Query 030083
Match_columns 183
No_of_seqs 154 out of 791
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 08:15:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030083.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030083hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00010 AAI_LTSS AAI_LTSS: Alp 99.5 4.6E-14 9.9E-19 96.5 3.6 62 5-69 1-63 (63)
2 cd01960 nsLTP1 nsLTP1: Non-spe 99.5 4E-14 8.7E-19 103.6 3.5 68 2-73 7-80 (89)
3 cd04660 nsLTP_like nsLTP_like: 99.4 2.6E-13 5.7E-18 96.6 4.0 68 3-76 6-73 (73)
4 PF14368 LTP_2: Probable lipid 99.3 2.2E-13 4.9E-18 98.8 -0.4 70 3-76 24-96 (96)
5 cd01959 nsLTP2 nsLTP2: Non-spe 99.1 1E-10 2.2E-15 82.9 3.9 61 3-72 4-64 (66)
6 smart00499 AAI Plant lipid tra 98.9 1.3E-09 2.8E-14 74.7 4.4 72 2-76 5-79 (79)
7 PF00234 Tryp_alpha_amyl: Prot 98.4 6.9E-09 1.5E-13 75.0 -5.1 66 4-76 14-90 (90)
8 cd01958 HPS_like HPS_like: Hyd 92.8 0.08 1.7E-06 39.6 2.2 72 4-76 10-85 (85)
9 PF14547 Hydrophob_seed: Hydro 91.3 0.039 8.4E-07 41.2 -1.0 73 4-77 8-85 (85)
10 KOG1924 RhoA GTPase effector D 46.4 1.6E+02 0.0035 30.8 9.5 11 63-73 521-531 (1102)
11 KOG0260 RNA polymerase II, lar 45.6 1.4E+02 0.0031 32.5 9.2 26 21-46 1388-1419(1605)
12 PF05283 MGC-24: Multi-glycosy 44.3 1.1E+02 0.0023 26.0 6.9 14 170-183 171-184 (186)
13 cd00261 AAI_SS AAI_SS: Alpha-A 43.9 11 0.00023 28.0 0.8 66 3-71 13-104 (110)
14 KOG1924 RhoA GTPase effector D 42.8 1.6E+02 0.0035 30.8 8.9 20 80-99 526-545 (1102)
15 KOG0260 RNA polymerase II, lar 30.1 3.6E+02 0.0079 29.6 9.3 6 38-43 1392-1397(1605)
16 PF03032 Brevenin: Brevenin/es 22.2 45 0.00098 22.2 0.9 13 169-181 7-19 (46)
No 1
>cd00010 AAI_LTSS AAI_LTSS: Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein family; a protein family unique to higher plants that includes cereal-type alpha-amylase inhibitors, lipid transfer proteins, seed storage proteins, and similar proteins. Proteins in this family are known to play important roles, in defending plants from insects and pathogens, lipid transport between intracellular membranes, and nutrient storage. Many proteins of this family have been identified as allergens in humans. These proteins contain a common pattern of eight cysteines that form four disulfide bridges.
