Query 042821
Match_columns 81
No_of_seqs 107 out of 691
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 09:50:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042821.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042821hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01397 Terpene_synth: Terpen 100.0 7.4E-36 1.6E-40 207.5 8.1 81 1-81 28-109 (183)
2 cd00684 Terpene_cyclase_plant_ 100.0 1.8E-31 3.9E-36 207.6 8.4 81 1-81 33-117 (542)
3 PLN02279 ent-kaur-16-ene synth 99.9 2.6E-22 5.5E-27 162.6 7.2 66 16-81 268-334 (784)
4 PLN02592 ent-copalyl diphospha 99.8 1.2E-21 2.5E-26 159.0 6.8 66 16-81 308-379 (800)
5 COG4738 Predicted transcriptio 75.3 5.2 0.00011 26.6 3.5 52 22-77 14-70 (124)
6 PF08373 RAP: RAP domain; Int 60.9 6.7 0.00015 21.5 1.6 17 63-79 18-34 (58)
7 PF02084 Bindin: Bindin; Inte 59.6 10 0.00022 27.8 2.7 36 37-75 105-140 (238)
8 cd03569 VHS_Hrs_Vps27p VHS dom 56.7 25 0.00053 23.3 4.0 22 60-81 120-141 (142)
9 PF14164 YqzH: YqzH-like prote 56.0 7.3 0.00016 23.1 1.2 12 70-81 12-23 (64)
10 PF11000 DUF2840: Protein of u 53.4 9.1 0.0002 26.2 1.5 16 20-35 96-111 (149)
11 PF03578 HGWP: HGWP repeat; I 52.3 5.7 0.00012 19.9 0.3 12 70-81 7-18 (28)
12 PF00601 Flu_NS2: Influenza no 51.4 15 0.00033 23.3 2.2 38 3-43 51-88 (94)
13 PF02847 MA3: MA3 domain; Int 50.2 38 0.00083 20.5 3.9 46 4-50 1-47 (113)
14 PF00233 PDEase_I: 3'5'-cyclic 47.9 11 0.00025 26.7 1.4 45 30-79 46-90 (237)
15 PF01963 TraB: TraB family; I 47.3 8.8 0.00019 26.6 0.7 13 69-81 246-258 (259)
16 PF11848 DUF3368: Domain of un 46.2 17 0.00038 19.7 1.7 13 69-81 25-37 (48)
17 PHA00438 hypothetical protein 45.7 11 0.00024 23.3 0.9 11 68-78 40-50 (81)
18 PF01585 G-patch: G-patch doma 44.0 17 0.00037 19.5 1.4 13 66-78 3-15 (45)
19 PF08041 PetM: PetM family of 43.8 30 0.00064 17.7 2.2 15 62-76 15-29 (31)
20 cd07604 BAR_ASAPs The Bin/Amph 36.6 95 0.0021 22.1 4.7 47 2-48 19-68 (215)
21 PF07862 Nif11: Nitrogen fixat 35.7 20 0.00043 19.2 0.9 11 71-81 35-45 (49)
22 KOG4082 Uncharacterized conser 35.0 33 0.00071 25.0 2.1 15 64-78 196-210 (268)
23 PF11121 DUF2639: Protein of u 34.7 31 0.00068 18.6 1.5 23 21-43 5-27 (40)
24 cd03568 VHS_STAM VHS domain fa 34.1 95 0.0021 20.6 4.1 21 60-80 116-136 (144)
25 PF00382 TFIIB: Transcription 33.5 94 0.002 17.5 4.8 51 29-80 6-56 (71)
26 COG1400 SEC65 Signal recogniti 33.2 31 0.00067 21.8 1.6 13 23-35 36-48 (93)
27 smart00544 MA3 Domain in DAP-5 31.2 1E+02 0.0023 18.6 3.8 39 5-44 2-40 (113)
28 PF14090 HTH_39: Helix-turn-he 31.0 18 0.0004 20.9 0.2 16 65-80 30-45 (70)
29 KOG3906 Tryptophan 2,3-dioxyge 30.7 97 0.0021 23.8 4.1 26 6-31 87-113 (399)
30 PF06327 DUF1053: Domain of Un 30.0 4.7 0.0001 24.8 -2.6 34 37-70 52-85 (101)
31 COG1060 ThiH Thiamine biosynth 29.6 54 0.0012 25.2 2.6 34 2-35 181-215 (370)
32 PF14068 YuiB: Putative membra 29.1 30 0.00066 22.3 1.0 16 64-79 86-101 (102)
33 PF12627 PolyA_pol_RNAbd: Prob 28.7 42 0.0009 18.5 1.5 37 4-44 27-63 (64)
34 PF11951 Fungal_trans_2: Funga 28.3 1.6E+02 0.0035 20.3 4.7 58 16-80 323-381 (383)
35 PF09278 MerR-DNA-bind: MerR, 27.7 56 0.0012 18.0 1.9 27 19-49 1-27 (65)
36 PF10866 DUF2704: Protein of u 27.2 1.7E+02 0.0036 20.4 4.4 43 4-49 70-112 (168)
37 PF08196 UL2: UL2 protein; In 26.8 34 0.00074 19.7 0.9 10 65-74 29-38 (60)
38 smart00443 G_patch glycine ric 26.2 54 0.0012 17.3 1.6 14 66-79 5-18 (47)
39 PF10390 ELL: RNA polymerase I 25.9 1.3E+02 0.0028 22.2 4.0 45 4-50 199-243 (284)
40 smart00265 BH4 BH4 Bcl-2 homol 25.7 43 0.00093 16.6 1.0 9 72-80 17-25 (27)
41 KOG4683 Uncharacterized conser 25.4 40 0.00087 27.0 1.3 20 18-37 244-263 (549)
42 PF12017 Tnp_P_element: Transp 25.3 2.7E+02 0.0058 20.2 5.5 14 68-81 90-103 (236)
43 PF07499 RuvA_C: RuvA, C-termi 24.9 1.2E+02 0.0026 16.1 3.3 24 24-50 6-29 (47)
44 PF09124 Endonuc-dimeris: T4 r 24.5 60 0.0013 18.6 1.6 18 19-36 16-33 (54)
45 PF11576 DUF3236: Protein of u 24.5 50 0.0011 22.7 1.5 14 20-33 140-153 (154)
46 PF02005 TRM: N2,N2-dimethylgu 24.2 1.5E+02 0.0033 22.7 4.2 61 19-80 280-354 (377)
47 PF09633 DUF2023: Protein of u 23.9 12 0.00026 24.1 -1.5 34 5-38 11-44 (101)
48 cd04908 ACT_Bt0572_1 N-termina 23.8 33 0.00071 19.0 0.4 11 70-80 55-65 (66)
49 PF00797 Acetyltransf_2: N-ace 23.6 53 0.0012 22.7 1.5 54 16-80 15-68 (240)
50 cd04778 HTH_MerR-like_sg2 Heli 23.4 1.4E+02 0.003 21.2 3.6 30 17-49 42-71 (219)
51 cd04783 HTH_MerR1 Helix-Turn-H 23.3 1.2E+02 0.0027 19.1 3.1 27 17-46 42-68 (126)
52 PRK10941 hypothetical protein; 22.9 1.6E+02 0.0034 21.7 3.9 24 3-26 40-63 (269)
53 PF05184 SapB_1: Saposin-like 22.8 1.1E+02 0.0025 15.0 2.9 25 25-49 11-35 (39)
54 TIGR02366 DHAK_reg probable di 22.8 92 0.002 20.1 2.5 34 16-50 18-56 (176)
55 cd07641 BAR_ASAP1 The Bin/Amph 22.7 1.9E+02 0.0041 21.0 4.2 47 2-48 19-68 (215)
56 PF08784 RPA_C: Replication pr 22.7 1.7E+02 0.0038 17.6 3.6 46 3-51 47-92 (102)
57 cd02071 MM_CoA_mut_B12_BD meth 22.6 70 0.0015 20.1 1.8 20 60-79 9-30 (122)
58 PRK04338 N(2),N(2)-dimethylgua 22.1 2.4E+02 0.0053 21.6 5.0 47 34-80 298-355 (382)
59 PF01316 Arg_repressor: Argini 22.1 37 0.0008 20.1 0.4 12 70-81 27-38 (70)
60 PHA00360 II replication initia 21.6 1.7E+02 0.0036 23.3 4.0 54 24-77 292-346 (421)
61 cd07603 BAR_ACAPs The Bin/Amph 21.4 2.2E+02 0.0047 19.9 4.3 46 3-48 20-66 (200)
62 cd04909 ACT_PDH-BS C-terminal 21.3 59 0.0013 17.8 1.2 15 65-79 55-69 (69)
63 KOG0856 Predicted pilin-like t 21.1 48 0.0011 22.6 0.9 14 65-78 26-39 (146)
64 PF10617 DUF2474: Protein of u 20.9 90 0.0019 16.8 1.7 12 61-72 21-32 (40)
65 PF03683 UPF0175: Uncharacteri 20.8 1.5E+02 0.0033 17.3 2.9 26 19-44 46-72 (76)
66 COG0632 RuvA Holliday junction 20.8 1.6E+02 0.0034 20.9 3.4 42 23-69 158-199 (201)
67 cd04882 ACT_Bt0572_2 C-termina 20.7 48 0.001 17.6 0.7 15 65-79 50-64 (65)
68 PRK05728 DNA polymerase III su 20.2 66 0.0014 21.1 1.4 20 61-80 116-135 (142)
69 PRK11876 petM cytochrome b6-f 20.1 70 0.0015 16.4 1.2 15 62-76 17-31 (32)
No 1
>PF01397 Terpene_synth: Terpene synthase, N-terminal domain; InterPro: IPR001906 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 2ONH_A 2ONG_B 3P5R_A 3P5P_A 3N0F_A 3N0G_B 3PYB_A 3PYA_A 3G4F_A 3G4D_B ....
