Query psy9697
Match_columns 128
No_of_seqs 181 out of 1240
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 17:18:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9697.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9697hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06911 rpsN 30S ribosomal pr 100.0 7.6E-31 1.6E-35 173.1 3.4 83 45-128 17-100 (100)
2 PRK08881 rpsN 30S ribosomal pr 100.0 4.7E-31 1E-35 174.6 1.8 83 45-128 17-101 (101)
3 CHL00074 rps14 ribosomal prote 100.0 4.5E-30 9.7E-35 169.6 2.6 82 45-128 17-100 (100)
4 KOG1741|consensus 99.9 1.2E-27 2.7E-32 155.0 0.4 83 46-128 20-103 (103)
5 COG0199 RpsN Ribosomal protein 99.9 6.4E-25 1.4E-29 131.8 4.2 54 75-128 8-61 (61)
6 PF00253 Ribosomal_S14: Riboso 99.9 1.6E-22 3.4E-27 120.3 5.3 54 74-127 2-55 (55)
7 PRK08061 rpsN 30S ribosomal pr 99.8 1.1E-21 2.3E-26 118.0 5.1 52 75-128 10-61 (61)
8 KOG0197|consensus 99.8 1.1E-18 2.3E-23 141.0 9.6 126 1-128 81-227 (468)
9 KOG4278|consensus 99.7 8.6E-18 1.9E-22 139.6 8.3 123 1-128 152-288 (1157)
10 cd00173 SH2 Src homology 2 dom 99.7 3.9E-17 8.5E-22 105.7 8.9 85 2-91 1-94 (94)
11 smart00252 SH2 Src homology 2 99.7 1.1E-16 2.3E-21 102.0 8.1 61 1-61 1-64 (84)
12 PF00017 SH2: SH2 domain; Int 99.7 1.6E-16 3.4E-21 99.8 6.7 54 3-56 1-57 (77)
13 PRK05766 rps14P 30S ribosomal 99.4 3.6E-13 7.7E-18 78.8 2.6 41 77-117 3-45 (52)
14 KOG1264|consensus 99.2 1.3E-11 2.8E-16 104.8 6.5 60 1-60 648-709 (1267)
15 KOG4792|consensus 99.2 1.9E-11 4.1E-16 90.8 5.5 52 2-53 12-65 (293)
16 KOG1264|consensus 99.1 1.6E-10 3.5E-15 98.2 7.4 113 2-116 535-665 (1267)
17 KOG4637|consensus 99.1 1.8E-10 4E-15 90.6 7.1 91 2-93 24-121 (464)
18 KOG4226|consensus 99.1 2.6E-10 5.6E-15 87.0 6.7 59 1-59 281-342 (379)
19 KOG0790|consensus 99.1 2.4E-10 5.2E-15 92.0 6.1 58 2-59 111-180 (600)
20 KOG4637|consensus 98.9 1.2E-09 2.6E-14 86.1 4.7 89 3-92 334-429 (464)
21 KOG0194|consensus 98.8 2.2E-08 4.7E-13 82.1 8.0 115 1-127 49-177 (474)
22 KOG0790|consensus 98.8 1.5E-08 3.3E-13 81.8 6.2 89 2-90 5-101 (600)
23 KOG2996|consensus 98.7 2.3E-08 5E-13 82.9 4.5 69 1-69 685-759 (865)
24 KOG1930|consensus 98.7 2.5E-08 5.5E-13 79.6 4.5 55 3-57 214-285 (483)
25 KOG3751|consensus 98.4 5.6E-08 1.2E-12 79.6 0.4 90 2-93 520-619 (622)
26 PTZ00218 40S ribosomal protein 98.4 1.5E-07 3.2E-12 55.1 1.6 32 86-117 14-47 (54)
27 KOG3601|consensus 98.3 1.5E-07 3.2E-12 69.4 0.5 57 2-58 59-118 (222)
28 PF14633 SH2_2: SH2 domain; PD 97.0 0.0027 5.8E-08 47.6 6.1 53 1-53 38-92 (220)
29 KOG3506|consensus 94.7 0.009 1.9E-07 35.0 0.1 31 87-117 17-49 (56)
30 KOG1856|consensus 91.0 0.39 8.4E-06 43.6 4.7 53 1-53 1108-1162(1299)
31 KOG3697|consensus 83.6 0.53 1.1E-05 36.8 1.0 37 1-39 201-239 (345)
32 TIGR01764 excise DNA binding d 83.5 1.1 2.4E-05 24.2 2.1 24 102-125 9-32 (49)
33 KOG4566|consensus 79.2 2.6 5.7E-05 32.4 3.4 53 2-54 53-107 (258)
34 PF12728 HTH_17: Helix-turn-he 70.1 5.5 0.00012 22.1 2.5 25 102-126 9-33 (51)
35 smart00557 IG_FLMN Filamin-typ 67.5 8 0.00017 24.5 3.1 28 17-44 51-79 (93)
36 PF05486 SRP9-21: Signal recog 64.2 33 0.00071 21.5 5.9 46 10-55 10-63 (79)
37 KOG1856|consensus 58.8 46 0.00099 31.1 7.0 71 7-77 1211-1289(1299)
38 cd04762 HTH_MerR-trunc Helix-T 57.3 9.3 0.0002 20.2 1.8 24 102-125 8-31 (49)
39 PF00630 Filamin: Filamin/ABP2 53.1 11 0.00023 23.7 1.8 27 18-44 66-93 (101)
40 PF02762 Cbl_N3: CBL proto-onc 50.2 64 0.0014 20.4 5.7 39 7-45 9-51 (86)
41 PF06353 DUF1062: Protein of u 40.6 14 0.00031 25.8 1.0 23 102-124 111-133 (142)
42 KOG3508|consensus 40.0 9.3 0.0002 34.4 -0.1 50 2-51 82-135 (932)
43 PF05930 Phage_AlpA: Prophage 40.0 5.5 0.00012 22.5 -1.0 22 100-121 9-30 (51)
44 PF14633 SH2_2: SH2 domain; PD 39.3 30 0.00065 26.0 2.6 64 6-69 140-211 (220)
45 PF11112 PyocinActivator: Pyoc 36.2 31 0.00066 21.5 1.9 19 103-121 24-43 (76)
46 PF09430 DUF2012: Protein of u 35.7 42 0.00092 22.4 2.7 35 18-53 26-61 (123)
47 KOG3667|consensus 34.3 43 0.00093 29.3 3.0 46 6-51 569-616 (682)
48 COG4332 Uncharacterized protei 33.8 23 0.00049 26.0 1.1 24 102-125 147-170 (203)
49 PF00432 Prenyltrans: Prenyltr 30.7 27 0.00058 18.8 0.9 22 7-28 1-24 (44)
50 KOG4257|consensus 30.6 39 0.00084 30.0 2.1 26 102-127 382-409 (974)
51 cd04761 HTH_MerR-SF Helix-Turn 30.3 38 0.00083 18.1 1.5 23 102-124 8-30 (49)
52 PF00408 PGM_PMM_IV: Phosphogl 25.0 45 0.00098 19.9 1.2 13 19-31 32-45 (73)
53 PF13309 HTH_22: HTH domain 24.8 32 0.0007 20.4 0.5 25 6-30 20-45 (64)
54 PF03330 DPBB_1: Rare lipoprot 24.0 31 0.00066 21.0 0.3 37 85-128 42-78 (78)
55 PF10743 Phage_Cox: Regulatory 23.9 85 0.0018 20.2 2.3 21 104-124 22-42 (87)
56 PF06200 tify: tify domain; I 21.8 1.2E+02 0.0026 16.1 2.4 15 35-49 6-20 (36)
No 1
>PRK06911 rpsN 30S ribosomal protein S14; Reviewed
Probab=99.96 E-value=7.6e-31 Score=173.10 Aligned_cols=83 Identities=20% Similarity=0.358 Sum_probs=76.6
Q ss_pred eeEEeeeeecccccccccCCCHHHH-HHHHHhhcCCCCCCCcccCCcccccCCCCccccccCCCHHHHHHhhccCCCCce
Q psy9697 45 AYNIFIRKRDDNKIGLGTFKPNEVM-AAREDATNHPRDSHPCRTQPRCVITSRPRGVVLRWRLSRIMFRHLADYNKLSGV 123 (128)
Q Consensus 45 v~hy~I~~~~~k~i~~n~~L~~~~r-~~~~~l~~l~~~~~~~rl~nrC~~tgr~~g~~~~~~l~R~~fr~~~~~G~~~gv 123 (128)
|.-|..++..+++++.|+++|.++- ++++ |+++|+|++|||++|||+.||||+||+++|+|||++|||+|+.|+||||
T Consensus 17 ~~k~~~kR~~lK~i~~~~~l~~~~~~a~~k-L~~lPrnss~~R~rNRC~~TGR~Rgv~r~FgLsRi~~Rela~~G~lPGv 95 (100)
T PRK06911 17 VEKYRQRRNELKQLIKSSDDFQVIMESQAK-LAKLPVNSNPVRYVTRCKQCGRPHAVYRKFNLCRICLRQQLMVGNIPGG 95 (100)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHH-HHhCCCccCcchhhcccCCCCCCcccccccCchHHHHHHHHHcCCCCCe
Confidence 4456777788899999999999865 6677 9999999999999999999999999999999999999999999999999
Q ss_pred EeccC
Q psy9697 124 QRAMW 128 (128)
Q Consensus 124 ~k~~W 128 (128)
+||||
T Consensus 96 ~KaSW 100 (100)
T PRK06911 96 RKSSW 100 (100)
T ss_pred ecccC
Confidence 99999
No 2
>PRK08881 rpsN 30S ribosomal protein S14; Reviewed
Probab=99.96 E-value=4.7e-31 Score=174.63 Aligned_cols=83 Identities=31% Similarity=0.488 Sum_probs=77.5
Q ss_pred eeEEeeeeecccccccccCCCHHHH--HHHHHhhcCCCCCCCcccCCcccccCCCCccccccCCCHHHHHHhhccCCCCc
Q psy9697 45 AYNIFIRKRDDNKIGLGTFKPNEVM--AAREDATNHPRDSHPCRTQPRCVITSRPRGVVLRWRLSRIMFRHLADYNKLSG 122 (128)
Q Consensus 45 v~hy~I~~~~~k~i~~n~~L~~~~r--~~~~~l~~l~~~~~~~rl~nrC~~tgr~~g~~~~~~l~R~~fr~~~~~G~~~g 122 (128)
