Query psy16431
Match_columns 87
No_of_seqs 104 out of 243
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 21:09:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16431.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16431hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2265|consensus 100.0 5.5E-38 1.2E-42 228.4 5.1 87 1-87 93-179 (179)
2 cd06465 p23_hB-ind1_like p23_l 95.8 0.0051 1.1E-07 40.2 1.7 30 1-30 74-103 (108)
3 TIGR00600 rad2 DNA excision re 84.4 1 2.2E-05 40.8 3.3 52 18-83 181-233 (1034)
4 PF05902 4_1_CTD: 4.1 protein 76.8 3.6 7.7E-05 28.6 3.2 16 65-80 87-102 (114)
5 PF14357 DUF4404: Domain of un 64.7 29 0.00064 22.3 5.4 48 32-79 16-69 (85)
6 KOG2265|consensus 58.2 3.1 6.7E-05 30.9 -0.1 26 61-86 120-145 (179)
7 PF11985 DUF3486: Protein of u 47.2 12 0.00026 26.6 1.4 23 28-50 3-25 (180)
8 PF15141 DUF4574: Domain of un 47.1 12 0.00025 24.7 1.3 22 57-78 26-47 (84)
9 COG3678 CpxP P pilus assembly/ 47.0 26 0.00056 25.2 3.1 36 32-67 55-90 (160)
10 PF00645 zf-PARP: Poly(ADP-rib 45.4 22 0.00048 21.8 2.3 24 20-47 58-81 (82)
11 PHA00159 endonuclease I 41.4 30 0.00066 25.0 2.7 26 56-84 68-97 (148)
12 PF10929 DUF2811: Protein of u 41.1 24 0.00052 21.7 1.9 15 66-80 11-25 (57)
13 PF12585 DUF3759: Protein of u 40.6 41 0.0009 22.6 3.1 25 47-72 31-55 (93)
14 cd01388 SOX-TCF_HMG-box SOX-TC 31.9 1.1E+02 0.0025 18.0 4.4 19 64-82 54-72 (72)
15 PF05367 Phage_endo_I: Phage e 31.8 39 0.00085 24.5 2.1 22 56-80 68-89 (149)
16 PF08863 YolD: YolD-like prote 31.8 98 0.0021 18.8 3.7 37 37-75 2-38 (92)
17 PF08897 DUF1841: Domain of un 30.9 1.3E+02 0.0029 21.3 4.6 39 39-80 2-41 (137)
18 PRK13676 hypothetical protein; 29.7 1.6E+02 0.0034 19.2 4.6 44 36-79 35-83 (114)
19 cd05837 MSH6_like The PWWP dom 28.6 29 0.00063 23.0 0.9 20 2-21 11-30 (110)
20 cd08470 PBP2_CrgA_like_1 The C 28.4 33 0.00071 21.9 1.1 18 65-82 16-33 (197)
21 PF11590 DNAPolymera_Pol: DNA 28.2 55 0.0012 18.9 1.9 32 41-72 5-36 (41)
22 PF13801 Metal_resist: Heavy-m 27.7 1.5E+02 0.0033 18.1 5.9 42 33-74 40-98 (125)
23 PF11637 UvsW: ATP-dependant D 27.1 56 0.0012 19.9 1.9 24 47-70 16-39 (54)
24 KOG4260|consensus 26.9 53 0.0011 26.6 2.2 32 51-82 60-93 (350)
25 TIGR03830 CxxCG_CxxCG_HTH puta 26.0 1.4E+02 0.0031 19.1 3.9 35 32-66 39-73 (127)
26 PF08947 BPS: BPS (Between PH 25.4 21 0.00045 21.4 -0.2 8 78-85 10-17 (49)
27 cd08477 PBP2_CrgA_like_8 The C 24.8 46 0.00099 21.1 1.3 17 66-82 17-33 (197)
28 cd08486 PBP2_CbnR The C-termin 24.2 42 0.00092 21.9 1.1 18 65-82 16-33 (198)
29 PRK13798 putative OHCU decarbo 23.9 87 0.0019 22.4 2.7 48 10-58 64-115 (166)
30 cd08466 PBP2_LeuO The C-termin 23.6 50 0.0011 21.1 1.3 18 65-82 15-32 (200)
31 cd08438 PBP2_CidR The C-termin 23.5 45 0.00098 21.0 1.1 18 65-82 15-32 (197)
32 cd05838 WHSC1_related The PWWP 23.1 39 0.00084 21.9 0.7 20 2-21 9-28 (95)
33 cd08476 PBP2_CrgA_like_7 The C 23.0 46 0.00099 21.0 1.0 17 66-82 15-31 (197)
34 PF08909 DUF1854: Domain of un 23.0 55 0.0012 23.1 1.5 16 31-46 36-51 (133)
35 cd08418 PBP2_TdcA The C-termin 22.2 55 0.0012 20.7 1.3 18 65-82 15-32 (201)
36 cd08422 PBP2_CrgA_like The C-t 22.1 46 0.001 20.9 0.9 18 65-82 16-33 (197)
37 TIGR02739 TraF type-F conjugat 21.5 3.7E+02 0.008 20.6 5.9 49 35-83 57-121 (256)
38 cd08440 PBP2_LTTR_like_4 TThe 21.4 58 0.0013 20.3 1.3 18 65-82 15-32 (197)
39 cd08452 PBP2_AlsR The C-termin 21.3 57 0.0012 21.0 1.3 18 65-82 15-32 (197)
40 cd08450 PBP2_HcaR The C-termin 21.3 55 0.0012 20.7 1.1 18 65-82 15-32 (196)
41 cd08464 PBP2_DntR_like_2 The C 21.3 58 0.0013 20.7 1.3 18 65-82 15-32 (200)
42 cd08471 PBP2_CrgA_like_2 The C 21.3 59 0.0013 20.7 1.3 18 65-82 16-33 (201)
43 cd08472 PBP2_CrgA_like_3 The C 20.8 61 0.0013 20.6 1.3 18 65-82 16-33 (202)
