BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 035508
(379 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GDK|B Chain B, Crystal Structure Of Human Atg12~atg5 Conjugate In Complex
With An N- Terminal Fragment Of Atg16l1
pdb|4GDK|E Chain E, Crystal Structure Of Human Atg12~atg5 Conjugate In Complex
With An N- Terminal Fragment Of Atg16l1
pdb|4GDL|B Chain B, Crystal Structure Of Human Atg12~atg5 Conjugate In Complex
With An N- Terminal Fragment Of Atg16l1
Length = 275
Score = 106 bits (265), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 85/326 (26%), Positives = 130/326 (39%), Gaps = 83/326 (25%)
Query: 55 VWEGAIPLQIHLHESEVTTXXXXXXXXXXXXRIGYLPLLVGLIKPYFGSSL-PPGVDTIW 113
VW G IP L++ E+T R+ YL L+ +K +F + + IW
Sbjct: 11 VWFGRIPTCFTLYQDEIT-EREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIW 69
Query: 114 FEYKGLPLKWYTPTGVLFDLLCAEPERPWNLTVHFRGYPVHVLIPCEGEDSVKWSFINSL 173
FEY+G PLKW+ P G+LFDLL + PWN+TVHF+ +P L+ C +D+++ F++ +
Sbjct: 70 FEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCM 129
Query: 174 KEAAYIINGNCKNVMNMSQSDQVELWRSVMNGNLEAYLRVSSKLKLITVEDDYTVKLNSS 233
KEA + + + M + D +LW + N + + ++ KL +Y + N
Sbjct: 130 KEAD-ALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLM------EYPAEENGF 182
Query: 234 SKSQQGTGETDFAGQVKTGRIPVRLYVWSVSEDFDDLEDAPDIDCWDKISFINRPVEVRT 293
IP R+Y + F I + RPV
Sbjct: 183 R------------------YIPFRIYQTTTERPF--------------IQKLFRPVAA-- 208
Query: 294 EEGKCFTLRDAIKTLLPEYFTDKPLFNDESPKLEDEEMNLSSEDAGSNKNTEVEEILYEH 353
+G+ TL D +K + P + ED G KN
Sbjct: 209 -DGQLHTLGDLLKEVCPS--------------------AIDPED-GEKKNQ--------- 237
Query: 354 VTRNAEIKLVRIQGIEPKLEIPFSWV 379
V I GIEP LE P W+
Sbjct: 238 ---------VMIHGIEPMLETPLQWL 254
>pdb|3VQI|A Chain A, Crystal Structure Of Kluyveromyces Marxianus Atg5
pdb|3VQI|B Chain B, Crystal Structure Of Kluyveromyces Marxianus Atg5
pdb|3VQI|C Chain C, Crystal Structure Of Kluyveromyces Marxianus Atg5
pdb|3VQI|D Chain D, Crystal Structure Of Kluyveromyces Marxianus Atg5
pdb|3VQI|E Chain E, Crystal Structure Of Kluyveromyces Marxianus Atg5
Length = 274
Score = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 57/198 (28%), Positives = 87/198 (43%), Gaps = 37/198 (18%)
Query: 48 HME-ARKYVWEGAIPLQIHLHESEVTTXXXXXXXXXXXXRIGYLPLLVGLIKPYFGSSLP 106
HME R+ VW G I +++ + ++ V +V L Y G LP
Sbjct: 3 HMEELRERVWNGTINVEVVVSDAIVVPNTTLADKSCH---------IVMLRDAYLGFYLP 53
Query: 107 PGV----DTI-----------WFEYKGLPLKWYTPTGVLFDLLCAEPERP---------- 141
V DTI WFEY G + W P GVLFDLL + ++
Sbjct: 54 TVVRKLADTIKVPYESDYRNWWFEYNGEGVPWEYPCGVLFDLLNKKRKKQGNELDDTSLQ 113
Query: 142 -WNLTV-HFRGYPVHVLIPCEGEDSVKWSFINSLKEAAYIINGNCKNVMNMSQSDQVELW 199
W L + H YP +L +G +K + + K+A +I+NG+ K +M++S D W
Sbjct: 114 MWELQLCHGDKYPRGILPLVDGHSQIKDYWRHQWKQACFILNGSAKRIMSLSIPDFENFW 173
Query: 200 RSVMNGNLEAYLRVSSKL 217
S+++ N ++ V SKL
Sbjct: 174 VSILSRNRSDFMAVRSKL 191
>pdb|2DYM|A Chain A, The Crystal Structure Of Saccharomyces Cerevisiae Atg5-
Atg16(1-46) Complex
pdb|2DYM|C Chain C, The Crystal Structure Of Saccharomyces Cerevisiae Atg5-
Atg16(1-46) Complex
