Query psy2747
Match_columns 557
No_of_seqs 456 out of 1956
Neff 6.9
Searched_HMMs 46136
Date Sat Aug 17 00:09:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2747.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2747hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1101|consensus 99.9 5.4E-25 1.2E-29 201.9 5.5 95 386-480 5-101 (147)
2 KOG1101|consensus 99.9 4.8E-24 1E-28 195.7 6.9 91 219-309 7-99 (147)
3 smart00238 BIR Baculoviral inh 99.9 2.8E-22 6E-27 163.1 5.8 70 3-72 1-70 (71)
4 PF00653 BIR: Inhibitor of Apo 99.8 3.4E-22 7.4E-27 162.2 3.0 66 7-72 1-70 (70)
5 cd00022 BIR Baculoviral inhibi 99.8 2.4E-21 5.3E-26 156.6 5.3 68 5-72 1-68 (69)
6 smart00238 BIR Baculoviral inh 99.8 4E-21 8.7E-26 156.3 6.2 70 139-208 1-70 (71)
7 cd00022 BIR Baculoviral inhibi 99.8 1.5E-20 3.2E-25 152.1 5.5 68 228-295 1-68 (69)
8 PF00653 BIR: Inhibitor of Apo 99.8 1.4E-20 3E-25 152.7 3.8 66 230-295 1-70 (70)
9 KOG4172|consensus 99.1 3.4E-12 7.3E-17 95.2 -4.0 50 508-557 8-62 (62)
10 PF13920 zf-C3HC4_3: Zinc fing 99.1 4.7E-11 1E-15 90.3 1.9 45 507-551 2-50 (50)
11 KOG4275|consensus 99.0 2.4E-11 5.2E-16 120.2 -1.2 51 507-557 300-350 (350)
12 KOG4265|consensus 99.0 9.7E-11 2.1E-15 119.9 1.2 52 505-556 288-343 (349)
13 KOG1571|consensus 98.7 2.2E-09 4.7E-14 110.2 -0.4 52 506-557 304-355 (355)
14 KOG1100|consensus 98.6 3.5E-08 7.6E-13 96.4 3.4 52 505-556 156-207 (207)
15 KOG1785|consensus 98.0 4.2E-06 9.2E-11 86.5 2.8 62 493-555 351-422 (563)
16 PF13923 zf-C3HC4_2: Zinc fing 97.6 1.8E-05 3.9E-10 56.5 1.2 34 510-544 1-39 (39)
17 PLN03208 E3 ubiquitin-protein 97.6 2.1E-05 4.4E-10 75.5 1.5 50 505-555 16-87 (193)
18 PHA02929 N1R/p28-like protein; 97.6 3E-05 6.5E-10 77.3 2.7 49 506-555 173-233 (238)
19 PF14634 zf-RING_5: zinc-RING 97.5 5.3E-05 1.2E-09 55.6 2.2 37 509-546 1-44 (44)
20 PF13639 zf-RING_2: Ring finge 97.4 7.1E-05 1.5E-09 54.8 1.1 36 509-545 2-44 (44)
21 KOG0978|consensus 97.3 5.2E-05 1.1E-09 85.1 0.3 61 495-556 631-698 (698)
22 PHA02926 zinc finger-like prot 97.3 8E-05 1.7E-09 72.3 1.0 53 500-553 163-234 (242)
23 KOG0317|consensus 97.2 9.9E-05 2.1E-09 74.2 1.0 48 507-555 239-290 (293)
24 KOG0320|consensus 97.1 0.00014 3E-09 68.3 0.7 49 507-556 131-187 (187)
25 smart00184 RING Ring finger. E 97.1 0.00038 8.1E-09 48.1 2.6 34 510-544 1-39 (39)
26 KOG0823|consensus 97.0 0.00041 8.8E-09 67.9 2.6 49 506-555 46-103 (230)
27 cd00162 RING RING-finger (Real 96.9 0.00071 1.5E-08 48.5 2.8 39 509-548 1-45 (45)
28 PF00097 zf-C3HC4: Zinc finger 96.9 0.0004 8.6E-09 49.8 1.2 34 510-544 1-41 (41)
29 PF15227 zf-C3HC4_4: zinc fing 96.6 0.0009 1.9E-08 48.7 1.5 34 510-544 1-42 (42)
30 TIGR00599 rad18 DNA repair pro 96.6 0.00069 1.5E-08 72.4 0.6 48 502-550 21-72 (397)
31 KOG2164|consensus 96.4 0.0013 2.9E-08 70.9 1.9 48 507-555 186-244 (513)
32 COG5236 Uncharacterized conser 96.4 0.0016 3.4E-08 66.9 1.7 47 505-552 59-111 (493)
33 PF14447 Prok-RING_4: Prokaryo 96.3 0.0018 3.8E-08 49.5 1.1 44 506-550 6-51 (55)
34 COG5574 PEX10 RING-finger-cont 96.2 0.0017 3.8E-08 64.6 0.9 42 507-549 215-262 (271)
35 KOG4692|consensus 96.1 0.0014 3E-08 67.4 0.1 45 506-551 421-469 (489)
36 smart00504 Ubox Modified RING 96.0 0.0041 8.8E-08 48.7 2.3 42 508-550 2-47 (63)
37 PF13445 zf-RING_UBOX: RING-ty 95.7 0.0038 8.3E-08 45.6 0.7 27 510-538 1-31 (43)
38 PF07967 zf-C3HC: C3HC zinc fi 95.5 0.015 3.2E-07 53.1 4.0 45 5-50 8-55 (133)
39 KOG2177|consensus 95.2 0.0064 1.4E-07 61.3 0.8 44 502-546 8-55 (386)
40 KOG0287|consensus 95.1 0.0065 1.4E-07 62.4 0.3 46 504-550 20-69 (442)
41 PF14835 zf-RING_6: zf-RING of 95.1 0.015 3.3E-07 45.9 2.2 47 502-549 2-51 (65)
42 COG5432 RAD18 RING-finger-cont 95.0 0.0087 1.9E-07 60.3 0.9 46 504-550 22-71 (391)
43 PF07967 zf-C3HC: C3HC zinc fi 95.0 0.029 6.3E-07 51.2 4.2 49 137-186 4-55 (133)
44 COG5243 HRD1 HRD ubiquitin lig 94.5 0.014 3.1E-07 60.6 1.0 45 504-549 284-345 (491)
45 PF12678 zf-rbx1: RING-H2 zinc 94.1 0.028 6E-07 45.9 1.8 36 509-545 21-73 (73)
46 COG5540 RING-finger-containing 93.7 0.042 9.2E-07 55.8 2.6 50 499-549 315-372 (374)
47 KOG0802|consensus 92.5 0.053 1.1E-06 61.0 1.2 43 505-548 289-340 (543)
48 KOG1039|consensus 90.9 0.092 2E-06 55.3 0.9 46 506-552 160-224 (344)
49 KOG3002|consensus 89.6 0.18 4E-06 52.2 1.8 45 505-551 46-93 (299)
50 PF04564 U-box: U-box domain; 88.7 0.29 6.3E-06 39.8 2.1 44 506-550 3-51 (73)
51 KOG4628|consensus 88.5 0.25 5.5E-06 51.9 2.0 43 508-551 230-280 (348)
52 KOG4159|consensus 88.2 0.14 3E-06 55.1 -0.2 45 505-550 82-130 (398)
53 KOG2113|consensus 87.7 0.47 1E-05 48.7 3.2 51 504-554 340-392 (394)
54 KOG1814|consensus 86.7 0.36 7.8E-06 51.3 1.9 30 507-537 184-216 (445)
55 KOG2932|consensus 84.8 0.22 4.8E-06 50.9 -0.7 43 509-553 92-138 (389)
56 COG5152 Uncharacterized conser 83.7 0.3 6.4E-06 46.9 -0.4 46 507-553 196-245 (259)
57 KOG3039|consensus 79.3 1.4 3E-05 43.9 2.5 45 506-551 220-272 (303)
58 PF04641 Rtf2: Rtf2 RING-finge 79.0 1.5 3.3E-05 44.6 2.9 45 506-551 112-163 (260)
59 KOG0311|consensus 78.9 0.29 6.3E-06 51.0 -2.4 51 500-551 36-92 (381)
60 KOG1001|consensus 78.8 0.8 1.7E-05 52.7 0.8 41 508-550 455-501 (674)
61 KOG0828|consensus 78.7 0.7 1.5E-05 50.1 0.3 45 505-550 569-635 (636)
62 KOG1813|consensus 78.5 0.85 1.8E-05 46.6 0.8 45 508-553 242-290 (313)
63 PF04710 Pellino: Pellino; In 76.7 0.8 1.7E-05 48.7 0.0 40 516-556 356-411 (416)
64 KOG2879|consensus 76.1 1.6 3.4E-05 44.3 1.9 45 506-551 238-289 (298)
65 PF12861 zf-Apc11: Anaphase-pr 71.9 2 4.3E-05 36.2 1.2 30 519-549 46-82 (85)
66 KOG0825|consensus 69.5 1.1 2.3E-05 51.2 -1.1 46 507-553 123-175 (1134)
67 KOG2113|consensus 68.6 1.8 4E-05 44.5 0.4 48 507-554 136-188 (394)
68 PF11682 DUF3279: Protein of u 66.3 6.8 0.00015 35.6 3.5 50 413-468 17-74 (128)
69 KOG4765|consensus 63.6 5.7 0.00012 42.1 2.8 50 135-185 49-101 (419)
70 COG5220 TFB3 Cdk activating ki 62.8 2.6 5.7E-05 41.8 0.2 40 506-546 9-61 (314)
71 KOG0297|consensus 61.6 3.3 7.1E-05 44.8 0.7 49 504-553 18-71 (391)
72 KOG0804|consensus 60.8 4.5 9.7E-05 43.7 1.5 41 505-546 173-219 (493)
73 KOG3497|consensus 60.7 4 8.6E-05 31.9 0.8 12 39-50 5-16 (69)
74 PF03854 zf-P11: P-11 zinc fin 59.5 3.5 7.6E-05 30.7 0.3 42 509-552 4-49 (50)
75 KOG4765|consensus 58.7 6.3 0.00014 41.8 2.1 48 223-271 50-100 (419)
76 COG1644 RPB10 DNA-directed RNA 58.3 3.9 8.5E-05 32.1 0.4 12 39-50 5-16 (63)
77 COG5175 MOT2 Transcriptional r 58.0 3 6.5E-05 43.3 -0.3 45 505-550 12-65 (480)
78 PLN00032 DNA-directed RNA poly 54.6 4.3 9.4E-05 32.8 0.1 12 39-50 5-16 (71)
79 KOG3842|consensus 54.6 5.7 0.00012 41.0 1.0 43 506-550 340-415 (429)
80 PF10272 Tmpp129: Putative tra 52.7 9.5 0.00021 40.7 2.3 42 507-548 271-350 (358)
81 PF14570 zf-RING_4: RING/Ubox 52.1 5 0.00011 30.1 0.1 38 510-548 1-47 (48)
82 PF11682 DUF3279: Protein of u 50.9 13 0.00027 33.9 2.5 48 242-295 15-70 (128)
83 PF08600 Rsm1: Rsm1-like; Int 50.5 6.5 0.00014 33.5 0.6 35 173-210 18-64 (91)
84 PF01194 RNA_pol_N: RNA polyme 49.9 4.4 9.6E-05 31.8 -0.5 12 39-50 5-16 (60)
85 PRK04016 DNA-directed RNA poly 49.6 5.8 0.00013 31.3 0.1 12 39-50 5-16 (62)
86 KOG1002|consensus 46.6 4.7 0.0001 44.4 -1.1 41 507-548 536-585 (791)
87 PF08600 Rsm1: Rsm1-like; Int 42.6 15 0.00034 31.2 1.7 34 38-74 19-64 (91)
88 smart00744 RINGv The RING-vari 41.2 17 0.00037 27.2 1.5 36 509-545 1-49 (49)
89 PF10367 Vps39_2: Vacuolar sor 39.5 14 0.0003 31.6 1.0 30 506-536 77-108 (109)
90 PF05290 Baculo_IE-1: Baculovi 37.3 13 0.00029 33.8 0.5 43 508-551 81-134 (140)
91 PF11793 FANCL_C: FANCL C-term 34.6 11 0.00024 30.4 -0.4 11 539-549 56-66 (70)
92 COG4416 Com Mu-like prophage p 33.6 38 0.00082 26.0 2.3 40 159-206 12-52 (60)
93 KOG0826|consensus 28.7 11 0.00025 39.2 -1.5 50 506-555 299-354 (357)
94 KOG3161|consensus 26.5 18 0.00039 40.9 -0.6 37 505-542 9-51 (861)
95 KOG1734|consensus 26.3 27 0.00058 35.6 0.6 44 506-550 223-282 (328)
96 PF10217 DUF2039: Uncharacteri 24.6 14 0.0003 31.7 -1.5 37 506-547 54-90 (92)
97 KOG2660|consensus 22.9 19 0.00042 37.6 -1.2 51 501-552 9-64 (331)
98 COG5219 Uncharacterized conser 22.5 28 0.00061 41.3 -0.1 12 539-550 1513-1524(1525)
99 PF10764 Gin: Inhibitor of sig 21.6 52 0.0011 24.4 1.2 28 509-538 1-28 (46)
100 KOG2817|consensus 20.5 37 0.00079 36.5 0.3 47 508-556 335-394 (394)
No 1
>KOG1101|consensus
Probab=99.91 E-value=5.4e-25 Score=201.94 Aligned_cols=95 Identities=41% Similarity=0.964 Sum_probs=88.8
Q ss_pred CCCCCCCCcChHhHhhhccCCCCCC--CCChhHhhhcCccccCCCCeEEEEecCCceeeccCCCCcHHHHhhhcCCcchh
Q psy2747 386 RVPKHPNLSTLDSRVLTFTTWPRDS--PLGPQSLAVAGFFYDGQGDWVRCFHCDGGLRKWTAMDEPWSEHARWFPECHFV 463 (557)
Q Consensus 386 ~~p~~p~~~~~~~Rl~Sf~~wp~~~--~~~~~~LA~AGFfy~g~~D~v~Cf~Cg~~l~~w~~~Ddpw~eH~~~~p~C~fv 463 (557)
..|.+|.|..+++||+||.+||... .++++.||+|||||+|.+|.++||+|+++|.+|+++||||.||++|+|.|.|+
T Consensus 5 ~~~~~~~~~~~~aRl~TF~~Wp~~~~~~c~p~~lA~AGFy~~g~~D~~~Cf~C~~~L~~We~~DDPW~EH~k~~p~C~F~ 84 (147)
T KOG1101|consen 5 FDPQNPKMAREEARLKTFKNWPYSDMDKCTPEQLAEAGFYYTGKQDCVKCFFCSGGLDDWEPGDDPWEEHAKWSPECEFL 84 (147)
T ss_pred ccccchhHHHHHHHHhhhhcCCCCCCCCcCHHHHHhCCceeeCCCCceECcccCcccccCCCCCCcHHHHHhhCCCCcee
Confidence 3577889999999999999999876 68999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhHHHhhhhcCC
Q psy2747 464 MLVKGEQFIEDTIKANP 480 (557)
Q Consensus 464 ~~~kG~~fv~~v~~~~~ 480 (557)
++.||++|+..++....