Probab=99.46 E-value=4.6e-14 Score=96.51 Aligned_cols=62 Identities=34% Similarity=0.795 Sum_probs=53.3
Q ss_pred ccCcHHHhhcCCCCCCCCCHHHHHHHHHhhCCCCCceeeeecCCCCcccCC-CHHHHhhccccCCC
Q 030083 5 FTPCMNFLTNSSGSGTSPSSDCCGSLKNLTGNSLDCVCLIVTASVPFRVPI-NRTLAISLPRACNM 69 (183)
Q Consensus 5 LaPCl~Yltg~s~~~~sPs~~CC~gLksl~~~~~~CLC~~~~~~~~~~i~I-N~trAlsLP~~Cgv 69 (183)
|++|++|++++ ...|+.+||++|+++++.+..|+|..+++......++ |.++++.||++||+
T Consensus 1 L~~C~~y~~~~---~~~Ps~~CC~~l~~~~~~~~~ClC~~~~~~~~~~~~~~~~~~a~~LP~~Cgv 63 (63)
T cd00010 1 LAPCLSYLTGG---ATAPPSDCCSGLKSVVKSDPKCLCAALNGPGASLLGLKNATRALALPAACGL 63 (63)
T ss_pred CcchHHHHcCC---CCCCChHHHHHHHHHHhcChhhHHHHHcCccccccCcccHHHHHhchHhcCC
Confidence 68999999985 3689999999999999889999999998754333345 89999999999996
No 2
>cd01960 nsLTP1 nsLTP1: Non-specific lipid-transfer protein type 1 (nsLTP1) subfamily; Plant nsLTPs are small, soluble proteins that facilitate the transfer of fatty acids, phospholipids, glycolipids, and steroids between membranes. In addition to lipid transport and assembly, nsLTPs also play a key role in the defense of plants against pathogens. There are two closely-related types of nsLTPs, types 1 and 2, which differ in protein sequence, molecular weight, and biological properties. nsLTPs contain an internal hydrophobic cavity, which serves as the binding site for lipids. The hydrophobic cavity accommodates various fatty acid ligands containing from ten to 18 carbon atoms. In general, the cavity is larger in nsLTP1 than in nsLTP2. nsLTP1 proteins are located in extracellular layers and in vacuolar structures. They may be involved in the formation of cutin layers on plant surfaces by transporting cutin monomers. Many nsLTP1 proteins have been characterized as allergens in humans.
Probab=99.45 E-value=4e-14 Score=103.58 Aligned_cols=68 Identities=26% Similarity=0.614 Sum_probs=53.2
Q ss_pred CCcccCcHHHhhcCCCCCCCCCHHHHHHHHHhhCC-----CCCceeeeecCCCCcccC-CCHHHHhhccccCCCCCCC
Q 030083 2 LTTFTPCMNFLTNSSGSGTSPSSDCCGSLKNLTGN-----SLDCVCLIVTASVPFRVP-INRTLAISLPRACNMPSVP 73 (183)
Q Consensus 2 l~~LaPCl~Yltg~s~~~~sPs~~CC~gLksl~~~-----~~~CLC~~~~~~~~~~i~-IN~trAlsLP~~Cgv~~pp 73 (183)
+..|++|++||+++ ...|+++||+++|+|++. +..|+|+.+++.. .++. ||.+||++||++||++.++
T Consensus 7 ~~~l~~C~~y~~g~---~~~Ps~~CC~~v~~l~~~~~t~~~~~~~C~C~~~~~-~~~~~i~~~~a~~LP~~C~v~~~~ 80 (89)
T cd01960 7 TSLLAPCLGYLTGG---GPAPSPACCSGVKSLNGLAKTTADRQAACNCLKSAA-AGISGLNPGRAAGLPGKCGVSIPY 80 (89)
T ss_pred HhhHHhHHHHHhCC---CCCCChHHhhhhHHHhhccCCCCchhhhhhcccccc-cccCCCCHHHHHhChHhcccCCCC
Confidence 46799999999986 368999999999999864 3345555444432 3454 9999999999999999765
No 3
>cd04660 nsLTP_like nsLTP_like: Non-specific lipid-transfer protein (nsLTP)-like subfamily; composed of predominantly uncharacterized proteins with similarity to nsLTPs, including Medicago truncatula MtN5, the root-specific Phaseolus vulgaris PVR3, Antirrhinum majus FIL1, and Lilium longiflorum LIM3. Plant nsLTPs are small, soluble proteins that facilitate the transfer of fatty acids, phospholipids, glycolipids, and steroids between membranes. The MtN5 gene is induced during root nodule development. FIL1 is thought to be important in petal and stamen formation. The LIM3 gene is induced during the early prophase stage of meiosis in lily microsporocytes.