pdb|2DYM|E Chain E, The Crystal Structure Of Saccharomyces Cerevisiae Atg5-
Atg16(1-46) Complex
pdb|2DYM|G Chain G, The Crystal Structure Of Saccharomyces Cerevisiae Atg5-
Atg16(1-46) Complex
pdb|2DYO|A Chain A, The Crystal Structure Of Saccharomyces Cerevisiae Atg5-
Atg16(1-57) Complex
Length = 297
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 40/152 (26%), Positives = 67/152 (44%), Gaps = 26/152 (17%)
Query: 87 IGYLPLLVGLIKPYFGSSLPPGVDT---IWFEYKGLPLKWYTPTGVLFDLLCAEPERPWN 143
+ Y+PL+ IK + S P D+ WFE+ P+ W P GVLFD L +
Sbjct: 49 VNYMPLIWNKIKSFL--SFDPLTDSEKYFWFEHNKTPIPWNYPVGVLFDCLAGKSA---T 103
Query: 144 LTVHFRGYPVHVL-----------------IPCEGEDSVKWSF-INSLKEAAYIINGNCK 185
T F VL IP + F + K+ +I+NG+ K
Sbjct: 104 FTTSFENQVKDVLTFLRIHLVMGDSLPPTIIPIASSKTQAEKFWFHQWKQVCFILNGSSK 163
Query: 186 NVMNMSQSDQVELWRSVMNGNLEAYLRVSSKL 217
+M++S ++ + W SV+ N + ++ +S+K+
Sbjct: 164 AIMSLSVNEARKFWGSVITRNFQDFIEISNKI 195
>pdb|3W1S|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Atg12-Atg5
Conjugate Bound To The N-Terminal Domain Of Atg16
Length = 284
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 40/152 (26%), Positives = 67/152 (44%), Gaps = 26/152 (17%)
Query: 87 IGYLPLLVGLIKPYFGSSLPPGVDT---IWFEYKGLPLKWYTPTGVLFDLLCAEPERPWN 143
+ Y+PL+ IK + S P D+ WFE+ P+ W P GVLFD L +
Sbjct: 46 VNYMPLIWNKIKSFL--SFDPLTDSEKYFWFEHNKTPIPWNYPVGVLFDCLAGKSA---T 100
Query: 144 LTVHFRGYPVHVL-----------------IPCEGEDSVKWSF-INSLKEAAYIINGNCK 185
T F VL IP + F + K+ +I+NG+ K
Sbjct: 101 FTTSFENQVKDVLTFLRIHLVMGDSLPPTIIPIASSKTQAEKFWFHQWKQVCFILNGSSK 160
Query: 186 NVMNMSQSDQVELWRSVMNGNLEAYLRVSSKL 217
+M++S ++ + W SV+ N + ++ +S+K+
Sbjct: 161 AIMSLSVNEARKFWGSVITRNFQDFIEISNKI 192
>pdb|3R0E|B Chain B, Structure Of Remusatia Vivipara Lectin
pdb|3R0E|D Chain D, Structure Of Remusatia Vivipara Lectin
Length = 110
Score = 33.5 bits (75), Expect = 0.20, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 5/67 (7%)
Query: 174 KEAAYIINGNCKNVMNMSQSDQVELWRSVMNGNLE-AYLRVSSKLKLITVEDDYTVKLNS 232
K ++ G+C V+ + W+S +GN E +LR++ K +LI +DD+ +S
Sbjct: 24 KNHQLVMQGDCNLVLYGGKYG----WQSNTHGNGEHCFLRLNHKGELIIKDDDFKTIWSS 79
Query: 233 SSKSQQG 239
S S+QG
Sbjct: 80 RSSSKQG 86
>pdb|1R76|A Chain A, Structure Of A Pectate Lyase From Azospirillum Irakense
Length = 408
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 278 CWDKISFINRPVEVRTEEGKCFTLRDAIKTLLPEYFT---DKPLFNDESPKLEDEEMNLS 334
W S I V++++G K L +++ +KP+F D + D+ M +S
Sbjct: 321 AWLNTSVIRDRAWVKSDQGYQLVTEQGAKPLWSRFYSLDGNKPVFGDRDKTIHDDVMGIS 380
Query: 335 SE 336
E
Sbjct: 381 QE 382
>pdb|1Z9U|A Chain A, Structural Genomics, The Crystal Structure Of The Acetyl
Transferase, Modifies N-Terminal Serine Of 50s Ribosomal
Subunit Protein L7L12 From Salmonella Typhimurium
pdb|1Z9U|B Chain B, Structural Genomics, The Crystal Structure Of The Acetyl
Transferase, Modifies N-Terminal Serine Of 50s Ribosomal
Subunit Protein L7L12 From Salmonella Typhimurium
Length = 179
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 143 NLTVHFRGYPVHVLIPCEGEDSVKWSF--INSLKEAAYI---INGNCKNVMNMSQSDQVE 197
N+ +H RGY LI C+ E + SF I + +AAYI ++ + + MSQS Q