T Consensus 85 ~~~k~~e~~~~v~~~~~ 101 (147)
T KOG1101|consen 85 KLKKGREFLGTVQSTAR 101 (147)
T ss_pred ecccchhhhhHHHHhHh
Confidence 99999999998876553
No 2
>KOG1101|consensus
Probab=99.89 E-value=4.8e-24 Score=195.71 Aligned_cols=91 Identities=38% Similarity=0.671 Sum_probs=83.6
Q ss_pred CCccccccHHHHHccCCCCCCCC--CCCHHHHHhcCceeccCCCeEEeeeccCcccccCCCCChHHHhhhcCCCCccccc
Q psy2747 219 ENEEVYKLESGRLATFNNWPVSF--IVTPEALAKTGFYYLKQGDKVKCAYCSVIIGRWEQGDNAESEHKRQSPNCPFLAR 296 (557)
Q Consensus 219 ~~~~~~~~~~~Rl~SF~~wp~~~--~~~~~~LA~aGFyy~g~~D~v~C~~C~~~l~~W~~~Ddp~~eH~~~~p~C~f~~~ 296 (557)
++.+.|..+++||+||.+||+.. .++|+.||+|||||+|.+|.|+||+|+++|.+|+++||||+||++|+|.|.|++.
T Consensus 7 ~~~~~~~~~~aRl~TF~~Wp~~~~~~c~p~~lA~AGFy~~g~~D~~~Cf~C~~~L~~We~~DDPW~EH~k~~p~C~F~~~ 86 (147)
T KOG1101|consen 7 PQNPKMAREEARLKTFKNWPYSDMDKCTPEQLAEAGFYYTGKQDCVKCFFCSGGLDDWEPGDDPWEEHAKWSPECEFLKL 86 (147)
T ss_pred ccchhHHHHHHHHhhhhcCCCCCCCCcCHHHHHhCCceeeCCCCceECcccCcccccCCCCCCcHHHHHhhCCCCceeec
Confidence 34568899999999999999986 5799999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhhhhhhh
Q psy2747 297 DNQATQANMINLR 309 (557)
Q Consensus 297 ~~~~~~~~~~~~~ 309 (557)
.||+++...++..
T Consensus 87 ~k~~e~~~~v~~~ 99 (147)
T KOG1101|consen 87 KKGREFLGTVQST 99 (147)
T ss_pred ccchhhhhHHHHh
Confidence 9998877766643
No 3
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=99.86 E-value=2.8e-22 Score=163.09 Aligned_cols=70 Identities=46% Similarity=0.992 Sum_probs=66.1
Q ss_pred chHHHHhhccCCCCCCCCCHHHHHHcCceeecCCCceeeeeecceecCCccCCchHHhhhcCCCCCCCCc
Q psy2747 3 FERSRLRTFQSWPSNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHRAKDPGCPFVK 72 (557)
Q Consensus 3 ~e~~Rl~TF~~wp~~~~~~~~~LA~aGFyytg~~d~V~Cf~Cg~~l~~w~~~d~~~~~H~~~~p~C~f~~ 72 (557)
+|++||+||.+||....+.++.||+|||||+|.+|.|+|++|+++|++|+.+|+|+++|.+++|+|+|++
T Consensus 1 ~~~~R~~sF~~w~~~~~~~~~~LA~~Gfyy~~~~d~v~C~~C~~~l~~w~~~d~p~~~H~~~~p~C~fv~ 70 (71)
T smart00238 1 SEEARLKTFQNWPYNSKLTPEQLAEAGFYYTGVGDEVKCFFCGGELDNWEPGDDPWEEHKKWSPNCPFVR 70 (71)
T ss_pred CHHHHHHHHHcCCCCccCCHHHHHHcCCeECCCCCEEEeCCCCCCcCCCCCCCCHHHHHhHhCcCCcCcc
Confidence 4789999999999745679999999999999999999999999999999999999999999999999985
No 4
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=99.85 E-value=3.4e-22 Score=162.17 Aligned_cols=66 Identities=47% Similarity=1.140 Sum_probs=58.4
Q ss_pred HHhhcc-CCCCC---CCCCHHHHHHcCceeecCCCceeeeeecceecCCccCCchHHhhhcCCCCCCCCc
Q psy2747 7 RLRTFQ-SWPSN---SPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHRAKDPGCPFVK 72 (557)
Q Consensus 7 Rl~TF~-~wp~~---~~~~~~~LA~aGFyytg~~d~V~Cf~Cg~~l~~w~~~d~~~~~H~~~~p~C~f~~ 72 (557)
||+||. +||.. ..++++.||+|||||+|.+|+|+||+||++|++|+++|||+++|++++|+|+|++
T Consensus 1 Rl~SF~~~wp~~~~~~~~~~~~LA~aGFyy~~~~d~v~C~~C~~~l~~w~~~Ddp~~~H~~~sp~C~f~k 70 (70)
T PF00653_consen 1 RLKSFRSNWPHSNDHDPVSPEKLARAGFYYTGTGDRVRCFYCGLELDNWEPNDDPWEEHKRHSPNCPFVK 70 (70)
T ss_dssp HHHGGTTGSSTTTTTSSSHHHHHHHTTEEEESSTTEEEETTTTEEEES-STT--HHHHHHHHSTTBHHHH
T ss_pred ChhHHCCcccCccccCCCCHHHHHHCCCEEcCCCCEEEEeccCCEEeCCCCCCCHHHHHHHHCcCCeecC
Confidence 999996 59963 3688999999999999999999999999999999999999999999999999873
No 5
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=99.83 E-value=2.4e-21 Score=156.64 Aligned_cols=68 Identities=43% Similarity=1.002 Sum_probs=64.5
Q ss_pred HHHHhhccCCCCCCCCCHHHHHHcCceeecCCCceeeeeecceecCCccCCchHHhhhcCCCCCCCCc
Q psy2747 5 RSRLRTFQSWPSNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHRAKDPGCPFVK 72 (557)
Q Consensus 5 ~~Rl~TF~~wp~~~~~~~~~LA~aGFyytg~~d~V~Cf~Cg~~l~~w~~~d~~~~~H~~~~p~C~f~~ 72 (557)
++||+||.+||......++.||+|||||+|.+|.|+|++|+.+|++|+.+|+|+++|.+++|+|+|++
T Consensus 1 ~~R~~TF~~w~~~~~~~~~~La~~Gfyy~~~~d~v~C~~C~~~~~~w~~~d~p~~~H~~~~p~C~fv~ 68 (69)
T cd00022 1 EARLKTFKNWPISLKVTPEKLAEAGFYYTGRGDEVKCFFCGLELKNWEPGDDPWEEHKRWSPNCPFVL 68 (69)
T ss_pred ChHHHHHHcCCCCccCCHHHHHHcCCeEcCCCCEEEeCCCCCCccCCCCCCCHHHHHhHhCcCCcCcc
Confidence 47999999999864678999999999999999999999999999999999999999999999999985
No 6
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=99.83 E-value=4e-21 Score=156.26 Aligned_cols=70 Identities=46% Similarity=0.992 Sum_probs=65.4
Q ss_pred hHHHHHhhccCCCCCCccCHHHHHHcCceecCCCCceeccccccccccccCCCChHHHhhcCCCCCCCcc
Q psy2747 139 FERSRLRTFQSWPSNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISNWTYNDSVMAKHRAKDPGCPFVK 208 (557)
Q Consensus 139 ~e~~Rl~TF~~wp~~~~~~~~~LA~aGFyy~g~~D~v~C~~C~~~l~~w~~~D~p~~eH~~~~p~C~f~~ 208 (557)
++++|++||.+||+.....+++||+|||||+|.+|.|+|++|++.|++|+.+|+|+++|++++|.|+|++
T Consensus 1 ~~~~R~~sF~~w~~~~~~~~~~LA~~Gfyy~~~~d~v~C~~C~~~l~~w~~~d~p~~~H~~~~p~C~fv~ 70 (71)
T smart00238 1 SEEARLKTFQNWPYNSKLTPEQLAEAGFYYTGVGDEVKCFFCGGELDNWEPGDDPWEEHKKWSPNCPFVR 70 (71)
T ss_pred CHHHHHHHHHcCCCCccCCHHHHHHcCCeECCCCCEEEeCCCCCCcCCCCCCCCHHHHHhHhCcCCcCcc
Confidence 3689999999999744478999999999999999999999999999999999999999999999999985
No 7
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=99.81 E-value=1.5e-20 Score=152.06 Aligned_cols=68 Identities=56% Similarity=1.136 Sum_probs=64.2
Q ss_pred HHHHccCCCCCCCCCCCHHHHHhcCceeccCCCeEEeeeccCcccccCCCCChHHHhhhcCCCCcccc
Q psy2747 228 SGRLATFNNWPVSFIVTPEALAKTGFYYLKQGDKVKCAYCSVIIGRWEQGDNAESEHKRQSPNCPFLA 295 (557)
Q Consensus 228 ~~Rl~SF~~wp~~~~~~~~~LA~aGFyy~g~~D~v~C~~C~~~l~~W~~~Ddp~~eH~~~~p~C~f~~ 295 (557)
++|++||.+||++....+++||++||||+|.+|.|+|++|++.|.+|+++|+|+.+|++++|.|+|++
T Consensus 1 ~~R~~TF~~w~~~~~~~~~~La~~Gfyy~~~~d~v~C~~C~~~~~~w~~~d~p~~~H~~~~p~C~fv~ 68 (69)
T cd00022 1 EARLKTFKNWPISLKVTPEKLAEAGFYYTGRGDEVKCFFCGLELKNWEPGDDPWEEHKRWSPNCPFVL 68 (69)
T ss_pred ChHHHHHHcCCCCccCCHHHHHHcCCeEcCCCCEEEeCCCCCCccCCCCCCCHHHHHhHhCcCCcCcc
Confidence 37999999999984458999999999999999999999999999999999999999999999999986
No 8
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=99.81 E-value=1.4e-20 Score=152.74 Aligned_cols=66 Identities=53% Similarity=1.118 Sum_probs=58.0
Q ss_pred HHccCC-CCCCCC---CCCHHHHHhcCceeccCCCeEEeeeccCcccccCCCCChHHHhhhcCCCCcccc
Q psy2747 230 RLATFN-NWPVSF---IVTPEALAKTGFYYLKQGDKVKCAYCSVIIGRWEQGDNAESEHKRQSPNCPFLA 295 (557)
Q Consensus 230 Rl~SF~-~wp~~~---~~~~~~LA~aGFyy~g~~D~v~C~~C~~~l~~W~~~Ddp~~eH~~~~p~C~f~~ 295 (557)
||+||. +||+.. .+++++||+|||||+|.+|+|+|++|++.|.+|+++||||++|.+++|+|+|++
T Consensus 1 Rl~SF~~~wp~~~~~~~~~~~~LA~aGFyy~~~~d~v~C~~C~~~l~~w~~~Ddp~~~H~~~sp~C~f~k 70 (70)
T PF00653_consen 1 RLKSFRSNWPHSNDHDPVSPEKLARAGFYYTGTGDRVRCFYCGLELDNWEPNDDPWEEHKRHSPNCPFVK 70 (70)
T ss_dssp HHHGGTTGSSTTTTTSSSHHHHHHHTTEEEESSTTEEEETTTTEEEES-STT--HHHHHHHHSTTBHHHH
T ss_pred ChhHHCCcccCccccCCCCHHHHHHCCCEEcCCCCEEEEeccCCEEeCCCCCCCHHHHHHHHCcCCeecC
Confidence 899996 599653 357999999999999999999999999999999999999999999999999974
No 9
>KOG4172|consensus
Probab=99.07 E-value=3.4e-12 Score=95.24 Aligned_cols=50 Identities=40% Similarity=0.931 Sum_probs=46.8
Q ss_pred cccccccccccceEEecCCccccchhhhcCC-----CCCCCCccccccEEEEeeC
Q psy2747 508 RLCKICMDKEVGVVLLPCGHLVTCVLCASSL-----PRCPVCRENIKATVRTFLS 557 (557)
Q Consensus 508 ~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~-----~~CP~CR~~i~~~i~i~~s 557 (557)
.+|.||++++.+.|+.-|||+|+|..|+.++ ..||+||++|..+|+.|.|
T Consensus 8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dvIkTY~s 62 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDVIKTYRS 62 (62)
T ss_pred cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHHHHhhcC
Confidence 6799999999999999999999999999876 5799999999999999875
No 10
>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=99.07 E-value=4.7e-11 Score=90.32 Aligned_cols=45 Identities=47% Similarity=1.088 Sum_probs=40.1
Q ss_pred ccccccccccccceEEecCCccccchhhhcCC----CCCCCCccccccE
Q psy2747 507 ARLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKAT 551 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~ 551 (557)
+..|.||+++.++++++||||.++|..|+.++ .+||+||++|+++
T Consensus 2 ~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~V 50 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIESV 50 (50)
T ss_dssp HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SEE
T ss_pred cCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcCC
Confidence 46899999999999999999999999999987 8999999999864
No 11
>KOG4275|consensus
Probab=99.04 E-value=2.4e-11 Score=120.22 Aligned_cols=51 Identities=47% Similarity=1.031 Sum_probs=48.9
Q ss_pred ccccccccccccceEEecCCccccchhhhcCCCCCCCCccccccEEEEeeC
Q psy2747 507 ARLCKICMDKEVGVVLLPCGHLVTCVLCASSLPRCPVCRENIKATVRTFLS 557 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~~~CP~CR~~i~~~i~i~~s 557 (557)
..+|.|||+.+++.+|++|||.+.|.+|...|..|||||+.|..+++||.+
T Consensus 300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm~eCPICRqyi~rvvrif~~ 350 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLECGHMVTCTKCGKRMNECPICRQYIVRVVRIFRV 350 (350)
T ss_pred HHHHHHHhcCCcceEEeecCcEEeehhhccccccCchHHHHHHHHHhhhcC
Confidence 678999999999999999999999999999999999999999999999964
No 12
>KOG4265|consensus
Probab=98.99 E-value=9.7e-11 Score=119.95 Aligned_cols=52 Identities=37% Similarity=0.912 Sum_probs=47.9
Q ss_pred HhccccccccccccceEEecCCccccchhhhcCC----CCCCCCccccccEEEEee
Q psy2747 505 REARLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKATVRTFL 556 (557)
Q Consensus 505 ~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~i~i~~ 556 (557)
++..+|+||++..++++++||.|+|+|..||..+ .+|||||++|...+.|+.
