Query 037233
Match_columns 88
No_of_seqs 102 out of 203
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 10:05:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037233.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037233hhsearch_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 2E-38 4.4E-43 202.1 5.2 60 29-88 1-60 (60)
2 PF07172 GRP: Glycine rich pro 85.1 0.87 1.9E-05 30.8 2.5 15 4-18 7-21 (95)
3 PF11912 DUF3430: Protein of u 76.8 2.3 5E-05 30.2 2.4 13 1-13 1-13 (212)
4 PF02950 Conotoxin: Conotoxin; 69.4 1.5 3.3E-05 26.9 0.0 15 1-16 1-15 (75)
5 PF08027 Albumin_I: Albumin I; 61.6 1 2.2E-05 32.5 -2.1 32 25-67 17-48 (120)
6 PF09257 BCMA-Tall_bind: BCMA, 54.5 9.9 0.00021 22.7 1.6 21 33-53 16-36 (39)
7 PF15284 PAGK: Phage-encoded v 53.4 15 0.00033 23.7 2.5 14 13-26 14-27 (61)
8 PF15240 Pro-rich: Proline-ric 52.6 10 0.00022 28.8 1.9 10 9-18 6-15 (179)
9 PF07127 Nodulin_late: Late no 50.6 14 0.0003 22.1 1.9 6 28-33 34-39 (54)
10 PF10690 Myticin-prepro: Mytic 46.4 9.9 0.00021 26.6 0.9 22 21-42 16-38 (98)
11 KOG4063 Major epididymal secre 41.7 28 0.00061 26.2 2.7 32 1-32 1-32 (158)
12 PRK00888 ftsB cell division pr 37.9 40 0.00086 22.8 2.8 15 1-15 1-15 (105)
13 PF15240 Pro-rich: Proline-ric 37.1 26 0.00055 26.7 1.9 16 12-27 3-18 (179)
14 PLN03207 stomagen; Provisional 35.3 50 0.0011 23.6 3.0 17 5-21 14-30 (113)
15 PF06607 Prokineticin: Prokine 33.0 12 0.00027 25.6 -0.3 11 69-79 75-85 (97)
16 PLN02995 Probable pectinestera 31.8 85 0.0018 27.1 4.4 16 34-49 37-52 (539)
17 PF15330 SIT: SHP2-interacting 31.2 65 0.0014 22.2 3.0 16 67-82 41-56 (107)
18 PF04202 Mfp-3: Foot protein 3 28.7 42 0.00092 22.3 1.7 17 10-26 9-25 (71)
19 TIGR02804 ExbD_2 TonB system t 28.1 63 0.0014 21.6 2.5 16 5-20 12-27 (121)
20 PF07699 GCC2_GCC3: GCC2 and G 27.9 79 0.0017 18.0 2.6 27 57-83 10-40 (48)
21 PRK11505 hypothetical protein; 27.5 61 0.0013 23.0 2.4 17 1-17 1-17 (106)
22 COG2991 Uncharacterized protei 26.9 95 0.0021 20.9 3.1 11 28-38 45-55 (77)
23 TIGR01614 PME_inhib pectineste 26.5 57 0.0012 22.4 2.1 18 33-50 31-48 (178)
24 PTZ00264 circumsporozoite-rela 25.8 62 0.0013 24.0 2.3 15 1-15 1-15 (148)
25 COG4537 ComGC Competence prote 25.2 64 0.0014 22.9 2.2 15 6-20 21-35 (107)
26 PF12606 RELT: Tumour necrosis 24.4 1.2E+02 0.0026 18.6 3.0 17 9-25 10-26 (50)
27 PF08396 Toxin_34: Spider toxi 24.1 49 0.0011 22.2 1.4 12 67-78 10-21 (75)
28 PRK08944 motB flagellar motor 23.6 75 0.0016 25.1 2.5 15 5-19 24-38 (302)
29 TIGR03516 ppisom_GldI peptidyl 23.3 51 0.0011 24.0 1.4 16 1-16 1-16 (177)
30 TIGR02801 tolR TolR protein. T 23.2 65 0.0014 21.5 1.8 15 5-19 13-27 (129)
31 PF13677 MotB_plug: Membrane M 23.0 93 0.002 18.9 2.4 13 6-18 25-37 (58)
32 PRK11024 colicin uptake protei 22.8 53 0.0012 22.6 1.4 16 5-20 23-38 (141)
33 PF15079 DUF4546: Domain of un 22.6 30 0.00066 26.8 0.1 20 47-66 169-189 (205)
34 PRK07734 motB flagellar motor 22.5 79 0.0017 24.0 2.4 14 5-18 26-39 (259)
35 PF07771 TSGP1: Tick salivary 22.3 44 0.00096 23.5 0.9 7 1-7 1-7 (120)
36 TIGR02803 ExbD_1 TonB system t 22.1 74 0.0016 21.2 2.0 16 5-20 12-27 (122)
37 PF12276 DUF3617: Protein of u 21.4 82 0.0018 21.5 2.1 7 1-7 1-7 (162)
38 PRK11443 lipoprotein; Provisio 21.2 77 0.0017 22.3 1.9 7 1-7 1-7 (124)
39 PF10868 DUF2667: Protein of u 21.0 59 0.0013 22.3 1.3 20 60-79 63-82 (90)
