Query psy13098
Match_columns 81
No_of_seqs 120 out of 426
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 19:28:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13098.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13098hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0467|consensus 100.0 9.4E-36 2E-40 247.4 3.2 80 1-80 808-887 (887)
2 KOG0469|consensus 99.7 9.3E-18 2E-22 137.7 3.6 58 2-77 785-842 (842)
3 KOG0468|consensus 99.6 4.9E-17 1.1E-21 135.9 2.6 63 1-67 886-948 (971)
4 PTZ00416 elongation factor 2; 99.6 1E-15 2.3E-20 127.8 4.3 57 1-75 778-834 (836)
5 PLN00116 translation elongatio 99.6 1.4E-15 3.1E-20 126.9 4.2 59 1-77 785-843 (843)
6 PRK07560 elongation factor EF- 98.9 6.2E-10 1.3E-14 91.9 3.3 49 1-73 681-729 (731)
7 TIGR00490 aEF-2 translation el 98.8 4E-09 8.6E-14 87.2 3.2 41 1-63 679-719 (720)
8 COG0480 FusA Translation elong 97.8 1.8E-05 3.8E-10 66.5 2.8 38 2-61 660-697 (697)
9 smart00838 EFG_C Elongation fa 97.2 0.0001 2.2E-09 45.8 0.8 25 2-26 60-84 (85)
10 TIGR00484 EF-G translation elo 96.6 0.00043 9.4E-09 57.1 -0.3 25 2-26 657-681 (689)
11 PF00679 EFG_C: Elongation fac 96.5 0.0004 8.6E-09 43.6 -1.1 25 2-26 62-86 (89)
12 PRK12739 elongation factor G; 96.5 0.00073 1.6E-08 55.9 0.1 23 2-24 657-679 (691)
13 PRK13351 elongation factor G; 96.4 0.00067 1.5E-08 55.8 -0.3 25 2-26 657-681 (687)
14 PRK12740 elongation factor G; 96.3 0.00081 1.8E-08 55.0 -0.5 25 2-26 639-663 (668)
15 PRK00007 elongation factor G; 96.0 0.0022 4.8E-08 53.2 0.4 24 2-25 660-683 (693)
16 PRK10218 GTP-binding protein; 64.5 3.8 8.2E-05 34.3 1.4 23 2-24 456-479 (607)
17 COG4851 CamS Protein involved 62.5 6.2 0.00013 31.6 2.2 37 21-62 187-224 (382)
18 TIGR01394 TypA_BipA GTP-bindin 62.4 4.4 9.5E-05 33.7 1.4 23 2-24 452-474 (594)
19 cd08325 CARD_CASP1-like Caspas 57.1 9.1 0.0002 23.9 1.9 29 30-58 31-60 (83)
20 cd02164 PPAT_CoAS phosphopante 55.0 6.2 0.00013 27.0 1.0 48 17-65 71-119 (143)
21 PRK05433 GTP-binding protein L 55.0 5.5 0.00012 33.1 0.8 20 2-21 462-481 (600)
22 TIGR01393 lepA GTP-binding pro 53.6 6.3 0.00014 32.7 0.9 19 2-20 459-477 (595)
23 COG2176 PolC DNA polymerase II 47.6 21 0.00045 33.2 3.2 31 43-80 1223-1253(1444)
24 PF07537 CamS: CamS sex pherom 47.3 8.1 0.00017 30.2 0.6 41 17-62 123-164 (319)
25 PF07421 Pro-NT_NN: Neurotensi 45.2 7.1 0.00015 28.3 0.0 15 14-28 114-128 (169)
26 PF10041 DUF2277: Uncharacteri 41.2 33 0.00071 22.0 2.6 21 26-55 11-31 (78)
27 PF12544 LAM_C: Lysine-2,3-ami 40.2 15 0.00033 25.5 1.0 16 1-16 4-19 (127)
28 PRK05473 hypothetical protein; 33.8 43 0.00094 21.8 2.3 23 20-56 46-68 (86)
29 PF07368 DUF1487: Protein of u 33.5 42 0.00092 25.0 2.5 35 44-79 42-76 (215)
30 PF04552 Sigma54_DBD: Sigma-54 32.9 39 0.00084 23.8 2.2 35 28-63 120-154 (160)
31 cd01671 CARD Caspase activatio 32.6 41 0.00088 19.7 2.0 30 30-60 28-57 (80)
32 PF07980 SusD: SusD family; I 32.2 44 0.00095 23.0 2.3 19 47-65 151-169 (266)
33 COG0813 DeoD Purine-nucleoside 31.6 28 0.0006 26.5 1.3 7 20-26 18-24 (236)
34 cd08329 CARD_BIRC2_BIRC3 Caspa 31.5 49 0.0011 21.1 2.3 30 30-60 38-67 (94)
35 PF06135 DUF965: Bacterial pro 30.7 48 0.001 21.3 2.1 23 20-56 43-65 (79)
36 PF00486 Trans_reg_C: Transcri 29.7 71 0.0015 18.2 2.7 32 29-60 24-58 (77)
37 PF13779 DUF4175: Domain of un 29.3 56 0.0012 28.7 2.9 39 22-60 761-803 (820)
38 PF06820 Phage_fiber_C: Putati 29.3 28 0.00061 21.5 0.8 18 11-28 41-58 (64)
39 PF15332 LIME1: Lck-interactin 28.8 37 0.00081 25.6 1.6 49 12-61 89-145 (228)
40 PF10937 DUF2638: Protein of u 28.1 28 0.0006 23.4 0.7 24 13-37 83-106 (112)
41 cd06909 M14_ASPA Aspartoacylas 27.9 17 0.00036 27.6 -0.4 22 10-31 226-248 (282)
42 PLN02388 phosphopantetheine ad 27.5 30 0.00065 24.8 0.9 47 18-65 92-139 (177)
43 COG1015 DeoB Phosphopentomutas 27.0 56 0.0012 26.6 2.4 40 16-63 88-127 (397)
44 PF11267 DUF3067: Protein of u 26.9 31 0.00067 23.0 0.8 53 5-62 23-82 (99)
45 PF00619 CARD: Caspase recruit 26.2 53 0.0012 19.4 1.7 29 30-58 31-59 (85)
46 TIGR03875 RNA_lig_partner RNA 25.7 31 0.00068 25.7 0.7 26 44-69 89-116 (206)
47 cd08330 CARD_ASC_NALP1 Caspase 24.8 74 0.0016 19.7 2.2 30 30-60 30-59 (82)
48 PRK04358 hypothetical protein; 23.8 25 0.00054 26.4 -0.1 29 44-72 93-123 (217)
49 PTZ00069 60S ribosomal protein 22.5 71 0.0015 25.2 2.1 46 5-53 56-101 (300)
50 PF08745 UPF0278: UPF0278 fami 22.4 29 0.00063 25.9 0.0 28 44-71 89-118 (205)
51 PF13758 Prefoldin_3: Prefoldi 21.6 1.4E+02 0.003 19.9 3.1 29 30-58 47-76 (99)
52 PLN02882 aminoacyl-tRNA ligase 21.5 84 0.0018 28.5 2.6 24 46-69 995-1021(1159)
53 PF01667 Ribosomal_S27e: Ribos 20.5 41 0.00088 20.1 0.4 19 2-20 7-25 (55)
No 1
>KOG0467|consensus
Probab=100.00 E-value=9.4e-36 Score=247.38 Aligned_cols=80 Identities=54% Similarity=0.850 Sum_probs=78.3
Q ss_pred CCcccCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCcccccCcchhhHHhhhhc
Q psy13098 1 MNLCCRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPVQDKLVAHAEKQRTVKRN 80 (81)
