RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16001
(318 letters)
>4ddp_A Beclin-1; ECD, autophagy, membrane binding, membrane protein; 1.55A
{Homo sapiens}
Length = 210
Score = 266 bits (681), Expect = 6e-90
Identities = 149/209 (71%), Positives = 173/209 (82%), Gaps = 3/209 (1%)
Query: 109 EYSDFLKTLELQLQYSLSQLNKFKSTNVFNATFHIWHSGHFGTINNFRLGTLPSAPVDWS 168
E D LK++E Q++Y+ +QL+K K TNVFNATFHIWHSG FGTINNFRLG LPS PV+W+
Sbjct: 2 ELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWN 61
Query: 169 EINAAWGQTALLLTALARKLNLTFQRYRIVPYGNHSYIEDTTEHKN-LPLFASGGAKFFW 227
EINAAWGQT LLL ALA K+ L FQRYR+VPYGNHSY+E T+ LPL+ SGG +FFW
Sbjct: 62 EINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFW 121
Query: 228 DTKFDMAMVAFLDCLQQFKEELEKGDSEFHLPYNMD-SKGKIED-ETTGNTYSVKYQFNS 285
D KFD AMVAFLDC+QQFKEE+EKG++ F LPY MD KGKIED +G +YS+K QFNS
Sbjct: 122 DNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFNS 181
Query: 286 QEQWTKALKFMLTNLKWGLAWVSSQFKNQ 314
+EQWTKALKFMLTNLKWGLAWVSSQF N+
Sbjct: 182 EEQWTKALKFMLTNLKWGLAWVSSQFYNK 210
>3vp7_A Vacuolar protein sorting-associated protein 30; targeting,
PI3-kinase complex I, PRE-autophagosomal structur
protein transport; 2.30A {Saccharomyces cerevisiae}
Length = 220
Score = 231 bits (590), Expect = 4e-76
Identities = 71/224 (31%), Positives = 99/224 (44%), Gaps = 54/224 (24%)
Query: 135 NVFNATFHIWHSGHFGTINNFRLGTLPSAPVDWSEINAAWGQTALLLTALARKLNLTFQR 194
N+FNATF I HSG F TIN RLG++P + V W EINAA GQ LLL + + L +
Sbjct: 2 NIFNATFKISHSGPFATINGLRLGSIPESVVPWKEINAALGQLILLLATINKNLKINLVD 61
Query: 195 YRIVPYGNHSYIEDTT---------------EHKNLPLFASG----GAKFFWDTKFDMAM 235
Y + P G+ S I+ + LP++ G F +TKFD ++
Sbjct: 62 YELQPMGSFSKIKKRMVNSVEYNNSTTNAPGDWLILPVYYDENFNLGRIFRKETKFDKSL 121
Query: 236 VAFLDCLQQFKEELEKGDSE---------------------------FHLPYNMDSKGKI 268
L+ + + +L S LPY M+ K KI
Sbjct: 122 ETTLEIISEITRQLSTIASSYSSQTLTTSQDESSMNNANDVENSTSILELPYIMN-KDKI 180
Query: 269 EDETTGNTYSVKYQFNSQE-QWTKALKFMLTNLKWGLAWVSSQF 311
SVK +S +WT A+KF+LTN+KW LA+ S+
Sbjct: 181 NG------LSVKLHGSSPNLEWTTAMKFLLTNVKWLLAFSSNLL 218
>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 = 36.4 bits (83), Expect = 0.012
Identities = 38/332 (11%), Positives = 87/332 (26%), Gaps = 96/332 (28%)
Query: 29 LDH-----FVPAFK-----LVDSTNGSNGFCLLGKDESSNSKGHQMKVY--ANLFDFLSS 76
L + AF L+ + L + S H + L
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK 309
Query: 77 NSGID-----------HPLCEECTDTLLDMMDKELKNTKQDFQEYSD-FLKTLELQLQYS 124
+P L ++ + +++ + + L ++ S
Sbjct: 310 YLDCRPQDLPREVLTTNPR-------RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS 362
Query: 125 LSQLN------KFKSTNVFNATFHIWHSGHFGTINNFRLGTLPSAPVDWSEINAAWGQTA 178
L+ L F +VF + HI L + W ++ +
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPSAHI-------PTI--LLSLI------WFDVIKS--DVM 405
Query: 179 LLLTALARKLNLTFQRYRIVPYGNHS-YIE-------DTTEHKNLPLFASGGAKFFWDTK 230
+++ L + L ++ + S Y+E + H+++
Sbjct: 406 VVVNKLHKYS-LVEKQPKESTISIPSIYLELKVKLENEYALHRSI--------------- 449
Query: 231 FDMAMVAFLDCLQQFKEELEKGDSEF--HLPYNMDSKGKIEDETTGNTYSVKYQFNSQEQ 288
+ D F H+ +++ + E + + + +
Sbjct: 450 --VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERM---TLFRMVF-LD---- 499
