Query psy6385
Match_columns 137
No_of_seqs 133 out of 152
Neff 4.2
Searched_HMMs 46136
Date Sat Aug 17 01:06:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6385hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3046|consensus 100.0 7.5E-36 1.6E-40 230.0 9.1 89 1-89 53-141 (147)
2 PF09748 Med10: Transcription 100.0 2.7E-34 5.9E-39 215.8 8.9 84 1-84 38-128 (128)
3 KOG3046|consensus 99.7 1E-17 2.2E-22 129.6 5.5 53 82-134 91-143 (147)
4 PF09748 Med10: Transcription 99.0 6E-10 1.3E-14 83.9 4.6 46 82-127 83-128 (128)
5 PF05823 Gp-FAR-1: Nematode fa 82.8 5.9 0.00013 30.7 6.6 101 19-122 9-138 (154)
6 cd08812 CARD_RIG-I_like Caspas 81.5 4.8 0.0001 28.3 5.2 74 6-85 6-80 (88)
7 PF13949 ALIX_LYPXL_bnd: ALIX 79.8 18 0.00039 29.3 8.7 71 39-117 90-171 (296)
8 PF11074 DUF2779: Domain of un 72.3 8.1 0.00018 29.2 4.5 75 21-108 42-118 (130)
9 smart00503 SynN Syntaxin N-ter 65.6 42 0.00091 23.2 9.1 88 41-129 9-110 (117)
10 cd00179 SynN Syntaxin N-termin 64.3 53 0.0011 23.9 9.2 86 42-128 8-108 (151)
11 cd09237 V_ScBro1_like Protein- 62.8 86 0.0019 26.8 9.4 28 39-66 134-161 (356)
12 smart00787 Spc7 Spc7 kinetocho 59.1 1.2E+02 0.0026 26.2 9.8 20 23-43 74-106 (312)
13 cd08789 CARD_IPS-1_RIG-I Caspa 58.1 28 0.00061 24.4 4.7 64 19-90 18-81 (84)
14 PF05823 Gp-FAR-1: Nematode fa 55.3 17 0.00038 28.1 3.6 41 49-89 108-148 (154)
15 cd08915 V_Alix_like Protein-in 53.8 1E+02 0.0023 26.0 8.3 68 39-114 139-217 (342)
16 PF10186 Atg14: UV radiation r 52.9 1.2E+02 0.0025 24.2 9.7 23 98-120 138-160 (302)
17 PF06133 DUF964: Protein of un 52.6 76 0.0016 22.0 7.4 74 42-117 25-101 (108)
18 cd09236 V_AnPalA_UmRIM20_like 48.9 1.7E+02 0.0038 25.1 9.8 38 39-76 140-180 (353)
19 PF10552 ORF6C: ORF6C domain; 48.3 99 0.0021 22.4 6.5 83 41-129 2-92 (116)
20 COG4079 Uncharacterized protei 47.0 18 0.00039 31.3 2.7 80 36-115 128-209 (293)
21 PF04229 GrpB: GrpB protein; 45.5 67 0.0014 24.7 5.5 49 59-115 117-165 (167)
22 PF05430 Methyltransf_30: S-ad 44.7 14 0.00031 27.6 1.6 17 31-47 62-78 (124)
23 smart00684 DM15 Tandem repeat 43.6 40 0.00088 20.8 3.2 25 99-123 4-28 (39)
24 PRK05255 hypothetical protein; 43.3 1.7E+02 0.0037 23.4 8.1 65 12-77 41-134 (171)
25 COG3028 Uncharacterized protei 41.9 2E+02 0.0043 23.7 8.2 99 12-110 51-181 (187)
26 COG5223 Uncharacterized conser 36.3 59 0.0013 27.4 4.1 42 19-60 142-185 (240)
27 TIGR03200 dearomat_oah 6-oxocy 36.0 91 0.002 27.7 5.4 56 31-86 220-293 (360)
28 PRK09432 metF 5,10-methylenete 34.5 82 0.0018 26.6 4.8 32 2-34 214-245 (296)
29 PF03682 UPF0158: Uncharacteri 34.4 1.4E+02 0.003 23.3 5.7 26 58-88 100-125 (163)
30 TIGR02606 antidote_CC2985 puta 33.5 1.5E+02 0.0032 19.9 5.1 54 17-77 3-62 (69)
31 PF09712 PHA_synth_III_E: Poly 32.8 2.2E+02 0.0047 24.2 7.1 56 58-121 177-232 (293)
32 PRK13740 conjugal transfer pro 32.7 55 0.0012 23.0 2.9 39 36-80 20-58 (70)
33 PF08535 KorB: KorB domain; I 32.2 82 0.0018 21.7 3.8 32 18-49 27-58 (93)
34 PRK07502 cyclohexadienyl dehyd 31.7 1.6E+02 0.0036 24.1 6.0 56 31-86 231-286 (307)
35 KOG0484|consensus 31.3 38 0.00083 25.9 2.0 18 26-43 34-51 (125)
36 PF03997 VPS28: VPS28 protein; 31.3 2.4E+02 0.0052 22.8 6.8 34 21-54 10-45 (188)
37 PLN02751 glutamyl-tRNA(Gln) am 30.9 2.8E+02 0.0062 26.0 8.0 99 14-114 427-542 (544)
38 PF02436 PYC_OADA: Conserved c 30.4 1.2E+02 0.0025 24.6 4.8 73 16-88 70-161 (196)
39 PF03693 RHH_2: Uncharacterise 28.1 1.5E+02 0.0032 20.6 4.5 53 17-76 6-64 (80)
40 PRK10167 hypothetical protein; 27.8 1.3E+02 0.0029 23.8 4.7 70 57-126 50-124 (169)
41 TIGR02044 CueR Cu(I)-responsiv 27.3 2.5E+02 0.0053 20.4 6.3 55 17-71 55-110 (127)
42 KOG0293|consensus 27.1 1.9E+02 0.004 27.1 6.0 40 82-121 126-168 (519)
43 PF08349 DUF1722: Protein of u 27.0 1.5E+02 0.0032 21.5 4.5 69 58-126 11-83 (117)
44 PRK03333 coaE dephospho-CoA ki 26.9 1.4E+02 0.0031 26.0 5.1 49 59-115 334-382 (395)
45 PF10057 DUF2294: Uncharacteri 26.9 99 0.0021 22.5 3.6 39 83-124 49-87 (118)
46 cd09234 V_HD-PTP_like Protein- 26.4 4.1E+02 0.0088 22.6 8.9 67 39-113 137-214 (337)
47 PF02637 GatB_Yqey: GatB domai 26.3 2.7E+02 0.0059 20.6 7.8 104 6-111 26-146 (148)
48 PRK14703 glutaminyl-tRNA synth 26.1 3.6E+02 0.0078 26.4 8.0 97 15-113 657-770 (771)
49 PRK15364 pathogenicity island 25.9 41 0.00089 27.8 1.5 13 18-30 97-109 (196)
50 PRK08645 bifunctional homocyst 25.5 95 0.002 28.8 3.9 45 2-46 527-571 (612)
51 PRK07417 arogenate dehydrogena 25.3 2.7E+02 0.0057 22.6 6.1 39 31-69 220-258 (279)
52 PF13413 HTH_25: Helix-turn-he 24.9 1.9E+02 0.004 18.9 4.3 36 8-46 13-52 (62)
53 PF00531 Death: Death domain; 24.8 1.3E+02 0.0029 19.3 3.6 47 18-67 22-68 (83)
54 cd08327 CARD_RAIDD Caspase act 23.7 1.2E+02 0.0027 21.7 3.5 59 18-86 20-91 (94)
55 cd03407 Band_7_4 A subgroup of 23.4 3E+02 0.0066 22.3 6.2 67 15-81 136-213 (262)
56 PF06632 XRCC4: DNA double-str 23.1 5.2E+02 0.011 22.7 8.8 43 29-71 119-161 (342)
57 cd09235 V_Alix Middle V-domain 22.8 4.3E+02 0.0094 22.5 7.2 38 39-76 137-177 (339)
58 PF15272 BBP1_C: Spindle pole 22.7 2.3E+02 0.005 23.3 5.2 32 100-131 44-81 (196)
59 PF06183 DinI: DinI-like famil 22.2 81 0.0018 21.3 2.2 20 58-77 5-24 (65)
60 PF11472 DUF3206: Protein of u 22.0 1.9E+02 0.0042 22.2 4.3 43 68-111 78-120 (128)
61 KOG2256|consensus 21.8 4E+02 0.0087 25.9 7.3 47 30-79 486-538 (661)
62 PF03433 EspA: EspA-like secre 21.6 31 0.00067 28.3 0.0 38 18-60 97-140 (188)
63 COG5094 TAF9 Transcription ini 21.5 1.5E+02 0.0033 23.3 3.8 52 17-74 33-87 (145)
64 TIGR00677 fadh2_euk methylenet 21.2 1.8E+02 0.0038 24.4 4.4 32 2-34 199-230 (281)
65 cd01282 HTH_MerR-like_sg3 Heli 21.1 3.2E+02 0.0068 19.5 5.5 53 18-70 55-111 (112)
66 PF02262 Cbl_N: CBL proto-onco 21.1 66 0.0014 25.0 1.7 19 102-120 108-126 (130)
67 COG3679 Regulatory protein inv 20.9 3.8E+02 0.0082 20.3 8.0 73 43-117 29-104 (118)
68 PF09164 VitD-bind_III: Vitami 20.8 1.2E+02 0.0027 21.1 2.9 22 58-79 10-31 (68)
69 KOG0679|consensus 20.8 74 0.0016 29.1 2.2 37 83-120 336-372 (426)
70 KOG0957|consensus 20.8 4.2E+02 0.0091 25.5 7.1 68 32-113 420-489 (707)
71 PF14006 YqzL: YqzL-like prote 20.7 60 0.0013 21.1 1.2 21 95-120 9-29 (47)
72 PF04751 DUF615: Protein of un 20.7 2.3E+02 0.005 22.1 4.7 68 12-80 30-119 (157)
73 PF11315 Med30: Mediator compl 20.6 1.5E+02 0.0032 23.4 3.6 42 20-61 81-136 (150)
74 PF09836 DUF2063: Uncharacteri 20.5 2.7E+02 0.0059 19.0 4.6 40 61-100 39-83 (94)
75 PRK13713 conjugal transfer pro 20.1 1.6E+02 0.0035 22.6 3.6 47 29-76 51-116 (118)
No 1
>KOG3046|consensus
Probab=100.00 E-value=7.5e-36 Score=230.04 Aligned_cols=89 Identities=54% Similarity=0.969 Sum_probs=86.0
Q ss_pred CchhhhhHHhhhhhcCCCCChHHHHHHHhcCCCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHH
Q psy6385 1 MISGLQEIDKLKSQVQDIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAK 80 (137)
Q Consensus 1 lV~~Lq~ld~~k~~~~~i~IPlEVl~yID~GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~ 80 (137)
||.+|+.++++.+.++++.||+||++|||||||||+|||+|+|+|+++||+++||++||++||++|+++|+++|||+++.
T Consensus 53 Lv~~L~~l~~~s~k~n~i~IPleVl~yIddGrNPd~ytke~le~~~~kNq~vkGK~~~~K~fr~~l~eEl~q~fPe~~~~ 132 (147)
T KOG3046|consen 53 LVRGLQDLDKLSSKLNDIQIPLEVLEYIDDGRNPDLYTKEFLEKCLAKNQYVKGKIDAFKKFRKHLAEELSQEFPELVDP 132 (147)
T ss_pred HHHHhhhhHHHHHhhccccCcHHHHHHHhcCCCccHHHHHHHHHHHHhhhHHhhhHHHHHHHHHHHHHHHHHHChHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhh
Q psy6385 81 YRAIREKAL 89 (137)
Q Consensus 81 y~~ireraL 89 (137)
|+.||++..
