Query 004933
Match_columns 723
No_of_seqs 148 out of 198
Neff 4.7
Searched_HMMs 46136
Date Thu Mar 28 15:18:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004933.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004933hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1356 Putative transcription 100.0 4E-185 9E-190 1548.9 34.4 642 2-721 237-885 (889)
2 PF02373 JmjC: JmjC domain, hy 99.5 1E-14 2.2E-19 131.2 5.5 84 569-668 29-114 (114)
3 PF13621 Cupin_8: Cupin-like d 99.0 1.1E-10 2.4E-15 117.3 -0.3 40 633-672 207-249 (251)
4 PF10497 zf-4CXXC_R1: Zinc-fin 98.4 1.3E-07 2.8E-12 87.2 3.4 59 3-61 16-85 (105)
5 smart00558 JmjC A domain famil 96.7 0.00044 9.6E-09 56.1 0.4 53 406-476 3-55 (57)
6 KOG2131 Uncharacterized conser 96.2 0.005 1.1E-07 67.6 4.6 58 630-687 263-321 (427)
7 cd02340 ZZ_NBR1_like Zinc fing 95.8 0.0045 9.7E-08 48.6 1.3 30 124-153 1-31 (43)
8 cd02249 ZZ Zinc finger, ZZ typ 95.2 0.0078 1.7E-07 47.6 1.0 32 125-156 2-34 (46)
9 cd02335 ZZ_ADA2 Zinc finger, Z 95.1 0.009 2E-07 48.0 1.2 30 125-154 2-33 (49)
10 KOG1356 Putative transcription 95.1 0.012 2.5E-07 70.2 2.4 104 44-155 145-261 (889)
11 cd02339 ZZ_Mind_bomb Zinc fing 94.6 0.017 3.6E-07 46.0 1.3 30 124-153 1-32 (45)
12 PF00569 ZZ: Zinc finger, ZZ t 94.5 0.021 4.5E-07 45.3 1.7 34 122-155 3-38 (46)
13 smart00291 ZnF_ZZ Zinc-binding 93.7 0.031 6.7E-07 43.9 1.3 35 123-157 4-39 (44)
14 COG1917 Uncharacterized conser 93.2 0.044 9.6E-07 51.3 1.6 58 604-666 56-115 (131)
15 PF07883 Cupin_2: Cupin domain 93.1 0.04 8.7E-07 45.3 1.0 26 636-661 38-63 (71)
16 cd02344 ZZ_HERC2 Zinc finger, 93.0 0.048 1E-06 43.5 1.4 31 124-154 1-33 (45)
17 cd02341 ZZ_ZZZ3 Zinc finger, Z 92.5 0.064 1.4E-06 43.3 1.5 31 125-155 2-36 (48)
18 KOG2130 Phosphatidylserine-spe 92.1 0.093 2E-06 57.1 2.5 43 633-675 261-303 (407)
19 cd02338 ZZ_PCMF_like Zinc fing 90.9 0.11 2.5E-06 41.8 1.2 31 124-154 1-33 (49)
20 PF13639 zf-RING_2: Ring finge 90.8 0.079 1.7E-06 40.9 0.3 30 7-44 15-44 (44)
21 COG0662 {ManC} Mannose-6-phosp 90.7 0.18 3.9E-06 47.6 2.7 42 634-675 74-115 (127)
22 cd02345 ZZ_dah Zinc finger, ZZ 90.7 0.13 2.7E-06 41.6 1.3 33 124-156 1-35 (49)
23 cd02337 ZZ_CBP Zinc finger, ZZ 88.3 0.19 4.1E-06 39.3 0.7 29 125-154 2-31 (41)
24 PHA02926 zinc finger-like prot 88.2 0.12 2.7E-06 53.8 -0.5 30 17-46 199-228 (242)
25 TIGR03214 ura-cupin putative a 87.0 0.32 6.9E-06 51.6 1.6 30 630-659 213-242 (260)
26 cd02334 ZZ_dystrophin Zinc fin 84.7 0.63 1.4E-05 37.8 2.0 34 124-157 1-36 (49)
27 PRK09943 DNA-binding transcrip 84.0 0.78 1.7E-05 45.7 2.7 55 613-672 129-183 (185)
28 PF13923 zf-C3HC4_2: Zinc fing 83.2 0.51 1.1E-05 35.7 0.8 29 8-43 11-39 (39)
29 PRK13290 ectC L-ectoine syntha 82.4 0.89 1.9E-05 43.4 2.3 37 634-672 74-110 (125)
30 cd02343 ZZ_EF Zinc finger, ZZ 81.8 0.7 1.5E-05 37.6 1.1 33 124-156 1-34 (48)
31 PF07649 C1_3: C1-like domain; 81.5 0.6 1.3E-05 33.7 0.6 27 125-151 2-29 (30)
32 cd00162 RING RING-finger (Real 80.0 0.83 1.8E-05 33.6 1.0 33 8-46 12-44 (45)
33 TIGR00218 manA mannose-6-phosp 79.7 0.92 2E-05 48.9 1.6 15 640-654 156-170 (302)
34 cd02342 ZZ_UBA_plant Zinc fing 78.5 1.1 2.5E-05 35.6 1.3 32 124-155 1-34 (43)
35 PF01050 MannoseP_isomer: Mann 77.7 1.2 2.6E-05 43.9 1.6 22 640-661 107-128 (151)
36 COG4101 Predicted mannose-6-ph 77.6 1.1 2.4E-05 43.0 1.2 27 636-662 89-115 (142)
37 PRK15131 mannose-6-phosphate i 77.5 1.2 2.5E-05 50.2 1.6 17 638-654 240-256 (389)
38 PF14634 zf-RING_5: zinc-RING 74.5 1.2 2.5E-05 34.7 0.4 28 11-45 17-44 (44)
39 PRK04190 glucose-6-phosphate i 73.4 2.5 5.3E-05 43.4 2.5 42 633-675 118-159 (191)
40 COG1482 ManA Phosphomannose is 72.6 1.9 4E-05 47.4 1.5 19 637-655 160-178 (312)
41 smart00184 RING Ring finger. E 70.6 1.7 3.8E-05 30.7 0.5 29 9-43 11-39 (39)
42 PLN02288 mannose-6-phosphate i 69.3 2.4 5.2E-05 47.9 1.5 15 640-654 256-270 (394)
43 PLN03208 E3 ubiquitin-protein 69.2 2.2 4.7E-05 43.9 1.1 35 12-47 34-78 (193)
44 PF00097 zf-C3HC4: Zinc finger 68.6 0.92 2E-05 34.2 -1.3 29 10-43 13-41 (41)
45 KOG4582 Uncharacterized conser 67.1 2.5 5.4E-05 45.6 1.0 33 123-155 152-186 (278)
46 PF10571 UPF0547: Uncharacteri 66.8 3.4 7.4E-05 29.5 1.3 23 125-147 2-24 (26)
47 PF13248 zf-ribbon_3: zinc-rib 66.6 2.7 5.9E-05 29.6 0.8 25 123-147 2-26 (26)
48 PF15227 zf-C3HC4_4: zinc fing 65.9 2.6 5.6E-05 32.9 0.6 29 12-43 14-42 (42)
49 PF13240 zinc_ribbon_2: zinc-r 64.7 3.2 6.9E-05 28.7 0.8 23 125-147 1-23 (23)
50 KOG2508 Predicted phospholipas 64.6 6.8 0.00015 43.9 3.8 39 298-336 33-74 (437)
51 PF00190 Cupin_1: Cupin; Inte 64.3 5.7 0.00012 38.0 2.8 38 636-673 81-125 (144)
52 KOG0823 Predicted E3 ubiquitin 63.9 3.7 8.1E-05 43.2 1.5 30 13-46 64-93 (230)
53 KOG1039 Predicted E3 ubiquitin 62.8 2.6 5.7E-05 46.8 0.2 32 13-45 186-218 (344)
54 PF13920 zf-C3HC4_3: Zinc fing 62.2 2.2 4.7E-05 33.9 -0.4 32 9-46 15-46 (50)
55 PF12678 zf-rbx1: RING-H2 zinc 60.2 4.8 0.0001 34.8 1.4 26 12-44 48-73 (73)
56 KOG2583 Ubiquinol cytochrome c 60.0 6.1 0.00013 44.7 2.4 46 267-314 158-206 (429)
57 PTZ00194 60S ribosomal protein 58.9 4.3 9.3E-05 40.0 0.9 43 608-652 18-60 (143)
58 PRK15460 cpsB mannose-1-phosph 57.7 6 0.00013 45.8 2.0 46 631-676 420-465 (478)
59 TIGR01479 GMP_PMI mannose-1-ph 57.2 7.8 0.00017 44.5 2.8 42 632-673 412-453 (468)
60 TIGR00599 rad18 DNA repair pro 57.0 6.7 0.00015 44.5 2.2 30 12-48 42-71 (397)
61 cd02336 ZZ_RSC8 Zinc finger, Z 55.8 6 0.00013 31.7 1.1 35 125-162 2-37 (45)
62 smart00835 Cupin_1 Cupin. This 53.7 10 0.00022 36.3 2.6 52 608-659 47-99 (146)
63 PF08007 Cupin_4: Cupin superf 53.0 13 0.00029 40.5 3.6 41 635-675 176-216 (319)
64 PF12861 zf-Apc11: Anaphase-pr 52.5 7.5 0.00016 35.3 1.3 34 7-45 46-79 (85)
65 PF02041 Auxin_BP: Auxin bindi 51.8 8.1 0.00018 38.6 1.5 41 614-659 75-115 (167)
66 KOG0457 Histone acetyltransfer 51.6 6 0.00013 45.1 0.7 33 121-153 12-46 (438)
67 COG5114 Histone acetyltransfer 50.7 5 0.00011 44.2 -0.1 31 123-153 5-37 (432)
68 TIGR03404 bicupin_oxalic bicup 50.2 12 0.00025 42.1 2.6 84 604-689 258-342 (367)
69 TIGR03214 ura-cupin putative a 50.1 11 0.00025 40.0 2.5 47 609-660 77-123 (260)
70 smart00504 Ubox Modified RING 48.0 8.7 0.00019 31.2 1.0 28 12-46 17-44 (63)
71 smart00647 IBR In Between Ring 47.5 12 0.00026 30.3 1.7 26 5-31 37-62 (64)
72 PF01238 PMI_typeI: Phosphoman 46.9 6.8 0.00015 43.8 0.2 18 638-655 253-270 (373)
73 PRK01191 rpl24p 50S ribosomal 45.9 9.1 0.0002 36.8 0.9 42 608-651 17-58 (120)
74 PF02938 GAD: GAD domain; Int 44.8 7.5 0.00016 35.1 0.1 41 607-657 53-93 (95)
75 PF14835 zf-RING_6: zf-RING of 43.5 10 0.00023 32.8 0.7 24 12-44 24-47 (65)
76 PF03107 C1_2: C1 domain; Int 42.3 14 0.00031 26.7 1.2 26 126-151 3-29 (30)
77 PRK11171 hypothetical protein; 42.1 14 0.00031 39.3 1.7 28 632-659 98-125 (266)
78 KOG2177 Predicted E3 ubiquitin 40.4 11 0.00023 37.9 0.4 25 13-44 30-54 (386)
79 KOG3905 Dynein light intermedi 39.5 13 0.00028 41.6 0.9 70 575-652 242-313 (473)
80 KOG1280 Uncharacterized conser 39.2 12 0.00026 41.7 0.6 36 119-154 4-41 (381)
81 KOG0311 Predicted E3 ubiquitin 39.2 16 0.00035 40.9 1.5 39 13-57 61-99 (381)
82 KOG2107 Uncharacterized conser 38.4 24 0.00052 35.8 2.5 56 583-655 80-136 (179)
83 PF06844 DUF1244: Protein of u 38.1 12 0.00026 32.5 0.3 13 18-30 11-23 (68)
84 PRK13264 3-hydroxyanthranilate 37.9 24 0.00053 36.0 2.5 45 633-677 74-118 (177)
85 TIGR03037 anthran_nbaC 3-hydro 37.7 24 0.00052 35.5 2.4 46 633-678 68-113 (159)
86 PRK10371 DNA-binding transcrip 37.6 26 0.00057 37.7 2.9 33 630-662 59-91 (302)
87 PRK14892 putative transcriptio 36.6 19 0.00042 33.5 1.4 28 119-146 17-51 (99)
88 PF14446 Prok-RING_1: Prokaryo 35.4 18 0.00038 30.4 0.9 24 119-145 17-44 (54)
89 PF05899 Cupin_3: Protein of u 34.6 21 0.00045 30.8 1.3 17 636-652 45-61 (74)
90 TIGR00570 cdk7 CDK-activating 34.4 23 0.0005 39.1 1.8 27 13-45 25-51 (309)
91 PF02944 BESS: BESS motif; In 34.1 47 0.001 25.2 2.9 24 77-100 6-29 (37)
92 PF08990 Docking: Erythronolid 32.0 34 0.00075 24.8 1.8 17 581-597 3-19 (27)
93 TIGR01080 rplX_A_E ribosomal p 31.6 26 0.00057 33.4 1.5 43 608-652 13-55 (114)
94 KOG3899 Uncharacterized conser 31.3 15 0.00033 40.2 -0.2 36 10-46 319-363 (381)
95 TIGR03404 bicupin_oxalic bicup 31.1 42 0.00092 37.7 3.2 40 633-672 108-152 (367)
96 PRK12380 hydrogenase nickel in 31.0 26 0.00056 33.0 1.3 24 122-145 69-94 (113)
97 PRK11171 hypothetical protein; 30.2 29 0.00064 37.0 1.8 30 630-659 218-247 (266)
98 KOG1814 Predicted E3 ubiquitin 30.0 89 0.0019 35.9 5.4 22 7-29 292-313 (445)
99 PF12852 Cupin_6: Cupin 29.6 31 0.00066 34.1 1.7 23 637-659 57-79 (186)
100 PF09845 DUF2072: Zn-ribbon co 29.4 37 0.00081 33.2 2.1 26 10-46 3-28 (131)
101 PF10122 Mu-like_Com: Mu-like 28.8 10 0.00022 31.3 -1.5 30 7-45 3-32 (51)
102 PF08271 TF_Zn_Ribbon: TFIIB z 28.6 32 0.00068 26.8 1.2 22 124-145 1-27 (43)
103 PF01485 IBR: IBR domain; Int 27.9 25 0.00055 28.3 0.6 23 8-31 40-62 (64)
104 PHA03096 p28-like protein; Pro 27.6 20 0.00043 39.1 -0.1 32 12-44 202-233 (284)
105 PF05883 Baculo_RING: Baculovi 27.2 66 0.0014 31.6 3.4 11 17-27 55-65 (134)
106 PF02311 AraC_binding: AraC-li 26.9 45 0.00096 29.6 2.1 46 630-676 36-83 (136)
107 PF06249 EutQ: Ethanolamine ut 26.9 47 0.001 33.2 2.4 21 632-652 110-130 (152)
108 PRK14559 putative protein seri 26.5 38 0.00082 40.9 2.0 33 120-154 12-50 (645)
109 PRK15457 ethanolamine utilizat 26.1 38 0.00081 36.1 1.6 75 570-658 142-216 (233)
110 TIGR02297 HpaA 4-hydroxyphenyl 25.5 55 0.0012 34.1 2.8 31 630-660 57-87 (287)
111 PRK13503 transcriptional activ 24.9 37 0.00081 35.1 1.4 31 630-660 48-78 (278)
112 PF08115 Toxin_28: SFI toxin f 23.9 37 0.00079 25.8 0.8 17 44-60 14-30 (35)
113 PF14816 FAM178: Family of unk 23.9 46 0.001 37.8 1.9 28 618-646 63-91 (377)
114 PF09567 RE_MamI: MamI restric 23.1 36 0.00078 36.7 0.8 21 125-145 84-104 (314)
115 COG3492 Uncharacterized protei 22.8 26 0.00056 32.4 -0.2 13 18-30 42-54 (104)
116 KOG4286 Dystrophin-like protei 22.3 43 0.00094 40.9 1.4 35 125-159 605-641 (966)
117 PF10367 Vps39_2: Vacuolar sor 21.9 74 0.0016 28.2 2.5 22 114-135 69-90 (109)
118 PRK13501 transcriptional activ 21.8 50 0.0011 34.8 1.6 28 630-657 51-78 (290)
119 smart00647 IBR In Between Ring 21.4 59 0.0013 26.2 1.7 32 122-153 17-56 (64)
120 PF04255 DUF433: Protein of un 20.2 68 0.0015 26.4 1.8 16 24-39 37-52 (56)
No 1
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=100.00 E-value=4.3e-185 Score=1548.91 Aligned_cols=642 Identities=42% Similarity=0.715 Sum_probs=577.7
Q ss_pred CCCCCceEecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCCCCCcccccccCcCCcccccccC----CChHHHHHHHH-
Q 004933 2 KSERKYVVPCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFCRRNCNCSVCLHTSGFIETSKIN----MTDCEKVEHLR- 76 (723)
Q Consensus 2 r~d~~~vv~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg~CNCk~CLr~~~~i~~~~~e----~~~~~k~~~~~- 76 (723)
+.++..+-+|++|+-+ ||++|++.|||.++.+|++++|+||+.+|||..|++..+++.+.+.. .+..+++.++.