Query: 289 WTKALKFMLTNLKW-GLAW-VSSQFKNQFQDL 318
+F+ ++ AW S N Q L
Sbjct: 500 ----FRFLEQKIRHDSTAWNASGSILNTLQQL 527
Score = 36.0 bits (82), Expect = 0.017
Identities = 27/171 (15%), Positives = 48/171 (28%), Gaps = 53/171 (30%)
Query: 3 DNSQTEIHLVPICSSQDIDLESQANSLD----HFVPAFKLVDSTNGSNGFCLLGKDESSN 58
S I I LE + + H +VD N F D
Sbjct: 422 KESTISIP--------SIYLELKVKLENEYALHR----SIVDHYNIPKTFD--SDDLIPP 467
Query: 59 SK--------GHQMK-------------VYANLFDFLSSNSGIDHPLCEECTDTLLDMMD 97
GH +K V+ + F FL I H D+
Sbjct: 468 YLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD-FRFLEQK--IRH-------DSTAWNAS 517
Query: 98 KELKNTKQDFQEYSDFLKTLELQLQYSLSQLNKFKSTNVFNATFHIWHSGH 148
+ NT Q + Y ++ + + + ++ + F + ++ S +
Sbjct: 518 GSILNTLQQLKFYKPYICDNDPKYERLVNAILDF----LPKIEENLICSKY 564
Score = 29.1 bits (64), Expect = 2.5
Identities = 38/294 (12%), Positives = 70/294 (23%), Gaps = 102/294 (34%)
Query: 2 VDNSQTEIHLVPICSSQDIDLESQANSLDHFVPAFKLVDSTNGSNGFCLLGKDESSNSKG 61
+D E +DI L F AF +
Sbjct: 7 MDFETGEHQY----QYKDI--------LSVFEDAFV---------------DNFDCK--- 36
Query: 62 HQMKVYANLFDFLS---SNSGIDH----PLCEECTDTLLDMMDKELKNTKQDF------Q 108
++ D S IDH T L + + + Q F
Sbjct: 37 -------DVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRI 89
Query: 109 EYSDFLKTLELQLQYS---------LSQLNKFKSTNVFNATFHIWHSGHFGTINNFRLGT 159
Y FL + ++ + + Q ++ + N A +++ + + L
Sbjct: 90 NY-KFLMS-PIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ-ALLE 146
Query: 160 LPSAPVDWSEIN--AAWGQTALLLTALARKLNLTFQRYRIVPYGNHSYIEDTTEHKNLPL 217
L P I+ G+T + L +
Sbjct: 147 L--RPAKNVLIDGVLGSGKTWVALDVCL----------------------SYKVQCKMDF 182
Query: 218 FASGGAKFFW-------DTKFDMAMVAFLDCLQQFKEELEKGDSEFHLPYNMDS 264
K FW + + M+ L Q + D ++ + S
Sbjct: 183 ------KIFWLNLKNCNSPETVLEMLQKL-LYQIDPNWTSRSDHSSNIKLRIHS 229
Score = 27.5 bits (60), Expect = 7.9
Identities = 14/82 (17%), Positives = 32/82 (39%), Gaps = 9/82 (10%)
Query: 242 LQQFKEELEKGDSEFHLPYNMDSKGKIED--ETTGNTYSVKYQF----NSQEQWTKALKF 295
F + + D + +P ++ SK +I+ + F + QE+ + KF
Sbjct: 26 EDAFVDNFDCKDVQ-DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQ--KF 82
Query: 296 MLTNLKWGLAWVSSQFKNQFQD 317
+ L+ ++ S K + +
Sbjct: 83 VEEVLRINYKFLMSPIKTEQRQ 104
>2p1l_B Beclin 1; apoptosis, autophagy, BH3 domain, BCL; 2.50A {Homo
sapiens} PDB: 3dvu_C 2pon_A
Length = 31
Score = 30.5 bits (68), Expect = 0.043
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 62 HQMKVYANLFDFLSSNSGIDHP 83
++KV +LFD +S + +DHP
Sbjct: 10 RRLKVTGDLFDIMSGQTDVDHP 31
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 32.6 bits (73), Expect = 0.074
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 7/30 (23%)
Query: 246 KEELEKGDSEFHLPYNMDS------KGKIE 269
K+ L+K + L Y DS K +E
Sbjct: 19 KQALKKLQASLKL-YADDSAPALAIKATME 47
>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 = 33.5 bits (76), Expect = 0.10
Identities = 45/284 (15%), Positives = 78/284 (27%), Gaps = 107/284 (37%)
Query: 57 SNSKGHQMKVYAN------LFD----FLSSNSGIDHPLCEECTDTLLDMMDKELKNTKQD 106
S +G M +Y +++ G ++LD++ N
Sbjct: 1626 SQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGF----------SILDIVINNPVNLTIH 1675
