Query 039784
Match_columns 88
No_of_seqs 102 out of 203
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 13:08:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039784.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039784hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02704 GASA: Gibberellin reg 100.0 2.1E-38 4.5E-43 202.0 5.2 60 29-88 1-60 (60)
2 PF07172 GRP: Glycine rich pro 83.4 1.1 2.5E-05 30.2 2.5 11 6-16 9-19 (95)
3 PF11912 DUF3430: Protein of u 76.2 2.5 5.4E-05 30.0 2.4 10 1-10 1-10 (212)
4 PF02950 Conotoxin: Conotoxin; 65.8 2 4.3E-05 26.4 0.0 15 1-16 1-15 (75)
5 PF08027 Albumin_I: Albumin I; 64.7 0.87 1.9E-05 32.8 -2.0 32 25-67 17-48 (120)
6 PF09257 BCMA-Tall_bind: BCMA, 59.8 7.1 0.00015 23.3 1.6 21 33-53 16-36 (39)
7 PF07127 Nodulin_late: Late no 49.6 14 0.0003 22.1 1.8 7 27-33 33-39 (54)
8 PF10690 Myticin-prepro: Mytic 48.1 9.4 0.0002 26.7 1.0 23 20-42 15-38 (98)
9 PF15284 PAGK: Phage-encoded v 45.7 25 0.00055 22.7 2.6 14 13-26 14-27 (61)
10 KOG4063 Major epididymal secre 36.7 36 0.00079 25.6 2.6 6 27-32 27-32 (158)
11 PRK00888 ftsB cell division pr 35.7 45 0.00098 22.6 2.8 12 1-12 1-12 (105)
12 PF15330 SIT: SHP2-interacting 35.3 53 0.0012 22.6 3.1 16 67-82 41-56 (107)
13 PF06607 Prokineticin: Prokine 34.4 12 0.00026 25.7 -0.2 12 68-79 74-85 (97)
14 PLN03207 stomagen; Provisional 32.4 58 0.0013 23.3 3.0 18 5-22 14-31 (113)
15 PF15240 Pro-rich: Proline-ric 32.2 29 0.00064 26.3 1.5 16 12-27 3-18 (179)
16 PF04202 Mfp-3: Foot protein 3 31.9 33 0.00072 22.8 1.6 17 10-26 9-25 (71)
17 PF13956 Ibs_toxin: Toxin Ibs, 31.0 22 0.00048 18.3 0.5 7 9-15 8-14 (19)
18 PLN02995 Probable pectinestera 30.3 93 0.002 26.9 4.4 16 34-49 37-52 (539)
19 PF07699 GCC2_GCC3: GCC2 and G 29.0 74 0.0016 18.1 2.6 27 57-83 10-40 (48)
20 PRK11505 hypothetical protein; 28.9 56 0.0012 23.2 2.4 17 1-17 1-17 (106)
21 PF08396 Toxin_34: Spider toxi 27.8 39 0.00084 22.7 1.4 12 67-78 10-21 (75)
22 TIGR02804 ExbD_2 TonB system t 26.9 69 0.0015 21.4 2.5 16 5-20 12-27 (121)
23 COG4537 ComGC Competence prote 26.7 58 0.0012 23.2 2.2 14 6-19 21-34 (107)
24 TIGR03516 ppisom_GldI peptidyl 23.3 51 0.0011 24.0 1.4 16 1-16 1-16 (177)
25 PTZ00264 circumsporozoite-rela 23.1 75 0.0016 23.6 2.3 15 1-15 1-15 (148)
26 PF07403 DUF1505: Protein of u 22.2 49 0.0011 23.6 1.1 15 1-15 1-15 (114)
27 PF12071 DUF3551: Protein of u 22.0 1.1E+02 0.0023 20.3 2.6 8 29-36 40-47 (82)
28 TIGR01614 PME_inhib pectineste 21.9 78 0.0017 21.7 2.1 18 33-50 31-48 (178)
29 PRK11024 colicin uptake protei 21.7 58 0.0012 22.4 1.4 16 5-20 23-38 (141)
30 TIGR02801 tolR TolR protein. T 21.6 73 0.0016 21.2 1.8 14 6-19 14-27 (129)
31 PF15079 DUF4546: Domain of un 21.3 34 0.00073 26.6 0.1 20 47-66 169-189 (205)
32 PF10868 DUF2667: Protein of u 21.3 52 0.0011 22.5 1.1 20 60-79 63-82 (90)
33 COG2991 Uncharacterized protei 20.9 1.4E+02 0.0031 20.1 3.1 9 29-37 46-54 (77)
34 PF01826 TIL: Trypsin Inhibito 20.8 3.2 7E-05 24.2 -4.4 39 28-70 8-46 (55)
35 TIGR02803 ExbD_1 TonB system t 20.6 83 0.0018 20.9 1.9 15 5-19 12-26 (122)
36 PF02402 Lysis_col: Lysis prot 20.2 45 0.00098 20.5 0.5 13 3-15 4-16 (46)
No 1
>PF02704 GASA: Gibberellin regulated protein; InterPro: IPR003854 This is the GASA gibberellin regulated cysteine rich protein family. The expression of these proteins is up-regulated by the plant hormone gibberellin, most of these proteins have some role in plant development. There are 12 cysteine residues conserved within the alignment giving the potential for these proteins to posses 6 disulphide bonds.
