RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3027
(300 letters)
>4dqv_A Probable peptide synthetase NRP (peptide synthase; GXXGXXG motif,
rossmann fold, short chain dehydrogenase/REDU family,
reductase; 2.30A {Mycobacterium tuberculosis}
Length = 478
Score = 53.8 bits (129), Expect = 2e-08
Identities = 24/148 (16%), Positives = 53/148 (35%), Gaps = 18/148 (12%)
Query: 1 LLHEWPNTYTFTKALAEDVLCK--EGKGLPLAVLRPAVIVSTYREPVRGWIDNVYGPIGM 58
+ W Y +K E +L + + LP+AV R +I++ + + + M
Sbjct: 241 VDGGWAGGYGTSKWAGEVLLREANDLCALPVAVFRCGMILADTSYAGQLNMSDWVT--RM 298
Query: 59 LVG-IATGVL-------HTHLINLNTVTDMVP-STVSDGPSEGVWQKKFPTSVFRPDPIP 109
++ +ATG+ + D +P + V++ + + +
Sbjct: 299 VLSLMATGIAPRSFYEPDSEGNRQRAHFDGLPVTFVAEAIAVLGAR----VAGSSLAGFA 354
Query: 110 IYNFVGSARNPISWGKL-DELATVCHPI 136
Y+ + + I + D L +PI
Sbjct: 355 TYHVMNPHDDGIGLDEYVDWLIEAGYPI 382
>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 = 40.0 bits (93), Expect = 7e-04
Identities = 35/227 (15%), Positives = 62/227 (27%), Gaps = 83/227 (36%)
Query: 39 STYREPVRGWIDNVYGPIGMLVGIATGVLHTHLINLNTVTDMVPSTVSDGPSEGVWQKKF 98
TY V I L L T + G + W
Sbjct: 178 QTYHVLVGDLIKFS---------------AETLSELIRTTLDAEKVFTQGLNILEW---- 218
Query: 99 PTSVFRPDPIPIYNFVGSARNPISWGKLDELATVCHPIWPTIRAIWYFSFIPASNKYTYY 158
+ P P +++ S PIS L + + H Y
Sbjct: 219 ---LENPSNTPDKDYLLSI--PISC-PLIGVIQLAH----------------------YV 250
Query: 159 ILSFFLHTIPGFILDSLASLSGR-KPMLMAIYKKIDKASDTLEYFAHRQWVWTDHNVQAL 217
+ + L PG + L +G + ++ A+ +D+ E F +A+
Sbjct: 251 VTAKLLGFTPGELRSYLKGATGHSQGLVTAV---AIAETDSWESF-------FVSVRKAI 300
Query: 218 FNKLDPEDQELFFFDMGQMKWEYYAEAMGLGLRVYLVHDDIHTLPAA 264
+ FF +G+R Y + + +LP +
Sbjct: 301 ---------TVLFF---------------IGVRCYEAYPNT-SLPPS 322
Score = 38.5 bits (89), Expect = 0.002
Identities = 48/309 (15%), Positives = 89/309 (28%), Gaps = 109/309 (35%)
Query: 32 LRPAVIVSTYREPVRGWIDNVYGPIGMLVGIATGVLHTHLINLNTVTDMVPSTVSDGPSE 91
RP + +G + ++ + T L + + + P+E
Sbjct: 6 TRPLTLS--------------HGSLEHVLLVPTA-SFFIASQLQ---EQFNKILPE-PTE 46
Query: 92 GVWQKKFPTSVFRPDPIPIY----NFVGSARNPISWGKLDELATVCHPIWPTIRAIWYF- 146
G PT+ P + +V S P G+ D++ + + F
Sbjct: 47 GFAADDEPTT-----PAELVGKFLGYVSSLVEPSKVGQFDQVLNL---------CLTEFE 92
Query: 147 -SFIPASNKYTYYILSFFLHTIPGFILDSLASLSGRKPMLMAIYKKIDKASDTLEYFAHR 205
++ ++ +H + A L + K++ K Y R
Sbjct: 93 NCYLEGND----------IHAL-------AAKLLQENDTTLVKTKELIKN-----YITAR 130
Query: 206 QWV---WTDHNVQALFNKLDPEDQELF-FFDMGQ-MKWEYYAEAMGLGLR----VY--LV 254
+ + ALF + + +L F GQ +Y+ E LR Y LV
Sbjct: 131 IMAKRPFDKKSNSALFRAVGEGNAQLVAIFG-GQGNTDDYFEE-----LRDLYQTYHVLV 184
Query: 255 HDDIHTL-----------PAARKKYQR-----------------LYIAHCALKIFCGLLL 286
D I A K + + Y+ I C L+
Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIP--ISCPLIG 242
Query: 287 LV-FLLYIV 294
++ Y+V
Sbjct: 243 VIQLAHYVV 251
>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 = 36.8 bits (84), Expect = 0.009
Identities = 47/305 (15%), Positives = 85/305 (27%), Gaps = 79/305 (25%)
Query: 24 GKG-LPLAVLRPAVIVSTYREPVRGWID--NVYGPIGMLVGIATGVLHTHLINLNTVTDM 80
GK + L V + + W++ N P +L L L D
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIF-WLNLKNCNSPETVL---------EMLQKLLYQIDP 211
Query: 81 VPSTVSDGPSEGVWQKKFPTSVFRPDPIPIYNFVGSARNPISWGKLDELATVCHP-IWP- 138