Q Consensus 1 ~~~~T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~~ekiv~~aekqr~L~k~ 80 (81)
||-.|||.|+|||+||||++++.||||+|+|+||+++||+++|..|+||.||++|||||||.++||||++|||||||+||
T Consensus 808 iRK~TSG~A~pQLvFShwEvId~DPFWvPtTEEEleefGekADs~N~ArkYMdaVRRRKGLfVEEkIVE~AEKQRTLkkn 887 (887)
T KOG0467|consen 808 IRKGTSGAASPQLVFSHWEVIDEDPFWVPTTEEELEEFGEKADSENIARKYMDAVRRRKGLFVEEKIVEHAEKQRTLKKN 887 (887)
T ss_pred HhhccccccchhhhccccEEecCCCccCCCcHHHHHHhhhcccchhHHHHHHHHHHhhcCCchHHHHhhhHHhhcccccC
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999998
No 2
>KOG0469|consensus
Probab=99.69 E-value=9.3e-18 Score=137.73 Aligned_cols=58 Identities=21% Similarity=0.261 Sum_probs=55.3
Q ss_pred CcccCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCcccccCcchhhHHhh
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPVQDKLVAHAEKQRTV 77 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~~ekiv~~aekqr~L 77 (81)
|..|+|||||||+||||++|||||+ ++.|.+.++|..+|||||| +|.++...+|.++|
T Consensus 785 rs~t~GqAfpq~vFdHws~lpgdp~----------------dp~sk~~~iV~~~RKrkgl--ke~~P~~~~y~Dkl 842 (842)
T KOG0469|consen 785 RSNTGGQAFPQMVFDHWSILPGDPL----------------DPTSKPGQIVLATRKRKGL--KEGVPDLDEYLDKL 842 (842)
T ss_pred hcccCCccccceeeeccccCCCCCC----------------CCCccchHHHHHHHHhcCC--CCCCCChHHHhhcC
Confidence 6789999999999999999999999 7899999999999999999 89999999999876
No 3
>KOG0468|consensus
Probab=99.65 E-value=4.9e-17 Score=135.89 Aligned_cols=63 Identities=22% Similarity=0.300 Sum_probs=55.2
Q ss_pred CCcccCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCccccc
Q psy13098 1 MNLCCRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPVQDKL 67 (81)
Q Consensus 1 ~~~~T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~~eki 67 (81)
.|++|+||||||++|+||++|||||++... .....+|++.+++||+||.++||||||.++..+
T Consensus 886 LR~hTqGqa~C~~vF~HW~~VPGDpLDKsi----~i~~Lep~p~~~LaReFmiKTRRRKGlsedvS~ 948 (971)
T KOG0468|consen 886 LRVHTQGQAFCLSVFDHWRIVPGDPLDKSI----AIRPLEPAPIRHLAREFMIKTRRRKGLSEDVSI 948 (971)
T ss_pred eeeeccchhHHHHhhhhcccCCCCcccccc----ccccCCCCCcchhHHHHHHHhhhhccccccccc
Confidence 378999999999999999999999998643 344678999999999999999999999877544
No 4
>PTZ00416 elongation factor 2; Provisional
Probab=99.58 E-value=1e-15 Score=127.77 Aligned_cols=57 Identities=25% Similarity=0.308 Sum_probs=47.8
Q ss_pred CCcccCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCcccccCcchhhHH
Q psy13098 1 MNLCCRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPVQDKLVAHAEKQR 75 (81)
Q Consensus 1 ~~~~T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~~ekiv~~aekqr 75 (81)
+|..|+|+|++++.||||+.||+||| +.+|+||+||++||+||||+ +++|.+.++-+
T Consensus 778 LRs~T~G~g~~~~~F~~y~~vp~dp~----------------~~~~~a~~~~~~~R~rKGl~--~~~~~~~~~~~ 834 (836)
T PTZ00416 778 LRAATSGQAFPQCVFDHWQVVPGDPL----------------EPGSKANEIVLSIRKRKGLK--PEIPDLDNYLD 834 (836)
T ss_pred HHhhCcCCceEEEEeccEEECCCCCC----------------CchhHHHHHHHHHHHhCCCC--CCCCCHHHhcc
Confidence 47899999999999999999999999 45799999999999999994 44654444433
No 5
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=99.57 E-value=1.4e-15 Score=126.94 Aligned_cols=59 Identities=20% Similarity=0.396 Sum_probs=53.0
Q ss_pred CCcccCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCcccccCcchhhHHhh
Q psy13098 1 MNLCCRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPVQDKLVAHAEKQRTV 77 (81)
Q Consensus 1 ~~~~T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~~ekiv~~aekqr~L 77 (81)
.|..|+|+|++++.||||+.||+||| +.+|+|++||++||+|||| .+++|.+.+|-++|
T Consensus 785 LRs~T~G~g~~~~~f~~y~~v~~dp~----------------~~~~~a~~~~~~~R~rKGl--~~~~~~~~~~~d~~ 843 (843)
T PLN00116 785 LRAATSGQAFPQCVFDHWDMMSSDPL----------------EAGSQAAQLVADIRKRKGL--KEQMPPLSEYEDKL 843 (843)
T ss_pred HHhhCCCCCeEEEEeceeEECCCCCC----------------CchhHHHHHHHHHHhhCCC--CCCCCCHHHhcccC
Confidence 37789999999999999999999999 4589999999999999999 57799888887764
No 6
>PRK07560 elongation factor EF-2; Reviewed
Probab=98.93 E-value=6.2e-10 Score=91.93 Aligned_cols=49 Identities=18% Similarity=0.191 Sum_probs=42.0
Q ss_pred CCcccCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCcccccCcchhh
Q psy13098 1 MNLCCRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPVQDKLVAHAEK 73 (81)
Q Consensus 1 ~~~~T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~~ekiv~~aek 73 (81)
.|..|+|+|++++.||||+.||+ |.|+++|.++|+|||| .++|+.+.++
T Consensus 681 Lrs~T~G~~~~~~~f~~y~~v~~----------------------~~~~~ii~~~r~rKGl--~~~~~~~~~~ 729 (731)
T PRK07560 681 IRSATEGRALWSTEFAGFEPVPD----------------------SLQLDIVRQIRERKGL--KPELPKPEDF 729 (731)
T ss_pred HHhhCcCCceEEEEeccceeCCH----------------------HHHHHHHHHHHhhCCC--CCCCCChhhh
Confidence 36789999999999999999972 5799999999999999 4677766554
No 7
>TIGR00490 aEF-2 translation elongation factor aEF-2. This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.