44 cd08415 PBP2_LysR_opines_like 20.7 61 0.0013 20.4 1.3 17 66-82 16-32 (196)
45 PF12995 DUF3879: Domain of un 20.5 3.8E+02 0.0081 20.1 6.1 68 10-77 58-126 (186)
46 cd08474 PBP2_CrgA_like_5 The C 20.4 55 0.0012 20.9 1.0 18 65-82 18-35 (202)
47 cd08481 PBP2_GcdR_like The C-t 20.3 54 0.0012 20.6 1.0 17 66-82 16-32 (194)
48 PF15060 PPDFL: Differentiatio 20.3 54 0.0012 22.6 1.0 19 1-19 46-64 (110)
49 cd08463 PBP2_DntR_like_4 The C 20.2 63 0.0014 21.3 1.3 19 64-82 14-32 (203)
50 cd08417 PBP2_Nitroaromatics_li 20.2 57 0.0012 20.7 1.1 18 65-82 15-32 (200)
51 PF07055 Eno-Rase_FAD_bd: Enoy 20.2 1.1E+02 0.0023 19.2 2.2 33 34-74 14-46 (65)
52 cd08435 PBP2_GbpR The C-termin 20.2 58 0.0012 20.6 1.1 19 64-82 14-32 (201)
53 cd08451 PBP2_BudR The C-termin 20.0 62 0.0013 20.5 1.2 16 66-81 17-32 (199)
No 1
>KOG2265|consensus
Probab=100.00 E-value=5.5e-38 Score=228.41 Aligned_cols=87 Identities=74% Similarity=1.148 Sum_probs=84.7
Q ss_pred CccccccccccccccCCcccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHhCCCCC
Q psy16431 1 MEKINKMEWWSKLVTTDPEINTKKINPEPSKLSDLDGETRGLVEKMMYDQRQKEMGLPTSDEQKKQDVLKKFMEQHPEMD 80 (87)
Q Consensus 1 L~K~~~~~WW~~vl~GdpeID~~kI~~~~~~l~dlD~etq~~veKmm~dq~qK~~G~ptsde~k~~e~Lkkf~~~~p~~d 80 (87)
|+|.++|+||+|+|+|+|+||+.+|+|+.+++++||++||++|+||||||+||.+|+|+||+.+++++|++||++||+||
T Consensus 93 l~K~~~~eWW~~ll~gep~ID~~ki~~e~skl~dldeEtra~vekmmfdq~qk~~~~p~sde~~~~d~Lkk~~~~~~~~~ 172 (179)
T KOG2265|consen 93 LKKSNKMEWWDSLLEGEPEIDTKKIEPEESKLSDLDEETRATVEKMMFDQRQKSMGLPTSDELKKHDMLKKFMDQHPEMD 172 (179)
T ss_pred eeccchHHHHHHHHcCCCCCCccccChhhhhhhhccHHHHHhhhccchhHHHhhcCCCCCchhhHHHHHHHHHHhCCCCC
Confidence 57888899999999999999999999988899999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCC
Q psy16431 81 FSNCKFG 87 (87)
Q Consensus 81 fs~~~~~ 87 (87)
||+|+||
T Consensus 173 f~~a~~~ 179 (179)
T KOG2265|consen 173 FSNAKFN 179 (179)
T ss_pred CchhccC
Confidence 9999997
No 2
>cd06465 p23_hB-ind1_like p23_like domain found in human (h) butyrate-induced transcript 1 (B-ind1) and similar proteins. hB-ind1 participates in signaling by the small GTPase Rac1. It binds to Rac1 and enhances different Rac1 effects including activation of nuclear factor (NF) kappaB and activation of c-Jun N-terminal kinase (JNK). hB-ind1 also plays a part in the RNA replication and particle production of Hepatitis C virus (HCV) through its interaction with heat shock protein Hsp90, HCV nonstructural protein 5A (NS5A), and the immunophilin FKBP8. hB-ind1 is upregulated in the outer layer of Chinese hamster V79 cells grown as multicell spheroids, versus in the same cells grown as monolayers. This group includes the Saccharomyces cerevisiae Sba1, a co-chaperone of the Hsp90. Sba1 has been shown to be is required for telomere length maintenance, and may modulate telomerase DNA-binding activity.
Probab=95.85 E-value=0.0051 Score=40.22 Aligned_cols=30 Identities=17% Similarity=0.337 Sum_probs=25.8
Q ss_pred CccccccccccccccCCcccccccCCCCCC
Q psy16431 1 MEKINKMEWWSKLVTTDPEINTKKINPEPS 30 (87)
Q Consensus 1 L~K~~~~~WW~~vl~GdpeID~~kI~~~~~ 30 (87)
|.|...+.||++|.+|+++++..+|+.++.
T Consensus 74 L~K~~~~~~W~~L~~~~~k~~~~~~d~~~w 103 (108)
T cd06465 74 LRKKEAGEYWPRLTKEKGKLPWLKVDFDKW 103 (108)
T ss_pred EEECCCCCCCcccccCCCCCCceECCchhc
Confidence 567763579999999999999999999874
No 3
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.41 E-value=1 Score=40.76 Aligned_cols=52 Identities=23% Similarity=0.176 Sum_probs=40.3
Q ss_pred cccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHhCCC-CCCCC
Q psy16431 18 PEINTKKINPEPSKLSDLDGETRGLVEKMMYDQRQKEMGLPTSDEQKKQDVLKKFMEQHPE-MDFSN 83 (87)
Q Consensus 18 peID~~kI~~~~~~l~dlD~etq~~veKmm~dq~qK~~G~ptsde~k~~e~Lkkf~~~~p~-~dfs~ 83 (87)
--+|+.+|++....+..|+.++|..|-.-|-.-++-+| .+|-+..|+ ||||.