T Consensus 237 ~tlfn~hw~C~~C~~~-~Cl~C~r~~~p~~~~~e~a~k~~~~~~~C~~~q~h~~~~Lm~Tq~i~~~al~~~~~~~h~~r~ 315 (889)
T KOG1356|consen 237 TTLFNIHWRCPRCGFG-VCLDCYRKWYPRLSKEEVAEKCEFSWLKCNKGQCHALSELMPTQIIPGSALLDLSDRVHAVRE 315 (889)
T ss_pred ccccceeEEccccCCe-eeecchhhccccchHhHhhhhhhHHHHhcCCccccchhhcccccccchhhhhhHHHHHHHHHH
Confidence 4567778899999977 99999999999999999999999999999999999999999988766 77789999999
Q ss_pred -HHHHHHhhhhHhhcHHHhhhhhhhhhhccccCCcccccccccCCCCceecCCcccccccccccCCCCCcccchhchHHH
Q 004933 77 -YLMVSLLPFIRQICEEQTQEIEFEASIQRVHSSKVGVSETLCGNDERVYCNHCATSIIDLHRSCPKCSYELCLTCCKEI 155 (723)
Q Consensus 77 -yll~~lLP~lkqi~~EQ~~E~e~Eaki~G~~~sei~i~~a~~~~DER~~CD~C~tSI~D~HRsC~~CsydLCL~CC~El 155 (723)
|+|..++|+|+.++..|-.+.+.||+|||..++. +++.+...++|++|||+|.|||.|+||+||+|+|++||.||.+|
T Consensus 316 k~~I~~~cpcl~~~~~~~~~~~~~e~~vq~~~~~~-~~~~~~~~~~e~~~~~~~~~si~~l~r~cP~~s~~~~l~~~~~i 394 (889)
T KOG1356|consen 316 KFGIKAHCPCLKKQNKQQPLDAETEASVQGTEPTS-KPPVTQANPEEPLYCDHCATSIGDLKRSCPDSSYAICLPWLADL 394 (889)
T ss_pred HhhHHhhChhHHhhhhhccccHHHHHHHhcCCCCC-CccccccCcCCCccccccccchhhccccCCCccccccchHHHHh
Confidence 9999999999999999999999999999999988 77777778899999999999999999999999999999999999
Q ss_pred hcCcCCCccccceeeeccCcccccCCCCCCCccCCCCCCCCCCCCcccccCCCCCccCCCCCCCCCCCcceeccccCCch
Q 004933 156 CEGRLSGRAEMKFQYVNRGYGYMQGGDPLPESCLHQTPDVHVEPSVMWSADDNGTISCPPTEMGGCGDCVLELTRILPDR 235 (723)
Q Consensus 156 R~g~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~~~~~~~~~W~a~~dGsI~CpP~e~ggCg~~~L~L~~if~~~ 235 (723)
|+|.+.-..+..+.|.+||..|.||.++...+-...... .+.+ ++++|+|.|-|...+||+...|+|||++|.-
T Consensus 395 ~~g~l~~~~e~~~~~~~r~~~~~~g~~~~~~~~~s~~~~---~~~~---~~~ng~~r~l~~~~~g~~~~~l~lkr~lpn~ 468 (889)
T KOG1356|consen 395 RRGDLKEKEECELMLRSRGVKYEHGPDPIEPSLSSVSVD---EPSS---ANENGSLRDLLLSLAGCLDRGLKLKRILPNI 468 (889)
T ss_pred hcCCcccchhHHHHHHHHHHHhhcCccccccccCCCCCC---CCcc---cccccchhhcccccCccchhhhhhhhcCchH
Confidence 999887776668889999999999988764332211111 1122 8899999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHhhcccccccccC-cccCCcccchhccccCCCCCCeeecCCCCCcCchhhHHHHHHHhhcCCCEEEE
Q 004933 236 WISDLEKEARDLVLILDNKLTNLRQN-RAETGTDMLCKAASREGSDDNLLYCPDSTKIQEDEELFRFQKHWIKGEPVIVR 314 (723)
Q Consensus 236 ~i~~L~~~aee~~~~~~~~~~~~~~c-~~~~~~~~~r~aa~re~s~dn~lYcP~~~d~~~~~~~~~FQ~hW~kGePVIV~ 314 (723)
|.+.++..||.-+..+.+.... .-| +...+.+.++++|.|+.+.|||||||.+.+.+. +|++|||+||++|||||||
T Consensus 469 ~~s~i~~~vE~k~~~~~~~~~l-~~~~~~~~~~~~~~s~~~~~~~cdn~Ll~l~~d~~~~-~n~~~FQEhWkqGqPViVs 546 (889)
T KOG1356|consen 469 LDSIIASVVENKLTSKLSKPPL-RLCRSSQDGSGLLLSAASHSWLCDNRLLSLKVDPLNQ-NNLKHFQEHWKQGQPVIVS 546 (889)
T ss_pred HHHHHHHHHHhhcccccCCchh-hcCccccccccCccccCCCCcCCCCceecCccCccch-hHHHHHHHHHhcCCcEEeh
Confidence 9999999999888775554433 233 223466778999999999999999999944554 9999999999999999999
Q ss_pred ecccccCCCCCChhHHHHHHhhhccccccccCCceeEeecCCCceeecchhhhhccccCCccCCCCccceeecCCCCCCC
Q 004933 315 NVLDKVTGLSWEPMVMWRALCENVDSEVSSKMSEVKAIDCLASCEVEISTRQFFKGYTQGRTYDNFWPEMLKLKDWPPSD 394 (723)
Q Consensus 315 ~vl~~~s~lsW~P~~mwra~~e~~~~~~~~~~~~vkaidCl~~~ev~i~~~~Ff~Gf~~gr~~~~~wp~mLKLKDWPps~ 394 (723)
||++++++++|+||+|||+|+++.+.-+...+.++.++||++ ++.+||.||++|+++++|||+|||||||||++
T Consensus 547 ~V~~~l~g~lW~P~a~~~~~g~q~~~l~n~~~~~i~s~d~~~------~fwegFe~~~kr~~~~~g~p~vLKLKDWpp~~ 620 (889)
T KOG1356|consen 547 GVHKKLNGLLWKPEALSRAFGDQVVDLSNCNNSQIISNDCVD------NFWEGFEGYSKRLKSENGWPEVLKLKDWPPGE 620 (889)
T ss_pred HhhhhccccccchHHHHHHhccchhhhhcCCCCCccccchhh------hHHHhhcccccCcccccCCeeEEeecCCCchH
Confidence 999999999999999999999988766667777888888887 78999999999999999999999999999999
Q ss_pred chhhhcccchHHHHhCCCCcCcCCCCCccccccccCCCCCCCCCCCcchhhccccccccCCCCCccccccchhhhhHhhh
Q 004933 395 KFEDLMPRHCDEFISALPFQEYSDPRAGILNLAVKLPSGVLKPDLGPKTYIAYGVAEELGRGDSVTKLHCDMSDAVNILT 474 (723)
Q Consensus 395 ~F~e~lP~h~~efi~~LP~~eYt~pr~G~LNLAs~LP~~~lkPDLGPK~YIAYG~~eelg~gdSvTkLH~DmSDAVNIL~ 474 (723)
+|+++||+||+|||++|||||||| +.|+||||++||.+|++||||||||||||+++++|||||||||||||||||||||
T Consensus 621 ~Fkd~lP~r~eell~sLPlpEYt~-r~G~LNlAs~LP~~fv~PDLGPk~y~AYG~~~e~gr~~gtTnLH~dvSDaVNILv 699 (889)
T KOG1356|consen 621 DFKDMLPRRFEELLASLPLPEYTD-RDGKLNLASKLPEGFVRPDLGPKLYNAYGVSTELGRGDGTTNLHLDVSDAVNILV 699 (889)
T ss_pred hHhhhhhHHHHHHHHcCCchhhhc-CCCccchHhhCcccccCCCCCchhhhhccccccccCCCCceeeceehhhhhhhee
Confidence 999999999999999999999999 8999999999999999999999999999999999999999999999999999999
Q ss_pred hccccccchHhHHHHHHHHHHHHHhhhhhhhccCCCcccccCCCCCCCCCCCccccccccCCCCCCcccccccccccccC
Q 004933 475 HTEEVLLTEEQHSAVERLKKEHRAQDLKENLVQDGMDESIEEPNSDNNKEDTDVSEINDSELLPSGIRGEFKMSRDEMQG 554 (723)
Q Consensus 475 ht~ev~~~~~~~~~i~~l~~~~~~q~~~e~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 (723)
||++++. +...|++++++..+++..|+.-. ++
T Consensus 700 yv~e~~~---~~~~~~~~~k~~~~~~~de~~~~----------------------~~----------------------- 731 (889)
T KOG1356|consen 700 YVGEPPG---QIEQIAKVLKKIQEGDLDEITRS----------------------RI----------------------- 731 (889)
T ss_pred eeccCCc---hHHhHHHHHHhhhhcchhhhhhh----------------------hc-----------------------
Confidence 9998876 44556666666655543222110 00
Q ss_pred CccccCCCCCCcCCCCccEeEeecCCChHHHHHHHHHHHHhhccccCCCCCcccCCcCCcceecCHHHHHHHHHHhCccc
Q 004933 555 TAFTCPHSEGTMVESGGALWDIFRRQDVPKLEAYLRKHFKEFRHVYCSPVEQVIHPIHDQCFYLSSEHKKKLKEEFGVEP 634 (723)
Q Consensus 555 ~~~~~~~~~~~~~~~~GAlWdIFrreDv~KLreyL~kh~~Ef~h~~~~p~~~v~dPIHDQ~fYL~~~hk~kLkeEyGVep 634 (723)
+ +..+.+|||||||||||||||||||+||++||+| ++.+|+||||||+||||.+||+||||||||||
T Consensus 732 -------~--~~~e~~GALWhIF~~~Dv~KireyL~k~~~E~~~----~~~~v~hPIhDQS~YLd~~lr~RLkeEyGVe~ 798 (889)
T KOG1356|consen 732 -------S--SVSETPGALWHIFRAQDVPKIREYLRKVCKEQGH----EVPKVHHPIHDQSWYLDRYLRRRLKEEYGVEP 798 (889)
T ss_pred -------c--ccccCCcchhhhhhhcchHHHHHHHHHhhHHhcC----CCCcccCCCcccceeccHHHHHHHHHHhCCCc
Confidence 0 0146899999999999999999999999999999 68999999999999999999999999999999
Q ss_pred eEEEeecCceeEecCCCccccccccccceeeccccCccchHHHHHHHHHhhcCCcccccchhhhhHhHHHHHHHHHHHHH
Q 004933 635 WTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDECLRLTKEFRLLPKNHRAREDKLEIKKMILYAVAQAIKD 714 (723)
Q Consensus 635 Wtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~ec~rLteEfR~Lp~~H~~keDkLevkkm~l~A~~~av~~ 714 (723)
|||+|+||||||||||||||||||+||||||+||||||||.||+|||+|||+||++|.+||||||||||+||||++||++
T Consensus 799 WtfvQ~LGdAVfIPAGaPHQVrNLkSCikVa~DFVSPE~v~ec~rLT~EfR~Lp~~h~~~eDKLqvK~mi~hAVk~Av~~ 878 (889)
T KOG1356|consen 799 WTFVQFLGDAVFIPAGAPHQVRNLKSCIKVAEDFVSPEHVSECFRLTQEFRQLPQNHKNHEDKLQVKNMIYHAVKDAVGT 878 (889)
T ss_pred cchhhcccceEEecCCCcHHhhhhhhHHHHHHhhCChhhHHHHHHHHHHHhhCCCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccC
Q 004933 715 ANSLIPA 721 (723)
Q Consensus 715 l~~l~~~ 721 (723)
|+.++..
T Consensus 879 L~~~~s~ 885 (889)
T KOG1356|consen 879 LKEAESS 885 (889)
T ss_pred HHHhhcc
Confidence 9987653
No 2
>PF02373 JmjC: JmjC domain, hydroxylase; InterPro: IPR013129 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with jmjN (see IPR003349 from INTERPRO) and belongs to the Cupin superfamily [].; PDB: 2YU2_A 2YU1_A 3AVR_A 3AVS_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=99.52 E-value=1e-14 Score=131.22 Aligned_cols=84 Identities=36% Similarity=0.578 Sum_probs=63.9
Q ss_pred CCccEeEeecCCChHHHHHHHHHHHHhhccccCCCCCcccCCc--CCcceecCHHHHHHHHHHhCccceEEEeecCceeE
Q 004933 569 SGGALWDIFRRQDVPKLEAYLRKHFKEFRHVYCSPVEQVIHPI--HDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVF 646 (723)
Q Consensus 569 ~~GAlWdIFrreDv~KLreyL~kh~~Ef~h~~~~p~~~v~dPI--HDQ~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVF 646 (723)
.+..+|-+++++|.+|++++++++... .+|+ +.....+.++. ..+.||+.|+|+|++||+||
T Consensus 29 g~~k~W~~v~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~p~~----l~~~gi~~~~~~Q~~Ge~V~ 92 (114)
T PF02373_consen 29 GGSKVWYIVPPEDADKFEKFLRSKESQ------------NCPQFLDHKNIFVSPEQ----LKKAGIPVYRFVQKPGEFVF 92 (114)
T ss_dssp ESEEEEEEE-GGGHHHHHHHHHHHHHH------------HSTTGGCTGGEEEGHHH----HHHTTS--EEEEEETT-EEE
T ss_pred CcceEeEEechhhhhhHHHHHhhcccc------------cccccccccccccceee----eeccCcccccceECCCCEEE
Confidence 356899999999999999999987221 2344 44444454444 67799999999999999999
Q ss_pred ecCCCccccccccccceeeccc
Q 004933 647 IPAGCPHQVRNLKSCTKVAVDF 668 (723)
Q Consensus 647 IPAGcPHQVrNL~SCIKVAlDF 668 (723)
||+|++|||.|+-.||++|.+|
T Consensus 93 i~pg~~H~v~n~g~~i~~a~Nf 114 (114)
T PF02373_consen 93 IPPGAYHQVFNLGDNISEAVNF 114 (114)
T ss_dssp E-TT-EEEEEESSSEEEEEEEE
T ss_pred ECCCceEEEEeCCceEEEEecC
Confidence 9999999999999999999998
No 3
>PF13621 Cupin_8: Cupin-like domain; PDB: 3AL6_C 3AL5_C 2XUM_A 2Y0I_A 1MZE_A 3KCY_A 1MZF_A 1YCI_A 2ILM_A 1H2L_A ....
Probab=98.95 E-value=1.1e-10 Score=117.35 Aligned_cols=40 Identities=35% Similarity=0.544 Sum_probs=33.2
Q ss_pred cceEEEeecCceeEecCCCccccccc--cc-cceeeccccCcc
Q 004933 633 EPWTFEQKLGEAVFIPAGCPHQVRNL--KS-CTKVAVDFVSPE 672 (723)
Q Consensus 633 epWtf~Q~~GeAVFIPAGcPHQVrNL--~S-CIKVAlDFVSPE 672 (723)
.+|++++.+||++|||+|-.|||+|| .. +|.|...|.+|.
T Consensus 207 ~~~~~~l~pGD~LfiP~gWwH~V~~~~~~~~sisvn~w~~~~~ 249 (251)
T PF13621_consen 207 PPYEVVLEPGDVLFIPPGWWHQVENLSDDDLSISVNYWFRTPF 249 (251)
T ss_dssp -EEEEEEETT-EEEE-TT-EEEEEESTTSSCEEEEEEEEESS-
T ss_pred ceeEEEECCCeEEEECCCCeEEEEEcCCCCeEEEEEEEecccc
Confidence 89999999999999999999999999 76 999999998764
No 4
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=98.44 E-value=1.3e-07 Score=87.18 Aligned_cols=59 Identities=29% Similarity=0.680 Sum_probs=46.2
Q ss_pred CCCCceEec------CCC--CCcccchhhhhhhCCCCCHHHH---HhhCCCCCCCcccccccCcCCcccc
Q 004933 3 SERKYVVPC------GKC--RTKVYCIQCIKQWYPKMSELDV---AEICPFCRRNCNCSVCLHTSGFIET 61 (723)
Q Consensus 3 ~d~~~vv~C------~~C--~~k~fC~~CI~~wYp~ls~~di---~~~CP~Crg~CNCk~CLr~~~~i~~ 61 (723)
+..+..++| ++| -+..||.+|+.++|.++.+|-. .-.||.|||+|||..|++.+|...+
T Consensus 16 Kt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiCnCs~Crrk~g~~PT 85 (105)
T PF10497_consen 16 KTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGICNCSFCRRKRGWAPT 85 (105)
T ss_pred CCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCeeCCHhhhccCCCCCc
Confidence 344556788 888 3477999999999998744422 2469999999999999999986654
No 5
>smart00558 JmjC A domain family that is part of the cupin metalloenzyme superfamily. Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).
Probab=96.72 E-value=0.00044 Score=56.14 Aligned_cols=53 Identities=42% Similarity=0.623 Sum_probs=42.5
Q ss_pred HHHhCCCCcCcCCCCCccccccccCCCCCCCCCCCcchhhccccccccCCCCCccccccchhhhhHhhhhc
Q 004933 406 EFISALPFQEYSDPRAGILNLAVKLPSGVLKPDLGPKTYIAYGVAEELGRGDSVTKLHCDMSDAVNILTHT 476 (723)
Q Consensus 406 efi~~LP~~eYt~pr~G~LNLAs~LP~~~lkPDLGPK~YIAYG~~eelg~gdSvTkLH~DmSDAVNIL~ht 476 (723)
..+..||+ .+||+.+++.....|+. +|+.+| ..+|+|.+|.|..|.+|++.+.
