Query 028899
Match_columns 202
No_of_seqs 154 out of 219
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 04:17:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028899.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028899hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4727 U1-like Zn-finger prot 100.0 9.6E-64 2.1E-68 411.3 11.9 191 6-202 3-193 (193)
2 smart00451 ZnF_U1 U1-like zinc 98.8 2.9E-09 6.4E-14 65.6 2.1 32 81-112 2-33 (35)
3 PF12171 zf-C2H2_jaz: Zinc-fin 98.7 7.2E-09 1.6E-13 61.2 2.1 26 83-108 2-27 (27)
4 PF12874 zf-met: Zinc-finger o 98.4 7.8E-08 1.7E-12 55.2 1.3 25 83-107 1-25 (25)
5 PF08648 DUF1777: Protein of u 98.0 1.9E-06 4E-11 71.3 1.3 16 186-201 127-142 (180)
6 PF06220 zf-U1: U1 zinc finger 97.8 1E-05 2.2E-10 52.0 1.8 31 81-111 2-34 (38)
7 KOG0717 Molecular chaperone (D 97.3 9.9E-05 2.1E-09 70.0 1.2 29 82-110 292-320 (508)
8 KOG3408 U1-like Zn-finger-cont 97.2 0.00017 3.7E-09 57.5 1.6 34 78-111 53-86 (129)
9 KOG3454 U1 snRNP-specific prot 96.9 0.00042 9.1E-09 57.6 1.2 31 81-111 2-34 (165)
10 PF00096 zf-C2H2: Zinc finger, 96.2 0.0014 3E-08 36.5 0.3 22 83-104 1-22 (23)
11 KOG2837 Protein containing a U 96.0 0.0013 2.8E-08 58.9 -0.9 34 79-112 22-55 (309)
12 KOG3263 Nucleic acid binding p 96.0 0.0034 7.4E-08 52.9 1.6 16 186-201 144-159 (196)
13 PF07535 zf-DBF: DBF zinc fing 95.9 0.0068 1.5E-07 41.1 2.4 42 83-129 6-47 (49)
14 KOG2384 Major histocompatibili 95.7 0.0045 9.7E-08 53.3 1.2 30 79-109 81-110 (223)
15 COG5112 UFD2 U1-like Zn-finger 95.6 0.0047 1E-07 48.5 0.8 34 78-111 51-84 (126)
16 PF13912 zf-C2H2_6: C2H2-type 95.3 0.0079 1.7E-07 34.7 0.9 22 83-104 2-23 (27)
17 PLN02748 tRNA dimethylallyltra 94.8 0.016 3.4E-07 55.5 2.0 32 81-112 417-449 (468)
18 PF13894 zf-C2H2_4: C2H2-type 94.6 0.015 3.1E-07 31.7 0.8 21 83-103 1-21 (24)
19 PF12756 zf-C2H2_2: C2H2 type 94.5 0.011 2.3E-07 42.8 -0.0 30 82-111 50-79 (100)
20 smart00586 ZnF_DBF Zinc finger 94.4 0.017 3.7E-07 39.2 0.8 26 83-111 6-31 (49)
21 PHA02768 hypothetical protein; 94.3 0.017 3.7E-07 40.1 0.8 26 81-108 4-29 (55)
22 COG5188 PRP9 Splicing factor 3 93.8 0.02 4.4E-07 53.2 0.4 31 80-110 236-266 (470)
23 COG4049 Uncharacterized protei 93.4 0.023 4.9E-07 40.0 -0.0 34 79-113 14-47 (65)
24 smart00355 ZnF_C2H2 zinc finge 93.2 0.045 9.8E-07 29.9 1.1 21 83-103 1-21 (26)
25 PF03194 LUC7: LUC7 N_terminus 93.1 0.1 2.2E-06 46.1 3.7 47 78-136 186-235 (254)
26 KOG0150 Spliceosomal protein F 91.1 0.098 2.1E-06 47.7 1.2 43 79-135 7-50 (336)
27 KOG2785 C2H2-type Zn-finger pr 90.9 0.075 1.6E-06 49.6 0.3 38 79-116 65-102 (390)
28 KOG3032 Uncharacterized conser 89.6 0.22 4.7E-06 44.0 2.0 36 72-108 25-60 (264)
29 PF11931 DUF3449: Domain of un 89.2 0.11 2.5E-06 44.5 0.0 36 80-115 99-138 (196)
30 PF14968 CCDC84: Coiled coil p 87.1 0.2 4.4E-06 46.1 0.2 55 54-110 32-92 (336)
31 PTZ00448 hypothetical protein; 86.4 0.52 1.1E-05 44.0 2.5 31 82-112 314-344 (373)
32 KOG0796 Spliceosome subunit [R 85.3 0.57 1.2E-05 42.9 2.1 47 79-137 183-232 (319)
33 KOG0227 Splicing factor 3a, su 85.2 0.37 7.9E-06 41.6 0.8 33 79-111 50-82 (222)
34 PHA00616 hypothetical protein 84.9 0.24 5.2E-06 32.9 -0.3 22 83-104 2-23 (44)
35 PF13913 zf-C2HC_2: zinc-finge 79.6 0.96 2.1E-05 26.2 0.9 20 83-103 3-22 (25)
36 PF09237 GAGA: GAGA factor; I 79.2 0.87 1.9E-05 31.4 0.7 22 82-103 24-45 (54)
37 KOG3792 Transcription factor N 78.3 0.71 1.5E-05 46.4 0.2 30 79-108 356-385 (816)
38 COG5246 PRP11 Splicing factor 78.2 0.99 2.2E-05 38.7 1.0 33 79-111 50-82 (222)
39 PF04988 AKAP95: A-kinase anch 71.1 1.1 2.4E-05 37.5 -0.5 49 81-129 90-140 (165)
40 PF13909 zf-H2C2_5: C2H2-type 70.9 2 4.3E-05 23.8 0.7 20 83-103 1-20 (24)
41 PF05605 zf-Di19: Drought indu 70.5 2.2 4.8E-05 28.6 1.0 22 82-104 2-23 (54)
42 PF13465 zf-H2C2_2: Zinc-finge 70.3 1.7 3.8E-05 25.0 0.4 12 82-93 14-25 (26)
43 KOG2785 C2H2-type Zn-finger pr 69.8 3.8 8.2E-05 38.5 2.7 57 81-137 2-59 (390)
44 KOG2636 Splicing factor 3a, su 66.3 4.1 8.9E-05 39.2 2.2 63 53-115 361-438 (497)
45 PF14968 CCDC84: Coiled coil p 62.7 3.5 7.6E-05 38.1 1.0 26 84-112 1-26 (336)
46 KOG2482 Predicted C2H2-type Zn 62.5 2.3 5.1E-05 39.7 -0.2 31 79-109 192-222 (423)
47 KOG3623 Homeobox transcription 62.5 2.4 5.2E-05 43.2 -0.1 24 79-102 891-914 (1007)
48 PF06658 DUF1168: Protein of u 61.5 16 0.00035 29.9 4.5 49 127-176 50-98 (142)
49 PF12756 zf-C2H2_2: C2H2 type 60.1 2.9 6.3E-05 29.8 0.0 27 85-112 2-28 (100)
50 COG5200 LUC7 U1 snRNP componen 58.5 3.5 7.5E-05 36.2 0.2 31 79-109 182-215 (258)
51 PHA00732 hypothetical protein 55.9 6.5 0.00014 28.8 1.2 21 83-103 2-22 (79)
52 PF04423 Rad50_zn_hook: Rad50 55.8 3.7 8E-05 27.5 -0.1 20 84-103 22-43 (54)
53 KOG1994 Predicted RNA binding 54.7 5.3 0.00011 35.5 0.7 26 79-104 236-261 (268)
54 KOG3634 Troponin [Cytoskeleton 53.8 17 0.00037 33.8 3.9 14 186-199 180-194 (361)
55 smart00734 ZnF_Rad18 Rad18-lik 53.5 7.5 0.00016 22.7 1.0 19 84-103 3-21 (26)
56 COG5136 U1 snRNP-specific prot 52.2 3.5 7.5E-05 34.8 -0.8 37 81-117 2-41 (188)
57 PHA00733 hypothetical protein 51.9 7.8 0.00017 30.7 1.2 22 82-103 99-120 (128)
58 PF04640 PLATZ: PLATZ transcri 46.0 20 0.00043 26.1 2.4 18 79-96 46-63 (72)
59 PHA00733 hypothetical protein 41.5 14 0.00031 29.2 1.2 23 81-103 72-94 (128)
60 KOG2462 C2H2-type Zn-finger pr 39.5 13 0.00029 33.5 0.9 23 82-104 215-237 (279)
61 PF07649 C1_3: C1-like domain; 38.9 13 0.00029 21.9 0.5 13 80-92 13-25 (30)
62 PHA02562 46 endonuclease subun 38.6 53 0.0012 31.1 4.8 16 82-97 284-299 (562)
63 COG5189 SFP1 Putative transcri 38.0 11 0.00023 35.2 0.0 22 82-103 398-419 (423)
64 KOG1144 Translation initiation 37.6 70 0.0015 33.4 5.6 13 15-27 11-23 (1064)
65 TIGR03831 YgiT_finger YgiT-typ 37.4 16 0.00034 22.8 0.7 16 79-94 29-44 (46)
66 COG5188 PRP9 Splicing factor 3 37.3 16 0.00035 34.5 1.0 35 80-114 372-410 (470)
67 PF04988 AKAP95: A-kinase anch 36.6 18 0.00038 30.4 1.1 43 83-125 1-44 (165)
68 PF08432 Vfa1: AAA-ATPase Vps4 35.7 56 0.0012 27.3 4.0 37 67-110 24-60 (182)
69 PF08262 Lem_TRP: Leucophaea m 35.6 16 0.00034 17.1 0.3 7 191-197 3-9 (10)
70 PF14401 RLAN: RimK-like ATPgr 33.6 22 0.00048 29.1 1.2 22 66-87 15-37 (153)
71 PF12855 Ecl1: Life-span regul 31.5 14 0.0003 24.3 -0.2 10 83-92 7-16 (43)
72 PF04959 ARS2: Arsenite-resist 31.0 20 0.00043 31.2 0.5 43 80-134 75-117 (214)
73 KOG2505 Ankyrin repeat protein 30.5 28 0.00061 34.2 1.5 50 81-130 65-115 (591)
74 KOG4432 Uncharacterized NUDIX 29.1 29 0.00063 32.2 1.3 36 56-91 107-143 (405)
75 KOG1842 FYVE finger-containing 28.7 19 0.00041 34.8 0.0 23 81-103 14-36 (505)
76 PF02892 zf-BED: BED zinc fing 28.4 27 0.00058 21.9 0.7 24 79-102 13-40 (45)
77 KOG4722 Zn-finger protein [Gen 28.3 28 0.0006 33.8 1.0 58 70-129 483-550 (672)
78 PF03879 Cgr1: Cgr1 family; I 28.1 2.3E+02 0.0051 22.1 6.0 20 118-137 39-58 (108)
79 PHA03123 dUTPase; Provisional 27.9 29 0.00063 32.9 1.1 15 188-202 387-401 (402)
80 PF04780 DUF629: Protein of un 26.6 30 0.00065 33.5 0.9 30 81-111 56-85 (466)
81 PRK09907 toxin MazF; Provision 26.5 53 0.0012 25.2 2.2 65 66-132 44-109 (111)
82 COG4469 CoiA Competence protei 26.0 27 0.00059 32.5 0.5 14 82-95 25-38 (342)
83 PF05477 SURF2: Surfeit locus 25.7 44 0.00094 29.7 1.7 48 79-126 76-124 (244)
84 TIGR02646 conserved hypothetic 25.5 22 0.00047 28.4 -0.1 29 80-108 22-50 (144)
85 PF00692 dUTPase: dUTPase; In 25.4 35 0.00077 26.2 1.0 10 191-200 119-128 (129)
86 KOG3623 Homeobox transcription 24.7 25 0.00054 36.2 0.0 41 81-124 949-989 (1007)
87 PHA03127 dUTPase; Provisional 24.6 34 0.00073 31.6 0.9 12 189-200 309-320 (322)
88 COG1645 Uncharacterized Zn-fin 24.3 34 0.00074 27.7 0.7 12 79-90 41-52 (131)
