RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3471
(227 letters)
>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 = 42.7 bits (100), Expect = 5e-05
Identities = 47/253 (18%), Positives = 76/253 (30%), Gaps = 90/253 (35%)
Query: 26 VDYDLGNAPY-----G------YVPFCDSRTEMDGFRFWNQGYWRNHLQGRKYH----IS 70
DY L + P G YV ++ G + G R++L+G H ++
Sbjct: 228 KDY-LLSIPISCPLIGVIQLAHYVVTA----KLLG---FTPGELRSYLKGATGHSQGLVT 279
Query: 71 ALYV---VDLKRFRKIAA---------GDRLRGQYQALSQDPNSLSNLDQDLPNNMIHQV 118
A+ + + F G +R +A S L+ L NN V
Sbjct: 280 AVAIAETDSWESFFVSVRKAITVLFFIG--VRCY-EAYPNTSLPPSILEDSLENN--EGV 334
Query: 119 P-----IKSLPQEWLWCETWCDDRSKSSAKTIDLCNNPLTKEAKLSAAMRILY------- 166
P I +L QE + ++ N+ L ++ + L
Sbjct: 335 PSPMLSISNLTQEQV-------------QDYVNKTNSHLPAGKQVEIS---LVNGAKNLV 378
Query: 167 ------SVYAFI--FRAYKFEYELVQYKWPRWLTQQTEKQRIIWGYKILFLDVLFP---- 214
S+Y R K L Q + P ++ K + FL V P
Sbjct: 379 VSGPPQSLYGLNLTLRKAKAPSGLDQSRIP--FSE--RKLKFSNR----FLPVASPFHSH 430
Query: 215 -L-DVKKIIFVDA 225
L +I D
Sbjct: 431 LLVPASDLINKDL 443
Score = 33.5 bits (76), Expect = 0.065
Identities = 26/174 (14%), Positives = 45/174 (25%), Gaps = 63/174 (36%)
Query: 74 VVDL-KRF-----RKIAAGDRLRGQYQALSQDPNSLSNLDQD-LPNNMIHQVPIKSLPQE 126
+L +F + GQ+ + L+ + L N IH + L QE
Sbjct: 57 PAELVGKFLGYVSSLVEPSKV--GQFDQVLN--LCLTEFENCYLEGNDIHAL-AAKLLQE 111
Query: 127 WLWCETWCDDRSKSSAKT----IDLCNNPLTKEAK---LSAA------------------ 161
++K K + P K++ A
Sbjct: 112 ----NDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTD 167
Query: 162 -----MRILYSVY-----AFIFRAYKFEYELVQ--------YKWP----RWLTQ 193
+R LY Y I + + EL++ + WL
Sbjct: 168 DYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLEN 221
>1g9r_A Glycosyl transferase; alpha-beta structure; HET: UPF; 2.00A
{Neisseria meningitidis} SCOP: c.68.1.4 PDB: 1ga8_A*
1ss9_A*
Length = 311
Score = 39.0 bits (91), Expect = 6e-04
Identities = 19/111 (17%), Positives = 40/111 (36%), Gaps = 10/111 (9%)
Query: 17 VVRADMKELVDYDLGNAPYGYVPFCDSRTEMDGFRFWNQGYWRNHLQGRKYHISALYVVD 76
+VR + L D DLG+ G ++ R G Y + + +++
Sbjct: 107 LVRDSLTPLWDTDLGDNWLGASI------DLFVERQEGYKQKIGMADGEYYFNAGVLLIN 160
Query: 77 LKRFRKIAAGDRLRGQYQALSQDPNSLSNLDQDLPNNMIHQVPIKSLPQEW 127
LK++R+ + + Q + + DQD+ N + + +
Sbjct: 161 LKKWRRHDIFKMS---SEWVEQYKDVMQYQDQDILNGLFKGG-VCYANSRF 207
>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 = 35.2 bits (80), Expect = 0.016
Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 21/95 (22%)
Query: 23 KELVDYDLGNAPYGYVPFCDSRTEMDGFRFWNQGYWRNHL----QGRKYHI-SALYVVDL 77
+ +VD+ N P + +D + + + G+ HL + + ++ +D
Sbjct: 447 RSIVDHY--NIPKTFDSDDLIPPYLDQYFYSHIGH---HLKNIEHPERMTLFRMVF-LDF 500
Query: 78 KRF--RKIAAGDRLRGQYQALSQDPNSLSNLDQDL 110
RF +KI R S+ N Q L
Sbjct: 501 -RFLEQKI----RHDS---TAWNASGSILNTLQQL 527
Score = 30.2 bits (67), Expect = 0.68
Identities = 31/215 (14%), Positives = 63/215 (29%), Gaps = 67/215 (31%)
Query: 48 DGFRFWNQGYWRNHLQGRKYHISALYVVDLKRFRKIAAGDRLRGQYQALSQDPNS----- 102
