Query psy6932
Match_columns 150
No_of_seqs 110 out of 347
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 22:12:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6932.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6932hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3198|consensus 100.0 4.5E-45 9.7E-50 283.7 8.8 138 1-142 1-150 (152)
2 PF01922 SRP19: SRP19 protein; 100.0 8.7E-40 1.9E-44 237.9 10.4 94 16-115 1-95 (95)
3 PRK00754 signal recognition pa 100.0 1.5E-36 3.3E-41 221.6 8.6 91 12-116 3-94 (95)
4 PRK03745 signal recognition pa 100.0 7.6E-34 1.7E-38 209.1 8.2 93 14-117 2-98 (100)
5 COG1400 SEC65 Signal recogniti 100.0 2.8E-29 6.1E-34 182.8 8.1 89 14-116 2-91 (93)
6 PF12387 Peptidase_C74: Pestiv 42.6 0.88 1.9E-05 37.3 -5.6 66 13-82 53-119 (200)
7 TIGR01565 homeo_ZF_HD homeobox 40.9 30 0.00065 23.1 2.5 19 41-59 27-45 (58)
8 COG3636 Predicted transcriptio 36.9 34 0.00073 25.6 2.5 22 42-63 74-95 (100)
9 PF02037 SAP: SAP domain; Int 32.7 29 0.00062 20.5 1.3 16 45-60 5-20 (35)
10 PF00046 Homeobox: Homeobox do 32.6 29 0.00063 21.5 1.4 20 41-60 22-41 (57)
11 smart00513 SAP Putative DNA-bi 32.2 45 0.00097 19.4 2.1 17 44-60 4-20 (35)
12 COG2104 ThiS Sulfur transfer p 31.2 37 0.00081 23.2 1.8 43 41-83 12-61 (68)
13 cd00086 homeodomain Homeodomai 29.7 55 0.0012 20.0 2.3 20 41-60 22-41 (59)
14 COG1871 CheD Chemotaxis protei 28.9 1E+02 0.0022 24.9 4.2 42 44-86 114-157 (164)
15 PF07524 Bromo_TP: Bromodomain 28.1 55 0.0012 22.0 2.3 19 42-60 57-75 (77)
16 PF13443 HTH_26: Cro/C1-type H 27.5 40 0.00086 21.2 1.4 20 41-60 35-54 (63)
17 PF07487 SopE_GEF: SopE GEF do 27.3 41 0.00088 27.1 1.6 22 43-64 63-84 (165)
18 TIGR03070 couple_hipB transcri 25.7 85 0.0018 18.7 2.6 18 42-59 40-57 (58)
19 COG0027 PurT Formate-dependent 25.6 56 0.0012 29.5 2.4 21 44-64 136-156 (394)
20 cd07245 Glo_EDI_BRP_like_9 Thi 25.4 1.3E+02 0.0028 19.4 3.7 44 39-92 68-111 (114)
21 PHA01976 helix-turn-helix prot 25.0 69 0.0015 20.3 2.2 23 38-60 36-58 (67)
22 KOG0683|consensus 24.9 1.1E+02 0.0025 27.7 4.2 56 49-121 232-291 (380)
23 cd08359 Glo_EDI_BRP_like_22 Th 24.1 1.4E+02 0.003 20.2 3.8 45 39-92 70-114 (119)
24 COG0602 NrdG Organic radical a 24.0 85 0.0018 25.5 3.0 28 44-71 86-114 (212)
25 smart00389 HOX Homeodomain. DN 23.8 82 0.0018 19.1 2.3 19 42-60 23-41 (56)
26 TIGR02684 dnstrm_HI1420 probab 23.6 90 0.002 22.2 2.8 21 42-62 68-88 (89)
27 PF04273 DUF442: Putative phos 23.3 51 0.0011 24.3 1.5 24 41-64 41-64 (110)
28 PRK09726 antitoxin HipB; Provi 22.8 1.2E+02 0.0025 20.9 3.2 32 40-71 48-80 (88)
29 smart00576 BTP Bromodomain tra 22.6 79 0.0017 21.5 2.2 19 42-60 57-75 (77)
30 PRK06724 hypothetical protein; 22.0 1.8E+02 0.0039 21.1 4.2 43 44-92 75-117 (128)
31 COG2524 Predicted transcriptio 21.8 1E+02 0.0022 27.1 3.2 62 44-109 218-292 (294)
32 PF02382 RTX: RTX N-terminal d 21.6 92 0.002 30.1 3.1 37 35-71 49-86 (653)
33 cd08794 Death_IRAK1 Death doma 21.4 56 0.0012 23.7 1.3 20 39-58 57-76 (84)
34 COG2313 IndA Uncharacterized e 21.3 87 0.0019 27.4 2.7 34 19-60 192-228 (310)
35 COG1828 PurS Phosphoribosylfor 21.3 87 0.0019 22.5 2.3 59 35-111 8-66 (83)
36 PTZ00172 40S ribosomal protein 21.3 48 0.001 25.1 1.0 54 30-86 25-89 (108)
37 KOG3802|consensus 20.7 86 0.0019 28.6 2.6 22 41-62 316-337 (398)
38 COG0107 HisF Imidazoleglycerol 20.4 65 0.0014 27.7 1.7 73 33-111 98-198 (256)
39 PF14830 Haemocyan_bet_s: Haem 20.3 1.1E+02 0.0024 22.8 2.7 38 45-97 56-93 (103)
No 1
>KOG3198|consensus
Probab=100.00 E-value=4.5e-45 Score=283.74 Aligned_cols=138 Identities=45% Similarity=0.733 Sum_probs=126.7
Q ss_pred CCccCCCCCCCccceEEEeeccccCCcCccccccccccccCCCCCHHHHHHHHHHcCCceeEec-CCCCccccccCCCcc
Q psy6932 1 MATIDTKKHTDVERWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIEN-KLYPREISKEHFVRG 79 (150)
Q Consensus 1 ~~~~~~~~~~~~~~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~iE~-K~yPR~w~~d~~~~G 79 (150)
|+.+..+++.+.++|+||||+|||+++|++||||||+++||+||+..||++||+.|||+|.+|. |+||||| .++|
T Consensus 1 m~~~~~~~~~~~~r~ivlYP~Y~d~krt~~EGRripke~aVeNP~a~eI~Dvl~~lgl~~~~E~~K~hPrD~----~n~G 76 (152)
T KOG3198|consen 1 MAFIASKDLEDQKRWIVLYPAYIDKKRTRKEGRRIPKEKAVENPLAKEIADVLRALGLNCLLEPNKKHPRDF----VNPG 76 (152)
T ss_pred CcccccCChhhccceEEEEEEEeccccchhhccccCHHHhhcCcchhHHHHHHHHhCCcccccccccCchhc----CCCc
Confidence 6788899999999999999999999999999999999999999999999999999999999995 9999988 6899
Q ss_pred eEEEEeecCCCCCCCCCCCCHHHHHHHHHHHchhhhhc-cCCCCCccccccc----------cCCCCCCCCccc
Q psy6932 80 RARVQLKNDDGSPVNPDFPTREAVMLHLGALIPKLKSR-QGKQANSEQNQQR----------DLSGGGGGGKKQ 142 (150)
Q Consensus 80 RVrV~l~~~~G~~~~~~~~~K~~Ll~~Ia~~I~~lrsR-~~~~~~~~~~~~~----------~~~~~~~~~~~~ 142 (150)
||||+|+++||++++.+|++++.+|..+|++|+++.+| .+.++++..+..+ +.++++|||+|+
T Consensus 77 RVRvqlk~edG~l~~~~~~sr~~~~~~~a~~ip~~~~R~~~~~~~a~~~~~q~~~~~t~~~~~~~~kkgkgkk~ 150 (152)
T KOG3198|consen 77 RVRVQLKNEDGTLYVIAFISRKSLMLPIAEMIPELKTRQPQKTGEAVHQYPQGVLGATISPLGSPGKKGKGKKK 150 (152)
T ss_pred eEEEEeeccCCcEEeecchhHHHHHHHhhhhCcccccccccccCCccccccccccccccccccccccccCCccc
Confidence 99999999999999999999999999999999999999 5566666655555 666777877776
No 2
>PF01922 SRP19: SRP19 protein; InterPro: IPR002778 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 3DLU_A 3DLV_B 2J37_B 1MFQ_B 3KTV_D 1RY1_B 1JID_A 1KVV_A 1KVN_A 3KTW_B ....