Probab=98.77 E-value=4e-09 Score=87.17 Aligned_cols=41 Identities=24% Similarity=0.286 Sum_probs=36.7
Q ss_pred CCcccCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCc
Q psy13098 1 MNLCCRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPV 63 (81)
Q Consensus 1 ~~~~T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~ 63 (81)
+|..|+|+|++++.||||+.+|+ +.++++|.++|+||||+.
T Consensus 679 Lrs~T~G~a~~~~~f~~y~~vp~----------------------~~~~~ii~~~r~rkgl~~ 719 (720)
T TIGR00490 679 IRGATSGRCLWSTEHAGFELVPQ----------------------NLQQEFVMEVRKRKGLKL 719 (720)
T ss_pred HHhhCCCCceEEEEecccccCCH----------------------HHHHHHHHHHHhhcCCCC
Confidence 37789999999999999999972 479999999999999975
No 8
>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]
Probab=97.75 E-value=1.8e-05 Score=66.47 Aligned_cols=38 Identities=24% Similarity=0.290 Sum_probs=35.3
Q ss_pred CcccCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGL 61 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL 61 (81)
|..|+|.|++++.||||+.+| .|.|.+++.++|+|||+
T Consensus 660 Rs~T~Gra~~~m~f~~y~~vp----------------------~~~a~~ii~~~~~~~~~ 697 (697)
T COG0480 660 RSATQGRASFSMEFDHYEEVP----------------------SSVAEEIIAKRRKRKGL 697 (697)
T ss_pred HhhcCCceeEEEEecccEeCC----------------------HHHHHHHHHHhhhhcCC
Confidence 788999999999999999887 57899999999999996
No 9
>smart00838 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
Probab=97.25 E-value=0.0001 Score=45.76 Aligned_cols=25 Identities=8% Similarity=-0.000 Sum_probs=22.2
Q ss_pred CcccCCcceeeceeccceecCCCCC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINIDPY 26 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gDP~ 26 (81)
|..|+|.|+.++.|+||+.+++|+.
T Consensus 60 rs~T~G~~~~~~~f~~y~~~~~~~~ 84 (85)
T smart00838 60 RSATQGRATWSMEFSHYEEVPKSIA 84 (85)
T ss_pred HHhcCCeEEEEEEeCcceECChhhc
Confidence 5789999999999999999997653
No 10
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=96.62 E-value=0.00043 Score=57.14 Aligned_cols=25 Identities=8% Similarity=-0.020 Sum_probs=22.8
Q ss_pred CcccCCcceeeceeccceecCCCCC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINIDPY 26 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gDP~ 26 (81)
|..|+|+|++++.||||+.+|+|++
T Consensus 657 rs~T~G~~~~~~~f~~y~~v~~~~~ 681 (689)
T TIGR00484 657 RSFTQGRGTYSMEFLHYGEVPSSVA 681 (689)
T ss_pred HHhcCCceEEEEEeccceeCCHHHH
Confidence 6789999999999999999998765
No 11
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=96.49 E-value=0.0004 Score=43.59 Aligned_cols=25 Identities=12% Similarity=-0.049 Sum_probs=21.7
Q ss_pred CcccCCcceeeceeccceecCCCCC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINIDPY 26 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gDP~ 26 (81)
|..|+|+|..++.|+||+.+++|++
T Consensus 62 r~~T~G~a~~~~~~~~y~~~~~~~~ 86 (89)
T PF00679_consen 62 RSLTSGRASFSMEFSGYRPVPGDIL 86 (89)
T ss_dssp HHHTTTS-EEEEEEEEEEEESHHHH
T ss_pred hccCCCEEEEEEEECeeEECCCChh
Confidence 5679999999999999999998875
No 12
>PRK12739 elongation factor G; Reviewed
Probab=96.48 E-value=0.00073 Score=55.90 Aligned_cols=23 Identities=9% Similarity=0.052 Sum_probs=20.8
Q ss_pred CcccCCcceeeceeccceecCCC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINID 24 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gD 24 (81)
|..|+|+|++++.||||+.+|++
T Consensus 657 r~~T~G~a~~~~~f~~y~~v~~~ 679 (691)
T PRK12739 657 RSATQGRATFSMEFDHYEEVPKN 679 (691)
T ss_pred HhhccCceEEEEEeccceECCHH
Confidence 67899999999999999999853
No 13
>PRK13351 elongation factor G; Reviewed
Probab=96.43 E-value=0.00067 Score=55.77 Aligned_cols=25 Identities=12% Similarity=-0.031 Sum_probs=23.0
Q ss_pred CcccCCcceeeceeccceecCCCCC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINIDPY 26 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gDP~ 26 (81)
|..|+|+|++++.||||+.+++|++
T Consensus 657 rs~T~G~a~~~~~f~~y~~v~~~~~ 681 (687)
T PRK13351 657 RSMTKGRGSFTMEFSHFDPVPPAVQ 681 (687)
T ss_pred HhhcCCceEEEEEeccceeCCHHHH
Confidence 6789999999999999999998775
No 14
>PRK12740 elongation factor G; Reviewed
Probab=96.31 E-value=0.00081 Score=54.97 Aligned_cols=25 Identities=8% Similarity=-0.080 Sum_probs=22.8
Q ss_pred CcccCCcceeeceeccceecCCCCC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINIDPY 26 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gDP~ 26 (81)
|..|+|+|++++.|+||+.+++|++
T Consensus 639 r~~T~G~a~~~~~f~~y~~~~~~~~ 663 (668)
T PRK12740 639 RSLTQGRGSFSMEFSHYEEVPGNVA 663 (668)
T ss_pred HHhcCCeEEEEEEecccccCCHHHH
Confidence 6789999999999999999998765
No 15
>PRK00007 elongation factor G; Reviewed
Probab=95.95 E-value=0.0022 Score=53.21 Aligned_cols=24 Identities=8% Similarity=0.022 Sum_probs=21.6
Q ss_pred CcccCCcceeeceeccceecCCCC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINIDP 25 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gDP 25 (81)
|..|+|+|++++.|+||+.+|+|.
T Consensus 660 rs~T~G~a~~~~~f~~y~~v~~~~ 683 (693)
T PRK00007 660 RSMTQGRATYSMEFDHYEEVPKNV 683 (693)
T ss_pred HhhcCCceEEEEEeceeeECCHHH
Confidence 678999999999999999998654
No 16
>PRK10218 GTP-binding protein; Provisional
Probab=64.48 E-value=3.8 Score=34.27 Aligned_cols=23 Identities=9% Similarity=-0.036 Sum_probs=20.6
Q ss_pred CcccCCcceeeceeccceecC-CC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVIN-ID 24 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~-gD 24 (81)
+..|+|.+...+.|+||+.++ |+
T Consensus 456 ~s~T~G~g~~~~~f~~Y~~~~~g~ 479 (607)
T PRK10218 456 MTMTSGTGLLYSTFSHYDDVRPGE 479 (607)
T ss_pred hhhCCCeEEEEEEecCccCCCCCC
Confidence 567999999999999999998 54
No 17
>COG4851 CamS Protein involved in sex pheromone biosynthesis [General function prediction only]
Probab=62.50 E-value=6.2 Score=31.61 Aligned_cols=37 Identities=19% Similarity=0.382 Sum_probs=29.1
Q ss_pred cCCCC-CCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCC
Q psy13098 21 INIDP-YWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLP 62 (81)
Q Consensus 21 l~gDP-~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~ 62 (81)
=+||+ |-...++.++..-|+ .+|.++++.+|+.+||.