89 COG5151 SSL1 RNA polymerase II 23.5 33 0.00071 32.0 0.6 12 79-90 305-316 (421)
90 PHA03126 dUTPase; Provisional 23.2 37 0.0008 31.4 0.8 13 188-200 312-324 (326)
91 KOG1146 Homeobox protein [Gene 23.2 25 0.00053 38.2 -0.3 33 81-113 1327-1359(1406)
92 KOG1144 Translation initiation 23.1 1.5E+02 0.0032 31.2 5.0 14 122-135 216-229 (1064)
93 TIGR03830 CxxCG_CxxCG_HTH puta 22.8 36 0.00079 25.7 0.6 18 80-97 29-46 (127)
94 PRK09812 toxin ChpB; Provision 22.5 78 0.0017 24.4 2.4 52 81-132 61-114 (116)
95 PF09888 DUF2115: Uncharacteri 22.4 42 0.00091 27.8 1.0 26 68-93 116-148 (163)
96 PF13240 zinc_ribbon_2: zinc-r 22.4 43 0.00093 18.9 0.7 13 84-96 1-13 (23)
97 PF10825 DUF2752: Protein of u 22.2 32 0.0007 23.1 0.2 12 80-91 7-18 (52)
98 TIGR02930 vnfG_nitrog V-contai 21.9 36 0.00078 26.8 0.4 14 11-24 16-29 (109)
99 smart00614 ZnF_BED BED zinc fi 21.3 43 0.00093 21.9 0.7 23 82-104 18-45 (50)
100 PHA03129 dUTPase; Provisional 20.6 45 0.00098 32.0 0.9 13 188-200 422-434 (436)
101 PF07430 PP1: Phloem filament 20.5 40 0.00088 29.1 0.5 38 81-125 47-84 (202)
102 PF13842 Tnp_zf-ribbon_2: DDE_ 20.3 47 0.001 20.2 0.6 13 80-92 14-26 (32)
103 cd00085 HNHc HNH nucleases; HN 20.2 44 0.00095 20.8 0.5 25 83-107 12-36 (57)
104 KOG1512 PHD Zn-finger protein 20.1 42 0.00092 30.9 0.6 15 81-95 328-342 (381)
No 1
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=100.00 E-value=9.6e-64 Score=411.29 Aligned_cols=191 Identities=59% Similarity=0.880 Sum_probs=168.8
Q ss_pred CCCCCCccccccCHHHHHHHHHhHHHHhhhcccccccCCCCCCCCCCcccccccchhhhcCCceEecCCCCCCCCCcccc
Q 028899 6 PAGVDNTFRRKFDREEYLERAREREREEADGRSKSKAKGPPVQRKPLKHRDYVVDLESRLGKTQVVTPIAPLSQQAGYYC 85 (202)
Q Consensus 6 ~~~~d~~~RRtWDreeYa~kA~~r~~~~~e~~~~~~~~~~~~~~~~Lk~R~~~ldL~~~lgK~~vv~~~~~~~~~~GfyC 85 (202)
..++.++||||||++||+..|++|....-. .+...+|+++++|++|+|.+||++.||+++||+..+|.+++|||||
T Consensus 3 ~~t~g~~~RRkwD~eEy~e~Ar~r~~d~~~----~~k~~~~vqre~L~~rdykvdl~sKLgkt~vitk~tp~sq~~GyyC 78 (193)
T KOG4727|consen 3 SGTTGNDFRRKWDKEEYEELARERLLDRIV----LKKDGPPVQREHLKHRDYKVDLESKLGKTVVITKSTPRSQKGGYYC 78 (193)
T ss_pred CCCCCcchhhccCHHHHHHHHHHhhhhhhH----HhhcCCchhHHHHhhhhhhhHhHhhccceeEeccCCcccccCceee
Confidence 345568899999999999999999876421 2235788999999999999999999999999999999999999999
Q ss_pred cCCCCccccchhhhhhhcCHHHHHHcCCCceeeeccHHHHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHH
Q 028899 86 SVCECVVKDSANYLDHINGKKHQRALGMSMRVERASLDQVRERFELLKKRKVPGSFSEQDLDERIIKQQEEEEERRRQRR 165 (202)
Q Consensus 86 ~vCd~~~kDs~~~ldH~n~k~H~~~~G~sm~VersTle~Vk~rl~~lk~kk~~~~~~~~~~~eRl~~~~eeEe~~r~~rk 165 (202)
+||||+|+||++|||||||+.|++++||||+|+|+||+||+.||+.++.+..+ ....++|++||.+.+++|++.+..++
T Consensus 79 dVCdcvvKDSinflDHiNgKkHqrnlgmsm~verst~~qv~erf~~~k~k~~~-~~ke~~vE~r~~e~qeee~rlkd~~k 157 (193)
T KOG4727|consen 79 DVCDCVVKDSINFLDHINGKKHQRNLGMSMRVERSTLDQVKERFEQNKKKMEE-KQKEYDVEERLRETQEEEERLKDTRK 157 (193)
T ss_pred eecceeehhhHHHHHHhccHHHHHHHhhhhcchhhhHHHHHHHHHHHHHhhhh-hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999995543 34688999999999999999999999
Q ss_pred HHHHHHHHHHHhhhhcCCCCHHHHHhcCCCCCCCCCC
Q 028899 166 EKKKEKKKEKAAVEEETEMDPDIAAMMGFGSFHSSKK 202 (202)
Q Consensus 166 ekkk~kk~~~~~~e~~~~~d~emaamMGF~gFGssKK 202 (202)
++++++|+...+. .+.+.+|+|+|||||||||+|||
T Consensus 158 EK~ke~K~~t~~d-i~~es~~~~~amMGFSgF~tsKk 193 (193)
T KOG4727|consen 158 EKKKEKKRATKED-IDFESKDEMAAMMGFSGFGTSKK 193 (193)
T ss_pred HHHHHHhhccccc-ccccccHHHHHHhCccccccCCC
Confidence 9997766664322 23345699999999999999997
No 2
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.78 E-value=2.9e-09 Score=65.56 Aligned_cols=32 Identities=31% Similarity=0.833 Sum_probs=29.8
Q ss_pred CcccccCCCCccccchhhhhhhcCHHHHHHcC
Q 028899 81 AGYYCSVCECVVKDSANYLDHINGKKHQRALG 112 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G 112 (202)
++|||++|+.+|.++.+|..|++|++|..++.
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~ 33 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKGKKHKKNVK 33 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHChHHHHHHHH
Confidence 68999999999999999999999999998764
No 3
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=98.71 E-value=7.2e-09 Score=61.21 Aligned_cols=26 Identities=27% Similarity=0.756 Sum_probs=25.3
Q ss_pred ccccCCCCccccchhhhhhhcCHHHH
Q 028899 83 YYCSVCECVVKDSANYLDHINGKKHQ 108 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n~k~H~ 108 (202)
|||++||+.|.+..+|..|++|+.|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCcccCCCCcCCHHHHHHHHccCCCC
Confidence 89999999999999999999999995
No 4
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=98.44 E-value=7.8e-08 Score=55.24 Aligned_cols=25 Identities=28% Similarity=0.783 Sum_probs=24.5
Q ss_pred ccccCCCCccccchhhhhhhcCHHH
Q 028899 83 YYCSVCECVVKDSANYLDHINGKKH 107 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n~k~H 107 (202)
|||++|+.+|.+..+|..|++|+.|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 8999999999999999999999998
No 5
>PF08648 DUF1777: Protein of unknown function (DUF1777); InterPro: IPR013957 This entry shows eukaryotic proteins of unknown function. Some of the proteins are putative nucleic acid binding proteins.
Probab=98.01 E-value=1.9e-06 Score=71.35 Aligned_cols=16 Identities=44% Similarity=0.929 Sum_probs=14.8
Q ss_pred HHHHHhcCCCCCCCCC
Q 028899 186 PDIAAMMGFGSFHSSK 201 (202)
Q Consensus 186 ~emaamMGF~gFGssK 201 (202)
.+||+||||+||||||
T Consensus 127 ~~mmk~MGf~gF~TTK 142 (180)
T PF08648_consen 127 EEMMKMMGFGGFGTTK 142 (180)
T ss_pred HHHHHhhcccccccCC
Confidence 4799999999999997
No 6
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=97.81 E-value=1e-05 Score=51.98 Aligned_cols=31 Identities=32% Similarity=0.621 Sum_probs=17.9
Q ss_pred CcccccCCCCcc-ccch-hhhhhhcCHHHHHHc
Q 028899 81 AGYYCSVCECVV-KDSA-NYLDHINGKKHQRAL 111 (202)
Q Consensus 81 ~GfyC~vCd~~~-kDs~-~~ldH~n~k~H~~~~ 111 (202)
+-|||++|++.| .|+. ....|.+|.+|+.+.
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv 34 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHERGWKHKENV 34 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT--THHHHHH
T ss_pred cCeecccccceecCCChHHHHHhhccHHHHHHH
Confidence 569999999999 7884 669999999999864
No 7
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=9.9e-05 Score=69.95 Aligned_cols=29 Identities=34% Similarity=0.609 Sum_probs=27.5
Q ss_pred cccccCCCCccccchhhhhhhcCHHHHHH
Q 028899 82 GYYCSVCECVVKDSANYLDHINGKKHQRA 110 (202)
Q Consensus 82 GfyC~vCd~~~kDs~~~ldH~n~k~H~~~ 110 (202)
-+||.||+.+|+.-.++.+|+||++|..+
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHken 320 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKEN 320 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHH
Confidence 39999999999999999999999999876
No 8
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=97.18 E-value=0.00017 Score=57.46 Aligned_cols=34 Identities=24% Similarity=0.485 Sum_probs=31.1
Q ss_pred CCCCcccccCCCCccccchhhhhhhcCHHHHHHc
Q 028899 78 SQQAGYYCSVCECVVKDSANYLDHINGKKHQRAL 111 (202)
Q Consensus 78 ~~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~ 111 (202)
.+.|-|||=.|.+.|.|+..+.-|..++.|.+++
T Consensus 53 PG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRv 86 (129)
T KOG3408|consen 53 PGGGQFYCIECARYFIDAKALKTHFKTKVHKRRV 86 (129)
T ss_pred CCCceeehhhhhhhhcchHHHHHHHhccHHHHHH
Confidence 3778899999999999999999999999998754
No 9
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=96.86 E-value=0.00042 Score=57.62 Aligned_cols=31 Identities=32% Similarity=0.731 Sum_probs=26.8
Q ss_pred CcccccCCC-Cccccch-hhhhhhcCHHHHHHc
Q 028899 81 AGYYCSVCE-CVVKDSA-NYLDHINGKKHQRAL 111 (202)
Q Consensus 81 ~GfyC~vCd-~~~kDs~-~~ldH~n~k~H~~~~ 111 (202)
.-|||++|| ..+.||+ .-.-|++|++|+.+.
