RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6249
(119 letters)
>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria,
structural genomics, structural genomics consortium,
SGC, unknown function; HET: GDP; 2.01A {Plasmodium
falciparum}
Length = 228
Score = 74.0 bits (182), Expect = 1e-17
Identities = 21/103 (20%), Positives = 47/103 (45%), Gaps = 5/103 (4%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRGRQ--V 72
S+ ++ ++ + SY FTT G ++K Q++D PG+++ A + + +
Sbjct: 43 SSFMNIVSRANVDVQSYSFTTKNLYVGHFDHKLNKYQIIDTPGLLDRAFENRNTIEMTTI 102
Query: 73 IAVARTADLVLMMLDATKQDVQRGLLE--KELESVGIRLNKKK 113
A+A ++L ++D ++Q + E S+ + K
Sbjct: 103 TALAHINGVILFIIDISEQCG-LTIKEQINLFYSIKSVFSNKS 144
>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP,
complex, structural G NPPSFA; HET: GDP; 2.35A
{Pyrococcus horikoshii}
Length = 357
Score = 64.9 bits (158), Expect = 1e-13
Identities = 25/93 (26%), Positives = 43/93 (46%), Gaps = 7/93 (7%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRG--RQV 72
STLL LT + E ASY FTT G E Q++D PG+++ + + +
Sbjct: 181 STLLKALTTAKPEIASYPFTTRGINVGQFEDGYFRYQIIDTPGLLDRPISERNEIEKQAI 240
Query: 73 IAVARTADLVLMMLDATKQDV-----QRGLLEK 100
+A+ +L++ + D ++ Q L E+
Sbjct: 241 LALRYLGNLIIYIFDPSEHCGFPLEEQIHLFEE 273
>1udx_A The GTP-binding protein OBG; TGS domain, riken structural
genomics/proteomics initiative, RSGI, structural
genomics; 2.07A {Thermus thermophilus} SCOP: b.117.1.1
c.37.1.8 d.242.1.1
Length = 416
Score = 58.3 bits (142), Expect = 2e-11
Identities = 38/103 (36%), Positives = 60/103 (58%), Gaps = 8/103 (7%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIP--GVIEYK-GANIQLLDLPGIIEGAAQGKGRGRQ 71
S+LL+ +T + A Y FTTL+ P GV+E L D+PGIIEGA++GKG G +
Sbjct: 171 SSLLAAMTRAHPKIAPYPFTTLS--PNLGVVEVSEEERFTLADIPGIIEGASEGKGLGLE 228
Query: 72 VIA-VARTADLVLMMLDATKQDVQR-GLLEKELESVGIRLNKK 112
+ +ART ++L +LDA + ++ L KE+ + L ++
Sbjct: 229 FLRHIARTR-VLLYVLDAADEPLKTLETLRKEVGAYDPALLRR 270
>1lnz_A SPO0B-associated GTP-binding protein; GTPase, OBG, stringent
factor, stress response, sporulation, large G-protein,
structural genomics, PSI; HET: G4P; 2.60A {Bacillus
subtilis} SCOP: b.117.1.1 c.37.1.8
Length = 342
Score = 56.4 bits (137), Expect = 9e-11
Identities = 35/107 (32%), Positives = 57/107 (53%), Gaps = 12/107 (11%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPGVIEYK-GANIQLLDLPGIIEGAAQGKGRGRQVI 73
STLLS ++ + + A Y FTTL G++E G + + DLPG+IEGA QG G G Q +
Sbjct: 172 STLLSVVSSAKPKIADYHFTTLVPNLGMVETDDGRSFVMADLPGLIEGAHQGVGLGHQFL 231
Query: 74 A-VARTADLVLMMLDATK-------QDVQRGLLEKELESVGIRLNKK 112
+ RT +++ ++D + D + +EL +RL ++
Sbjct: 232 RHIERTR-VIVHVIDMSGLEGRDPYDDYL--TINQELSEYNLRLTER 275
>1wxq_A GTP-binding protein; structural genomics, riken structural
genomics/proteomics initiative, RSGI, NPPSFA; 2.60A
{Pyrococcus horikoshii} SCOP: c.37.1.8 d.15.10.2
Length = 397
Score = 45.0 bits (107), Expect = 8e-07
Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 30/101 (29%)