40 PRK11267 biopolymer transport 20.9 76 0.0016 21.9 1.9 15 5-19 26-40 (141)
41 PRK06667 motB flagellar motor 20.5 93 0.002 23.5 2.4 14 5-18 25-38 (252)
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=2e-38 Score=202.09 Aligned_cols=60 Identities=65% Similarity=1.546 Sum_probs=59.5
Q ss_pred CChHHhhHHHhhcCcchHHHHHHhHhhccccccCCCCCCCCCCCCcccccccCCCCCCCC
Q 037233 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=85.10 E-value=0.87 Score=30.82 Aligned_cols=15 Identities=33% Similarity=0.565 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHHh
Q 037233 4 ALVTFLLVSLVVTST 18 (88)
Q Consensus 4 ~~~~~ll~~lll~~~ 18 (88)
+++.+||++|||++|
T Consensus 7 llL~l~LA~lLlisS 21 (95)
T PF07172_consen 7 LLLGLLLAALLLISS 21 (95)
T ss_pred HHHHHHHHHHHHHHh
Confidence 344444444444433
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=76.81 E-value=2.3 Score=30.19 Aligned_cols=13 Identities=46% Similarity=0.636 Sum_probs=7.1
Q ss_pred ChHHHHHHHHHHH
Q 037233 1 MKLALVTFLLVSL 13 (88)
Q Consensus 1 mk~~~~~~ll~~l 13 (88)
|||++.++||+++
T Consensus 1 MKll~~lilli~~ 13 (212)
T PF11912_consen 1 MKLLISLILLILL 13 (212)
T ss_pred CcHHHHHHHHHHH
Confidence 9987554333333
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=69.42 E-value=1.5 Score=26.90 Aligned_cols=15 Identities=40% Similarity=0.662 Sum_probs=0.0
Q ss_pred ChHHHHHHHHHHHHHH
Q 037233 1 MKLALVTFLLVSLVVT 16 (88)
Q Consensus 1 mk~~~~~~ll~~lll~ 16 (88)
|||-++ |+|++|||+
T Consensus 1 mKLt~v-liVavLllt 15 (75)
T PF02950_consen 1 MKLTCV-LIVAVLLLT 15 (75)
T ss_dssp ----------------
T ss_pred CCcchH-HHHHHHHHH
Confidence 787755 244445554
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=61.63 E-value=1 Score=32.48 Aligned_cols=32 Identities=28% Similarity=0.661 Sum_probs=14.1
Q ss_pred cCCCCChHHhhHHHhhcCcchHHHHHHhHhhccccccCCCCCC
Q 037233 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~-----ppCgs--s~CrCiP~~l~~ 48 (120)
T PF08027_consen 17 VEACDCSGV----CSPFEM-----PPCGS--SDCRCIPWGLFV 48 (120)
T ss_dssp -----SECE----E-TTSS-----SCCC---TTSEEEE-SSS-
T ss_pred eeeeccCcc----ccCCcC-----CCCCC--CCeeEEEeeecc
Confidence 344677776 443322 12443 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=54.47 E-value=9.9 Score=22.67 Aligned_cols=21 Identities=33% Similarity=0.871 Sum_probs=16.2
Q ss_pred HhhHHHhhcCcchHHHHHHhH
Q 037233 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 378899997788899999984
No 7
>PF15284 PAGK: Phage-encoded virulence factor
Probab=53.39 E-value=15 Score=23.74 Aligned_cols=14 Identities=21% Similarity=0.375 Sum_probs=6.3
Q ss_pred HHHHHhhhhhhccC
Q 037233 13 LVVTSTFFEVSMAG 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 33334444455553
No 8
>PF15240 Pro-rich: Proline-rich
Probab=52.65 E-value=10 Score=28.79 Aligned_cols=10 Identities=40% Similarity=0.491 Sum_probs=3.9
Q ss_pred HHHHHHHHHh
Q 037233 9 LLVSLVVTST 18 (88)
Q Consensus 9 ll~~lll~~~ 18 (88)
|.+.||+++|
T Consensus 6 LSvALLALSS 15 (179)
T PF15240_consen 6 LSVALLALSS 15 (179)
T ss_pred HHHHHHHhhh
Confidence 3333444333
No 9
>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=50.58 E-value=14 Score=22.11 Aligned_cols=6 Identities=17% Similarity=0.412 Sum_probs=4.3
Q ss_pred CCChHH
Q 037233 28 DFCDSK 33 (88)
Q Consensus 28 ~~C~~~ 33 (88)
.||+..