Probab=100.00 E-value=2.1e-38 Score=201.99 Aligned_cols=60 Identities=65% Similarity=1.546 Sum_probs=59.5
Q ss_pred CChHHhhHHHhhcCcchHHHHHHhHhhccccccCCCCCCCCCCCCcccccccCCCCCCCC
Q 039784 29 FCDSKCAVRCSKAGREDRCLKYCGICCDKCHCVPSGTYGHKDECPCYRDLKNSKGKPKCP 88 (88)
Q Consensus 29 ~C~~~C~~RCs~~~~~~~C~~~C~~CC~~C~CVP~Gtygnk~~CpCY~~m~t~~g~pKCP 88 (88)
||+++|++|||+++++++||++||+||++|+|||||||||+|+||||+||+||+|+||||
T Consensus 1 ~C~~~C~~RCs~~~~~~~C~~~C~~CC~~C~CVP~GT~gn~~~CpCY~~m~t~~g~pKCP 60 (60)
T PF02704_consen 1 DCGGACSVRCSKASRKKRCMRACGTCCAKCKCVPPGTYGNKEECPCYRDMKTHGGKPKCP 60 (60)
T ss_pred CcchHHHHHHhccCCchHHHHHHHHHhccCcccCCCCCCCCccCCChhhhhccCCCCCCc
Confidence 799999999999999999999999999999999999999999999999999999999999
No 2
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=83.36 E-value=1.1 Score=30.23 Aligned_cols=11 Identities=36% Similarity=0.640 Sum_probs=4.3
Q ss_pred HHHHHHHHHHH
Q 039784 6 VTFLLVSLVLT 16 (88)
Q Consensus 6 ~~~ll~~lll~ 16 (88)
+.+||++|||+
T Consensus 9 L~l~LA~lLli 19 (95)
T PF07172_consen 9 LGLLLAALLLI 19 (95)
T ss_pred HHHHHHHHHHH
Confidence 33333344443
No 3
>PF11912 DUF3430: Protein of unknown function (DUF3430); InterPro: IPR021837 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 209 to 265 amino acids in length.
Probab=76.16 E-value=2.5 Score=30.04 Aligned_cols=10 Identities=50% Similarity=0.660 Sum_probs=5.9
Q ss_pred ChHHHHHHHH
Q 039784 1 MKLALVTFLL 10 (88)
Q Consensus 1 mk~~~~~~ll 10 (88)
|||++.++||
T Consensus 1 MKll~~lill 10 (212)
T PF11912_consen 1 MKLLISLILL 10 (212)
T ss_pred CcHHHHHHHH
Confidence 8987554333
No 4
>PF02950 Conotoxin: Conotoxin; InterPro: IPR004214 Cone snail toxins, conotoxins, are small neurotoxic peptides with disulphide connectivity that target ion-channels or G-protein coupled receptors. Based on the number and pattern of disulphide bonds and biological activities, conotoxins can be classified into several families []. Omega, delta and kappa families of conotoxins have a knottin or inhibitor cysteine knot scaffold. The knottin scaffold is a very special disulphide-through-disulphide knot, in which the III-VI disulphide bond crosses the macrocycle formed by two other disulphide bonds (I-IV and II-V) and the interconnecting backbone segments, where I-VI indicates the six cysteine residues starting from the N terminus. The disulphide bonding network, as well as specific amino acids in inter-cysteine loops, provide the specificity of conotoxins []. The cysteine arrangements are the same for omega, delta and kappa families, even though omega conotoxins are calcium channel blockers, whereas delta conotoxins delay the inactivation of sodium channels, and kappa conotoxins are potassium channel blockers []. Mu conotoxins have two types of cysteine arrangements, but the knottin scaffold is not observed. Mu conotoxins target the voltage-gated sodium channels [], and are useful probes for investigating voltage-dependent sodium channels of excitable tissues []. Alpha conotoxins have two types of cysteine arrangements [], and are competitive nicotinic acetylcholine receptor antagonists. ; GO: 0008200 ion channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 2EFZ_A 1FYG_A 1RMK_A 1DG0_A 1DFY_A 1DFZ_A 2JQC_A 2YYF_A 2JQB_A 1F3K_A ....
Probab=65.76 E-value=2 Score=26.36 Aligned_cols=15 Identities=47% Similarity=0.638 Sum_probs=0.0
Q ss_pred ChHHHHHHHHHHHHHH
Q 039784 1 MKLALVTFLLVSLVLT 16 (88)
Q Consensus 1 mk~~~~~~ll~~lll~ 16 (88)
|||-+++ +|++|||+
T Consensus 1 mKLt~vl-iVavLllt 15 (75)
T PF02950_consen 1 MKLTCVL-IVAVLLLT 15 (75)
T ss_dssp ----------------
T ss_pred CCcchHH-HHHHHHHH
Confidence 7877442 44545554
No 5
>PF08027 Albumin_I: Albumin I; InterPro: IPR012512 The albumin I protein, a hormone-like peptide, stimulates kinase activity upon binding a membrane bound 43 kDa receptor. The structure of this region reveals a knottin like fold, comprise of three beta strands [].; GO: 0045735 nutrient reservoir activity, 0009405 pathogenesis; PDB: 1P8B_A 1JU8_A.
