Query psy13230
Match_columns 132
No_of_seqs 117 out of 218
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 23:27:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13230hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3151|consensus 100.0 2.2E-41 4.8E-46 273.4 9.9 118 13-130 86-227 (260)
2 PF10075 PCI_Csn8: COP9 signal 99.9 6.1E-24 1.3E-28 157.4 8.2 107 24-131 2-132 (143)
3 PF03399 SAC3_GANP: SAC3/GANP/ 99.2 1.1E-11 2.5E-16 94.8 6.0 89 19-107 92-204 (204)
4 KOG4414|consensus 98.1 6.8E-06 1.5E-10 64.0 4.9 63 65-128 102-164 (197)
5 PF01399 PCI: PCI domain; Int 97.1 0.0056 1.2E-07 41.3 8.5 79 32-119 5-83 (105)
6 KOG1861|consensus 93.1 0.6 1.3E-05 42.2 8.5 100 25-126 386-509 (540)
7 smart00753 PAM PCI/PINT associ 92.7 0.46 9.9E-06 31.6 5.7 45 74-119 3-47 (88)
8 smart00088 PINT motif in prote 92.7 0.46 9.9E-06 31.6 5.7 45 74-119 3-47 (88)
9 KOG3252|consensus 90.9 1 2.2E-05 36.4 6.6 52 77-128 133-184 (217)
10 KOG2581|consensus 90.0 0.84 1.8E-05 40.8 6.0 72 39-119 330-401 (493)
11 PF04800 ETC_C1_NDUFA4: ETC co 84.3 0.68 1.5E-05 33.4 1.8 22 103-124 51-72 (101)
12 KOG3442|consensus 82.2 4.9 0.00011 30.4 5.7 60 72-131 15-97 (132)
13 KOG3389|consensus 77.4 1.2 2.6E-05 34.7 1.1 30 96-125 120-149 (178)
14 PF03374 ANT: Phage antirepres 75.8 7.1 0.00015 27.1 4.7 39 86-125 15-53 (111)
15 PF08727 P3A: Poliovirus 3A pr 71.8 2.1 4.6E-05 28.1 1.1 18 109-126 28-45 (57)
16 PF03683 UPF0175: Uncharacteri 70.4 24 0.00052 23.5 6.0 46 77-124 17-62 (76)
17 COG5079 SAC3 Nuclear protein e 69.5 9.8 0.00021 35.1 5.1 61 65-125 309-377 (646)
18 PF10098 DUF2336: Uncharacteri 68.8 9.5 0.0002 30.4 4.5 77 30-106 165-259 (262)
19 COG2522 Predicted transcriptio 68.8 14 0.00031 27.3 5.0 44 74-120 3-46 (119)
20 KOG1464|consensus 62.5 92 0.002 27.2 9.4 96 13-118 289-386 (440)
21 PF02042 RWP-RK: RWP-RK domain 60.7 14 0.0003 23.6 3.2 29 92-121 12-40 (52)
22 PF14791 DNA_pol_B_thumb: DNA 59.8 9 0.0002 25.1 2.3 21 111-131 13-33 (64)
23 PF12728 HTH_17: Helix-turn-he 51.3 22 0.00047 21.2 2.9 24 96-120 2-25 (51)
24 PF04433 SWIRM: SWIRM domain; 47.9 56 0.0012 21.8 4.8 45 79-123 36-84 (86)
25 KOG2582|consensus 46.7 41 0.00088 29.9 4.9 33 87-119 309-341 (422)
26 PF01466 Skp1: Skp1 family, di 44.3 85 0.0018 20.7 5.2 46 75-124 29-77 (78)
27 PF05687 DUF822: Plant protein 44.0 17 0.00036 28.2 1.9 46 77-127 17-65 (150)
28 PF00392 GntR: Bacterial regul 39.6 64 0.0014 20.1 3.9 49 75-123 3-54 (64)
29 COG5249 RER1 Golgi protein inv 37.8 12 0.00026 29.3 0.2 63 29-94 64-132 (180)
30 TIGR01764 excise DNA binding d 37.5 51 0.0011 18.6 3.0 24 96-120 2-25 (49)
31 PF09691 PulS_OutS: Bacterial 36.2 26 0.00056 25.6 1.8 16 112-127 54-69 (109)
32 PF06888 Put_Phosphatase: Puta 36.1 62 0.0013 26.3 4.1 71 49-131 21-103 (234)
33 smart00345 HTH_GNTR helix_turn 35.4 57 0.0012 19.1 3.0 45 78-123 2-50 (60)
34 PF12959 DUF3848: Protein of u 35.2 60 0.0013 23.6 3.5 32 78-111 35-66 (101)
35 PF14555 UBA_4: UBA-like domai 33.9 32 0.0007 20.3 1.7 29 98-127 4-32 (43)
36 cd07377 WHTH_GntR Winged helix 33.6 1.1E+02 0.0023 18.2 4.6 46 77-123 6-55 (66)
37 PF12833 HTH_18: Helix-turn-he 32.2 1.4E+02 0.0029 19.0 5.8 42 78-119 28-69 (81)
38 smart00874 B5 tRNA synthetase 31.3 92 0.002 19.7 3.7 31 95-125 5-36 (71)
39 TIGR01004 PulS_OutS lipoprotei 30.6 29 0.00063 26.1 1.3 15 112-126 70-84 (128)
40 KOG1688|consensus 30.1 14 0.0003 29.4 -0.5 11 67-77 104-114 (188)
41 KOG1860|consensus 29.4 1.7E+02 0.0037 28.7 6.4 96 28-125 309-416 (927)
42 cd04762 HTH_MerR-trunc Helix-T 28.6 80 0.0017 17.5 2.8 23 96-119 1-23 (49)
43 PF01418 HTH_6: Helix-turn-hel 27.9 1.1E+02 0.0024 20.0 3.7 38 84-122 20-60 (77)
44 PF10524 NfI_DNAbd_pre-N: Nucl 27.6 51 0.0011 20.4 1.8 32 65-103 5-36 (44)
45 COG3357 Predicted transcriptio 27.2 99 0.0021 22.3 3.5 37 79-115 2-38 (97)
46 PF14647 FAM91_N: FAM91 N-term 26.7 1E+02 0.0023 26.4 4.1 49 69-124 88-143 (308)
47 TIGR00517 acyl_carrier acyl ca 26.4 1.2E+02 0.0026 19.4 3.6 35 83-120 41-76 (77)
48 PRK12529 RNA polymerase sigma 24.6 70 0.0015 23.7 2.5 21 93-114 141-161 (178)
49 PHA02992 hypothetical protein; 23.5 48 0.001 31.5 1.6 32 75-106 5-36 (728)
50 PF10255 Paf67: RNA polymerase 23.2 2E+02 0.0043 25.4 5.3 44 72-116 298-341 (404)
51 PF14542 Acetyltransf_CG: GCN5 23.0 76 0.0016 21.0 2.2 18 110-127 44-61 (78)
52 PRK10878 hypothetical protein; 23.0 91 0.002 21.0 2.5 44 36-79 18-62 (72)
53 PF07862 Nif11: Nitrogen fixat 22.9 83 0.0018 18.8 2.1 20 107-126 26-45 (49)
54 PF00607 Gag_p24: gag gene pro 22.7 34 0.00073 27.1 0.4 29 65-93 131-159 (206)
55 smart00549 TAFH TAF homology. 22.2 2.5E+02 0.0054 20.1 4.7 45 39-92 39-83 (92)
56 PHA02962 hypothetical protein; 22.1 1.3E+02 0.0029 28.6 4.2 53 35-94 297-360 (722)
57 PF04760 IF2_N: Translation in 21.9 90 0.002 19.0 2.2 28 95-123 3-31 (54)
58 COG5114 Histone acetyltransfer 21.9 2.1E+02 0.0045 25.3 5.0 45 80-124 383-429 (432)
59 PF02646 RmuC: RmuC family; I 21.7 75 0.0016 26.4 2.3 40 72-111 145-186 (304)
60 PF11640 TAN: Telomere-length 21.7 3.4E+02 0.0073 20.0 6.3 55 31-88 7-64 (155)
61 cd04761 HTH_MerR-SF Helix-Turn 21.6 1.2E+02 0.0026 17.2 2.7 25 96-122 1-25 (49)
62 PF12840 HTH_20: Helix-turn-he 21.1 2.1E+02 0.0046 17.5 5.2 43 73-117 3-45 (61)
63 TIGR02809 phasin_3 phasin fami 20.6 3.1E+02 0.0068 20.1 5.1 51 70-120 17-69 (110)
64 cd00141 NT_POLXc Nucleotidyltr 20.6 85 0.0018 26.1 2.4 32 99-130 242-277 (307)
65 PF06393 BID: BH3 interacting 20.6 65 0.0014 26.0 1.6 37 21-57 9-45 (196)
66 PF01221 Dynein_light: Dynein 20.4 1.4E+02 0.0031 20.1 3.1 34 80-124 16-56 (89)
67 smart00420 HTH_DEOR helix_turn 20.3 1.8E+02 0.0039 16.3 4.5 30 94-124 13-45 (53)
No 1
>KOG3151|consensus
Probab=100.00 E-value=2.2e-41 Score=273.42 Aligned_cols=118 Identities=41% Similarity=0.658 Sum_probs=110.3
Q ss_pred cccCCC-CCCCcCcchhhHHHHHHHhccCChhHHHHHHhhhchhhh-----------------------HHhccCCCCCc
Q psy13230 13 SLSFSR-VPESPYKNEMLGLNLLYLLSQNRVAEFHMELERIQYEDM-----------------------IFLAKDGVPSP 68 (132)
Q Consensus 13 ~~~~~~-lp~S~~~~~ilgL~LL~LLsqnriaeFHteLE~l~~~~~-----------------------V~~~~~~vP~~ 68 (132)
||.|.. +|+|++|++++|||||+|||||||||||||||+||.+.+ |+++++++|+|
T Consensus 86 Y~d~~~~l~~S~~~~~l~GLnLL~LLsqNRiaeFHteLe~lp~~~l~~~~~I~~~v~LEq~~MEGaYnKv~~a~~s~p~~ 165 (260)
T KOG3151|consen 86 YFDYNEKLSESEKKHKLLGLNLLYLLSQNRIAEFHTELELLPKKILQHNPYISHPVSLEQSLMEGAYNKVLSAKQSIPSE 165 (260)
T ss_pred hcccccccCcchhhhHHHHHHHHHHHHhccHHHHHHHHHhccHHHhhccchhhhHHHHHHHHHhhHHHHHHHHHhcCCcH
Confidence 455544 999999999999999999999999999999999998766 88999999999
Q ss_pred cHHHHHHHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhhcCCeeeceeee
Q psy13230 69 RYNAFMETLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKKVKNIVYFYIFY 130 (132)
Q Consensus 69 ~y~~Fm~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~ergW~vd~~~~~ 130 (132)
+|.+||++|++|||+|||.|+||||+.||+++|++||+|++++++.+|+.+|+|.++..-.|
T Consensus 166 ~y~~FmdIl~~tiRdEIA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~~~~~r~W~l~~~~~~ 227 (260)
T KOG3151|consen 166 EYTYFMDILLDTIRDEIAGCIEKSYDKLSASDATQMLLFNNDKELKKFATERQWPLDEKGVF 227 (260)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHhcCChHHHHHHHHhcCCcccccccc
Confidence 99999999999999999999999999999999999999999999999999999999954433
No 2
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=99.90 E-value=6.1e-24 Score=157.44 Aligned_cols=107 Identities=31% Similarity=0.361 Sum_probs=84.3
Q ss_pred CcchhhHHHHHHHhccCChhHHHHHHhhhchhhh-----------------------HHh-ccCCCCCccHHHHHHHHHH
Q psy13230 24 YKNEMLGLNLLYLLSQNRVAEFHMELERIQYEDM-----------------------IFL-AKDGVPSPRYNAFMETLID 79 (132)
Q Consensus 24 ~~~~ilgL~LL~LLsqnriaeFHteLE~l~~~~~-----------------------V~~-~~~~vP~~~y~~Fm~~L~~ 79 (132)
.+..+.|++|+.+|.+|++++||..++++|.+.. +|. .+++.|++.|..||..+.+
T Consensus 2 ~~~~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~ 81 (143)
T PF10075_consen 2 LNPEIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFED 81 (143)