T Consensus 34 ~DCp~~ 39 (54)
T PF07127_consen 34 SDCPKD 39 (54)
T ss_pred ccCCCC
Confidence 678776
No 10
>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=46.40 E-value=9.9 Score=26.64 Aligned_cols=22 Identities=36% Similarity=0.440 Sum_probs=9.9
Q ss_pred hhhccCCCCChHH-hhHHHhhcC
Q 037233 21 EVSMAGSDFCDSK-CAVRCSKAG 42 (88)
Q Consensus 21 ~~~~a~~~~C~~~-C~~RCs~~~ 42 (88)
..-+|+++.|.+- |+.+|..++
T Consensus 16 ~v~ea~s~~CtS~yC~~fCgsa~ 38 (98)
T PF10690_consen 16 GVQEAQSISCTSYYCKKFCGSAR 38 (98)
T ss_dssp ---------HHHH-HHHHHHHTT
T ss_pred ccccccccccchhHHHHhcCCCC
Confidence 3444556788888 888887543
No 11
>KOG4063 consensus Major epididymal secretory protein HE1 [Function unknown]
Probab=41.68 E-value=28 Score=26.18 Aligned_cols=32 Identities=13% Similarity=0.284 Sum_probs=12.3
Q ss_pred ChHHHHHHHHHHHHHHHhhhhhhccCCCCChH
Q 037233 1 MKLALVTFLLVSLVVTSTFFEVSMAGSDFCDS 32 (88)
Q Consensus 1 mk~~~~~~ll~~lll~~~~~~~~~a~~~~C~~ 32 (88)
|+..+..++++.+||+++..|....+-.+|++
T Consensus 1 m~ms~~~~v~l~alls~a~aq~~~t~~k~C~s 32 (158)
T KOG4063|consen 1 MMMSFLKTVILLALLSLAAAQAISTGVKQCGS 32 (158)
T ss_pred CchHHHHHHHHHHHHHHhhhcccCcccccccC
Confidence 44333333333334433333322223356655
No 12
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=37.88 E-value=40 Score=22.83 Aligned_cols=15 Identities=20% Similarity=0.324 Sum_probs=8.1
Q ss_pred ChHHHHHHHHHHHHH
Q 037233 1 MKLALVTFLLVSLVV 15 (88)
Q Consensus 1 mk~~~~~~ll~~lll 15 (88)
||+++++++++++++
T Consensus 1 m~~~~~vll~ll~~l 15 (105)
T PRK00888 1 MRLLTLLLLALLVWL 15 (105)
T ss_pred CcHHHHHHHHHHHHH
Confidence 787766544443333
No 13
>PF15240 Pro-rich: Proline-rich
Probab=37.09 E-value=26 Score=26.67 Aligned_cols=16 Identities=19% Similarity=0.306 Sum_probs=10.9
Q ss_pred HHHHHHhhhhhhccCC
Q 037233 12 SLVVTSTFFEVSMAGS 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 4666667778877754
No 14
>PLN03207 stomagen; Provisional
Probab=35.29 E-value=50 Score=23.62 Aligned_cols=17 Identities=24% Similarity=0.376 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHhhhh
Q 037233 5 LVTFLLVSLVVTSTFFE 21 (88)
Q Consensus 5 ~~~~ll~~lll~~~~~~ 21 (88)
++.|||.+|||.+.++|
T Consensus 14 ~lffLl~~llla~~v~q 30 (113)
T PLN03207 14 TLFFLLFFLLLGAYVIQ 30 (113)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 34445555566565554
No 15
>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=33.04 E-value=12 Score=25.62 Aligned_cols=11 Identities=36% Similarity=0.661 Sum_probs=4.8
Q ss_pred CCCCCcccccc
Q 037233 69 KDECPCYRDLK 79 (88)
Q Consensus 69 k~~CpCY~~m~ 79 (88)
.+.|||-.++.
