: Predicted in 22.6 82 0.0018 20.9 2.2 9 46-54 25-33 (54)
97 PF07295 DUF1451: Protein of u 22.3 81 0.0017 24.8 2.5 33 62-94 110-142 (146)
98 PF14599 zinc_ribbon_6: Zinc-r 21.8 1.4E+02 0.003 20.5 3.3 31 98-128 26-56 (61)
99 PRK14892 putative transcriptio 21.4 95 0.0021 23.1 2.6 9 81-89 20-28 (99)
100 PF08792 A2L_zn_ribbon: A2L zi 20.9 1E+02 0.0022 18.6 2.2 11 27-37 5-15 (33)
101 COG2023 RPR2 RNase P subunit R 20.6 66 0.0014 24.6 1.6 44 62-117 54-97 (105)
102 PF13901 DUF4206: Domain of un 20.4 51 0.0011 26.6 1.0 28 66-93 154-183 (202)
103 PRK03564 formate dehydrogenase 20.2 88 0.0019 27.6 2.5 11 43-53 187-197 (309)
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=99.51 E-value=8.7e-15 Score=88.74 Aligned_cols=31 Identities=61% Similarity=1.243 Sum_probs=23.9
Q ss_pred eeeccCccceeecccCCCeeecCCCCcccCC
Q 032227 25 QLVCSGCRNLLLYPVGATSVCCAVCNAVTAV 55 (145)
Q Consensus 25 QlvC~gCr~lL~YprGA~~VrC~~C~tvn~v 55 (145)
|++|++||++|+||+||++|||+.|++||.+
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 6778888888888888888888888877753
No 2
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=99.45 E-value=3e-14 Score=83.21 Aligned_cols=25 Identities=64% Similarity=1.364 Sum_probs=16.8
Q ss_pred ccCccceeecccCCCeeecCCCCcc
Q 032227 28 CSGCRNLLLYPVGATSVCCAVCNAV 52 (145)
Q Consensus 28 C~gCr~lL~YprGA~~VrC~~C~tv 52 (145)
|+|||++|+||+||++|||+.|++|
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 5666666666666666666666664
No 3
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=99.43 E-value=5.6e-14 Score=85.20 Aligned_cols=30 Identities=73% Similarity=1.381 Sum_probs=21.0
Q ss_pred eEEeCcccceEeeecCCceEECCCCCcccc
Q 032227 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVNL 93 (145)
Q Consensus 64 ql~CGgCr~lLmYP~GA~sVrC~~C~tVn~ 93 (145)
|++|++||++|+||+||.+|||+.|++||.
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 566777777777777777777777777664
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=99.39 E-value=1.3e-13 Score=80.51 Aligned_cols=25 Identities=80% Similarity=1.666 Sum_probs=15.8
Q ss_pred eCcccceEeeecCCceEECCCCCcc
Q 032227 67 CGGCHTLLMYIRGATSVQCSCCHTV 91 (145)
Q Consensus 67 CGgCr~lLmYP~GA~sVrC~~C~tV 91 (145)
||+||++||||+||+||||+.|++|
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 5666666666666666666666654
No 5
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=97.77 E-value=0.00023 Score=60.80 Aligned_cols=112 Identities=23% Similarity=0.534 Sum_probs=86.7
Q ss_pred ccceeeccCccceeeccc--CCCeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCC--CCcc-ccccc
Q 032227 22 AQSQLVCSGCRNLLLYPV--GATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSC--CHTV-NLALE 96 (145)
Q Consensus 22 ~~sQlvC~gCr~lL~Ypr--GA~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~--C~tV-n~v~~ 96 (145)
.+--+.|.=|+.++--.- ----|+|..||-.|...++.....-+.|- |+-||+-...++-+-|+. |..| |+.+.
T Consensus 62 ~~p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRCP-CNCLLICk~sS~rIaCPRp~CkRiI~L~~~ 140 (256)
T PF09788_consen 62 GAPVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRCP-CNCLLICKSSSQRIACPRPNCKRIINLGPS 140 (256)
T ss_pred CCceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEecC-CceEEEeecccccccCCCCCCcceEEeCCc
Confidence 345688999998876542 22358999999999876555556677774 788999999999999988 9877 44332
Q ss_pred -----------cceeEEEEcCCcCeEEEEecCC--ceEeCCCCCceeeccC
Q 032227 97 -----------ANQVAHVNCGNCRMLLMYQYGA--RSVKCAVCNFVTAVGA 134 (145)
Q Consensus 97 -----------~~q~~~v~Cg~Crt~LmyP~GA--~sVkCa~C~~VT~i~~ 134 (145)
......++||+|+.+.+++.=. .-.||+-|+.|..|+.
T Consensus 141 ~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~ 191 (256)
T PF09788_consen 141 HQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGP 191 (256)
T ss_pred cCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccccc
Confidence 2355789999999999999766 5569999999999974
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=95.93 E-value=0.0029 Score=42.68 Aligned_cols=39 Identities=28% Similarity=0.613 Sum_probs=26.5
Q ss_pred EEEcCCcCeEEEEe--cCCceEeCCCCCceeeccCCCCccc
Q 032227 102 HVNCGNCRMLLMYQ--YGARSVKCAVCNFVTAVGASTSTTE 140 (145)
Q Consensus 102 ~v~Cg~Crt~LmyP--~GA~sVkCa~C~~VT~i~~~~~~~~ 140 (145)
.++|++|+.+|+.- +.....||+.|.+++.|++.+...|
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~~~~~ 44 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATSPEPE 44 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceEeccCCCCC
Confidence 46777777777774 4445777888888777776654443
No 7
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=94.77 E-value=0.014 Score=39.33 Aligned_cols=34 Identities=26% Similarity=0.591 Sum_probs=26.5
Q ss_pred eeEEeCcccceEeee--cCCceEECCCCCccccccc
Q 032227 63 AQLVCGGCHTLLMYI--RGATSVQCSCCHTVNLALE 96 (145)
Q Consensus 63 aql~CGgCr~lLmYP--~GA~sVrC~~C~tVn~v~~ 96 (145)
-.+.|++|+.+|+.- ..-..+||+.|.++|.+..
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 367899999998885 3335889999999998754
No 8
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=93.88 E-value=0.042 Score=38.01 Aligned_cols=53 Identities=26% Similarity=0.590 Sum_probs=41.2
Q ss_pred cceeEEeCcccceEeeecC-CceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCce
Q 032227 61 EMAQLVCGGCHTLLMYIRG-ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV 129 (145)
Q Consensus 61 q~aql~CGgCr~lLmYP~G-A~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~V 129 (145)
++.-.+|-+|...| .|.+ +..+.|+.|..+.. .+|..||.+ +..++|+.|+|.
T Consensus 4 ~~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I---------~RC~~CRk~------~~~Y~CP~CGF~ 57 (59)
T PRK14890 4 MMEPPKCTSCGIEI-APREKAVKFLCPNCGEVII---------YRCEKCRKQ------SNPYTCPKCGFE 57 (59)
T ss_pred cccCccccCCCCcc-cCCCccCEeeCCCCCCeeE---------eechhHHhc------CCceECCCCCCc
Confidence 34455799999888 5666 99999999976533 569999986 467899999885
No 9
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=93.56 E-value=0.083 Score=35.92 Aligned_cols=42 Identities=19% Similarity=0.426 Sum_probs=27.8
Q ss_pred eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCC
Q 032227 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCA 124 (145)
Q Consensus 82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa 124 (145)
.|+|+.|..++.+-+.. ...+.|.+|.++|..|.|-..-.=.
T Consensus 7 ~VkCp~C~~~q~vFSha-~t~V~C~~Cg~~L~~PtGGKa~l~~ 48 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHA-QTVVKCVVCGTVLAQPTGGKARLTE 48 (55)
T ss_dssp EEE-TTT-SEEEEETT--SS-EE-SSSTSEEEEE-SSSEEESS
T ss_pred EEECCCCCCeeEEEecC-CeEEEcccCCCEecCCCCcCeEEeC
Confidence 58999999998875433 3479999999999999997654433
No 10
>PLN00209 ribosomal protein S27; Provisional
Probab=92.75 E-value=0.19 Score=37.12 Aligned_cols=46 Identities=24% Similarity=0.611 Sum_probs=32.9
Q ss_pred eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCc
Q 032227 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNF 128 (145)
Q Consensus 82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~ 128 (145)
.|+|+.|..++.+-+. -...+.|..|.++|..|.|-....=.-|.|
T Consensus 36 ~VkCp~C~n~q~VFSh-A~t~V~C~~Cg~~L~~PTGGKa~l~~gc~f 81 (86)
T PLN00209 36 DVKCQGCFNITTVFSH-SQTVVVCGSCQTVLCQPTGGKARLTEGCSF 81 (86)
T ss_pred EEECCCCCCeeEEEec-CceEEEccccCCEeeccCCCCeEecCCceE
Confidence 5788888888776543 334788999999999998877655444443
No 11
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=92.62 E-value=0.21 Score=36.85 Aligned_cols=44 Identities=23% Similarity=0.520 Sum_probs=31.3
Q ss_pred eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCC
Q 032227 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVC 126 (145)
Q Consensus 82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C 126 (145)
.|+|+.|..++.+-+.. ...+.|.+|.++|.-|.|-....=.-|
T Consensus 35 ~VkCp~C~n~q~VFShA-~t~V~C~~Cg~~L~~PTGGKa~l~~gc 78 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHA-QTVVLCGGCSSQLCQPTGGKAKLTEGC 78 (85)
T ss_pred EEECCCCCCeeEEEecC-ceEEEccccCCEeeccCCCCeEecCCc
Confidence 47888888887765433 347888888888888888766543333
No 12
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=91.87 E-value=0.12 Score=35.76 Aligned_cols=38 Identities=21% Similarity=0.436 Sum_probs=26.3
Q ss_pred eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCce
Q 032227 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120 (145)
Q Consensus 82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~s 120 (145)
.|+|+.|..++.+-+. -...+.|..|.++|.-|.|-..