T Consensus 288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~i~~ 343 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEELLEIYV 343 (349)
T ss_pred cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHhhheecc
Confidence 3467899999999999999999999999999987 579999999999999875
No 13
>KOG1571|consensus
Probab=98.71 E-value=2.2e-09 Score=110.16 Aligned_cols=52 Identities=40% Similarity=1.090 Sum_probs=49.3
Q ss_pred hccccccccccccceEEecCCccccchhhhcCCCCCCCCccccccEEEEeeC
Q psy2747 506 EARLCKICMDKEVGVVLLPCGHLVTCVLCASSLPRCPVCRENIKATVRTFLS 557 (557)
Q Consensus 506 ~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~~~CP~CR~~i~~~i~i~~s 557 (557)
....|+||.+++.+++|+||||+|+|..|+..+.+||+||..|...+++|.+
T Consensus 304 ~p~lcVVcl~e~~~~~fvpcGh~ccct~cs~~l~~CPvCR~rI~~~~k~y~~ 355 (355)
T KOG1571|consen 304 QPDLCVVCLDEPKSAVFVPCGHVCCCTLCSKHLPQCPVCRQRIRLVRKRYRS 355 (355)
T ss_pred CCCceEEecCCccceeeecCCcEEEchHHHhhCCCCchhHHHHHHHHHHhcC
Confidence 3578999999999999999999999999999999999999999999999975
No 14
>KOG1100|consensus
Probab=98.56 E-value=3.5e-08 Score=96.44 Aligned_cols=52 Identities=38% Similarity=0.893 Sum_probs=47.7
Q ss_pred HhccccccccccccceEEecCCccccchhhhcCCCCCCCCccccccEEEEee
Q psy2747 505 REARLCKICMDKEVGVVLLPCGHLVTCVLCASSLPRCPVCRENIKATVRTFL 556 (557)
Q Consensus 505 ~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~~~CP~CR~~i~~~i~i~~ 556 (557)
.....|+.|.++++.++++||.|+++|..|...+..||+|+.++.+.+.||+
T Consensus 156 ~~~~~Cr~C~~~~~~VlllPCrHl~lC~~C~~~~~~CPiC~~~~~s~~~v~~ 207 (207)
T KOG1100|consen 156 KRMRSCRKCGEREATVLLLPCRHLCLCGICDESLRICPICRSPKTSSVEVNF 207 (207)
T ss_pred hccccceecCcCCceEEeecccceEecccccccCccCCCCcChhhceeeccC
Confidence 3344499999999999999999999999999999999999999999999985
No 15
>KOG1785|consensus
Probab=97.95 E-value=4.2e-06 Score=86.52 Aligned_cols=62 Identities=37% Similarity=0.759 Sum_probs=48.2
Q ss_pred cccChHHHHHHHHh----ccccccccccccceEEecCCccccchhhhcCC------CCCCCCccccccEEEEe
Q psy2747 493 FVKSLEEEVRRLRE----ARLCKICMDKEVGVVLLPCGHLVTCVLCASSL------PRCPVCRENIKATVRTF 555 (557)
Q Consensus 493 ~~~~~~~~~~~~~~----~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~------~~CP~CR~~i~~~i~i~ 555 (557)
.+...+||.+-.-+ -.+|+||-++++++-+-||||+ +|..|.... +.||.||..|.++-.|-
T Consensus 351 ~i~VtqEQyeLYceMgsTFeLCKICaendKdvkIEPCGHL-lCt~CLa~WQ~sd~gq~CPFCRcEIKGte~vi 422 (563)
T KOG1785|consen 351 RIKVTQEQYELYCEMGSTFELCKICAENDKDVKIEPCGHL-LCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVI 422 (563)
T ss_pred ceeeeHHHHHHHHHccchHHHHHHhhccCCCcccccccch-HHHHHHHhhcccCCCCCCCceeeEecccccee
Confidence 34444555443222 2589999999999999999999 899998764 69999999999876553
No 16
>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=97.65 E-value=1.8e-05 Score=56.50 Aligned_cols=34 Identities=47% Similarity=1.196 Sum_probs=28.4
Q ss_pred cccccccccce-EEecCCccccchhhhcCC----CCCCCC
Q psy2747 510 CKICMDKEVGV-VLLPCGHLVTCVLCASSL----PRCPVC 544 (557)
Q Consensus 510 C~IC~~~~~~~-~~~PCgH~~~C~~Ca~~~----~~CP~C 544 (557)
|.||++...+. +++||||. +|.+|..+. .+||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~-fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHS-FCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEE-EEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCc-hhHHHHHHHHHCcCCCcCC
Confidence 78999999998 68999999 899999754 789987
No 17
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.62 E-value=2.1e-05 Score=75.49 Aligned_cols=50 Identities=34% Similarity=0.817 Sum_probs=41.5
Q ss_pred HhccccccccccccceEEecCCccccchhhhcC--------------------CCCCCCCcccccc--EEEEe
Q psy2747 505 REARLCKICMDKEVGVVLLPCGHLVTCVLCASS--------------------LPRCPVCRENIKA--TVRTF 555 (557)
Q Consensus 505 ~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~--------------------~~~CP~CR~~i~~--~i~i~ 555 (557)
.+...|.||++...+.++.+|||. +|..|... ...||+||.+|.. ++.||
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~-FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiy 87 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHL-FCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIY 87 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCch-hHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEee
Confidence 346789999999999999999998 89999953 1489999999976 45555
No 18
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.62 E-value=3e-05 Score=77.27 Aligned_cols=49 Identities=31% Similarity=0.777 Sum_probs=39.2
Q ss_pred hccccccccccccc--------eEEecCCccccchhhhcCC----CCCCCCccccccEEEEe
Q psy2747 506 EARLCKICMDKEVG--------VVLLPCGHLVTCVLCASSL----PRCPVCRENIKATVRTF 555 (557)
Q Consensus 506 ~~~~C~IC~~~~~~--------~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~i~i~ 555 (557)
+...|.||++.-.+ .++.||||. +|..|.... ..||+||.++..+++..
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~-FC~~CI~~Wl~~~~tCPlCR~~~~~v~~~r 233 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHV-FCIECIDIWKKEKNTCPVCRTPFISVIKSR 233 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCc-ccHHHHHHHHhcCCCCCCCCCEeeEEeeee
Confidence 45789999986322 466789998 999999643 79999999999988754
No 19
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=97.52 E-value=5.3e-05 Score=55.59 Aligned_cols=37 Identities=41% Similarity=1.039 Sum_probs=31.4
Q ss_pred ccccccccc---cceEEecCCccccchhhhcCCC----CCCCCcc
Q psy2747 509 LCKICMDKE---VGVVLLPCGHLVTCVLCASSLP----RCPVCRE 546 (557)
Q Consensus 509 ~C~IC~~~~---~~~~~~PCgH~~~C~~Ca~~~~----~CP~CR~ 546 (557)
.|.||++.- ...++++|||. +|..|+..+. .||+||+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~-~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHI-FCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCH-HHHHHHHhhcCCCCCCcCCCC
Confidence 378888655 56788999999 8999999886 9999985
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=97.35 E-value=7.1e-05 Score=54.80 Aligned_cols=36 Identities=44% Similarity=0.980 Sum_probs=29.8
Q ss_pred ccccccccc---cceEEecCCccccchhhhcCC----CCCCCCc
Q psy2747 509 LCKICMDKE---VGVVLLPCGHLVTCVLCASSL----PRCPVCR 545 (557)
Q Consensus 509 ~C~IC~~~~---~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR 545 (557)
.|.||++.- ..++.+||||. +|.+|.... ..||+||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHV-FHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEE-EEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCe-eCHHHHHHHHHhCCcCCccC
Confidence 699999754 57888899998 899999865 7999998
No 21
>KOG0978|consensus
Probab=97.34 E-value=5.2e-05 Score=85.14 Aligned_cols=61 Identities=30% Similarity=0.672 Sum_probs=52.4
Q ss_pred cChHHHHHHHHhccccccccccccceEEecCCccccchhhhcCC-----CCCCCCcccccc--EEEEee
Q psy2747 495 KSLEEEVRRLREARLCKICMDKEVGVVLLPCGHLVTCVLCASSL-----PRCPVCRENIKA--TVRTFL 556 (557)
Q Consensus 495 ~~~~~~~~~~~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~-----~~CP~CR~~i~~--~i~i~~ 556 (557)
..|.+++++......|.+|.++.+++|+.-|||+ +|..|.... .+||.|.+++-. +.+||+
T Consensus 631 ~~L~EElk~yK~~LkCs~Cn~R~Kd~vI~kC~H~-FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 631 EVLAEELKEYKELLKCSVCNTRWKDAVITKCGHV-FCEECVQTRYETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred HHHHHHHHHHHhceeCCCccCchhhHHHHhcchH-HHHHHHHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence 4467888888889999999999999999999999 999999864 899999998754 566654
No 22
>PHA02926 zinc finger-like protein; Provisional
Probab=97.29 E-value=8e-05 Score=72.32 Aligned_cols=53 Identities=26% Similarity=0.688 Sum_probs=40.2
Q ss_pred HHHHHHhccccccccccc---------cceEEecCCccccchhhhcCC----------CCCCCCccccccEEE
Q psy2747 500 EVRRLREARLCKICMDKE---------VGVVLLPCGHLVTCVLCASSL----------PRCPVCRENIKATVR 553 (557)
Q Consensus 500 ~~~~~~~~~~C~IC~~~~---------~~~~~~PCgH~~~C~~Ca~~~----------~~CP~CR~~i~~~i~ 553 (557)
.+-+..++..|.||++.. +-.++.+|+|. +|..|.... ..||+||..+..++.
T Consensus 163 ~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHs-FCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~p 234 (242)
T PHA02926 163 DVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHI-FCITCINIWHRTRRETGASDNCPICRTRFRNITM 234 (242)
T ss_pred HHHhccCCCCCccCccccccccccccccccccCCCCch-HHHHHHHHHHHhccccCcCCcCCCCcceeeeecc
Confidence 334445578999999863 23678899999 999999754 239999999886643
No 23
>KOG0317|consensus
Probab=97.24 E-value=9.9e-05 Score=74.21 Aligned_cols=48 Identities=29% Similarity=0.823 Sum_probs=40.7
Q ss_pred ccccccccccccceEEecCCccccchhhhcCC----CCCCCCccccccEEEEe
Q psy2747 507 ARLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKATVRTF 555 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~i~i~ 555 (557)
...|.+|++...+-...||||+ +|-.|.... ..||+||.+..-.--|.