T Consensus 3 ~~l~~lP~---------~~~ll~~~~~~~~~~~~---~~~~~G------~~~s~t~~H~d~~~~~n~~~~~ 55 (57)
T smart00558 3 NNLAKLPF---------KLNLLSDLPEDILGPDV---PYLYMG------MAGSVTPWHIDDYDLVNYLHQG 55 (57)
T ss_pred chhhhCCC---------cchHHHHCCcccCCCCc---ceEEEe------CCCCccceeEcCCCeEEEEEec
Confidence 34567776 68999999988887777 666667 4488999999999999988654
No 6
>KOG2131 consensus Uncharacterized conserved protein, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=96.21 E-value=0.005 Score=67.63 Aligned_cols=58 Identities=28% Similarity=0.422 Sum_probs=47.0
Q ss_pred hCccceEEEeecCceeEecCCCccccccccccceeeccccCccchHHHHH-HHHHhhcC
Q 004933 630 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDECLR-LTKEFRLL 687 (723)
Q Consensus 630 yGVepWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~ec~r-LteEfR~L 687 (723)
+.+.+.++-|.+||+||+|.|==|||-||-..|.|-..++--=|+..=.+ |-+++-.+
T Consensus 263 ~~~~~lei~Qepge~VFvPsGW~hQV~NL~dTISINHNW~N~~nl~~~w~~Lk~~y~a~ 321 (427)
T KOG2131|consen 263 FRGPLLEIFQEPGETVFVPSGWHHQVLNLGDTISINHNWCNATNLAWMWDALKEDYPAL 321 (427)
T ss_pred cccchhhhhccCCceeeccCccccccccccceeeecccccccccHHHHHHHHHhhhhhh
Confidence 34677899999999999999999999999999999999988877766554 33344333
No 7
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=95.75 E-value=0.0045 Score=48.64 Aligned_cols=30 Identities=33% Similarity=0.952 Sum_probs=28.3
Q ss_pred eecCCcccccccccccCCCC-CcccchhchH
Q 004933 124 VYCNHCATSIIDLHRSCPKC-SYELCLTCCK 153 (723)
Q Consensus 124 ~~CD~C~tSI~D~HRsC~~C-sydLCL~CC~ 153 (723)
+.||.|+++|..+...|..| .||||..|..
T Consensus 1 v~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~ 31 (43)
T cd02340 1 VICDGCQGPIVGVRYKCLVCPDYDLCESCEA 31 (43)
T ss_pred CCCCCCCCcCcCCeEECCCCCCccchHHhhC
Confidence 57999999999999999999 7999999987
No 8
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=95.23 E-value=0.0078 Score=47.57 Aligned_cols=32 Identities=25% Similarity=0.783 Sum_probs=29.4
Q ss_pred ecCCcccccccccccCCCCC-cccchhchHHHh
Q 004933 125 YCNHCATSIIDLHRSCPKCS-YELCLTCCKEIC 156 (723)
Q Consensus 125 ~CD~C~tSI~D~HRsC~~Cs-ydLCL~CC~ElR 156 (723)
.||.|..+|...+..|..|. ||||..|..+-.
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 59999999999999999999 999999998543
No 9
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=95.13 E-value=0.009 Score=47.96 Aligned_cols=30 Identities=30% Similarity=1.000 Sum_probs=28.1
Q ss_pred ecCCccccccc-ccccCCCC-CcccchhchHH
Q 004933 125 YCNHCATSIID-LHRSCPKC-SYELCLTCCKE 154 (723)
Q Consensus 125 ~CD~C~tSI~D-~HRsC~~C-sydLCL~CC~E 154 (723)
.||+|...|.. ++-.|..| .||||+.|...
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~ 33 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSA 33 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhC
Confidence 59999999999 99999999 99999999984
No 10
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=95.09 E-value=0.012 Score=70.25 Aligned_cols=104 Identities=23% Similarity=0.511 Sum_probs=64.0
Q ss_pred CCCcccccccCcCCcccccc---------cCCCh---HHHHHHHHHHHHHHhhhhHhhcHHHhhhhhhhhhhccccC-Cc
Q 004933 44 RRNCNCSVCLHTSGFIETSK---------INMTD---CEKVEHLRYLMVSLLPFIRQICEEQTQEIEFEASIQRVHS-SK 110 (723)
Q Consensus 44 rg~CNCk~CLr~~~~i~~~~---------~e~~~---~~k~~~~~yll~~lLP~lkqi~~EQ~~E~e~Eaki~G~~~-se 110 (723)
|..=+=+.|++-.+...+-. .+++. .-.++-+.|+|-.+= .++.+.=+.|.|.=+ +..+ ..
T Consensus 145 rl~~~~~~~~~~~~~~~p~~~~~e~~~l~~~~s~~~~~~~~e~~k~il~~~g---d~~c~~~~se~eAl~---~~~~~~~ 218 (889)
T KOG1356|consen 145 RLQFTKKGVLRVQGFLSPDQYDPEAISLWGPISGSDSRLDTETAKYILANLG---DQFCQLVRSEKEALS---MQRPDQK 218 (889)
T ss_pred hccccccceEeeeeecCcccCCchhhhhcccCCCcccccchHHHHHHhhhcc---chhhhhhhccchhhc---ccCcccc
Confidence 55666777777766555321 11111 123455555543321 256666666655432 2111 11
Q ss_pred ccccccccCCCCceecCCcccccccccccCCCCCcccchhchHHH
Q 004933 111 VGVSETLCGNDERVYCNHCATSIIDLHRSCPKCSYELCLTCCKEI 155 (723)
Q Consensus 111 i~i~~a~~~~DER~~CD~C~tSI~D~HRsC~~CsydLCL~CC~El 155 (723)
+....| ....|-.||.|.|++|++|+.|++|++.+|+.|.+.-
T Consensus 219 ~a~k~a--~~g~~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~ 261 (889)
T KOG1356|consen 219 VAWKRA--VKGIREMCDRCETTLFNIHWRCPRCGFGVCLDCYRKW 261 (889)
T ss_pred cchhhc--ccCcchhhhhhcccccceeEEccccCCeeeecchhhc
Confidence 222222 4677889999999999999999999999999999865
No 11
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=94.59 E-value=0.017 Score=46.03 Aligned_cols=30 Identities=37% Similarity=1.124 Sum_probs=28.0
Q ss_pred eecCCcc-cccccccccCCCC-CcccchhchH
Q 004933 124 VYCNHCA-TSIIDLHRSCPKC-SYELCLTCCK 153 (723)
Q Consensus 124 ~~CD~C~-tSI~D~HRsC~~C-sydLCL~CC~ 153 (723)
+.||.|+ .+|.-....|..| .||||..|..
T Consensus 1 i~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~ 32 (45)
T cd02339 1 IICDTCRKQGIIGIRWKCAECPNYDLCTTCYH 32 (45)
T ss_pred CCCCCCCCCCcccCeEECCCCCCccchHHHhC
Confidence 5799999 7899999999999 7999999998
No 12
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=94.47 E-value=0.021 Score=45.28 Aligned_cols=34 Identities=32% Similarity=0.806 Sum_probs=27.3
Q ss_pred CceecCCccc-ccccccccCCCCC-cccchhchHHH
Q 004933 122 ERVYCNHCAT-SIIDLHRSCPKCS-YELCLTCCKEI 155 (723)
Q Consensus 122 ER~~CD~C~t-SI~D~HRsC~~Cs-ydLCL~CC~El 155 (723)
..+.||.|++ +|.-....|..|. ||||..|..+-
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g 38 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKG 38 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH-
T ss_pred CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCc
Confidence 4578999999 9999999999998 99999999873
No 13
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=93.71 E-value=0.031 Score=43.87 Aligned_cols=35 Identities=26% Similarity=0.788 Sum_probs=30.8
Q ss_pred ceecCCcccccccccccCCCC-CcccchhchHHHhc
Q 004933 123 RVYCNHCATSIIDLHRSCPKC-SYELCLTCCKEICE 157 (723)
Q Consensus 123 R~~CD~C~tSI~D~HRsC~~C-sydLCL~CC~ElR~ 157 (723)
.+.||.|...|......|..| .||||..|..+-+.
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~ 39 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSA 39 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcCc
Confidence 357999999999999999999 89999999986544
No 14
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=93.15 E-value=0.044 Score=51.31 Aligned_cols=58 Identities=22% Similarity=0.379 Sum_probs=46.0
Q ss_pred CCcccCCcCCcceecCHHHHHHHHHHhCccceEEEeecCceeEecCCCcccccccccc--ceeec
Q 004933 604 VEQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSC--TKVAV 666 (723)
Q Consensus 604 ~~~v~dPIHDQ~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVFIPAGcPHQVrNL~SC--IKVAl 666 (723)
+....||-++|.+|..+-.-+ |.+++=+++=+.||.|+||||.+|-+.|..+. +.+++
T Consensus 56 ~~~H~hp~~~~~~~Vl~G~~~-----~~~~g~~~~l~~Gd~i~ip~g~~H~~~a~~~~~~~~l~v 115 (131)
T COG1917 56 IPWHTHPLGEQTIYVLEGEGT-----VQLEGEKKELKAGDVIIIPPGVVHGLKAVEDEPMVLLLV 115 (131)
T ss_pred cccccCCCcceEEEEEecEEE-----EEecCCceEecCCCEEEECCCCeeeeccCCCCceeEEEE
Confidence 345689989999998776543 55556667778999999999999999999999 55543
No 15
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=93.07 E-value=0.04 Score=45.32 Aligned_cols=26 Identities=50% Similarity=0.814 Sum_probs=22.5
Q ss_pred EEEeecCceeEecCCCcccccccccc
Q 004933 636 TFEQKLGEAVFIPAGCPHQVRNLKSC 661 (723)
Q Consensus 636 tf~Q~~GeAVFIPAGcPHQVrNL~SC 661 (723)
++.=..||+++||||++|+++|..+-
T Consensus 38 ~~~l~~Gd~~~i~~~~~H~~~n~~~~ 63 (71)
T PF07883_consen 38 RVELKPGDAIYIPPGVPHQVRNPGDE 63 (71)
T ss_dssp EEEEETTEEEEEETTSEEEEEEESSS
T ss_pred EeEccCCEEEEECCCCeEEEEECCCC
Confidence 55567899999999999999998754
No 16
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=93.03 E-value=0.048 Score=43.54 Aligned_cols=31 Identities=29% Similarity=0.834 Sum_probs=28.1
Q ss_pred eecCCccc-ccccccccCCCCC-cccchhchHH
Q 004933 124 VYCNHCAT-SIIDLHRSCPKCS-YELCLTCCKE 154 (723)
Q Consensus 124 ~~CD~C~t-SI~D~HRsC~~Cs-ydLCL~CC~E 154 (723)
|.||.|.+ +|+-....|..|. ||||..|...
T Consensus 1 V~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 1 VTCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 56999985 8999999999998 9999999986
No 17
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=92.55 E-value=0.064 Score=43.32 Aligned_cols=31 Identities=26% Similarity=0.809 Sum_probs=28.5
Q ss_pred ecCCccc-ccccccccCCCCC---cccchhchHHH
Q 004933 125 YCNHCAT-SIIDLHRSCPKCS---YELCLTCCKEI 155 (723)
Q Consensus 125 ~CD~C~t-SI~D~HRsC~~Cs---ydLCL~CC~El 155 (723)
.||+|.. +|.-+...|..|. ||||..|...-
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 4999998 9999999999999 99999999843
No 18
>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=92.13 E-value=0.093 Score=57.10 Aligned_cols=43 Identities=37% Similarity=0.560 Sum_probs=40.3
Q ss_pred cceEEEeecCceeEecCCCccccccccccceeeccccCccchH
Q 004933 633 EPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVD 675 (723)
Q Consensus 633 epWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~ 675 (723)
+|=...|++||.||||.|==|=|-||--.|-|.+.|+|=||.+
T Consensus 261 kPIEc~q~pGEt~fVP~GWWHvVlNle~TIAiTqNf~s~eNf~ 303 (407)
T KOG2130|consen 261 KPIECLQKPGETMFVPSGWWHVVLNLEPTIAITQNFASKENFP 303 (407)
T ss_pred CCceeeecCCceEEecCCeEEEEeccCceeeeeeccccccCCc
Confidence 4667899999999999999999999999999999999999965
No 19
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=90.85 E-value=0.11 Score=41.77 Aligned_cols=31 Identities=29% Similarity=0.870 Sum_probs=27.9
Q ss_pred eecCCcc-cccccccccCCCC-CcccchhchHH
Q 004933 124 VYCNHCA-TSIIDLHRSCPKC-SYELCLTCCKE 154 (723)
Q Consensus 124 ~~CD~C~-tSI~D~HRsC~~C-sydLCL~CC~E 154 (723)
|.||.|+ .+|.-....|..| .||||..|...
T Consensus 1 i~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~ 33 (49)
T cd02338 1 VSCDGCGKSNFTGRRYKCLICYDYDLCADCYDS 33 (49)
T ss_pred CCCCCCcCCCcEEeeEEeCCCCCCccchhHHhC
Confidence 5799999 8999999999998 79999999984
No 20
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=90.82 E-value=0.079 Score=40.94 Aligned_cols=30 Identities=40% Similarity=0.977 Sum_probs=22.7
Q ss_pred ceEecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCCC
Q 004933 7 YVVPCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFCR 44 (723)
Q Consensus 7 ~vv~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Cr 44 (723)
.++... |+ ..||..||.+|.-. ...||+||
T Consensus 15 ~~~~l~-C~-H~fh~~Ci~~~~~~------~~~CP~CR 44 (44)
T PF13639_consen 15 KVVKLP-CG-HVFHRSCIKEWLKR------NNSCPVCR 44 (44)
T ss_dssp CEEEET-TS-EEEEHHHHHHHHHH------SSB-TTTH
T ss_pred eEEEcc-CC-CeeCHHHHHHHHHh------CCcCCccC
Confidence 455555 97 89999999999843 34999997
No 21
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=90.74 E-value=0.18 Score=47.62 Aligned_cols=42 Identities=38% Similarity=0.597 Sum_probs=31.7
Q ss_pred ceEEEeecCceeEecCCCccccccccccceeeccccCccchH
Q 004933 634 PWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVD 675 (723)
Q Consensus 634 pWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~ 675 (723)
.=.++=+.||+|+||||.||.++|.-+.-=+.++=-+|+..+
T Consensus 74 ~~~~~v~~gd~~~iP~g~~H~~~N~G~~~L~liei~~p~~~~ 115 (127)
T COG0662 74 GEEVEVKAGDSVYIPAGTPHRVRNTGKIPLVLIEVQSPPYLG 115 (127)
T ss_pred CEEEEecCCCEEEECCCCcEEEEcCCCcceEEEEEecCCcCC
Confidence 566777899999999999999999999443444444555544
No 22
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=90.68 E-value=0.13 Score=41.59 Aligned_cols=33 Identities=30% Similarity=0.803 Sum_probs=28.7
Q ss_pred eecCCccc-ccccccccCCCC-CcccchhchHHHh
Q 004933 124 VYCNHCAT-SIIDLHRSCPKC-SYELCLTCCKEIC 156 (723)
Q Consensus 124 ~~CD~C~t-SI~D~HRsC~~C-sydLCL~CC~ElR 156 (723)
+.||+|+. +|.-++..|..| .||||+.|...-+
T Consensus 1 ~~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~ 35 (49)
T cd02345 1 LSCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGR 35 (49)
T ss_pred CcCCCCCCCCceEeeEECCCCCCcCchHHHHhCCC
Confidence 36999998 999999999999 4999999998443
No 23
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=88.33 E-value=0.19 Score=39.25 Aligned_cols=29 Identities=34% Similarity=1.040 Sum_probs=25.6
Q ss_pred ecCCcccccccccccCCCC-CcccchhchHH
Q 004933 125 YCNHCATSIIDLHRSCPKC-SYELCLTCCKE 154 (723)
Q Consensus 125 ~CD~C~tSI~D~HRsC~~C-sydLCL~CC~E 154 (723)
.||.|.. |.-..+.|..| .||||..|...
T Consensus 2 ~C~~C~~-~~~~r~~C~~C~dfDLC~~C~~~ 31 (41)
T cd02337 2 TCNECKH-HVETRWHCTVCEDYDLCITCYNT 31 (41)
T ss_pred cCCCCCC-cCCCceECCCCcchhhHHHHhCC
Confidence 4999988 66799999999 89999999875
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=88.22 E-value=0.12 Score=53.83 Aligned_cols=30 Identities=33% Similarity=0.976 Sum_probs=23.8
Q ss_pred cccchhhhhhhCCCCCHHHHHhhCCCCCCC
Q 004933 17 KVYCIQCIKQWYPKMSELDVAEICPFCRRN 46 (723)
Q Consensus 17 k~fC~~CI~~wYp~ls~~di~~~CP~Crg~ 46 (723)
..||..||++|-..-.+..+...||.||..