Probab=100.00 E-value=8.7e-40 Score=237.86 Aligned_cols=94 Identities=45% Similarity=0.778 Sum_probs=85.3
Q ss_pred EEEeeccccCCcCccccccccccccCCCCCHHHHHHHHHHcCCceeEe-cCCCCccccccCCCcceEEEEeecCCCCCCC
Q psy6932 16 VCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIE-NKLYPREISKEHFVRGRARVQLKNDDGSPVN 94 (150)
Q Consensus 16 ~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~iE-~K~yPR~w~~d~~~~GRVrV~l~~~~G~~~~ 94 (150)
+||||+|||+++|+++|||||+++||++|+++||++||++|||++++| +|+|||+|| +++|||+|+++++ ++|
T Consensus 1 ~vIyP~Y~Ds~~sr~~GRrv~k~~aV~~P~~~EI~~a~~~Lgl~~~~E~~K~yPr~~~---~~~GRV~V~~~~~---~~~ 74 (95)
T PF01922_consen 1 IVIYPAYFDSKKSRSEGRRVPKELAVENPTLEEIADACKKLGLPCVVEPDKRYPRDWW---ENPGRVRVQLKND---PVN 74 (95)
T ss_dssp EEEEGGGGBTTSSTTTT--SSTTTSBSS--HHHHHHHHHHTTSEEEEETTECTTCGST---SCTTEEEEE-CST---BSS
T ss_pred CEEccchhcCCCChhhccccChhhcCCCCCHHHHHHHHHHcCCCEEEccccCcChhhc---ccCceEEEEeCCC---ccc
Confidence 699999999999999999999999999999999999999999999999 599999975 6999999999876 999
Q ss_pred CCCCCHHHHHHHHHHHchhhh
Q psy6932 95 PDFPTREAVMLHLGALIPKLK 115 (150)
Q Consensus 95 ~~~~~K~~Ll~~Ia~~I~~lr 115 (150)
++|++|++||++||+.|+++|
T Consensus 75 ~~~~~K~~Ll~~Ia~~i~~~r 95 (95)
T PF01922_consen 75 PEIKSKKELLKKIAEKIKKIR 95 (95)
T ss_dssp TTSSSHHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHhC
Confidence 999999999999999999886
No 3
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=100.00 E-value=1.5e-36 Score=221.57 Aligned_cols=91 Identities=30% Similarity=0.470 Sum_probs=84.0
Q ss_pred ccceEEEeeccccCCcCccccccccccccCCCCCHHHHHHHHHHcCCceeEec-CCCCccccccCCCcceEEEEeecCCC
Q psy6932 12 VERWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIEN-KLYPREISKEHFVRGRARVQLKNDDG 90 (150)
Q Consensus 12 ~~~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~iE~-K~yPR~w~~d~~~~GRVrV~l~~~~G 90 (150)
...++||||+|||+++|+++|||||+++||+||+++||++||++|||+|++|+ |.|||+|| +++|||+|+.
T Consensus 3 ~~~r~vIyP~Y~d~~~tr~eGRrv~k~~aV~~P~~~EI~~a~~~lgl~~~~e~~K~yPr~~~---e~~GRv~V~~----- 74 (95)
T PRK00754 3 DKGRIVIWPAYIDSTRSRSEGRIISRKLAVKEPRLEEIIEAAEKLGLNPEVEPDKAYPRSWW---EVSGRVLVDK----- 74 (95)
T ss_pred CcCcEEEeeccccCCCChhhcCccCHHHhccCCCHHHHHHHHHHcCCCeEEeeCCCCCchHh---cCCCEEEECC-----
Confidence 35579999999999999999999999999999999999999999999999995 99999996 4999999953
Q ss_pred CCCCCCCCCHHHHHHHHHHHchhhhh
Q psy6932 91 SPVNPDFPTREAVMLHLGALIPKLKS 116 (150)
Q Consensus 91 ~~~~~~~~~K~~Ll~~Ia~~I~~lrs 116 (150)
+.+|.+||++||+.|+++|.
T Consensus 75 ------~~~K~~ll~~Ia~~I~~~R~ 94 (95)
T PRK00754 75 ------VGSKTNTLRMIAKEIKKLRG 94 (95)
T ss_pred ------CCCHHHHHHHHHHHHHHHhc
Confidence 36899999999999999875
No 4
>PRK03745 signal recognition particle protein Srp19; Provisional
Probab=100.00 E-value=7.6e-34 Score=209.12 Aligned_cols=93 Identities=25% Similarity=0.410 Sum_probs=83.6
Q ss_pred ceEEEeeccccCCcCccccccccccccCCCCCHHHHHHHHHHcCCce-eEec-CCCCccccc--cCCCcceEEEEeecCC
Q psy6932 14 RWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKY-HIEN-KLYPREISK--EHFVRGRARVQLKNDD 89 (150)
Q Consensus 14 ~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~-~iE~-K~yPR~w~~--d~~~~GRVrV~l~~~~ 89 (150)
.++||||+|||+++|++||||||+++||+||+++||++||++|||+| ++|. |.|||+|.. +|...|||+|+..
