Query psy3967
Match_columns 324
No_of_seqs 259 out of 1221
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 21:53:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3967.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3967hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1101|consensus 99.9 7.1E-28 1.5E-32 206.9 6.2 94 165-258 5-100 (147)
2 smart00238 BIR Baculoviral inh 99.9 3.2E-23 6.9E-28 157.1 6.5 70 174-243 1-70 (71)
3 KOG1101|consensus 99.9 5.4E-23 1.2E-27 176.7 5.2 81 30-117 6-89 (147)
4 cd00022 BIR Baculoviral inhibi 99.9 1.1E-22 2.5E-27 153.2 5.5 68 176-243 1-68 (69)
5 PF00653 BIR: Inhibitor of Apo 99.9 7.5E-23 1.6E-27 155.1 4.1 66 178-243 1-70 (70)
6 smart00238 BIR Baculoviral inh 99.9 1.9E-22 4.2E-27 152.8 6.0 69 38-113 1-70 (71)
7 cd00022 BIR Baculoviral inhibi 99.9 3.8E-22 8.2E-27 150.3 5.3 67 40-113 1-68 (69)
8 PF00653 BIR: Inhibitor of Apo 99.8 8.1E-22 1.7E-26 149.4 4.0 66 42-113 1-70 (70)
9 PF13920 zf-C3HC4_3: Zinc fing 97.8 1E-05 2.2E-10 57.0 2.1 26 298-323 2-27 (50)
10 KOG4275|consensus 97.7 1.3E-05 2.9E-10 75.4 1.0 26 298-323 300-325 (350)
11 KOG4265|consensus 97.6 2E-05 4.3E-10 76.2 1.3 28 297-324 289-316 (349)
12 KOG1571|consensus 97.2 0.00018 3.8E-09 69.8 2.8 29 295-323 302-330 (355)
13 KOG1100|consensus 96.4 0.0018 3.9E-08 59.2 2.1 26 299-324 159-184 (207)
14 KOG4172|consensus 96.1 0.00047 1E-08 49.6 -2.4 25 299-323 8-32 (62)
15 PF07967 zf-C3HC: C3HC zinc fi 96.1 0.0077 1.7E-07 51.0 4.2 48 36-90 4-54 (133)
16 PF07967 zf-C3HC: C3HC zinc fi 95.8 0.0088 1.9E-07 50.6 3.3 47 173-220 5-54 (133)
17 PF13923 zf-C3HC4_2: Zinc fing 94.8 0.02 4.3E-07 38.0 1.9 21 301-321 1-22 (39)
18 smart00184 RING Ring finger. E 93.8 0.031 6.7E-07 35.3 1.2 20 301-320 1-20 (39)
19 PF13445 zf-RING_UBOX: RING-ty 92.8 0.072 1.6E-06 36.6 1.8 20 301-321 1-24 (43)
20 PF00097 zf-C3HC4: Zinc finger 90.8 0.16 3.4E-06 33.6 1.7 21 301-321 1-22 (41)
21 KOG4692|consensus 88.8 0.14 3.1E-06 50.0 0.3 26 296-321 420-445 (489)
22 PF15227 zf-C3HC4_4: zinc fing 88.4 0.37 8E-06 32.7 2.1 21 301-321 1-21 (42)
23 KOG1785|consensus 86.1 0.18 3.9E-06 50.0 -0.7 24 298-321 369-392 (563)
24 PF13639 zf-RING_2: Ring finge 84.7 0.61 1.3E-05 31.4 1.6 22 300-321 2-26 (44)
25 PF14447 Prok-RING_4: Prokaryo 84.2 0.53 1.2E-05 34.0 1.2 25 297-321 6-30 (55)
26 PF14634 zf-RING_5: zinc-RING 81.9 0.59 1.3E-05 31.7 0.6 22 300-321 1-25 (44)
27 cd00162 RING RING-finger (Real 81.2 0.76 1.6E-05 29.8 1.0 21 300-320 1-22 (45)
28 KOG0823|consensus 80.2 0.82 1.8E-05 42.3 1.1 24 298-321 47-70 (230)
29 COG5574 PEX10 RING-finger-cont 77.4 0.79 1.7E-05 43.2 0.2 25 298-322 215-239 (271)
30 KOG0317|consensus 74.9 0.84 1.8E-05 43.5 -0.3 24 298-321 239-262 (293)
31 KOG4765|consensus 74.6 1.7 3.8E-05 42.9 1.7 53 32-91 47-102 (419)
32 PF11682 DUF3279: Protein of u 71.0 3.5 7.5E-05 35.0 2.5 60 190-255 15-83 (128)
33 smart00504 Ubox Modified RING 70.6 2.8 6.1E-05 29.9 1.6 23 299-321 2-24 (63)
34 KOG4765|consensus 67.3 3.7 8.1E-05 40.7 2.2 52 168-220 47-101 (419)
35 KOG1814|consensus 66.9 1.8 3.9E-05 43.3 -0.1 24 298-321 184-210 (445)
36 PHA02929 N1R/p28-like protein; 65.7 3.2 7E-05 38.8 1.4 25 297-321 173-205 (238)
37 PF08600 Rsm1: Rsm1-like; Int 64.3 3.7 7.9E-05 32.6 1.3 34 78-114 18-63 (91)
38 PLN00032 DNA-directed RNA poly 59.5 4.5 9.6E-05 30.8 0.9 11 210-220 5-15 (71)
39 KOG3497|consensus 58.6 4 8.6E-05 30.2 0.5 15 209-223 4-19 (69)
40 COG5243 HRD1 HRD ubiquitin lig 57.6 4.7 0.0001 40.0 0.9 25 296-320 285-322 (491)
41 PRK04016 DNA-directed RNA poly 55.5 6 0.00013 29.4 1.0 12 209-220 4-15 (62)
42 KOG2164|consensus 54.5 5.6 0.00012 40.9 0.9 26 298-323 186-211 (513)
43 COG5236 Uncharacterized conser 52.2 7.1 0.00015 38.4 1.2 27 295-321 58-84 (493)
44 PF01194 RNA_pol_N: RNA polyme 48.7 5.7 0.00012 29.3 -0.0 11 210-220 5-15 (60)
45 COG1644 RPB10 DNA-directed RNA 48.3 12 0.00025 27.8 1.5 12 209-220 4-15 (63)
46 KOG4628|consensus 46.9 12 0.00026 36.9 1.9 22 299-320 230-254 (348)
47 PHA02926 zinc finger-like prot 46.4 7.1 0.00015 36.2 0.2 26 296-321 168-202 (242)
48 PF12678 zf-rbx1: RING-H2 zinc 44.2 19 0.0004 27.2 2.2 20 301-320 22-54 (73)
49 KOG0978|consensus 41.6 3.9 8.5E-05 43.7 -2.5 31 291-321 636-666 (698)
50 PF10367 Vps39_2: Vacuolar sor 41.3 21 0.00045 28.0 2.2 27 295-321 75-103 (109)
51 smart00744 RINGv The RING-vari 40.7 17 0.00038 25.3 1.4 18 300-317 1-20 (49)
52 COG5540 RING-finger-containing 37.3 18 0.00039 35.1 1.4 26 295-320 320-348 (374)
53 PF04564 U-box: U-box domain; 31.9 41 0.00088 25.2 2.3 24 297-320 3-26 (73)
54 PF04710 Pellino: Pellino; In 28.7 19 0.00041 36.1 0.0 13 309-321 358-370 (416)
55 KOG0320|consensus 23.6 24 0.00052 31.6 -0.3 24 298-321 131-156 (187)
56 COG4416 Com Mu-like prophage p 20.4 86 0.0019 22.7 2.0 37 58-103 12-48 (60)
57 KOG0802|consensus 20.2 40 0.00088 35.1 0.5 24 297-320 290-318 (543)
No 1
>KOG1101|consensus
Probab=99.94 E-value=7.1e-28 Score=206.92 Aligned_cols=94 Identities=48% Similarity=0.989 Sum_probs=88.6
Q ss_pred CCCCCCCCCCHHHHHhccccCCCCC--CCChHHHHHcCCcccCCCCceEEeeeCCcccCCCCCCChHHHHHhhcCCCchh
Q psy3967 165 SPPAFPNYATYESRLRSFDSWPISL--RLKPVTLTEAGFFYTGKADQTLCFRCGGGLKHWEETDDPWTEHARWFSSCPYV 242 (324)
Q Consensus 165 ~~p~~~~y~~~~~Rl~SF~~Wp~~~--~~~~~~LA~AGFyytg~~D~v~Cf~Cg~~l~~W~~~DdP~~eH~~~~p~C~f~ 242 (324)
..|.++.|..+++|++||.+||+.. .+.|+.||+|||||+|..|.++||+|+++|.+|+++||||+||++|+|.|.|+
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 4567888999999999999999986 68999999999999999999999999999999999999999999999999999
Q ss_pred hhccchhHHHhhhccc
Q psy3967 243 KLVKGQEFINQVIGHK 258 (324)
Q Consensus 243 ~~~kg~~~i~~v~~~~ 258 (324)
+..||++|+..|+...
