RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2895
(293 letters)
>3t7v_A Methylornithine synthase PYLB; TIM-barrel fold, mutase,
[4Fe-4S]-cluster, SAM, lysine, transferase; HET: SAM
MD0; 1.50A {Methanosarcina barkeri}
Length = 350
Score = 68.8 bits (169), Expect = 2e-13
Identities = 39/197 (19%), Positives = 77/197 (39%), Gaps = 14/197 (7%)
Query: 55 ECFGRGVATFMIM--GSICTRRCKFCNISHGRPDP---LDIEEPKKIAYTINKLKLNYVV 109
FG V + + C +C FC + L +EE K+ T+ + V
Sbjct: 53 HYFGNRVFLNCFIYFSTYCKNQCSFCYYNCRNEINRYRLTMEEIKETCKTLKGAGFHMVD 112
Query: 110 ITSVNRDDLHDGGSSHFVSCIKHIRKLSTKIKIEILIPDFRNQINHVLKIFKQALPDVLN 169
+T D + + FV ++ +++ + I I N L ++ + L
Sbjct: 113 LTM-GEDPYYYEDPNRFVELVQIVKE-ELGLPIMISPGLMDN---ATLLKAREKGANFLA 167
Query: 170 HNIET-VPRLYKKVRPGSDYKHSLNLLKNFKKLYPNILTKSGIMVGLGENDEEILTVIHD 228
ET LY+K+R G + +N + K+ + GI+ G+G + E + +
Sbjct: 168 LYQETYDTELYRKLRVGQSFDGRVNARRFAKQQ--GYCVEDGILTGVGNDIESTILSLRG 225
Query: 229 MRNHNIDILTIGQYLMP 245
M ++ D++ + +P
Sbjct: 226 MSTNDPDMVRVMT-FLP 241
>3iix_A Biotin synthetase, putative; adoMet radical, SAM radical, adoMet
cleavage, Fe4S4 cluster, HYDE, hydrogenase, maturation,
beta barrel; HET: OTY CSO 5AD CPS; 1.25A {Thermotoga
maritima} PDB: 3ciw_A* 3iiz_A* 3cix_A*
Length = 348
Score = 56.9 bits (137), Expect = 2e-09
Identities = 49/271 (18%), Positives = 104/271 (38%), Gaps = 34/271 (12%)
Query: 9 IEILKKPNWIRVKLISNIDNFNKTKN--ILRANNLVTVCEEASCPNIGECFGRGVATFMI 66
+E L++ + R L + ++ N + + + + + G V I
Sbjct: 7 LEKLERREFTREVLKEALSINDRGFNEALFKLADEIRR----------KYVGDEVHIRAI 56
Query: 67 MGSI---CTRRCKFCNISHGRPD----PLDIEEPKKIAYTINKLKLNYVVITSVNRDDLH 119
+ C + C +C + + + EE + A + +V+ S
Sbjct: 57 I-EFSNVCRKNCLYCGLRRDNKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYXM 115
Query: 120 DGGSSHFVSCIKHIRKLSTKIKIEILIPDFRNQINHVLKIFKQALPDVLNHNIETV-PRL 178
+K I+K+ + + + + +K+A D ET P L
Sbjct: 116 P---DVISDIVKEIKKMGVAVTLSLGEWPREY-----YEKWKEAGADRYLLRHETANPVL 167
Query: 179 YKKVRPGSDYKHSLNLLKNFKKLYPNILTKSGIMVGL-GENDEEILTVIHDMRNHNIDIL 237
++K+RP + +++ LN L K+L T +G MVGL G+ ++++ + ++ H+ D++
Sbjct: 168 HRKLRPDTSFENRLNCLLTLKEL--GYETGAGSMVGLPGQTIDDLVDDLLFLKEHDFDMV 225
Query: 238 TIGQYLMPSRLHLPVHRYLHPKFFEKFKKIA 268
IG ++ P+ F K +A
Sbjct: 226 GIGPFI--PHPDTPLANEKKGDFTLTLKMVA 254
>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 = 46.4 bits (109), Expect = 7e-06
Identities = 35/277 (12%), Positives = 82/277 (29%), Gaps = 73/277 (26%)
Query: 52 NIGECFGRGVATFMIMGSICTR-RCKFC-NISHGRPDPLDIEEPK---KIAYTINKLKLN 106
N+ C ++ + + + H L I + + +
Sbjct: 188 NLKNCN-SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 107 YVVITSVNRDDLHDGGS-SHF-VSCIKHIRKLST---KIKIEILIPDFRNQI--NHVLKI 159
+V+ ++ + + + F +SC + L T K + L I +H
Sbjct: 247 LLVL-----LNVQNAKAWNAFNLSC----KILLTTRFKQVTDFLSAATTTHISLDHHSMT 297
Query: 160 F-----KQALPDVLNHNIETVPRLYKKVRP------------GSD----YKH-------- 190
K L L+ + +PR P G +KH
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT 357
Query: 191 ----SLNLLK--NFKKLY-------PNILTKSGIMVGL-----GENDEEILTVIHDM--- 229
SLN+L+ ++K++ P+ + ++ + + ++ +H
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 230 -RNHNIDILTIGQYLMPSRLHLPVHRYLHPKFFEKFK 265
