Query psy1883
Match_columns 81
No_of_seqs 43 out of 45
Neff 2.8
Searched_HMMs 46136
Date Fri Aug 16 18:42:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1883.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1883hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09058 L27_1: L27_1; InterP 100.0 9.5E-30 2E-34 162.7 4.5 56 14-69 3-58 (64)
2 PF09045 L27_2: L27_2; InterP 97.7 3.2E-05 6.9E-10 49.2 3.1 49 18-66 1-49 (58)
3 smart00569 L27 domain in recep 97.3 0.00095 2.1E-08 38.0 4.9 44 19-68 2-45 (55)
4 PF02828 L27: L27 domain; Int 93.4 0.5 1.1E-05 27.9 5.8 43 19-66 2-44 (56)
5 PRK14736 atpC F0F1 ATP synthas 82.9 3.2 6.9E-05 28.8 4.6 38 18-55 90-127 (133)
6 PF04818 CTD_bind: RNA polymer 74.4 6.7 0.00015 23.1 3.6 23 33-55 38-60 (64)
7 KOG3550|consensus 73.5 14 0.00031 28.3 6.0 45 17-66 12-56 (207)
8 TIGR00208 fliS flagellar biosy 70.4 31 0.00066 23.4 8.1 59 16-74 51-111 (124)
9 COG1516 FliS Flagellin-specifi 70.0 28 0.0006 25.0 6.5 57 18-74 53-111 (132)
10 PF02561 FliS: Flagellar prote 62.9 41 0.00089 22.2 8.4 59 17-75 50-110 (122)
11 PF14278 TetR_C_8: Transcripti 59.7 30 0.00064 19.4 5.5 52 28-79 17-75 (77)
12 PF09413 DUF2007: Domain of un 59.0 4.8 0.0001 23.6 0.8 21 10-30 46-66 (67)
13 PF04064 DUF384: Domain of unk 59.0 18 0.0004 22.3 3.4 30 22-54 20-49 (58)
14 COG5393 Predicted membrane pro 54.3 63 0.0014 23.5 6.0 28 53-80 44-78 (131)
15 PF13840 ACT_7: ACT domain ; P 54.1 4 8.7E-05 24.4 -0.1 22 7-28 44-65 (65)
16 KOG4357|consensus 52.7 4.1 8.8E-05 30.4 -0.3 34 35-68 78-111 (164)
17 PF14144 DOG1: Seed dormancy c 51.2 22 0.00049 22.9 3.0 35 25-60 2-38 (80)
18 PRK13448 atpC F0F1 ATP synthas 49.3 38 0.00082 23.4 4.1 35 18-53 89-123 (135)
19 PF09106 SelB-wing_2: Elongati 47.3 11 0.00024 22.1 1.1 39 23-64 2-44 (59)
20 smart00582 RPR domain present 46.3 76 0.0016 20.2 8.0 76 5-80 16-106 (121)
21 PF11363 DUF3164: Protein of u 44.3 46 0.00099 24.7 4.1 34 18-51 97-130 (195)
22 PF12177 Proho_convert: Prohor 41.6 15 0.00034 22.1 1.1 10 55-64 29-38 (41)
23 cd03562 CID CID (CTD-Interacti 41.0 82 0.0018 20.0 4.5 27 6-32 22-48 (114)
24 PF12424 ATP_Ca_trans_C: Plasm 40.4 9.3 0.0002 24.2 0.0 10 47-56 17-26 (66)
25 PF12209 SAC3: Leucine permeas 38.4 61 0.0013 20.9 3.6 16 47-62 37-52 (79)
26 PF01756 ACOX: Acyl-CoA oxidas 38.3 1E+02 0.0023 21.4 5.0 42 11-52 46-88 (187)
27 PF10635 DisA-linker: DisA bac 38.2 17 0.00036 26.1 1.0 18 17-34 9-26 (145)
28 cd08807 CARD_CARD10_CARMA3 Cas 37.9 95 0.0021 21.2 4.6 27 41-67 48-77 (86)
29 PF09349 OHCU_decarbox: OHCU d 37.3 62 0.0013 22.6 3.7 35 22-56 123-157 (159)
30 PF10540 Membr_traf_MHD: Munc1 36.8 62 0.0013 22.2 3.6 40 19-68 87-127 (137)
31 PF03368 Dicer_dimer: Dicer di 35.6 35 0.00075 21.8 2.1 16 22-37 1-16 (90)
32 PRK05685 fliS flagellar protei 35.5 1.4E+02 0.0031 20.2 8.1 57 18-74 57-115 (132)
33 TIGR02302 aProt_lowcomp conser 34.2 55 0.0012 29.6 3.7 39 14-52 812-851 (851)
34 PF13628 DUF4142: Domain of un 33.5 1.4E+02 0.0031 19.6 6.2 47 9-58 87-135 (139)
35 TIGR02672 cas_csm6 CRISPR-asso 32.7 1.3E+02 0.0028 25.1 5.4 53 18-72 139-201 (362)
36 PF14293 YWFCY: YWFCY protein 32.5 46 0.00099 21.4 2.2 16 58-73 7-22 (61)
37 PRK13798 putative OHCU decarbo 32.3 88 0.0019 22.5 3.9 35 22-56 125-159 (166)
38 TIGR03164 UHCUDC OHCU decarbox 32.1 89 0.0019 22.1 3.9 35 22-56 120-154 (157)
39 COG3602 Uncharacterized protei 29.8 37 0.0008 24.8 1.7 22 10-31 110-131 (134)
40 smart00345 HTH_GNTR helix_turn 29.7 71 0.0015 17.1 2.5 26 4-29 22-47 (60)
41 TIGR01216 ATP_synt_epsi ATP sy 29.7 1.6E+02 0.0034 19.8 4.7 40 16-55 86-125 (130)
42 PF09426 Nyv1_N: Vacuolar R-SN 29.4 1E+02 0.0023 22.7 3.9 35 23-57 102-136 (141)
43 PF03820 Mtc: Tricarboxylate c 28.8 78 0.0017 25.1 3.4 43 11-53 21-65 (308)
44 PF14661 HAUS6_N: HAUS augmin- 28.6 1E+02 0.0022 22.9 3.9 48 7-54 40-87 (247)
45 PF00392 GntR: Bacterial regul 28.2 71 0.0015 18.5 2.4 27 3-29 25-51 (64)
46 PF11640 TAN: Telomere-length 27.6 1.2E+02 0.0027 20.7 3.9 28 28-55 8-35 (155)
47 COG5424 Pyrroloquinoline quino 27.5 2E+02 0.0044 22.7 5.5 48 6-55 174-221 (242)
48 COG1202 Superfamily II helicas 27.5 42 0.00091 30.5 1.9 33 39-71 688-722 (830)
49 TIGR02132 phaR_Bmeg polyhydrox 26.9 1.1E+02 0.0024 23.5 3.8 51 18-68 50-103 (189)
50 PF11123 DNA_Packaging_2: DNA 26.1 2.1E+02 0.0045 19.4 4.7 40 12-53 6-45 (82)
51 PHA01623 hypothetical protein 26.0 1.2E+02 0.0025 18.3 3.2 28 23-50 25-52 (56)
52 COG1516 FliS Flagellin-specifi 25.8 1.7E+02 0.0037 21.0 4.4 25 35-60 44-68 (132)
53 TIGR03180 UraD_2 OHCU decarbox 25.2 1.4E+02 0.0031 21.2 3.9 35 22-56 120-154 (158)
54 KOG1758|consensus 25.0 1.8E+02 0.0039 21.8 4.5 29 17-45 116-144 (159)
55 PF05760 IER: Immediate early 25.0 41 0.0009 26.9 1.3 22 42-64 246-267 (300)
56 PF12297 EVC2_like: Ellis van 24.9 1.5E+02 0.0033 25.2 4.6 38 9-55 314-351 (429)
57 PHA00425 DNA packaging protein 24.3 1.9E+02 0.0042 19.8 4.3 40 12-53 8-47 (88)
58 PF15469 Sec5: Exocyst complex 24.2 2.5E+02 0.0053 19.3 5.5 54 18-73 108-165 (182)
59 cd01048 Ferritin_like_AB2 Unch 23.8 1.3E+02 0.0029 20.2 3.4 31 26-56 98-128 (135)
60 PF00858 ASC: Amiloride-sensit 23.7 1.2E+02 0.0025 22.5 3.4 26 54-79 411-436 (439)
61 PF00497 SBP_bac_3: Bacterial 23.5 1.7E+02 0.0037 18.7 3.8 27 36-62 193-220 (225)
62 PF13446 RPT: A repeated domai 23.4 1.2E+02 0.0027 17.6 2.9 28 47-74 21-48 (62)
63 smart00509 TFS2N Domain in the 23.2 1.2E+02 0.0025 19.0 2.9 24 32-55 49-72 (75)
64 PF08785 Ku_PK_bind: Ku C term 22.4 2.5E+02 0.0053 18.7 4.5 43 27-69 7-55 (120)
65 KOG2160|consensus 21.1 2.4E+02 0.0051 23.2 4.9 43 15-57 96-157 (342)
66 PF13233 Complex1_LYR_2: Compl 20.2 88 0.0019 19.8 1.9 25 24-48 77-101 (104)
67 PRK10512 selenocysteinyl-tRNA- 20.1 1.3E+02 0.0029 25.5 3.4 44 19-65 420-466 (614)
68 COG4493 Uncharacterized protei 20.1 65 0.0014 25.1 1.5 21 37-57 150-170 (209)
No 1
>PF09058 L27_1: L27_1; InterPro: IPR015143 The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices []. ; PDB: 3LRA_A 1RSO_A.
Probab=99.96 E-value=9.5e-30 Score=162.70 Aligned_cols=56 Identities=59% Similarity=0.800 Sum_probs=51.8
Q ss_pred hchHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhHHhH
Q psy1883 14 LNYLEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALLGQLGGAIG 69 (81)
Q Consensus 14 ~~~~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALLDI~e~~~~ 69 (81)
++++||||||++||+||++|++|+|++||++|+||||+|||+||||||||||||+.