T Consensus 133 yr~Ir~e~~ 141 (147)
T KOG3046|consen 133 YRSIRAEDA 141 (147)
T ss_pred HHHHHhccC
Confidence 999997654
No 2
>PF09748 Med10: Transcription factor subunit Med10 of Mediator complex; InterPro: IPR019145 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med10 is one of the protein subunits of the Mediator complex, tethered to Med14 (Rgr1) protein. Med10 specifically mediates basal-level HIS4 transcription via Gcn4. In addition, there is a putative requirement for Med10 in Bas2-mediated transcription []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=100.00 E-value=2.7e-34 Score=215.75 Aligned_cols=84 Identities=45% Similarity=0.836 Sum_probs=81.0
Q ss_pred CchhhhhHHhhhhh-------cCCCCChHHHHHHHhcCCCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhh
Q psy6385 1 MISGLQEIDKLKSQ-------VQDIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGA 73 (137)
Q Consensus 1 lV~~Lq~ld~~k~~-------~~~i~IPlEVl~yID~GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~ 73 (137)
||++|++|+++++. +++++||+|||+|||+|||||+|||||||+|+++||+++||++||++||++|+++|+++
T Consensus 38 lv~~L~~l~~~~~~~~~~~~~~~~~~IP~evl~yID~GrNPDiyTre~vE~~~~~Nq~~kGK~~a~~~fr~~L~~el~~~ 117 (128)
T PF09748_consen 38 LVTSLQELDKLAQQTNDPDSPLQDIQIPLEVLEYIDDGRNPDIYTREFVELVRRENQYVKGKMEAFKSFRDVLAEELASA 117 (128)
T ss_pred HHHHHHHHHHHhcccCCCCcccccCCCCHHHHHHHhCCCCchHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999998 77999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHH
Q psy6385 74 FPNELAKYRAI 84 (137)
Q Consensus 74 FPel~~~y~~i 84 (137)
|||+.+.|+.|
T Consensus 118 fPe~~~~~~~i 128 (128)
T PF09748_consen 118 FPELKEDVRRI 128 (128)
T ss_pred ChHHHHHHhhC
Confidence 99999999875
No 3
>KOG3046|consensus
Probab=99.71 E-value=1e-17 Score=129.62 Aligned_cols=53 Identities=47% Similarity=0.771 Sum_probs=48.1
Q ss_pred HHHHhhhhhhhhhccchHHHHHHHHHHHHHHHHhhChHHHHHHhHhhCCCCCC
Q psy6385 82 RAIREKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIRGGDETP 134 (137)
Q Consensus 82 ~~ireraLakN~~~~gk~~~~~~~r~~l~~el~~~fp~~~~~yr~ir~~~~~~ 134 (137)
+..-++|++|||.||||||+||+||+||++||+|+|||+|+.||.||+.++++
T Consensus 91 ke~le~~~~kNq~vkGK~~~~K~fr~~l~eEl~q~fPe~~~~yr~Ir~e~~~~ 143 (147)
T KOG3046|consen 91 KEFLEKCLAKNQYVKGKIDAFKKFRKHLAEELSQEFPELVDPYRSIRAEDAPE 143 (147)
T ss_pred HHHHHHHHHhhhHHhhhHHHHHHHHHHHHHHHHHHChHHHHHHHHHHhccCcc
Confidence 45668899999999999999999999999999999999999999999955443
No 4
>PF09748 Med10: Transcription factor subunit Med10 of Mediator complex; InterPro: IPR019145 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med10 is one of the protein subunits of the Mediator complex, tethered to Med14 (Rgr1) protein. Med10 specifically mediates basal-level HIS4 transcription via Gcn4. In addition, there is a putative requirement for Med10 in Bas2-mediated transcription []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=98.98 E-value=6e-10 Score=83.89 Aligned_cols=46 Identities=35% Similarity=0.555 Sum_probs=42.7
Q ss_pred HHHHhhhhhhhhhccchHHHHHHHHHHHHHHHHhhChHHHHHHhHh
Q psy6385 82 RAIREKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAI 127 (137)
Q Consensus 82 ~~ireraLakN~~~~gk~~~~~~~r~~l~~el~~~fp~~~~~yr~i 127 (137)
++.-+.+..+|+.+|||+++|++||.+|.+||+++||++++.|+.|
T Consensus 83 re~vE~~~~~Nq~~kGK~~a~~~fr~~L~~el~~~fPe~~~~~~~i 128 (128)
T PF09748_consen 83 REFVELVRRENQYVKGKMEAFKSFRDVLAEELASAFPELKEDVRRI 128 (128)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHChHHHHHHhhC
Confidence 3455788999999999999999999999999999999999999986
No 5
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=82.80 E-value=5.9 Score=30.69 Aligned_cols=101 Identities=18% Similarity=0.302 Sum_probs=50.3
Q ss_pred CChHHHHHHHhc------------CCCCchhH--HHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHH-------
Q psy6385 19 HVPLEVFDYIDQ------------GRNPQLYT--KDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNE------- 77 (137)
Q Consensus 19 ~IPlEVl~yID~------------GrNPDiYT--refvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel------- 77 (137)
-||.||++++++ .+|..-|+ -|++...-.++--+.+|++.+ ++.+.+.+..-=|+=
T Consensus 9 ~iP~ev~~~~~~Lt~eeK~~lkev~~~~~~~~~~de~i~~LK~ksP~L~~k~~~l---~~~~k~ki~~L~peak~Fv~~l 85 (154)
T PF05823_consen 9 LIPSEVVEFYKNLTPEEKAELKEVAKNYAKFKNEDEMIAALKEKSPSLYEKAEKL---RDKLKKKIDKLSPEAKAFVKEL 85 (154)
T ss_dssp T--HHHHHHHHH--TTTHHHHHHHHTT-------TTHHHHHHHH-HHHHHHHHHH---HHHHHHTTTT--HHHHHHHHHH
T ss_pred hCcHHHHHHHHcCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCHHHHHHHHHH---HHHHHHHHHcCCHHHHHHHHHH
Confidence 478888887654 34444444 457777778888888777644 555555554444442
Q ss_pred HHHHHHHHhhhhhh--------hhhccchHHHHHHHHHHHHHHHHhhChHHHH
Q psy6385 78 LAKYRAIREKALTK--------NEQVKGKIDAYRKFKAHMLVELSGAFPNELA 122 (137)
Q Consensus 78 ~~~y~~ireraLak--------N~~~~gk~~~~~~~r~~l~~el~~~fp~~~~ 122 (137)
.+.++.+....++. .+..++-++.|+.|-.-.=.+|..+||.-+.
T Consensus 86 i~~~~~l~~~~~~G~~~~~~~lk~~~k~~~~~ykaLs~~ak~dL~k~FP~i~~ 138 (154)
T PF05823_consen 86 IAKARSLYAQYSAGEKPDLEELKQLAKKVIDSYKALSPEAKDDLKKNFPIIAS 138 (154)
T ss_dssp HHHHHHHHHHHHHT----THHHHHHH----HHHHTS-HHHHHHHHHH-TT---
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHhhhHHHHHcCCHHHHHHHHHHCccchh
Confidence 23333333332221 1334566688888888888899999997654
No 6
>cd08812 CARD_RIG-I_like Caspase activation and recruitment domains found in RIG-I-like DEAD box helicases. Caspase activation and recruitment domains (CARDs) found in Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. These helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I and MDA5 have been shown to recognize different sets of viruses. MDA5 and RIG-I associate with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mec
Probab=81.49 E-value=4.8 Score=28.34 Aligned_cols=74 Identities=22% Similarity=0.351 Sum_probs=57.6
Q ss_pred hhHHhhhhhcCCCCChHHHHHHHhcCCCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHH-HHHhhchHHHHHHHHH
Q psy6385 6 QEIDKLKSQVQDIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLV-ELSGAFPNELAKYRAI 84 (137)
Q Consensus 6 q~ld~~k~~~~~i~IPlEVl~yID~GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~-el~~~FPel~~~y~~i 84 (137)
+-|.+....+...-.|.+|+.|+-. .+|.+.+|.++++ ...+|.+.|...|=+.|.+ .=...||...+..+..
T Consensus 6 ~lL~~~~~~l~~~l~p~~il~~l~~-----~L~~~~~e~I~a~-~~~~g~~~aa~~Ll~~L~~~r~~~wf~~Fl~AL~~~ 79 (88)
T cd08812 6 RLLERLQPLLKDTIIPRDILDHLPE-----CLTDEDKEQILAE-ERNKGNIAAAEELLDRLERCDKPGWFQAFLDALRRT 79 (88)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHH-----HcCHHHHHHHHHH-HhccChHHHHHHHHHHHHHhccCCcHHHHHHHHHHc
Confidence 4455556666566789999999976 9999999999986 4556999999999888887 5567788887776654
Q ss_pred H
Q psy6385 85 R 85 (137)
Q Consensus 85 r 85 (137)
-
T Consensus 80 g 80 (88)
T cd08812 80 G 80 (88)
T ss_pred C
Confidence 3
No 7
>PF13949 ALIX_LYPXL_bnd: ALIX V-shaped domain binding to HIV ; PDB: 2XS1_A 2XS8_A 2R03_A 2R02_A 2OEX_B 2OEV_A 2OJQ_A 2R05_A.
Probab=79.80 E-value=18 Score=29.30 Aligned_cols=71 Identities=20% Similarity=0.366 Sum_probs=44.0
Q ss_pred HHHHHHHHHHhHHHhhHHHHHHHHHHHHHH---HHHhhchHHH--------HHHHHHHhhhhhhhhhccchHHHHHHHHH
Q psy6385 39 KDCIEKALTKNEQVKGKIDAYRKFKAHMLV---ELSGAFPNEL--------AKYRAIREKALTKNEQVKGKIDAYRKFKA 107 (137)
Q Consensus 39 refvE~~~~~Nq~~kGK~~a~~~fR~~L~~---el~~~FPel~--------~~y~~ireraLakN~~~~gk~~~~~~~r~ 107 (137)
+..++.+...+..+..+++.+...=..|.. +|...+|... ..+..++.-. ++++.++.=|.
T Consensus 90 ~~~L~~A~~sD~~~~~~~~~~~~~l~~L~~~~~~L~~~lp~~~~~~~~~~~~~i~~L~~ll--------~~l~~l~~eR~ 161 (296)
T PF13949_consen 90 REYLEQASESDSQLRSKLESIEENLELLSGPIEELEASLPSSSPSDSPQVSEVIRQLRELL--------NKLEELKKERE 161 (296)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSHHHHHHHS--B---SSGSS-HHHHHHHHHH--------HHHHHHHHHHH
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHcCChhhHHhhCCCCCcccccchhHHHHHHHHHH--------HHHHHHHHHHH
Confidence 467788888999999999888777777754 6777788754 4444444322 55555555555
Q ss_pred HHHHHHHhhC
Q psy6385 108 HMLVELSGAF 117 (137)
Q Consensus 108 ~l~~el~~~f 117 (137)
.++.+|.+.+
T Consensus 162 ~~~~~lk~~~ 171 (296)
T PF13949_consen 162 ELLEQLKEKL 171 (296)
T ss_dssp HHHHHHHH--
T ss_pred HHHHHHHHHH
Confidence 5555555533
No 8
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=72.31 E-value=8.1 Score=29.21 Aligned_cols=75 Identities=31% Similarity=0.504 Sum_probs=52.7
Q ss_pred hHHHHHHHhc-CCCCchhHHHHHHHHHHHhHHHhhHHHHHHH-HHHHHHHHHHhhchHHHHHHHHHHhhhhhhhhhccch
Q psy6385 21 PLEVFDYIDQ-GRNPQLYTKDCIEKALTKNEQVKGKIDAYRK-FKAHMLVELSGAFPNELAKYRAIREKALTKNEQVKGK 98 (137)
Q Consensus 21 PlEVl~yID~-GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~-fR~~L~~el~~~FPel~~~y~~ireraLakN~~~~gk 98 (137)
+++-.+|+++ |..|-...-+-+-.+..++- |-+=+|.+ |-..-..+|++.||+..+....|.++.
T Consensus 42 ~~~h~efL~~~~~DPr~~~~~~L~~~i~~~~---g~ivvyN~sfE~~rL~ela~~~p~~~~~l~~I~~r~---------- 108 (130)
T PF11074_consen 42 ELEHVEFLADPGEDPRRELIEALIKAIGSIY---GSIVVYNKSFEKTRLKELAELFPDYAEKLNSIIERT---------- 108 (130)
T ss_pred chhhHHHhccCCCCchHHHHHHHHHHhhhhc---CeEEEechHHHHHHHHHHHHHhHHHHHHHHHHHHHH----------
Confidence 4566677754 67887655555555555443 66666655 778888899999999999999999776
Q ss_pred HHHHHHHHHH
Q psy6385 99 IDAYRKFKAH 108 (137)
Q Consensus 99 ~~~~~~~r~~ 108 (137)
+|.+.=||++
T Consensus 109 vDL~~~f~~~ 118 (130)
T PF11074_consen 109 VDLLDPFKNH 118 (130)
T ss_pred HHHHHHHhhC
Confidence 4555555543
No 9
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=65.56 E-value=42 Score=23.19 Aligned_cols=88 Identities=10% Similarity=0.201 Sum_probs=59.4
Q ss_pred HHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHhhhhhhhhhccchHHHHHH--------------HH
Q psy6385 41 CIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIREKALTKNEQVKGKIDAYRK--------------FK 106 (137)
Q Consensus 41 fvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~y~~ireraLakN~~~~gk~~~~~~--------------~r 106 (137)
-++.+...=+.+++.+..++.+...+..... ..|++......+...+-..-..++..+..+.+ .|
T Consensus 9 ~v~~I~~~I~~i~~~v~~l~~l~~~~l~~~~-~~~~~~~~l~~~~~~~~~~~~~i~~~lk~l~~~~~~~~~~~~~~~r~~ 87 (117)
T smart00503 9 KVEEIRANIQKISQNVAELQKLHEELLTPPD-ADKELREKLERLIDDIKRLAKEIRAKLKELEKENLENRASGSASDRTR 87 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccCc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhcccCCHhhhHH
Confidence 4566666667777788887777777765433 33667777777777777777777777665443 33
Q ss_pred HHHHHHHHhhChHHHHHHhHhhC
Q psy6385 107 AHMLVELSGAFPNELAKYRAIRG 129 (137)
Q Consensus 107 ~~l~~el~~~fp~~~~~yr~ir~ 129 (137)
+-...=|...|=+.|..|+.+..
T Consensus 88 ~~q~~~L~~~f~~~m~~fq~~Q~ 110 (117)
T smart00503 88 KAQTEKLRKKFKEVMNEFQRLQR 110 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555577788888888887753
No 10
>cd00179 SynN Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain
Probab=64.34 E-value=53 Score=23.89 Aligned_cols=86 Identities=13% Similarity=0.271 Sum_probs=60.9
Q ss_pred HHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHhhhhhhhhhccchHHHHHHH---------------H
Q psy6385 42 IEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIREKALTKNEQVKGKIDAYRKF---------------K 106 (137)
Q Consensus 42 vE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~y~~ireraLakN~~~~gk~~~~~~~---------------r 106 (137)
++.+...=+.++..+..++.+...|..... .-|++......+...+-..-..+++++..++.. |
T Consensus 8 v~~I~~~i~~i~~~v~~l~~l~~~~~t~~~-~~~~~~~~l~~~~~~~~~~~~~ik~~lk~l~~~~~~~~~~~~s~~~r~~ 86 (151)
T cd00179 8 VEEIRGNIDKISEDVEELQKLHSQLLTAPD-ADPELKQELESLVQEIKKLAKEIKGKLKELEESNEQNEALNGSSVDRIR 86 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHH
Confidence 344555666677777777777777766544 346778888888888888888888888776642 3
Q ss_pred HHHHHHHHhhChHHHHHHhHhh
Q psy6385 107 AHMLVELSGAFPNELAKYRAIR 128 (137)
Q Consensus 107 ~~l~~el~~~fp~~~~~yr~ir 128 (137)
+-...=|.+.|=+.|..|..+.