T Consensus 11 ~VkCp~C~n~q~vFsh-a~t~V~C~~Cg~~L~~PtGGKa 48 (59)
T PRK00415 11 KVKCPDCGNEQVVFSH-ASTVVRCLVCGKTLAEPTGGKA 48 (59)
T ss_pred EEECCCCCCeEEEEec-CCcEEECcccCCCcccCCCcce
Confidence 4777777777765433 2336788888888888887544
No 13
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=91.46 E-value=0.2 Score=32.96 Aligned_cols=37 Identities=30% Similarity=0.726 Sum_probs=18.8
Q ss_pred CCCeeecCCCCcccCCCCC----CCcceeEEeCcccceEee
Q 032227 40 GATSVCCAVCNAVTAVPPP----GTEMAQLVCGGCHTLLMY 76 (145)
Q Consensus 40 GA~~VrC~~C~tvn~vpp~----~~q~aql~CGgCr~lLmY 76 (145)
||+-|-|..|..+-..|.. .....+|.||.|...|.|
T Consensus 3 GAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~ 43 (46)
T PF11331_consen 3 GAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSF 43 (46)
T ss_pred CCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEE
Confidence 5555555555555544421 112445566666655555
No 14
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=91.11 E-value=0.47 Score=34.96 Aligned_cols=45 Identities=22% Similarity=0.537 Sum_probs=30.2
Q ss_pred eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCC
Q 032227 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCN 127 (145)
Q Consensus 82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~ 127 (145)
-|||+.|..||-+-+..|. -+.|++|.+.|.-|.|-..+.=..|.
T Consensus 34 ~VkC~gc~~iT~vfSHaqt-vVvc~~c~~il~~~tggra~ls~~cs 78 (84)
T KOG1779|consen 34 DVKCPGCFKITTVFSHAQT-VVVCEGCSTILCQPTGGKAKLSEGCS 78 (84)
T ss_pred EEEcCCceEEEEEeecCce-EEEcCCCceEEEEecCCcEEecCCCc
Confidence 3667777666666544444 67888888888888887766544443
No 15
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=90.10 E-value=0.26 Score=29.51 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=15.0
Q ss_pred EECCCCCcccccccc---ceeEEEEcCCcCeEE
Q 032227 83 VQCSCCHTVNLALEA---NQVAHVNCGNCRMLL 112 (145)
Q Consensus 83 VrC~~C~tVn~v~~~---~q~~~v~Cg~Crt~L 112 (145)
++|+.|++.+.+.++ ..-..++|++|+..+
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 456666665544321 111256666666554
No 16
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=90.07 E-value=0.39 Score=34.07 Aligned_cols=39 Identities=21% Similarity=0.428 Sum_probs=28.3
Q ss_pred eEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceE
Q 032227 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSV 121 (145)
Q Consensus 82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sV 121 (145)
-|+|+-|.....+-. +-...++|..|.++|..|.|-.+.
T Consensus 19 ~VkCpdC~N~q~vFs-hast~V~C~~CG~~l~~PTGGka~ 57 (67)
T COG2051 19 RVKCPDCGNEQVVFS-HASTVVTCLICGTTLAEPTGGKAK 57 (67)
T ss_pred EEECCCCCCEEEEec-cCceEEEecccccEEEecCCCeEE
Confidence 578888887766543 333478888899999999886543
No 17
>PLN00209 ribosomal protein S27; Provisional
Probab=89.45 E-value=0.29 Score=36.16 Aligned_cols=40 Identities=30% Similarity=0.546 Sum_probs=29.9
Q ss_pred eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEE
Q 032227 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ 84 (145)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVr 84 (145)
.|+|+.|..++.+ =++....+.|.+|.++|..|.|--...
T Consensus 36 ~VkCp~C~n~q~V--FShA~t~V~C~~Cg~~L~~PTGGKa~l 75 (86)
T PLN00209 36 DVKCQGCFNITTV--FSHSQTVVVCGSCQTVLCQPTGGKARL 75 (86)
T ss_pred EEECCCCCCeeEE--EecCceEEEccccCCEeeccCCCCeEe
Confidence 4888888888876 245566788888888888888865543
No 18
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.20 E-value=0.43 Score=29.23 Aligned_cols=12 Identities=42% Similarity=1.018 Sum_probs=6.3
Q ss_pred CceEeCCCCCce
Q 032227 118 ARSVKCAVCNFV 129 (145)
Q Consensus 118 A~sVkCa~C~~V 129 (145)
...|||+.|+++
T Consensus 23 ~~~vrC~~C~~~ 34 (37)
T PF13719_consen 23 GRKVRCPKCGHV 34 (37)
T ss_pred CcEEECCCCCcE
Confidence 445555555544
No 19
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=89.05 E-value=0.33 Score=35.81 Aligned_cols=39 Identities=28% Similarity=0.603 Sum_probs=28.5
Q ss_pred eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceE
Q 032227 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSV 83 (145)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sV 83 (145)
.|+|+.|..++.+ =++....+.|.+|.++|..|.|--..
T Consensus 35 ~VkCp~C~n~q~V--FShA~t~V~C~~Cg~~L~~PTGGKa~ 73 (85)
T PTZ00083 35 DVKCPGCSQITTV--FSHAQTVVLCGGCSSQLCQPTGGKAK 73 (85)
T ss_pred EEECCCCCCeeEE--EecCceEEEccccCCEeeccCCCCeE
Confidence 4788888888776 24556678888888888888876543
No 20
>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=88.86 E-value=0.64 Score=40.12 Aligned_cols=65 Identities=22% Similarity=0.598 Sum_probs=44.0
Q ss_pred ccceeecccCCCeeecCC--CCcc-cCCCC---C-------CCcceeEEeCcccceEeeecCC--ceEECCCCCcccccc
Q 032227 31 CRNLLLYPVGATSVCCAV--CNAV-TAVPP---P-------GTEMAQLVCGGCHTLLMYIRGA--TSVQCSCCHTVNLAL 95 (145)
Q Consensus 31 Cr~lL~YprGA~~VrC~~--C~tv-n~vpp---~-------~~q~aql~CGgCr~lLmYP~GA--~sVrC~~C~tVn~v~ 95 (145)
|.-||+=..-++-|-|++ |..| |+.+. + ...+..++||+|+...+|+.=. .-.||+.|+.|..+.
T Consensus 111 CNCLLICk~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG 190 (256)
T PF09788_consen 111 CNCLLICKSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVG 190 (256)
T ss_pred CceEEEeecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceecccc
Confidence 334555555555555555 6544 44332 1 2467889999999999999655 456999999998885
No 21
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.83 E-value=0.36 Score=29.56 Aligned_cols=9 Identities=33% Similarity=0.896 Sum_probs=4.4
Q ss_pred EEEcCCcCe
Q 032227 102 HVNCGNCRM 110 (145)
Q Consensus 102 ~v~Cg~Crt 110 (145)
.++|+.|+.
T Consensus 25 ~vrC~~C~~ 33 (37)
T PF13719_consen 25 KVRCPKCGH 33 (37)
T ss_pred EEECCCCCc
Confidence 455555544
No 22
>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=88.00 E-value=0.42 Score=32.48 Aligned_cols=38 Identities=24% Similarity=0.417 Sum_probs=22.8
Q ss_pred eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCce
Q 032227 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS 82 (145)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~s 82 (145)
.|+|+.|..++.+ =++....+.|.+|.++|..|.|-..
T Consensus 7 ~VkCp~C~~~q~v--FSha~t~V~C~~Cg~~L~~PtGGKa 44 (55)
T PF01667_consen 7 DVKCPGCYNIQTV--FSHAQTVVKCVVCGTVLAQPTGGKA 44 (55)
T ss_dssp EEE-TTT-SEEEE--ETT-SS-EE-SSSTSEEEEE-SSSE
T ss_pred EEECCCCCCeeEE--EecCCeEEEcccCCCEecCCCCcCe
Confidence 4788888888766 2445567788888888888877544
No 23
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=87.99 E-value=0.67 Score=30.52 Aligned_cols=37 Identities=27% Similarity=0.594 Sum_probs=23.3
Q ss_pred CCceEECCCCCccccccc-----cceeEEEEcCCcCeEEEEe
Q 032227 79 GATSVQCSCCHTVNLALE-----ANQVAHVNCGNCRMLLMYQ 115 (145)
Q Consensus 79 GA~sVrC~~C~tVn~v~~-----~~q~~~v~Cg~Crt~LmyP 115 (145)
||+-|-|..|.-+=..+. ...+..++||.|...|.|-
T Consensus 3 GAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 3 GAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred CCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe
Confidence 555555555554433321 2236699999999999874
No 24
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.51 E-value=0.74 Score=28.93 Aligned_cols=23 Identities=22% Similarity=0.605 Sum_probs=8.6
Q ss_pred cCCcCeEEEEecCCceEeCCCCC
Q 032227 105 CGNCRMLLMYQYGARSVKCAVCN 127 (145)
Q Consensus 105 Cg~Crt~LmyP~GA~sVkCa~C~ 127 (145)
|++|...+.+......++|+.|+
T Consensus 6 C~~CG~~~~~~~~~~~~~Cp~CG 28 (46)
T PRK00398 6 CARCGREVELDEYGTGVRCPYCG 28 (46)
T ss_pred CCCCCCEEEECCCCCceECCCCC
Confidence 33333333333333333333333
No 25
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=87.17 E-value=0.35 Score=33.45 Aligned_cols=34 Identities=24% Similarity=0.331 Sum_probs=15.7
Q ss_pred eecCCCCcccCCCCCCCcceeEEeCcccceEeeecC
Q 032227 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRG 79 (145)
Q Consensus 44 VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~G 79 (145)
|+|+.|..++.+= ++....+.|..|.++|..|.|
T Consensus 12 VkCp~C~n~q~vF--sha~t~V~C~~Cg~~L~~PtG 45 (59)
T PRK00415 12 VKCPDCGNEQVVF--SHASTVVRCLVCGKTLAEPTG 45 (59)
T ss_pred EECCCCCCeEEEE--ecCCcEEECcccCCCcccCCC
Confidence 4555555554331 222334455555555555544
No 26
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.92 E-value=1.3 Score=27.76 Aligned_cols=26 Identities=23% Similarity=0.471 Sum_probs=12.7
Q ss_pred EEeCcccceEeeecCCceEECCCCCc
Q 032227 65 LVCGGCHTLLMYIRGATSVQCSCCHT 90 (145)
Q Consensus 65 l~CGgCr~lLmYP~GA~sVrC~~C~t 90 (145)
..|.+|...+.+..+...++|+.|++
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCC
Confidence 34555555555544444445544443
No 27
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.33 E-value=1.8 Score=26.50 Aligned_cols=13 Identities=15% Similarity=0.406 Sum_probs=7.4
Q ss_pred EECCCCCcccccc
Q 032227 83 VQCSCCHTVNLAL 95 (145)
Q Consensus 83 VrC~~C~tVn~v~ 95 (145)
+.|+.|++.-.+.