T Consensus 199 HsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~ 228 (242)
T PHA02926 199 HIFCITCINIWHRTRRETGASDNCPICRTR 228 (242)
T ss_pred chHHHHHHHHHHHhccccCcCCcCCCCcce
Confidence 359999999998754345677889999975
No 25
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=86.99 E-value=0.32 Score=51.62 Aligned_cols=30 Identities=13% Similarity=0.287 Sum_probs=24.7
Q ss_pred hCccceEEEeecCceeEecCCCcccccccc
Q 004933 630 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLK 659 (723)
Q Consensus 630 yGVepWtf~Q~~GeAVFIPAGcPHQVrNL~ 659 (723)
|.+.+=...=..||+|||||||||+..|.=
T Consensus 213 ~~~~g~~~~V~~GD~i~i~~~~~h~~~~~G 242 (260)
T TIGR03214 213 YNLDNNWVPVEAGDYIWMGAYCPQACYAGG 242 (260)
T ss_pred EEECCEEEEecCCCEEEECCCCCEEEEecC
Confidence 455566667778999999999999999964
No 26
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=84.74 E-value=0.63 Score=37.78 Aligned_cols=34 Identities=32% Similarity=0.766 Sum_probs=28.5
Q ss_pred eecCCccc-ccccccccCCCC-CcccchhchHHHhc
Q 004933 124 VYCNHCAT-SIIDLHRSCPKC-SYELCLTCCKEICE 157 (723)
Q Consensus 124 ~~CD~C~t-SI~D~HRsC~~C-sydLCL~CC~ElR~ 157 (723)
+-||.|+. +|.-+.-.|..| .||||..|+..=+.
T Consensus 1 ~~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~ 36 (49)
T cd02334 1 AKCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRT 36 (49)
T ss_pred CCCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCc
Confidence 46999995 799999999988 49999999985443
No 27
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=83.96 E-value=0.78 Score=45.68 Aligned_cols=55 Identities=13% Similarity=0.160 Sum_probs=41.9
Q ss_pred CcceecCHHHHHHHHHHhCccceEEEeecCceeEecCCCccccccccccceeeccccCcc
Q 004933 613 DQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPE 672 (723)
Q Consensus 613 DQ~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPE 672 (723)
++.+|+-.-.- ++-|..=++.-..||.++||||.||..+|..+.-=+++-+++|-
T Consensus 129 ~E~~~Vl~G~~-----~~~~~~~~~~l~~Gd~~~~~~~~~H~~~n~~~~~~~~l~~~~p~ 183 (185)
T PRK09943 129 EEIGTVLEGEI-----VLTINGQDYHLVAGQSYAINTGIPHSFSNTSAGICRIISAHTPT 183 (185)
T ss_pred cEEEEEEEeEE-----EEEECCEEEEecCCCEEEEcCCCCeeeeCCCCCCeEEEEEeCCC
Confidence 45555544332 25567778889999999999999999999887766777777774
No 28
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=83.20 E-value=0.51 Score=35.67 Aligned_cols=29 Identities=31% Similarity=0.900 Sum_probs=23.4
Q ss_pred eEecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCC
Q 004933 8 VVPCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFC 43 (723)
Q Consensus 8 vv~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~C 43 (723)
.+.-+.|+ ..||.+||.+|... . ..||+|
T Consensus 11 ~~~~~~CG-H~fC~~C~~~~~~~-~-----~~CP~C 39 (39)
T PF13923_consen 11 PVVVTPCG-HSFCKECIEKYLEK-N-----PKCPVC 39 (39)
T ss_dssp EEEECTTS-EEEEHHHHHHHHHC-T-----SB-TTT
T ss_pred cCEECCCC-CchhHHHHHHHHHC-c-----CCCcCC
Confidence 45678999 78999999999776 2 799987
No 29
>PRK13290 ectC L-ectoine synthase; Reviewed
Probab=82.41 E-value=0.89 Score=43.38 Aligned_cols=37 Identities=16% Similarity=0.098 Sum_probs=27.3
Q ss_pred ceEEEeecCceeEecCCCccccccccccceeeccccCcc
Q 004933 634 PWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPE 672 (723)
Q Consensus 634 pWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPE 672 (723)
.=++.=..||+++||||-||+.+|...+.=++. ++|.
T Consensus 74 g~~~~L~aGD~i~~~~~~~H~~~N~e~~~~l~v--~tP~ 110 (125)
T PRK13290 74 GEVHPIRPGTMYALDKHDRHYLRAGEDMRLVCV--FNPP 110 (125)
T ss_pred CEEEEeCCCeEEEECCCCcEEEEcCCCEEEEEE--ECCC
Confidence 344556789999999999999999855544333 5554
No 30
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=81.83 E-value=0.7 Score=37.56 Aligned_cols=33 Identities=24% Similarity=0.569 Sum_probs=26.6
Q ss_pred eecCCcccccccccccCCCCC-cccchhchHHHh
Q 004933 124 VYCNHCATSIIDLHRSCPKCS-YELCLTCCKEIC 156 (723)
Q Consensus 124 ~~CD~C~tSI~D~HRsC~~Cs-ydLCL~CC~ElR 156 (723)
+.||.|...|.-+.-.|-.|. ||||..|...=+
T Consensus 1 i~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~ 34 (48)
T cd02343 1 ISCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGV 34 (48)
T ss_pred CCCCCCCCcCCCceEECCCCCCchhHHHHHhCCc
Confidence 359999988888877888884 999999987433
No 31
>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=81.53 E-value=0.6 Score=33.72 Aligned_cols=27 Identities=26% Similarity=0.806 Sum_probs=12.8
Q ss_pred ecCCccccccc-ccccCCCCCcccchhc
Q 004933 125 YCNHCATSIID-LHRSCPKCSYELCLTC 151 (723)
Q Consensus 125 ~CD~C~tSI~D-~HRsC~~CsydLCL~C 151 (723)
.|+.|+.+|.. +.-+|+.|.|.|.+.|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 59999999998 8888999999999887
No 32
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=80.00 E-value=0.83 Score=33.64 Aligned_cols=33 Identities=33% Similarity=0.870 Sum_probs=24.6
Q ss_pred eEecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCCCCC
Q 004933 8 VVPCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFCRRN 46 (723)
Q Consensus 8 vv~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg~ 46 (723)
.+.-..|+ ..||..|++.|+.. ....||.|+..
T Consensus 12 ~~~~~~C~-H~~c~~C~~~~~~~-----~~~~Cp~C~~~ 44 (45)
T cd00162 12 PVVLLPCG-HVFCRSCIDKWLKS-----GKNTCPLCRTP 44 (45)
T ss_pred ceEecCCC-ChhcHHHHHHHHHh-----CcCCCCCCCCc
Confidence 34556688 77999999999764 34569999863
No 33
>TIGR00218 manA mannose-6-phosphate isomerase, class I. The names phosphomannose isomerase and mannose-6-phosphate isomerase are synonomous. This family contains two rather deeply branched groups. One group contains an experimentally determined phosphomannose isomerase of Streptococcus mutans as well as three uncharacterized paralogous proteins of Bacillus subtilis, all at more than 50 % identity to each other, plus a more distant homolog from Archaeoglobus fulgidus. The other group contains members from E. coli, budding yeast, Borrelia burgdorferi, etc.
Probab=79.69 E-value=0.92 Score=48.93 Aligned_cols=15 Identities=40% Similarity=0.986 Sum_probs=13.7
Q ss_pred ecCceeEecCCCccc
Q 004933 640 KLGEAVFIPAGCPHQ 654 (723)
Q Consensus 640 ~~GeAVFIPAGcPHQ 654 (723)
++||+||||||.||=
T Consensus 156 ~~Gd~i~ipaGt~HA 170 (302)
T TIGR00218 156 KPGDFFYVPSGTPHA 170 (302)
T ss_pred CCCCEEEeCCCCccc
Confidence 479999999999995
No 34
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=78.51 E-value=1.1 Score=35.60 Aligned_cols=32 Identities=22% Similarity=0.607 Sum_probs=27.4
Q ss_pred eecCCcc-cccccccccCCCC-CcccchhchHHH
Q 004933 124 VYCNHCA-TSIIDLHRSCPKC-SYELCLTCCKEI 155 (723)
Q Consensus 124 ~~CD~C~-tSI~D~HRsC~~C-sydLCL~CC~El 155 (723)
+.||.|. +||+-+-..|..| .||||-.|..+-
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 4699999 5999999999977 699999998753
No 35
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=77.73 E-value=1.2 Score=43.88 Aligned_cols=22 Identities=36% Similarity=0.724 Sum_probs=19.4
Q ss_pred ecCceeEecCCCcccccccccc
Q 004933 640 KLGEAVFIPAGCPHQVRNLKSC 661 (723)
Q Consensus 640 ~~GeAVFIPAGcPHQVrNL~SC 661 (723)
..||.|+||+|+.|++.|.-+.
T Consensus 107 ~~g~sv~Ip~g~~H~i~n~g~~ 128 (151)
T PF01050_consen 107 KEGDSVYIPRGAKHRIENPGKT 128 (151)
T ss_pred cCCCEEEECCCCEEEEECCCCc
Confidence 5799999999999999997654
No 36
>COG4101 Predicted mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=77.57 E-value=1.1 Score=42.96 Aligned_cols=27 Identities=37% Similarity=0.583 Sum_probs=23.4
Q ss_pred EEEeecCceeEecCCCccccccccccc
Q 004933 636 TFEQKLGEAVFIPAGCPHQVRNLKSCT 662 (723)
Q Consensus 636 tf~Q~~GeAVFIPAGcPHQVrNL~SCI 662 (723)
+.+-.+||...||+|.|||--||.+=-
T Consensus 89 ha~~~pGDf~YiPpgVPHqp~N~S~ep 115 (142)
T COG4101 89 HAEVGPGDFFYIPPGVPHQPANLSTEP 115 (142)
T ss_pred eEEecCCCeEEcCCCCCCcccccCCCC
Confidence 567789999999999999999997533
No 37
>PRK15131 mannose-6-phosphate isomerase; Provisional
Probab=77.51 E-value=1.2 Score=50.21 Aligned_cols=17 Identities=41% Similarity=0.643 Sum_probs=14.9
Q ss_pred EeecCceeEecCCCccc
Q 004933 638 EQKLGEAVFIPAGCPHQ 654 (723)
Q Consensus 638 ~Q~~GeAVFIPAGcPHQ 654 (723)
.=++|||+|||||.||=
T Consensus 240 ~l~pGeaifipAg~~HA 256 (389)
T PRK15131 240 KLNPGEAMFLFAETPHA 256 (389)
T ss_pred EeCCCCEEEeCCCCCeE
Confidence 34689999999999996
No 38
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=74.53 E-value=1.2 Score=34.73 Aligned_cols=28 Identities=29% Similarity=0.925 Sum_probs=23.0
Q ss_pred cCCCCCcccchhhhhhhCCCCCHHHHHhhCCCCCC
Q 004933 11 CGKCRTKVYCIQCIKQWYPKMSELDVAEICPFCRR 45 (723)
Q Consensus 11 C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg 45 (723)
=++|+ ..||..||+++. .....||+||.
T Consensus 17 l~~Cg-H~~C~~C~~~~~------~~~~~CP~C~k 44 (44)
T PF14634_consen 17 LTSCG-HIFCEKCLKKLK------GKSVKCPICRK 44 (44)
T ss_pred EcccC-CHHHHHHHHhhc------CCCCCCcCCCC
Confidence 36777 789999999998 55678999984
No 39
>PRK04190 glucose-6-phosphate isomerase; Provisional
Probab=73.38 E-value=2.5 Score=43.36 Aligned_cols=42 Identities=21% Similarity=0.278 Sum_probs=30.9
Q ss_pred cceEEEeecCceeEecCCCccccccccccceeeccccCccchH
Q 004933 633 EPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVD 675 (723)
Q Consensus 633 epWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~ 675 (723)
+.+.+.=..||+|+||+|..|++.|.-+.-=+.+- +.|...+
T Consensus 118 ~~~~~~v~pGd~v~IPpg~~H~~iN~G~epl~fl~-v~p~~~~ 159 (191)
T PRK04190 118 EARWIEMEPGTVVYVPPYWAHRSVNTGDEPLVFLA-CYPADAG 159 (191)
T ss_pred cEEEEEECCCCEEEECCCCcEEeEECCCCCEEEEE-EEcCCcc
Confidence 37889999999999999999999998654333332 4444443
No 40
>COG1482 ManA Phosphomannose isomerase [Carbohydrate transport and metabolism]
Probab=72.60 E-value=1.9 Score=47.41 Aligned_cols=19 Identities=53% Similarity=0.903 Sum_probs=16.5
Q ss_pred EEeecCceeEecCCCcccc
Q 004933 637 FEQKLGEAVFIPAGCPHQV 655 (723)
Q Consensus 637 f~Q~~GeAVFIPAGcPHQV 655 (723)
+.=++|||+|||||.||=.
T Consensus 160 v~lkpGe~~fl~Agt~HA~ 178 (312)
T COG1482 160 VKLKPGEAFFLPAGTPHAY 178 (312)
T ss_pred EecCCCCEEEecCCCceee
Confidence 5567999999999999964
No 41
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=70.58 E-value=1.7 Score=30.67 Aligned_cols=29 Identities=28% Similarity=0.907 Sum_probs=21.6
Q ss_pred EecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCC
Q 004933 9 VPCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFC 43 (723)
Q Consensus 9 v~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~C 43 (723)
..-..|+ ..||..|++.|+. .....||+|
T Consensus 11 ~~~~~C~-H~~c~~C~~~~~~-----~~~~~CP~C 39 (39)
T smart00184 11 PVVLPCG-HTFCRSCIRKWLK-----SGNNTCPIC 39 (39)
T ss_pred cEEecCC-ChHHHHHHHHHHH-----hCcCCCCCC
Confidence 3445688 5699999999986 334569887
No 42
>PLN02288 mannose-6-phosphate isomerase
Probab=69.25 E-value=2.4 Score=47.95 Aligned_cols=15 Identities=40% Similarity=0.720 Sum_probs=13.9
Q ss_pred ecCceeEecCCCccc
Q 004933 640 KLGEAVFIPAGCPHQ 654 (723)
Q Consensus 640 ~~GeAVFIPAGcPHQ 654 (723)
.+|||||||||-||=
T Consensus 256 ~PGeaifl~ag~~HA 270 (394)
T PLN02288 256 NPGEALYLGANEPHA 270 (394)
T ss_pred CCCCEEEecCCCCce
Confidence 589999999999995
No 43
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=69.19 E-value=2.2 Score=43.92 Aligned_cols=35 Identities=29% Similarity=0.827 Sum_probs=23.6
Q ss_pred CCCCCcccchhhhhhhCC--CCCHHHH--------HhhCCCCCCCc
Q 004933 12 GKCRTKVYCIQCIKQWYP--KMSELDV--------AEICPFCRRNC 47 (723)
Q Consensus 12 ~~C~~k~fC~~CI~~wYp--~ls~~di--------~~~CP~Crg~C 47 (723)
+.|+ ..||..||.+|.- ..+.+.+ ...||+||..-
T Consensus 34 T~CG-H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~I 78 (193)
T PLN03208 34 TLCG-HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV 78 (193)
T ss_pred cCCC-chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcC
Confidence 6788 7999999999942 1111111 24799999743
No 44
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=68.64 E-value=0.92 Score=34.18 Aligned_cols=29 Identities=24% Similarity=0.873 Sum_probs=22.1
Q ss_pred ecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCC
Q 004933 10 PCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFC 43 (723)
Q Consensus 10 ~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~C 43 (723)
.=..|+ ..||..||.+|+.. .-...||.|
T Consensus 13 ~~~~C~-H~fC~~C~~~~~~~----~~~~~CP~C 41 (41)
T PF00097_consen 13 ILLPCG-HSFCRDCLRKWLEN----SGSVKCPLC 41 (41)
T ss_dssp EETTTS-EEEEHHHHHHHHHH----TSSSBTTTT
T ss_pred EEecCC-CcchHHHHHHHHHh----cCCccCCcC
Confidence 346788 77999999999875 334558877
No 45
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=67.09 E-value=2.5 Score=45.63 Aligned_cols=33 Identities=30% Similarity=0.825 Sum_probs=29.3
Q ss_pred ceecCCccc-ccccccccCCCCC-cccchhchHHH
Q 004933 123 RVYCNHCAT-SIIDLHRSCPKCS-YELCLTCCKEI 155 (723)
Q Consensus 123 R~~CD~C~t-SI~D~HRsC~~Cs-ydLCL~CC~El 155 (723)
-+-||+|.+ .|+-.-..|.-|. ||||-.|-...