+..|.+.+..+++++.|+++|.+++ ++.+ |+++|+|++||+++|||+.||||+|++++|+|||++||++|+.|+|||
T Consensus 17 ~~k~~~kR~~lK~i~~~~~l~~~~r~~~~~k-L~~lPr~ss~tRi~NRC~~TGR~Rgv~r~F~LsRi~fRela~~G~lpG 95 (101)
T PRK08881 17 VAKYAAKRAELKAIISDPNLSDEERYEARLK-LQKLPRNSSPTRLRNRCELTGRPRGYYRKFGLSRIKLRELAHRGEIPG 95 (101)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH-HHhCCcccchHHHhccccCCCCCCccccCcCchHHHHHHHHHcCCCCC
Confidence 4567778888999999999999998 5555 999999999999999999999999999999999999999999999999
Q ss_pred eEeccC
Q psy9697 123 VQRAMW 128 (128)
Q Consensus 123 v~k~~W 128 (128)
|+||||
T Consensus 96 v~KsSW 101 (101)
T PRK08881 96 VVKASW 101 (101)
T ss_pred eecccC
Confidence 999999
No 3
>CHL00074 rps14 ribosomal protein S14
Probab=99.96 E-value=4.5e-30 Score=169.62 Aligned_cols=82 Identities=29% Similarity=0.460 Sum_probs=75.9
Q ss_pred eeEEeeeeecccccccccCCCHHHH--HHHHHhhcCCCCCCCcccCCcccccCCCCccccccCCCHHHHHHhhccCCCCc
Q psy9697 45 AYNIFIRKRDDNKIGLGTFKPNEVM--AAREDATNHPRDSHPCRTQPRCVITSRPRGVVLRWRLSRIMFRHLADYNKLSG 122 (128)
Q Consensus 45 v~hy~I~~~~~k~i~~n~~L~~~~r--~~~~~l~~l~~~~~~~rl~nrC~~tgr~~g~~~~~~l~R~~fr~~~~~G~~~g 122 (128)
|.-|++.+..+++++.|+++|.+ + ++++ ++++|+|++||+++|||+.||||+||+++|+|||++|||+|+.|+|||
T Consensus 17 ~~k~~~kR~~lK~i~~~~~l~~~-r~~a~~k-L~~lpr~ss~tRi~NRC~~TGR~Rgv~r~F~LsRi~~Re~a~~G~ipG 94 (100)
T CHL00074 17 VQKYHLKRRSLKKEIKKVSSLSE-KWEIHGK-LQSLPRNSAPTRLHNRCFLTGRPRGNYRDFGLSRHVLREMAHACLLPG 94 (100)
T ss_pred HHHHHHHHHHHHHHHhCCCCcHH-HHHHHHH-HHhCCcccchHHHhccccCCCCCCccccCcCchHHHHHHHHHcCCCCC
Confidence 34566777888999999999999 7 5555 999999999999999999999999999999999999999999999999
Q ss_pred eEeccC
Q psy9697 123 VQRAMW 128 (128)
Q Consensus 123 v~k~~W 128 (128)
|+||||
T Consensus 95 v~KaSW 100 (100)
T CHL00074 95 VTKSSW 100 (100)
T ss_pred cccccC
Confidence 999999
No 4
>KOG1741|consensus
Probab=99.93 E-value=1.2e-27 Score=155.02 Aligned_cols=83 Identities=41% Similarity=0.666 Sum_probs=75.6
Q ss_pred eEEeeeeecccccccccCCCHHHH-HHHHHhhcCCCCCCCcccCCcccccCCCCccccccCCCHHHHHHhhccCCCCceE
Q psy9697 46 YNIFIRKRDDNKIGLGTFKPNEVM-AAREDATNHPRDSHPCRTQPRCVITSRPRGVVLRWRLSRIMFRHLADYNKLSGVQ 124 (128)
Q Consensus 46 ~hy~I~~~~~k~i~~n~~L~~~~r-~~~~~l~~l~~~~~~~rl~nrC~~tgr~~g~~~~~~l~R~~fr~~~~~G~~~gv~ 124 (128)
+.|.+.+..+++|.+|++||..++ ....+++++|+|+.||+++|+|+.||||||+++.|+|||+.||++|..|.+|||+
T Consensus 20 ~e~~~~R~slk~i~knp~LP~~~r~ea~~kl~alPrns~ptrI~NRCv~TGR~R~v~r~frLsR~~FR~~A~~~~LpGv~ 99 (103)
T KOG1741|consen 20 KEYELERRSLKEISKNPILPEKLRDEAAEKLQALPRNSAPTRIKNRCVFTGRPRGVYRDFRLSRHVFRELADAGALPGVT 99 (103)
T ss_pred HHHHHHHHHHHHHHhCCcccHHHHHHHHHHHhcCccccchHHHHHHHHhcCCcccccchhhhHHHHHHHHHHhccCcCcc
Confidence 445566666799999999999999 4444499999999999999999999999999999999999999999999999999
Q ss_pred eccC
Q psy9697 125 RAMW 128 (128)
Q Consensus 125 k~~W 128 (128)
||||
T Consensus 100 rasW 103 (103)
T KOG1741|consen 100 RASW 103 (103)
T ss_pred cccC
Confidence 9999
No 5
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=6.4e-25 Score=131.80 Aligned_cols=54 Identities=41% Similarity=0.776 Sum_probs=53.2
Q ss_pred hhcCCCCCCCcccCCcccccCCCCccccccCCCHHHHHHhhccCCCCceEeccC
Q psy9697 75 ATNHPRDSHPCRTQPRCVITSRPRGVVLRWRLSRIMFRHLADYNKLSGVQRAMW 128 (128)
Q Consensus 75 l~~l~~~~~~~rl~nrC~~tgr~~g~~~~~~l~R~~fr~~~~~G~~~gv~k~~W 128 (128)
+.++|++..+++..|+|..||||+||+++|+|||++|||+|++|+||||+|+||
T Consensus 8 ~~~~p~~~~~~r~~nRC~~cGRprg~~Rkf~lcR~cfRE~A~~g~ipGv~K~sW 61 (61)
T COG0199 8 LKALPRPKSPGRGRNRCRRCGRPRGVIRKFGLCRICFRELAHKGEIPGVKKASW 61 (61)
T ss_pred hhcCCCCCccccccccccccCCCccchhhhhhHHHHHHHHhhccCCCCeEeccC
Confidence 778999999999999999999999999999999999999999999999999999
No 6
>PF00253 Ribosomal_S14: Ribosomal protein S14p/S29e; InterPro: IPR001209 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 [, ]. S14 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S14 is known to be required for the assembly of 30S particles and may also be responsible for determining the conformation of 16S rRNA at the A site. It belongs to a family of ribosomal proteins [, ] that include, bacterial, algal and plant chloroplast, yeast mitochondrial, cyanelle and archael, Methanococcus vannielii S14's, as well as yeast mitochondrial MRP2, yeast YS29A/B and mammalian S29.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_N 2XZM_N 1S1H_N 3IZ6_N 2YKR_N 2QBB_N 3I1Z_N 3OAQ_N 3R8O_N 2Z4K_N ....
Probab=99.87 E-value=1.6e-22 Score=120.31 Aligned_cols=54 Identities=46% Similarity=0.790 Sum_probs=51.7
Q ss_pred HhhcCCCCCCCcccCCcccccCCCCccccccCCCHHHHHHhhccCCCCceEecc
Q psy9697 74 DATNHPRDSHPCRTQPRCVITSRPRGVVLRWRLSRIMFRHLADYNKLSGVQRAM 127 (128)
Q Consensus 74 ~l~~l~~~~~~~rl~nrC~~tgr~~g~~~~~~l~R~~fr~~~~~G~~~gv~k~~ 127 (128)
++.++|++++++++.|+|+.|||++|++++|+|||++||++|..|+||||+|||
T Consensus 2 kl~~~p~~s~~~r~~nrC~~tGR~rgv~r~f~lsR~~fR~~a~~g~l~G~~KsS 55 (55)
T PF00253_consen 2 KLSKLPRNSSPTRIKNRCVITGRSRGVIRKFGLSRICFRELASKGLLPGVKKSS 55 (55)
T ss_dssp HSTSSSSSSSCTGSCSSBSSSCSSSSBETTTSSBHHHHHHHHHTTSSTTEEES-
T ss_pred hhhhCCCCCCCCCCCeecccCCCceeeeccccccHHHHHHHHHcCCCCCEEeCC
Confidence 378999999999999999999999999999999999999999999999999997
No 7
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=99.85 E-value=1.1e-21 Score=118.03 Aligned_cols=52 Identities=37% Similarity=0.659 Sum_probs=48.2
Q ss_pred hhcCCCCCCCcccCCcccccCCCCccccccCCCHHHHHHhhccCCCCceEeccC
Q psy9697 75 ATNHPRDSHPCRTQPRCVITSRPRGVVLRWRLSRIMFRHLADYNKLSGVQRAMW 128 (128)
Q Consensus 75 l~~l~~~~~~~rl~nrC~~tgr~~g~~~~~~l~R~~fr~~~~~G~~~gv~k~~W 128 (128)
..+.|++ +|+++|+|+.||||+|++++|+|||++|||+|..|+||||+||||
T Consensus 10 ~~~~~k~--~~r~~nRC~~tGR~rgvir~fgl~R~~FRe~A~~G~ipGv~KasW 61 (61)
T PRK08061 10 AKRKPKF--KVRAYTRCERCGRPHSVYRKFGLCRICFRELAYKGQIPGVKKASW 61 (61)
T ss_pred hhcCCCC--CcccceeeecCCCCcceeccCCccHHHHHHHHHcCcCCCeeeccC
Confidence 5556655 599999999999999999999999999999999999999999999
No 8
>KOG0197|consensus
Probab=99.78 E-value=1.1e-18 Score=141.04 Aligned_cols=126 Identities=20% Similarity=0.286 Sum_probs=99.6
Q ss_pred CCCCC-CCCHHHHHHhH--hcCCcccEEEeeCCC-CCCEEEEEEeCC------EeeEEeeeeeccccc---ccc-cCCCH
Q psy9697 1 MAWFH-SVNRERAVQMV--AAGGEGCFLVRPSSS-SEPLTLTLWYGG------RAYNIFIRKRDDNKI---GLG-TFKPN 66 (128)
Q Consensus 1 ~~W~~-~i~r~~ae~ll--~~~~~G~FlvR~s~~-~~~~~lsv~~~~------~v~hy~I~~~~~k~i---~~n-~~L~~ 66 (128)
+|||+ +|+|++||+.| ..+..|+||||+|++ +|+|+|||+... .|+||+|+..+.+.+ +.. ..++.