T Consensus 3 i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 3 ITCPNCQAKYEID 15 (36)
T ss_pred EECCCCCCEEeCC
Confidence 4566666665553
No 28
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.95 E-value=1.1 Score=31.40 Aligned_cols=50 Identities=28% Similarity=0.654 Sum_probs=40.1
Q ss_pred EEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCce
Q 032227 65 LVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV 129 (145)
Q Consensus 65 l~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~V 129 (145)
-+|-+|...|.--.++.+..|+.|.-+. -.+|..||.+ ...++|+.|.|.
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~---------I~Rc~~CRk~------g~~Y~Cp~CGF~ 59 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEVE---------IYRCAKCRKL------GNPYRCPKCGFE 59 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCCcee---------eehhhhHHHc------CCceECCCcCcc
Confidence 5899999999888899999999998542 4578889875 345789999885
No 29
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=81.77 E-value=1.5 Score=31.13 Aligned_cols=38 Identities=24% Similarity=0.337 Sum_probs=23.9
Q ss_pred eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCce
Q 032227 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATS 82 (145)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~s 82 (145)
.|+|..|..++-+= ++....+.|..|.++|..|-|-..
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 47777777666542 333456677777777777776543
No 30
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=80.15 E-value=1.9 Score=26.42 Aligned_cols=13 Identities=23% Similarity=0.657 Sum_probs=6.2
Q ss_pred eecCCCCcccCCC
Q 032227 44 VCCAVCNAVTAVP 56 (145)
Q Consensus 44 VrC~~C~tvn~vp 56 (145)
+.|..|++.-.++
T Consensus 3 i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 3 ITCPNCQAKYEID 15 (36)
T ss_pred EECCCCCCEEeCC
Confidence 3455555554443
No 31
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=79.07 E-value=2 Score=29.78 Aligned_cols=53 Identities=21% Similarity=0.477 Sum_probs=40.4
Q ss_pred ccceeeccCccceeecccC-CCeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCCCCcc
Q 032227 22 AQSQLVCSGCRNLLLYPVG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (145)
Q Consensus 22 ~~sQlvC~gCr~lL~YprG-A~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~C~tV 91 (145)
++.-.+|.+|...| .|++ |..--|+.|..+... .|..||++ +...+|+.|.+.
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 34556899999888 5666 999999999876543 48888886 367788888764
No 32
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=79.06 E-value=3 Score=30.76 Aligned_cols=40 Identities=30% Similarity=0.537 Sum_probs=28.4
Q ss_pred eeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEE
Q 032227 43 SVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQ 84 (145)
Q Consensus 43 ~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVr 84 (145)
.|+|+.|-.||.+= ++...-++|+||.+.|.-|.|-..+.
T Consensus 34 ~VkC~gc~~iT~vf--SHaqtvVvc~~c~~il~~~tggra~l 73 (84)
T KOG1779|consen 34 DVKCPGCFKITTVF--SHAQTVVVCEGCSTILCQPTGGKAKL 73 (84)
T ss_pred EEEcCCceEEEEEe--ecCceEEEcCCCceEEEEecCCcEEe
Confidence 47888888887763 34455678888888888887766554
No 33
>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=78.86 E-value=4.9 Score=23.89 Aligned_cols=29 Identities=24% Similarity=0.605 Sum_probs=17.4
Q ss_pred EEEcCCcCeEEEEec-----CCceEeCCCCCcee
Q 032227 102 HVNCGNCRMLLMYQY-----GARSVKCAVCNFVT 130 (145)
Q Consensus 102 ~v~Cg~Crt~LmyP~-----GA~sVkCa~C~~VT 130 (145)
.+.|.+|.+...++. +...|+|+.|+.+-
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 356777777666663 22357777776543
No 34
>PF12773 DZR: Double zinc ribbon
Probab=77.95 E-value=1.1 Score=28.08 Aligned_cols=28 Identities=25% Similarity=0.421 Sum_probs=16.7
Q ss_pred eEEeCcccceEeeecCCceEECCCCCccc
Q 032227 64 QLVCGGCHTLLMYIRGATSVQCSCCHTVN 92 (145)
Q Consensus 64 ql~CGgCr~lLmYP~GA~sVrC~~C~tVn 92 (145)
...|..|.+.|. ......+.|+.|.+.+
T Consensus 12 ~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 12 AKFCPHCGTPLP-PPDQSKKICPNCGAEN 39 (50)
T ss_pred ccCChhhcCChh-hccCCCCCCcCCcCCC
Confidence 556666666666 4444455666666653
No 35
>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=69.84 E-value=3.7 Score=33.37 Aligned_cols=40 Identities=33% Similarity=0.549 Sum_probs=26.3
Q ss_pred eeecCCCCcccCCCCCC---CcceeEEeCcccceEeeecCCce
Q 032227 43 SVCCAVCNAVTAVPPPG---TEMAQLVCGGCHTLLMYIRGATS 82 (145)
Q Consensus 43 ~VrC~~C~tvn~vpp~~---~q~aql~CGgCr~lLmYP~GA~s 82 (145)
.|+|.-|+||-+|.-+. -.+--+.||+|-.+|..--++..
T Consensus 12 YVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~ 54 (170)
T PF04690_consen 12 YVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALL 54 (170)
T ss_pred EEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccc
Confidence 58888888888775443 33445667777777776655554
No 36
>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=67.74 E-value=8.3 Score=26.51 Aligned_cols=29 Identities=28% Similarity=0.565 Sum_probs=15.9
Q ss_pred eEEEEcCCcCeEEEEecCCce--EeCCCCCc
Q 032227 100 VAHVNCGNCRMLLMYQYGARS--VKCAVCNF 128 (145)
Q Consensus 100 ~~~v~Cg~Crt~LmyP~GA~s--VkCa~C~~ 128 (145)
...|.||.|++.+.+-.-.-+ ..|+.|+.
T Consensus 39 ~~~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 39 VKRVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp --EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred ccCeECCCCCCccChhhhhcCCCccCcCcCC
Confidence 337888888888776553333 67777764
No 37
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=67.42 E-value=4.3 Score=25.13 Aligned_cols=19 Identities=16% Similarity=0.429 Sum_probs=10.8
Q ss_pred cCCceEeCCCCCceeeccC
Q 032227 116 YGARSVKCAVCNFVTAVGA 134 (145)
Q Consensus 116 ~GA~sVkCa~C~~VT~i~~ 134 (145)
.+..+.+|..|.+.|+++.
T Consensus 20 ~~~~~w~C~~C~~~N~lp~ 38 (40)
T PF04810_consen 20 DGGKTWICNFCGTKNPLPP 38 (40)
T ss_dssp TTTTEEEETTT--EEE--G
T ss_pred CCCCEEECcCCCCcCCCCC
Confidence 3667778888888777764
No 38
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=66.39 E-value=6.3 Score=24.48 Aligned_cols=31 Identities=19% Similarity=0.597 Sum_probs=18.3
Q ss_pred cCCcCeEEEEecCCc--eEeCCCCCceeeccCC
Q 032227 105 CGNCRMLLMYQYGAR--SVKCAVCNFVTAVGAS 135 (145)
Q Consensus 105 Cg~Crt~LmyP~GA~--sVkCa~C~~VT~i~~~ 135 (145)
|..|..+|....+.. .+.|+.|.++-.+...
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeEECCCc
Confidence 556666554443432 5668778777766543
No 39
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=66.27 E-value=5.1 Score=34.72 Aligned_cols=75 Identities=23% Similarity=0.496 Sum_probs=48.1
Q ss_pred ccCCCeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCCCCcccccccc-ceeEEEEcCCcCeEEEEec
Q 032227 38 PVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEA-NQVAHVNCGNCRMLLMYQY 116 (145)
Q Consensus 38 prGA~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~-~q~~~v~Cg~Crt~LmyP~ 116 (145)
.-+++-|-|..|+..-.+ ++ .+-| --|||-.|+--|.++.+ ..--+++|. |+.+|+-=.
T Consensus 75 ~g~~PmvtCRVCq~~i~~--eg-k~~Q----------------HVVKC~~CnEATPIrnAPpGKKYVRCP-CNCLLICK~ 134 (275)
T KOG4684|consen 75 LGQFPMVTCRVCQVAISL--EG-KNQQ----------------HVVKCHSCNEATPIRNAPPGKKYVRCP-CNCLLICKA 134 (275)
T ss_pred cCCCceEeehhhhHHhcc--cc-ccce----------------eeEeecccCccccCCCCCCCCceeecC-CcEEEEEec
Confidence 467888888888876654 23 2222 23677777777776543 244467775 777887777
Q ss_pred CCceEeCCC--CCceeec
Q 032227 117 GARSVKCAV--CNFVTAV 132 (145)
Q Consensus 117 GA~sVkCa~--C~~VT~i 132 (145)
..+-.-|+. |.-|-++
T Consensus 135 sSqRIACPRpnCkRiInL 152 (275)
T KOG4684|consen 135 SSQRIACPRPNCKRIINL 152 (275)
T ss_pred ccceeccCCCCcceeeec
Confidence 777777753 5555444
No 40
>PRK05580 primosome assembly protein PriA; Validated
Probab=64.53 E-value=13 Score=35.18 Aligned_cols=68 Identities=24% Similarity=0.422 Sum_probs=51.4
Q ss_pred cceeecc-cC-CCeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcC
Q 032227 32 RNLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCR 109 (145)
Q Consensus 32 r~lL~Yp-rG-A~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Cr 109 (145)
+.||+-+ || |+.+.|..|..+- .|..|...|.|.......+|.-|......+ -.|.+|.