T Consensus 152 ~v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~ 186 (278)
T KOG4582|consen 152 SVPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN 186 (278)
T ss_pred cccCCCccCCccccceeeecCCCccchhHHhhcCC
Confidence 377999999 9999999999985 99999998753
No 46
>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=66.81 E-value=3.4 Score=29.47 Aligned_cols=23 Identities=26% Similarity=0.959 Sum_probs=20.7
Q ss_pred ecCCcccccccccccCCCCCccc
Q 004933 125 YCNHCATSIIDLHRSCPKCSYEL 147 (723)
Q Consensus 125 ~CD~C~tSI~D~HRsC~~CsydL 147 (723)
.|..|..-|-.--+.||.|+|++
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 48899999999999999999985
No 47
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=66.65 E-value=2.7 Score=29.58 Aligned_cols=25 Identities=28% Similarity=0.814 Sum_probs=22.0
Q ss_pred ceecCCcccccccccccCCCCCccc
Q 004933 123 RVYCNHCATSIIDLHRSCPKCSYEL 147 (723)
Q Consensus 123 R~~CD~C~tSI~D~HRsC~~CsydL 147 (723)
.++|.+|.+.|-+=.+-|++|+..|
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 3689999999999999999999765
No 48
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=65.88 E-value=2.6 Score=32.88 Aligned_cols=29 Identities=24% Similarity=0.673 Sum_probs=20.1
Q ss_pred CCCCCcccchhhhhhhCCCCCHHHHHhhCCCC
Q 004933 12 GKCRTKVYCIQCIKQWYPKMSELDVAEICPFC 43 (723)
Q Consensus 12 ~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~C 43 (723)
..|+ ..||..||.+|..+..... ..||.|
T Consensus 14 l~CG-H~FC~~Cl~~~~~~~~~~~--~~CP~C 42 (42)
T PF15227_consen 14 LPCG-HSFCRSCLERLWKEPSGSG--FSCPEC 42 (42)
T ss_dssp -SSS-SEEEHHHHHHHHCCSSSST-----SSS
T ss_pred cCCc-CHHHHHHHHHHHHccCCcC--CCCcCC
Confidence 3677 8899999999988765444 689987
No 49
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=64.72 E-value=3.2 Score=28.72 Aligned_cols=23 Identities=39% Similarity=0.969 Sum_probs=20.5
Q ss_pred ecCCcccccccccccCCCCCccc
Q 004933 125 YCNHCATSIIDLHRSCPKCSYEL 147 (723)
Q Consensus 125 ~CD~C~tSI~D~HRsC~~CsydL 147 (723)
||-+|...|-|=.+-|++|+..|
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCcC
Confidence 68999999999999999999865
No 50
>KOG2508 consensus Predicted phospholipase [Lipid transport and metabolism]
Probab=64.57 E-value=6.8 Score=43.88 Aligned_cols=39 Identities=26% Similarity=0.491 Sum_probs=30.6
Q ss_pred HHHHHHHh-hcCCCEEEEecccccCCC-CCChh-HHHHHHhh
Q 004933 298 LFRFQKHW-IKGEPVIVRNVLDKVTGL-SWEPM-VMWRALCE 336 (723)
Q Consensus 298 ~~~FQ~hW-~kGePVIV~~vl~~~s~l-sW~P~-~mwra~~e 336 (723)
-.+|=+-| .+..|||+|+.+..-.++ .|.+. ++..|++.
T Consensus 33 pl~Fyr~fvs~n~PvIIrkAL~hWpal~lWs~p~Yl~~algd 74 (437)
T KOG2508|consen 33 PLDFYRKFVSTNTPVIIRKALPHWPALKLWSQPDYLLSALGD 74 (437)
T ss_pred hHHHHHhhhcCCCcEEEecccccCchhhccCchHHHHHhccC
Confidence 35777777 789999999999877777 89887 77666543
No 51
>PF00190 Cupin_1: Cupin; InterPro: IPR006045 This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. ; GO: 0045735 nutrient reservoir activity; PDB: 2E9Q_A 2EVX_A 1OD5_A 1UCX_A 1UD1_C 1FXZ_C 3KGL_C 3KSC_D 1UIJ_F 1IPK_B ....
Probab=64.28 E-value=5.7 Score=37.96 Aligned_cols=38 Identities=32% Similarity=0.496 Sum_probs=26.7
Q ss_pred EEEee----cCceeEecCCCccccccc--cccceeeccccC-ccc
Q 004933 636 TFEQK----LGEAVFIPAGCPHQVRNL--KSCTKVAVDFVS-PEN 673 (723)
Q Consensus 636 tf~Q~----~GeAVFIPAGcPHQVrNL--~SCIKVAlDFVS-PEn 673 (723)
.+.|. .||.++||+|.||=+.|. .+.+.++.=+.+ |++
T Consensus 81 ~~~~~v~l~~Gdv~~vP~G~~h~~~n~~~~~~~~~~~f~~~~~~~ 125 (144)
T PF00190_consen 81 DFSQKVRLKAGDVFVVPAGHPHWIINDGDDEALVLIIFDTNNPPN 125 (144)
T ss_dssp EEEEEEEEETTEEEEE-TT-EEEEEECSSSSEEEEEEEEESSTTG
T ss_pred eeeceeeeecccceeeccceeEEEEcCCCCCCEEEEEEECCCCcc
Confidence 45566 999999999999999999 577666654443 434
No 52
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.86 E-value=3.7 Score=43.24 Aligned_cols=30 Identities=27% Similarity=0.923 Sum_probs=21.0
Q ss_pred CCCCcccchhhhhhhCCCCCHHHHHhhCCCCCCC
Q 004933 13 KCRTKVYCIQCIKQWYPKMSELDVAEICPFCRRN 46 (723)
Q Consensus 13 ~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg~ 46 (723)
-|+ ..||-+||-+|.--- .-.+.||||++.
T Consensus 64 lCG-HLFCWpClyqWl~~~---~~~~~cPVCK~~ 93 (230)
T KOG0823|consen 64 LCG-HLFCWPCLYQWLQTR---PNSKECPVCKAE 93 (230)
T ss_pred ecc-cceehHHHHHHHhhc---CCCeeCCccccc
Confidence 588 889999999994311 123567998753
No 53
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.82 E-value=2.6 Score=46.84 Aligned_cols=32 Identities=34% Similarity=1.070 Sum_probs=25.1
Q ss_pred CCCCcccchhhhhhhCCC-CCHHHHHhhCCCCCC
Q 004933 13 KCRTKVYCIQCIKQWYPK-MSELDVAEICPFCRR 45 (723)
Q Consensus 13 ~C~~k~fC~~CI~~wYp~-ls~~di~~~CP~Crg 45 (723)
+|+ ..||..||.+|=.- -.+-.|-+.||+||.
T Consensus 186 nC~-H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv 218 (344)
T KOG1039|consen 186 NCN-HSFCLNCIRKWRQATQFESKTSKSCPFCRV 218 (344)
T ss_pred Ccc-hhhhhcHhHhhhhhhccccccccCCCcccC
Confidence 477 77999999999631 126678899999985
No 54
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=62.16 E-value=2.2 Score=33.87 Aligned_cols=32 Identities=25% Similarity=0.672 Sum_probs=24.8
Q ss_pred EecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCCCCC
Q 004933 9 VPCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFCRRN 46 (723)
Q Consensus 9 v~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg~ 46 (723)
+.-..|+=..||..|+.+|.. -...||+||..
T Consensus 15 ~~~~pCgH~~~C~~C~~~~~~------~~~~CP~Cr~~ 46 (50)
T PF13920_consen 15 VVLLPCGHLCFCEECAERLLK------RKKKCPICRQP 46 (50)
T ss_dssp EEEETTCEEEEEHHHHHHHHH------TTSBBTTTTBB
T ss_pred eEEeCCCChHHHHHHhHHhcc------cCCCCCcCChh
Confidence 344578844499999999987 45789999963
No 55
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=60.17 E-value=4.8 Score=34.85 Aligned_cols=26 Identities=38% Similarity=1.216 Sum_probs=20.8
Q ss_pred CCCCCcccchhhhhhhCCCCCHHHHHhhCCCCC
Q 004933 12 GKCRTKVYCIQCIKQWYPKMSELDVAEICPFCR 44 (723)
Q Consensus 12 ~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Cr 44 (723)
..|+ ..|-..||.+|.-.-+ .||.||
T Consensus 48 ~~C~-H~FH~~Ci~~Wl~~~~------~CP~CR 73 (73)
T PF12678_consen 48 GPCG-HIFHFHCISQWLKQNN------TCPLCR 73 (73)
T ss_dssp ETTS-EEEEHHHHHHHHTTSS------B-TTSS
T ss_pred cccC-CCEEHHHHHHHHhcCC------cCCCCC
Confidence 5687 8899999999986433 999998
No 56
>KOG2583 consensus Ubiquinol cytochrome c reductase, subunit QCR2 [Energy production and conversion]
Probab=59.97 E-value=6.1 Score=44.73 Aligned_cols=46 Identities=37% Similarity=0.557 Sum_probs=39.5
Q ss_pred cccchhccccCCCCCCeeecCC--CCCcCchhhHHHH-HHHhhcCCCEEEE
Q 004933 267 TDMLCKAASREGSDDNLLYCPD--STKIQEDEELFRF-QKHWIKGEPVIVR 314 (723)
Q Consensus 267 ~~~~r~aa~re~s~dn~lYcP~--~~d~~~~~~~~~F-Q~hW~kGePVIV~ 314 (723)
-++|.+||+|. +-.|-||||. ...+.. .+|++| ++|..+|.-|+|.
T Consensus 158 ~e~lH~aAfRn-gLgnslY~p~~~vg~vss-~eL~~Fa~k~fv~gn~~lvg 206 (429)
T KOG2583|consen 158 IEQLHAAAFRN-GLGNSLYSPGYQVGSVSS-SELKDFAAKHFVKGNAVLVG 206 (429)
T ss_pred HHHHHHHHHhc-ccCCcccCCcccccCccH-HHHHHHHHHHhhccceEEEe
Confidence 46789999998 7899999996 666777 889999 6899999999885
No 57
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=58.94 E-value=4.3 Score=40.02 Aligned_cols=43 Identities=19% Similarity=0.317 Sum_probs=39.0
Q ss_pred cCCcCCcceecCHHHHHHHHHHhCccceEEEeecCceeEecCCCc
Q 004933 608 IHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCP 652 (723)
Q Consensus 608 ~dPIHDQ~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVFIPAGcP 652 (723)
.-|+|...-.+.+.+=+.|+++|||..|.| +-||-|.|=+|=.
T Consensus 18 ~Ap~h~r~k~msa~LSkeLr~k~~~Rs~~I--kkGD~V~Vi~Gk~ 60 (143)
T PTZ00194 18 TAPSHLRRKLMSAPLSKELRAKYNVRSMPV--RKDDEVMVVRGHH 60 (143)
T ss_pred cCcHHHHHHHhcCccCHHHHHHhCCcccee--ecCCEEEEecCCC
Confidence 568999999999999999999999999987 7799999988864
No 58
>PRK15460 cpsB mannose-1-phosphate guanyltransferase; Provisional
Probab=57.74 E-value=6 Score=45.83 Aligned_cols=46 Identities=17% Similarity=0.198 Sum_probs=30.3
Q ss_pred CccceEEEeecCceeEecCCCccccccccccceeeccccCccchHH
Q 004933 631 GVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDE 676 (723)
Q Consensus 631 GVepWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~e 676 (723)
.|..=++.=..||.|+||+|.||+.+|.-+=-=+.+--.+|+-++|
T Consensus 420 ~idg~~~~L~~GDSi~ip~g~~H~~~N~g~~~l~iI~V~~g~yl~e 465 (478)
T PRK15460 420 TIDGDIKLLGENESIYIPLGATHCLENPGKIPLDLIEVRSGSYLEE 465 (478)
T ss_pred EECCEEEEecCCCEEEECCCCcEEEEcCCCCCEEEEEEEcCCCCCC
Confidence 3444556668999999999999999998542222222355554443
No 59
>TIGR01479 GMP_PMI mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase. This enzyme is known to be bifunctional, as both mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in Pseudomonas aeruginosa, Xanthomonas campestris, and Gluconacetobacter xylinus. The literature on the enzyme from E. coli attributes mannose-6-phosphate isomerase activity to an adjacent gene, but the present sequence has not been shown to lack the activity. The PMI domain is C-terminal.
Probab=57.24 E-value=7.8 Score=44.53 Aligned_cols=42 Identities=19% Similarity=0.217 Sum_probs=29.5
Q ss_pred ccceEEEeecCceeEecCCCccccccccccceeeccccCccc
Q 004933 632 VEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPEN 673 (723)
Q Consensus 632 VepWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEn 673 (723)
+.+=++.=..||.|+||+|.||+.+|.-+--=+.+--.+|+-
T Consensus 412 ~dg~~~~l~~GDsi~ip~~~~H~~~N~g~~~~~~i~v~~~~~ 453 (468)
T TIGR01479 412 IGDETLLLTENESTYIPLGVIHRLENPGKIPLELIEVQSGSY 453 (468)
T ss_pred ECCEEEEecCCCEEEECCCCcEEEEcCCCCCEEEEEEEcCCC
Confidence 444566778999999999999999998764333333344543
No 60
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.98 E-value=6.7 Score=44.50 Aligned_cols=30 Identities=27% Similarity=0.838 Sum_probs=24.8
Q ss_pred CCCCCcccchhhhhhhCCCCCHHHHHhhCCCCCCCcc
Q 004933 12 GKCRTKVYCIQCIKQWYPKMSELDVAEICPFCRRNCN 48 (723)
Q Consensus 12 ~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg~CN 48 (723)
+.|+ ..||..||..|.... ..||.|+..+.
T Consensus 42 tpCg-H~FCs~CI~~~l~~~------~~CP~Cr~~~~ 71 (397)
T TIGR00599 42 TSCS-HTFCSLCIRRCLSNQ------PKCPLCRAEDQ 71 (397)
T ss_pred CCCC-CchhHHHHHHHHhCC------CCCCCCCCccc
Confidence 5788 889999999998753 47999998764
No 61
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=55.77 E-value=6 Score=31.72 Aligned_cols=35 Identities=29% Similarity=0.690 Sum_probs=27.0
Q ss_pred ecCCcccccccccccCCCCC-cccchhchHHHhcCcCCC
Q 004933 125 YCNHCATSIIDLHRSCPKCS-YELCLTCCKEICEGRLSG 162 (723)
Q Consensus 125 ~CD~C~tSI~D~HRsC~~Cs-ydLCL~CC~ElR~g~~~~ 162 (723)
.||.|..-+..-+-+|.++. ||||..|+.+ |+.++
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~---G~f~~ 37 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE---GRFPS 37 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC---cCCCC
Confidence 58888887777666788887 9999999985 55543
No 62
>smart00835 Cupin_1 Cupin. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.
Probab=53.72 E-value=10 Score=36.31 Aligned_cols=52 Identities=19% Similarity=0.365 Sum_probs=33.6
Q ss_pred cCCcCCcceecCHHH-HHHHHHHhCccceEEEeecCceeEecCCCcccccccc
Q 004933 608 IHPIHDQCFYLSSEH-KKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLK 659 (723)
Q Consensus 608 ~dPIHDQ~fYL~~~h-k~kLkeEyGVepWtf~Q~~GeAVFIPAGcPHQVrNL~ 659 (723)
.||-.++-+|+-.-. +-.+-++.|=+-+++.-..||+++||+|-+|+..|.-
T Consensus 47 ~H~~~~e~~~Vl~G~~~~~~~~~~~~~~~~~~l~~GD~~~ip~g~~H~~~n~~ 99 (146)
T smart00835 47 YHPRATELLYVVRGEGRVGVVDPNGNKVYDARLREGDVFVVPQGHPHFQVNSG 99 (146)
T ss_pred eCCCCCEEEEEEeCeEEEEEEeCCCCeEEEEEecCCCEEEECCCCEEEEEcCC
Confidence 455445666644321 2111122222557888999999999999999999974
No 63
>PF08007 Cupin_4: Cupin superfamily protein; InterPro: IPR022777 This signature represents primarily the cupin fold found in JmjC transcription factors. The fold is also found in lysine-specific demethylase NO66.; PDB: 2XDV_A 1VRB_B 4DIQ_B.
Probab=52.98 E-value=13 Score=40.48 Aligned_cols=41 Identities=22% Similarity=0.366 Sum_probs=31.0
Q ss_pred eEEEeecCceeEecCCCccccccccccceeeccccCccchH
Q 004933 635 WTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVD 675 (723)
Q Consensus 635 Wtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~ 675 (723)
..|+=.+||..+||.|++|++.....|+.+++-|..|-...
T Consensus 176 ~~~~L~pGD~LYlPrG~~H~~~~~~~S~hltv~~~~~t~~d 216 (319)
T PF08007_consen 176 EEVVLEPGDVLYLPRGWWHQAVTTDPSLHLTVGFRAPTWAD 216 (319)
T ss_dssp EEEEE-TT-EEEE-TT-EEEEEESS-EEEEEEEECCEBHHH
T ss_pred EEEEECCCCEEEECCCccCCCCCCCCceEEEEeeeCCchhh
Confidence 35777899999999999999999999999999999984433
No 64
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=52.50 E-value=7.5 Score=35.26 Aligned_cols=34 Identities=26% Similarity=0.731 Sum_probs=26.7
Q ss_pred ceEecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCCCC
Q 004933 7 YVVPCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFCRR 45 (723)
Q Consensus 7 ~vv~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg 45 (723)
.+|+++ |+ .-|=+.||.+|...- .....||.||.