T Consensus 81 ~~Wf~~~isR~~ae~~ll~p~~~~G~flvR~se~~~g~yslsv~~~~~~~~~~~v~hyri~~~~~~~~~~~~~~~~~F~~ 160 (468)
T KOG0197|consen 81 EPWFFGKISREEAERQLLAPENKEGAFLVRESESDKGDYSLSVREGDSGGLGAKVKHYRIRQLDGGGLYPYIDERELFSS 160 (468)
T ss_pred CCchhccccHHHHHHhhcCCCCCccceeeecccCCcCCeeEEEEeccccCCccceeeeeeeEcCCCCeecCCCHHHhhhh
Confidence 58999 89999999655 677889999999987 899999999976 999999999887532 211 11111
Q ss_pred HHHHHHHHhhcCCCCCCCcccCCcccccC----CCCcc-ccccCCCHHHH--HHhhccCCCCceEeccC
Q psy9697 67 EVMAAREDATNHPRDSHPCRTQPRCVITS----RPRGV-VLRWRLSRIMF--RHLADYNKLSGVQRAMW 128 (128)
Q Consensus 67 ~~r~~~~~l~~l~~~~~~~rl~nrC~~tg----r~~g~-~~~~~l~R~~f--r~~~~~G~~~gv~k~~W 128 (128)
. .++..++...+++..+++..+|...+ .+.+. ...|+++|..+ -+.+++|+|+.|..+.|
T Consensus 161 l--~~lv~~~~~~~~gl~~~l~~p~~~~~~~~p~~~~~~~d~wei~r~~l~l~~~LG~G~FG~V~~g~~ 227 (468)
T KOG0197|consen 161 L--QQLVNYYSKNADGLCTRLRDPCSKQGHTKPQTPDLARDPWEIPREELKLIRELGSGQFGEVWLGKW 227 (468)
T ss_pred H--HHHHhhhhccCcchhhcccCchhccCCCCCCCCccccCCeeecHHHHHHHHHhcCCccceEEEEEE
Confidence 1 33444888999999999999998642 23344 68899999966 67899999999999987
No 9
>KOG4278|consensus
Probab=99.73 E-value=8.6e-18 Score=139.59 Aligned_cols=123 Identities=25% Similarity=0.425 Sum_probs=104.0
Q ss_pred CCCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeecc-cccccccCCCHHHH----HHHH
Q psy9697 1 MAWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDD-NKIGLGTFKPNEVM----AARE 73 (128)
Q Consensus 1 ~~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~-k~i~~n~~L~~~~r----~~~~ 73 (128)
+.||| .++|+.||-+|...-.|+||||+|++ +|.|++|++|.|.||||+|..... |.|+.. +.| +-+.
T Consensus 152 hsWYHGpvSRsaaEy~LsSgInGSFLVRESEsSpgQ~sISlRyeGRVyHYRINt~~dgK~yvt~-----EsrF~TLaELV 226 (1157)
T KOG4278|consen 152 HSWYHGPVSRSAAEYILSSGINGSFLVRESESSPGQYSISLRYEGRVYHYRINTDNDGKMYVTQ-----ESRFRTLAELV 226 (1157)
T ss_pred cccccCccccchhhhhhhcCcccceEEeeccCCCcceeEEEEecceEEEEEeeccCCccEEEee-----hhhhhHHHHHH
Confidence 47999 79999999999888889999999997 899999999999999999998765 555432 223 3444
Q ss_pred HhhcCCCCCCCcccCCcccccCCCC--ccc---cccCCCHHHH--HHhhccCCCCceEeccC
Q psy9697 74 DATNHPRDSHPCRTQPRCVITSRPR--GVV---LRWRLSRIMF--RHLADYNKLSGVQRAMW 128 (128)
Q Consensus 74 ~l~~l~~~~~~~rl~nrC~~tgr~~--g~~---~~~~l~R~~f--r~~~~~G~~~gv~k~~W 128 (128)
..+..-.|++.|-|.-+-.+++.|+ |+. ++|++.|..+ +.+++-||.+.|..+.|
T Consensus 227 HHHStvADGLittLhYPApK~nKptvygvSPn~DkWEmeRtdItMkhKLGGGQYGeVYeGvW 288 (1157)
T KOG4278|consen 227 HHHSTVADGLITTLHYPAPKKNKPTVYGVSPNADKWEMERTDITMKHKLGGGQYGEVYEGVW 288 (1157)
T ss_pred hhccccccceeEeeeccCccCCCCceeeecCCcchhhccchheeeeeccCCCcccceeeeee
Confidence 4677888999999999999988887 333 8999999966 88999999999999998
No 10
>cd00173 SH2 Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
Probab=99.72 E-value=3.9e-17 Score=105.66 Aligned_cols=85 Identities=25% Similarity=0.394 Sum_probs=64.9
Q ss_pred CCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeeccccccc--c---cCCCHHHHHHHHH
Q psy9697 2 AWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDDNKIGL--G---TFKPNEVMAARED 74 (128)
Q Consensus 2 ~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~k~i~~--n---~~L~~~~r~~~~~ 74 (128)
+||| .|+|++||++|+...+|+||||.|++ ++.|+||+..++.|+||+|......+... . +++++.+.
T Consensus 1 ~w~~g~i~r~~Ae~~L~~~~~G~FLiR~s~~~~~~~~Lsv~~~~~v~H~~I~~~~~~~~~~~~~~~f~sl~eLv~----- 75 (94)
T cd00173 1 PWYHGPISREEAEELLKKKPDGTFLVRDSESSPGDYVLSVRVKGKVKHYRIERTDDGYYLLGEGRSFPSLPELIE----- 75 (94)
T ss_pred CccccCCCHHHHHHHHhcCCCceEEEEecCCCCCCEEEEEEECCEEEEEEEEECCCCeEEecCCCccCCHHHHHH-----
Confidence 7999 89999999999778999999999996 89999999999999999999887655433 3 33333333
Q ss_pred hhcCCC--CCCCcccCCcc
Q psy9697 75 ATNHPR--DSHPCRTQPRC 91 (128)
Q Consensus 75 l~~l~~--~~~~~rl~nrC 91 (128)
++..+. +..++.+..+|
T Consensus 76 ~y~~~~~~~~~~~~L~~p~ 94 (94)
T cd00173 76 HYQKNPLSDGLGVKLRYPV 94 (94)
T ss_pred HHhhCccCCCcccEeCCcC
Confidence 333333 66666666665
No 11
>smart00252 SH2 Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
Probab=99.70 E-value=1.1e-16 Score=102.03 Aligned_cols=61 Identities=30% Similarity=0.502 Sum_probs=53.9
Q ss_pred CCCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeec-ccccccc
Q psy9697 1 MAWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRD-DNKIGLG 61 (128)
Q Consensus 1 ~~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~-~k~i~~n 61 (128)
++||| .|+|++||++|..+.+|+||||.|++ ++.|+||+..++.|+||+|.... .++.+.+
T Consensus 1 ~~w~~g~i~r~~Ae~lL~~~~~G~FLvR~s~~~~~~~~Lsv~~~~~~~h~~I~~~~~~~~~l~~ 64 (84)
T smart00252 1 QPWYHGFISREEAEKLLKNEGDGDFLVRDSESEPGDYVLSVRVKGKVKHYRIRRNEDGKFYLDG 64 (84)
T ss_pred CCeecccCCHHHHHHHHhcCCCcEEEEEcCCCCCCCEEEEEEECCEEEEEEEEECCCCcEEECC
Confidence 58999 89999999999666799999999998 89999999999999999999877 4555544
No 12
>PF00017 SH2: SH2 domain; InterPro: IPR000980 The Src homology 2 (SH2) domain is a protein domain of about 100 amino-acid residues first identified as a conserved sequence region between the oncoproteins Src and Fps []. Similar sequences were later found in many other intracellular signal-transducing proteins []. SH2 domains function as regulatory modules of intracellular signalling cascades by interacting with high affinity to phosphotyrosine-containing target peptides in a sequence-specific, SH2 domains recognise between 3-6 residues C-terminal to the phosphorylated tyrosine in a fashion that differs from one SH2 domain to another, and strictly phosphorylation-dependent manner [, , , ]. They are found in a wide variety of protein contexts e.g., in association with catalytic domains of phospholipase Cy (PLCy) and the non-receptor protein tyrosine kinases; within structural proteins such as fodrin and tensin; and in a group of small adaptor molecules, i.e Crk and Nck. The domains are frequently found as repeats in a single protein sequence and will then often bind both mono- and di-phosphorylated substrates. The structure of the SH2 domain belongs to the alpha+beta class, its overall shape forming a compact flattened hemisphere. The core structural elements comprise a central hydrophobic anti-parallel beta-sheet, flanked by 2 short alpha-helices. The loop between strands 2 and 3 provides many of the binding interactions with the phosphate group of its phosphopeptide ligand, and is hence designated the phosphate binding loop, the phosphorylated ligand binds perpendicular to the beta-sheet and typically interacts with the phosphate binding loop and a hydrophobic binding pocket that interacts with a pY+3 side chain. The N- and C-termini of the domain are close together in space and on the opposite face from the phosphopeptide binding surface and it has been speculated that this has facilitated their integration into surface-exposed regions of host proteins [].; GO: 0005515 protein binding; PDB: 1M27_A 1KA6_A 1D4W_B 1D4T_A 1D1Z_B 1KA7_A 1UUR_A 1UUS_A 1BLJ_A 1BLK_A ....
Probab=99.67 E-value=1.6e-16 Score=99.83 Aligned_cols=54 Identities=31% Similarity=0.671 Sum_probs=50.7
Q ss_pred CCC-CCCHHHHHHhHhc-CCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeeccc
Q psy9697 3 WFH-SVNRERAVQMVAA-GGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDDN 56 (128)
Q Consensus 3 W~~-~i~r~~ae~ll~~-~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~k 56 (128)
||| .|+|++||++|.. .++|+||||.|.+ +|.|+||++.+++|+||+|.+.+.+
T Consensus 1 W~~g~isr~~Ae~~L~~~~~~G~FLvR~s~~~~~~~~Lsv~~~~~v~h~~I~~~~~~ 57 (77)
T PF00017_consen 1 WFHGFISRQEAERLLMQGKPDGTFLVRPSSSKPGKYVLSVRFDGKVKHFRINRTENG 57 (77)
T ss_dssp TBEESSHHHHHHHHHHTTSSTTEEEEEEESSSTTSEEEEEEETTEEEEEEEEEETTS
T ss_pred CcCCCCCHHHHHHHHHhcCCCCeEEEEeccccccccccccccccccEEEEEEecCCc
Confidence 998 8999999999966 7899999999996 8999999999999999999999876
No 13
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=99.36 E-value=3.6e-13 Score=78.84 Aligned_cols=41 Identities=22% Similarity=0.443 Sum_probs=39.1
Q ss_pred cCCCCCCCcccCCcccccCCCCccccccC--CCHHHHHHhhcc
Q psy9697 77 NHPRDSHPCRTQPRCVITSRPRGVVLRWR--LSRIMFRHLADY 117 (128)
Q Consensus 77 ~l~~~~~~~rl~nrC~~tgr~~g~~~~~~--l~R~~fr~~~~~ 117 (128)
..|+++++++..|+|+.||||+|++++|+ |||++|||+|..
T Consensus 3 ~~p~~~~~~r~~nrC~~~Gr~rgvirkf~l~lcR~~FRe~A~~ 45 (52)
T PRK05766 3 KPPKKRKYGKGARECQRCGRKQGLIRKYGLYLCRQCFREVAPK 45 (52)
T ss_pred CCCCCCCCCCCCceeecCCCCceeHHhhCCcccHHHHHHHHHH
Confidence 47999999999999999999999999999 999999999976
No 14
>KOG1264|consensus
Probab=99.24 E-value=1.3e-11 Score=104.77 Aligned_cols=60 Identities=23% Similarity=0.439 Sum_probs=52.6
Q ss_pred CCCCC-CCCHHHHHHhH-hcCCcccEEEeeCCCCCCEEEEEEeCCEeeEEeeeeeccccccc
Q psy9697 1 MAWFH-SVNRERAVQMV-AAGGEGCFLVRPSSSSEPLTLTLWYGGRAYNIFIRKRDDNKIGL 60 (128)
Q Consensus 1 ~~W~~-~i~r~~ae~ll-~~~~~G~FlvR~s~~~~~~~lsv~~~~~v~hy~I~~~~~k~i~~ 60 (128)
.|||| .++|++||++| ....||+||||.++.++.|++|+..+++|+|++|.+.+--+.+.