T Consensus 3 v~k~dA~rALelLe~y~~~L~~~~D~~lr~~ierli~ifkS~LF~ALLDIqe~YE~ 58 (64)
T PF09058_consen 3 VRKEDAHRALELLEEYHNKLSRPEDEELRTAIERLINIFKSRLFQALLDIQEFYEV 58 (64)
T ss_dssp --HHHHHHHHHHHHHHHHTTSSSS-CCHHHHHHHHHHHHHSHHHHHHHHHCCCCCE
T ss_pred CcHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57889999999999999999999999999999999999999999999999999983
No 2
>PF09045 L27_2: L27_2; InterPro: IPR015132 The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer []. ; PDB: 3UIT_A 1VF6_B.
Probab=97.74 E-value=3.2e-05 Score=49.17 Aligned_cols=49 Identities=24% Similarity=0.380 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q psy1883 18 EAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALLGQLGG 66 (81)
Q Consensus 18 dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALLDI~e~ 66 (81)
|++|||..||..++||.+.+|.+--..+..+.++.||.||+-+|-+|.-
T Consensus 1 d~~~al~~lerlq~KL~~rGd~s~~e~L~~l~~~LqSPLF~~iL~LQqS 49 (58)
T PF09045_consen 1 DTQRALQALERLQAKLKERGDTSHSEKLSLLKDTLQSPLFNQILTLQQS 49 (58)
T ss_dssp --CHHHHHHHHHHHHHHHCT--TTHHHHHHHHHHHH-HHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHHHHHHccCcccHHHHHHHHHHHhChHHHHHHHHHHH
Confidence 6789999999999999999999999999999999999999999987753
No 3
>smart00569 L27 domain in receptor targeting proteins Lin-2 and Lin-7.
Probab=97.26 E-value=0.00095 Score=38.03 Aligned_cols=44 Identities=34% Similarity=0.465 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhHHh
Q psy1883 19 AHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALLGQLGGAI 68 (81)
Q Consensus 19 AhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALLDI~e~~~ 68 (81)
.++++++|++++...+.+.| ++-+.++|+|.-|+||+.+.|...
T Consensus 2 ~~~~~~~L~~l~~~~~~~~~------~~~L~~ll~~~~~~all~~hd~v~ 45 (55)
T smart00569 2 VQRLLELLEELQSLLSPSED------LQELRRLLQSPHLQALLKIHDKVA 45 (55)
T ss_pred hHHHHHHHHHHHhccCCCcc------HHHHHHHHcCHHHHHHHHHHHHHH
Confidence 57999999999988877644 455788999999999999988754
No 4
>PF02828 L27: L27 domain; InterPro: IPR014775 The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7, as well as some protein kinases and human MPP2 protein.; PDB: 1ZL8_B 1VA8_A 3LRA_A 3UIT_A 1Y74_D 1RSO_B.
Probab=93.35 E-value=0.5 Score=27.90 Aligned_cols=43 Identities=30% Similarity=0.416 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q psy1883 19 AHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALLGQLGG 66 (81)
Q Consensus 19 AhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALLDI~e~ 66 (81)
-+|++++|++-+...+.+ ...+.=+-++|+|.-|+||+.+-|-
T Consensus 2 v~~~~e~L~~L~~~~~~~-----~~~~~eL~~lL~~p~~~aLl~~hD~ 44 (56)
T PF02828_consen 2 VQRVLELLEELQSLSSAS-----QEDAQELQQLLQSPHFQALLEVHDK 44 (56)
T ss_dssp HHHHHHHHHHHHHHTSST-----HHHHHHHHHHHHSHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHhccCCC-----hHHHHHHHHHHcCHHHHHHHHHHHH
Confidence 368999999999876665 4556778889999999999977653
No 5
>PRK14736 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=82.89 E-value=3.2 Score=28.79 Aligned_cols=38 Identities=13% Similarity=0.071 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHH
Q psy1883 18 EAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSR 55 (81)
Q Consensus 18 dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~ 55 (81)
|..||-+.+++..+.|+...|++-|.++++.+..++|=
T Consensus 90 D~~~a~~a~~~Ae~~~~~~~~~~~~~~~~~~~~~~~~~ 127 (133)
T PRK14736 90 TPEMIDREIEAVEMERDATQDLDKREALNAQIVQMQEA 127 (133)
T ss_pred CHHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHH
Confidence 66777777788888999999999999999999988763
No 6
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=74.40 E-value=6.7 Score=23.09 Aligned_cols=23 Identities=22% Similarity=0.517 Sum_probs=18.3
Q ss_pred cCCCCcHHHHHHHHHHHHHHHHH
Q psy1883 33 LTDPSDKQLRSAIERVIRIFKSR 55 (81)
Q Consensus 33 L~~~~D~~Lr~aiervIniFkS~ 55 (81)
.-+..|++.+..+.|++++.++|
T Consensus 38 ~~~~~~~~~~~kv~rll~iW~~r 60 (64)
T PF04818_consen 38 AYKNVDPEVRKKVQRLLNIWEER 60 (64)
T ss_dssp HCCCS-HHHHHHHHHHHHHHHHC
T ss_pred HHhcCCHHHHHHHHHHHHHhhCC
Confidence 34456999999999999999875
No 7
>KOG3550|consensus
Probab=73.45 E-value=14 Score=28.31 Aligned_cols=45 Identities=20% Similarity=0.259 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q psy1883 17 LEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALLGQLGG 66 (81)
Q Consensus 17 ~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALLDI~e~ 66 (81)
+|-.||+||||..+..=.- .++= ++-+-.+.||..|.|.-++-|+
T Consensus 12 rdv~r~ielleklq~sgev--p~~k---l~alq~vlqsef~~avrevye~ 56 (207)
T KOG3550|consen 12 RDVQRAIELLEKLQRSGEV--PPQK---LQALQKVLQSEFCTAVREVYEH 56 (207)
T ss_pred HHHHHHHHHHHHHHHcCCC--CHHH---HHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999988863221 2222 3344456789999998777665
No 8
>TIGR00208 fliS flagellar biosynthetic protein FliS. The function of this protein in flagellar biosynthesis is unknown, but appears to be regulatory. The member of this family in Vibrio parahaemolyticus is designated FlaJ (creating a synonym for FliS) and was shown essential for flagellin biosynthesis.
Probab=70.43 E-value=31 Score=23.41 Aligned_cols=59 Identities=14% Similarity=0.104 Sum_probs=49.0
Q ss_pred hHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHH--HhhhHHhHHHHhh
Q psy1883 16 YLEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALL--GQLGGAIGISVLG 74 (81)
Q Consensus 16 ~~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALL--DI~e~~~~~~~~~ 74 (81)
...-.+|..++.+-+..|+.....++-..+.++=+-...+|.+|-+ |.-..-+.+.++.
T Consensus 51 ~~~i~ka~~Ii~eL~~~Ld~e~ggeiA~nL~~LY~y~~~~L~~An~~~d~~~l~ev~~~l~ 111 (124)
T TIGR00208 51 NENLIKAQNIIQELNFTLDREKNIELSASLGALYDYMYRRLVQANIKNDTSKLAEVEGYVR 111 (124)
T ss_pred HHHHHHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Confidence 3445789999999999999999999999999999999999999988 5555555665554
No 9
>COG1516 FliS Flagellin-specific chaperone FliS [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=70.01 E-value=28 Score=24.99 Aligned_cols=57 Identities=16% Similarity=0.228 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHH--HhhhHHhHHHHhh
Q psy1883 18 EAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALL--GQLGGAIGISVLG 74 (81)
Q Consensus 18 dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALL--DI~e~~~~~~~~~ 74 (81)
--.||..++++-...|+...-.++-..+..+=+.+-.+|++|-+ |+..-.+.+.++-
T Consensus 53 ~i~ka~~Ii~eL~~~Ld~E~Ggeia~nL~~LY~y~~~rL~~ANl~nd~~~i~eV~~ll~ 111 (132)
T COG1516 53 SIDKAIDIITELRASLDYEKGGEIAQNLDALYDYMVRRLVQANLKNDASKIDEVIGLLR 111 (132)
T ss_pred HHHHHHHHHHHHHHhcCHhhcchHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence 44678899999999999999999999999999999999999988 6666555555543
No 10
>PF02561 FliS: Flagellar protein FliS; InterPro: IPR003713 The fliD operon of several bacteria consists of three flagellar genes, fliD, fliS, and fliT, and is transcribed in this order []. In Bacillus subtilis the operon encoding the flagellar proteins FliD, FliS, and FliT is sigma D-dependent [].; GO: 0009296 flagellum assembly, 0009288 bacterial-type flagellum; PDB: 1VH6_A 3IQC_B 3K1I_B 1ORJ_B 1ORY_A.
Probab=62.90 E-value=41 Score=22.15 Aligned_cols=59 Identities=17% Similarity=0.142 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHH--HhhhHHhHHHHhhh
Q psy1883 17 LEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALL--GQLGGAIGISVLGI 75 (81)
Q Consensus 17 ~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALL--DI~e~~~~~~~~~~ 75 (81)
..-.+|..++.+-...|+.....++-..+.++=+-+..+|-+|-+ |.-.+-+.+.++.-
T Consensus 50 ~~l~ka~~Ii~~L~~~Ld~e~g~eia~~L~~lY~y~~~~L~~A~~~~d~~~l~~v~~~l~~ 110 (122)
T PF02561_consen 50 EALQKAQDIITELQSSLDFEKGGEIADNLFRLYDYMIRQLVQANLKKDPERLDEVIRILEE 110 (122)
T ss_dssp HHHHHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 345688999999999999998999999999999999999999988 65666666666653
No 11
>PF14278 TetR_C_8: Transcriptional regulator C-terminal region
Probab=59.66 E-value=30 Score=19.45 Aligned_cols=52 Identities=13% Similarity=0.280 Sum_probs=32.3
Q ss_pred HHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh----HHh---HHHHhhhhhhc
Q psy1883 28 DYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALLGQLG----GAI---GISVLGIFKIW 79 (81)
Q Consensus 28 ~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALLDI~e----~~~---~~~~~~~~~~~ 79 (81)
-|+.=|+.++|+.+...+..++.-.-.+.++....... |+. .-+.+|+++-|
T Consensus 17 ~~~~ll~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~y~~~f~~sg~igvi~~W 75 (77)
T PF14278_consen 17 FYKILLSPNGDPNFQERLKELIKEWITEYINENSPDNDDPEEYLISFIVSGIIGVIQWW 75 (77)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHHHH
Confidence 46667889999999777766665554444444432111 322 44567888777
No 12
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=59.00 E-value=4.8 Score=23.62 Aligned_cols=21 Identities=24% Similarity=0.313 Sum_probs=17.7
Q ss_pred HHHhhchHHHHHHHHHHHHHH
Q psy1883 10 TYYLLNYLEAHRALELLEDYH 30 (81)
Q Consensus 10 ~~~~~~~~dAhRALeLLE~Y~ 30 (81)
+.+++...|..+|.++|++|.