T Consensus 2 pRYyCDYCdt~LthDslsvRK~H~~GrkH~~nv 34 (165)
T KOG3454|consen 2 PRYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNV 34 (165)
T ss_pred CcchhhhhhhhhhcccHHHHHhhhhhHHHHHHH
Confidence 469999999 8899998 567999999998763
No 10
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.24 E-value=0.0014 Score=36.50 Aligned_cols=22 Identities=23% Similarity=0.587 Sum_probs=20.4
Q ss_pred ccccCCCCccccchhhhhhhcC
Q 028899 83 YYCSVCECVVKDSANYLDHING 104 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n~ 104 (202)
|-|++|+..|.+..+|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 6799999999999999999874
No 11
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=95.98 E-value=0.0013 Score=58.85 Aligned_cols=34 Identities=29% Similarity=0.602 Sum_probs=30.7
Q ss_pred CCCcccccCCCCccccchhhhhhhcCHHHHHHcC
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHINGKKHQRALG 112 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G 112 (202)
+..-|||..|.+.|+|-+.|..|+-|..|+|.+-
T Consensus 22 QKlRwyCqmCQkQcrDeNGFkCH~~SeSHqRql~ 55 (309)
T KOG2837|consen 22 QKLRWYCQMCQKQCRDENGFKCHTMSESHQRQLL 55 (309)
T ss_pred HHHHHHHHHHHHHhccccccccccCCHHHHHHHH
Confidence 3468999999999999999999999999998654
No 12
>KOG3263 consensus Nucleic acid binding protein [General function prediction only]
Probab=95.98 E-value=0.0034 Score=52.90 Aligned_cols=16 Identities=31% Similarity=0.756 Sum_probs=14.9
Q ss_pred HHHHHhcCCCCCCCCC
Q 028899 186 PDIAAMMGFGSFHSSK 201 (202)
Q Consensus 186 ~emaamMGF~gFGssK 201 (202)
.||++||||+||-|||
T Consensus 144 iEMmk~MGf~gFDtTk 159 (196)
T KOG3263|consen 144 IEMMKIMGFSGFDTTK 159 (196)
T ss_pred HHHHHHhCcCcccCCC
Confidence 5899999999999987
No 13
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=95.85 E-value=0.0068 Score=41.07 Aligned_cols=42 Identities=24% Similarity=0.474 Sum_probs=30.8
Q ss_pred ccccCCCCccccchhhhhhhcCHHHHHHcCCCceeeeccHHHHHHHH
Q 028899 83 YYCSVCECVVKDSANYLDHINGKKHQRALGMSMRVERASLDQVRERF 129 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~sm~VersTle~Vk~rl 129 (202)
-||+.|-..|.| |..||.|++|+.-..-+.+.. .||.+-.+|
T Consensus 6 GYCE~C~~ky~~---l~~Hi~s~~Hr~FA~~~~Nf~--~lD~li~~l 47 (49)
T PF07535_consen 6 GYCENCRVKYDD---LEEHIQSEKHRKFAENDSNFK--ELDSLISQL 47 (49)
T ss_pred ccCccccchhhh---HHHHhCCHHHHHHHcCcccHH--HHHHHHHHh
Confidence 499999999986 999999999998665555432 255554443
No 14
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=95.68 E-value=0.0045 Score=53.32 Aligned_cols=30 Identities=27% Similarity=0.616 Sum_probs=24.4
Q ss_pred CCCcccccCCCCccccchhhhhhhcCHHHHH
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHINGKKHQR 109 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~ 109 (202)
.-.+|||++||..|.+|. +..|+.|--|+-
T Consensus 81 ~e~lfyCE~Cd~~ip~~~-~snH~tSttHll 110 (223)
T KOG2384|consen 81 DEALFYCEVCDIYIPNSK-KSNHFTSTTHLL 110 (223)
T ss_pred CCccchhhhhhhhccCCC-CccchhhHHHHh
Confidence 668999999999999863 567888888863
No 15
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=95.55 E-value=0.0047 Score=48.48 Aligned_cols=34 Identities=24% Similarity=0.443 Sum_probs=31.0
Q ss_pred CCCCcccccCCCCccccchhhhhhhcCHHHHHHc
Q 028899 78 SQQAGYYCSVCECVVKDSANYLDHINGKKHQRAL 111 (202)
Q Consensus 78 ~~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~ 111 (202)
.+.+.|||=.|++.|-.+..++.|..|+-|.|++
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~ 84 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKKGKVHKRRA 84 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhccchhHHHH
Confidence 3677899999999999999999999999998764
No 16
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=95.25 E-value=0.0079 Score=34.66 Aligned_cols=22 Identities=14% Similarity=0.379 Sum_probs=20.2
Q ss_pred ccccCCCCccccchhhhhhhcC
Q 028899 83 YYCSVCECVVKDSANYLDHING 104 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n~ 104 (202)
|.|.+|+..|.+..+|..|+..
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCccCCccCChhHHHHHhHH
Confidence 7899999999999999999853
No 17
>PLN02748 tRNA dimethylallyltransferase
Probab=94.80 E-value=0.016 Score=55.46 Aligned_cols=32 Identities=22% Similarity=0.642 Sum_probs=28.9
Q ss_pred CcccccCCCC-ccccchhhhhhhcCHHHHHHcC
Q 028899 81 AGYYCSVCEC-VVKDSANYLDHINGKKHQRALG 112 (202)
Q Consensus 81 ~GfyC~vCd~-~~kDs~~~ldH~n~k~H~~~~G 112 (202)
--|+|++|+. ++.--.+|.-|++|+.|.+++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~ 449 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQ 449 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHh
Confidence 5689999997 9999999999999999998754
No 18
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=94.61 E-value=0.015 Score=31.72 Aligned_cols=21 Identities=14% Similarity=0.607 Sum_probs=17.6
Q ss_pred ccccCCCCccccchhhhhhhc
Q 028899 83 YYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n 103 (202)
|-|++|+..|.+...|..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 789999999999999999975
No 19
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=94.46 E-value=0.011 Score=42.76 Aligned_cols=30 Identities=17% Similarity=0.530 Sum_probs=26.0
Q ss_pred cccccCCCCccccchhhhhhhcCHHHHHHc
Q 028899 82 GYYCSVCECVVKDSANYLDHINGKKHQRAL 111 (202)
Q Consensus 82 GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~ 111 (202)
.|.|.+|+..|.+..++..|+++..|....
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~ 79 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRN 79 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCcc
Confidence 699999999999999999999999887643
No 20
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=94.38 E-value=0.017 Score=39.19 Aligned_cols=26 Identities=27% Similarity=0.496 Sum_probs=22.3
Q ss_pred ccccCCCCccccchhhhhhhcCHHHHHHc
Q 028899 83 YYCSVCECVVKDSANYLDHINGKKHQRAL 111 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n~k~H~~~~ 111 (202)
-||+.|-.-|. .|..||.|++|..-.
T Consensus 6 GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA 31 (49)
T smart00586 6 GYCENCREKYD---DLETHLLSEKHRRFA 31 (49)
T ss_pred cccccHhHHHh---hHHHHhccHHHHHHH
Confidence 49999999997 488999999998643
No 21
>PHA02768 hypothetical protein; Provisional
Probab=94.32 E-value=0.017 Score=40.08 Aligned_cols=26 Identities=23% Similarity=0.657 Sum_probs=23.7
Q ss_pred CcccccCCCCccccchhhhhhhcCHHHH
Q 028899 81 AGYYCSVCECVVKDSANYLDHINGKKHQ 108 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n~k~H~ 108 (202)
.||.|+.|+..|..+.+|..|.+. |.
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~--H~ 29 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRK--HN 29 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHh--cC
Confidence 599999999999999999999776 66
No 22
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=93.80 E-value=0.02 Score=53.21 Aligned_cols=31 Identities=26% Similarity=0.498 Sum_probs=28.9
Q ss_pred CCcccccCCCCccccchhhhhhhcCHHHHHH
Q 028899 80 QAGYYCSVCECVVKDSANYLDHINGKKHQRA 110 (202)
Q Consensus 80 ~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~ 110 (202)
-.+|||++|.+-|.-+.-|.-|+-|+.|.++
T Consensus 236 ~~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~ 266 (470)
T COG5188 236 FPKVYCVKCGREFSRSKVFEYHLEGKRHCKE 266 (470)
T ss_pred ccceeeHhhhhHhhhhHHHHHHHhhhhhhhh
Confidence 3689999999999999999999999999875
No 23
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.37 E-value=0.023 Score=39.98 Aligned_cols=34 Identities=26% Similarity=0.550 Sum_probs=27.4
Q ss_pred CCCcccccCCCCccccchhhhhhhcCHHHHHHcCC
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHINGKKHQRALGM 113 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~ 113 (202)
+.--|-|+-||..|+++-+|..|.| +.|....|-
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVN-KaH~~~~~r 47 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVN-KAHGWLFGR 47 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhh-HHhhhhhcC
Confidence 3345789999999999999999999 667655543
No 24
>smart00355 ZnF_C2H2 zinc finger.
Probab=93.23 E-value=0.045 Score=29.87 Aligned_cols=21 Identities=29% Similarity=0.657 Sum_probs=19.5
Q ss_pred ccccCCCCccccchhhhhhhc
Q 028899 83 YYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n 103 (202)
|-|+.|+..|....++..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 679999999999999999986
No 25
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=93.10 E-value=0.1 Score=46.09 Aligned_cols=47 Identities=34% Similarity=0.591 Sum_probs=35.3
Q ss_pred CCCCcccccCCC--Cccccch-hhhhhhcCHHHHHHcCCCceeeeccHHHHHHHHHHHHHhh
Q 028899 78 SQQAGYYCSVCE--CVVKDSA-NYLDHINGKKHQRALGMSMRVERASLDQVRERFELLKKRK 136 (202)
Q Consensus 78 ~~~~GfyC~vCd--~~~kDs~-~~ldH~n~k~H~~~~G~sm~VersTle~Vk~rl~~lk~kk 136 (202)
..+-.-.|+||+ ++.-|+. .+.||+.||.|+- --.||..|+.|+++.
T Consensus 186 ~~qkl~VCeVCGA~Ls~~D~d~RladH~~GK~HlG------------y~~IR~~l~el~e~~ 235 (254)
T PF03194_consen 186 QQQKLEVCEVCGAFLSVGDNDRRLADHFGGKQHLG------------YAKIREKLKELKEKR 235 (254)
T ss_pred cccCccchhhhhhHHhccchHHHHHHHhccchhhh------------HHHHHHHHHHHHHHH
Confidence 356678999999 5566886 5789999999974 445677777776653
No 26
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=91.09 E-value=0.098 Score=47.74 Aligned_cols=43 Identities=26% Similarity=0.531 Sum_probs=34.2
Q ss_pred CCCcccccCCCCccccch-hhhhhhcCHHHHHHcCCCceeeeccHHHHHHHHHHHHHh
Q 028899 79 QQAGYYCSVCECVVKDSA-NYLDHINGKKHQRALGMSMRVERASLDQVRERFELLKKR 135 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~-~~ldH~n~k~H~~~~G~sm~VersTle~Vk~rl~~lk~k 135 (202)
.++-+||++|-|-|.|+. +-.-|-.|+.|+-+ |..||..+.++
T Consensus 7 S~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~--------------V~Kritdi~rk 50 (336)
T KOG0150|consen 7 SQPKKFCDYCKIWIKDNPASVRFHERGKRHKEN--------------VAKRITDIHRK 50 (336)
T ss_pred hccchhhhhhhhhhcCChHHHHhHhhhhHHHHH--------------HHHHHHHHHHh
Confidence 467899999999999997 67789999999854 56666665554
No 27
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=90.92 E-value=0.075 Score=49.62 Aligned_cols=38 Identities=24% Similarity=0.441 Sum_probs=32.5
Q ss_pred CCCcccccCCCCccccchhhhhhhcCHHHHHHcCCCce
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHINGKKHQRALGMSMR 116 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~sm~ 116 (202)
..+-|||.+|.+.|.-..++.+||+|+.|.-++....+
T Consensus 65 ~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 65 AESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred cccceehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 56788999999999999999999999999876654433
No 28
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.58 E-value=0.22 Score=44.03 Aligned_cols=36 Identities=31% Similarity=0.643 Sum_probs=30.2
Q ss_pred cCCCCCCCCCcccccCCCCccccchhhhhhhcCHHHH
Q 028899 72 TPIAPLSQQAGYYCSVCECVVKDSANYLDHINGKKHQ 108 (202)
Q Consensus 72 ~~~~~~~~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~ 108 (202)
+....+...+-..|-||+...+ -.-|.-|+||++|.
