RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3230
(151 letters)
>2xzm_K RPS14E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_K 3j0o_K 3j0l_K 2zkq_k 3iz6_K 3jyv_K*
Length = 151
Score = 202 bits (515), Expect = 3e-68
Identities = 109/151 (72%), Positives = 124/151 (82%)
Query: 1 MAPRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGM 60
MAP+K ++EV+ P V E+VFGV HI A++NDTF+HVTDLSGRET+ R+TGGM
Sbjct: 1 MAPKKTAPVQKEVISYGPPNVGANENVFGVCHIMATWNDTFIHVTDLSGRETLVRVTGGM 60
Query: 61 KVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALA 120
KVKADR+E+SPYAAM AA DV +CK L I ALHIKLRA GG TK PGPGAQSALRALA
Sbjct: 61 KVKADREESSPYAAMQAAIDVVNRCKELKINALHIKLRAKGGVETKQPGPGAQSALRALA 120
Query: 121 RSNMKIGRIEDVTPIPSDSTRRKGGRRGRRL 151
RS MKIGRIEDVTPIP+DSTRR+GGRRGRRL
Sbjct: 121 RSGMKIGRIEDVTPIPTDSTRREGGRRGRRL 151
>3u5c_O RP59A, 40S ribosomal protein S14-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_K 3o30_H 3o2z_H 3u5g_O 1s1h_K
3jyv_K*
Length = 137
Score = 201 bits (513), Expect = 6e-68
Identities = 107/133 (80%), Positives = 122/133 (91%)
Query: 19 PQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAA 78
Q ++ VFGVA I+ASFNDTFVHVTDLSG+ETIAR+TGGMKVKADRDE+SPYAAMLAA
Sbjct: 5 VQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAMLAA 64
Query: 79 QDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSD 138
QDVA KCK +GITA+H+K+RATGG RTKTPGPG Q+ALRALARS ++IGRIEDVTP+PSD
Sbjct: 65 QDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPVPSD 124
Query: 139 STRRKGGRRGRRL 151
STR+KGGRRGRRL
Sbjct: 125 STRKKGGRRGRRL 137
>3r8n_K 30S ribosomal protein S11; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_K 3fih_K* 3iy8_K 2wwl_K
3oar_K 3oaq_K 3ofb_K 3ofa_K 3ofp_K 3ofx_K 3ofy_K 3ofo_K
3r8o_K 4a2i_K 3i1m_K 1vs7_K* 3e1a_C 3e1c_C 1vs5_K 3i1o_K
...
Length = 117
Score = 148 bits (376), Expect = 2e-47
Identities = 47/119 (39%), Positives = 64/119 (53%), Gaps = 9/119 (7%)
Query: 29 GVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTL 88
GVAHI ASFN+T V +TD G GG + R +++P+AA +AA+ A+ K
Sbjct: 7 GVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSR-KSTPFAAQVAAERCADAVKEY 65
Query: 89 GITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRR 147
GI L + + K PGPG +S +RAL + +I I DVTPIP + R RR
Sbjct: 66 GIKNLEVMV--------KGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRR 116
>3bbn_K Ribosomal protein S11; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 140
Score = 137 bits (348), Expect = 8e-43
Identities = 41/148 (27%), Positives = 63/148 (42%), Gaps = 10/148 (6%)
Query: 1 MAPRKGKVQKEEVLVSLGPQVKEGEDV-FGVAHIFASFNDTFVHVTDLSGRETIARITGG 59
MA K+ + + GV H+ ASFN+T V VTD+ G ++ + G
Sbjct: 1 MAKPIPKIGSRRNGRISSRKSASARKIPKGVIHVQASFNNTIVTVTDVRG-RVVSWASAG 59
Query: 60 MKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRAL 119
+P+AA AA + G+ + + K PG G +ALRA+
Sbjct: 60 TCGFRGTKRGTPFAAQTAAGNAIRTVVEQGMQRAEVMI--------KGPGLGRDAALRAI 111
Query: 120 ARSNMKIGRIEDVTPIPSDSTRRKGGRR 147
RS + + + DVTP+P + R RR
Sbjct: 112 RRSGILLSFVRDVTPMPHNGCRPPKKRR 139
>2vqe_K 30S ribosomal protein S11, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: c.55.4.1
PDB: 1gix_N* 1hnw_K* 1hnx_K* 1hnz_K* 1hr0_K 1ibk_K*
1ibl_K* 1ibm_K 1j5e_K 1jgo_N* 1jgp_N* 1jgq_N* 1ml5_N*
1n32_K* 1n33_K* 1n34_K 1n36_K 1xmo_K* 1xmq_K* 1xnq_K*
...