T ss_dssp --HHHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHH
T ss_pred CchhHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHH
Confidence 4567999999999999999999999999998754 555 5777899999999999999
Q ss_pred HHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhhcCCeeeceeeee
Q psy13230 80 TTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKKVKNIVYFYIFYI 131 (132)
Q Consensus 80 TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~ergW~vd~~~~~~ 131 (132)
+||++|+.|+++||++|++++++++|+++ ++|+.++++++||++|++...+
T Consensus 82 ~iR~~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~~~gW~~d~~~~~~ 132 (143)
T PF10075_consen 82 TIRERIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIKSRGWTVDGDGVLF 132 (143)
T ss_dssp HHHHHHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHHHHT-EE-----EE
T ss_pred HHHHHHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHHHcCCEECCCccEE
Confidence 99999999999999999999999999999 9999999999999999887644
No 3
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=99.25 E-value=1.1e-11 Score=94.78 Aligned_cols=89 Identities=33% Similarity=0.504 Sum_probs=68.7
Q ss_pred CCCCcCcchhhHHHHHHHhccCChhHHHHHHhhhchhhh----------------------HHh-ccCCCCCccHHHHHH
Q psy13230 19 VPESPYKNEMLGLNLLYLLSQNRVAEFHMELERIQYEDM----------------------IFL-AKDGVPSPRYNAFME 75 (132)
Q Consensus 19 lp~S~~~~~ilgL~LL~LLsqnriaeFHteLE~l~~~~~----------------------V~~-~~~~vP~~~y~~Fm~ 75 (132)
.++++++..++|++||++|++|+.++||+.++.+|.+.. +|. .+++-+++.+..+|+
T Consensus 92 ~~~~~~~~ef~~y~lL~~l~~~~~~~~~~~l~~l~~~~~~~~~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~ 171 (204)
T PF03399_consen 92 LPPSPNEAEFIAYYLLYLLCQNNIPDFHMELELLPSEILSSPYIQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLME 171 (204)
T ss_dssp T---TTHHHHHHHHHHHTT-T---THHHHHHTTS-HHHHTSHHHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHG
T ss_pred CCCCCCHHHHHHHHHHHHHHcccchHHHHHHHHCchhhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHH
Confidence 578999999999999999999999999999999986544 233 223455688999999
Q ss_pred HHHHHHHHHHHHhHHHhcCc-ccHHHHHhhhCC
Q psy13230 76 TLIDTTRNEIASCIEKAYTV-ISVGDTAQKLHI 107 (132)
Q Consensus 76 ~L~~TIR~eIA~ciEkAY~s-Lsl~~a~~LL~~ 107 (132)
..+++||..++.|+++||.+ +|++.++++|+|
T Consensus 172 ~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 172 RFFNRIRLRALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp GGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 99999999999999999999 999999999986
No 4
>KOG4414|consensus
Probab=98.05 E-value=6.8e-06 Score=63.99 Aligned_cols=63 Identities=19% Similarity=0.029 Sum_probs=59.4
Q ss_pred CCCccHHHHHHHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhhcCCeeecee
Q psy13230 65 VPSPRYNAFMETLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKKVKNIVYFYI 128 (132)
Q Consensus 65 vP~~~y~~Fm~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~ergW~vd~~~ 128 (132)
-=|++.+..|..+.+..|.+....+-+||++|..+|.+..|++. +++..+.+.|.||++|+.+
T Consensus 102 dWSeeak~imaAf~D~~~kR~FaLl~qAYssI~~~D~A~FlGl~-~ddAtk~ilEnGWqaDaas 164 (197)
T KOG4414|consen 102 DWSEEAKDIMAAFRDATRKRAFALLLQAYSSIIADDFAAFLGLP-EDDATKGILENGWQADAAS 164 (197)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-HHHHHHHHHHcccchhhHH
Confidence 34789999999999999999999999999999999999999999 9999999999999999764
No 5
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=97.13 E-value=0.0056 Score=41.33 Aligned_cols=79 Identities=23% Similarity=0.370 Sum_probs=63.1
Q ss_pred HHHHHhccCChhHHHHHHhhhchhhhHHhccCCCCCccHHHHHHHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHH
Q psy13230 32 NLLYLLSQNRVAEFHMELERIQYEDMIFLAKDGVPSPRYNAFMETLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEK 111 (132)
Q Consensus 32 ~LL~LLsqnriaeFHteLE~l~~~~~V~~~~~~vP~~~y~~Fm~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~ 111 (132)
.|+..+.+|++.+|+..++..... .+ ..+.....++.+...+|.....-+-+.|+++++++.+++++++ .+
T Consensus 5 ~l~~~~~~~~~~~~~~~l~~~~~~--~~------~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~ 75 (105)
T PF01399_consen 5 ELLRAFRSGDLQEFEEFLEKHSES--LF------KDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EE 75 (105)
T ss_dssp HHHHHHHCT-HHHHHHHHHHTCHH--HH------HCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HH
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHH--HH------cCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hH
Confidence 578889999999999999988221 11 1234456888999999999999999999999999999999998 78
Q ss_pred HHHHHHhh
Q psy13230 112 QMVEFGKK 119 (132)
Q Consensus 112 el~~Fa~e 119 (132)
+++....+
T Consensus 76 ~vE~~l~~ 83 (105)
T PF01399_consen 76 EVESILID 83 (105)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 88888654
No 6
>KOG1861|consensus
Probab=93.12 E-value=0.6 Score=42.15 Aligned_cols=100 Identities=20% Similarity=0.247 Sum_probs=77.7
Q ss_pred cchhhHHHHHHHhc-cCChhHHHHHHhhhchhhh-------HHhccC---------------CCCCccHHHHHHHHHHHH
Q psy13230 25 KNEMLGLNLLYLLS-QNRVAEFHMELERIQYEDM-------IFLAKD---------------GVPSPRYNAFMETLIDTT 81 (132)
Q Consensus 25 ~~~ilgL~LL~LLs-qnriaeFHteLE~l~~~~~-------V~~~~~---------------~vP~~~y~~Fm~~L~~TI 81 (132)
....++-.+||-+- .|++ |.-++|-.|..++. .++-++ +.|.-. .+.||..++.-
T Consensus 386 ~~EF~AYriLY~i~tkN~~-di~sll~~lt~E~ked~~V~hAL~vR~A~~~GNY~kFFrLY~~AP~M~-~yLmdlF~erE 463 (540)
T KOG1861|consen 386 YLEFTAYRILYYIFTKNYP-DILSLLRDLTEEDKEDEAVAHALEVRSAVTLGNYHKFFRLYLTAPNMS-GYLMDLFLERE 463 (540)
T ss_pred hhhHHHHHHHHHHHhcCch-HHHHHHHhccHhhccCHHHHHHHHHHHHHHhccHHHHHHHHhhcccch-hHHHHHHHHHH
Confidence 55667777776554 5555 99999988887655 122222 234222 56788899999
Q ss_pred HHHHHHhHHHhcC-cccHHHHHhhhCCCCHHHHHHHHhhcCCeeec
Q psy13230 82 RNEIASCIEKAYT-VISVGDTAQKLHIGSEKQMVEFGKKVKNIVYF 126 (132)
Q Consensus 82 R~eIA~ciEkAY~-sLsl~~a~~LL~~~s~~el~~Fa~ergW~vd~ 126 (132)
|...-.-|.|||. +|+++..++-|-|++-++++.|-++.+|+-+.
T Consensus 464 R~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~c~~~l~~~~~~~~~ 509 (540)
T KOG1861|consen 464 RKKALTIICKSYRPTITVDFIASELAFDSMEDCVNFLNEQNLTYDS 509 (540)
T ss_pred HHHHHHHHHHHcCCCccHHHHhhhhhhchHHHHHHHHhccCccccc
Confidence 9999999999999 99999999999999999999999999998654
No 7
>smart00753 PAM PCI/PINT associated module.
Probab=92.73 E-value=0.46 Score=31.63 Aligned_cols=45 Identities=22% Similarity=0.251 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhh
Q psy13230 74 METLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKK 119 (132)
Q Consensus 74 m~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~e 119 (132)
.+.+...+|...-....+.|+++++++.++.+.++ .++++.++.+
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~ 47 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSK 47 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHH
Confidence 46688899999989999999999999999999998 5578777654
No 8
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=92.73 E-value=0.46 Score=31.63 Aligned_cols=45 Identities=22% Similarity=0.251 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhh
Q psy13230 74 METLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKK 119 (132)
Q Consensus 74 m~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~e 119 (132)
.+.+...+|...-....+.|+++++++.++.+.++ .++++.++.+
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~ 47 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSK 47 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHH
Confidence 46688899999989999999999999999999998 5578777654
No 9
>KOG3252|consensus
Probab=90.90 E-value=1 Score=36.41 Aligned_cols=52 Identities=19% Similarity=-0.003 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhhcCCeeecee
Q psy13230 77 LIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKKVKNIVYFYI 128 (132)
Q Consensus 77 L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~ergW~vd~~~ 128 (132)
.-+.||.-+..-+.-.|.+|+-+-.++|||-.+.+++...+++-||..+...
