RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4101
(82 letters)
>3q9t_A Choline dehydrogenase and related flavoproteins;
glucose-methanol-choline oxidoreductase family, formate
OXID formyl-FAD, oxidoreductase; HET: FAY; 2.24A
{Aspergillus oryzae}
Length = 577
Score = 109 bits (274), Expect = 7e-30
Identities = 28/68 (41%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 13 VILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLR-VGDNLQDHVGMAGLTFLVDKPV 71
VILS G +P++LM+SGIGP L GI I D R VG NL DH G+ V
Sbjct: 262 VILSQGVFETPKLLMLSGIGPTRELSRHGINTIVDSRHVGQNLMDHPGV-PFVLRVKDGF 320
Query: 72 SIVQNRLQ 79
+ L+
Sbjct: 321 GMDDVLLR 328
>3qvp_A Glucose oxidase; oxidoreductase; HET: NAG BMA MAN FAD; 1.20A
{Aspergillus niger} PDB: 1gal_A* 1cf3_A* 3qvr_A*
Length = 583
Score = 108 bits (273), Expect = 8e-30
Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 13 VILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLRVGDNLQDHVGMAGLTFLVDKPVS 72
V+L+AG+ SP IL SGIG K L+ +GI + DL VG NLQD + + +
Sbjct: 285 VLLAAGSAVSPTILEYSGIGMKSILEPLGIDTVVDLPVGLNLQDQTTA-TVRSRITSAGA 343
Query: 73 I 73
Sbjct: 344 G 344
>1gpe_A Protein (glucose oxidase); oxidoreductase(flavoprotein); HET: NAG
BMA MAN FAD; 1.80A {Penicillium amagasakiense} SCOP:
c.3.1.2 d.16.1.1
Length = 587
Score = 108 bits (272), Expect = 1e-29
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 13 VILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLRVGDNLQDHVGMAGLTFLVDKPVS 72
V+L+AG+ SP IL SGIG K L + + DL VG N+QD ++ +
Sbjct: 289 VLLAAGSAISPLILEYSGIGLKSVLDQANVTQLLDLPVGINMQDQT-TTTVSSRASSAGA 347
Query: 73 I 73
Sbjct: 348 G 348
>3fim_B ARYL-alcohol oxidase; AAO, lignin degradation, oxidoreductase,
flavoprotein; HET: FAD; 2.55A {Pleurotus eryngii}
Length = 566
Score = 106 bits (267), Expect = 5e-29
Identities = 24/62 (38%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 13 VILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLR-VGDNLQDHVGMAGLTFLVDKPV 71
V+LSAG++G+P +L +SGIG ++ L +GI I + VG NL DH+ + F V+
Sbjct: 268 VVLSAGSVGTPILLQLSGIGDENDLSSVGIDTIVNNPSVGRNLSDHLLL-PAAFFVNSNQ 326
Query: 72 SI 73
+
Sbjct: 327 TF 328
>1ju2_A HydroxynitrIle lyase; flavin, GMC oxidoreductase, almond,
cyanogenesis; HET: NAG NDG FUC BMA MAN FAD; 1.47A
{Prunus dulcis} SCOP: c.3.1.2 d.16.1.1 PDB: 3gdp_A*
3gdn_A*
Length = 536
Score = 104 bits (261), Expect = 3e-28
Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 2/61 (3%)
Query: 13 VILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLR-VGDNLQDHVGMAGLTFLVDKPV 71
VI+SAGTIG+PQ+L++SG+GP+ +L + IPV+ VG L D+ + L P+
Sbjct: 253 VIVSAGTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQFLHDNP-RNFINILPPNPI 311
Query: 72 S 72
Sbjct: 312 E 312
>3t37_A Probable dehydrogenase; BET alpha beta fold, ADP binding,
oxidoreductase; HET: FAD; 2.19A {Mesorhizobium loti}
Length = 526
Score = 102 bits (257), Expect = 1e-27
Identities = 28/69 (40%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 5 RHRPQASNVILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLR-VGDNLQDHVGMAGL 63
A ++L AG + SP +LM SGIGP D L G+ + D+ +G NLQDH+ AG
Sbjct: 255 SAEVFADQIVLCAGALESPALLMRSGIGPHDVLDAAGVGCLIDMPDIGRNLQDHLLGAGN 314
Query: 64 TFLVDKPVS 72
+ KPV
Sbjct: 315 LYAARKPVP 323
>2jbv_A Choline oxidase; alcohol oxidation, flavoenyzme oxidase, covalently
linked FAD, C4A-adduct, flavoprotein, oxidoreductase;
HET: FAO; 1.86A {Arthrobacter globiformis} PDB: 3nne_A*
3ljp_A*