T Consensus 368 qvll~~nrrGy~~~~~C~~Cg~~~------------~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~-------~~Cp~Cg 428 (679)
T PRK05580 368 QVLLFLNRRGYAPFLLCRDCGWVA------------ECPHCDASLTLHRFQRRLRCHHCGYQEPIP-------KACPECG 428 (679)
T ss_pred eEEEEEcCCCCCCceEhhhCcCcc------------CCCCCCCceeEECCCCeEECCCCcCCCCCC-------CCCCCCc
Confidence 3556665 45 6789999998753 588999999999999999999999876543 2588887
Q ss_pred eEEEEecCC
Q 032227 110 MLLMYQYGA 118 (145)
Q Consensus 110 t~LmyP~GA 118 (145)
-.-+.+.|.
T Consensus 429 ~~~l~~~g~ 437 (679)
T PRK05580 429 STDLVPVGP 437 (679)
T ss_pred CCeeEEeec
Confidence 665555443
No 41
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=63.31 E-value=23 Score=30.80 Aligned_cols=109 Identities=23% Similarity=0.539 Sum_probs=74.6
Q ss_pred eeeccCccceeecc--cCCCeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECC--CCCcc-cccc----
Q 032227 25 QLVCSGCRNLLLYP--VGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCS--CCHTV-NLAL---- 95 (145)
Q Consensus 25 QlvC~gCr~lL~Yp--rGA~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~--~C~tV-n~v~---- 95 (145)
-+.|.-|+.++.-. +----|.|-.|+--|....+..-...+.|- |+-+|+--...+-.-|+ .|..| |+.+
T Consensus 80 mvtCRVCq~~i~~egk~~QHVVKC~~CnEATPIrnAPpGKKYVRCP-CNCLLICK~sSqRIACPRpnCkRiInL~p~~~~ 158 (275)
T KOG4684|consen 80 MVTCRVCQVAISLEGKNQQHVVKCHSCNEATPIRNAPPGKKYVRCP-CNCLLICKASSQRIACPRPNCKRIINLDPLIEK 158 (275)
T ss_pred eEeehhhhHHhccccccceeeEeecccCccccCCCCCCCCceeecC-CcEEEEEecccceeccCCCCcceeeecCCCCCC
Confidence 36788898877543 223458999999999876443344455553 66677777777777775 46554 4431
Q ss_pred -----ccceeEEEEcCCcCeEEEEec-CCceEeCCCCCceeeccC
Q 032227 96 -----EANQVAHVNCGNCRMLLMYQY-GARSVKCAVCNFVTAVGA 134 (145)
Q Consensus 96 -----~~~q~~~v~Cg~Crt~LmyP~-GA~sVkCa~C~~VT~i~~ 134 (145)
.+...-.+.||.|+-+.+|-. --.-.+|+-|+.|..|+.
T Consensus 159 p~~P~~~P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrKvSsvGs 203 (275)
T KOG4684|consen 159 PRDPGTAPTGCRVKCGHCNETFLFNTLTNALARCPHCRKVSSVGS 203 (275)
T ss_pred CCCCCCCCcceEEEecCccceeehhhHHHHHhcCCcccchhhhhh
Confidence 124556899999998887743 224579999999998864
No 42
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=62.83 E-value=5.2 Score=41.37 Aligned_cols=54 Identities=22% Similarity=0.450 Sum_probs=34.1
Q ss_pred cceeEEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCc
Q 032227 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNF 128 (145)
Q Consensus 61 q~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~ 128 (145)
|+++..|-.|.+.... .+|+.|.+-+.. ...|.+|+..+-.-... +.+|+-|..
T Consensus 664 EV~~rkCPkCG~~t~~------~fCP~CGs~te~-------vy~CPsCGaev~~des~-a~~CP~CGt 717 (1337)
T PRK14714 664 EVGRRRCPSCGTETYE------NRCPDCGTHTEP-------VYVCPDCGAEVPPDESG-RVECPRCDV 717 (1337)
T ss_pred EEEEEECCCCCCcccc------ccCcccCCcCCC-------ceeCccCCCccCCCccc-cccCCCCCC
Confidence 5566777777765421 278877777542 23788888776544333 667888874
No 43
>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=61.64 E-value=6.2 Score=22.84 Aligned_cols=9 Identities=33% Similarity=0.900 Sum_probs=4.1
Q ss_pred CceEECCCC
Q 032227 80 ATSVQCSCC 88 (145)
Q Consensus 80 A~sVrC~~C 88 (145)
+....|+.|
T Consensus 14 ~v~f~CPnC 22 (24)
T PF07754_consen 14 AVPFPCPNC 22 (24)
T ss_pred CceEeCCCC
Confidence 444444444
No 44
>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=60.65 E-value=10 Score=34.61 Aligned_cols=28 Identities=25% Similarity=0.723 Sum_probs=12.5
Q ss_pred EcCCcCeEEEEecCCceEeCCCCCceee
Q 032227 104 NCGNCRMLLMYQYGARSVKCAVCNFVTA 131 (145)
Q Consensus 104 ~Cg~Crt~LmyP~GA~sVkCa~C~~VT~ 131 (145)
.|.+|...|-|=......+|.-|++...
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCC
Confidence 3444444444444444444444444433
No 45
>PRK05580 primosome assembly protein PriA; Validated
Probab=60.26 E-value=9.2 Score=36.07 Aligned_cols=51 Identities=27% Similarity=0.582 Sum_probs=40.7
Q ss_pred ceEeeec-C-CceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCceeecc
Q 032227 72 TLLMYIR-G-ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVG 133 (145)
Q Consensus 72 ~lLmYP~-G-A~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~VT~i~ 133 (145)
++|..++ | |+.+.|..|..+ .+|.+|...|.|.......+|.-|++...++
T Consensus 369 vll~~nrrGy~~~~~C~~Cg~~-----------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~ 421 (679)
T PRK05580 369 VLLFLNRRGYAPFLLCRDCGWV-----------AECPHCDASLTLHRFQRRLRCHHCGYQEPIP 421 (679)
T ss_pred EEEEEcCCCCCCceEhhhCcCc-----------cCCCCCCCceeEECCCCeEECCCCcCCCCCC
Confidence 4555563 4 678999999876 5799999999999988888899888876653
No 46
>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=60.00 E-value=14 Score=26.30 Aligned_cols=39 Identities=10% Similarity=0.296 Sum_probs=19.1
Q ss_pred ceEECCCCCccccc----cccceeEEEEcCCcCeEEEEecCCc
Q 032227 81 TSVQCSCCHTVNLA----LEANQVAHVNCGNCRMLLMYQYGAR 119 (145)
Q Consensus 81 ~sVrC~~C~tVn~v----~~~~q~~~v~Cg~Crt~LmyP~GA~ 119 (145)
..+.|+.|+.-+.+ ...+.++.+.|+.|...-.+..+..
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 45678888755443 2346788999999977766665544
No 47
>PRK14873 primosome assembly protein PriA; Provisional
Probab=55.79 E-value=14 Score=35.30 Aligned_cols=68 Identities=22% Similarity=0.427 Sum_probs=44.3
Q ss_pred cCccceeecc-cC-CCeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcC
Q 032227 29 SGCRNLLLYP-VG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCG 106 (145)
Q Consensus 29 ~gCr~lL~Yp-rG-A~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg 106 (145)
.| +.||+-+ || |+.+.|..|.. .+.|..|...|.|..+....+|.-|.+. .. .-.|.
T Consensus 368 ~g-qvll~lnRrGyap~l~C~~Cg~------------~~~C~~C~~~L~~h~~~~~l~Ch~CG~~-~~-------p~~Cp 426 (665)
T PRK14873 368 HG-PVLVQVPRRGYVPSLACARCRT------------PARCRHCTGPLGLPSAGGTPRCRWCGRA-AP-------DWRCP 426 (665)
T ss_pred cC-cEEEEecCCCCCCeeEhhhCcC------------eeECCCCCCceeEecCCCeeECCCCcCC-Cc-------CccCC
Confidence 46 6676655 45 45668888864 5788888888888777777777777763 11 23677
Q ss_pred CcCeEEEEecC
Q 032227 107 NCRMLLMYQYG 117 (145)
Q Consensus 107 ~Crt~LmyP~G 117 (145)
+|...-+-+.|
T Consensus 427 ~Cgs~~l~~~g 437 (665)
T PRK14873 427 RCGSDRLRAVV 437 (665)
T ss_pred CCcCCcceeee
Confidence 77655333433
No 48
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=55.73 E-value=3 Score=31.87 Aligned_cols=27 Identities=26% Similarity=0.635 Sum_probs=24.1
Q ss_pred eeeccCccceeecccCCCeeecCCCCc
Q 032227 25 QLVCSGCRNLLLYPVGATSVCCAVCNA 51 (145)
Q Consensus 25 QlvC~gCr~lL~YprGA~~VrC~~C~t 51 (145)
-++||-||.+|.+..=-..++|+.|++
T Consensus 62 ~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 62 AIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred cEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 389999999999998888888999975
No 49
>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=54.54 E-value=9.1 Score=23.30 Aligned_cols=31 Identities=23% Similarity=0.562 Sum_probs=16.3
Q ss_pred EcCCcCeEEEEecCCce-EeCCCCCceeeccC
Q 032227 104 NCGNCRMLLMYQYGARS-VKCAVCNFVTAVGA 134 (145)
Q Consensus 104 ~Cg~Crt~LmyP~GA~s-VkCa~C~~VT~i~~ 134 (145)
-|..|..+|....+... +.|..|.|+-+|..