T Consensus 239 ~~kC~LCLe~~~~pSaTpCGHi-FCWsCI~~w~~ek~eCPlCR~~~~pskvi~ 290 (293)
T KOG0317|consen 239 TRKCSLCLENRSNPSATPCGHI-FCWSCILEWCSEKAECPLCREKFQPSKVIC 290 (293)
T ss_pred CCceEEEecCCCCCCcCcCcch-HHHHHHHHHHccccCCCcccccCCCcceee
Confidence 4789999999999999999999 899998754 68999999887654443
No 24
>KOG0320|consensus
Probab=97.13 E-value=0.00014 Score=68.33 Aligned_cols=49 Identities=35% Similarity=0.834 Sum_probs=38.7
Q ss_pred ccccccccccccceE-E-ecCCccccchhhhcCC----CCCCCCcccccc--EEEEee
Q psy2747 507 ARLCKICMDKEVGVV-L-LPCGHLVTCVLCASSL----PRCPVCRENIKA--TVRTFL 556 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~-~-~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~--~i~i~~ 556 (557)
.-.|.|||+.....+ + --|||+ +|..|+... .+||+||.+|+. +.+|||
T Consensus 131 ~~~CPiCl~~~sek~~vsTkCGHv-FC~~Cik~alk~~~~CP~C~kkIt~k~~~rI~L 187 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVPVSTKCGHV-FCSQCIKDALKNTNKCPTCRKKITHKQFHRIYL 187 (187)
T ss_pred ccCCCceecchhhccccccccchh-HHHHHHHHHHHhCCCCCCcccccchhhheeccC
Confidence 357999998766655 2 589999 999999864 799999977765 577775
No 25
>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=97.10 E-value=0.00038 Score=48.13 Aligned_cols=34 Identities=41% Similarity=1.096 Sum_probs=30.1
Q ss_pred cccccccccceEEecCCccccchhhhcC-----CCCCCCC
Q psy2747 510 CKICMDKEVGVVLLPCGHLVTCVLCASS-----LPRCPVC 544 (557)
Q Consensus 510 C~IC~~~~~~~~~~PCgH~~~C~~Ca~~-----~~~CP~C 544 (557)
|.||++.....+++||||. +|..|... ...||+|
T Consensus 1 C~iC~~~~~~~~~~~C~H~-~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLPCGHT-FCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEecCCCh-HHHHHHHHHHHhCcCCCCCC
Confidence 7899999999999999999 89999974 3579987
No 26
>KOG0823|consensus
Probab=97.00 E-value=0.00041 Score=67.94 Aligned_cols=49 Identities=33% Similarity=0.732 Sum_probs=41.7
Q ss_pred hccccccccccccceEEecCCccccchhhhcCC-------CCCCCCcccccc--EEEEe
Q psy2747 506 EARLCKICMDKEVGVVLLPCGHLVTCVLCASSL-------PRCPVCRENIKA--TVRTF 555 (557)
Q Consensus 506 ~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~-------~~CP~CR~~i~~--~i~i~ 555 (557)
....|-||+|..++.|+-+|||+ +|=.|.-+. +.||+|++.|.. ++.||
T Consensus 46 ~~FdCNICLd~akdPVvTlCGHL-FCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlY 103 (230)
T KOG0823|consen 46 GFFDCNICLDLAKDPVVTLCGHL-FCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLY 103 (230)
T ss_pred CceeeeeeccccCCCEEeecccc-eehHHHHHHHhhcCCCeeCCccccccccceEEeee
Confidence 35689999999999999999999 899999764 789999997654 56666
No 27
>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=96.93 E-value=0.00071 Score=48.46 Aligned_cols=39 Identities=44% Similarity=1.025 Sum_probs=30.3
Q ss_pred ccccccccccce-EEecCCccccchhhhcC-----CCCCCCCcccc
Q psy2747 509 LCKICMDKEVGV-VLLPCGHLVTCVLCASS-----LPRCPVCRENI 548 (557)
Q Consensus 509 ~C~IC~~~~~~~-~~~PCgH~~~C~~Ca~~-----~~~CP~CR~~i 548 (557)
.|.||++..... .+.||||. +|..|... ...||+||..+
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~-~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHV-FCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhCceEecCCCCh-hcHHHHHHHHHhCcCCCCCCCCcC
Confidence 489999887444 44559999 89999973 35799999864
No 28
>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=96.89 E-value=0.0004 Score=49.84 Aligned_cols=34 Identities=44% Similarity=1.086 Sum_probs=29.9
Q ss_pred cccccccccceE-EecCCccccchhhhcCC------CCCCCC
Q psy2747 510 CKICMDKEVGVV-LLPCGHLVTCVLCASSL------PRCPVC 544 (557)
Q Consensus 510 C~IC~~~~~~~~-~~PCgH~~~C~~Ca~~~------~~CP~C 544 (557)
|.||++.....+ ++||||. +|..|..++ ..||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~-fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHS-FCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEE-EEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCc-chHHHHHHHHHhcCCccCCcC
Confidence 789999988888 9999999 899999754 579887
No 29
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=96.65 E-value=0.0009 Score=48.67 Aligned_cols=34 Identities=47% Similarity=1.015 Sum_probs=26.4
Q ss_pred cccccccccceEEecCCccccchhhhcCC--------CCCCCC
Q psy2747 510 CKICMDKEVGVVLLPCGHLVTCVLCASSL--------PRCPVC 544 (557)
Q Consensus 510 C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~--------~~CP~C 544 (557)
|.||++--.+-+.++|||. +|..|..+. ..||.|
T Consensus 1 CpiC~~~~~~Pv~l~CGH~-FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHS-FCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSE-EEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCccccCCcCH-HHHHHHHHHHHccCCcCCCCcCC
Confidence 7899999999999999999 899999764 268887
No 30
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.57 E-value=0.00069 Score=72.38 Aligned_cols=48 Identities=35% Similarity=0.718 Sum_probs=40.6
Q ss_pred HHHHhccccccccccccceEEecCCccccchhhhcC----CCCCCCCcccccc
Q psy2747 502 RRLREARLCKICMDKEVGVVLLPCGHLVTCVLCASS----LPRCPVCRENIKA 550 (557)
Q Consensus 502 ~~~~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~----~~~CP~CR~~i~~ 550 (557)
..+.....|.||.+.-.+.++.||||. +|..|... ...||+||..+..
T Consensus 21 ~~Le~~l~C~IC~d~~~~PvitpCgH~-FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 21 YPLDTSLRCHICKDFFDVPVLTSCSHT-FCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred cccccccCCCcCchhhhCccCCCCCCc-hhHHHHHHHHhCCCCCCCCCCcccc
Confidence 445567899999999989899999999 89999974 2579999998764
No 31
>KOG2164|consensus
Probab=96.44 E-value=0.0013 Score=70.91 Aligned_cols=48 Identities=31% Similarity=0.728 Sum_probs=41.4
Q ss_pred ccccccccccccceEEecCCccccchhhhcCC---------CCCCCCcccccc--EEEEe
Q psy2747 507 ARLCKICMDKEVGVVLLPCGHLVTCVLCASSL---------PRCPVCRENIKA--TVRTF 555 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~---------~~CP~CR~~i~~--~i~i~ 555 (557)
...|.||++.+...+..-|||. +|-.|.-.+ ..||+||..|.. +..|+
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHi-FC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHI-FCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVF 244 (513)
T ss_pred CCcCCcccCCCCcccccccCce-eeHHHHHHHHhhhcccCCccCCchhhhccccceeeee
Confidence 6789999999999999999999 899998643 799999999987 55554
No 32
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.36 E-value=0.0016 Score=66.86 Aligned_cols=47 Identities=38% Similarity=0.829 Sum_probs=41.2
Q ss_pred HhccccccccccccceEEecCCccccchhhhcCC------CCCCCCccccccEE
Q psy2747 505 REARLCKICMDKEVGVVLLPCGHLVTCVLCASSL------PRCPVCRENIKATV 552 (557)
Q Consensus 505 ~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~------~~CP~CR~~i~~~i 552 (557)
++...|+||-+.-.-+.++||+|. +|..|+.++ +.||+||..-..++
T Consensus 59 Een~~C~ICA~~~TYs~~~PC~H~-~CH~Ca~RlRALY~~K~C~~CrTE~e~V~ 111 (493)
T COG5236 59 EENMNCQICAGSTTYSARYPCGHQ-ICHACAVRLRALYMQKGCPLCRTETEAVV 111 (493)
T ss_pred cccceeEEecCCceEEEeccCCch-HHHHHHHHHHHHHhccCCCccccccceEE
Confidence 456789999999999999999999 799999875 89999999877654
No 33
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.27 E-value=0.0018 Score=49.47 Aligned_cols=44 Identities=30% Similarity=0.677 Sum_probs=37.7
Q ss_pred hccccccccccccceEEecCCccccchhhhcC--CCCCCCCcccccc
Q psy2747 506 EARLCKICMDKEVGVVLLPCGHLVTCVLCASS--LPRCPVCRENIKA 550 (557)
Q Consensus 506 ~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~--~~~CP~CR~~i~~ 550 (557)
....|+.|......-+++||||+ .|..|-.. ..-||+|-.++..
T Consensus 6 ~~~~~~~~~~~~~~~~~~pCgH~-I~~~~f~~~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTVLPCGHL-ICDNCFPGERYNGCPFCGTPFEF 51 (55)
T ss_pred cceeEEEccccccccccccccce-eeccccChhhccCCCCCCCcccC
Confidence 35679999999899999999999 69999875 4799999998864
No 34
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.18 E-value=0.0017 Score=64.64 Aligned_cols=42 Identities=31% Similarity=0.777 Sum_probs=36.7
Q ss_pred ccccccccccccceEEecCCccccchhhhcCC------CCCCCCccccc
Q psy2747 507 ARLCKICMDKEVGVVLLPCGHLVTCVLCASSL------PRCPVCRENIK 549 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~------~~CP~CR~~i~ 549 (557)
...|.||++..-...-.||||+ +|-.|.-.+ ..||+||+.+.
T Consensus 215 d~kC~lC~e~~~~ps~t~CgHl-FC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 215 DYKCFLCLEEPEVPSCTPCGHL-FCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccceeeeecccCCcccccccch-hhHHHHHHHHHhhccccCchhhhhcc
Confidence 5689999999999999999999 899998762 57999999764
No 35
>KOG4692|consensus
Probab=96.15 E-value=0.0014 Score=67.38 Aligned_cols=45 Identities=31% Similarity=0.804 Sum_probs=39.5
Q ss_pred hccccccccccccceEEecCCccccchhhhcC----CCCCCCCccccccE
Q psy2747 506 EARLCKICMDKEVGVVLLPCGHLVTCVLCASS----LPRCPVCRENIKAT 551 (557)
Q Consensus 506 ~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~----~~~CP~CR~~i~~~ 551 (557)
++.+|.||+..+++++|-||+|. .|..|... .+.|-.|...|...
T Consensus 421 Ed~lCpICyA~pi~Avf~PC~H~-SC~~CI~qHlmN~k~CFfCktTv~~~ 469 (489)
T KOG4692|consen 421 EDNLCPICYAGPINAVFAPCSHR-SCYGCITQHLMNCKRCFFCKTTVIDV 469 (489)
T ss_pred ccccCcceecccchhhccCCCCc-hHHHHHHHHHhcCCeeeEecceeeeh
Confidence 46799999999999999999999 79999975 38999999987753
No 36
>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=96.04 E-value=0.0041 Score=48.70 Aligned_cols=42 Identities=21% Similarity=0.289 Sum_probs=36.4
Q ss_pred cccccccccccceEEecCCccccchhhhcCC----CCCCCCcccccc
Q psy2747 508 RLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKA 550 (557)
Q Consensus 508 ~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~ 550 (557)
..|.||.+--.+-+..||||. +|..|.... ..||+|+.++..
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v-~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQT-YERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCE-EeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 469999999888999999998 899999865 689999998843
No 37
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=95.71 E-value=0.0038 Score=45.64 Aligned_cols=27 Identities=41% Similarity=0.974 Sum_probs=17.3
Q ss_pred cccccccccc----eEEecCCccccchhhhcCC
Q psy2747 510 CKICMDKEVG----VVLLPCGHLVTCVLCASSL 538 (557)
Q Consensus 510 C~IC~~~~~~----~~~~PCgH~~~C~~Ca~~~ 538 (557)
|.||.+ ..+ -+.+||||. +|.+|..++
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~-~c~~cl~~l 31 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHV-FCKDCLQKL 31 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-E-EEHHHHHHH
T ss_pred CCcccc-ccCCCCCCEEEeCccH-HHHHHHHHH
Confidence 788888 555 678899999 899999876
No 38
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 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 zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=95.49 E-value=0.015 Score=53.12 Aligned_cols=45 Identities=27% Similarity=0.561 Sum_probs=37.7
Q ss_pred HHHHhhccC--CC-CCCCCCHHHHHHcCceeecCCCceeeeeecceecC
Q psy2747 5 RSRLRTFQS--WP-SNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISN 50 (557)
Q Consensus 5 ~~Rl~TF~~--wp-~~~~~~~~~LA~aGFyytg~~d~V~Cf~Cg~~l~~ 50 (557)
..||+||.. |. ....+++-.+|+.|+..++ +|.++|-.||..+.-
T Consensus 8 l~RL~Tf~~~~W~~kp~~lspl~cA~~GW~~~~-~d~l~C~~C~~~l~~ 55 (133)
T PF07967_consen 8 LRRLETFKSLTWFPKPPWLSPLECARRGWICVS-KDMLKCESCGARLCV 55 (133)
T ss_pred HHHHHHcccccccCCCcccCHHHHHHcCCCcCC-CCEEEeCCCCCEEEE
Confidence 369999985 83 3467999999999999977 889999999999643
No 39
>KOG2177|consensus
Probab=95.25 E-value=0.0064 Score=61.28 Aligned_cols=44 Identities=43% Similarity=0.883 Sum_probs=37.5
Q ss_pred HHHHhccccccccccccceEEecCCccccchhhhcCC----CCCCCCcc
Q psy2747 502 RRLREARLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRE 546 (557)
Q Consensus 502 ~~~~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~ 546 (557)
..+.+...|.||++.-....++||||. +|..|...+ -.||.||.
T Consensus 8 ~~~~~~~~C~iC~~~~~~p~~l~C~H~-~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 8 EVLQEELTCPICLEYFREPVLLPCGHN-FCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred hhccccccChhhHHHhhcCccccccch-HhHHHHHHhcCCCcCCcccCC
Confidence 344567899999998888899999999 899999875 48999993
No 40
>KOG0287|consensus
Probab=95.11 E-value=0.0065 Score=62.37 Aligned_cols=46 Identities=30% Similarity=0.782 Sum_probs=40.0
Q ss_pred HHhccccccccccccceEEecCCccccchhhhcCC----CCCCCCcccccc
Q psy2747 504 LREARLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKA 550 (557)
Q Consensus 504 ~~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~ 550 (557)
+.+...|-||++--.-.++.||+|- +|.-|.... ..||.|+.+++.
T Consensus 20 lD~lLRC~IC~eyf~ip~itpCsHt-fCSlCIR~~L~~~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 20 LDDLLRCGICFEYFNIPMITPCSHT-FCSLCIRKFLSYKPQCPTCCVTVTE 69 (442)
T ss_pred hHHHHHHhHHHHHhcCceeccccch-HHHHHHHHHhccCCCCCceecccch
Confidence 4455679999999999999999999 899999864 799999998765
No 41
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.05 E-value=0.015 Score=45.92 Aligned_cols=47 Identities=36% Similarity=0.698 Sum_probs=27.0
Q ss_pred HHHHhccccccccccccceE-EecCCccccchhhhcCC--CCCCCCccccc
Q psy2747 502 RRLREARLCKICMDKEVGVV-LLPCGHLVTCVLCASSL--PRCPVCRENIK 549 (557)
Q Consensus 502 ~~~~~~~~C~IC~~~~~~~~-~~PCgH~~~C~~Ca~~~--~~CP~CR~~i~ 549 (557)
+++++...|.+|.+--+..| +--|.|. +|..|.... ..||+|+.|..