Length = 546
Score = 98.8 bits (247), Expect = 3e-26
Identities = 27/62 (43%), Positives = 39/62 (62%), Gaps = 2/62 (3%)
Query: 13 VILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLR-VGDNLQDHVGMAGLTFLVDKPV 71
V+LS G I +P++LM+SGIGP HL + GI V+ D VG++LQDH + F +P+
Sbjct: 265 VVLSTGAIDTPKLLMLSGIGPAAHLAEHGIEVLVDSPGVGEHLQDHPEG-VVQFEAKQPM 323
Query: 72 SI 73
Sbjct: 324 VA 325
>1kdg_A CDH, cellobiose dehydrogenase; GMC oxidoreductase, PHBH fold,
alpha/beta structure, rossman 6-hydroxylated FAD,
oxidoreductase; HET: NAG MAN 6FA EMT; 1.50A
{Phanerochaete chrysosporium} SCOP: c.3.1.2 d.16.1.1
PDB: 1naa_A*
Length = 546
Score = 93.4 bits (233), Expect = 3e-24
Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 12/72 (16%)
Query: 13 VILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLR-----------VGDNLQDHVGMA 61
VILSAG G+ +IL SGIGP D +Q + VG N QD+ +
Sbjct: 253 VILSAGAFGTSRILFQSGIGPTDMIQTVQSNPTAAAALPPQNQWINLPVGMNAQDNPSI- 311
Query: 62 GLTFLVDKPVSI 73
L F +
Sbjct: 312 NLVFTHPSIDAY 323
>3pl8_A Pyranose 2-oxidase; substrate complex, H167A mutant, homotetramer,
GMC oxidoredu PHBH fold, rossmann domain,
oxidoreductase; HET: FAD MES G3F; 1.35A {Trametes
ochracea} PDB: 2igo_A* 3lsm_A* 2ign_A* 3k4c_A* 1tt0_A*
2igk_A* 3k4b_A* 3lsk_A* 3bg6_A* 3lsh_A* 3lsi_A* 2igm_A*
3k4j_A* 3k4m_A* 3bg7_A* 3k4k_A* 3k4l_A* 3bly_A* 1tzl_A*
3fdy_A* ...
Length = 623
Score = 46.4 bits (109), Expect = 9e-08
Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 5 RHRPQASNVILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLRVGDNLQDHVGMAGLT 64
R +A +L+AG + + Q+L+ SG G P + +G + + + T
Sbjct: 308 RFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPANPPELLPS-LGSYITEQSLVFCQT 366
Query: 65 FLVDKPVS 72
+ + +
Sbjct: 367 VMSTELID 374
>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 = 31.9 bits (72), Expect = 0.012
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 6/38 (15%)
Query: 38 QDMGIPVIHDLRVGDNLQDHVGMAGLTFLVD----KPV 71
+D+ IPV +D G +L+ G +VD PV
Sbjct: 453 KDIQIPV-YDTFDGSDLRVLSGSI-SERIVDCIIRLPV 488
>1n4w_A CHOD, cholesterol oxidase; flavoenzyme, steroid metabolism,
oxidoreductase, atomic RESO; HET: FAD; 0.92A
{Streptomyces SP} SCOP: c.3.1.2 d.16.1.1 PDB: 1b4v_A*
1n1p_A* 1n4u_A* 1n4v_A* 1mxt_A* 2gew_A* 1b8s_A* 3gyi_A*
1cc2_A* 3gyj_A* 1ijh_A* 1cbo_A* 3b3r_A* 3b6d_A* 3cnj_A*
Length = 504
Score = 31.2 bits (70), Expect = 0.019
Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 8/53 (15%)
Query: 5 RHRPQASNVILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLRVGDNLQDH 57
+ L AG++GS ++L+ + +P ++ VG +
Sbjct: 272 TKEISCRYLFLGAGSLGSTELLVRAR-------DTGTLPNLNS-EVGAGWGPN 316
>1coy_A Cholesterol oxidase; oxidoreductase(oxygen receptor); HET: AND FAD;
1.80A {Brevibacterium sterolicum} SCOP: c.3.1.2 d.16.1.1
PDB: 3cox_A*
Length = 507
Score = 30.5 bits (68), Expect = 0.037
Identities = 9/53 (16%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 5 RHRPQASNVILSAGTIGSPQILMISGIGPKDHLQDMGIPVIHDLRVGDNLQDH 57
A V +AG++G+ ++L+ +P + +VG+ ++
Sbjct: 277 TKVVTADRVFFAAGSVGTSKLLVSMKAQG-------HLPNLSS-QVGEGWGNN 321
>3osn_A DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA complex,
Y-family DNA polym translesion synthesis, nucleoside
triphosphate; HET: DNA DOC 6OG TTP; 1.90A {Homo sapiens}
PDB: 2dpj_A* 2fll_A* 2fln_A* 2flp_A* 3epg_A* 3epi_A*
2dpi_A* 3g6v_A* 3g6y_A* 3g6x_A* 3gv7_B* 3gv8_B* 3ngd_A*
3gv5_B* 3q8p_B* 3q8q_B* 3q8r_B* 3q8s_B* 3h4d_A* 3h4b_A*
...