T Consensus 85 ~~~k~~e~~~~v~~~~ 100 (147)
T KOG1101|consen 85 KLKKGREFLGTVQSTA 100 (147)
T ss_pred ecccchhhhhHHHHhH
Confidence 9999999999998654
No 2
>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=99.88 E-value=3.2e-23 Score=157.07 Aligned_cols=70 Identities=50% Similarity=1.208 Sum_probs=65.4
Q ss_pred CHHHHHhccccCCCCCCCChHHHHHcCCcccCCCCceEEeeeCCcccCCCCCCChHHHHHhhcCCCchhh
Q psy3967 174 TYESRLRSFDSWPISLRLKPVTLTEAGFFYTGKADQTLCFRCGGGLKHWEETDDPWTEHARWFSSCPYVK 243 (324)
Q Consensus 174 ~~~~Rl~SF~~Wp~~~~~~~~~LA~AGFyytg~~D~v~Cf~Cg~~l~~W~~~DdP~~eH~~~~p~C~f~~ 243 (324)
++++|++||.+||+...+.++.||+|||||+|.+|.|+|++|++.|.+|+++|+||++|++++|+|.|++
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 3689999999999744578999999999999999999999999999999999999999999999999985
No 3
>KOG1101|consensus
Probab=99.87 E-value=5.4e-23 Score=176.75 Aligned_cols=81 Identities=47% Similarity=0.929 Sum_probs=74.9
Q ss_pred cccccCCcCHHHHHhccCCCCCCCC---cCHHHHHHcCceecCCCCCCCCCCeEeecccCceeccccCCCChhhhhcccC
Q psy3967 30 CSRKQNMTLECDRLDSFKNSWPLTY---LSAKQMAAAGFYFLGKKENGRFSDDVKCIFCGIELGKWVQGDDPLKDHEKWS 106 (324)
Q Consensus 30 ~~~~~~~~~e~~RL~SF~~~Wp~~~---~~~~~LA~aGFyy~g~~~~~~~~D~V~C~~C~~~l~~w~~~Ddp~~eH~~~s 106 (324)
+.....|..+++||+||.+ ||++. +.|+.||+|||||+|. +|.|+||+|++.|.+|+++||||.||.+|+
T Consensus 6 ~~~~~~~~~~~aRl~TF~~-Wp~~~~~~c~p~~lA~AGFy~~g~------~D~~~Cf~C~~~L~~We~~DDPW~EH~k~~ 78 (147)
T KOG1101|consen 6 DPQNPKMAREEARLKTFKN-WPYSDMDKCTPEQLAEAGFYYTGK------QDCVKCFFCSGGLDDWEPGDDPWEEHAKWS 78 (147)
T ss_pred cccchhHHHHHHHHhhhhc-CCCCCCCCcCHHHHHhCCceeeCC------CCceECcccCcccccCCCCCCcHHHHHhhC
Confidence 3456679999999999999 99985 8999999999999999 899999999999999999999999999999
Q ss_pred CCCcccccccc
Q psy3967 107 PNCWFLRRLKK 117 (324)
Q Consensus 107 P~C~f~~~~~~ 117 (324)
|.|.|++..+.
