RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1332
(103 letters)
>2kdo_A Ribosome maturation protein SBDS; SBDS protein, protein structure,
RNA-interacting protein mutation, phosphoprotein,
ribosome biogenesis; NMR {Homo sapiens} PDB: 2l9n_A
Length = 252
Score = 88.9 bits (220), Expect = 2e-23
Identities = 50/98 (51%), Positives = 70/98 (71%), Gaps = 3/98 (3%)
Query: 6 QVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLI 65
+VI LK+ M IERA MR+R + + KKLKEKL +E+E++ G L ++CLI
Sbjct: 158 EVIKQLKEKMKIERAHMRLRFILPV--NEGKKLKEKLKPLIKVIESEDY-GQQLEIVCLI 214
Query: 66 DPGKYREIDELVRTETRGQGTLELLNLKEVTEGEEVLE 103
DPG +REIDEL++ ET+G+G+LE+LNLK+V EG+E E
Sbjct: 215 DPGCFREIDELIKKETKGKGSLEVLNLKDVEEGDEKFE 252
>1t95_A Hypothetical protein AF0491; shwachman-bodian-diamond syndrome
protein orthologue, unknown function; 1.90A
{Archaeoglobus fulgidus} SCOP: a.5.8.1 d.235.1.2
d.58.11.3 PDB: 1p9q_C
Length = 240
Score = 81.6 bits (201), Expect = 1e-20
Identities = 12/86 (13%), Positives = 34/86 (39%), Gaps = 2/86 (2%)
Query: 6 QVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLI 65
++ LK + ++ +M + +++ + + L E G + + I
Sbjct: 154 DIVKALKPILPLKFEEMEIAIKIPP--EHTGRAISALYNFGGVTREEWQRDGSWICVMRI 211
Query: 66 DPGKYREIDELVRTETRGQGTLELLN 91
G Y ++ +L+ +G+ ++L
Sbjct: 212 PSGMYGDLMDLLGKVAKGEALTKVLR 237
>2wbm_A MTHSBDS, ribosome maturation protein SDO1 homolog;
shwachman-bodian-diamond syndrome protein; 1.75A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 252
Score = 66.6 bits (162), Expect = 6e-15
Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 4/86 (4%)
Query: 6 QVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLI 65
V+ ++ + I+ ++RV +++ + + + NEEW G + +
Sbjct: 169 IVLKAIRTKIPIKFEKVRVAIKIPG--EMAGSAYGVISNFGK-ITNEEWQNDGSWIAVVE 225
Query: 66 DPGKYR-EIDELVRTETRGQGTLELL 90
PG + + + T G L+
Sbjct: 226 IPGGLQDSFYQKLSELTGGNVETRLI 251
>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 = 31.0 bits (69), Expect = 0.058
Identities = 26/122 (21%), Positives = 46/122 (37%), Gaps = 30/122 (24%)
Query: 1 MYYYSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLL 60
Y+YS + LK ER + V + D + L++K+ +T+ W+ G +
Sbjct: 471 QYFYSHIGHHLKNIEHPERMTLFRMVFL-----DFRFLEQKIRHDSTA-----WNASGSI 520
Query: 61 LICLIDPGKYRE----------------IDELVRTET---RGQGTLELLNLKEVTEGEEV 101
L L Y+ +D L + E + T +LL + + E E +
Sbjct: 521 LNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYT-DLLRIALMAEDEAI 579
Query: 102 LE 103
E
Sbjct: 580 FE 581
Score = 26.7 bits (58), Expect = 1.4
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 71 REIDELVRTETRGQGTLELLNLKEVTEGEEVLE 103
EID ++ ++ GTL L ++ EE+++
Sbjct: 49 EEIDHIIMSKDAVSGTLRLFWTLL-SKQEEMVQ 80
Score = 24.8 bits (53), Expect = 8.4
Identities = 15/82 (18%), Positives = 25/82 (30%), Gaps = 16/82 (19%)
Query: 26 VEVSAGV--KDVKKLKEKLVKCATSVENEEWSGGGLLLICLI-----------DPGKYRE 72
S + +VK L K + C E + +I D K+
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVN 351
Query: 73 IDELVRTETRGQGTLELLNLKE 94
D+L + +L +L E
Sbjct: 352 CDKLTTII---ESSLNVLEPAE 370
>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 = 28.9 bits (64), Expect = 0.26
Identities = 13/97 (13%), Positives = 28/97 (28%), Gaps = 15/97 (15%)
Query: 3 YYSQVIPTLKQCM-----SIERAQMRVRVEVSAGVKDVKKLK----EKLVKCATSVENEE 53
+ + + S +++ V + D++ L E++V C +
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIR-LPVK 489
Query: 54 W----SGGGLLLICLIDPGKYREIDELVRTETRGQGT 86
W ++ PG + L G G
Sbjct: 490 WETTTQFKATHILDF-GPGGASGLGVLTHRNKDGTGV 525
>1pix_A Glutaconyl-COA decarboxylase A subunit; biotin-dependent ION