Probab=64.74 E-value=0.87 Score=32.81 Aligned_cols=32 Identities=28% Similarity=0.662 Sum_probs=14.3
Q ss_pred cCCCCChHHhhHHHhhcCcchHHHHHHhHhhccccccCCCCCC
Q 039784 25 AGSDFCDSKCAVRCSKAGREDRCLKYCGICCDKCHCVPSGTYG 67 (88)
Q Consensus 25 a~~~~C~~~C~~RCs~~~~~~~C~~~C~~CC~~C~CVP~Gtyg 67 (88)
....+|.+. ||.-..+ -||. .+|.|+|-|..+
T Consensus 17 VEA~~C~g~----Cs~Fe~p-----pCgs--s~CrCiP~~l~~ 48 (120)
T PF08027_consen 17 VEACDCSGV----CSPFEMP-----PCGS--SDCRCIPWGLFV 48 (120)
T ss_dssp -----SECE----E-TTSSS-----CCC---TTSEEEE-SSS-
T ss_pred eeeeccCcc----ccCCcCC-----CCCC--CCeeEEEeeecc
Confidence 445678776 4543321 2443 579999988653
No 6
>PF09257 BCMA-Tall_bind: BCMA, TALL-1 binding; InterPro: IPR015337 Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [, , ]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [, ]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide []. There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. Members of this entry, which are predominantly found in the tumour necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumour necrosis factor ligand TALL-1 []. ; PDB: 2KN1_A 1OQD_R 1XU2_T.
Probab=59.81 E-value=7.1 Score=23.27 Aligned_cols=21 Identities=33% Similarity=0.871 Sum_probs=16.3
Q ss_pred HhhHHHhhcCcchHHHHHHhH
Q 039784 33 KCAVRCSKAGREDRCLKYCGI 53 (88)
Q Consensus 33 ~C~~RCs~~~~~~~C~~~C~~ 53 (88)
-|.-|||+..-+-.|.+||+.
T Consensus 16 PChLRCsn~tPP~~Cq~YCna 36 (39)
T PF09257_consen 16 PCHLRCSNNTPPLPCQRYCNA 36 (39)
T ss_dssp EHHHHHTSSS--TTTHHHHHH
T ss_pred cceeecCCCCCCccchhhccc
Confidence 388999997888899999974
No 7
>PF07127 Nodulin_late: Late nodulin protein; InterPro: IPR009810 This family consists of several plant specific late nodulin sequences which are homologous to the Pisum sativum (Garden pea) ENOD3 protein. ENOD3 is expressed in the late stages of root nodule formation and contains two pairs of cysteine residues toward the proteins C terminus which may be involved in metal-binding [].; GO: 0046872 metal ion binding, 0009878 nodule morphogenesis
Probab=49.57 E-value=14 Score=22.10 Aligned_cols=7 Identities=14% Similarity=0.377 Sum_probs=4.7
Q ss_pred CCCChHH
Q 039784 27 SDFCDSK 33 (88)
Q Consensus 27 ~~~C~~~ 33 (88)
..||+..
T Consensus 33 d~DCp~~ 39 (54)
T PF07127_consen 33 DSDCPKD 39 (54)
T ss_pred cccCCCC
Confidence 3677776
No 8
>PF10690 Myticin-prepro: Myticin pre-proprotein from the mussel; InterPro: IPR019631 Myticin is a cysteine-rich peptide produced in three isoforms, A, B and C, by Mytilus galloprovincialis (Mediterranean mussel). Isoforms A and B show antibacterial activity against Gram-positive bacteria, while isoform B is additionally active against the fungus Fusarium oxysporum and a Gram-negative bacterium, Escherichia coli (streptomycin resistant strain D31) []. Myticin-prepro is the precursor peptide. The mature molecule, named myticin, consists of 40 residues, with four intramolecular disulphide bridges and a cysteine array in the primary structure different from that of previously characterised cysteine-rich antimicrobial peptides. The first 20 amino acids are a putative signal peptide, and the antimicrobial peptide sequence is a 36-residue C-terminal extension. Such a structure suggests that myticins are synthesised as prepro-proteins that are then processed by various proteolytic events before storage in the haemocytes as the active peptide. Myticin precursors are expressed mainly in the haemocytes. ; PDB: 2EEM_A.