T Consensus 181 ~~~d~~~ID~~S~~F~sLP~~~qyeILs~lRlrSRlRm--------------eQLeemfpdSmDFSk 233 (1034)
T TIGR00600 181 FFHNPSAIDIESEEFSSLPPEVKHEILTDMKLFTKRRR--------------TLFEAMPENSMDFSQ 233 (1034)
T ss_pred ccCChhhcCCCCHHHHhCCHHHHHHHHHHHHHHHHHHH--------------HHHhhcCCCchhhhH
Confidence 45899999999889999999999999776654444333 666667776 88885
No 4
>PF05902 4_1_CTD: 4.1 protein C-terminal domain (CTD); InterPro: IPR008379 There is a unique sequence domain at the C terminus of all known 4.1 proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24 kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates [].; GO: 0003779 actin binding, 0005198 structural molecule activity, 0005856 cytoskeleton
Probab=76.75 E-value=3.6 Score=28.57 Aligned_cols=16 Identities=38% Similarity=0.617 Sum_probs=12.5
Q ss_pred HHHHHHHHHHhCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMD 80 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~d 80 (87)
-...++.++++||+|-
T Consensus 87 La~aI~eAk~q~Pdm~ 102 (114)
T PF05902_consen 87 LAQAIKEAKEQHPDMS 102 (114)
T ss_pred HHHHHHHHHHhCCCce
Confidence 3457788899999984
No 5
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=64.74 E-value=29 Score=22.25 Aligned_cols=48 Identities=21% Similarity=0.272 Sum_probs=33.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHcCC-----CC-cHHHHHHHHHHHHHHhCCCC
Q psy16431 32 LSDLDGETRGLVEKMMYDQRQKEMGL-----PT-SDEQKKQDVLKKFMEQHPEM 79 (87)
Q Consensus 32 l~dlD~etq~~veKmm~dq~qK~~G~-----pt-sde~k~~e~Lkkf~~~~p~~ 79 (87)
...+|+++++.+..++-|-+...-.. +. +--.+......+|-..||.+
T Consensus 16 ~~~ld~~~~~~L~~l~~dIe~~L~~~~~~~~~~~~l~d~l~~av~~FE~~HP~l 69 (85)
T PF14357_consen 16 NPPLDEETRAELSSLDDDIEAQLAEEDEAEAEDESLVDRLNEAVERFEASHPKL 69 (85)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCcccccchhHHHHHHHHHHHHHHhCCcH
Confidence 45689999999999998876654441 11 11234455778899999974
No 6
>KOG2265|consensus
Probab=58.21 E-value=3.1 Score=30.89 Aligned_cols=26 Identities=19% Similarity=0.169 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCCCC
Q psy16431 61 DEQKKQDVLKKFMEQHPEMDFSNCKF 86 (87)
Q Consensus 61 de~k~~e~Lkkf~~~~p~~dfs~~~~ 86 (87)
++-+..+++++|++..|.|+|+++.+
T Consensus 120 e~skl~dldeEtra~vekmmfdq~qk 145 (179)
T KOG2265|consen 120 EESKLSDLDEETRATVEKMMFDQRQK 145 (179)
T ss_pred hhhhhhhccHHHHHhhhccchhHHHh
Confidence 34577888999999999999998764
No 7
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=47.21 E-value=12 Score=26.56 Aligned_cols=23 Identities=30% Similarity=0.394 Sum_probs=19.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHH
Q psy16431 28 EPSKLSDLDGETRGLVEKMMYDQ 50 (87)
Q Consensus 28 ~~~~l~dlD~etq~~veKmm~dq 50 (87)
.+|+|+-||++.|..|..|+-+.
T Consensus 3 r~SkId~LP~eir~~l~~~L~~~ 25 (180)
T PF11985_consen 3 RRSKIDLLPPEIREWLDQMLRDG 25 (180)
T ss_pred CCchHhhCCHHHHHHHHHHHHhC
Confidence 35789999999999999988774
No 8
>PF15141 DUF4574: Domain of unknown function (DUF4574)
Probab=47.06 E-value=12 Score=24.73 Aligned_cols=22 Identities=45% Similarity=0.705 Sum_probs=15.3
Q ss_pred CCCcHHHHHHHHHHHHHHhCCC
Q psy16431 57 LPTSDEQKKQDVLKKFMEQHPE 78 (87)
Q Consensus 57 ~ptsde~k~~e~Lkkf~~~~p~ 78 (87)
+-||-+++|++|||..-++||-
T Consensus 26 LvtPgeerK~e~lK~~pe~~p~ 47 (84)
T PF15141_consen 26 LVTPGEERKQEMLKEMPEQNPR 47 (84)
T ss_pred EeCCcHHHHHHHHHHccccCch
Confidence 3456677777788777777764
No 9
>COG3678 CpxP P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism]
Probab=46.95 E-value=26 Score=25.19 Aligned_cols=36 Identities=19% Similarity=0.206 Sum_probs=24.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHH
Q psy16431 32 LSDLDGETRGLVEKMMYDQRQKEMGLPTSDEQKKQD 67 (87)
Q Consensus 32 l~dlD~etq~~veKmm~dq~qK~~G~ptsde~k~~e 67 (87)
.-+|-.+.|..|..+||.+|+..+...-+.-....+
T Consensus 55 ~l~lT~~Qrqqi~~i~~~~~~a~~~~~~~~r~~l~~ 90 (160)
T COG3678 55 GLDLTRAQRQQIRDLMQAQRRAQREQLRSKRRALHE 90 (160)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445677899999999999997665544444333333
No 10
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=45.39 E-value=22 Score=21.83 Aligned_cols=24 Identities=17% Similarity=0.356 Sum_probs=17.5
Q ss_pred cccccCCCCCCCCCCCCHHHHHHHHHHH
Q psy16431 20 INTKKINPEPSKLSDLDGETRGLVEKMM 47 (87)
Q Consensus 20 ID~~kI~~~~~~l~dlD~etq~~veKmm 47 (87)
.++..|. .+++|.++-|..|++++
T Consensus 58 ~~~~~i~----G~~~L~~~Dq~~i~~~i 81 (82)
T PF00645_consen 58 GDIEEIK----GFDELKPEDQEKIRKLI 81 (82)
T ss_dssp SCGGGCE----TCCCS-HHHHHHHHHHH
T ss_pred CCHHHCC----ChHHCCHHHHHHHHHHh
Confidence 4455554 69999999999998764
No 11
>PHA00159 endonuclease I
Probab=41.44 E-value=30 Score=25.01 Aligned_cols=26 Identities=50% Similarity=0.777 Sum_probs=18.9
Q ss_pred CCCCcHHHHHHHHHHHHHHhCCCCC----CCCC
Q psy16431 56 GLPTSDEQKKQDVLKKFMEQHPEMD----FSNC 84 (87)
Q Consensus 56 G~ptsde~k~~e~Lkkf~~~~p~~d----fs~~ 84 (87)
|.=.+|+.+|+.+.+ +|||++| ||+.
T Consensus 68 G~w~~ddR~K~lli~---eQ~P~ldiR~VFs~s 97 (148)
T PHA00159 68 GLWDSDDRKKHLLIR---EQYPELDIRFVFSSS 97 (148)
T ss_pred ccCChHHHHHHHHHH---HHCCCccEEEEEecC
Confidence 555677777776655 6999999 6654
No 12
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=41.05 E-value=24 Score=21.72 Aligned_cols=15 Identities=40% Similarity=0.888 Sum_probs=13.1
Q ss_pred HHHHHHHHHhCCCCC
Q psy16431 66 QDVLKKFMEQHPEMD 80 (87)
Q Consensus 66 ~e~Lkkf~~~~p~~d 80 (87)
++-|++|.+.||+.|
T Consensus 11 ~~~m~~fie~hP~WD 25 (57)
T PF10929_consen 11 HQAMKDFIETHPNWD 25 (57)
T ss_pred HHHHHHHHHcCCCch
Confidence 556899999999988
No 13
>PF12585 DUF3759: Protein of unknown function (DUF3759); InterPro: IPR022234 This family of proteins is found in eukaryotes. Proteins in this family are typically between 107 and 132 amino acids in length. There is a single completely conserved residue H that may be functionally important.