Query: 15 STLLSTLTHTQSEAASYEFTT---------------------------LTCIPGVIEYKG 47
ST S T E A+Y FTT G+
Sbjct: 14 STFFSAATLVDVEIANYPFTTIEANVGVTYAITDHPCKELGCSPNPQNYEYRNGLA---L 70
Query: 48 ANIQLLDLPGIIEGAAQGKGRGRQVIAVARTADLVLMMLDA 88
++++D+ G++ GA +G+G G + + R A ++ ++DA
Sbjct: 71 IPVKMVDVAGLVPGAHEGRGLGNKFLDDLRMASALIHVVDA 111
>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 = 37.3 bits (86), Expect = 4e-04
Identities = 28/160 (17%), Positives = 51/160 (31%), Gaps = 57/160 (35%)
Query: 12 SHESTLLSTLT-HTQ-----SEAASY---------------------EFTTLTCIPGVIE 44
E LL + T TQ E A++ E+ L + V+
Sbjct: 1720 RSEKGLL-SATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMS 1778
Query: 45 YKGANIQLLDLPGI-IEGAAQGKGRGRQ---VIAVARTADLVLMMLDATKQDVQR----- 95
+ ++++ G+ ++ A GR +IA+ +A + V+R
Sbjct: 1779 IESL-VEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRT 1837
Query: 96 -GLLE-----------------KELESVGIRLNK-KKPNI 116
L+E + L++V LN K I
Sbjct: 1838 GWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKI 1877
Score = 26.2 bits (57), Expect = 3.4
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 52 LLDL-PGIIEG-----AAQGKGRGRQVIAVARTAD 80
+LD PG G G G +VI VA T D
Sbjct: 501 ILDFGPGGASGLGVLTHRNKDGTGVRVI-VAGTLD 534
>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation,
GTP-binding domain, maturation enzyme, oxidoreductase;
2.99A {Thermotoga neapolitana}
Length = 423
Score = 37.3 bits (87), Expect = 5e-04
Identities = 19/105 (18%), Positives = 39/105 (37%), Gaps = 15/105 (14%)
Query: 15 STLLSTLTHTQ----SEAASYEFTTLTCIPGVIEYKGAN-IQLLDLPGIIEGAAQGKGRG 69
S+ ++ L S+ A TT + +E + L+D PG+ + G+ R
Sbjct: 48 SSFMNALVGQNVSIVSDYAG---TTTDPVYKSMELHPIGPVTLVDTPGLDDVGELGRLRV 104
Query: 70 RQVIAVARTADLVLMMLDATKQDVQRGLLEKELESVGIRLNKKKP 114
+ V AD +++ D+ + ++ E + P
Sbjct: 105 EKARRVFYRADCGILVTDSAPTPYEDDVVNLFKE-------MEIP 142
>2qpt_A EH domain-containing protein-2; protein-nucleotide complex,
membrane protein, endocytosis; HET: ANP; 3.10A {Mus
musculus}
Length = 550
Score = 36.7 bits (84), Expect = 7e-04
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 10/73 (13%)
Query: 49 NIQLLDLPGIIEGAAQGKGRGRQVIAVART----ADLVLMMLDATKQDVQR------GLL 98
+I ++D PGI+ GA Q RG AV R DL++++ DA K ++ G L
Sbjct: 155 SISIIDTPGILSGAKQRVSRGYDFPAVLRWFAERVDLIILLFDAHKLEISDEFSEAIGAL 214
Query: 99 EKELESVGIRLNK 111
+ + + LNK
Sbjct: 215 RGHEDKIRVVLNK 227
>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP;
1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A*
2j3e_A*
Length = 262
Score = 30.6 bits (69), Expect = 0.089
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 9/69 (13%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGAA---QGKGRGRQVIAVARTADLVLMMLDA-- 88
L + G I ++D PG++E Q + + RT D++L +
Sbjct: 70 EGLRPVMVSRTMGGFTINIIDTPGLVEAGYVNHQALELIKGFLV-NRTIDVLLYVDRLDV 128
Query: 89 ---TKQDVQ 94
+ D Q
Sbjct: 129 YAVDELDKQ 137
>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer,
alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A
{Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A*