Probab=99.39 E-value=2.6e-13 Score=96.61 Aligned_cols=68 Identities=29% Similarity=0.723 Sum_probs=54.5
Q ss_pred CcccCcHHHhhcCCCCCCCCCHHHHHHHHHhhCCCCCceeeeecCCCCcccCCCHHHHhhccccCCCCCCCCCc
Q 030083 3 TTFTPCMNFLTNSSGSGTSPSSDCCGSLKNLTGNSLDCVCLIVTASVPFRVPINRTLAISLPRACNMPSVPVQC 76 (183)
Q Consensus 3 ~~LaPCl~Yltg~s~~~~sPs~~CC~gLksl~~~~~~CLC~~~~~~~~~~i~IN~trAlsLP~~Cgv~~pp~~C 76 (183)
..|++|++||++++ +...|+..||++||++ +..|+|.+.+... .. .||.+||++||++||+++++.+|
T Consensus 6 ~~L~~C~~yl~~~~-~~~~Ps~~CC~~vk~~---~~~C~C~~~~~~~-~~-~i~~~~a~~Lp~~Cgv~~p~~~C 73 (73)
T cd04660 6 DLLAECQPYVTGPN-PPPPPSRECCAALRRA---DLPCLCRYKTSLV-LQ-IIDPDKAVYLPAKCGLPLPPSSC 73 (73)
T ss_pred HHHHHHHHHHcCCC-CCCCCCHHHHHHHHcC---CcCCEeeccCCCc-cc-ccCHHHHHHHHHHcCCCCCCCCC
Confidence 57899999999863 1246999999999984 5569999987532 22 49999999999999999876555
No 4
>PF14368 LTP_2: Probable lipid transfer; PDB: 2RKN_A 1N89_A 1TUK_A.
Probab=99.31 E-value=2.2e-13 Score=98.83 Aligned_cols=70 Identities=33% Similarity=0.789 Sum_probs=47.3
Q ss_pred CcccCc---HHHhhcCCCCCCCCCHHHHHHHHHhhCCCCCceeeeecCCCCcccCCCHHHHhhccccCCCCCCCCCc
Q 030083 3 TTFTPC---MNFLTNSSGSGTSPSSDCCGSLKNLTGNSLDCVCLIVTASVPFRVPINRTLAISLPRACNMPSVPVQC 76 (183)
Q Consensus 3 ~~LaPC---l~Yltg~s~~~~sPs~~CC~gLksl~~~~~~CLC~~~~~~~~~~i~IN~trAlsLP~~Cgv~~pp~~C 76 (183)
..|++| +.|+++ ...|+.+||+++|++++.+..|||..+++....+++||.+|++.||++||++.++.+|
T Consensus 24 ~~l~~c~~~~~~~~~----~~~Ps~~CC~~l~~~~~~~~~ClC~~~~~~~~~~~~in~~~a~~Lp~~Cg~~~~~~~C 96 (96)
T PF14368_consen 24 NSLLPCCPCLCYVTG----GPAPSAACCSALKSVVQADPPCLCQLLNSPGAPGFGINVTRALALPAACGVPVPPSKC 96 (96)
T ss_dssp CCCCHH--HHHHHCC---------HHHHHHHCC----HCCHHHCCCC-CCHCHHCCTCHHHHHHHHHCTSS-S----
T ss_pred HHHhccccchhccCC----CCCCCHHHHHHHHHhccCCCCCHHHhcCccccccCCcCHHHHHHHHHHcCCCCCCCCC
Confidence 357777 788875 4789999999999998889999999998753245689999999999999999877555
No 5
>cd01959 nsLTP2 nsLTP2: Non-specific lipid-transfer protein type 2 (nsLTP2) subfamily; Plant nsLTPs are small, soluble proteins that facilitate the transfer of fatty acids, phospholipids, glycolipids, and steroids between membranes. In addition to lipid transport and assembly, nsLTPs also play a key role in the defense of plants against pathogens. There are two closely-related types of nsLTPs, types 1 and 2, which differ in protein sequence, molecular weight, and biological properties. nsLTPs contain an internal hydrophobic cavity, which serves as the binding site for lipids. nsLTP2 can bind lipids and sterols. Structure studies of rice nsLTPs show that the plasticity of the hydrophobic cavity is an important factor in ligand binding. The flexibility of the sLTP2 cavity allows its binding to rigid sterol molecules, whereas nsLTP1 cannot bind sterols despite its larger cavity size. The resulting nsLTP2/sterol complexes may bind to receptors that trigger defense responses. nsLTP2 gene exp
Probab=99.08 E-value=1e-10 Score=82.92 Aligned_cols=61 Identities=26% Similarity=0.628 Sum_probs=51.0
Q ss_pred CcccCcHHHhhcCCCCCCCCCHHHHHHHHHhhCCCCCceeeeecCCCCcccCCCHHHHhhccccCCCCCC
Q 030083 3 TTFTPCMNFLTNSSGSGTSPSSDCCGSLKNLTGNSLDCVCLIVTASVPFRVPINRTLAISLPRACNMPSV 72 (183)
Q Consensus 3 ~~LaPCl~Yltg~s~~~~sPs~~CC~gLksl~~~~~~CLC~~~~~~~~~~i~IN~trAlsLP~~Cgv~~p 72 (183)
..|++|++|++++ ..|+.+||+.||. +..|||.++++.. +...||..+|+.|+++|||..+
T Consensus 4 ~~L~~C~~ai~~~----~~Ps~~CC~~Lk~----~~~CLC~y~~~p~-l~~~i~~~~A~~l~~~Cgv~~P 64 (66)
T cd01959 4 TQLSPCLPAILGG----SPPSAACCAKLKE----QQSCLCQYAKNPS-LKQYVNSPNARKVLAACGVPYP 64 (66)
T ss_pred hhcccCHHHHhCC----CCCCHHHHHHHhc----CCCCeeeeecCcc-HHhhcCcHHHHHHHHHcCCCCC
Confidence 5799999999974 5899999999998 3389999987643 3334999999999999999874
No 6
>smart00499 AAI Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family.