Probab=100.00 E-value=7.4e-36 Score=207.48 Aligned_cols=81 Identities=49% Similarity=0.854 Sum_probs=68.8
Q ss_pred ChHHHHHHHHHHHhhc-ChhhHHHHHHHHHHhccccchHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHhhCCCCC
Q 042821 1 AEELKGKVKTTIKYAT-EPLDQLEQIDNLQRLGLAYHFQTEIRNILHGIYNNNKDDNWRNKNVYAASVEFRLLRQHGYNV 79 (81)
Q Consensus 1 ~e~LkeeVk~ml~~~~-~~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~~~~~dL~~~aL~FRLLRq~Gy~V 79 (81)
+++||++||.|+.... ++.++|+|||+||||||+|||++||+++|+++|+.+........|||+|||+|||||||||+|
T Consensus 28 ~~~Lk~~v~~~l~~~~~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~dL~~~AL~FRLLRqhGy~V 107 (183)
T PF01397_consen 28 AEELKEEVRNMLPASYPDPLEKLELIDTLQRLGISYHFEDEIKEILDSIYRSWDEDNEEIDDLYTTALRFRLLRQHGYYV 107 (183)
T ss_dssp HHHHHHHHHHHHHSSSSHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHHTTTTTSHTSSCHHHHHHHHHHHHHTT---
T ss_pred HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhhhccccccccCchhHHHHHHHHHHHcCCcc
Confidence 3789999999998754 799999999999999999999999999999999987764322259999999999999999999
Q ss_pred CC
Q 042821 80 SQ 81 (81)
Q Consensus 80 S~ 81 (81)
||
T Consensus 108 S~ 109 (183)
T PF01397_consen 108 SS 109 (183)
T ss_dssp -G
T ss_pred cH
Confidence 97
No 2
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=99.97 E-value=1.8e-31 Score=207.63 Aligned_cols=81 Identities=43% Similarity=0.738 Sum_probs=72.2
Q ss_pred ChHHHHHHHHHHHh---hcChhhHHHHHHHHHHhccccchHHHHHHHHHHHhhcCCCCC-CCCCCHHHHHHHHHHHhhCC
Q 042821 1 AEELKGKVKTTIKY---ATEPLDQLEQIDNLQRLGLAYHFQTEIRNILHGIYNNNKDDN-WRNKNVYAASVEFRLLRQHG 76 (81)
Q Consensus 1 ~e~LkeeVk~ml~~---~~~~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~-~~~~dL~~~aL~FRLLRq~G 76 (81)
+++||++||+||.. +.++.++|++||+||||||+|||++||+++|+.+|+.|...+ ....|||+|||+||||||||
T Consensus 33 ~~~lk~~v~~~~~~~~~~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~~~~~~dl~~~al~FRlLR~~G 112 (542)
T cd00684 33 IEELKEEVRKMLEDSEYPVDLFERLWLIDRLQRLGISYHFEDEIKEILDYIYRYWTERGESNEDDLYTTALGFRLLRQHG 112 (542)
T ss_pred HHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHcCchhhhHHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHHHHHcC
Confidence 37899999999976 568999999999999999999999999999999999875432 12369999999999999999
Q ss_pred CCCCC
Q 042821 77 YNVSQ 81 (81)
Q Consensus 77 y~VS~ 81 (81)
|+|||
T Consensus 113 y~vs~ 117 (542)
T cd00684 113 YNVSS 117 (542)
T ss_pred CCcCH
Confidence 99996
No 3
>PLN02279 ent-kaur-16-ene synthase
Probab=99.87 E-value=2.6e-22 Score=162.57 Aligned_cols=66 Identities=30% Similarity=0.568 Sum_probs=58.5
Q ss_pred cChhhHHHHHHHHHHhccccchHHHHHHHHHHHhhcCCCCCCC-CCCHHHHHHHHHHHhhCCCCCCC
Q 042821 16 TEPLDQLEQIDNLQRLGLAYHFQTEIRNILHGIYNNNKDDNWR-NKNVYAASVEFRLLRQHGYNVSQ 81 (81)
Q Consensus 16 ~~~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~~~-~~dL~~~aL~FRLLRq~Gy~VS~ 81 (81)
.+.++++++||+||||||+|||++||+++|+.+|+.|...+.. ..|+++|||+|||||||||+|||
T Consensus 268 ~~~fe~l~lvd~L~rlGi~~hF~~EI~~~L~~~~~~~~~~~~~~~~Dl~~tAl~FRLLR~hGy~VS~ 334 (784)
T PLN02279 268 LDQYARLSMVDTLERLGIDRHFRKEIKSVLDETYRYWLQGEEEIFLDLATCALAFRILRLNGYDVSS 334 (784)
T ss_pred ccHHHHhHHHHHHHHhCCccccHHHHHHHHHHHHHhhcccccCCCCCHHHHHHHHHHHHHcCCCCCh
Confidence 4679999999999999999999999999999999877542111 26999999999999999999997
No 4
>PLN02592 ent-copalyl diphosphate synthase
Probab=99.85 E-value=1.2e-21 Score=158.98 Aligned_cols=66 Identities=27% Similarity=0.483 Sum_probs=57.8
Q ss_pred cChhhHHHHHHHHHHhccccchHHHHHHHHHHHhhcCCCCC----CC--CCCHHHHHHHHHHHhhCCCCCCC
Q 042821 16 TEPLDQLEQIDNLQRLGLAYHFQTEIRNILHGIYNNNKDDN----WR--NKNVYAASVEFRLLRQHGYNVSQ 81 (81)
Q Consensus 16 ~~~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~----~~--~~dL~~~aL~FRLLRq~Gy~VS~ 81 (81)
.+++++|++||+||||||+|||++||+++|+.+|+.|...+ .+ ..|+++|||+|||||||||+|||
T Consensus 308 ~d~fE~LwlVDtLqRLGIs~hF~~EI~~iLd~iy~~w~~~g~~~a~~~~~~Dld~TALaFRLLRqhGy~VS~ 379 (800)
T PLN02592 308 VDLFEHIWAVDRLQRLGISRYFEPEIKECIDYVHRYWTENGICWARNSHVHDIDDTAMGFRLLRLHGHQVSA 379 (800)
T ss_pred CcHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhcCcccccCCCcCCHHHHHHHHHHHHHcCCCCCh
Confidence 57899999999999999999999999999999998654321 11 26999999999999999999996
No 5
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=75.29 E-value=5.2 Score=26.56 Aligned_cols=52 Identities=21% Similarity=0.374 Sum_probs=31.1
Q ss_pred HHHHHHHHHhccccchHHHHHHHHHHHhhcCCCCCCCC---CCHH--HHHHHHHHHhhCCC
Q 042821 22 LEQIDNLQRLGLAYHFQTEIRNILHGIYNNNKDDNWRN---KNVY--AASVEFRLLRQHGY 77 (81)
Q Consensus 22 L~lID~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~~~~---~dL~--~~aL~FRLLRq~Gy 77 (81)
=.+|+.|+.|||++.-- .+|-.+-+.......++ ..|- .||++-|.||.+|+
T Consensus 14 ~~~ie~L~~lgi~R~vA----~tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gW 70 (124)
T COG4738 14 YEIIELLRILGIPRNVA----TTLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENGW 70 (124)
T ss_pred HHHHHHHHHcCCCchHH----HHHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccc
Confidence 45899999999998752 23333322111000000 1222 59999999999996
No 6
>PF08373 RAP: RAP domain; InterPro: IPR013584 The ~60-residue RAP (an acronym for RNA-binding domain abundant in Apicomplexans) domain is found in various proteins in eukaryotes. It is particularly abundant in apicomplexans and might mediate a range of cellular functions through its potential interactions with RNA []. The RAP domain consists of multiple blocks of charged and aromatics residues and is predicted to be composed of alpha helical and beta strand structures. Two predicted loop regions that are dominated by glycine and tryptophan residues are found before and after the central beta sheet []. Some proteins known to contain a RAP domain are listed below: Human hypothetical protein MGC5297, Mammalian FAST kinase domain-containing proteins (FASTKDs), Chlamydomonas reinhardtii chloroplastic trans-splicing factor Raa3.
Probab=60.89 E-value=6.7 Score=21.48 Aligned_cols=17 Identities=29% Similarity=0.524 Sum_probs=15.7
Q ss_pred HHHHHHHHHHhhCCCCC
Q 042821 63 YAASVEFRLLRQHGYNV 79 (81)
Q Consensus 63 ~~~aL~FRLLRq~Gy~V 79 (81)
-.++|.=|+|+..||.|
T Consensus 18 g~t~lk~r~L~~~G~~V 34 (58)
T PF08373_consen 18 GSTKLKHRHLKALGYKV 34 (58)
T ss_pred hHHHHHHHHHHHCCCEE
Confidence 57999999999999987
No 7
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=59.59 E-value=10 Score=27.77 Aligned_cols=36 Identities=19% Similarity=0.273 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHhhC
Q 042821 37 FQTEIRNILHGIYNNNKDDNWRNKNVYAASVEFRLLRQH 75 (81)
Q Consensus 37 F~~EI~~~L~~i~~~~~~~~~~~~dL~~~aL~FRLLRq~ 75 (81)
--+.|+.+|-..--... -++.|.|+.-|-.|-||.|
T Consensus 105 vm~~ikavLgaTKiDLP---VDINDPYDlGLLLRhLRHH 140 (238)
T PF02084_consen 105 VMEDIKAVLGATKIDLP---VDINDPYDLGLLLRHLRHH 140 (238)
T ss_pred HHHHHHHHhcccccccc---cccCChhhHHHHHHHHHHH
Confidence 34667777765421222 2567999999999999987
No 8
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=56.73 E-value=25 Score=23.27 Aligned_cols=22 Identities=9% Similarity=0.265 Sum_probs=18.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCCC
Q 042821 60 KNVYAASVEFRLLRQHGYNVSQ 81 (81)
Q Consensus 60 ~dL~~~aL~FRLLRq~Gy~VS~ 81 (81)
.++-.+.=.|..||..||..++
T Consensus 120 ~~l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 120 PQLKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred cccHHHHHHHHHHHHcCCCCCC
Confidence 4677788889999999998764
No 9
>PF14164 YqzH: YqzH-like protein
Probab=55.96 E-value=7.3 Score=23.15 Aligned_cols=12 Identities=50% Similarity=0.717 Sum_probs=9.4
Q ss_pred HHHhhCCCCCCC
Q 042821 70 RLLRQHGYNVSQ 81 (81)
Q Consensus 70 RLLRq~Gy~VS~ 81 (81)
+-|||.||++++
T Consensus 12 ~~l~QYg~d~~~ 23 (64)
T PF14164_consen 12 NCLRQYGYDVEC 23 (64)
T ss_pred HHHHHhCCcccC
Confidence 568999998764
No 10
>PF11000 DUF2840: Protein of unknown function (DUF2840); InterPro: IPR021263 This bacterial family of proteins have no known function.