T Consensus 46 ~~v~V~~~d~~~A~~il~~~~ 66 (67)
T PF09413_consen 46 VEVYVPEEDYERAREILEEFE 66 (67)
T ss_dssp EEEEEEGGGHHHHHHHHHHTT
T ss_pred eEEEECHHHHHHHHHHHHHhc
Confidence 446677899999999999986
No 13
>PF04064 DUF384: Domain of unknown function (DUF384); InterPro: IPR007206 This is a protein of unknown function. It is found C-terminal to another domain of unknown function (IPR007205 from INTERPRO).
Probab=58.99 E-value=18 Score=22.35 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHH
Q psy1883 22 ALELLEDYHSKLTDPSDKQLRSAIERVIRIFKS 54 (81)
Q Consensus 22 ALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS 54 (81)
+-.+|.++|.. .+|+.++.+++|+++++.+
T Consensus 20 vY~IlRe~h~~---E~d~~V~e~~erlV~iLir 49 (58)
T PF04064_consen 20 VYPILRELHKW---EEDEEVQEACERLVQILIR 49 (58)
T ss_pred chHHHHHHHhc---cCCHHHHHHHHHHHHHHhc
Confidence 34566777764 7899999999999998754
No 14
>COG5393 Predicted membrane protein [Function unknown]
Probab=54.33 E-value=63 Score=23.55 Aligned_cols=28 Identities=32% Similarity=0.312 Sum_probs=18.2
Q ss_pred HHHHHHHHHH-------hhhHHhHHHHhhhhhhcc
Q psy1883 53 KSRLFQALLG-------QLGGAIGISVLGIFKIWD 80 (81)
Q Consensus 53 kS~LFqALLD-------I~e~~~~~~~~~~~~~~~ 80 (81)
|.||||.|+= +.=-.++.+++-|+-+||
T Consensus 44 Kanll~lllm~gLtl~fa~~~lmsL~vLvi~~f~~ 78 (131)
T COG5393 44 KANLLQLLLMAGLTLLFAAFGLMSLMVLVIWAFDP 78 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 5677777651 122245778888888887
No 15
>PF13840 ACT_7: ACT domain ; PDB: 3S1T_A 1ZHV_A 3AB4_K 3AB2_O 2DTJ_A 3AAW_A 2RE1_B 3MAH_A 1ZVP_D.
Probab=54.08 E-value=4 Score=24.43 Aligned_cols=22 Identities=27% Similarity=0.377 Sum_probs=18.5
Q ss_pred hhhHHHhhchHHHHHHHHHHHH
Q psy1883 7 ELSTYYLLNYLEAHRALELLED 28 (81)
Q Consensus 7 ~~~~~~~~~~~dAhRALeLLE~ 28 (81)
+.+.+++++..|+++|++.|++
T Consensus 44 ~~~~~ilV~~~~~~~A~~~L~~ 65 (65)
T PF13840_consen 44 EISISILVKEEDLEKAVEALHE 65 (65)
T ss_dssp SSEEEEEEEGGGHHHHHHHHHH
T ss_pred eeeEEEEEeHHHHHHHHHHhcC
Confidence 4566789999999999999875
No 16
>KOG4357|consensus
Probab=52.69 E-value=4.1 Score=30.36 Aligned_cols=34 Identities=26% Similarity=0.469 Sum_probs=29.0
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhHHh
Q psy1883 35 DPSDKQLRSAIERVIRIFKSRLFQALLGQLGGAI 68 (81)
Q Consensus 35 ~~~D~~Lr~aiervIniFkS~LFqALLDI~e~~~ 68 (81)
+|..++.|---|..-.+.||+||+|=.|.|.|..
T Consensus 78 qp~~kd~rpftee~tqiwq~qlfn~~~dlq~fii 111 (164)
T KOG4357|consen 78 QPDEKDIRPFTEEITQIWQGQLFNAHVDLQRFII 111 (164)
T ss_pred CCChhhccchhHHHHHHHHHHhhccccceEEEEe
Confidence 4666677777799999999999999999998865
No 17
>PF14144 DOG1: Seed dormancy control
Probab=51.21 E-value=22 Score=22.87 Aligned_cols=35 Identities=26% Similarity=0.519 Sum_probs=25.8
Q ss_pred HHHHHHhhcCCC--CcHHHHHHHHHHHHHHHHHHHHHH
Q psy1883 25 LLEDYHSKLTDP--SDKQLRSAIERVIRIFKSRLFQAL 60 (81)
Q Consensus 25 LLE~Y~~kL~~~--~D~~Lr~aiervIniFkS~LFqAL 60 (81)
++.+-++.|+.+ .|.+|+.-+++++.-| .++|.+-
T Consensus 2 ~l~eLr~al~~~~~~~~~L~~lV~~~~~Hy-~~y~~~K 38 (80)
T PF14144_consen 2 QLNELRAALQSHADSDDELRSLVDKVMSHY-DEYYRAK 38 (80)
T ss_pred cHHHHHHHHHhcCCCHHHHHHHHHHHHHHH-HHHHHHH
Confidence 355666677776 5999999999999988 4455543
No 18
>PRK13448 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=49.33 E-value=38 Score=23.41 Aligned_cols=35 Identities=23% Similarity=0.380 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHH
Q psy1883 18 EAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFK 53 (81)
Q Consensus 18 dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFk 53 (81)
|..+|-+.+++=..+|....+..++.++.| ++.++
T Consensus 89 D~~~a~~~~~~Ae~~l~~~~~~~l~ra~~r-l~~~~ 123 (135)
T PRK13448 89 DLAQFAATIAEMEAQLAGKVGDELDRAIER-LDHFK 123 (135)
T ss_pred CHHHHHHHHHHHHHHHhhCChHHHHHHHHH-HHHHH
Confidence 334444444444556766677889999988 55544
No 19
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=47.29 E-value=11 Score=22.13 Aligned_cols=39 Identities=38% Similarity=0.639 Sum_probs=22.8
Q ss_pred HHHHHHHHhhcCC---CCcHHHHHHHHHHHH-HHHHHHHHHHHHhh
Q psy1883 23 LELLEDYHSKLTD---PSDKQLRSAIERVIR-IFKSRLFQALLGQL 64 (81)
Q Consensus 23 LeLLE~Y~~kL~~---~~D~~Lr~aiervIn-iFkS~LFqALLDI~ 64 (81)
++.|++||.+=.- ..-++||+ |+-. .+..++|+++|+.+
T Consensus 2 ~~~L~~yH~~~Plr~G~~keeLrs---rl~~~~l~~k~~~~ll~~l 44 (59)
T PF09106_consen 2 LEILAEYHRENPLRPGMPKEELRS---RLFKPRLPPKLFNALLEAL 44 (59)
T ss_dssp HHHHHHHHHH-TTSS-EEHHHHHH---HCST-TS-HCCHHHHHHHH
T ss_pred hHHHHHHHHHCcCccCcCHHHHHH---HHhhccCCHHHHHHHHHHH
Confidence 5789999986221 11234444 3333 55678888888755
No 20
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=46.33 E-value=76 Score=20.19 Aligned_cols=76 Identities=18% Similarity=0.299 Sum_probs=46.0
Q ss_pred cchhhHHHhhchHHHHHHHHHHHHHHhhcCCC--------CcHHHHHHHHHHHHHHHHHHHHHHHHhhhHHh-------H
Q psy1883 5 KKELSTYYLLNYLEAHRALELLEDYHSKLTDP--------SDKQLRSAIERVIRIFKSRLFQALLGQLGGAI-------G 69 (81)
Q Consensus 5 ~~~~~~~~~~~~~dAhRALeLLE~Y~~kL~~~--------~D~~Lr~aiervIniFkS~LFqALLDI~e~~~-------~ 69 (81)
-+.++.+.+.+...|..-.++++++..+-+.+ -|.=++++..+....|...+...+-++..... -
T Consensus 16 I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~ 95 (121)
T smart00582 16 IQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQDALRDVLGAANDETK 95 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHhCCHHHH
Confidence 35678888888888888888899888764432 13445555555445555544444433333222 2
Q ss_pred HHHhhhhhhcc
Q psy1883 70 ISVLGIFKIWD 80 (81)
Q Consensus 70 ~~~~~~~~~~~ 80 (81)
-++.-++.||+
T Consensus 96 ~ki~kll~iW~ 106 (121)
T smart00582 96 KKIRRLLNIWE 106 (121)
T ss_pred HHHHHHHHHHh
Confidence 35666777885
No 21
>PF11363 DUF3164: Protein of unknown function (DUF3164); InterPro: IPR021505 This entry is represented by Bacteriophage B3, Orf6. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=44.34 E-value=46 Score=24.67 Aligned_cols=34 Identities=18% Similarity=0.400 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHH
Q psy1883 18 EAHRALELLEDYHSKLTDPSDKQLRSAIERVIRI 51 (81)
Q Consensus 18 dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIni 51 (81)
+.+-|.+++.+|-+.++...+++++.-+++...+
T Consensus 97 ~l~~Ak~lIde~l~~w~~g~~~~l~~lV~~af~~ 130 (195)
T PF11363_consen 97 RLQAAKALIDECLNEWAKGADPELRALVNRAFQV 130 (195)
T ss_pred HHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHhc
Confidence 6788999999999999999999999998887665
No 22
>PF12177 Proho_convert: Prohormone convertase enzyme; InterPro: IPR022005 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with PF01483 from PFAM, PF00082 from PFAM. There are two completely conserved residues (Y and D) that may be functionally important. This protein is the C-terminal domain of a prohormone convertase enzyme which targets hormones in dense core secretory granules. This C-terminal tail domain is the domain responsible for targeting these dense core secretory granules. The domain adopts an alpha helical structure []. ; PDB: 2KE3_A 2KDT_A.
