>gi|297820134|ref|XP_002877950.1| protease inhibitor/seed storage/lipid transfer protein family protein [Arabidopsis lyrata subsp. lyrata] gi|297323788|gb|EFH54209.1| protease inhibitor/seed storage/lipid transfer protein family protein [Arabidopsis lyrata subsp. lyrata]
>gi|357505755|ref|XP_003623166.1| Protease inhibitor/seed storage/LTP family protein [Medicago truncatula] gi|355498181|gb|AES79384.1| Protease inhibitor/seed storage/LTP family protein [Medicago truncatula] gi|388494356|gb|AFK35244.1| unknown [Medicago truncatula]
Score = 87 (35.7 bits), Expect = 0.00045, P = 0.00045
Identities = 19/57 (33%), Positives = 28/57 (49%)
Query: 52 QDEKASVSASCCAQVKRIGQNPICLCAVLLSDTAKASGVNPQVAMSIPKRCNFANRP 108
++ S S CC +K CLC S + GV+P++A S+PK C+ N P
Sbjct: 45 KNNPTSPSLLCCNALKHADYT--CLCGYKNSPWLGSFGVDPKLASSLPKECDLTNAP 99
Parameters:
V=100
filter=SEG
E=0.001
ctxfactor=1.00
Query ----- As Used ----- ----- Computed ----
Frame MatID Matrix name Lambda K H Lambda K H
+0 0 BLOSUM62 0.320 0.133 0.407 same same same
Q=9,R=2 0.244 0.0300 0.180 n/a n/a n/a
Query
Frame MatID Length Eff.Length E S W T X E2 S2
+0 0 119 108 0.00091 102 3 11 22 0.42 30
29 0.40 32
Statistics:
Database: /share/blast/go-seqdb.fasta
Title: go_20130330-seqdb.fasta
Posted: 5:47:42 AM PDT Apr 1, 2013
Created: 5:47:42 AM PDT Apr 1, 2013
Format: XDF-1
# of letters in database: 169,044,731
# of sequences in database: 368,745
# of database sequences satisfying E: 6
No. of states in DFA: 506 (54 KB)
Total size of DFA: 104 KB (2073 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Elapsed: 00:00:00
No. of threads or processors used: 24
Search cpu time: 9.08u 0.15s 9.23t Elapsed: 00:00:00
Total cpu time: 9.08u 0.15s 9.23t Elapsed: 00:00:00
Start: Sat May 11 03:01:01 2013 End: Sat May 11 03:01:01 2013
>gnl|CDD|237980 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. Length = 63
>gnl|CDD|215810 pfam00234, Tryp_alpha_amyl, Protease inhibitor/seed storage/LTP family
Score = 36.7 bits (85), Expect = 3e-04
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 41 ALKLAPCAAAAQ-DEKASVSASCCAQVKRIGQNPI-CLCAVLLSDTAKASGVNPQVAMSI 98
A L PC + A+ S +CCA +K + + CLC ++ S A G+N A+++
Sbjct: 23 ADSLLPCLGYCYVNGTAAPSPACCAALKAAVKADVPCLCDLVTSPLAAGFGINLTRAVAL 82
Query: 99 PKRCN 103
PK C
Sbjct: 83 PKACG 87
The members of this family are probably involved in lipid transfer. The family has several highly conserved cysteines, paired in various ways. Length = 95
GRP: Glycine rich protein family; InterPro: IPR010
89.42
>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.
>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
>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.
>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.
>smart00499 AAI Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family
>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 [, ]
Probab=98.86 E-value=8.4e-11 Score=75.75 Aligned_cols=68 Identities=26% Similarity=0.631 Sum_probs=54.6
Q ss_pred cccccCHHHhhCCCCCCCHHHHHHHHhhcCCCCccceecccccccc----------CCCChHHHhhhhhhcCCCCCCCCC
Q 033430 42 LKLAPCAAAAQDEKASVSASCCAQVKRIGQNPICLCAVLLSDTAKA----------SGVNPQVAMSIPKRCNFANRPVGY 111 (119)
Q Consensus 42 ~~L~pC~~yv~~~~~~Ps~~CC~~vk~l~~~~~ClC~~~~~~~~~~----------~~i~~~~a~~lP~~Cgv~~~p~g~ 111 (119)
..+.+|..|++++...|+..||++|+++ +..|.|..+....... .+++..+|..||+.||++ .|. +
T Consensus 13 ~~l~~c~~~~~~~~~~~~~~CC~~L~~l--~~~C~C~~i~~~~~~~~~q~~~~~~~~~~~~~~a~~LP~~C~v~-~~~-~ 88 (90)
T PF00234_consen 13 VRLSPCLPYLQGGCQQPSQQCCQQLRQL--DPQCRCEAIRQMVRQVIQQQQQGGQEMQIMAQRAQNLPSMCNVS-PPY-T 88 (90)
T ss_dssp SHHHGGHHHHTTSSSHHHHHHHHHHHHH--HHHHHHHHHHHHHHHSHHCTSTCSHHHHHHHHHHHHHHHHTTSS-SSS-S
T ss_pred ccccccHHHHhcccccchHHHhHHHHHH--hHHhhCHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHCCCC-CCC-C
Confidence 4588999999987657999999999999 8999999887543331 257889999999999999 554 5
Q ss_pred CC
Q 033430 112 KC 113 (119)
Q Consensus 112 ~C 113 (119)
+|
T Consensus 89 ~C 90 (90)
T PF00234_consen 89 DC 90 (90)
T ss_dssp -G
T ss_pred CC
Confidence 55
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 ....
>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
Probab=97.18 E-value=0.00056 Score=44.14 Aligned_cols=68 Identities=22% Similarity=0.566 Sum_probs=47.7
Q ss_pred cccccCHHHhhCC----CCCCCHHHHHHHHhhc--CCCCccceeccccccccCCCC--hH-HHhhhhhhcCCCCCCCCCC
Q 033430 42 LKLAPCAAAAQDE----KASVSASCCAQVKRIG--QNPICLCAVLLSDTAKASGVN--PQ-VAMSIPKRCNFANRPVGYK 112 (119)
Q Consensus 42 ~~L~pC~~yv~~~----~~~Ps~~CC~~vk~l~--~~~~ClC~~~~~~~~~~~~i~--~~-~a~~lP~~Cgv~~~p~g~~ 112 (119)
.+|.-|..-+-.. +.+|..+||+-++.+. .-..|+|..++.+ .+||+ .. +..-|-+.||.. .|.||+
T Consensus 9 lkLgvCanvL~l~~~~~g~~~~~~CC~ll~GL~dldAA~CLCtaikan---~lgi~~~~pv~l~llln~CGk~-~P~gf~ 84 (85)
T cd01958 9 LKLGVCANVLGLSLLLLGTPAVQPCCPLIGGLADLDAAVCLCTAIKAN---ILGISINIPVALSLLLNSCGRN-VPPGFT 84 (85)
T ss_pred HHhchhHhhhhccccccCCCccchHHHHHcCchhhheeeeeeeeeecc---ccCcccccChhHHHHHHHHcCc-CCCCCc
Confidence 5677787766321 2367789999999996 3356999988643 34543 33 344556789999 999999
Q ss_pred C
Q 033430 113 C 113 (119)
Q Consensus 113 C 113 (119)
|
T Consensus 85 C 85 (85)
T cd01958 85 C 85 (85)
T ss_pred C
Confidence 8
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