T Consensus 79 p~C~F~~~~k~ 89 (147)
T KOG1101|consen 79 PECEFLKLKKG 89 (147)
T ss_pred CCCceeecccc
Confidence 99999987643
No 4
>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=99.87 E-value=1.1e-22 Score=153.18 Aligned_cols=68 Identities=56% Similarity=1.263 Sum_probs=64.3
Q ss_pred HHHHhccccCCCCCCCChHHHHHcCCcccCCCCceEEeeeCCcccCCCCCCChHHHHHhhcCCCchhh
Q psy3967 176 ESRLRSFDSWPISLRLKPVTLTEAGFFYTGKADQTLCFRCGGGLKHWEETDDPWTEHARWFSSCPYVK 243 (324)
Q Consensus 176 ~~Rl~SF~~Wp~~~~~~~~~LA~AGFyytg~~D~v~Cf~Cg~~l~~W~~~DdP~~eH~~~~p~C~f~~ 243 (324)
++|++||.+||++....++.||+|||||+|.+|.++|++|++.|.+|+++|+||++|.+++|+|+|++
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 36999999999985578999999999999999999999999999999999999999999999999986
No 5
>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=99.87 E-value=7.5e-23 Score=155.05 Aligned_cols=66 Identities=52% Similarity=1.115 Sum_probs=58.3
Q ss_pred HHhccc-cCCCCC---CCChHHHHHcCCcccCCCCceEEeeeCCcccCCCCCCChHHHHHhhcCCCchhh
Q psy3967 178 RLRSFD-SWPISL---RLKPVTLTEAGFFYTGKADQTLCFRCGGGLKHWEETDDPWTEHARWFSSCPYVK 243 (324)
Q Consensus 178 Rl~SF~-~Wp~~~---~~~~~~LA~AGFyytg~~D~v~Cf~Cg~~l~~W~~~DdP~~eH~~~~p~C~f~~ 243 (324)
|++||. +||+.. .+.+++||+|||||+|.+|+|+|++|++.|.+|+++||||++|.+++|+|+|++
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 899995 599753 467899999999999999999999999999999999999999999999999984
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=99.86 E-value=1.9e-22 Score=152.76 Aligned_cols=69 Identities=55% Similarity=1.172 Sum_probs=65.2
Q ss_pred CHHHHHhccCCCCCC-CCcCHHHHHHcCceecCCCCCCCCCCeEeecccCceeccccCCCChhhhhcccCCCCcccc
Q psy3967 38 LECDRLDSFKNSWPL-TYLSAKQMAAAGFYFLGKKENGRFSDDVKCIFCGIELGKWVQGDDPLKDHEKWSPNCWFLR 113 (324)
Q Consensus 38 ~e~~RL~SF~~~Wp~-~~~~~~~LA~aGFyy~g~~~~~~~~D~V~C~~C~~~l~~w~~~Ddp~~eH~~~sP~C~f~~ 113 (324)
++++||+||.+ ||+ ....++.||++||||+|. +|.|+|++|+++|.+|+++|+|+++|++++|.|+|++
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 SEEARLKTFQN-WPYNSKLTPEQLAEAGFYYTGV------GDEVKCFFCGGELDNWEPGDDPWEEHKKWSPNCPFVR 70 (71)
T ss_pred CHHHHHHHHHc-CCCCccCCHHHHHHcCCeECCC------CCEEEeCCCCCCcCCCCCCCCHHHHHhHhCcCCcCcc
Confidence 47899999998 996 567999999999999998 8999999999999999999999999999999999986
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=99.86 E-value=3.8e-22 Score=150.32 Aligned_cols=67 Identities=51% Similarity=1.220 Sum_probs=64.1
Q ss_pred HHHHhccCCCCCCC-CcCHHHHHHcCceecCCCCCCCCCCeEeecccCceeccccCCCChhhhhcccCCCCcccc
Q psy3967 40 CDRLDSFKNSWPLT-YLSAKQMAAAGFYFLGKKENGRFSDDVKCIFCGIELGKWVQGDDPLKDHEKWSPNCWFLR 113 (324)
Q Consensus 40 ~~RL~SF~~~Wp~~-~~~~~~LA~aGFyy~g~~~~~~~~D~V~C~~C~~~l~~w~~~Ddp~~eH~~~sP~C~f~~ 113 (324)
++||+||.+ ||++ ...+++||++||||+|. +|.|+|++|++++.+|+++|+|+++|++++|.|+|++
T Consensus 1 ~~R~~TF~~-w~~~~~~~~~~La~~Gfyy~~~------~d~v~C~~C~~~~~~w~~~d~p~~~H~~~~p~C~fv~ 68 (69)
T cd00022 1 EARLKTFKN-WPISLKVTPEKLAEAGFYYTGR------GDEVKCFFCGLELKNWEPGDDPWEEHKRWSPNCPFVL 68 (69)
T ss_pred ChHHHHHHc-CCCCccCCHHHHHHcCCeEcCC------CCEEEeCCCCCCccCCCCCCCHHHHHhHhCcCCcCcc
Confidence 479999998 9998 68999999999999999 8999999999999999999999999999999999985
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=99.84 E-value=8.1e-22 Score=149.40 Aligned_cols=66 Identities=45% Similarity=1.102 Sum_probs=57.5
Q ss_pred HHhccCCCCCCC----CcCHHHHHHcCceecCCCCCCCCCCeEeecccCceeccccCCCChhhhhcccCCCCcccc
Q psy3967 42 RLDSFKNSWPLT----YLSAKQMAAAGFYFLGKKENGRFSDDVKCIFCGIELGKWVQGDDPLKDHEKWSPNCWFLR 113 (324)
Q Consensus 42 RL~SF~~~Wp~~----~~~~~~LA~aGFyy~g~~~~~~~~D~V~C~~C~~~l~~w~~~Ddp~~eH~~~sP~C~f~~ 113 (324)
||+||...||+. .+++++||+|||||+|. +|+|+|++|+++|.+|+++|||+++|++++|+|+|++
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 RLKSFRSNWPHSNDHDPVSPEKLARAGFYYTGT------GDRVRCFYCGLELDNWEPNDDPWEEHKRHSPNCPFVK 70 (70)
T ss_dssp HHHGGTTGSSTTTTTSSSHHHHHHHTTEEEESS------TTEEEETTTTEEEES-STT--HHHHHHHHSTTBHHHH
T ss_pred ChhHHCCcccCccccCCCCHHHHHHCCCEEcCC------CCEEEEeccCCEEeCCCCCCCHHHHHHHHCcCCeecC
Confidence 999995339964 36899999999999999 9999999999999999999999999999999999973
No 9
>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=97.83 E-value=1e-05 Score=57.01 Aligned_cols=26 Identities=42% Similarity=1.072 Sum_probs=22.6
Q ss_pred cccccccccccccEEEecCCceeecc
Q psy3967 298 GRLCKICYQREMGVVFLPCGHIVACV 323 (324)
Q Consensus 298 ~~~C~iC~~~~~~~~~~PCgH~~~C~ 323 (324)
+.+|.||+++.++++|+||||++.|.
T Consensus 2 ~~~C~iC~~~~~~~~~~pCgH~~~C~ 27 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLPCGHLCFCE 27 (50)
T ss_dssp HSB-TTTSSSBSSEEEETTCEEEEEH
T ss_pred cCCCccCCccCCceEEeCCCChHHHH
Confidence 46899999999999999999998774
No 10
>KOG4275|consensus
Probab=97.67 E-value=1.3e-05 Score=75.41 Aligned_cols=26 Identities=50% Similarity=1.131 Sum_probs=24.9
Q ss_pred cccccccccccccEEEecCCceeecc
Q psy3967 298 GRLCKICYQREMGVVFLPCGHIVACV 323 (324)
Q Consensus 298 ~~~C~iC~~~~~~~~~~PCgH~~~C~ 323 (324)
..+|+|||+.++|.|||+|||.|+|.
T Consensus 300 ~~LC~ICmDaP~DCvfLeCGHmVtCt 325 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLECGHMVTCT 325 (350)
T ss_pred HHHHHHHhcCCcceEEeecCcEEeeh
Confidence 68999999999999999999999996
No 11
>KOG4265|consensus
Probab=97.61 E-value=2e-05 Score=76.20 Aligned_cols=28 Identities=36% Similarity=0.841 Sum_probs=25.7
Q ss_pred ccccccccccccccEEEecCCceeeccC
Q psy3967 297 DGRLCKICYQREMGVVFLPCGHIVACVI 324 (324)
Q Consensus 297 ~~~~C~iC~~~~~~~~~~PCgH~~~C~~ 324 (324)
..++|+||+...||+++|||+|+|.|.+
T Consensus 289 ~gkeCVIClse~rdt~vLPCRHLCLCs~ 316 (349)
T KOG4265|consen 289 SGKECVICLSESRDTVVLPCRHLCLCSG 316 (349)
T ss_pred CCCeeEEEecCCcceEEecchhhehhHh
Confidence 4688999999999999999999999963
No 12
>KOG1571|consensus
Probab=97.25 E-value=0.00018 Score=69.83 Aligned_cols=29 Identities=34% Similarity=0.961 Sum_probs=25.8
Q ss_pred CCccccccccccccccEEEecCCceeecc
Q psy3967 295 NSDGRLCKICYQREMGVVFLPCGHIVACV 323 (324)
Q Consensus 295 ~~~~~~C~iC~~~~~~~~~~PCgH~~~C~ 323 (324)
......|+||.+++.+++|+||||+|||.