+ ++I + ++ L LH + +
Sbjct: 418 EKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYN 454
Score = 36.4 bits (83), Expect = 0.011
Identities = 24/179 (13%), Positives = 52/179 (29%), Gaps = 45/179 (25%)
Query: 142 IEILIPDFRNQI--NHVLKIFKQALP-----DVLN--HNIETVPRLYKKVR--PGSDYKH 190
+ + F + V + K L ++ + RL+ + +
Sbjct: 22 LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK 81
Query: 191 SLN--LLKNFKKLYPNILTKSGIMVGLGENDEEILTVIH-DMRNHNIDILTIGQYLMPSR 247
+ L N+K L I T+ ++T ++ + R+ + Q
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQ--------RQPSMMTRMYIEQRDR---LYNDNQVFAK-- 128
Query: 248 LHLPVHRYLHPKFFEKFKKIAYKL------------GF-KNVLVGSMIRSSYMADKHFF 293
V R + + K ++ +L G K + + S + K F
Sbjct: 129 --YNVSR---LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182
>1r30_A Biotin synthase; SAM radical protein, TIM barrel, FES cluster,
transferase; HET: SAM DTB; 3.40A {Escherichia coli}
SCOP: c.1.28.1
Length = 369
Score = 36.2 bits (84), Expect = 0.010
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 169 NHNIETVPRLYKKVRPGSDYKHSLNLLKNFKKLYPNILTKSGIMVGLGENDEEILTVIHD 228
NHN++T P Y + Y+ L+ L+ + I SG +VGLGE ++ ++
Sbjct: 174 NHNLDTSPEFYGNIITTRTYQERLDTLEKVRD--AGIKVCSGGIVGLGETVKDRAGLLLQ 231
Query: 229 MRN 231
+ N
Sbjct: 232 LAN 234
>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 = 34.6 bits (79), Expect = 0.039
Identities = 32/190 (16%), Positives = 52/190 (27%), Gaps = 79/190 (41%)
Query: 82 HGRPDP------LDIEEPKKIAYTINK-LKLN-YVVITSVNRDDLHDGGSSHFVSC---- 129
G P P L E+ + N L V I+ VN G+ + V
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVN-------GAKNLVVSGPPQ 384
Query: 130 -----IKHIRKLSTKIKIEIL-IPDFRNQINHVLKIFKQALPDVLNHNIETVPRLYKKVR 183
+RK ++ IP F + LK + LP + P
Sbjct: 385 SLYGLNLTLRKAKAPSGLDQSRIP-FSER---KLKFSNRFLP------V-ASP------- 426
Query: 184 PGSDYKHSLNLLKNFKKLYPNILTKSGIMVGLGENDEEILTVIHDMRNHNIDILTIGQYL 243
+ HS +LL L + D+ +N+
Sbjct: 427 ----F-HS-HLLVPASDL-----------------------INKDLVKNNVSFN------ 451
Query: 244 MPSRLHLPVH 253
+ +PV+
Sbjct: 452 -AKDIQIPVY 460
Score = 33.9 bits (77), Expect = 0.068
Identities = 24/150 (16%), Positives = 43/150 (28%), Gaps = 54/150 (36%)
Query: 165 PDVLNH-NIET---VPRLYKKVRPGSDYKHSLNLLKNFKKLYPNILTKSGIMVGLGENDE 220
P L+H ++E VP + + + L + F K+ P D+
Sbjct: 8 PLTLSHGSLEHVLLVPT--------ASFFIASQLQEQFNKILPEPTEGF-------AADD 52
Query: 221 EILTVIH------DMRNHNIDILTIGQYLMPSRLHLPVHRYLHPKFFEKFKKIAYKLGFK 274
E T + ++ +GQ+ L L FE Y L
Sbjct: 53 EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCL--------TEFEN----CY-LEGN 99
Query: 275 NV--LVGSM--------------IRSSYMA 288
++ L + I++ A
Sbjct: 100 DIHALAAKLLQENDTTLVKTKELIKNYITA 129
>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 = 31.1 bits (69), Expect = 0.20
Identities = 6/44 (13%), Positives = 15/44 (34%), Gaps = 17/44 (38%)
Query: 131 KHIRKLSTKIKIEILIPDFRNQINHVLKIFKQALPDV-LNHNIE 173
+ ++KL +K + D + P + + +E
Sbjct: 20 QALKKLQASLK--LYADD--------------SAPALAIKATME 47
Score = 29.1 bits (64), Expect = 1.1
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 5/28 (17%)
Query: 189 KHSLNLLKNFKKLY-----PNILTKSGI 211
K +L L+ KLY P + K+ +
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATM 46