++ SD S + + R + S L L V + W
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELR-------RLLKSKPYENC---LLVLLNVQNAKAWNA 261
Query: 139 ---------TIRAIWYFSFIPASNKYTYYILSFFLHTIPGFILDSLASLSGRK------- 182
T R F+ A T+ L H D + SL +
Sbjct: 262 FNLSCKILLTTRFKQVTDFLSA-ATTTHISLD---HHSMTLTPDEVKSLLLKYLDCRPQD 317
Query: 183 ---------PMLMA-IYKKIDKASDTLEYFAHRQWVWTDHNVQALFNKLDPEDQELFFFD 232
P ++ I + I T + + H +++ N L+P + F
Sbjct: 318 LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377
Query: 233 MG-------------QMKWEY--YAEAMGLGLRVYLVHDDIH--TLPAARKKYQRLYIAH 275
+ + W ++ M +V + +H +L + K + I
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVM-------VVVNKLHKYSLVEKQPKESTISIPS 430
Query: 276 CALKI 280
L++
Sbjct: 431 IYLEL 435
Score = 29.8 bits (66), Expect = 1.3
Identities = 42/284 (14%), Positives = 70/284 (24%), Gaps = 91/284 (32%)
Query: 11 FTKALAEDVLCKEGKGLPLAVLRPAVIVSTYREPVRGWIDNVYGPIGMLVGIATGVLHTH 70
F A ++ CK+ + +P ++L I + L+
Sbjct: 25 FEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDA--VSGTLRLFWTLL---------- 72
Query: 71 LINLNTVTDMVPSTVSDGPSEGVWQKKFPTSVFRPDPIPIYNFVGSA-----RNPISWGK 125
E V +KF V R + Y F+ S R P +
Sbjct: 73 ----------------SKQEEMV--QKFVEEVLRIN----YKFLMSPIKTEQRQPSMMTR 110
Query: 126 L-----DELATVCHPIWP----------TIRAIWYFSFIPASNKYTYYILSFFLHTIPGF 170
+ D L +R PA N + + G
Sbjct: 111 MYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ-ALLELRPAKN--------VLIDGVLGS 161
Query: 171 -----ILDSLASLSGRKPMLMAIY----KKIDKASDTLEYFAHRQWVWTDHNVQALFNKL 221
LD S + M I+ K + LE +Q L ++
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE------------MLQKLLYQI 209
Query: 222 DPEDQELFFFDMG---QMKWEYYAEAMGLGLRVY----LVHDDI 258
DP ++ L + Y LV ++
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV 253
>2x4g_A Nucleoside-diphosphate-sugar epimerase; isomerase; 2.65A
{Pseudomonas aeruginosa}
Length = 342
Score = 30.7 bits (70), Expect = 0.55
Identities = 6/33 (18%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 7 NTYTFTKALAED-VLCKEGKGLPLAVLRPAVIV 38
++Y K ++ + GLP+ + P +++
Sbjct: 153 SSYVLCKWALDEQAREQARNGLPVVIGIPGMVL 185
>3oxp_A Phosphotransferase enzyme II, A component; structural genomics,
center for structural genomics of infec diseases, csgid,
pestis CO92; HET: GOL; 1.20A {Yersinia pestis}
Length = 150
Score = 28.8 bits (65), Expect = 1.2
Identities = 8/51 (15%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 30 AVLRPAVIVSTYREPVRGWIDNVYGPIGMLVGIATGVLHTHLINLNTVTDM 80
V R ++ ++ E V + P+ +L+ +A ++H+ ++ + +
Sbjct: 75 GVNRLSLALTVITEGVT-FNAEGNDPVKLLIVLAATDSNSHIEAISQLAQL 124
>1xty_A PTH, peptidyl-tRNA hydrolase; mixed beta sheet; 1.80A {Pyrococcus
abyssi}
Length = 120
Score = 27.9 bits (62), Expect = 2.0
Identities = 9/75 (12%), Positives = 20/75 (26%), Gaps = 12/75 (16%)
Query: 186 MAIYKKIDKASDTLEYFAHRQWVWTDHNVQALFNKLDPEDQELFFFDMGQMKWEYYAEAM 245
+ + I +++ +W H Q E+ +A
Sbjct: 28 VTLVVSIINSNNLRWKEWLNEW---LHQGQPKIIVKVNSLDEII---------SRAKKAE 75
Query: 246 GLGLRVYLVHDDIHT 260
+ L ++ D T
Sbjct: 76 TMNLPFSIIEDAGKT 90
>3sxp_A ADP-L-glycero-D-mannoheptose-6-epimerase; rossman fold, NAD
binding, isomerase; HET: NAD; 2.55A {Helicobacter
pylori}
Length = 362
Score = 28.8 bits (65), Expect = 2.1
Identities = 11/49 (22%), Positives = 15/49 (30%), Gaps = 15/49 (30%)