Probab=98.92 E-value=1.3e-09 Score=74.71 Aligned_cols=72 Identities=39% Similarity=0.794 Sum_probs=55.1
Q ss_pred CCcccCcHHHhhcCCCCCCCCCHHHHHHHHHhhCCCCCceeeeecCCCCccc---CCCHHHHhhccccCCCCCCCCCc
Q 030083 2 LTTFTPCMNFLTNSSGSGTSPSSDCCGSLKNLTGNSLDCVCLIVTASVPFRV---PINRTLAISLPRACNMPSVPVQC 76 (183)
Q Consensus 2 l~~LaPCl~Yltg~s~~~~sPs~~CC~gLksl~~~~~~CLC~~~~~~~~~~i---~IN~trAlsLP~~Cgv~~pp~~C 76 (183)
+..+.+|+.|+++.. ....|+.+||++|+.+. +..|+|.++.......+ .+|..++..||+.||+..++..|
T Consensus 5 ~~~~~~c~~~~~~~~-~~~~p~~~CC~~l~~~~--~~~C~C~~~~~~~~~~~~~~~~~~~~a~~lp~~C~~~~~~~~C 79 (79)
T smart00499 5 LLQLAPCLSYLTGGS-PGAPPSQQCCSQLRGLN--SAQCRCLALRAAVLGILEIPGVNAQNAASLPSACGVPPPYTDC 79 (79)
T ss_pred hhhHHhhHHHHcCCC-CCCCCchHHHHHHHHhc--ccCCcchhhhcccccccchhhhhHHHHHhhHHhcCCCCCCCCC
Confidence 345679999999752 13678899999999986 77899998876432122 26999999999999998764444
No 7
>PF00234 Tryp_alpha_amyl: Protease inhibitor/seed storage/LTP family This is a small subfamily; InterPro: IPR003612 This domain is found is several proteins, including plant lipid transfer proteins [], seed storage proteins [] and trypsin-alpha amylase inhibitors [, ]. The domain forms a four-helical bundle in a right-handed superhelix with a folded leaf topology, which is stabilised by disulphide bonds, and which has an internal cavity. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; PDB: 1BFA_A 1BEA_A 1MID_A 1BE2_A 1LIP_A 3GSH_A 1JTB_A 1UVC_B 1BV2_A 1UVB_A ....