T Consensus 2 ~~~vIyP~Y~D~~~sr~eGRrv~k~~aV~~P~~~EI~~a~~~lgl~~~~~E~~K~yPr~~g~~~~~~~~Grv~V~~~--- 78 (100)
T PRK03745 2 GRFVVWPSELDSRLSRKYGRIVPKNLAVERPTLEEIVDAAEALGFKVIEVDREKLNPRLSGIDEELRTRGRIVIESP--- 78 (100)
T ss_pred CcEEEeeccccCcCChhhcCccCHHHcccCCCHHHHHHHHHHcCCCcEeeccCCCCCCccCCccchhcCCEEEecCC---
Confidence 47999999999999999999999999999999999999999999999 5995 999999422 2468999999643
Q ss_pred CCCCCCCCCCHHHHHHHHHHHchhhhhc
Q psy6932 90 GSPVNPDFPTREAVMLHLGALIPKLKSR 117 (150)
Q Consensus 90 G~~~~~~~~~K~~Ll~~Ia~~I~~lrsR 117 (150)
.+|..||++||+.|+++|.+
T Consensus 79 --------~~K~~ll~~Ia~~ik~~R~~ 98 (100)
T PRK03745 79 --------YGKSKSLKMIAQKIREFRKR 98 (100)
T ss_pred --------CCHHHHHHHHHHHHHHHHhc
Confidence 37999999999999999875
No 5
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=99.96 E-value=2.8e-29 Score=182.78 Aligned_cols=89 Identities=30% Similarity=0.572 Sum_probs=81.1
Q ss_pred ceEEEeeccccCCcCccccccccccccCCCCCHHHHHHHHHHcCCceeEe-cCCCCccccccCCCcceEEEEeecCCCCC
Q psy6932 14 RWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIE-NKLYPREISKEHFVRGRARVQLKNDDGSP 92 (150)
Q Consensus 14 ~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~iE-~K~yPR~w~~d~~~~GRVrV~l~~~~G~~ 92 (150)
..+||||+|||+++||++|||||+++||+||+++||++|+++|||+|.++ +|.|||.||+ ..|||.|+..
T Consensus 2 ~~~vlwp~YfDs~~srs~GRrvpk~laV~~P~~~ei~~a~~~LGl~~~v~~dk~yPr~~w~---~~g~vive~~------ 72 (93)
T COG1400 2 MRIVLWPAYFDSDLSRSEGRRVPKELAVENPSLEEIAEALRELGLKPKVERDKKYPRLWWE---ISGRVIVESN------ 72 (93)
T ss_pred CceEEeehhhcCccChhhccccchhhcccCCCHHHHHHHHHHcCCCeeechhhcCCCchhh---hCceEEEecC------
Confidence 46899999999999999999999999999999999999999999999765 5999999975 6699999754
Q ss_pred CCCCCCCHHHHHHHHHHHchhhhh
Q psy6932 93 VNPDFPTREAVMLHLGALIPKLKS 116 (150)
Q Consensus 93 ~~~~~~~K~~Ll~~Ia~~I~~lrs 116 (150)
.+|.++|+.||+.|+.++.
T Consensus 73 -----~~K~~~lk~ia~~lr~~r~ 91 (93)
T COG1400 73 -----GKKSKLLKAIAAKLREKRE 91 (93)
T ss_pred -----ccHhHHHHHHHHHHHHhhc
Confidence 3699999999999998853
No 6
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=42.57 E-value=0.88 Score=37.30 Aligned_cols=66 Identities=20% Similarity=0.274 Sum_probs=56.0
Q ss_pred cceEEEeeccccCCcCccccccccccccCCCCCHHHHHHHHHHcCCceeEec-CCCCccccccCCCcceEE
Q psy6932 13 ERWVCIYPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLSTTGLKYHIEN-KLYPREISKEHFVRGRAR 82 (150)
Q Consensus 13 ~~~~vIYP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~~Lgl~~~iE~-K~yPR~w~~d~~~~GRVr 82 (150)
+.|.++|.+||--..+.---|||-.+.|=-.=-++-+..|+-+|+....-|+ |.+-+. |..+|||+
T Consensus 53 S~Wq~~Yl~yL~ie~~Yy~H~kIIeEiaGgtN~iSR~iAaliElNW~~d~eE~kGlKKF----flLS~R~r 119 (200)
T PF12387_consen 53 SKWQCFYLLYLIIELSYYMHRKIIEEIAGGTNFISRLIAALIELNWAMDEEESKGLKKF----FLLSGRVR 119 (200)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHhhccccchhhcCccee----eeehhHHH
Confidence 5799999999999999999999999999777778888888889998887776 888774 47788886
No 7
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=40.86 E-value=30 Score=23.08 Aligned_cols=19 Identities=5% Similarity=0.316 Sum_probs=17.0
Q ss_pred CCCCCHHHHHHHHHHcCCc
Q psy6932 41 VDNPTYKDIDDVLSTTGLK 59 (150)
Q Consensus 41 V~~Pt~~EI~~A~~~Lgl~ 59 (150)
+..|+..++.+.|..|||+
T Consensus 27 ~~~~~~~~r~~la~~lgl~ 45 (58)
T TIGR01565 27 LKDKRREEVREFCEEIGVT 45 (58)
T ss_pred CCCCCHHHHHHHHHHhCCC
Confidence 4569999999999999997
No 8
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=36.91 E-value=34 Score=25.56 Aligned_cols=22 Identities=36% Similarity=0.608 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHHHHcCCceeEe
Q psy6932 42 DNPTYKDIDDVLSTTGLKYHIE 63 (150)
Q Consensus 42 ~~Pt~~EI~~A~~~Lgl~~~iE 63 (150)
-||++.-|..+|+.|||...+.
T Consensus 74 GNPtf~Til~V~kAlG~rl~~~ 95 (100)
T COG3636 74 GNPTFDTILAVLKALGLRLSAQ 95 (100)
T ss_pred CCCcHHHHHHHHHHcCceeecc
Confidence 4999999999999999987654
No 9
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=32.69 E-value=29 Score=20.47 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=12.4
Q ss_pred CHHHHHHHHHHcCCce
Q psy6932 45 TYKDIDDVLSTTGLKY 60 (150)
Q Consensus 45 t~~EI~~A~~~Lgl~~ 60 (150)
++.|+.+.|+++||+.
T Consensus 5 ~v~eLk~~l~~~gL~~ 20 (35)
T PF02037_consen 5 TVAELKEELKERGLST 20 (35)
T ss_dssp HHHHHHHHHHHTTS-S
T ss_pred cHHHHHHHHHHCCCCC
Confidence 5788999999998863
No 10
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=32.63 E-value=29 Score=21.54 Aligned_cols=20 Identities=15% Similarity=0.283 Sum_probs=17.8
Q ss_pred CCCCCHHHHHHHHHHcCCce
Q psy6932 41 VDNPTYKDIDDVLSTTGLKY 60 (150)
Q Consensus 41 V~~Pt~~EI~~A~~~Lgl~~ 60 (150)
-..|+..++.+.+..|||+.