2gja_A* 1rfl_A
Length = 172
Score = 29.4 bits (67), Expect = 0.18
Identities = 31/116 (26%), Positives = 42/116 (36%), Gaps = 28/116 (24%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPG----VIE----YKGANIQLLDLPGI------IE 60
S+LL+ L EAA +T I G V+ G + ++D G+ +E
Sbjct: 18 SSLLNALAG--REAA-----IVTDIAGTTRDVLREHIHIDGMPLHIIDTAGLREASDEVE 70
Query: 61 GAAQGKGRGRQVIAVARTADLVLMMLDATKQDVQRGLLEKELESVGIRLNKKKPNI 116
G R Q I AD VL M+D T D + RL K P
Sbjct: 71 --RIGIERAWQEIE---QADRVLFMVDGTTTDAV--DPAEIWPEFIARLPAKLPIT 119
>3i8s_A Ferrous iron transport protein B; GTPase, GPCR, iron uptake, FEO,
cell inner membrane, cell ME GTP-binding, ION
transport, membrane; 1.80A {Escherichia coli} PDB:
3i8x_A* 3i92_A* 3hyr_A 3hyt_A* 2wic_A* 2wib_A* 2wia_A*
Length = 274
Score = 29.2 bits (66), Expect = 0.23
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 41 GVIEYKGANIQLLDLPGIIE-GAAQGKGRGRQVIA----VARTADLVLMMLDAT 89
G + L+DLPG + + IA ++ ADL++ ++DA+
Sbjct: 43 GQFSTTDHQVTLVDLPGTYSLTTISSQTSLDEQIACHYILSGDADLLINVVDAS 96
>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA,
national P protein structural and functional analyses;
HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8
Length = 190
Score = 29.2 bits (66), Expect = 0.25
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 16/63 (25%)
Query: 40 PGV----IEYKGANIQLLDLPGIIEGAAQGKGRG----------RQVIAVARTADLVLMM 85
PGV IE + N +++D+PG G G + + A+ D+ +++
Sbjct: 32 PGVTRKIIEIEWKNHKIIDMPGF--GFMMGLPKEVQERIKDEIVHFIEDNAKNIDVAVLV 89
Query: 86 LDA 88
+D
Sbjct: 90 VDG 92
>3a1s_A Iron(II) transport protein B; FEOB, iron transporter, small
GTPase, G protein, GDI; HET: GDP; 1.50A {Thermotoga
maritima} PDB: 3a1t_A* 3a1u_A* 3a1v_A* 3a1w_A
Length = 258
Score = 28.8 bits (65), Expect = 0.33
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 15/57 (26%)
Query: 41 GVIEYKGANIQLLDLPGII--------EGAAQGKGRGRQVIAVARTADLVLMMLDAT 89
GV YKG I L+DLPG E A R + + ADLV+++ D+
Sbjct: 45 GVFTYKGYTINLIDLPGTYSLGYSSIDEKIA------RDYL-LKGDADLVILVADSV 94
>3iby_A Ferrous iron transport protein B; G protein, G domain, iron
uptake, cell inner membrane, cell GTP-binding, ION
transport, membrane; 2.50A {Legionella pneumophila}
Length = 256
Score = 28.8 bits (65), Expect = 0.40
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 41 GVIEYKGANIQLLDLPGIIEGAAQGKGRG------RQVIAVARTADLVLMMLDAT 89
G I++ DLPG+ A +G Q + + D ++ ++DA
Sbjct: 41 GEFLLGEHLIEITDLPGVYSLVANAEGISQDEQIAAQSV-IDLEYDCIINVIDAC 94
>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins,
cell membrane, ION transport, transmembrane; HET: GNP;
1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A*
2wjh_A*
Length = 165
Score = 28.2 bits (64), Expect = 0.43
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 15/57 (26%)
Query: 41 GVIEYKGANIQLLDLPGII--------EGAAQGKGRGRQVIAVARTADLVLMMLDAT 89
G EY G +++DLPG+ E A R I + DLV+ ++DAT
Sbjct: 43 GEFEYNGEKFKVVDLPGVYSLTANSIDEIIA------RDYI-INEKPDLVVNIVDAT 92