Probab=48.12 E-value=9.4 Score=26.74 Aligned_cols=23 Identities=35% Similarity=0.423 Sum_probs=9.9
Q ss_pred hhhhhcCCCCChHH-hhHHHhhcC
Q 039784 20 FEVSMAGSDFCDSK-CAVRCSKAG 42 (88)
Q Consensus 20 ~~~~~a~~~~C~~~-C~~RCs~~~ 42 (88)
+...+|.+.-|.+. |+.+|..++
T Consensus 15 v~v~ea~s~~CtS~yC~~fCgsa~ 38 (98)
T PF10690_consen 15 VGVQEAQSISCTSYYCKKFCGSAR 38 (98)
T ss_dssp ----------HHHH-HHHHHHHTT
T ss_pred cccccccccccchhHHHHhcCCCC
Confidence 34445566788888 888887543
No 9
>PF15284 PAGK: Phage-encoded virulence factor
Probab=45.72 E-value=25 Score=22.72 Aligned_cols=14 Identities=21% Similarity=0.349 Sum_probs=6.4
Q ss_pred HHHHHhhhhhhhcC
Q 039784 13 LVLTSTFFEVSMAG 26 (88)
Q Consensus 13 lll~~~~~~~~~a~ 26 (88)
+|.++.|...++|+
T Consensus 14 ~LsA~~FSasamAa 27 (61)
T PF15284_consen 14 ILSAAGFSASAMAA 27 (61)
T ss_pred HHHHhhhhHHHHHH
Confidence 33344444555553
No 10
>KOG4063 consensus Major epididymal secretory protein HE1 [Function unknown]
Probab=36.66 E-value=36 Score=25.59 Aligned_cols=6 Identities=33% Similarity=0.595 Sum_probs=3.2
Q ss_pred CCCChH
Q 039784 27 SDFCDS 32 (88)
Q Consensus 27 ~~~C~~ 32 (88)
-.+|++
T Consensus 27 ~k~C~s 32 (158)
T KOG4063|consen 27 VKQCGS 32 (158)
T ss_pred cccccC
Confidence 356655
No 11
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=35.66 E-value=45 Score=22.56 Aligned_cols=12 Identities=25% Similarity=0.376 Sum_probs=6.7
Q ss_pred ChHHHHHHHHHH
Q 039784 1 MKLALVTFLLVS 12 (88)
Q Consensus 1 mk~~~~~~ll~~ 12 (88)
||++++++++++
T Consensus 1 m~~~~~vll~ll 12 (105)
T PRK00888 1 MRLLTLLLLALL 12 (105)
T ss_pred CcHHHHHHHHHH
Confidence 777755544333
No 12
>PF15330 SIT: SHP2-interacting transmembrane adaptor protein, SIT
Probab=35.28 E-value=53 Score=22.60 Aligned_cols=16 Identities=25% Similarity=0.671 Sum_probs=11.3
Q ss_pred CCCCCCCcccccccCC
Q 039784 67 GHKDECPCYRDLKNSK 82 (88)
Q Consensus 67 gnk~~CpCY~~m~t~~ 82 (88)
+..|+=|||.|...+.
T Consensus 41 ~~~E~~p~YgNL~~~q 56 (107)
T PF15330_consen 41 QPTEDDPCYGNLELQQ 56 (107)
T ss_pred CCCCCCcccccccccc
Confidence 4557778999986643
No 13
>PF06607 Prokineticin: Prokineticin; InterPro: IPR023569 The prokineticin family includes prokinectin itself and related proteins such as BM8 and the AVIToxins. The suprachiasmatic nucleus (SCN) controls the circadian rhythm of physiological and behavioural processes in mammals. It has been shown that prokineticin 2 (PK2), a cysteine-rich secreted protein, functions as an output molecule from the SCN circadian clock. PK2 messenger RNA is rhythmically expressed in the SCN, and the phase of PK2 rhythm is responsive to light entrainment. Molecular and genetic studies have revealed that PK2 is a gene that is controlled by a circadian clock []. The prokinectin domain is found in the prokinectin family and the hainantoxins, where it comprises the whole length of the protein. This domain is also found at the C terminus of some members of the Dickkopf family.; PDB: 1IMT_A 2KRA_A.
Probab=34.41 E-value=12 Score=25.69 Aligned_cols=12 Identities=33% Similarity=0.545 Sum_probs=4.9
Q ss_pred CCCCCCcccccc
Q 039784 68 HKDECPCYRDLK 79 (88)
Q Consensus 68 nk~~CpCY~~m~ 79 (88)
..+.|||-.++.
T Consensus 74 ~~~~CPC~~gL~ 85 (97)
T PF06607_consen 74 YFWRCPCAPGLV 85 (97)
T ss_dssp -SSS--B-TT-E
T ss_pred eEeeCCCCCCcE
Confidence 347888888773
No 14
>PLN03207 stomagen; Provisional
Probab=32.39 E-value=58 Score=23.27 Aligned_cols=18 Identities=28% Similarity=0.335 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHhhhhh
Q 039784 5 LVTFLLVSLVLTSTFFEV 22 (88)
Q Consensus 5 ~~~~ll~~lll~~~~~~~ 22 (88)
++.|||.+|||.+.+.|.
T Consensus 14 ~lffLl~~llla~~v~qg 31 (113)
T PLN03207 14 TLFFLLFFLLLGAYVIQG 31 (113)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 344455556666665543
No 15
>PF15240 Pro-rich: Proline-rich
Probab=32.18 E-value=29 Score=26.34 Aligned_cols=16 Identities=25% Similarity=0.351 Sum_probs=10.5
Q ss_pred HHHHHHhhhhhhhcCC
Q 039784 12 SLVLTSTFFEVSMAGS 27 (88)
Q Consensus 12 ~lll~~~~~~~~~a~~ 27 (88)
+|||+++++.+++|.+
T Consensus 3 lVLLSvALLALSSAQ~ 18 (179)
T PF15240_consen 3 LVLLSVALLALSSAQS 18 (179)
T ss_pred hHHHHHHHHHhhhccc
Confidence 3566667777777753
No 16
>PF04202 Mfp-3: Foot protein 3; InterPro: IPR007328 Mytilus foot protein-3 (Mfp-3) is a highly polymorphic protein family located in the byssal adhesive plaques of blue mussels.