>2dce_A KIAA1915 protein; swirm domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 111
Score = 26.7 bits (59), Expect = 3.6
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 143 EILIPDFRN--QINHVLKIFKQALPDVLNHNIETVPRLYKKVR 183
E+ P+ N + + KQA+P+ P Y K+R
Sbjct: 12 ELKPPEQEIEIDRNIIQEEEKQAIPEFFEGRQAKTPERYLKIR 54
>2a9f_A Putative malic enzyme ((S)-malate:NAD+ oxidoreductase
(decarboxylating)); hypothetical protein, structural
genomics, PSI; 2.50A {Streptococcus pyogenes}
Length = 398
Score = 27.5 bits (62), Expect = 5.1
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 4/23 (17%)
Query: 148 DFRNQINHVLK---IFKQALPDV 167
DF NQIN+VL IF+ AL D
Sbjct: 314 DFPNQINNVLAFPGIFRGAL-DA 335
>1vl6_A Malate oxidoreductase; TM0542, NAD-dependent malic enzyme,
structural genomics, JCS protein structure initiative,
PSI; 2.61A {Thermotoga maritima} SCOP: c.2.1.7 c.58.1.3
PDB: 2hae_A*
Length = 388
Score = 27.5 bits (62), Expect = 5.6
Identities = 8/23 (34%), Positives = 13/23 (56%), Gaps = 4/23 (17%)
Query: 148 DFRNQINHVLK---IFKQALPDV 167
D NQ+N++L I K A+ +
Sbjct: 319 DHPNQVNNLLAFPGIMKGAV-EK 340
>3nv9_A Malic enzyme; rossmann fold, oxidoreductase; 2.25A {Entamoeba
histolytica}
Length = 487
Score = 27.6 bits (62), Expect = 5.6
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 4/23 (17%)
Query: 148 DFRNQINHVLK---IFKQALPDV 167
DF NQ+N+ + I K AL V
Sbjct: 352 DFPNQVNNSVGFPGILKGAL-IV 373
>1g62_A Ribosome anti-association factor EIF6; alpha-beta barrel, velcro
closure, subdomain, structural genomics, PSI; 2.50A
{Saccharomyces cerevisiae} SCOP: d.126.1.1 PDB: 2x7n_B
Length = 224
Score = 27.2 bits (60), Expect = 6.4
Identities = 23/123 (18%), Positives = 51/123 (41%), Gaps = 17/123 (13%)
Query: 2 NLTKDKNIEILKKPNWIRVKLISNIDNFNKTKNILRANNLVTVC----EEASCPNIGECF 57
T D+ ++ L+ VK+ + + N++ N+ V + + + I +
Sbjct: 74 TQTTDQELQHLRNSLPDSVKIQRVEERLSALGNVICCNDYVALVHPDIDRETEELISDVL 133
Query: 58 G----RG-VATFMIMGSICTRRCKFCNISHGRPDPLDIEEPKKIAYTINKLKLNYVVITS 112
G R ++ +++GS C+ + + H + D EE + L++ +V +
Sbjct: 134 GVEVFRQTISGNILVGSYCSLSNQGG-LVHPQTSVQDQEELSSL------LQVP-LVAGT 185
Query: 113 VNR 115
VNR
Sbjct: 186 VNR 188
>2dvm_A Malic enzyme, 439AA long hypothetical malate oxidoreductase; NAD,
structural genomics, NPPSFA; HET: NAD MES; 1.60A
{Pyrococcus horikoshii} PDB: 1ww8_A*
Length = 439
Score = 27.2 bits (61), Expect = 6.8
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 4/23 (17%)
Query: 148 DFRNQINHVLK---IFKQALPDV 167
D+ NQIN++L IF+ AL DV
Sbjct: 321 DYPNQINNLLGFPGIFRGAL-DV 342
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
0.324 0.141 0.424
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,554,996
Number of extensions: 278759
Number of successful extensions: 632
Number of sequences better than 10.0: 1
Number of HSP's gapped: 629
Number of HSP's successfully gapped: 28
Length of query: 293
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 200
Effective length of database: 4,105,140
Effective search space: 821028000
Effective search space used: 821028000
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: 41 (22.0 bits)
S2: 57 (25.7 bits)