RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3766
(470 letters)
>2isb_A Fumarase, FUM-1; NP_069927.1, fumarase of FUM-1, structural
genomics, PSI-2, structure initiative, joint center for
structural genomics; HET: MSE; 1.66A {Archaeoglobus
fulgidus} SCOP: c.8.9.1
Length = 192
Score = 199 bits (507), Expect = 5e-62
Identities = 64/175 (36%), Positives = 106/175 (60%), Gaps = 5/175 (2%)
Query: 281 VNLNT-LTKKEVSSWRSGEILLLNGKILTGRDAAHNRIQYMLSKGEKIPVNFNNRVIYYV 339
L T L K ++ + G+++ + G+I T RD AH R + +G+++P +F+ V+Y+
Sbjct: 17 YELRTPLVKDQILKLKVGDVVYITGEIFTARDEAHARALEWMEEGKELPFSFDKGVVYHC 76
Query: 340 GPINPVRNE-VIGPAGPTTASRMDHFTNLILEKIGLIAMIGKAERSDKIIKLIKKQKIAY 398
GP+ +E + AGPTT++RM+ FT ILEK+ + +IGK S+++++ ++ K AY
Sbjct: 77 GPLVKKNDEWRVVSAGPTTSARMNPFTPKILEKVECMGIIGKGGMSEEVVEAMRG-KAAY 135
Query: 399 LVAVGGAAYLISKAIKSAKIICFEDLGM-EAIYEFNVENM-PVTVAIDSLGKSIH 451
GGA L + +IK K + +EDLGM EA++ VE P VAID+ G S++
Sbjct: 136 FAFTGGAGALAAMSIKKVKGVVWEDLGMPEAVWLLEVERFGPCIVAIDAHGNSLY 190
>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 = 50.6 bits (120), Expect = 8e-07
Identities = 54/428 (12%), Positives = 118/428 (27%), Gaps = 104/428 (24%)
Query: 66 YTNPNNILRASIVSDPHFIR----KNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKT 121
Y +IL V + F+ K+ QD ++++ E +I + + T
Sbjct: 16 YQY-KDILS---VFEDAFVDNFDCKDVQDMPKSILSKE-------EIDHIIMSKDAVSGT 64
Query: 122 KF---AMLNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINM 178
+L+ + +V ++ V + + I + M + ++ + N
Sbjct: 65 LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY--ND 122
Query: 179 NSIIKNGP---KNKIEELRLELFNKINSLGIGAQGMGG-------LSTVLDVKI---MMY 225
N + +LR L + + G+ G L L K+ M +
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182
Query: 226 PTH-----AASKPVAIIPNCAATRHGHIILNG-SGPVFMKPPSLS-NWPKIKFTTNNKKF 278
+ P ++ + I N S L + + + K
Sbjct: 183 KIFWLNLKNCNSPETVLEMLQKLLY-QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241
Query: 279 HYVN-LNTLTKKEVSSWRSGEILLLNGKIL-TGRDAAHNRIQYMLSKGEKIPVNFNNRVI 336
Y N L L V + ++ L+ KIL T R V
Sbjct: 242 PYENCLLVL--LNVQNAKAWNAFNLSCKILLTTRFKQ---------------------VT 278
Query: 337 YYVGPINPVRNEVIGPAGP-TTASRMDHFTNLILEKIG------------LIAMIGKAER 383
++ + + T + + +++I ++ R
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR 338
Query: 384 SDKII----------KLIKKQKIAYLVAVGGAAYLISKAIKSAKIICFEDLGMEAIYEFN 433
KL + + L + F+ L +++ +
Sbjct: 339 DGLATWDNWKHVNCDKLTTIIESSL-------NVLEPAEYRK----MFDRL---SVFPPS 384
Query: 434 VENMPVTV 441
++P +
Sbjct: 385 A-HIPTIL 391
Score = 45.2 bits (106), Expect = 5e-05
Identities = 31/186 (16%), Positives = 66/186 (35%), Gaps = 36/186 (19%)
Query: 269 IKFTTNNKKFHYVN-LNTLTKKEVSSWRSGEILLLNGKILTGRDAAH--------NRIQY 319
+ F T ++ Y + L+ V ++ ++ + IL+ + H +
Sbjct: 7 MDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR 66
Query: 320 M----LSKGEKIPVNFNNRVIY--YVGPINPVRNEVIGPAGPTTA-----SRMDHFTNLI 368
+ LSK E++ F V+ Y ++P++ E P+ T R+ + N +
Sbjct: 67 LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL-YNDNQV 125
Query: 369 LEKIGLIAMIGKAERSDKIIKLIKK----QKIAYLVAVG----GAAYLISKAIKSAKIIC 420