Probab=31.90 E-value=33 Score=22.78 Aligned_cols=17 Identities=47% Similarity=0.571 Sum_probs=8.5
Q ss_pred HHHHHHHHhhhhhhhcC
Q 039784 10 LVSLVLTSTFFEVSMAG 26 (88)
Q Consensus 10 l~~lll~~~~~~~~~a~ 26 (88)
|+.|+|+.+|...++|+
T Consensus 9 LlaLvLIg~fAVqSdag 25 (71)
T PF04202_consen 9 LLALVLIGSFAVQSDAG 25 (71)
T ss_pred HHHHHHHhhheeeecCc
Confidence 33444445555555554
No 17
>PF13956 Ibs_toxin: Toxin Ibs, type I toxin-antitoxin system
Probab=30.98 E-value=22 Score=18.32 Aligned_cols=7 Identities=43% Similarity=0.747 Sum_probs=2.7
Q ss_pred HHHHHHH
Q 039784 9 LLVSLVL 15 (88)
Q Consensus 9 ll~~lll 15 (88)
|+++|++
T Consensus 8 lvvLLli 14 (19)
T PF13956_consen 8 LVVLLLI 14 (19)
T ss_pred HHHHHhc
Confidence 3333433
No 18
>PLN02995 Probable pectinesterase/pectinesterase inhibitor
Probab=30.29 E-value=93 Score=26.85 Aligned_cols=16 Identities=25% Similarity=0.335 Sum_probs=11.6
Q ss_pred hhHHHhhcCcchHHHH
Q 039784 34 CAVRCSKAGREDRCLK 49 (88)
Q Consensus 34 C~~RCs~~~~~~~C~~ 49 (88)
=...|+.+.+++.|.+
T Consensus 37 Irs~C~~T~YP~lC~s 52 (539)
T PLN02995 37 IDGWCDKTPYPDPCKC 52 (539)
T ss_pred HHhhcCCCCChHHHHH
Confidence 3345888888988853
No 19
>PF07699 GCC2_GCC3: GCC2 and GCC3; InterPro: IPR011641 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Tyrosine-protein kinases can transfer a phosphate group from ATP to a tyrosine residue in a protein. These enzymes can be divided into two main groups []: Receptor tyrosine kinases (RTK), which are transmembrane proteins involved in signal transduction; they play key roles in growth, differentiation, metabolism, adhesion, motility, death and oncogenesis []. RTKs are composed of 3 domains: an extracellular domain (binds ligand), a transmembrane (TM) domain, and an intracellular catalytic domain (phosphorylates substrate). The TM domain plays an important role in the dimerisation process necessary for signal transduction []. Cytoplasmic / non-receptor tyrosine kinases, which act as regulatory proteins, playing key roles in cell differentiation, motility, proliferation, and survival. For example, the Src-family of protein-tyrosine kinases []. This entry represents various ephrin type A and B receptors, which have tyrosine kinase activity.
Probab=29.04 E-value=74 Score=18.10 Aligned_cols=27 Identities=37% Similarity=0.801 Sum_probs=19.2
Q ss_pred cccccCCCCCCCC---CCC-CcccccccCCC
Q 039784 57 KCHCVPSGTYGHK---DEC-PCYRDLKNSKG 83 (88)
Q Consensus 57 ~C~CVP~Gtygnk---~~C-pCY~~m~t~~g 83 (88)
.|.=-|.|||-+. .+| +|-.+..|...
T Consensus 10 ~C~~Cp~GtYq~~~g~~~C~~Cp~g~~T~~~ 40 (48)
T PF07699_consen 10 KCQPCPKGTYQDEEGQTSCTPCPPGSTTSSE 40 (48)
T ss_pred ccCCCCCCccCCccCCccCccCcCCCccCCc
Confidence 3444588999654 579 89998877553
No 20
>PRK11505 hypothetical protein; Provisional
Probab=28.90 E-value=56 Score=23.17 Aligned_cols=17 Identities=41% Similarity=0.639 Sum_probs=10.4
Q ss_pred ChHHHHHHHHHHHHHHH
Q 039784 1 MKLALVTFLLVSLVLTS 17 (88)
Q Consensus 1 mk~~~~~~ll~~lll~~ 17 (88)
||+.+++.|++.|+++.
T Consensus 1 mk~~~l~~ll~g~~~~~ 17 (106)
T PRK11505 1 MKITLLVTLLFGLVFLT 17 (106)
T ss_pred CchHHHHHHHHHHHHhh
Confidence 67665555666666654
No 21
>PF08396 Toxin_34: Spider toxin omega agatoxin/Tx1 family; InterPro: IPR013605 The Tx1 family lethal spider neurotoxin induces excitatory symptoms in mice [].