T Consensus 25 splakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHr 60 (264)
T KOG3032|consen 25 SPLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHR 60 (264)
T ss_pred cHhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHH
Confidence 3344456778889999999999 77899999999996
No 29
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=89.22 E-value=0.11 Score=44.47 Aligned_cols=36 Identities=25% Similarity=0.543 Sum_probs=0.0
Q ss_pred CCcccccCCC-CccccchhhhhhhcCHHHH---HHcCCCc
Q 028899 80 QAGYYCSVCE-CVVKDSANYLDHINGKKHQ---RALGMSM 115 (202)
Q Consensus 80 ~~GfyC~vCd-~~~kDs~~~ldH~n~k~H~---~~~G~sm 115 (202)
.--|+|+||+ .+|+-..+|..|++...|. +.||.+.
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI~n 138 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGIPN 138 (196)
T ss_dssp ----------------------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcChhHHHccChhcCCCC
Confidence 4579999996 6788999999999999995 7788773
No 30
>PF14968 CCDC84: Coiled coil protein 84
Probab=87.05 E-value=0.2 Score=46.12 Aligned_cols=55 Identities=20% Similarity=0.509 Sum_probs=38.8
Q ss_pred ccccccchhhhcCCceEecCCCCCCCCCcccccCCCCccccc------hhhhhhhcCHHHHHH
Q 028899 54 HRDYVVDLESRLGKTQVVTPIAPLSQQAGYYCSVCECVVKDS------ANYLDHINGKKHQRA 110 (202)
Q Consensus 54 ~R~~~ldL~~~lgK~~vv~~~~~~~~~~GfyC~vCd~~~kDs------~~~ldH~n~k~H~~~ 110 (202)
.+...-|+-.-|.+.++..... .....|+|-.||+-+.+. ...|.||.|+.|+.+
T Consensus 32 f~~Kl~d~R~~lk~p~v~~~~~--~~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLaS~eH~k~ 92 (336)
T PF14968_consen 32 FRSKLSDARFFLKKPSVLRYDP--EHRNRFWCVFCDCEVREHDSSFACGGAIEHLASPEHRKN 92 (336)
T ss_pred HHHHHHHHHHHHhCCccCCCCc--cccceeEeeCccchhhhccchhhhccHHhhcCCHHHHHH
Confidence 3444444544455555544322 356789999999999998 688999999999853
No 31
>PTZ00448 hypothetical protein; Provisional
Probab=86.37 E-value=0.52 Score=44.02 Aligned_cols=31 Identities=16% Similarity=0.281 Sum_probs=28.4
Q ss_pred cccccCCCCccccchhhhhhhcCHHHHHHcC
Q 028899 82 GYYCSVCECVVKDSANYLDHINGKKHQRALG 112 (202)
Q Consensus 82 GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G 112 (202)
-|-|..|+..|.|+..+-+|..|--|..|+-
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLK 344 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEWHIFNTK 344 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhHHHHHHH
Confidence 5889999999999999999999999997764
No 32
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=85.28 E-value=0.57 Score=42.94 Aligned_cols=47 Identities=36% Similarity=0.545 Sum_probs=34.3
Q ss_pred CCCcccccCCCCccc--cch-hhhhhhcCHHHHHHcCCCceeeeccHHHHHHHHHHHHHhhC
Q 028899 79 QQAGYYCSVCECVVK--DSA-NYLDHINGKKHQRALGMSMRVERASLDQVRERFELLKKRKV 137 (202)
Q Consensus 79 ~~~GfyC~vCd~~~k--Ds~-~~ldH~n~k~H~~~~G~sm~VersTle~Vk~rl~~lk~kk~ 137 (202)
.+..=.|+||+..+. |+. .+.||++||.|+- --.|+++|+.|++...
T Consensus 183 ~qkl~VCeVCGa~L~~~D~d~RlaDHf~GKlHlG------------y~~iR~~l~eLk~~~~ 232 (319)
T KOG0796|consen 183 QQKLRVCEVCGAFLSVNDADRRLADHFGGKLHLG------------YVLIREKLAELKKEKA 232 (319)
T ss_pred hhhhhHHHhhhHHHhccchHHHHHHhhcchHHHH------------HHHHHHHHHHHHHHHh
Confidence 455669999997654 554 6779999999974 3456777777776543
No 33
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=85.15 E-value=0.37 Score=41.56 Aligned_cols=33 Identities=36% Similarity=0.736 Sum_probs=29.2
Q ss_pred CCCcccccCCCCccccchhhhhhhcCHHHHHHc
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHINGKKHQRAL 111 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~ 111 (202)
-.+-|-|.+|-..--.-.+|+.|.-|++|+-|+
T Consensus 50 h~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nl 82 (222)
T KOG0227|consen 50 HLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNL 82 (222)
T ss_pred cCcceeehhhhhhhcchhhhhhhhccchhhHHH
Confidence 557899999998888889999999999998755
No 34
>PHA00616 hypothetical protein
Probab=84.88 E-value=0.24 Score=32.89 Aligned_cols=22 Identities=18% Similarity=0.603 Sum_probs=20.3
Q ss_pred ccccCCCCccccchhhhhhhcC
Q 028899 83 YYCSVCECVVKDSANYLDHING 104 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n~ 104 (202)
|-|..|+..|....++..|+++
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~ 23 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLS 23 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHH
Confidence 7899999999999999999953
No 35
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=79.56 E-value=0.96 Score=26.16 Aligned_cols=20 Identities=15% Similarity=0.370 Sum_probs=15.7
Q ss_pred ccccCCCCccccchhhhhhhc
Q 028899 83 YYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n 103 (202)
.-|++|++.| -..++..|++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3599999999 5667878864
No 36
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=79.19 E-value=0.87 Score=31.43 Aligned_cols=22 Identities=27% Similarity=0.655 Sum_probs=16.0
Q ss_pred cccccCCCCccccchhhhhhhc
Q 028899 82 GYYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 82 GfyC~vCd~~~kDs~~~ldH~n 103 (202)
.--|++|+.++.-+.++-.|+-
T Consensus 24 PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCcchhhccchhhHHHHHH
Confidence 4589999999999999999874
No 37
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=78.28 E-value=0.71 Score=46.44 Aligned_cols=30 Identities=23% Similarity=0.718 Sum_probs=27.7
Q ss_pred CCCcccccCCCCccccchhhhhhhcCHHHH
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHINGKKHQ 108 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~ 108 (202)
+---|.|.+|||-|.|-++-+=|||+.+|.
T Consensus 356 K~~~f~cKlcdckf~d~nak~mhl~grRhr 385 (816)
T KOG3792|consen 356 KLLRFHCKLCDCKFNDPNAKEMHLKGRRHR 385 (816)
T ss_pred chHhhhhhhhcCCCCCcchHHhhhhccccc
Confidence 456799999999999999999999999995
No 38
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=78.17 E-value=0.99 Score=38.73 Aligned_cols=33 Identities=27% Similarity=0.590 Sum_probs=29.8
Q ss_pred CCCcccccCCCCccccchhhhhhhcCHHHHHHc
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHINGKKHQRAL 111 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~ 111 (202)
-.+-|-|-+|...--.-.+|+.|+-|++|.-|+
T Consensus 50 h~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~ 82 (222)
T COG5246 50 HTGKYVCLLCKTKHLTEMSYVKHREGKKHKENS 82 (222)
T ss_pred CCCcEEeeeeccccccHHHHHHhhccchhhhhH
Confidence 567899999999999999999999999998664
No 39
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=71.07 E-value=1.1 Score=37.49 Aligned_cols=49 Identities=20% Similarity=0.404 Sum_probs=35.8
Q ss_pred CcccccCCCCccccch-hhhhhhcCHHHHHHcCCCc-eeeeccHHHHHHHH
Q 028899 81 AGYYCSVCECVVKDSA-NYLDHINGKKHQRALGMSM-RVERASLDQVRERF 129 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~-~~ldH~n~k~H~~~~G~sm-~VersTle~Vk~rl 129 (202)
-.++|..||...-... +...||.|..|++|.-.-| ..+|++|.=-+.-|
T Consensus 90 Ea~hCsACd~~IP~~~~~vQ~Hl~S~~H~~Nrr~~~eq~Kr~sl~vA~Sil 140 (165)
T PF04988_consen 90 EAAHCSACDVFIPMQHSSVQKHLKSQDHNKNRRAMMEQSKRSSLSVARSIL 140 (165)
T ss_pred HHhhhhHhhhhccCcHHHHHHHhccHHHHhhHHHHHHHHHHHHHHHHHHHh
Confidence 3569999999999886 5569999999998875444 45666665444444
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=70.88 E-value=2 Score=23.85 Aligned_cols=20 Identities=25% Similarity=0.635 Sum_probs=15.2
Q ss_pred ccccCCCCccccchhhhhhhc
Q 028899 83 YYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n 103 (202)
|-|+.|+-... ...+..|+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~ 20 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLK 20 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHH
Confidence 67999998888 778999875
No 41
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=70.52 E-value=2.2 Score=28.58 Aligned_cols=22 Identities=14% Similarity=0.437 Sum_probs=18.4
Q ss_pred cccccCCCCccccchhhhhhhcC
Q 028899 82 GYYCSVCECVVKDSANYLDHING 104 (202)
Q Consensus 82 GfyC~vCd~~~kDs~~~ldH~n~ 104 (202)
.|-|++|+. .-|..+|+.|++.
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~ 23 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCED 23 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHh
Confidence 488999999 5677899999874
No 42
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=70.35 E-value=1.7 Score=25.02 Aligned_cols=12 Identities=25% Similarity=0.612 Sum_probs=10.6
Q ss_pred cccccCCCCccc
Q 028899 82 GYYCSVCECVVK 93 (202)
Q Consensus 82 GfyC~vCd~~~k 93 (202)
-|-|++|+..|.
T Consensus 14 ~~~C~~C~k~F~ 25 (26)
T PF13465_consen 14 PYKCPYCGKSFS 25 (26)
T ss_dssp SEEESSSSEEES
T ss_pred CCCCCCCcCeeC
Confidence 499999999985
No 43
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=69.83 E-value=3.8 Score=38.54 Aligned_cols=57 Identities=16% Similarity=0.287 Sum_probs=48.3
Q ss_pred CcccccCCCCccccchhhhhhhcCHHHHHHcCC-CceeeeccHHHHHHHHHHHHHhhC
Q 028899 81 AGYYCSVCECVVKDSANYLDHINGKKHQRALGM-SMRVERASLDQVRERFELLKKRKV 137 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~-sm~VersTle~Vk~rl~~lk~kk~ 137 (202)
.||-|..|...|.+.-.--.|..|--|..||-- --.+.-.|+++.-+|+......++
T Consensus 2 t~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~ 59 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKE 59 (390)
T ss_pred CcceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhh
Confidence 689999999999999999999999999987743 235778899999999988776654
No 44
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=66.26 E-value=4.1 Score=39.20 Aligned_cols=63 Identities=21% Similarity=0.273 Sum_probs=42.9
Q ss_pred cccccccchhhhcCCceEecCCCCC-----------CCCCcccccCCC-CccccchhhhhhhcCHHHH---HHcCCCc
Q 028899 53 KHRDYVVDLESRLGKTQVVTPIAPL-----------SQQAGYYCSVCE-CVVKDSANYLDHINGKKHQ---RALGMSM 115 (202)
Q Consensus 53 k~R~~~ldL~~~lgK~~vv~~~~~~-----------~~~~GfyC~vCd-~~~kDs~~~ldH~n~k~H~---~~~G~sm 115 (202)
..++..+|=+.-++...-.+.+-.+ +-.--|-|+||+ .+++-..+|..|.|.-.|. |-+|++.