Sbjct: 58 NILLHQRGYAKMYLIFCQNEMAGVLSFNAIEPINKAAYIGYWLDESFQGQGIMSQSLQAL 117
Query: 198 LWRSVMNGNLEAYL 211
+ G++ ++
Sbjct: 118 MTHYARRGDIRRFV 131
>pdb|1S7F|A Chain A, Riml- Ribosomal L7L12 ALPHA-N-Protein Acetyltransferase
Crystal Form I (Apo)
Length = 199
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 143 NLTVHFRGYPVHVLIPCEGEDSVKWSF--INSLKEAAYI---INGNCKNVMNMSQSDQVE 197
N+ +H RGY LI C+ E + SF I + +AAYI ++ + + MSQS Q
Sbjct: 78 NILLHQRGYAKMYLIFCQNEMAGVLSFNAIEPINKAAYIGYWLDESFQGQGIMSQSLQAL 137
Query: 198 LWRSVMNGNLEAYL 211
+ G++ ++
Sbjct: 138 MTHYARRGDIRRFV 151
>pdb|1S7K|A Chain A, Riml- Ribosomal L7L12 ALPHA-N-Protein Acetyltransferase
Crystal Form 2 (Apo)
pdb|1S7L|A Chain A, Riml- Ribosomal L7L12 ALPHA-N-Protein Acetyltransferase In
Complex With Coenzyme A (Coa-Cys134 Disulfide)
pdb|1S7N|A Chain A, Ribosomal L7L12 ALPHA-N-Protein Acetyltransferase In
Complex With Coenzyme A (Coa Free Sulfhydryl)
pdb|1S7N|B Chain B, Ribosomal L7L12 ALPHA-N-Protein Acetyltransferase In
Complex With Coenzyme A (Coa Free Sulfhydryl)
pdb|1S7N|C Chain C, Ribosomal L7L12 ALPHA-N-Protein Acetyltransferase In
Complex With Coenzyme A (Coa Free Sulfhydryl)
pdb|1S7N|D Chain D, Ribosomal L7L12 ALPHA-N-Protein Acetyltransferase In
Complex With Coenzyme A (Coa Free Sulfhydryl)
Length = 182
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 143 NLTVHFRGYPVHVLIPCEGEDSVKWSF--INSLKEAAYI---INGNCKNVMNMSQSDQVE 197
N+ +H RGY LI C+ E + SF I + +AAYI ++ + + MSQS Q
Sbjct: 61 NILLHQRGYAKMYLIFCQNEMAGVLSFNAIEPINKAAYIGYWLDESFQGQGIMSQSLQAL 120
Query: 198 LWRSVMNGNLEAYL 211
+ G++ ++
Sbjct: 121 MTHYARRGDIRRFV 134
>pdb|2GEY|A Chain A, Crystal Structure Of Aclr A Putative Hydroxylase From
Streptomyces Galilaeus
pdb|2GEY|B Chain B, Crystal Structure Of Aclr A Putative Hydroxylase From
Streptomyces Galilaeus
pdb|2GEY|C Chain C, Crystal Structure Of Aclr A Putative Hydroxylase From
Streptomyces Galilaeus
pdb|2GEY|D Chain D, Crystal Structure Of Aclr A Putative Hydroxylase From
Streptomyces Galilaeus
Length = 158
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 48/103 (46%), Gaps = 15/103 (14%)
Query: 190 MSQSDQVELWRSVMNGNLEAYLRVSSKLKLITVEDDYTVKLNSSSKSQQGTGETDFAGQV 249
+S +D V+L M G L+A+ + ++K I E+D + + + QG +F G
Sbjct: 42 VSSADMVKL----MEGGLKAFPDLQLEVKSIMAEEDRVALRITVTATHQG----EFMGVQ 93
Query: 250 KTGRIPVRLYVWSVSEDFDDLEDAPDIDCWDKISFINRPVEVR 292
TG + W + E+ D ++ WD I+ RP+ VR
Sbjct: 94 PTG----QRVSWHLVEEL-RFVDGKVVEHWDVINM--RPLLVR 129
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.135 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,913,354
Number of Sequences: 62578
Number of extensions: 459076
Number of successful extensions: 916
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 907
Number of HSP's gapped (non-prelim): 11
length of query: 379
length of database: 14,973,337
effective HSP length: 100
effective length of query: 279
effective length of database: 8,715,537
effective search space: 2431634823
effective search space used: 2431634823
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)