T Consensus 187 kdg~~~fe~eisds~l~~qGe-----kiaqeVlnRlR~~d~lk 224 (382)
T COG4851 187 KDGDTYFETEISDSKLLEQGE-----KIAQEVLNRLRREDGLK 224 (382)
T ss_pred ccCCccceeecCHHHHHHHHH-----HHHHHHHHHHHhhcCCc
Confidence 36899 544577888877664 48999999999999983
No 18
>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA. This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.
Probab=62.44 E-value=4.4 Score=33.68 Aligned_cols=23 Identities=13% Similarity=-0.126 Sum_probs=20.9
Q ss_pred CcccCCcceeeceeccceecCCC
Q psy13098 2 NLCCRGSVDGLRYFFWFQVINID 24 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l~gD 24 (81)
+..|+|.++....|+||+.++++
T Consensus 452 ~s~T~G~g~~~~~f~~Y~~~~~~ 474 (594)
T TIGR01394 452 LTDTRGTGIMNHVFDEYEPWKGE 474 (594)
T ss_pred HhhcCCeEEEEEEeccceeCCCc
Confidence 56799999999999999999975
No 19
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=57.11 E-value=9.1 Score=23.94 Aligned_cols=29 Identities=28% Similarity=0.382 Sum_probs=23.0
Q ss_pred cchHHHhhcCC-CCCccCHHHHHHHHHHHh
Q psy13098 30 RTEEEYLHFGD-KADTENRARKYMDSVRKR 58 (81)
Q Consensus 30 ~t~ee~e~~g~-~~~~~n~Ar~~v~~iRkR 58 (81)
.|++|++..++ .......||.+|+.+.++
T Consensus 31 l~~~E~e~i~~~~~t~~dkar~Lid~v~~K 60 (83)
T cd08325 31 LNEEEMEKIKEENNTIMDKARVLVDSVTEK 60 (83)
T ss_pred CCHHHHHHHHhccCCHHHHHHHHHHHHHHH
Confidence 47889998777 445788999999999854
No 20
>cd02164 PPAT_CoAS phosphopantetheine adenylyltransferase domain of eukaryotic and archaeal bifunctional enzymes. The PPAT domain of the bifunctional enzyme with PPAT and DPCK functions. The final two steps of the CoA biosynthesis pathway are catalyzed by phosphopantetheine adenylyltransferase (PPAT) and dephospho-CoA (dPCoA) kinase (DPCK). The PPAT reaction involves the reversible adenylation of 4'-phosphopantetheine to form 3'-dPCoA and PPi, and DPCK catalyses phosphorylation of the 3'-hydroxy group of the ribose moiety of dPCoA. In eukaryotes the two enzymes are part of a large multienzyme complex . Studies in Corynebacterium ammoniagenes suggested that separate enzymes were present, and this was confirmed through identification of the bacterial PPAT/CoAD.
Probab=55.01 E-value=6.2 Score=27.00 Aligned_cols=48 Identities=15% Similarity=0.234 Sum_probs=29.8
Q ss_pred cceecC-CCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCccc
Q psy13098 17 WFQVIN-IDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPVQD 65 (81)
Q Consensus 17 HW~~l~-gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~~e 65 (81)
++++++ .|||--..|+.+++-+ --.++...--..|+.+|+.+||+.-+
T Consensus 71 ~~~i~~i~d~~Gpt~~~~~~d~l-VVS~ET~~~~~~iN~~R~~~gl~pl~ 119 (143)
T cd02164 71 KYEIVPIDDPYGPTGTDPDLEAI-VVSPETYPGALKINRKREENGLSPLE 119 (143)
T ss_pred eEEEEEccCCCCCcccCCCCCEE-EEcHHHhhhHHHHHHHHHHCCCCcee
Confidence 566776 4887544544443332 11123334578999999999997665
No 21
>PRK05433 GTP-binding protein LepA; Provisional
Probab=54.95 E-value=5.5 Score=33.07 Aligned_cols=20 Identities=15% Similarity=0.049 Sum_probs=17.8
Q ss_pred CcccCCcceeeceeccceec
Q psy13098 2 NLCCRGSVDGLRYFFWFQVI 21 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~l 21 (81)
|..|+|.|+..+-|+||+.-
T Consensus 462 ks~T~G~gs~~~~~~~Y~~~ 481 (600)
T PRK05433 462 KSVSRGYASLDYEFIGYRES 481 (600)
T ss_pred HhhcCCEEEEEEEECCcccc
Confidence 67899999999999999854
No 22
>TIGR01393 lepA GTP-binding protein LepA. LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown.
Probab=53.63 E-value=6.3 Score=32.72 Aligned_cols=19 Identities=11% Similarity=-0.036 Sum_probs=17.4
Q ss_pred CcccCCcceeeceecccee
Q psy13098 2 NLCCRGSVDGLRYFFWFQV 20 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~ 20 (81)
+..|+|.|+..+.|+||+.
T Consensus 459 ks~T~G~gs~~~~~~~Y~~ 477 (595)
T TIGR01393 459 KSISRGYASFDYELIGYRP 477 (595)
T ss_pred hhhcCCEEEEEEEECCccc
Confidence 6789999999999999984
No 23
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=47.61 E-value=21 Score=33.23 Aligned_cols=31 Identities=42% Similarity=0.382 Sum_probs=24.5
Q ss_pred CccCHHHHHHHHHHHhcCCCcccccCcchhhHHhhhhc
Q psy13098 43 DTENRARKYMDSVRKRKGLPVQDKLVAHAEKQRTVKRN 80 (81)
Q Consensus 43 ~~~n~Ar~~v~~iRkRKGL~~~ekiv~~aekqr~L~k~ 80 (81)
-+++.|-.||..+||=|||.. +|++..++.|
T Consensus 1223 lep~~AFkIME~VRKGk~lk~-------~e~~~~Mke~ 1253 (1444)
T COG2176 1223 LEPSLAFKIMEFVRKGKGLKP-------AEYEELMKEN 1253 (1444)
T ss_pred CCcchHHHHHHHHhccCCCCh-------HHHHHHHHHc
Confidence 578899999999999999964 5666655554
No 24
>PF07537 CamS: CamS sex pheromone cAM373 precursor; InterPro: IPR011426 This family includes CamS (Q8L313 from SWISSPROT), from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. It also includes a number of uncharacterised bacterial proteins.; PDB: 3N2Q_A 3IB5_A 2QX2_A.
Probab=47.33 E-value=8.1 Score=30.22 Aligned_cols=41 Identities=32% Similarity=0.516 Sum_probs=29.4
Q ss_pred cceecCCCC-CCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCC
Q psy13098 17 WFQVINIDP-YWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLP 62 (81)
Q Consensus 17 HW~~l~gDP-~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~ 62 (81)
.|+.-.+.| |-+..++++++..| ...|.++|..+|++++|.
