RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8965
(193 letters)
>2j3w_B ZGC 92866, trafficking protein particle complex protein 2;
multisubunit tethering factor, trapp, palmitate,
transport, lipoprotein; HET: PLM; 2.1A {Brachydanio
rerio} SCOP: d.278.1.2 PDB: 2j3r_B*
Length = 188
Score = 211 bits (538), Expect = 2e-70
Identities = 103/184 (55%), Positives = 145/184 (78%), Gaps = 1/184 (0%)
Query: 10 ISISIIQPKTSILDKPINTKVKHDISINLYALLFSELVQYCQNKSLSVPEFQSKLHEVGQ 69
+ + + K++IL++ + + K ++S++ +ALLFSE+VQYCQ++ SV E Q++L ++GQ
Sbjct: 1 MEVRFTRGKSAILERSLT-RPKTEVSVSAFALLFSEMVQYCQSRVYSVSELQARLADMGQ 59
Query: 70 SIGAKLIDINFYREKNGKREIKLLNILQFVKINLWKNIFGKECDKLERANDDERTYYLIE 129
+GA L+D+ REKNGKRE K+LNIL F+K+N+WK +FGKE DKLE+ANDD++TYY+IE
Sbjct: 60 GVGASLLDVLVMREKNGKRETKVLNILLFIKVNVWKALFGKEADKLEQANDDDKTYYIIE 119
Query: 130 QESLVNKFISVPKDKGSLNCAIFVAGIVEAVLNNCGFKSTVTAHWHKGTTYMIQFDEQVI 189
+E L+N +ISVPK+ +LNCA F GIVEA+L + GF + VT HWHKGTT MI+FDE VI
Sbjct: 120 KEPLINAYISVPKENSTLNCAAFTGGIVEAILTHSGFPAKVTVHWHKGTTLMIKFDESVI 179
Query: 190 ARDK 193
ARDK
Sbjct: 180 ARDK 183
>3cue_B Transport protein particle 31 kDa subunit; membrane traffic, GEF,
tethering complex, RAB activation, GU nucleotide
exchange factor; HET: PLM; 3.70A {Saccharomyces
cerevisiae}
Length = 283
Score = 155 bits (391), Expect = 4e-47
Identities = 47/183 (25%), Positives = 80/183 (43%), Gaps = 15/183 (8%)
Query: 22 LDKPINTKVKHDISINLYALLFSELVQYCQNKSLSVPEFQSKLHEVGQSIGAKLI----- 76
L + + L +E N S S + S +L
Sbjct: 101 LLNFRASVSPSSLPRASAFLSQNESSSKLSNASNSPGMLANSSTATSASANERLQEKQTE 160
Query: 77 DINFYREKNGKREIKLLNILQFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNK 136
++ Y K +R++K+L+ILQF+ LW +F D L ++++ + Y +++ + +
Sbjct: 161 SLSNYITKMRRRDLKILDILQFIHGTLWSYLFNHVSDDLVKSSERDNEYMIVDNFPTLTQ 220
Query: 137 FISVPKDKGSLNCAIFVAGIVEAVLNNCGFKSTVTAH------WHKGTTYMIQFDEQVIA 190
FI +++C FV GI++ L N GF VTAH + T Y+IQFD QV+
Sbjct: 221 FIPGE----NVSCEYFVCGIIKGFLFNAGFPCGVTAHRMPQGGHSQRTVYLIQFDRQVLD 276
Query: 191 RDK 193
R+
Sbjct: 277 REG 279
Score = 73.1 bits (178), Expect = 5e-16
Identities = 18/128 (14%), Positives = 45/128 (35%), Gaps = 1/128 (0%)
Query: 3 SATNTAGISISIIQPKTSILDKPINTKVKHDISINLYALLFSELVQYCQNKSLSVPEFQS 62
S + I + + K + + S++ A LF E++ + +F++
Sbjct: 27 GPKQAITSEASTTYIPSRIYSESLLFK-RQEASLSAMAFLFQEMISQLHRTCKTAGDFET 85
Query: 63 KLHEVGQSIGAKLIDINFYREKNGKREIKLLNILQFVKINLWKNIFGKECDKLERANDDE 122
KL + G +IG +L+++ +R + + + K + +
Sbjct: 86 KLSDYGHNIGIRLLELLNFRASVSPSSLPRASAFLSQNESSSKLSNASNSPGMLANSSTA 145
Query: 123 RTYYLIEQ 130
+ E+
Sbjct: 146 TSASANER 153
>1sz7_A BET3 homolog, trafficking protein particle complex subunit 3;
alpha-beta plait, trapp complex, palmitoylated,