T Consensus 648 k~W~~as~treqAE~mL~rvp~DGaFLiR~~~~~nsy~iSfr~~gkikHcRi~rdGr~fvl~ 709 (1267)
T KOG1264|consen 648 KPWYHASLTREQAEDMLMRVPRDGAFLIRKREGSNSYAISFRARGKIKHCRINRDGRHFVLG 709 (1267)
T ss_pred CccccccccHHHHHHHHhhCccCcceEEEeccCCceEEEEEEEcCcEeEEEEccCceEEEec
Confidence 48999 89999999999 77899999999666688999999999999999999877655443
No 15
>KOG4792|consensus
Probab=99.22 E-value=1.9e-11 Score=90.85 Aligned_cols=52 Identities=27% Similarity=0.510 Sum_probs=48.5
Q ss_pred CCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeee
Q psy9697 2 AWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKR 53 (128)
Q Consensus 2 ~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~ 53 (128)
+||. .+||++|..+|+....|.||||||++ +|+|+|||.-+.+|-||-|.+.
T Consensus 12 swYfg~mSRqeA~~lL~~~r~G~FLvRDSst~pGdYvLsV~E~srVshYiIn~~ 65 (293)
T KOG4792|consen 12 SWYFGPMSRQEAVALLQGQRHGVFLVRDSSTSPGDYVLSVSENSRVSHYIINSS 65 (293)
T ss_pred ceecCcccHHHHHHHhcCcceeeEEEecCCCCCCceEEEEecCcceeeeeecCC
Confidence 5997 79999999999877799999999998 9999999999999999999873
No 16
>KOG1264|consensus
Probab=99.12 E-value=1.6e-10 Score=98.22 Aligned_cols=113 Identities=22% Similarity=0.369 Sum_probs=73.5
Q ss_pred CCCC-CCC-HHHHHHhHh------cCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeee-cc---cccccccCCCHHH
Q psy9697 2 AWFH-SVN-RERAVQMVA------AGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKR-DD---NKIGLGTFKPNEV 68 (128)
Q Consensus 2 ~W~~-~i~-r~~ae~ll~------~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~-~~---k~i~~n~~L~~~~ 68 (128)
.||| ++- |.+||++|+ ..+||+||||+|+. .|+|+||+|.+|+|.|-+|+.. .. |||..++..-+.+
T Consensus 535 ~WFHgkle~R~eAekll~eycke~G~~dGtFlVReS~tFvgDytLSfwr~grv~HcRIrsk~e~gt~Kyyl~dN~vfdsl 614 (1267)
T KOG1264|consen 535 KWFHGKLEGRTEAEKLLQEYCKETGGKDGTFLVRESETFVGDYTLSFWRSGRVQHCRIRSKMEGGTLKYYLTDNLVFDSL 614 (1267)
T ss_pred hhhhcccccchHHHHHHHHHHHHhCCCCccEEEeeccccccceeeeeeECCceeeEEEEeeecCCceeEEEecchhHHHH
Confidence 6999 787 999999992 13699999999998 9999999999999999999854 32 6665543322222
Q ss_pred HHHHHHhh--cCCCCCCCcccCCcccccCCCCccccccC---CCHHHHHHhhc
Q psy9697 69 MAAREDAT--NHPRDSHPCRTQPRCVITSRPRGVVLRWR---LSRIMFRHLAD 116 (128)
Q Consensus 69 r~~~~~l~--~l~~~~~~~rl~nrC~~tgr~~g~~~~~~---l~R~~fr~~~~ 116 (128)
-+....|. -+...---.+|..||.... |+- .+.|= ++|.+--++++
T Consensus 615 Y~LI~~Y~~~~Lr~aeF~m~LtePvPqp~-~He-~k~W~~as~treqAE~mL~ 665 (1267)
T KOG1264|consen 615 YALIQHYRETHLRCAEFEMRLTEPVPQPN-PHE-SKPWYHASLTREQAEDMLM 665 (1267)
T ss_pred HHHHHHHHhccccccceEEEecCCCCCCC-ccc-CCccccccccHHHHHHHHh
Confidence 12222121 2333333467889998744 331 13332 66665544444
No 17
>KOG4637|consensus
Probab=99.12 E-value=1.8e-10 Score=90.63 Aligned_cols=91 Identities=24% Similarity=0.248 Sum_probs=69.0
Q ss_pred CCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeecccc-cccccCCCHHHH----HHHHH
Q psy9697 2 AWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDDNK-IGLGTFKPNEVM----AARED 74 (128)
Q Consensus 2 ~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~k~-i~~n~~L~~~~r----~~~~~ 74 (128)
+||. +|||+++.+.|.+.+||+||||+-++ +|+||||++.++-++-++|-..+.|| ++...++...++ +....
T Consensus 24 ~WYWgdisReev~~~L~d~PDGsFlVRdAstm~GdYTLtl~k~g~~KLikI~h~DgKyGF~d~ltf~SVVelIn~yr~~S 103 (464)
T KOG4637|consen 24 EWYWGDISREEVNKKLRDQPDGSFLVRDASTMQGDYTLTLRKGGNNKLIKIVHRDGKYGFSDPLTFNSVVELINHYRNES 103 (464)
T ss_pred cccccccCHHHHHHHhcCCCCCcEEeeccccCCCceEEEEecCCccceeeeEEecCccCCCCchhhHHHHHHHHHHhhhH
Confidence 7997 89999999999999999999999988 99999999999999999999888877 332233333333 22222
Q ss_pred hhcCCCCCCCcccCCcccc
Q psy9697 75 ATNHPRDSHPCRTQPRCVI 93 (128)
Q Consensus 75 l~~l~~~~~~~rl~nrC~~ 93 (128)
|. +-...+-+++.+|-..
T Consensus 104 L~-~yN~~LDvrLlyPVs~ 121 (464)
T KOG4637|consen 104 LA-QYNPKLDVRLLYPVSR 121 (464)
T ss_pred HH-hhCcccceeeechHHH
Confidence 22 3344566777777664
No 18
>KOG4226|consensus
Probab=99.09 E-value=2.6e-10 Score=86.95 Aligned_cols=59 Identities=25% Similarity=0.396 Sum_probs=52.2
Q ss_pred CCCCC-CCCHHHHHHhH-hcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeecccccc
Q psy9697 1 MAWFH-SVNRERAVQMV-AAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDDNKIG 59 (128)
Q Consensus 1 ~~W~~-~i~r~~ae~ll-~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~k~i~ 59 (128)
.|||. +|+|.+||.+| ..+.+|.||||+|++ +|+|++|+...++-+||++...+.-+-|
T Consensus 281 ~~WYyG~itR~qae~~Ln~hG~eGdFLiRDSEsnpgD~SvSlka~grNKHFkVq~~d~~ycI 342 (379)
T KOG4226|consen 281 RPWYYGNITRHQAECALNEHGHEGDFLIRDSESNPGDFSVSLKASGRNKHFKVQLVDNVYCI 342 (379)
T ss_pred CcceeccccHHHHHHHHhccCccCceEEecCCCCCcceeEEeeccCCCcceEEEEecceEEe
Confidence 37997 89999999999 667899999999998 9999999999999999999877664433
No 19
>KOG0790|consensus
Probab=99.07 E-value=2.4e-10 Score=92.01 Aligned_cols=58 Identities=26% Similarity=0.491 Sum_probs=52.9
Q ss_pred CCCC-CCCHHHHHHhH-hcCCcccEEEeeCCC-CCCEEEEEEeCC---------EeeEEeeeeecccccc
Q psy9697 2 AWFH-SVNRERAVQMV-AAGGEGCFLVRPSSS-SEPLTLTLWYGG---------RAYNIFIRKRDDNKIG 59 (128)
Q Consensus 2 ~W~~-~i~r~~ae~ll-~~~~~G~FlvR~s~~-~~~~~lsv~~~~---------~v~hy~I~~~~~k~i~ 59 (128)
-||| +++-.+||.|| +..+.|+||||+|.+ ||+|+|||+.++ +|.|..|+..+.+|-+
T Consensus 111 rWfHG~LsgkeAekLl~ekgk~gsfLvReSqs~PGdfVlSvrTdd~~~~~~~~~kVtHvmI~~q~~kydV 180 (600)
T KOG0790|consen 111 RWFHGHLSGKEAEKLLQEKGKHGSFLVRESQSHPGDFVLSVRTDDKKESNDSKLKVTHVMIRCQEGKYDV 180 (600)
T ss_pred hhhccCCCchhHHHHHHhcCCCccEEEeccccCCCceEEEEEcCCcccCCCCccceEEEEEEeccccccc
Confidence 4999 89999999999 778999999999988 999999999976 8999999999888744
No 20
>KOG4637|consensus
Probab=98.93 E-value=1.2e-09 Score=86.13 Aligned_cols=89 Identities=18% Similarity=0.249 Sum_probs=68.8
Q ss_pred CCC-CCCHHHHHHhHhcCCcccEEEeeCCCCCCEEEEEEeCCEeeEEeeeeecccc-cc----cccCCCHHHH-HHHHHh
Q psy9697 3 WFH-SVNRERAVQMVAAGGEGCFLVRPSSSSEPLTLTLWYGGRAYNIFIRKRDDNK-IG----LGTFKPNEVM-AAREDA 75 (128)
Q Consensus 3 W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~~~~~~lsv~~~~~v~hy~I~~~~~k~-i~----~n~~L~~~~r-~~~~~l 75 (128)
|+- .+.|.+||++|+..+||+||||+|+..|.|+|||.+++.|+|--|...+.++ +. --.+|.+.++ ++...|
T Consensus 334 w~~~~a~r~kAe~llrg~~dGtFLIR~ss~~g~yalSV~~~~~V~HClIy~tatG~GFa~pyn~y~tlk~lV~hY~h~SL 413 (464)
T KOG4637|consen 334 WRVRDANRDKAEELLRGKPDGTFLIRESSKGGCYALSVVHDGEVKHCLIYQTATGFGFAEPYNLYSTLKELVLHYQHTSL 413 (464)
T ss_pred hHHhhhhHHHHHHHhcCCCCCeEEEeeccCCCceEEEEEECCceeeeEEeeccccccccchhHHHHHHHHHHHHHhhhhH
Confidence 775 7999999999999999999999987789999999999999999998887644 32 2256777777 444323
Q ss_pred hcCCCCCCCcccCCccc
Q psy9697 76 TNHPRDSHPCRTQPRCV 92 (128)
Q Consensus 76 ~~l~~~~~~~rl~nrC~ 92 (128)
- ...|+.-|.++.|-.