DG W+ W++ + I + L+ R + LS P S
Sbjct: 339 DGLATWD--NWKHVNCDKLTTIIESSLNVLEP-------AEYRKMFDRLSVFPPSAHIPT 389
Query: 103 --LS----NLDQDLPNNMIHQVPIKSLPQEWLWCETWCDDRSKSSAKTIDLCNNPLTKEA 156
LS ++ + +++++ SL ++ K S +I L +
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ----------PKESTISIPSIYLELKVKL 439
Query: 157 KLSAAM--RIL--YSV----------------YAFIFRAY------------KFEYELVQ 184
+ A+ I+ Y++ Y + + F +
Sbjct: 440 ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD 499
Query: 185 YKWPRWLTQQTEKQRIIWGYKILFLDVLFPLDVKK 219
+ R+L Q+ W L+ L +K
Sbjct: 500 F---RFLEQKIRHDSTAWNASGSILNTL--QQLKF 529
>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine
rich repeat domain, type three effector, salmonella
virulence factor; 1.90A {Salmonella typhimurium}
Length = 622
Score = 29.5 bits (66), Expect = 1.1
Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 19/61 (31%)
Query: 96 LSQDPNSLSNLDQ-DLPNNMIHQVP--IKSLPQEWLWCETWCDDRSKSSAKTIDLCNNPL 152
L+ P S L + N + ++P + L E T++L NPL
Sbjct: 253 LTSLPMLPSGLLSLSVYRNQLTRLPESLIHLSSE----------------TTVNLEGNPL 296
Query: 153 T 153
+
Sbjct: 297 S 297
>3cww_A Insulysin, insulin-degrading enzyme, insulinase; A-beta degrading
enzyme, criptidase, kinins, hydrolase; 1.96A {Homo
sapiens} PDB: 3ofi_A 2wc0_A 3h44_A 3n56_A 3n57_A 2wby_A
3qz2_A 3e4z_A 2wk3_A 3e4a_A* 2g47_A 2g48_A 2g49_A 2g54_A
2g56_A 2jbu_A 3e50_A 2jg4_A 3hgz_A 2yb3_A* ...
Length = 990
Score = 28.6 bits (63), Expect = 1.9
Identities = 21/123 (17%), Positives = 41/123 (33%), Gaps = 4/123 (3%)
Query: 87 DRLRGQYQALSQDPNSLSN-LDQDLPNNMIHQVPIKSLPQEWLWCETWCDDRSKSSAKTI 145
+ L +Y P+ + LD+ P N+ + KS + E W + K A
Sbjct: 419 EVLTAEYLLEEFRPDLIEMVLDKLRPENVRVAIVSKSFEGKTDRTEEWYGTQYKQEAIPD 478
Query: 146 DLCNNPLTKEAKLSAAMRILYSVYAFIFRAYKFEYELVQYKWPRWLTQQTEKQRIIWGYK 205
+ + A L+ + L + FI ++ L + T ++ +
Sbjct: 479 AVIAKW--QNAALNGKFK-LPTKNEFIPTNFEILPLEAAATPYPALIKDTAMSKLWFKQD 535
Query: 206 ILF 208
F
Sbjct: 536 DKF 538
>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A
resolution, N-formylmethionine, alpha subunit; HET: FME;
2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1
c.10.2.2 PDB: 1ltx_A*
Length = 567
Score = 28.6 bits (63), Expect = 1.9
Identities = 19/132 (14%), Positives = 42/132 (31%), Gaps = 22/132 (16%)
Query: 49 GFRFWNQGYWRNHLQGRKYHISALYVVDL--KRFRKIAAGDRLRG------QYQALSQDP 100
+ + + K + + V+ L K + ++L + L P
Sbjct: 420 AYLDDLRSKFLLENSVLKMEYADVRVLHLAHKDLTVLCHLEQLLLVTHLDLSHNRLRALP 479
Query: 101 NSLSNLDQ----DLPNNMIHQVP-IKSLPQ-EWLWC-----ETWCDD---RSKSSAKTID 146
+L+ L +N + V + +LP+ + L + S ++
Sbjct: 480 PALAALRCLEVLQASDNALENVDGVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLLN 539
Query: 147 LCNNPLTKEAKL 158
L N L +E +
Sbjct: 540 LQGNSLCQEEGI 551
>3pe5_A Uncharacterized protein; structural genomics, PSI-biology, protein
structure initiati northeast structural genomics
consortium, NESG; 2.38A {Clostridium leptum}
Length = 403