Probab=27.77 E-value=39 Score=22.68 Aligned_cols=12 Identities=50% Similarity=1.168 Sum_probs=10.2
Q ss_pred CCCCCCCccccc
Q 039784 67 GHKDECPCYRDL 78 (88)
Q Consensus 67 gnk~~CpCY~~m 78 (88)
|+|++|.|++++
T Consensus 10 G~k~dCqCc~~n 21 (75)
T PF08396_consen 10 GDKSDCQCCRDN 21 (75)
T ss_pred CCcccccccCCC
Confidence 788899888876
No 22
>TIGR02804 ExbD_2 TonB system transport protein ExbD, group 2. Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR family modeled by TIGRFAMs TIGR02801. Members always are encoded next to a protein designated ExbB (TIGR02797), related to the TolQ family modeled by TIGRFAMs TIGR02796. ExbD and ExbB together form a proton channel through which they can harness the proton-motive force to energize TonB, which in turn energizes TonB-dependent receptors in the outer membrane. TonB-dependent receptors with known specificity tend to import siderophores or vitamin B12. A TonB system and Tol-Pal system often will co-exist in a single bacterial genome.
Probab=26.86 E-value=69 Score=21.42 Aligned_cols=16 Identities=31% Similarity=0.584 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHhhh
Q 039784 5 LVTFLLVSLVLTSTFF 20 (88)
Q Consensus 5 ~~~~ll~~lll~~~~~ 20 (88)
++.+||+++++++++.
T Consensus 12 VvflLLiFFmvtt~~~ 27 (121)
T TIGR02804 12 IMLVLLAIVLIISTFI 27 (121)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444555566665554
No 23
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=26.74 E-value=58 Score=23.17 Aligned_cols=14 Identities=21% Similarity=0.505 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHhh
Q 039784 6 VTFLLVSLVLTSTF 19 (88)
Q Consensus 6 ~~~ll~~lll~~~~ 19 (88)
++||++|+|++.++
T Consensus 21 iVLlIISiLlLl~i 34 (107)
T COG4537 21 IVLLIISILLLLFI 34 (107)
T ss_pred HHHHHHHHHHHHHc
Confidence 44577777776554
No 24
>TIGR03516 ppisom_GldI peptidyl-prolyl isomerase, gliding motility-associated. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldI is a FKBP-type peptidyl-prolyl cis-trans isomerase (pfam00254) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockout of this gene abolishes the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. This family is only found in Bacteroidetes containing the suite of genes proposed to confer the gliding motility phenotype.
Probab=23.30 E-value=51 Score=24.05 Aligned_cols=16 Identities=38% Similarity=0.515 Sum_probs=8.3
Q ss_pred ChHHHHHHHHHHHHHH
Q 039784 1 MKLALVTFLLVSLVLT 16 (88)
Q Consensus 1 mk~~~~~~ll~~lll~ 16 (88)
||.+++++|++++|++
T Consensus 1 ~~~~~~~~~~~~~~~~ 16 (177)
T TIGR03516 1 MKHLIAVILLLLLLLG 16 (177)
T ss_pred CceeHHHHHHHHHHhh
Confidence 6766555444444443
No 25
>PTZ00264 circumsporozoite-related antigen; Provisional
Probab=23.13 E-value=75 Score=23.58 Aligned_cols=15 Identities=47% Similarity=0.653 Sum_probs=9.2
Q ss_pred ChHHHHHHHHHHHHH
Q 039784 1 MKLALVTFLLVSLVL 15 (88)
Q Consensus 1 mk~~~~~~ll~~lll 15 (88)
|||+.++|||.++.|
T Consensus 1 mkils~vFllF~~il 15 (148)
T PTZ00264 1 MKLLSAVFLLFCAIL 15 (148)
T ss_pred ChHHHHHHHHHHHHH
Confidence 788866655444444
No 26
>PF07403 DUF1505: Protein of unknown function (DUF1505); InterPro: IPR009981 This family consists of several uncharacterised Caenorhabditis elegans proteins of around 115 resides in length. Members of this family contain 6 highly conserved cysteine residues. The function of this family is unknown.
Probab=22.16 E-value=49 Score=23.58 Aligned_cols=15 Identities=33% Similarity=0.439 Sum_probs=7.3
Q ss_pred ChHHHHHHHHHHHHH
Q 039784 1 MKLALVTFLLVSLVL 15 (88)
Q Consensus 1 mk~~~~~~ll~~lll 15 (88)
|++++++.||+++++
T Consensus 1 Mnf~~~~vl~lsv~v 15 (114)
T PF07403_consen 1 MNFFPSTVLLLSVTV 15 (114)
T ss_pred CCchhhhHHHHHHHH
Confidence 665544445555433
No 27
>PF12071 DUF3551: Protein of unknown function (DUF3551); InterPro: IPR021937 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 79 to 104 amino acids in length. This protein has a single completely conserved residue C that may be functionally important.