T Consensus 87 ~~q~~~L~~~f~~~m~~fq~~Q 108 (151)
T cd00179 87 KTQHSGLSKKFVEVMTEFNKAQ 108 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455557888888888887764
No 11
>cd09237 V_ScBro1_like Protein-interacting V-domain of Saccharomyces cerevisiae Bro1 and related domains. This family contains the V-shaped (V) domain of Saccharomyces cerevisiae Bro1, and related domains. It belongs to the V_Alix_like superfamily which also includes the V-domain of Saccharomyces cerevisiae Rim20 (also known as PalA), mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Bro1 interacts with the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in endosomal trafficking. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Bro1 also has an N-terminal Bro1-like domain, which binds Snf7, a component of the ESCRT-III complex, and a C-terminal proline-rich
Probab=62.77 E-value=86 Score=26.82 Aligned_cols=28 Identities=18% Similarity=0.223 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhHHHhhHHHHHHHHHHHH
Q psy6385 39 KDCIEKALTKNEQVKGKIDAYRKFKAHM 66 (137)
Q Consensus 39 refvE~~~~~Nq~~kGK~~a~~~fR~~L 66 (137)
|.-++.+...+..+.+|++..+.--..|
T Consensus 134 ~~~L~~A~~SD~~l~~~~~~~~~~l~lL 161 (356)
T cd09237 134 KKSLVEASASDEKLFSLVDPVKEDIALL 161 (356)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 3556666667777777777666555555
No 12
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=59.15 E-value=1.2e+02 Score=26.19 Aligned_cols=20 Identities=45% Similarity=0.913 Sum_probs=13.2
Q ss_pred HHHHHHhcCC-------------CCchhHHHHHH
Q psy6385 23 EVFDYIDQGR-------------NPQLYTKDCIE 43 (137)
Q Consensus 23 EVl~yID~Gr-------------NPDiYTrefvE 43 (137)
|+-.||.+|| ||-+| ||.+.
T Consensus 74 EL~~~I~egr~~~~~~E~et~~~nPpLF-~EY~~ 106 (312)
T smart00787 74 ELKKYISEGRDLFKEIEEETLINNPPLF-KEYFS 106 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcCcHHH-HHHHc
Confidence 5556777774 77777 66653
No 13
>cd08789 CARD_IPS-1_RIG-I Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases. Caspase activation and recruitment domains (CARDs) found in IPS-1 (Interferon beta promoter stimulator protein 1) and Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. RIG-I-like helicases and IPS-1 play important roles in the induction of interferons in response to viral infection. They are crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. RIG-I-like helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. MDA5 and RIG-I associate with IPS-1 through a CARD-CAR
Probab=58.05 E-value=28 Score=24.35 Aligned_cols=64 Identities=19% Similarity=0.137 Sum_probs=50.2
Q ss_pred CChHHHHHHHhcCCCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHhhhhh
Q psy6385 19 HVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIREKALT 90 (137)
Q Consensus 19 ~IPlEVl~yID~GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~y~~ireraLa 90 (137)
-+|.+|+.|+- ++|.+-.|.+++. ...+|.++|-..|=+.|. .=...||.+.+..++.-.+.||
T Consensus 18 l~~~~il~~L~------~Lt~~d~e~I~a~-~~~~G~~~aa~~Ll~~L~-r~~~Wf~~Fl~AL~~~~~~~LA 81 (84)
T cd08789 18 IDVEEVLPYLT------CLTAEDKERIQAA-ENNSGNIKAAWTLLDTLV-RRDNWLEPFLDALRECGLGHLA 81 (84)
T ss_pred CcHHHHHhhCC------cCCHHHHHHHHHH-HhcCChHHHHHHHHHHHh-ccCChHHHHHHHHHHcCCHHHH
Confidence 58999999986 9999999999887 456799999999888888 5667788777776665444443
No 14
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=55.30 E-value=17 Score=28.06 Aligned_cols=41 Identities=22% Similarity=0.275 Sum_probs=18.3
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHhhhh
Q psy6385 49 NEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIREKAL 89 (137)
Q Consensus 49 Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~y~~ireraL 89 (137)
.+..++-+..|+.+-..-.+.|..+||..+.-..+=+.+++
T Consensus 108 k~~~k~~~~~ykaLs~~ak~dL~k~FP~i~~~~~~~k~~~~ 148 (154)
T PF05823_consen 108 KQLAKKVIDSYKALSPEAKDDLKKNFPIIASFLQNDKFQAL 148 (154)
T ss_dssp HHHH----HHHHTS-HHHHHHHHHH-TT-------------
T ss_pred HHHHhhhHHHHHcCCHHHHHHHHHHCccchhhhhhhhhhhc
Confidence 45566777888888888889999999998766655544443
No 15
>cd08915 V_Alix_like Protein-interacting V-domain of mammalian Alix and related domains. This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains
Probab=53.81 E-value=1e+02 Score=25.95 Aligned_cols=68 Identities=15% Similarity=0.215 Sum_probs=40.7
Q ss_pred HHHHHHHHHHhHHHhhHHHHHHHHHHHHH---HHHHhhch--------HHHHHHHHHHhhhhhhhhhccchHHHHHHHHH
Q psy6385 39 KDCIEKALTKNEQVKGKIDAYRKFKAHML---VELSGAFP--------NELAKYRAIREKALTKNEQVKGKIDAYRKFKA 107 (137)
Q Consensus 39 refvE~~~~~Nq~~kGK~~a~~~fR~~L~---~el~~~FP--------el~~~y~~ireraLakN~~~~gk~~~~~~~r~ 107 (137)
|..++.+...+..+..|++..+..=..|. .+|...+| +....+..+| ..=.+++.+++=|.
T Consensus 139 ~~~L~~A~~sD~~l~~~~~~~~~~l~lL~~~~~~l~~~~Ps~~~~~~~~~~~~v~~Lr--------~~l~~l~~lk~eR~ 210 (342)
T cd08915 139 RGYLEQASNSDNEVLQCYESIDPNLVLLCGGYKELKAFIPSPYPALDPEVSEVVSSLR--------PLLNEVSELEKERE 210 (342)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHHHHHhcCChHHHHHhCCCccccCCchhhHHHHHHH--------HHHHHHHHHHHHHH
Confidence 45677777788888888877766555553 34666777 1222333333 23366666666666
Q ss_pred HHHHHHH
Q psy6385 108 HMLVELS 114 (137)
Q Consensus 108 ~l~~el~ 114 (137)
.++++|.
T Consensus 211 ~~~~~lk 217 (342)
T cd08915 211 RFISELE 217 (342)
T ss_pred HHHHHHH
Confidence 6666663
No 16
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=52.93 E-value=1.2e+02 Score=24.22 Aligned_cols=23 Identities=26% Similarity=0.381 Sum_probs=18.5
Q ss_pred hHHHHHHHHHHHHHHHHhhChHH
Q psy6385 98 KIDAYRKFKAHMLVELSGAFPNE 120 (137)
Q Consensus 98 k~~~~~~~r~~l~~el~~~fp~~ 120 (137)
-...+..-|+.++.||...||=+
T Consensus 138 l~~~l~~~r~~l~~~l~~ifpI~ 160 (302)
T PF10186_consen 138 LQSQLARRRRQLIQELSEIFPIE 160 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHhCce
Confidence 34556678899999999999963
No 17
>PF06133 DUF964: Protein of unknown function (DUF964); InterPro: IPR010368 This entry consists of several relatively short bacterial and archaeal hypothetical sequences. It also includes YlbF and YmcA proteins which are involved in the formation of biofilms []. YlbF regulates sporulation prior to stage II, positively controlling the competence regulator ComK at a post-transcriptional level. It may also modulate the translation, stability or activity of ComS and may work together with YmcA to regulate community development [].; PDB: 2IAZ_C 2OEE_A 2OEQ_D 2PIH_A.
Probab=52.56 E-value=76 Score=22.00 Aligned_cols=74 Identities=19% Similarity=0.390 Sum_probs=53.4
Q ss_pred HHHHHHHhHHHhhHHHHHHHHHHHHHHH-HHhhch--HHHHHHHHHHhhhhhhhhhccchHHHHHHHHHHHHHHHHhhC
Q psy6385 42 IEKALTKNEQVKGKIDAYRKFKAHMLVE-LSGAFP--NELAKYRAIREKALTKNEQVKGKIDAYRKFKAHMLVELSGAF 117 (137)
Q Consensus 42 vE~~~~~Nq~~kGK~~a~~~fR~~L~~e-l~~~FP--el~~~y~~ireraLakN~~~~gk~~~~~~~r~~l~~el~~~f 117 (137)
.+.....|..++..+.-|+..+..+... .....| +....+..+. +.+..|+.|+...++...|-. ||.++.+..
T Consensus 25 a~~~l~~d~e~~~l~~~f~~~q~~~~~~q~~g~~~~~e~~~~l~~~~-~~l~~~p~v~~y~~ae~~~~~-ll~~i~~~I 101 (108)
T PF06133_consen 25 AEEALEADPEAQKLIEEFQKLQQELQNAQMYGKEPPKEEIEELQELQ-EELMQNPVVKEYLQAEQALQD-LLQDINQII 101 (108)
T ss_dssp HHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHH-HHHHTSHHHHHHHHHHHHHHH-HHHHHHHHH
T ss_pred HHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhccCCcHHHHHHHHHHH-HHHHcCHHHHHHHHHHHHHHH-HHHHHHHHH
Confidence 3456777889999999999999988773 223333 4556666555 788999999999999988854 555555443
No 18
>cd09236 V_AnPalA_UmRIM20_like Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins. This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas Pa
Probab=48.90 E-value=1.7e+02 Score=25.08 Aligned_cols=38 Identities=18% Similarity=0.357 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhHHHhhHHHHHHHHHHHHH---HHHHhhchH
Q psy6385 39 KDCIEKALTKNEQVKGKIDAYRKFKAHML---VELSGAFPN 76 (137)
Q Consensus 39 refvE~~~~~Nq~~kGK~~a~~~fR~~L~---~el~~~FPe 76 (137)
+.-++.+...+..+..|++..+..=+.|. ..|...+|.
T Consensus 140 ~~~L~~A~~sD~~v~~k~~~~~~~l~lL~~~~~~l~~~~Ps 180 (353)
T cd09236 140 EGYLKQAGASDELVRRKLDEWEDLIQILTGDERDLENFVPS 180 (353)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHcCCHHHHHHhCCC
Confidence 45677888888888888888876655662 345566664
No 19
>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 [].
Probab=48.25 E-value=99 Score=22.43 Aligned_cols=83 Identities=18% Similarity=0.329 Sum_probs=48.2
Q ss_pred HHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHHHHHHH---hhhhhhhhhccchH-HHHHH--HHHHHHHHHH
Q psy6385 41 CIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIR---EKALTKNEQVKGKI-DAYRK--FKAHMLVELS 114 (137)
Q Consensus 41 fvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~y~~ir---eraLakN~~~~gk~-~~~~~--~r~~l~~el~ 114 (137)
.+......+..++.++..++.-= ..|.+.+|=-..++..|+ .+... ..+.|+- .+|++ +++.+...+.
T Consensus 2 ~i~l~~~~~~~~~~ki~~ve~~V----~~l~~~~~i~~~q~~~i~~~v~~rv~--~~lgg~~s~ay~~~~~~~k~f~~i~ 75 (116)
T PF10552_consen 2 QIKLLMQATEEHNEKIEEVENRV----DDLEENMPIDPGQQKEIQKAVKSRVY--ELLGGKGSPAYKDKSFRRKLFSDIY 75 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH----HHHHhcCCCCHHHHHHHHHHHHHHHH--HHHhccccchhhhhHHhHHHHHHHH
Confidence 35566777777777777664432 334455554444444443 22222 3444552 56666 7777777666
Q ss_pred hhChH--HHHHHhHhhC
Q psy6385 115 GAFPN--ELAKYRAIRG 129 (137)
Q Consensus 115 ~~fp~--~~~~yr~ir~ 129 (137)
..|=+ .|.+|++|+.
T Consensus 76 ~~lk~~F~V~sY~~I~~ 92 (116)
T PF10552_consen 76 RDLKRHFGVPSYKDIPR 92 (116)
T ss_pred HHHHHHhCCchHHhhhH
Confidence 65554 4789999875
No 20
>COG4079 Uncharacterized protein conserved in archaea [Function unknown]
Probab=47.02 E-value=18 Score=31.30 Aligned_cols=80 Identities=19% Similarity=0.218 Sum_probs=58.5
Q ss_pred hhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHhhhhh--hhhhccchHHHHHHHHHHHHHHH
Q psy6385 36 LYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIREKALT--KNEQVKGKIDAYRKFKAHMLVEL 113 (137)
Q Consensus 36 iYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~y~~ireraLa--kN~~~~gk~~~~~~~r~~l~~el 113 (137)
-|||+..+.+..+|=..+-++......=+.|.+.+++--|-....|.-..-..-. .-.-++-.|+++.+-|+.|-+|+
T Consensus 128 k~~Ke~aneflk~~l~~k~~lqd~~dal~elfe~vss~tpsVskeydiy~vs~~~d~~~rl~kkDie~L~k~R~~L~~em 207 (293)
T COG4079 128 KFTKEVANEFLKDNLTKKSKLQDAVDALMELFETVSSKTPSVSKEYDIYQVSSNVDPVLRLVKKDIETLRKHRRRLAEEM 207 (293)
T ss_pred HHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHhhcCCCcccceeEEEEecCCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4899999999999888887777777777777778887888877766543222211 12334577899999999999887
Q ss_pred Hh
Q psy6385 114 SG 115 (137)
Q Consensus 114 ~~ 115 (137)
-+
T Consensus 208 ld 209 (293)
T COG4079 208 LD 209 (293)
T ss_pred HH
Confidence 65
No 21
>PF04229 GrpB: GrpB protein; InterPro: IPR007344 This family of uncharacterised proteins is also known as GrpB.; PDB: 2NRK_A.