K + R +KL + + ++ G G ++ S K+ C
Sbjct: 126 FAKYNV-------SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQC 178
Query: 421 FEDLGM 426
D +
Sbjct: 179 KMDFKI 184
>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 = 37.0 bits (85), Expect = 0.014
Identities = 49/280 (17%), Positives = 85/280 (30%), Gaps = 117/280 (41%)
Query: 207 GAQ--GMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRH-----GHIILNGSGPVFMK 259
G+Q GMG +D +Y T A++ V A H G IL+ V
Sbjct: 1625 GSQEQGMG-----MD----LYKTSKAAQDVWN----RADNHFKDTYGFSILD---IVINN 1668
Query: 260 PPSLS-------------NWPKIKFTTNN-------KKFHYVNLNT-------------L 286
P +L+ N+ + F T K F +N ++
Sbjct: 1669 PVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSA 1728
Query: 287 TKK--------EVSSWR-----------------S-GEI--LLLNGKILTGRDAA---HN 315
T+ E +++ S GE L +++
Sbjct: 1729 TQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFY 1788
Query: 316 R---IQYMLSKGEKIPVNFNNRVIYYVGPINPVRNEVIGPAGPTTASRMDHFTNLILEKI 372
R +Q + + E R Y + INP R + + A + + + ++
Sbjct: 1789 RGMTMQVAVPRDE------LGRSNYGMIAINPGR---VAASFSQEA--LQYVVERVGKRT 1837
Query: 373 GLIAMI-------------G--KA-ERSDKIIKLIKKQKI 396
G + I G +A + ++ IK QKI
Sbjct: 1838 GWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKI 1877
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 33.7 bits (77), Expect = 0.14
Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 16/62 (25%)
Query: 205 GIGAQGMGGLSTVLDVKIMMYPTHAASKPV-------AIIPNCAATRHGHI-ILNGS-GP 255
GMGG+S + M+ +PV + I +A +L S GP
Sbjct: 1046 NCSGSGMGGVSALRG----MFKDRFKDEPVQNDILQESFINTMSA---WVNMLLISSSGP 1098
Query: 256 VF 257
+
Sbjct: 1099 IK 1100
Score = 27.9 bits (62), Expect = 8.6
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 130 DSLVDWIMKTVPTMGAGWCP 149
++L+++I T G GW
Sbjct: 547 EALIEFIYDTEKNGGLGWDL 566
>4fbw_A DNA repair protein RAD32; DNA double-strand break repair, nuclease,
hydrolase; HET: DNA; 2.20A {Schizosaccharomyces pombe}
PDB: 4fcx_B*
Length = 417
Score = 29.1 bits (64), Expect = 3.8
Identities = 22/138 (15%), Positives = 52/138 (37%), Gaps = 9/138 (6%)
Query: 329 VNFNNRVIYYVGPINPVRNEVIGPAGPTTASRMDHFTNLILEKIGLIAMIGKAERSDKI- 387
+N+ + I P+ + P+G S +D IL+ GL+ G+ +D I
Sbjct: 110 INYLDPNINVAIPVFSIHGNHDDPSGDGRYSALD-----ILQVTGLVNYFGRVPENDNIV 164
Query: 388 IKLIKKQKIAYLVAVGGAAYLISKAIKSA---KIICFEDLGMEAIYEFNVENMPVTVAID 444
+ I QK +A+ G + + + + + + F + FN+ + +
Sbjct: 165 VSPILLQKGFTKLALYGISNVRDERLYHSFRENKVKFLRPDLYRDEWFNLLTVHQNHSAH 224
Query: 445 SLGKSIHIDGPKKWKKYI 462
+ + + + ++
Sbjct: 225 TPTSYLPESFIQDFYDFV 242
>1zzo_A RV1677; thioredoxin fold, structural genomics, PSI, protein
structure initiative, TB structural genomics consortium,
TBSGC; 1.60A {Mycobacterium tuberculosis} SCOP:
c.47.1.10 PDB: 3ios_A
Length = 136
Score = 27.6 bits (62), Expect = 4.4
Identities = 7/43 (16%), Positives = 12/43 (27%), Gaps = 3/43 (6%)
Query: 423 DLGMEAIYEFNVENMPVTVAIDSLGKSIHIDGP---KKWKKYI 462
D F V P +D G + G + + +
Sbjct: 88 DTDGSVWANFGVTQQPAYAFVDPHGNVDVVRGRMSQDELTRRV 130
>3djc_A Type III pantothenate kinase; structural genomics, putative