T Consensus 123 yy~~e~~g~~~~~~Is~~e~~~~G-----k~~A~~iv~rlR~~~~l~ 164 (319)
T PF07537_consen 123 YYQKEEDGPTYEVEISDEEMEAYG-----KEMANKIVKRLRKKKGLK 164 (319)
T ss_dssp EEESSTTS-EEEEES-HHHHHHHH-----HHHHHHHHHHHHHCCCGS
T ss_pred eecccCCCceeeEecCHHHHHHHH-----HHHHHHHHHHHHhccccC
Confidence 344444444 35568889999986 458999999999999983
No 25
>PF07421 Pro-NT_NN: Neurotensin/neuromedin N precursor; InterPro: IPR008055 Neurotensin is a 13-residue peptide transmitter, sharing significant similarity in its 6 C-terminal amino acid residues with several other neuropeptides, including neuromedin N (which is derived from the same precursor). This C-terminal region is responsible for the full biological activity, the N-terminal portion having a modulatory role. Neurotensin is distributed throughout the central nervous system, with highest levels in the hypothalamus, amygdala and nucleus accumbens. It induces a variety of effects, including: analgesia, hypothermia and increased locomotor activity. It is also involved in regulation of dopamine pathways. In the periphery, neurotensin is found in endocrine cells of the small intestine, where it leads to secretion and smooth muscle contraction []. The neurotensin/neuromedin N precursor can also be processed to produce large 125-138 amino acid peptides with the neurotensin or neuromedin N sequence at their C terminus. These large peptides appear to be less potent than their smaller counterparts, but are also less sensitive to degradation and may represent endogenous, long-lasting activators in a number of pathophysiological situations.; GO: 0005184 neuropeptide hormone activity, 0005576 extracellular region; PDB: 3F6K_N.
Probab=45.17 E-value=7.1 Score=28.26 Aligned_cols=15 Identities=20% Similarity=0.144 Sum_probs=0.0
Q ss_pred eeccceecCCCCCCC
Q psy13098 14 YFFWFQVINIDPYWE 28 (81)
Q Consensus 14 ~FsHW~~l~gDP~~~ 28 (81)
.|.||+++.+|-++.
T Consensus 114 ~fqhwel~qed~l~~ 128 (169)
T PF07421_consen 114 AFQHWELIQEDYLDP 128 (169)
T ss_dssp ---------------
T ss_pred cchHHHHHHHHHhhc
Confidence 699999999998853
No 26
>PF10041 DUF2277: Uncharacterized conserved protein (DUF2277); InterPro: IPR018735 Members of this family of hypothetical bacterial proteins have no known function.
Probab=41.20 E-value=33 Score=22.05 Aligned_cols=21 Identities=33% Similarity=0.445 Sum_probs=14.8
Q ss_pred CCCCcchHHHhhcCCCCCccCHHHHHHHHH
Q psy13098 26 YWEPRTEEEYLHFGDKADTENRARKYMDSV 55 (81)
Q Consensus 26 ~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~i 55 (81)
|.-|.|++||..- |.+||.+|
T Consensus 11 fePpaT~~EI~aA---------AlQyVRKv 31 (78)
T PF10041_consen 11 FEPPATDEEIRAA---------ALQYVRKV 31 (78)
T ss_pred CCCCCCHHHHHHH---------HHHHHHHH
Confidence 5556899998763 77886554
No 27
>PF12544 LAM_C: Lysine-2,3-aminomutase ; PDB: 2A5H_D.
Probab=40.23 E-value=15 Score=25.50 Aligned_cols=16 Identities=6% Similarity=-0.243 Sum_probs=10.3
Q ss_pred CCcccCCcceeeceec
Q psy13098 1 MNLCCRGSVDGLRYFF 16 (81)
Q Consensus 1 ~~~~T~G~A~~ql~Fs 16 (81)
+|-+|||-|.|+.|.|
T Consensus 4 LRGhtSGlAvPtyVvD 19 (127)
T PF12544_consen 4 LRGHTSGLAVPTYVVD 19 (127)
T ss_dssp TCTTC-GGG--EEEEE
T ss_pred ccccccccccceEEEE
Confidence 4678999999988874
No 28
>PRK05473 hypothetical protein; Provisional
Probab=33.76 E-value=43 Score=21.84 Aligned_cols=23 Identities=26% Similarity=0.525 Sum_probs=16.7
Q ss_pred ecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHH
Q psy13098 20 VINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVR 56 (81)
Q Consensus 20 ~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iR 56 (81)
+|.|||-+.+ .-|-||.+|.++=
T Consensus 46 llSGDPaYIt--------------sh~nAR~lIrkiE 68 (86)
T PRK05473 46 LLSGDPAYIP--------------RHNDARNLIRKLE 68 (86)
T ss_pred hccCCCCccC--------------CcccHHHHHHHHh
Confidence 4678998763 4567888888764
No 29
>PF07368 DUF1487: Protein of unknown function (DUF1487); InterPro: IPR009961 This family consists of several uncharacterised proteins from Drosophila melanogaster. The function of this family is unknown.
Probab=33.52 E-value=42 Score=25.03 Aligned_cols=35 Identities=23% Similarity=0.506 Sum_probs=30.0
Q ss_pred ccCHHHHHHHHHHHhcCCCcccccCcchhhHHhhhh
Q psy13098 44 TENRARKYMDSVRKRKGLPVQDKLVAHAEKQRTVKR 79 (81)
Q Consensus 44 ~~n~Ar~~v~~iRkRKGL~~~ekiv~~aekqr~L~k 79 (81)
.+++..+||..||.|-. +..+.|-.|+.|.|+|++
T Consensus 42 qEsireefi~rvr~~m~-pl~~~va~Hpny~rsl~~ 76 (215)
T PF07368_consen 42 QESIREEFIERVRSRMK-PLSPQVANHPNYLRSLKK 76 (215)
T ss_pred eHHHHHHHHHHHHHhCc-cCChhhccCcHHHHHHHH
Confidence 57788999999999965 347899999999999975
No 30
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=32.91 E-value=39 Score=23.76 Aligned_cols=35 Identities=17% Similarity=0.366 Sum_probs=21.1
Q ss_pred CCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCc
Q psy13098 28 EPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPV 63 (81)
Q Consensus 28 ~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~ 63 (81)
.|.||++|.+.... .+=++||..|.+-|..-|++.
T Consensus 120 ~PlSD~~i~~~L~~-~gi~isRRTVaKYR~~L~Ip~ 154 (160)
T PF04552_consen 120 KPLSDQEIAELLKE-EGIKISRRTVAKYREELGIPS 154 (160)
T ss_dssp S---HHHHHHHHTT-TTS---HHHHHHHHHHHT-S-
T ss_pred CCCCHHHHHHHHHH-cCCCccHHHHHHHHHHcCCCC
Confidence 47789998885543 236799999999999988853
No 31
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=32.58 E-value=41 Score=19.73 Aligned_cols=30 Identities=37% Similarity=0.615 Sum_probs=22.3
Q ss_pred cchHHHhhcCCCCCccCHHHHHHHHHHHhcC
Q psy13098 30 RTEEEYLHFGDKADTENRARKYMDSVRKRKG 60 (81)
Q Consensus 30 ~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKG 60 (81)
.|.++.+...........|+++++.+.+ ||
T Consensus 28 lt~~e~~~i~~~~~~~~k~~~Lld~l~~-kg 57 (80)
T cd01671 28 LTEEEYEKIRSESTRQDKARKLLDILPR-KG 57 (80)
T ss_pred CCHHHHHHHHcCCChHHHHHHHHHHHHh-cC
Confidence 4667777765555677789999999886 66
No 32
>PF07980 SusD: SusD family; InterPro: IPR012944 This domain occurs in several hypothetical proteins. It also occurs in RagB, Q9ZA59 from SWISSPROT, a protein involved in signalling [] and SusD, Q8A1G2 from SWISSPROT, an outer membrane protein involved in nutrient binding [].; PDB: 3IHV_A 3LEW_A 3JQ1_A 3JQ0_A 3NQP_B 3SNX_A 3L22_A 3OTN_A 3IV0_A 3QNK_C ....