>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle,
G-protein, prokaryote, GTP-BIND nucleotide-binding,
metal transport; 2.70A {Pyrococcus furiosus}
Length = 271
Score = 28.4 bits (64), Expect = 0.45
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 15/57 (26%)
Query: 41 GVIEYKGANIQLLDLPGII--------EGAAQGKGRGRQVIAVARTADLVLMMLDAT 89
G++EY+ ++DLPGI E A R I + AD+++ ++D+T
Sbjct: 43 GIMEYREKEFLVVDLPGIYSLTAHSIDELIA------RNFI-LDGNADVIVDIVDST 92
>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane
G-proteins, cell membrane, ION transport,
transmembrane; HET: GDP; 2.20A {Methanocaldococcus
jannaschii}
Length = 188
Score = 28.3 bits (64), Expect = 0.46
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 15/57 (26%)
Query: 41 GVIEYKGANIQLLDLPGII--------EGAAQGKGRGRQVIAVARTADLVLMMLDAT 89
G EY G +++DLPG+ E A R I + DLV+ ++DAT
Sbjct: 47 GEFEYNGEKFKVVDLPGVYSLTANSIDEIIA------RDYI-INEKPDLVVNIVDAT 96
>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like,
hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8
d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X
Length = 301
Score = 28.6 bits (65), Expect = 0.47
Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 2/59 (3%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGKGRG--RQVIAVARTADLVLMMLDATK 90
TT I G+ +D PG+ + R + + +LV+ +++ T+
Sbjct: 42 TTRHRIVGIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTR 100
>2dby_A GTP-binding protein; GDP, structural genomics, NPPSFA, natio
project on protein structural and functional analyses;
HET: GDP; 1.76A {Thermus thermophilus} PDB: 2dwq_A
Length = 368
Score = 28.2 bits (64), Expect = 0.63
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 21/78 (26%)
Query: 15 STLLSTLTHTQSEAASYEFTT-----------------LTCIPGVIEYKG----ANIQLL 53
STL + LT + AA+Y F T L E +++ +
Sbjct: 15 STLFNALTRANALAANYPFATIDKNVGVVPLEDERLYALQRTFAKGERVPPVVPTHVEFV 74
Query: 54 DLPGIIEGAAQGKGRGRQ 71
D+ G+++GA +G+G G Q
Sbjct: 75 DIAGLVKGAHKGEGLGNQ 92
>1jal_A YCHF protein; nucleotide-binding fold, structural genomics,
structure 2 function project, S2F, unknown function;
2.40A {Haemophilus influenzae} SCOP: c.37.1.8 d.15.10.2
Length = 363
Score = 27.4 bits (62), Expect = 0.96
Identities = 24/88 (27%), Positives = 37/88 (42%), Gaps = 28/88 (31%)
Query: 15 STLLSTLTHTQSEAASYEFTT-----------------LTCI--PGVIEYKGANIQLLDL 55
STL + LT EAA+Y F T L I P I ++ +D+
Sbjct: 16 STLFNALTKAGIEAANYPFCTIEPNTGVVPMPDPRLDALAEIVKPERILP--TTMEFVDI 73
Query: 56 PGIIEGAAQGKGRG-------RQVIAVA 76
G++ GA++G+G G R+ A+
Sbjct: 74 AGLVAGASKGEGLGNKFLANIRETDAIG 101
>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 = 27.5 bits (60), Expect = 1.2
Identities = 16/106 (15%), Positives = 32/106 (30%), Gaps = 31/106 (29%)
Query: 42 VIEYKGANIQLLDLPGI-IEGAAQGKGRGRQVIA--VAR--------------------- 77
++ + A ++L + I+G G G+ +A V
Sbjct: 137 YLKLRQALLELRPAKNVLIDG---VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN 193
Query: 78 TADLVLMMLDATKQDVQRGLLEKELESVGIRLN----KKKPNIYFK 119
+ + VL ML + + S I+L + + K