T Consensus 133 Fedsvr~yachvv~iTyQkI~k~lLaellG~~sDs~le~~~~~~GW~a~e~G 184 (217)
T KOG3252|consen 133 FEDSVRKYACHVVGITYQKIDKWLLAELLGGLSDSQLEVWMTKYGWIADESG 184 (217)
T ss_pred HHHHHHHHHHHheechHhhchHHHHHHhhCcccHHHHHHHHHHccceecCCc
Confidence 4689999999999999999999999999999999999999999999998653
No 10
>KOG2581|consensus
Probab=90.04 E-value=0.84 Score=40.78 Aligned_cols=72 Identities=25% Similarity=0.293 Sum_probs=50.1
Q ss_pred cCChhHHHHHHhhhchhhhHHhccCCCCCccHHHHHHHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHh
Q psy13230 39 QNRVAEFHMELERIQYEDMIFLAKDGVPSPRYNAFMETLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGK 118 (132)
Q Consensus 39 qnriaeFHteLE~l~~~~~V~~~~~~vP~~~y~~Fm~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~ 118 (132)
-|+++.|...||..-.. +++.+ .|.. +-.|...|=..-.+.|.-+|++||+.|.|+-|+++|+++++-.+.
T Consensus 330 ~gdlkkF~~~leq~k~~---f~~D~-----ty~L-ivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~EyiVa 400 (493)
T KOG2581|consen 330 LGDLKKFNETLEQFKDK---FQADG-----TYTL-IVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYIVA 400 (493)
T ss_pred HhhHHHHHHHHHHHHHH---HhhCC-----cchH-HHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHHHH
Confidence 58999999999987432 33332 2333 233444444444567899999999999999999999887766554
Q ss_pred h
Q psy13230 119 K 119 (132)
Q Consensus 119 e 119 (132)
+
T Consensus 401 k 401 (493)
T KOG2581|consen 401 K 401 (493)
T ss_pred H
Confidence 4
No 11
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=84.33 E-value=0.68 Score=33.39 Aligned_cols=22 Identities=9% Similarity=0.191 Sum_probs=18.6
Q ss_pred hhhCCCCHHHHHHHHhhcCCee
Q psy13230 103 QKLHIGSEKQMVEFGKKVKNIV 124 (132)
Q Consensus 103 ~LL~~~s~~el~~Fa~ergW~v 124 (132)
.-|.|+|.+++++||+++||..
T Consensus 51 v~l~F~skE~Ai~yaer~G~~Y 72 (101)
T PF04800_consen 51 VRLKFDSKEDAIAYAERNGWDY 72 (101)
T ss_dssp CEEEESSHHHHHHHHHHCT-EE
T ss_pred eEeeeCCHHHHHHHHHHcCCeE
Confidence 4578899999999999999985
No 12
>KOG3442|consensus
Probab=82.25 E-value=4.9 Score=30.38 Aligned_cols=60 Identities=18% Similarity=0.236 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHHhHHHh-----------------cCcccHHHHHhhhCCC---CHHHHHHHHhh---cCCeeecee
Q psy13230 72 AFMETLIDTTRNEIASCIEKA-----------------YTVISVGDTAQKLHIG---SEKQMVEFGKK---VKNIVYFYI 128 (132)
Q Consensus 72 ~Fm~~L~~TIR~eIA~ciEkA-----------------Y~sLsl~~a~~LL~~~---s~~el~~Fa~e---rgW~vd~~~ 128 (132)
.+-..+..+.|++||.....| |..|++.+|+.+|+.+ |.+++.+-=+. -+=+-.++.
T Consensus 15 vvgrAf~~A~RQeia~s~~aa~~~~a~k~g~~~~~~~~~~~iTlqEa~qILnV~~~ln~eei~k~yehLFevNdkskGGS 94 (132)
T KOG3442|consen 15 VVGRAFVQAYRQEIAASQQAAARQAAGKSGTRSAEANSNGKITLQEAQQILNVKEPLNREEIEKRYEHLFEVNDKSKGGS 94 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccccccccccccHHHHhhHhCCCCCCCHHHHHHHHHHHHhccCcccCcc
Confidence 344568899999998876532 6789999999999998 55555543211 122223466
Q ss_pred eee
Q psy13230 129 FYI 131 (132)
Q Consensus 129 ~~~ 131 (132)
||+
T Consensus 95 FYL 97 (132)
T KOG3442|consen 95 FYL 97 (132)
T ss_pred eee
Confidence 775
No 13
>KOG3389|consensus
Probab=77.45 E-value=1.2 Score=34.72 Aligned_cols=30 Identities=10% Similarity=0.050 Sum_probs=25.8
Q ss_pred ccHHHHHhhhCCCCHHHHHHHHhhcCCeee
Q psy13230 96 ISVGDTAQKLHIGSEKQMVEFGKKVKNIVY 125 (132)
Q Consensus 96 Lsl~~a~~LL~~~s~~el~~Fa~ergW~vd 125 (132)
=|+++.-.-|.|++.+++..||++.||..|
T Consensus 120 DPlsNvgm~L~F~tkEdA~sFaEkngW~yd 149 (178)
T KOG3389|consen 120 DPLSNVGMALAFDTKEDAKSFAEKNGWDYD 149 (178)
T ss_pred CcccccceeeeeccHHHHHHHHHHcCCccc
Confidence 366677777889999999999999999876
No 14
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=75.77 E-value=7.1 Score=27.14 Aligned_cols=39 Identities=10% Similarity=0.194 Sum_probs=32.9
Q ss_pred HHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhhcCCeee
Q psy13230 86 ASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKKVKNIVY 125 (132)
Q Consensus 86 A~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~ergW~vd 125 (132)
++.+-.+=..+++.++|++|++. +..+.++-.++||-.+
T Consensus 15 ~d~~~~~~~~~ti~~~AK~L~i~-~~~l~~~Lr~~g~l~~ 53 (111)
T PF03374_consen 15 YDAFVDSDGLYTIREAAKLLGIG-RNKLFQWLREKGWLYR 53 (111)
T ss_pred HHHHHcCCCCccHHHHHHHhCCC-HHHHHHHHHhCCceEE
Confidence 33444445889999999999998 9999999999999887
No 15
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=71.81 E-value=2.1 Score=28.08 Aligned_cols=18 Identities=11% Similarity=0.113 Sum_probs=12.0
Q ss_pred CHHHHHHHHhhcCCeeec
Q psy13230 109 SEKQMVEFGKKVKNIVYF 126 (132)
Q Consensus 109 s~~el~~Fa~ergW~vd~ 126 (132)
..+|+.+|++++||.+..
T Consensus 28 ~~~eV~~YC~~~GWIip~ 45 (57)
T PF08727_consen 28 DSPEVREYCEEQGWIIPA 45 (57)
T ss_dssp --HHHHHHHHHHT--TT-
T ss_pred CCHHHHHHHHHCCccccC
Confidence 467899999999998865
No 16
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=70.37 E-value=24 Score=23.54 Aligned_cols=46 Identities=20% Similarity=0.180 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhhcCCee
Q psy13230 77 LIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKKVKNIV 124 (132)
Q Consensus 77 L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~ergW~v 124 (132)
+..-+|.++|--.=+ -.+||+..|+++.+++ .-++.++..+||=.+
T Consensus 17 ~~~~~r~~~Ai~lY~-~g~iS~gkAAelag~s-~~eF~~~L~~~gI~~ 62 (76)
T PF03683_consen 17 FEQELREELAIKLYE-EGKISLGKAAELAGMS-RWEFLELLKERGIPI 62 (76)
T ss_pred HHHHHHHHHHHHHHH-cCCCCHHHHHHHhCCC-HHHHHHHHHHCCCCC
Confidence 345666666655443 4689999999999995 999999999998553
No 17
>COG5079 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]
Probab=69.55 E-value=9.8 Score=35.11 Aligned_cols=61 Identities=23% Similarity=0.199 Sum_probs=49.0
Q ss_pred CCCccHHHHHHHHHHH----HHHHHH----HhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhhcCCeee
Q psy13230 65 VPSPRYNAFMETLIDT----TRNEIA----SCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKKVKNIVY 125 (132)
Q Consensus 65 vP~~~y~~Fm~~L~~T----IR~eIA----~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~ergW~vd 125 (132)
+-++...+||..|++. ||.-.- +|+++|-..+|.-+...+|.|++.+|.++|++=.|-++.
T Consensus 309 ~qSpsv~~lmg~lle~h~~sir~~aLkAm~k~~~sahk~ipf~~l~~il~f~~~~e~~efckyy~lei~ 377 (646)
T COG5079 309 IQSPSVQYLMGCLLEKHNISIRGGALKAMEKEIESAHKNIPFVDLSGILDFEEKGEGEEFCKYYGLEIR 377 (646)
T ss_pred HhCccHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhcCCCeehhhhhccccccchhHHHhhhcceeee
Confidence 4567788888888765 454443 566677788999999999999999999999998888773
No 18
>PF10098 DUF2336: Uncharacterized protein conserved in bacteria (DUF2336); InterPro: IPR019285 Members of this family of hypothetical bacterial proteins have no known function.
Probab=68.82 E-value=9.5 Score=30.41 Aligned_cols=77 Identities=19% Similarity=0.160 Sum_probs=56.5
Q ss_pred HHHHHHHhccCChhHHHHHHhhhchhhh----------------HHhccCCCCCccHHHHHHHHHHHHHH--HHHHhHHH
Q psy13230 30 GLNLLYLLSQNRVAEFHMELERIQYEDM----------------IFLAKDGVPSPRYNAFMETLIDTTRN--EIASCIEK 91 (132)
Q Consensus 30 gL~LL~LLsqnriaeFHteLE~l~~~~~----------------V~~~~~~vP~~~y~~Fm~~L~~TIR~--eIA~ciEk 91 (132)
.=-|++.+.+|+...|...|-.+..=.. ++-..-.+|.+.|..|...+...-+. +-..-...
T Consensus 165 ~~lL~~a~~~g~~~~f~aaLA~lsgl~~~~v~~il~d~~~~~L~~l~kaaGL~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (262)
T PF10098_consen 165 EALLLRAACSGRLAFFAAALAELSGLPPARVRRILADGGGEALAALCKAAGLPWATFPAFLAALAPWRRISRGDLEEALA 244 (262)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHCcCHHHHHHHHhCCCchHHHHHHHHcCCCHHHHHHHHHHHhhhcccCcchHHHHHH
Confidence 3457899999999999999987753211 23345568989999999887665542 22333667
Q ss_pred hcCcccHHHHHhhhC
Q psy13230 92 AYTVISVGDTAQKLH 106 (132)
Q Consensus 92 AY~sLsl~~a~~LL~ 106 (132)
.|..|+.+.|..+|.