Length = 129
Score = 135 bits (342), Expect = 4e-42
Identities = 41/119 (34%), Positives = 62/119 (52%), Gaps = 9/119 (7%)
Query: 29 GVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTL 88
G A+I AS+N+T V +TD G I +GG+ + +PYAA LAA D A+K
Sbjct: 17 GRAYIHASYNNTIVTITDPDG-NPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAY 75
Query: 89 GITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIPSDSTRRKGGRR 147
G+ ++ + +R G G + A+RAL S +++ I D TP+P + R K R
Sbjct: 76 GMQSVDVIVRG--------TGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFR 126
>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 = 38.1 bits (88), Expect = 6e-04
Identities = 30/166 (18%), Positives = 41/166 (24%), Gaps = 76/166 (45%)
Query: 32 HIFAS-FN--DTFVHVT----DLSGRETIARITGGMKVKA----DRDEA----------- 69
+ S N V V+ L G R K KA D+
Sbjct: 365 QVEISLVNGAKNLV-VSGPPQSLYGLNLTLR-----KAKAPSGLDQSRIPFSERKLKFSN 418
Query: 70 ----------SPY---AAMLAAQDVAE-----KCKTLGITALHIK----LRATGGNRTKT 107
S A+ L +D+ + K + I LR G+ ++
Sbjct: 419 RFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISER 478
Query: 108 --------P-----------------GPGAQSALRALARSNMKIGR 128
P GPG S L L N K G
Sbjct: 479 IVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRN-KDGT 523
Score = 28.1 bits (62), Expect = 1.2
Identities = 26/153 (16%), Positives = 44/153 (28%), Gaps = 50/153 (32%)
Query: 2 APRKGKVQKEEV-----LVS--LG---PQVKEGE-----DVFGVAHIFASFNDTFVHVTD 46
P +G +E LV LG V+ + V + F + ++ D
Sbjct: 43 EPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQV--LNLCLTEFENCYLEGND 100
Query: 47 LSGRETIARITGGMKVKADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGGNRTK 106
+ +A A +L D I +I R +
Sbjct: 101 I---HALA------------------AKLLQENDTTLVKTKELIKN-YITARIMAK---R 135
Query: 107 TPGPGAQSAL-RALARSNMKI-------GRIED 131
+ SAL RA+ N ++ G +D
Sbjct: 136 PFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDD 168
>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 = 32.6 bits (73), Expect = 0.024
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 50 RETIARITGGMKVKADRDEASPYAAMLAA 78
++ + ++ +K+ AD D A P A+ A
Sbjct: 19 KQALKKLQASLKLYAD-DSA-PALAIKAT 45
>2ri0_A Glucosamine-6-phosphate deaminase; carbohydrate metabolism,; HET:
BTB; 1.60A {Streptococcus mutans} PDB: 2ri1_A*
Length = 234
Score = 27.6 bits (62), Expect = 1.4
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 10/45 (22%)
Query: 60 MKVK--ADRDEASPYAAMLAAQDVAEKCKTLGITALHIKLRATGG 102
MK ++ E S A + +++ KTLG+ ATG
Sbjct: 2 MKTIKVKNKTEGSKVAFRMLEEEITFGAKTLGL--------ATGS 38
>3p0j_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase,
AARS, tyrrs, pseudod translation, ATP-binding,