Probab=98.38 E-value=6.9e-09 Score=74.98 Aligned_cols=66 Identities=29% Similarity=0.677 Sum_probs=53.3
Q ss_pred cccCcHHHhhcCCCCCCCCCHHHHHHHHHhhCCCCCceeeeecCCCCcc-----------cCCCHHHHhhccccCCCCCC
Q 030083 4 TFTPCMNFLTNSSGSGTSPSSDCCGSLKNLTGNSLDCVCLIVTASVPFR-----------VPINRTLAISLPRACNMPSV 72 (183)
Q Consensus 4 ~LaPCl~Yltg~s~~~~sPs~~CC~gLksl~~~~~~CLC~~~~~~~~~~-----------i~IN~trAlsLP~~Cgv~~p 72 (183)
.|.+|..|++++ ...+..+||++|++| +..|+|..+.... .+ ..++..+|..||+.||+..+
T Consensus 14 ~l~~c~~~~~~~---~~~~~~~CC~~L~~l---~~~C~C~~i~~~~-~~~~~q~~~~~~~~~~~~~~a~~LP~~C~v~~~ 86 (90)
T PF00234_consen 14 RLSPCLPYLQGG---CQQPSQQCCQQLRQL---DPQCRCEAIRQMV-RQVIQQQQQGGQEMQIMAQRAQNLPSMCNVSPP 86 (90)
T ss_dssp HHHGGHHHHTTS---SSHHHHHHHHHHHHH---HHHHHHHHHHHHH-HHSHHCTSTCSHHHHHHHHHHHHHHHHTTSSSS
T ss_pred cccccHHHHhcc---cccchHHHhHHHHHH---hHHhhCHHHHHHH-HhhhhhhhhhHHHHHHHHHHHHHHHHHCCCCCC
Confidence 388999999986 347899999999998 6789999887532 12 26899999999999999987
Q ss_pred CCCc
Q 030083 73 PVQC 76 (183)
Q Consensus 73 p~~C 76 (183)
+++|
T Consensus 87 ~~~C 90 (90)
T PF00234_consen 87 YTDC 90 (90)
T ss_dssp SS-G
T ss_pred CCCC
Confidence 6455
No 8
>cd01958 HPS_like HPS_like: Hydrophobic Protein from Soybean (HPS)-like subfamily; composed of proteins with similarity to HPS, a small hydrophobic protein with unknown function related to cereal-type alpha-amylase inhibitors and lipid transfer proteins. In addition to HPS, members of this subfamily include a hybrid proline-rich protein (HyPRP) from maize, a dark-inducible protein (LeDI-2) from Lithospermum erythrorhizon, maize ZRP3 protein, and rice RcC3 protein. HyPRP is an embryo-specific protein that contains an N-terminal proline-rich domain and a C-terminal HPS-like cysteine-rich domain. It has been suggested that HyPRP may be involved in the stability and defense of the developing embryo. LeDI-2 is a root-specific protein that may be involved in regulating the biosynthesis of shikonin derivatives in L. erythrorhizon. Maize ZRP3 and rice RcC3 are root-specific proteins whose functions are yet to be determined. It has been reported that ZRP3 largely accumulates in a distinct subset
Probab=92.79 E-value=0.08 Score=39.63 Aligned_cols=72 Identities=28% Similarity=0.535 Sum_probs=45.9
Q ss_pred cccCcHHHhhcCCC-CCCCCCHHHHHHHHHhhCCC-CCceeeeecCCCCcccCCCHHHHhh-ccccCCCCCCC-CCc
Q 030083 4 TFTPCMNFLTNSSG-SGTSPSSDCCGSLKNLTGNS-LDCVCLIVTASVPFRVPINRTLAIS-LPRACNMPSVP-VQC 76 (183)
Q Consensus 4 ~LaPCl~Yltg~s~-~~~sPs~~CC~gLksl~~~~-~~CLC~~~~~~~~~~i~IN~trAls-LP~~Cgv~~pp-~~C 76 (183)
+|--|.+-+..... .+..+..+||.-++.+.+.+ ..|+|..++.+. +++.+|....++ |-..||-..+. |+|
T Consensus 10 kLgvCanvL~l~~~~~g~~~~~~CC~ll~GL~dldAA~CLCtaikan~-lgi~~~~pv~l~llln~CGk~~P~gf~C 85 (85)
T cd01958 10 KLGVCANVLGLSLLLLGTPAVQPCCPLIGGLADLDAAVCLCTAIKANI-LGISINIPVALSLLLNSCGRNVPPGFTC 85 (85)
T ss_pred HhchhHhhhhccccccCCCccchHHHHHcCchhhheeeeeeeeeeccc-cCcccccChhHHHHHHHHcCcCCCCCcC
Confidence 35557776632100 12467799999999998875 579999998753 455444444443 33568887654 455
No 9
>PF14547 Hydrophob_seed: Hydrophobic seed protein
Probab=91.30 E-value=0.039 Score=41.17 Aligned_cols=73 Identities=25% Similarity=0.508 Sum_probs=46.9
Q ss_pred cccCcHHHhhcC-CCCCCCCCHHHHHHHHHhhCCC-CCceeeeecCCCCcc-cCCCHHHHh-hccccCCCCCCC-CCcC
Q 030083 4 TFTPCMNFLTNS-SGSGTSPSSDCCGSLKNLTGNS-LDCVCLIVTASVPFR-VPINRTLAI-SLPRACNMPSVP-VQCK 77 (183)
Q Consensus 4 ~LaPCl~Yltg~-s~~~~sPs~~CC~gLksl~~~~-~~CLC~~~~~~~~~~-i~IN~trAl-sLP~~Cgv~~pp-~~C~ 77 (183)
+|--|.+.+--. -..+..+..+||.-++.+.+.+ ..|||..++.+. ++ +.||....+ .|-..||...+. |+|.