Probab=40.62 E-value=41 Score=22.57 Aligned_cols=25 Identities=32% Similarity=0.582 Sum_probs=20.1
Q ss_pred HHHHHHHHcCCCCcHHHHHHHHHHHH
Q psy16431 47 MYDQRQKEMGLPTSDEQKKQDVLKKF 72 (87)
Q Consensus 47 m~dq~qK~~G~ptsde~k~~e~Lkkf 72 (87)
+|+.+|+.-|+|.|...-|+ +|--|
T Consensus 31 ayEdhq~~~Gkp~sHa~AKE-llAg~ 55 (93)
T PF12585_consen 31 AYEDHQRKNGKPVSHAFAKE-LLAGF 55 (93)
T ss_pred HHHHHHHHcCCCCcHHHHHH-HHHHH
Confidence 59999999999999987775 44433
No 14
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=31.87 E-value=1.1e+02 Score=18.05 Aligned_cols=19 Identities=11% Similarity=0.303 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHhCCCCCCC
Q psy16431 64 KKQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 64 k~~e~Lkkf~~~~p~~dfs 82 (87)
.-....+++..+||++-|+
T Consensus 54 ~a~~~k~~y~~~~p~y~y~ 72 (72)
T cd01388 54 EAKKLKELHMKLYPDYKWR 72 (72)
T ss_pred HHHHHHHHHHHHCcCCCCC
Confidence 4455678899999998664
No 15
>PF05367 Phage_endo_I: Phage endonuclease I; InterPro: IPR008029 Endonuclease I (3.1.21.2 from EC) is a junction-resolving enzyme encoded by bacteriophage T7, that selectively binds and cleaves four-way Holliday DNA junctions []. The structure of the enzyme shows that it forms a symmetric homodimer arranged in two well-separated domains. Each domain, however, is composed of elements from both subunits, and amino acid side chains from both protomers contribute to the active site []. ; GO: 0008833 deoxyribonuclease IV (phage-T4-induced) activity, 0015074 DNA integration, 0016032 viral reproduction; PDB: 3CAE_A 1M0D_A 1M0I_C 1FZR_B 2PFJ_B.
Probab=31.80 E-value=39 Score=24.47 Aligned_cols=22 Identities=36% Similarity=0.641 Sum_probs=14.6
Q ss_pred CCCCcHHHHHHHHHHHHHHhCCCCC
Q psy16431 56 GLPTSDEQKKQDVLKKFMEQHPEMD 80 (87)
Q Consensus 56 G~ptsde~k~~e~Lkkf~~~~p~~d 80 (87)
|.=.+++.+|+.+++ ++||++|
T Consensus 68 G~f~~~DR~K~l~Ik---~q~P~LD 89 (149)
T PF05367_consen 68 GRFDAEDRRKHLLIK---EQYPELD 89 (149)
T ss_dssp SS--HHHHHHHHHHH---HH-TTSE
T ss_pred eccCcchhHHHHHHH---HhCCCcc
Confidence 445567888887666 5999999
No 16
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=31.79 E-value=98 Score=18.83 Aligned_cols=37 Identities=22% Similarity=0.364 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHh
Q psy16431 37 GETRGLVEKMMYDQRQKEMGLPTSDEQKKQDVLKKFMEQ 75 (87)
Q Consensus 37 ~etq~~veKmm~dq~qK~~G~ptsde~k~~e~Lkkf~~~ 75 (87)
||.+.++.++.-++... -+|.-++.+..++...+..+
T Consensus 2 PEH~e~L~~~~~e~~k~--~kp~Lde~~leei~~~l~~a 38 (92)
T PF08863_consen 2 PEHKEALRELIKEQNKV--EKPELDEQQLEEINEKLSEA 38 (92)
T ss_pred ChHHHHHHHHHHHhccc--CCCCCcHHHHHHHHHHHHHH
Confidence 35667777766554443 37788888888888777654
No 17
>PF08897 DUF1841: Domain of unknown function (DUF1841); InterPro: IPR014993 This group of proteins are functionally uncharacterised.
Probab=30.88 E-value=1.3e+02 Score=21.33 Aligned_cols=39 Identities=26% Similarity=0.477 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHc-CCCCcHHHHHHHHHHHHHHhCCCCC
Q psy16431 39 TRGLVEKMMYDQRQKEM-GLPTSDEQKKQDVLKKFMEQHPEMD 80 (87)
Q Consensus 39 tq~~veKmm~dq~qK~~-G~ptsde~k~~e~Lkkf~~~~p~~d 80 (87)
+|..|+++.+|--+|.. |.|-+.-.. +.-....+|||+.
T Consensus 2 sr~~~R~ff~~~w~K~~~~~~L~~lE~---~a~~~i~~HPEYh 41 (137)
T PF08897_consen 2 SRDQVRRFFCDAWRKYRAGEPLTPLEQ---IAADVIEEHPEYH 41 (137)
T ss_pred CHHHHHHHHHHHHHHHHCCCCCCHHHH---HHHHHHHHCcchH
Confidence 46789999999888755 666654333 2356677999963
No 18
>PRK13676 hypothetical protein; Provisional
Probab=29.67 E-value=1.6e+02 Score=19.20 Aligned_cols=44 Identities=27% Similarity=0.360 Sum_probs=26.9
Q ss_pred CHHHHHHHHHHHH---HHHHH-HcCC-CCcHHHHHHHHHHHHHHhCCCC
Q psy16431 36 DGETRGLVEKMMY---DQRQK-EMGL-PTSDEQKKQDVLKKFMEQHPEM 79 (87)
Q Consensus 36 D~etq~~veKmm~---dq~qK-~~G~-ptsde~k~~e~Lkkf~~~~p~~ 79 (87)
|++++..|....- ...++ ..|. ++.++.+...-|.+-...||.+
T Consensus 35 d~~a~~li~~F~~~q~~~~~~q~~g~~~~~e~~~~l~~l~~~i~~n~~i 83 (114)
T PRK13676 35 DEEAKKLFDEFRALQLEIQQKQMTGQEITEEEQQKAQELGQKIQQNELL 83 (114)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhcCHHH
Confidence 6788888776542 21112 4576 4555666666777766778764
No 19
>cd05837 MSH6_like The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. The role of the PWWP domain in MSH6 is not clear; MSH6 orthologs found in S. cerevisiae, Caenorhabditis elegans and Arabidopsis thaliana lack the PWWP domain. Histone methyltransferases (HMTases) induce the posttranslational methylation of lysine residues in histones and play a role in apoptosis. In the HMTase Whistle, the PWWP domain is necessary for HMTase activity. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain pro
Probab=28.59 E-value=29 Score=23.00 Aligned_cols=20 Identities=30% Similarity=0.855 Sum_probs=16.2
Q ss_pred ccccccccccccccCCcccc
Q psy16431 2 EKINKMEWWSKLVTTDPEIN 21 (87)
Q Consensus 2 ~K~~~~~WW~~vl~GdpeID 21 (87)
.|+..--||+|+|..+|.+.