T Consensus 414 e-~HnDal~ttLr~Pv~ 429 (464)
T KOG4637|consen 414 E-QHNDALTTTLRYPVF 429 (464)
T ss_pred H-hhcccccccccccee
Confidence 2 345667777776654
No 21
>KOG0194|consensus
Probab=98.79 E-value=2.2e-08 Score=82.09 Aligned_cols=115 Identities=17% Similarity=0.221 Sum_probs=79.0
Q ss_pred CCCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CC---CE-EEEEEeC--CEeeEEeeeeecccccccc----cCCCHHH
Q psy9697 1 MAWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SE---PL-TLTLWYG--GRAYNIFIRKRDDNKIGLG----TFKPNEV 68 (128)
Q Consensus 1 ~~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~---~~-~lsv~~~--~~v~hy~I~~~~~k~i~~n----~~L~~~~ 68 (128)
++||| -+.|++|+.+|.. +|.||||.|+. +| .+ .|||... .+++||.|++.+.+++... +++++.+
T Consensus 49 ~~~yHG~l~red~~~lL~~--~GDfLvR~s~~~~~~~~~~~vlSv~~~~~~~~~h~vi~~~~~~~~~~~~~~F~si~~li 126 (474)
T KOG0194|consen 49 LPYYHGLLPREDAEKLLKN--DGDFLVRASEPKEGEKREFVVLSVKWSVFKKIKHYVIKRNGNLFFFEGLRKFPTISELV 126 (474)
T ss_pred CccccccccHhHHHHHhCC--CCceEEEeecccCCcceeEEEEEEEeecCCceeEEEEEEcCCeeEEeccccCCcHHHHH
Confidence 58999 5999999999954 79999999986 44 23 8888875 7899999999887665433 3333333
Q ss_pred HHHHHHhhcCCCCCCCcccCCcccccCCCCccccccCC--CHHHHHHhhccCCCCceEecc
Q psy9697 69 MAAREDATNHPRDSHPCRTQPRCVITSRPRGVVLRWRL--SRIMFRHLADYNKLSGVQRAM 127 (128)
Q Consensus 69 r~~~~~l~~l~~~~~~~rl~nrC~~tgr~~g~~~~~~l--~R~~fr~~~~~G~~~gv~k~~ 127 (128)
..+. .+..+--+..+.|++|-.. ..|+| +-+.+-+++|+|.|+.|.+|.
T Consensus 127 -~~~~-~~~~~~~~~~~~L~~PI~r--------~~Wel~H~~v~l~kkLGeGaFGeV~~G~ 177 (474)
T KOG0194|consen 127 -NYYK-FSKLEITGKNFFLKRPIPR--------QKWELSHSDIELGKKLGEGAFGEVFKGK 177 (474)
T ss_pred -HHHH-hcccceeccceeecccccc--------cccEEeccCccccceeecccccEEEEEE
Confidence 2222 3334444433344444333 44774 445667999999999999875
No 22
>KOG0790|consensus
Probab=98.77 E-value=1.5e-08 Score=81.79 Aligned_cols=89 Identities=20% Similarity=0.269 Sum_probs=67.4
Q ss_pred CCCC-CCCHHHHHHhH-hcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeeccccc-c---cccCCCHHHH-HHHH
Q psy9697 2 AWFH-SVNRERAVQMV-AAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDDNKI-G---LGTFKPNEVM-AARE 73 (128)
Q Consensus 2 ~W~~-~i~r~~ae~ll-~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~k~i-~---~n~~L~~~~r-~~~~ 73 (128)
.||| +|+-.+||.|| ....||.||.|.|++ +|.|+|++..+++|.|++|...+..+- . +-.++++.+. +...
T Consensus 5 ~wfh~~~~g~~ae~Ll~~~g~dgsfl~r~s~sNp~~fsl~~r~~~~v~hikiq~~~~~~~l~~gekfat~~ELvqyyme~ 84 (600)
T KOG0790|consen 5 RWFHPDLSGVEAETLLKERGVDGSFLARPSESNPGDFSLSVRRGDKVTHIKIQNSGDFYDLYGGEKFATLAELVQYYMEH 84 (600)
T ss_pred hhcCCCccchhHHHHHHHhccccchhhccccCCCcceeEEEEeCCceEEEEEeecCccccccCCccccchHHHHHHHHhh
Confidence 4999 89999999999 567999999999997 899999999999999999998876542 2 2256666666 2222
Q ss_pred HhhcCCCCCCCcccCCc
Q psy9697 74 DATNHPRDSHPCRTQPR 90 (128)
Q Consensus 74 ~l~~l~~~~~~~rl~nr 90 (128)
.-....+|+....++.|
T Consensus 85 ~~~lkekng~~ielK~p 101 (600)
T KOG0790|consen 85 HGQLKEKNGDVIELKYP 101 (600)
T ss_pred hHHHHhcCCCEEEecCC
Confidence 11234566666666665
No 23
>KOG2996|consensus
Probab=98.67 E-value=2.3e-08 Score=82.90 Aligned_cols=69 Identities=17% Similarity=0.291 Sum_probs=57.5
Q ss_pred CCCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeecccccc-cc---cCCCHHHH
Q psy9697 1 MAWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDDNKIG-LG---TFKPNEVM 69 (128)
Q Consensus 1 ~~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~k~i~-~n---~~L~~~~r 69 (128)
.+||. .+-|.+||..|....+|+||||.+.. .+.|++|+.++..|+|++|...+.++.+ .+ .++.+.+.
T Consensus 685 ~~WyaG~MERaqaes~Lk~~~ngT~LVR~r~kea~e~AISikynnevKHikI~~~dg~~~i~E~k~F~sl~ELVe 759 (865)
T KOG2996|consen 685 FPWYAGEMERAQAESTLKNRPNGTYLVRYRTKEAKEFAISIKYNNEVKHIKIETNDGKVHITEDKKFNSLVELVE 759 (865)
T ss_pred hhhhcchHhhhhhhhHhhcCCCceEEEEecccchhheeEEEEeccccceEEEEecCCeEEechhhhhhhHHHHHH
Confidence 47997 79999999999888999999999976 7889999999999999999988776644 33 34444444
No 24
>KOG1930|consensus
Probab=98.66 E-value=2.5e-08 Score=79.65 Aligned_cols=55 Identities=24% Similarity=0.437 Sum_probs=46.5
Q ss_pred CCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEe---------------CCEeeEEeeeeecccc
Q psy9697 3 WFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWY---------------GGRAYNIFIRKRDDNK 57 (128)
Q Consensus 3 W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~---------------~~~v~hy~I~~~~~k~ 57 (128)
||. +|+|+||-.||++.+-|+|+||||.+ .|.|-|.|.- +.-|+||-|....-+.
T Consensus 214 WYKP~isREQAIalLrdkePGtFvvRDS~SfrGayGLAlKVstPPPs~~~~~g~~~neLVRHFLIE~spkGV 285 (483)
T KOG1930|consen 214 WYKPNISREQAIALLRDKEPGTFVVRDSHSFRGAYGLALKVSTPPPSVQPGDGSDSNELVRHFLIEPSPKGV 285 (483)
T ss_pred ccCCCCCHHHHHHHhhcCCCCeEEEecCCcCCCccceEEEeccCCCcccCCCCCchhhhhhhheeccCCCce
Confidence 997 89999999999888889999999998 9999888754 1359999998664433
No 25
>KOG3751|consensus
Probab=98.41 E-value=5.6e-08 Score=79.65 Aligned_cols=90 Identities=23% Similarity=0.396 Sum_probs=70.1
Q ss_pred CCCC-CCCHHHHHHhH-hcC-CcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeecccc---cccc---cCCCHHHHHH
Q psy9697 2 AWFH-SVNRERAVQMV-AAG-GEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDDNK---IGLG---TFKPNEVMAA 71 (128)
Q Consensus 2 ~W~~-~i~r~~ae~ll-~~~-~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~k~---i~~n---~~L~~~~r~~ 71 (128)
.||| +|+|+++..+| +.+ .||.|++|+|.+ |..|++++.+..+|+||+|.-...+. +..+ +.+++. .+
T Consensus 520 ~~~~~kis~~es~~~ikq~glv~~~~l~r~sqsnP~~~~~~~~~~~~v~~~~~~P~~~~~~~~~t~~~g~t~~sd~--~q 597 (622)
T KOG3751|consen 520 TWFHGKISRDESQRLIKQQGLVDGLFLVRDSQSNPKIFVLSLCHPQKVKHFQILPVEDDGCTFFTLDDGPTKFSDL--IQ 597 (622)
T ss_pred cCcccccCchhhhhHHHhcccceeeeeecccccCcchhhhhccCCccccceEEecCCCCCceeeccCCCCcccccc--cc
Confidence 6998 89999999988 444 789999999987 88899999999999999998654422 2222 222222 55
Q ss_pred HHHhhcCCCCCCCcccCCcccc
Q psy9697 72 REDATNHPRDSHPCRTQPRCVI 93 (128)
Q Consensus 72 ~~~l~~l~~~~~~~rl~nrC~~ 93 (128)
+.+++.++++-.|+.++.+|..
T Consensus 598 l~~~~ql~k~~l~~al~~~~~r 619 (622)
T KOG3751|consen 598 LVEFYQLNKGVLPCALKHCCER 619 (622)
T ss_pred ccchhhcCCCcchHHHHHHHHh
Confidence 6667889999999999998864
No 26
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=98.38 E-value=1.5e-07 Score=55.14 Aligned_cols=32 Identities=22% Similarity=0.519 Sum_probs=29.1
Q ss_pred ccCCcccccCCCCccccccC--CCHHHHHHhhcc
Q psy9697 86 RTQPRCVITSRPRGVVLRWR--LSRIMFRHLADY 117 (128)
Q Consensus 86 rl~nrC~~tgr~~g~~~~~~--l~R~~fr~~~~~ 117 (128)
+-.++|..||+++|++++|+ +||++|||.|..
T Consensus 14 kGsr~C~vCg~~~gliRkygL~~CRqCFRe~A~~ 47 (54)
T PTZ00218 14 KGSRQCRVCSNRHGLIRKYGLNVCRQCFRENAEL 47 (54)
T ss_pred CCCCeeecCCCcchhhhhcCcchhhHHHHHhhHh
Confidence 34588999999999999999 999999999975
No 27
>KOG3601|consensus
Probab=98.31 E-value=1.5e-07 Score=69.36 Aligned_cols=57 Identities=16% Similarity=0.271 Sum_probs=51.0
Q ss_pred CCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeecc-ccc
Q psy9697 2 AWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDD-NKI 58 (128)
Q Consensus 2 ~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~-k~i 58 (128)
+||+ .|+|..||++|....+|.|++|.++. +|+|++++.+...|+|+++-+-+- +++
T Consensus 59 ~wve~~i~r~~ae~~l~~~~~G~fl~r~s~sSPg~fsgsvr~~d~vqhfkvvrpa~~k~~ 118 (222)
T KOG3601|consen 59 EWVEGLIPRPLAEDLLSKKRDGDFLIRLSESSPGDFSGSVRFPDGVQHFKVVRPAFGKYF 118 (222)
T ss_pred cceecccccchhhhhhhccCcchhhhhhhhcCcccccccccCCCCceeccccccCccccc
Confidence 7998 79999999999668999999999987 999999999999999999886654 553
No 28
>PF14633 SH2_2: SH2 domain; PDB: 3GXX_A 3GXW_B 3PJP_B 2XP1_A.