T Consensus 245 ~y~~L~~~~A~~~L~ 259 (262)
T PF10098_consen 245 LYDRLSPDAAQRVLR 259 (262)
T ss_pred HHHcCCHHHHHHHHH
Confidence 799999999998874
No 19
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=68.81 E-value=14 Score=27.34 Aligned_cols=44 Identities=14% Similarity=0.131 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhhc
Q psy13230 74 METLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKKV 120 (132)
Q Consensus 74 m~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~er 120 (132)
.+.++-+||-.+|.=+-.- -+|..+.|+|||++ +..|.+|.+..
T Consensus 3 ~~~vlPaiRa~lA~~L~ee--G~Sq~~iA~LLGlt-qaAVS~Yls~k 46 (119)
T COG2522 3 VEEVLPAIRALLAKELIEE--GLSQYRIAKLLGLT-QAAVSQYLSGK 46 (119)
T ss_pred hHHHHHHHHHHHHHHHHHc--CCcHHHHHHHhCCC-HHHHHHHHccC
Confidence 4567889999999754443 88899999999998 99999998763
No 20
>KOG1464|consensus
Probab=62.50 E-value=92 Score=27.23 Aligned_cols=96 Identities=19% Similarity=0.277 Sum_probs=71.7
Q ss_pred cccCCCCCCCcCcchhhHH-HHHHHhccCChhHHHHHHhhhchhhhHHhccCC-CCCccHHHHHHHHHHHHHHHHHHhHH
Q psy13230 13 SLSFSRVPESPYKNEMLGL-NLLYLLSQNRVAEFHMELERIQYEDMIFLAKDG-VPSPRYNAFMETLIDTTRNEIASCIE 90 (132)
Q Consensus 13 ~~~~~~lp~S~~~~~ilgL-~LL~LLsqnriaeFHteLE~l~~~~~V~~~~~~-vP~~~y~~Fm~~L~~TIR~eIA~ciE 90 (132)
-|..+.-.|=.+.+.|+++ ||..-.-.|.|.+|..-|- .-+++ +..|-...-|+-|+..||-.+---+-
T Consensus 289 PFDsQEAKPyKNdPEIlAMTnlv~aYQ~NdI~eFE~Il~---------~~~~~IM~DpFIReh~EdLl~niRTQVLlkLI 359 (440)
T KOG1464|consen 289 PFDSQEAKPYKNDPEILAMTNLVAAYQNNDIIEFERILK---------SNRSNIMDDPFIREHIEDLLRNIRTQVLLKLI 359 (440)
T ss_pred CCcccccCCCCCCHHHHHHHHHHHHHhcccHHHHHHHHH---------hhhccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4555555566677777775 6666667889988865442 22233 45567778889999999999999999
Q ss_pred HhcCcccHHHHHhhhCCCCHHHHHHHHh
Q psy13230 91 KAYTVISVGDTAQKLHIGSEKQMVEFGK 118 (132)
Q Consensus 91 kAY~sLsl~~a~~LL~~~s~~el~~Fa~ 118 (132)
|-|+.+.+...++-|..+ +.+|...-.
T Consensus 360 kPYt~i~Ipfis~~Lnv~-~~dV~~LLV 386 (440)
T KOG1464|consen 360 KPYTNIGIPFISKELNVP-EADVESLLV 386 (440)
T ss_pred ccccccCchhhHhhcCCC-HHHHHHHHH
Confidence 999999999999999998 888776643
No 21
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=60.70 E-value=14 Score=23.63 Aligned_cols=29 Identities=10% Similarity=0.274 Sum_probs=25.3
Q ss_pred hcCcccHHHHHhhhCCCCHHHHHHHHhhcC
Q psy13230 92 AYTVISVGDTAQKLHIGSEKQMVEFGKKVK 121 (132)
Q Consensus 92 AY~sLsl~~a~~LL~~~s~~el~~Fa~erg 121 (132)
+|=.+|+++||+-|++. ...+..-+.+.|
T Consensus 12 ~~fhlp~~eAA~~Lgv~-~T~LKr~CR~~G 40 (52)
T PF02042_consen 12 QYFHLPIKEAAKELGVS-VTTLKRRCRRLG 40 (52)
T ss_pred HHhCCCHHHHHHHhCCC-HHHHHHHHHHcC
Confidence 47789999999999998 888998888865
No 22
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=59.80 E-value=9 Score=25.11 Aligned_cols=21 Identities=14% Similarity=0.244 Sum_probs=17.6
Q ss_pred HHHHHHHhhcCCeeeceeeee
Q psy13230 111 KQMVEFGKKVKNIVYFYIFYI 131 (132)
Q Consensus 111 ~el~~Fa~ergW~vd~~~~~~ 131 (132)
..++..|+++||+++.+..+.
T Consensus 13 r~lR~~A~~~g~~L~~~Gl~~ 33 (64)
T PF14791_consen 13 RDLRQYAKKKGMKLSEYGLFK 33 (64)
T ss_dssp HHHHHHHHHTTEEEESSEEEE
T ss_pred HHHHHHHHHcCCeeCcccccc
Confidence 468899999999999987663
No 23
>PF12728 HTH_17: Helix-turn-helix domain
Probab=51.30 E-value=22 Score=21.21 Aligned_cols=24 Identities=17% Similarity=0.284 Sum_probs=20.3
Q ss_pred ccHHHHHhhhCCCCHHHHHHHHhhc
Q psy13230 96 ISVGDTAQKLHIGSEKQMVEFGKKV 120 (132)
Q Consensus 96 Lsl~~a~~LL~~~s~~el~~Fa~er 120 (132)
++.+++|.+|+.+ .+.+.+.+++.
T Consensus 2 lt~~e~a~~l~is-~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGIS-RSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHHcC
Confidence 6789999999996 88898888764
No 24
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=47.87 E-value=56 Score=21.82 Aligned_cols=45 Identities=16% Similarity=0.186 Sum_probs=31.3
Q ss_pred HHHHHHHHHh-HHHhcCcccHHHHHhhhC-CC--CHHHHHHHHhhcCCe
Q psy13230 79 DTTRNEIASC-IEKAYTVISVGDTAQKLH-IG--SEKQMVEFGKKVKNI 123 (132)
Q Consensus 79 ~TIR~eIA~c-iEkAY~sLsl~~a~~LL~-~~--s~~el~~Fa~ergW~ 123 (132)
=.||+.|-+. ....-..++.++|.+++. .+ ....+-+|-...||-
T Consensus 36 l~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G~I 84 (86)
T PF04433_consen 36 LKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYDFLERWGLI 84 (86)
T ss_dssp HHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHHHHHHTTSS
T ss_pred HHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHHHHHHcCcc
Confidence 3588888777 677889999999999998 44 233556677778883
No 25
>KOG2582|consensus
Probab=46.72 E-value=41 Score=29.92 Aligned_cols=33 Identities=15% Similarity=0.370 Sum_probs=28.7
Q ss_pred HhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhh
Q psy13230 87 SCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKK 119 (132)
Q Consensus 87 ~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~e 119 (132)
.-.-|.|.+|++++.+++..+.+.+|+.+++-+
T Consensus 309 ~rltktF~sLsL~dIA~~vQLa~~qevek~Ilq 341 (422)
T KOG2582|consen 309 QRLTKTFLSLSLSDIASRVQLASAQEVEKYILQ 341 (422)
T ss_pred HHHHHHHHHhhHHHHHHHHHhcchHHHHHHHHH
Confidence 345677999999999999999999999998755
No 26
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=44.32 E-value=85 Score=20.74 Aligned_cols=46 Identities=20% Similarity=0.139 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCC---CHHHHHHHHhhcCCee
Q psy13230 75 ETLIDTTRNEIASCIEKAYTVISVGDTAQKLHIG---SEKQMVEFGKKVKNIV 124 (132)
Q Consensus 75 ~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~---s~~el~~Fa~ergW~v 124 (132)
+.|++.+-..||+.+. .-|..+..+++++. +++|..+.-++--|..
T Consensus 29 ~~L~~~~~~~iA~~i~----gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~ 77 (78)
T PF01466_consen 29 KGLLDLCCKYIANMIK----GKSPEEIRKYFGIENDLTPEEEEEIRKENEWAF 77 (78)
T ss_dssp HHHHHHHHHHHHHHHT----TS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB
T ss_pred hHHHHHHHHHHHHHhc----CCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhc
Confidence 3477777778888776 36889999999997 5566677777778853
No 27
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=44.05 E-value=17 Score=28.15 Aligned_cols=46 Identities=15% Similarity=0.018 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhHHH---hcCcccHHHHHhhhCCCCHHHHHHHHhhcCCeeece
Q psy13230 77 LIDTTRNEIASCIEK---AYTVISVGDTAQKLHIGSEKQMVEFGKKVKNIVYFY 127 (132)
Q Consensus 77 L~~TIR~eIA~ciEk---AY~sLsl~~a~~LL~~~s~~el~~Fa~ergW~vd~~ 127 (132)
+.+.=|.-||+-|-. +|-.-.+. =+-|+.+-+.+.|.|-||+|+++
T Consensus 17 ~RERrRRAIaakIfaGLR~~Gny~Lp-----~~aD~NeVLkALc~eAGw~Ve~D 65 (150)
T PF05687_consen 17 RRERRRRAIAAKIFAGLRAHGNYKLP-----KHADNNEVLKALCREAGWTVEPD 65 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCC-----CcCCHHHHHHHHHHhCCEEEccC
Confidence 455566666665543 22221111 12254555668899999999764
No 28
>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=39.55 E-value=64 Score=20.12 Aligned_cols=49 Identities=16% Similarity=0.105 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHhHHHhcCcc-cHHHHHhhhCCC--CHHHHHHHHhhcCCe
Q psy13230 75 ETLIDTTRNEIASCIEKAYTVI-SVGDTAQKLHIG--SEKQMVEFGKKVKNI 123 (132)
Q Consensus 75 ~~L~~TIR~eIA~ciEkAY~sL-sl~~a~~LL~~~--s~~el~~Fa~ergW~ 123 (132)
+.+.+.+++.|.++-=+.=++| +..+.++.++.+ +..++...-.+.||-
T Consensus 3 ~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i 54 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLI 54 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcE
Confidence 3466777777777766666799 999999999997 333444445667775
No 29
>COG5249 RER1 Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion]
Probab=37.81 E-value=12 Score=29.30 Aligned_cols=63 Identities=22% Similarity=0.328 Sum_probs=37.4
Q ss_pred hHHHHHHHhccCChhHHHHHHhhhchhhhHHhccCCCCCccHHHHHHHH------HHHHHHHHHHhHHHhcC
Q psy13230 29 LGLNLLYLLSQNRVAEFHMELERIQYEDMIFLAKDGVPSPRYNAFMETL------IDTTRNEIASCIEKAYT 94 (132)
Q Consensus 29 lgL~LL~LLsqnriaeFHteLE~l~~~~~V~~~~~~vP~~~y~~Fm~~L------~~TIR~eIA~ciEkAY~ 94 (132)
+|+|||.++--=-..+|.+-+|++..++- ++.++ -++||.+|+..| ...+|.-..+.+..-+.