T Consensus 75 ~~~CPC~~gL~ 85 (97)
T PF06607_consen 75 FWRCPCAPGLV 85 (97)
T ss_dssp SSS--B-TT-E
T ss_pred EeeCCCCCCcE
Confidence 47888888773
No 16
>PLN02995 Probable pectinesterase/pectinesterase inhibitor
Probab=31.75 E-value=85 Score=27.10 Aligned_cols=16 Identities=25% Similarity=0.335 Sum_probs=11.6
Q ss_pred hhHHHhhcCcchHHHH
Q 037233 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 3445888889988853
No 17
>PF15330 SIT: SHP2-interacting transmembrane adaptor protein, SIT
Probab=31.22 E-value=65 Score=22.18 Aligned_cols=16 Identities=25% Similarity=0.671 Sum_probs=11.4
Q ss_pred CCCCCCCcccccccCC
Q 037233 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 4556778999987643
No 18
>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=28.68 E-value=42 Score=22.31 Aligned_cols=17 Identities=41% Similarity=0.528 Sum_probs=8.0
Q ss_pred HHHHHHHHhhhhhhccC
Q 037233 10 LVSLVVTSTFFEVSMAG 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 33444445554445543
No 19
>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=28.06 E-value=63 Score=21.61 Aligned_cols=16 Identities=31% Similarity=0.590 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHhhh
Q 037233 5 LVTFLLVSLVVTSTFF 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 3444555566655554
No 20
>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=27.88 E-value=79 Score=17.98 Aligned_cols=27 Identities=37% Similarity=0.801 Sum_probs=19.0
Q ss_pred cccccCCCCCCCC---CCC-CcccccccCCC
Q 037233 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 3444588999644 579 89998877654
No 21
>PRK11505 hypothetical protein; Provisional
Probab=27.51 E-value=61 Score=22.98 Aligned_cols=17 Identities=41% Similarity=0.602 Sum_probs=10.4
Q ss_pred ChHHHHHHHHHHHHHHH
Q 037233 1 MKLALVTFLLVSLVVTS 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 22
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.89 E-value=95 Score=20.95 Aligned_cols=11 Identities=27% Similarity=0.519 Sum_probs=6.6
Q ss_pred CCChHHhhHHH
Q 037233 28 DFCDSKCAVRC 38 (88)
Q Consensus 28 ~~C~~~C~~RC 38 (88)
=||+..|+.|=
T Consensus 45 CdC~~pCDt~~ 55 (77)
T COG2991 45 CDCDEPCDTHK 55 (77)
T ss_pred cCCCCchHHHH
Confidence 36766776653
No 23
>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=26.46 E-value=57 Score=22.36 Aligned_cols=18 Identities=17% Similarity=0.294 Sum_probs=12.1
Q ss_pred HhhHHHhhcCcchHHHHH
Q 037233 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 24
>PTZ00264 circumsporozoite-related antigen; Provisional
Probab=25.78 E-value=62 Score=24.00 Aligned_cols=15 Identities=40% Similarity=0.605 Sum_probs=9.0
Q ss_pred ChHHHHHHHHHHHHH
Q 037233 1 MKLALVTFLLVSLVV 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 888866655444444
No 25
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=25.21 E-value=64 Score=22.94 Aligned_cols=15 Identities=13% Similarity=0.339 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHhhh
Q 037233 6 VTFLLVSLVVTSTFF 20 (88)
Q Consensus 6 ~~~ll~~lll~~~~~ 20 (88)
++||++|+|++.++.
T Consensus 21 iVLlIISiLlLl~iP 35 (107)
T COG4537 21 IVLLIISILLLLFIP 35 (107)
T ss_pred HHHHHHHHHHHHHcc
Confidence 445777777766553
No 26
>PF12606 RELT: Tumour necrosis factor receptor superfamily member 19; InterPro: IPR022248 The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 []. RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues [].