transport PR; HET: PLM; 1.55A {Homo sapiens} PDB:
2cfh_A* 2pwn_A* 3kxc_A* 1wc8_A* 2j3w_D* 2j3r_A* 2j3t_A*
1wc9_A* 2c0j_A*
Length = 200
Score = 148 bits (375), Expect = 1e-45
Identities = 29/187 (15%), Positives = 64/187 (34%), Gaps = 12/187 (6%)
Query: 17 PKTSILDKPINTKVKHD-ISINLYALLFSELVQYCQNKSLSVPEFQSKLHEVGQSIGAKL 75
+ N + +S L+ L + LV + + +L ++G +IG +L
Sbjct: 5 HHHHGSSRQANRGTESKKMSSELFTLTYGALVTQLCKDYENDEDVNKQLDKMGFNIGVRL 64
Query: 76 IDINFYREKNGKREIKLLNILQFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVN 135
I+ R N R + +K G + + ++E LV+
Sbjct: 65 IEDFLARS-NVGRCHDFRETADVIAKVAFKMYLGITPSITNWSPAGDEFSLILENNPLVD 123
Query: 136 KFISVPKDKGSLNCAIFVAGIVEAVLNNCGFKSTVT--AHWHKG-------TTYMIQFDE 186
F+ +P + SL + + G++ L KG ++ + ++
Sbjct: 124 -FVELPDNHSSLIYSNLLCGVLRGALEMVQMAVEAKFVQDTLKGDGVTEIRMRFIRRIED 182
Query: 187 QVIARDK 193
+ A ++
Sbjct: 183 NLPAGEE 189
>2bjn_A TPC6, trafficking protein particle complex subunit 6B; trapp
complex, tethering, transport protein; 1.7A {Homo
sapiens} PDB: 3kxc_C* 2cfh_C*
Length = 160
Score = 131 bits (332), Expect = 1e-39
Identities = 35/162 (21%), Positives = 63/162 (38%), Gaps = 13/162 (8%)
Query: 33 DISINLYALLFSELVQYCQNKS----LSVPEFQSKLHEVGQSIGAKLIDINFYREKNGKR 88
L+ LL +E+V + + +KL +G +G LI+ K+ R
Sbjct: 3 MADEALFLLLHNEMVSGVYKSAEQGEVENGRCITKLENMGFRVGQGLIE---RFTKDTAR 59
Query: 89 EIKLLNILQFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLN 148
L+I++F+ + W +F K+ D L + Y L + + + +S K
Sbjct: 60 FKDELDIMKFICKDFWTTVFKKQIDNLRTNHQG--IYVLQDNKFRLLTQMSAGKQYLEHA 117
Query: 149 CAI--FVAGIVEAVLNNCGFKSTVTAHWHK--GTTYMIQFDE 186
F G++ L+N G KS VTA + + +
Sbjct: 118 SKYLAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQK 159
>2c0j_B R32611_2; palmitate; HET: PLM; 2.20A {Homo sapiens} PDB: 2j3t_B*
Length = 160
Score = 123 bits (310), Expect = 2e-36
Identities = 33/162 (20%), Positives = 59/162 (36%), Gaps = 14/162 (8%)
Query: 34 ISINLYALLFSELVQYCQNKSLSVPEFQ-----SKLHEVGQSIGAKLIDINFYREKNGKR 88
L+ L +E+V S L +G +G L + RE R
Sbjct: 3 ADTVLFEFLHTEMVAELWAHDPDPGPGGQKMSLSVLEGMGFRVGQALGER-LPRETLAFR 61
Query: 89 EIKLLNILQFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKD--KGS 146
E L++L+F+ +LW +F K+ D L + TY L + + ++ + +
Sbjct: 62 EE--LDVLKFLCKDLWVAVFQKQMDSLRTNHQG--TYVLQDNSFPLLLPMASGLQYLEEA 117
Query: 147 LNCAIFVAGIVEAVLNNCGFKSTVTAHWHK--GTTYMIQFDE 186
F G++ L G +S VTA + + +
Sbjct: 118 PKFLAFTCGLLRGALYTLGIESVVTASVAALPVCKFQVVIPK 159
>3cue_D Transport protein particle 22 kDa subunit; membrane traffic, GEF,
tethering complex, RAB activation, GU nucleotide
exchange factor; HET: PLM; 3.70A {Saccharomyces
cerevisiae}
Length = 193
Score = 42.3 bits (99), Expect = 2e-05
Identities = 29/140 (20%), Positives = 60/140 (42%), Gaps = 4/140 (2%)