Probab=53.44 E-value=9.1 Score=26.23 Aligned_cols=16 Identities=31% Similarity=0.542 Sum_probs=13.6
Q ss_pred hHHHHHHHHHHhcccc
Q 042821 20 DQLEQIDNLQRLGLAY 35 (81)
Q Consensus 20 ~~L~lID~lqrLGi~~ 35 (81)
.-|..||+++.|||+-
T Consensus 96 ~VL~~IDaiEalGidp 111 (149)
T PF11000_consen 96 RVLQAIDAIEALGIDP 111 (149)
T ss_pred HHHHHHhHHHHcCCCh
Confidence 3488999999999974
No 11
>PF03578 HGWP: HGWP repeat; InterPro: IPR005213 This short (30 amino acids) repeat is found in a number of plant proteins. It contains a conserved HGWP motif, hence its name. The function of these proteins is unknown.
Probab=52.30 E-value=5.7 Score=19.95 Aligned_cols=12 Identities=33% Similarity=0.592 Sum_probs=9.3
Q ss_pred HHHhhCCCCCCC
Q 042821 70 RLLRQHGYNVSQ 81 (81)
Q Consensus 70 RLLRq~Gy~VS~ 81 (81)
.-||.||+.|+|
T Consensus 7 Wc~rLhGW~i~p 18 (28)
T PF03578_consen 7 WCLRLHGWPIMP 18 (28)
T ss_pred hheeeccCcccC
Confidence 347899998875
No 12
>PF00601 Flu_NS2: Influenza non-structural protein (NS2); InterPro: IPR000968 The Influenza A virus belongs to the class of ssRNA negative-strand viruses. Nonstructural protein 2 (NS2) may play a role in promoting normal replication of the genomic RNAs by preventing the replication of short-length RNA species []. NS1 and NS2 proteins are produced from the same gene by alternative splicing.; GO: 0006405 RNA export from nucleus, 0042025 host cell nucleus; PDB: 1PD3_B.
Probab=51.42 E-value=15 Score=23.27 Aligned_cols=38 Identities=24% Similarity=0.347 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhhcChhhHHHHHHHHHHhccccchHHHHHH
Q 042821 3 ELKGKVKTTIKYATEPLDQLEQIDNLQRLGLAYHFQTEIRN 43 (81)
Q Consensus 3 ~LkeeVk~ml~~~~~~~~~L~lID~lqrLGi~~hF~~EI~~ 43 (81)
-|.+++|..+..+++.++++.+.-+||-| +--++||..
T Consensus 51 wlI~e~r~~l~~tensf~qItfmqaLqlL---lEve~eirt 88 (94)
T PF00601_consen 51 WLIEEHRHRLKITENSFEQITFMQALQLL---LEVEQEIRT 88 (94)
T ss_dssp HHHHHHHHC----TTSHHHHHHHHHHHHH---HHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHH---HHHHHHHHH
Confidence 45677777777777888888887777765 455555554
No 13
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=50.16 E-value=38 Score=20.55 Aligned_cols=46 Identities=22% Similarity=0.230 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhhcChhhHHHHHHHHHHhccccchHHHH-HHHHHHHhh
Q 042821 4 LKGKVKTTIKYATEPLDQLEQIDNLQRLGLAYHFQTEI-RNILHGIYN 50 (81)
Q Consensus 4 LkeeVk~ml~~~~~~~~~L~lID~lqrLGi~~hF~~EI-~~~L~~i~~ 50 (81)
+|+.|+..+.+..+....-+.+..|+.|+++ .|..|+ ..++.....
T Consensus 1 ~rk~i~~~l~ey~~~~d~~ea~~~l~el~~~-~~~~~vv~~~l~~~le 47 (113)
T PF02847_consen 1 LRKKIFSILMEYFSSGDVDEAVECLKELKLP-SQHHEVVKVILECALE 47 (113)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHHHHTT-G-GGHHHHHHHHHHHHHT
T ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHhCCC-ccHHHHHHHHHHHHhh
Confidence 4677888877643334556677888999999 555554 444444443
No 14
>PF00233 PDEase_I: 3'5'-cyclic nucleotide phosphodiesterase; InterPro: IPR002073 The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction. PDE enzymes are often targets for pharmacological inhibition due to their unique tissue distribution, structural properties, and functional properties. Inhibitors include: Roflumilast for chronic obstructive pulmonary disease and asthma [], Sildenafil for erectile dysfunction [] and Cilostazol for peripheral arterial occlusive disease [], amongst others. Retinal 3',5'-cGMP phosphodiesterase is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion. This entry represents the catalytic domain of PDE which is multihelical and can be divided into three subdomains.; GO: 0004114 3',5'-cyclic-nucleotide phosphodiesterase activity, 0007165 signal transduction; PDB: 3I8V_A 3TVX_A 2QYK_A 1ZKL_A 3G3N_A 4DFF_B 2OUS_B 3SNL_A 2OUY_A 2OUP_B ....
Probab=47.91 E-value=11 Score=26.69 Aligned_cols=45 Identities=22% Similarity=0.357 Sum_probs=31.8
Q ss_pred HhccccchHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHhhCCCCC
Q 042821 30 RLGLAYHFQTEIRNILHGIYNNNKDDNWRNKNVYAASVEFRLLRQHGYNV 79 (81)
Q Consensus 30 rLGi~~hF~~EI~~~L~~i~~~~~~~~~~~~dL~~~aL~FRLLRq~Gy~V 79 (81)
.=|++.-|.-..+..|-.+|+... .-.-|-+|+.|++|+..|+++
T Consensus 46 HpG~~N~flv~~~~~LA~~Y~d~S-----vLE~~H~~~~~~lL~~~~~ni 90 (237)
T PF00233_consen 46 HPGVNNAFLVKTNSPLAILYNDRS-----VLENHHCALAFQLLRKEECNI 90 (237)
T ss_dssp -SSSCHHHHHHTTSHHHHHTTTSS-----HHHHHHHHHHHHHHTSTTTTT
T ss_pred CCccccchhhccccchhhhcCccC-----CccccHHHHHHHHHHhhhhhh
Confidence 447777777777777777765411 124578999999999999876
No 15
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=47.27 E-value=8.8 Score=26.62 Aligned_cols=13 Identities=46% Similarity=0.892 Sum_probs=11.1
Q ss_pred HHHHhhCCCCCCC
Q 042821 69 FRLLRQHGYNVSQ 81 (81)
Q Consensus 69 FRLLRq~Gy~VS~ 81 (81)
..+||+.||.|++
T Consensus 246 l~lLr~~Gy~V~~ 258 (259)
T PF01963_consen 246 LDLLRKKGYTVEP 258 (259)
T ss_pred HHHHHhCCceeec
Confidence 3899999999975
No 16
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=46.16 E-value=17 Score=19.68 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=7.7
Q ss_pred HHHHhhCCCCCCC
Q 042821 69 FRLLRQHGYNVSQ 81 (81)
Q Consensus 69 FRLLRq~Gy~VS~ 81 (81)
+.-|+++||++|+
T Consensus 25 l~~l~~~g~~is~ 37 (48)
T PF11848_consen 25 LDRLQQAGFRISP 37 (48)
T ss_pred HHHHHHcCcccCH
Confidence 4444666776663
No 17
>PHA00438 hypothetical protein
Probab=45.74 E-value=11 Score=23.35 Aligned_cols=11 Identities=73% Similarity=1.186 Sum_probs=9.2
Q ss_pred HHHHHhhCCCC
Q 042821 68 EFRLLRQHGYN 78 (81)
Q Consensus 68 ~FRLLRq~Gy~ 78 (81)
..|+||++||.
T Consensus 40 ~i~~lR~~G~S 50 (81)
T PHA00438 40 EIRLLRQAGYS 50 (81)
T ss_pred hHHHHHHcCCc
Confidence 45899999995
No 18
>PF01585 G-patch: G-patch domain; InterPro: IPR000467 The D111/G-patch domain [] is a short conserved region of about 40 amino acids which occurs in a number of putative RNA-binding proteins, including tumor suppressor and DNA-damage-repair proteins, suggesting that this domain may have an RNA binding function. This domain has seven highly conserved glycines. A multiple alignment of a small subset of D111/G-patch domains is shown in Fig. 2b of [].; GO: 0003676 nucleic acid binding, 0005622 intracellular
Probab=44.04 E-value=17 Score=19.53 Aligned_cols=13 Identities=31% Similarity=0.907 Sum_probs=11.4
Q ss_pred HHHHHHHhhCCCC
Q 042821 66 SVEFRLLRQHGYN 78 (81)
Q Consensus 66 aL~FRLLRq~Gy~ 78 (81)
+..||+|++.||.