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239
>1xzp_A Probable tRNA modification GTPase TRME; GTP-binding, THF-binding,
hydrolase; 2.30A {Thermotoga maritima} SCOP: a.24.25.1
c.37.1.8 d.250.1.2 PDB: 1xzq_A* 1xzp_B 1xzq_B*
Length = 482
Score = 27.1 bits (61), Expect = 1.4
Identities = 27/91 (29%), Positives = 40/91 (43%), Gaps = 27/91 (29%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPG----VIE----YKGANIQLLDLPGI-------I 59
STLL+ L + + A +T IPG VI +G +++D G+ +
Sbjct: 257 STLLNRLLN--EDRA-----IVTDIPGTTRDVISEEIVIRGILFRIVDTAGVRSETNDLV 309
Query: 60 EGAAQGKGRGRQVIAVARTADLVLMMLDATK 90
E G R Q I AD+VL +LDA+
Sbjct: 310 E--RLGIERTLQEIE---KADIVLFVLDASS 335
>3geh_A MNME, tRNA modification GTPase MNME; G protein, U34, GTP-binding,
HYDR magnesium, metal-binding, nucleotide-binding,
potassium, TR processing; HET: GDP FON; 3.20A {Nostoc
SP}
Length = 462
Score = 27.1 bits (61), Expect = 1.4
Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 19/66 (28%)
Query: 39 IPG----VIE----YKGANIQLLDLPGI------IEGAAQGKGRGRQVIAVARTADLVLM 84
+PG V+E G +Q+LD GI +E G R RQ TADLVL+
Sbjct: 255 LPGTTRDVVESQLVVGGIPVQVLDTAGIRETSDQVE--KIGVERSRQAAN---TADLVLL 309
Query: 85 MLDATK 90
+DA
Sbjct: 310 TIDAAT 315
>2ohf_A Protein OLA1, GTP-binding protein 9; ATPase, GTPase, P-loop,
OBG-like, hydrolase; HET: ACP; 2.70A {Homo sapiens}
Length = 396
Score = 27.1 bits (61), Expect = 1.7
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 23/77 (29%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCI-P--GVIE------------YK-----GANIQLLD 54
ST + LT++Q+ A ++ F T I P + +K A + ++D
Sbjct: 36 STFFNVLTNSQASAENFPFCT---IDPNESRVPVPDERFDFLCQYHKPASKIPAFLNVVD 92
Query: 55 LPGIIEGAAQGKGRGRQ 71
+ G+++GA G+G G
Sbjct: 93 IAGLVKGAHNGQGLGNA 109
>3gee_A MNME, tRNA modification GTPase MNME; G protein, cytoplasm, GTP-
binding, hydrolase, magnesium, metal-binding,
nucleotide- binding, potassium; HET: GDP FON; 2.95A
{Chlorobium tepidum} PDB: 3gei_A*
Length = 476
Score = 26.7 bits (60), Expect = 1.9
Identities = 27/89 (30%), Positives = 38/89 (42%), Gaps = 26/89 (29%)
Query: 15 STLLSTLTHTQSEAASYEFTTLTCIPG----VIE----YKGANIQLLDLPGI------IE 60
STLL+TL E A ++ +PG IE + +L D G+ IE
Sbjct: 247 STLLNTLLG--QERA-----IVSHMPGTTRDYIEECFIHDKTMFRLTDTAGLREAGEEIE 299
Query: 61 GAAQGKGRGRQVIAVARTADLVLMMLDAT 89
+G R R +A ADL+L +LD
Sbjct: 300 --HEGIRRSRMKMA---EADLILYLLDLG 323
>2hjg_A GTP-binding protein ENGA; GTPase ENGA KH-domain, hydrolase; HET:
GDP; 2.50A {Bacillus subtilis}
Length = 436
Score = 26.7 bits (60), Expect = 2.1
Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 18/64 (28%)
Query: 42 VIEYKGANIQLLDLPGIIEGAAQGKGRGRQVI---AVART------ADLVLMMLDA---- 88
Y ++D G+ + KG+ + +V R +++V ++LD
Sbjct: 217 SFTYNQQEFVIVDTAGMRK-----KGKVYETTEKYSVLRALKAIDRSEVVAVVLDGEEGI 271
Query: 89 TKQD 92
+QD
Sbjct: 272 IEQD 275
>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET:
GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*
Length = 270
Score = 26.1 bits (57), Expect = 2.8