T Consensus 361 ~~~e~~~de~~~~ynp~~lPLGwDGkPiPyWLyKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCLGIpn 438 (497)
T KOG2636|consen 361 SDEESDDDEEELIYNPKNLPLGWDGKPIPYWLYKLHGLDIEYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCLGIPN 438 (497)
T ss_pred cccccccchhhccCCcccCCCCCCCCcCchHHHhhcCCCcccceeeccCccccCcHHHHHHhHHHHHhhcceecCCCC
Confidence 3445555555455555545443221 123468999999 9999999999999999997 5667664
No 45
>PF14968 CCDC84: Coiled coil protein 84
Probab=62.67 E-value=3.5 Score=38.14 Aligned_cols=26 Identities=35% Similarity=0.650 Sum_probs=22.1
Q ss_pred cccCCCCccccchhhhhhhcCHHHHHHcC
Q 028899 84 YCSVCECVVKDSANYLDHINGKKHQRALG 112 (202)
Q Consensus 84 yC~vCd~~~kDs~~~ldH~n~k~H~~~~G 112 (202)
||.||.++.- +...|+-++.|+++|-
T Consensus 1 yC~vCr~~h~---~gr~H~Y~~~Hq~~L~ 26 (336)
T PF14968_consen 1 YCEVCRRNHD---QGRRHVYSPKHQKSLS 26 (336)
T ss_pred CcchhhCccc---ccCCCccCHHHHHHHH
Confidence 9999998753 4899999999998774
No 46
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=62.54 E-value=2.3 Score=39.70 Aligned_cols=31 Identities=26% Similarity=0.592 Sum_probs=27.7
Q ss_pred CCCcccccCCCCccccchhhhhhhcCHHHHH
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHINGKKHQR 109 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~ 109 (202)
+--.|-|=+|...|+|...+.+|.|-+.|.+
T Consensus 192 kL~r~~CLyCekifrdkntLkeHMrkK~Hrr 222 (423)
T KOG2482|consen 192 KLERLRCLYCEKIFRDKNTLKEHMRKKRHRR 222 (423)
T ss_pred HHhhheeeeeccccCCcHHHHHHHHhccCcc
Confidence 3457889999999999999999999999975
No 47
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=62.46 E-value=2.4 Score=43.19 Aligned_cols=24 Identities=17% Similarity=0.472 Sum_probs=21.5
Q ss_pred CCCcccccCCCCccccchhhhhhh
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHI 102 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~ 102 (202)
..+.|-|+.||.+|--+.+++.|-
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHK 914 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHK 914 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhh
Confidence 568899999999999999999883
No 48
>PF06658 DUF1168: Protein of unknown function (DUF1168); InterPro: IPR009548 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=61.52 E-value=16 Score=29.89 Aligned_cols=49 Identities=22% Similarity=0.466 Sum_probs=30.0
Q ss_pred HHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028899 127 ERFELLKKRKVPGSFSEQDLDERIIKQQEEEEERRRQRREKKKEKKKEKA 176 (202)
Q Consensus 127 ~rl~~lk~kk~~~~~~~~~~~eRl~~~~eeEe~~r~~rkekkk~kk~~~~ 176 (202)
+||..+-..-... .....|+.++.+....++++-.++++++..+|+++.
T Consensus 50 ~Rl~~me~~~~~e-~~~~eF~~kree~~~~~eekTaKkR~KR~KkK~kk~ 98 (142)
T PF06658_consen 50 ERLEYMEEEAKKE-KEDEEFQRKREERKKEAEEKTAKKRAKRQKKKQKKK 98 (142)
T ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555554432211 123468889988888888877777777655555544
No 49
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=60.12 E-value=2.9 Score=29.77 Aligned_cols=27 Identities=26% Similarity=0.551 Sum_probs=0.0
Q ss_pred ccCCCCccccchhhhhhhcCHHHHHHcC
Q 028899 85 CSVCECVVKDSANYLDHINGKKHQRALG 112 (202)
Q Consensus 85 C~vCd~~~kDs~~~ldH~n~k~H~~~~G 112 (202)
|.+|+..|.+-..++.|++ ..|.-.+.
T Consensus 2 C~~C~~~f~~~~~l~~H~~-~~H~~~~~ 28 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMK-KKHGFDIP 28 (100)
T ss_dssp ----------------------------
T ss_pred ccccccccccccccccccc-cccccccc
Confidence 9999999999999999995 55654433
No 50
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=58.45 E-value=3.5 Score=36.25 Aligned_cols=31 Identities=29% Similarity=0.495 Sum_probs=23.6
Q ss_pred CCCcccccCCCCccccc---hhhhhhhcCHHHHH
Q 028899 79 QQAGYYCSVCECVVKDS---ANYLDHINGKKHQR 109 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs---~~~ldH~n~k~H~~ 109 (202)
.|--=.|.||+..+.-+ ..+.||+||+-|+-
T Consensus 182 hqklqvC~iCgayLsrlDtdrrladHf~GklHlG 215 (258)
T COG5200 182 HQKLQVCGICGAYLSRLDTDRRLADHFNGKLHLG 215 (258)
T ss_pred hhhhhhhhhhhhHHHhcchhhHHHHHhccchhhh
Confidence 34456899999876544 47889999999974
No 51
>PHA00732 hypothetical protein
Probab=55.93 E-value=6.5 Score=28.82 Aligned_cols=21 Identities=14% Similarity=0.411 Sum_probs=19.3
Q ss_pred ccccCCCCccccchhhhhhhc
Q 028899 83 YYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n 103 (202)
|-|+.|+..|....++..|+.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhh
Confidence 679999999999999999975
No 52
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=55.79 E-value=3.7 Score=27.52 Aligned_cols=20 Identities=10% Similarity=0.488 Sum_probs=10.6
Q ss_pred cccCCCCccccch--hhhhhhc
Q 028899 84 YCSVCECVVKDSA--NYLDHIN 103 (202)
Q Consensus 84 yC~vCd~~~kDs~--~~ldH~n 103 (202)
-||||++.|.+.. .++.+++
T Consensus 22 ~CPlC~r~l~~e~~~~li~~~~ 43 (54)
T PF04423_consen 22 CCPLCGRPLDEEHRQELIKKYK 43 (54)
T ss_dssp E-TTT--EE-HHHHHHHHHHHH
T ss_pred cCCCCCCCCCHHHHHHHHHHHH
Confidence 8999999998764 4444433
No 53
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=54.73 E-value=5.3 Score=35.46 Aligned_cols=26 Identities=31% Similarity=0.707 Sum_probs=23.4
Q ss_pred CCCcccccCCCCccccchhhhhhhcC
Q 028899 79 QQAGYYCSVCECVVKDSANYLDHING 104 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~~~ldH~n~ 104 (202)
...-|||=.|+..|+|.-.++.|.-|
T Consensus 236 R~eh~YC~fCG~~y~~~edl~ehCPG 261 (268)
T KOG1994|consen 236 RSEHYYCFFCGIKYKDEEDLYEHCPG 261 (268)
T ss_pred hccceEEEEeccccCCHHHHHHhCCC
Confidence 45789999999999999999999755
No 54
>KOG3634 consensus Troponin [Cytoskeleton]
Probab=53.83 E-value=17 Score=33.80 Aligned_cols=14 Identities=14% Similarity=0.052 Sum_probs=10.4
Q ss_pred HHHHHh-cCCCCCCC
Q 028899 186 PDIAAM-MGFGSFHS 199 (202)
Q Consensus 186 ~emaam-MGF~gFGs 199 (202)
--++.| ++|+|||.
T Consensus 180 ftvakk~a~~~~fgn 194 (361)
T KOG3634|consen 180 FTVAKKGAQNDGFGN 194 (361)
T ss_pred ceeecccccchhHHH
Confidence 456666 89999985
No 55
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=53.45 E-value=7.5 Score=22.67 Aligned_cols=19 Identities=26% Similarity=0.431 Sum_probs=14.5
Q ss_pred cccCCCCccccchhhhhhhc
Q 028899 84 YCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 84 yC~vCd~~~kDs~~~ldH~n 103 (202)
-|+||...+ .....-.||.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 599999999 5556667765
No 56
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=52.23 E-value=3.5 Score=34.77 Aligned_cols=37 Identities=24% Similarity=0.442 Sum_probs=26.5
Q ss_pred CcccccCCCCccc-cch-hhhhhhcCHHHHHHc-CCCcee
Q 028899 81 AGYYCSVCECVVK-DSA-NYLDHINGKKHQRAL-GMSMRV 117 (202)
Q Consensus 81 ~GfyC~vCd~~~k-Ds~-~~ldH~n~k~H~~~~-G~sm~V 117 (202)
+.|||++|...+. |++ ...-|+-|+.|.++. .+-|++
T Consensus 2 pRY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~dYY~~~ 41 (188)
T COG5136 2 PRYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDYYMEM 41 (188)
T ss_pred cchHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 4699999998764 555 456799999998654 334444
No 57
>PHA00733 hypothetical protein
Probab=51.91 E-value=7.8 Score=30.70 Aligned_cols=22 Identities=27% Similarity=0.602 Sum_probs=18.8
Q ss_pred cccccCCCCccccchhhhhhhc
Q 028899 82 GYYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 82 GfyC~vCd~~~kDs~~~ldH~n 103 (202)
.|-|++|+..|....++.+|+.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~ 120 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVC 120 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHH
Confidence 4889999999999999988864
No 58
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=45.99 E-value=20 Score=26.12 Aligned_cols=18 Identities=22% Similarity=0.606 Sum_probs=15.7
Q ss_pred CCCcccccCCCCccccch
Q 028899 79 QQAGYYCSVCECVVKDSA 96 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs~ 96 (202)
++++..|.+|++.+.|..
T Consensus 46 ~~~~~~C~~C~R~L~d~~ 63 (72)
T PF04640_consen 46 KGSGNICETCHRSLQDPY 63 (72)
T ss_pred CCCCCccCCCCCCCCCCC
Confidence 567999999999999873
No 59
>PHA00733 hypothetical protein
Probab=41.52 E-value=14 Score=29.20 Aligned_cols=23 Identities=26% Similarity=0.564 Sum_probs=20.6
Q ss_pred CcccccCCCCccccchhhhhhhc
Q 028899 81 AGYYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n 103 (202)
.-|-|+.|+..|....++..|+.
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHh
Confidence 45899999999999999998876
No 60
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=39.53 E-value=13 Score=33.55 Aligned_cols=23 Identities=22% Similarity=0.496 Sum_probs=18.5
Q ss_pred cccccCCCCccccchhhhhhhcC
Q 028899 82 GYYCSVCECVVKDSANYLDHING 104 (202)
Q Consensus 82 GfyC~vCd~~~kDs~~~ldH~n~ 104 (202)
-|-|+.|.+.|-|..++--|+..