T Consensus 3 ~~g~~lm~kmGw~ 15 (45)
T PF01585_consen 3 SIGFKLMKKMGWK 15 (45)
T ss_pred cHHHHHHHHCCCC
Confidence 5689999999996
No 19
>PF08041 PetM: PetM family of cytochrome b6f complex subunit 7; InterPro: IPR012595 This family consists of the PetM family of cytochrome b6f complex subunit IV. The cytochrome b6f complex consists of 7 subunits and contains 2 beta haem's and 1 chlorophyll alpha per cytochrome f. It is highly active in transferring electrons from decylplastoquinol to oxidised plastocyanin [].; GO: 0009512 cytochrome b6f complex; PDB: 2ZT9_F 1Q90_M 2E76_F 2E75_F 2E74_F 2D2C_S 1VF5_S.
Probab=43.76 E-value=30 Score=17.73 Aligned_cols=15 Identities=27% Similarity=0.527 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHhhCC
Q 042821 62 VYAASVEFRLLRQHG 76 (81)
Q Consensus 62 L~~~aL~FRLLRq~G 76 (81)
|--.|+.|=|||-+|
T Consensus 15 lvGla~Gf~LLkiQG 29 (31)
T PF08041_consen 15 LVGLALGFVLLKIQG 29 (31)
T ss_dssp HHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHhheeec
Confidence 456899999999887
No 20
>cd07604 BAR_ASAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ASAPs (ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) with similarity to ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins) in that they contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and ankyrin (ANK) repeats. However, ASAPs contain an additional C-terminal SH3 domain. ASAPs function in regulating cell growth, migration, and invasion. Vertebrates contain at least three members, ASAP1, ASAP2, and ASAP3. ASAP1 and ASAP2 shows GTPase activating protein (GAP) activity towards Arf1 and Arf5. They do not show GAP activity towards Arf6, but is able to mediate
Probab=36.60 E-value=95 Score=22.07 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=30.4
Q ss_pred hHHHHHHHHHHHhhcC-hhhHHHHHHHHHHhccccc--hHHHHHHHHHHH
Q 042821 2 EELKGKVKTTIKYATE-PLDQLEQIDNLQRLGLAYH--FQTEIRNILHGI 48 (81)
Q Consensus 2 e~LkeeVk~ml~~~~~-~~~~L~lID~lqrLGi~~h--F~~EI~~~L~~i 48 (81)
++++.-+|.|..+..+ ......++++|+.||=..- .+.+|..+|...
T Consensus 19 ~Kl~K~~k~~~~~g~~~~~~~~~F~~aL~~~g~~~~~~~~~~i~~~l~kF 68 (215)
T cd07604 19 QKLKKAVKAIHNSGLAHVENELQFAEALEKLGSKALSREEEDLGAAFLKF 68 (215)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhccccCcccHHHHHHHHHH
Confidence 4567777777755433 4567889999999993221 233577776554
No 21
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=35.74 E-value=20 Score=19.22 Aligned_cols=11 Identities=36% Similarity=0.857 Sum_probs=8.7
Q ss_pred HHhhCCCCCCC
Q 042821 71 LLRQHGYNVSQ 81 (81)
Q Consensus 71 LLRq~Gy~VS~ 81 (81)
+-|.+||.+|+
T Consensus 35 lA~~~Gy~ft~ 45 (49)
T PF07862_consen 35 LAREAGYDFTE 45 (49)
T ss_pred HHHHcCCCCCH
Confidence 45999999873
No 22
>KOG4082 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.01 E-value=33 Score=24.98 Aligned_cols=15 Identities=40% Similarity=0.616 Sum_probs=10.8
Q ss_pred HHHHHHHHHhhCCCC
Q 042821 64 AASVEFRLLRQHGYN 78 (81)
Q Consensus 64 ~~aL~FRLLRq~Gy~ 78 (81)
.+-..|.-||||||=
T Consensus 196 ~iqasf~tLrq~Gki 210 (268)
T KOG4082|consen 196 CIQASFKTLRQHGKI 210 (268)
T ss_pred HHHHHHHHHHHhCCC
Confidence 344467789999983
No 23
>PF11121 DUF2639: Protein of unknown function (DUF2639); InterPro: IPR022580 This family is conserved in the Bacillaceae family. Several members are named as being YflJ, but the function is not known.
Probab=34.67 E-value=31 Score=18.64 Aligned_cols=23 Identities=17% Similarity=0.306 Sum_probs=17.3
Q ss_pred HHHHHHHHHHhccccchHHHHHH
Q 042821 21 QLEQIDNLQRLGLAYHFQTEIRN 43 (81)
Q Consensus 21 ~L~lID~lqrLGi~~hF~~EI~~ 43 (81)
|=|.|..|..+||.+|=..-++.
T Consensus 5 KGw~V~eLKk~GI~~h~~rKles 27 (40)
T PF11121_consen 5 KGWYVKELKKLGIRRHEGRKLES 27 (40)
T ss_pred chHHHHHHHHhCccccchhHHHH
Confidence 34788999999999987554443
No 24
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=34.13 E-value=95 Score=20.55 Aligned_cols=21 Identities=14% Similarity=0.237 Sum_probs=17.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCC
Q 042821 60 KNVYAASVEFRLLRQHGYNVS 80 (81)
Q Consensus 60 ~dL~~~aL~FRLLRq~Gy~VS 80 (81)
.++-.++=.+..|+..||..+
T Consensus 116 ~~l~~i~~~y~~L~~~G~~f~ 136 (144)
T cd03568 116 PSLSLMSDLYKKLKNEGPDLV 136 (144)
T ss_pred cccHHHHHHHHHHHHcCCCCC
Confidence 477788888999999999753
No 25
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=33.48 E-value=94 Score=17.52 Aligned_cols=51 Identities=16% Similarity=0.173 Sum_probs=31.8
Q ss_pred HHhccccchHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHhhCCCCCC
Q 042821 29 QRLGLAYHFQTEIRNILHGIYNNNKDDNWRNKNVYAASVEFRLLRQHGYNVS 80 (81)
Q Consensus 29 qrLGi~~hF~~EI~~~L~~i~~~~~~~~~~~~dL~~~aL~FRLLRq~Gy~VS 80 (81)
.+||++.+..+.=..+.....+.+...+.. ..--..|--|--=|++|.+.|
T Consensus 6 ~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~-~~~iaAA~iY~acr~~~~~~t 56 (71)
T PF00382_consen 6 SKLGLPEDVRERAKEIYKKAQERGLLKGRS-PESIAAACIYLACRLNGVPRT 56 (71)
T ss_dssp HHTT--HHHHHHHHHHHHHHHHTTTSTTS--HHHHHHHHHHHHHHHTTSSSS
T ss_pred hHcCCCHHHHHHHHHHHHHHHHcCCcccCC-HHHHHHHHHHHHHHHcCCCcC
Confidence 578899888888888888887765432222 233344555556688888765
No 26
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=33.24 E-value=31 Score=21.81 Aligned_cols=13 Identities=38% Similarity=0.521 Sum_probs=11.2
Q ss_pred HHHHHHHHhcccc
Q 042821 23 EQIDNLQRLGLAY 35 (81)
Q Consensus 23 ~lID~lqrLGi~~ 35 (81)
++.++++.||+.+
T Consensus 36 ei~~a~~~LGl~~ 48 (93)
T COG1400 36 EIAEALRELGLKP 48 (93)
T ss_pred HHHHHHHHcCCCe
Confidence 5788999999988
No 27
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=31.22 E-value=1e+02 Score=18.62 Aligned_cols=39 Identities=23% Similarity=0.186 Sum_probs=22.9
Q ss_pred HHHHHHHHHhhcChhhHHHHHHHHHHhccccchHHHHHHH
Q 042821 5 KGKVKTTIKYATEPLDQLEQIDNLQRLGLAYHFQTEIRNI 44 (81)
Q Consensus 5 keeVk~ml~~~~~~~~~L~lID~lqrLGi~~hF~~EI~~~ 44 (81)
++.+...+.+..++-.--+.+..|..|++. +|..|+=..
T Consensus 2 ~k~i~~~l~ey~~~~D~~ea~~~l~~L~~~-~~~~~vv~~ 40 (113)
T smart00544 2 KKKIFLIIEEYLSSGDTDEAVHCLLELKLP-EQHHEVVKV 40 (113)
T ss_pred hhHHHHHHHHHHHcCCHHHHHHHHHHhCCC-cchHHHHHH
Confidence 445555555433333445567778888888 566665443
No 28
>PF14090 HTH_39: Helix-turn-helix domain
Probab=30.99 E-value=18 Score=20.93 Aligned_cols=16 Identities=25% Similarity=0.517 Sum_probs=10.9
Q ss_pred HHHHHHHHhhCCCCCC
Q 042821 65 ASVEFRLLRQHGYNVS 80 (81)
Q Consensus 65 ~aL~FRLLRq~Gy~VS 80 (81)
.|=+-.=||++||+|.
T Consensus 30 ~~aRI~eLR~~G~~I~ 45 (70)
T PF14090_consen 30 LAARISELRKKGYPIV 45 (70)
T ss_pred HHHHHHHHHHcCCeee
Confidence 3444455899999874
No 29
>KOG3906 consensus Tryptophan 2,3-dioxygenase [Amino acid transport and metabolism]
Probab=30.73 E-value=97 Score=23.82 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=15.9
Q ss_pred HHHHHHHHhh-cChhhHHHHHHHHHHh
Q 042821 6 GKVKTTIKYA-TEPLDQLEQIDNLQRL 31 (81)
Q Consensus 6 eeVk~ml~~~-~~~~~~L~lID~lqrL 31 (81)
+.||+||.+. .|....|+.|-.+-|.