Probab=24.42 E-value=1.2e+02 Score=18.57 Aligned_cols=17 Identities=12% Similarity=0.067 Sum_probs=7.4
Q ss_pred HHHHHHHHHhhhhhhcc
Q 037233 9 LLVSLVVTSTFFEVSMA 25 (88)
Q Consensus 9 ll~~lll~~~~~~~~~a 25 (88)
++++.+|..++.++.-+
T Consensus 10 ~iv~~lLg~~I~~~~K~ 26 (50)
T PF12606_consen 10 FIVMGLLGLSICTTLKA 26 (50)
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 33444444444444443
No 27
>PF08396 Toxin_34: Spider toxin omega agatoxin/Tx1 family; InterPro: IPR013605 The Tx1 family lethal spider neurotoxin induces excitatory symptoms in mice [].
Probab=24.13 E-value=49 Score=22.20 Aligned_cols=12 Identities=50% Similarity=1.168 Sum_probs=10.1
Q ss_pred CCCCCCCccccc
Q 037233 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 788888888876
No 28
>PRK08944 motB flagellar motor protein MotB; Reviewed
Probab=23.60 E-value=75 Score=25.15 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHhh
Q 037233 5 LVTFLLVSLVVTSTF 19 (88)
Q Consensus 5 ~~~~ll~~lll~~~~ 19 (88)
+++||+.|++|+.+|
T Consensus 24 lmTLLm~FFVlL~S~ 38 (302)
T PRK08944 24 LMSLLMCFFVLLLSF 38 (302)
T ss_pred HHHHHHHHHHHHHHH
Confidence 455566666665554
No 29
>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=23.29 E-value=51 Score=24.05 Aligned_cols=16 Identities=31% Similarity=0.470 Sum_probs=8.1
Q ss_pred ChHHHHHHHHHHHHHH
Q 037233 1 MKLALVTFLLVSLVVT 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 6766554444444443
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=23.18 E-value=65 Score=21.48 Aligned_cols=15 Identities=27% Similarity=0.538 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHhh
Q 037233 5 LVTFLLVSLVVTSTF 19 (88)
Q Consensus 5 ~~~~ll~~lll~~~~ 19 (88)
++.+||+++++++++
T Consensus 13 VvFlLLiFFmvts~~ 27 (129)
T TIGR02801 13 VMLVLLIIFMVTAPL 27 (129)
T ss_pred HHHHHHHHHHhhhcc
Confidence 344455555555555
No 31
>PF13677 MotB_plug: Membrane MotB of proton-channel complex MotA/MotB
Probab=22.99 E-value=93 Score=18.90 Aligned_cols=13 Identities=31% Similarity=0.411 Sum_probs=5.5
Q ss_pred HHHHHHHHHHHHh
Q 037233 6 VTFLLVSLVVTST 18 (88)
Q Consensus 6 ~~~ll~~lll~~~ 18 (88)
+++|+++++++.+
T Consensus 25 mTLLl~fFVlL~s 37 (58)
T PF13677_consen 25 MTLLLAFFVLLFS 37 (58)
T ss_pred HHHHHHHHHHHHH
Confidence 4444444444433
No 32
>PRK11024 colicin uptake protein TolR; Provisional
Probab=22.80 E-value=53 Score=22.59 Aligned_cols=16 Identities=19% Similarity=0.414 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHhhh
Q 037233 5 LVTFLLVSLVVTSTFF 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 33
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=22.59 E-value=30 Score=26.84 Aligned_cols=20 Identities=40% Similarity=1.157 Sum_probs=16.1
Q ss_pred HHHHHhHhhcccc-ccCCCCC
Q 037233 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 8877665
No 34
>PRK07734 motB flagellar motor protein MotB; Reviewed
Probab=22.48 E-value=79 Score=23.99 Aligned_cols=14 Identities=36% Similarity=0.508 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHh
Q 037233 5 LVTFLLVSLVVTST 18 (88)
Q Consensus 5 ~~~~ll~~lll~~~ 18 (88)
+++||++|++|+.+
T Consensus 26 ~vTlLlaFFvlL~s 39 (259)
T PRK07734 26 LLTLLLALFIVLFA 39 (259)
T ss_pred HHHHHHHHHHHHHH
Confidence 45555555555443
No 35
>PF07771 TSGP1: Tick salivary peptide group 1; InterPro: IPR011694 This entry contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis (Black-legged tick) []. Also present are peptides from a related tick species, Ixodes ricinus (Sheep tick). They are characterised by a putative signal peptide, indicative of secretion, and conserved cysteine residues.