Query: 34 ISINLYALLFSELV-QYCQNKSLSVPEFQSKLHEVGQSIGAKLIDINFYREKNGKREIKL 92
I+ L+ L + +V Q CQ+ + L+ +G +IG +LI+ +F R L
Sbjct: 25 INTELFTLTYGSIVAQLCQDYERDFNKVNDHLYSMGYNIGCRLIE-DFLARTALPRCENL 83
Query: 93 LNILQFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKD-KGSLNCAI 151
+ + + +K + + + ++ T+ LI E+ + F+ +P D SL +
Sbjct: 84 VKTSEVLSKCAFKIFLNITPN-ITNWSHNKDTFSLILDENPLADFVELPMDAMKSLWYSN 142
Query: 152 FVAGIVEAVLNNCGFKSTVT 171
+ G+++ L V
Sbjct: 143 ILCGVLKGSLEMVQLDCDVW 162
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 41.0 bits (95), Expect = 1e-04
Identities = 26/210 (12%), Positives = 51/210 (24%), Gaps = 79/210 (37%)
Query: 20 SILDKPINTKVKHDISINLYALLFSE------LVQYCQNKSLSVPEFQSKLHEVGQS-IG 72
+ D H IS++ +++ + L++Y + +P + S I
Sbjct: 276 QVTDFLSAATTTH-ISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIA 334
Query: 73 AKLIDINFYREKNGKREIKLLNILQFVKINLWKNIFGKECDKLERAND---------DER 123
+ D + W N CDKL + + R
Sbjct: 335 ESIRD----------------------GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372
Query: 124 TYYLIEQESLVNKFISVPKDKGSLNCAIFVAGI------------------VEAVLNNCG 165
+ ++F V V+N
Sbjct: 373 KMF--------------------DRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLH 412
Query: 166 FKSTVTAHWHKGTT--YMIQFDEQVIARDK 193
S V + T I + +V ++
Sbjct: 413 KYSLVEKQPKESTISIPSIYLELKVKLENE 442
Score = 41.0 bits (95), Expect = 1e-04
Identities = 18/87 (20%), Positives = 31/87 (35%), Gaps = 12/87 (13%)
Query: 61 QSKLHEVGQSIGAK------LIDINFYR----EKNGKREIKLLNILQFVKINLWKNIF-G 109
+ K+ + A L + FY+ + + K E + IL F+ + +N+
Sbjct: 504 EQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP-KIEENLICS 562
Query: 110 KECDKLERANDDERTYYLIEQESLVNK 136
K D L A E E V +
Sbjct: 563 KYTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 39.1 bits (90), Expect = 5e-04
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 14/77 (18%)
Query: 76 IDINFYREKNGKREIKLLNILQFVK-------INLWKNIFGK-ECDK-LERANDDERTYY 126
+D + ++I + FV ++ K+I K E D + + T
Sbjct: 7 MDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66
Query: 127 LI-----EQESLVNKFI 138
L +QE +V KF+
Sbjct: 67 LFWTLLSKQEEMVQKFV 83
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 32.3 bits (73), Expect = 0.094
Identities = 26/125 (20%), Positives = 42/125 (33%), Gaps = 34/125 (27%)
Query: 43 FS--ELVQYCQN-KSLSVPEFQSKLHEVGQSIGAKLIDINFYREKNGKREIKLLNILQFV 99
FS ++V N +L++ F E G+ I + F E ++K I + +
Sbjct: 1659 FSILDIVI--NNPVNLTI-HFGG---EKGKRIRENYSAMIF--ETIVDGKLKTEKIFKEI 1710
Query: 100 KINLWKNIFGKECDKLERANDDERTYY------LIEQ---ESLVNKFISVPKDKGSLNCA 150
+ F E L T + L+E+ E L K KG +
Sbjct: 1711 NEHSTSYTFRSEKGLLSA------TQFTQPALTLMEKAAFEDL--------KSKGLIPAD 1756
Query: 151 IFVAG 155
AG