Identities = 10/59 (16%), Positives = 21/59 (35%), Gaps = 4/59 (6%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGAA---QGKGRGRQVIAVARTADLVLMMLDAT 89
+ G + ++D PG+IEG + + +T D++L +
Sbjct: 73 EGPRPVMVSRSRAGFTLNIIDTPGLIEGGYINDMALNIIKSFLL-DKTIDVLLYVDRLD 130
>1n8i_A Probable malate synthase G; glyoxylate pathway, acetyl coenzyme A,
isocitrate lyase, persistence, GLCB, structural
genomics, PSI; 2.10A {Mycobacterium tuberculosis} SCOP:
c.1.13.1 PDB: 1n8w_A* 2gq3_A*
Length = 741
Score = 26.3 bits (58), Expect = 3.1
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 60 EGAAQGKG----RGRQVIAVAR 77
+GA +G RG +VIA AR
Sbjct: 152 DGAEKGPTYNKVRGDKVIAYAR 173
>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 = 25.9 bits (58), Expect = 3.3
Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 34 TTLTCIPGVIEYKGANIQLLDLPGIIEGA-AQGKGRGRQVIAVARTADLVLMMLDATK 90
TT + G++ I +D PG+ + A G+ ++V + V+ ++D
Sbjct: 41 TTRKRLRGILTEGRRQIVFVDTPGLHKPMDALGEFMDQEVYEALADVNAVVWVVDLRH 98
>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem
G-domains, ligand binding protein; HET: GDP; 1.90A
{Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1
Length = 439
Score = 25.9 bits (58), Expect = 3.5
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 13/50 (26%)
Query: 74 AVART------ADLVLMMLDA----TKQDVQR--GLLEKELESVGIRLNK 111
+ R AD+V+++LDA T+QD QR GL+E+ + + NK
Sbjct: 253 SNYRVVDSIEKADVVVIVLDATQGITRQD-QRMAGLMERRGRASVVVFNK 301
Score = 24.8 bits (55), Expect = 9.8
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 10/61 (16%)
Query: 39 IPGV--------IEYKGANIQLLDLPGIIEGAAQGKGRG--RQVIAVARTADLVLMMLDA 88
GV +E+ G +L+D G+ + + + + R ADLVL ++D
Sbjct: 32 EEGVTRDPVQDTVEWYGKTFKLVDTCGVFDNPQDIISQKMKEVTLNMIREADLVLFVVDG 91
Query: 89 T 89
Sbjct: 92 K 92
>1xa0_A Putative NADPH dependent oxidoreductases; structural genomics,
protein structure initiative, MCSG; HET: DTY; 2.80A
{Geobacillus stearothermophilus} SCOP: b.35.1.2 c.2.1.1
Length = 328
Score = 26.1 bits (58), Expect = 3.5
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 50 IQLLDLPGIIEGAAQGKGRGRQVIAVA 76
I L +LP ++ +G+ RGR V+ +A
Sbjct: 302 ISLAELPQALKRILRGELRGRTVVRLA 328
>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural
genomics; HET: PLP; 1.15A {Thermus thermophilus}
Length = 407
Score = 26.0 bits (58), Expect = 3.6
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 16/62 (25%)
Query: 66 KGRGRQVIAVART---------ADLV-------LMMLDATKQDVQRGLLEKELESVGIRL 109
K R V+ A+ +V L ++D + + E+ L++VGI +
Sbjct: 280 KEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITV 339
Query: 110 NK 111
NK
Sbjct: 340 NK 341
>2vi8_A Serine hydroxymethyltransferase; SHMT, E53Q, FTHF, enzyme memory,
pyridoxal phosphate, one-carbon metabolism,
PLP-dependent enzymes; HET: PLP; 1.67A {Bacillus
stearothermophilus} PDB: 2vi9_A* 2via_A* 2vib_A* 1kkj_A*
1kkp_A* 1kl1_A* 1kl2_A* 1yjs_A* 2w7f_A* 2w7d_A* 2w7e_A*
2w7g_A* 2w7h_A* 1yjz_A* 1yjy_A* 2vgu_A* 2vgs_A* 2vgt_A*
2vgv_A* 2vgw_A* ...