Query: 7 NTYTFTKALAEDVLCKEGKGLPLAVLRPAVIVSTYREPVRGWIDNVYGP 55
N Y F+K ++ + LR NVYGP
Sbjct: 159 NVYGFSKLCMDEFVLSHSNDNVQVGLRYF---------------NVYGP 192
>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote
initiative, RSGI, structural genomics, hydrolase; HET:
GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8
d.52.3.1
Length = 301
Score = 28.6 bits (65), Expect = 2.5
Identities = 15/78 (19%), Positives = 23/78 (29%), Gaps = 22/78 (28%)
Query: 170 FILDSLASLSGRKPMLMAIYKKIDKASDTLEYFAHRQWVW-----------TDHNVQALF 218
+ +L L G+ P+L+ K+D A E + + V L
Sbjct: 106 LVARALKPLVGKVPILLVG-NKLDAAKYPEEAMKAYHELLPEAEPRMLSALDERQVAELK 164
Query: 219 NKLD----------PEDQ 226
L PED
Sbjct: 165 ADLLALMPEGPFFYPEDY 182
>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 = 27.6 bits (60), Expect = 3.6
Identities = 5/16 (31%), Positives = 7/16 (43%), Gaps = 2/16 (12%)
Query: 96 KKFPTSV--FRPDPIP 109
KK S+ + D P
Sbjct: 23 KKLQASLKLYADDSAP 38
>3d00_A Tungsten formylmethanofuran dehydrogenase subunit; FWDE/GAPDH
domain-like fold, structural genomics, joint CENT
structural genomics; HET: MSE; 1.90A {Syntrophus
aciditrophicus}
Length = 191
Score = 26.9 bits (59), Expect = 6.1
Identities = 11/44 (25%), Positives = 18/44 (40%)
Query: 228 LFFFDMGQMKWEYYAEAMGLGLRVYLVHDDIHTLPAARKKYQRL 271
L MG Y + G G+RV+L + + R + +L
Sbjct: 77 LTVLPMGLFAVSLYDKFTGEGVRVFLDVEKMGPWQEIRNWFLKL 120
>1a3a_A Mannitol-specific EII; phosphoenolpyruvate dependent
phosphotransferase system, IIA histidine
phosphorylation, phosphotransferase; 1.80A {Escherichia
coli} SCOP: d.112.1.1 PDB: 1j6t_A 2few_A*
Length = 148
Score = 26.4 bits (59), Expect = 7.1
Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 23 EGKGLPLA-------VLRPAVIVSTYREPVRGWIDNVYGPIGMLVGIATGVLHTHLINLN 75
E +P VL+ V+ Y E VR + + +++GIA + H+ +
Sbjct: 59 ESIAVPHGTVEAKDRVLKTGVVFCQYPEGVR-FGEEEDDIARLVIGIA-ARNNEHIQVIT 116
Query: 76 TVTDM 80
++T+
Sbjct: 117 SLTNA 121
>1rxt_A Myristoyl-, glycylpeptide N-tetradecanoyltransferase 1; alpha-beta
structure, unique N-myristoyltransferase fold; 3.00A
{Homo sapiens} SCOP: d.108.1.2 d.108.1.2
Length = 496
Score = 27.0 bits (59), Expect = 9.5
Identities = 20/128 (15%), Positives = 38/128 (29%), Gaps = 24/128 (18%)
Query: 91 EGVWQKKFPTSVFRPDPIPIYNFVGSARNPISWGKLDELATVCHPIWPTIRAIWYFSFIP 150
EG++Q + V P P+ + ++ KL E+ FS +
Sbjct: 274 EGIFQAVYTAGVVLPKPVGTCRYWHR---SLNPRKLIEVK---------------FSHLS 315
Query: 151 ASNKYTYYILSFFLHTIP---GFILDSLASLSGRKPMLMAIYKKIDKASD-TLEYFAHRQ 206
+ + + L P G + +L K+ + E H
Sbjct: 316 RNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEH-- 373
Query: 207 WVWTDHNV 214
W + N+
Sbjct: 374 WFYPQENI 381
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
0.326 0.142 0.462
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,926,366
Number of extensions: 297794
Number of successful extensions: 749
Number of sequences better than 10.0: 1
Number of HSP's gapped: 743
Number of HSP's successfully gapped: 20
Length of query: 300
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 207
Effective length of database: 4,105,140
Effective search space: 849763980
Effective search space used: 849763980
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 (21.6 bits)
S2: 57 (26.0 bits)