Length = 420
Score = 30.1 bits (68), Expect = 0.046
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 23 PQILMISGIGPK--DHLQDMGIPVIHDLRVGD--NLQDHVGMA 61
I I GIG K L+ +GI + DL+ L+ +G++
Sbjct: 234 NHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGIS 276
>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family,
transferase-D complex; HET: DNA MSE ADI; 1.70A
{Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB:
1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A*
1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A*
2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ...
Length = 352
Score = 28.3 bits (64), Expect = 0.21
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 28 ISGIGPK--DHLQDMGIPVIHDLRVGD--NLQDHVGMAGLTFL 66
+ GIG + L+ +GI + D + L+ +G A +L
Sbjct: 183 VPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYL 225
>1r5j_A Putative phosphotransacetylase; lactate dehydrogenase-like
nucleotide-binding fold, structural genomics, BSGC
structure funded by NIH; 2.70A {Streptococcus pyogenes}
SCOP: c.77.1.5
Length = 337
Score = 25.6 bits (57), Expect = 1.8
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 31 IGPKDHLQDMGIPVIHDLRVGDNLQDHVGMAGLT 64
IGP LQ + PV +DL G + +D +A +T
Sbjct: 298 IGPI--LQGLNKPV-NDLSRGSSAEDIYKLAIIT 328
>1td9_A Phosphate acetyltransferase; structural genomics, BSGC structure
funded by NIH, protein structure initiative, PSI; 2.75A
{Bacillus subtilis} SCOP: c.77.1.5 PDB: 1xco_A
Length = 329
Score = 25.6 bits (57), Expect = 1.8
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 31 IGPKDHLQDMGIPVIHDLRVGDNLQDHVGMAGLT 64
+GP LQ + +PV +DL G N +D +A +T
Sbjct: 294 VGPI--LQGLNMPV-NDLSRGCNAEDVYNLALIT 324
>1vmi_A Putative phosphate acetyltransferase; NP_416953.1, structura
genomics, JCSG, protein structure initiative, PSI, joint
CE structural genomics; 2.32A {Escherichia coli} SCOP:
c.77.1.5
Length = 355
Score = 25.6 bits (57), Expect = 1.8
Identities = 10/34 (29%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 31 IGPKDHLQDMGIPVIHDLRVGDNLQDHVGMAGLT 64
+GP +Q + P+ HDL G ++Q+ + +A +
Sbjct: 301 VGPL--IQGLAAPM-HDLSRGCSVQEIIELALVA 331
>4e4r_A Phosphate acetyltransferase; structural genomics, EUTD, center for
structural genomics of infectious diseases, csgid; HET:
TRS; 1.44A {Staphylococcus aureus subsp}
Length = 331
Score = 25.6 bits (57), Expect = 2.0
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 31 IGPKDHLQDMGIPVIHDLRVGDNLQDHVGMAGLT 64
+GP LQ + PV +DL G +++D ++ +T
Sbjct: 295 VGPV--LQGLNSPV-NDLSRGCSIEDVYNLSFIT 325
>2af4_C Phosphate acetyltransferase; PTA dimer with one COA ligand bound
PER monomer, acyltransferase; HET: COA; 2.15A
{Methanosarcina thermophila} SCOP: c.77.1.5 PDB: 1qzt_A*
2af3_C*
Length = 333
Score = 25.6 bits (57), Expect = 2.2
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 31 IGPKDHLQDMGIPVIHDLRVGDNLQDHVGMAGLT 64
GP Q + P+ +DL G + +D VG +T
Sbjct: 294 YGPI--TQGLAKPI-NDLSRGCSDEDIVGAVAIT 324
>3psh_A Protein HI_1472; substrate binding protein, periplasmic binding
protein, MOLY binding protein, metal transport; 1.50A
{Haemophilus influenzae} PDB: 3psa_A
Length = 326
Score = 25.0 bits (55), Expect = 3.5