Score = 27.6 bits (61), Expect = 3.2
Identities = 20/109 (18%), Positives = 28/109 (25%), Gaps = 28/109 (25%)
Query: 16 YVVRADM---KELVDYDLG----NAPYGYVPFCDSRTEMDGFRFWNQGYWRNHLQGRKYH 68
+VD LG + + F +G +N L G
Sbjct: 190 RYAVVYFDTFPGIVD-TLGGIEVEMTQTEADVMNESVGPEFANF-TEG--KNTLNGAT-- 243
Query: 69 ISAL-YVVDLKRFRKIAAGDRLRGQYQ-----AL---SQDPNSLSNLDQ 108
AL YV R R D R Q Q + + + L
Sbjct: 244 --ALVYV----RIRYGVGDDFGRTQRQRDFMLQVLNKVKGTRDVGTLLT 286
>4fmz_A Internalin; leucine rich repeat, structural genomic center for
structural genomics, JCSG, protein structure INI
PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes
serotype 4B}
Length = 347
Score = 26.7 bits (60), Expect = 7.2
Identities = 11/63 (17%), Positives = 20/63 (31%), Gaps = 21/63 (33%)
Query: 97 SQDPNSLSNLDQ----DLPNNMIHQV-PIKSLPQEWLWCETWCDDRSKSSAKTIDLCNNP 151
++D + L L N I + P+ SL + + + D N
Sbjct: 301 NEDMEVIGGLTNLTTLFLSQNHITDIRPLASLSK--M--------------DSADFANQV 344
Query: 152 LTK 154
+ K
Sbjct: 345 IKK 347
>3tzt_A Glycosyl transferase family 8; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG, putative
glycosyl transferase; HET: MSE CIT; 2.10A {Anaerococcus
prevotii}
Length = 276
Score = 26.4 bits (58), Expect = 7.5
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 204 YKILFLDVLFPLDVKKIIFVDAD 226
Y L P ++ +I+++D D
Sbjct: 88 YYRLLAGEFLPENLGEILYLDPD 110
>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold,
ligase; 2.80A {Shigella flexneri 2A}
Length = 571
Score = 26.9 bits (59), Expect = 7.7
Identities = 18/125 (14%), Positives = 35/125 (28%), Gaps = 21/125 (16%)
Query: 96 LSQDPNSLSNLDQ-DLPNNMIHQVP--IKSLPQ-EWLWCETWCDD----------RSKSS 141
L+ P +L+ D+ N++ +P E C + S
Sbjct: 172 LTFLPELPESLEALDVSTNLLESLPAVPVRNHHSEETEIFFRCRENRITHIPENILSLDP 231
Query: 142 AKTIDLCNNPLTKEAKLSAAMRILYSVYA-------FIFRAYKFEYELVQYKWPRWLTQQ 194
TI L +NPL+ + S + + Y + + W +
Sbjct: 232 TCTIILEDNPLSSRIRESLSQQTAQPDYHGPRIYFSMSDGQQNTLHRPLADAVTAWFPEN 291
Query: 195 TEKQR 199
+
Sbjct: 292 KQSDV 296
>3aj7_A Oligo-1,6-glucosidase; (beta/alpha)8-barrel, hydrolase; 1.30A
{Saccharomyces cerevisiae} PDB: 3a4a_A* 3a47_A 3axi_A*
3axh_A*
Length = 589
Score = 26.4 bits (59), Expect = 8.4
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 40 FCDSRTEMDGFRFWNQGYWRNHLQGRKYHISALYVVDLKRFRKIAA 85
+ ++G W+ Y NH Q R I+ + D + R I+
Sbjct: 330 LAELFRYINGTDCWSTIYLENHDQPR--SITR-FGDDSPKNRVISG 372
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
0.323 0.139 0.451
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,665,211
Number of extensions: 203127
Number of successful extensions: 420
Number of sequences better than 10.0: 1
Number of HSP's gapped: 415
Number of HSP's successfully gapped: 19
Length of query: 227
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 137
Effective length of database: 4,188,903
Effective search space: 573879711
Effective search space used: 573879711
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.8 bits)