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~~ 34 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEPISQ 34 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE-SS
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccCCCC
Confidence 36667666644433322 24777777776653
No 50
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=53.93 E-value=5.2 Score=36.16 Aligned_cols=28 Identities=32% Similarity=0.630 Sum_probs=23.6
Q ss_pred EeCcccceEeeecCCceEECCCCCcccccc
Q 032227 66 VCGGCHTLLMYIRGATSVQCSCCHTVNLAL 95 (145)
Q Consensus 66 ~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~ 95 (145)
.|. |++.++-|.||.. +|+.||+|+.+.
T Consensus 6 ~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~ 33 (362)
T KOG1546|consen 6 GCN-CQRPMAPPPGARY-QCAGCHAVTQIA 33 (362)
T ss_pred cCC-CCCCCCCCCCCcc-cccccceeeeec
Confidence 355 8999999999999 999999998764
No 51
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=53.13 E-value=28 Score=28.35 Aligned_cols=48 Identities=31% Similarity=0.609 Sum_probs=26.4
Q ss_pred CCcceeEEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCce
Q 032227 59 GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARS 120 (145)
Q Consensus 59 ~~q~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~s 120 (145)
..+.-.+.|+-|.|.|. .+|-|+. -. .+--|+||.|--+|..=-++.+
T Consensus 7 sE~lCYVhCnFC~TiLa-----VsVP~ss--L~-------~~VTVRCGHCtNLLSVNm~~~~ 54 (170)
T PF04690_consen 7 SEQLCYVHCNFCNTILA-----VSVPCSS--LL-------KTVTVRCGHCTNLLSVNMRALL 54 (170)
T ss_pred CCcEEEEEcCCcCeEEE-----Eecchhh--hh-------hhhceeccCccceeeeeccccc
Confidence 45555666666666664 3444442 11 2225677777777765444443
No 52
>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=52.39 E-value=19 Score=32.83 Aligned_cols=61 Identities=20% Similarity=0.491 Sum_probs=47.3
Q ss_pred ccC-CCeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcCeEEEEec
Q 032227 38 PVG-ATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQY 116 (145)
Q Consensus 38 prG-A~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~ 116 (145)
.|| |+.+.|..|..+- .|..|...|.|-......+|.-|...-.++ -.|..|...-+-+.
T Consensus 207 rrGya~~~~C~~Cg~~~------------~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~-------~~Cp~C~s~~l~~~ 267 (505)
T TIGR00595 207 RRGYSKNLLCRSCGYIL------------CCPNCDVSLTYHKKEGKLRCHYCGYQEPIP-------KTCPQCGSEDLVYK 267 (505)
T ss_pred CCcCCCeeEhhhCcCcc------------CCCCCCCceEEecCCCeEEcCCCcCcCCCC-------CCCCCCCCCeeEee
Confidence 455 5788999998754 588999999999998999999999876553 36888877655555
Q ss_pred C
Q 032227 117 G 117 (145)
Q Consensus 117 G 117 (145)
|
T Consensus 268 g 268 (505)
T TIGR00595 268 G 268 (505)
T ss_pred c
Confidence 5
No 53
>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=52.35 E-value=6.9 Score=24.18 Aligned_cols=17 Identities=18% Similarity=0.575 Sum_probs=7.3
Q ss_pred EEecCCceEeCCCCCce
Q 032227 113 MYQYGARSVKCAVCNFV 129 (145)
Q Consensus 113 myP~GA~sVkCa~C~~V 129 (145)
.+-+..-.+-|+.|..|
T Consensus 12 ~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 12 VFDPERGELVCPNCGLV 28 (43)
T ss_dssp EEETTTTEEEETTT-BB
T ss_pred EEcCCCCeEECCCCCCE
Confidence 34444444444444444
No 54
>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=51.38 E-value=11 Score=26.71 Aligned_cols=26 Identities=19% Similarity=0.543 Sum_probs=11.2
Q ss_pred cCCcCeEEEEecCCceEeCCCCCceeec
Q 032227 105 CGNCRMLLMYQYGARSVKCAVCNFVTAV 132 (145)
Q Consensus 105 Cg~Crt~LmyP~GA~sVkCa~C~~VT~i 132 (145)
|..|+.+| +|.+ ..++|..|.+...+
T Consensus 3 C~~Cg~~l-~~~~-~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 3 CPKCGSLM-TPKN-GVYVCPSCGYEKEK 28 (104)
T ss_pred CcccCccc-ccCC-CeEECcCCCCcccc
Confidence 44444444 2222 23455555554443
No 55
>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=50.94 E-value=7.9 Score=30.00 Aligned_cols=32 Identities=25% Similarity=0.468 Sum_probs=22.1
Q ss_pred CceEECCCCCccccccccceeEEEEcCCcCeEEEEe
Q 032227 80 ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQ 115 (145)
Q Consensus 80 A~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP 115 (145)
|..|+|+.|+-+|...-.. -.|-.|++.|-..
T Consensus 67 av~V~CP~C~K~TKmLGr~----D~CM~C~~pLTLd 98 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGRV----DACMHCKEPLTLD 98 (114)
T ss_pred ceeeECCCCCChHhhhchh----hccCcCCCcCccC
Confidence 5678888888888765322 2688888776543
No 56
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=50.64 E-value=4.3 Score=28.22 Aligned_cols=30 Identities=30% Similarity=0.640 Sum_probs=14.9
Q ss_pred EEeCcccceEeeecCC--ceEECCCCCccccc
Q 032227 65 LVCGGCHTLLMYIRGA--TSVQCSCCHTVNLA 94 (145)
Q Consensus 65 l~CGgCr~lLmYP~GA--~sVrC~~C~tVn~v 94 (145)
+.|..|..+|.=..|- .-++|+.|..||..
T Consensus 5 iRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 5 IRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred eehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 3344444444333222 45667777777654
No 57
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=50.00 E-value=12 Score=38.87 Aligned_cols=55 Identities=20% Similarity=0.405 Sum_probs=31.9
Q ss_pred ccceeeccCccceeecccCCCeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCCCCcc
Q 032227 22 AQSQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (145)
Q Consensus 22 ~~sQlvC~gCr~lL~YprGA~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~C~tV 91 (145)
+.++..|..|.+.... .+|+.|.+.+.. ...|.+|+..+-..... +.+|+-|.+-
T Consensus 664 EV~~rkCPkCG~~t~~------~fCP~CGs~te~--------vy~CPsCGaev~~des~-a~~CP~CGtp 718 (1337)
T PRK14714 664 EVGRRRCPSCGTETYE------NRCPDCGTHTEP--------VYVCPDCGAEVPPDESG-RVECPRCDVE 718 (1337)
T ss_pred EEEEEECCCCCCcccc------ccCcccCCcCCC--------ceeCccCCCccCCCccc-cccCCCCCCc
Confidence 4455777777775422 277777776632 23677777665543222 5566666654
No 58
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.46 E-value=24 Score=34.38 Aligned_cols=41 Identities=17% Similarity=0.489 Sum_probs=25.2
Q ss_pred CeeecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCCCCccccc
Q 032227 42 TSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLA 94 (145)
Q Consensus 42 ~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v 94 (145)
+.+.|..|..+ ..|-+|...|.|-.....-+|--|..-..+
T Consensus 434 ~~l~C~~Cg~v------------~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~ 474 (730)
T COG1198 434 PLLLCRDCGYI------------AECPNCDSPLTLHKATGQLRCHYCGYQEPI 474 (730)
T ss_pred ceeecccCCCc------------ccCCCCCcceEEecCCCeeEeCCCCCCCCC
Confidence 36666666542 566666666666666666666666665443
No 59
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.24 E-value=22 Score=33.99 Aligned_cols=48 Identities=25% Similarity=0.515 Sum_probs=28.8
Q ss_pred cceEeeec-C-CceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCce
Q 032227 71 HTLLMYIR-G-ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFV 129 (145)
Q Consensus 71 r~lLmYP~-G-A~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~V 129 (145)
.++|+-++ | ++.+.|..|..+ .+|.+|...|-|..+....+|.-|++.
T Consensus 370 qvll~lnRrGyap~l~C~~Cg~~-----------~~C~~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 370 PVLVQVPRRGYVPSLACARCRTP-----------ARCRHCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred cEEEEecCCCCCCeeEhhhCcCe-----------eECCCCCCceeEecCCCeeECCCCcCC
Confidence 45555453 3 355577777654 456666666666666666666666663
No 60
>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=47.06 E-value=29 Score=24.70 Aligned_cols=33 Identities=30% Similarity=0.601 Sum_probs=23.7
Q ss_pred EEEcCCcCeEEEEecCCceEeCCCCCceeeccCCC
Q 032227 102 HVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGAST 136 (145)
Q Consensus 102 ~v~Cg~Crt~LmyP~GA~sVkCa~C~~VT~i~~~~ 136 (145)
-.+| .|.-.|.-..|+.+-|| .|.+..+|....