T Consensus 302 ~~~p~lcVVcl~e~~~~~fvpcGh~ccct 330 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKSAVFVPCGHVCCCT 330 (355)
T ss_pred cCCCCceEEecCCccceeeecCCcEEEch
Confidence 34467899999999999999999999985
No 13
>KOG1100|consensus
Probab=96.38 E-value=0.0018 Score=59.17 Aligned_cols=26 Identities=46% Similarity=1.018 Sum_probs=23.8
Q ss_pred ccccccccccccEEEecCCceeeccC
Q psy3967 299 RLCKICYQREMGVVFLPCGHIVACVI 324 (324)
Q Consensus 299 ~~C~iC~~~~~~~~~~PCgH~~~C~~ 324 (324)
..|+.|.++++.|+++||.|+|.|.+
T Consensus 159 ~~Cr~C~~~~~~VlllPCrHl~lC~~ 184 (207)
T KOG1100|consen 159 RSCRKCGEREATVLLLPCRHLCLCGI 184 (207)
T ss_pred ccceecCcCCceEEeecccceEeccc
Confidence 33999999999999999999999974
No 14
>KOG4172|consensus
Probab=96.12 E-value=0.00047 Score=49.56 Aligned_cols=25 Identities=36% Similarity=1.014 Sum_probs=23.3
Q ss_pred ccccccccccccEEEecCCceeecc
Q psy3967 299 RLCKICYQREMGVVFLPCGHIVACV 323 (324)
Q Consensus 299 ~~C~iC~~~~~~~~~~PCgH~~~C~ 323 (324)
.+|.||+++.+|.|+.-|||+|.|.
T Consensus 8 dECTICye~pvdsVlYtCGHMCmCy 32 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLYTCGHMCMCY 32 (62)
T ss_pred cceeeeccCcchHHHHHcchHHhHH
Confidence 5699999999999999999999884
No 15
>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=96.06 E-value=0.0077 Score=50.98 Aligned_cols=48 Identities=31% Similarity=0.529 Sum_probs=39.0
Q ss_pred CcCHHHHHhccCC-CCCCC--CcCHHHHHHcCceecCCCCCCCCCCeEeecccCceec
Q psy3967 36 MTLECDRLDSFKN-SWPLT--YLSAKQMAAAGFYFLGKKENGRFSDDVKCIFCGIELG 90 (324)
Q Consensus 36 ~~~e~~RL~SF~~-~Wp~~--~~~~~~LA~aGFyy~g~~~~~~~~D~V~C~~C~~~l~ 90 (324)
...+-.||+||.. +|... .+++-.+|+.|+...+ .|.++|..|+..+.
T Consensus 4 r~~~l~RL~Tf~~~~W~~kp~~lspl~cA~~GW~~~~-------~d~l~C~~C~~~l~ 54 (133)
T PF07967_consen 4 REDFLRRLETFKSLTWFPKPPWLSPLECARRGWICVS-------KDMLKCESCGARLC 54 (133)
T ss_pred HHHHHHHHHHcccccccCCCcccCHHHHHHcCCCcCC-------CCEEEeCCCCCEEE
Confidence 3456799999986 58432 3899999999998866 58999999999875
No 16
>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=95.78 E-value=0.0088 Score=50.64 Aligned_cols=47 Identities=30% Similarity=0.625 Sum_probs=38.6
Q ss_pred CCHHHHHhcccc--C-CCCCCCChHHHHHcCCcccCCCCceEEeeeCCccc
Q psy3967 173 ATYESRLRSFDS--W-PISLRLKPVTLTEAGFFYTGKADQTLCFRCGGGLK 220 (324)
Q Consensus 173 ~~~~~Rl~SF~~--W-p~~~~~~~~~LA~AGFyytg~~D~v~Cf~Cg~~l~ 220 (324)
..+-.||+||.. | +.+..+++-.+|+.||...+ .|+++|-.|+..+.
T Consensus 5 ~~~l~RL~Tf~~~~W~~kp~~lspl~cA~~GW~~~~-~d~l~C~~C~~~l~ 54 (133)
T PF07967_consen 5 EDFLRRLETFKSLTWFPKPPWLSPLECARRGWICVS-KDMLKCESCGARLC 54 (133)
T ss_pred HHHHHHHHHcccccccCCCcccCHHHHHHcCCCcCC-CCEEEeCCCCCEEE
Confidence 456889999985 8 33445789999999999987 68999999998664
No 17
>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=94.76 E-value=0.02 Score=38.00 Aligned_cols=21 Identities=38% Similarity=0.860 Sum_probs=17.9
Q ss_pred ccccccccccE-EEecCCceee
Q psy3967 301 CKICYQREMGV-VFLPCGHIVA 321 (324)
Q Consensus 301 C~iC~~~~~~~-~~~PCgH~~~ 321 (324)
|.||++..++. ++++|||+.+
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC 22 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFC 22 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEE
T ss_pred CCCCCCcccCcCEECCCCCchh
Confidence 78999999999 7999999964
No 18
>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=93.78 E-value=0.031 Score=35.34 Aligned_cols=20 Identities=45% Similarity=1.021 Sum_probs=18.5
Q ss_pred ccccccccccEEEecCCcee
Q psy3967 301 CKICYQREMGVVFLPCGHIV 320 (324)
Q Consensus 301 C~iC~~~~~~~~~~PCgH~~ 320 (324)
|.||++...+++++||||..