T Consensus 11 aK~~g~PwWPa~V~~~~~~~ 30 (110)
T cd05837 11 AKVSGYPWWPCMVCSDPLLG 30 (110)
T ss_pred EeCCCCCCCCEEEecccccc
Confidence 36666689999999998775
No 20
>cd08470 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene
Probab=28.42 E-value=33 Score=21.90 Aligned_cols=18 Identities=17% Similarity=0.540 Sum_probs=14.7
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|.+|.++||+.+++
T Consensus 16 l~~~l~~f~~~~P~v~l~ 33 (197)
T cd08470 16 IAPLVNDFMQRYPKLEVD 33 (197)
T ss_pred HHHHHHHHHHHCCCeEEE
Confidence 356889999999998764
No 21
>PF11590 DNAPolymera_Pol: DNA polymerase catalytic subunit Pol; InterPro: IPR021639 This family of proteins represents the catalytic subunit, Pol, of the Herpes simplex virus DNA polymerase. Pol binds UL42, making up the DNA polymerase. UL42 is a processivity subunit which binds to the C-terminal of Pol in a similar way that the cell cycle regulator p21 binds to PCNA []. ; GO: 0003887 DNA-directed DNA polymerase activity, 0004523 ribonuclease H activity; PDB: 1DML_H.
Probab=28.20 E-value=55 Score=18.94 Aligned_cols=32 Identities=19% Similarity=0.357 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHH
Q psy16431 41 GLVEKMMYDQRQKEMGLPTSDEQKKQDVLKKF 72 (87)
Q Consensus 41 ~~veKmm~dq~qK~~G~ptsde~k~~e~Lkkf 72 (87)
..+..-+|..-.---|+|.++|.+.+-.|.+.
T Consensus 5 ~Rl~~AgF~~i~~g~g~~~~~eeEt~qkL~~A 36 (41)
T PF11590_consen 5 ERLRSAGFATIGSGAGLPSSEEEETRQKLRRA 36 (41)
T ss_dssp HHHHHTT-EEECTTS------HHHHHHHHHHH
T ss_pred HHHHHHhHHHhccCccccchhhHHHHHHHHHH
Confidence 33333444433344588999999999888764
No 22
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=27.70 E-value=1.5e+02 Score=18.07 Aligned_cols=42 Identities=24% Similarity=0.356 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHHHHHHHHH-----------------HHcCCCCcHHHHHHHHHHHHHH
Q psy16431 33 SDLDGETRGLVEKMMYDQRQ-----------------KEMGLPTSDEQKKQDVLKKFME 74 (87)
Q Consensus 33 ~dlD~etq~~veKmm~dq~q-----------------K~~G~ptsde~k~~e~Lkkf~~ 74 (87)
.+|+++.+..|+.++-+.+. ..+..|+.|+.+...++++..+
T Consensus 40 l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ll~~~~~D~~~i~a~~~~~~~ 98 (125)
T PF13801_consen 40 LNLTPEQQAKLRALMDEFRQEMRALRQELRAARQELRALLAAPPPDEAAIEALLEEIRE 98 (125)
T ss_dssp S-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSS-HHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 46899999999998876554 2455666666666655555543
No 23
>PF11637 UvsW: ATP-dependant DNA helicase UvsW; InterPro: IPR020975 This entry represents the DNA helicase UvsW from Enterobacteria phage T4. The protein is a member of the monomeric SF2 helicase superfamily and shows structural homology to the eukaryotic SF2 helicase Rad54. UvsW is thought to have a role in recombination and the rescue of stalled replication forks []. ; PDB: 2JPN_A.
Probab=27.13 E-value=56 Score=19.94 Aligned_cols=24 Identities=38% Similarity=0.589 Sum_probs=20.3
Q ss_pred HHHHHHHHcCCCCcHHHHHHHHHH
Q psy16431 47 MYDQRQKEMGLPTSDEQKKQDVLK 70 (87)
Q Consensus 47 m~dq~qK~~G~ptsde~k~~e~Lk 70 (87)
.|.+|-|...+..|+++..++.|.
T Consensus 16 yY~kR~KEv~l~~sdDIsiRDAl~ 39 (54)
T PF11637_consen 16 YYKKRKKEVELKDSDDISIRDALA 39 (54)
T ss_dssp HHHHHTTTS--TTHHHHHHHHHHH
T ss_pred HHHHhhhhcccCCcccccHHHHhc
Confidence 599999999999999999999984
No 24
>KOG4260|consensus
Probab=26.92 E-value=53 Score=26.56 Aligned_cols=32 Identities=22% Similarity=0.451 Sum_probs=26.3
Q ss_pred HHHHcCCCCcHHHHHHHHHHHHHH--hCCCCCCC
Q psy16431 51 RQKEMGLPTSDEQKKQDVLKKFME--QHPEMDFS 82 (87)
Q Consensus 51 ~qK~~G~ptsde~k~~e~Lkkf~~--~~p~~dfs 82 (87)
..|.+++..+-|.+-.|+|+.+=. .-|+|||-
T Consensus 60 EEknL~kYk~SE~RLvEilEglCsks~~~n~Dfe 93 (350)
T KOG4260|consen 60 EEKNLSKYKTSETRLVEILEGLCSKSSLPNMDFE 93 (350)
T ss_pred hhhhhhhccccchhHHHHHHHhhhccCCCCCChH
Confidence 346778888889999999999876 56999984
No 25
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=26.04 E-value=1.4e+02 Score=19.07 Aligned_cols=35 Identities=26% Similarity=0.134 Sum_probs=29.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHcCCCCcHHHHHH
Q psy16431 32 LSDLDGETRGLVEKMMYDQRQKEMGLPTSDEQKKQ 66 (87)
Q Consensus 32 l~dlD~etq~~veKmm~dq~qK~~G~ptsde~k~~ 66 (87)
=.-++++.-..+.+++++...+..|+.++.+++..