T Consensus 2 ~~le~lLrCs~C~~~l~~pv~l~~CeH~-fCs~Ci~~~~~~~CPvC~~Paw 51 (65)
T PF14835_consen 2 ERLEELLRCSICFDILKEPVCLGGCEHI-FCSSCIRDCIGSECPVCHTPAW 51 (65)
T ss_dssp HHHHHTTS-SSS-S--SS-B---SSS---B-TTTGGGGTTTB-SSS--B-S
T ss_pred hHHHHhcCCcHHHHHhcCCceeccCccH-HHHHHhHHhcCCCCCCcCChHH
Confidence 45667789999998877765 5689999 899999875 78999998763
No 42
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=95.00 E-value=0.0087 Score=60.25 Aligned_cols=46 Identities=37% Similarity=0.710 Sum_probs=39.1
Q ss_pred HHhccccccccccccceEEecCCccccchhhhcCC----CCCCCCcccccc
Q psy2747 504 LREARLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKA 550 (557)
Q Consensus 504 ~~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~ 550 (557)
+.....|.||.+.-+--++-||||. +|.-|...- ..||+||.+...
T Consensus 22 LDs~lrC~IC~~~i~ip~~TtCgHt-FCslCIR~hL~~qp~CP~Cr~~~~e 71 (391)
T COG5432 22 LDSMLRCRICDCRISIPCETTCGHT-FCSLCIRRHLGTQPFCPVCREDPCE 71 (391)
T ss_pred chhHHHhhhhhheeecceecccccc-hhHHHHHHHhcCCCCCccccccHHh
Confidence 3456689999999999999999999 899999763 799999987543
No 43
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 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 zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=94.98 E-value=0.029 Score=51.22 Aligned_cols=49 Identities=24% Similarity=0.453 Sum_probs=39.6
Q ss_pred chhHHHHHhhccC--CC-CCCccCHHHHHHcCceecCCCCceecccccccccc
Q psy2747 137 MNFERSRLRTFQS--WP-SNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKISN 186 (557)
Q Consensus 137 ~~~e~~Rl~TF~~--wp-~~~~~~~~~LA~aGFyy~g~~D~v~C~~C~~~l~~ 186 (557)
....-.||+||.. |. ....+++-.+|+.|+.-.+ .|.++|..|+..+.-
T Consensus 4 r~~~l~RL~Tf~~~~W~~kp~~lspl~cA~~GW~~~~-~d~l~C~~C~~~l~~ 55 (133)
T PF07967_consen 4 REDFLRRLETFKSLTWFPKPPWLSPLECARRGWICVS-KDMLKCESCGARLCV 55 (133)
T ss_pred HHHHHHHHHHcccccccCCCcccCHHHHHHcCCCcCC-CCEEEeCCCCCEEEE
Confidence 3445789999984 83 3446999999999998865 789999999998763
No 44
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=94.49 E-value=0.014 Score=60.59 Aligned_cols=45 Identities=36% Similarity=0.862 Sum_probs=33.5
Q ss_pred HHhccccccccccc-------------cceEEecCCccccchhhhcC----CCCCCCCccccc
Q psy2747 504 LREARLCKICMDKE-------------VGVVLLPCGHLVTCVLCASS----LPRCPVCRENIK 549 (557)
Q Consensus 504 ~~~~~~C~IC~~~~-------------~~~~~~PCgH~~~C~~Ca~~----~~~CP~CR~~i~ 549 (557)
..+.+.|.||||.- +.-.=+||||. +=-.|... -++||+||.++.
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHi-lHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHI-LHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccce-eeHHHHHHHHHhccCCCcccCccc
Confidence 35678999999871 11245799998 67778764 489999999953
No 45
>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=94.11 E-value=0.028 Score=45.91 Aligned_cols=36 Identities=39% Similarity=0.912 Sum_probs=26.5
Q ss_pred ccccccccc-------------cceEEecCCccccchhhhcCC----CCCCCCc
Q psy2747 509 LCKICMDKE-------------VGVVLLPCGHLVTCVLCASSL----PRCPVCR 545 (557)
Q Consensus 509 ~C~IC~~~~-------------~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR 545 (557)
.|.||++.- ..+++.+|||. +-..|..+. ..||+||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~-FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHI-FHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEE-EEHHHHHHHHTTSSB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCC-EEHHHHHHHHhcCCcCCCCC
Confidence 488887543 45577799999 899998743 7999998
No 46
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.73 E-value=0.042 Score=55.84 Aligned_cols=50 Identities=34% Similarity=0.708 Sum_probs=37.6
Q ss_pred HHHHHHHhcccccccccc---ccceEEecCCccccchhhhcCC-----CCCCCCccccc
Q psy2747 499 EEVRRLREARLCKICMDK---EVGVVLLPCGHLVTCVLCASSL-----PRCPVCRENIK 549 (557)
Q Consensus 499 ~~~~~~~~~~~C~IC~~~---~~~~~~~PCgH~~~C~~Ca~~~-----~~CP~CR~~i~ 549 (557)
+...+....-.|.|||+. .-..+.+||.|. +=..|..+. .+||+||.+|.
T Consensus 315 e~~~ea~~GveCaICms~fiK~d~~~vlPC~H~-FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 315 ERAVEADKGVECAICMSNFIKNDRLRVLPCDHR-FHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred HhHHhcCCCceEEEEhhhhcccceEEEeccCce-echhHHHHHHhhhcccCCccCCCCC
Confidence 334444445789999964 333778899999 788898875 69999999875
No 47
>KOG0802|consensus
Probab=92.46 E-value=0.053 Score=61.04 Aligned_cols=43 Identities=35% Similarity=0.780 Sum_probs=36.9
Q ss_pred Hhccccccccccccc-----eEEecCCccccchhhhcCC----CCCCCCcccc
Q psy2747 505 REARLCKICMDKEVG-----VVLLPCGHLVTCVLCASSL----PRCPVCRENI 548 (557)
Q Consensus 505 ~~~~~C~IC~~~~~~-----~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i 548 (557)
.....|.||.+.-.. ...+||||. ++..|..+. ..||+||..+
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hi-fh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHI-FHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccc-hHHHHHHHHHHHhCcCCcchhhh
Confidence 346789999998777 789999999 899999864 8999999944
No 48
>KOG1039|consensus
Probab=90.87 E-value=0.092 Score=55.32 Aligned_cols=46 Identities=26% Similarity=0.599 Sum_probs=37.4
Q ss_pred hccccccccccccceE-----E---ecCCccccchhhhcC-----------CCCCCCCccccccEE
Q psy2747 506 EARLCKICMDKEVGVV-----L---LPCGHLVTCVLCASS-----------LPRCPVCRENIKATV 552 (557)
Q Consensus 506 ~~~~C~IC~~~~~~~~-----~---~PCgH~~~C~~Ca~~-----------~~~CP~CR~~i~~~i 552 (557)
.+..|.|||+.....+ | .+|.|. +|..|... .+.||+||.+...++
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~-~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~ 224 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNCNHS-FCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVN 224 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCcchh-hhhcHhHhhhhhhccccccccCCCcccCcccccc
Confidence 4678999998776666 5 679999 89999964 268999999887654
No 49
>KOG3002|consensus
Probab=89.57 E-value=0.18 Score=52.21 Aligned_cols=45 Identities=29% Similarity=0.748 Sum_probs=36.3
Q ss_pred HhccccccccccccceEEecC--CccccchhhhcC-CCCCCCCccccccE
Q psy2747 505 REARLCKICMDKEVGVVLLPC--GHLVTCVLCASS-LPRCPVCRENIKAT 551 (557)
Q Consensus 505 ~~~~~C~IC~~~~~~~~~~PC--gH~~~C~~Ca~~-~~~CP~CR~~i~~~ 551 (557)
.+-..|.||++.-.--++- | ||+ +|..|..+ ..+||.||.+|..+
T Consensus 46 ~~lleCPvC~~~l~~Pi~Q-C~nGHl-aCssC~~~~~~~CP~Cr~~~g~~ 93 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLSPPIFQ-CDNGHL-ACSSCRTKVSNKCPTCRLPIGNI 93 (299)
T ss_pred hhhccCchhhccCccccee-cCCCcE-ehhhhhhhhcccCCccccccccH
Confidence 3456799999887777775 6 899 79999954 58999999999843
No 50
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=88.75 E-value=0.29 Score=39.82 Aligned_cols=44 Identities=23% Similarity=0.298 Sum_probs=33.2
Q ss_pred hccccccccccccceEEecCCccccchhhhcCC-----CCCCCCcccccc
Q psy2747 506 EARLCKICMDKEVGVVLLPCGHLVTCVLCASSL-----PRCPVCRENIKA 550 (557)
Q Consensus 506 ~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~-----~~CP~CR~~i~~ 550 (557)
+...|.|+.+--.+-|++|+||. ++..|.... ..||+|+.++..
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~t-yer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHT-YERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEE-EEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cccCCcCcCcHhhCceeCCcCCE-EcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 46789999999999999999977 899988643 679999998875
No 51
>KOG4628|consensus
Probab=88.48 E-value=0.25 Score=51.93 Aligned_cols=43 Identities=33% Similarity=0.833 Sum_probs=31.6
Q ss_pred ccccccccc---ccceEEecCCccccchhhhcCC-----CCCCCCccccccE
Q psy2747 508 RLCKICMDK---EVGVVLLPCGHLVTCVLCASSL-----PRCPVCRENIKAT 551 (557)
Q Consensus 508 ~~C~IC~~~---~~~~~~~PCgH~~~C~~Ca~~~-----~~CP~CR~~i~~~ 551 (557)
..|.||+|. .--+.++||.|. +=..|.... ..||+|+..|...
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~-FH~~CIDpWL~~~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHK-FHVNCIDPWLTQTRTFCPVCKRDIRTD 280 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCc-hhhccchhhHhhcCccCCCCCCcCCCC
Confidence 389999974 334566899999 455677654 4599999987653
No 52
>KOG4159|consensus
Probab=88.23 E-value=0.14 Score=55.12 Aligned_cols=45 Identities=31% Similarity=0.775 Sum_probs=37.6
Q ss_pred HhccccccccccccceEEecCCccccchhhhcC----CCCCCCCcccccc
Q psy2747 505 REARLCKICMDKEVGVVLLPCGHLVTCVLCASS----LPRCPVCRENIKA 550 (557)
Q Consensus 505 ~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~----~~~CP~CR~~i~~ 550 (557)
..+..|.||+..--..+..||||. +|..|..+ -..||.||..+..
T Consensus 82 ~sef~c~vc~~~l~~pv~tpcghs-~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVVTPCGHS-FCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCCCcccccccc-ccHHHHHHHhccCCCCccccccccc
Confidence 456789999998888888899999 89999543 3799999998875
No 53
>KOG2113|consensus
Probab=87.68 E-value=0.47 Score=48.66 Aligned_cols=51 Identities=14% Similarity=-0.014 Sum_probs=44.5
Q ss_pred HHhccccccccccccceEEecCCccccchhhhcCC--CCCCCCccccccEEEE
Q psy2747 504 LREARLCKICMDKEVGVVLLPCGHLVTCVLCASSL--PRCPVCRENIKATVRT 554 (557)
Q Consensus 504 ~~~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~--~~CP~CR~~i~~~i~i 554 (557)
+...++|.+|-..-...++.||||..+|.+||..- ..||.|...+-..++|
T Consensus 340 ~~s~~~~~~~~~~~~st~~~~~~~n~~~~~~a~~s~~~~~~~c~~~~~~~~~i 392 (394)
T KOG2113|consen 340 LMSSLKGTSAGFGLLSTIWSGGNMNLSPGSLASASASPTSSTCDHNDHTLVPI 392 (394)
T ss_pred chhhcccccccCceeeeEeecCCcccChhhhhhcccCCccccccccceeeeec
Confidence 34567899999999999999999999999999843 7999999888777765
No 54
>KOG1814|consensus
Probab=86.73 E-value=0.36 Score=51.30 Aligned_cols=30 Identities=33% Similarity=0.881 Sum_probs=26.0
Q ss_pred ccccccccccccc---eEEecCCccccchhhhcC
Q psy2747 507 ARLCKICMDKEVG---VVLLPCGHLVTCVLCASS 537 (557)
Q Consensus 507 ~~~C~IC~~~~~~---~~~~PCgH~~~C~~Ca~~ 537 (557)
...|.||++.... ++|+||+|+ +|..|...
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC~Hv-~Ck~C~kd 216 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPCSHV-FCKSCLKD 216 (445)
T ss_pred cccceeeehhhcCcceeeecccchH-HHHHHHHH
Confidence 5689999998766 789999999 89999974
No 55
>KOG2932|consensus
Probab=84.83 E-value=0.22 Score=50.87 Aligned_cols=43 Identities=30% Similarity=0.901 Sum_probs=32.0
Q ss_pred ccccccccccceE--EecCCccccchhhhcCC--CCCCCCccccccEEE
Q psy2747 509 LCKICMDKEVGVV--LLPCGHLVTCVLCASSL--PRCPVCRENIKATVR 553 (557)
Q Consensus 509 ~C~IC~~~~~~~~--~~PCgH~~~C~~Ca~~~--~~CP~CR~~i~~~i~ 553 (557)
.|.-| +.++-+. ++||.|+ +|.+||..- +.||.|-.+|..+-+
T Consensus 92 fCd~C-d~PI~IYGRmIPCkHv-FCl~CAr~~~dK~Cp~C~d~VqrIeq 138 (389)
T KOG2932|consen 92 FCDRC-DFPIAIYGRMIPCKHV-FCLECARSDSDKICPLCDDRVQRIEQ 138 (389)
T ss_pred eeccc-CCcceeeecccccchh-hhhhhhhcCccccCcCcccHHHHHHH
Confidence 46666 3444443 6899999 999999865 799999988876543
No 56
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=83.73 E-value=0.3 Score=46.94 Aligned_cols=46 Identities=33% Similarity=0.642 Sum_probs=37.8
Q ss_pred ccccccccccccceEEecCCccccchhhhcCC----CCCCCCccccccEEE
Q psy2747 507 ARLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKATVR 553 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~i~ 553 (557)
...|.||...-..-|.--|||. +|..|+..- .+|.+|.+...+...