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQT 237 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQT 237 (279)
T ss_pred CccCCcccchhcchHHHHHHHHh
Confidence 47899999999898888877643
No 61
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=38.92 E-value=13 Score=21.88 Aligned_cols=13 Identities=31% Similarity=0.521 Sum_probs=5.7
Q ss_pred CCcccccCCCCcc
Q 028899 80 QAGYYCSVCECVV 92 (202)
Q Consensus 80 ~~GfyC~vCd~~~ 92 (202)
+..|+|..||-.+
T Consensus 13 ~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 13 GWFYRCSECDFDL 25 (30)
T ss_dssp --EEE-TTT----
T ss_pred CceEECccCCCcc
Confidence 5789999999765
No 62
>PHA02562 46 endonuclease subunit; Provisional
Probab=38.63 E-value=53 Score=31.08 Aligned_cols=16 Identities=19% Similarity=0.619 Sum_probs=13.1
Q ss_pred cccccCCCCccccchh
Q 028899 82 GYYCSVCECVVKDSAN 97 (202)
Q Consensus 82 GfyC~vCd~~~kDs~~ 97 (202)
.-.|++|...|.++.+
T Consensus 284 ~~~Cp~C~~~~~~~~~ 299 (562)
T PHA02562 284 GGVCPTCTQQISEGPD 299 (562)
T ss_pred CCCCCCCCCcCCCcHH
Confidence 3489999999999833
No 63
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=37.97 E-value=11 Score=35.22 Aligned_cols=22 Identities=27% Similarity=0.466 Sum_probs=19.1
Q ss_pred cccccCCCCccccchhhhhhhc
Q 028899 82 GYYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 82 GfyC~vCd~~~kDs~~~ldH~n 103 (202)
-|.|+|||.-|+..+.+.=|+-
T Consensus 398 PYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 398 PYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ceeccccchhhccCccceeccc
Confidence 5789999999999998887764
No 64
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=37.56 E-value=70 Score=33.36 Aligned_cols=13 Identities=15% Similarity=0.187 Sum_probs=7.5
Q ss_pred cccCHHHHHHHHH
Q 028899 15 RKFDREEYLERAR 27 (202)
Q Consensus 15 RtWDreeYa~kA~ 27 (202)
..||-+.-+....
T Consensus 11 ~kwd~d~~ea~l~ 23 (1064)
T KOG1144|consen 11 KKWDGDASEALLA 23 (1064)
T ss_pred ccccccHHHHHHH
Confidence 4577666555444
No 65
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=37.40 E-value=16 Score=22.81 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=12.4
Q ss_pred CCCcccccCCCCcccc
Q 028899 79 QQAGYYCSVCECVVKD 94 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kD 94 (202)
.-++|+|+.|+-.+-|
T Consensus 29 ~vp~~~C~~CGE~~~~ 44 (46)
T TIGR03831 29 NVPALVCPQCGEEYLD 44 (46)
T ss_pred CCCccccccCCCEeeC
Confidence 3468999999987654
No 66
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=37.30 E-value=16 Score=34.49 Aligned_cols=35 Identities=20% Similarity=0.514 Sum_probs=28.8
Q ss_pred CCcccccCCC-CccccchhhhhhhcCHHHHH---HcCCC
Q 028899 80 QAGYYCSVCE-CVVKDSANYLDHINGKKHQR---ALGMS 114 (202)
Q Consensus 80 ~~GfyC~vCd-~~~kDs~~~ldH~n~k~H~~---~~G~s 114 (202)
.--|-|++|+ .++--...|..|.|...|.. -+|.+
T Consensus 372 d~ef~CEICgNyvy~GR~~FdrHF~E~rHiygl~clGi~ 410 (470)
T COG5188 372 DIEFECEICGNYVYYGRDRFDRHFEEDRHIYGLECLGIK 410 (470)
T ss_pred CcceeeeecccccccchHHHHhhhhhhhhhhheeecccc
Confidence 3468999999 88888999999999999975 44544
No 67
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=36.64 E-value=18 Score=30.42 Aligned_cols=43 Identities=19% Similarity=0.461 Sum_probs=30.0
Q ss_pred ccccCCCCccccchhhhhhhcCHHHHHHcCC-CceeeeccHHHH
Q 028899 83 YYCSVCECVVKDSANYLDHINGKKHQRALGM-SMRVERASLDQV 125 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~-sm~VersTle~V 125 (202)
|.|.+|--.-=..-....||.|+-|+--+-. .++..+.|++=+
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i~tkl~k~~~dFL 44 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKYIQTKLPKKTMDFL 44 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHHHHhcCChHHHHHH
Confidence 8899998777677788999999999832211 445555555433
No 68
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=35.70 E-value=56 Score=27.26 Aligned_cols=37 Identities=27% Similarity=0.466 Sum_probs=25.8
Q ss_pred CceEecCCCCCCCCCcccccCCCCccccchhhhhhhcCHHHHHH
Q 028899 67 KTQVVTPIAPLSQQAGYYCSVCECVVKDSANYLDHINGKKHQRA 110 (202)
Q Consensus 67 K~~vv~~~~~~~~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~ 110 (202)
.++|||.. ..-=|| ||+..+.|+ +|--.|-+......
T Consensus 24 ttVL~t~~----~~DfFY--~C~~HL~D~-~F~~p~~~~~~~~~ 60 (182)
T PF08432_consen 24 TTVLITPD----NKDFFY--VCPSHLKDR-QFATPIYDEEYVEA 60 (182)
T ss_pred ceEEecCC----CCCeEE--eCcccccCc-ccCCCCCCHHHHHH
Confidence 45666543 334577 799999999 99888777765543
No 69
>PF08262 Lem_TRP: Leucophaea maderae tachykinin-related peptide ; InterPro: IPR013206 These peptides are designated Leucophaea maderae (Madeira cockroach) tachykinin-related peptides (Lem TRPs). Some were isolated from the midgut of L. maderae, whereas others appear to be brain specific. The Lem TRPs of the brain are myotropic and induce increases in the amplitude and frequency of spontaneous contractions and tonus of hindgut muscle in L. maderae []. They were also isolated from brain-corpora, cardiaca-corpora, allata-suboesophageal ganglion extracts of Locusta migratoria (Migratory locust). They stimulate visceral muscle contractions of the oviduct and the foregut of L. migratoria [].
Probab=35.57 E-value=16 Score=17.13 Aligned_cols=7 Identities=43% Similarity=0.814 Sum_probs=5.3
Q ss_pred hcCCCCC
Q 028899 191 MMGFGSF 197 (202)
Q Consensus 191 mMGF~gF 197 (202)
.|||-|.
T Consensus 3 smgf~g~ 9 (10)
T PF08262_consen 3 SMGFHGM 9 (10)
T ss_pred ccccccc
Confidence 5999773
No 70
>PF14401 RLAN: RimK-like ATPgrasp N-terminal domain
Probab=33.65 E-value=22 Score=29.11 Aligned_cols=22 Identities=32% Similarity=0.685 Sum_probs=16.9
Q ss_pred CCceEecCCCCCC-CCCcccccC
Q 028899 66 GKTQVVTPIAPLS-QQAGYYCSV 87 (202)
Q Consensus 66 gK~~vv~~~~~~~-~~~GfyC~v 87 (202)
..+.|||.-.+.. .+-||||.+
T Consensus 15 ~~~rViNLcrsy~Yls~GYY~SL 37 (153)
T PF14401_consen 15 RRTRVINLCRSYRYLSEGYYCSL 37 (153)
T ss_pred CCceEEEecCCccccCcceeeeH
Confidence 3478888877666 788999965
No 71
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=31.52 E-value=14 Score=24.28 Aligned_cols=10 Identities=40% Similarity=1.036 Sum_probs=8.9
Q ss_pred ccccCCCCcc
Q 028899 83 YYCSVCECVV 92 (202)
Q Consensus 83 fyC~vCd~~~ 92 (202)
=||-+||+.+
T Consensus 7 ~yC~~Cdk~~ 16 (43)
T PF12855_consen 7 DYCIVCDKQI 16 (43)
T ss_pred hHHHHhhccc
Confidence 3999999999
No 72
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=31.05 E-value=20 Score=31.19 Aligned_cols=43 Identities=21% Similarity=0.477 Sum_probs=29.7
Q ss_pred CCcccccCCCCccccchhhhhhhcCHHHHHHcCCCceeeeccHHHHHHHHHHHHH
Q 028899 80 QAGYYCSVCECVVKDSANYLDHINGKKHQRALGMSMRVERASLDQVRERFELLKK 134 (202)
Q Consensus 80 ~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~sm~VersTle~Vk~rl~~lk~ 134 (202)
..-|-|.+|...|+-..=+..||..| |--. |++|++.+.....
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nK-H~e~-----------ve~~~~ev~~fnn 117 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNK-HPEK-----------VEEVKKEVEYFNN 117 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH--HHH-----------HHHHHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhc-CHHH-----------HHHHHHHHHHHHH
Confidence 34699999999999999999999854 5432 5677766655443
No 73
>KOG2505 consensus Ankyrin repeat protein [General function prediction only]
Probab=30.47 E-value=28 Score=34.22 Aligned_cols=50 Identities=14% Similarity=0.169 Sum_probs=35.6
Q ss_pred CcccccCCCCccccchhhhhhhcCHHHHHHcCCCce-eeeccHHHHHHHHH
Q 028899 81 AGYYCSVCECVVKDSANYLDHINGKKHQRALGMSMR-VERASLDQVRERFE 130 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~sm~-VersTle~Vk~rl~ 130 (202)
--+.|.+|++.|-+..-...|+.+--|.-|+-...+ ..=.|.+++-.=+.
T Consensus 65 d~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krkl~~~~ils~edFe~i~s 115 (591)
T KOG2505|consen 65 DSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRKLRGKPILSEEDFEGIIS 115 (591)
T ss_pred ccccccccCCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhh
Confidence 357999999999999999999999999865544432 12235666544333
No 74
>KOG4432 consensus Uncharacterized NUDIX family hydrolase [General function prediction only]
Probab=29.07 E-value=29 Score=32.21 Aligned_cols=36 Identities=25% Similarity=0.281 Sum_probs=21.6
Q ss_pred ccccchhhhcCCceEec-CCCCCCCCCcccccCCCCc
Q 028899 56 DYVVDLESRLGKTQVVT-PIAPLSQQAGYYCSVCECV 91 (202)
Q Consensus 56 ~~~ldL~~~lgK~~vv~-~~~~~~~~~GfyC~vCd~~ 91 (202)
-|.+|.++-+--.+.+. ..++.+.+.-|||+||+-.
T Consensus 107 gy~v~~d~l~hv~~~~~g~~~s~sa~~l~y~ei~es~ 143 (405)
T KOG4432|consen 107 GYRVDPDDLIHVITFVVGAHQSGSAQHLYYAEIDESM 143 (405)
T ss_pred CCcCChhHceEEEEEEeccccCccchheeeeecchhh
Confidence 35555555444333332 3444457889999999854
No 75
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=28.72 E-value=19 Score=34.81 Aligned_cols=23 Identities=22% Similarity=0.664 Sum_probs=20.0
Q ss_pred CcccccCCCCccccchhhhhhhc
Q 028899 81 AGYYCSVCECVVKDSANYLDHIN 103 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n 103 (202)
-||-|++|-.-|..-.++.+|+-
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d 36 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLD 36 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHh
Confidence 58999999999988888888874
No 76
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=28.44 E-value=27 Score=21.93 Aligned_cols=24 Identities=29% Similarity=0.493 Sum_probs=15.3
Q ss_pred CCCcccccCCCCccccc----hhhhhhh
Q 028899 79 QQAGYYCSVCECVVKDS----ANYLDHI 102 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs----~~~ldH~ 102 (202)
......|.+|+..++-+ .++..||
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 44567999999999985 4788887
No 77
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=28.32 E-value=28 Score=33.81 Aligned_cols=58 Identities=26% Similarity=0.548 Sum_probs=39.6
Q ss_pred EecCCCCCCCCCcccccCCCCccccchhhhhhhcCHHHHHHcCCCc----------eeeeccHHHHHHHH
Q 028899 70 VVTPIAPLSQQAGYYCSVCECVVKDSANYLDHINGKKHQRALGMSM----------RVERASLDQVRERF 129 (202)
Q Consensus 70 vv~~~~~~~~~~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~sm----------~VersTle~Vk~rl 129 (202)
..+..||+-. .-.|.+|+.......-+.-|..|++|+..+.-.. .|+-.||+-.--+|
T Consensus 483 yapkltpyer--kkqcslcnvlissevylfshvkgrkhqqal~e~~~iegrel~deevehlSle~~~idi 550 (672)
T KOG4722|consen 483 YAPKLTPYER--KKQCSLCNVLISSEVYLFSHVKGRKHQQALNELLLIEGRELEDEEVEHLSLEHLAIDI 550 (672)
T ss_pred cccccChHHh--hhccchhhhhhhhhhhhhhhhcchhHHHHHHHHhccCcccCCccccccccHHhhhhHH
Confidence 3345566531 1269999999998888999999999997654332 36666665544444
No 78
>PF03879 Cgr1: Cgr1 family; InterPro: IPR005579 Cgr1 is involved in nucleolar integrity and is required for processing pre-rRNA for the 60S ribosome subunit. In Saccharomyces cerevisiae, this protein is conserved and contributes to compartmentalisation of nucleolar constituents []. Cgr1 is a small hydrophilic protein and members of this family are coiled-coil proteins []. Its primary role appears to be in ribosome biogenesis [, ]. Expression of CGR1 is also associated with a cessation of yeast cell growth, which is a prerequisite for germination in this organism [].