T Consensus 46 plv~g~-C~-H~FH~hCI~kWl~~~---~~~~~CPmCR~ 79 (85)
T PF12861_consen 46 PLVWGK-CS-HNFHMHCILKWLSTQ---SSKGQCPMCRQ 79 (85)
T ss_pred ceeecc-Cc-cHHHHHHHHHHHccc---cCCCCCCCcCC
Confidence 456666 88 679999999998752 33679999996
No 65
>PF02041 Auxin_BP: Auxin binding protein; InterPro: IPR000526 Auxin binding protein is located in the lumen of the endoplasmic reticulum (ER). The primary structure contains an N-terminal hydrophobic leader sequence of 30-40 amino acids, which could represent a signal for translocation of the protein to the ER [, ]. The mature protein comprises around 165 residues, and contains a number of potential N-glycosylation sites. In vitro transport studies have demonstrated co-translational glycosylation []. Retention within the lumen of the ER correlates with an additional signal located at the C terminus, represented by the sequence Lys-Asp-Glu-Leu, known to be responsible for preventing secretion of proteins from the lumen of the ER in eukaryotic cells [, ].; GO: 0004872 receptor activity, 0005788 endoplasmic reticulum lumen; PDB: 1LR5_D 1LRH_D.
Probab=51.81 E-value=8.1 Score=38.59 Aligned_cols=41 Identities=32% Similarity=0.456 Sum_probs=24.4
Q ss_pred cceecCHHHHHHHHHHhCccceEEEeecCceeEecCCCcccccccc
Q 004933 614 QCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLK 659 (723)
Q Consensus 614 Q~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVFIPAGcPHQVrNL~ 659 (723)
++.||...+ ++|.-+|=.|.=.++.-.-||.+++|||.|-.
T Consensus 75 GTl~l~~~~-----~~~pG~pqef~~~pnSTf~IPvn~~HQv~NT~ 115 (167)
T PF02041_consen 75 GTLYLASSH-----EKYPGKPQEFPIFPNSTFHIPVNDAHQVWNTN 115 (167)
T ss_dssp EEEEE--SS-----SSS--S-EEEEE-TTEEEEE-TT--EEEE---
T ss_pred eEEEEeccc-----ccCCCCceEEEecCCCeEEeCCCCcceeecCC
Confidence 466777433 26999999999999999999999999999964
No 66
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=51.65 E-value=6 Score=45.06 Aligned_cols=33 Identities=30% Similarity=0.896 Sum_probs=29.4
Q ss_pred CCceecCCccccccccc-ccCCCCC-cccchhchH
Q 004933 121 DERVYCNHCATSIIDLH-RSCPKCS-YELCLTCCK 153 (723)
Q Consensus 121 DER~~CD~C~tSI~D~H-RsC~~Cs-ydLCL~CC~ 153 (723)
.+-..||+|..-|-+.- -.|..|- |||||-|+.
T Consensus 12 g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs 46 (438)
T KOG0457|consen 12 GGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFS 46 (438)
T ss_pred CCCCCCccHhHHhccceEEEeecCCCcchhHHHHh
Confidence 46778999999999865 8999999 999999986
No 67
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=50.71 E-value=5 Score=44.16 Aligned_cols=31 Identities=32% Similarity=0.929 Sum_probs=27.2
Q ss_pred ceecCCcccccccc-cccCCCC-CcccchhchH
Q 004933 123 RVYCNHCATSIIDL-HRSCPKC-SYELCLTCCK 153 (723)
Q Consensus 123 R~~CD~C~tSI~D~-HRsC~~C-sydLCL~CC~ 153 (723)
...||+|..-|.|. |-+|..| .||||+-|+-
T Consensus 5 k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~ 37 (432)
T COG5114 5 KIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFV 37 (432)
T ss_pred eeeehHHHHhhhcceeeeeecccccceehhhhh
Confidence 45799999999986 5689999 9999999985
No 68
>TIGR03404 bicupin_oxalic bicupin, oxalate decarboxylase family. Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.
Probab=50.15 E-value=12 Score=42.05 Aligned_cols=84 Identities=21% Similarity=0.312 Sum_probs=49.6
Q ss_pred CCcccCCcCCcceecCHH-HHHHHHHHhCccceEEEeecCceeEecCCCccccccccccceeeccccCccchHHHHHHHH
Q 004933 604 VEQVIHPIHDQCFYLSSE-HKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDECLRLTK 682 (723)
Q Consensus 604 ~~~v~dPIHDQ~fYL~~~-hk~kLkeEyGVepWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~ec~rLte 682 (723)
.....||--+..+|+-.- -+..+-..-| ...++.=..||++|||+|.+|.++|.-+--=+-+-+.+....+.- .|++
T Consensus 258 ~~~H~H~~~~E~~yvl~G~~~~~v~d~~g-~~~~~~l~~GD~~~iP~g~~H~i~N~G~e~l~fL~if~s~~~~~i-~l~~ 335 (367)
T TIGR03404 258 RELHWHPNADEWQYFIQGQARMTVFAAGG-NARTFDYQAGDVGYVPRNMGHYVENTGDETLVFLEVFKADRFADV-SLNQ 335 (367)
T ss_pred cCCeeCcCCCeEEEEEEEEEEEEEEecCC-cEEEEEECCCCEEEECCCCeEEEEECCCCCEEEEEEECCCCCcee-EHHH
Confidence 345678877776665433 3221111111 356777889999999999999999997643333334333333222 2566
Q ss_pred HhhcCCc
Q 004933 683 EFRLLPK 689 (723)
Q Consensus 683 EfR~Lp~ 689 (723)
=+..+|.
T Consensus 336 ~l~~~p~ 342 (367)
T TIGR03404 336 WLALTPP 342 (367)
T ss_pred HHhhCCH
Confidence 6666664
No 69
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=50.14 E-value=11 Score=39.98 Aligned_cols=47 Identities=17% Similarity=0.240 Sum_probs=32.5
Q ss_pred CCcCCcceecCHHHHHHHHHHhCccceEEEeecCceeEecCCCccccccccc
Q 004933 609 HPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRNLKS 660 (723)
Q Consensus 609 dPIHDQ~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVFIPAGcPHQVrNL~S 660 (723)
|+-.++-+|+-.---. .-+..-++.=..||+++||||.||..+|..+
T Consensus 77 ~~g~ee~iyVl~G~l~-----v~~~g~~~~L~~Gd~~y~pa~~~H~~~N~~~ 123 (260)
T TIGR03214 77 GEGIETFLFVISGEVN-----VTAEGETHELREGGYAYLPPGSKWTLANAQA 123 (260)
T ss_pred CCceEEEEEEEeCEEE-----EEECCEEEEECCCCEEEECCCCCEEEEECCC
Confidence 3444455665443221 2345667788889999999999999999763
No 70
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=47.98 E-value=8.7 Score=31.18 Aligned_cols=28 Identities=14% Similarity=0.241 Sum_probs=22.7
Q ss_pred CCCCCcccchhhhhhhCCCCCHHHHHhhCCCCCCC
Q 004933 12 GKCRTKVYCIQCIKQWYPKMSELDVAEICPFCRRN 46 (723)
Q Consensus 12 ~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg~ 46 (723)
+.|+ ..||-.||.+|.-. ...||+|+..
T Consensus 17 ~~~G-~v~~~~~i~~~~~~------~~~cP~~~~~ 44 (63)
T smart00504 17 LPSG-QTYERRAIEKWLLS------HGTDPVTGQP 44 (63)
T ss_pred CCCC-CEEeHHHHHHHHHH------CCCCCCCcCC
Confidence 4677 88999999999854 4689999854
No 71
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=47.55 E-value=12 Score=30.30 Aligned_cols=26 Identities=27% Similarity=0.713 Sum_probs=21.2
Q ss_pred CCceEecCCCCCcccchhhhhhhCCCC
Q 004933 5 RKYVVPCGKCRTKVYCIQCIKQWYPKM 31 (723)
Q Consensus 5 ~~~vv~C~~C~~k~fC~~CI~~wYp~l 31 (723)
....|.|.+|+ ..||..|-..|=+.+
T Consensus 37 ~~~~v~C~~C~-~~fC~~C~~~~H~~~ 62 (64)
T smart00647 37 GCNRVTCPKCG-FSFCFRCKVPWHSPV 62 (64)
T ss_pred CCCeeECCCCC-CeECCCCCCcCCCCC
Confidence 45688999998 779999999986655
No 72
>PF01238 PMI_typeI: Phosphomannose isomerase type I; InterPro: IPR001250 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. Type I includes eukaryotic PMI and the enzyme encoded by the manA gene in enterobacteria. PMI has a bound zinc ion, which is essential for activity. A crystal structure of PMI from Candida albicans shows that the enzyme has three distinct domains []. The active site lies in the central domain, contains a single essential zinc atom, and forms a deep, open cavity of suitable dimensions to contain M6P or F6P The central domain is flanked by a helical domain on one side and a jelly-roll like domain on the other.; GO: 0004476 mannose-6-phosphate isomerase activity, 0008270 zinc ion binding, 0005975 carbohydrate metabolic process; PDB: 1PMI_A 1QWR_B 1ZX5_A 3H1Y_A 2WFP_A 3H1M_A 3H1W_A.
Probab=46.85 E-value=6.8 Score=43.82 Aligned_cols=18 Identities=56% Similarity=0.973 Sum_probs=13.8
Q ss_pred EeecCceeEecCCCcccc
Q 004933 638 EQKLGEAVFIPAGCPHQV 655 (723)
Q Consensus 638 ~Q~~GeAVFIPAGcPHQV 655 (723)
.=.+|||+|+|||-||-.
T Consensus 253 ~L~pGeaifl~a~~~HAY 270 (373)
T PF01238_consen 253 ELQPGEAIFLPAGEPHAY 270 (373)
T ss_dssp EE-TT-EEEEHTTHHEEE
T ss_pred EecCCceEEecCCCcccc
Confidence 335999999999999973
No 73
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=45.92 E-value=9.1 Score=36.77 Aligned_cols=42 Identities=24% Similarity=0.426 Sum_probs=36.9
Q ss_pred cCCcCCcceecCHHHHHHHHHHhCccceEEEeecCceeEecCCC
Q 004933 608 IHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGC 651 (723)
Q Consensus 608 ~dPIHDQ~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVFIPAGc 651 (723)
.-|.|...-.+.+.+=+.|+++|||..|.| +.||-|.|=||-
T Consensus 17 ~a~~~~r~k~msa~LSkeLr~~y~ir~~~I--kkGD~V~VisG~ 58 (120)
T PRK01191 17 NAPLHLRQKLMSAPLSKELREKYGIRSLPV--RKGDTVKVMRGD 58 (120)
T ss_pred cCCHHHHHHHhcCccCHHHHHHhCCccceE--eCCCEEEEeecC
Confidence 457888888888888899999999999977 589999999985
No 74
>PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D.
Probab=44.80 E-value=7.5 Score=35.10 Aligned_cols=41 Identities=34% Similarity=0.570 Sum_probs=32.0
Q ss_pred ccCCcCCcceecCHHHHHHHHHHhCccceEEEeecCceeEecCCCcccccc
Q 004933 607 VIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCPHQVRN 657 (723)
Q Consensus 607 v~dPIHDQ~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVFIPAGcPHQVrN 657 (723)
...||-. ||+++.+++|.+.+|.++ ||+||+=||-.+.|++
T Consensus 53 ~~s~i~k---fl~e~~~~~l~~~~~a~~-------GD~ll~~Ag~~~~v~~ 93 (95)
T PF02938_consen 53 LKSPIAK---FLSEEELKALIERLGAKP-------GDLLLFVAGKKEIVNK 93 (95)
T ss_dssp EECTTCC---CCHHHHHHHHHHHTT--T-------TEEEEEEEESHHHHHH
T ss_pred ccCcccc---cCCHHHHHHHHHHhCCCC-------CCEEEEECCCHHHHHh
Confidence 3455543 499999999999999975 9999999999887764
No 75
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=43.50 E-value=10 Score=32.79 Aligned_cols=24 Identities=33% Similarity=1.201 Sum_probs=13.5
Q ss_pred CCCCCcccchhhhhhhCCCCCHHHHHhhCCCCC
Q 004933 12 GKCRTKVYCIQCIKQWYPKMSELDVAEICPFCR 44 (723)
Q Consensus 12 ~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Cr 44 (723)
.+|. ..||-.||++- |...||+|.
T Consensus 24 ~~Ce-H~fCs~Ci~~~--------~~~~CPvC~ 47 (65)
T PF14835_consen 24 GGCE-HIFCSSCIRDC--------IGSECPVCH 47 (65)
T ss_dssp -SSS---B-TTTGGGG--------TTTB-SSS-
T ss_pred ccCc-cHHHHHHhHHh--------cCCCCCCcC
Confidence 4666 78999999873 335699986
No 76
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=42.34 E-value=14 Score=26.74 Aligned_cols=26 Identities=27% Similarity=0.874 Sum_probs=21.7
Q ss_pred cCCcccccccc-cccCCCCCcccchhc
Q 004933 126 CNHCATSIIDL-HRSCPKCSYELCLTC 151 (723)
Q Consensus 126 CD~C~tSI~D~-HRsC~~CsydLCL~C 151 (723)
|+.|...+-.+ --+|..|.|.|-+.|
T Consensus 3 C~~C~~~~~~~~~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 3 CDVCRRKIDGFYFYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCcCCCEeEEeCCCCCeEcCcc
Confidence 78888888888 888888888888776
No 77
>PRK11171 hypothetical protein; Provisional
Probab=42.09 E-value=14 Score=39.34 Aligned_cols=28 Identities=25% Similarity=0.372 Sum_probs=23.6
Q ss_pred ccceEEEeecCceeEecCCCcccccccc
Q 004933 632 VEPWTFEQKLGEAVFIPAGCPHQVRNLK 659 (723)
Q Consensus 632 VepWtf~Q~~GeAVFIPAGcPHQVrNL~ 659 (723)
+..=++.=..||.|+||+|.||+.+|.-
T Consensus 98 ~~g~~~~L~~GDsi~~p~~~~H~~~N~g 125 (266)
T PRK11171 98 LEGKTHALSEGGYAYLPPGSDWTLRNAG 125 (266)
T ss_pred ECCEEEEECCCCEEEECCCCCEEEEECC
Confidence 3444677788999999999999999975
No 78
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.39 E-value=11 Score=37.86 Aligned_cols=25 Identities=28% Similarity=0.883 Sum_probs=21.7
Q ss_pred CCCCcccchhhhhhhCCCCCHHHHHhhCCCCC
Q 004933 13 KCRTKVYCIQCIKQWYPKMSELDVAEICPFCR 44 (723)
Q Consensus 13 ~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Cr 44 (723)
.|. ..||..||..+-. ....||.||
T Consensus 30 ~C~-H~~c~~C~~~~~~------~~~~Cp~cr 54 (386)
T KOG2177|consen 30 PCG-HNFCRACLTRSWE------GPLSCPVCR 54 (386)
T ss_pred ccc-chHhHHHHHHhcC------CCcCCcccC
Confidence 466 7799999999988 558999999
No 79
>KOG3905 consensus Dynein light intermediate chain [Cell motility]
Probab=39.54 E-value=13 Score=41.60 Aligned_cols=70 Identities=21% Similarity=0.255 Sum_probs=34.2
Q ss_pred EeecCCChHHHHHHHHHHHHhhccccC-CCCCcccCCcCCcceecCHHHHHHHHHHhCccceEEEe-ecCceeEecCCCc
Q 004933 575 DIFRRQDVPKLEAYLRKHFKEFRHVYC-SPVEQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQ-KLGEAVFIPAGCP 652 (723)
Q Consensus 575 dIFrreDv~KLreyL~kh~~Ef~h~~~-~p~~~v~dPIHDQ~fYL~~~hk~kLkeEyGVepWtf~Q-~~GeAVFIPAGcP 652 (723)
|=||-+-.++|+..|+|-+-.++..-- ..++... -+|-=-|=-...-||.---|=.| -.-||||||||--
T Consensus 242 ~eyrDehfdfiq~~lRkFCLr~GaaLiyTSvKE~K--------NidllyKYivhr~yG~~fttpAlVVEkdaVfIPAGWD 313 (473)
T KOG3905|consen 242 HEYRDEHFDFIQSHLRKFCLRYGAALIYTSVKETK--------NIDLLYKYIVHRSYGFPFTTPALVVEKDAVFIPAGWD 313 (473)
T ss_pred chhhHHHHHHHHHHHHHHHHHcCceeEEeeccccc--------chHHHHHHHHHHhcCcccCCcceEeecceeEeccCCC
Confidence 457777777777777776655432100 0011000 00111111122346654433333 3469999999963
No 80
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=39.25 E-value=12 Score=41.73 Aligned_cols=36 Identities=33% Similarity=0.989 Sum_probs=29.1
Q ss_pred CCCCceecCCcccccccccc-cCCCCC-cccchhchHH
Q 004933 119 GNDERVYCNHCATSIIDLHR-SCPKCS-YELCLTCCKE 154 (723)
Q Consensus 119 ~~DER~~CD~C~tSI~D~HR-sC~~Cs-ydLCL~CC~E 154 (723)
+--|+|-||.|..--|-|.| -|-.|+ ||||-+|+..