transfera 2, protein structure initiative; 2.40A
{Legionella pneumophila subsp}
Length = 266
Score = 28.4 bits (64), Expect = 4.5
Identities = 13/71 (18%), Positives = 22/71 (30%), Gaps = 15/71 (21%)
Query: 373 GLIAMIGKAERSDKIIKLIKKQ----KIAYLVAVGGAAYLISKAIKSAKIICFEDL---G 425
G++ ++I+ I + ++A GG A L K DL G
Sbjct: 197 GVLGAC------KELIQRIHHEAFNGDQILILATGGFASLFDKQGL--YDHLVPDLVLQG 248
Query: 426 MEAIYEFNVEN 436
+ N
Sbjct: 249 IRLAAMMNTAE 259
>3vpi_A Type VI secretion exported 1; hydrolase; HET: MSE; 1.50A
{Pseudomonas aeruginosa} PDB: 3vpj_A
Length = 174
Score = 27.9 bits (61), Expect = 4.7
Identities = 7/34 (20%), Positives = 15/34 (44%)
Query: 236 IIPNCAATRHGHIILNGSGPVFMKPPSLSNWPKI 269
+I +GH+ + SGP++ + + I
Sbjct: 100 VIAGLKGRTYGHVAVVISGPLYRQKYPMCWCGSI 133
>2q3l_A Uncharacterized protein; SPOIIAA-like fold, structural genomics,
joint center for STR genomics, JCSG, protein structure
initiative; HET: MSE; 2.25A {Shewanella loihica pv-4}
SCOP: c.13.2.2
Length = 126
Score = 27.6 bits (61), Expect = 4.7
Identities = 5/46 (10%), Positives = 14/46 (30%)
Query: 40 KIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSDPHFIR 85
+I + +G + ++ G + R +I+
Sbjct: 53 EIVALIDITELDGLSLHAAWDDLKLGLKHGKEFKRVAIIGQGELQE 98
>2qv6_A MJ0145, GTP cyclohydrolase III, MJGC; enzyme, FAPY; HET: GTP; 2.00A
{Methanocaldococcus jannaschii}
Length = 268
Score = 28.1 bits (62), Expect = 6.9
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 154 GIGIGGTPEKAMLMAKKVL 172
GIGIG T E A +A L
Sbjct: 215 GIGIGRTAEDASNLADIGL 233
>3erw_A Sporulation thiol-disulfide oxidoreductase A; thioredoxin-like
fold, RESA-like fold, dithiol, STOA, redox-active
center; 2.50A {Bacillus subtilis}
Length = 145
Score = 26.9 bits (60), Expect = 8.0
Identities = 8/74 (10%), Positives = 26/74 (35%), Gaps = 20/74 (27%)
Query: 375 IAMIGKAERSDKIIKLIKKQKIAYLVAVGGAAYLISKAIKSAKIICFEDLGMEAIYEFNV 434
+ ++ + + IK K+ + + + D E + E+++
Sbjct: 73 VNLVNSEQNQQVVEDFIKANKLTFPIVL--------------------DSKGELMKEYHI 112
Query: 435 ENMPVTVAIDSLGK 448
+P + ++ G+
Sbjct: 113 ITIPTSFLLNEKGE 126
>2o3i_A Hypothetical protein; NESG, CVR68, Q7NTB2, structural genomics,
PSI-2, protein structure initiative; 2.30A
{Chromobacterium violaceum} SCOP: e.73.1.1
Length = 405
Score = 27.8 bits (61), Expect = 9.6
Identities = 8/32 (25%), Positives = 11/32 (34%)
Query: 152 ILGIGIGGTPEKAMLMAKKVLMQDINMNSIIK 183
G G GGT A +A D ++
Sbjct: 19 FFGSGGGGTMISARHLAANFRKGDYYPTDKVR 50
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
0.319 0.137 0.401
Gapped
Lambda K H
0.267 0.0450 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,314,960
Number of extensions: 467025
Number of successful extensions: 1001
Number of sequences better than 10.0: 1
Number of HSP's gapped: 995
Number of HSP's successfully gapped: 25
Length of query: 470
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 373
Effective length of database: 3,993,456
Effective search space: 1489559088
Effective search space used: 1489559088
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.2 bits)