pump, carboxyltransferase, lyase; 2.20A
{Acidaminococcus fermentans} SCOP: c.14.1.4 c.14.1.4
Length = 587
Score = 26.2 bits (58), Expect = 2.0
Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 7/80 (8%)
Query: 1 MYYYSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLL 60
M Y Q +P + + + A +++ +++ +L ++ + + + G L
Sbjct: 6 MPRYFQNMPQVGKPLKKADAANEEQLK--KIEEEIHQLIKEAQEAGKADADVN-KRGELT 62
Query: 61 ----LICLIDPGKYREIDEL 76
+ L++PG +R ++ L
Sbjct: 63 ALQRIEKLVEPGSWRPLNTL 82
>1nsj_A PRAI, phosphoribosyl anthranilate isomerase; thermostability; 2.00A
{Thermotoga maritima} SCOP: c.1.2.4 PDB: 1lbm_A 1dl3_A
Length = 205
Score = 25.9 bits (58), Expect = 2.2
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 26 VEVSAGVKDVKKLKE 40
VE G KD +K
Sbjct: 183 VEAFPGKKDHDSIKM 197
>2cve_A Hypothetical protein TTHA1053; COG1739, UPF0029, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; HET: TLA; 1.60A {Thermus thermophilus}
SCOP: d.14.1.11 d.58.11.2
Length = 191
Score = 26.0 bits (57), Expect = 2.5
Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 2/86 (2%)
Query: 3 YYSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLI 62
Y L++ + + V + +V ++ L A E G+
Sbjct: 108 YGGVAAEALRRAPKVPLVER-VGLAFLVPFAEVGRVYALLEARALKAEETYT-PEGVRFA 165
Query: 63 CLIDPGKYREIDELVRTETRGQGTLE 88
L+ + + TRGQ LE
Sbjct: 166 LLLPKPEREGFLRALLDATRGQVALE 191
>1v5x_A PRA isomerase, phosphoribosylanthranilate isomerase; alpha-beta
barrel, TRPF, riken structural genomics/proteomics
initiative, RSGI; 2.00A {Thermus thermophilus} SCOP:
c.1.2.4
Length = 203
Score = 25.6 bits (57), Expect = 2.9
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 26 VEVSAGVKDVKKLKE 40
VE + GVK +KL+
Sbjct: 177 VEEAPGVKSAEKLRA 191
>1t6c_A Exopolyphosphatase; alpha/beta protein, actin-like fold,
hydrolase; 1.53A {Aquifex aeolicus} SCOP: c.55.1.8
c.55.1.8 PDB: 1t6d_A 2j4r_A*
Length = 315
Score = 25.6 bits (57), Expect = 3.4
Identities = 10/27 (37%), Positives = 10/27 (37%), Gaps = 2/27 (7%)
Query: 60 LLICLIDPGKYREIDELVRTETR-GQG 85
L I I GK I E R T G
Sbjct: 26 LTIAQIKDGKLSIILERGRI-TSLGTK 51
>2qx0_A 7,8-dihydro-6-hydroxymethylpterin- pyrophosphokinase; 3-layered
alpha-BATA-alpha fold, homodimer, ternary complex,
transferase; HET: APC PH2; 1.80A {Yersinia pestis}
Length = 159
Score = 25.1 bits (56), Expect = 4.5
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 11 LKQCMSIERAQMRVRVEV 28
L +IER Q RVR E
Sbjct: 71 LDHTQAIERNQGRVRKEQ 88
>1vrg_A Propionyl-COA carboxylase, beta subunit; TM0716, structural joint
center for structural genomics, JCSG, protein structu
initiative, PSI; HET: MSE; 2.30A {Thermotoga maritima}
SCOP: c.14.1.4 c.14.1.4
Length = 527
Score = 25.2 bits (56), Expect = 5.1
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 64 LIDPGKYREIDELVRTETRGQG 85
L+DPG + EID+ V G
Sbjct: 56 LLDPGTFVEIDKFVEHRNTYFG 77
>3n6r_B Propionyl-COA carboxylase, beta subunit; protein complex,
biotin-dependent carboxylase, ligase; HET: BTI; 3.20A
{Roseobacter denitrificans}
Length = 531
Score = 24.8 bits (55), Expect = 5.9
Identities = 6/22 (27%), Positives = 8/22 (36%)
Query: 64 LIDPGKYREIDELVRTETRGQG 85
L+D G + E D V
Sbjct: 63 LLDEGSFEEFDMFVTHRCTDFN 84
>3r8n_C 30S ribosomal protein S3; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2gyb_C 2gy9_C* 2ykr_C 3fih_C*
2wwl_C 3oar_C 3oaq_C 3ofb_C 3ofa_C 3ofp_C 3ofx_C 3ofy_C
3ofo_C 3r8o_C 4a2i_C
Length = 206
Score = 24.4 bits (54), Expect = 6.7
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 17 IERAQMRVRVEVSA---GV------KDVKKLKEKLVK 44