Probab=22.35 E-value=44 Score=23.53 Aligned_cols=7 Identities=57% Similarity=0.738 Sum_probs=3.9
Q ss_pred ChHHHHH
Q 037233 1 MKLALVT 7 (88)
Q Consensus 1 mk~~~~~ 7 (88)
|++++++
T Consensus 1 m~~~~~~ 7 (120)
T PF07771_consen 1 MGLTVVT 7 (120)
T ss_pred Ccceeeh
Confidence 6666444
No 36
>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=22.15 E-value=74 Score=21.16 Aligned_cols=16 Identities=19% Similarity=0.418 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHhhh
Q 037233 5 LVTFLLVSLVVTSTFF 20 (88)
Q Consensus 5 ~~~~ll~~lll~~~~~ 20 (88)
++.+||+++++++.+.
T Consensus 12 VvflLLiFFmvts~~~ 27 (122)
T TIGR02803 12 VMLVLLIIFMVAAPLA 27 (122)
T ss_pred HHHHHHHHHHHhhhcc
Confidence 3444555555555443
No 37
>PF12276 DUF3617: Protein of unknown function (DUF3617); InterPro: IPR022061 This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 179 amino acids in length. There is a single completely conserved residue C that may be functionally important.
Probab=21.44 E-value=82 Score=21.48 Aligned_cols=7 Identities=43% Similarity=0.439 Sum_probs=3.3
Q ss_pred ChHHHHH
Q 037233 1 MKLALVT 7 (88)
Q Consensus 1 mk~~~~~ 7 (88)
||.+++.
T Consensus 1 M~~~~~~ 7 (162)
T PF12276_consen 1 MKRRLLL 7 (162)
T ss_pred CchHHHH
Confidence 5544343
No 38
>PRK11443 lipoprotein; Provisional
Probab=21.21 E-value=77 Score=22.32 Aligned_cols=7 Identities=29% Similarity=0.292 Sum_probs=3.9
Q ss_pred ChHHHHH
Q 037233 1 MKLALVT 7 (88)
Q Consensus 1 mk~~~~~ 7 (88)
||.++++
T Consensus 1 Mk~~~~~ 7 (124)
T PRK11443 1 MKKFIAP 7 (124)
T ss_pred ChHHHHH
Confidence 7755443
No 39
>PF10868 DUF2667: Protein of unknown function (DUF2667); InterPro: IPR022618 This family of proteins with unknown function appears to be restricted to Arabidopsis thaliana.
Probab=20.99 E-value=59 Score=22.31 Aligned_cols=20 Identities=35% Similarity=0.677 Sum_probs=12.3
Q ss_pred ccCCCCCCCCCCCCcccccc
Q 037233 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 67765544567786655543
No 40
>PRK11267 biopolymer transport protein ExbD; Provisional
Probab=20.92 E-value=76 Score=21.88 Aligned_cols=15 Identities=20% Similarity=0.496 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHhh
Q 037233 5 LVTFLLVSLVVTSTF 19 (88)
Q Consensus 5 ~~~~ll~~lll~~~~ 19 (88)
++.+||+++++++.+
T Consensus 26 Vvf~LLiFFmvts~~ 40 (141)
T PRK11267 26 VMLVLLIIFMVAAPL 40 (141)
T ss_pred HHHHHHHHHHhhhhc
Confidence 344455555555544
No 41
>PRK06667 motB flagellar motor protein MotB; Validated
Probab=20.47 E-value=93 Score=23.52 Aligned_cols=14 Identities=43% Similarity=0.508 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHHHh
Q 037233 5 LVTFLLVSLVVTST 18 (88)
Q Consensus 5 ~~~~ll~~lll~~~ 18 (88)
+++|||.|++|+.+
T Consensus 25 l~TLLL~FFVlL~s 38 (252)
T PRK06667 25 MVTLLLCFFVMLFT 38 (252)
T ss_pred HHHHHHHHHHHHHH
Confidence 34545555444433
Done!