RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6336
(73 letters)
>2r2q_A Gamma-aminobutyric acid receptor-associated protein-like 1;
autophagy, ubiquitin homolog, structural genomics
consortium, SGC, microtubule; 1.65A {Homo sapiens} PDB:
2l8j_A 1kjt_A 1kot_A 3d32_A 3dow_A 1gnu_A 1klv_A 1km7_A
Length = 110
Score = 84.6 bits (209), Expect = 1e-23
Identities = 58/68 (85%), Positives = 63/68 (92%)
Query: 4 RVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSA 63
VIVEKAPKAR+ DLDK+KYLVPSDLTVGQFYFLIRKR+ LRPEDALFFFVNN IPPTSA
Sbjct: 29 PVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSA 88
Query: 64 TMGSLYQE 71
TMG LY++
Sbjct: 89 TMGQLYED 96
>1eo6_A GATE-16, golgi-associated ATPase enhancer of 16 KD; ubiquitin
fold, protein binding; 1.80A {Bos taurus} SCOP:
d.15.1.3
Length = 117
Score = 82.3 bits (203), Expect = 1e-22
Identities = 38/68 (55%), Positives = 52/68 (76%)
Query: 4 RVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSA 63
VIVEK ++I D+DK+KYLVPSD+TV QF ++IRKR+QL E A+F FV+ +P +S
Sbjct: 30 PVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSSL 89
Query: 64 TMGSLYQE 71
TMG LY++
Sbjct: 90 TMGQLYEK 97
>3rui_B Autophagy-related protein 8; autophagosome formation,
non-canonical E1, ATP BI UBL, ATG8, ATG12, ATG10, ATG3,
UBL activation, thiolation; 1.91A {Saccharomyces
cerevisiae} PDB: 2kq7_A 2zpn_A 2kwc_A 2li5_A 3vh3_B
3vh4_B*
Length = 118
Score = 82.0 bits (202), Expect = 2e-22
Identities = 41/68 (60%), Positives = 55/68 (80%)
Query: 4 RVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSA 63
VI EKA K+ I ++DK+KYLVP+DLTVGQF ++IRKR+ L PE A+F FVN+ +PPT+A
Sbjct: 32 PVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAA 91
Query: 64 TMGSLYQE 71
M ++YQE
Sbjct: 92 LMSAIYQE 99
>3m95_A Autophagy related protein ATG8; alpha slash beta, receptor,
transport protein; 2.40A {Bombyx mori}
Length = 125
Score = 81.2 bits (200), Expect = 5e-22
Identities = 64/68 (94%), Positives = 66/68 (97%)
Query: 4 RVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSA 63
VIVEKAPKAR+GDLDKKKYLVPSDLTVGQFYFLIRKR+ LRPEDALFFFVNNVIPPTSA
Sbjct: 38 PVIVEKAPKARLGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNVIPPTSA 97
Query: 64 TMGSLYQE 71
TMGSLYQE
Sbjct: 98 TMGSLYQE 105
>3h9d_A ATG8, microtubule-associated protein 1A/1B, light chain putative;
autophagy, lipidation, ubiquitin-like, S protein; 2.30A
{Trypanosoma brucei}
Length = 119
Score = 77.4 bits (190), Expect = 1e-20
Identities = 35/67 (52%), Positives = 48/67 (71%)
Query: 5 VIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVNNVIPPTSAT 64
+I EK + IG+LD+ K+LVPSDLTVGQF ++RKRVQL E ALF + N+ + P+SA
Sbjct: 34 IICEKVYNSDIGELDRCKFLVPSDLTVGQFVSVLRKRVQLEAESALFVYTNDTVLPSSAQ 93
Query: 65 MGSLYQE 71
M +Y +
Sbjct: 94 MADIYSK 100
>2zjd_A Microtubule-associated proteins 1A/1B light chain 3B precursor;
autophagy, LC3, microtubule-associated protein 1 light
chain 3, cytoplasm, cytoplasmic vesicle, lipoprotein;
1.56A {Homo sapiens} SCOP: d.15.1.3 PDB: 2z0e_B 2zzp_B
2z0d_B 1ugm_A 1v49_A 2k6q_A 3eci_A
Length = 130
Score = 66.6 bits (162), Expect = 3e-16
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 5 VIVEKAPKAR-IGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALFFFVN-NVIPPTS 62
VI+E+ + + LDK K+LVP + + + +IR+R+QL A F VN + + S
Sbjct: 38 VIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVS 97
Query: 63 ATMGSLYQE 71
+ +Y+
Sbjct: 98 TPISEVYES 106
>1l0w_A Aspartyl-tRNA synthetase; space-grown crystal, dimeric enzyme,
flexible domains, ligase; 2.01A {Thermus thermophilus}
SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1efw_A* 1g51_A
Length = 580
Score = 24.8 bits (55), Expect = 2.9
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 23 YLVPSDLTVGQFYFL 37
+LVP G FY L
Sbjct: 182 FLVPYRHEPGLFYAL 196
>1c0a_A Aspartyl tRNA synthetase; protein-RNA complex, ligase/RNA complex;
HET: 4SU H2U QUO G7M 5MU PSU AMP AMO; 2.40A {Escherichia
coli} SCOP: b.40.4.1 d.74.4.1 d.104.1.1 PDB: 1il2_A*
1eqr_A*
Length = 585
Score = 24.8 bits (55), Expect = 3.2
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 23 YLVPSDLTVGQFYFL 37
YLVPS + G+FY L
Sbjct: 176 YLVPSRVHKGKFYAL 190
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 23.4 bits (51), Expect = 5.8
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 2 MWRVIVEKAPKARIGDLDKKKY 23
MW+ + +K+ DK++Y
Sbjct: 41 MWKELKDKSKWEDAAAKDKQRY 62
>2cv8_A TRNA-splicing endonuclease; tRNA-intron endonuclease, structural
genomics, NPPSFA; 2.80A {Sulfolobus tokodaii}
Length = 180
Score = 23.8 bits (51), Expect = 6.2
Identities = 6/48 (12%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 4 RVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRVQLRPEDALF 51
+++++ AR+ Y P ++ + I + L + ++
Sbjct: 9 KILIKNIEDARLI-YKMGYYGKPIGISKPKSAEEINSELILSLIEGVY 55
>3nm9_A HMG-D, high mobility group protein D; DNA bending,
non-sequence-specific, HMG chromosomal protein; HET:
DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A*
1hma_A 1qrv_A*
Length = 73
Score = 23.0 bits (50), Expect = 7.2
Identities = 5/22 (22%), Positives = 9/22 (40%)
Query: 2 MWRVIVEKAPKARIGDLDKKKY 23
+WR + +K+ K Y
Sbjct: 41 LWRAMKDKSEWEAKAAKAKDDY 62
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
0.327 0.143 0.424
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,168,076
Number of extensions: 56575
Number of successful extensions: 147
Number of sequences better than 10.0: 1
Number of HSP's gapped: 146
Number of HSP's successfully gapped: 16
Length of query: 73
Length of database: 6,701,793
Length adjustment: 43
Effective length of query: 30
Effective length of database: 5,501,190
Effective search space: 165035700
Effective search space used: 165035700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.5 bits)