Probab=96.96 E-value=0.0027 Score=47.59 Aligned_cols=53 Identities=26% Similarity=0.363 Sum_probs=39.0
Q ss_pred CCCCCCCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEe-CCEeeEEeeeee
Q psy9697 1 MAWFHSVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWY-GGRAYNIFIRKR 53 (128)
Q Consensus 1 ~~W~~~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~-~~~v~hy~I~~~ 53 (128)
+|-|++++-.+||+.|.....|.++||+|+. ....++|..- ++...|+.|.-.
T Consensus 38 HP~F~n~~~~qAe~~L~~~~~Ge~iIRPSSkG~dhL~vTwKv~d~vyqHidV~E~ 92 (220)
T PF14633_consen 38 HPLFKNFNYKQAEEYLADQDVGEVIIRPSSKGPDHLTVTWKVADGVYQHIDVKEE 92 (220)
T ss_dssp STTEESS-HHHHHHHHCCS-TT-EEEEE-TTTTTEEEEEEEEETTEEEEEEEEEE
T ss_pred CCCccCCCHHHHHHHHhcCCCCCEEEeeCCCCCCeEEEEEEEcCCcEEEEEEEEC
Confidence 4667899999999999777779999999987 4557788755 566779988744
No 29
>KOG3506|consensus
Probab=94.69 E-value=0.009 Score=35.00 Aligned_cols=31 Identities=23% Similarity=0.486 Sum_probs=26.9
Q ss_pred cCCcccccCCCCccccccC--CCHHHHHHhhcc
Q psy9697 87 TQPRCVITSRPRGVVLRWR--LSRIMFRHLADY 117 (128)
Q Consensus 87 l~nrC~~tgr~~g~~~~~~--l~R~~fr~~~~~ 117 (128)
-...|..|+.-+|++++|| +||.+||+.|..
T Consensus 17 GsrsC~vCsn~~gLIrKYGL~vcr~cfr~~a~d 49 (56)
T KOG3506|consen 17 GSRSCRVCSNRHGLIRKYGLNVCRQCFREYAND 49 (56)
T ss_pred CCcceeeeccchhHHHHhhhHHhHHHHHhhccc
Confidence 3466999999999999988 799999998865
No 30
>KOG1856|consensus
Probab=90.99 E-value=0.39 Score=43.65 Aligned_cols=53 Identities=25% Similarity=0.354 Sum_probs=41.4
Q ss_pred CCCCCCCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEeC-CEeeEEeeeee
Q psy9697 1 MAWFHSVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWYG-GRAYNIFIRKR 53 (128)
Q Consensus 1 ~~W~~~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~~-~~v~hy~I~~~ 53 (128)
+|-|++++=+|||.+|..-..|-++||+|+. ....|++..-. +.-.|+.|+-.
T Consensus 1108 HP~F~n~n~eQAe~yL~~~d~ge~iiRpSSrgddhLvvtwKVsD~iYqhidV~E~ 1162 (1299)
T KOG1856|consen 1108 HPLFKNLNAEQAEAYLSDMDQGELIIRPSSRGDDHLVVTWKVSDGIYQHIDVQEL 1162 (1299)
T ss_pred CccccCCCHHHHHHHHHhcccccEEeccccCCCCceEEEEEecCchhhhhhhhhh
Confidence 4788999999999999777789999999987 45567776554 44467777643
No 31
>KOG3697|consensus
Probab=83.56 E-value=0.53 Score=36.81 Aligned_cols=37 Identities=5% Similarity=-0.047 Sum_probs=31.4
Q ss_pred CCCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEE
Q psy9697 1 MAWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTL 39 (128)
Q Consensus 1 ~~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv 39 (128)
||||+ .+++..+++.| ..+|.|+++.+.. ++.+.|+=
T Consensus 201 ~pp~~g~l~~~~~q~~l--~~~a~~~a~~~~~~p~~~~ls~ 239 (345)
T KOG3697|consen 201 MPPPGGFLDTRLKQRPL--APDAAQFAGKEQTYPQGRHLSD 239 (345)
T ss_pred CCCCCCccchhhhhccC--CcccchhhhhccCCcccccccc
Confidence 79999 89999999998 3468999999987 78887775
No 32
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=83.52 E-value=1.1 Score=24.25 Aligned_cols=24 Identities=13% Similarity=0.012 Sum_probs=21.4
Q ss_pred cccCCCHHHHHHhhccCCCCceEe
Q psy9697 102 LRWRLSRIMFRHLADYNKLSGVQR 125 (128)
Q Consensus 102 ~~~~l~R~~fr~~~~~G~~~gv~k 125 (128)
+.+++|+..+++++..|.||.++.
T Consensus 9 ~~lgis~~ti~~~~~~g~i~~~~~ 32 (49)
T TIGR01764 9 EYLGVSKDTVYRLIHEGELPAYRV 32 (49)
T ss_pred HHHCCCHHHHHHHHHcCCCCeEEe
Confidence 568999999999999999999864
No 33
>KOG4566|consensus
Probab=79.21 E-value=2.6 Score=32.40 Aligned_cols=53 Identities=23% Similarity=0.240 Sum_probs=39.2
Q ss_pred CCCC-CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeec
Q psy9697 2 AWFH-SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRD 54 (128)
Q Consensus 2 ~W~~-~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~ 54 (128)
+||- -.+.++|+..|.....|.|+||+|.. +--++|++.....-+.-+|...+
T Consensus 53 g~~w~~~~~~~~~~~l~~~p~~~~l~Rdss~~~~~~~I~vk~~~g~~~~r~~~~~ 107 (258)
T KOG4566|consen 53 GHYWGLETANEAELCLGQEPRGTFLVRDSSHRPYLFTISVKTHSGPKNLRIQYQD 107 (258)
T ss_pred CcccccccchhHHHhhcCCCccceeeecCcCccccceeEeeeccCCCCccccccc
Confidence 3554 57888888888555889999999987 55688888876666666665544
No 34
>PF12728 HTH_17: Helix-turn-helix domain
Probab=70.06 E-value=5.5 Score=22.13 Aligned_cols=25 Identities=12% Similarity=0.015 Sum_probs=21.6
Q ss_pred cccCCCHHHHHHhhccCCCCceEec
Q psy9697 102 LRWRLSRIMFRHLADYNKLSGVQRA 126 (128)
Q Consensus 102 ~~~~l~R~~fr~~~~~G~~~gv~k~ 126 (128)
+..++|+..+++++..|.||.++.+
T Consensus 9 ~~l~is~~tv~~~~~~g~i~~~~~g 33 (51)
T PF12728_consen 9 ELLGISRSTVYRWIRQGKIPPFKIG 33 (51)
T ss_pred HHHCcCHHHHHHHHHcCCCCeEEeC
Confidence 4578999999999999999998653
No 35
>smart00557 IG_FLMN Filamin-type immunoglobulin domains. These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).
Probab=67.51 E-value=8 Score=24.46 Aligned_cols=28 Identities=25% Similarity=0.538 Sum_probs=23.1
Q ss_pred hcCCcccEEEeeCCC-CCCEEEEEEeCCE
Q psy9697 17 AAGGEGCFLVRPSSS-SEPLTLTLWYGGR 44 (128)
Q Consensus 17 ~~~~~G~FlvR~s~~-~~~~~lsv~~~~~ 44 (128)
.++.||.|.|...-. .|.|.++|..++.
T Consensus 51 ~d~~dGty~v~y~P~~~G~~~i~V~~~g~ 79 (93)
T smart00557 51 KDNGDGTYTVSYTPTEPGDYTVTVKFGGE 79 (93)
T ss_pred EeCCCCEEEEEEEeCCCEeEEEEEEECCE
Confidence 467889999998865 7899999998873
No 36
>PF05486 SRP9-21: Signal recognition particle 9 kDa protein (SRP9); InterPro: IPR008832 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 9 kDa SRP9 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0045900 negative regulation of translational elongation, 0048500 signal recognition particle; PDB: 1E8O_A 1RY1_C.
Probab=64.20 E-value=33 Score=21.45 Aligned_cols=46 Identities=13% Similarity=0.096 Sum_probs=31.5
Q ss_pred HHHHHhHhcCCc-ccEEEeeCC-----CCCCEEEEEEeCCE--eeEEeeeeecc
Q psy9697 10 ERAVQMVAAGGE-GCFLVRPSS-----SSEPLTLTLWYGGR--AYNIFIRKRDD 55 (128)
Q Consensus 10 ~~ae~ll~~~~~-G~FlvR~s~-----~~~~~~lsv~~~~~--v~hy~I~~~~~ 55 (128)
++++.|++.+++ =.|.++-+. ..|..+|.+.++.. +..|+..+..+
T Consensus 10 ~~s~~L~~a~P~~TR~~~kY~~~~~~~~~~~l~lK~td~~~g~clKykT~k~~d 63 (79)
T PF05486_consen 10 EQSEKLYEANPSTTRYSIKYRHPSKKPPTGKLVLKTTDPHSGVCLKYKTDKAKD 63 (79)
T ss_dssp HHHHHHHHH-TTT-EEEEEBBT-----TTTBEEEEEE-SS---EEEEEE-SGGG
T ss_pred HHHHHHHHhCCCceEEEEEEecccccCCCceEEEEEeCCCceeEEEEEeCHHHH
Confidence 577888866654 458888887 56789999999866 89999876544
No 37
>KOG1856|consensus
Probab=58.84 E-value=46 Score=31.06 Aligned_cols=71 Identities=4% Similarity=-0.060 Sum_probs=52.1
Q ss_pred CCHHHHHHhHh--cCCcc---cEEEeeCCC-CCCEEEEEEeCCEeeEEeeeeecccccccccCCCHHHH--HHHHHhhc
Q psy9697 7 VNRERAVQMVA--AGGEG---CFLVRPSSS-SEPLTLTLWYGGRAYNIFIRKRDDNKIGLGTFKPNEVM--AAREDATN 77 (128)
Q Consensus 7 i~r~~ae~ll~--~~~~G---~FlvR~s~~-~~~~~lsv~~~~~v~hy~I~~~~~k~i~~n~~L~~~~r--~~~~~l~~ 77 (128)
=++++.|++|. .+.++ .|-..-|.. ||.|.|+...+++++|--+.....++...+..++...+ ...+.+.+
T Consensus 1211 Gt~~~~ek~L~~~k~~np~~~~Y~F~~s~~~PG~F~L~y~~~~k~~heyv~v~p~g~~~rg~~f~tld~L~~~FK~h~~ 1289 (1299)
T KOG1856|consen 1211 GTKKEVEKLLRDYKKVNPKKSVYFFCASHEHPGKFCLSYKPSSKPRHEYVKVVPEGFRFRGQNFGTLDELCRWFKRHYK 1289 (1299)
T ss_pred CCHHHHHHHHHHHhccCCCeeeEEEEecccCCceEEEEeccCCCccceeEEEcccceEEecccchhHHHHHHHHHHHhc
Confidence 35788899883 33344 444666765 99999999999999999999888888888878887666 44443433
No 38
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=57.34 E-value=9.3 Score=20.22 Aligned_cols=24 Identities=17% Similarity=0.156 Sum_probs=20.4
Q ss_pred cccCCCHHHHHHhhccCCCCceEe
Q psy9697 102 LRWRLSRIMFRHLADYNKLSGVQR 125 (128)
Q Consensus 102 ~~~~l~R~~fr~~~~~G~~~gv~k 125 (128)
+.+++++..++.....|.+|..+.