T Consensus 39 e~~~~~e~~~~~~~~i~~~~~~~~~~~~~~~i~~~ 73 (127)
T TIGR03830 39 EELLDPEESKRNSAALADFYRKVDGLLTPPEIRRI 73 (127)
T ss_pred CEEEcHHHHHHHHHHHHHHHHHccCCcCHHHHHHH
Confidence 34467788899999999999999999999887654
No 26
>PF08947 BPS: BPS (Between PH and SH2) ; InterPro: IPR015042 The BPS (Between PH and SH2) domain, comprised of 2 beta strands and a C-terminal helix, is an approximately 45 residue region found in the adaptor proteins Grb7/10/14 that mediates inhibition of the tyrosine kinase domain of the insulin receptor by binding of the N-terminal portion of the BPS domain to the substrate peptide groove of the kinase, acting as a pseudosubstrate inhibitor []. ; PDB: 2AUH_B.
Probab=25.35 E-value=21 Score=21.42 Aligned_cols=8 Identities=50% Similarity=0.679 Sum_probs=5.2
Q ss_pred CCCCCCCC
Q psy16431 78 EMDFSNCK 85 (87)
Q Consensus 78 ~~dfs~~~ 85 (87)
-||||+..
T Consensus 10 aMDFsG~~ 17 (49)
T PF08947_consen 10 AMDFSGQT 17 (49)
T ss_dssp EEE-SSSS
T ss_pred EeeecCCc
Confidence 48999864
No 27
>cd08477 PBP2_CrgA_like_8 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=24.82 E-value=46 Score=21.13 Aligned_cols=17 Identities=12% Similarity=0.464 Sum_probs=14.1
Q ss_pred HHHHHHHHHhCCCCCCC
Q psy16431 66 QDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 66 ~e~Lkkf~~~~p~~dfs 82 (87)
-.+|..|.++||++.|+
T Consensus 17 ~~~l~~~~~~~P~i~l~ 33 (197)
T cd08477 17 TPALAEYLARYPDVRVD 33 (197)
T ss_pred HHHHHHHHHHCCCcEEE
Confidence 46789999999998764
No 28
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=24.23 E-value=42 Score=21.91 Aligned_cols=18 Identities=22% Similarity=0.381 Sum_probs=14.8
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|++|..+||++.++
T Consensus 16 l~~~l~~f~~~~P~v~i~ 33 (198)
T cd08486 16 LPLLLRAFLTSTPTATVS 33 (198)
T ss_pred HHHHHHHHHHhCCCeEEE
Confidence 347889999999998764
No 29
>PRK13798 putative OHCU decarboxylase; Provisional
Probab=23.90 E-value=87 Score=22.39 Aligned_cols=48 Identities=15% Similarity=0.163 Sum_probs=34.7
Q ss_pred ccccccCCccccccc----CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q psy16431 10 WSKLVTTDPEINTKK----INPEPSKLSDLDGETRGLVEKMMYDQRQKEMGLP 58 (87)
Q Consensus 10 W~~vl~GdpeID~~k----I~~~~~~l~dlD~etq~~veKmm~dq~qK~~G~p 58 (87)
|..+|.+||.|--.. -..+.+.|+.|++++...+..+=-.++.|= |.|
T Consensus 64 ~~~~l~~HP~lg~~~~~~~S~~EQ~gl~~l~~~~~~~l~~lN~~Y~~kF-Gfp 115 (166)
T PRK13798 64 IDEALAGHPRIGERPASKASAREQAGVADADEAVMAALAAGNRAYEEKF-GFV 115 (166)
T ss_pred HHHHHHhCCcccCccccccCHHHhcccccCCHHHHHHHHHHHHHHHHhC-CCe
Confidence 567889999987533 223456788999999999888877777764 544
No 30
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=23.64 E-value=50 Score=21.10 Aligned_cols=18 Identities=11% Similarity=0.348 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|..|..+||++.++
T Consensus 15 l~~~l~~f~~~~P~v~l~ 32 (200)
T cd08466 15 LPRLLARLKQLAPNISLR 32 (200)
T ss_pred HHHHHHHHHHHCCCCEEE
Confidence 356889999999998753
No 31
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=23.50 E-value=45 Score=21.00 Aligned_cols=18 Identities=17% Similarity=0.427 Sum_probs=14.8
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
-..+|.+|.++||+..++
T Consensus 15 l~~~l~~~~~~~p~v~i~ 32 (197)
T cd08438 15 FAPLLAAFRQRYPNIELE 32 (197)
T ss_pred cHHHHHHHHHHCcCeEEE
Confidence 356889999999998764
No 32
>cd05838 WHSC1_related The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as plasmacytoma. WHCS1 proteins typically contain two copies of the PWWP domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=23.10 E-value=39 Score=21.86 Aligned_cols=20 Identities=20% Similarity=0.787 Sum_probs=15.4
Q ss_pred ccccccccccccccCCcccc
Q psy16431 2 EKINKMEWWSKLVTTDPEIN 21 (87)
Q Consensus 2 ~K~~~~~WW~~vl~GdpeID 21 (87)
.|+..-.||+++|...+++.
T Consensus 9 aK~~g~pwWPa~V~~~~~~p 28 (95)
T cd05838 9 AKLGNFRWWPAIICDPREVP 28 (95)
T ss_pred EECCCCCCCCeEEcChhhcC
Confidence 36666789999999876654
No 33
>cd08476 PBP2_CrgA_like_7 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=22.99 E-value=46 Score=20.97 Aligned_cols=17 Identities=35% Similarity=0.696 Sum_probs=14.2
Q ss_pred HHHHHHHHHhCCCCCCC
Q psy16431 66 QDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 66 ~e~Lkkf~~~~p~~dfs 82 (87)
..+|.+|..+||+.+++
T Consensus 15 ~~~l~~~~~~~P~v~i~ 31 (197)
T cd08476 15 LPVLAAFMQRYPEIELD 31 (197)
T ss_pred HHHHHHHHHHCCCeEEE
Confidence 45899999999998764
No 34
>PF08909 DUF1854: Domain of unknown function (DUF1854); InterPro: IPR015005 These protein is functionally uncharacterised. It is found at the C terminus of a number of ATP transporter proteins suggesting it may be involved in ligand binding.