T Consensus 3 ifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~r 35 (68)
T PF09082_consen 3 IFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERR 35 (68)
T ss_dssp EEEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS
T ss_pred EEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEE
Confidence 4678 69999999999999999 899999986654
No 61
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=46.66 E-value=31 Score=28.69 Aligned_cols=29 Identities=28% Similarity=0.580 Sum_probs=21.2
Q ss_pred eeEEEEcCCcCeEEEEecCCceEeCCCCCce
Q 032227 99 QVAHVNCGNCRMLLMYQYGARSVKCAVCNFV 129 (145)
Q Consensus 99 q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~V 129 (145)
.+-..+|-+|+..|++ .-...+|+.|+.+
T Consensus 146 GVI~A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 146 GVIYARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred eEEEEEccCCCcceEE--cCcEEECCCCCCE
Confidence 4445678888888888 6677888888764
No 62
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=45.35 E-value=4.7 Score=30.82 Aligned_cols=28 Identities=25% Similarity=0.650 Sum_probs=24.4
Q ss_pred eEEeCcccceEeeecCCceEECCCCCcc
Q 032227 64 QLVCGGCHTLLMYIRGATSVQCSCCHTV 91 (145)
Q Consensus 64 ql~CGgCr~lLmYP~GA~sVrC~~C~tV 91 (145)
-++||-||.+|.+..=-..+.|+-|+.=
T Consensus 62 ~iiCGvC~~~LT~~EY~~~~~Cp~C~sp 89 (105)
T COG4357 62 AIICGVCRKLLTRAEYGMCGSCPYCQSP 89 (105)
T ss_pred cEEhhhhhhhhhHHHHhhcCCCCCcCCC
Confidence 3899999999999888888889999864
No 63
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=43.93 E-value=11 Score=34.08 Aligned_cols=26 Identities=42% Similarity=0.855 Sum_probs=23.7
Q ss_pred ccCccceeecccCCCeeecCCCCcccCC
Q 032227 28 CSGCRNLLLYPVGATSVCCAVCNAVTAV 55 (145)
Q Consensus 28 C~gCr~lL~YprGA~~VrC~~C~tvn~v 55 (145)
|+ ||+-++-|-||.. ||+.|++++..
T Consensus 7 ~~-~~~p~~~pp~ar~-q~~~~~~~~~~ 32 (362)
T KOG1546|consen 7 CN-CQRPMAPPPGARY-QCAGCHAVTQI 32 (362)
T ss_pred CC-CCCCCCCCCCCcc-cccccceeeee
Confidence 55 9999999999999 99999999964
No 64
>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=37.83 E-value=25 Score=31.47 Aligned_cols=31 Identities=19% Similarity=0.423 Sum_probs=17.1
Q ss_pred eEECCCCCccccccccceeEEEEcCCcCeEE
Q 032227 82 SVQCSCCHTVNLALEANQVAHVNCGNCRMLL 112 (145)
Q Consensus 82 sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~L 112 (145)
.+.|+.|+.+...++-..-....|..|+..|
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 4456666666655432233345566666666
No 65
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=36.02 E-value=32 Score=28.64 Aligned_cols=30 Identities=17% Similarity=0.546 Sum_probs=23.6
Q ss_pred Cccee--EEeCcccceEeeecCCceEECCCCCcc
Q 032227 60 TEMAQ--LVCGGCHTLLMYIRGATSVQCSCCHTV 91 (145)
Q Consensus 60 ~q~aq--l~CGgCr~lLmYP~GA~sVrC~~C~tV 91 (145)
++++- -.|..|+..|++ .-...+|+.|..+
T Consensus 143 ~dlGVI~A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 143 NDLGVIYARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred CcceEEEEEccCCCcceEE--cCcEEECCCCCCE
Confidence 44444 469999999999 6688899999876
No 66
>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=35.45 E-value=25 Score=20.86 Aligned_cols=21 Identities=24% Similarity=0.729 Sum_probs=9.4
Q ss_pred eccCccceeecccCCCeeecCCCCc
Q 032227 27 VCSGCRNLLLYPVGATSVCCAVCNA 51 (145)
Q Consensus 27 vC~gCr~lL~YprGA~~VrC~~C~t 51 (145)
.|..|.++..||| ..|+.|..
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 4677777777776 35566643
No 67
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=35.21 E-value=20 Score=34.25 Aligned_cols=50 Identities=24% Similarity=0.492 Sum_probs=34.3
Q ss_pred eecCCCCcccCCCCCCCcceeEEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcCeEE
Q 032227 44 VCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLL 112 (145)
Q Consensus 44 VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~L 112 (145)
..|+.|++.|.. +.-.|..|.+.|- .-.|+.|.+.+.. ..-.|++|.+-+
T Consensus 2 ~~Cp~Cg~~n~~-------~akFC~~CG~~l~------~~~Cp~CG~~~~~------~~~fC~~CG~~~ 51 (645)
T PRK14559 2 LICPQCQFENPN-------NNRFCQKCGTSLT------HKPCPQCGTEVPV------DEAHCPNCGAET 51 (645)
T ss_pred CcCCCCCCcCCC-------CCccccccCCCCC------CCcCCCCCCCCCc------ccccccccCCcc
Confidence 468999988842 2457889988873 2368888887653 234688887653
No 68
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=34.80 E-value=5.5 Score=24.50 Aligned_cols=24 Identities=29% Similarity=0.751 Sum_probs=15.5
Q ss_pred ceeEEeCcccceEeeecCCceEECCCCC
Q 032227 62 MAQLVCGGCHTLLMYIRGATSVQCSCCH 89 (145)
Q Consensus 62 ~aql~CGgCr~lLmYP~GA~sVrC~~C~ 89 (145)
=+|+.|..|-..++ ...++|+.|+
T Consensus 20 CgH~~C~~C~~~~~----~~~~~CP~C~ 43 (44)
T PF14634_consen 20 CGHIFCEKCLKKLK----GKSVKCPICR 43 (44)
T ss_pred cCCHHHHHHHHhhc----CCCCCCcCCC
Confidence 35666666777666 6666777665
No 69
>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=33.41 E-value=48 Score=19.23 Aligned_cols=23 Identities=26% Similarity=0.678 Sum_probs=7.7
Q ss_pred cCCcCeEEEEecCCceEeCCCCC
Q 032227 105 CGNCRMLLMYQYGARSVKCAVCN 127 (145)
Q Consensus 105 Cg~Crt~LmyP~GA~sVkCa~C~ 127 (145)
|+.|...+..-.+-.+-+|+.|+
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~Cg 28 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSCG 28 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSSS
T ss_pred cCcCCccccCCCCcCEeECCCCc
Confidence 44444444444444444444443
No 70
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.23 E-value=26 Score=35.93 Aligned_cols=56 Identities=18% Similarity=0.384 Sum_probs=39.8
Q ss_pred cceeEEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCceeeccCC
Q 032227 61 EMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGAS 135 (145)
Q Consensus 61 q~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~VT~i~~~ 135 (145)
+.+.-.|..|.... ...+|+.|...|.. ..+|..|++..- ...|+.|.+.+.-...
T Consensus 623 EVg~RfCpsCG~~t------~~frCP~CG~~Te~-------i~fCP~CG~~~~------~y~CPKCG~El~~~s~ 678 (1121)
T PRK04023 623 EIGRRKCPSCGKET------FYRRCPFCGTHTEP-------VYRCPRCGIEVE------EDECEKCGREPTPYSK 678 (1121)
T ss_pred cccCccCCCCCCcC------CcccCCCCCCCCCc-------ceeCccccCcCC------CCcCCCCCCCCCccce
Confidence 45566788888774 56799999988543 458999966532 2569999988765443
No 71
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=31.88 E-value=36 Score=21.94 Aligned_cols=29 Identities=31% Similarity=0.574 Sum_probs=17.2
Q ss_pred ceeeccCccceeecc------cCCCeeecCCCCcc
Q 032227 24 SQLVCSGCRNLLLYP------VGATSVCCAVCNAV 52 (145)
Q Consensus 24 sQlvC~gCr~lL~Yp------rGA~~VrC~~C~tv 52 (145)
..-+|+||+.-|.-- ++...+.|+.|+.|
T Consensus 21 ~~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 21 EGGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred eCCccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 344788888766432 34456666666543
No 72
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=30.43 E-value=56 Score=24.65 Aligned_cols=13 Identities=31% Similarity=0.800 Sum_probs=6.0
Q ss_pred EEEEcCCcCeEEE
Q 032227 101 AHVNCGNCRMLLM 113 (145)
Q Consensus 101 ~~v~Cg~Crt~Lm 113 (145)
...+|+.|+-.|.
T Consensus 132 ~~y~C~~C~g~l~ 144 (146)
T smart00731 132 SRYRCGKCGGKLI 144 (146)
T ss_pred ceEEcCCCCCEEE
Confidence 3444555544443
No 73
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=30.15 E-value=24 Score=28.50 Aligned_cols=28 Identities=21% Similarity=0.605 Sum_probs=21.7
Q ss_pred EcCCcC-eEEEEecCC-ceEeCCCCCceee
Q 032227 104 NCGNCR-MLLMYQYGA-RSVKCAVCNFVTA 131 (145)
Q Consensus 104 ~Cg~Cr-t~LmyP~GA-~sVkCa~C~~VT~ 131 (145)
.|.-|+ ..++||+.. .+++|+.|..|-.
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~H 183 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVFH 183 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCccccc
Confidence 577777 478888888 8888888887754
No 74
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=30.03 E-value=19 Score=29.08 Aligned_cols=63 Identities=35% Similarity=0.696 Sum_probs=35.6
Q ss_pred cccCCCeeecCCCCcccCCCCCCCcceeEEeCcccceEee-----ecCCceEECCCCCccccccccceeEEEEcCCcCe
Q 032227 37 YPVGATSVCCAVCNAVTAVPPPGTEMAQLVCGGCHTLLMY-----IRGATSVQCSCCHTVNLALEANQVAHVNCGNCRM 110 (145)
Q Consensus 37 YprGA~~VrC~~C~tvn~vpp~~~q~aql~CGgCr~lLmY-----P~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt 110 (145)
-+.|+....|+.|..-..+ +.+|+.|...|=- ..+=..+-|+.|.++|.. ++..++.|-+|.+
T Consensus 105 ~~~~~~~~aCs~C~r~~~~--------~~~C~~Cdr~lC~~C~~~C~~C~~~~Cs~Cs~~~y~---~~~e~~lC~~C~m 172 (175)
T PF05458_consen 105 DPSGPASRACSVCQRTQRI--------KSVCSQCDRALCESCIRSCSSCSEVFCSLCSTVNYS---DQYERVLCLSCSM 172 (175)
T ss_pred CCCCCcCccCcCCcCCCCC--------CccccccCcHHHHHHHhhhhchhhhhhcCccccccC---CcccccccCCCCC
Confidence 3456566678999633322 3456666555432 445556667777766553 2345566666653
No 75
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=29.67 E-value=1.1e+02 Score=19.40 Aligned_cols=32 Identities=22% Similarity=0.451 Sum_probs=18.1
Q ss_pred EECCCCCccccccccceeEEEEcCCcCeEEEEecC
Q 032227 83 VQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYG 117 (145)
Q Consensus 83 VrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~G 117 (145)
.+|..|...+... ....++|..|.--++|-.-
T Consensus 3 Y~C~~Cg~~~~~~---~~~~irC~~CG~rIlyK~R 34 (44)
T smart00659 3 YICGECGRENEIK---SKDVVRCRECGYRILYKKR 34 (44)
T ss_pred EECCCCCCEeecC---CCCceECCCCCceEEEEeC
Confidence 4566666655443 2345667666666666443
No 76
>PRK02935 hypothetical protein; Provisional
Probab=29.15 E-value=37 Score=26.22 Aligned_cols=32 Identities=25% Similarity=0.430 Sum_probs=19.8
Q ss_pred CCceEECCCCCccccccccceeEEEEcCCcCeEEEE
Q 032227 79 GATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMY 114 (145)
Q Consensus 79 GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~Lmy 114 (145)
-|..|.|+.|+-+|..+-.. -.|-.|++.|-.