Identities = 6/26 (23%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 23 PQILMISGIGPKDH---LQDMGIPVI 45
P ++ ++ P + + D+ IPV+
Sbjct: 85 PDVVFVTNYAPSEMIKQISDVNIPVV 110
>4a01_A Proton pyrophosphatase; hydrolase, membrane protein, proton
pumping; HET: DMU; 2.35A {Vigna radiata}
Length = 766
Score = 24.8 bits (54), Expect = 4.3
Identities = 12/29 (41%), Positives = 13/29 (44%), Gaps = 9/29 (31%)
Query: 41 GIP--------VIHDLRVGDNLQDHVGMA 61
IP VI D VGDN+ D GM
Sbjct: 265 NIPEDDPRNPAVIADN-VGDNVGDIAGMG 292
>1g7s_A Translation initiation factor IF2/EIF5B; translational GTPase; HET:
GDP; 2.00A {Methanothermobacterthermautotrophicus} SCOP:
b.43.3.1 b.43.3.1 c.20.1.1 c.37.1.8 PDB: 1g7r_A* 1g7t_A*
Length = 594
Score = 24.5 bits (54), Expect = 4.4
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 12 NVILSAGTIGSPQILMISGIGPKDHLQDMGIPVIH 46
V++ A T+GS + + L+DM +P+
Sbjct: 352 GVVVKADTLGSLEAV-------VKILRDMYVPIKV 379
>3vh1_A Ubiquitin-like modifier-activating enzyme ATG7; autophagy, zinc
binding, metal binding protein; 3.00A {Saccharomyces
cerevisiae} PDB: 3vh2_A
Length = 598
Score = 24.4 bits (53), Expect = 4.9
Identities = 7/26 (26%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 9 QASNVILSAGTIGSP--QILMISGIG 32
++L AGT+G + L+ G+
Sbjct: 327 NTKVLLLGAGTLGCYVSRALIAWGVR 352
>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin
enzyme, photoreactivating enzyme; HET: FAD; 1.80A
{Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB:
1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A*
Length = 484
Score = 24.5 bits (54), Expect = 5.1
Identities = 7/18 (38%), Positives = 10/18 (55%), Gaps = 4/18 (22%)
Query: 40 MGIPVIH----DLRVGDN 53
M P++ DLR+ DN
Sbjct: 1 MAAPILFWHRRDLRLSDN 18
>3cqy_A Anhydro-N-acetylmuramic acid kinase; APC7501, SO_1313, structural
genomics, PSI-2, shewanella one MR-1, protein structure
initiative; 2.30A {Shewanella oneidensis}
Length = 370
Score = 23.7 bits (52), Expect = 9.2
Identities = 14/51 (27%), Positives = 17/51 (33%), Gaps = 16/51 (31%)
Query: 4 LRHRPQASNVILSAGT--IGSPQILMISGIGPKDHLQDMGIPVIHDLRVGD 52
+RH P T IG P + + GI VI D R D
Sbjct: 102 VRHMPNLEV----GFTLQIGDPNTIA----------TETGIDVIADFRRKD 138
>2fds_A Orotidine-monophosphate-decarboxylase; TIM barrel, structural
genomics, structural genomics consortium, SGC, unknown
function; 1.72A {Plasmodium berghei} SCOP: c.1.2.3 PDB:
2aqw_A
Length = 352
Score = 23.7 bits (50), Expect = 9.2
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 35 DHLQDMGIPVIHDLRVGD 52
D+L M IP + D+++ D
Sbjct: 145 DYLNSMNIPTMLDMKIND 162
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
0.323 0.141 0.408
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,209,801
Number of extensions: 63226
Number of successful extensions: 231
Number of sequences better than 10.0: 1
Number of HSP's gapped: 224
Number of HSP's successfully gapped: 33
Length of query: 82
Length of database: 6,701,793
Length adjustment: 51
Effective length of query: 31
Effective length of database: 5,277,822
Effective search space: 163612482
Effective search space used: 163612482
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 (21.9 bits)
S2: 51 (23.3 bits)