Probab=22.97 E-value=55 Score=23.05 Aligned_cols=16 Identities=44% Similarity=0.648 Sum_probs=14.0
Q ss_pred CCCCCCHHHHHHHHHH
Q psy16431 31 KLSDLDGETRGLVEKM 46 (87)
Q Consensus 31 ~l~dlD~etq~~veKm 46 (87)
.|++||+++|+.|+.-
T Consensus 36 ~l~~L~~~~r~lle~e 51 (133)
T PF08909_consen 36 DLDDLPEESRALLEEE 51 (133)
T ss_pred ChhHCCHHHHHHHHHH
Confidence 5999999999999763
No 35
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=22.17 E-value=55 Score=20.75 Aligned_cols=18 Identities=33% Similarity=0.659 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
-..+|..|.+.||+..|+
T Consensus 15 l~~~l~~~~~~~P~i~l~ 32 (201)
T cd08418 15 MPAVINRFKEQFPDVQIS 32 (201)
T ss_pred hHHHHHHHHHHCCCceEE
Confidence 346789999999998764
No 36
>cd08422 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own
Probab=22.08 E-value=46 Score=20.89 Aligned_cols=18 Identities=17% Similarity=0.492 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|..|.++||+.+++
T Consensus 16 l~~~l~~~~~~~P~v~i~ 33 (197)
T cd08422 16 LAPLLAEFLARYPDVRLE 33 (197)
T ss_pred HHHHHHHHHHhCCceEEE
Confidence 456889999999997763
No 37
>TIGR02739 TraF type-F conjugative transfer system pilin assembly protein TraF. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se.
Probab=21.51 E-value=3.7e+02 Score=20.62 Aligned_cols=49 Identities=20% Similarity=0.331 Sum_probs=36.7
Q ss_pred CCH-HHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHH---------------HhCCCCCCCC
Q psy16431 35 LDG-ETRGLVEKMMYDQRQKEMGLPTSDEQKKQDVLKKFM---------------EQHPEMDFSN 83 (87)
Q Consensus 35 lD~-etq~~veKmm~dq~qK~~G~ptsde~k~~e~Lkkf~---------------~~~p~~dfs~ 83 (87)
++. +.-+.+++.+=+-+-++.--||.+..+.-..|.+++ -+||++|++.
T Consensus 57 ~~~~~~~~~l~~~~~~~~~~Ai~~Pt~ENv~~y~~lq~~~~dka~~Fa~~~~~v~l~~PeLdy~l 121 (256)
T TIGR02739 57 LSPTEQMKLLRQETKEALNQAILNPSVENFARYMRLQRFWTKQSSQFSMTWQKALLAHPELDYTL 121 (256)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCccc
Confidence 444 555667777778888899999999888776666654 4689999864
No 38
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=21.42 E-value=58 Score=20.35 Aligned_cols=18 Identities=28% Similarity=0.477 Sum_probs=14.7
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
-..+|.+|.++||+..+.
T Consensus 15 l~~~l~~~~~~~p~v~i~ 32 (197)
T cd08440 15 LPPVLAAFRRRHPGIRVR 32 (197)
T ss_pred HHHHHHHHHHhCCCcEEE
Confidence 457889999999998753
No 39
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=21.32 E-value=57 Score=21.03 Aligned_cols=18 Identities=6% Similarity=0.409 Sum_probs=14.8
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|..|..+||+.+++
T Consensus 15 l~~~l~~~~~~~P~v~i~ 32 (197)
T cd08452 15 LPPIVREYRKKFPSVKVE 32 (197)
T ss_pred HHHHHHHHHHHCCCcEEE
Confidence 357899999999998764
No 40
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=21.30 E-value=55 Score=20.74 Aligned_cols=18 Identities=33% Similarity=0.645 Sum_probs=14.4
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|+.|..+||++.++
T Consensus 15 l~~~l~~~~~~~P~i~l~ 32 (196)
T cd08450 15 LPEVLPILREEHPDLDVE 32 (196)
T ss_pred HHHHHHHHHhhCCCcEEE
Confidence 356889999999998653
No 41
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=21.26 E-value=58 Score=20.68 Aligned_cols=18 Identities=11% Similarity=0.261 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|..|...||+.++.
T Consensus 15 l~~~l~~~~~~~P~v~l~ 32 (200)
T cd08464 15 APPLLAALRAEAPGVRLV 32 (200)
T ss_pred HHHHHHHHHHHCCCcEEE
Confidence 456789999999997753
No 42
>cd08471 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=21.25 E-value=59 Score=20.69 Aligned_cols=18 Identities=17% Similarity=0.479 Sum_probs=14.4
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|.+|.+.||+.+++
T Consensus 16 l~~~l~~~~~~~P~v~i~ 33 (201)
T cd08471 16 VLPIITDFLDAYPEVSVR 33 (201)
T ss_pred HHHHHHHHHHHCCCcEEE
Confidence 346889999999987764
No 43
>cd08472 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=20.76 E-value=61 Score=20.63 Aligned_cols=18 Identities=17% Similarity=0.490 Sum_probs=14.6
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|.+|.++||++.++
T Consensus 16 l~~~l~~~~~~~P~i~v~ 33 (202)
T cd08472 16 LIPALPDFLARYPDIELD 33 (202)
T ss_pred HHHHHHHHHHHCCCcEEE
Confidence 346889999999998764
No 44
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=20.67 E-value=61 Score=20.43 Aligned_cols=17 Identities=24% Similarity=0.634 Sum_probs=13.8
Q ss_pred HHHHHHHHHhCCCCCCC
Q psy16431 66 QDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 66 ~e~Lkkf~~~~p~~dfs 82 (87)
..+|.+|.++||+.+++
T Consensus 16 ~~~l~~~~~~~P~i~l~ 32 (196)
T cd08415 16 PRAIARFRARHPDVRIS 32 (196)
T ss_pred HHHHHHHHHHCCCcEEE
Confidence 46889999999997753
No 45
>PF12995 DUF3879: Domain of unknown function, E. rectale Gene description (DUF3879); InterPro: IPR024540 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=20.47 E-value=3.8e+02 Score=20.08 Aligned_cols=68 Identities=16% Similarity=0.285 Sum_probs=52.9