Probab=41.59 E-value=15 Score=22.08 Aligned_cols=10 Identities=60% Similarity=0.800 Sum_probs=7.8
Q ss_pred HHHHHHHHhh
Q psy1883 55 RLFQALLGQL 64 (81)
Q Consensus 55 ~LFqALLDI~ 64 (81)
+|.|||+||+
T Consensus 29 rLlQAL~~~l 38 (41)
T PF12177_consen 29 RLLQALFDIL 38 (41)
T ss_dssp HHHHHHHHHC
T ss_pred HHHHHHHHHH
Confidence 6778888875
No 23
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=41.04 E-value=82 Score=20.03 Aligned_cols=27 Identities=22% Similarity=0.270 Sum_probs=14.8
Q ss_pred chhhHHHhhchHHHHHHHHHHHHHHhh
Q psy1883 6 KELSTYYLLNYLEAHRALELLEDYHSK 32 (81)
Q Consensus 6 ~~~~~~~~~~~~dAhRALeLLE~Y~~k 32 (81)
..|+.....+.+.|..-.+.++++..+
T Consensus 22 ~~lt~~a~~~~~~a~~iv~~i~~~i~~ 48 (114)
T cd03562 22 QTLTKLAIENRKHAKEIVEIIEKHIKK 48 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345555555555555555555555544
No 24
>PF12424 ATP_Ca_trans_C: Plasma membrane calcium transporter ATPase C terminal; InterPro: IPR022141 This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with PF00689 from PFAM, PF00122 from PFAM, PF00702 from PFAM, PF00690 from PFAM. There is a conserved QTQ sequence motif. This family is the C-terminal of a calcium transporting ATPase located in the plasma membrane. ; GO: 0005388 calcium-transporting ATPase activity; PDB: 2KNE_B 1CFF_B.
Probab=40.43 E-value=9.3 Score=24.22 Aligned_cols=10 Identities=50% Similarity=0.879 Sum_probs=0.0
Q ss_pred HHHHHHHHHH
Q psy1883 47 RVIRIFKSRL 56 (81)
Q Consensus 47 rvIniFkS~L 56 (81)
||+|+|+|.+
T Consensus 17 rVV~AFrs~l 26 (66)
T PF12424_consen 17 RVVNAFRSSL 26 (66)
T ss_dssp ----------
T ss_pred HHHHHHcCCc
Confidence 7999999998
No 25
>PF12209 SAC3: Leucine permease transcriptional regulator helical domain; InterPro: IPR024293 This domain is found in fungal proteins, including the nuclear mRNA export protein SAC3. It has been suggested this domain provides a scaffold within the yeast Sac3:Cdc31:Sus1:Thp1 (TREX-2) complex to integrate interactions between protein complexes to facilitate the coupling of transcription and mRNA export during gene expression [].; PDB: 3FWC_N 3FWB_B.
Probab=38.38 E-value=61 Score=20.93 Aligned_cols=16 Identities=19% Similarity=0.522 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHH
Q psy1883 47 RVIRIFKSRLFQALLG 62 (81)
Q Consensus 47 rvIniFkS~LFqALLD 62 (81)
++|+.+.+.||+|.+-
T Consensus 37 ~iI~sLs~ELy~AFi~ 52 (79)
T PF12209_consen 37 QIIDSLSEELYDAFIH 52 (79)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5699999999999983
No 26
>PF01756 ACOX: Acyl-CoA oxidase; InterPro: IPR002655 Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids []. Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain []. Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments []. Experimental data indicate that, in the pumpkin, the expression pattern of ACOX is very similar to that of the glyoxysomal enzyme 3-ketoacyl-CoA thiolase []. In humans, defects in ACOX1 are the cause of pseudoneonatal adrenoleukodystrophy, also known as peroxisomal acyl-CoA oxidase deficiency. Pseudo-NALD is a peroxisomal single-enzyme disorder. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly and hearing deficit. Pseudo-NALD is characterised by increased plasma levels of very-long chain fatty acids due to a decrease in, or absence of, peroxisome acyl-CoA oxidase activity, despite the peroxisomes being intact and functioning. This entry represents the Acyl-CoA oxidase C-terminal.; GO: 0003997 acyl-CoA oxidase activity, 0006635 fatty acid beta-oxidation, 0055114 oxidation-reduction process, 0005777 peroxisome; PDB: 2FON_A 1IS2_B 2DDH_A 1W07_B.
Probab=38.31 E-value=1e+02 Score=21.38 Aligned_cols=42 Identities=17% Similarity=0.372 Sum_probs=36.9
Q ss_pred HHhhchHHHHHHHHHHHHHHhhcC-CCCcHHHHHHHHHHHHHH
Q psy1883 11 YYLLNYLEAHRALELLEDYHSKLT-DPSDKQLRSAIERVIRIF 52 (81)
Q Consensus 11 ~~~~~~~dAhRALeLLE~Y~~kL~-~~~D~~Lr~aiervIniF 52 (81)
..+.+...||--.-+++.+..++. ...|++.+..+..+...|
T Consensus 46 ~~l~~~a~Ah~e~~i~~~f~~~i~~~~~~~~~~~vL~~L~~Ly 88 (187)
T PF01756_consen 46 VQLVRAAKAHAERYILEQFIEAIQSSCADPEVRQVLRQLCQLY 88 (187)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTSG-SSTTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccCCChHHHHHHHHHHHHH
Confidence 455677799999999999999999 999999999999999888
No 27
>PF10635 DisA-linker: DisA bacterial checkpoint controller linker region ; InterPro: IPR018906 The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. the first, N-terminal region, from 1-145 is globular and is represented by IPR003390 from INTERPRO; the next 146-289 residues is this domain that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), thus forming a spine like-linker between domains 1 and 3. The C-terminal residues of domain 3 (IPR000445 from INTERPRO), represent the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis []. ; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A.
Probab=38.22 E-value=17 Score=26.14 Aligned_cols=18 Identities=39% Similarity=0.641 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHhhcC
Q psy1883 17 LEAHRALELLEDYHSKLT 34 (81)
Q Consensus 17 ~dAhRALeLLE~Y~~kL~ 34 (81)
..|-+||.-||.|++.|+
T Consensus 9 ~raNQAl~TLErYr~~ld 26 (145)
T PF10635_consen 9 ARANQALQTLERYRARLD 26 (145)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 368999999999998643
No 28
>cd08807 CARD_CARD10_CARMA3 Caspase activation and recruitment domain of CARD10-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD10, also known as CARMA3 (caspase recruitment domain-containing membrane-associated guanylate kinase protein 3) or BIMP1. The CARMA3-BCL10-MALT1 signalosome plays a role in the GPCR-induced NF-kB activation. CARMA3 is more widely expressed than CARMA1, which is found only in hematopoietic cells. In endothelial and smooth muscle cells, CARMA3-mediated NF-kB activation induces pro-inflammatory signals within the vasculature and is a key factor in atherogenesis. In bronchial epithelial cells, CARMA3-mediated NF-kB signaling is important for the development of allergic airway inflammation. 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 mechanisms. DDs are protein-protein interaction domains fo
Probab=37.93 E-value=95 Score=21.15 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHHhhhHH
Q psy1883 41 LRSAIERVIRIFKSR---LFQALLGQLGGA 67 (81)
Q Consensus 41 Lr~aiervIniFkS~---LFqALLDI~e~~ 67 (81)
-++...++++|.+++ =|.|-|+-+||+
T Consensus 48 ~~~k~~~LLDIL~trG~~gf~aFLeSLE~~ 77 (86)
T cd08807 48 RINRTGRLMDILRGRGKRGYEAFLEALEFY 77 (86)
T ss_pred HHHHHHHHHHHHHhcCchHHHHHHHHHHhh
Confidence 345567888999885 788888888854
No 29
>PF09349 OHCU_decarbox: OHCU decarboxylase; InterPro: IPR018020 The proteins in this entry are OHCU decarboxylase, an enzyme of the purine catabolism that catalyses the conversion of OHCU into S(+)-allantoin []; it is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalysed by urate oxidase (IPR002042 from INTERPRO) and step two is catalysed by hydroxyisourate hydrolase (IPR000895 from INTERPRO). ; PDB: 3O7I_B 3O7H_B 3O7J_A 3O7K_A 2Q37_A 2O70_B 2O73_C 2O74_C 2O8I_A.
Probab=37.27 E-value=62 Score=22.63 Aligned_cols=35 Identities=34% Similarity=0.559 Sum_probs=29.8
Q ss_pred HHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHH
Q psy1883 22 ALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRL 56 (81)
Q Consensus 22 ALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~L 56 (81)
+=++|+.-+.+|+...+.|++.+++=+..|-..||
T Consensus 123 ~~~Il~~l~~Rl~n~~~~E~~~A~~Ev~kIa~~RL 157 (159)
T PF09349_consen 123 AAEILAALERRLNNDPEEELRIALEEVAKIARLRL 157 (159)
T ss_dssp HHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHh
Confidence 35688888899999999999999999999888776
No 30
>PF10540 Membr_traf_MHD: Munc13 (mammalian uncoordinated) homology domain; InterPro: IPR019558 Mammalian uncoordinated homology 13 (Munc13) proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana (Mouse-ear cress), C. elegans, Drosophila melanogaster (Fruit fly), Mus musculus (Mouse), Rattus norvegicus (Rat) and Homo sapiens (Human), some of which may function in a Munc13-like manner to regulate membrane trafficking. The MHD1 and MHD2 domains are predicted to be alpha-helical. ; PDB: 3SWH_A.
Probab=36.77 E-value=62 Score=22.21 Aligned_cols=40 Identities=23% Similarity=0.227 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHH-HHHHHHHHHHhhhHHh
Q psy1883 19 AHRALELLEDYHSKLTDPSDKQLRSAIERVIRIF-KSRLFQALLGQLGGAI 68 (81)
Q Consensus 19 AhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniF-kS~LFqALLDI~e~~~ 68 (81)
-+.||+.|.+|-+. .+ +.+. ...+ ||.-||+|..++.||.