Probab=32.17 E-value=44 Score=23.03 Aligned_cols=19 Identities=47% Similarity=0.793 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHhcCCCccc
Q psy13098 47 RARKYMDSVRKRKGLPVQD 65 (81)
Q Consensus 47 ~Ar~~v~~iRkRKGL~~~e 65 (81)
.|.++|+.||+|-|++...
T Consensus 151 ~A~~~lN~vR~Rag~~~~~ 169 (266)
T PF07980_consen 151 EALEYLNQVRKRAGLPPLT 169 (266)
T ss_dssp HHHHHHHHHHHHTTTTCGG
T ss_pred HHHHHHHHHHHHcCCCccc
Confidence 4999999999999986543
No 33
>COG0813 DeoD Purine-nucleoside phosphorylase [Nucleotide transport and metabolism]
Probab=31.58 E-value=28 Score=26.53 Aligned_cols=7 Identities=29% Similarity=0.534 Sum_probs=6.2
Q ss_pred ecCCCCC
Q psy13098 20 VINIDPY 26 (81)
Q Consensus 20 ~l~gDP~ 26 (81)
+||||||
T Consensus 18 LmPGDPl 24 (236)
T COG0813 18 LMPGDPL 24 (236)
T ss_pred ecCCCCc
Confidence 5899999
No 34
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=31.54 E-value=49 Score=21.14 Aligned_cols=30 Identities=40% Similarity=0.477 Sum_probs=23.9
Q ss_pred cchHHHhhcCCCCCccCHHHHHHHHHHHhcC
Q psy13098 30 RTEEEYLHFGDKADTENRARKYMDSVRKRKG 60 (81)
Q Consensus 30 ~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKG 60 (81)
.|++|++....+......||.+++.+. .||
T Consensus 38 lt~ee~e~I~~~~t~~~qAr~Lld~l~-~KG 67 (94)
T cd08329 38 ITEQEYDVIKQKTQTPLQARELIDTVL-VKG 67 (94)
T ss_pred CCHHHHHHHHcCCChHHHHHHHHHHHH-hhh
Confidence 578888887666666789999999988 566
No 35
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=30.69 E-value=48 Score=21.29 Aligned_cols=23 Identities=22% Similarity=0.469 Sum_probs=16.4
Q ss_pred ecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHH
Q psy13098 20 VINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVR 56 (81)
Q Consensus 20 ~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iR 56 (81)
+|.|||-+.+ .-|-||.+|.++=
T Consensus 43 llSGDPaYIt--------------sh~nAR~lIr~~e 65 (79)
T PF06135_consen 43 LLSGDPAYIT--------------SHNNARNLIRKIE 65 (79)
T ss_pred eecCCCcccc--------------CcccHHHHHHHHh
Confidence 3788998763 4567888887764
No 36
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=29.74 E-value=71 Score=18.16 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=23.2
Q ss_pred CcchHHHhh--cCCCC-CccCHHHHHHHHHHHhcC
Q psy13098 29 PRTEEEYLH--FGDKA-DTENRARKYMDSVRKRKG 60 (81)
Q Consensus 29 ~~t~ee~e~--~g~~~-~~~n~Ar~~v~~iRkRKG 60 (81)
++|.++|.+ ||... ...+.-+.+|..+|+.=+
T Consensus 24 ~vs~~~l~~~~w~~~~~~~~~~l~~~I~rLR~kL~ 58 (77)
T PF00486_consen 24 VVSREELIEALWGDEEDVSDNSLDVHISRLRKKLE 58 (77)
T ss_dssp EEEHHHHHHHHTSSSSTTCTHHHHHHHHHHHHHHH
T ss_pred CCCHHHhCChhhhcccccchhhHHHHHHHHHHHHh
Confidence 456677665 77765 566677999999998854
No 37
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=29.32 E-value=56 Score=28.70 Aligned_cols=39 Identities=28% Similarity=0.313 Sum_probs=24.3
Q ss_pred CCCCCCCCcchHHHh-hcCCCCCccC---HHHHHHHHHHHhcC
Q psy13098 22 NIDPYWEPRTEEEYL-HFGDKADTEN---RARKYMDSVRKRKG 60 (81)
Q Consensus 22 ~gDP~~~~~t~ee~e-~~g~~~~~~n---~Ar~~v~~iRkRKG 60 (81)
+.|||-.|....... ..+..++.++ .||+|++.||||-|
T Consensus 761 ~~DPLGR~~~~~~~~~~~~~~vp~e~~~~RAR~IleELRrR~g 803 (820)
T PF13779_consen 761 GRDPLGRPLGGQGPGGDDDVKVPDEIDRQRAREILEELRRRLG 803 (820)
T ss_pred CCCCCCCCCCCCCCCCCCCccCCChhHHHHHHHHHHHHHHhcC
Confidence 468887775433221 1222223322 89999999999988
No 38
>PF06820 Phage_fiber_C: Putative prophage tail fibre C-terminus; InterPro: IPR009640 This entry represents the C terminus of phage 933W tail fibre protein. This domain is found together with conserved RLGP motif. The characteristics of the protein distribution suggest prophage matches.
Probab=29.25 E-value=28 Score=21.50 Aligned_cols=18 Identities=28% Similarity=0.187 Sum_probs=14.6
Q ss_pred eeceeccceecCCCCCCC
Q psy13098 11 GLRYFFWFQVINIDPYWE 28 (81)
Q Consensus 11 ~ql~FsHW~~l~gDP~~~ 28 (81)
.|++|+|-++.=+|--|+
T Consensus 41 vq~~f~~LQv~fgDGpWq 58 (64)
T PF06820_consen 41 VQGVFRHLQVRFGDGPWQ 58 (64)
T ss_pred heeeeeeeEEEeccCChh
Confidence 489999999998876554
No 39
>PF15332 LIME1: Lck-interacting transmembrane adapter 1
Probab=28.85 E-value=37 Score=25.61 Aligned_cols=49 Identities=22% Similarity=0.208 Sum_probs=26.2
Q ss_pred eceeccceecCCC-CCCCCcc--hHHHhhcCCCC-CccCHHHHHHH----HHHHhcCC
Q psy13098 12 LRYFFWFQVINID-PYWEPRT--EEEYLHFGDKA-DTENRARKYMD----SVRKRKGL 61 (81)
Q Consensus 12 ql~FsHW~~l~gD-P~~~~~t--~ee~e~~g~~~-~~~n~Ar~~v~----~iRkRKGL 61 (81)
--+|+||+ +|.- |.-.+.+ +-..-..|..+ +..++|..-|. -|+|.||-
T Consensus 89 p~aF~hre-lP~~~PaA~~s~~peATYSNVgLAAiPraslAaspVvAEYAciqK~KgT 145 (228)
T PF15332_consen 89 PSAFSHRE-LPQAPPAASPSIGPEATYSNVGLAAIPRASLAASPVVAEYACIQKLKGT 145 (228)
T ss_pred CCCCChhh-cCCCCcccccccCccceeccccccccCccccccchhHHHHHHHHHhccC
Confidence 45899999 6654 5543322 22233333322 34445544333 38899985
No 40
>PF10937 DUF2638: Protein of unknown function (DUF2638); InterPro: IPR020373 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a component of the mitochondrial small ribosomal subunit. Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S). This entry is represented by a mitochondrial ribosomal protein of the small subunit, which has similarity to human mitochondrial ribosomal protein MRP-S36 [, , ].