T Consensus 87 DsvR~~l~~~v~DEtktLkiVsrl~Rv 113 (399)
T KOG3906|consen 87 DSVRKLLNNTVVDETKTLKIVSRLDRV 113 (399)
T ss_pred HHHHHHhcchhhcchhHHHHHHhHHHH
Confidence 5688888753 3555556666555554
No 30
>PF06327 DUF1053: Domain of Unknown Function (DUF1053); InterPro: IPR009398 Cyclic AMP (cAMP) is a ubiquitous signalling molecule which mediates many cellular processes by activating cAMP-dependent kinases and also inducing protein-protein interactions. This molecule is produced by the adenylate cyclase (AC) enzyme, using ATP as its substrate. Mammalian adenylate cyclase has nine closely related membrane-bound isoforms (AC1-9) showing significant sequence homology and sharing the same overall structure: two hydrophobic transmembrane domains, and two cytoplasmic domains that are responsible for the catalytic activity. These isoforms differ in both their tissue specificity and their regulation. Regulatory factors known to influence one or more of these isoforms include G proteins, protein kinases, calcium and calmodulin. For more information see [, ]. This entry represents a region of unknown function found in many of these isoforms. It is part of the N-terminal cytoplasmic domain but its presence is not necessary for catalytic activity []. ; GO: 0004016 adenylate cyclase activity, 0009190 cyclic nucleotide biosynthetic process, 0016021 integral to membrane
Probab=29.95 E-value=4.7 Score=24.83 Aligned_cols=34 Identities=15% Similarity=0.288 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHH
Q 042821 37 FQTEIRNILHGIYNNNKDDNWRNKNVYAASVEFR 70 (81)
Q Consensus 37 F~~EI~~~L~~i~~~~~~~~~~~~dL~~~aL~FR 70 (81)
+++||++.|.+.-..-........+++..+|.|+
T Consensus 52 ~eeevn~~l~~aIe~~S~~r~rse~~~~~tL~F~ 85 (101)
T PF06327_consen 52 PEEEVNERLMQAIEARSSDRMRSEHINRFTLRFK 85 (101)
T ss_pred cHHHHHHHHHHHHHHHHHHhHhhhhcceeeEEEC
Confidence 7889988887765431110012257777777764
No 31
>COG1060 ThiH Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]
Probab=29.65 E-value=54 Score=25.21 Aligned_cols=34 Identities=26% Similarity=0.308 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHHhh-cChhhHHHHHHHHHHhcccc
Q 042821 2 EELKGKVKTTIKYA-TEPLDQLEQIDNLQRLGLAY 35 (81)
Q Consensus 2 e~LkeeVk~ml~~~-~~~~~~L~lID~lqrLGi~~ 35 (81)
+.|.++||+.+... .++-..|+.++..-||||..
T Consensus 181 eil~e~vr~~~~p~K~~~~~wle~~~~Ah~lGI~~ 215 (370)
T COG1060 181 EILSEEVRKIHCPPKKSPEEWLEIHERAHRLGIPT 215 (370)
T ss_pred eechHHHHHhhCCCCCCHHHHHHHHHHHHHcCCCc
Confidence 56788999888753 58899999999999999863
No 32
>PF14068 YuiB: Putative membrane protein
Probab=29.05 E-value=30 Score=22.30 Aligned_cols=16 Identities=31% Similarity=0.760 Sum_probs=12.5
Q ss_pred HHHHHHHHHhhCCCCC
Q 042821 64 AASVEFRLLRQHGYNV 79 (81)
Q Consensus 64 ~~aL~FRLLRq~Gy~V 79 (81)
.....-|.||..||.+
T Consensus 86 ~SG~tIr~LRk~GYqM 101 (102)
T PF14068_consen 86 VSGITIRTLRKKGYQM 101 (102)
T ss_pred HHHHHHHHHHHccccC
Confidence 3446679999999975
No 33
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=28.72 E-value=42 Score=18.46 Aligned_cols=37 Identities=16% Similarity=0.291 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhhcChhhHHHHHHHHHHhccccchHHHHHHH
Q 042821 4 LKGKVKTTIKYATEPLDQLEQIDNLQRLGLAYHFQTEIRNI 44 (81)
Q Consensus 4 LkeeVk~ml~~~~~~~~~L~lID~lqrLGi~~hF~~EI~~~ 44 (81)
..+|+.++|... ++ -..+..+..+|+-.+.-.|++.+
T Consensus 27 i~~El~kil~~~-~~---~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 27 IREELEKILSSP-NP---SRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp HHHHHHHHHTST-TH---HHHHHHHHHTTCHHHHSTTHHT-
T ss_pred HHHHHHHHHcCC-CH---HHHHHHHHHcCCHHHHCcccccc
Confidence 345555555432 12 23445566777655544555544
No 34
>PF11951 Fungal_trans_2: Fungal specific transcription factor domain; InterPro: IPR021858 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 454 to 826 amino acids in length. This protein is found associated with PF00172 from PFAM.
Probab=28.29 E-value=1.6e+02 Score=20.26 Aligned_cols=58 Identities=19% Similarity=0.307 Sum_probs=39.4
Q ss_pred cChhhHHHHHHHHHHhc-cccchHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHhhCCCCCC
Q 042821 16 TEPLDQLEQIDNLQRLG-LAYHFQTEIRNILHGIYNNNKDDNWRNKNVYAASVEFRLLRQHGYNVS 80 (81)
Q Consensus 16 ~~~~~~L~lID~lqrLG-i~~hF~~EI~~~L~~i~~~~~~~~~~~~dL~~~aL~FRLLRq~Gy~VS 80 (81)
.++.++-++++.+++++ .++-.-..+.++|+.+++........ .| +..+++..|+.|+
T Consensus 323 ~~~~~R~~~~~~l~~~~~~~~~~~~~~~~~l~~vW~~~~~~~~~-~~------W~~~~~~~~~~~~ 381 (383)
T PF11951_consen 323 RDPEQRDWILARLRRLQSSGFGNVRRARELLEEVWRRRDDGGPR-WD------WRDIMRELGWDVL 381 (383)
T ss_pred CCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhhcCCCcC-CC------cchHHHhCCCCEE
Confidence 46678888999999999 55555778888999998764421111 12 4566777777664
No 35
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=27.75 E-value=56 Score=17.95 Aligned_cols=27 Identities=37% Similarity=0.751 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHhccccchHHHHHHHHHHHh
Q 042821 19 LDQLEQIDNLQRLGLAYHFQTEIRNILHGIY 49 (81)
Q Consensus 19 ~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~ 49 (81)
.++|.+|=.++.||.+ =+||.+.| .++
T Consensus 1 v~rL~~I~~~r~lGfs---L~eI~~~l-~l~ 27 (65)
T PF09278_consen 1 VERLQFIRRLRELGFS---LEEIRELL-ELY 27 (65)
T ss_dssp HHHHHHHHHHHHTT-----HHHHHHHH-HHC
T ss_pred ChHHHHHHHHHHcCCC---HHHHHHHH-hcc
Confidence 3678999999999988 47899888 443
No 36
>PF10866 DUF2704: Protein of unknown function (DUF2704); InterPro: IPR022594 This group of viral proteins has no known function.
Probab=27.17 E-value=1.7e+02 Score=20.43 Aligned_cols=43 Identities=19% Similarity=0.176 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhhcChhhHHHHHHHHHHhccccchHHHHHHHHHHHh
Q 042821 4 LKGKVKTTIKYATEPLDQLEQIDNLQRLGLAYHFQTEIRNILHGIY 49 (81)
Q Consensus 4 LkeeVk~ml~~~~~~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~ 49 (81)
|-|-+|+.|+ +.+-|||+...=++|-.+--|.++|-..|+.-.
T Consensus 70 LyE~lr~~FV---dePfKlWle~Na~qLaad~efrd~i~K~l~~~L 112 (168)
T PF10866_consen 70 LYEILRGDFV---DEPFKLWLEQNAAQLAADAEFRDKIHKILQDQL 112 (168)
T ss_pred HHHHHHHHhc---CCchHHHHHhhHHHHhhhHHHHHHHHHHHHHHH
Confidence 3344444443 556689999999999999999888887776543
No 37
>PF08196 UL2: UL2 protein; InterPro: IPR013269 This entry contains Orf UL2 of Human cytomegalovirus (HHV-5) (Human herpesvirus 5), which is a short protein of unknown function [].
Probab=26.83 E-value=34 Score=19.75 Aligned_cols=10 Identities=60% Similarity=0.803 Sum_probs=7.8
Q ss_pred HHHHHHHHhh
Q 042821 65 ASVEFRLLRQ 74 (81)
Q Consensus 65 ~aL~FRLLRq 74 (81)
.--.||+||-
T Consensus 29 aqygfrllrg 38 (60)
T PF08196_consen 29 AQYGFRLLRG 38 (60)
T ss_pred HHHHHHHHHH
Confidence 4568999994
No 38
>smart00443 G_patch glycine rich nucleic binding domain. A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.
Probab=26.20 E-value=54 Score=17.30 Aligned_cols=14 Identities=29% Similarity=0.797 Sum_probs=11.8
Q ss_pred HHHHHHHhhCCCCC
Q 042821 66 SVEFRLLRQHGYNV 79 (81)
Q Consensus 66 aL~FRLLRq~Gy~V 79 (81)
...+++|+..||..