T Consensus 87 l~~~L~~L~~FFhA---~G-~Gl~------~~~L~ks~~yq~L~~~l~ly~ 127 (137)
T PF10540_consen 87 LFKWLDTLKDFFHA---EG-NGLP------LEFLEKSPEYQSLRYILSLYD 127 (137)
T ss_dssp HHHHHHHHHHHHHC---CC-TS--------HHHHHC-HHHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHHhC---CC-CCCC------HHHHccCHHHHHHHHHHHHhc
Confidence 35688888888874 22 2333 5667 8999999999999986
No 31
>PF03368 Dicer_dimer: Dicer dimerisation domain; InterPro: IPR005034 This domain is found in members of the Dicer protein family of dsRNA nucleases. This entry represents a dsRNA-binding domain. RNA interference (RNAi) is an ancient gene-silencing process that plays a fundamental role in diverse eukaryotic functions including viral defence, chromatin remodelling, genome rearrangement, developmental timing, brain morphogenesis, and stem cell maintenance. All RNAi pathways require the multidomain ribonuclease Dicer, which initiates RNAi by cleaving double-stranded RNA (dsRNA) substrates into small fragments ~25 nuleotides in length. A typical eukaryotic Dicer consists of a helicase domain (PDOC51192 from PROSITEDOC), a domain of unknown function, and a PAZ domain (PDOC50821 from PROSITEDOC) at the amino (N)-terminus as well as two ribonuclease III domains (PDOC00448 from PROSITEDOC) and a dsRNA-binding domain (dsRBD) (PDOC50137 from PROSITEDOC) at the carboxy (C)-terminus. The domain of unknown function of ~100 amino acids is predicted to adopt the canonical alpha-beta-beta-beta-alpha-fold found in all dsRBDs [, , , ].; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters; PDB: 2KOU_A.
Probab=35.57 E-value=35 Score=21.80 Aligned_cols=16 Identities=44% Similarity=0.603 Sum_probs=13.1
Q ss_pred HHHHHHHHHhhcCCCC
Q psy1883 22 ALELLEDYHSKLTDPS 37 (81)
Q Consensus 22 ALeLLE~Y~~kL~~~~ 37 (81)
|+.+|..||++|.+..
T Consensus 1 Ai~lL~~yC~~Lp~d~ 16 (90)
T PF03368_consen 1 AISLLNRYCSTLPSDS 16 (90)
T ss_dssp HHHHHHHHHTTSSS-T
T ss_pred CHHHHHHHHhcCCCCC
Confidence 7889999999998753
No 32
>PRK05685 fliS flagellar protein FliS; Validated
Probab=35.48 E-value=1.4e+02 Score=20.23 Aligned_cols=57 Identities=12% Similarity=0.131 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHH--HhhhHHhHHHHhh
Q psy1883 18 EAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALL--GQLGGAIGISVLG 74 (81)
Q Consensus 18 dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALL--DI~e~~~~~~~~~ 74 (81)
.-.+|.+++.+-+..|+.....++-..+..+=+-...+|.+|-+ |.-..-+.+.++.
T Consensus 57 ~l~ka~~Ii~eL~~sLd~e~ggeiA~~L~~LY~y~~~~L~~A~~~~d~~~l~ev~~il~ 115 (132)
T PRK05685 57 YLSKAINIINGLRNSLDMEKGGEVAKNLSALYDYMIRRLLEANLRNDVQAIDEVEGLLR 115 (132)
T ss_pred HHHHHHHHHHHHHhhcCCccccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 44588899999999999888889999999999999999999887 3444444555544
No 33
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=34.25 E-value=55 Score=29.62 Aligned_cols=39 Identities=26% Similarity=0.427 Sum_probs=31.2
Q ss_pred hchHHHHHHHHHHHHHHhhcCCCCcHHH-HHHHHHHHHHH
Q psy1883 14 LNYLEAHRALELLEDYHSKLTDPSDKQL-RSAIERVIRIF 52 (81)
Q Consensus 14 ~~~~dAhRALeLLE~Y~~kL~~~~D~~L-r~aiervIniF 52 (81)
-...|.+||=++||+-+.++..+.-++. +.-+|||+.-|
T Consensus 812 p~~~d~qRAReILeElRRR~gd~~rPq~E~dYLeRLL~~f 851 (851)
T TIGR02302 812 PGEIDVQRARRILEEIRRKLGDSLRPQIELDYLERLLKDY 851 (851)
T ss_pred CChHhHHHHHHHHHHHHHhhCCCCCcHHHHHHHHHHhccC
Confidence 3445899999999999999998755544 67789988755
No 34
>PF13628 DUF4142: Domain of unknown function (DUF4142)
Probab=33.46 E-value=1.4e+02 Score=19.63 Aligned_cols=47 Identities=23% Similarity=0.398 Sum_probs=33.8
Q ss_pred hHHHhhchHHHH-HHHHHHHH-HHhhcCCCCcHHHHHHHHHHHHHHHHHHHH
Q psy1883 9 STYYLLNYLEAH-RALELLED-YHSKLTDPSDKQLRSAIERVIRIFKSRLFQ 58 (81)
Q Consensus 9 ~~~~~~~~~dAh-RALeLLE~-Y~~kL~~~~D~~Lr~aiervIniFkS~LFq 58 (81)
..-|+.....+| +++.+++. +- .+..|++||..+...+.+++..|=.
T Consensus 87 D~~yl~~~i~~h~~~l~~~~~~~~---~~~~~~~lk~~a~~~lp~l~~hl~~ 135 (139)
T PF13628_consen 87 DRAYLDAQIKAHEKALALFEKQLA---ASGKDPELKAFAQETLPVLEAHLEM 135 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh---ccCCCHHHHHHHHHHhHHHHHHHHH
Confidence 334444444454 56777777 54 4799999999999999999887743
No 35
>TIGR02672 cas_csm6 CRISPR-associated protein, Csm6 family. Members of this family as found in CRISPR-associated (cas) gene regions in Streptococcus thermophilus CNRZ1066, Staphylococcus epidermidis RP62A, and Mycobacterium tuberculosis (strains CDC1551 and H37Rv), as part of Mtube-type CRISPR/Cas systems. CRISPR is a widespread form of direct repeat found in archaea and bacteria, with distinctive subtypes each of which has a characteristic sporadic distribution.
Probab=32.73 E-value=1.3e+02 Score=25.07 Aligned_cols=53 Identities=17% Similarity=0.168 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHH-HHHHHHHH---------HhhhHHhHHHH
Q psy1883 18 EAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFK-SRLFQALL---------GQLGGAIGISV 72 (81)
Q Consensus 18 dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFk-S~LFqALL---------DI~e~~~~~~~ 72 (81)
|=+.||+++.+-+. .+....-+|.++.+..++|| .+.+.... ++.+||..+-+
T Consensus 139 DY~AAL~il~~~~~--~~~~~~llr~aL~d~~~v~K~~~~~~~~~~~p~~~~~kk~~eY~L~idl 201 (362)
T TIGR02672 139 DYSAALTIAADSRL--FDNVKNLIRGKLHRSRLEHKVAPKFFKITAFTYDDANKKVLEYYLALAL 201 (362)
T ss_pred cHHHHHHHHHhCcc--cccHHHHHHHHHHhHHHHHhhhhhhhhhhccccchHHHHHHHHHHHHHH
Confidence 56788888886552 23333469999999999999 66655322 56666665544
No 36
>PF14293 YWFCY: YWFCY protein
Probab=32.49 E-value=46 Score=21.35 Aligned_cols=16 Identities=31% Similarity=0.233 Sum_probs=13.6
Q ss_pred HHHHHhhhHHhHHHHh
Q psy1883 58 QALLGQLGGAIGISVL 73 (81)
Q Consensus 58 qALLDI~e~~~~~~~~ 73 (81)
+||=-|++|.++||++
T Consensus 7 r~L~KImdf~R~iSI~ 22 (61)
T PF14293_consen 7 RALRKIMDFMRAISIL 22 (61)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 6778899999999875
No 37
>PRK13798 putative OHCU decarboxylase; Provisional
Probab=32.25 E-value=88 Score=22.46 Aligned_cols=35 Identities=23% Similarity=0.361 Sum_probs=31.3
Q ss_pred HHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHH
Q psy1883 22 ALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRL 56 (81)
Q Consensus 22 ALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~L 56 (81)
+=++|+.-..+|.+..+.|++.+++=+..|-.-||
T Consensus 125 ~~~IL~~l~~Rl~n~~e~E~~~al~Ev~kIa~lRL 159 (166)
T PRK13798 125 ADEMLAALQQRLHNDPETERKVVREELAKINRLRL 159 (166)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 45688888999999999999999999999988887
No 38
>TIGR03164 UHCUDC OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model.
Probab=32.06 E-value=89 Score=22.13 Aligned_cols=35 Identities=20% Similarity=0.448 Sum_probs=29.4
Q ss_pred HHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHH
Q psy1883 22 ALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRL 56 (81)
Q Consensus 22 ALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~L 56 (81)
+=++|++-+.+|.+..+.|++.+++-+..|=.-||
T Consensus 120 ~~~Il~~l~~Rl~n~~~~E~~~a~~Ev~kIa~~RL 154 (157)
T TIGR03164 120 KQSILAAFEARLNNDRETEFARALREIERIARFRL 154 (157)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45788888899999999999999999888877665
No 39
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.80 E-value=37 Score=24.79 Aligned_cols=22 Identities=18% Similarity=0.182 Sum_probs=19.0
Q ss_pred HHHhhchHHHHHHHHHHHHHHh
Q psy1883 10 TYYLLNYLEAHRALELLEDYHS 31 (81)
Q Consensus 10 ~~~~~~~~dAhRALeLLE~Y~~ 31 (81)
-|+|+-+++|.+|+.+|....+
T Consensus 110 DHlFVp~e~a~~A~~~L~~laa 131 (134)
T COG3602 110 DHLFVPAERAKEALVVLQGLAA 131 (134)
T ss_pred ceeeeeHHHHHHHHHHHHHHHh
Confidence 4789999999999999987664
No 40
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=29.73 E-value=71 Score=17.07 Aligned_cols=26 Identities=23% Similarity=0.213 Sum_probs=18.8
Q ss_pred ccchhhHHHhhchHHHHHHHHHHHHH
Q psy1883 4 RKKELSTYYLLNYLEAHRALELLEDY 29 (81)
Q Consensus 4 ~~~~~~~~~~~~~~dAhRALeLLE~Y 29 (81)
..++++..+=..+.-..+|+..|++.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 45566777777777788888888764
No 41
>TIGR01216 ATP_synt_epsi ATP synthase, F1 epsilon subunit (delta in mitochondria). This model describes one of the five types of subunits in the F1 part of F1/F0 ATP synthases. Members of this family are designated epsilon in bacterial and chloroplast systems but designated delta in mitochondria, where the counterpart of the bacterial delta subunit is designated OSCP. In a few cases (Propionigenium modestum, Acetobacterium woodii) scoring above the trusted cutoff and designated here as exceptions, Na+ replaces H+ for translocation.