Query: 107 F---------QEYSDFLKTLELQLQYSLSQLNKFKSTNVFNATFHIWHSGHFGTINNFRL 157
F + YS E + L FK N ++T + + G ++
Sbjct: 1676 FGGEKGKRIRENYSAM--IFETIVDGKLKTEKIFKEIN-EHSTSYTF-RSEKGLLSA--- 1728
Query: 158 GTLPSAPVDWSEINAAWGQTALLLTALARKLNLTFQRYR---IVPYGN----HS---Y-- 205
T Q AL L A F+ + ++P HS Y
Sbjct: 1729 -T----------QFT---QPALTLMEKA-----AFEDLKSKGLIPADATFAGHSLGEYAA 1769
Query: 206 ---------IEDT---------TEHKNLPLFASGGAKFFWDTKFDMA------MVAFL-- 239
IE T +P G + + M + A
Sbjct: 1770 LASLADVMSIESLVEVVFYRGMTMQVAVPRDELGR------SNYGMIAINPGRVAASFSQ 1823
Query: 240 DCLQQFKEELEKGDSEFHLP--YNMDSK-----GKIED-ETTGN 275
+ LQ E + K YN++++ G + +T N
Sbjct: 1824 EALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTN 1867
Score = 30.8 bits (69), Expect = 0.80
Identities = 32/192 (16%), Positives = 60/192 (31%), Gaps = 74/192 (38%)
Query: 6 QTEIHLVPICSSQDIDLESQANSLDHFV---PAFKLVDSTNGSNGFCLL--------GKD 54
+T HL P + + +++ S N + V P L G L G D
Sbjct: 355 KTNSHL-P--AGKQVEI-SLVNGAKNLVVSGPPQSLY-------GLNLTLRKAKAPSGLD 403
Query: 55 ESSNSKGHQMK-VYANLFDFLSS--NSGIDHPLCEECTDTLLDMMDKELKNTKQDFQEYS 111
+S + K ++N F ++S +S L +D + +D + +
Sbjct: 404 QS-RIPFSERKLKFSNRFLPVASPFHS----HLLVPASDLIN-----------KDLVKNN 447
Query: 112 DFLKTLELQLQYSLSQLNKFKSTNVFNATFHIWHSGHFGTINNFRL--GTLP-------- 161
++Q+ V++ TF G + R+ G++
Sbjct: 448 VSFNAKDIQIP-------------VYD-TF----DGS-----DLRVLSGSISERIVDCII 484
Query: 162 SAPVDWSEINAA 173
PV W
Sbjct: 485 RLPVKWETTTQF 496
>2ppq_A HSK, HK, homoserine kinase; structural genomics, MCSG, PSI-2,
protein structure initiative; 2.00A {Agrobacterium
tumefaciens str} SCOP: d.144.1.6
Length = 322
Score = 29.1 bits (64), Expect = 1.7
Identities = 21/183 (11%), Positives = 39/183 (21%), Gaps = 9/183 (4%)
Query: 47 GFCLLGKDESSNSKGHQMKVYANLFDF--LSSNSGIDHPLCEECTDTLLDMMDKELKNTK 104
L G H +V L S I P + E + +
Sbjct: 102 ISFLEGMWLRKPEAKHCREVGKALAAMHLASEGFEIKRPNALSVDGWKVLWDKSEERADE 161
Query: 105 QDFQEYSDFLKTLELQLQYSLSQLNKFKSTNVFNATFHIWHSGHFGTINNFRLGTLPSAP 164
+ + ++ + L + + +F
Sbjct: 162 VEKGLREEIRPEIDYLAAHWPKDLPAGVIHADLFQDNVFFLGDELSGLIDFYFAC----- 216
Query: 165 VDWSEINAAWGQTALLLTALARKLNLTFQRYRIVPYGNHSYIEDTTEHKNLPLFASGGAK 224
D + + A + E E + LPL + G A
Sbjct: 217 NDLLAYDVSICLNAWCFEKDGAYNVTKGKALLEGYQSVRPLSEA--ELEALPLLSRGSAL 274
Query: 225 FFW 227
F+
Sbjct: 275 RFF 277
>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus
norvegicus}
Length = 96
Score = 26.4 bits (58), Expect = 5.2
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 98 KELKNTKQDFQEYSDFLKTLELQLQYSLSQLNKFK 132
+E K+ E D LK++E Q++Y+ QL+K K
Sbjct: 60 REYSEFKRQQLELDDELKSVENQMRYAQMQLDKLK 94
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
0.318 0.132 0.402
Gapped
Lambda K H
0.267 0.0566 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,638,805
Number of extensions: 255808
Number of successful extensions: 459
Number of sequences better than 10.0: 1
Number of HSP's gapped: 451
Number of HSP's successfully gapped: 15
Length of query: 318
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 224
Effective length of database: 4,077,219
Effective search space: 913297056
Effective search space used: 913297056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.1 bits)