T Consensus 67 kavqV~CP~C~K~TKmLGrv----D~CM~C~~PLTL 98 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGRV----DACMHCNQPLTL 98 (110)
T ss_pred cceeeECCCCCchhhhccce----eecCcCCCcCCc
Confidence 35667788888887764322 256666666544
No 77
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=28.62 E-value=26 Score=20.95 Aligned_cols=26 Identities=19% Similarity=0.465 Sum_probs=16.4
Q ss_pred EcCCcCeEEEEecCCceEeCCCCCcee
Q 032227 104 NCGNCRMLLMYQYGARSVKCAVCNFVT 130 (145)
Q Consensus 104 ~Cg~Crt~LmyP~GA~sVkCa~C~~VT 130 (145)
.|-.|+..|... +.+..+|+.|..+-
T Consensus 13 ~C~~C~~~i~~~-~~~~~~C~~C~~~~ 38 (50)
T cd00029 13 FCDVCRKSIWGL-FKQGLRCSWCKVKC 38 (50)
T ss_pred Chhhcchhhhcc-ccceeEcCCCCCch
Confidence 466666666543 56777777776553
No 78
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.20 E-value=74 Score=20.78 Aligned_cols=14 Identities=36% Similarity=0.525 Sum_probs=7.9
Q ss_pred ceEECCCCCccccc
Q 032227 81 TSVQCSCCHTVNLA 94 (145)
Q Consensus 81 ~sVrC~~C~tVn~v 94 (145)
+|-.|+.|..+...
T Consensus 27 TSq~C~~CG~~~~~ 40 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK 40 (69)
T ss_pred CccCccCccccccc
Confidence 55556666665543
No 79
>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=28.17 E-value=41 Score=20.83 Aligned_cols=28 Identities=21% Similarity=0.723 Sum_probs=17.8
Q ss_pred EEcCCcCeEEEEecCCceEeCCCCCceee
Q 032227 103 VNCGNCRMLLMYQYGARSVKCAVCNFVTA 131 (145)
Q Consensus 103 v~Cg~Crt~LmyP~GA~sVkCa~C~~VT~ 131 (145)
..|..|+..| .-.+.+.++|+.|+.+-.
T Consensus 12 ~~C~~C~~~i-~g~~~~g~~C~~C~~~~H 39 (53)
T PF00130_consen 12 TYCDVCGKFI-WGLGKQGYRCSWCGLVCH 39 (53)
T ss_dssp EB-TTSSSBE-CSSSSCEEEETTTT-EEE
T ss_pred CCCcccCccc-CCCCCCeEEECCCCChHh
Confidence 4677777777 336777788888877643
No 80
>PRK04351 hypothetical protein; Provisional
Probab=27.77 E-value=51 Score=25.85 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=11.7
Q ss_pred EEEEcCCcCeEEEEe
Q 032227 101 AHVNCGNCRMLLMYQ 115 (145)
Q Consensus 101 ~~v~Cg~Crt~LmyP 115 (145)
..-+||.|+..|.+-
T Consensus 131 ~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 131 KRYRCGKCRGKLKLI 145 (149)
T ss_pred CcEEeCCCCcEeeec
Confidence 577888888888764
No 81
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=27.65 E-value=94 Score=30.47 Aligned_cols=52 Identities=25% Similarity=0.604 Sum_probs=39.4
Q ss_pred ceEeeec-C-CceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCceeeccC
Q 032227 72 TLLMYIR-G-ATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGA 134 (145)
Q Consensus 72 ~lLmYP~-G-A~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~VT~i~~ 134 (145)
++|+-+| | ++.+.|..|.+| ..|.+|...|.|-.....-+|--|++...++.
T Consensus 423 ~llflnRRGys~~l~C~~Cg~v-----------~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~ 476 (730)
T COG1198 423 VLLFLNRRGYAPLLLCRDCGYI-----------AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQ 476 (730)
T ss_pred EEEEEccCCccceeecccCCCc-----------ccCCCCCcceEEecCCCeeEeCCCCCCCCCCC
Confidence 3455444 3 457889999887 46888999999998888888888888866653
No 82
>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=27.07 E-value=24 Score=20.84 Aligned_cols=24 Identities=21% Similarity=0.708 Sum_probs=14.2
Q ss_pred EcCCcCeEEEEecCCceEeCCCCCce
Q 032227 104 NCGNCRMLLMYQYGARSVKCAVCNFV 129 (145)
Q Consensus 104 ~Cg~Crt~LmyP~GA~sVkCa~C~~V 129 (145)
.|-.|+..|.... +.++|+.|..+
T Consensus 13 ~C~~C~~~i~~~~--~~~~C~~C~~~ 36 (49)
T smart00109 13 KCCVCRKSIWGSF--QGLRCSWCKVK 36 (49)
T ss_pred CccccccccCcCC--CCcCCCCCCch
Confidence 4666666665432 46777777654
No 83
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=25.74 E-value=14 Score=27.31 Aligned_cols=59 Identities=17% Similarity=0.419 Sum_probs=35.2
Q ss_pred ceeEEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcCeEEEEecCCceEeCCCCCceeeccCCC
Q 032227 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGAST 136 (145)
Q Consensus 62 ~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~VT~i~~~~ 136 (145)
++.-.|.-|...+-+-. .....|..|. +-.|..|+.. -.+.....|.+|+.-.++...+
T Consensus 52 ~~~~~C~~C~~~fg~l~-~~~~~C~~C~------------~~VC~~C~~~---~~~~~~WlC~vC~k~rel~~~s 110 (118)
T PF02318_consen 52 YGERHCARCGKPFGFLF-NRGRVCVDCK------------HRVCKKCGVY---SKKEPIWLCKVCQKQRELKKKS 110 (118)
T ss_dssp HCCSB-TTTS-BCSCTS-TTCEEETTTT------------EEEETTSEEE---TSSSCCEEEHHHHHHHHHHHHC
T ss_pred cCCcchhhhCCcccccC-CCCCcCCcCC------------ccccCccCCc---CCCCCCEEChhhHHHHHHHHHh
Confidence 34456666666554432 2336777665 5578888876 4466777888887766654433
No 84
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=25.58 E-value=22 Score=27.72 Aligned_cols=36 Identities=22% Similarity=0.377 Sum_probs=24.3
Q ss_pred EEEcCCcCeEEEEecCCceEeCCCCCceeeccCCCC
Q 032227 102 HVNCGNCRMLLMYQYGARSVKCAVCNFVTAVGASTS 137 (145)
Q Consensus 102 ~v~Cg~Crt~LmyP~GA~sVkCa~C~~VT~i~~~~~ 137 (145)
-.-|+-|..+|+.|.-...|-|..|..+..+.+-.+
T Consensus 7 ~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~~~~ 42 (116)
T KOG2907|consen 7 LDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQFSG 42 (116)
T ss_pred cchhhhhhhhcccccccCceEeccccccCCHHHhCC
Confidence 345777777777777777777777777766655433
No 85
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=25.20 E-value=87 Score=19.47 Aligned_cols=25 Identities=28% Similarity=0.788 Sum_probs=13.4
Q ss_pred EcC--CcCeEEEEec--CCceEeCCCCCc
Q 032227 104 NCG--NCRMLLMYQY--GARSVKCAVCNF 128 (145)
Q Consensus 104 ~Cg--~Crt~LmyP~--GA~sVkCa~C~~ 128 (145)
.|. +|...+.... +...|+|+.|++
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~~ 48 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCGF 48 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCCC
Confidence 355 5555555542 555666655554
No 86
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=25.12 E-value=73 Score=21.37 Aligned_cols=7 Identities=29% Similarity=1.004 Sum_probs=3.2
Q ss_pred ECCCCCc
Q 032227 84 QCSCCHT 90 (145)
Q Consensus 84 rC~~C~t 90 (145)
+|+.|..
