RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16812
(359 letters)
>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 = 39.1 bits (90), Expect = 0.003
Identities = 58/387 (14%), Positives = 105/387 (27%), Gaps = 148/387 (38%)
Query: 22 RLWSHHSYKAKWPMRLLL--------AIFQTIGIQYSILNWVRDHRLHHKYTDTDADPHN 73
RL Y+ LL + + IL R ++ TD
Sbjct: 236 RLLKSKPYE-----NCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQV------TDFLSAA 284
Query: 74 STRGFFFSHIGWSLILPHPEVTEKV--KVIDTS--DVEKDWVVVWQYKNINPTENLFVSV 129
+T H +L P+ + + K +D D+ + + NP +S+
Sbjct: 285 TTTHISLDHHSMTL---TPDEVKSLLLKYLDCRPQDLPR------EVLTTNP---RRLSI 332
Query: 130 --ASFGDG---WHNYHHVF----------------PWDYKNAELWNYK----F----NIS 160
S DG W N+ HV P +Y+ + F +I
Sbjct: 333 IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK----MFDRLSVFPPSAHIP 388
Query: 161 TAFVDLCALIGWAYDLKTVPTDMIQKR-----VARTGDGSHHHHHDGGTSFLRFRLYAPF 215
T L + W +K+ ++ K V + S +L ++
Sbjct: 389 TIL--LSLI--WFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI---YLELKV---- 437
Query: 216 AVFLCYILPTWVPWYFWGEDLWVAHCVATQLRHVITLHGTFLINSVAHMWGNKPYDKNIN 275
+L + LH + V H K +D +
Sbjct: 438 -----------------------------KLENEYALHRSI----VDHYNIPKTFDSDDL 464
Query: 276 PTENLFVSVASFGDG-WHNY--HHVFPWDYKNAELWNYKFNISTAFVDLCALIGWAYDLK 332
L D ++++ HH+ KN E F+D +
Sbjct: 465 IPPYL--------DQYFYSHIGHHL-----KNIEHPERMTLFRMVFLDF----RF----- 502
Query: 333 TVPTDMIQKRVARTGMFTNVKKSNGNV 359
+++++ N S N
Sbjct: 503 ------LEQKIRHDSTAWNASGSILNT 523
Score = 28.3 bits (62), Expect = 4.6
Identities = 42/310 (13%), Positives = 78/310 (25%), Gaps = 102/310 (32%)
Query: 61 HHKYTDTDADPHNSTRGFFFSHIGWSLILPH--PEVTEKVKVIDTSDVEKDWVVVWQYKN 118
HH + D + H + IL + D D+ K + + +
Sbjct: 3 HHHHMDFETGEH---------QYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDH 53
Query: 119 I----NPTENLFVSVASFGDGWHNYHHVFPWDYKNAELWNYKFNISTAFVDLCALIGWAY 174
I + + F + NYKF L + I
Sbjct: 54 IIMSKDAVSGTLRLFWTLLSKQEEMVQKF---VEEVLRINYKF--------LMSPIKTEQ 102
Query: 175 DLKTVPTDMIQKRVARTGDGSHHHHHDGGTSFLRFRLYAPFAVFLCYILPTWVPWYFWGE 234
++ T M ++ R ++D +++A + V +
Sbjct: 103 RQPSMMTRMYIEQRDRL-------YNDN-------QVFAKYNV--------SRL-----Q 135
Query: 235 DLWVAHCVATQLRHV--ITLHG------TFLINSVA-------HM-----W---GNKPYD 271
+LR + + G T++ V M W N
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195
Query: 272 KNI-NPTENLFVSV----ASFGDGWHNY------------HHVFPWDYKNA-----ELWN 309
+ + + L + S D N + Y+N + N
Sbjct: 196 ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN 255
Query: 310 YK----FNIS 315
K FN+S
Sbjct: 256 AKAWNAFNLS 265
>2x8s_A Endo-alpha-1,5-L-arabinanase; hydrolase; HET: AHR; 1.50A {Bacillus
subtilis} PDB: 2x8f_A 2x8t_A 3lv4_A
Length = 470
Score = 31.9 bits (72), Expect = 0.37
Identities = 10/102 (9%), Positives = 29/102 (28%)
Query: 78 FFFSHIGWSLILPHPEVTEKVKVIDTSDVEKDWVVVWQYKNINPTENLFVSVASFGDGWH 137
F + GW + P+ E +K + D+ + ++ K+I+ +++ +
Sbjct: 352 LFMNKDGWPVAAPYRYAGETLKEVKQKDITGTYKLIQHGKDISADIKQTINIQLNKNHTI 411
Query: 138 NYHHVFPWDYKNAELWNYKFNISTAFVDLCALIGWAYDLKTV 179
+ W + + +
Sbjct: 412 SGEMTGTWRKTGKNTADITLAGKKYNGVFLRQWDSVREKNVM 453
>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate
synthase, structural genomics, PSI, protein structure
initiative, nysgrc; 1.90A {Corynebacterium glutamicum}
PDB: 3q2q_A*
Length = 360
Score = 31.1 bits (71), Expect = 0.60
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 188 VARTGDGSHHHHH 200
V R G+G HHHHH
Sbjct: 348 VKRVGEGHHHHHH 360
>2kcd_A Uncharacterized protein SSP0047; alpha beta, structural genomics,
unknown function, PSI-2, protein structure initiative;
NMR {Staphylococcus saprophyticus subsp}