Probab=28.09 E-value=28 Score=23.37 Aligned_cols=24 Identities=25% Similarity=0.224 Sum_probs=17.5
Q ss_pred ceeccceecCCCCCCCCcchHHHhh
Q psy13098 13 RYFFWFQVINIDPYWEPRTEEEYLH 37 (81)
Q Consensus 13 l~FsHW~~l~gDP~~~~~t~ee~e~ 37 (81)
-+||.|+ ||.-=-..+.+++|||-
T Consensus 83 ~~~~~~e-LP~Rfrr~p~se~EiE~ 106 (112)
T PF10937_consen 83 EYFDRSE-LPARFRRKPISEEEIEA 106 (112)
T ss_pred ceeeHHH-cCHhHccCCCCHHHHHH
Confidence 4678888 77655566788899875
No 41
>cd06909 M14_ASPA Aspartoacylase (ASPA) belongs to the Succinylglutamate desuccinylase/aspartoacylase subfamily of the M14 family of metallocarboxypeptidases. ASPA (also known as aminoacylase 2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=27.86 E-value=17 Score=27.56 Aligned_cols=22 Identities=14% Similarity=-0.088 Sum_probs=18.3
Q ss_pred eeeceeccceecC-CCCCCCCcc
Q psy13098 10 DGLRYFFWFQVIN-IDPYWEPRT 31 (81)
Q Consensus 10 ~~ql~FsHW~~l~-gDP~~~~~t 31 (81)
.|+|+...|+.|. |||++....
T Consensus 226 hp~lq~~d~~~l~~Gdp~f~~~~ 248 (282)
T cd06909 226 HPQLQDRDWQPLKPGDPLFLTFD 248 (282)
T ss_pred CchhcCCCCcccCCCCceEecCC
Confidence 7999999999995 999766543
No 42
>PLN02388 phosphopantetheine adenylyltransferase
Probab=27.51 E-value=30 Score=24.82 Aligned_cols=47 Identities=19% Similarity=0.200 Sum_probs=27.5
Q ss_pred ceecC-CCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCccc
Q psy13098 18 FQVIN-IDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPVQD 65 (81)
Q Consensus 18 W~~l~-gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~~e 65 (81)
+++++ .|||--..++.+++-+ --.++...-...|+.+|+.+||+.-+
T Consensus 92 ~~i~~i~D~~Gpt~~~~~~d~L-VVS~ET~~g~~~IN~~R~e~Gl~pL~ 139 (177)
T PLN02388 92 VQAEPIIDPYGPSIVDENLEAI-VVSKETLPGGLSVNKKRAERGLSQLK 139 (177)
T ss_pred EEEEEecCCCCCcccCCCCCEE-EEcHhHhhhHHHHHHHHHHCCCCCeE
Confidence 56666 4777544443333221 11123334578999999999996654
No 43
>COG1015 DeoB Phosphopentomutase [Carbohydrate transport and metabolism]
Probab=26.96 E-value=56 Score=26.63 Aligned_cols=40 Identities=15% Similarity=0.230 Sum_probs=23.7
Q ss_pred ccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHHHHHHhcCCCc
Q psy13098 16 FWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMDSVRKRKGLPV 63 (81)
Q Consensus 16 sHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKGL~~ 63 (81)
-|||++. =|...|. ..| +...+....+++.+|+++-|++.
T Consensus 88 GHWEimG-~pv~~~~-----~~f--~~~~~~fp~el~~~i~~~~g~~~ 127 (397)
T COG1015 88 GHWEIMG-VPVLFPF-----GYF--PDTVNGFPEELLDEIERRTGRKG 127 (397)
T ss_pred cchhhcC-Ccccccc-----ccc--ccccccChHHHHHHHHhhcCCce
Confidence 6999885 4442211 112 11235567899999999866643
No 44
>PF11267 DUF3067: Protein of unknown function (DUF3067); InterPro: IPR021420 This family of proteins has no known function. ; PDB: 2LJW_A.
Probab=26.87 E-value=31 Score=22.99 Aligned_cols=53 Identities=28% Similarity=0.463 Sum_probs=29.4
Q ss_pred cCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCC-------CccCHHHHHHHHHHHhcCCC
Q psy13098 5 CRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKA-------DTENRARKYMDSVRKRKGLP 62 (81)
Q Consensus 5 T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~-------~~~n~Ar~~v~~iRkRKGL~ 62 (81)
+.|..+.|+. |.-+.+-.| |.||+|..++.+.+ ......+.++.++|+|-.|.