T Consensus 5 ~~g~~~l~~mGw~~ 18 (47)
T smart00443 5 NIGYKLLRKMGWKE 18 (47)
T ss_pred cHHHHHHHHcCCCC
Confidence 46789999999975
No 39
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=25.91 E-value=1.3e+02 Score=22.21 Aligned_cols=45 Identities=27% Similarity=0.377 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhcChhhHHHHHHHHHHhccccchHHHHHHHHHHHhh
Q 042821 4 LKGKVKTTIKYATEPLDQLEQIDNLQRLGLAYHFQTEIRNILHGIYN 50 (81)
Q Consensus 4 LkeeVk~ml~~~~~~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~~ 50 (81)
+++-|=.+|. -.|..+=+|+..|+|-|+.--=.+++..+|+.+-+
T Consensus 199 lReRvIHLLA--LkpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~ 243 (284)
T PF10390_consen 199 LRERVIHLLA--LKPYKKPELLLRLQKDGLSPKDKDELDSILQEVAN 243 (284)
T ss_dssp HHHHHHHHHH--HS-EEHHHHHHHHHHH---HHHHHHHHHHHHHCCE
T ss_pred ccccchhhhh--cCccccHHHHHHHHhcCCChHHHHHHHHHHHHHhc
Confidence 4455555553 35566778999999999998888999999999843
No 40
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=25.67 E-value=43 Score=16.56 Aligned_cols=9 Identities=44% Similarity=0.774 Sum_probs=6.1
Q ss_pred HhhCCCCCC
Q 042821 72 LRQHGYNVS 80 (81)
Q Consensus 72 LRq~Gy~VS 80 (81)
|+|+||.-+
T Consensus 17 LsQrgy~w~ 25 (27)
T smart00265 17 LSQNGYEWD 25 (27)
T ss_pred HhhcCCCCC
Confidence 678887643
No 41
>KOG4683 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.44 E-value=40 Score=26.96 Aligned_cols=20 Identities=40% Similarity=0.650 Sum_probs=17.8
Q ss_pred hhhHHHHHHHHHHhccccch
Q 042821 18 PLDQLEQIDNLQRLGLAYHF 37 (81)
Q Consensus 18 ~~~~L~lID~lqrLGi~~hF 37 (81)
..++|++.-.|||+|++|--
T Consensus 244 dve~lR~mGILQr~~~ayLV 263 (549)
T KOG4683|consen 244 DVEQLRIMGILQRFGVAYLV 263 (549)
T ss_pred cHHHHHHHHHHHHhhHHHHH
Confidence 47899999999999999964
No 42
>PF12017 Tnp_P_element: Transposase protein; InterPro: IPR021896 Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with PF05485 from PFAM.
Probab=25.34 E-value=2.7e+02 Score=20.17 Aligned_cols=14 Identities=29% Similarity=0.764 Sum_probs=10.5
Q ss_pred HHHHHhhCCCCCCC
Q 042821 68 EFRLLRQHGYNVSQ 81 (81)
Q Consensus 68 ~FRLLRq~Gy~VS~ 81 (81)
+++-|+..||+.|+
T Consensus 90 ~Y~yL~kk~~pLPs 103 (236)
T PF12017_consen 90 AYNYLRKKGYPLPS 103 (236)
T ss_pred HHHHHHHcCCCCCC
Confidence 47778767999875
No 43
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=24.92 E-value=1.2e+02 Score=16.07 Aligned_cols=24 Identities=17% Similarity=0.353 Sum_probs=19.5
Q ss_pred HHHHHHHhccccchHHHHHHHHHHHhh
Q 042821 24 QIDNLQRLGLAYHFQTEIRNILHGIYN 50 (81)
Q Consensus 24 lID~lqrLGi~~hF~~EI~~~L~~i~~ 50 (81)
.+.+|.-||- -+.||..++..+..
T Consensus 6 ~~~AL~~LGy---~~~e~~~av~~~~~ 29 (47)
T PF07499_consen 6 ALEALISLGY---SKAEAQKAVSKLLE 29 (47)
T ss_dssp HHHHHHHTTS----HHHHHHHHHHHHH
T ss_pred HHHHHHHcCC---CHHHHHHHHHHhhc
Confidence 5778899994 47899999999975
No 44
>PF09124 Endonuc-dimeris: T4 recombination endonuclease VII, dimerisation; InterPro: IPR015208 This entry represents a dimerisation domain predominantly found in Bacteriophage T4 recombination endonuclease VII. It adopts a helical secondary structure, with three alpha helices oriented parallel to each other. As well as mediating dimerisation of the protein, this domain is also involved in binding to the DNA major groove []. ; PDB: 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=24.54 E-value=60 Score=18.57 Aligned_cols=18 Identities=28% Similarity=0.584 Sum_probs=10.9
Q ss_pred hhHHHHHHHHHHhccccc
Q 042821 19 LDQLEQIDNLQRLGLAYH 36 (81)
Q Consensus 19 ~~~L~lID~lqrLGi~~h 36 (81)
+.+-+||+.++..|++|.
T Consensus 16 l~k~eMiaem~~~G~~y~ 33 (54)
T PF09124_consen 16 LTKPEMIAEMDSYGFEYN 33 (54)
T ss_dssp S-HHHHHHHHHHTT----
T ss_pred cCHHHHHHHHHHhCCcCC
Confidence 345679999999999886
No 45
>PF11576 DUF3236: Protein of unknown function (DUF3236); InterPro: IPR012019 This family of proteins with unknown function appears to be restricted to Methanobacteria. ; PDB: 3BRC_B.
Probab=24.53 E-value=50 Score=22.71 Aligned_cols=14 Identities=36% Similarity=0.665 Sum_probs=11.5
Q ss_pred hHHHHHHHHHHhcc
Q 042821 20 DQLEQIDNLQRLGL 33 (81)
Q Consensus 20 ~~L~lID~lqrLGi 33 (81)
-+.+++++|+|+|+
T Consensus 140 v~~E~~~AL~RiG~ 153 (154)
T PF11576_consen 140 VKKEMIEALKRIGI 153 (154)
T ss_dssp HHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHhCC
Confidence 46889999999996
No 46
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=24.24 E-value=1.5e+02 Score=22.70 Aligned_cols=61 Identities=18% Similarity=0.176 Sum_probs=34.0
Q ss_pred hhHHHHHHHHHHhccc---cchHHHHHHHHHHHhhcCCCCCCCCCCHHHHH-----------HHHHHHhhCCCCCC
Q 042821 19 LDQLEQIDNLQRLGLA---YHFQTEIRNILHGIYNNNKDDNWRNKNVYAAS-----------VEFRLLRQHGYNVS 80 (81)
Q Consensus 19 ~~~L~lID~lqrLGi~---~hF~~EI~~~L~~i~~~~~~~~~~~~dL~~~a-----------L~FRLLRq~Gy~VS 80 (81)
+..-.+++.+....-. .++.+.|...|..+..+.... .-..+++..| .-..-||+.||.+|
T Consensus 280 L~d~~fl~~ml~~~~~~~~~~~~~ri~~lL~~i~eE~~~~-P~yY~l~~ias~lk~~~P~~~~ii~aL~~~Gy~aS 354 (377)
T PF02005_consen 280 LHDKEFLEKMLEEAEEMPELNTSKRIEKLLETIKEELIDP-PFYYDLHEIASRLKCNPPPLDKIISALRNAGYRAS 354 (377)
T ss_dssp SB-HHHHHHHHHHHCT-S-TTTHHHHHHHHHHHHHCHS-S-SS-EEHHHHHHHHT-SC--HHHHHHHHHHTTTTEE
T ss_pred cCCHHHHHHHHhhhhccchhhhHHHHhhhcchhhhhcccc-eeEEeHHHHHHhcCCCCCCHHHHHHHHhhcceEEE
Confidence 3334444444444333 456888888888886652111 1112555554 23456999999987
No 47
>PF09633 DUF2023: Protein of unknown function (DUF2023); InterPro: IPR018594 This protein of approx.120 residues consists of three beta strands and five alpha helices, thought to fold into a homo-dimer. ; PDB: 2GUK_B.
Probab=23.90 E-value=12 Score=24.07 Aligned_cols=34 Identities=24% Similarity=0.256 Sum_probs=19.1
Q ss_pred HHHHHHHHHhhcChhhHHHHHHHHHHhccccchH
Q 042821 5 KGKVKTTIKYATEPLDQLEQIDNLQRLGLAYHFQ 38 (81)
Q Consensus 5 keeVk~ml~~~~~~~~~L~lID~lqrLGi~~hF~ 38 (81)
++=||.|+.-+.+.-..-..+..|++-||+|+.+
T Consensus 11 ~KGvR~LvL~T~~~~~~~~~~~rL~~~~I~y~iq 44 (101)
T PF09633_consen 11 KKGVRQLVLHTLPKRYEEFAIARLERQGIDYFIQ 44 (101)
T ss_dssp HCTS-SEEEEEEEGGGHHHHHHHHHHTT--EEEE
T ss_pred hhhhhhHhhhhCCHhhHHHHHHHHHHCCCCEEEE
Confidence 4445555543333334445788999999999874
No 48
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=23.80 E-value=33 Score=19.01 Aligned_cols=11 Identities=27% Similarity=0.658 Sum_probs=9.5
Q ss_pred HHHhhCCCCCC
Q 042821 70 RLLRQHGYNVS 80 (81)
Q Consensus 70 RLLRq~Gy~VS 80 (81)
+.|+++||.|.
