RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16188
(395 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 = 54.7 bits (131), Expect = 4e-08
Identities = 71/417 (17%), Positives = 116/417 (27%), Gaps = 155/417 (37%)
Query: 25 YSSVDTNPIGIYVM-------HPFWNKLVE----YFPRWLAPNLITFVGFLFTVLSFVWL 73
+ +V + + ++ +L + Y L +LI F + L L
Sbjct: 146 FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHV--LVGDLIKFSAETLSELIRTTL 203
Query: 74 SFYDYHYYA----SSLTHPNYPPVPKWL----FSLVGICV--FLAYTLDGIDGKQARRTG 123
L +P+ P +L S I V Y + A+ G
Sbjct: 204 DAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVT------AKLLG 257
Query: 124 NSGPVGELFDH--GL----------------DSWTAMFVPA-----LLYSI-------FG 153
+ P GEL + G DSW + FV +L+ I +
Sbjct: 258 FT-P-GELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYP 315
Query: 154 RSDFSVS------------PFRMYLICWNVFISFYASHWEKYNTGVLYLPWSYDLSM-L- 199
+ S P M L N+ + K N+ +LP + + L
Sbjct: 316 NTSLPPSILEDSLENNEGVPSPM-LSISNLTQEQVQDYVNKTNS---HLPAGKQVEISLV 371
Query: 200 --GTTVVFWVTGY----YGIEFWKVYLYRDITLGHLLE---ITF------YVSSFISNLP 244
+V V+G YG+ R L+ I F + + F LP
Sbjct: 372 NGAKNLV--VSGPPQSLYGLNLT----LRKAKAPSGLDQSRIPFSERKLKFSNRF---LP 422
Query: 245 VVIYNIYHS------------------------------YKTGTGKN-RPLLEAMRP-LY 272
V +HS Y T G + R L ++ +
Sbjct: 423 VAS--PFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIV 480
Query: 273 PLVAFVALSYYW---VRTSPNDIMDLDPRAVF--------ITTGTIFSNICCRLIVA 318
+ + + W + I+D P GT R+IVA
Sbjct: 481 DCIIRLPV--KWETTTQFKATHILDFGPGGASGLGVLTHRNKDGT-----GVRVIVA 530
Score = 41.2 bits (96), Expect = 6e-04
Identities = 65/375 (17%), Positives = 109/375 (29%), Gaps = 140/375 (37%)
Query: 38 MHPFWNKLVEYFPRWLA---------------PNLIT-FVGFL------------FTVLS 69
++L E F + L L+ F+G++ VL+
Sbjct: 26 SFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLN 85
Query: 70 FVWLSF---Y----DYHYYASSLTHPNYPPVPKWLFSLVGICVFLAYTLDGIDGKQARRT 122
F Y D H A+ L N + K + Y AR
Sbjct: 86 LCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKE------LIKNYI-------TARIM 132
Query: 123 GNSGPVGE-----LFDHGLDSWTAMFVPALLYSIF---GRSD--FS--VSPFRMYLICWN 170
P + LF + A L +IF G +D F ++ Y +
Sbjct: 133 AKR-PFDKKSNSALFRAVGEG------NAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVG 185
Query: 171 VFISFYASHWEKYNTGVLYLPWSYDLSMLGTTVVFWVTGYYGIEFWKVYLYRDITLGHLL 230
I F A LS L T + + KV+ + + + L
Sbjct: 186 DLIKFSAET----------------LSELIRTTL---------DAEKVF-TQGLNILEWL 219
Query: 231 EITFYVSSFISNLPVVIYNIYHSYKTGTGKNRPLLEAMRPL-YPLVAFVALSYYWVRTSP 289
E SN P Y LL P+ PL+ + L++Y V
Sbjct: 220 ENP-------SNTPDKDY---------------LLSI--PISCPLIGVIQLAHYVVTAK- 254
Query: 290 NDIMDLDPRAVF-ITTGTIFSNICCRLIVA----QMSNTRCDAFNWLLVAQAVDIVLSSF 344
++ P + G + +V +++ ++F + V +A+ + F
Sbjct: 255 --LLGFTPGELRSYLKGAT---GHSQGLVTAVAIAETDSW-ESFF-VSVRKAITV---LF 304
Query: 345 FVG------MPRAEL 353
F+G P L