T Consensus 64 LgiyLLn~flaFLTPKfdms~eq~e~d~e-ieeg~--kd~EFrPFIRrLPEFkFWy~s~rat~~aLi~s~F~ 132 (180)
T COG5249 64 LGIYLLNAFLAFLTPKFDMSFEQIEDDDE-IEEGE--KDNEFRPFIRRLPEFKFWYFSTRATGMALIGSYFG 132 (180)
T ss_pred HHHHHHHHHHHHhCCCCcccHhhhccccc-ccccc--ccchhhHHHHcCchhHHHHHHHHHHHHHHHHHHHh
Confidence 67788777655556667777777755432 22222 246777777765 45566665555554333
No 30
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=37.54 E-value=51 Score=18.57 Aligned_cols=24 Identities=13% Similarity=0.236 Sum_probs=20.3
Q ss_pred ccHHHHHhhhCCCCHHHHHHHHhhc
Q psy13230 96 ISVGDTAQKLHIGSEKQMVEFGKKV 120 (132)
Q Consensus 96 Lsl~~a~~LL~~~s~~el~~Fa~er 120 (132)
+++.+++++|+++ ...+...+++.
T Consensus 2 lt~~e~a~~lgis-~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVS-KDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCC-HHHHHHHHHcC
Confidence 6789999999997 88888888763
No 31
>PF09691 PulS_OutS: Bacterial chaperone lipoprotein (PulS_OutS); InterPro: IPR019114 This family comprises lipoproteins from gamma proteobacterial species: pullulanase secretion protein PulS protein of Klebsiella pneumoniae (P20440 from SWISSPROT), the lipoprotein OutS protein of Erwinia chrysanthemi (Q01567 from SWISSPROT) and the functionally uncharacterised type II secretion protein EtpO (Q7BSV3 from SWISSPROT) from Escherichia coli O157:H7. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family. In addition to the PulS/OutS proteins this entry also includes other functionally uncharacterised proteins, such as YacC from Escherischia coli (P0AA95 from SWISSPROT).; PDB: 3SOL_A 3UYM_A 3UTK_A 4A56_A.
Probab=36.16 E-value=26 Score=25.56 Aligned_cols=16 Identities=19% Similarity=0.057 Sum_probs=10.7
Q ss_pred HHHHHHhhcCCeeece
Q psy13230 112 QMVEFGKKVKNIVYFY 127 (132)
Q Consensus 112 el~~Fa~ergW~vd~~ 127 (132)
.+..||++|||.+.++
T Consensus 54 ~a~~~A~~~gWd~~~~ 69 (109)
T PF09691_consen 54 AAVIFAQQRGWDTSNY 69 (109)
T ss_dssp HHHHHHHHTT--CGG-
T ss_pred HHHHHHHHcCCCcchh
Confidence 5677899999998763
No 32
>PF06888 Put_Phosphatase: Putative Phosphatase; InterPro: IPR016965 This group represents phosphatases related to PHOSPHO1 and PHOSPHO2 []. It includes plant phosphatases with homology to the haloacid dehalogenase (HAD) superfamily [, ]. PHOSPHO1 is a phosphoethanolamine/phosphocholine phosphatase [], while PHOSPHO2 has high activity toward pyridoxal 5'-phosphate (PLP), and it is active at much lower level toward pyrophosphate, phosphoethanolamine (PEA)and phosphocholine (PCho) []. ; GO: 0016791 phosphatase activity
Probab=36.08 E-value=62 Score=26.26 Aligned_cols=71 Identities=14% Similarity=0.290 Sum_probs=41.3
Q ss_pred HhhhchhhhHHhccCCCCCccHHHHHHHHHHHHH------HHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHH--hhc
Q psy13230 49 LERIQYEDMIFLAKDGVPSPRYNAFMETLIDTTR------NEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFG--KKV 120 (132)
Q Consensus 49 LE~l~~~~~V~~~~~~vP~~~y~~Fm~~L~~TIR------~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa--~er 120 (132)
+|.+|.+....+.+...|...+..+|+.++..+. ++|.+++ .++|+.. .-.++.+++ +++
T Consensus 21 ~~~l~~~~~~~~l~~~~~~~~wt~~m~~vl~~L~~~gvt~~~I~~~l----~~ip~~p--------gm~~~l~~l~~~~~ 88 (234)
T PF06888_consen 21 IELLPPEELPEELRESYPKGGWTEYMDRVLQLLHEQGVTPEDIRDAL----RSIPIDP--------GMKELLRFLAKNQR 88 (234)
T ss_pred HHhcCCcccHHHHHHhccccchHHHHHHHHHHHHHcCCCHHHHHHHH----HcCCCCc--------cHHHHHHHHHhcCC
Confidence 4444444322222333444567788888877774 5555554 4577543 345777777 346
Q ss_pred CCee----eceeeee
Q psy13230 121 KNIV----YFYIFYI 131 (132)
Q Consensus 121 gW~v----d~~~~~~ 131 (132)
|+.+ |+++|||
T Consensus 89 ~~~~~IiSDaNs~fI 103 (234)
T PF06888_consen 89 GFDLIIISDANSFFI 103 (234)
T ss_pred CceEEEEeCCcHhHH
Confidence 8876 6666666
No 33
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=35.43 E-value=57 Score=19.08 Aligned_cols=45 Identities=16% Similarity=0.099 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhHHHhcCcc-cHHHHHhhhCCCCHHHHHHH---HhhcCCe
Q psy13230 78 IDTTRNEIASCIEKAYTVI-SVGDTAQKLHIGSEKQMVEF---GKKVKNI 123 (132)
Q Consensus 78 ~~TIR~eIA~ciEkAY~sL-sl~~a~~LL~~~s~~el~~F---a~ergW~ 123 (132)
.+.+|..|..+.-..=..+ |..+.++.++.+ ..-+.+. -.+.||-
T Consensus 2 ~~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs-~~tv~~~l~~L~~~g~i 50 (60)
T smart00345 2 AERLREDIVSGELRPGDKLPSERELAAQLGVS-RTTVREALSRLEAEGLV 50 (60)
T ss_pred HHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCE
Confidence 4567777766643333467 799999999996 5544444 3447884
No 34
>PF12959 DUF3848: Protein of unknown function (DUF3848); InterPro: IPR024380 This domain is found in a family of uncharacterised proteins found by clustering human gut metagenomic sequences[].
Probab=35.18 E-value=60 Score=23.55 Aligned_cols=32 Identities=16% Similarity=0.089 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHH
Q psy13230 78 IDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEK 111 (132)
Q Consensus 78 ~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~ 111 (132)
--|||++|+-|+|-. -||-..|+.||...++=
T Consensus 35 Ey~VkeDi~m~~ee~--~l~~~qa~ALl~sp~PL 66 (101)
T PF12959_consen 35 EYTVKEDILMAMEEL--ELPDQQAKALLKSPSPL 66 (101)
T ss_pred HHHHHHHHHHHHHHc--cCCHHHHHHHHcCCChH
Confidence 458999999999987 49999999999877653
No 35
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=33.93 E-value=32 Score=20.30 Aligned_cols=29 Identities=3% Similarity=-0.104 Sum_probs=21.4
Q ss_pred HHHHHhhhCCCCHHHHHHHHhhcCCeeece
Q psy13230 98 VGDTAQKLHIGSEKQMVEFGKKVKNIVYFY 127 (132)
Q Consensus 98 l~~a~~LL~~~s~~el~~Fa~ergW~vd~~ 127 (132)
+.....+.+. +++.+..|-+..+|.++.+
T Consensus 4 i~~F~~iTg~-~~~~A~~~L~~~~wdle~A 32 (43)
T PF14555_consen 4 IAQFMSITGA-DEDVAIQYLEANNWDLEAA 32 (43)
T ss_dssp HHHHHHHH-S-SHHHHHHHHHHTTT-HHHH
T ss_pred HHHHHHHHCc-CHHHHHHHHHHcCCCHHHH
Confidence 4567777887 5899999999999998754
No 36
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=33.61 E-value=1.1e+02 Score=18.23 Aligned_cols=46 Identities=17% Similarity=0.104 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhHHHhcCccc-HHHHHhhhCCCCHHHHHHHH---hhcCCe
Q psy13230 77 LIDTTRNEIASCIEKAYTVIS-VGDTAQKLHIGSEKQMVEFG---KKVKNI 123 (132)
Q Consensus 77 L~~TIR~eIA~ciEkAY~sLs-l~~a~~LL~~~s~~el~~Fa---~ergW~ 123 (132)
+.+.++..+....-..-..++ ..+.++.++++ ...+.+.. .+.||-
T Consensus 6 ~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is-~~~v~~~l~~L~~~G~i 55 (66)
T cd07377 6 IADQLREAILSGELKPGDRLPSERELAEELGVS-RTTVREALRELEAEGLV 55 (66)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCE
Confidence 445555555554333344556 89999999996 66655554 347884
No 37
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=32.17 E-value=1.4e+02 Score=18.98 Aligned_cols=42 Identities=17% Similarity=0.172 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhh
Q psy13230 78 IDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKK 119 (132)
Q Consensus 78 ~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~e 119 (132)
+...|-+.|.-.=..++..|+.+++...||.|...+....++
T Consensus 28 ~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~ 69 (81)
T PF12833_consen 28 LRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKR 69 (81)
T ss_dssp HHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHH
Confidence 344444444333223689999999999999999988776654
No 38
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=31.29 E-value=92 Score=19.65 Aligned_cols=31 Identities=16% Similarity=0.119 Sum_probs=26.1
Q ss_pred cccHHHHHhhhCCC-CHHHHHHHHhhcCCeee
Q psy13230 95 VISVGDTAQKLHIG-SEKQMVEFGKKVKNIVY 125 (132)
Q Consensus 95 sLsl~~a~~LL~~~-s~~el~~Fa~ergW~vd 125 (132)
.++.+...+++|.+ +.+++.+.-+.-|.+++
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEILKRLGFEVE 36 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHHHHCCCeEE
Confidence 46788899999988 78899999888888775
No 39
>TIGR01004 PulS_OutS lipoprotein, PulS/OutS family. This family comprises lipoproteins from four gamma proteobacterial species: PulS protein of Klebsiella pneumoniae, the OutS protein of Erwinia chrysanthemi and Pectobacterium chrysanthemi, and the functionally uncharacterized E. coli protein EtpO. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family.