T Consensus 55 ~~L~~~G~~v~ 65 (66)
T cd04908 55 EALKEAGFAVK 65 (66)
T ss_pred HHHHHCCCEEE
Confidence 78999999875
No 49
>PF00797 Acetyltransf_2: N-acetyltransferase; InterPro: IPR001447 Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30 kDa. It facilitates the transfer of an acetyl group from acetyl coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (Mycobacterium tuberculosis, Mycobacterium smegmatis etc) to Homo sapiens (Human). It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid. NAT catalyses the reaction: Acetyl-coA + arylamine = coA + N-acetylarylamine NAT is the target of a common genetic polymorphism of clinical relevance in humans. The N-acetylation polymorphism is determined by low or high NAT activity in liver. NAT has been implicated in the action and toxicity of amine-containing drugs, and in the susceptibility to cancer and systematic lupus erythematosus. Two highly similar human genes for NAT, termed NAT1 and NAT2, encode genetically invariant and variant NAT proteins, respectively. ; GO: 0016407 acetyltransferase activity, 0008152 metabolic process; PDB: 1W6F_A 1W5R_A 1GX3_D 2PQT_A 2IJA_A 1W4T_A 2BSZ_B 3D9W_B 3LTW_A 3LNB_A ....
Probab=23.63 E-value=53 Score=22.66 Aligned_cols=54 Identities=19% Similarity=0.285 Sum_probs=27.5
Q ss_pred cChhhHHHHHHHHHHhccccchHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHhhCCCCCC
Q 042821 16 TEPLDQLEQIDNLQRLGLAYHFQTEIRNILHGIYNNNKDDNWRNKNVYAASVEFRLLRQHGYNVS 80 (81)
Q Consensus 16 ~~~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~~~~~dL~~~aL~FRLLRq~Gy~VS 80 (81)
.=|++.+.+... ++. .=+++.+.++|... .........-.|-.++|++-||+|+
T Consensus 15 ~iPFENl~~~~~-~~~------~l~~~~i~~kiv~~----~rGG~C~elN~lf~~lL~~lGf~v~ 68 (240)
T PF00797_consen 15 TIPFENLDIHLG-EPI------SLDPDAIFDKIVRR----GRGGYCFELNGLFYWLLRELGFDVT 68 (240)
T ss_dssp HS-EE-HHHHTT------------SHHHHHHHHTTT----T--B-HHHHHHHHHHHHHHCT-EEE
T ss_pred cCCCCChhhhcC-Ccc------ccCHHHHHHHHHhc----CCCeEhHHHHHHHHHHHHHCCCeEE
Confidence 356677765532 111 22334455555322 1122467778899999999999985
No 50
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). 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=23.37 E-value=1.4e+02 Score=21.22 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=25.0
Q ss_pred ChhhHHHHHHHHHHhccccchHHHHHHHHHHHh
Q 042821 17 EPLDQLEQIDNLQRLGLAYHFQTEIRNILHGIY 49 (81)
Q Consensus 17 ~~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~ 49 (81)
...++|.+|-.+++.|.+ -.+|+++|+..-
T Consensus 42 ~~v~rL~~I~~l~~~G~~---L~~I~~~l~~~~ 71 (219)
T cd04778 42 SHLARLRLINQLLERGYT---LAHIAELLAAWE 71 (219)
T ss_pred HHHHHHHHHHHHHHCCCC---HHHHHHHHHhhh
Confidence 347899999999999986 788998888753
No 51
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.28 E-value=1.2e+02 Score=19.12 Aligned_cols=27 Identities=33% Similarity=0.541 Sum_probs=21.7
Q ss_pred ChhhHHHHHHHHHHhccccchHHHHHHHHH
Q 042821 17 EPLDQLEQIDNLQRLGLAYHFQTEIRNILH 46 (81)
Q Consensus 17 ~~~~~L~lID~lqrLGi~~hF~~EI~~~L~ 46 (81)
+.+.+|.+|-.+..+|++- +||..+++
T Consensus 42 ~~l~~l~~I~~lr~~G~sL---~eI~~~l~ 68 (126)
T cd04783 42 ETVTRLRFIKRAQELGFTL---DEIAELLE 68 (126)
T ss_pred HHHHHHHHHHHHHHcCCCH---HHHHHHHh
Confidence 3467899999999999885 77887765
No 52
>PRK10941 hypothetical protein; Provisional
Probab=22.94 E-value=1.6e+02 Score=21.65 Aligned_cols=24 Identities=21% Similarity=0.173 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHhhcChhhHHHHHH
Q 042821 3 ELKGKVKTTIKYATEPLDQLEQID 26 (81)
Q Consensus 3 ~LkeeVk~ml~~~~~~~~~L~lID 26 (81)
.|..+||..+....++.+++..+.
T Consensus 40 ~l~~~~~~~l~~~~~~~~~l~~L~ 63 (269)
T PRK10941 40 RLVSLAREEISQLLPQDEQLEKLI 63 (269)
T ss_pred HHHHHHHHhccccCCHHHHHHHHH
Confidence 344445544443334444444433
No 53
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=22.80 E-value=1.1e+02 Score=14.97 Aligned_cols=25 Identities=16% Similarity=0.266 Sum_probs=14.9
Q ss_pred HHHHHHhccccchHHHHHHHHHHHh
Q 042821 25 IDNLQRLGLAYHFQTEIRNILHGIY 49 (81)
Q Consensus 25 ID~lqrLGi~~hF~~EI~~~L~~i~ 49 (81)
|..++.+=-+.-.++||.+.|+.+=
T Consensus 11 v~~i~~~l~~~~t~~~I~~~l~~~C 35 (39)
T PF05184_consen 11 VKEIEKLLKNNKTEEEIKKALEKAC 35 (39)
T ss_dssp HHHHHHHHHSTCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCccHHHHHHHHHHHH
Confidence 3333333336667788888887753
No 54
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=22.75 E-value=92 Score=20.08 Aligned_cols=34 Identities=18% Similarity=0.337 Sum_probs=24.2
Q ss_pred cChhhHHHHHHHHHHhccc-----cchHHHHHHHHHHHhh
Q 042821 16 TEPLDQLEQIDNLQRLGLA-----YHFQTEIRNILHGIYN 50 (81)
Q Consensus 16 ~~~~~~L~lID~lqrLGi~-----~hF~~EI~~~L~~i~~ 50 (81)
..+++++.+=|..++-||+ +||.+ +.+.|..++.
T Consensus 18 ~k~~~~ITV~~I~~~AgvsR~TFY~hF~d-K~dLl~~~~~ 56 (176)
T TIGR02366 18 VQAFSKISVSDIMSTAQIRRQTFYNHFQD-KYELLTWIFE 56 (176)
T ss_pred HCCCccCCHHHHHHHhCCCHHHHHHHCCC-HHHHHHHHHH
Confidence 4567788888888899998 57755 6666665543
No 55
>cd07641 BAR_ASAP1 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP1 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 1) is also known as DDEF1 (Development and Differentiation Enhancing Factor 1), AMAP1, centaurin beta-4, or PAG2. ASAP1 is an Arf GTPase activating protein (GAP) with activity towards Arf1 and Arf5 but not Arf6 However, it has been shown to bind GTP-Arf6 stably without GAP activity. It has been implicated in cell growth, migration, and survival, as well as in tumor invasion and malignancy. It binds paxillin and cortactin, two components of invadopodia which are essential for tumor invasiveness. It also binds focal adhesion kinase (FAK) and the SH2/SH3 adaptor CrkL. ASAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Ar
Probab=22.74 E-value=1.9e+02 Score=20.97 Aligned_cols=47 Identities=11% Similarity=0.209 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHHhh-cChhhHHHHHHHHHHhcccc--chHHHHHHHHHHH
Q 042821 2 EELKGKVKTTIKYA-TEPLDQLEQIDNLQRLGLAY--HFQTEIRNILHGI 48 (81)
Q Consensus 2 e~LkeeVk~ml~~~-~~~~~~L~lID~lqrLGi~~--hF~~EI~~~L~~i 48 (81)
+++|.-|+.|..+. .=....-.+|+.|.+||=.. -=+.+|.++|...
T Consensus 19 ~Kl~K~~kam~~SG~~yv~n~~~f~~~l~~Lg~~~~~~dd~~i~~a~~kf 68 (215)
T cd07641 19 QKVKKSVKAIYNSGQDHVQNEENYAQALDKFGSNFLSRDNPDLGTAFVKF 68 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchhHHHHHHHH
Confidence 56778888888654 22344566999999999444 2255666666554
No 56
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=22.65 E-value=1.7e+02 Score=17.58 Aligned_cols=46 Identities=26% Similarity=0.336 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhhcChhhHHHHHHHHHHhccccchHHHHHHHHHHHhhc
Q 042821 3 ELKGKVKTTIKYATEPLDQLEQIDNLQRLGLAYHFQTEIRNILHGIYNN 51 (81)
Q Consensus 3 ~LkeeVk~ml~~~~~~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i~~~ 51 (81)
.++++|=..|......-+-+.+=+..++||++ +++|..+++.+-..