Probab=22.02 E-value=1.1e+02 Score=20.27 Aligned_cols=8 Identities=13% Similarity=0.252 Sum_probs=3.3
Q ss_pred CChHHhhH
Q 039784 29 FCDSKCAV 36 (88)
Q Consensus 29 ~C~~~C~~ 36 (88)
+.++.|++
T Consensus 40 g~~g~C~y 47 (82)
T PF12071_consen 40 GYPGDCSY 47 (82)
T ss_pred CCCccCCc
Confidence 34444443
No 28
>TIGR01614 PME_inhib pectinesterase inhibitor domain. This model describes a plant domain of about 200 amino acids, characterized by four conserved Cys residues, shown in a pectinesterase inhibitor from Kiwi to form two disulfide bonds: first to second and third to fourth. Roughly half the members of this family have the region described by this model followed immediately by a pectinesterase domain, pfam01095. This suggests that the pairing of the enzymatic domain and its inhibitor reflects a conserved regulatory mechanism for this enzyme family.
Probab=21.93 E-value=78 Score=21.66 Aligned_cols=18 Identities=17% Similarity=0.294 Sum_probs=12.0
Q ss_pred HhhHHHhhcCcchHHHHH
Q 039784 33 KCAVRCSKAGREDRCLKY 50 (88)
Q Consensus 33 ~C~~RCs~~~~~~~C~~~ 50 (88)
.=+.-|..+.+++.|...
T Consensus 31 ~i~~~C~~t~~~~~C~~~ 48 (178)
T TIGR01614 31 LIKRICKKTEYPNFCIST 48 (178)
T ss_pred HHHHHHcCCCChHHHHHH
Confidence 444557777788888654
No 29
>PRK11024 colicin uptake protein TolR; Provisional
Probab=21.75 E-value=58 Score=22.42 Aligned_cols=16 Identities=19% Similarity=0.387 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHhhh
Q 039784 5 LVTFLLVSLVLTSTFF 20 (88)
Q Consensus 5 ~~~~ll~~lll~~~~~ 20 (88)
++.+||++++++++|.
T Consensus 23 VvfvLLiFFmvts~~~ 38 (141)
T PRK11024 23 VLLVLLLIFMATAPII 38 (141)
T ss_pred HHHHHHHHHHhccccc
Confidence 3444555555555553
No 30
>TIGR02801 tolR TolR protein. The model describes the inner membrane protein TolR, part of the TolR/TolQ complex that transduces energy from the proton-motive force, through TolA, to an outer membrane complex made up of TolB and Pal (peptidoglycan-associated lipoprotein). The complex is required to maintain outer membrane integrity, and defects may cause a defect in the import of some organic compounds in addition to the resulting morphologic. While several gene pairs homologous to talR and tolQ may be found in a single genome, but the scope of this model is set to favor finding only bone fide TolR, supported by operon structure as well as by score.
Probab=21.63 E-value=73 Score=21.23 Aligned_cols=14 Identities=21% Similarity=0.496 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHhh
Q 039784 6 VTFLLVSLVLTSTF 19 (88)
Q Consensus 6 ~~~ll~~lll~~~~ 19 (88)
+.+||+++++++++
T Consensus 14 vFlLLiFFmvts~~ 27 (129)
T TIGR02801 14 MLVLLIIFMVTAPL 27 (129)
T ss_pred HHHHHHHHHhhhcc
Confidence 33455555555555
No 31
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=21.28 E-value=34 Score=26.60 Aligned_cols=20 Identities=40% Similarity=1.157 Sum_probs=16.1
Q ss_pred HHHHHhHhhcccc-ccCCCCC
Q 039784 47 CLKYCGICCDKCH-CVPSGTY 66 (88)
Q Consensus 47 C~~~C~~CC~~C~-CVP~Gty 66 (88)
-+-.|++||++|. |..-.+|
T Consensus 169 ~lH~C~tCcekcllCalk~n~ 189 (205)
T PF15079_consen 169 SLHQCRTCCEKCLLCALKNNY 189 (205)
T ss_pred chhhchhhhhhhhhhhccccc
Confidence 4567999999998 8877655
No 32
>PF10868 DUF2667: Protein of unknown function (DUF2667); InterPro: IPR022618 This family of proteins with unknown function appears to be restricted to Arabidopsis thaliana.
Probab=21.27 E-value=52 Score=22.55 Aligned_cols=20 Identities=35% Similarity=0.677 Sum_probs=12.3
Q ss_pred ccCCCCCCCCCCCCcccccc
Q 039784 60 CVPSGTYGHKDECPCYRDLK 79 (88)
Q Consensus 60 CVP~Gtygnk~~CpCY~~m~ 79 (88)
|+|-|.-.-...|-|..+-+
T Consensus 63 C~~~~~~~~~~~C~Cc~~~~ 82 (90)
T PF10868_consen 63 CVPVGPPPGDGVCYCCYYVK 82 (90)
T ss_pred eccCCCCCCCcEEEEeccCC
Confidence 67755544567786655543
No 33
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.90 E-value=1.4e+02 Score=20.11 Aligned_cols=9 Identities=33% Similarity=0.855 Sum_probs=5.7
Q ss_pred CChHHhhHH
Q 039784 29 FCDSKCAVR 37 (88)
Q Consensus 29 ~C~~~C~~R 37 (88)
||+..|+.|
T Consensus 46 dC~~pCDt~ 54 (77)
T COG2991 46 DCDEPCDTH 54 (77)
T ss_pred CCCCchHHH
Confidence 566666655
No 34
>PF01826 TIL: Trypsin Inhibitor like cysteine rich domain; InterPro: IPR002919 This domain is found in proteinase inhibitors as well as in many extracellular proteins. The domain typically contains ten cysteine residues that form five disulphide bonds. The cysteine residues that form the disulphide bonds are 1-7, 2-6, 3-5, 4-10 and 8-9. This inhibitor domain belongs to MEROPS inhibitor family I8 (clan IA). Proteins containing this domain inhibit peptidases belonging to families S1 (IPR001254 from INTERPRO), S8 (IPR000209 from INTERPRO), and M4 (IPR001570 from INTERPRO) [] and are restricted to the chordata, nematoda, arthropoda and echinodermata. Examples of proteins containing this domain are: chymotrypsin/elastase inhibitor from Ascaris suum (pig roundworm) Acp62F protein from Drosophila melanogaster Bombina trypsin inhibitor from Bombina maxima (large-webbed bell toad) Bombyx subtilisin inhibitor from Bombyx mori (silk moth) von Willebrand factor ; PDB: 2P3F_N 1HX2_A 1CCV_A 1EAI_D 2H9E_C 1COU_A 1ATE_A 1ATB_A 1ATD_A 1ATA_A ....