Probab=29.71 E-value=1.6e+02 Score=19.78 Aligned_cols=40 Identities=13% Similarity=0.092 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHH
Q psy1883 16 YLEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSR 55 (81)
Q Consensus 16 ~~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~ 55 (81)
..|..+|-+.+++-+.+|+...|..=+..++.-+..-.++
T Consensus 86 ~id~~~a~~~~~~ae~~l~~~~~~~~~~~a~~~l~~a~~r 125 (130)
T TIGR01216 86 DIDEAEAEKALEAAEKLLESAEDDKDLAEALLKLKKARAQ 125 (130)
T ss_pred cCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHH
Confidence 3477788888888888888766644444444444444443
No 42
>PF09426 Nyv1_N: Vacuolar R-SNARE Nyv1 N terminal; InterPro: IPR019005 This entry represents the N-terminal domain of vacuolar R-SNARE Nyv1, which adopts a longin fold []. Vacuolar v-SNARE is required for docking and is only involved in homotypic vacuole fusion. Nyv1 is required for Ca(2+) efflux from the vacuolar lumen, a required signal for subsequent membrane fusion events, by inhibiting vacuolar Ca(2+)-ATPase PMC1 and promoting Ca(2+) release when forming trans-SNARE assemblies during the docking step. In yeast, the N-terminal domain of Nyv1 is sufficient to direct the transport of Nyv1 to limiting membrane of the vacuole []. ; PDB: 2FZ0_A.
Probab=29.36 E-value=1e+02 Score=22.66 Aligned_cols=35 Identities=17% Similarity=0.431 Sum_probs=24.1
Q ss_pred HHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHH
Q psy1883 23 LELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLF 57 (81)
Q Consensus 23 LeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LF 57 (81)
|++|.+-..-=....|++|...+..+++-|...|.
T Consensus 102 iRlLSeLK~~~~~~~D~~L~~~v~~IlD~FH~ELl 136 (141)
T PF09426_consen 102 IRLLSELKGLENNDTDEELSAHVGNILDEFHEELL 136 (141)
T ss_dssp HHHHHHHTTSS---STTSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhhccccCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34444444322238999999999999999998775
No 43
>PF03820 Mtc: Tricarboxylate carrier; InterPro: IPR004686 The MTC family consists of a limited number of homologues, all from eukaryotes. One member of the family has been functionally characterised as a tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism. The rest of the characterised proteins appear to be sideroflexins involved in iron transport.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016020 membrane
Probab=28.79 E-value=78 Score=25.12 Aligned_cols=43 Identities=30% Similarity=0.349 Sum_probs=33.1
Q ss_pred HHhhchHHHHHHHHHHHHHHhhcCCC--CcHHHHHHHHHHHHHHH
Q psy1883 11 YYLLNYLEAHRALELLEDYHSKLTDP--SDKQLRSAIERVIRIFK 53 (81)
Q Consensus 11 ~~~~~~~dAhRALeLLE~Y~~kL~~~--~D~~Lr~aiervIniFk 53 (81)
.+|....+-+.|-++|++|++.-..+ +|++|..|=.....+|.
T Consensus 21 ~l~~S~~~l~~a~~ll~~~~~g~~~~~~~~~~lw~Ak~l~~Sa~H 65 (308)
T PF03820_consen 21 NLFASEAELEEAKELLEDYRAGKVPPGLTDDELWKAKKLYDSAFH 65 (308)
T ss_pred hhcCCHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHhhcccC
Confidence 45666778899999999999876666 78998887666555544
No 44
>PF14661 HAUS6_N: HAUS augmin-like complex subunit 6 N-terminus
Probab=28.58 E-value=1e+02 Score=22.85 Aligned_cols=48 Identities=19% Similarity=0.279 Sum_probs=41.4
Q ss_pred hhhHHHhhchHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHH
Q psy1883 7 ELSTYYLLNYLEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKS 54 (81)
Q Consensus 7 ~~~~~~~~~~~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS 54 (81)
|...|+++..-|+.+|-+.+..|-==++..+|..+|.++-+.++..+.
T Consensus 40 e~vl~~Lf~~lD~~~~~~~f~~~wP~~d~~q~~~fR~~~~~~L~~l~~ 87 (247)
T PF14661_consen 40 EWVLHFLFTILDPEEAKKKFRPCWPPLDKKQSANFRKALFRWLKELKK 87 (247)
T ss_pred HHHHHHHHHHcCHHHHHHHhhccCCCCCchhhHHHHHHHHHHHHHHHH
Confidence 556789999999999988888877788889999999999999888776
No 45
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=28.17 E-value=71 Score=18.51 Aligned_cols=27 Identities=30% Similarity=0.388 Sum_probs=18.7
Q ss_pred CccchhhHHHhhchHHHHHHHHHHHHH
Q psy1883 3 PRKKELSTYYLLNYLEAHRALELLEDY 29 (81)
Q Consensus 3 ~~~~~~~~~~~~~~~dAhRALeLLE~Y 29 (81)
|...+|+-.+=+.+.-+.+|+..|++.
T Consensus 25 ps~~~la~~~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 25 PSERELAERYGVSRTTVREALRRLEAE 51 (64)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCHHHHHHHhccCCcHHHHHHHHHHHC
Confidence 555677777778888888888888764
No 46
>PF11640 TAN: Telomere-length maintenance and DNA damage repair; InterPro: IPR021668 ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of the DNA damage signal transducer kinase Rad53 (an orthologue of mammalian CHK2). In addition to functioning in the response to DSBs, numerous findings indicate that Tel1/ATM regulates telomeres. The overall domain structure of Tel1/ATM is shared by proteins of the phosphatidylinositol 3-kinase (PI3K)-related kinase (PIKK) family, but this family carries a unique and functionally important TAN sequence motif, near its N-terminal, LxxxKxxE/DRxxxL. which is conserved specifically in the Tel1/ATM subclass of the PIKKs. The TAN motif is essential for both telomere length maintenance and Tel1 action in response to DNA damage []. It is classified as an 2.7.11.1 from EC. ; GO: 0004674 protein serine/threonine kinase activity
Probab=27.60 E-value=1.2e+02 Score=20.67 Aligned_cols=28 Identities=21% Similarity=0.195 Sum_probs=16.8
Q ss_pred HHHhhcCCCCcHHHHHHHHHHHHHHHHH
Q psy1883 28 DYHSKLTDPSDKQLRSAIERVIRIFKSR 55 (81)
Q Consensus 28 ~Y~~kL~~~~D~~Lr~aiervIniFkS~ 55 (81)
+.+..|.+..-++=+.+++.+..+++++
T Consensus 8 ~~~~~L~S~k~keR~~al~~L~~il~~~ 35 (155)
T PF11640_consen 8 SILRLLSSDKIKERNKALEDLRHILSSP 35 (155)
T ss_pred HHHHHHhccccchHHHHHHHHHHHHcCc
Confidence 3445555566666666666666666655
No 47
>COG5424 Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C [Coenzyme metabolism]
Probab=27.52 E-value=2e+02 Score=22.70 Aligned_cols=48 Identities=10% Similarity=0.109 Sum_probs=37.9
Q ss_pred chhhHHHhhchHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHH
Q psy1883 6 KELSTYYLLNYLEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSR 55 (81)
Q Consensus 6 ~~~~~~~~~~~~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~ 55 (81)
+-+.+|+-...++|.-||+++.++-.. +..+++++.++.+..++|-+-
T Consensus 174 ~yf~~h~eaD~~Ha~Ealkiv~~~~~t--~E~~~~~~~~~~~~~D~lw~f 221 (242)
T COG5424 174 AYFREHLEADVRHAEEALKIVLELAGT--RELQDQVLDALQKSLDVLWLF 221 (242)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHhc--hhhHHHHHHHHHHHHHHHHHH
Confidence 345677788889999999999987653 677888999998888876543
No 48
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=27.51 E-value=42 Score=30.49 Aligned_cols=33 Identities=42% Similarity=0.433 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHH-HHHHHHH-HHHHhhhHHhHHH
Q psy1883 39 KQLRSAIERVIRI-FKSRLFQ-ALLGQLGGAIGIS 71 (81)
Q Consensus 39 ~~Lr~aiervIni-FkS~LFq-ALLDI~e~~~~~~ 71 (81)
.-|+++|++..+. +.||+|+ |++||.+=..-++
T Consensus 688 ~~l~r~i~~~~~~~vpsr~f~~a~~~I~~e~d~ii 722 (830)
T COG1202 688 GFLKRAIESALRGRVPSRLFDSALLDILEEGDKII 722 (830)
T ss_pred hHHHHHHHHHhcCCCchhhhhHHHHHHHhchhhhh
Confidence 3467778887764 8999999 9999998766554
No 49
>TIGR02132 phaR_Bmeg polyhydroxyalkanoic acid synthase, PhaR subunit. This model describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit.
Probab=26.91 E-value=1.1e+02 Score=23.47 Aligned_cols=51 Identities=16% Similarity=0.283 Sum_probs=38.5
Q ss_pred HHHHHH-HHHHHHHhhcCCCCcHHHHHHHHHHHHH-HHHHHHHHHH-HhhhHHh
Q psy1883 18 EAHRAL-ELLEDYHSKLTDPSDKQLRSAIERVIRI-FKSRLFQALL-GQLGGAI 68 (81)
Q Consensus 18 dAhRAL-eLLE~Y~~kL~~~~D~~Lr~aiervIni-FkS~LFqALL-DI~e~~~ 68 (81)
.+++|+ +.++.|-++|.=|+-.++-+-+++|||+ +|=+.....+ |+.++..