Probab=45.55 E-value=67 Score=24.70 Aligned_cols=49 Identities=20% Similarity=0.289 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhhchHHHHHHHHHHhhhhhhhhhccchHHHHHHHHHHHHHHHHh
Q psy6385 59 YRKFKAHMLVELSGAFPNELAKYRAIREKALTKNEQVKGKIDAYRKFKAHMLVELSG 115 (137)
Q Consensus 59 ~~~fR~~L~~el~~~FPel~~~y~~ireraLakN~~~~gk~~~~~~~r~~l~~el~~ 115 (137)
.-.|||.|. +.|++...|.+++.+...++. +..+.|..-|+-.++++.+
T Consensus 117 ~l~FRDyLr-----~~p~~~~~Y~~lK~~la~~~~---~d~~~Y~~~K~~fi~~il~ 165 (167)
T PF04229_consen 117 HLLFRDYLR-----AHPELRREYEALKRELAKRFP---NDRDAYTAAKSAFIKEILQ 165 (167)
T ss_dssp HHHHHHHHH-----H-HHHHHHHHHHHHHHHTT-S---S-HHHH----HHHHHHHHH
T ss_pred HHHHHHHHh-----hCHHHHHHHHHHHHHHHHHCC---CCHHHHHHHHHHHHHHHHh
Confidence 346888886 689999999999966553433 3677777777777776543
No 22
>PF05430 Methyltransf_30: S-adenosyl-L-methionine-dependent methyltransferase; InterPro: IPR008471 This entry contains several uncharacterised bacterial proteins with no known function.; GO: 0016645 oxidoreductase activity, acting on the CH-NH group of donors, 0055114 oxidation-reduction process; PDB: 2E58_D 3SGL_A 3PVC_A 3AWI_D 3PS9_A 2QY6_A.
Probab=44.66 E-value=14 Score=27.56 Aligned_cols=17 Identities=24% Similarity=0.610 Sum_probs=15.3
Q ss_pred CCCCchhHHHHHHHHHH
Q psy6385 31 GRNPQLYTKDCIEKALT 47 (137)
Q Consensus 31 GrNPDiYTrefvE~~~~ 47 (137)
.+||++||.+++..+.+
T Consensus 62 ~~nPelWs~e~~~~l~~ 78 (124)
T PF05430_consen 62 AKNPELWSEELFKKLAR 78 (124)
T ss_dssp TTSGGGSSHHHHHHHHH
T ss_pred cCCcccCCHHHHHHHHH
Confidence 89999999999988765
No 23
>smart00684 DM15 Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function.
Probab=43.56 E-value=40 Score=20.84 Aligned_cols=25 Identities=20% Similarity=0.197 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHhhChHHHHH
Q psy6385 99 IDAYRKFKAHMLVELSGAFPNELAK 123 (137)
Q Consensus 99 ~~~~~~~r~~l~~el~~~fp~~~~~ 123 (137)
-.||.+||+..|++-....+-+|+.
T Consensus 4 ~~~Y~eFr~laled~~~~~~~gm~~ 28 (39)
T smart00684 4 QNMYEEFRQLCLEDRKSLGRYELNC 28 (39)
T ss_pred hhHHHHHHHHHHHHHHHcCChhHHH
Confidence 3689999999999998888877764
No 24
>PRK05255 hypothetical protein; Provisional
Probab=43.31 E-value=1.7e+02 Score=23.39 Aligned_cols=65 Identities=15% Similarity=0.349 Sum_probs=47.9
Q ss_pred hhhcCCCCChHHHHHHHhcCC----------------------CCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHH
Q psy6385 12 KSQVQDIHVPLEVFDYIDQGR----------------------NPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVE 69 (137)
Q Consensus 12 k~~~~~i~IPlEVl~yID~Gr----------------------NPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~e 69 (137)
++++..+++|.++++.|..++ +|+ =-+..++.....++....+.+.++..|+.|.++
T Consensus 41 ~~ql~~lpL~e~L~~Ai~ea~ri~~~eA~RRqlqyIGKLmR~~d~e-~I~~al~~~~~~~~~~~~~~h~lE~wRdrLi~~ 119 (171)
T PRK05255 41 KDQLAKLPLDEDLRDAILEAQRITSHEARRRQLQYIGKLMRNEDVE-PIRAALDKLKNKHNQETARFHKLERWRDRLLAE 119 (171)
T ss_pred HHHHhcCCCCHHHHHHHHHHhhhccchHHHHHHHHHHHHHhhCCHH-HHHHHHHHHhchhHHHHHHHHHHHHHHHHHHhC
Confidence 355667788888888765543 222 246678888888999999999999999999884
Q ss_pred -------HHhhchHH
Q psy6385 70 -------LSGAFPNE 77 (137)
Q Consensus 70 -------l~~~FPel 77 (137)
+.+.||+.
T Consensus 120 ~d~al~e~~~~~P~~ 134 (171)
T PRK05255 120 GDDALTEFLEEYPDA 134 (171)
T ss_pred CHHHHHHHHHHCchh
Confidence 55666653
No 25
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.87 E-value=2e+02 Score=23.69 Aligned_cols=99 Identities=14% Similarity=0.316 Sum_probs=58.4
Q ss_pred hhhcCCCCChHHHHHHHhcC--------------------CCCchhH-HHHHHHHHHHhHHHhhHHHHHHHHHHHHHHH-
Q psy6385 12 KSQVQDIHVPLEVFDYIDQG--------------------RNPQLYT-KDCIEKALTKNEQVKGKIDAYRKFKAHMLVE- 69 (137)
Q Consensus 12 k~~~~~i~IPlEVl~yID~G--------------------rNPDiYT-refvE~~~~~Nq~~kGK~~a~~~fR~~L~~e- 69 (137)
++.+.-+++|-++...|... |+-|+-+ ++++.+....-+......+.++.+|+.|.++
T Consensus 51 ~~~L~KiPL~E~L~~Ai~~aqri~~~~arrRQlQyIGKlmR~~DvepI~~~Ldkl~~~~~q~~a~lHklE~~RdrLia~G 130 (187)
T COG3028 51 KAALAKIPLDEDLLEAIELAQRIKSEIARRRQLQYIGKLMRDRDVEPIRAALDKLRNRHNQQVALLHKLEQLRDRLIAEG 130 (187)
T ss_pred HHHHhhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhcC
Confidence 45556678888887766432 2223332 5677777777778888999999999999877
Q ss_pred ------HHhhchHH-HHHHHHHH---hhhhhhhhhccchHHHHHHHHHHHH
Q psy6385 70 ------LSGAFPNE-LAKYRAIR---EKALTKNEQVKGKIDAYRKFKAHML 110 (137)
Q Consensus 70 ------l~~~FPel-~~~y~~ir---eraLakN~~~~gk~~~~~~~r~~l~ 110 (137)
+-..||+- ..+.+.+- ..--+.|+--|..=+.|.-||-.++
T Consensus 131 D~Alt~~l~~~P~aDrq~LR~LvRna~kE~a~NKPPks~ReifQ~lk~l~~ 181 (187)
T COG3028 131 DGALTEFLNQYPDADRQQLRTLIRNAKKEQAQNKPPKSFREIFQYLKELME 181 (187)
T ss_pred chHHHHHHHHCCcccHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHH
Confidence 44556652 12222111 1223445555555555655554443
No 26
>COG5223 Uncharacterized conserved protein [Function unknown]
Probab=36.26 E-value=59 Score=27.38 Aligned_cols=42 Identities=24% Similarity=0.329 Sum_probs=35.4
Q ss_pred CChHHHHHHHhc--CCCCchhHHHHHHHHHHHhHHHhhHHHHHH
Q psy6385 19 HVPLEVFDYIDQ--GRNPQLYTKDCIEKALTKNEQVKGKIDAYR 60 (137)
Q Consensus 19 ~IPlEVl~yID~--GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~ 60 (137)
-||.|.+++.|+ +|--...+|+.|+.-.-.|+.+.||.++=.
T Consensus 142 f~peeFf~tt~elV~r~enrl~kdqi~nNel~~sv~~~~~~~k~ 185 (240)
T COG5223 142 FIPEEFFRTTEELVVRRENRLEKDQIENNELEDSVFSGKLHSKL 185 (240)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCChhhHHHH
Confidence 589999999887 666778899999988889999999987643
No 27
>TIGR03200 dearomat_oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase. Members of this protein family are 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase, a ring-hydrolyzing enzyme in the anaerobic metabolism of aromatic enzymes by way of benzoyl-CoA, as seen in Thauera aromatica, Geobacter metallireducens, and Azoarcus sp. Note that Rhodopseudomonas palustris uses a different pathway to perform a similar degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Probab=36.05 E-value=91 Score=27.72 Aligned_cols=56 Identities=14% Similarity=0.210 Sum_probs=30.3
Q ss_pred CCCCchhHHHHHHHHH---HHhHHHhhHHHHHH-----------HHHHH---HHHHHHhhchHH-HHHHHHHHh
Q psy6385 31 GRNPQLYTKDCIEKAL---TKNEQVKGKIDAYR-----------KFKAH---MLVELSGAFPNE-LAKYRAIRE 86 (137)
Q Consensus 31 GrNPDiYTrefvE~~~---~~Nq~~kGK~~a~~-----------~fR~~---L~~el~~~FPel-~~~y~~ire 86 (137)
-+||++.|-+.++... ..|-..--...+.+ .+... |..++...||+- ......+|.
T Consensus 220 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 293 (360)
T TIGR03200 220 VANPLVVTDRYLDEFGRIVHGEFKAGDELKAGKELIKQGTIDLSLLDEAVEALCAKLLNTFPECLTKSIEELRK 293 (360)
T ss_pred hcCcccchHHHHHHHhHHhcCCCcchhHHHHHHHHHhcccchHhHHHHHHHHHHHHHHHhchHHHHHHHHHhhh
Confidence 4899999988887621 11111100222222 23344 777889999984 444444543
No 28
>PRK09432 metF 5,10-methylenetetrahydrofolate reductase; Provisional
Probab=34.48 E-value=82 Score=26.64 Aligned_cols=32 Identities=13% Similarity=0.368 Sum_probs=26.1
Q ss_pred chhhhhHHhhhhhcCCCCChHHHHHHHhcCCCC
Q psy6385 2 ISGLQEIDKLKSQVQDIHVPLEVFDYIDQGRNP 34 (137)
Q Consensus 2 V~~Lq~ld~~k~~~~~i~IPlEVl~yID~GrNP 34 (137)
|.+++.+.++ ..+..+.||.++++-++...+.
T Consensus 214 i~s~~~~~~~-~~~~Gv~vP~~l~~~l~~~~d~ 245 (296)
T PRK09432 214 VSNFKQLKKF-ADMTNVRIPAWMAKMFDGLDDD 245 (296)
T ss_pred cCCHHHHHHH-HHccCCCCCHHHHHHHHhcCCC
Confidence 5677888888 4677999999999999987543
No 29
>PF03682 UPF0158: Uncharacterised protein family (UPF0158); InterPro: IPR005361 This is a small family of hypothetical bacterial proteins of unknown function.
Probab=34.38 E-value=1.4e+02 Score=23.32 Aligned_cols=26 Identities=31% Similarity=0.607 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHhhchHHHHHHHHHHhhh
Q psy6385 58 AYRKFKAHMLVELSGAFPNELAKYRAIREKA 88 (137)
Q Consensus 58 a~~~fR~~L~~el~~~FPel~~~y~~irera 88 (137)
||+.||+.|.+ +|++.+.+-+.+...
T Consensus 100 afrrFKd~L~~-----~~~~~e~Wy~F~~~~ 125 (163)
T PF03682_consen 100 AFRRFKDILSE-----YPELRERWYAFREER 125 (163)
T ss_pred HHHHHHHHHHH-----CHHHHHHHHHHHHHH
Confidence 89999998863 677666665555443
No 30
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=33.53 E-value=1.5e+02 Score=19.94 Aligned_cols=54 Identities=6% Similarity=0.111 Sum_probs=40.0
Q ss_pred CCCChHHHHHHHh----cCC--CCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHH
Q psy6385 17 DIHVPLEVFDYID----QGR--NPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNE 77 (137)
Q Consensus 17 ~i~IPlEVl~yID----~Gr--NPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel 77 (137)
+|.+|.+.-.||+ .|+ |..-+-|+-+......++ .++.+|+.+.+.+++..|+.
T Consensus 3 ~isL~~~~~~~i~~~V~sG~Y~s~SEVir~aLR~le~~e~-------~~~~Lr~~i~~g~~sg~~~~ 62 (69)
T TIGR02606 3 SVSLGEHLESFIRSQVQSGRYGSASEVVRAALRLLEERET-------KLQALRDAIEEGEQSGEAGR 62 (69)
T ss_pred eeecCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhCCCCCC
Confidence 6788988888775 476 667777777766666552 36789999999999887764
No 31
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=32.84 E-value=2.2e+02 Score=24.23 Aligned_cols=56 Identities=16% Similarity=0.254 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHhhchHHHHHHHHHHhhhhhhhhhccchHHHHHHHHHHHHHHHHhhChHHH
Q psy6385 58 AYRKFKAHMLVELSGAFPNELAKYRAIREKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNEL 121 (137)
Q Consensus 58 a~~~fR~~L~~el~~~FPel~~~y~~ireraLakN~~~~gk~~~~~~~r~~l~~el~~~fp~~~ 121 (137)
++..|-..|.+-..+++..+...+.+.- .....+++++.|+..=++-++.+|=+.+
T Consensus 177 a~~ey~~~l~~~~~~a~~~~~~~l~~~~--------~~g~~~~s~re~~d~Wi~~ae~~~~~~~ 232 (293)
T PF09712_consen 177 ASQEYQAQLSEAWMKAFERMMEKLQERA--------EEGEQIKSWREFYDIWIDAAEEAYEELF 232 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh--------ccCCCCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444445544444443322 2224466777777777777777765554
No 32
>PRK13740 conjugal transfer protein TraY; Provisional
Probab=32.74 E-value=55 Score=22.98 Aligned_cols=39 Identities=15% Similarity=0.197 Sum_probs=28.8
Q ss_pred hhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHH
Q psy6385 36 LYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAK 80 (137)
Q Consensus 36 iYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~ 80 (137)
--|-+.+..+...+-..|.+--.+ .++|||.. |||....