T Consensus 8 kLgvC~~vL~l~~~~~g~~~~~~CC~li~gL~d~~AA~CLC~aika~v-lg~i~~~ipv~l~~lln~CGk~~p~gf~C~ 85 (85)
T PF14547_consen 8 KLGVCANVLGLVNLVIGNPPRQPCCSLIAGLADLDAAVCLCTAIKANV-LGLINVNIPVALNLLLNACGKTVPSGFTCP 85 (85)
T ss_pred hhhhhhhhhhhhccccCCCCCCCcChHHhCcccchHHHHHHHHHhhhc-ccccccccccHHHHHHHHhCCcCcCCCcCC
Confidence 566788888110 0012357899999999998875 579999887653 34 343333333 456779987654 5773
No 10
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=46.45 E-value=1.6e+02 Score=30.77 Aligned_cols=11 Identities=36% Similarity=0.715 Sum_probs=6.3
Q ss_pred ccccCCCCCCC
Q 030083 63 LPRACNMPSVP 73 (183)
Q Consensus 63 LP~~Cgv~~pp 73 (183)
||..||+..++
T Consensus 521 ~~~~~~iP~PP 531 (1102)
T KOG1924|consen 521 LPIDGGIPPPP 531 (1102)
T ss_pred CCCCCCCCCCC
Confidence 45566665554
No 11
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=45.64 E-value=1.4e+02 Score=32.47 Aligned_cols=26 Identities=15% Similarity=0.277 Sum_probs=15.0
Q ss_pred CCCHHHHHHHHHhhCC------CCCceeeeec
Q 030083 21 SPSSDCCGSLKNLTGN------SLDCVCLIVT 46 (183)
Q Consensus 21 sPs~~CC~gLksl~~~------~~~CLC~~~~ 46 (183)
.-..++|.++....-. .--|.|+++.
T Consensus 1388 ~~ekd~~rgvsEnImlgqlap~gTg~~d~~ld 1419 (1605)
T KOG0260|consen 1388 HAEKDPCRGVSENIMLGQLAPMGTGCFDLMLD 1419 (1605)
T ss_pred hhccCCCccceeeeeecccccCCCcceeeecc
Confidence 4456677776654322 3358887754
No 12
>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor. Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.
Probab=44.26 E-value=1.1e+02 Score=26.02 Aligned_cols=14 Identities=21% Similarity=0.441 Sum_probs=9.9
Q ss_pred HHHHHHHHHHhhcC
Q 030083 170 LLLFVLGFVVLKYY 183 (183)
Q Consensus 170 ~~~~~~~~~~~~~~ 183 (183)
|-|++|+|+++|||
T Consensus 171 LGv~aI~ff~~KF~ 184 (186)
T PF05283_consen 171 LGVLAIIFFLYKFC 184 (186)
T ss_pred HHHHHHHHHHhhhc
Confidence 34456777788998
No 13
>cd00261 AAI_SS AAI_SS: Alpha-Amylase Inhibitors (AAIs) and Seed Storage (SS) Protein subfamily; composed of cereal-type AAIs and SS proteins. They are mainly present in the seeds of a variety of plants. AAIs play an important role in the natural defenses of plants against insects and pathogens such as fungi, bacteria and viruses. AAIs impede the digestion of plant starch and proteins by inhibiting digestive alpha-amylases and proteinases. Also included in this subfamily are SS proteins such as 2S albumin, gamma-gliadin, napin, and prolamin. These AAIs and SS proteins are also known allergens in humans.