Probab=30.61 E-value=29 Score=26.15 Aligned_cols=15 Identities=0% Similarity=-0.507 Sum_probs=12.2
Q ss_pred HHHHHHhhcCCeeec
Q psy13230 112 QMVEFGKKVKNIVYF 126 (132)
Q Consensus 112 el~~Fa~ergW~vd~ 126 (132)
.+..||++|||.+.+
T Consensus 70 aai~~A~~~gWd~~~ 84 (128)
T TIGR01004 70 TANNVAIGKGWDSGR 84 (128)
T ss_pred HHHHHHHHcCCchhh
Confidence 577899999997753
No 40
>KOG1688|consensus
Probab=30.08 E-value=14 Score=29.45 Aligned_cols=11 Identities=27% Similarity=0.646 Sum_probs=8.8
Q ss_pred CccHHHHHHHH
Q psy13230 67 SPRYNAFMETL 77 (132)
Q Consensus 67 ~~~y~~Fm~~L 77 (132)
++||.+|+..|
T Consensus 104 ~dEFrPFIRRL 114 (188)
T KOG1688|consen 104 SDEFRPFIRRL 114 (188)
T ss_pred ccccchHHHcC
Confidence 57888888876
No 41
>KOG1860|consensus
Probab=29.43 E-value=1.7e+02 Score=28.74 Aligned_cols=96 Identities=16% Similarity=0.222 Sum_probs=66.0
Q ss_pred hhHHHHHHHhccCChhHHHHHHhhhchhhh--------HHhccCCCCCccHHHHHHHHHHHHHHHHHHhHHHhcC----c
Q psy13230 28 MLGLNLLYLLSQNRVAEFHMELERIQYEDM--------IFLAKDGVPSPRYNAFMETLIDTTRNEIASCIEKAYT----V 95 (132)
Q Consensus 28 ilgL~LL~LLsqnriaeFHteLE~l~~~~~--------V~~~~~~vP~~~y~~Fm~~L~~TIR~eIA~ciEkAY~----s 95 (132)
-+++.+.....+|....||. +=.+-.+.. ++.....+| ..-..+++.+...||.-.-..++.+|. .
T Consensus 309 k~al~~~~a~~~nn~~~~~r-~~~~~t~a~~~l~~~~~~l~q~p~~~-~L~~~v~~~~f~~ir~~al~~~~~~~~~~~~~ 386 (927)
T KOG1860|consen 309 KLALCLRRAFQSNNFRRFFR-LSSLRTEALQNLYTRFFKLMQSPALP-YLMGCVLELFFPDIRWAALRAMSHAYNSKHVP 386 (927)
T ss_pred HHHHHHHHHhccCCeeeeee-ccchhHHHHHHHHHHHHHHhcCcchH-HHHHHHHHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 35677777788888777774 111111111 111122222 133566777788888888888888885 6
Q ss_pred ccHHHHHhhhCCCCHHHHHHHHhhcCCeee
Q psy13230 96 ISVGDTAQKLHIGSEKQMVEFGKKVKNIVY 125 (132)
Q Consensus 96 Lsl~~a~~LL~~~s~~el~~Fa~ergW~vd 125 (132)
+|+.+...+|.|+++++...+..-+|=+++
T Consensus 387 vp~~~l~~~l~f~~~e~~~~~~~~y~Leis 416 (927)
T KOG1860|consen 387 VPLGKLDRILLFDGEEELKVVCNYYGLEIS 416 (927)
T ss_pred cchhHHHHHHhcCChhhhHhhhhheeeEee
Confidence 899999999999999999999999998885
No 42
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=28.55 E-value=80 Score=17.50 Aligned_cols=23 Identities=13% Similarity=0.293 Sum_probs=19.0
Q ss_pred ccHHHHHhhhCCCCHHHHHHHHhh
Q psy13230 96 ISVGDTAQKLHIGSEKQMVEFGKK 119 (132)
Q Consensus 96 Lsl~~a~~LL~~~s~~el~~Fa~e 119 (132)
++..++|++|+.+ ...+..++++
T Consensus 1 ~s~~e~a~~lgvs-~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVS-PSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHHc
Confidence 4678999999987 8888888765
No 43
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=27.92 E-value=1.1e+02 Score=20.00 Aligned_cols=38 Identities=26% Similarity=0.352 Sum_probs=24.2
Q ss_pred HHHHhHHHhc---CcccHHHHHhhhCCCCHHHHHHHHhhcCC
Q psy13230 84 EIASCIEKAY---TVISVGDTAQKLHIGSEKQMVEFGKKVKN 122 (132)
Q Consensus 84 eIA~ciEkAY---~sLsl~~a~~LL~~~s~~el~~Fa~ergW 122 (132)
+||+.+-+-+ ..+++.+.|+..+.+ +.-+..|+++-|-
T Consensus 20 ~Ia~yil~~~~~~~~~si~elA~~~~vS-~sti~Rf~kkLG~ 60 (77)
T PF01418_consen 20 KIADYILENPDEIAFMSISELAEKAGVS-PSTIVRFCKKLGF 60 (77)
T ss_dssp HHHHHHHH-HHHHCT--HHHHHHHCTS--HHHHHHHHHHCTT
T ss_pred HHHHHHHhCHHHHHHccHHHHHHHcCCC-HHHHHHHHHHhCC
Confidence 3444444433 467888888888875 8889999888653
No 44
>PF10524 NfI_DNAbd_pre-N: Nuclear factor I protein pre-N-terminus; InterPro: IPR019548 Nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF) [, ] (also known as TGGCA-binding proteins) are a family of vertebrate nuclear proteins which recognise and bind, as dimers, the palindromic DNA sequence 5'-TGGCANNNTGCCA-3'. CTF/NF-I binding sites are present in viral and cellular promoters and in the origin of DNA replication of Human adenovirus 2 (HAdV-2). The CTF/NF-I proteins were first identified as nuclear factor I, a collection of proteins that activate the replication of several Adenovirus serotypes (together with NF-II and NF-III) []. The family of proteins was also identified as the CTF transcription factors, before the NFI and CTF families were found to be identical []. The CTF/NF-I proteins are individually capable of activating transcription and DNA replication. In a given species, there are a large number of different CTF/NF-I proteins, generated both by alternative splicing and by the occurrence of four different genes. CTF/NF-1 proteins contain 400 to 600 amino acids. The N-terminal 200 amino-acid sequence, almost perfectly conserved in all species and genes sequenced, mediates site-specific DNA recognition, protein dimerisation and Adenovirus DNA replication. The C-terminal 100 amino acids contain the transcriptional activation domain. This activation domain is the target of gene expression regulatory pathways elicited by growth factors and it interacts with basal transcription factors and with histone H3 []. This entry represents the N terminus, of which 200 residues contain the DNA-binding and dimerisation domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerisation-ability and the stimulation of adenovirus DNA replication [].
Probab=27.60 E-value=51 Score=20.44 Aligned_cols=32 Identities=19% Similarity=0.381 Sum_probs=23.7
Q ss_pred CCCccHHHHHHHHHHHHHHHHHHhHHHhcCcccHHHHHh
Q psy13230 65 VPSPRYNAFMETLIDTTRNEIASCIEKAYTVISVGDTAQ 103 (132)
Q Consensus 65 vP~~~y~~Fm~~L~~TIR~eIA~ciEkAY~sLsl~~a~~ 103 (132)
.+.++|.+|++.|+--||. -||.=..+..+++
T Consensus 5 ~~~de~hpFiEalLP~Vk~-------fay~WfnLQA~KR 36 (44)
T PF10524_consen 5 SQQDEFHPFIEALLPYVKA-------FAYTWFNLQAAKR 36 (44)
T ss_pred chHHHhhhHHHHHHHHHHH-------HHHHHHhHHHHHH
Confidence 3567899999999999985 3666666655544
No 45
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=27.21 E-value=99 Score=22.26 Aligned_cols=37 Identities=24% Similarity=0.320 Sum_probs=31.1
Q ss_pred HHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHH
Q psy13230 79 DTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVE 115 (132)
Q Consensus 79 ~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~ 115 (132)
.|.|++|.+.+..+=+-+++..+.++++...++++-+
T Consensus 2 ~t~rEkii~lL~e~~eplt~~ei~~~~~~~~~~~v~~ 38 (97)
T COG3357 2 ETTREKIISLLLESDEPLTVAEIFELLNGEKEKEVYD 38 (97)
T ss_pred chHHHHHHHHHHcCCCcchHHHHHHHHcCCchHHHHH
Confidence 5889999999888888999999999999886665544
No 46
>PF14647 FAM91_N: FAM91 N-terminus
Probab=26.71 E-value=1e+02 Score=26.42 Aligned_cols=49 Identities=20% Similarity=0.428 Sum_probs=34.3
Q ss_pred cHHHHHHHHHHHHHHHHHHhHHHhcCccc---HHHHHhhhCCCCHHHHHHHHhh----cCCee
Q psy13230 69 RYNAFMETLIDTTRNEIASCIEKAYTVIS---VGDTAQKLHIGSEKQMVEFGKK----VKNIV 124 (132)
Q Consensus 69 ~y~~Fm~~L~~TIR~eIA~ciEkAY~sLs---l~~a~~LL~~~s~~el~~Fa~e----rgW~v 124 (132)
-|++..+++.+.+++ ||+|++|| ..|+-++||.. ..|-.+..++ +.|..
T Consensus 88 PF~YY~~ml~~lm~~------ekSYDsLPNFTAaD~LRllGIG-RNqYIdlmn~~RS~~~~~~ 143 (308)
T PF14647_consen 88 PFSYYIDMLAELMKS------EKSYDSLPNFTAADCLRLLGIG-RNQYIDLMNKCRSKKRWFR 143 (308)
T ss_pred cHHHHHHHHHHHHHc------CCCcccCCCCcHHHHHHHhcch-HHHHHHHHHHhchhHHHhh
Confidence 477777888887775 69999997 56677888887 5555555433 45654
No 47
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=26.43 E-value=1.2e+02 Score=19.38 Aligned_cols=35 Identities=14% Similarity=0.250 Sum_probs=26.5
Q ss_pred HHHHHhHHHhcC-cccHHHHHhhhCCCCHHHHHHHHhhc
Q psy13230 83 NEIASCIEKAYT-VISVGDTAQKLHIGSEKQMVEFGKKV 120 (132)
Q Consensus 83 ~eIA~ciEkAY~-sLsl~~a~~LL~~~s~~el~~Fa~er 120 (132)
-+++..+|+.|. ++|-+++ -.+.+.+++.+|..++
T Consensus 41 veli~~lE~~f~i~i~~~~~---~~~~tv~~l~~~i~~~ 76 (77)
T TIGR00517 41 VELVMALEEEFDIEIPDEEA---EKIATVGDAVDYIEEN 76 (77)
T ss_pred HHHHHHHHHHHCCCCCHHHH---HHCCcHHHHHHHHHhc
Confidence 467888999998 5776664 4567899999998764
No 48
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.58 E-value=70 Score=23.69 Aligned_cols=21 Identities=24% Similarity=0.175 Sum_probs=12.9
Q ss_pred cCcccHHHHHhhhCCCCHHHHH
Q psy13230 93 YTVISVGDTAQKLHIGSEKQMV 114 (132)
Q Consensus 93 Y~sLsl~~a~~LL~~~s~~el~ 114 (132)
++-+|.++.++.|+.+ ++-+.