Length = 405
Score = 26.0 bits (58), Expect = 3.6
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 16/62 (25%)
Query: 66 KGRGRQVIAVART---------ADLV-------LMMLDATKQDVQRGLLEKELESVGIRL 109
K ++V+ A+ LV L+++D Q + EK L+ VGI +
Sbjct: 279 KAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITV 338
Query: 110 NK 111
NK
Sbjct: 339 NK 340
>3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A,
one-carbon metabolism, pyridoxa phosphate, structural
genomics; 1.60A {Burkholderia pseudomallei}
Length = 425
Score = 25.7 bits (57), Expect = 4.0
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 16/62 (25%)
Query: 66 KGRGRQVIAVART---------ADLV-------LMMLDATKQDVQRGLLEKELESVGIRL 109
K +V+A A+ DLV L+++D + ++ +E+ LE GI
Sbjct: 289 KTYIDRVLANAQALGDVLKAGGVDLVTGGTDNHLLLVDLRPKGLKGAQVEQALERAGITC 348
Query: 110 NK 111
NK
Sbjct: 349 NK 350
>1rv3_A Serine hydroxymethyltransferase, cytosolic; one-carbon metabolism;
HET: GLY PLP; 2.40A {Oryctolagus cuniculus} SCOP:
c.67.1.4 PDB: 1rv4_A* 1rvu_A* 1rvy_A* 1ls3_A* 1cj0_A*
1bj4_A* 1eji_A*
Length = 483
Score = 25.3 bits (56), Expect = 5.2
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 83 LMMLDATKQDVQRGLLEKELESVGIRLNK 111
L+++D + G EK LE+ I NK
Sbjct: 357 LILVDLRSKGTDGGRAEKVLEACSIACNK 385
>3gbx_A Serine hydroxymethyltransferase; structural genomics, IDP01011,
serine hydroxymethyltransfera salmonella typhimurium.;
HET: MSE; 1.80A {Salmonella typhimurium} PDB: 1dfo_A*
3g8m_A* 1eqb_A*
Length = 420
Score = 25.2 bits (56), Expect = 5.9
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 83 LMMLDATKQDVQRGLLEKELESVGIRLNK 111
L +LD +++ + L I +NK
Sbjct: 321 LFLLDLVDKNLTGKEADAALGRANITVNK 349
>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron
transport, GTPase, transmembrane, potassium; HET: GGM;
1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A*
3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*
Length = 272
Score = 25.3 bits (56), Expect = 6.3
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 15/53 (28%)
Query: 45 YKGANIQLLDLPGII--------EGAAQGKGRGRQVIAVARTADLVLMMLDAT 89
K ++++ DLPGI A R + +++ AD +L ++DAT
Sbjct: 46 KKNKDLEIQDLPGIYSMSPYSPEAKVA------RDYL-LSQRADSILNVVDAT 91
>2a7v_A Serine hydroxymethyltransferase; structural genomics, structural
genomics consortium, SGC; 2.04A {Homo sapiens} SCOP:
c.67.1.4 PDB: 3ou5_A
Length = 490
Score = 25.4 bits (56), Expect = 6.3
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 83 LMMLDATKQDVQRGLLEKELESVGIRLNK 111
L+++D + + E+ LE V I NK
Sbjct: 367 LVLVDLRPKGLDGARAERVLELVSITANK 395
>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA,
30S ribosome ASSE GTP-binding, nucleotide-binding; HET:
GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*
Length = 308
Score = 25.1 bits (56), Expect = 6.8
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 9/69 (13%)
Query: 52 LLDLPGIIEGAAQGK-GRG--RQVIAVARTADLVLMMLDATKQ--DVQRGLLEKELESVG 106
LD PGI E G AD++L M+DAT+ + + ++ +
Sbjct: 63 FLDTPGIYEPKKSDVLGHSMVEIAKQSLEEADVILFMIDATEGWRPRDEEIYQNFIKPLN 122
Query: 107 IR----LNK 111
+NK
Sbjct: 123 KPVIVVINK 131
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 25.3 bits (56), Expect = 6.9
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 83 LMMLDATKQDVQRGLLEKELESVGIRLNK 111
L+++D + E L VGI +N+
Sbjct: 339 LVLVDLRDSPLDGQAAEDLLHEVGITVNR 367
>3n0l_A Serine hydroxymethyltransferase; alpha beta class, 3-layer(ABA)
sandwich, CSGI transferase, structural genomics; HET:
MSE; 1.80A {Campylobacter jejuni}
Length = 417
Score = 25.2 bits (56), Expect = 7.0
Identities = 6/29 (20%), Positives = 13/29 (44%)
Query: 83 LMMLDATKQDVQRGLLEKELESVGIRLNK 111
L+++ ++ + L + GI NK
Sbjct: 314 LVLMSFLDREFSGKDADLALGNAGITANK 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
0.319 0.135 0.373
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,668,298
Number of extensions: 92873
Number of successful extensions: 349
Number of sequences better than 10.0: 1
Number of HSP's gapped: 347
Number of HSP's successfully gapped: 55
Length of query: 119
Length of database: 6,701,793
Length adjustment: 81
Effective length of query: 38
Effective length of database: 4,440,192
Effective search space: 168727296
Effective search space used: 168727296
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 (21.8 bits)
S2: 51 (23.4 bits)