T Consensus 4 ~rHe~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen 41 (381)
T KOG1280|consen 4 SRHEGVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYEN 41 (381)
T ss_pred CCcCCceeccccccceeeeeeEeeeecchhHHHHHhhc
Confidence 34589999999887777766 488885 9999999873
No 81
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.18 E-value=16 Score=40.91 Aligned_cols=39 Identities=23% Similarity=0.560 Sum_probs=30.7
Q ss_pred CCCCcccchhhhhhhCCCCCHHHHHhhCCCCCCCcccccccCcCC
Q 004933 13 KCRTKVYCIQCIKQWYPKMSELDVAEICPFCRRNCNCSVCLHTSG 57 (723)
Q Consensus 13 ~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg~CNCk~CLr~~~ 57 (723)
.|- +|||.+||-+=.-. =-+.||.||.+|-=|.=||.|.
T Consensus 61 eCl-hrfc~~ci~~a~r~-----gn~ecptcRk~l~SkrsLr~Dp 99 (381)
T KOG0311|consen 61 ECL-HRFCFDCIWKALRS-----GNNECPTCRKKLVSKRSLRIDP 99 (381)
T ss_pred HHH-HHHHHHHHHHHHHh-----cCCCCchHHhhccccccCCCCc
Confidence 566 78999999664332 2357999999999999998875
No 82
>KOG2107 consensus Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=38.45 E-value=24 Score=35.82 Aligned_cols=56 Identities=23% Similarity=0.460 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHhhccccCCCCCcccCCcCCcceecCHHHHHHHHHHhCccceEEEe-ecCceeEecCCCcccc
Q 004933 583 PKLEAYLRKHFKEFRHVYCSPVEQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQ-KLGEAVFIPAGCPHQV 655 (723)
Q Consensus 583 ~KLreyL~kh~~Ef~h~~~~p~~~v~dPIHDQ~fYL~~~hk~kLkeEyGVepWtf~Q-~~GeAVFIPAGcPHQV 655 (723)
+||..|...|..++ ..+-=|-+++-|.|.+.+. +-|-=.+ .-||-|+||||.=|--
T Consensus 80 eKvk~FfEEhlh~d---------eeiR~il~GtgYfDVrd~d--------d~WIRi~vekGDlivlPaGiyHRF 136 (179)
T KOG2107|consen 80 EKVKSFFEEHLHED---------EEIRYILEGTGYFDVRDKD--------DQWIRIFVEKGDLIVLPAGIYHRF 136 (179)
T ss_pred HHHHHHHHHhcCch---------hheEEEeecceEEeeccCC--------CCEEEEEEecCCEEEecCcceeee
Confidence 68888888776654 2345577888999988775 6776444 4699999999998864
No 83
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=38.10 E-value=12 Score=32.54 Aligned_cols=13 Identities=31% Similarity=1.275 Sum_probs=9.7
Q ss_pred ccchhhhhhhCCC
Q 004933 18 VYCIQCIKQWYPK 30 (723)
Q Consensus 18 ~fC~~CI~~wYp~ 30 (723)
+||-.|+.+||..
T Consensus 11 gFCRNCLskWy~~ 23 (68)
T PF06844_consen 11 GFCRNCLSKWYRE 23 (68)
T ss_dssp S--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 6999999999974
No 84
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=37.85 E-value=24 Score=36.01 Aligned_cols=45 Identities=16% Similarity=0.265 Sum_probs=38.7
Q ss_pred cceEEEeecCceeEecCCCccccccccccceeeccccCccchHHH
Q 004933 633 EPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDEC 677 (723)
Q Consensus 633 epWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~ec 677 (723)
+..++.=+.||..+||+|.||..+.-..||-+.+.=..|+..-.+
T Consensus 74 ~~~~v~L~eGd~fllP~gvpHsP~r~~~tv~LviE~~r~~~~~d~ 118 (177)
T PRK13264 74 KRRDVPIREGEMFLLPPHVPHSPQREAGSIGLVIERKRPEGELDG 118 (177)
T ss_pred ceeeEEECCCCEEEeCCCCCcCCccCCCeEEEEEEeCCCCCCccc
Confidence 346788899999999999999998899999999988888866553
No 85
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=37.66 E-value=24 Score=35.46 Aligned_cols=46 Identities=11% Similarity=0.237 Sum_probs=40.3
Q ss_pred cceEEEeecCceeEecCCCccccccccccceeeccccCccchHHHH
Q 004933 633 EPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAVDFVSPENVDECL 678 (723)
Q Consensus 633 epWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAlDFVSPEnV~ec~ 678 (723)
+..++.=..||..+||+|.||..+--..+|=+.+.=.+|++...++
T Consensus 68 ~~~~v~L~eGd~flvP~gvpHsP~r~~~t~~LvIE~~r~~~~~d~~ 113 (159)
T TIGR03037 68 KREDVPIREGDIFLLPPHVPHSPQRPAGSIGLVIERKRPQGELDGF 113 (159)
T ss_pred cEEEEEECCCCEEEeCCCCCcccccCCCcEEEEEEeCCCCCCCcce
Confidence 3567888899999999999999988999999999999999877643
No 86
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=37.56 E-value=26 Score=37.66 Aligned_cols=33 Identities=18% Similarity=0.322 Sum_probs=27.9
Q ss_pred hCccceEEEeecCceeEecCCCccccccccccc
Q 004933 630 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLKSCT 662 (723)
Q Consensus 630 yGVepWtf~Q~~GeAVFIPAGcPHQVrNL~SCI 662 (723)
|-|.+-++.-.+||+||||+|.||+......|-
T Consensus 59 ~~i~g~~~~l~~Gd~ili~s~~~H~~~~~~~~~ 91 (302)
T PRK10371 59 YLINNEKVQINQGHITLFWACTPHQLTDPGNCR 91 (302)
T ss_pred EEECCEEEEEcCCcEEEEecCCcccccccCCCc
Confidence 667888899999999999999999976655553
No 87
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.57 E-value=19 Score=33.45 Aligned_cols=28 Identities=18% Similarity=0.382 Sum_probs=22.6
Q ss_pred CCCCceecCCccccccc-------ccccCCCCCcc
Q 004933 119 GNDERVYCNHCATSIID-------LHRSCPKCSYE 146 (723)
Q Consensus 119 ~~DER~~CD~C~tSI~D-------~HRsC~~Csyd 146 (723)
..+-.+.|.+|....+. .|+.|++|+|-
T Consensus 17 klpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 17 KLPKIFECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred CCCcEeECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 34456779999987777 79999999983
No 88
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=35.36 E-value=18 Score=30.35 Aligned_cols=24 Identities=33% Similarity=0.787 Sum_probs=19.9
Q ss_pred CCCCceecCCcccccccccccCC----CCCc
Q 004933 119 GNDERVYCNHCATSIIDLHRSCP----KCSY 145 (723)
Q Consensus 119 ~~DER~~CD~C~tSI~D~HRsC~----~Csy 145 (723)
+.|..|.|.-|.|+ |||.|- .|.+
T Consensus 17 ~~dDiVvCp~Cgap---yHR~C~~~~g~C~~ 44 (54)
T PF14446_consen 17 DGDDIVVCPECGAP---YHRDCWEKAGGCIN 44 (54)
T ss_pred CCCCEEECCCCCCc---ccHHHHhhCCceEe
Confidence 47888999999998 899996 5554
No 89
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=34.63 E-value=21 Score=30.82 Aligned_cols=17 Identities=41% Similarity=0.714 Sum_probs=12.8
Q ss_pred EEEeecCceeEecCCCc
Q 004933 636 TFEQKLGEAVFIPAGCP 652 (723)
Q Consensus 636 tf~Q~~GeAVFIPAGcP 652 (723)
+..=..||+||||+|..
T Consensus 45 ~~~~~aGD~~~~p~G~~ 61 (74)
T PF05899_consen 45 TVTFKAGDAFFLPKGWT 61 (74)
T ss_dssp EEEEETTEEEEE-TTEE
T ss_pred EEEEcCCcEEEECCCCE
Confidence 34557999999999984
No 90
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.43 E-value=23 Score=39.06 Aligned_cols=27 Identities=26% Similarity=0.735 Sum_probs=20.5
Q ss_pred CCCCcccchhhhhhhCCCCCHHHHHhhCCCCCC
Q 004933 13 KCRTKVYCIQCIKQWYPKMSELDVAEICPFCRR 45 (723)
Q Consensus 13 ~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg 45 (723)
.|+ .+||-+||.+.+..-+ ..||.|+.
T Consensus 25 ~CG-H~~C~sCv~~l~~~~~-----~~CP~C~~ 51 (309)
T TIGR00570 25 VCG-HTLCESCVDLLFVRGS-----GSCPECDT 51 (309)
T ss_pred CCC-CcccHHHHHHHhcCCC-----CCCCCCCC
Confidence 588 8899999999765433 37997753
No 91
>PF02944 BESS: BESS motif; InterPro: IPR004210 The BESS domain has been named after the three proteins that originally defined the domain: BEAF (Boundary element associated factor 32) [], Suvar(3)7 [] and Stonewall []). The BESS domain is 40 amino acid residues long and is predicted to be composed of three alpha helices, as such it might be related to the myb/SANT HTH domain. The BESS domain directs a variety of protein-protein interactions, including interactions with itself, with Dorsal, and with a TBP-associated factor. It is found in a single copy in Drosophila proteins and is often associated with the MADF domain [, , ]. Proteins known to contain a BESS domain include: Drosophila Boundary element associated factor 32 (BEAF-32). Drosophila Suppressor of variegation protein 3-7 (Su(var)3-7), which could play a role in chromosome condensation. Drosophila Ravus, which is homologous to the C-terminal part of Su(var)3-7 []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation. Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3). It functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. ; GO: 0003677 DNA binding
Probab=34.14 E-value=47 Score=25.21 Aligned_cols=24 Identities=21% Similarity=0.539 Sum_probs=20.4
Q ss_pred HHHHHHhhhhHhhcHHHhhhhhhh
Q 004933 77 YLMVSLLPFIRQICEEQTQEIEFE 100 (723)
Q Consensus 77 yll~~lLP~lkqi~~EQ~~E~e~E 100 (723)
+.|-+++|.+|++...|..+.+++
T Consensus 6 ~Fl~Sl~p~~k~L~~~~k~~~k~~ 29 (37)
T PF02944_consen 6 LFLLSLLPHMKRLPPKQKLKFKMK 29 (37)
T ss_pred HHHHHhHHHHHhCCHHHHHHHHHH
Confidence 567889999999999999876655
No 92
>PF08990 Docking: Erythronolide synthase docking; InterPro: IPR015083 The N-terminal docking domain found in modular polyketide synthase assumes an alpha-helical structure, wherein two alpha-helices are connected by a short loop. Two such N-terminal domains dimerise to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function []. ; GO: 0016740 transferase activity, 0048037 cofactor binding; PDB: 2HG4_E.
Probab=32.02 E-value=34 Score=24.84 Aligned_cols=17 Identities=35% Similarity=0.585 Sum_probs=14.0
Q ss_pred ChHHHHHHHHHHHHhhc
Q 004933 581 DVPKLEAYLRKHFKEFR 597 (723)
Q Consensus 581 Dv~KLreyL~kh~~Ef~ 597 (723)
+-+||++||++...|.+
T Consensus 3 ~e~kLr~YLkr~t~eL~ 19 (27)
T PF08990_consen 3 NEDKLRDYLKRVTAELR 19 (27)
T ss_dssp -HCHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 45799999999998874
No 93
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=31.56 E-value=26 Score=33.38 Aligned_cols=43 Identities=26% Similarity=0.376 Sum_probs=38.8
Q ss_pred cCCcCCcceecCHHHHHHHHHHhCccceEEEeecCceeEecCCCc
Q 004933 608 IHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPAGCP 652 (723)
Q Consensus 608 ~dPIHDQ~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVFIPAGcP 652 (723)
.-|+|...-++.+.+=+.|+++||++.+.| +-||-|-|=+|-=
T Consensus 13 ~a~~~~r~~~~~a~ls~elr~~y~~r~~~I--kkGD~V~Vi~Gk~ 55 (114)
T TIGR01080 13 TAPLHVRRKLMSAPLSKELREKYGKRALPV--RKGDKVRIMRGDF 55 (114)
T ss_pred cCcHhhhhheeecccCHHHHHHcCccccee--ecCCEEEEecCCC
Confidence 568999999999999999999999999966 7899999999864
No 94
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.31 E-value=15 Score=40.16 Aligned_cols=36 Identities=33% Similarity=0.918 Sum_probs=26.6
Q ss_pred ecCCCC-CcccchhhhhhhCCCCCHHHH--------HhhCCCCCCC
Q 004933 10 PCGKCR-TKVYCIQCIKQWYPKMSELDV--------AEICPFCRRN 46 (723)
Q Consensus 10 ~C~~C~-~k~fC~~CI~~wYp~ls~~di--------~~~CP~Crg~ 46 (723)
.|.+|= |-+.|.+|+.+|+-.- .++| ...||.||+|
T Consensus 319 ~c~nc~crp~wc~~cla~~f~~r-q~~v~r~~~~~~~~~cp~cr~~ 363 (381)
T KOG3899|consen 319 PCENCICRPLWCRSCLAQIFIGR-QDNVYRYEYHRGSAQCPTCRKN 363 (381)
T ss_pred cccccccccHHHHHHHHHHHhhc-ccchhHHHHHhcCCCCcchhhc
Confidence 688875 4689999999998765 2444 2468888875
No 95
>TIGR03404 bicupin_oxalic bicupin, oxalate decarboxylase family. Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.
Probab=31.07 E-value=42 Score=37.69 Aligned_cols=40 Identities=18% Similarity=0.425 Sum_probs=28.6
Q ss_pred cceEEEeecCceeEecCCCccccccccccceeec-----cccCcc
Q 004933 633 EPWTFEQKLGEAVFIPAGCPHQVRNLKSCTKVAV-----DFVSPE 672 (723)
Q Consensus 633 epWtf~Q~~GeAVFIPAGcPHQVrNL~SCIKVAl-----DFVSPE 672 (723)
+-+++.=..||.++||+|.+|-.+|...=..+.. .|-|+.
T Consensus 108 ~~~~~~L~~GD~~~fP~g~~H~~~n~~~~~~~l~vf~~~~f~~~~ 152 (367)
T TIGR03404 108 RNYIDDVGAGDLWYFPPGIPHSLQGLDEGCEFLLVFDDGNFSEDG 152 (367)
T ss_pred cEEEeEECCCCEEEECCCCeEEEEECCCCeEEEEEeCCcccCCcc
Confidence 3455567899999999999999999854333333 355565
No 96
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=31.04 E-value=26 Score=32.99 Aligned_cols=24 Identities=25% Similarity=0.758 Sum_probs=18.7
Q ss_pred CceecCCccc--ccccccccCCCCCc
Q 004933 122 ERVYCNHCAT--SIIDLHRSCPKCSY 145 (723)
Q Consensus 122 ER~~CD~C~t--SI~D~HRsC~~Csy 145 (723)
-+.+|..|.. ++-+++..||+|+-
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCCcCccCcCCCC
Confidence 3679999975 55567788999984
No 97
>PRK11171 hypothetical protein; Provisional
Probab=30.24 E-value=29 Score=37.01 Aligned_cols=30 Identities=17% Similarity=0.286 Sum_probs=26.9
Q ss_pred hCccceEEEeecCceeEecCCCcccccccc
Q 004933 630 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLK 659 (723)
Q Consensus 630 yGVepWtf~Q~~GeAVFIPAGcPHQVrNL~ 659 (723)
+.+.+-++.=..||++++|+++||+.+|.-
T Consensus 218 ~~~~~~~~~l~~GD~i~~~~~~~h~~~N~g 247 (266)
T PRK11171 218 YRLNNDWVEVEAGDFIWMRAYCPQACYAGG 247 (266)
T ss_pred EEECCEEEEeCCCCEEEECCCCCEEEECCC
Confidence 677888888899999999999999999964
No 98
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.05 E-value=89 Score=35.93 Aligned_cols=22 Identities=27% Similarity=0.801 Sum_probs=19.6
Q ss_pred ceEecCCCCCcccchhhhhhhCC
Q 004933 7 YVVPCGKCRTKVYCIQCIKQWYP 29 (723)
Q Consensus 7 ~vv~C~~C~~k~fC~~CI~~wYp 29 (723)
.++.|++|+ -.||.-|..+|=-
T Consensus 292 ~l~~CskCn-FaFCtlCk~t~HG 313 (445)
T KOG1814|consen 292 ALAICSKCN-FAFCTLCKLTWHG 313 (445)
T ss_pred hhhhhccCc-cHHHHHHHHhhcC
Confidence 478999999 8899999999965
No 99
>PF12852 Cupin_6: Cupin
Probab=29.65 E-value=31 Score=34.12 Aligned_cols=23 Identities=22% Similarity=0.469 Sum_probs=18.3
Q ss_pred EEeecCceeEecCCCcccccccc
Q 004933 637 FEQKLGEAVFIPAGCPHQVRNLK 659 (723)
Q Consensus 637 f~Q~~GeAVFIPAGcPHQVrNL~ 659 (723)
+.=..||.||+|.|.||...--.