Probab=28.10 E-value=2.3e+02 Score=22.12 Aligned_cols=20 Identities=30% Similarity=0.433 Sum_probs=11.1
Q ss_pred eeccHHHHHHHHHHHHHhhC
Q 028899 118 ERASLDQVRERFELLKKRKV 137 (202)
Q Consensus 118 ersTle~Vk~rl~~lk~kk~ 137 (202)
.|..+.+|+++...|+..++
T Consensus 39 ~R~~~~~~K~~ekElKeEKe 58 (108)
T PF03879_consen 39 KRLELKAIKEKEKELKEEKE 58 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34445566666666655543
No 79
>PHA03123 dUTPase; Provisional
Probab=27.92 E-value=29 Score=32.93 Aligned_cols=15 Identities=27% Similarity=0.222 Sum_probs=11.1
Q ss_pred HHHhcCCCCCCCCCC
Q 028899 188 IAAMMGFGSFHSSKK 202 (202)
Q Consensus 188 maamMGF~gFGssKK 202 (202)
.-..=|++|||||-|
T Consensus 387 ppS~Rg~~GFGSTg~ 401 (402)
T PHA03123 387 PPSDRGNKGFGSTDK 401 (402)
T ss_pred CcccccCCCCCCCCC
Confidence 345569999999854
No 80
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=26.63 E-value=30 Score=33.50 Aligned_cols=30 Identities=23% Similarity=0.500 Sum_probs=24.7
Q ss_pred CcccccCCCCccccchhhhhhhcCHHHHHHc
Q 028899 81 AGYYCSVCECVVKDSANYLDHINGKKHQRAL 111 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~ 111 (202)
--|-|++|+..|.|..+++.|+-. .|...+
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~-eH~~~l 85 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQ-EHPAGL 85 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHH-hhhhhc
Confidence 366899999999999999999964 466554
No 81
>PRK09907 toxin MazF; Provisional
Probab=26.53 E-value=53 Score=25.16 Aligned_cols=65 Identities=14% Similarity=0.176 Sum_probs=42.1
Q ss_pred CCceEecCCCCCCCCCcccccCCCCccccchhhhhhhcCHH-HHHHcCCCceeeeccHHHHHHHHHHH
Q 028899 66 GKTQVVTPIAPLSQQAGYYCSVCECVVKDSANYLDHINGKK-HQRALGMSMRVERASLDQVRERFELL 132 (202)
Q Consensus 66 gK~~vv~~~~~~~~~~GfyC~vCd~~~kDs~~~ldH~n~k~-H~~~~G~sm~VersTle~Vk~rl~~l 132 (202)
|.+++++. |+......|+..+- -..++|..+.+++.+=. +.|..-.-..|..-++++|.+.|..+
T Consensus 44 ~~viv~Pi-Ts~~~~~p~~v~i~-gl~~~s~v~~~Qirtld~~~R~~~~ig~l~~~~~~~v~~~l~~~ 109 (111)
T PRK09907 44 GMCLCVPC-TTQSKGYPFEVVLS-GQERDGVALADQVKSIAWRARGATKKGTVAPEELQLIKAKINVL 109 (111)
T ss_pred CeEEEEEe-cCCCcCCceEEEec-CCCCCEEEEeecceeecHHHhCCcEeeEeCHHHHHHHHHHHHHH
Confidence 44444444 44344556666553 34688889999999999 54544445567777778888777654
No 82
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=25.97 E-value=27 Score=32.48 Aligned_cols=14 Identities=14% Similarity=0.627 Sum_probs=10.7
Q ss_pred cccccCCCCccccc
Q 028899 82 GYYCSVCECVVKDS 95 (202)
Q Consensus 82 GfyC~vCd~~~kDs 95 (202)
-|||++|+-.+.=.
T Consensus 25 ~ffCPaC~~~l~lK 38 (342)
T COG4469 25 RFFCPACGSQLILK 38 (342)
T ss_pred ccccCCCCCeeeee
Confidence 69999999765443
No 83
>PF05477 SURF2: Surfeit locus protein 2 (SURF2); InterPro: IPR008833 Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown [].
Probab=25.70 E-value=44 Score=29.69 Aligned_cols=48 Identities=21% Similarity=0.387 Sum_probs=33.2
Q ss_pred CCCcccccCCCCccccc-hhhhhhhcCHHHHHHcCCCceeeeccHHHHH
Q 028899 79 QQAGYYCSVCECVVKDS-ANYLDHINGKKHQRALGMSMRVERASLDQVR 126 (202)
Q Consensus 79 ~~~GfyC~vCd~~~kDs-~~~ldH~n~k~H~~~~G~sm~VersTle~Vk 126 (202)
...-+||.|..+.+--+ ...+.||||++.++++-.--.-....++-|-
T Consensus 76 ~~~~LfCkLT~~~iNk~pe~V~rHv~GKRf~kaLek~ee~~~~g~e~vp 124 (244)
T PF05477_consen 76 NPHKLFCKLTGRHINKSPEHVERHVNGKRFQKALEKYEECQKQGVEFVP 124 (244)
T ss_pred CCceeEEechHhHhccCHHHHHHHhhhHHHHHHHHHHHHHHhhcccchh
Confidence 44578999988877655 4788999999999887654443333333333
No 84
>TIGR02646 conserved hypothetical protein TIGR02646. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins.
Probab=25.54 E-value=22 Score=28.37 Aligned_cols=29 Identities=21% Similarity=0.363 Sum_probs=23.3
Q ss_pred CCcccccCCCCccccchhhhhhhcCHHHH
Q 028899 80 QAGYYCSVCECVVKDSANYLDHINGKKHQ 108 (202)
Q Consensus 80 ~~GfyC~vCd~~~kDs~~~ldH~n~k~H~ 108 (202)
-+|+.|.+|...+.....-+||+-.+.+-
T Consensus 22 ~~~~~C~YC~~~~~~~~~~ieH~~Pk~~~ 50 (144)
T TIGR02646 22 LQGGLCAYCEREIELLGSHIEHFRPKGAY 50 (144)
T ss_pred HhCCCcCccCCCcCCCCcceeeecccCCC
Confidence 35789999999777677889999887653
No 85
>PF00692 dUTPase: dUTPase; InterPro: IPR008180 Synonym(s): dUTP diphosphatase, Deoxyuridine-triphosphatase The essential enzyme dUTP pyrophosphatase (3.6.1.23 from EC) is specific for dUTP and is critical for the fidelity of DNA replication and repair. dUTPase hydrolyzes dUTP to dUMP and pyrophosphate, simultaneously reducing dUTP levels and providing the dUMP for dTTP biosynthesis. dUTPase decreases the intracellular concentration of dUPT so that uracil cannot be incorporated into DNA []. The crystal structure of human dUTPase reveals that each subunit of the dUTPase trimer folds into an eight-stranded jelly-roll beta barrel, with the C-terminal beta strands interchanged among the subunits. The structure is similar to that of the Escherichia coli enzyme, despite low sequence homology between the two enzymes []. Other enzymes like deoxycytidine triphosphate deaminase (dCTP) (3.5.4.13 from EC) that specifically bind uridine also belong to this group suggesting that the signature may recognise a putative uridine-binding motif. Some retroviruses encode dUTPases. Retroviral dUTPase is synthesised as part of POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, dUTPase and RNase H. ; GO: 0016787 hydrolase activity, 0046080 dUTP metabolic process; PDB: 4DHK_A 1DUC_A 1DUN_A 3LQW_A 2BT1_A 2WE1_A 2WE0_A 2WE2_A 2BSY_A 2WE3_A ....
Probab=25.36 E-value=35 Score=26.19 Aligned_cols=10 Identities=40% Similarity=0.511 Sum_probs=4.9
Q ss_pred hcCCCCCCCC
Q 028899 191 MMGFGSFHSS 200 (202)
Q Consensus 191 mMGF~gFGss 200 (202)
.+|-+|||||
T Consensus 119 ~rg~~Gfgst 128 (129)
T PF00692_consen 119 ERGEGGFGST 128 (129)
T ss_dssp SSTTTSTTTT
T ss_pred cCCCCCCCCC
Confidence 3455555554
No 86
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=24.70 E-value=25 Score=36.20 Aligned_cols=41 Identities=27% Similarity=0.433 Sum_probs=28.1
Q ss_pred CcccccCCCCccccchhhhhhhcCHHHHHHcCCCceeeeccHHH
Q 028899 81 AGYYCSVCECVVKDSANYLDHINGKKHQRALGMSMRVERASLDQ 124 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~sm~VersTle~ 124 (202)
--|.|+-|..-|..|-+|-.|+|++ .--=-..+-+|++.++
T Consensus 949 KPfQCdKClKRFSHSGSYSQHMNHR---YSYCKpyrEer~s~e~ 989 (1007)
T KOG3623|consen 949 KPFQCDKCLKRFSHSGSYSQHMNHR---YSYCKPYREERASPED 989 (1007)
T ss_pred CcchhhhhhhhcccccchHhhhccc---hhcccchhhccCChhh
Confidence 4688999999999999999998843 2222223455666655
No 87
>PHA03127 dUTPase; Provisional
Probab=24.62 E-value=34 Score=31.62 Aligned_cols=12 Identities=25% Similarity=0.296 Sum_probs=9.9
Q ss_pred HHhcCCCCCCCC
Q 028899 189 AAMMGFGSFHSS 200 (202)
Q Consensus 189 aamMGF~gFGss 200 (202)
-..=|.+|||||
T Consensus 309 ~S~Rg~~GFGST 320 (322)
T PHA03127 309 SSARGDRGFGST 320 (322)
T ss_pred cccccCCCCCCC
Confidence 466799999998
No 88
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=24.28 E-value=34 Score=27.71 Aligned_cols=12 Identities=25% Similarity=0.877 Sum_probs=10.4
Q ss_pred CCCcccccCCCC
Q 028899 79 QQAGYYCSVCEC 90 (202)
Q Consensus 79 ~~~GfyC~vCd~ 90 (202)
+.|--||++|+.