T Consensus 50 ~yQKafnE~MekYLe~lNlPSr~DiarvA~lvinlE~kvD~lee~fdd~~d~l~ 103 (189)
T TIGR02132 50 FYQKALNDTTGNYLEQVNVPTKEDIANVASLVINLEEKVDLIEEFFDDKFDELE 103 (189)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466776 5789999999999999999999999997 4555555544 4455544
No 50
>PF11123 DNA_Packaging_2: DNA packaging protein ; InterPro: IPR024345 This entry represents Gp18 (gene 18 product), also known as DNA maturase A, from T7-like bacteriophages. In Bacteriophage T3, this protein is required for DNA packaging and functions in a complex with Gp19 [].
Probab=26.08 E-value=2.1e+02 Score=19.43 Aligned_cols=40 Identities=28% Similarity=0.406 Sum_probs=32.9
Q ss_pred HhhchHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHH
Q psy1883 12 YLLNYLEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFK 53 (81)
Q Consensus 12 ~~~~~~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFk 53 (81)
.++...|++.|=.+|.+.+. +....+||-+||.|+...-|
T Consensus 6 klLemlDtEmA~~mL~DLr~--dekRsPQLYnAI~k~L~RHk 45 (82)
T PF11123_consen 6 KLLEMLDTEMAQQMLADLRD--DEKRSPQLYNAIGKLLDRHK 45 (82)
T ss_pred HHHHHHHHHHHHHHHHHhcc--hhhcChHHHHHHHHHHHHcc
Confidence 45667799999999999887 46778999999999987644
No 51
>PHA01623 hypothetical protein
Probab=25.97 E-value=1.2e+02 Score=18.33 Aligned_cols=28 Identities=18% Similarity=0.190 Sum_probs=21.3
Q ss_pred HHHHHHHHhhcCCCCcHHHHHHHHHHHH
Q psy1883 23 LELLEDYHSKLTDPSDKQLRSAIERVIR 50 (81)
Q Consensus 23 LeLLE~Y~~kL~~~~D~~Lr~aiervIn 50 (81)
++-|+.||.+..-...+-+|.+|+..+.
T Consensus 25 ~~~Ld~y~~~~g~~rSe~IreAI~~yL~ 52 (56)
T PHA01623 25 KTRLKVYCAKNNLQLTQAIEEAIKEYLQ 52 (56)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 4668899998777777777777776664
No 52
>COG1516 FliS Flagellin-specific chaperone FliS [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=25.81 E-value=1.7e+02 Score=20.98 Aligned_cols=25 Identities=20% Similarity=0.320 Sum_probs=17.8
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHH
Q psy1883 35 DPSDKQLRSAIERVIRIFKSRLFQAL 60 (81)
Q Consensus 35 ~~~D~~Lr~aiervIniFkS~LFqAL 60 (81)
...=++--.+|.|+++||. .|...|
T Consensus 44 ~~~i~~k~~~i~ka~~Ii~-eL~~~L 68 (132)
T COG1516 44 QEDIEEKNESIDKAIDIIT-ELRASL 68 (132)
T ss_pred hccHHHHHHHHHHHHHHHH-HHHHhc
Confidence 3444567788999999998 555544
No 53
>TIGR03180 UraD_2 OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. This model is a separate (but related) clade from that represented by TIGR3164. This model places a second homolog in streptomyces species which (are not in the vicinity of other urate catabolism associated genes) below the trusted cutoff.
Probab=25.22 E-value=1.4e+02 Score=21.19 Aligned_cols=35 Identities=29% Similarity=0.480 Sum_probs=30.4
Q ss_pred HHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHH
Q psy1883 22 ALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRL 56 (81)
Q Consensus 22 ALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~L 56 (81)
+=++|+.-+.+|.+..+.|++.+++=+..|-.-||
T Consensus 120 ~~~IL~~l~~Rl~n~~e~E~~~al~Ev~kIa~~RL 154 (158)
T TIGR03180 120 AEEMLDALQARLPNDPEQELTIAAEQLRKINRLRL 154 (158)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45788888899999999999999999988877775
No 54
>KOG1758|consensus
Probab=25.01 E-value=1.8e+02 Score=21.84 Aligned_cols=29 Identities=28% Similarity=0.406 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHhhcCCCCcHHHHHHH
Q psy1883 17 LEAHRALELLEDYHSKLTDPSDKQLRSAI 45 (81)
Q Consensus 17 ~dAhRALeLLE~Y~~kL~~~~D~~Lr~ai 45 (81)
-|+..|=++||+++++|...+|+--+-.+
T Consensus 116 id~~~a~q~Le~aqa~l~~a~de~~~AEA 144 (159)
T KOG1758|consen 116 IDPSEAQQLLEKAQAKLVSASDEREAAEA 144 (159)
T ss_pred CCHHHHHHHHHHHHHHhcccccHHHHHHH
Confidence 37888999999999999999998655433
No 55
>PF05760 IER: Immediate early response protein (IER); InterPro: IPR008653 This family consists of several eukaryotic immediate early response (IER) 2 and 5 proteins. The role of IER5 is unclear although it play an important role in mediating the cellular response to mitogenic signals. Again, little is known about the function of IER2 although it is thought to play a role in mediating the cellular responses to a variety of extracellular signals [, ].
Probab=24.97 E-value=41 Score=26.94 Aligned_cols=22 Identities=32% Similarity=0.561 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Q psy1883 42 RSAIERVIRIFKSRLFQALLGQL 64 (81)
Q Consensus 42 r~aiervIniFkS~LFqALLDI~ 64 (81)
-.+|.-||.||.|. |+.||.-+
T Consensus 246 t~NvsnLIsIfgSs-FSGLls~~ 267 (300)
T PF05760_consen 246 TGNVSNLISIFGSS-FSGLLSKQ 267 (300)
T ss_pred ccchhHHHHHHhhh-hhhhhcCC
Confidence 47899999999999 99998643
No 56
>PF12297 EVC2_like: Ellis van Creveld protein 2 like protein; InterPro: IPR022076 This family of proteins is found in eukaryotes. Proteins in this family are typically between 571 and 1310 amino acids in length. There are two conserved sequence motifs: LPA and ELH. EVC2 is implicated in Ellis van Creveld chondrodysplastic dwarfism in humans. Mutations in this protein can give rise to this congenital condition. LIMBIN is a protein which shares around 80% sequence homology with EVC2 and it is implicated in a similar condition in bovine chondrodysplastic dwarfism.
Probab=24.91 E-value=1.5e+02 Score=25.17 Aligned_cols=38 Identities=21% Similarity=0.443 Sum_probs=29.8
Q ss_pred hHHHhhchHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHH
Q psy1883 9 STYYLLNYLEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSR 55 (81)
Q Consensus 9 ~~~~~~~~~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~ 55 (81)
.--+..+.-++..|=.+|++|.. ....+|+|++.|+|+
T Consensus 314 ~~ai~~GeL~~e~Ak~Ll~~y~~---------~Q~~vEelMD~~qA~ 351 (429)
T PF12297_consen 314 KSAIFKGELKPEAAKSLLQDYSK---------IQENVEELMDFFQAN 351 (429)
T ss_pred HHHHHhCCCCHHHHHHHHHHHHH---------HHHHHHHHHHHHHHh
Confidence 33455666778888889999974 567899999999986
No 57
>PHA00425 DNA packaging protein, small subunit
Probab=24.29 E-value=1.9e+02 Score=19.83 Aligned_cols=40 Identities=25% Similarity=0.375 Sum_probs=32.6
Q ss_pred HhhchHHHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHH
Q psy1883 12 YLLNYLEAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFK 53 (81)
Q Consensus 12 ~~~~~~dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFk 53 (81)
-|+--.|++.|=.+|++.+. ++...+||-+||.++...-|
T Consensus 8 k~LemlDTE~a~~mL~DL~d--dekRtPQLYnAIgKlL~RHk 47 (88)
T PHA00425 8 KFLEMLDTEMAQRMLADLKD--DEKRTPQLYNAIGKLLDRHK 47 (88)
T ss_pred HHHHHHhHHHHHHHHHHhcC--ccccChHHHHHHHHHHHHhc
Confidence 35566799999999999876 46778999999999987654
No 58
>PF15469 Sec5: Exocyst complex component Sec5
Probab=24.15 E-value=2.5e+02 Score=19.35 Aligned_cols=54 Identities=26% Similarity=0.378 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh----hhHHhHHHHh
Q psy1883 18 EAHRALELLEDYHSKLTDPSDKQLRSAIERVIRIFKSRLFQALLGQ----LGGAIGISVL 73 (81)
Q Consensus 18 dAhRALeLLE~Y~~kL~~~~D~~Lr~aiervIniFkS~LFqALLDI----~e~~~~~~~~ 73 (81)
|=.||-.++++|+. ..+-=..+...+|..|..|+..|++-|.+. .++...|+.|
T Consensus 108 dY~kak~l~~~~~~--~~~vf~~v~~eve~ii~~~r~~l~~~L~~~~~s~~~~~~~i~~L 165 (182)
T PF15469_consen 108 DYKKAKSLFEKYKQ--QVPVFQKVWSEVEKIIEEFREKLWEKLLSPPSSQEEFLKLIRKL 165 (182)
T ss_pred HHHHHHHHHHHhhh--hHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 33678888888853 122334467789999999999999999843 3444455444
No 59
>cd01048 Ferritin_like_AB2 Uncharacterized family of ferritin-like proteins found in archaea and bacteria. Ferritin-like domain found in archaea and bacteria, subgroup 2 (Ferritin_like_AB2). This uncharacterized domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown. The conserved residues of a diiron center are present within the putative active site.