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~---~~~v~~al~~L~~e 92 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMS---ENEVRKALDFLSNE 92 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHSTS----HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhCcC---HHHHHHHHHHHHhC
Confidence 34566666665421222233344456777776 78999999998654
No 57
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=22.60 E-value=70 Score=20.08 Aligned_cols=20 Identities=25% Similarity=0.398 Sum_probs=13.5
Q ss_pred CCHHHHHHHH--HHHhhCCCCC
Q 042821 60 KNVYAASVEF--RLLRQHGYNV 79 (81)
Q Consensus 60 ~dL~~~aL~F--RLLRq~Gy~V 79 (81)
.|.|+..+.+ .+||.+||.|
T Consensus 9 gd~H~lG~~~~~~~l~~~G~~v 30 (122)
T cd02071 9 LDGHDRGAKVIARALRDAGFEV 30 (122)
T ss_pred CChhHHHHHHHHHHHHHCCCEE
Confidence 3555554443 5799999986
No 58
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=22.12 E-value=2.4e+02 Score=21.55 Aligned_cols=47 Identities=17% Similarity=0.193 Sum_probs=27.9
Q ss_pred ccchHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHH-----------HHHHhhCCCCCC
Q 042821 34 AYHFQTEIRNILHGIYNNNKDDNWRNKNVYAASVE-----------FRLLRQHGYNVS 80 (81)
Q Consensus 34 ~~hF~~EI~~~L~~i~~~~~~~~~~~~dL~~~aL~-----------FRLLRq~Gy~VS 80 (81)
...+.+.+...|..+..+..-...-..+++..|=. .--||+.||.+|
T Consensus 298 ~~~~~~~~~~ll~~~~~E~~~~~p~~y~~~~i~~~~k~~~p~~~~~~~~L~~~Gy~as 355 (382)
T PRK04338 298 ELGTSKKALKLLKTIEEESKLDTPTFYDLHELAKKLKVSAPPMDEILEALREAGFEAS 355 (382)
T ss_pred hccchHHHHHHHHHHHhccCCCCCcEEcHHHHHhhcCCCCCCHHHHHHHHHHCCCeEE
Confidence 34567888888888865411100111255554433 567999999987
No 59
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=22.06 E-value=37 Score=20.12 Aligned_cols=12 Identities=42% Similarity=0.703 Sum_probs=6.6
Q ss_pred HHHhhCCCCCCC
Q 042821 70 RLLRQHGYNVSQ 81 (81)
Q Consensus 70 RLLRq~Gy~VS~ 81 (81)
+.|+.+||.|++
T Consensus 27 ~~L~~~Gi~vTQ 38 (70)
T PF01316_consen 27 ELLEEEGIEVTQ 38 (70)
T ss_dssp HHHHHTT-T--H
T ss_pred HHHHHcCCCcch
Confidence 567778888864
No 60
>PHA00360 II replication initiation protein
Probab=21.59 E-value=1.7e+02 Score=23.27 Aligned_cols=54 Identities=9% Similarity=0.048 Sum_probs=34.4
Q ss_pred HHHHHHHhccccchHHHHHHHHHHHhhcCCCCCCCCC-CHHHHHHHHHHHhhCCC
Q 042821 24 QIDNLQRLGLAYHFQTEIRNILHGIYNNNKDDNWRNK-NVYAASVEFRLLRQHGY 77 (81)
Q Consensus 24 lID~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~~~~~-dL~~~aL~FRLLRq~Gy 77 (81)
+.|+++++-++..=.++|...|...|......+.-+. ==..+.-.++.|.++||
T Consensus 292 ~~~a~eg~~m~~~~~~~I~~~L~s~~~t~t~~G~~s~~ka~nl~~~Y~~lw~~G~ 346 (421)
T PHA00360 292 LFDAFEGDDMNIYDDSAVLDAIINKFFSITKSGKISFAKANRLFGFYRRLVNEGY 346 (421)
T ss_pred HHHHhccccccccChHHHHHHHHhhhcccccCCccchHHHHHHHHHHHHHHHhhH
Confidence 4568888888888888888888777665443211100 11234456677999999
No 61
>cd07603 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=21.40 E-value=2.2e+02 Score=19.91 Aligned_cols=46 Identities=11% Similarity=0.084 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhhcC-hhhHHHHHHHHHHhccccchHHHHHHHHHHH
Q 042821 3 ELKGKVKTTIKYATE-PLDQLEQIDNLQRLGLAYHFQTEIRNILHGI 48 (81)
Q Consensus 3 ~LkeeVk~ml~~~~~-~~~~L~lID~lqrLGi~~hF~~EI~~~L~~i 48 (81)
+++..++.|+....+ ......++++|+.||-.+-=...|..+|...
T Consensus 20 kl~K~~~~~~~ag~~~~~a~~~F~~~L~~~~~~~~~d~~i~~~l~kF 66 (200)
T cd07603 20 KLLKLCNGMVDSGKTYVNANSLFVNSLNDLSDYFRDDSLVQNCLNKF 66 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH
Confidence 444555555543222 2346779999999997543344565555544
No 62
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.28 E-value=59 Score=17.81 Aligned_cols=15 Identities=27% Similarity=0.530 Sum_probs=11.1
Q ss_pred HHHHHHHHhhCCCCC
Q 042821 65 ASVEFRLLRQHGYNV 79 (81)
Q Consensus 65 ~aL~FRLLRq~Gy~V 79 (81)
..-.-..|+++||.|
T Consensus 55 ~~~~~~~L~~~G~~v 69 (69)
T cd04909 55 RERAKEILKEAGYEV 69 (69)
T ss_pred HHHHHHHHHHcCCcC
Confidence 445557799999976
No 63
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.10 E-value=48 Score=22.63 Aligned_cols=14 Identities=36% Similarity=0.748 Sum_probs=11.6
Q ss_pred HHHHHHHHhhCCCC
Q 042821 65 ASVEFRLLRQHGYN 78 (81)
Q Consensus 65 ~aL~FRLLRq~Gy~ 78 (81)
+-.+||+|||-|-.
T Consensus 26 sPeQ~~v~RekgTE 39 (146)
T KOG0856|consen 26 SPEQFRVLREKGTE 39 (146)
T ss_pred CHHHhhhhHhhccc
Confidence 56799999999854
No 64
>PF10617 DUF2474: Protein of unknown function (DUF2474); InterPro: IPR018895 This family of short proteins has no known function.
Probab=20.85 E-value=90 Score=16.79 Aligned_cols=12 Identities=33% Similarity=0.481 Sum_probs=10.0
Q ss_pred CHHHHHHHHHHH
Q 042821 61 NVYAASVEFRLL 72 (81)
Q Consensus 61 dL~~~aL~FRLL 72 (81)
-|..+|..||++
T Consensus 21 aL~~va~~~Rll 32 (40)
T PF10617_consen 21 ALGVVAMLFRLL 32 (40)
T ss_pred HHHHHHHHHHHH
Confidence 477899999986
No 65
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=20.79 E-value=1.5e+02 Score=17.35 Aligned_cols=26 Identities=15% Similarity=0.413 Sum_probs=19.0
Q ss_pred hhHHHHHHHHHHhccccch-HHHHHHH
Q 042821 19 LDQLEQIDNLQRLGLAYHF-QTEIRNI 44 (81)
Q Consensus 19 ~~~L~lID~lqrLGi~~hF-~~EI~~~ 44 (81)
..+..+++.|.+-||+.++ ++|+..=
T Consensus 46 ~s~~eF~~~L~~~gI~~~~~~eel~~d 72 (76)
T PF03683_consen 46 MSRWEFLELLKERGIPINYDEEELEED 72 (76)
T ss_pred CCHHHHHHHHHHCCCCCCCCHHHHHHH
Confidence 4788999999999999554 4444443
No 66
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=20.78 E-value=1.6e+02 Score=20.94 Aligned_cols=42 Identities=14% Similarity=0.353 Sum_probs=29.5
Q ss_pred HHHHHHHHhccccchHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHH
Q 042821 23 EQIDNLQRLGLAYHFQTEIRNILHGIYNNNKDDNWRNKNVYAASVEF 69 (81)
Q Consensus 23 ~lID~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~~~~~dL~~~aL~F 69 (81)
+.|.+|.-||-+ +.||+.++..+... .. ..+..++-..||..
T Consensus 158 ~~v~AL~~LGy~---~~e~~~av~~v~~~-~~-~~~~~~~Ik~aLk~ 199 (201)
T COG0632 158 EAVEALVALGYK---EKEIKKAVKKVLKE-NP-DADVEELIKEALKL 199 (201)
T ss_pred HHHHHHHHcCCC---HHHHHHHHHHHHhc-CC-CCCHHHHHHHHHHh
Confidence 348899999977 99999999999865 21 11224566666654
No 67
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.69 E-value=48 Score=17.63 Aligned_cols=15 Identities=13% Similarity=0.377 Sum_probs=11.6
Q ss_pred HHHHHHHHhhCCCCC
Q 042821 65 ASVEFRLLRQHGYNV 79 (81)
Q Consensus 65 ~aL~FRLLRq~Gy~V 79 (81)
..-....|+++||.|
T Consensus 50 ~~~~~~~L~~~G~~v 64 (65)
T cd04882 50 IEKAIEVLQERGVEL 64 (65)
T ss_pred HHHHHHHHHHCCceE
Confidence 455668899999976
No 68
>PRK05728 DNA polymerase III subunit chi; Validated
Probab=20.22 E-value=66 Score=21.12 Aligned_cols=20 Identities=25% Similarity=0.428 Sum_probs=16.3
Q ss_pred CHHHHHHHHHHHhhCCCCCC
Q 042821 61 NVYAASVEFRLLRQHGYNVS 80 (81)
Q Consensus 61 dL~~~aL~FRLLRq~Gy~VS 80 (81)
.+...=-+||-.|+.||.++
T Consensus 116 ~~~~aR~r~r~Yr~~G~~l~ 135 (142)
T PRK05728 116 AKQAARERWKAYRAAGYALT 135 (142)
T ss_pred HHHHHHHHHHHHHHCCCCce
Confidence 56666788999999999875
No 69
>PRK11876 petM cytochrome b6-f complex subunit PetM; Reviewed
Probab=20.07 E-value=70 Score=16.44 Aligned_cols=15 Identities=20% Similarity=0.131 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHhhCC
Q 042821 62 VYAASVEFRLLRQHG 76 (81)
Q Consensus 62 L~~~aL~FRLLRq~G 76 (81)
|--.|+.|-|||-+|
T Consensus 17 lvGlalGf~LLkiqg 31 (32)
T PRK11876 17 PVGLAGGALLLKLQG 31 (32)
T ss_pred HHHHHHHHHheeeec
Confidence 456789999998776
Done!