T Consensus 22 ~~~p~~~~~~~la~~l~l~~ 41 (57)
T PF00046_consen 22 NPYPSKEEREELAKELGLTE 41 (57)
T ss_dssp SSSCHHHHHHHHHHHHTSSH
T ss_pred hccccccccccccccccccc
Confidence 46799999999999999975
No 11
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=32.24 E-value=45 Score=19.39 Aligned_cols=17 Identities=24% Similarity=0.362 Sum_probs=14.1
Q ss_pred CCHHHHHHHHHHcCCce
Q psy6932 44 PTYKDIDDVLSTTGLKY 60 (150)
Q Consensus 44 Pt~~EI~~A~~~Lgl~~ 60 (150)
=++.|+.+.|+.+||+.
T Consensus 4 l~~~~Lk~~l~~~gl~~ 20 (35)
T smart00513 4 LKVSELKDELKKRGLST 20 (35)
T ss_pred CcHHHHHHHHHHcCCCC
Confidence 36889999999999874
No 12
>COG2104 ThiS Sulfur transfer protein involved in thiamine biosynthesis [Coenzyme metabolism]
Probab=31.18 E-value=37 Score=23.19 Aligned_cols=43 Identities=23% Similarity=0.417 Sum_probs=28.8
Q ss_pred CCCCCHHHHHHHHHHcCCc---eeEe-c-CCCCccccccCCCcc--eEEE
Q psy6932 41 VDNPTYKDIDDVLSTTGLK---YHIE-N-KLYPREISKEHFVRG--RARV 83 (150)
Q Consensus 41 V~~Pt~~EI~~A~~~Lgl~---~~iE-~-K~yPR~w~~d~~~~G--RVrV 83 (150)
++-+.-.-+++.+.+|||+ +.++ + ...||+-|.|..... ||.|
T Consensus 12 ~e~~~~~tv~dLL~~l~~~~~~vav~vNg~iVpr~~~~~~~l~~gD~iev 61 (68)
T COG2104 12 VEIAEGTTVADLLAQLGLNPEGVAVAVNGEIVPRSQWADTILKEGDRIEV 61 (68)
T ss_pred EEcCCCCcHHHHHHHhCCCCceEEEEECCEEccchhhhhccccCCCEEEE
Confidence 3333335677888999997 4556 5 899998877665554 4444
No 13
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=29.73 E-value=55 Score=19.96 Aligned_cols=20 Identities=15% Similarity=0.288 Sum_probs=17.8
Q ss_pred CCCCCHHHHHHHHHHcCCce
Q psy6932 41 VDNPTYKDIDDVLSTTGLKY 60 (150)
Q Consensus 41 V~~Pt~~EI~~A~~~Lgl~~ 60 (150)
-..|+..|+.+.+..+||+.
T Consensus 22 ~~~P~~~~~~~la~~~~l~~ 41 (59)
T cd00086 22 NPYPSREEREELAKELGLTE 41 (59)
T ss_pred CCCCCHHHHHHHHHHHCcCH
Confidence 46899999999999999875
No 14
>COG1871 CheD Chemotaxis protein; stimulates methylation of MCP proteins [Cell motility and secretion / Signal transduction mechanisms]
Probab=28.88 E-value=1e+02 Score=24.88 Aligned_cols=42 Identities=21% Similarity=0.188 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHcCCceeEec--CCCCccccccCCCcceEEEEee
Q psy6932 44 PTYKDIDDVLSTTGLKYHIEN--KLYPREISKEHFVRGRARVQLK 86 (150)
Q Consensus 44 Pt~~EI~~A~~~Lgl~~~iE~--K~yPR~w~~d~~~~GRVrV~l~ 86 (150)
=.++-+.+.++.+|++.+-|+ ..|||.-+ -+...|||+|..-
T Consensus 114 rNv~~~~~~L~~~~IpilaeD~Gg~~gR~i~-F~p~tG~v~vr~v 157 (164)
T COG1871 114 RNVEFAKEFLKDEGIPILAEDTGGDSGRTIE-FNPSTGRVRVRTV 157 (164)
T ss_pred HHHHHHHHHHHHcCCcEEEhhhCCCCCcEEE-EecCCCcEEEEEc
Confidence 356678899999999999997 89999863 2367899999765
No 15
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=28.11 E-value=55 Score=22.04 Aligned_cols=19 Identities=21% Similarity=0.595 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHcCCce
Q psy6932 42 DNPTYKDIDDVLSTTGLKY 60 (150)
Q Consensus 42 ~~Pt~~EI~~A~~~Lgl~~ 60 (150)
..|++.||..|+..+|+++
T Consensus 57 t~~~~~Dv~~al~~~gi~v 75 (77)
T PF07524_consen 57 TEPNLQDVEQALEEMGISV 75 (77)
T ss_pred CCCCHHHHHHHHHHhCCCC
Confidence 4689999999999999964
No 16
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=27.51 E-value=40 Score=21.24 Aligned_cols=20 Identities=10% Similarity=0.257 Sum_probs=12.4
Q ss_pred CCCCCHHHHHHHHHHcCCce
Q psy6932 41 VDNPTYKDIDDVLSTTGLKY 60 (150)
Q Consensus 41 V~~Pt~~EI~~A~~~Lgl~~ 60 (150)
+.+|++++|..+|..||+++
T Consensus 35 ~~~~~~~~l~~ia~~l~~~~ 54 (63)
T PF13443_consen 35 PSNPSLDTLEKIAKALNCSP 54 (63)
T ss_dssp -----HHHHHHHHHHHT--H
T ss_pred cccccHHHHHHHHHHcCCCH
Confidence 46899999999999999975
No 17
>PF07487 SopE_GEF: SopE GEF domain; InterPro: IPR016019 The type III secretion system of Gram-negative bacteria is used to transport virulence factors from the pathogen directly into the host cell [] and is only triggered when the bacterium comes into close contact with the host. Effector proteins secreted by the type III system do not possess a secretion signal, and are considered unique because of this. Salmonella spp. secrete an effector protein called SopE that is responsible for stimulating the reorganisation of the host cell actin cytoskeleton, and ruffling of the cellular membrane []. It acts as a guanyl-nucleotide-exchange factor on Rho-GTPase proteins such as Cdc42 and Rac. As it is imperative for the bacterium to revert the cell back to its "normal" state as quickly as possible, another tyrosine phosphatase effector called SptP reverses the actions brought about by SopE []. Recently, it has been found that SopE and its protein homologue SopE2 can activate different sets of Rho-GTPases in the host cell []. Far from being a redundant set of two similar type III effectors, they both act in unison to specifically activate different Rho-GTPase signalling cascades in the host cell during infection. This entry represents the guanine nucleotide exchange factor domain of SopE. This domain has an alpha-helical structure consisting of two three-helix bundles arranged in a lamdba shape [, ].; GO: 0005085 guanyl-nucleotide exchange factor activity, 0009405 pathogenesis, 0031532 actin cytoskeleton reorganization, 0032862 activation of Rho GTPase activity, 0005576 extracellular region; PDB: 1GZS_B 1R9K_A 1R6E_A 2JOL_A 2JOK_A.