T Consensus 20 ~etn~lL~~A~~RSGRSK~~EA~l-RL~DHL~r-----FpDfy~s 58 (70)
T PRK13740 20 EDTNNKLIEAKERSGRSKTNEVQI-RLRDHLKR-----FPDFYNS 58 (70)
T ss_pred HHHHHHHHHHHHHcCCcccHHHHH-HHHHHHHh-----Cccccch
Confidence 345667777777777777765555 89999987 9998655
No 33
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=32.19 E-value=82 Score=21.68 Aligned_cols=32 Identities=22% Similarity=0.348 Sum_probs=20.3
Q ss_pred CCChHHHHHHHhcCCCCchhHHHHHHHHHHHh
Q psy6385 18 IHVPLEVFDYIDQGRNPQLYTKDCIEKALTKN 49 (137)
Q Consensus 18 i~IPlEVl~yID~GrNPDiYTrefvE~~~~~N 49 (137)
...|.+|.+.|++|+-.|+.+..-+.....+|
T Consensus 27 l~lP~~i~~~v~~g~~~~~~a~~~L~~~~~~~ 58 (93)
T PF08535_consen 27 LDLPEEIKELVRSGRISDIRALYELRKLAEKN 58 (93)
T ss_dssp GS--HHHHHHHHTTS---HHHHHHHHHHHHH-
T ss_pred HcCCHHHHHHHHcCCCchHHHHHHHHHHHHhC
Confidence 57999999999999999988776665555554
No 34
>PRK07502 cyclohexadienyl dehydrogenase; Validated
Probab=31.69 E-value=1.6e+02 Score=24.07 Aligned_cols=56 Identities=13% Similarity=0.145 Sum_probs=37.3
Q ss_pred CCCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHh
Q psy6385 31 GRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIRE 86 (137)
Q Consensus 31 GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~y~~ire 86 (137)
+.||++|+-=|+...-.--+....-++.+..||+.|...=.+++-+..+.-++.|.
T Consensus 231 ~~~~~~w~~i~~~N~~~~~~~l~~~~~~l~~~~~~l~~~d~~~l~~~~~~~~~~r~ 286 (307)
T PRK07502 231 ASDPTMWRDVFLHNKDAVLEMLGRFTEDLAALQRAIRWGDGDALFDLFTRTRAIRR 286 (307)
T ss_pred cCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 56999998877765444446677778888888888876544455555555555553
No 35
>KOG0484|consensus
Probab=31.30 E-value=38 Score=25.94 Aligned_cols=18 Identities=22% Similarity=0.503 Sum_probs=13.6
Q ss_pred HHHhcCCCCchhHHHHHH
Q psy6385 26 DYIDQGRNPQLYTKDCIE 43 (137)
Q Consensus 26 ~yID~GrNPDiYTrefvE 43 (137)
...-..+=|||||||-+-
T Consensus 34 rvF~ETHYPDIYTREEiA 51 (125)
T KOG0484|consen 34 RVFAETHYPDIYTREEIA 51 (125)
T ss_pred HHHHhhcCCcchhHHHHH
Confidence 344567889999999664
No 36
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=31.29 E-value=2.4e+02 Score=22.82 Aligned_cols=34 Identities=24% Similarity=0.342 Sum_probs=23.6
Q ss_pred hHHHHH--HHhcCCCCchhHHHHHHHHHHHhHHHhh
Q psy6385 21 PLEVFD--YIDQGRNPQLYTKDCIEKALTKNEQVKG 54 (137)
Q Consensus 21 PlEVl~--yID~GrNPDiYTrefvE~~~~~Nq~~kG 54 (137)
-+|.++ ||.+.-+|+-||..|-....+=.-..+.
T Consensus 10 tle~LEkayikD~It~~eYt~~c~kLl~Qyk~~~~~ 45 (188)
T PF03997_consen 10 TLEHLEKAYIKDSITEKEYTTACNKLLNQYKTILKQ 45 (188)
T ss_dssp HHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 345554 8999999999999998776554444443
No 37
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=30.88 E-value=2.8e+02 Score=26.02 Aligned_cols=99 Identities=20% Similarity=0.308 Sum_probs=54.8
Q ss_pred hcCCCCChHH----HHHHHhcCCCCchhHHHHHHHHHHHhHHHhhHHHH--------HHHHHHHHHHHHHhhchHHHHHH
Q psy6385 14 QVQDIHVPLE----VFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDA--------YRKFKAHMLVELSGAFPNELAKY 81 (137)
Q Consensus 14 ~~~~i~IPlE----Vl~yID~GrNPDiYTrefvE~~~~~Nq~~kGK~~a--------~~~fR~~L~~el~~~FPel~~~y 81 (137)
.+.+..|+++ +|..|++|.==.--.|+.++.....+.-...-++. -..+.+ +.+++-.+.|+.++.|
T Consensus 427 ~i~~~~l~p~~laeLi~li~~g~Is~~~AK~vl~~~~~~~~~p~~iiee~gL~qisD~~~l~~-iv~evi~~np~~V~~~ 505 (544)
T PLN02751 427 SISEIKLTPKELAELIASIKDGTISGKIGKEILPELLAKGGTVKGLVEEKGLVQISDPAEIEA-MVDKVLEENPKQLEQY 505 (544)
T ss_pred ChhhcCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCCHHHHHHhcCCcccCCHHHHHH-HHHHHHHHCHHHHHHH
Confidence 3444556654 55688887766667788888777544322222221 112333 4455556789998888
Q ss_pred HHHHhhhhh-----hhhhccchHHHHHHHHHHHHHHHH
Q psy6385 82 RAIREKALT-----KNEQVKGKIDAYRKFKAHMLVELS 114 (137)
Q Consensus 82 ~~ireraLa-----kN~~~~gk~~~~~~~r~~l~~el~ 114 (137)
+.-..+.+. =-+.++||.|-= ..+..|.+.|.
T Consensus 506 k~Gk~k~~g~lvGqVMK~tkGkAnp~-~v~~iL~e~L~ 542 (544)
T PLN02751 506 RGGKTKLQGFFAGQVMKASKGKANPG-LLNKILMEKLN 542 (544)
T ss_pred HcccHHHHHHHHHHHHHHhCCCCCHH-HHHHHHHHHhc
Confidence 865444431 124466776653 45555555543
No 38
>PF02436 PYC_OADA: Conserved carboxylase domain; InterPro: IPR003379 This domain represents a conserved region in pyruvate carboxylase (PYC) (6.4.1.1 from EC), oxaloacetate decarboxylase alpha chain (OADA) (4.1.1.3 from EC), and transcarboxylase 5s subunit (2.1.3.1 from EC). The domain is found adjacent to the HMGL-like domain (IPR000891 from INTERPRO) and often close to the biotin_lipoyl domain (IPR000089 from INTERPRO) of biotin requiring enzymes.; PDB: 2NX9_B 3HBL_A 3HB9_C 3HO8_A 3BG5_C 1S3H_A 1RQE_A 1U5J_A 1RQB_A 2QF7_B ....
Probab=30.41 E-value=1.2e+02 Score=24.58 Aligned_cols=73 Identities=21% Similarity=0.353 Sum_probs=49.8
Q ss_pred CCCCChHHHHHHHhc--CCCCchhHHHHHHHHHHHhHHHhhHHH------HHHHHHHHHHHHH-----------HhhchH
Q psy6385 16 QDIHVPLEVFDYIDQ--GRNPQLYTKDCIEKALTKNEQVKGKID------AYRKFKAHMLVEL-----------SGAFPN 76 (137)
Q Consensus 16 ~~i~IPlEVl~yID~--GrNPDiYTrefvE~~~~~Nq~~kGK~~------a~~~fR~~L~~el-----------~~~FPe 76 (137)
.-..||-+|++|+-. |+=|-=+..++.+++++..+...|.=. .|+.+|+.|.+.. .--||.
T Consensus 70 r~~~~p~~v~~~~~G~~G~pp~~~~~~l~~~vl~~~~~i~~RP~~~l~p~d~~~~r~~l~~~~g~~~~dedvlsyal~P~ 149 (196)
T PF02436_consen 70 RYKDFPDSVVDYLLGKYGKPPGGFPEELRKKVLKGEEPITGRPGDLLPPADLDKLRKELEEKAGREPTDEDVLSYALFPK 149 (196)
T ss_dssp TTSS-BHHHHHHHTTTT---TTSS-HHHHHHHHTTS---SSSGGGCS----HHHHHHHHHHHCTSTSCHHHHHHHHHCHH
T ss_pred cccchhHHHHHHhCcccCCCCCCCCHHHHHHHhcCCCCCCCCccccCChhhHHHHHHHHHHHcCCCCCHHHHHHHhcCch
Confidence 357899999999955 999999999999999988776555421 6788888888754 335888
Q ss_pred HHHHHHHHHhhh
Q psy6385 77 ELAKYRAIREKA 88 (137)
Q Consensus 77 l~~~y~~irera 88 (137)
....|.+.|...
T Consensus 150 v~~~f~~~~~~~ 161 (196)
T PF02436_consen 150 VAEDFLKFRAKY 161 (196)
T ss_dssp HHHHHHHHHHHH
T ss_pred hHHHHHHHHHhc
Confidence 888888887654
No 39
>PF03693 RHH_2: Uncharacterised protein family (UPF0156); InterPro: IPR022789 This family of proteins are about 80 amino acids in length and their function is unknown. The proteins contain a conserved GRY motif. This family appears to be related to ribbon-helix-helix DNA-binding proteins. ; PDB: 3KXE_C.
Probab=28.08 E-value=1.5e+02 Score=20.57 Aligned_cols=53 Identities=9% Similarity=0.213 Sum_probs=34.7
Q ss_pred CCCChHHHHHHHhc----C--CCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchH
Q psy6385 17 DIHVPLEVFDYIDQ----G--RNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPN 76 (137)
Q Consensus 17 ~i~IPlEVl~yID~----G--rNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPe 76 (137)
+|.+|.+.-.||++ | .|-.-|-|+.|......+. -+..||+.|.+.+.+..|.
T Consensus 6 sisL~~~~~~~i~~~V~sG~Y~s~SEvvR~aLRlle~~e~-------~~~~Lr~~l~~g~~sG~~~ 64 (80)
T PF03693_consen 6 SISLTPELEAFIEEQVASGRYSSASEVVREALRLLEEREA-------KLEALREALQEGLESGESE 64 (80)
T ss_dssp EE---HHHHHHHHHHHCTTS-SSHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHCT-EES
T ss_pred eEecCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhCCCCC
Confidence 68899998888865 4 4777777777765544332 3456899999888877666
No 40
>PRK10167 hypothetical protein; Provisional
Probab=27.78 E-value=1.3e+02 Score=23.80 Aligned_cols=70 Identities=16% Similarity=0.209 Sum_probs=51.1
Q ss_pred HHHHHHHHHHHHHHHh-hchHHHHHHHHHHhhhhhhhhhccchHHHH----HHHHHHHHHHHHhhChHHHHHHhH
Q psy6385 57 DAYRKFKAHMLVELSG-AFPNELAKYRAIREKALTKNEQVKGKIDAY----RKFKAHMLVELSGAFPNELAKYRA 126 (137)
Q Consensus 57 ~a~~~fR~~L~~el~~-~FPel~~~y~~ireraLakN~~~~gk~~~~----~~~r~~l~~el~~~fp~~~~~yr~ 126 (137)
.+++.++..++..=.. .+-++...|...--.++++-+..++-|.++ --||++|=.+=.+.|=+-+++||.
T Consensus 50 ~~yr~LG~lva~~~~~~~~~~~~~~Y~~~lm~al~~~~t~~~~~NvL~Hi~GYFKk~Ls~~EKq~l~~lI~~Yr~ 124 (169)
T PRK10167 50 PEYRKLGPFVADIHQWQSLDDFYNQYRQRVIVLLSHPANVRDHTNVLMHVQGYFRPHIDSTERQQLAALIDSYRR 124 (169)
T ss_pred HHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHHHHcCCCCcchhHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHc
Confidence 4455566666543222 677788999999999998888888888765 457777777766778888888885
No 41
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=27.29 E-value=2.5e+02 Score=20.40 Aligned_cols=55 Identities=15% Similarity=0.258 Sum_probs=40.4
Q ss_pred CCCChHHHHH-HHhcCCCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHH
Q psy6385 17 DIHVPLEVFD-YIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELS 71 (137)
Q Consensus 17 ~i~IPlEVl~-yID~GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~ 71 (137)
..-+|++-|. +++...+|+.-..+..+.....-+.+..++..+..+++.|...+.