Q ss_pred ccccccCCcccccccCCC-CCCCCCCCCHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHhCC
Q psy16431 10 WSKLVTTDPEINTKKINP-EPSKLSDLDGETRGLVEKMMYDQRQKEMGLPTSDEQKKQDVLKKFMEQHP 77 (87)
Q Consensus 10 W~~vl~GdpeID~~kI~~-~~~~l~dlD~etq~~veKmm~dq~qK~~G~ptsde~k~~e~Lkkf~~~~p 77 (87)
|-....|..-+|++--.+ ...+|--.+++.+..|..+.+...-+.-|....|..+..++.+....+-|
T Consensus 58 ~~np~~g~aGldVTg~~~~s~~rIi~VsE~~~q~mfdlvkkef~~enG~snGDttkrs~i~k~y~~sv~ 126 (186)
T PF12995_consen 58 WINPNNGLAGLDVTGKNCASWQRIIPVSEEVRQKMFDLVKKEFKNENGVSNGDTTKRSDIIKDYYMSVP 126 (186)
T ss_pred ccCCCCCcccccccCCCccchhheecCCHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHHHHHhcC
Confidence 333445666677766653 33467778899999999999999999999999999999999998876555
No 46
>cd08474 PBP2_CrgA_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene a
Probab=20.43 E-value=55 Score=20.92 Aligned_cols=18 Identities=17% Similarity=0.536 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.+|.+|.+.||+.+++
T Consensus 18 l~~~l~~~~~~~P~v~i~ 35 (202)
T cd08474 18 LAPLLARFLARYPDIRLE 35 (202)
T ss_pred HHHHHHHHHHHCCCeEEE
Confidence 447899999999997753
No 47
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=20.31 E-value=54 Score=20.64 Aligned_cols=17 Identities=24% Similarity=0.597 Sum_probs=13.8
Q ss_pred HHHHHHHHHhCCCCCCC
Q psy16431 66 QDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 66 ~e~Lkkf~~~~p~~dfs 82 (87)
-.+|.+|...||++.++
T Consensus 16 ~~~l~~f~~~~P~i~i~ 32 (194)
T cd08481 16 IPRLPDFLARHPDITVN 32 (194)
T ss_pred HhhhhHHHHHCCCceEE
Confidence 45789999999997764
No 48
>PF15060 PPDFL: Differentiation and proliferation regulator
Probab=20.25 E-value=54 Score=22.64 Aligned_cols=19 Identities=16% Similarity=0.569 Sum_probs=15.3
Q ss_pred CccccccccccccccCCcc
Q psy16431 1 MEKINKMEWWSKLVTTDPE 19 (87)
Q Consensus 1 L~K~~~~~WW~~vl~Gdpe 19 (87)
|-|+..+.||.+.|-|.+.
T Consensus 46 Lpkad~g~WW~sfFF~k~~ 64 (110)
T PF15060_consen 46 LPKADPGHWWASFFFGKST 64 (110)
T ss_pred ccccCCCcceEEeEecccc
Confidence 4577888999999988853
No 49
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=20.21 E-value=63 Score=21.30 Aligned_cols=19 Identities=11% Similarity=0.310 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHhCCCCCCC
Q psy16431 64 KKQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 64 k~~e~Lkkf~~~~p~~dfs 82 (87)
---.+|.+|...||++++.
T Consensus 14 ~~~~~l~~~~~~~P~~~v~ 32 (203)
T cd08463 14 FLPELVARFRREAPGARLE 32 (203)
T ss_pred HhHHHHHHHHHHCCCCEEE
Confidence 3456899999999998763
No 50
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=20.19 E-value=57 Score=20.72 Aligned_cols=18 Identities=11% Similarity=0.333 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhCCCCCCC
Q psy16431 65 KQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 65 ~~e~Lkkf~~~~p~~dfs 82 (87)
--.++.+|...||+.+|+
T Consensus 15 ~~~~i~~~~~~~P~i~l~ 32 (200)
T cd08417 15 LPPLLARLRQEAPGVRLR 32 (200)
T ss_pred HHHHHHHHHhhCCCeEEE
Confidence 456789999999997764
No 51
>PF07055 Eno-Rase_FAD_bd: Enoyl reductase FAD binding domain; InterPro: IPR010758 This family contains a number of bacterial putative reductases. ; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3S8M_A 3ZU5_A 3ZU3_A 3ZU4_A 3ZU2_A.
Probab=20.18 E-value=1.1e+02 Score=19.21 Aligned_cols=33 Identities=12% Similarity=0.180 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHH
Q psy16431 34 DLDGETRGLVEKMMYDQRQKEMGLPTSDEQKKQDVLKKFME 74 (87)
Q Consensus 34 dlD~etq~~veKmm~dq~qK~~G~ptsde~k~~e~Lkkf~~ 74 (87)
+|++++|+.|.+++ ..-|++.....-=++-|+.
T Consensus 14 El~~dvQ~~V~~lw--------~~it~en~~el~D~~gy~~ 46 (65)
T PF07055_consen 14 ELRPDVQAEVAELW--------EQITTENFKELGDYDGYRQ 46 (65)
T ss_dssp CCSHHHHHHHHHHH--------CCT-CCCHHHHS-HHHHHH
T ss_pred hcCHHHHHHHHHHH--------HHhccccHHHHHhHHHHHH
Confidence 67999999997754 4555665554443444333
No 52
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=20.18 E-value=58 Score=20.58 Aligned_cols=19 Identities=11% Similarity=0.406 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHhCCCCCCC
Q psy16431 64 KKQDVLKKFMEQHPEMDFS 82 (87)
Q Consensus 64 k~~e~Lkkf~~~~p~~dfs 82 (87)
--..+|..|..+||+..++
T Consensus 14 ~l~~~l~~~~~~~P~v~i~ 32 (201)
T cd08435 14 LLPPAIARLLARHPRLTVR 32 (201)
T ss_pred HHHHHHHHHHHHCCCeEEE
Confidence 3467899999999987654
No 53
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=20.02 E-value=62 Score=20.48 Aligned_cols=16 Identities=19% Similarity=0.688 Sum_probs=13.2
Q ss_pred HHHHHHHHHhCCCCCC
Q psy16431 66 QDVLKKFMEQHPEMDF 81 (87)
Q Consensus 66 ~e~Lkkf~~~~p~~df 81 (87)
-.+|.+|...||+.++
T Consensus 17 ~~~l~~~~~~~P~i~l 32 (199)
T cd08451 17 PGLIRRFREAYPDVEL 32 (199)
T ss_pred HHHHHHHHHHCCCcEE
Confidence 4578999999998764
Done!