T Consensus 8 ~~lgvs~~tl~~~~~~g~~~~~~~ 31 (49)
T cd04762 8 ELLGVSPSTLRRWVKEGKLKAIRT 31 (49)
T ss_pred HHHCcCHHHHHHHHHcCCCCceeC
Confidence 568899999999999999997653
No 39
>PF00630 Filamin: Filamin/ABP280 repeat; InterPro: IPR017868 The many different actin cross-linking proteins share a common architecture, consisting of a globular actin-binding domain and an extended rod. Whereas their actin-binding domains consist of two calponin homology domains (see IPR001715 from INTERPRO), their rods fall into three families. The rod domain of the family including the Dictyostelium discoideum (Slime mould) gelation factor (ABP120) and human filamin (ABP280) is constructed from tandem repeats of a 100-residue motif that is glycine and proline rich []. The gelation factor's rod contains 6 copies of the repeat, whereas filamin has a rod constructed from 24 repeats. The resolution of the 3D structure of rod repeats from the gelation factor has shown that they consist of a beta-sandwich, formed by two beta-sheets arranged in an immunoglobulin-like fold [, ]. Because conserved residues that form the core of the repeats are preserved in filamin, the repeat structure should be common to the members of the gelation factor/filamin family. The head to tail homodimerisation is crucial to the function of the ABP120 and ABP280 proteins. This interaction involves a small portion at the distal end of the rod domains. For the gelation factor it has been shown that the carboxy-terminal repeat 6 dimerises through a double edge-to-edge extension of the beta-sheet and that repeat 5 contributes to dimerisation to some extent [, , ].; PDB: 2DI9_A 2EEC_A 2DIC_A 2EEA_A 2DMC_A 2EE9_A 2D7O_A 2D7N_A 2K7P_A 2NQC_A ....
Probab=53.10 E-value=11 Score=23.75 Aligned_cols=27 Identities=15% Similarity=0.400 Sum_probs=20.2
Q ss_pred cCCcccEEEeeCCC-CCCEEEEEEeCCE
Q psy9697 18 AGGEGCFLVRPSSS-SEPLTLTLWYGGR 44 (128)
Q Consensus 18 ~~~~G~FlvR~s~~-~~~~~lsv~~~~~ 44 (128)
++.||.|.|...-. +|.|.|+|..++.
T Consensus 66 ~~~~G~y~v~y~p~~~G~y~i~V~~~g~ 93 (101)
T PF00630_consen 66 DNGDGTYTVSYTPTEPGKYKISVKINGQ 93 (101)
T ss_dssp EESSSEEEEEEEESSSEEEEEEEEESSE
T ss_pred ECCCCEEEEEEEeCccEeEEEEEEECCE
Confidence 45678888887754 7888888887763
No 40
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=50.21 E-value=64 Score=20.43 Aligned_cols=39 Identities=10% Similarity=0.199 Sum_probs=28.5
Q ss_pred CCHHHHHHhHh--cCCcccEEEeeCCC-CCCEEEEEEe-CCEe
Q psy9697 7 VNRERAVQMVA--AGGEGCFLVRPSSS-SEPLTLTLWY-GGRA 45 (128)
Q Consensus 7 i~r~~ae~ll~--~~~~G~FlvR~s~~-~~~~~lsv~~-~~~v 45 (128)
++=+|+...|+ .++-|+|+.|-|.+ .|.+++-... +++|
T Consensus 9 lTYdevk~~L~~~~~kpGsYiFRlSCTrLGQWAIGyV~~dg~I 51 (86)
T PF02762_consen 9 LTYDEVKARLQHYRDKPGSYIFRLSCTRLGQWAIGYVTQDGKI 51 (86)
T ss_dssp --HHHHHHHHGGGTTSTTEEEEEEESSSTTSEEEEEEETTSEE
T ss_pred EeHHHHHHHHHHHhCCcccEEEeeccccccceeEEEEcCCCcE
Confidence 77889988883 45779999999987 7888877655 3444
No 41
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=40.64 E-value=14 Score=25.81 Aligned_cols=23 Identities=17% Similarity=0.186 Sum_probs=20.5
Q ss_pred cccCCCHHHHHHhhccCCCCceE
Q psy9697 102 LRWRLSRIMFRHLADYNKLSGVQ 124 (128)
Q Consensus 102 ~~~~l~R~~fr~~~~~G~~~gv~ 124 (128)
++++|||..++++...|.|-+..
T Consensus 111 ~~L~lSrs~l~~l~~~G~I~~~~ 133 (142)
T PF06353_consen 111 RQLGLSRSRLKRLIEQGLIRSDP 133 (142)
T ss_pred HHhCcCHHHHHHHHHCCCEEecC
Confidence 67999999999999999987753
No 42
>KOG3508|consensus
Probab=40.04 E-value=9.3 Score=34.41 Aligned_cols=50 Identities=14% Similarity=0.221 Sum_probs=38.1
Q ss_pred CCCC-CCCHHHHHHhH-hcCCcccEEEeeCCC-CCCEEEEEEeC-CEeeEEeee
Q psy9697 2 AWFH-SVNRERAVQMV-AAGGEGCFLVRPSSS-SEPLTLTLWYG-GRAYNIFIR 51 (128)
Q Consensus 2 ~W~~-~i~r~~ae~ll-~~~~~G~FlvR~s~~-~~~~~lsv~~~-~~v~hy~I~ 51 (128)
.||| ++.|.-||..+ ....-|.++||++.. ++.+.++..-. +.+-|+++.
T Consensus 82 ~~~~~~lrr~i~e~r~r~~e~s~~~wi~e~~~lp~~~~l~~~~~~d~~l~~r~~ 135 (932)
T KOG3508|consen 82 KWYMENLRRTIAESRLRRAENSGSYWIREAKRLPGKGKLSCLLQLDGTLYARTI 135 (932)
T ss_pred hhhhcchhhhcccchhhccCCceeEEeeccCcCCCcceeehhhccchhHHhhhh
Confidence 4898 89999999887 445679999999987 77776665443 337888775
No 43
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=40.01 E-value=5.5 Score=22.49 Aligned_cols=22 Identities=23% Similarity=0.151 Sum_probs=15.9
Q ss_pred cccccCCCHHHHHHhhccCCCC
Q psy9697 100 VVLRWRLSRIMFRHLADYNKLS 121 (128)
Q Consensus 100 ~~~~~~l~R~~fr~~~~~G~~~ 121 (128)
+.+..++||..+.++...|.||
T Consensus 9 v~~~~g~s~~ti~~~~k~g~FP 30 (51)
T PF05930_consen 9 VAELLGVSRSTIYRLIKDGKFP 30 (51)
T ss_dssp HHHHHSS-HHHHHHHHHHHH--
T ss_pred HHHHHCCCHHHHHHHHhcccCC
Confidence 3456889999999999999997
No 44
>PF14633 SH2_2: SH2 domain; PDB: 3GXX_A 3GXW_B 3PJP_B 2XP1_A.
Probab=39.32 E-value=30 Score=25.96 Aligned_cols=64 Identities=9% Similarity=-0.040 Sum_probs=39.1
Q ss_pred CCCHHHHHHhH-h---cC-CcccEEEeeCCC-CCCEEEEEEeCCEeeEEe--eeeecccccccccCCCHHHH
Q psy9697 6 SVNRERAVQMV-A---AG-GEGCFLVRPSSS-SEPLTLTLWYGGRAYNIF--IRKRDDNKIGLGTFKPNEVM 69 (128)
Q Consensus 6 ~i~r~~ae~ll-~---~~-~~G~FlvR~s~~-~~~~~lsv~~~~~v~hy~--I~~~~~k~i~~n~~L~~~~r 69 (128)
.=+++++|++| . .+ .--.|-+..+.. ||.|.|+...+....|.. |.....++......++...+
T Consensus 140 ~g~~~e~e~~L~~~k~~nP~~i~Y~f~~~~~~PG~F~L~y~~~~~~~~~~~~v~V~p~Gf~~r~~~f~~~~~ 211 (220)
T PF14633_consen 140 DGTKEEVEEWLKEEKKANPKRIPYAFCISKEHPGYFILSYKPNKNPRHEYWPVKVTPDGFRFRKQVFPSLDR 211 (220)
T ss_dssp SS-CCCCHHHHHCHHHHSTTS-EEEEEE-TTSTTEEEEEEESSTTS-EEEEEEEE-SSSEEETTEEESSHHH
T ss_pred CCCHHHHHHHHHHHHHhCCCCceEEEEECCCCCCEEEEEEEcCCCCceEEeeEEEecCcEEEecccCCCHHH
Confidence 45677888888 2 23 334666777755 999999998876655554 87777777665555555433
No 45
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=36.16 E-value=31 Score=21.50 Aligned_cols=19 Identities=16% Similarity=0.205 Sum_probs=17.2
Q ss_pred cc-CCCHHHHHHhhccCCCC
Q psy9697 103 RW-RLSRIMFRHLADYNKLS 121 (128)
Q Consensus 103 ~~-~l~R~~fr~~~~~G~~~ 121 (128)
.| +|+...|+++|..|.||
T Consensus 24 yf~~lt~~~a~rk~~~g~lp 43 (76)
T PF11112_consen 24 YFPHLTPKTAKRKANAGELP 43 (76)
T ss_pred HHccCCHHHHHHHHHCCCCC
Confidence 35 89999999999999987
No 46
>PF09430 DUF2012: Protein of unknown function (DUF2012); InterPro: IPR019008 This domain is found in different proteins, including uncharacterised protein family UPF0480 and nodal modulators. A nodal modulator has been identified as part of a protein complex that participates in the nodal signaling pathway during vertebrate development [].
Probab=35.67 E-value=42 Score=22.45 Aligned_cols=35 Identities=9% Similarity=0.082 Sum_probs=25.2
Q ss_pred cCCcccEEEeeCCCCCCEEEEEEeCCEe-eEEeeeee
Q psy9697 18 AGGEGCFLVRPSSSSEPLTLTLWYGGRA-YNIFIRKR 53 (128)
Q Consensus 18 ~~~~G~FlvR~s~~~~~~~lsv~~~~~v-~hy~I~~~ 53 (128)
-++||+|.+.+- .+|.|.|.|.+.+-+ -.|+|.-.