T Consensus 1 C~iC~~~~~~~~~~~C~H~~ 20 (39)
T smart00184 1 CPICLEELKDPVVLPCGHTF 20 (39)
T ss_pred CCcCccCCCCcEEecCCChH
Confidence 78999999999999999984
No 19
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=92.79 E-value=0.072 Score=36.56 Aligned_cols=20 Identities=40% Similarity=0.981 Sum_probs=10.5
Q ss_pred cccccccccc----EEEecCCceee
Q psy3967 301 CKICYQREMG----VVFLPCGHIVA 321 (324)
Q Consensus 301 C~iC~~~~~~----~~~~PCgH~~~ 321 (324)
|-||++ -.+ -+.|||||+.+
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c 24 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFC 24 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEE
T ss_pred CCcccc-ccCCCCCCEEEeCccHHH
Confidence 678887 455 58899999986
No 20
>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=90.79 E-value=0.16 Score=33.62 Aligned_cols=21 Identities=43% Similarity=0.944 Sum_probs=18.8
Q ss_pred ccccccccccEE-EecCCceee
Q psy3967 301 CKICYQREMGVV-FLPCGHIVA 321 (324)
Q Consensus 301 C~iC~~~~~~~~-~~PCgH~~~ 321 (324)
|.||++.-.+.+ ++||||..+
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC 22 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFC 22 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEE
T ss_pred CCcCCccccCCCEEecCCCcch
Confidence 789999999888 999999865
No 21
>KOG4692|consensus
Probab=88.77 E-value=0.14 Score=50.01 Aligned_cols=26 Identities=42% Similarity=0.981 Sum_probs=23.5
Q ss_pred CccccccccccccccEEEecCCceee
Q psy3967 296 SDGRLCKICYQREMGVVFLPCGHIVA 321 (324)
Q Consensus 296 ~~~~~C~iC~~~~~~~~~~PCgH~~~ 321 (324)
.++.+|-||+..+++.||-||||-.|
T Consensus 420 sEd~lCpICyA~pi~Avf~PC~H~SC 445 (489)
T KOG4692|consen 420 SEDNLCPICYAGPINAVFAPCSHRSC 445 (489)
T ss_pred cccccCcceecccchhhccCCCCchH
Confidence 35789999999999999999999876
No 22
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=88.40 E-value=0.37 Score=32.68 Aligned_cols=21 Identities=43% Similarity=0.844 Sum_probs=17.6
Q ss_pred ccccccccccEEEecCCceee
Q psy3967 301 CKICYQREMGVVFLPCGHIVA 321 (324)
Q Consensus 301 C~iC~~~~~~~~~~PCgH~~~ 321 (324)
|-||++--.+=|.|+|||..+
T Consensus 1 CpiC~~~~~~Pv~l~CGH~FC 21 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHSFC 21 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSEEE
T ss_pred CCccchhhCCccccCCcCHHH
Confidence 789999999999999999876
No 23
>KOG1785|consensus
Probab=86.09 E-value=0.18 Score=50.03 Aligned_cols=24 Identities=42% Similarity=0.934 Sum_probs=21.9
Q ss_pred cccccccccccccEEEecCCceee
Q psy3967 298 GRLCKICYQREMGVVFLPCGHIVA 321 (324)
Q Consensus 298 ~~~C~iC~~~~~~~~~~PCgH~~~ 321 (324)
-.+||||-+++.||-+-||||+.|
T Consensus 369 FeLCKICaendKdvkIEPCGHLlC 392 (563)
T KOG1785|consen 369 FELCKICAENDKDVKIEPCGHLLC 392 (563)
T ss_pred HHHHHHhhccCCCcccccccchHH
Confidence 357999999999999999999876
No 24
>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=84.66 E-value=0.61 Score=31.43 Aligned_cols=22 Identities=45% Similarity=0.913 Sum_probs=18.0
Q ss_pred ccccccccc---ccEEEecCCceee
Q psy3967 300 LCKICYQRE---MGVVFLPCGHIVA 321 (324)
Q Consensus 300 ~C~iC~~~~---~~~~~~PCgH~~~ 321 (324)
.|.||++.- ..++.+||||+..
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh 26 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFH 26 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEE
T ss_pred CCcCCChhhcCCCeEEEccCCCeeC
Confidence 599999754 6899999999753
No 25
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=84.15 E-value=0.53 Score=34.03 Aligned_cols=25 Identities=28% Similarity=0.638 Sum_probs=21.8
Q ss_pred ccccccccccccccEEEecCCceee
Q psy3967 297 DGRLCKICYQREMGVVFLPCGHIVA 321 (324)
Q Consensus 297 ~~~~C~iC~~~~~~~~~~PCgH~~~ 321 (324)
....|..|......=+++||||+++
T Consensus 6 ~~~~~~~~~~~~~~~~~~pCgH~I~ 30 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTVLPCGHLIC 30 (55)
T ss_pred cceeEEEccccccccccccccceee
Confidence 3567999999988899999999986
No 26
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=81.93 E-value=0.59 Score=31.73 Aligned_cols=22 Identities=32% Similarity=0.848 Sum_probs=17.3
Q ss_pred ccccccccc---ccEEEecCCceee
Q psy3967 300 LCKICYQRE---MGVVFLPCGHIVA 321 (324)
Q Consensus 300 ~C~iC~~~~---~~~~~~PCgH~~~ 321 (324)
.|.||++.- +..++++|||+.+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C 25 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFC 25 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHH
Confidence 377888655 6799999999864
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=81.18 E-value=0.76 Score=29.79 Aligned_cols=21 Identities=43% Similarity=0.980 Sum_probs=15.4
Q ss_pred cccccccccccEE-EecCCcee
Q psy3967 300 LCKICYQREMGVV-FLPCGHIV 320 (324)
Q Consensus 300 ~C~iC~~~~~~~~-~~PCgH~~ 320 (324)
.|.||++.-.+.+ +.||||..