Probab=27.28 E-value=41 Score=27.10 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=18.4
Q ss_pred CCCHHHHHHHHHHcCCceeEec
Q psy6932 43 NPTYKDIDDVLSTTGLKYHIEN 64 (150)
Q Consensus 43 ~Pt~~EI~~A~~~Lgl~~~iE~ 64 (150)
+|-+.||-+||+..||+++.-+
T Consensus 63 ~pFL~eiGeaak~aGLPge~KN 84 (165)
T PF07487_consen 63 QPFLFEIGEAAKNAGLPGENKN 84 (165)
T ss_dssp HHHHHHHHHHHHHTT-SEEEET
T ss_pred cHHHHHHHHHHHHCCCCccccC
Confidence 5789999999999999998654
No 18
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=25.73 E-value=85 Score=18.75 Aligned_cols=18 Identities=22% Similarity=0.309 Sum_probs=16.0
Q ss_pred CCCCHHHHHHHHHHcCCc
Q psy6932 42 DNPTYKDIDDVLSTTGLK 59 (150)
Q Consensus 42 ~~Pt~~EI~~A~~~Lgl~ 59 (150)
.+|++.++..+|+.||++
T Consensus 40 ~~~~~~~~~~i~~~lgv~ 57 (58)
T TIGR03070 40 PTVRLDKVLRVLDALGLE 57 (58)
T ss_pred CCCCHHHHHHHHHHcCCC
Confidence 478999999999999986
No 19
>COG0027 PurT Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]
Probab=25.61 E-value=56 Score=29.53 Aligned_cols=21 Identities=5% Similarity=0.278 Sum_probs=18.9
Q ss_pred CCHHHHHHHHHHcCCceeEec
Q psy6932 44 PTYKDIDDVLSTTGLKYHIEN 64 (150)
Q Consensus 44 Pt~~EI~~A~~~Lgl~~~iE~ 64 (150)
=+++|+.+||.++||||++.+
T Consensus 136 ~s~~e~~~a~~~iGfPcvvKP 156 (394)
T COG0027 136 DSLEELRAAVEKIGFPCVVKP 156 (394)
T ss_pred ccHHHHHHHHHHcCCCeeccc
Confidence 378999999999999999875
No 20
>cd07245 Glo_EDI_BRP_like_9 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases.
Probab=25.40 E-value=1.3e+02 Score=19.43 Aligned_cols=44 Identities=16% Similarity=0.198 Sum_probs=28.7
Q ss_pred ccCCCCCHHHHHHHHHHcCCceeEecCCCCccccccCCCcceEEEEeecCCCCC
Q psy6932 39 KAVDNPTYKDIDDVLSTTGLKYHIENKLYPREISKEHFVRGRARVQLKNDDGSP 92 (150)
Q Consensus 39 ~aV~~Pt~~EI~~A~~~Lgl~~~iE~K~yPR~w~~d~~~~GRVrV~l~~~~G~~ 92 (150)
.|..-+.++++.+.+++.|+++..+... .| .++ .+.+.|.+|..
T Consensus 68 ~~~~v~d~~~~~~~l~~~g~~~~~~~~~---~~------~~~-~~~~~DP~G~~ 111 (114)
T cd07245 68 IAFRVDDLDAFRARLKAAGVPYTESDVP---GD------GVR-QLFVRDPDGNR 111 (114)
T ss_pred EEEEeCCHHHHHHHHHHcCCCcccccCC---CC------Ccc-EEEEECCCCCE
Confidence 3444456999999999999997665432 11 122 34567888753
No 21
>PHA01976 helix-turn-helix protein
Probab=25.05 E-value=69 Score=20.34 Aligned_cols=23 Identities=13% Similarity=0.190 Sum_probs=19.0
Q ss_pred cccCCCCCHHHHHHHHHHcCCce
Q psy6932 38 AKAVDNPTYKDIDDVLSTTGLKY 60 (150)
Q Consensus 38 ~~aV~~Pt~~EI~~A~~~Lgl~~ 60 (150)
+.....|+...+.++|+.||+++
T Consensus 36 e~g~~~p~~~~l~~ia~~l~v~~ 58 (67)
T PHA01976 36 EADKRLPNLKTLLRLADALGVTL 58 (67)
T ss_pred HcCCCCCCHHHHHHHHHHHCcCH
Confidence 34556799999999999999875
No 22
>KOG0683|consensus
Probab=24.94 E-value=1.1e+02 Score=27.71 Aligned_cols=56 Identities=21% Similarity=0.322 Sum_probs=39.4
Q ss_pred HHHHHHHcCCceeEecCCCCccccccCCCcceEEEEeecCCCCCCCCCCCCHH----HHHHHHHHHchhhhhccCCC
Q psy6932 49 IDDVLSTTGLKYHIENKLYPREISKEHFVRGRARVQLKNDDGSPVNPDFPTRE----AVMLHLGALIPKLKSRQGKQ 121 (150)
Q Consensus 49 I~~A~~~Lgl~~~iE~K~yPR~w~~d~~~~GRVrV~l~~~~G~~~~~~~~~K~----~Ll~~Ia~~I~~lrsR~~~~ 121 (150)
|.++|++.|+-+.+.+|-++-+|+ ..| +.-.|.+|. ..++.|++.|+++..|..-+
T Consensus 232 l~rVae~~Gviasf~pKp~~g~Wn----gaG-------------~Htn~ST~~mr~~~g~~~i~~a~~~ls~rh~~h 291 (380)
T KOG0683|consen 232 LHRVAEKFGVIASFDPKPILGDWN----GAG-------------CHTNFSTKEMREAGGLKIIEEAIPKLSKRHREH 291 (380)
T ss_pred HHHHHHHhCeeEEecCCCCCCccc----Ccc-------------cccccchhHHHhccCHHHHHHHhhhcchhhhhh
Confidence 678899999999999999999993 333 233333343 35778888888887765433
No 23
>cd08359 Glo_EDI_BRP_like_22 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=24.08 E-value=1.4e+02 Score=20.21 Aligned_cols=45 Identities=13% Similarity=0.169 Sum_probs=29.0
Q ss_pred ccCCCCCHHHHHHHHHHcCCceeEecCCCCccccccCCCcceEEEEeecCCCCC
Q psy6932 39 KAVDNPTYKDIDDVLSTTGLKYHIENKLYPREISKEHFVRGRARVQLKNDDGSP 92 (150)
Q Consensus 39 ~aV~~Pt~~EI~~A~~~Lgl~~~iE~K~yPR~w~~d~~~~GRVrV~l~~~~G~~ 92 (150)
.++.-..++++.+.+..+|.++..++...| | |-..+.+.|.+|..