Sbjct: 1757 ATFAG 1761
Score = 28.9 bits (64), Expect = 1.3
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 22/62 (35%)
Query: 61 QSKLHEVGQSIGAK---LIDI-NFYREKN---------GKREI--KLLNILQFVKINLWK 105
Q L V + +G + L++I N+ N G + N+L F+K+ +
Sbjct: 1823 QEALQYVVERVGKRTGWLVEIVNY----NVENQQYVAAGDLRALDTVTNVLNFIKL---Q 1875
Query: 106 NI 107
I
Sbjct: 1876 KI 1877
>1b7y_B Phers, protein (phenylalanyl-tRNA synthetase); enzyme, alpha/beta
homodimer, ligase; HET: FYA; 2.50A {Thermus
thermophilus} SCOP: a.6.1.1 a.6.1.1 b.40.4.4 b.153.1.1
d.58.13.1 d.104.1.1 PDB: 1b70_B* 1eiy_B 1jjc_B* 1pys_B
2akw_B* 2aly_B* 2amc_B* 3hfz_B* 3teh_B* 2iy5_B*
Length = 785
Score = 31.3 bits (72), Expect = 0.19
Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 4/40 (10%)
Query: 155 GIVEAVLNNCGFKSTVTA----HWHKGTTYMIQFDEQVIA 190
G +EA+ G V A H G + + + + +
Sbjct: 611 GYLEALFARLGLAFRVEAQAFPFLHPGVSGRVLVEGEEVG 650
>3pco_B Phenylalanyl-tRNA synthetase, beta chain; aminoacylation,
tRNA-binding, DNA-binding domain, four-helix
aminoacyl-tRNA synthetase, ATP-binding; HET: PHE AMP;
3.02A {Escherichia coli}
Length = 795
Score = 29.4 bits (67), Expect = 0.73
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 153 VAGIVEAVLNNCGFKSTVT------AHWHKGTTYMIQFDEQVIA 190
+ G +E+VL+ G + V H G + I + I
Sbjct: 617 LKGDLESVLDLTGKLNEVEFRAEANPALHPGQSAAIYLKGERIG 660
>2rhq_B Phenylalanyl-tRNA synthetase beta chain; heterotetramer,
phenylalanine, aminoacyl-tRNA synthetase, ATP-binding,
cytoplasm, ligase; HET: GAX; 2.20A {Staphylococcus
haemolyticus} PDB: 2rhs_B*
Length = 795
Score = 29.4 bits (67), Expect = 0.78
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 4/39 (10%)
Query: 155 GIVEAVLNNCGFKSTVTA----HWHKGTTYMIQFDEQVI 189
G+V+ V + + A H G T ++ + Q I
Sbjct: 623 GVVDRVAEKLNLEFSYKAGKIEGLHPGRTAIVSLEGQDI 661
>3e6s_A Ferritin; iron storage, ferroxidase, oxidoreductase; 1.95A
{Pseudo-nitzschia multiseries} PDB: 3e6r_A
Length = 168
Score = 27.2 bits (61), Expect = 2.7
Identities = 3/26 (11%), Positives = 8/26 (30%)
Query: 113 DKLERANDDERTYYLIEQESLVNKFI 138
K+ N ++ S + +
Sbjct: 140 AKVTDENRTPGLLRSLDVVSFLGPCL 165
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.135 0.387
Gapped
Lambda K H
0.267 0.0840 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,744,316
Number of extensions: 147921
Number of successful extensions: 299
Number of sequences better than 10.0: 1
Number of HSP's gapped: 285
Number of HSP's successfully gapped: 22
Length of query: 193
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 105
Effective length of database: 4,244,745
Effective search space: 445698225
Effective search space used: 445698225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.8 bits)