Sbjct: 305 FIGVRCYEAYPNTSL 319
Score = 33.5 bits (76), Expect = 0.15
Identities = 44/289 (15%), Positives = 74/289 (25%), Gaps = 106/289 (36%)
Query: 134 HG-LDSWTAMFVPALLYSIFG--RSDFSVS---PFRMY-----------LICWNVFISFY 176
HG L+ + VP + I + F+ P + L F+ +
Sbjct: 13 HGSLE--HVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAEL--VGKFLGYV 68
Query: 177 ASHWEKYNTGVLYLPWSYDLSMLGTTVVFWVTGYYGIEFWKVYLY-RDI-TL-GHLLEI- 232
+S E G +D +L + EF YL DI L LL+
Sbjct: 69 SSLVEPSKVG------QFD-QVLNLCLT---------EFENCYLEGNDIHALAAKLLQEN 112
Query: 233 ------------TFYVSSFISNLPVV-----------------IYNIYHSYKTGTGKNRP 263
+ + ++ P + I+ G G
Sbjct: 113 DTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF----GGQGNTDD 168
Query: 264 LLEAMRPLYPLVAFVALSYYWVRTSPNDIMDLDPRAVFITTGTIFSNICCRLIVAQMSNT 323
E +R LY +T + DL + + LI +
Sbjct: 169 YFEELRDLY-------------QTYHVLVGDLIKFS---------AETLSELIRTTLDAE 206
Query: 324 R-----CDAFNWLLVAQAV--DIVLSSFFVGMPR---AELCLLYVFCTV 362
+ + WL L S + P +L V +
Sbjct: 207 KVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKL 255
>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 = 37.1 bits (85), Expect = 0.009
Identities = 30/189 (15%), Positives = 55/189 (29%), Gaps = 58/189 (30%)
Query: 204 VFWVT-GYYGIEFWKVYLYRDITLGHLLEITFYVSSFISNLPVVIYNIYHSYKTGTGKNR 262
+FW+ + L L ++ + + ++ NI + + R
Sbjct: 184 IFWLNLKNCNSP--------ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR 235
Query: 263 PLLEAMRPLYP---LVAFVALSYYWVRTSPNDIMDLDPRAV--FITTGTIFSNICCRLIV 317
LL Y LV L + +A F N+ C++++
Sbjct: 236 RLL--KSKPYENCLLV----LLNVQ-----------NAKAWNAF--------NLSCKILL 270
Query: 318 AQMSNTRCDA--FNWLLVAQAVDIVLSSFFVGMPRAE---LCLLYVFCTVALLAHIHYGS 372
TR ++L A I L + + E L L Y+ C L
Sbjct: 271 T----TR-FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP------ 319
Query: 373 CVVRQMCKH 381
R++
Sbjct: 320 ---REVLTT 325
Score = 29.8 bits (66), Expect = 1.8
Identities = 43/272 (15%), Positives = 79/272 (29%), Gaps = 75/272 (27%)
Query: 12 LDKHHLNGFDNYKYSSVDTNPIGIYVMHPFWNKLVEYFPRWLAPNLI--TFVGF-LF--- 65
+ L +DN+K+ + D ++E L P F +F
Sbjct: 336 SIRDGLATWDNWKHVNCDK-----------LTTIIESSLNVLEPAEYRKMFDRLSVFPPS 384
Query: 66 -----TVLSFVW--LSFYDYHYYASSLTHPNYPPVPKW----LFSLVGICVFLAYTLDGI 114
+LS +W + D + L Y V K S+ I +L +
Sbjct: 385 AHIPTILLSLIWFDVIKSDVMVVVNKLH--KYSLVEKQPKESTISIPSI--YLELKVKLE 440
Query: 115 DGKQARRTGNSGPVGELFDHGLDSWTAMFVPALLYSI---FGRSDFSVSPFRMYLICWNV 171
+ R+ + DH Y+I F D Y
Sbjct: 441 NEYALHRS--------IVDH--------------YNIPKTFDSDDLIPPYLDQY-FYS-- 475
Query: 172 FISFY---ASHWEKYNT-GVLYLPWSYDLSMLG-----TTVVFWVTGYYGIEFWKVYLYR 222
I + H E+ +++L D L + + +G ++ Y+
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFL----DFRFLEQKIRHDSTAWNASGSILNTLQQLKFYK 531
Query: 223 D-ITLGHLLEITFYVSSFISNLPVVIYNIYHS 253
I + V++ + LP + N+ S
Sbjct: 532 PYICDND-PKYERLVNAILDFLPKIEENLICS 562