T Consensus 70 ~~~~v~did~~~~~l~~~G~~~~~~~~~~~--~-------g~~~~~~~DP~G~~ 114 (119)
T cd08359 70 LNFEVDDVDAEYERLKAEGLPIVLPLRDEP--W-------GQRHFIVRDPNGVL 114 (119)
T ss_pred EEEEECCHHHHHHHHHhcCCCeeeccccCC--C-------cceEEEEECCCCCE
Confidence 333445699999999999998665544444 2 32233466888764
No 24
>COG0602 NrdG Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=23.96 E-value=85 Score=25.54 Aligned_cols=28 Identities=18% Similarity=0.345 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHcCCceeEec-CCCCccc
Q psy6932 44 PTYKDIDDVLSTTGLKYHIEN-KLYPREI 71 (150)
Q Consensus 44 Pt~~EI~~A~~~Lgl~~~iE~-K~yPR~w 71 (150)
|.+.++.+.++.+|+++.+|. ..+|..|
T Consensus 86 ~~l~~Ll~~l~~~g~~~~lETngti~~~~ 114 (212)
T COG0602 86 PNLLELLELLKRLGFRIALETNGTIPVWT 114 (212)
T ss_pred ccHHHHHHHHHhCCceEEecCCCCccccc
Confidence 478999999999999999996 9999876
No 25
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=23.76 E-value=82 Score=19.10 Aligned_cols=19 Identities=16% Similarity=0.363 Sum_probs=17.1
Q ss_pred CCCCHHHHHHHHHHcCCce
Q psy6932 42 DNPTYKDIDDVLSTTGLKY 60 (150)
Q Consensus 42 ~~Pt~~EI~~A~~~Lgl~~ 60 (150)
..|+..++.+.+..+||+.
T Consensus 23 ~~P~~~~~~~la~~~~l~~ 41 (56)
T smart00389 23 PYPSREEREELAAKLGLSE 41 (56)
T ss_pred CCCCHHHHHHHHHHHCcCH
Confidence 4799999999999999974
No 26
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=23.61 E-value=90 Score=22.19 Aligned_cols=21 Identities=38% Similarity=0.545 Sum_probs=18.6
Q ss_pred CCCCHHHHHHHHHHcCCceeE
Q psy6932 42 DNPTYKDIDDVLSTTGLKYHI 62 (150)
Q Consensus 42 ~~Pt~~EI~~A~~~Lgl~~~i 62 (150)
.+|++.-|..+|+.||++..|
T Consensus 68 ~~Ps~~tL~kI~~aLgi~l~v 88 (89)
T TIGR02684 68 GNPTFDTILKVTKALGLKLTA 88 (89)
T ss_pred CCCCHHHHHHHHHHcCCceee
Confidence 489999999999999998754
No 27
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=23.34 E-value=51 Score=24.27 Aligned_cols=24 Identities=17% Similarity=0.220 Sum_probs=16.5
Q ss_pred CCCCCHHHHHHHHHHcCCceeEec
Q psy6932 41 VDNPTYKDIDDVLSTTGLKYHIEN 64 (150)
Q Consensus 41 V~~Pt~~EI~~A~~~Lgl~~~iE~ 64 (150)
-..|...++.++|+++||.++.-+
T Consensus 41 ~~qp~~~~~~~~a~~~Gl~y~~iP 64 (110)
T PF04273_consen 41 PGQPSSAEEAAAAEALGLQYVHIP 64 (110)
T ss_dssp TT-T-HHCHHHHHHHCT-EEEE--
T ss_pred CCCCCHHHHHHHHHHcCCeEEEee
Confidence 346899999999999999987544
No 28
>PRK09726 antitoxin HipB; Provisional
Probab=22.76 E-value=1.2e+02 Score=20.90 Aligned_cols=32 Identities=22% Similarity=0.160 Sum_probs=23.9
Q ss_pred cCCCCCHHHHHHHHHHcCCceeEe-cCCCCccc
Q psy6932 40 AVDNPTYKDIDDVLSTTGLKYHIE-NKLYPREI 71 (150)
Q Consensus 40 aV~~Pt~~EI~~A~~~Lgl~~~iE-~K~yPR~w 71 (150)
....|++..|..+|..||++..+- ...+.-+|
T Consensus 48 g~~~ps~~~l~~ia~~lgv~~~~~~~~~~~~~~ 80 (88)
T PRK09726 48 NPDNTTLTTFFKILQSLELSMTLCDAKNASPES 80 (88)
T ss_pred CCCCCCHHHHHHHHHHcCCCcchhcccCCCCCc
Confidence 445799999999999999997653 24444465
No 29
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=22.59 E-value=79 Score=21.51 Aligned_cols=19 Identities=21% Similarity=0.364 Sum_probs=16.5
Q ss_pred CCCCHHHHHHHHHHcCCce
Q psy6932 42 DNPTYKDIDDVLSTTGLKY 60 (150)
Q Consensus 42 ~~Pt~~EI~~A~~~Lgl~~ 60 (150)
..|++.||..|+..+|++.
T Consensus 57 ~~~~~~Dv~~Al~~~gi~~ 75 (77)
T smart00576 57 TEPNLGDVVLALENLGISV 75 (77)
T ss_pred CCCCHHHHHHHHHHhCccc
Confidence 3689999999999999863
No 30
>PRK06724 hypothetical protein; Provisional
Probab=22.01 E-value=1.8e+02 Score=21.12 Aligned_cols=43 Identities=14% Similarity=0.205 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHcCCceeEecCCCCccccccCCCcceEEEEeecCCCCC
Q psy6932 44 PTYKDIDDVLSTTGLKYHIENKLYPREISKEHFVRGRARVQLKNDDGSP 92 (150)
Q Consensus 44 Pt~~EI~~A~~~Lgl~~~iE~K~yPR~w~~d~~~~GRVrV~l~~~~G~~ 92 (150)
-.++++.+.+.+.|+++..++..+|. ...|.-.+.+.|.||..