Probab=20.84 E-value=3.2 Score=24.17 Aligned_cols=39 Identities=26% Similarity=0.795 Sum_probs=24.8
Q ss_pred CCChHHhhHHHhhcCcchHHHHHHhHhhccccccCCCCCCCCC
Q 039784 28 DFCDSKCAVRCSKAGREDRCLKYCGICCDKCHCVPSGTYGHKD 70 (88)
Q Consensus 28 ~~C~~~C~~RCs~~~~~~~C~~~C~~CC~~C~CVP~Gtygnk~ 70 (88)
.+|++.|...|+.......|.. .|=+-|.| |+|++-|.+
T Consensus 8 ~~C~~~C~~tC~~~~~~~~C~~---~C~~gC~C-~~G~v~~~~ 46 (55)
T PF01826_consen 8 SECGSPCPRTCDNPNNPEPCSE---PCVEGCFC-PPGYVRNDN 46 (55)
T ss_dssp ESSETSTTCBSSCTTTSSSCSS---S-ESEEEE-TTTEEEETT
T ss_pred CcccCCcCCcCCCCCCCcCcCC---CCCccCCC-CCCeeEcCC
Confidence 4688888888887666655663 33344667 557775544
No 35
>TIGR02803 ExbD_1 TonB system transport protein ExbD, group 1. Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR family modeled by TIGRFAMs TIGR02801. Members always are encoded next to a protein designated ExbB (TIGR02797), related to the TolQ family modeled by TIGRFAMs TIGR02796. ExbD and ExbB together form a proton channel through which they can harness the proton-motive force to energize TonB, which in turn energizes TonB-dependent receptors in the outer membrane. TonB-dependent receptors with known specificity tend to import siderophores or vitamin B12. A TonB system and Tol-Pal system often will co-exist in a single bacterial genome.
Probab=20.60 E-value=83 Score=20.92 Aligned_cols=15 Identities=13% Similarity=0.461 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHhh
Q 039784 5 LVTFLLVSLVLTSTF 19 (88)
Q Consensus 5 ~~~~ll~~lll~~~~ 19 (88)
++.+||+++++++.+
T Consensus 12 VvflLLiFFmvts~~ 26 (122)
T TIGR02803 12 VMLVLLIIFMVAAPL 26 (122)
T ss_pred HHHHHHHHHHHhhhc
Confidence 333455555555544
No 36
>PF02402 Lysis_col: Lysis protein; InterPro: IPR003059 The DNA sequence of the entire colicin E2 operon has been determined []. The operon comprises the colicin activity gene (ceaB), the colicin immunity gene (ceiB) and the lysis gene (celB), which is essential for colicin release from producing cells []. A putative LexA binding site is located upstream from ceaB, and a rho-independent terminator structure is located downstream from celB []. Comparison of the amino acid sequences of colicin E2 and cloacin DF13 reveal extensive similarity. These colicins have different modes of action and recognise different cell surface receptors; the two major regions of heterology at the C terminus, and in the C-terminal end of the central region are thought to correspond to the catalytic and receptor-recognition domains, respectively []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. By contrast, the lysis proteins of the ColE2, ColE1 and CloDF13 plasmids are almost identical except in the N-terminal regions, which themselves are similar to lipoprotein signal peptides []. Processing of the ColE2 prolysis protein to the mature form is prevented by globomycin, a specific inhibitor of the lipoprotein signal peptidase []. The mature ColE2 lysis protein is located in the cell envelope [].; GO: 0009405 pathogenesis, 0019835 cytolysis, 0019867 outer membrane
Probab=20.17 E-value=45 Score=20.54 Aligned_cols=13 Identities=15% Similarity=0.639 Sum_probs=5.3
Q ss_pred HHHHHHHHHHHHH
Q 039784 3 LALVTFLLVSLVL 15 (88)
Q Consensus 3 ~~~~~~ll~~lll 15 (88)
+++..++++.++|
T Consensus 4 i~~~~i~~~~~~L 16 (46)
T PF02402_consen 4 IIFIGIFLLTMLL 16 (46)
T ss_pred EEEeHHHHHHHHH
Confidence 3433334444444
Done!