Probab=43.86 E-value=11 Score=28.01 Aligned_cols=66 Identities=23% Similarity=0.477 Sum_probs=42.8
Q ss_pred CcccCcHHHhhcCCCCCC-----------CCCHHHHHHHHHhhCCCCCceeeeecCCCC---cc------------cCCC
Q 030083 3 TTFTPCMNFLTNSSGSGT-----------SPSSDCCGSLKNLTGNSLDCVCLIVTASVP---FR------------VPIN 56 (183)
Q Consensus 3 ~~LaPCl~Yltg~s~~~~-----------sPs~~CC~gLksl~~~~~~CLC~~~~~~~~---~~------------i~IN 56 (183)
..|.+|..||.--..... ..-..||.-++.+ +..|.|..+..-.. .. ...-
T Consensus 13 ~~L~~C~~yl~qq~~~~~~~~~~~~~~~~~~~qqCCqqL~~i---~~qcrC~al~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (110)
T cd00261 13 QPLNSCREYLRQQCSGVGGPPVWPQQSCEVLRQQCCQQLAQI---PEQCRCEALRQMVQGVIQQQQQQQEQQQGQEVERM 89 (110)
T ss_pred ccCcHHHHHHHHhccCCCCCCCcCccccHHHHHHHHHHHHhC---cHhhhHHHHHHHHHHHHHhhhccccccCcChHHHH
Confidence 468899999874210011 1237899999996 56799988753110 00 1233
Q ss_pred HHHHhhccccCCCCC
Q 030083 57 RTLAISLPRACNMPS 71 (183)
Q Consensus 57 ~trAlsLP~~Cgv~~ 71 (183)
...|..||..||+..
T Consensus 90 ~~~a~~Lp~~C~~~~ 104 (110)
T cd00261 90 RQAAQNLPSMCNLYP 104 (110)
T ss_pred HHHHHhhchhcCCCC
Confidence 457889999999986
No 14
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=42.80 E-value=1.6e+02 Score=30.76 Aligned_cols=20 Identities=40% Similarity=0.821 Sum_probs=8.6
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 030083 80 GAPLPAPGPASLGSAPSPGE 99 (183)
Q Consensus 80 gap~pap~pa~~~p~~~p~~ 99 (183)
|.|.|-+-|...|+..+|++
T Consensus 526 ~iP~PP~~pp~gG~g~pppP 545 (1102)
T KOG1924|consen 526 GIPPPPPLPPTGGTGPPPPP 545 (1102)
T ss_pred CCCCCCCCCCCCCCCCCCCC
Confidence 44444433334444444433
No 15
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=30.14 E-value=3.6e+02 Score=29.60 Aligned_cols=6 Identities=17% Similarity=0.257 Sum_probs=3.3
Q ss_pred CCceee
Q 030083 38 LDCVCL 43 (183)
Q Consensus 38 ~~CLC~ 43 (183)
..|.|.
T Consensus 1392 d~~rgv 1397 (1605)
T KOG0260|consen 1392 DPCRGV 1397 (1605)
T ss_pred CCCccc
Confidence 456664
No 16
>PF03032 Brevenin: Brevenin/esculentin/gaegurin/rugosin family; InterPro: IPR004275 In addition to the highly specific cell-mediated immune system, vertebrates possess an efficient host-defence mechanism against invading microorganisms which involves the synthesis of highly potent antimicrobial peptides with a large spectrum of activity. This entry represents a number of these defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins.; GO: 0006952 defense response, 0042742 defense response to bacterium, 0005576 extracellular region
Probab=22.24 E-value=45 Score=22.21 Aligned_cols=13 Identities=54% Similarity=0.810 Sum_probs=9.7
Q ss_pred hHHHHHHHHHHhh
Q 030083 169 SLLLFVLGFVVLK 181 (183)
Q Consensus 169 ~~~~~~~~~~~~~ 181 (183)
-++||++|+|-|-
T Consensus 7 llLlfflG~ISlS 19 (46)
T PF03032_consen 7 LLLLFFLGTISLS 19 (46)
T ss_pred HHHHHHHHHcccc
Confidence 4667799998763
Done!