T Consensus 75 ~dvd~~~~~l~~~G~~~~~~p~~~~~------~~~g~~~~~f~DPdG~~ 117 (128)
T PRK06724 75 KVVDEVAEFLSSTKIKIIRGPMEMNH------YSEGYYTIDFYDPNGFI 117 (128)
T ss_pred HHHHHHHHHHHHCCCEEecCCcccCC------CCCCEEEEEEECCCCCE
Confidence 45778888888899987666543331 12454556677888874
No 31
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=21.85 E-value=1e+02 Score=27.06 Aligned_cols=62 Identities=21% Similarity=0.348 Sum_probs=42.7
Q ss_pred CCHHHHHHHHHHcCCceeEec--CCCCccccc-----------cCCCcceEEEEeecCCCCCCCCCCCCHHHHHHHHHH
Q psy6932 44 PTYKDIDDVLSTTGLKYHIEN--KLYPREISK-----------EHFVRGRARVQLKNDDGSPVNPDFPTREAVMLHLGA 109 (150)
Q Consensus 44 Pt~~EI~~A~~~Lgl~~~iE~--K~yPR~w~~-----------d~~~~GRVrV~l~~~~G~~~~~~~~~K~~Ll~~Ia~ 109 (150)
-|+.+|++|..+-.++..+++ ..-+=.-++ .+.+-||..|. |.+|.|+ -+-+|..+|..||-
T Consensus 218 it~~dI~~aia~g~~~~kV~~~M~k~vitI~eDe~i~dAir~M~~~nVGRLlV~--ds~gkpv--GiITrTDIL~~ia~ 292 (294)
T COG2524 218 ITLSDIAKAIANGNLDAKVSDYMRKNVITINEDEDIYDAIRLMNKNNVGRLLVT--DSNGKPV--GIITRTDILTRIAG 292 (294)
T ss_pred EEHHHHHHHHHcCCccccHHHHhccCCceEcCchhHHHHHHHHHhcCcceEEEE--ccCCcEE--EEEehHHHHHHhhc
Confidence 478899999998877766654 332222111 33678999995 6677763 35689999999984
No 32
>PF02382 RTX: RTX N-terminal domain; InterPro: IPR018504 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior []. Four principal exotoxin secretion systems have been described. In the type II and IV secretion systems, toxins are first exported to the periplasm by way of a cleaved N-terminal signal sequence; a second set of proteins is used for extracellular transport (type II), or the C terminus of the exotoxin itself is used (type IV). Type III secretion involves at least 20 molecules that assemble into a needle; effector proteins are then translocated through this without need of a signal sequence. In the Type I system, a complete channel is formed through both membranes, and the secretion signal is carried on the C terminus of the exotoxin. The RTX (repeats in toxin) family of cytolytic toxins belong to the Type I secretion system, and are important virulence factors in Gram-negative bacteria. As well as the C-terminal signal sequence, several glycine-rich repeats are also found. These are essential for binding calcium, and are critical for the biological activity of the secreted toxins []. All RTX toxin operons exist in the order rtxCABD, RtxA protein being the structural component of the exotoxin, both RtxB and D being required for its export from the bacterial cell; RtxC is an acyl-carrier-protein-dependent acyl- modification enzyme, required to convert RtxA to its active form []. Escherichia coli haemolysin (HlyA) is often quoted as the model for RTX toxins. Recent work on its relative rtxC gene product HlyC [] has revealed that it provides the acylation aspect for post-translational modification of two internal lysine residues in the HlyA protein. To cause pathogenicity, the HlyA toxin must first bind Ca2+ ions to the set of glycine-rich repeats and then be activated by HlyC []. This has been demonstrated both in vitro and in vivo. A number of the sequences in this family are metallopeptidases belonging to MEROPS peptidase family M10 (clan MA(M)), subfamily M10B: serralysin, epralysin and unassigned peptidases.; GO: 0005509 calcium ion binding, 0009405 pathogenesis, 0005576 extracellular region
Probab=21.57 E-value=92 Score=30.08 Aligned_cols=37 Identities=16% Similarity=0.205 Sum_probs=30.0
Q ss_pred ccccccC-CCCCHHHHHHHHHHcCCceeEecCCCCccc
Q psy6932 35 IPKAKAV-DNPTYKDIDDVLSTTGLKYHIENKLYPREI 71 (150)
Q Consensus 35 V~k~~aV-~~Pt~~EI~~A~~~Lgl~~~iE~K~yPR~w 71 (150)
|||++=. .--.+.|+++|+.+||+++.-|++-.+..-
T Consensus 49 IPKdYd~~~GngLndLVKAAdeLGIev~~eern~~a~A 86 (653)
T PF02382_consen 49 IPKDYDASQGNGLNDLVKAADELGIEVQREERNGTATA 86 (653)
T ss_pred cccccccccCccHHHHHHHHHHcCceeeeecCCcHHHH
Confidence 5666443 455899999999999999999998888764
No 33
>cd08794 Death_IRAK1 Death domain of Interleukin 1 Receptor Associated Kinase-1. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 1 (IRAK1). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK1 is an active kinase and also plays adaptor functions. It binds to the MyD88-IRAK4 complex via its DD, which facilitates its phosphorylation by IRAK4, activating it for further auto-phosphorylation. Hyper-phosphorylated IRAK1 forms a cytosolic complex with TRAF6, leading to the activation of NF-kB and MAPK pathways. IRAK1 is involved in autoimmunity and may be associated with lupus pathogenesis. DDs are protein-protein interaction domains found in a variety of domain architectures.
Probab=21.43 E-value=56 Score=23.67 Aligned_cols=20 Identities=20% Similarity=0.149 Sum_probs=17.9
Q ss_pred ccCCCCCHHHHHHHHHHcCC
Q psy6932 39 KAVDNPTYKDIDDVLSTTGL 58 (150)
Q Consensus 39 ~aV~~Pt~~EI~~A~~~Lgl 58 (150)
=+..|+|+.|+.++++.|++
T Consensus 57 W~~Rn~tV~~Ll~iL~~L~l 76 (84)
T cd08794 57 WENRNGRVGELLDILERLQL 76 (84)
T ss_pred HHhcccHHHHHHHHHHHhhh
Confidence 36789999999999999987
No 34
>COG2313 IndA Uncharacterized enzyme involved in pigment biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.33 E-value=87 Score=27.45 Aligned_cols=34 Identities=26% Similarity=0.541 Sum_probs=25.9
Q ss_pred eeccccCCcCccccccccccccCCCCCHHHHHHHHH---HcCCce
Q psy6932 19 YPAYINRKKTLAEGRRIPKAKAVDNPTYKDIDDVLS---TTGLKY 60 (150)
Q Consensus 19 YP~Y~Ds~~sr~eGRRV~k~~aV~~Pt~~EI~~A~~---~Lgl~~ 60 (150)
+|++| ||+.|+++|...- +.+||+++.. +|||+.