T Consensus 196 PF~C~iCKkdy~spvvt~CGH~-FC~~Cai~~y~kg~~C~~Cgk~t~G~f~ 245 (259)
T COG5152 196 PFLCGICKKDYESPVVTECGHS-FCSLCAIRKYQKGDECGVCGKATYGRFW 245 (259)
T ss_pred ceeehhchhhccchhhhhcchh-HHHHHHHHHhccCCcceecchhhcccee
Confidence 3589999988888888899999 899999753 799999887666543
No 57
>KOG3039|consensus
Probab=79.34 E-value=1.4 Score=43.88 Aligned_cols=45 Identities=27% Similarity=0.453 Sum_probs=36.8
Q ss_pred hcccccccccc----ccceEEecCCccccchhhhcCC----CCCCCCccccccE
Q psy2747 506 EARLCKICMDK----EVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKAT 551 (557)
Q Consensus 506 ~~~~C~IC~~~----~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~ 551 (557)
....|.||.+. ...++|-||||+ +|.+|+.++ ..||+|-.+....
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~V-v~~ecvEklir~D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHV-VTKECVEKLIRKDMVDPVTDKPLKDR 272 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcE-eeHHHHHHhccccccccCCCCcCccc
Confidence 45689999864 445678899999 699999987 6999999887764
No 58
>PF04641 Rtf2: Rtf2 RING-finger
Probab=78.98 E-value=1.5 Score=44.56 Aligned_cols=45 Identities=24% Similarity=0.501 Sum_probs=35.9
Q ss_pred hcccccccccc----ccceEEecCCccccchhhhcCCC---CCCCCccccccE
Q psy2747 506 EARLCKICMDK----EVGVVLLPCGHLVTCVLCASSLP---RCPVCRENIKAT 551 (557)
Q Consensus 506 ~~~~C~IC~~~----~~~~~~~PCgH~~~C~~Ca~~~~---~CP~CR~~i~~~ 551 (557)
....|.|.... .+-++|.||||+ ++..+...++ .||+|-.++...
T Consensus 112 ~~~~CPvt~~~~~~~~~fv~l~~cG~V-~s~~alke~k~~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 112 GRFICPVTGKEFNGKHKFVYLRPCGCV-FSEKALKELKKSKKCPVCGKPFTEE 163 (260)
T ss_pred ceeECCCCCcccCCceeEEEEcCCCCE-eeHHHHHhhcccccccccCCccccC
Confidence 35678888743 355677799999 7999999886 899999998764
No 59
>KOG0311|consensus
Probab=78.95 E-value=0.29 Score=51.01 Aligned_cols=51 Identities=22% Similarity=0.534 Sum_probs=39.7
Q ss_pred HHHHHHhccccccccccccce-EEecCCccccchhhhcCC-----CCCCCCccccccE
Q psy2747 500 EVRRLREARLCKICMDKEVGV-VLLPCGHLVTCVLCASSL-----PRCPVCRENIKAT 551 (557)
Q Consensus 500 ~~~~~~~~~~C~IC~~~~~~~-~~~PCgH~~~C~~Ca~~~-----~~CP~CR~~i~~~ 551 (557)
.++.+..+..|.||++--..+ ...-|+|. +|.+|..+- ..||.||+...+.
T Consensus 36 ~l~~~~~~v~c~icl~llk~tmttkeClhr-fc~~ci~~a~r~gn~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 36 DLAMFDIQVICPICLSLLKKTMTTKECLHR-FCFDCIWKALRSGNNECPTCRKKLVSK 92 (381)
T ss_pred cHHHhhhhhccHHHHHHHHhhcccHHHHHH-HHHHHHHHHHHhcCCCCchHHhhcccc
Confidence 345566678999999865544 45579999 899999853 7999999987764
No 60
>KOG1001|consensus
Probab=78.82 E-value=0.8 Score=52.72 Aligned_cols=41 Identities=37% Similarity=0.865 Sum_probs=35.6
Q ss_pred cccccccccccceEEecCCccccchhhhcCC------CCCCCCcccccc
Q psy2747 508 RLCKICMDKEVGVVLLPCGHLVTCVLCASSL------PRCPVCRENIKA 550 (557)
Q Consensus 508 ~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~------~~CP~CR~~i~~ 550 (557)
..|.+|.+ ....++.+|||. .|.+|.... ..||+||..+..
T Consensus 455 ~~c~ic~~-~~~~~it~c~h~-~c~~c~~~~i~~~~~~~~~~cr~~l~~ 501 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRCGHD-FCVECLKKSIQQSENAPCPLCRNVLKE 501 (674)
T ss_pred cccccccc-cccceeecccch-HHHHHHHhccccccCCCCcHHHHHHHH
Confidence 78999999 888888999999 899999754 579999987653
No 61
>KOG0828|consensus
Probab=78.71 E-value=0.7 Score=50.11 Aligned_cols=45 Identities=33% Similarity=0.699 Sum_probs=33.3
Q ss_pred Hhcccccccccc-----------------ccceEEecCCccccchhhhcCC----C-CCCCCcccccc
Q psy2747 505 REARLCKICMDK-----------------EVGVVLLPCGHLVTCVLCASSL----P-RCPVCRENIKA 550 (557)
Q Consensus 505 ~~~~~C~IC~~~-----------------~~~~~~~PCgH~~~C~~Ca~~~----~-~CP~CR~~i~~ 550 (557)
.+...|+|||.. .++.++-||.|+ +=..|.... + .||+||.++..
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~Hi-fH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHI-FHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHH-HHHHHHHHHHhhhcccCCccCCCCCC
Confidence 456789999962 234566799999 678888653 3 89999998753
No 62
>KOG1813|consensus
Probab=78.53 E-value=0.85 Score=46.61 Aligned_cols=45 Identities=29% Similarity=0.620 Sum_probs=38.2
Q ss_pred cccccccccccceEEecCCccccchhhhcCC----CCCCCCccccccEEE
Q psy2747 508 RLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKATVR 553 (557)
Q Consensus 508 ~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~i~ 553 (557)
..|-||..--.+-|.--|||. +|..||.+- .+|++|.+.+.++..
T Consensus 242 f~c~icr~~f~~pVvt~c~h~-fc~~ca~~~~qk~~~c~vC~~~t~g~~~ 290 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVVTKCGHY-FCEVCALKPYQKGEKCYVCSQQTHGSFN 290 (313)
T ss_pred ccccccccccccchhhcCCce-eehhhhccccccCCcceecccccccccc
Confidence 459999988888888899999 899999863 689999999887643
No 63
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=76.72 E-value=0.8 Score=48.65 Aligned_cols=40 Identities=28% Similarity=0.576 Sum_probs=0.0
Q ss_pred cccceEEecCCccccchhhhc-----CC--------CCCCCCcccccc---EEEEee
Q psy2747 516 KEVGVVLLPCGHLVTCVLCAS-----SL--------PRCPVCRENIKA---TVRTFL 556 (557)
Q Consensus 516 ~~~~~~~~PCgH~~~C~~Ca~-----~~--------~~CP~CR~~i~~---~i~i~~ 556 (557)
.....+|.||||++ =+..+. .+ ..||.|-.++.. .+|+++
T Consensus 356 ~~pthaF~PCGHv~-SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g~~g~vrLiF 411 (416)
T PF04710_consen 356 GPPTHAFNPCGHVC-SEKTAKYWSQIPLPHGTHAFHAACPFCATPLDGEQGYVRLIF 411 (416)
T ss_dssp ---------------------------------------------------------
T ss_pred CCCceeeccccccc-chhhhhhhhcCCCCCCcccccccCCcccCcccCCCCceEEEE
Confidence 34567899999993 122222 11 589999999876 455543
No 64
>KOG2879|consensus
Probab=76.09 E-value=1.6 Score=44.28 Aligned_cols=45 Identities=29% Similarity=0.741 Sum_probs=35.6
Q ss_pred hccccccccccccce-EEecCCccccchhhhcCC------CCCCCCccccccE
Q psy2747 506 EARLCKICMDKEVGV-VLLPCGHLVTCVLCASSL------PRCPVCRENIKAT 551 (557)
Q Consensus 506 ~~~~C~IC~~~~~~~-~~~PCgH~~~C~~Ca~~~------~~CP~CR~~i~~~ 551 (557)
...+|.+|.+.+..- +..||||. .|.-|+..- -.||.|.+++...
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~Hi-yCY~Ci~ts~~~~asf~Cp~Cg~~~~~l 289 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHI-YCYYCIATSRLWDASFTCPLCGENVEPL 289 (298)
T ss_pred CCceeeccCCCCCCCeeeccccce-eehhhhhhhhcchhhcccCccCCCCcch
Confidence 356899999887664 55689998 899999753 3899999987743
No 65
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=71.85 E-value=2 Score=36.18 Aligned_cols=30 Identities=30% Similarity=0.607 Sum_probs=22.7
Q ss_pred ceEEecCCccccchhhhcC-------CCCCCCCccccc
Q psy2747 519 GVVLLPCGHLVTCVLCASS-------LPRCPVCRENIK 549 (557)
Q Consensus 519 ~~~~~PCgH~~~C~~Ca~~-------~~~CP~CR~~i~ 549 (557)
.+++--|+|. +=..|..+ -..||+||++.+
T Consensus 46 plv~g~C~H~-FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 46 PLVWGKCSHN-FHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred ceeeccCccH-HHHHHHHHHHccccCCCCCCCcCCeee
Confidence 3466789998 77888653 269999999764
No 66
>KOG0825|consensus
Probab=69.55 E-value=1.1 Score=51.19 Aligned_cols=46 Identities=22% Similarity=0.399 Sum_probs=34.9
Q ss_pred ccccccccccccceEE---ecCCccccchhhhcCC----CCCCCCccccccEEE
Q psy2747 507 ARLCKICMDKEVGVVL---LPCGHLVTCVLCASSL----PRCPVCRENIKATVR 553 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~---~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~i~ 553 (557)
...|.+|+..-.+-+. .+|+|. +|..|.... .+||+||..+..++.
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~-FC~~Ci~sWsR~aqTCPiDR~EF~~v~V 175 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHY-FCEECVGSWSRCAQTCPVDRGEFGEVKV 175 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccc-cHHHHhhhhhhhcccCchhhhhhheeee
Confidence 3468888765444333 499999 899999875 799999998877643
No 67
>KOG2113|consensus
Probab=68.56 E-value=1.8 Score=44.48 Aligned_cols=48 Identities=15% Similarity=0.167 Sum_probs=40.2
Q ss_pred ccccccccccccceEEecCCccccchhhhcCC-----CCCCCCccccccEEEE
Q psy2747 507 ARLCKICMDKEVGVVLLPCGHLVTCVLCASSL-----PRCPVCRENIKATVRT 554 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~-----~~CP~CR~~i~~~i~i 554 (557)
.-.|++|+++..-+.++||+|-++|.+|+.+. ..|++|...+.....|
T Consensus 136 ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta~~ra~~i 188 (394)
T KOG2113|consen 136 TIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTAVTRAGQI 188 (394)
T ss_pred ccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhhhhhhhhcc
Confidence 44699999999999999999999999997765 4699998877766554
No 68
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=66.31 E-value=6.8 Score=35.59 Aligned_cols=50 Identities=26% Similarity=0.447 Sum_probs=36.5
Q ss_pred ChhHhhhcCccccCCCCeEEEEecCCceeec--cCCCCcHHHHhhhcC------Ccchhhhhhh
Q psy2747 413 GPQSLAVAGFFYDGQGDWVRCFHCDGGLRKW--TAMDEPWSEHARWFP------ECHFVMLVKG 468 (557)
Q Consensus 413 ~~~~LA~AGFfy~g~~D~v~Cf~Cg~~l~~w--~~~Ddpw~eH~~~~p------~C~fv~~~kG 468 (557)
++.+.+.+ ..|...|.+||..|.-- .....||.||....- .|.|+...++
T Consensus 17 ~A~~a~~~------~~~~~tC~~Cg~~L~lh~~~~~~~pWFEH~~~~~~~~~l~~C~yl~pe~k 74 (128)
T PF11682_consen 17 GARTAASA------PYDHWTCHSCGCPLILHPGTDTEPPWFEHDQHSLAENGLMQCPYLDPEEK 74 (128)
T ss_pred ehhhhhhC------CCCeEEEecCCceEEEecCCcCCCCccccCccccChhhcccCceECcccc
Confidence 46666666 67899999999887554 567799999997652 4777664443
No 69
>KOG4765|consensus
Probab=63.57 E-value=5.7 Score=42.07 Aligned_cols=50 Identities=24% Similarity=0.385 Sum_probs=39.4
Q ss_pred ccchhHHHHHhhcc--CCC-CCCccCHHHHHHcCceecCCCCceeccccccccc
Q psy2747 135 ITMNFERSRLRTFQ--SWP-SNSPVSSKRIAKAGFFYTGHQHEVQCFACGVKIS 185 (557)
Q Consensus 135 ~~~~~e~~Rl~TF~--~wp-~~~~~~~~~LA~aGFyy~g~~D~v~C~~C~~~l~ 185 (557)
-++...-.||+||+ +|= ....+++..+|+-|+--. ..|.++|-+|+..|.