T Consensus 23 ~~~~v~lqVM---W~yLeQ~SF--PltE~eY~~hL~~va~~L~~wG~~~~Vr~~l~~t~~rPRlG 82 (99)
T PF11267_consen 23 RRGRVYLQVM---WKYLEQRSF--PLTEEEYLEHLDAVAEYLNAWGQADQVRAFLEETRERPRLG 82 (99)
T ss_dssp ETTEEEEEEE---EEETTSTT---SS-HHHHHHHHHHHHHHHHHHS-HHHHHHHHHH-----BTT
T ss_pred EcCEEEEEEe---hhhccCCCc--CCCHHHHHHHHHHHHHHHHHcccHHHHHHHHHhCCCCCCCC
Confidence 4556667766 555888888 78988855543222 23446789999999887764
No 45
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=26.24 E-value=53 Score=19.39 Aligned_cols=29 Identities=31% Similarity=0.584 Sum_probs=21.0
Q ss_pred cchHHHhhcCCCCCccCHHHHHHHHHHHh
Q psy13098 30 RTEEEYLHFGDKADTENRARKYMDSVRKR 58 (81)
Q Consensus 30 ~t~ee~e~~g~~~~~~n~Ar~~v~~iRkR 58 (81)
.|++|.+.........+.++.+++.+.++
T Consensus 31 lt~~e~e~I~~~~t~~~k~~~LLd~l~~k 59 (85)
T PF00619_consen 31 LTEEEYEEIRSEPTRQDKARKLLDILKRK 59 (85)
T ss_dssp SSHHHHHHHHTSSSHHHHHHHHHHHHHHC
T ss_pred CCHHHHHHHHccCChHHHHHHHHHHHHHH
Confidence 36777777655556777899999987743
No 46
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=25.70 E-value=31 Score=25.73 Aligned_cols=26 Identities=35% Similarity=0.562 Sum_probs=20.3
Q ss_pred ccCHHHHHHHHHHHh--cCCCcccccCc
Q psy13098 44 TENRARKYMDSVRKR--KGLPVQDKLVA 69 (81)
Q Consensus 44 ~~n~Ar~~v~~iRkR--KGL~~~ekiv~ 69 (81)
+...-++||..+|.| |||-+-|+-+-
T Consensus 89 PA~i~ye~I~e~R~RInkGLRVAEe~vr 116 (206)
T TIGR03875 89 PAEIFYEYIEEVRERIDKGLRVAEEHVR 116 (206)
T ss_pred cHHHHHHHHHHHHHHHhcchhHHHHHHH
Confidence 445779999999999 99987765443
No 47
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=24.75 E-value=74 Score=19.70 Aligned_cols=30 Identities=27% Similarity=0.406 Sum_probs=21.6
Q ss_pred cchHHHhhcCCCCCccCHHHHHHHHHHHhcC
Q psy13098 30 RTEEEYLHFGDKADTENRARKYMDSVRKRKG 60 (81)
Q Consensus 30 ~t~ee~e~~g~~~~~~n~Ar~~v~~iRkRKG 60 (81)
.|+++.+..-........||++++.+.+ ||
T Consensus 30 it~e~~~~I~a~~T~~~kar~Lld~l~~-kG 59 (82)
T cd08330 30 ITQEQYSEVRAEKTNQEKMRKLFSFVRS-WG 59 (82)
T ss_pred CCHHHHHHHHcCCCcHHHHHHHHHHHHc-cC
Confidence 5777777744444667789999999886 55
No 48
>PRK04358 hypothetical protein; Provisional
Probab=23.79 E-value=25 Score=26.44 Aligned_cols=29 Identities=31% Similarity=0.527 Sum_probs=22.6
Q ss_pred ccCHHHHHHHHHHHh--cCCCcccccCcchh
Q psy13098 44 TENRARKYMDSVRKR--KGLPVQDKLVAHAE 72 (81)
Q Consensus 44 ~~n~Ar~~v~~iRkR--KGL~~~ekiv~~ae 72 (81)
+..+-++||..+|.| |||.+-|+-+-.|.
T Consensus 93 PA~i~ye~I~~mR~RInkGLRVAEeavrea~ 123 (217)
T PRK04358 93 PAEIFYEYIEDMRERINKGLRVAEEAVREAA 123 (217)
T ss_pred cHHHHHHHHHHHHHHHhcchHHHHHHHHHHH
Confidence 445779999999999 99988876655543
No 49
>PTZ00069 60S ribosomal protein L5; Provisional
Probab=22.54 E-value=71 Score=25.16 Aligned_cols=46 Identities=17% Similarity=0.068 Sum_probs=37.7
Q ss_pred cCCcceeeceeccceecCCCCCCCCcchHHHhhcCCCCCccCHHHHHHH
Q psy13098 5 CRGSVDGLRYFFWFQVINIDPYWEPRTEEEYLHFGDKADTENRARKYMD 53 (81)
Q Consensus 5 T~G~A~~ql~FsHW~~l~gDP~~~~~t~ee~e~~g~~~~~~n~Ar~~v~ 53 (81)
|+-.++||++.+. +.||--....+..||..+|-++...|.|--|+.
T Consensus 56 TN~~ii~Qiv~~~---~~GD~vl~sA~S~eL~kyG~k~gl~N~~AAY~T 101 (300)
T PTZ00069 56 TNKDIICQIVYAT---IVGDKVLAAAYSHELPRFGIPVGLTNYAAAYAT 101 (300)
T ss_pred ECCcEEEEEEEee---cCCCEEEEEeehhhHhhcCcCCCCccHHHHHHH
Confidence 4556789999877 889988888888999999999999997766554
No 50
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=22.40 E-value=29 Score=25.88 Aligned_cols=28 Identities=32% Similarity=0.542 Sum_probs=0.0
Q ss_pred ccCHHHHHHHHHHHh--cCCCcccccCcch
Q psy13098 44 TENRARKYMDSVRKR--KGLPVQDKLVAHA 71 (81)
Q Consensus 44 ~~n~Ar~~v~~iRkR--KGL~~~ekiv~~a 71 (81)
+..+-++||..+|.| |||.+-|+-+-.|
T Consensus 89 PA~i~yEyI~emR~RInKGLRVAEeavrea 118 (205)
T PF08745_consen 89 PAEIFYEYIEEMRERINKGLRVAEEAVREA 118 (205)
T ss_dssp ------------------------------
T ss_pred cccccccccccccccccccccccccccccc
Confidence 455779999999999 9998887665543
No 51
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=21.59 E-value=1.4e+02 Score=19.88 Aligned_cols=29 Identities=21% Similarity=0.352 Sum_probs=21.7
Q ss_pred cchHHHhh-cCCCCCccCHHHHHHHHHHHh
Q psy13098 30 RTEEEYLH-FGDKADTENRARKYMDSVRKR 58 (81)
Q Consensus 30 ~t~ee~e~-~g~~~~~~n~Ar~~v~~iRkR 58 (81)
.|+.||.+ +|++....-.+.++|+-|-||
T Consensus 47 v~~kEi~~ilG~~~~i~Rt~~Qvv~~l~RR 76 (99)
T PF13758_consen 47 VTEKEIKEILGEGQGITRTREQVVDVLSRR 76 (99)
T ss_pred ccHHHHHHHhCCCCCCCcCHHHHHHHHHHH
Confidence 45666666 887766666788899888888
No 52
>PLN02882 aminoacyl-tRNA ligase
Probab=21.51 E-value=84 Score=28.52 Aligned_cols=24 Identities=33% Similarity=0.520 Sum_probs=20.0
Q ss_pred CHHHHHHHH---HHHhcCCCcccccCc
Q psy13098 46 NRARKYMDS---VRKRKGLPVQDKLVA 69 (81)
Q Consensus 46 n~Ar~~v~~---iRkRKGL~~~ekiv~ 69 (81)
-.||++|+. .||..||.+.++|-.
T Consensus 995 G~ARE~v~rIQ~lRK~~gl~~~D~I~v 1021 (1159)
T PLN02882 995 GVAREVVNRIQKLRKKAGLEPTDKVEV 1021 (1159)
T ss_pred hHHHHHHHHHHHHHHhCCCCCCcEEEE
Confidence 379999987 699999999987743
No 53
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=20.50 E-value=41 Score=20.08 Aligned_cols=19 Identities=21% Similarity=0.282 Sum_probs=10.7
Q ss_pred CcccCCcceeeceecccee
Q psy13098 2 NLCCRGSVDGLRYFFWFQV 20 (81)
Q Consensus 2 ~~~T~G~A~~ql~FsHW~~ 20 (81)
+..+.|=-.-|.+|||=+.
T Consensus 7 ~VkCp~C~~~q~vFSha~t 25 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQT 25 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS
T ss_pred EEECCCCCCeeEEEecCCe
Confidence 3445555567899999553
Done!