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~ 22 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVF 22 (45)
T ss_pred CCCcCchhhhCceEecCCCChh
Confidence 4899998874444 44599975
No 28
>KOG0823|consensus
Probab=80.17 E-value=0.82 Score=42.31 Aligned_cols=24 Identities=29% Similarity=0.534 Sum_probs=22.0
Q ss_pred cccccccccccccEEEecCCceee
Q psy3967 298 GRLCKICYQREMGVVFLPCGHIVA 321 (324)
Q Consensus 298 ~~~C~iC~~~~~~~~~~PCgH~~~ 321 (324)
.-.|-||+|...|-|+-+|||+-|
T Consensus 47 ~FdCNICLd~akdPVvTlCGHLFC 70 (230)
T KOG0823|consen 47 FFDCNICLDLAKDPVVTLCGHLFC 70 (230)
T ss_pred ceeeeeeccccCCCEEeeccccee
Confidence 456999999999999999999977
No 29
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=77.40 E-value=0.79 Score=43.24 Aligned_cols=25 Identities=24% Similarity=0.583 Sum_probs=23.1
Q ss_pred cccccccccccccEEEecCCceeec
Q psy3967 298 GRLCKICYQREMGVVFLPCGHIVAC 322 (324)
Q Consensus 298 ~~~C~iC~~~~~~~~~~PCgH~~~C 322 (324)
...|.||++..-+-+..||||+-||
T Consensus 215 d~kC~lC~e~~~~ps~t~CgHlFC~ 239 (271)
T COG5574 215 DYKCFLCLEEPEVPSCTPCGHLFCL 239 (271)
T ss_pred ccceeeeecccCCcccccccchhhH
Confidence 5689999999999999999999875
No 30
>KOG0317|consensus
Probab=74.94 E-value=0.84 Score=43.54 Aligned_cols=24 Identities=33% Similarity=0.815 Sum_probs=22.2
Q ss_pred cccccccccccccEEEecCCceee
Q psy3967 298 GRLCKICYQREMGVVFLPCGHIVA 321 (324)
Q Consensus 298 ~~~C~iC~~~~~~~~~~PCgH~~~ 321 (324)
...|.+|++...+--..||||+-|
T Consensus 239 ~~kC~LCLe~~~~pSaTpCGHiFC 262 (293)
T KOG0317|consen 239 TRKCSLCLENRSNPSATPCGHIFC 262 (293)
T ss_pred CCceEEEecCCCCCCcCcCcchHH
Confidence 578999999999999999999876
No 31
>KOG4765|consensus
Probab=74.65 E-value=1.7 Score=42.93 Aligned_cols=53 Identities=26% Similarity=0.370 Sum_probs=40.5
Q ss_pred cccCCcCHHHHHhccCC-CCCCC--CcCHHHHHHcCceecCCCCCCCCCCeEeecccCceecc
Q psy3967 32 RKQNMTLECDRLDSFKN-SWPLT--YLSAKQMAAAGFYFLGKKENGRFSDDVKCIFCGIELGK 91 (324)
Q Consensus 32 ~~~~~~~e~~RL~SF~~-~Wp~~--~~~~~~LA~aGFyy~g~~~~~~~~D~V~C~~C~~~l~~ 91 (324)
+.-++-.+-.||+||.. +|-.. .+++..+|+.|+-... .|.++|-+|+..|.-
T Consensus 47 k~wdred~lrRl~Tfks~tWygkp~~iS~lnCA~~GWv~vd-------~D~lkCe~C~a~L~~ 102 (419)
T KOG4765|consen 47 KPWDREDLLRRLATFKSRTWYGKPFEISPLNCAKYGWVCVD-------CDMLKCESCGAFLCA 102 (419)
T ss_pred CcccHHHHHHHHHhccCchhccCCcccchHHHhhcCeeecc-------CCeeehhhhhhHHhc
Confidence 44446667799999986 35332 3899999999997554 699999999998853
No 32
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=71.04 E-value=3.5 Score=34.99 Aligned_cols=60 Identities=27% Similarity=0.478 Sum_probs=42.8
Q ss_pred CCChHHHHHcCCcccCCCCceEEeeeCCcccCC--CCCCChHHHHHhhc------CCCchhhhccch-hHHHhhh
Q psy3967 190 RLKPVTLTEAGFFYTGKADQTLCFRCGGGLKHW--EETDDPWTEHARWF------SSCPYVKLVKGQ-EFINQVI 255 (324)
Q Consensus 190 ~~~~~~LA~AGFyytg~~D~v~Cf~Cg~~l~~W--~~~DdP~~eH~~~~------p~C~f~~~~kg~-~~i~~v~ 255 (324)
.+++...+.+ ..|...|.+||..|.== ..+..||-||.... -.|.|+.-.++. ..|..+.
T Consensus 15 ~v~A~~a~~~------~~~~~tC~~Cg~~L~lh~~~~~~~pWFEH~~~~~~~~~l~~C~yl~pe~k~~~ri~~L~ 83 (128)
T PF11682_consen 15 FVGARTAASA------PYDHWTCHSCGCPLILHPGTDTEPPWFEHDQHSLAENGLMQCPYLDPEEKERRRIKRLR 83 (128)
T ss_pred EEehhhhhhC------CCCeEEEecCCceEEEecCCcCCCCccccCccccChhhcccCceECcccchHHHHHHHH
Confidence 3566777766 56899999999877533 45678999998875 359999866554 4554444
No 33
>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=70.56 E-value=2.8 Score=29.93 Aligned_cols=23 Identities=30% Similarity=0.473 Sum_probs=20.1
Q ss_pred ccccccccccccEEEecCCceee
Q psy3967 299 RLCKICYQREMGVVFLPCGHIVA 321 (324)
Q Consensus 299 ~~C~iC~~~~~~~~~~PCgH~~~ 321 (324)
..|.||++--.+-|.+||||+..
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v~~ 24 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQTYE 24 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCEEe
Confidence 46999999989999999999865
No 34
>KOG4765|consensus
Probab=67.34 E-value=3.7 Score=40.67 Aligned_cols=52 Identities=21% Similarity=0.400 Sum_probs=39.6
Q ss_pred CCCCCCCHHHHHhccc--cCC-CCCCCChHHHHHcCCcccCCCCceEEeeeCCccc
Q psy3967 168 AFPNYATYESRLRSFD--SWP-ISLRLKPVTLTEAGFFYTGKADQTLCFRCGGGLK 220 (324)
Q Consensus 168 ~~~~y~~~~~Rl~SF~--~Wp-~~~~~~~~~LA~AGFyytg~~D~v~Cf~Cg~~l~ 220 (324)
..-+...+-.|++||+ +|- .+..+++...|+.|+-.-. .|.++|-+||..|.
T Consensus 47 k~wdred~lrRl~Tfks~tWygkp~~iS~lnCA~~GWv~vd-~D~lkCe~C~a~L~ 101 (419)
T KOG4765|consen 47 KPWDREDLLRRLATFKSRTWYGKPFEISPLNCAKYGWVCVD-CDMLKCESCGAFLC 101 (419)
T ss_pred CcccHHHHHHHHHhccCchhccCCcccchHHHhhcCeeecc-CCeeehhhhhhHHh
Confidence 3445677899999998 462 2234689999999997664 58999999997663
No 35
>KOG1814|consensus
Probab=66.87 E-value=1.8 Score=43.28 Aligned_cols=24 Identities=38% Similarity=0.866 Sum_probs=19.9
Q ss_pred cccccccccccc---cEEEecCCceee
Q psy3967 298 GRLCKICYQREM---GVVFLPCGHIVA 321 (324)
Q Consensus 298 ~~~C~iC~~~~~---~~~~~PCgH~~~ 321 (324)
.-.|-|||+... .++|+||+|+-|
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC~Hv~C 210 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPCSHVFC 210 (445)
T ss_pred cccceeeehhhcCcceeeecccchHHH
Confidence 346999998875 599999999865
No 36
>PHA02929 N1R/p28-like protein; Provisional
Probab=65.72 E-value=3.2 Score=38.78 Aligned_cols=25 Identities=20% Similarity=0.663 Sum_probs=18.2
Q ss_pred cccccccccccccc--------EEEecCCceee
Q psy3967 297 DGRLCKICYQREMG--------VVFLPCGHIVA 321 (324)
Q Consensus 297 ~~~~C~iC~~~~~~--------~~~~PCgH~~~ 321 (324)
+...|.||++.-.+ .++.+|||.-+
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC 205 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFC 205 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCccc
Confidence 35689999996332 46778999755
No 37
>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=64.26 E-value=3.7 Score=32.57 Aligned_cols=34 Identities=29% Similarity=0.749 Sum_probs=27.4
Q ss_pred CeEeecccCceeccccCC------------CChhhhhcccCCCCccccc
Q psy3967 78 DDVKCIFCGIELGKWVQG------------DDPLKDHEKWSPNCWFLRR 114 (324)
Q Consensus 78 D~V~C~~C~~~l~~w~~~------------Ddp~~eH~~~sP~C~f~~~ 114 (324)
..+.|-+|..++.-|.-. =||+.+|+.+ ||++..