IER +RV + G+ +DV+KL++ +
Sbjct: 56 IERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVAD 92
>3iav_A Propionyl-COA carboxylase complex B subunit; accase, pccase, ACC,
PCC, CT, carboxyltransfe polyketide, fatty acid, PKS,
FAS; 1.75A {Streptomyces coelicolor} PDB: 1xnw_A
3ib9_A* 3ibb_A 3mfm_C 1xny_A* 1xnv_A* 1xo6_A
Length = 530
Score = 24.8 bits (55), Expect = 6.7
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 64 LIDPGKYREIDELVRTETRGQG 85
L+D G + E+DE R + G
Sbjct: 55 LLDEGSFVELDEFARHRSTNFG 76
>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C*
1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C
1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C
1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ...
Length = 239
Score = 24.5 bits (54), Expect = 7.3
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 17 IERAQMRVRVEVSA---GV------KDVKKLKEKLVK 44
IERA V V V GV + ++ L+E+L K
Sbjct: 57 IERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAK 93
>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA
complex, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
{Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O
1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 3izv_G*
3izw_G* 3kc4_C 3or9_C 3ora_C 3sfs_C* 3uoq_C* 2qal_C*
1p6g_C 1p87_C 2aw7_C ...
Length = 233
Score = 24.5 bits (54), Expect = 7.6
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 17 IERAQMRVRVEVSA---GV------KDVKKLKEKLVK 44
IER +RV + G+ +DV+KL++ +
Sbjct: 57 IERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVAD 93
>1cbk_A Protein (7,8-dihydro-6-hydroxymethylpterin- pyrophosphokinase);
transferase; HET: ROI; 2.02A {Haemophilus influenzae}
SCOP: d.58.30.1
Length = 160
Score = 24.4 bits (54), Expect = 7.8
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 11 LKQCMSIERAQMRVRVE 27
L + IE Q RVR+
Sbjct: 71 LDELQRIENEQGRVRLR 87
>1x0u_A Hypothetical methylmalonyl-COA decarboxylase ALPH; lyase; 2.20A
{Sulfolobus tokodaii}
Length = 522
Score = 24.4 bits (54), Expect = 7.8
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 64 LIDPGKYREIDELVRTETRGQG 85
L D GK+ EI T G
Sbjct: 49 LFDDGKFNEIMTFATTRATEFG 70
>2bzr_A Propionyl-COA carboxylase beta chain 5; fatty acid biosynthesis,
accase, ligase, transferase; 2.2A {Mycobacterium
tuberculosis} PDB: 2a7s_A
Length = 548
Score = 24.5 bits (54), Expect = 8.2
Identities = 5/22 (22%), Positives = 10/22 (45%)
Query: 64 LIDPGKYREIDELVRTETRGQG 85
L+D + E+D L + +
Sbjct: 66 LLDEDSFVELDALAKHRSTNFN 87
>1on3_A Methylmalonyl-COA carboxyltransferase 12S subunit; domain
duplication, multienzyme complex, transcarboxylase;
HET: MCA; 1.90A {Propionibacterium freudenreichii}
SCOP: c.14.1.4 c.14.1.4 PDB: 1on9_A*
Length = 523
Score = 24.4 bits (54), Expect = 9.3
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 64 LIDPGKYREIDELVRTETRGQG 85
L+DP + E+ + T G
Sbjct: 53 LLDPHSFDEVGAFRKHRTTLFG 74
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
0.315 0.134 0.373
Gapped
Lambda K H
0.267 0.0659 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,565,489
Number of extensions: 81072
Number of successful extensions: 127
Number of sequences better than 10.0: 1
Number of HSP's gapped: 122
Number of HSP's successfully gapped: 40
Length of query: 103
Length of database: 6,701,793
Length adjustment: 68
Effective length of query: 35
Effective length of database: 4,803,165
Effective search space: 168110775
Effective search space used: 168110775
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (23.6 bits)