T Consensus 55 ~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~ 110 (127)
T TIGR02044 55 QVGFSLEECKELLNLWNDPNRTSADVKARTLEKVAEIERKISELQSMRDQLEALAQ 110 (127)
T ss_pred HCCCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567776664 666555555444566677778889999999999999999887654
No 42
>KOG0293|consensus
Probab=27.07 E-value=1.9e+02 Score=27.07 Aligned_cols=40 Identities=20% Similarity=0.327 Sum_probs=30.2
Q ss_pred HHHHhhhhhhhhhccchHHH---HHHHHHHHHHHHHhhChHHH
Q psy6385 82 RAIREKALTKNEQVKGKIDA---YRKFKAHMLVELSGAFPNEL 121 (137)
Q Consensus 82 ~~ireraLakN~~~~gk~~~---~~~~r~~l~~el~~~fp~~~ 121 (137)
.++--.-+..|.+.+|..++ +-..|.+||.||++-.|-++
T Consensus 126 ~el~~sll~sn~~~~ne~~~~~~~~n~R~~ll~elskyi~p~i 168 (519)
T KOG0293|consen 126 HELASSLLVSNDQFSNEENTTAQLNNERDKLLDELSKYIPPNI 168 (519)
T ss_pred HHHHHHHhccccccccccchhhhhchhHHHHHHHHHhhCCHhh
Confidence 33444456778888887776 55689999999999988764
No 43
>PF08349 DUF1722: Protein of unknown function (DUF1722); InterPro: IPR013560 This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Probab=27.03 E-value=1.5e+02 Score=21.49 Aligned_cols=69 Identities=19% Similarity=0.297 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHhhchHHHHHHHHHHhhhhhhhhhccchHHH----HHHHHHHHHHHHHhhChHHHHHHhH
Q psy6385 58 AYRKFKAHMLVELSGAFPNELAKYRAIREKALTKNEQVKGKIDA----YRKFKAHMLVELSGAFPNELAKYRA 126 (137)
Q Consensus 58 a~~~fR~~L~~el~~~FPel~~~y~~ireraLakN~~~~gk~~~----~~~~r~~l~~el~~~fp~~~~~yr~ 126 (137)
.++.++..++..=...+.++.+.|...-..++++-+..++-+.+ +--||+++=++=.+.|=+-++.||+
T Consensus 11 ~y~~lg~~va~~~~~~~~~~~~~Y~~~l~~al~~~~~~~~~~Nvl~Hi~Gyfk~~ls~~EK~~~~~~i~~yr~ 83 (117)
T PF08349_consen 11 IYRELGRLVANAGKRPLEEVFEEYEELLMEALSKPPTRGSHINVLQHIFGYFKKKLSSEEKQHFLDLIEDYRE 83 (117)
T ss_pred HHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHc
Confidence 45566666666555557788888888888888777666666654 4567777777777778888888886
No 44
>PRK03333 coaE dephospho-CoA kinase/protein folding accessory domain-containing protein; Provisional
Probab=26.94 E-value=1.4e+02 Score=26.04 Aligned_cols=49 Identities=22% Similarity=0.321 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHhhchHHHHHHHHHHhhhhhhhhhccchHHHHHHHHHHHHHHHHh
Q psy6385 59 YRKFKAHMLVELSGAFPNELAKYRAIREKALTKNEQVKGKIDAYRKFKAHMLVELSG 115 (137)
Q Consensus 59 ~~~fR~~L~~el~~~FPel~~~y~~ireraLakN~~~~gk~~~~~~~r~~l~~el~~ 115 (137)
.=.|||.|. +.|++...|.+++-+.-.+. .+.++.|..-|...++++.+
T Consensus 334 ~l~FRDyLr-----~~p~~~~~Y~~lK~~la~~~---~~d~~~Y~~~K~~fi~~i~~ 382 (395)
T PRK03333 334 ALLFRDWLR-----ADPAARAEYLAVKRRAARRA---DGDTAAYADAKEPWFLDAYP 382 (395)
T ss_pred HHHHHHHHh-----cCHHHHHHHHHHHHHHHHhC---CccHHHHHhcchHHHHHHHH
Confidence 347999986 89999999999995544333 35778888888888887765
No 45
>PF10057 DUF2294: Uncharacterized conserved protein (DUF2294); InterPro: IPR018745 This domain of unknown function is found in a family of hypothetical bacterial proteins with no known function. It is also found at the C terminus of proteins provisionally annotated as response regulators.
Probab=26.86 E-value=99 Score=22.54 Aligned_cols=39 Identities=10% Similarity=0.198 Sum_probs=31.1
Q ss_pred HHHhhhhhhhhhccchHHHHHHHHHHHHHHHHhhChHHHHHH
Q psy6385 83 AIREKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKY 124 (137)
Q Consensus 83 ~ireraLakN~~~~gk~~~~~~~r~~l~~el~~~fp~~~~~y 124 (137)
.-.|..|+++ +|-.++.+..|..|.+.+.+.++..++.-
T Consensus 49 Tp~Ek~L~~~---~~g~~lv~~~R~~l~~~~~~~l~~~ie~i 87 (118)
T PF10057_consen 49 TPAEKFLAET---EEGRELVKQVRTSLIESLKPELKEMIEEI 87 (118)
T ss_pred CHHHHHHHhC---cchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446666666 57788999999999999999999888753
No 46
>cd09234 V_HD-PTP_like Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains. This family contains the V-shaped (V) domain of mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23) and related domains. It belongs to the V_Alix_like superfamily which includes the V domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X/ also known as apoptosis-linked gene-2 interacting protein 1, AIP1), and related domains. HD_PTP interacts with the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in cell migration and endosomal trafficking. The related Alix V-domain (belonging to a different family in this superfamily) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. In addi
Probab=26.45 E-value=4.1e+02 Score=22.63 Aligned_cols=67 Identities=21% Similarity=0.246 Sum_probs=38.5
Q ss_pred HHHHHHHHHHhHHHhhHHHHHHHHHHHH---HHHHHhhchHH--------HHHHHHHHhhhhhhhhhccchHHHHHHHHH
Q psy6385 39 KDCIEKALTKNEQVKGKIDAYRKFKAHM---LVELSGAFPNE--------LAKYRAIREKALTKNEQVKGKIDAYRKFKA 107 (137)
Q Consensus 39 refvE~~~~~Nq~~kGK~~a~~~fR~~L---~~el~~~FPel--------~~~y~~ireraLakN~~~~gk~~~~~~~r~ 107 (137)
++-++.+..+|..+..|++....-=+.| .++|.+..|.. ...+..+|+-. .|++.++.=|.
T Consensus 137 ~~~L~~A~~sD~~l~~~~~~~~~~l~lL~~~~~~l~~~iPs~~~~~~~~~~~~v~~Lr~ll--------~kl~~lk~eR~ 208 (337)
T cd09234 137 KEAHEKASQSNTELHKAMNLHIANLKLLAGPLDELQKKLPSPSLLDRPEDEAIEKELKRIL--------NKVNEMRKQRR 208 (337)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHhhCCCccccCCcccHHHHHHHHHHH--------HHHHHHHHHHH
Confidence 5677888889999999988765444444 23444555552 22233333222 45555655555
Q ss_pred HHHHHH
Q psy6385 108 HMLVEL 113 (137)
Q Consensus 108 ~l~~el 113 (137)
.++++|
T Consensus 209 ~l~~~L 214 (337)
T cd09234 209 SLEQQL 214 (337)
T ss_pred HHHHHH
Confidence 555555
No 47
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=26.33 E-value=2.7e+02 Score=20.57 Aligned_cols=104 Identities=17% Similarity=0.309 Sum_probs=50.6
Q ss_pred hhHHhhhhhcCCCCChHHH----HHHHhcCCCCchhHHHHHHHHHHHhHHHhhHHHHH--------HHHHHHHHHHHHhh
Q psy6385 6 QEIDKLKSQVQDIHVPLEV----FDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAY--------RKFKAHMLVELSGA 73 (137)
Q Consensus 6 q~ld~~k~~~~~i~IPlEV----l~yID~GrNPDiYTrefvE~~~~~Nq~~kGK~~a~--------~~fR~~L~~el~~~ 73 (137)
..+.+..-.+.+..|+++- ++.+++|+=-.-=.|+.+........-...-++.. ..++ .+.+++-++
T Consensus 26 ~~l~~~~~~~~~~~i~~~~l~~li~l~~~~~Is~~~ak~ll~~~~~~~~~~~~ii~~~~l~~i~d~~el~-~~v~~vi~~ 104 (148)
T PF02637_consen 26 GLLNKKGLDIEDSPISPEHLAELINLLEDGKISKKSAKELLRELLENGKSPEEIIEENGLWQISDEEELE-ALVEEVIAE 104 (148)
T ss_dssp HHHHHHT--TTTSSSTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTS-HHHHHHHTT---B--CCHHH-HHHHHHHHC
T ss_pred HHHHHCCCChhhcCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCcCCCHHHHH-HHHHHHHHH
Confidence 3444444445566677654 45777776555555666666664433222222221 1122 334455556
Q ss_pred chHHHHHHHHHHhhhhh-----hhhhccchHHHHHHHHHHHHH
Q psy6385 74 FPNELAKYRAIREKALT-----KNEQVKGKIDAYRKFKAHMLV 111 (137)
Q Consensus 74 FPel~~~y~~ireraLa-----kN~~~~gk~~~~~~~r~~l~~ 111 (137)
.|+.++.|+.-..+.+. =-+.++|+.|.= .++..|-+
T Consensus 105 n~~~v~~~~~Gk~k~~~~LvGqvMk~t~G~adp~-~v~~~l~~ 146 (148)
T PF02637_consen 105 NPKEVEDYRNGKKKAIGFLVGQVMKETKGRADPK-EVKELLKE 146 (148)
T ss_dssp -HHHHHHHCTT-TTCCHHHHHHHHHCTTS-C-HH-HHHHHHHH
T ss_pred CHHHHHHHHcChHHHHHHHHHHHHHHcCCCCCHH-HHHHHHHh
Confidence 78888888766554431 134467777653 45544443
No 48
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=26.15 E-value=3.6e+02 Score=26.41 Aligned_cols=97 Identities=19% Similarity=0.306 Sum_probs=49.9
Q ss_pred cCCCCChHH----HHHHHhcCCCCchhHHHHHHHHHHHhHHHhhHHHHH--------HHHHHHHHHHHHhhchHHHHHHH
Q psy6385 15 VQDIHVPLE----VFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAY--------RKFKAHMLVELSGAFPNELAKYR 82 (137)
Q Consensus 15 ~~~i~IPlE----Vl~yID~GrNPDiYTrefvE~~~~~Nq~~kGK~~a~--------~~fR~~L~~el~~~FPel~~~y~ 82 (137)
+.+..|+.+ ++..|++|.=-.-=-|+.++.....+.-..--++.. ..+.. +.+++-++.|+.++.|+
T Consensus 657 i~~~~l~pe~LaeLv~lV~~g~IS~~~AK~VL~~m~~~~~~p~~IIee~GL~qisDe~~Le~-iV~eVI~~NP~~Ve~yk 735 (771)
T PRK14703 657 LAALPFTPAALARLVALVDAGRISTRIAKDVLAELAASGGDPEAIVEAKGLEQVSDAGALEP-IVEEVLAAHPDKVAAYR 735 (771)
T ss_pred CccCCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHhcCCCHHHHHHhcCCcccCCHHHHHH-HHHHHHHHCHHHHHHHh
Confidence 334455543 456777776544445666666554332221111111 22333 44555577899999998
Q ss_pred HHHhhhhh-----hhhhccchHHHHHHHHHHHHHHH
Q psy6385 83 AIREKALT-----KNEQVKGKIDAYRKFKAHMLVEL 113 (137)
Q Consensus 83 ~ireraLa-----kN~~~~gk~~~~~~~r~~l~~el 113 (137)
+-..+++. ==+.++||.|.= ..+..|.+.|
T Consensus 736 ~GK~kalgfLVGqVMK~tkGKAdP~-~V~elLke~L 770 (771)
T PRK14703 736 AGKTKLLGFFVGQVMRETGGKANPQ-QVRELLQKKL 770 (771)
T ss_pred cchHHHHHHHHHHHHHHhCCCCCHH-HHHHHHHHHh
Confidence 65554441 134556666653 4444444443
No 49
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=25.93 E-value=41 Score=27.76 Aligned_cols=13 Identities=31% Similarity=0.626 Sum_probs=11.1
Q ss_pred CCChHHHHHHHhc
Q psy6385 18 IHVPLEVFDYIDQ 30 (137)
Q Consensus 18 i~IPlEVl~yID~ 30 (137)
.++|.|||+||.+
T Consensus 97 ~~LPddVI~Ymrd 109 (196)
T PRK15364 97 EEVPEDVIKYMRD 109 (196)
T ss_pred ccCCHHHHHHHHH
Confidence 4899999999943
No 50
>PRK08645 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein; Reviewed
Probab=25.47 E-value=95 Score=28.80 Aligned_cols=45 Identities=13% Similarity=0.214 Sum_probs=33.2
Q ss_pred chhhhhHHhhhhhcCCCCChHHHHHHHhcCCCCchhHHHHHHHHH
Q psy6385 2 ISGLQEIDKLKSQVQDIHVPLEVFDYIDQGRNPQLYTKDCIEKAL 46 (137)
Q Consensus 2 V~~Lq~ld~~k~~~~~i~IPlEVl~yID~GrNPDiYTrefvE~~~ 46 (137)
|.+.+.+..++..+..+.||.++++-++.+.+|+-+-..-++.|.
T Consensus 527 i~s~k~~~~~~~~~~Gv~vP~~l~~~l~~~~d~~~~~~~gv~~a~ 571 (612)
T PRK08645 527 LVSYRNAEFLHNEVPGITLPEEIRERMRAVEDKEEAREEGVAIAR 571 (612)
T ss_pred cCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCCchHHHHHHHHHHH
Confidence 455677778877777899999999999999888654444444443
No 51
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=25.28 E-value=2.7e+02 Score=22.63 Aligned_cols=39 Identities=13% Similarity=0.072 Sum_probs=25.8
Q ss_pred CCCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHH
Q psy6385 31 GRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVE 69 (137)
Q Consensus 31 GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~e 69 (137)
+.||++|+-=|....-.==+....-++.+..||+.|.++
T Consensus 220 ~~~p~~w~~i~~~N~~~i~~~l~~~~~~l~~~~~~l~~~ 258 (279)
T PRK07417 220 GGNPELGVMMAEYNRAALLRSLASYRQSLDQLEELIEQE 258 (279)
T ss_pred CCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 568999987777654333345566666677777777654
No 52
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=24.91 E-value=1.9e+02 Score=18.94 Aligned_cols=36 Identities=11% Similarity=0.424 Sum_probs=23.0
Q ss_pred HHhhhhhcCCCCChHHHHHHHhcCC----CCchhHHHHHHHHH
Q psy6385 8 IDKLKSQVQDIHVPLEVFDYIDQGR----NPQLYTKDCIEKAL 46 (137)
Q Consensus 8 ld~~k~~~~~i~IPlEVl~yID~Gr----NPDiYTrefvE~~~ 46 (137)
++.++. ...||...|+.||+|. .+..|.|-||....