Length = 120
Score = 28.9 bits (64), Expect = 1.0
Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 7/87 (8%)
Query: 115 QYKNINPTENLFVSVASFGDGWHNYHHVFPW-DYKNAELWNYKFNISTAFVDLCALIGWA 173
QY + P N + ++ + +++P+ Y +L I+ F+D + +
Sbjct: 39 QYVRLGPLSNKILQTNTYYSDTLHKSNIYPFILYYQKQL------IAIGFIDENHDMDFL 92
Query: 174 YDLKTVPTDMIQKRVARTGDGSHHHHH 200
Y TV + Q+ + G HHHHH
Sbjct: 93 YLHNTVMPLLDQRYLLTGGQLEHHHHH 119
>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 = 29.5 bits (66), Expect = 2.2
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 148 KNAELWNYKFNISTAFVDLCALIGWAYD 175
K + L FN + D+ ALI + YD
Sbjct: 529 KGSTLIVVPFNQG-SKQDVEALIEFIYD 555
Score = 29.5 bits (66), Expect = 2.2
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 303 KNAELWNYKFNISTAFVDLCALIGWAYD 330
K + L FN + D+ ALI + YD
Sbjct: 529 KGSTLIVVPFNQG-SKQDVEALIEFIYD 555
>2fgx_A Putative thioredoxin; NET3, NESG, GFT-glutaredoxin-like, structural
genomics, PSI, protein structure initiative; NMR
{Nitrosomonas europaea}
Length = 107
Score = 27.4 bits (61), Expect = 2.8
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 192 GDGSHHHHHDGGTSFLRFR 210
G HHHHH G L F+
Sbjct: 2 GTSHHHHHHSSGRENLYFQ 20
>3fdu_A Putative enoyl-COA hydratase/isomerase; structural genomics, PSI-2;
2.00A {Acinetobacter baumannii}
Length = 266
Score = 28.7 bits (65), Expect = 2.9
Identities = 9/18 (50%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 184 IQKRVAR-TGDGSHHHHH 200
+QKR + +G HHHHH
Sbjct: 249 MQKRQPDFSQEGHHHHHH 266
>2jyl_A Capsid protein P24 (Ca); HIV-1, carboxy-terminal, dimerization
domain, CTD, 3D- NMR, capsid protein (Ca), double
mutant; NMR {Human immunodeficiency virus 1} PDB:
2k1c_A* 2l6e_A*
Length = 105
Score = 26.8 bits (59), Expect = 4.8
Identities = 9/27 (33%), Positives = 11/27 (40%), Gaps = 3/27 (11%)
Query: 192 GDGSHHHHHDGGTSFLRFRLYAPFAVF 218
G HHHHH G L R ++
Sbjct: 2 GSSHHHHHHSSG---LVPRGSHMTSIL 25
>2a1v_A Conserved hypothetical protein; structural genomics, PSI, protein
structure initiative; 2.15A {Deinococcus radiodurans}
SCOP: d.198.3.1
Length = 144
Score = 27.2 bits (60), Expect = 5.4
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 142 VFPWDYKNAELWN-YKFNISTAFVDLCALIGWAYDL--KTVPTDMIQKRVAR---TGDGS 195
+ P + N + W + + L L+ +Y L K T +K + GS
Sbjct: 79 IAPGYHLNKKHWVTVTLDGTVPAELLGELLRGSYLLVTKKGFTKAERKELGLPDSLEGGS 138
Query: 196 HHHHH 200
HHHHH
Sbjct: 139 HHHHH 143
>3na5_A Phosphoglucomutase; isomerase, metal binding; HET: BTB; 1.70A
{Salmonella enterica subsp} PDB: 3olp_A 2fuv_A*
Length = 570
Score = 27.7 bits (62), Expect = 7.2
Identities = 8/17 (47%), Positives = 8/17 (47%)
Query: 196 HHHHHDGGTSFLRFRLY 212
HHHHH G LY
Sbjct: 3 HHHHHSSGVDLGTENLY 19
>1o63_A ATP phosphoribosyltransferase; structural genomics; 2.00A
{Thermotoga maritima} SCOP: c.94.1.1 PDB: 1o64_A 1usy_E*
1usy_H*
Length = 219
Score = 26.8 bits (60), Expect = 8.7
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 185 QKRVARTGDGSHHHHH 200
+R GSHHHHH
Sbjct: 203 SNEQSRGEGGSHHHHH 218
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
0.325 0.138 0.482
Gapped
Lambda K H
0.267 0.0548 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,131,181
Number of extensions: 372436
Number of successful extensions: 3039
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3030
Number of HSP's successfully gapped: 37
Length of query: 359
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 264
Effective length of database: 4,049,298
Effective search space: 1069014672
Effective search space used: 1069014672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.5 bits)