T Consensus 49 wdred~lrRl~Tfks~tWygkp~~iS~lnCA~~GWv~v-d~D~lkCe~C~a~L~ 101 (419)
T KOG4765|consen 49 WDREDLLRRLATFKSRTWYGKPFEISPLNCAKYGWVCV-DCDMLKCESCGAFLC 101 (419)
T ss_pred ccHHHHHHHHHhccCchhccCCcccchHHHhhcCeeec-cCCeeehhhhhhHHh
Confidence 34666678999999 462 234589999999999754 578999999999875
No 70
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=62.78 E-value=2.6 Score=41.81 Aligned_cols=40 Identities=30% Similarity=0.842 Sum_probs=29.3
Q ss_pred hcccccccccc---ccceE--Eec-CCccccchhhhcCC-----CCCC--CCcc
Q psy2747 506 EARLCKICMDK---EVGVV--LLP-CGHLVTCVLCASSL-----PRCP--VCRE 546 (557)
Q Consensus 506 ~~~~C~IC~~~---~~~~~--~~P-CgH~~~C~~Ca~~~-----~~CP--~CR~ 546 (557)
..+.|.||... ..++. +-| |-|. +|.+|..++ ..|| -|..
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHr-mCESCvdRIFs~GpAqCP~~gC~k 61 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHR-MCESCVDRIFSRGPAQCPYKGCGK 61 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHH-HHHHHHHHHhcCCCCCCCCccHHH
Confidence 35689999742 33444 448 9999 799999976 6899 6754
No 71
>KOG0297|consensus
Probab=61.64 E-value=3.3 Score=44.78 Aligned_cols=49 Identities=37% Similarity=0.756 Sum_probs=39.8
Q ss_pred HHhccccccccccccceEE-ecCCccccchhhhcCC----CCCCCCccccccEEE
Q psy2747 504 LREARLCKICMDKEVGVVL-LPCGHLVTCVLCASSL----PRCPVCRENIKATVR 553 (557)
Q Consensus 504 ~~~~~~C~IC~~~~~~~~~-~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~i~ 553 (557)
+.+...|.+|+.--.+.+. ..|||. +|..|.... ..||.|+..+.....
T Consensus 18 ~~~~l~C~~C~~vl~~p~~~~~cgh~-fC~~C~~~~~~~~~~cp~~~~~~~~~~~ 71 (391)
T KOG0297|consen 18 LDENLLCPICMSVLRDPVQTTTCGHR-FCAGCLLESLSNHQKCPVCRQELTQAEE 71 (391)
T ss_pred CcccccCccccccccCCCCCCCCCCc-ccccccchhhccCcCCcccccccchhhc
Confidence 3456789999998888888 599999 899999875 689999887765433
No 72
>KOG0804|consensus
Probab=60.81 E-value=4.5 Score=43.73 Aligned_cols=41 Identities=29% Similarity=0.784 Sum_probs=29.4
Q ss_pred Hhcccccccccccc----ceEEecCCccccchhhhcCC--CCCCCCcc
Q psy2747 505 REARLCKICMDKEV----GVVLLPCGHLVTCVLCASSL--PRCPVCRE 546 (557)
Q Consensus 505 ~~~~~C~IC~~~~~----~~~~~PCgH~~~C~~Ca~~~--~~CP~CR~ 546 (557)
.+...|+||+++-- .++-++|.|-. =..|..+. ..||+||=
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsf-h~~cl~~w~~~scpvcR~ 219 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSF-HCSCLMKWWDSSCPVCRY 219 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeeccccc-chHHHhhcccCcChhhhh
Confidence 34678999997643 24567999994 44576654 69999985
No 73
>KOG3497|consensus
Probab=60.73 E-value=4 Score=31.87 Aligned_cols=12 Identities=42% Similarity=1.248 Sum_probs=10.7
Q ss_pred eeeeeecceecC
Q psy2747 39 VQCFACGVKISN 50 (557)
Q Consensus 39 V~Cf~Cg~~l~~ 50 (557)
|+||.||++|.+
T Consensus 5 iRCFtCGKvig~ 16 (69)
T KOG3497|consen 5 IRCFTCGKVIGD 16 (69)
T ss_pred eEeeeccccccc
Confidence 899999999864
No 74
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=59.49 E-value=3.5 Score=30.72 Aligned_cols=42 Identities=26% Similarity=0.789 Sum_probs=25.0
Q ss_pred ccccccccccceEEecCCccccchhhhcCC----CCCCCCccccccEE
Q psy2747 509 LCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPVCRENIKATV 552 (557)
Q Consensus 509 ~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~CR~~i~~~i 552 (557)
-|+-|.-+.++.| -|.---+|-.|...| ..||+|..++...+
T Consensus 4 nCKsCWf~~k~Li--~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtki 49 (50)
T PF03854_consen 4 NCKSCWFANKGLI--KCSDHYLCLNCLTLMLSRSDRCPICGKPLPTKI 49 (50)
T ss_dssp ---SS-S--SSEE--E-SS-EEEHHHHHHT-SSSSEETTTTEE----S
T ss_pred cChhhhhcCCCee--eecchhHHHHHHHHHhccccCCCcccCcCcccc
Confidence 4888887777766 587666999999987 79999999887654
No 75
>KOG4765|consensus
Probab=58.73 E-value=6.3 Score=41.77 Aligned_cols=48 Identities=31% Similarity=0.521 Sum_probs=37.3
Q ss_pred ccccHHHHHccCC--CCCC-CCCCCHHHHHhcCceeccCCCeEEeeeccCcc
Q psy2747 223 VYKLESGRLATFN--NWPV-SFIVTPEALAKTGFYYLKQGDKVKCAYCSVII 271 (557)
Q Consensus 223 ~~~~~~~Rl~SF~--~wp~-~~~~~~~~LA~aGFyy~g~~D~v~C~~C~~~l 271 (557)
++..+-.||+||+ +|-. +..+++...|+.|+-... .|.++|-+|+..|
T Consensus 50 dred~lrRl~Tfks~tWygkp~~iS~lnCA~~GWv~vd-~D~lkCe~C~a~L 100 (419)
T KOG4765|consen 50 DREDLLRRLATFKSRTWYGKPFEISPLNCAKYGWVCVD-CDMLKCESCGAFL 100 (419)
T ss_pred cHHHHHHHHHhccCchhccCCcccchHHHhhcCeeecc-CCeeehhhhhhHH
Confidence 5666778999998 4632 233689999999997664 5899999999765
No 76
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=58.31 E-value=3.9 Score=32.10 Aligned_cols=12 Identities=50% Similarity=1.243 Sum_probs=10.4
Q ss_pred eeeeeecceecC
Q psy2747 39 VQCFACGVKISN 50 (557)
Q Consensus 39 V~Cf~Cg~~l~~ 50 (557)
|+||+||+.|..
T Consensus 5 iRCFsCGkvi~~ 16 (63)
T COG1644 5 VRCFSCGKVIGH 16 (63)
T ss_pred eEeecCCCCHHH
Confidence 899999999854
No 77
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=57.97 E-value=3 Score=43.35 Aligned_cols=45 Identities=29% Similarity=0.866 Sum_probs=33.3
Q ss_pred Hhcccccccccc----ccceEEecCCccccchhhhcCC-----CCCCCCcccccc
Q psy2747 505 REARLCKICMDK----EVGVVLLPCGHLVTCVLCASSL-----PRCPVCRENIKA 550 (557)
Q Consensus 505 ~~~~~C~IC~~~----~~~~~~~PCgH~~~C~~Ca~~~-----~~CP~CR~~i~~ 550 (557)
.++..|..|++. .++-.-.|||-. .|.-|...+ ..||.||.....
T Consensus 12 deed~cplcie~mditdknf~pc~cgy~-ic~fc~~~irq~lngrcpacrr~y~d 65 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFFPCPCGYQ-ICQFCYNNIRQNLNGRCPACRRKYDD 65 (480)
T ss_pred cccccCcccccccccccCCcccCCcccH-HHHHHHHHHHhhccCCChHhhhhccc
Confidence 346679999974 334444578887 699999865 699999987654
No 78
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=54.63 E-value=4.3 Score=32.83 Aligned_cols=12 Identities=58% Similarity=1.301 Sum_probs=10.6
Q ss_pred eeeeeecceecC
Q psy2747 39 VQCFACGVKISN 50 (557)
Q Consensus 39 V~Cf~Cg~~l~~ 50 (557)
|+||.||+.|.+
T Consensus 5 VRCFTCGkvig~ 16 (71)
T PLN00032 5 VRCFTCGKVIGN 16 (71)
T ss_pred eeecCCCCCcHH
Confidence 899999999854
No 79
>KOG3842|consensus
Probab=54.61 E-value=5.7 Score=41.04 Aligned_cols=43 Identities=26% Similarity=0.614 Sum_probs=28.2
Q ss_pred hccccccccc-------------------cccceEEecCCccccchhhhcC------C--------CCCCCCcccccc
Q psy2747 506 EARLCKICMD-------------------KEVGVVLLPCGHLVTCVLCASS------L--------PRCPVCRENIKA 550 (557)
Q Consensus 506 ~~~~C~IC~~-------------------~~~~~~~~PCgH~~~C~~Ca~~------~--------~~CP~CR~~i~~ 550 (557)
.++.|.+|.. -+...+|-||||++ .+=..+ + ..||.|-..+.+
T Consensus 340 ~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~--sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~g 415 (429)
T KOG3842|consen 340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVC--SEKTVKYWSQIPLPHGTHAFHAACPFCATQLAG 415 (429)
T ss_pred ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCccccc--chhhhhHhhcCcCCCccccccccCcchhhhhcc
Confidence 3667888875 23456788999993 322211 1 589999887765
No 80
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=52.67 E-value=9.5 Score=40.66 Aligned_cols=42 Identities=29% Similarity=0.673 Sum_probs=27.7
Q ss_pred ccccccccccccceEEe-cC----------------Cccc----cchhhhcCC-----------------CCCCCCcccc
Q psy2747 507 ARLCKICMDKEVGVVLL-PC----------------GHLV----TCVLCASSL-----------------PRCPVCRENI 548 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~~-PC----------------gH~~----~C~~Ca~~~-----------------~~CP~CR~~i 548 (557)
...|.-|+..+.++.+. -| +.-. =|.+|..+. ..||+||+++
T Consensus 271 ~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 271 LEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF 350 (358)
T ss_pred cCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence 44677777777777765 23 2111 288887653 4899999975
No 81
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=52.15 E-value=5 Score=30.08 Aligned_cols=38 Identities=32% Similarity=0.851 Sum_probs=16.1
Q ss_pred cccccccc--cceEEe--cCCccccchhhhcCC-----CCCCCCcccc
Q psy2747 510 CKICMDKE--VGVVLL--PCGHLVTCVLCASSL-----PRCPVCRENI 548 (557)
Q Consensus 510 C~IC~~~~--~~~~~~--PCgH~~~C~~Ca~~~-----~~CP~CR~~i 548 (557)
|.+|.+.- .+.-|. +||+. +|..|...+ ..||.||.+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~-IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQ-ICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS-----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCc-HHHHHHHHHHhccCCCCCCCCCCC
Confidence 45565432 233344 67888 799996543 6899999874
No 82
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=50.89 E-value=13 Score=33.87 Aligned_cols=48 Identities=23% Similarity=0.358 Sum_probs=35.7
Q ss_pred CCCHHHHHhcCceeccCCCeEEeeeccCcccc--cCCCCChHHHhhhcCC------CCcccc
Q psy2747 242 IVTPEALAKTGFYYLKQGDKVKCAYCSVIIGR--WEQGDNAESEHKRQSP------NCPFLA 295 (557)
Q Consensus 242 ~~~~~~LA~aGFyy~g~~D~v~C~~C~~~l~~--W~~~Ddp~~eH~~~~p------~C~f~~ 295 (557)
.+++.+.+.+ ..|...|.+|+..|.- =..++.||-||...+- .|+|+.
T Consensus 15 ~v~A~~a~~~------~~~~~tC~~Cg~~L~lh~~~~~~~pWFEH~~~~~~~~~l~~C~yl~ 70 (128)
T PF11682_consen 15 FVGARTAASA------PYDHWTCHSCGCPLILHPGTDTEPPWFEHDQHSLAENGLMQCPYLD 70 (128)
T ss_pred EEehhhhhhC------CCCeEEEecCCceEEEecCCcCCCCccccCccccChhhcccCceEC
Confidence 3577777776 6689999999976643 3667899999976642 387776
No 83
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=50.52 E-value=6.5 Score=33.48 Aligned_cols=35 Identities=23% Similarity=0.589 Sum_probs=27.2
Q ss_pred CceeccccccccccccCC------------CChHHHhhcCCCCCCCccCC
Q psy2747 173 HEVQCFACGVKISNWTYN------------DSVMAKHRAKDPGCPFVKNP 210 (557)
Q Consensus 173 D~v~C~~C~~~l~~w~~~------------D~p~~eH~~~~p~C~f~~~~ 210 (557)
..+.|-+|..++.-|... =||++||+ ..||++...
T Consensus 18 ~~~~C~~C~Rr~GLW~f~~~~ss~~~~~~~~d~~~eHr---~~CPwv~~~ 64 (91)
T PF08600_consen 18 GLLSCSYCFRRLGLWMFKSKESSDSDPMSPFDPLEEHR---EYCPWVNPS 64 (91)
T ss_pred CeEEccccCcEeeeeecccCccCCCCcCCCCCCccccc---ccCCccCCc
Confidence 379999999999988432 26889997 479998653
No 84
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=49.87 E-value=4.4 Score=31.80 Aligned_cols=12 Identities=58% Similarity=1.301 Sum_probs=9.5
Q ss_pred eeeeeecceecC
Q psy2747 39 VQCFACGVKISN 50 (557)
Q Consensus 39 V~Cf~Cg~~l~~ 50 (557)
|+||.||+.|.+
T Consensus 5 VRCFTCGkvi~~ 16 (60)
T PF01194_consen 5 VRCFTCGKVIGN 16 (60)
T ss_dssp SS-STTTSBTCG
T ss_pred eecCCCCCChhH
Confidence 899999999963
No 85
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=49.64 E-value=5.8 Score=31.33 Aligned_cols=12 Identities=50% Similarity=1.240 Sum_probs=10.8
Q ss_pred eeeeeecceecC
Q psy2747 39 VQCFACGVKISN 50 (557)
Q Consensus 39 V~Cf~Cg~~l~~ 50 (557)
|+||.||+.|.+
T Consensus 5 vRCFTCGkvi~~ 16 (62)
T PRK04016 5 VRCFTCGKVIAE 16 (62)
T ss_pred eEecCCCCChHH
Confidence 899999999965
No 86
>KOG1002|consensus
Probab=46.61 E-value=4.7 Score=44.35 Aligned_cols=41 Identities=29% Similarity=0.714 Sum_probs=35.1
Q ss_pred ccccccccccccceEEecCCccccchhhhcCC---------CCCCCCcccc
Q psy2747 507 ARLCKICMDKEVGVVLLPCGHLVTCVLCASSL---------PRCPVCRENI 548 (557)
Q Consensus 507 ~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~---------~~CP~CR~~i 548 (557)
+..|.+|.+.-.+.+.-.|.|. +|..|.... -+||.|....