T Consensus 13 l~~va~---~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya 52 (62)
T PF13413_consen 13 LEDVAE---ETKISVSYLEAIENGDFDSLPSPVYARGYLRKYA 52 (62)
T ss_dssp HHHHHH---HCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHH
T ss_pred HHHHHH---HhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHH
Confidence 344444 3579999999999874 34578888876544
No 53
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=24.81 E-value=1.3e+02 Score=19.28 Aligned_cols=47 Identities=13% Similarity=0.214 Sum_probs=30.5
Q ss_pred CCChHHHHHHHhcCCCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHH
Q psy6385 18 IHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHML 67 (137)
Q Consensus 18 i~IPlEVl~yID~GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~ 67 (137)
..+|...|+.|+. .||+ .++....++..=+...|.-.++..|-+.|.
T Consensus 22 Lg~~~~~i~~i~~-~~~~--~~~~~~~~L~~W~~~~~~~at~~~L~~aL~ 68 (83)
T PF00531_consen 22 LGLSESEIENIEE-ENPD--LREQTYEMLQRWRQREGPNATVDQLIQALR 68 (83)
T ss_dssp TTS-HHHHHHHHH-HSTS--HHHHHHHHHHHHHHHHGSTSSHHHHHHHHH
T ss_pred hCcCHHHHHHHHH-hCCC--hHHHHHHHHHHHHHhcCCCCcHHHHHHHHH
Confidence 4788889999988 8887 555555555554444666666666665554
No 54
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=23.69 E-value=1.2e+02 Score=21.72 Aligned_cols=59 Identities=24% Similarity=0.381 Sum_probs=35.9
Q ss_pred CCChHHHHHHH-hcCCCCchhHHHHHHHHHHHhHHHhhHH------------HHHHHHHHHHHHHHHhhchHHHHHHHHH
Q psy6385 18 IHVPLEVFDYI-DQGRNPQLYTKDCIEKALTKNEQVKGKI------------DAYRKFKAHMLVELSGAFPNELAKYRAI 84 (137)
Q Consensus 18 i~IPlEVl~yI-D~GrNPDiYTrefvE~~~~~Nq~~kGK~------------~a~~~fR~~L~~el~~~FPel~~~y~~i 84 (137)
+.+.-.|++|+ +.| |+|-+-.+.+.+.- ....|+ .||..|.+.|.+ ||-+.+.....
T Consensus 20 l~~~~~v~~~L~~~g----IlT~~~~e~I~a~~-T~~~k~~~LLdiLp~RG~~AF~~F~~aL~e-----~~~l~~~l~~~ 89 (94)
T cd08327 20 LLVDGLVIQYLYQEG----ILTESHVEEIESQT-TSRRKTMKLLDILPSRGPKAFHAFLDSLEE-----FPWVRDKLLKL 89 (94)
T ss_pred ccchHHHHHHHHhCC----CCCHHHHHHHHccC-ChHHHHHHHHHHHHhhChhHHHHHHHHHHH-----HHHHHHHHHHH
Confidence 33433466644 333 88888887776421 112222 578888888843 89888877765
Q ss_pred Hh
Q psy6385 85 RE 86 (137)
Q Consensus 85 re 86 (137)
++
T Consensus 90 ~~ 91 (94)
T cd08327 90 RE 91 (94)
T ss_pred Hh
Confidence 53
No 55
>cd03407 Band_7_4 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic H
Probab=23.44 E-value=3e+02 Score=22.27 Aligned_cols=67 Identities=12% Similarity=-0.008 Sum_probs=37.1
Q ss_pred cCCCCChHHHHHHHhcCCCC-----------chhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHHH
Q psy6385 15 VQDIHVPLEVFDYIDQGRNP-----------QLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKY 81 (137)
Q Consensus 15 ~~~i~IPlEVl~yID~GrNP-----------DiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~y 81 (137)
+.++..|.+|.+.+++=..= +-|-...+-.+..+.+...=.-+|.+..+...++.+.+.|=.+.+.|
T Consensus 136 I~~i~~p~~v~~A~~~~~~A~~~~~a~~~~Aea~~~~~i~~A~~ea~a~~~~Aeg~a~a~~~~A~g~~~~~~~~~~~~ 213 (262)
T cd03407 136 ITDIDPDAEVKRAMNEINAAQRQRVAAVHKAEAEKIKDIKAAEADAEAKRLQGVGAAEQRQAIADGLRESILSLADAV 213 (262)
T ss_pred EEecCCCHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46788899998887761100 11111233344444444444445566666666776666666665555
No 56
>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants. XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.
Probab=23.11 E-value=5.2e+02 Score=22.73 Aligned_cols=43 Identities=16% Similarity=0.224 Sum_probs=30.3
Q ss_pred hcCCCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHH
Q psy6385 29 DQGRNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELS 71 (137)
Q Consensus 29 D~GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~ 71 (137)
..-.||..-.++++.-|+..+.....+...+..-.+.|..+..
T Consensus 119 ~~~~~p~e~i~el~d~~l~~~~~l~~~~~~L~~enerL~~e~~ 161 (342)
T PF06632_consen 119 KQVDNPAEVIRELFDWCLDANSRLQAENEHLQKENERLESEAN 161 (342)
T ss_dssp EE-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446787777889999999998888888877665555555443
No 57
>cd09235 V_Alix Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules. This family contains the middle V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X) and related domains. It belongs to the V_Alix_like superfamily which includes the V-domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), is part of the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in membrane remodeling processes, including the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), the abscission reactions of mammalian cell division, and in apoptosis. The Alix V-domain is a dimerization domain, and contains a binding site, partially conserved in the
Probab=22.76 E-value=4.3e+02 Score=22.53 Aligned_cols=38 Identities=21% Similarity=0.344 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhHHHhhHHHHHHHHHHHHH---HHHHhhchH
Q psy6385 39 KDCIEKALTKNEQVKGKIDAYRKFKAHML---VELSGAFPN 76 (137)
Q Consensus 39 refvE~~~~~Nq~~kGK~~a~~~fR~~L~---~el~~~FPe 76 (137)
++-++.+...+..+..|++..+.-=+.|. .+|...+|.
T Consensus 137 r~~L~~A~~sD~~v~~k~~~~~~~l~lLs~~~~~l~~~lPs 177 (339)
T cd09235 137 RTILDNAVQADKIVREKYESHREGIELLSKPEEELANAIPS 177 (339)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHcCCHHHHHHhCCC
Confidence 45567777777888888777766555552 235555554
No 58
>PF15272 BBP1_C: Spindle pole body component BBP1, C-terminal
Probab=22.66 E-value=2.3e+02 Score=23.31 Aligned_cols=32 Identities=16% Similarity=0.487 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHh------hChHHHHHHhHhhCCC
Q psy6385 100 DAYRKFKAHMLVELSG------AFPNELAKYRAIRGGD 131 (137)
Q Consensus 100 ~~~~~~r~~l~~el~~------~fp~~~~~yr~ir~~~ 131 (137)
+-|..+|.-+|.||.+ ++=....+|++++..+
T Consensus 44 ~KY~~lR~ElI~ELkqsKklydnYYkL~~KY~~LK~~~ 81 (196)
T PF15272_consen 44 EKYQQLRQELINELKQSKKLYDNYYKLYSKYQELKKSS 81 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4567788888888764 5677888899888743
No 59
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=22.22 E-value=81 Score=21.27 Aligned_cols=20 Identities=15% Similarity=0.414 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHhhchHH
Q psy6385 58 AYRKFKAHMLVELSGAFPNE 77 (137)
Q Consensus 58 a~~~fR~~L~~el~~~FPel 77 (137)
|+..|+..|...|...||+.
T Consensus 5 a~~AL~~EL~kRl~~~yPd~ 24 (65)
T PF06183_consen 5 ALEALESELTKRLHRQYPDA 24 (65)
T ss_dssp HHHHHHHHHHHHHHHH-SS-
T ss_pred HHHHHHHHHHHHHHHHCCCc
Confidence 56778999999999999994
No 60
>PF11472 DUF3206: Protein of unknown function (DUF3206); InterPro: IPR021571 This bacterial family of proteins has no known function. ; PDB: 2AU5_A.
Probab=21.99 E-value=1.9e+02 Score=22.17 Aligned_cols=43 Identities=23% Similarity=0.348 Sum_probs=32.6
Q ss_pred HHHHhhchHHHHHHHHHHhhhhhhhhhccchHHHHHHHHHHHHH
Q psy6385 68 VELSGAFPNELAKYRAIREKALTKNEQVKGKIDAYRKFKAHMLV 111 (137)
Q Consensus 68 ~el~~~FPel~~~y~~ireraLakN~~~~gk~~~~~~~r~~l~~ 111 (137)
++|..+|--+..-|...|.+.|+.|+. +=..+.+.||-..||-
T Consensus 78 ~~L~~E~~~Li~LY~~~~~~~LT~N~~-~L~~~i~DKF~~LLL~ 120 (128)
T PF11472_consen 78 EQLMDEFNCLINLYFRARQRNLTSNQD-NLFVNIFDKFTFLLLC 120 (128)
T ss_dssp HHHHHHHHHHHHHHHHHHTT---HHHH-HHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHhhccccch-hhhhhHHHHHHHHHHc
Confidence 456666777888999999999999976 5688999999998873
No 61
>KOG2256|consensus
Probab=21.82 E-value=4e+02 Score=25.88 Aligned_cols=47 Identities=15% Similarity=0.148 Sum_probs=32.9
Q ss_pred cCCCCchhH-HHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHh-----hchHHHH
Q psy6385 30 QGRNPQLYT-KDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSG-----AFPNELA 79 (137)
Q Consensus 30 ~GrNPDiYT-refvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~-----~FPel~~ 79 (137)
.++++|.++ -.+=..+++.+++..|=++. +=+.|.+.++. +|||++-
T Consensus 486 ~~k~~D~~~~Lk~sk~~L~sk~yq~~~ieq---v~~lL~ey~a~~s~~IaFPELv~ 538 (661)
T KOG2256|consen 486 SVKPIDFDSTLKLSKRYLRSKAYQDGVIEQ---VIELLLEYFALFSKSIAFPELVL 538 (661)
T ss_pred ccCCCCeeEEeecCHHHhccHHHHHHHHHH---HHHHHHHHHHHHhccCCchhhhH
Confidence 356778763 45556778889999998874 45566666654 8999853
No 62
>PF03433 EspA: EspA-like secreted protein ; InterPro: IPR005095 EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system. These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell [, ].; PDB: 1XOU_A.
Probab=21.60 E-value=31 Score=28.28 Aligned_cols=38 Identities=26% Similarity=0.430 Sum_probs=0.0
Q ss_pred CCChHHHHHHHhc------CCCCchhHHHHHHHHHHHhHHHhhHHHHHH
Q psy6385 18 IHVPLEVFDYIDQ------GRNPQLYTKDCIEKALTKNEQVKGKIDAYR 60 (137)
Q Consensus 18 i~IPlEVl~yID~------GrNPDiYTrefvE~~~~~Nq~~kGK~~a~~ 60 (137)
.++|.|||+|+++ |.+=+-|-++.-. -+.-+|...|++
T Consensus 97 ~~lp~dVi~Ym~~ngI~VdG~si~~Yl~~n~~-----~~LdkG~LqaVK 140 (188)
T PF03433_consen 97 APLPDDVIDYMRDNGIKVDGKSIDDYLKKNGS-----GGLDKGQLQAVK 140 (188)
T ss_dssp -------------------------------------------------
T ss_pred ccCCHHHHHHHHHcCCeecCeeccchhhhhhh-----ccCCchhHHHHH
Confidence 4899999999965 6666666665433 455666666654
No 63
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=21.47 E-value=1.5e+02 Score=23.25 Aligned_cols=52 Identities=23% Similarity=0.526 Sum_probs=44.3
Q ss_pred CCCChHHHHHHHhcCCCCchhHHHHHHHHHHHhHHH-hhHHHH--HHHHHHHHHHHHHhhc
Q psy6385 17 DIHVPLEVFDYIDQGRNPQLYTKDCIEKALTKNEQV-KGKIDA--YRKFKAHMLVELSGAF 74 (137)
Q Consensus 17 ~i~IPlEVl~yID~GrNPDiYTrefvE~~~~~Nq~~-kGK~~a--~~~fR~~L~~el~~~F 74 (137)
.-.||++++++- .-||.+.++-++--|..+ +|-+.+ .+..|=.|+..+...|
T Consensus 33 e~~VplQLl~FA------hRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F 87 (145)
T COG5094 33 EPKVPLQLLEFA------HRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHF 87 (145)
T ss_pred CccchHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCc
Confidence 347999999986 469999999999999998 777765 5788889999998888
No 64
>TIGR00677 fadh2_euk methylenetetrahydrofolate reductase, eukaryotic type. This protein is an FAD-containing flavoprotein.
Probab=21.19 E-value=1.8e+02 Score=24.42 Aligned_cols=32 Identities=9% Similarity=0.258 Sum_probs=24.3
Q ss_pred chhhhhHHhhhhhcCCCCChHHHHHHHhcCCCC
Q psy6385 2 ISGLQEIDKLKSQVQDIHVPLEVFDYIDQGRNP 34 (137)
Q Consensus 2 V~~Lq~ld~~k~~~~~i~IPlEVl~yID~GrNP 34 (137)
+++++.+.++ ..+..+.||.++++-++...+.