T Consensus 141 ~~g~s~~EIA~~lgis-~~tVk 161 (178)
T PRK12529 141 LDGMKQKDIAQALDIA-LPTVK 161 (178)
T ss_pred HcCCCHHHHHHHHCCC-HHHHH
Confidence 4566777777777665 44443
No 49
>PHA02992 hypothetical protein; Provisional
Probab=23.52 E-value=48 Score=31.50 Aligned_cols=32 Identities=13% Similarity=0.229 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHhHHHhcCcccHHHHHhhhC
Q psy13230 75 ETLIDTTRNEIASCIEKAYTVISVGDTAQKLH 106 (132)
Q Consensus 75 ~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~ 106 (132)
..|.++....-+.++.+||.+||++||-+|+.
T Consensus 5 ~~Lr~~f~~~~~~~l~~aF~~L~i~da~~Li~ 36 (728)
T PHA02992 5 SPLREAFLSNNCHTLTKAFKKLRIDDAMRLII 36 (728)
T ss_pred HHHHHHHHhCccchHHHHHHhcCHHHHHHHHH
Confidence 45777777777788999999999999999874
No 50
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=23.16 E-value=2e+02 Score=25.42 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHH
Q psy13230 72 AFMETLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEF 116 (132)
Q Consensus 72 ~Fm~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~F 116 (132)
.|++.+.....--.-++-=|=|++|+++-.|++|..+ ++++..-
T Consensus 298 ~Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~vd-~~~lr~~ 341 (404)
T PF10255_consen 298 LFLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLDVD-EEELRSQ 341 (404)
T ss_pred HHHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcCCC-HHHHHHH
Confidence 3444443333333445556778999999999999997 6655543
No 51
>PF14542 Acetyltransf_CG: GCN5-related N-acetyl-transferase; PDB: 2H5M_A 2Q44_A 1XMT_A 2Q4Y_A 2IL4_A 2EVN_A 1R57_A.
Probab=23.01 E-value=76 Score=21.03 Aligned_cols=18 Identities=6% Similarity=0.014 Sum_probs=14.0
Q ss_pred HHHHHHHHhhcCCeeece
Q psy13230 110 EKQMVEFGKKVKNIVYFY 127 (132)
Q Consensus 110 ~~el~~Fa~ergW~vd~~ 127 (132)
.+++.++|+++||+|.+.
T Consensus 44 ~~~~l~~a~~~~~kv~p~ 61 (78)
T PF14542_consen 44 VEAALDYARENGLKVVPT 61 (78)
T ss_dssp HHHHHHHHHHTT-EEEET
T ss_pred HHHHHHHHHHCCCEEEEE
Confidence 468899999999998753
No 52
>PRK10878 hypothetical protein; Provisional
Probab=22.99 E-value=91 Score=20.99 Aligned_cols=44 Identities=11% Similarity=0.068 Sum_probs=30.2
Q ss_pred HhccCChhHHHHHHhhhchhhhHH-hccCCCCCccHHHHHHHHHH
Q psy13230 36 LLSQNRVAEFHMELERIQYEDMIF-LAKDGVPSPRYNAFMETLID 79 (132)
Q Consensus 36 LLsqnriaeFHteLE~l~~~~~V~-~~~~~vP~~~y~~Fm~~L~~ 79 (132)
-|+....+.|...||.=+++..-| ..++..|.++...+++.+.+
T Consensus 18 ~l~~~e~~~Fe~LL~~~D~dL~~W~~g~~~p~d~~l~~iV~~Ir~ 62 (72)
T PRK10878 18 SLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELERMVRLIQT 62 (72)
T ss_pred hCCHHHHHHHHHHHcCCCHHHHHHHhCCCCCCCHHHHHHHHHHHH
Confidence 466777888888888877765544 45566777888876655444
No 53
>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=22.89 E-value=83 Score=18.84 Aligned_cols=20 Identities=5% Similarity=0.014 Sum_probs=16.9
Q ss_pred CCCHHHHHHHHhhcCCeeec
Q psy13230 107 IGSEKQMVEFGKKVKNIVYF 126 (132)
Q Consensus 107 ~~s~~el~~Fa~ergW~vd~ 126 (132)
..+.+++.++|+++|-.+..
T Consensus 26 ~~~~~e~~~lA~~~Gy~ft~ 45 (49)
T PF07862_consen 26 CQNPEEVVALAREAGYDFTE 45 (49)
T ss_pred cCCHHHHHHHHHHcCCCCCH
Confidence 45899999999999988764
No 54
>PF00607 Gag_p24: gag gene protein p24 (core nucleocapsid protein); InterPro: IPR000721 The Gag protein from retroviruses, also known as p24, forms the inner protein layer of the nucleocapsid. This protein performs highly complex orchestrated tasks during the assembly, budding, maturation and infection stages of the viral replication cycle. During viral assembly, the proteins form membrane associations and self-associations that ultimately result in budding of an immature virion from the infected cell. Gag precursors also function during viral assembly to selectively bind and package two plus strands of genomic RNA. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.; GO: 0016032 viral reproduction; PDB: 1BMX_A 1SJH_C 1SJE_C 1U57_A 1FGL_B 1G03_A 2XT1_A 2JO0_A 2L6E_A 2HJL_C ....
Probab=22.75 E-value=34 Score=27.09 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=24.5
Q ss_pred CCCccHHHHHHHHHHHHHHHHHHhHHHhc
Q psy13230 65 VPSPRYNAFMETLIDTTRNEIASCIEKAY 93 (132)
Q Consensus 65 vP~~~y~~Fm~~L~~TIR~eIA~ciEkAY 93 (132)
=|.|.|.-|++.|..++|.+.+...-+.+
T Consensus 131 Gp~Epf~dFv~rl~~a~~~~~~~~~~~~~ 159 (206)
T PF00607_consen 131 GPKEPFADFVDRLQKAIRREQGENEVKNI 159 (206)
T ss_dssp -TTSHHHHHHHHHHHHHHCSSSTHHHHHH
T ss_pred ccccchHHHHHHHHHHHhhcccccchhhH
Confidence 48899999999999999999887666554
No 55
>smart00549 TAFH TAF homology. Domain in Drosophila nervy, CBFA2T1, human TAF105, human TAF130, and Drosophila TAF110. Also known as nervy homology region 1 (NHR1).
Probab=22.19 E-value=2.5e+02 Score=20.06 Aligned_cols=45 Identities=18% Similarity=0.292 Sum_probs=34.4
Q ss_pred cCChhHHHHHHhhhchhhhHHhccCCCCCccHHHHHHHHHHHHHHHHHHhHHHh
Q psy13230 39 QNRVAEFHMELERIQYEDMIFLAKDGVPSPRYNAFMETLIDTTRNEIASCIEKA 92 (132)
Q Consensus 39 qnriaeFHteLE~l~~~~~V~~~~~~vP~~~y~~Fm~~L~~TIR~eIA~ciEkA 92 (132)
.=.+.|||..|+..= ...|-|..-+|...=+..+|.+++.|....
T Consensus 39 ~i~~EeF~~~Lq~~l---------ns~~qP~lvPFLK~slp~Lr~~l~~~~~~i 83 (92)
T smart00549 39 TITAEEFTSRLQEAL---------NSPLQPYLIPFLKNSLPLLRRELLHCARLI 83 (92)
T ss_pred CCCHHHHHHHHHHHH---------cCCCCchhHHHHHHhhHHHHHHHHHHHHHh
Confidence 334568888876542 233888999999999999999999997653
No 56
>PHA02962 hypothetical protein; Provisional
Probab=22.08 E-value=1.3e+02 Score=28.61 Aligned_cols=53 Identities=21% Similarity=0.373 Sum_probs=41.3
Q ss_pred HHhccCChhHHHHHHhhhchhhh--------HHhccCCCC-CccH--HHHHHHHHHHHHHHHHHhHHHhcC
Q psy13230 35 YLLSQNRVAEFHMELERIQYEDM--------IFLAKDGVP-SPRY--NAFMETLIDTTRNEIASCIEKAYT 94 (132)
Q Consensus 35 ~LLsqnriaeFHteLE~l~~~~~--------V~~~~~~vP-~~~y--~~Fm~~L~~TIR~eIA~ciEkAY~ 94 (132)
+||..|++.=+|+-+..+|.+.+ |-.+..+|| -... -.+.+.+| +.|+++.|+
T Consensus 297 ~ll~~~~~DLLa~Iid~vP~d~ltEelcirIV~~s~~kv~~ik~l~~pihS~~VM-------~~Ci~~gye 360 (722)
T PHA02962 297 LLIDNSNYSLLASIIDRIPDDMHNENLYMNIIRHSNDKKPKIKNFKADFFSECLM-------VMCYLRGYE 360 (722)
T ss_pred HHHhccchhHHHHHHHhccHhhhhHHHHHHHHHHcCCccchhhhccchhhHHHHH-------HHHHHcCCc
Confidence 57788999999999999998866 557888888 5555 55555554 679999995
No 57
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=21.94 E-value=90 Score=18.97 Aligned_cols=28 Identities=21% Similarity=0.305 Sum_probs=21.4
Q ss_pred cccHHHHHhhhCCCCHHHHHHHH-hhcCCe
Q psy13230 95 VISVGDTAQKLHIGSEKQMVEFG-KKVKNI 123 (132)
Q Consensus 95 sLsl~~a~~LL~~~s~~el~~Fa-~ergW~ 123 (132)
.+++.+.|+.|+.+ .+++.+.. ++.|=.
T Consensus 3 ~i~V~elAk~l~v~-~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 3 KIRVSELAKELGVP-SKEIIKKLFKELGIM 31 (54)
T ss_dssp EE-TTHHHHHHSSS-HHHHHHHH-HHHTS-
T ss_pred ceEHHHHHHHHCcC-HHHHHHHHHHhCCcC
Confidence 57889999999998 88888887 556655
No 58
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=21.92 E-value=2.1e+02 Score=25.30 Aligned_cols=45 Identities=16% Similarity=0.186 Sum_probs=38.2
Q ss_pred HHHHHHHHhHHHhcCcccHHHHHhhhCCC--CHHHHHHHHhhcCCee
Q psy13230 80 TTRNEIASCIEKAYTVISVGDTAQKLHIG--SEKQMVEFGKKVKNIV 124 (132)
Q Consensus 80 TIR~eIA~ciEkAY~sLsl~~a~~LL~~~--s~~el~~Fa~ergW~v 124 (132)
..+.++.+|.=++=..++-+++.+|++++ -.+.+-+|-.+|||--
T Consensus 383 ~LK~~~is~~l~t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 383 ELKKEVISCFLRTRGEFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred HHHHHHHHHHHHhCCCccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 35788889999988999999999999976 4567888999999964
No 59
>PF02646 RmuC: RmuC family; InterPro: IPR003798 This protein contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures []. Proteins in this family are predicted to contain a central endonuclease-like fold domain, surrounded by coiled coils, consistent with a direct role in DNA cleavage [, ].