T Consensus 536 ~~~C~lc~d~aed~i~s~ChH~-FCrlCi~eyv~~f~~~~nvtCP~C~i~L 585 (791)
T KOG1002|consen 536 EVECGLCHDPAEDYIESSCHHK-FCRLCIKEYVESFMENNNVTCPVCHIGL 585 (791)
T ss_pred ceeecccCChhhhhHhhhhhHH-HHHHHHHHHHHhhhcccCCCCccccccc
Confidence 5689999999999999999999 899999431 5999998754
No 87
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=42.57 E-value=15 Score=31.18 Aligned_cols=34 Identities=24% Similarity=0.643 Sum_probs=27.4
Q ss_pred ceeeeeecceecCCccC------------CchHHhhhcCCCCCCCCcCC
Q psy2747 38 EVQCFACGVKISNWTYN------------DSVMAKHRAKDPGCPFVKNP 74 (557)
Q Consensus 38 ~V~Cf~Cg~~l~~w~~~------------d~~~~~H~~~~p~C~f~~~~ 74 (557)
-+.|-.|...|.-|... =||+++|+.+ ||++...
T Consensus 19 ~~~C~~C~Rr~GLW~f~~~~ss~~~~~~~~d~~~eHr~~---CPwv~~~ 64 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKSKESSDSDPMSPFDPLEEHREY---CPWVNPS 64 (91)
T ss_pred eEEccccCcEeeeeecccCccCCCCcCCCCCCccccccc---CCccCCc
Confidence 69999999999888842 2689999865 9998653
No 88
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=41.21 E-value=17 Score=27.18 Aligned_cols=36 Identities=28% Similarity=0.803 Sum_probs=24.1
Q ss_pred ccccccc--cccceEEecCC-----ccccchhhhcCC------CCCCCCc
Q psy2747 509 LCKICMD--KEVGVVLLPCG-----HLVTCVLCASSL------PRCPVCR 545 (557)
Q Consensus 509 ~C~IC~~--~~~~~~~~PCg-----H~~~C~~Ca~~~------~~CP~CR 545 (557)
.|.||++ .+.+.++.||. |. +=..|..+. ..||+|.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~-vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKY-VHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhH-HHHHHHHHHHHHcCCCcCCCCC
Confidence 4899996 66677888995 33 224565532 4799985
No 89
>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=39.54 E-value=14 Score=31.56 Aligned_cols=30 Identities=30% Similarity=0.722 Sum_probs=21.5
Q ss_pred hccccccccccc--cceEEecCCccccchhhhc
Q psy2747 506 EARLCKICMDKE--VGVVLLPCGHLVTCVLCAS 536 (557)
Q Consensus 506 ~~~~C~IC~~~~--~~~~~~PCgH~~~C~~Ca~ 536 (557)
+...|.+|...- ...++.||||+ +-..|+.
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v-~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHV-VHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeE-Eeccccc
Confidence 467899998654 34556699988 5777764
No 90
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=37.34 E-value=13 Score=33.82 Aligned_cols=43 Identities=35% Similarity=0.849 Sum_probs=34.9
Q ss_pred cccccccccccceEEe----cCCccccchhhhcCC-------CCCCCCccccccE
Q psy2747 508 RLCKICMDKEVGVVLL----PCGHLVTCVLCASSL-------PRCPVCRENIKAT 551 (557)
Q Consensus 508 ~~C~IC~~~~~~~~~~----PCgH~~~C~~Ca~~~-------~~CP~CR~~i~~~ 551 (557)
-+|-||.|...+--|+ =||-. .|..|...+ ..||+|+....+.
T Consensus 81 YeCnIC~etS~ee~FLKPneCCgY~-iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 81 YECNICKETSAEERFLKPNECCGYS-ICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred eeccCcccccchhhcCCcccccchH-HHHHHHHHHHHHcccCCCCCccccccccc
Confidence 4799999988887776 27755 899998765 7999999988764
No 91
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=34.59 E-value=11 Score=30.36 Aligned_cols=11 Identities=36% Similarity=0.954 Sum_probs=7.3
Q ss_pred CCCCCCccccc
Q psy2747 539 PRCPVCRENIK 549 (557)
Q Consensus 539 ~~CP~CR~~i~ 549 (557)
.+||.|+++|.
T Consensus 56 G~CP~C~~~i~ 66 (70)
T PF11793_consen 56 GECPYCSSPIS 66 (70)
T ss_dssp EE-TTT-SEEE
T ss_pred cCCcCCCCeee
Confidence 37999999886
No 92
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=33.56 E-value=38 Score=25.99 Aligned_cols=40 Identities=23% Similarity=0.303 Sum_probs=30.4
Q ss_pred HHHHHcCce-ecCCCCceeccccccccccccCCCChHHHhhcCCCCCCC
Q psy2747 159 KRIAKAGFF-YTGHQHEVQCFACGVKISNWTYNDSVMAKHRAKDPGCPF 206 (557)
Q Consensus 159 ~~LA~aGFy-y~g~~D~v~C~~C~~~l~~w~~~D~p~~eH~~~~p~C~f 206 (557)
+-||+||+- |. .++|.-|+..-.-..+..-|...|+ .|.|
T Consensus 12 KlLa~a~~~~yl----e~KCPrCK~vN~~~~~~e~~t~~~k----s~k~ 52 (60)
T COG4416 12 KLLAEAEGQAYL----EKKCPRCKEVNEFYIKEEATTQIHK----SNKF 52 (60)
T ss_pred HHHHhcccceee----eecCCccceeeeeecccccchhhhh----cccc
Confidence 679999996 54 6999999987666666667777786 5655
No 93
>KOG0826|consensus
Probab=28.70 E-value=11 Score=39.18 Aligned_cols=50 Identities=26% Similarity=0.624 Sum_probs=32.6
Q ss_pred hccccccccccccceEEecCCccccchhhhcCC----CCCCC--CccccccEEEEe
Q psy2747 506 EARLCKICMDKEVGVVLLPCGHLVTCVLCASSL----PRCPV--CRENIKATVRTF 555 (557)
Q Consensus 506 ~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~----~~CP~--CR~~i~~~i~i~ 555 (557)
+...|.||.....+-..+---=.++|..|+.+- +.||+ |.+.+...+|+|
T Consensus 299 ~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~~l~rl~ 354 (357)
T KOG0826|consen 299 DREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVDHLIRLF 354 (357)
T ss_pred ccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcchHHHHHHHh
Confidence 456899999776664444343344999999763 89998 444444444443
No 94
>KOG3161|consensus
Probab=26.49 E-value=18 Score=40.94 Aligned_cols=37 Identities=38% Similarity=0.863 Sum_probs=28.5
Q ss_pred Hhccccccccc----cccceEEecCCccccchhhhcCC--CCCC
Q psy2747 505 REARLCKICMD----KEVGVVLLPCGHLVTCVLCASSL--PRCP 542 (557)
Q Consensus 505 ~~~~~C~IC~~----~~~~~~~~PCgH~~~C~~Ca~~~--~~CP 542 (557)
.+-..|.||+. ....-+++-|||. .|..|+..+ ..||
T Consensus 9 ~~~l~c~ic~n~f~~~~~~Pvsl~cght-ic~~c~~~lyn~scp 51 (861)
T KOG3161|consen 9 VLLLLCDICLNLFVVQRLEPVSLQCGHT-ICGHCVQLLYNASCP 51 (861)
T ss_pred HHHhhchHHHHHHHHHhcCcccccccch-HHHHHHHhHhhccCC
Confidence 34457999954 4455667789999 799999987 7888
No 95
>KOG1734|consensus
Probab=26.34 E-value=27 Score=35.61 Aligned_cols=44 Identities=25% Similarity=0.698 Sum_probs=30.7
Q ss_pred hccccccccccc---c-------ceEEecCCccccchhhhcC------CCCCCCCcccccc
Q psy2747 506 EARLCKICMDKE---V-------GVVLLPCGHLVTCVLCASS------LPRCPVCRENIKA 550 (557)
Q Consensus 506 ~~~~C~IC~~~~---~-------~~~~~PCgH~~~C~~Ca~~------~~~CP~CR~~i~~ 550 (557)
+...|.||-.+- . ++.-+.|+|+ +=+.|... .++||.|...|+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHv-FHEfCIrGWcivGKkqtCPYCKekVdl 282 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHV-FHEFCIRGWCIVGKKQTCPYCKEKVDL 282 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccc-hHHHhhhhheeecCCCCCchHHHHhhH
Confidence 355788886432 2 3445789999 66777754 3899999998864
No 96
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=24.60 E-value=14 Score=31.65 Aligned_cols=37 Identities=30% Similarity=0.700 Sum_probs=29.5
Q ss_pred hccccccccccccceEEecCCccccchhhhcCCCCCCCCccc
Q psy2747 506 EARLCKICMDKEVGVVLLPCGHLVTCVLCASSLPRCPVCREN 547 (557)
Q Consensus 506 ~~~~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~~~CP~CR~~ 547 (557)
....|..|..+.+-.+. |. +|..||..+..|+-|..+
T Consensus 54 ~p~kC~~C~qktVk~AY----h~-iC~~Ca~~~~vCaKC~k~ 90 (92)
T PF10217_consen 54 QPKKCNKCQQKTVKHAY----HV-ICDPCAKELKVCAKCGKP 90 (92)
T ss_pred CCccccccccchHHHHH----HH-HHHHHHHhhccCcccCCC
Confidence 35679999877666553 44 799999999999999875
No 97
>KOG2660|consensus
Probab=22.94 E-value=19 Score=37.60 Aligned_cols=51 Identities=24% Similarity=0.487 Sum_probs=39.4
Q ss_pred HHHHHhccccccccccccceEE-ecCCccccchhhhcC----CCCCCCCccccccEE
Q psy2747 501 VRRLREARLCKICMDKEVGVVL-LPCGHLVTCVLCASS----LPRCPVCRENIKATV 552 (557)
Q Consensus 501 ~~~~~~~~~C~IC~~~~~~~~~-~PCgH~~~C~~Ca~~----~~~CP~CR~~i~~~i 552 (557)
+.++.....|.+|-.=-+++.. .-|-|- +|..|.-+ ...||.|...|-+..
T Consensus 9 ~~~~n~~itC~LC~GYliDATTI~eCLHT-FCkSCivk~l~~~~~CP~C~i~ih~t~ 64 (331)
T KOG2660|consen 9 LTELNPHITCRLCGGYLIDATTITECLHT-FCKSCIVKYLEESKYCPTCDIVIHKTH 64 (331)
T ss_pred hhhcccceehhhccceeecchhHHHHHHH-HHHHHHHHHHHHhccCCccceeccCcc
Confidence 3445566789999876666554 369999 89999975 389999999988764
No 98
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=22.48 E-value=28 Score=41.26 Aligned_cols=12 Identities=42% Similarity=1.129 Sum_probs=10.3
Q ss_pred CCCCCCcccccc
Q psy2747 539 PRCPVCRENIKA 550 (557)
Q Consensus 539 ~~CP~CR~~i~~ 550 (557)
.+||+||..|+-
T Consensus 1513 s~CPlCRseitf 1524 (1525)
T COG5219 1513 SNCPLCRSEITF 1524 (1525)
T ss_pred CCCCcccccccc
Confidence 699999998864
No 99
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=21.64 E-value=52 Score=24.44 Aligned_cols=28 Identities=21% Similarity=0.589 Sum_probs=22.7
Q ss_pred ccccccccccceEEecCCccccchhhhcCC
Q psy2747 509 LCKICMDKEVGVVLLPCGHLVTCVLCASSL 538 (557)
Q Consensus 509 ~C~IC~~~~~~~~~~PCgH~~~C~~Ca~~~ 538 (557)
.|.||-....+.+.+ .|++ .|.+|...|
T Consensus 1 ~CiiC~~~~~~GI~I-~~~f-IC~~CE~~i 28 (46)
T PF10764_consen 1 KCIICGKEKEEGIHI-YGKF-ICSDCEKEI 28 (46)
T ss_pred CeEeCCCcCCCCEEE-ECeE-ehHHHHHHh
Confidence 489999888876666 7888 799999876
No 100
>KOG2817|consensus
Probab=20.52 E-value=37 Score=36.45 Aligned_cols=47 Identities=23% Similarity=0.532 Sum_probs=28.4
Q ss_pred ccccccc----ccccceEEecCCccccchhhhcCC-------CCCCCCcccc--ccEEEEee
Q psy2747 508 RLCKICM----DKEVGVVLLPCGHLVTCVLCASSL-------PRCPVCRENI--KATVRTFL 556 (557)
Q Consensus 508 ~~C~IC~----~~~~~~~~~PCgH~~~C~~Ca~~~-------~~CP~CR~~i--~~~i~i~~ 556 (557)
..|.|=. +.+.-+- ++|||+ .|.+=..+| -+||.|.... ....+||+
T Consensus 335 F~CPVlKeqtsdeNPPm~-L~CGHV-ISkdAlnrLS~ng~~sfKCPYCP~e~~~~~~kql~F 394 (394)
T KOG2817|consen 335 FICPVLKEQTSDENPPMM-LICGHV-ISKDALNRLSKNGSQSFKCPYCPVEQLASDTKQLYF 394 (394)
T ss_pred eecccchhhccCCCCCee-eeccce-ecHHHHHHHhhCCCeeeeCCCCCcccCHHhcccccC
Confidence 4566543 2333333 469999 677766655 3899998743 33455553
Done!