T Consensus 199 i~s~~~~~~~-~~~~Gi~vP~~l~~~l~~~~~~ 230 (281)
T TIGR00677 199 INNYASFLRR-AKWSKTKIPQEIMSRLEPIKDD 230 (281)
T ss_pred cCCHHHHHHH-HhcCCCCCCHHHHHHHHhccCC
Confidence 3456666667 4577899999999999887554
No 65
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.14 E-value=3.2e+02 Score=19.47 Aligned_cols=53 Identities=11% Similarity=0.122 Sum_probs=37.0
Q ss_pred CCChHHHH-HHHhcCCCCc---hhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHH
Q psy6385 18 IHVPLEVF-DYIDQGRNPQ---LYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVEL 70 (137)
Q Consensus 18 i~IPlEVl-~yID~GrNPD---iYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el 70 (137)
.-+|++-| ++++...+++ .=..+..+.....-+.+..++..++..++.|...|
T Consensus 55 ~G~sl~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~l 111 (112)
T cd01282 55 AGLTLEEIREFLPCLRGGEPTFRPCPDLLAVLRRELARIDRQIADLTRSRDRLDAYL 111 (112)
T ss_pred cCCCHHHHHHHHHHhhCCCccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45666555 4555444332 33456678888888999999999999999987765
No 66
>PF02262 Cbl_N: CBL proto-oncogene N-terminal domain 1; InterPro: IPR003153 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the N-terminal four-helical bundle domain.; GO: 0004871 signal transducer activity, 0007166 cell surface receptor linked signaling pathway, 0005634 nucleus; PDB: 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B 1B47_C 3BUO_D ....
Probab=21.09 E-value=66 Score=24.98 Aligned_cols=19 Identities=37% Similarity=0.595 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHhhChHH
Q psy6385 102 YRKFKAHMLVELSGAFPNE 120 (137)
Q Consensus 102 ~~~~r~~l~~el~~~fp~~ 120 (137)
+.-.=+|++.||.-.||+-
T Consensus 108 LsLiFSHMlaELkAlFP~G 126 (130)
T PF02262_consen 108 LSLIFSHMLAELKALFPDG 126 (130)
T ss_dssp HHHHHHHHHHHHHHHSGGG
T ss_pred HHHHHHHHHHHHHHhCCCC
Confidence 4455699999999999984
No 67
>COG3679 Regulatory protein involved in competence development and sporulation [Replication, recombination and repair; Signal transduction mechanisms]
Probab=20.92 E-value=3.8e+02 Score=20.33 Aligned_cols=73 Identities=16% Similarity=0.275 Sum_probs=54.6
Q ss_pred HHHHHHhHHHhhHHHHHHHHHHHHHHHHHhh-chHHHHHHHHHH--hhhhhhhhhccchHHHHHHHHHHHHHHHHhhC
Q psy6385 43 EKALTKNEQVKGKIDAYRKFKAHMLVELSGA-FPNELAKYRAIR--EKALTKNEQVKGKIDAYRKFKAHMLVELSGAF 117 (137)
Q Consensus 43 E~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~-FPel~~~y~~ir--eraLakN~~~~gk~~~~~~~r~~l~~el~~~f 117 (137)
..++..|+-++-.++.|..++..+.+..... .|+.... ..+| .+.+..|+.|.-..++.-.| .++|.||++-.
T Consensus 29 ~~~v~~d~eA~~lf~~F~~~q~~~q~~q~~G~~~d~~~~-~~~q~~~~~i~~~e~v~~f~eaE~~L-~~~l~el~~iI 104 (118)
T COG3679 29 KRAVEADEEAKKLFEEFRQLQEQFQEKQRFGYEPDYEEV-TKAQELKQEIQLNEKVSAFMEAEQAL-SSLLDELNKII 104 (118)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHH-HHHHHHHHHHhhcHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 4677889999999999999999999988877 6664222 2443 37788888888777777665 56788887643
No 68
>PF09164 VitD-bind_III: Vitamin D binding protein, domain III; InterPro: IPR015247 This domain is predominantly found in Vitamin D binding proteins, and adopts a multihelical structure. It is required for formation of an actin 'clamp', allowing the protein to bind to actin []. ; PDB: 1MA9_A 1KW2_A 1KXP_D 1J7E_A 1J78_A 1LOT_A.
Probab=20.85 E-value=1.2e+02 Score=21.13 Aligned_cols=22 Identities=14% Similarity=0.455 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHhhchHHHH
Q psy6385 58 AYRKFKAHMLVELSGAFPNELA 79 (137)
Q Consensus 58 a~~~fR~~L~~el~~~FPel~~ 79 (137)
.|-.|++.|++.|..-||+-..
T Consensus 10 tFtEyKKrL~e~l~~k~P~at~ 31 (68)
T PF09164_consen 10 TFTEYKKRLAERLRAKLPDATP 31 (68)
T ss_dssp -HHHHHHHHHHHHHHH-TTS-H
T ss_pred cHHHHHHHHHHHHHHHCCCCCH
Confidence 5778999999999999998644
No 69
>KOG0679|consensus
Probab=20.81 E-value=74 Score=29.11 Aligned_cols=37 Identities=30% Similarity=0.352 Sum_probs=32.8
Q ss_pred HHHhhhhhhhhhccchHHHHHHHHHHHHHHHHhhChHH
Q psy6385 83 AIREKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNE 120 (137)
Q Consensus 83 ~ireraLakN~~~~gk~~~~~~~r~~l~~el~~~fp~~ 120 (137)
+|| ..|.-|=++-|-+-.+.+|.-+|.+||++.+|--
T Consensus 336 diR-~~L~~nVivtGGtSliqG~s~RL~~ELs~~~P~s 372 (426)
T KOG0679|consen 336 DIR-SSLLGNVIVTGGTSLIQGFSERLNKELSKRAPSS 372 (426)
T ss_pred HHH-HHhhccEEEecCcchhhhHHHHHHHHHHHhCCcc
Confidence 344 6788999999999999999999999999999964
No 70
>KOG0957|consensus
Probab=20.75 E-value=4.2e+02 Score=25.54 Aligned_cols=68 Identities=24% Similarity=0.325 Sum_probs=40.1
Q ss_pred CCCchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHh--hhhhhhhhccchHHHHHHHHHHH
Q psy6385 32 RNPQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVELSGAFPNELAKYRAIRE--KALTKNEQVKGKIDAYRKFKAHM 109 (137)
Q Consensus 32 rNPDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~el~~~FPel~~~y~~ire--raLakN~~~~gk~~~~~~~r~~l 109 (137)
+=|--||+||++--...|..+.|.. ....+...+.-|.+.++-+--++ ....-|+. .|....||
T Consensus 420 Hv~pafs~efi~yy~~rn~rm~~i~-------~~m~e~~s~~~~le~eq~~l~~ey~~~~e~~~e-------~k~~~~~L 485 (707)
T KOG0957|consen 420 HVPPAFSKEFIEYYTKRNERMSGIS-------SFMQERDSQIIPLEEEQLRLSREYLAETEANQE-------KKSSQKHL 485 (707)
T ss_pred cCCccccHHHHHHHHHHHHHHHHHH-------HHHHHHhhcccchhhHHHHHHHHHHHHHHHHHH-------HHHhHHHH
Confidence 5577799999999999998876643 33344445555665544443332 12223333 34556666
Q ss_pred HHHH
Q psy6385 110 LVEL 113 (137)
Q Consensus 110 ~~el 113 (137)
++++
T Consensus 486 ~~~~ 489 (707)
T KOG0957|consen 486 VERF 489 (707)
T ss_pred HHHh
Confidence 6654
No 71
>PF14006 YqzL: YqzL-like protein
Probab=20.74 E-value=60 Score=21.11 Aligned_cols=21 Identities=38% Similarity=0.523 Sum_probs=14.7
Q ss_pred ccchHHHHHHHHHHHHHHHHhhChHH
Q psy6385 95 VKGKIDAYRKFKAHMLVELSGAFPNE 120 (137)
Q Consensus 95 ~~gk~~~~~~~r~~l~~el~~~fp~~ 120 (137)
..|.||+| .|.+|+++...+.
T Consensus 9 ~TG~i~aY-----llyke~E~~~~~~ 29 (47)
T PF14006_consen 9 QTGSIDAY-----LLYKELEEESEDE 29 (47)
T ss_pred hcCCHHHH-----HHHHHHHhhcccc
Confidence 45999999 5666677666543
No 72
>PF04751 DUF615: Protein of unknown function (DUF615); InterPro: IPR006839 The proteins in this entry are functionally uncharacterised. The entry contains the Escherichia coli (strain K12) protein YjgA (P0A8X0 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2P0T_A.
Probab=20.67 E-value=2.3e+02 Score=22.14 Aligned_cols=68 Identities=18% Similarity=0.354 Sum_probs=44.0
Q ss_pred hhhcCCCCChHHHHHHHhcCCC----------------------CchhHHHHHHHHHHHhHHHhhHHHHHHHHHHHHHHH
Q psy6385 12 KSQVQDIHVPLEVFDYIDQGRN----------------------PQLYTKDCIEKALTKNEQVKGKIDAYRKFKAHMLVE 69 (137)
Q Consensus 12 k~~~~~i~IPlEVl~yID~GrN----------------------PDiYTrefvE~~~~~Nq~~kGK~~a~~~fR~~L~~e 69 (137)
++++..+++|.++.+.|..++- |+ =-+..++.+...++......+.++..|+.|.++
T Consensus 30 ~~ql~~lpL~e~l~~Ai~~a~ri~~~~arrRQ~qyIGKLmR~~d~e-~I~~al~~~~~~~~~~~~~~h~lE~wRdrLi~~ 108 (157)
T PF04751_consen 30 PKQLAKLPLPEELRDAIMEARRITSHEARRRQLQYIGKLMREEDPE-AIRAALDALKNKSQQETARFHRLERWRDRLIAD 108 (157)
T ss_dssp HHHHTTS---HHHHHHHHHGGG--SHHHHHHHHHHHHHHGGGS-HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred HHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHhCCHH-HHHHHHHHHHcccHHHHHHHHHHHHHHHHHHhC
Confidence 3556678889888887765432 22 135677888888888899999999999998765
Q ss_pred HHhhchHHHHH
Q psy6385 70 LSGAFPNELAK 80 (137)
Q Consensus 70 l~~~FPel~~~ 80 (137)
=..++.++.+.
T Consensus 109 ~~~al~e~~~~ 119 (157)
T PF04751_consen 109 DDSALTEFLAE 119 (157)
T ss_dssp -HHHHHHHHHH
T ss_pred ChHHHHHHHHH
Confidence 44444444333
No 73
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=20.58 E-value=1.5e+02 Score=23.42 Aligned_cols=42 Identities=33% Similarity=0.510 Sum_probs=30.9
Q ss_pred ChH-HHHHHHhcCCCCchhH-------------HHHHHHHHHHhHHHhhHHHHHHH
Q psy6385 20 VPL-EVFDYIDQGRNPQLYT-------------KDCIEKALTKNEQVKGKIDAYRK 61 (137)
Q Consensus 20 IPl-EVl~yID~GrNPDiYT-------------refvE~~~~~Nq~~kGK~~a~~~ 61 (137)
+|. ++|-|+|...+..--+ ++.+|.+..+|+.++--|+-++.
T Consensus 81 ~~iEsLIP~~~~~~~k~e~~~~s~~~~~~~~er~el~e~v~~KN~qLk~iid~lR~ 136 (150)
T PF11315_consen 81 TPIESLIPYKEEPRNKEEERDSSEEYRQLLEERKELIEQVKQKNQQLKEIIDQLRN 136 (150)
T ss_pred CCHHHhccccCCccccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 354 4678999988866442 56788899999999888876544
No 74
>PF09836 DUF2063: Uncharacterized protein conserved in bacteria (DUF2063); InterPro: IPR018640 This entry contains proteins that have no known function. ; PDB: 3DEE_A.
Probab=20.51 E-value=2.7e+02 Score=18.98 Aligned_cols=40 Identities=13% Similarity=0.312 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHhhchHH-----HHHHHHHHhhhhhhhhhccchHH
Q psy6385 61 KFKAHMLVELSGAFPNE-----LAKYRAIREKALTKNEQVKGKID 100 (137)
Q Consensus 61 ~fR~~L~~el~~~FPel-----~~~y~~ireraLakN~~~~gk~~ 100 (137)
.++..|.+.|+..||-+ .+.+..+-.+=+..++-..+...
T Consensus 39 ~~~~~l~~~L~~~fP~~~~llG~~~f~~la~~y~~~~p~~s~~l~ 83 (94)
T PF09836_consen 39 NYRARLIEALEATFPVVRALLGEEFFDALARAYIRAHPSRSPDLN 83 (94)
T ss_dssp HHHHHHHHHHHHHTTTGGGGS-HHHHHHHHHHHHHSGGGG-S-GG
T ss_pred HHHHHHHHHHHHHhHHHHHHhCHHHHHHHHHHHHHhCCCCCCcHH
Confidence 47788899999999986 34555565565666666555443
No 75
>PRK13713 conjugal transfer protein TraM; Provisional
Probab=20.07 E-value=1.6e+02 Score=22.57 Aligned_cols=47 Identities=21% Similarity=0.306 Sum_probs=33.7
Q ss_pred hcCCCCchhHHHHHHHHHHHhHHHhhHHH-------------------HHHHHHHHHHHHHHhhchH
Q psy6385 29 DQGRNPQLYTKDCIEKALTKNEQVKGKID-------------------AYRKFKAHMLVELSGAFPN 76 (137)
Q Consensus 29 D~GrNPDiYTrefvE~~~~~Nq~~kGK~~-------------------a~~~fR~~L~~el~~~FPe 76 (137)
+.|-|-+.|.|-.+|.|.+.+..+. ||- ....+|+-..++|..=||+
T Consensus 51 es~Fnq~eFnK~lLE~v~kt~~~~~-~IL~~~~lsp~v~~~~~~ey~~mv~~I~~~v~e~m~~FFpe 116 (118)
T PRK13713 51 ESGFNQTEFNKLLLECVVKTQSTVA-KILGIESLSPHVSGNPKFEYANMVEDIREKVSEEMERFFPE 116 (118)
T ss_pred cCcccHHHHHHHHHHHHHHHHHHHH-HHHccccccHhhcCCCcccHHHHHHHHHHHHHHHHHhcCCC
Confidence 6799999999999999998855433 232 3355666666777777775
Done!