T Consensus 41 KdG~v~CPvC~~ 52 (131)
T COG1645 41 KDGEVFCPVCGY 52 (131)
T ss_pred eCCeEECCCCCc
Confidence 677889999996
No 89
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=23.53 E-value=33 Score=32.02 Aligned_cols=12 Identities=42% Similarity=1.115 Sum_probs=10.0
Q ss_pred CCCcccccCCCC
Q 028899 79 QQAGYYCSVCEC 90 (202)
Q Consensus 79 ~~~GfyC~vCd~ 90 (202)
.++||+|++|.-
T Consensus 305 ~~gGy~CP~Ckt 316 (421)
T COG5151 305 KGGGYECPVCKT 316 (421)
T ss_pred ccCceeCCcccc
Confidence 679999998863
No 90
>PHA03126 dUTPase; Provisional
Probab=23.24 E-value=37 Score=31.44 Aligned_cols=13 Identities=23% Similarity=0.335 Sum_probs=10.2
Q ss_pred HHHhcCCCCCCCC
Q 028899 188 IAAMMGFGSFHSS 200 (202)
Q Consensus 188 maamMGF~gFGss 200 (202)
.-..=|++|||||
T Consensus 312 p~S~Rg~~GFGST 324 (326)
T PHA03126 312 PSSLRADGGFGST 324 (326)
T ss_pred CcccccCCCCCCC
Confidence 3566799999997
No 91
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=23.20 E-value=25 Score=38.16 Aligned_cols=33 Identities=21% Similarity=0.455 Sum_probs=28.9
Q ss_pred CcccccCCCCccccchhhhhhhcCHHHHHHcCC
Q 028899 81 AGYYCSVCECVVKDSANYLDHINGKKHQRALGM 113 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~ 113 (202)
--|||.+|.+.|.++..+--|+.+--|.++.-.
T Consensus 1327 ~~~~c~~c~~~~~~~~alqihm~~~~~~~kt~~ 1359 (1406)
T KOG1146|consen 1327 CTYHCLACEVLLSGREALQIHMRSSAHRRKTAP 1359 (1406)
T ss_pred ccccchHHHhhcchhHHHHHHHHHhhhcccCCC
Confidence 456899999999999999999999999876543
No 92
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=23.06 E-value=1.5e+02 Score=31.16 Aligned_cols=14 Identities=7% Similarity=0.197 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHHHh
Q 028899 122 LDQVRERFELLKKR 135 (202)
Q Consensus 122 le~Vk~rl~~lk~k 135 (202)
|-..+..|+.+++.
T Consensus 216 v~~~qe~La~~qe~ 229 (1064)
T KOG1144|consen 216 VRAMQEALAKRQEE 229 (1064)
T ss_pred HHHHHHHHHHHHHH
Confidence 55555555555444
No 93
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=22.76 E-value=36 Score=25.66 Aligned_cols=18 Identities=28% Similarity=0.756 Sum_probs=14.6
Q ss_pred CCcccccCCCCccccchh
Q 028899 80 QAGYYCSVCECVVKDSAN 97 (202)
Q Consensus 80 ~~GfyC~vCd~~~kDs~~ 97 (202)
.++|+|+.|+-.|-|...
T Consensus 29 ~~~~~C~~CGe~~~~~e~ 46 (127)
T TIGR03830 29 VPGWYCPACGEELLDPEE 46 (127)
T ss_pred eeeeECCCCCCEEEcHHH
Confidence 458999999998887754
No 94
>PRK09812 toxin ChpB; Provisional
Probab=22.51 E-value=78 Score=24.44 Aligned_cols=52 Identities=10% Similarity=0.059 Sum_probs=37.8
Q ss_pred CcccccCC-CCccccchhhhhhhcCHHH-HHHcCCCceeeeccHHHHHHHHHHH
Q 028899 81 AGYYCSVC-ECVVKDSANYLDHINGKKH-QRALGMSMRVERASLDQVRERFELL 132 (202)
Q Consensus 81 ~GfyC~vC-d~~~kDs~~~ldH~n~k~H-~~~~G~sm~VersTle~Vk~rl~~l 132 (202)
.+|+..+- +-.-++|..+.++|.+=.. .|....-..+...++++|.++|..+
T Consensus 61 ~p~~v~l~~~gl~~~s~v~~~QirtiD~~~R~~~~ig~l~~~~~~~v~~~~~~~ 114 (116)
T PRK09812 61 AGFAVPLHCEEGDTQGVVLVNQVRMMDLEARLAKRIGLAADEVVEDALLRLQAV 114 (116)
T ss_pred cceEEEeccCCCccceEEEeeeccccCHHHhcCceeeecCHHHHHHHHHHHHHH
Confidence 46666653 3234788888999999885 4655566678888899999988765
No 95
>PF09888 DUF2115: Uncharacterized protein conserved in archaea (DUF2115); InterPro: IPR019215 This entry represents various hypothetical archaeal proteins, has no known function.
Probab=22.43 E-value=42 Score=27.83 Aligned_cols=26 Identities=19% Similarity=0.399 Sum_probs=17.3
Q ss_pred ceEecCCCCCC-------CCCcccccCCCCccc
Q 028899 68 TQVVTPIAPLS-------QQAGYYCSVCECVVK 93 (202)
Q Consensus 68 ~~vv~~~~~~~-------~~~GfyC~vCd~~~k 93 (202)
.=+.+.++|.. ..+.|||+|=|..-.
T Consensus 116 ~PlHPvG~~FPGG~~V~~~~g~YYCPVKdkq~d 148 (163)
T PF09888_consen 116 EPLHPVGMPFPGGFKVEEKNGNYYCPVKDKQKD 148 (163)
T ss_pred CCCCCCCCCCCCCeEEEEECCEEeCccchhhcC
Confidence 33455555532 568999999988654
No 96
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=22.38 E-value=43 Score=18.91 Aligned_cols=13 Identities=38% Similarity=0.991 Sum_probs=6.4
Q ss_pred cccCCCCccccch
Q 028899 84 YCSVCECVVKDSA 96 (202)
Q Consensus 84 yC~vCd~~~kDs~ 96 (202)
||+-|+....|..
T Consensus 1 ~Cp~CG~~~~~~~ 13 (23)
T PF13240_consen 1 YCPNCGAEIEDDA 13 (23)
T ss_pred CCcccCCCCCCcC
Confidence 4555555544443
No 97
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=22.19 E-value=32 Score=23.06 Aligned_cols=12 Identities=25% Similarity=0.562 Sum_probs=10.0
Q ss_pred CCcccccCCCCc
Q 028899 80 QAGYYCSVCECV 91 (202)
Q Consensus 80 ~~GfyC~vCd~~ 91 (202)
-.|++|+-|+.+
T Consensus 7 ltG~~CPgCG~t 18 (52)
T PF10825_consen 7 LTGIPCPGCGMT 18 (52)
T ss_pred hhCCCCCCCcHH
Confidence 469999999875
No 98
>TIGR02930 vnfG_nitrog V-containing nitrogenase, delta subunit. Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, VnfG, represents the delta subunit of the V-containing (vanadium) alternative nitrogenase. It is homologous to AnfG, the delta subunit of the Fe-only nitrogenase.
Probab=21.94 E-value=36 Score=26.78 Aligned_cols=14 Identities=50% Similarity=0.840 Sum_probs=11.0
Q ss_pred CccccccCHHHHHH
Q 028899 11 NTFRRKFDREEYLE 24 (202)
Q Consensus 11 ~~~RRtWDreeYa~ 24 (202)
++|-|+|||++-.+
T Consensus 16 QF~SRsWDRe~q~e 29 (109)
T TIGR02930 16 QFFSRTWDREENIE 29 (109)
T ss_pred hhcccchhHHHhHH
Confidence 57889999987443
No 99
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=21.34 E-value=43 Score=21.87 Aligned_cols=23 Identities=22% Similarity=0.374 Sum_probs=17.6
Q ss_pred cccccCCCCccccc-----hhhhhhhcC
Q 028899 82 GYYCSVCECVVKDS-----ANYLDHING 104 (202)
Q Consensus 82 GfyC~vCd~~~kDs-----~~~ldH~n~ 104 (202)
.=.|..|...+.-. .+|..||++
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHh
Confidence 45899999999754 477777765
No 100
>PHA03129 dUTPase; Provisional
Probab=20.61 E-value=45 Score=32.04 Aligned_cols=13 Identities=23% Similarity=0.307 Sum_probs=9.9
Q ss_pred HHHhcCCCCCCCC
Q 028899 188 IAAMMGFGSFHSS 200 (202)
Q Consensus 188 maamMGF~gFGss 200 (202)
+-..=|.+|||||
T Consensus 422 p~S~Rg~~GFGST 434 (436)
T PHA03129 422 MTSERQEGGFGST 434 (436)
T ss_pred CcccccCCCCCCC
Confidence 3566788999987
No 101
>PF07430 PP1: Phloem filament protein PP1; InterPro: IPR009994 This domain represents a conserved region approximately 200 residues long, four copies of which are found within the plant phloem filament protein PP1. This is one of the constituents of the proteinaceous filaments found in the sieve elements of Cucurbita phloem [].
Probab=20.50 E-value=40 Score=29.13 Aligned_cols=38 Identities=24% Similarity=0.494 Sum_probs=25.1
Q ss_pred CcccccCCCCccccchhhhhhhcCHHHHHHcCCCceeeeccHHHH
Q 028899 81 AGYYCSVCECVVKDSANYLDHINGKKHQRALGMSMRVERASLDQV 125 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs~~~ldH~n~k~H~~~~G~sm~VersTle~V 125 (202)
-|+||++|+-+ +.|-=|+.-- ..+|-|...+=.-++|+
T Consensus 47 egwy~el~~~~----~~yrlhv~a~---d~l~r~l~~e~ii~e~~ 84 (202)
T PF07430_consen 47 EGWYFELCPNS----LKYRLHVKAI---DFLGRSLKYEAIIIEEK 84 (202)
T ss_pred eceeecccccc----eeEEEeehhh---hhhccccceeeeeeehh
Confidence 49999999944 4455454432 34666777666677777
No 102
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=20.27 E-value=47 Score=20.20 Aligned_cols=13 Identities=31% Similarity=0.879 Sum_probs=10.1
Q ss_pred CCcccccCCCCcc
Q 028899 80 QAGYYCSVCECVV 92 (202)
Q Consensus 80 ~~GfyC~vCd~~~ 92 (202)
...|+|+.||..+
T Consensus 14 ~T~~~C~~C~v~l 26 (32)
T PF13842_consen 14 DTRYMCSKCDVPL 26 (32)
T ss_pred eeEEEccCCCCcc
Confidence 3689999998543
No 103
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=20.18 E-value=44 Score=20.84 Aligned_cols=25 Identities=20% Similarity=0.189 Sum_probs=18.9
Q ss_pred ccccCCCCccccchhhhhhhcCHHH
Q 028899 83 YYCSVCECVVKDSANYLDHINGKKH 107 (202)
Q Consensus 83 fyC~vCd~~~kDs~~~ldH~n~k~H 107 (202)
+.|.+|+..+....-=++||.....
T Consensus 12 ~~C~~c~~~~~~~~~~v~Hi~p~~~ 36 (57)
T cd00085 12 GLCPYCGKPGGTEGLEVDHIIPLSD 36 (57)
T ss_pred CcCccCCCcCCCCCceEEeecchhh
Confidence 7899999998555566788876543
No 104
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=20.09 E-value=42 Score=30.94 Aligned_cols=15 Identities=20% Similarity=0.545 Sum_probs=11.9
Q ss_pred CcccccCCCCccccc
Q 028899 81 AGYYCSVCECVVKDS 95 (202)
Q Consensus 81 ~GfyC~vCd~~~kDs 95 (202)
-..||++||+.|..-
T Consensus 328 E~~FCD~CDRG~HT~ 342 (381)
T KOG1512|consen 328 EHLFCDVCDRGPHTL 342 (381)
T ss_pred heeccccccCCCCcc
Confidence 355999999999753
Done!