T Consensus 18 ~~~~C~~C~Rr~GLW~f~~~~ss~~~~~~~~d~~~eHr~~---CPwv~~ 63 (91)
T PF08600_consen 18 GLLSCSYCFRRLGLWMFKSKESSDSDPMSPFDPLEEHREY---CPWVNP 63 (91)
T ss_pred CeEEccccCcEeeeeecccCccCCCCcCCCCCCccccccc---CCccCC
Confidence 489999999999888642 3788899875 999875
No 38
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=59.55 E-value=4.5 Score=30.80 Aligned_cols=11 Identities=36% Similarity=0.954 Sum_probs=10.3
Q ss_pred eEEeeeCCccc
Q psy3967 210 TLCFRCGGGLK 220 (324)
Q Consensus 210 v~Cf~Cg~~l~ 220 (324)
|+||.||..+.
T Consensus 5 VRCFTCGkvig 15 (71)
T PLN00032 5 VRCFTCGKVIG 15 (71)
T ss_pred eeecCCCCCcH
Confidence 79999999997
No 39
>KOG3497|consensus
Probab=58.59 E-value=4 Score=30.17 Aligned_cols=15 Identities=40% Similarity=1.086 Sum_probs=11.8
Q ss_pred ceEEeeeCCcccC-CC
Q psy3967 209 QTLCFRCGGGLKH-WE 223 (324)
Q Consensus 209 ~v~Cf~Cg~~l~~-W~ 223 (324)
-++||.||.++.+ |+
T Consensus 4 PiRCFtCGKvig~KWe 19 (69)
T KOG3497|consen 4 PIRCFTCGKVIGDKWE 19 (69)
T ss_pred eeEeeeccccccccHH
Confidence 3799999999863 54
No 40
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=57.56 E-value=4.7 Score=40.00 Aligned_cols=25 Identities=40% Similarity=0.881 Sum_probs=17.4
Q ss_pred CccccccccccccccE-------------EEecCCcee
Q psy3967 296 SDGRLCKICYQREMGV-------------VFLPCGHIV 320 (324)
Q Consensus 296 ~~~~~C~iC~~~~~~~-------------~~~PCgH~~ 320 (324)
.+++.|.||||+-... ==|||||..
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHil 322 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHIL 322 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCccccccccee
Confidence 4578999999982111 248999974
No 41
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=55.49 E-value=6 Score=29.35 Aligned_cols=12 Identities=33% Similarity=0.888 Sum_probs=10.8
Q ss_pred ceEEeeeCCccc
Q psy3967 209 QTLCFRCGGGLK 220 (324)
Q Consensus 209 ~v~Cf~Cg~~l~ 220 (324)
-|+||.||..+.
T Consensus 4 PvRCFTCGkvi~ 15 (62)
T PRK04016 4 PVRCFTCGKVIA 15 (62)
T ss_pred CeEecCCCCChH
Confidence 489999999998
No 42
>KOG2164|consensus
Probab=54.46 E-value=5.6 Score=40.85 Aligned_cols=26 Identities=31% Similarity=0.512 Sum_probs=23.4
Q ss_pred cccccccccccccEEEecCCceeecc
Q psy3967 298 GRLCKICYQREMGVVFLPCGHIVACV 323 (324)
Q Consensus 298 ~~~C~iC~~~~~~~~~~PCgH~~~C~ 323 (324)
...|-||++.+.-.+..-|||+-||.
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHiFC~~ 211 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHIFCGP 211 (513)
T ss_pred CCcCCcccCCCCcccccccCceeeHH
Confidence 56799999999999999999999863
No 43
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=52.23 E-value=7.1 Score=38.42 Aligned_cols=27 Identities=26% Similarity=0.624 Sum_probs=23.5
Q ss_pred CCccccccccccccccEEEecCCceee
Q psy3967 295 NSDGRLCKICYQREMGVVFLPCGHIVA 321 (324)
Q Consensus 295 ~~~~~~C~iC~~~~~~~~~~PCgH~~~ 321 (324)
..+...|.||-+.---++++||+|-.|
T Consensus 58 DEen~~C~ICA~~~TYs~~~PC~H~~C 84 (493)
T COG5236 58 DEENMNCQICAGSTTYSARYPCGHQIC 84 (493)
T ss_pred ccccceeEEecCCceEEEeccCCchHH
Confidence 345788999999999999999999765
No 44
>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=48.73 E-value=5.7 Score=29.31 Aligned_cols=11 Identities=36% Similarity=0.954 Sum_probs=9.1
Q ss_pred eEEeeeCCccc
Q psy3967 210 TLCFRCGGGLK 220 (324)
Q Consensus 210 v~Cf~Cg~~l~ 220 (324)
|+||.||..+.
T Consensus 5 VRCFTCGkvi~ 15 (60)
T PF01194_consen 5 VRCFTCGKVIG 15 (60)
T ss_dssp SS-STTTSBTC
T ss_pred eecCCCCCChh
Confidence 68999999997
No 45
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=48.31 E-value=12 Score=27.81 Aligned_cols=12 Identities=33% Similarity=0.869 Sum_probs=10.5
Q ss_pred ceEEeeeCCccc
Q psy3967 209 QTLCFRCGGGLK 220 (324)
Q Consensus 209 ~v~Cf~Cg~~l~ 220 (324)
-|+||.||..+.