T Consensus 57 ~~L~~GDivllp~g~~H~l~~~~ 79 (186)
T PF12852_consen 57 IRLEAGDIVLLPRGTAHVLSSDP 79 (186)
T ss_pred EEecCCCEEEEcCCCCeEeCCCC
Confidence 44467999999999999985433
No 100
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=29.40 E-value=37 Score=33.17 Aligned_cols=26 Identities=31% Similarity=0.673 Sum_probs=20.4
Q ss_pred ecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCCCCC
Q 004933 10 PCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFCRRN 46 (723)
Q Consensus 10 ~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg~ 46 (723)
+|++|++. |++=+ .+|-.-||.|-||
T Consensus 3 ~Ct~Cg~~----------f~dgs-~eil~GCP~CGg~ 28 (131)
T PF09845_consen 3 QCTKCGRV----------FEDGS-KEILSGCPECGGN 28 (131)
T ss_pred ccCcCCCC----------cCCCc-HHHHccCcccCCc
Confidence 69999976 78764 4599999998664
No 101
>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=28.77 E-value=10 Score=31.35 Aligned_cols=30 Identities=20% Similarity=0.555 Sum_probs=20.3
Q ss_pred ceEecCCCCCcccchhhhhhhCCCCCHHHHHhhCCCCCC
Q 004933 7 YVVPCGKCRTKVYCIQCIKQWYPKMSELDVAEICPFCRR 45 (723)
Q Consensus 7 ~vv~C~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Crg 45 (723)
+-|+|..|+|.-+=. -.-.+|+.+||-|+.
T Consensus 3 ~eiRC~~CnklLa~~---------g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKA---------GEVIELEIKCPRCKT 32 (51)
T ss_pred cceeccchhHHHhhh---------cCccEEEEECCCCCc
Confidence 358999999764311 123467899999864
No 102
>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=28.55 E-value=32 Score=26.77 Aligned_cols=22 Identities=32% Similarity=1.019 Sum_probs=15.4
Q ss_pred eecCCcccc--cccccc---cCCCCCc
Q 004933 124 VYCNHCATS--IIDLHR---SCPKCSY 145 (723)
Q Consensus 124 ~~CD~C~tS--I~D~HR---sC~~Csy 145 (723)
|.|.+|..+ ++|+.+ .|++|++
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCC
Confidence 568888886 678664 6777776
No 103
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=27.90 E-value=25 Score=28.32 Aligned_cols=23 Identities=26% Similarity=0.933 Sum_probs=18.4
Q ss_pred eEecCCCCCcccchhhhhhhCCCC
Q 004933 8 VVPCGKCRTKVYCIQCIKQWYPKM 31 (723)
Q Consensus 8 vv~C~~C~~k~fC~~CI~~wYp~l 31 (723)
.|.|..|+ ..||..|-..|=+.+
T Consensus 40 ~~~C~~C~-~~fC~~C~~~~H~~~ 62 (64)
T PF01485_consen 40 IVTCPSCG-TEFCFKCGEPWHEGV 62 (64)
T ss_dssp -CCTTSCC-SEECSSSTSESCTTS
T ss_pred eeECCCCC-CcCccccCcccCCCC
Confidence 38999999 779999999885554
No 104
>PHA03096 p28-like protein; Provisional
Probab=27.59 E-value=20 Score=39.11 Aligned_cols=32 Identities=16% Similarity=0.239 Sum_probs=22.0
Q ss_pred CCCCCcccchhhhhhhCCCCCHHHHHhhCCCCC
Q 004933 12 GKCRTKVYCIQCIKQWYPKMSELDVAEICPFCR 44 (723)
Q Consensus 12 ~~C~~k~fC~~CI~~wYp~ls~~di~~~CP~Cr 44 (723)
+.|+ .-||..||+.|=..-...++...||.|+
T Consensus 202 ~~c~-h~fc~~ci~~wr~~~~~~e~~~~c~~~~ 233 (284)
T PHA03096 202 SEIK-HEFNIFCIKIWMTESLYKETEPENRRLN 233 (284)
T ss_pred ccCC-cHHHHHHHHHHHHhhhhcccCccccchh
Confidence 4677 7799999999987655545544444443
No 105
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=27.19 E-value=66 Score=31.64 Aligned_cols=11 Identities=45% Similarity=1.455 Sum_probs=10.6
Q ss_pred cccchhhhhhh
Q 004933 17 KVYCIQCIKQW 27 (723)
Q Consensus 17 k~fC~~CI~~w 27 (723)
|+||..|+++|
T Consensus 55 kmfc~~C~~rw 65 (134)
T PF05883_consen 55 KMFCADCDKRW 65 (134)
T ss_pred HHHHHHHHHHH
Confidence 78999999999
No 106
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=26.95 E-value=45 Score=29.64 Aligned_cols=46 Identities=24% Similarity=0.404 Sum_probs=28.1
Q ss_pred hCccceEEEeecCceeEecCCCcccccccc--ccceeeccccCccchHH
Q 004933 630 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLK--SCTKVAVDFVSPENVDE 676 (723)
Q Consensus 630 yGVepWtf~Q~~GeAVFIPAGcPHQVrNL~--SCIKVAlDFVSPEnV~e 676 (723)
+.|..=++.=.+||++|||+|-+|...--. .+....+.| +|+-+.+
T Consensus 36 ~~~~~~~~~l~~g~~~li~p~~~H~~~~~~~~~~~~~~i~~-~~~~~~~ 83 (136)
T PF02311_consen 36 LHIDGQEYPLKPGDLFLIPPGQPHSYYPDSNEPWEYYWIYF-SPDFLEE 83 (136)
T ss_dssp EEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEEEEE----GGGG
T ss_pred EEECCEEEEEECCEEEEecCCccEEEecCCCCCEEEEEEEE-CHHHHHH
Confidence 445666677889999999999999987777 666666666 5554444
No 107
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=26.87 E-value=47 Score=33.19 Aligned_cols=21 Identities=33% Similarity=0.670 Sum_probs=16.1
Q ss_pred ccceEEEeecCceeEecCCCc
Q 004933 632 VEPWTFEQKLGEAVFIPAGCP 652 (723)
Q Consensus 632 VepWtf~Q~~GeAVFIPAGcP 652 (723)
+++-++.=++||+||||.|.-
T Consensus 110 ~~G~~~~A~~GDvi~iPkGs~ 130 (152)
T PF06249_consen 110 IDGQTVTAKPGDVIFIPKGST 130 (152)
T ss_dssp ETTEEEEEETT-EEEE-TT-E
T ss_pred ECCEEEEEcCCcEEEECCCCE
Confidence 668899999999999999963
No 108
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.49 E-value=38 Score=40.92 Aligned_cols=33 Identities=36% Similarity=1.020 Sum_probs=24.0
Q ss_pred CCCceecCCcccccccccccCCCCCcc------cchhchHH
Q 004933 120 NDERVYCNHCATSIIDLHRSCPKCSYE------LCLTCCKE 154 (723)
Q Consensus 120 ~DER~~CD~C~tSI~D~HRsC~~Csyd------LCL~CC~E 154 (723)
.+.--||..|.+++. +..|++|+.. +|..|=..
T Consensus 12 ~~~akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 12 PNNNRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CCCCccccccCCCCC--CCcCCCCCCCCCcccccccccCCc
Confidence 455568888888874 4678888887 77777544
No 109
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=26.08 E-value=38 Score=36.08 Aligned_cols=75 Identities=19% Similarity=0.099 Sum_probs=52.7
Q ss_pred CccEeEeecCCChHHHHHHHHHHHHhhccccCCCCCcccCCcCCcceecCHHHHHHHHHHhCccceEEEeecCceeEecC
Q 004933 570 GGALWDIFRRQDVPKLEAYLRKHFKEFRHVYCSPVEQVIHPIHDQCFYLSSEHKKKLKEEFGVEPWTFEQKLGEAVFIPA 649 (723)
Q Consensus 570 ~GAlWdIFrreDv~KLreyL~kh~~Ef~h~~~~p~~~v~dPIHDQ~fYL~~~hk~kLkeEyGVepWtf~Q~~GeAVFIPA 649 (723)
.=.+-|+|-.+|.+.|-- -|-.+... ....+--|||.+|+-.-.-. +-|.+=++.=.+||.+|||.
T Consensus 142 ~v~~~d~~~~~d~s~m~a-------Gf~~~~~~--sf~wtl~~dEi~YVLEGe~~-----l~IdG~t~~l~pGDvlfIPk 207 (233)
T PRK15457 142 CVGLTDLVTGDDGSSMAA-------GFMQWENA--FFPWTLNYDEIDMVLEGELH-----VRHEGETMIAKAGDVMFIPK 207 (233)
T ss_pred cEEeeeeeccCCCCceee-------EEEEEecC--ccceeccceEEEEEEEeEEE-----EEECCEEEEeCCCcEEEECC
Confidence 345678888888888722 11111122 33477889999887655443 77889999999999999999
Q ss_pred CCccccccc
Q 004933 650 GCPHQVRNL 658 (723)
Q Consensus 650 GcPHQVrNL 658 (723)
|.+|.-.+-
T Consensus 208 Gs~~hf~tp 216 (233)
T PRK15457 208 GSSIEFGTP 216 (233)
T ss_pred CCeEEecCC
Confidence 999876443
No 110
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=25.48 E-value=55 Score=34.13 Aligned_cols=31 Identities=10% Similarity=0.177 Sum_probs=25.0
Q ss_pred hCccceEEEeecCceeEecCCCccccccccc
Q 004933 630 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLKS 660 (723)
Q Consensus 630 yGVepWtf~Q~~GeAVFIPAGcPHQVrNL~S 660 (723)
+.|..=++.=..||+||||+|.+|+++.-.+
T Consensus 57 ~~~~~~~~~l~~g~~~ii~~~~~H~~~~~~~ 87 (287)
T TIGR02297 57 LQLDEHEYSEYAPCFFLTPPSVPHGFVTDLD 87 (287)
T ss_pred EEECCEEEEecCCeEEEeCCCCccccccCCC
Confidence 6666667777899999999999999875443
No 111
>PRK13503 transcriptional activator RhaS; Provisional
Probab=24.93 E-value=37 Score=35.13 Aligned_cols=31 Identities=10% Similarity=0.083 Sum_probs=23.5
Q ss_pred hCccceEEEeecCceeEecCCCccccccccc
Q 004933 630 FGVEPWTFEQKLGEAVFIPAGCPHQVRNLKS 660 (723)
Q Consensus 630 yGVepWtf~Q~~GeAVFIPAGcPHQVrNL~S 660 (723)
+.|..=++.=..||++|||+|.+|...+..+
T Consensus 48 ~~i~~~~~~l~~g~~~~i~~~~~h~~~~~~~ 78 (278)
T PRK13503 48 HVFNGQPYTLSGGTVCFVRDHDRHLYEHTDN 78 (278)
T ss_pred eEecCCcccccCCcEEEECCCccchhhhccC
Confidence 3444445555789999999999998877665
No 112
>PF08115 Toxin_28: SFI toxin family; InterPro: IPR012633 This family consists of the SFI family of spider toxins. This family of toxins might share structural, evolutionary and functional relationships with other small, highly structurally constrained spider neurotoxins. These toxins are highly selective agonists/antagonists of different voltage-dependent calcium channels and are extremely valuable reagents in the analysis of neuromuscular function.; GO: 0009405 pathogenesis, 0005576 extracellular region
Probab=23.92 E-value=37 Score=25.79 Aligned_cols=17 Identities=29% Similarity=0.546 Sum_probs=14.6
Q ss_pred CCCcccccccCcCCccc
Q 004933 44 RRNCNCSVCLHTSGFIE 60 (723)
Q Consensus 44 rg~CNCk~CLr~~~~i~ 60 (723)
-.||+|-.||++++++-
T Consensus 14 n~n~~~G~CL~~~~~~A 30 (35)
T PF08115_consen 14 NHNDCCGSCLCSNGPHA 30 (35)
T ss_pred cCCCcccceeccCCccC
Confidence 47999999999998764
No 113
>PF14816 FAM178: Family of unknown function, FAM178
Probab=23.92 E-value=46 Score=37.76 Aligned_cols=28 Identities=32% Similarity=0.576 Sum_probs=23.2
Q ss_pred cCHHHHHHHHHHhCccceEEE-eecCceeE
Q 004933 618 LSSEHKKKLKEEFGVEPWTFE-QKLGEAVF 646 (723)
Q Consensus 618 L~~~hk~kLkeEyGVepWtf~-Q~~GeAVF 646 (723)
|++|||. +.|.|+|..-.|- +|+||.||
T Consensus 63 l~~Ehr~-~lekfsv~~~~Ip~~HPGE~IF 91 (377)
T PF14816_consen 63 LTPEHRE-FLEKFSVSLQAIPDVHPGEEIF 91 (377)
T ss_pred CCHHHHH-HHHHhchhhccCCCCCCchhhc
Confidence 5688886 7778999888875 78899999
No 114
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=23.07 E-value=36 Score=36.69 Aligned_cols=21 Identities=38% Similarity=1.043 Sum_probs=19.8
Q ss_pred ecCCcccccccccccCCCCCc
Q 004933 125 YCNHCATSIIDLHRSCPKCSY 145 (723)
Q Consensus 125 ~CD~C~tSI~D~HRsC~~Csy 145 (723)
-|++|.+-+.-|.-+||+|+.
T Consensus 84 ~C~~CGa~V~~~e~~Cp~C~S 104 (314)
T PF09567_consen 84 KCNNCGANVSRLEESCPNCGS 104 (314)
T ss_pred hhccccceeeehhhcCCCCCc
Confidence 699999999999999999976
No 115
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.84 E-value=26 Score=32.36 Aligned_cols=13 Identities=31% Similarity=1.255 Sum_probs=11.6
Q ss_pred ccchhhhhhhCCC
Q 004933 18 VYCIQCIKQWYPK 30 (723)
Q Consensus 18 ~fC~~CI~~wYp~ 30 (723)
.||-.|+.+||-+
T Consensus 42 gFCRNCLs~Wy~e 54 (104)
T COG3492 42 GFCRNCLSNWYRE 54 (104)
T ss_pred HHHHHHHHHHHHH
Confidence 6999999999974
No 116
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=22.27 E-value=43 Score=40.90 Aligned_cols=35 Identities=26% Similarity=0.538 Sum_probs=29.9
Q ss_pred ecCCcc-cccccccccCCCCC-cccchhchHHHhcCc
Q 004933 125 YCNHCA-TSIIDLHRSCPKCS-YELCLTCCKEICEGR 159 (723)
Q Consensus 125 ~CD~C~-tSI~D~HRsC~~Cs-ydLCL~CC~ElR~g~ 159 (723)
-|+.|+ .+|+-|...|-+|. ||||++|+--=|.|.
T Consensus 605 kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak 641 (966)
T KOG4286|consen 605 KCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAK 641 (966)
T ss_pred hcchhhhCccceeeeeehhhcChhHHhhHhhhccccc
Confidence 499997 59999999999995 899999998766554
No 117
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=21.88 E-value=74 Score=28.24 Aligned_cols=22 Identities=14% Similarity=0.249 Sum_probs=14.2
Q ss_pred cccccCCCCceecCCccccccc
Q 004933 114 SETLCGNDERVYCNHCATSIID 135 (723)
Q Consensus 114 ~~a~~~~DER~~CD~C~tSI~D 135 (723)
.+..+.-++-..|..|..+|.+
T Consensus 69 ~~~~v~i~~~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 69 RSRSVVITESTKCSVCGKPLGN 90 (109)
T ss_pred cCceEEECCCCCccCcCCcCCC
Confidence 3333444455569999998875
No 118
>PRK13501 transcriptional activator RhaR; Provisional
Probab=21.80 E-value=50 Score=34.80 Aligned_cols=28 Identities=14% Similarity=0.281 Sum_probs=23.5
Q ss_pred hCccceEEEeecCceeEecCCCcccccc
Q 004933 630 FGVEPWTFEQKLGEAVFIPAGCPHQVRN 657 (723)
Q Consensus 630 yGVepWtf~Q~~GeAVFIPAGcPHQVrN 657 (723)
+-|.+-++.=..||.||||+|.+|+++.
T Consensus 51 ~~i~~~~~~l~~g~~~~I~p~~~H~~~~ 78 (290)
T PRK13501 51 HVLNDHPYRITCGDVFYIQAADHHSYES 78 (290)
T ss_pred EEECCeeeeecCCeEEEEcCCCcccccc
Confidence 5567777777899999999999999764
No 119
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=21.43 E-value=59 Score=26.22 Aligned_cols=32 Identities=31% Similarity=0.956 Sum_probs=23.5
Q ss_pred CceecC--Ccccccc------cccccCCCCCcccchhchH
Q 004933 122 ERVYCN--HCATSII------DLHRSCPKCSYELCLTCCK 153 (723)
Q Consensus 122 ER~~CD--~C~tSI~------D~HRsC~~CsydLCL~CC~ 153 (723)
...+|- .|...|. +.+..|++|++..|..|=.
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~ 56 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKV 56 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCC
Confidence 344677 7766554 4588899999999999943
No 120
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=20.22 E-value=68 Score=26.37 Aligned_cols=16 Identities=25% Similarity=0.432 Sum_probs=11.6
Q ss_pred hhhhCCCCCHHHHHhh
Q 004933 24 IKQWYPKMSELDVAEI 39 (723)
Q Consensus 24 I~~wYp~ls~~di~~~ 39 (723)
|..+||+||.++|..+
T Consensus 37 I~~~yp~Lt~~~i~aA 52 (56)
T PF04255_consen 37 IAEDYPSLTLEDIRAA 52 (56)
T ss_dssp HHHHSTT--HHHHHHH
T ss_pred HHHHCCCCCHHHHHHH
Confidence 6678999999999864
Done!