T Consensus 192 fPaF~----sR~Sg~~~pl~l~----~pe~ia~~~~t~~~lgleg 228 (310)
T COG2313 192 FPAFF----SRESGFRVPLRLE----SPEEIARILATKWQLGLEG 228 (310)
T ss_pred ccchh----cccCCCcCccccC----CHHHHHHHHHHHHHhCCCC
Confidence 56665 7889999997765 6678887775 788875
No 35
>COG1828 PurS Phosphoribosylformylglycinamidine (FGAM) synthase, PurS component [Nucleotide transport and metabolism]
Probab=21.30 E-value=87 Score=22.52 Aligned_cols=59 Identities=14% Similarity=0.148 Sum_probs=37.6
Q ss_pred ccccccCCCCCHHHHHHHHHHcCCceeEecCCCCccccccCCCcceEEEEeecCCCCCCCCCCCCHHHHHHHHHHHc
Q psy6932 35 IPKAKAVDNPTYKDIDDVLSTTGLKYHIENKLYPREISKEHFVRGRARVQLKNDDGSPVNPDFPTREAVMLHLGALI 111 (150)
Q Consensus 35 V~k~~aV~~Pt~~EI~~A~~~Lgl~~~iE~K~yPR~w~~d~~~~GRVrV~l~~~~G~~~~~~~~~K~~Ll~~Ia~~I 111 (150)
|.....|-+|.-+-|..|+..||++-+-+- ...=++.+.+..++- ..=.+.++.||+.|
T Consensus 8 V~lK~~VlDPqG~ti~~aL~~lg~~~V~~v-----------R~gK~~el~ld~~~~-------e~a~~~v~~mcekL 66 (83)
T COG1828 8 VTLKPGVLDPEGETIEKALHRLGYNEVSDV-----------RVGKVIELELDAESE-------EKAEEEVKEMCEKL 66 (83)
T ss_pred EEeCCcccCchhHHHHHHHHHcCCccccee-----------eeeeEEEEEecCcch-------hHHHHHHHHHHHHH
Confidence 455678999999999999999999844331 122234455543221 12346777888765
No 36
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=21.30 E-value=48 Score=25.07 Aligned_cols=54 Identities=26% Similarity=0.316 Sum_probs=31.7
Q ss_pred cccccccccccCC---------CCCHHHHHHHHHHcCCceeEecCCCCccccc--cCCCcceEEEEee
Q psy6932 30 AEGRRIPKAKAVD---------NPTYKDIDDVLSTTGLKYHIENKLYPREISK--EHFVRGRARVQLK 86 (150)
Q Consensus 30 ~eGRRV~k~~aV~---------~Pt~~EI~~A~~~Lgl~~~iE~K~yPR~w~~--d~~~~GRVrV~l~ 86 (150)
.-||.||+++||. .-.+.||.+|+-.-++. -+|.|=..||. =.-+.+=|+|...
T Consensus 25 nCgr~vPKDKAIkrf~irniVe~aa~rDl~~a~v~~~y~---lPKly~k~~YCVSCAIH~~iVRvRs~ 89 (108)
T PTZ00172 25 NCGRCVPKDKAIKRFVVRNIVDAASVRDIAEASVYYGYP---LPKLYMKQQYCVSCAIHSRVVRVRSR 89 (108)
T ss_pred CccccccccceEEEEeccCCccHHHHHHHHHhhchhccc---cccceeeeEEeeehhhcCCeeecCCh
Confidence 3589999999964 34567777776643321 14555544432 1135677777543
No 37
>KOG3802|consensus
Probab=20.68 E-value=86 Score=28.61 Aligned_cols=22 Identities=18% Similarity=0.344 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHHHHHcCCceeE
Q psy6932 41 VDNPTYKDIDDVLSTTGLKYHI 62 (150)
Q Consensus 41 V~~Pt~~EI~~A~~~Lgl~~~i 62 (150)
+..|+.+||.+++.+|+|+=+|
T Consensus 316 npKPt~qEIt~iA~~L~leKEV 337 (398)
T KOG3802|consen 316 NPKPTSQEITHIAESLQLEKEV 337 (398)
T ss_pred CCCCCHHHHHHHHHHhccccce
Confidence 5789999999999999997443
No 38
>COG0107 HisF Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]
Probab=20.36 E-value=65 Score=27.73 Aligned_cols=73 Identities=14% Similarity=0.174 Sum_probs=46.6
Q ss_pred cccccc-ccCCCCCHHHHHHHHHHcCCceeEe--c-CCCC---ccccccCCCc---------------------ceEEEE
Q psy6932 33 RRIPKA-KAVDNPTYKDIDDVLSTTGLKYHIE--N-KLYP---REISKEHFVR---------------------GRARVQ 84 (150)
Q Consensus 33 RRV~k~-~aV~~Pt~~EI~~A~~~Lgl~~~iE--~-K~yP---R~w~~d~~~~---------------------GRVrV~ 84 (150)
-|||.+ .||.||.+ |.+++..+|-.|++- + |+-| ..||+=|.+. |.|.+.
T Consensus 98 DKVSINsaAv~~p~l--I~~~a~~FGsQciVvaIDakr~~~g~~~~~~v~~~gGr~~t~~d~~~Wa~~~e~~GAGEIlLt 175 (256)
T COG0107 98 DKVSINSAAVKDPEL--ITEAADRFGSQCIVVAIDAKRVPDGENGWYEVFTHGGREDTGLDAVEWAKEVEELGAGEILLT 175 (256)
T ss_pred CeeeeChhHhcChHH--HHHHHHHhCCceEEEEEEeeeccCCCCCcEEEEecCCCcCCCcCHHHHHHHHHHcCCceEEEe
Confidence 567776 67999975 889999999999754 4 6654 3355422222 556666
Q ss_pred eecCCCCCCCCCCCCHHHHHHHHHHHc
Q psy6932 85 LKNDDGSPVNPDFPTREAVMLHLGALI 111 (150)
Q Consensus 85 l~~~~G~~~~~~~~~K~~Ll~~Ia~~I 111 (150)
.-|.||+-. .==..|++.|++.+
T Consensus 176 smD~DGtk~----GyDl~l~~~v~~~v 198 (256)
T COG0107 176 SMDRDGTKA----GYDLELTRAVREAV 198 (256)
T ss_pred eeccccccc----CcCHHHHHHHHHhC
Confidence 556666521 11247788887764
No 39
>PF14830 Haemocyan_bet_s: Haemocyanin beta-sandwich; PDB: 1JS8_B 3QJO_A 1LNL_A.
Probab=20.32 E-value=1.1e+02 Score=22.83 Aligned_cols=38 Identities=24% Similarity=0.277 Sum_probs=24.4
Q ss_pred CHHHHHHHHHHcCCceeEecCCCCccccccCCCcceEEEEeecCCCCCCCCCC
Q psy6932 45 TYKDIDDVLSTTGLKYHIENKLYPREISKEHFVRGRARVQLKNDDGSPVNPDF 97 (150)
Q Consensus 45 t~~EI~~A~~~Lgl~~~iE~K~yPR~w~~d~~~~GRVrV~l~~~~G~~~~~~~ 97 (150)
---||.+++++|||+ + ...=.|+|++.+-||+.+.+.+
T Consensus 56 ykydIT~~l~~l~l~-----------~----~~~f~i~~~i~~~nGt~l~~~~ 93 (103)
T PF14830_consen 56 YKYDITDALKKLGLH-----------Y----DDPFHIKVEITAVNGTELPSDI 93 (103)
T ss_dssp EEEE-HHHHHHCT-------------T----TSSEEEEEEEEESSSSBE-CCC
T ss_pred chhhHHHHHHHcCCC-----------C----CCCEEEEEEEEecCCCCCcccc
Confidence 335899999999998 1 1333678888888998876653
Done!