T Consensus 26 v~~dG~F~f~~V-p~GsY~L~V~s~~~~F~~~RVdV~ 61 (123)
T PF09430_consen 26 VRSDGSFVFHNV-PPGSYLLEVHSPDYVFPPYRVDVS 61 (123)
T ss_pred ecCCCEEEeCCC-CCceEEEEEECCCccccCEEEEEe
Confidence 357999999864 358999999886544 34666644
No 47
>KOG3667|consensus
Probab=34.30 E-value=43 Score=29.32 Aligned_cols=46 Identities=20% Similarity=0.297 Sum_probs=31.6
Q ss_pred CCCHHHHHHhHhcCCcccEEEeeCCC-CCCEEEEEEe-CCEeeEEeee
Q psy9697 6 SVNRERAVQMVAAGGEGCFLVRPSSS-SEPLTLTLWY-GGRAYNIFIR 51 (128)
Q Consensus 6 ~i~r~~ae~ll~~~~~G~FlvR~s~~-~~~~~lsv~~-~~~v~hy~I~ 51 (128)
.++++++-.+|....+|+|++|-|++ -|..++.-.. +....|+-|.
T Consensus 569 finkq~~~~ll~~~~~GtflLrfs~S~~GgiT~~~v~~~~~~~~~~i~ 616 (682)
T KOG3667|consen 569 FINKQQERALLMTKPDGTFLLRFSASEEGGITIAWVEDQKQNLIMMIM 616 (682)
T ss_pred ecchhhhhhhhhcCCCCCceeeeeccccCceeEEecccccccceeEec
Confidence 48888888888888889999999987 4544444322 2223455555
No 48
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.81 E-value=23 Score=26.03 Aligned_cols=24 Identities=21% Similarity=0.275 Sum_probs=21.6
Q ss_pred cccCCCHHHHHHhhccCCCCceEe
Q psy9697 102 LRWRLSRIMFRHLADYNKLSGVQR 125 (128)
Q Consensus 102 ~~~~l~R~~fr~~~~~G~~~gv~k 125 (128)
++.+|||.+|..++..|+|-|...
T Consensus 147 seL~LSrS~lq~lie~g~Irgdtd 170 (203)
T COG4332 147 SELGLSRSELQRLIETGQIRGDTD 170 (203)
T ss_pred HHhCcCHHHHHHHHHcCceeecch
Confidence 678999999999999999998754
No 49
>PF00432 Prenyltrans: Prenyltransferase and squalene oxidase repeat This Prosite family is a subset of the Pfam family.; InterPro: IPR001330 The beta subunit of the farnesyltransferases is responsible for peptide binding. Squalene-hopene cyclase is a bacterial enzyme that catalyzes the cyclization of squalene into hopene, a key step in hopanoid (triterpenoid) metabolism []. Lanosterol synthase (5.4.99.7 from EC) (oxidosqualene-lanosterol cyclase) catalyzes the cyclization of (S)-2,3-epoxysqualene to lanosterol, the initial precursor of cholesterol, steroid hormones and vitamin D in vertebrates and of ergosterol in fungi []. Cycloartenol synthase () (2,3-epoxysqualene-cycloartenol cyclase) is a plant enzyme that catalyzes the cyclization of (S)-2,3-epoxysqualene to cycloartenol.; GO: 0003824 catalytic activity; PDB: 2IEJ_B 1LD7_B 1LD8_B 2H6G_B 1TN6_B 1S63_B 1MZC_B 2H6I_B 2H6F_B 1JCQ_B ....
Probab=30.66 E-value=27 Score=18.83 Aligned_cols=22 Identities=23% Similarity=0.522 Sum_probs=15.2
Q ss_pred CCHHHHHHhH--hcCCcccEEEee
Q psy9697 7 VNRERAVQMV--AAGGEGCFLVRP 28 (128)
Q Consensus 7 i~r~~ae~ll--~~~~~G~FlvR~ 28 (128)
|+++++.+-| .++.||.|--+.
T Consensus 1 id~~~~~~~l~~~Q~~dGGf~~~~ 24 (44)
T PF00432_consen 1 IDVEKLIRFLLSCQNPDGGFGGRP 24 (44)
T ss_dssp SHHHHHHHHHHHTBBTTSSBBSST
T ss_pred CCHHHHHHHHHHHCCCCCCCCCCC
Confidence 4577888866 455889886554
No 50
>KOG4257|consensus
Probab=30.63 E-value=39 Score=29.98 Aligned_cols=26 Identities=15% Similarity=0.317 Sum_probs=22.9
Q ss_pred cccCCCHH--HHHHhhccCCCCceEecc
Q psy9697 102 LRWRLSRI--MFRHLADYNKLSGVQRAM 127 (128)
Q Consensus 102 ~~~~l~R~--~fr~~~~~G~~~gv~k~~ 127 (128)
+.|+|.|. .+.+++|.|+|+.|.++.
T Consensus 382 rnyel~Re~Itl~r~iG~GqFGdVy~gv 409 (974)
T KOG4257|consen 382 RNYELRRELITLKRLIGEGQFGDVYKGV 409 (974)
T ss_pred CcceeehhhccHHHhhcCCcccceeeeE
Confidence 67998887 669999999999999885
No 51
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=30.28 E-value=38 Score=18.06 Aligned_cols=23 Identities=17% Similarity=0.001 Sum_probs=19.5
Q ss_pred cccCCCHHHHHHhhccCCCCceE
Q psy9697 102 LRWRLSRIMFRHLADYNKLSGVQ 124 (128)
Q Consensus 102 ~~~~l~R~~fr~~~~~G~~~gv~ 124 (128)
+.++++...+|....+|.+|..+
T Consensus 8 ~~~gv~~~tlr~~~~~g~l~~~~ 30 (49)
T cd04761 8 KLTGVSPSTLRYYERIGLLSPAR 30 (49)
T ss_pred HHHCcCHHHHHHHHHCCCCCCCc
Confidence 56889999999999999998543
No 52
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=25.03 E-value=45 Score=19.94 Aligned_cols=13 Identities=46% Similarity=0.588 Sum_probs=11.1
Q ss_pred CCcccEE-EeeCCC
Q psy9697 19 GGEGCFL-VRPSSS 31 (128)
Q Consensus 19 ~~~G~Fl-vR~s~~ 31 (128)
..||..+ ||.|.+
T Consensus 32 ~~dG~~l~vR~SgT 45 (73)
T PF00408_consen 32 FEDGWRLLVRPSGT 45 (73)
T ss_dssp ETTEEEEEEEEESS
T ss_pred CCCceEEEEECCCC
Confidence 3789999 999977
No 53
>PF13309 HTH_22: HTH domain
Probab=24.84 E-value=32 Score=20.41 Aligned_cols=25 Identities=20% Similarity=0.391 Sum_probs=18.9
Q ss_pred CCCHHHHHHhH-hcCCcccEEEeeCC
Q psy9697 6 SVNRERAVQMV-AAGGEGCFLVRPSS 30 (128)
Q Consensus 6 ~i~r~~ae~ll-~~~~~G~FlvR~s~ 30 (128)
.+++++-.+++ .-...|.|.++.+-
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav 45 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAV 45 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHH
Confidence 36777777777 44677999999873
No 54
>PF03330 DPBB_1: Rare lipoprotein A (RlpA)-like double-psi beta-barrel; InterPro: IPR009009 Beta barrels are commonly observed in protein structures. They are classified in terms of two integral parameters: the number of strands in the sheet, n, and the shear number, S, a measure of the stagger of the strands in the beta-sheet. These two parameters have been shown to determine the major geometrical features of beta-barrels. Six-stranded beta-barrels with a pseudo-twofold axis are found in several proteins. One involving parallel strands forming two psi structures is known as the double-psi barrel. The first psi structure consists of the loop connecting strands beta1 and beta2 (a 'psi loop') and the strand beta5, whereas the second psi structure consists of the loop connecting strands beta4 and beta5 and the strand beta2. All the psi structures in double-psi barrels have a unique handedness, in that beta1 (beta4), beta2 (beta5) and the loop following beta5 (beta2) form a right-handed helix. The unique handedness may be related to the fact that the twisting angle between the parallel pair of strands is always larger than that between the antiparallel pair [].; PDB: 1N10_B 3D30_A 2BH0_A 2HCZ_X.
Probab=23.99 E-value=31 Score=20.96 Aligned_cols=37 Identities=30% Similarity=0.408 Sum_probs=25.5
Q ss_pred cccCCcccccCCCCccccccCCCHHHHHHhhccCCCCceEeccC
Q psy9697 85 CRTQPRCVITSRPRGVVLRWRLSRIMFRHLADYNKLSGVQRAMW 128 (128)
Q Consensus 85 ~rl~nrC~~tgr~~g~~~~~~l~R~~fr~~~~~G~~~gv~k~~W 128 (128)
+++.++|..++. ..+.||+..|.+++.... |+..=.|
T Consensus 42 v~V~D~Cp~~~~-----~~lDLS~~aF~~la~~~~--G~i~V~w 78 (78)
T PF03330_consen 42 VTVVDRCPGCPP-----NHLDLSPAAFKALADPDA--GVIPVEW 78 (78)
T ss_dssp EEEEEE-TTSSS-----SEEEEEHHHHHHTBSTTC--SSEEEEE
T ss_pred EEEEccCCCCcC-----CEEEeCHHHHHHhCCCCc--eEEEEEC
Confidence 567788887553 568999999999887743 5544433
No 55
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=23.88 E-value=85 Score=20.17 Aligned_cols=21 Identities=14% Similarity=0.136 Sum_probs=18.3
Q ss_pred cCCCHHHHHHhhccCCCCceE
Q psy9697 104 WRLSRIMFRHLADYNKLSGVQ 124 (128)
Q Consensus 104 ~~l~R~~fr~~~~~G~~~gv~ 124 (128)
-|-+....|+++..|+||.+.
T Consensus 22 IGKt~sAVr~Mi~~gKLP~i~ 42 (87)
T PF10743_consen 22 IGKTPSAVRKMIKAGKLPVIE 42 (87)
T ss_pred HCCCHHHHHHHHHcCCCCeEe
Confidence 467788999999999999986
No 56
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=21.78 E-value=1.2e+02 Score=16.06 Aligned_cols=15 Identities=33% Similarity=0.625 Sum_probs=12.0
Q ss_pred EEEEEEeCCEeeEEe
Q psy9697 35 LTLTLWYGGRAYNIF 49 (128)
Q Consensus 35 ~~lsv~~~~~v~hy~ 49 (128)
--|+++++|.|.=|.
T Consensus 6 ~qLTIfY~G~V~Vfd 20 (36)
T PF06200_consen 6 AQLTIFYGGQVCVFD 20 (36)
T ss_pred CcEEEEECCEEEEeC
Confidence 358999999997764
Done!