>3ayf_A Nitric oxide reductase; oxidoreductase; HET: HEM BOG EPE LOP; 2.50A
{Geobacillus stearothermophilus} PDB: 3ayg_A*
Length = 800
Score = 28.1 bits (62), Expect = 7.1
Identities = 16/171 (9%), Positives = 43/171 (25%), Gaps = 19/171 (11%)
Query: 52 WLAPNLITFVGFLFTVLSFVWLSFYDYHYYASSLTHPNYPPVPKWLFSLVGICVFLAYTL 111
+ + +G V ++ ++ + W LV + + +
Sbjct: 397 LVVLVGGSMIGQWLGVNGYLGNEWFLLGHQGWEYIELGRI----WQIILVVGMLLWLFIV 452
Query: 112 DGIDGKQARRTGNSGPVGELFDHGLDSWTAMFVPALLYSIFGRSDFSVSPFRMYLICWNV 171
+ +R + G + L + + Y + W +
Sbjct: 453 FRGVKRGLKRESDKGGLIHLL------FYSAIAVPFFYIFAFFIQPDTNFTMADFWRWWI 506
Query: 172 FISFYASHWEKYNTGVLYL---------PWSYDLSMLGTTVVFWVTGYYGI 213
+ +E + V+ S ++ + +G GI
Sbjct: 507 IHLWVEGIFEVFAVVVIGFLLVQLRLVTKKSTVRALYFQFTILLGSGVIGI 557
>3jwd_A HIV-1 GP120 envelope glycoprotein; HIV-1 viral spike, molecular
motion, protein architecture, R triggered entry, type 1
fusion protein, cell membrane, DISU bond; HET: YCM NAG;
2.61A {Human immunodeficiency virus 1} PDB: 1meq_A
Length = 379
Score = 27.5 bits (62), Expect = 7.8
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 206 WVTGYYGIEFWK 217
WVT YYG+ WK
Sbjct: 5 WVTVYYGVPVWK 16
>2bo4_A Mannosylglycerate synthase; catalysis, glycosyltransferase,
mannose, transferase, stereoselectivity; HET: FLC; 1.95A
{Rhodothermus marinus} SCOP: c.68.1.18 PDB: 2bo6_A
2bo7_A* 2bo8_A* 2xw2_A 2y4j_A 2xw3_A* 2xw4_A* 2xw5_A*
2y4k_A* 2y4l_A* 2y4m_A*
Length = 397
Score = 27.8 bits (61), Expect = 7.8
Identities = 13/97 (13%), Positives = 26/97 (26%), Gaps = 11/97 (11%)
Query: 131 LFDHGLDSWTAMFVPALLYSIFGRSDFSVSPFRMYL----ICWNVFISFYASHWEKYNTG 186
+D + S+ ++ + F I W + + +A W
Sbjct: 98 FYDADITSFGPDWITKAEEAADFGYGLVRHYFPRASTDAMITWMITRTGFALLWPHTELS 157
Query: 187 VLYLPWSYDLSM-------LGTTVVFWVTGYYGIEFW 216
+ P +L M L +GI+
Sbjct: 158 WIEQPLGGELLMRREVAAMLYEDERVRRRSDWGIDTL 194
>3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A
{Bacillus phage PHI29} PDB: 3gqk_A*
Length = 163
Score = 26.9 bits (59), Expect = 9.5
Identities = 9/54 (16%), Positives = 18/54 (33%), Gaps = 3/54 (5%)
Query: 2 TLANLFNYKYLDKHHLNGFDNYKYSSV---DTNPIGIYVMHPFWNKLVEYFPRW 52
+ ++++ N F Y V D + +P ++ Y PR
Sbjct: 46 FVLGESSFEWQGAVLKNEFGGIIYEEVTTEDGVKFKRPLPNPDFDPNKNYIPRS 99
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
0.330 0.143 0.482
Gapped
Lambda K H
0.267 0.0457 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,618,782
Number of extensions: 401660
Number of successful extensions: 1009
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1006
Number of HSP's successfully gapped: 20
Length of query: 395
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 299
Effective length of database: 4,021,377
Effective search space: 1202391723
Effective search space used: 1202391723
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 (21.8 bits)
S2: 58 (26.8 bits)