Probab=23.81 E-value=1.3e+02 Score=20.25 Aligned_cols=31 Identities=16% Similarity=0.333 Sum_probs=27.3
Q ss_pred HHHHHhhcCCCCcHHHHHHHHHHHHHHHHHH
Q psy1883 26 LEDYHSKLTDPSDKQLRSAIERVIRIFKSRL 56 (81)
Q Consensus 26 LE~Y~~kL~~~~D~~Lr~aiervIniFkS~L 56 (81)
++.|..-+.+.+|+.+|...+++.+--+.++
T Consensus 98 i~~ye~~~~~~~d~d~k~v~~~L~~~e~~H~ 128 (135)
T cd01048 98 IADYDRLLERTQNPDIRDVFENLQAASRNHH 128 (135)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999998877765
No 60
>PF00858 ASC: Amiloride-sensitive sodium channel; InterPro: IPR001873 The apical membrane of many tight epithelia contains sodium channels that are primarily characterised by their high affinity to the diuretic blocker amiloride [, , , ]. These channels mediate the first step of active sodium reabsorption essential for the maintenance of body salt and water homeostasis []. In vertebrates, the channels control reabsorption of sodium in kidney, colon, lung and sweat glands; they also play a role in taste perception. Members of the epithelial Na+ channel (ENaC) family fall into four subfamilies, termed alpha, beta, gamma and delta []. The proteins exhibit the same apparent topology, each with two transmembrane (TM) spanning segments, separated by a large extracellular loop. In most ENaC proteins studied to date, the extracellular domains are highly conserved and contain numerous cysteine residues, with flanking C-terminal amphipathic TM regions, postulated to contribute to the formation of the hydrophilic pores of the oligomeric channel protein complexes. It is thought that the well-conserved extracellular domains serve as receptors to control the activities of the channels. Vertebrate ENaC proteins are similar to degenerins of Caenorhabditis elegans []: deg-1, del-1, mec-4, mec-10 and unc-8. These proteins can be mutated to cause neuronal degradation, and are also thought to form sodium channels. Structurally, the proteins that belong to this family consist of about 510 to 920 amino acid residues. They are made of an intracellular N terminus region followed by a transmembrane domain, a large extracellular loop, a second transmembrane segment and a C-terminal intracellular tail [].; GO: 0005272 sodium channel activity, 0006814 sodium ion transport, 0016020 membrane; PDB: 2QTS_B 3S3W_C 3IJ4_A 3S3X_A 3HGC_A 2K2B_A.
Probab=23.74 E-value=1.2e+02 Score=22.51 Aligned_cols=26 Identities=35% Similarity=0.494 Sum_probs=20.6
Q ss_pred HHHHHHHHHhhhHHhHHHHhhhhhhc
Q psy1883 54 SRLFQALLGQLGGAIGISVLGIFKIW 79 (81)
Q Consensus 54 S~LFqALLDI~e~~~~~~~~~~~~~~ 79 (81)
++|+..+=+++...+|+|+++++.|-
T Consensus 411 ~~ll~~iGG~~gLflG~S~is~~E~i 436 (439)
T PF00858_consen 411 SDLLSDIGGILGLFLGASVISLVEII 436 (439)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHhhhHHHHHHhHHHHHHHHHe
Confidence 45666666888999999999998764
No 61
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=23.52 E-value=1.7e+02 Score=18.70 Aligned_cols=27 Identities=22% Similarity=0.324 Sum_probs=22.4
Q ss_pred CCcHHHHHHHHHHHHHHHHH-HHHHHHH
Q psy1883 36 PSDKQLRSAIERVIRIFKSR-LFQALLG 62 (81)
Q Consensus 36 ~~D~~Lr~aiervIniFkS~-LFqALLD 62 (81)
+.+++|+..+++.|..++.+ -++.+++
T Consensus 193 ~~~~~l~~~~n~~i~~l~~~G~~~~i~~ 220 (225)
T PF00497_consen 193 KKNPELLEIFNKAIRELKQSGEIQKILK 220 (225)
T ss_dssp TTTHHHHHHHHHHHHHHHHTTHHHHHHH
T ss_pred ccccHHHHHHHHHHHHHHhCcHHHHHHH
Confidence 67899999999999999876 7777643
No 62
>PF13446 RPT: A repeated domain in UCH-protein
Probab=23.36 E-value=1.2e+02 Score=17.62 Aligned_cols=28 Identities=14% Similarity=0.106 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHhhhHHhHHHHhh
Q psy1883 47 RVIRIFKSRLFQALLGQLGGAIGISVLG 74 (81)
Q Consensus 47 rvIniFkS~LFqALLDI~e~~~~~~~~~ 74 (81)
=+|++|++++...=-++-.+.+++.++|
T Consensus 21 ~Ii~~f~~~~~~~P~~~~~~r~AL~~Ia 48 (62)
T PF13446_consen 21 FIISAFQSKVNDDPSQKDTLREALRVIA 48 (62)
T ss_pred HHHHHHHHHHHcChHhHHHHHHHHHHHH
Confidence 4566666666644334445555555554
No 63
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=23.24 E-value=1.2e+02 Score=18.95 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=18.2
Q ss_pred hcCCCCcHHHHHHHHHHHHHHHHH
Q psy1883 32 KLTDPSDKQLRSAIERVIRIFKSR 55 (81)
Q Consensus 32 kL~~~~D~~Lr~aiervIniFkS~ 55 (81)
+|.+|.|++++..+..++...+..
T Consensus 49 ~Lrkh~~~~I~~~A~~Li~~WK~~ 72 (75)
T smart00509 49 GLRKHKNEEIRKLAKKLIKSWKKL 72 (75)
T ss_pred HHHcCCcHHHHHHHHHHHHHHHHH
Confidence 466678888888888888776653
No 64
>PF08785 Ku_PK_bind: Ku C terminal domain like; InterPro: IPR014893 The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C-terminal of Ku which binds to DNA-PKcs []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 1RW2_A 1Q2Z_A 3ISM_C.
Probab=22.36 E-value=2.5e+02 Score=18.70 Aligned_cols=43 Identities=16% Similarity=0.287 Sum_probs=25.0
Q ss_pred HHHHhhcCCCCc------HHHHHHHHHHHHHHHHHHHHHHHHhhhHHhH
Q psy1883 27 EDYHSKLTDPSD------KQLRSAIERVIRIFKSRLFQALLGQLGGAIG 69 (81)
Q Consensus 27 E~Y~~kL~~~~D------~~Lr~aiervIniFkS~LFqALLDI~e~~~~ 69 (81)
+||.+-|.+..+ ++++..|..++.-..++.|+-.++.+.-++.
T Consensus 7 ~DFk~ll~~~d~~~~~A~~qM~~vI~~Lv~~s~~~~y~kalecl~~lR~ 55 (120)
T PF08785_consen 7 QDFKALLAQRDSDFQKAIQQMKNVIEQLVSDSGDQNYDKALECLRALRE 55 (120)
T ss_dssp HHHHHHCCCCSSCCCHHHHHHHHHHHHHHHCSHCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHH
Confidence 466666666554 4555566666665555556655566555553
No 65
>KOG2160|consensus
Probab=21.13 E-value=2.4e+02 Score=23.17 Aligned_cols=43 Identities=26% Similarity=0.341 Sum_probs=34.1
Q ss_pred chHHHHHHHHHHHHHHhhcCC------------------CCcHHHHHHHHHHHHH-HHHHHH
Q psy1883 15 NYLEAHRALELLEDYHSKLTD------------------PSDKQLRSAIERVIRI-FKSRLF 57 (81)
Q Consensus 15 ~~~dAhRALeLLE~Y~~kL~~------------------~~D~~Lr~aiervIni-FkS~LF 57 (81)
..+|=+.||+.||+|....+. ++|..||..+-+||++ +|+|-+
T Consensus 96 ~le~ke~ald~Le~lve~iDnAndl~~~ggl~~ll~~l~~~~~~lR~~Aa~Vigt~~qNNP~ 157 (342)
T KOG2160|consen 96 DLEDKEDALDNLEELVEDIDNANDLISLGGLVPLLGYLENSDAELRELAARVIGTAVQNNPK 157 (342)
T ss_pred CHHHHHHHHHHHHHHHHhhhhHHhHhhccCHHHHHHHhcCCcHHHHHHHHHHHHHHHhcCHH
Confidence 346778999999999888775 7899999999999974 455443
No 66
>PF13233 Complex1_LYR_2: Complex1_LYR-like
Probab=20.22 E-value=88 Score=19.76 Aligned_cols=25 Identities=36% Similarity=0.594 Sum_probs=14.2
Q ss_pred HHHHHHHhhcCCCCcHHHHHHHHHH
Q psy1883 24 ELLEDYHSKLTDPSDKQLRSAIERV 48 (81)
Q Consensus 24 eLLE~Y~~kL~~~~D~~Lr~aierv 48 (81)
+|+|.|.--++-.+++-++.++.||
T Consensus 77 eL~erYnpg~~m~qee~v~~tA~~V 101 (104)
T PF13233_consen 77 ELLERYNPGLDMTQEERVRRTARRV 101 (104)
T ss_pred HHHhhcccccCCCHHHHHHHHHHHh
Confidence 4566665545545555566666554
No 67
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=20.15 E-value=1.3e+02 Score=25.53 Aligned_cols=44 Identities=20% Similarity=0.378 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhhcCC--CCc-HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy1883 19 AHRALELLEDYHSKLTD--PSD-KQLRSAIERVIRIFKSRLFQALLGQLG 65 (81)
Q Consensus 19 AhRALeLLE~Y~~kL~~--~~D-~~Lr~aiervIniFkS~LFqALLDI~e 65 (81)
.++.++.|++||++=.- .-. ++|+ .++...+...+|+++|+-+.
T Consensus 420 ~~~~~~~l~~~h~~~p~~~g~~~~~l~---~~~~~~~~~~~~~~~l~~l~ 466 (614)
T PRK10512 420 QRKLLDTLATYHEQHRDEPGPGRERLR---RMALPMEDEALVLLLIEKMR 466 (614)
T ss_pred HHHHHHHHHHHHHHCCcccCCCHHHHH---hhcccCCCHHHHHHHHHHHH
Confidence 46778899999986222 111 2243 33444577899999987663
No 68
>COG4493 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.14 E-value=65 Score=25.07 Aligned_cols=21 Identities=33% Similarity=0.512 Sum_probs=18.9
Q ss_pred CcHHHHHHHHHHHHHHHHHHH
Q psy1883 37 SDKQLRSAIERVIRIFKSRLF 57 (81)
Q Consensus 37 ~D~~Lr~aiervIniFkS~LF 57 (81)
.|.+|+.++||+.++=|+.|+
T Consensus 150 ~~~~l~~~~eRl~~VKK~Ell 170 (209)
T COG4493 150 TDDALKEAAERLRDVKKGELL 170 (209)
T ss_pred cHHHHHHHHHHHHhcchhheE
Confidence 389999999999999998875
Done!