T Consensus 4 ~CP~CG~ 10 (54)
T TIGR01206 4 ECPDCGA 10 (54)
T ss_pred CCCCCCC
Confidence 4444444
No 87
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=24.68 E-value=44 Score=30.14 Aligned_cols=30 Identities=17% Similarity=0.426 Sum_probs=16.4
Q ss_pred EECCCCCccccccccceeEEEEcCCcCeEE
Q 032227 83 VQCSCCHTVNLALEANQVAHVNCGNCRMLL 112 (145)
Q Consensus 83 VrC~~C~tVn~v~~~~q~~~v~Cg~Crt~L 112 (145)
+.|+.|+.+...++-+.-...+|..|...|
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 40 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL 40 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence 446666666655433333345566666665
No 88
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=24.51 E-value=48 Score=22.31 Aligned_cols=20 Identities=25% Similarity=0.564 Sum_probs=11.8
Q ss_pred ccceeeccCccceeecccCC
Q 032227 22 AQSQLVCSGCRNLLLYPVGA 41 (145)
Q Consensus 22 ~~sQlvC~gCr~lL~YprGA 41 (145)
+..+.+|..|.++|..-..+
T Consensus 43 ~~kr~~Ck~C~~~liPG~~~ 62 (85)
T PF04032_consen 43 EIKRTICKKCGSLLIPGVNC 62 (85)
T ss_dssp TCCCTB-TTT--B--CTTTE
T ss_pred HHhcccccCCCCEEeCCCcc
Confidence 46788999999999987654
No 89
>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=24.20 E-value=76 Score=19.45 Aligned_cols=24 Identities=17% Similarity=0.382 Sum_probs=12.0
Q ss_pred cCCcCeEEEEecCCceEeCCCCCce
Q 032227 105 CGNCRMLLMYQYGARSVKCAVCNFV 129 (145)
Q Consensus 105 Cg~Crt~LmyP~GA~sVkCa~C~~V 129 (145)
|+.|+-. .|-...-...|..|+++
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 90
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=23.96 E-value=32 Score=22.46 Aligned_cols=27 Identities=30% Similarity=0.803 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCCCCCCccccceeeccCccc
Q 032227 4 PLAPYPTPPAPYTPPANGAQSQLVCSGCRN 33 (145)
Q Consensus 4 ~l~p~~~~~~p~~~~~~~~~sQlvC~gCr~ 33 (145)
+|..|.-|| .+..+.+.+-++|.-|+.
T Consensus 18 ~L~vy~Vpp---~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 18 PLVVYAVPP---SSDVTADNSVMLCDTCHS 44 (47)
T ss_pred CceEEecCC---CCCCCccceeeechHHHH
Confidence 566666543 344677889999998875
No 91
>PRK11827 hypothetical protein; Provisional
Probab=23.71 E-value=1e+02 Score=21.19 Aligned_cols=32 Identities=19% Similarity=0.407 Sum_probs=19.7
Q ss_pred EEEcCCcCeEEEEecCCceEeCCCCCceeecc
Q 032227 102 HVNCGNCRMLLMYQYGARSVKCAVCNFVTAVG 133 (145)
Q Consensus 102 ~v~Cg~Crt~LmyP~GA~sVkCa~C~~VT~i~ 133 (145)
.+.|..|+..|.|=.++....|..|+-+-.|+
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFPLR 39 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeecccc
Confidence 35566666666665556666666666665554
No 92
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=23.33 E-value=32 Score=26.79 Aligned_cols=33 Identities=30% Similarity=0.556 Sum_probs=28.7
Q ss_pred ceeeccCccceeecccCCCeeecCCCCcccCCC
Q 032227 24 SQLVCSGCRNLLLYPVGATSVCCAVCNAVTAVP 56 (145)
Q Consensus 24 sQlvC~gCr~lL~YprGA~~VrC~~C~tvn~vp 56 (145)
+-+.|+.|.+||.=|.-+..|-|..|..+..+.
T Consensus 6 ~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~ 38 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVS 38 (116)
T ss_pred CcchhhhhhhhcccccccCceEeccccccCCHH
Confidence 557799999999999999999999999988764
No 93
>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=23.17 E-value=34 Score=19.76 Aligned_cols=21 Identities=19% Similarity=0.600 Sum_probs=10.3
Q ss_pred cCCcCeEEEEecCCceEeCCCCCce
Q 032227 105 CGNCRMLLMYQYGARSVKCAVCNFV 129 (145)
Q Consensus 105 Cg~Crt~LmyP~GA~sVkCa~C~~V 129 (145)
|..|+..+ -....+|+.|+|+
T Consensus 3 CP~C~~~V----~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 3 CPECGAEV----PESAKFCPHCGYD 23 (26)
T ss_pred CCCCcCCc----hhhcCcCCCCCCC
Confidence 44444443 2344556666553
No 94
>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=23.01 E-value=30 Score=24.26 Aligned_cols=30 Identities=23% Similarity=0.561 Sum_probs=19.0
Q ss_pred eeccCccc-------eeecccCCCeeecCCCCcccCC
Q 032227 26 LVCSGCRN-------LLLYPVGATSVCCAVCNAVTAV 55 (145)
Q Consensus 26 lvC~gCr~-------lL~YprGA~~VrC~~C~tvn~v 55 (145)
..|..|.+ -.+|-+|.-.|||+.|+..-..
T Consensus 5 FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 5 FTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred EEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeee
Confidence 44555543 2578899999999999876654
No 95
>PF14369 zf-RING_3: zinc-finger
Probab=22.80 E-value=65 Score=19.60 Aligned_cols=23 Identities=26% Similarity=0.761 Sum_probs=10.2
Q ss_pred eCcccceEeee-cCCceEECCCCC
Q 032227 67 CGGCHTLLMYI-RGATSVQCSCCH 89 (145)
Q Consensus 67 CGgCr~lLmYP-~GA~sVrC~~C~ 89 (145)
|..|+..+.-. .+...+.|+.|+
T Consensus 5 Ch~C~~~V~~~~~~~~~~~CP~C~ 28 (35)
T PF14369_consen 5 CHQCNRFVRIAPSPDSDVACPRCH 28 (35)
T ss_pred CccCCCEeEeCcCCCCCcCCcCCC
Confidence 44555444442 233333455554
No 96
>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=22.63 E-value=82 Score=20.91 Aligned_cols=9 Identities=22% Similarity=0.719 Sum_probs=4.0
Q ss_pred cCCCCcccC
Q 032227 46 CAVCNAVTA 54 (145)
Q Consensus 46 C~~C~tvn~ 54 (145)
|+.|+..|-
T Consensus 25 C~~C~~hNG 33 (54)
T PF10058_consen 25 CSKCFSHNG 33 (54)
T ss_pred Ccccchhhc
Confidence 444444443
No 97
>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=22.28 E-value=81 Score=24.83 Aligned_cols=33 Identities=18% Similarity=0.404 Sum_probs=19.0
Q ss_pred ceeEEeCcccceEeeecCCceEECCCCCccccc
Q 032227 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLA 94 (145)
Q Consensus 62 ~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v 94 (145)
.+.++|-+|...+.|-.-..--.|+.|+.....
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~ 142 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERLPPCPKCGHTEFT 142 (146)
T ss_pred CceEecccCCCEEEecCCCcCCCCCCCCCCeee
Confidence 345666666666665555555566666655544
No 98
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=21.83 E-value=1.4e+02 Score=20.46 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=11.2
Q ss_pred ceeEEEEcCCcCeEEEEecCCceEeCCCCCc
Q 032227 98 NQVAHVNCGNCRMLLMYQYGARSVKCAVCNF 128 (145)
Q Consensus 98 ~q~~~v~Cg~Crt~LmyP~GA~sVkCa~C~~ 128 (145)
+...++.|..|+..=-.++--.-.||+.|+.
T Consensus 26 ~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 26 NKKVWILCNDCNAKSEVPFHFLGHKCSHCGS 56 (61)
T ss_dssp --EEEEEESSS--EEEEE--TT----TTTS-
T ss_pred CCEEEEECCCCCCccceeeeHhhhcCCCCCC
Confidence 3445555555555555555555555555554
No 99
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.38 E-value=95 Score=23.13 Aligned_cols=9 Identities=22% Similarity=0.737 Sum_probs=4.7
Q ss_pred ceEECCCCC
Q 032227 81 TSVQCSCCH 89 (145)
Q Consensus 81 ~sVrC~~C~ 89 (145)
..+.|+.|+
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 345555555
No 100
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=20.89 E-value=1e+02 Score=18.58 Aligned_cols=11 Identities=27% Similarity=0.489 Sum_probs=4.4
Q ss_pred eccCccceeec
Q 032227 27 VCSGCRNLLLY 37 (145)
Q Consensus 27 vC~gCr~lL~Y 37 (145)
.|.+|+.-++|
T Consensus 5 ~C~~C~~~~i~ 15 (33)
T PF08792_consen 5 KCSKCGGNGIV 15 (33)
T ss_pred EcCCCCCCeEE
Confidence 34444443333
No 101
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=20.58 E-value=66 Score=24.56 Aligned_cols=44 Identities=25% Similarity=0.452 Sum_probs=23.0
Q ss_pred ceeEEeCcccceEeeecCCceEECCCCCccccccccceeEEEEcCCcCeEEEEecC
Q 032227 62 MAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLALEANQVAHVNCGNCRMLLMYQYG 117 (145)
Q Consensus 62 ~aql~CGgCr~lLmYP~GA~sVrC~~C~tVn~v~~~~q~~~v~Cg~Crt~LmyP~G 117 (145)
+--..|-+|.+.|....+|.. +-....--++|-.|....=||+|
T Consensus 54 iKR~~CkkC~t~Lvpg~n~rv------------R~~~~~v~vtC~~CG~~~R~p~~ 97 (105)
T COG2023 54 IKRTICKKCYTPLVPGKNARV------------RLRKGRVVVTCLECGTIRRYPYG 97 (105)
T ss_pred HHHHhccccCcccccCcceEE------------EEcCCeEEEEecCCCcEEEeccc
Confidence 334456666666655544421 11112245666666666666666
No 102
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=20.35 E-value=51 Score=26.62 Aligned_cols=28 Identities=25% Similarity=0.605 Sum_probs=23.2
Q ss_pred EeCccc-ceEeeecCC-ceEECCCCCcccc
Q 032227 66 VCGGCH-TLLMYIRGA-TSVQCSCCHTVNL 93 (145)
Q Consensus 66 ~CGgCr-~lLmYP~GA-~sVrC~~C~tVn~ 93 (145)
+|--|+ ..++||... ..++|..|.+|--
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~H 183 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVFH 183 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCccccc
Confidence 566777 489999999 9999999998843
No 103
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.18 E-value=88 Score=27.56 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=6.1
Q ss_pred eeecCCCCccc
Q 032227 43 SVCCAVCNAVT 53 (145)
Q Consensus 43 ~VrC~~C~tvn 53 (145)
.-.|+.|...-
T Consensus 187 ~~~CPvCGs~P 197 (309)
T PRK03564 187 RQFCPVCGSMP 197 (309)
T ss_pred CCCCCCCCCcc
Confidence 44566666544
Done!