Probab=21.72 E-value=75 Score=26.43 Aligned_cols=40 Identities=25% Similarity=0.198 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHhHHHhcCcccHHHH--HhhhCCCCHH
Q psy13230 72 AFMETLIDTTRNEIASCIEKAYTVISVGDT--AQKLHIGSEK 111 (132)
Q Consensus 72 ~Fm~~L~~TIR~eIA~ciEkAY~sLsl~~a--~~LL~~~s~~ 111 (132)
.++..+...||..|-...+|.|..+.-... =.+||+.++.
T Consensus 145 ~~~k~~~~~vr~hi~~Ls~K~Y~~i~~~~t~dfvimFiP~E~ 186 (304)
T PF02646_consen 145 AALKEHAKSVRKHIKELSSKDYWNIIPPNTPDFVIMFIPSES 186 (304)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCccCCCCCCCEEEEEecChH
Confidence 445568999999999999999977622222 2356666554
No 60
>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=21.65 E-value=3.4e+02 Score=20.01 Aligned_cols=55 Identities=22% Similarity=0.379 Sum_probs=45.6
Q ss_pred HHHHHHhccCChhHHHHHHhhhchhhhHHhcc---CCCCCccHHHHHHHHHHHHHHHHHHh
Q psy13230 31 LNLLYLLSQNRVAEFHMELERIQYEDMIFLAK---DGVPSPRYNAFMETLIDTTRNEIASC 88 (132)
Q Consensus 31 L~LL~LLsqnriaeFHteLE~l~~~~~V~~~~---~~vP~~~y~~Fm~~L~~TIR~eIA~c 88 (132)
-..+.+|..+++.|=..+||.|.. ++... ...|...|....+.|...|..|-...
T Consensus 7 ~~~~~~L~S~k~keR~~al~~L~~---il~~~~~~~~l~~k~~~~ifeaL~~~i~~Ek~~y 64 (155)
T PF11640_consen 7 NSILRLLSSDKIKERNKALEDLRH---ILSSPPRVDSLNDKQWHSIFEALFRCIEKEKEAY 64 (155)
T ss_pred HHHHHHHhccccchHHHHHHHHHH---HHcCccccccCCcchHHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999998853 45444 77888999999999999999997766
No 61
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.63 E-value=1.2e+02 Score=17.23 Aligned_cols=25 Identities=8% Similarity=0.244 Sum_probs=19.3
Q ss_pred ccHHHHHhhhCCCCHHHHHHHHhhcCC
Q psy13230 96 ISVGDTAQKLHIGSEKQMVEFGKKVKN 122 (132)
Q Consensus 96 Lsl~~a~~LL~~~s~~el~~Fa~ergW 122 (132)
+++.+++++++++ +.-+..+.+ +|+
T Consensus 1 ~~~~e~a~~~gv~-~~tlr~~~~-~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVS-PSTLRYYER-IGL 25 (49)
T ss_pred CcHHHHHHHHCcC-HHHHHHHHH-CCC
Confidence 3678999999998 888887755 444
No 62
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=21.05 E-value=2.1e+02 Score=17.50 Aligned_cols=43 Identities=21% Similarity=0.257 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHH
Q psy13230 73 FMETLIDTTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFG 117 (132)
Q Consensus 73 Fm~~L~~TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa 117 (132)
+.+.|.+..|.+|-..+ ..-...+..+.++.++++ ...+..-.
T Consensus 3 i~~aL~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~-~~t~s~hL 45 (61)
T PF12840_consen 3 IFKALSDPTRLRILRLL-ASNGPMTVSELAEELGIS-QSTVSYHL 45 (61)
T ss_dssp HHHHHTSHHHHHHHHHH-HHCSTBEHHHHHHHHTS--HHHHHHHH
T ss_pred HHHHhCCHHHHHHHHHH-hcCCCCCHHHHHHHHCCC-HHHHHHHH
Confidence 56778999999999999 668899999999999987 55554443
No 63
>TIGR02809 phasin_3 phasin family protein. Members of this protein family are encoded in polyhydroxyalkanoic acid storage system regions in Vibrio, Photobacterium profundum SS9, Acinetobacter sp., Aeromonas hydrophila, and several species of Vibrio. Members appear distantly related to the phasin family proteins modeled by TIGR01841 and TIGR01985.
Probab=20.64 E-value=3.1e+02 Score=20.13 Aligned_cols=51 Identities=12% Similarity=0.309 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHH--HHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhhc
Q psy13230 70 YNAFMETLIDTTRN--EIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKKV 120 (132)
Q Consensus 70 y~~Fm~~L~~TIR~--eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~er 120 (132)
|.-|...+++.+-. +.--..-++|+.|.++.+++.+-.++++.+..|..++
T Consensus 17 ~~kfN~L~~kN~E~ltelQL~a~rsYsdlGl~Q~raaseVkD~~sl~sf~t~Q 69 (110)
T TIGR02809 17 YTKFNKLLAKNVEQLTELQLAAARTYSELGLNQLKAAGEVKDAQSLAAFNTQQ 69 (110)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHH
Confidence 34455555444432 2333456889999999999999999999999998664
No 64
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=20.62 E-value=85 Score=26.14 Aligned_cols=32 Identities=16% Similarity=0.066 Sum_probs=24.0
Q ss_pred HHHHhhhCCCCHH----HHHHHHhhcCCeeeceeee
Q psy13230 99 GDTAQKLHIGSEK----QMVEFGKKVKNIVYFYIFY 130 (132)
Q Consensus 99 ~~a~~LL~~~s~~----el~~Fa~ergW~vd~~~~~ 130 (132)
+-.+.+++|+..+ .+...|+++||+++.+-+|
T Consensus 242 ~~~~all~fTGs~~~nr~lR~~A~~~G~~L~~~GL~ 277 (307)
T cd00141 242 EFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLF 277 (307)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHHHcCCeeeccccc
Confidence 3457888887444 6788899999999986544
No 65
>PF06393 BID: BH3 interacting domain (BID); InterPro: IPR010479 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. BID is a member of the Bcl-2 superfamily of proteins that are key regulators of programmed cell death, hence this family is related to the Apoptosis regulator Bcl-2 protein BH domain. BID is a pro-apoptotic member of the Bcl-2 superfamily and as such posses the ability to target intracellular membranes and contains the BH3 death domain. The activity of BID is regulated by a Caspase 8-mediated cleavage event, exposing the BH3 domain and significantly changing the surface charge and hydrophobicity, which causes a change of cellular localisation [].; GO: 0043065 positive regulation of apoptosis, 0005737 cytoplasm; PDB: 2BID_A 1ZY3_B 2KBW_B 1DDB_A 2VOI_B.
Probab=20.60 E-value=65 Score=25.96 Aligned_cols=37 Identities=24% Similarity=0.218 Sum_probs=27.5
Q ss_pred CCcCcchhhHHHHHHHhccCChhHHHHHHhhhchhhh
Q psy13230 21 ESPYKNEMLGLNLLYLLSQNRVAEFHMELERIQYEDM 57 (132)
Q Consensus 21 ~S~~~~~ilgL~LL~LLsqnriaeFHteLE~l~~~~~ 57 (132)
++.+...|+.|=|+-.|-...-..||.|||-+..+..
T Consensus 9 ~~~~~e~iT~lLlf~FLq~~~~~~F~~EL~~Lg~El~ 45 (196)
T PF06393_consen 9 SGLQDEHITNLLLFGFLQSCSNCNFHEELEVLGRELP 45 (196)
T ss_dssp -----THHHHHHHHHHHHHTCSSSSHHHHHHHHGG--
T ss_pred CCcchhhHHHHHHHHHHhcCCCccHHHHHHHHccccc
Confidence 4566777999999999999999999999999976644
No 66
>PF01221 Dynein_light: Dynein light chain type 1 ; InterPro: IPR001372 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits (see IPR004273 from INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, ]. Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].; GO: 0007017 microtubule-based process, 0005875 microtubule associated complex; PDB: 1F95_A 1F96_A 1F3C_A 3P8M_B 2XQQ_C 1RE6_A 1CMI_A 1PWK_A 1PWJ_A 4DS1_C ....
Probab=20.39 E-value=1.4e+02 Score=20.06 Aligned_cols=34 Identities=21% Similarity=0.190 Sum_probs=18.4
Q ss_pred HHHHHHHHhHHHhcCcccHHHHHhhhCCCCHHHHHHHHhh-------cCCee
Q psy13230 80 TTRNEIASCIEKAYTVISVGDTAQKLHIGSEKQMVEFGKK-------VKNIV 124 (132)
Q Consensus 80 TIR~eIA~ciEkAY~sLsl~~a~~LL~~~s~~el~~Fa~e-------rgW~v 124 (132)
.+++++.+.+-.|+..-+ +++++.++.++ ++|.+
T Consensus 16 ~~~~~~~~~~~~a~~~~~-----------~~~eiA~~iK~~lD~~yG~~Wh~ 56 (89)
T PF01221_consen 16 EMQEEAIELAKEALKKYQ-----------DEKEIAEFIKQELDKKYGPTWHC 56 (89)
T ss_dssp HHHHHHHHHHHHHHHHCS-----------SHHHHHHHHHHHHHHHHSS-EEE
T ss_pred HHHHHHHHHHHHHHHHCC-----------cHHHHHHHHHHHHhcccCCceEE
Confidence 455555555555554322 45666666555 68876
No 67
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=20.30 E-value=1.8e+02 Score=16.33 Aligned_cols=30 Identities=17% Similarity=0.156 Sum_probs=21.0
Q ss_pred CcccHHHHHhhhCCCCHHHH---HHHHhhcCCee
Q psy13230 94 TVISVGDTAQKLHIGSEKQM---VEFGKKVKNIV 124 (132)
Q Consensus 94 ~sLsl~~a~~LL~~~s~~el---~~Fa~ergW~v 124 (132)
..++..+.++.++++ ...+ .+.-.+.||-.
T Consensus 13 ~~~s~~~l~~~l~~s-~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 13 GKVSVEELAELLGVS-EMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred CCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE
Confidence 568999999999996 4433 33345578854
Done!