T Consensus 4 PiRCFsCGkvi~ 15 (63)
T COG1644 4 PVRCFSCGKVIG 15 (63)
T ss_pred ceEeecCCCCHH
Confidence 379999999997
No 46
>KOG4628|consensus
Probab=46.91 E-value=12 Score=36.90 Aligned_cols=22 Identities=32% Similarity=0.754 Sum_probs=17.2
Q ss_pred ccccccccc---cccEEEecCCcee
Q psy3967 299 RLCKICYQR---EMGVVFLPCGHIV 320 (324)
Q Consensus 299 ~~C~iC~~~---~~~~~~~PCgH~~ 320 (324)
-.|.||+|. .--+..|||+|.-
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~F 254 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKF 254 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCch
Confidence 389999975 4457889999963
No 47
>PHA02926 zinc finger-like protein; Provisional
Probab=46.43 E-value=7.1 Score=36.23 Aligned_cols=26 Identities=31% Similarity=0.607 Sum_probs=19.4
Q ss_pred Ccccccccccccc---------ccEEEecCCceee
Q psy3967 296 SDGRLCKICYQRE---------MGVVFLPCGHIVA 321 (324)
Q Consensus 296 ~~~~~C~iC~~~~---------~~~~~~PCgH~~~ 321 (324)
+.+.+|.|||+.- +--++.+|+|.-|
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFC 202 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFC 202 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHH
Confidence 3467899999863 2258889999854
No 48
>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=44.20 E-value=19 Score=27.18 Aligned_cols=20 Identities=45% Similarity=1.029 Sum_probs=14.7
Q ss_pred cccccccc-------------ccEEEecCCcee
Q psy3967 301 CKICYQRE-------------MGVVFLPCGHIV 320 (324)
Q Consensus 301 C~iC~~~~-------------~~~~~~PCgH~~ 320 (324)
|.||++.- ..++..+|||.-
T Consensus 22 C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~F 54 (73)
T PF12678_consen 22 CAICREPLEDPCPECQAPQDECPIVWGPCGHIF 54 (73)
T ss_dssp ETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEE
T ss_pred ccccChhhhChhhhhcCCccccceEecccCCCE
Confidence 88887654 667888999974
No 49
>KOG0978|consensus
Probab=41.61 E-value=3.9 Score=43.68 Aligned_cols=31 Identities=23% Similarity=0.493 Sum_probs=26.9
Q ss_pred CCCCCCccccccccccccccEEEecCCceee
Q psy3967 291 RPEPNSDGRLCKICYQREMGVVFLPCGHIVA 321 (324)
Q Consensus 291 ~~~~~~~~~~C~iC~~~~~~~~~~PCgH~~~ 321 (324)
+++.+.....|.+|.++..|+|+.-|||+-|
T Consensus 636 Elk~yK~~LkCs~Cn~R~Kd~vI~kC~H~FC 666 (698)
T KOG0978|consen 636 ELKEYKELLKCSVCNTRWKDAVITKCGHVFC 666 (698)
T ss_pred HHHHHHhceeCCCccCchhhHHHHhcchHHH
Confidence 3455667788999999999999999999976
No 50
>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=41.34 E-value=21 Score=27.98 Aligned_cols=27 Identities=30% Similarity=0.714 Sum_probs=20.0
Q ss_pred CCcccccccccccc--ccEEEecCCceee
Q psy3967 295 NSDGRLCKICYQRE--MGVVFLPCGHIVA 321 (324)
Q Consensus 295 ~~~~~~C~iC~~~~--~~~~~~PCgH~~~ 321 (324)
.++...|.+|...- ..+++.||||++-
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~p~~~v~H 103 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVFPCGHVVH 103 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEeCCCeEEe
Confidence 34567899998654 4577789999874
No 51
>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=40.73 E-value=17 Score=25.31 Aligned_cols=18 Identities=33% Similarity=0.874 Sum_probs=14.9
Q ss_pred ccccccc--ccccEEEecCC
Q psy3967 300 LCKICYQ--REMGVVFLPCG 317 (324)
Q Consensus 300 ~C~iC~~--~~~~~~~~PCg 317 (324)
.|.||++ .+.+.++.||.
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~ 20 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCR 20 (49)
T ss_pred CccCCCCCCCCCCeeEeccc
Confidence 4899996 67788899995
No 52
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.31 E-value=18 Score=35.14 Aligned_cols=26 Identities=31% Similarity=0.681 Sum_probs=19.5
Q ss_pred CCccccccccccc---cccEEEecCCcee
Q psy3967 295 NSDGRLCKICYQR---EMGVVFLPCGHIV 320 (324)
Q Consensus 295 ~~~~~~C~iC~~~---~~~~~~~PCgH~~ 320 (324)
....-.|.|||+. .-.++.+||.|.-
T Consensus 320 a~~GveCaICms~fiK~d~~~vlPC~H~F 348 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLRVLPCDHRF 348 (374)
T ss_pred cCCCceEEEEhhhhcccceEEEeccCcee
Confidence 3445789999974 3348999999974
No 53
>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=31.93 E-value=41 Score=25.16 Aligned_cols=24 Identities=38% Similarity=0.504 Sum_probs=19.6
Q ss_pred ccccccccccccccEEEecCCcee
Q psy3967 297 DGRLCKICYQREMGVVFLPCGHIV 320 (324)
Q Consensus 297 ~~~~C~iC~~~~~~~~~~PCgH~~ 320 (324)
+.-.|-|+.+-=+|=|++|+||..
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~ty 26 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHTY 26 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEEE
T ss_pred cccCCcCcCcHhhCceeCCcCCEE
Confidence 467899999999999999999874
No 54
>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=28.72 E-value=19 Score=36.12 Aligned_cols=13 Identities=38% Similarity=0.884 Sum_probs=0.0
Q ss_pred ccEEEecCCceee
Q psy3967 309 MGVVFLPCGHIVA 321 (324)
Q Consensus 309 ~~~~~~PCgH~~~ 321 (324)
-..+|.||||++.
T Consensus 358 pthaF~PCGHv~S 370 (416)
T PF04710_consen 358 PTHAFNPCGHVCS 370 (416)
T ss_dssp -------------
T ss_pred Cceeecccccccc
Confidence 4678999999984
No 55
>KOG0320|consensus
Probab=23.60 E-value=24 Score=31.64 Aligned_cols=24 Identities=29% Similarity=0.635 Sum_probs=19.1
Q ss_pred cccccccccccccEE-E-ecCCceee
Q psy3967 298 GRLCKICYQREMGVV-F-LPCGHIVA 321 (324)
Q Consensus 298 ~~~C~iC~~~~~~~~-~-~PCgH~~~ 321 (324)
.-.|-|||+.....+ + --|||+-|
T Consensus 131 ~~~CPiCl~~~sek~~vsTkCGHvFC 156 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVPVSTKCGHVFC 156 (187)
T ss_pred ccCCCceecchhhccccccccchhHH
Confidence 356999998877776 3 69999876
No 56
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=20.38 E-value=86 Score=22.73 Aligned_cols=37 Identities=19% Similarity=0.169 Sum_probs=23.2
Q ss_pred HHHHHcCceecCCCCCCCCCCeEeecccCceeccccCCCChhhhhc
Q psy3967 58 KQMAAAGFYFLGKKENGRFSDDVKCIFCGIELGKWVQGDDPLKDHE 103 (324)
Q Consensus 58 ~~LA~aGFyy~g~~~~~~~~D~V~C~~C~~~l~~w~~~Ddp~~eH~ 103 (324)
+-||+|||- +. -+++|.-|+..-.-..+..-|.+.|+
T Consensus 12 KlLa~a~~~--~y-------le~KCPrCK~vN~~~~~~e~~t~~~k 48 (60)
T COG4416 12 KLLAEAEGQ--AY-------LEKKCPRCKEVNEFYIKEEATTQIHK 48 (60)
T ss_pred HHHHhcccc--ee-------eeecCCccceeeeeecccccchhhhh
Confidence 567888773 21 25778888776555555556666665
No 57
>KOG0802|consensus
Probab=20.23 E-value=40 Score=35.08 Aligned_cols=24 Identities=42% Similarity=0.852 Sum_probs=21.0
Q ss_pred cccccccccccccc-----EEEecCCcee
Q psy3967 297 DGRLCKICYQREMG-----VVFLPCGHIV 320 (324)
Q Consensus 297 ~~~~C~iC~~~~~~-----~~~~PCgH~~ 320 (324)
....|.||.|.-.. .-.+||||+.
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hif 318 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIF 318 (543)
T ss_pred cCCeeeeechhhccccccccceeecccch
Confidence 36789999999888 7999999975
Done!