nucleotide-binding, ligase; HET: TYE; 2.89A {Leishmania
major} PDB: 3p0i_A* 3p0h_A*
Length = 690
Score = 27.5 bits (61), Expect = 1.9
Identities = 14/74 (18%), Positives = 26/74 (35%), Gaps = 7/74 (9%)
Query: 11 EEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADRDEAS 70
EV + G + + ++ I + + + V D+ + TIARI + E +
Sbjct: 105 IEVWKAAGMDMDKVLFLWSSEEITSHADTYWRMVLDIGRQNTIARIK-KCCTIMGKTEGT 163
Query: 71 P------YAAMLAA 78
Y M
Sbjct: 164 LTAAQVLYPLMQCC 177
>1o2d_A Alcohol dehydrogenase, iron-containing; TM0920, structural
genomics, JCSG, PSI, protein structure initiative; HET:
MSE NAP TRS; 1.30A {Thermotoga maritima} SCOP: e.22.1.2
PDB: 1vhd_A*
Length = 371
Score = 26.4 bits (59), Expect = 3.6
Identities = 15/74 (20%), Positives = 24/74 (32%), Gaps = 5/74 (6%)
Query: 77 AAQDVAEKCKTLGITALHIKLRATGGNRTKTPGPGAQSALRALARSNMKIGRIEDVTPIP 136
+ LG AL + TG + +K G + L + + ++V P
Sbjct: 28 ILEKRGNIIDLLGKRALVV----TGKSSSKKNGS-LDDLKKLLDETEISYEIFDEVEENP 82
Query: 137 SDSTRRKGGRRGRR 150
S K R R
Sbjct: 83 SFDNVMKAVERYRN 96
>2vd8_A Alanine racemase; pyridoxal 5'-phosphate, peptidoglycan synthesis,
PLP, OPPF, L-alanine, isomerase, D- alanine, pyridoxal
phosphate; HET: MLY LLP; 1.47A {Bacillus anthracis} PDB:
2vd9_A* 3ha1_A*
Length = 391
Score = 26.5 bits (58), Expect = 4.6
Identities = 11/53 (20%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 2 APRKGKVQKEEVLVSLGPQVKEGEDVFGVAHIFASFNDTFVHVTDLSGR-ETI 53
P G+V ++ ++ L +V G V + D ++ T+++ TI
Sbjct: 311 VPIVGRVTMDQFMIHLPCEVPLGTXVT----LIGRQGDEYISATEVAEYSGTI 359
>3bhn_A THIJ/PFPI domain protein; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: MSE; 1.76A {Shewanella loihica pv-4}
Length = 236
Score = 25.7 bits (57), Expect = 6.0
Identities = 10/49 (20%), Positives = 16/49 (32%), Gaps = 4/49 (8%)
Query: 26 DVFGVAHIFASFNDTFVHVTDLSGRETIARITGGMKVKADR--DEASPY 72
D F + + +D++ L + GM VK D E
Sbjct: 35 DFFLMNDLLGRTSDSWTVRI-LGTKPEH-HSQLGMTVKTDGHVSEVKEQ 81
>3n6r_A Propionyl-COA carboxylase, alpha subunit; protein complex,
biotin-dependent carboxylase, ligase; HET: BTI; 3.20A
{Ruegeria pomeroyi}
Length = 681
Score = 25.7 bits (57), Expect = 6.6
Identities = 6/24 (25%), Positives = 11/24 (45%), Gaps = 2/24 (8%)
Query: 2 APRKGKVQKEEVLVSLGPQVKEGE 25
A +KG V ++ S G + +
Sbjct: 654 AEKKGVV--AKINASAGNSLAVDD 675
>1f5v_A Oxygen-insensitive NADPH nitroreductase; flavoprotein,
oxidoreduction, nitrocompound, oxidoreductase; HET:
FMN; 1.70A {Escherichia coli} SCOP: d.90.1.1
Length = 240
Score = 25.3 bits (56), Expect = 9.3
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 40 TFVHVTDLSGRETIARITGGMK 61
+ + +TD + RE + +TGG K
Sbjct: 47 SIIRITDKALREELVTLTGGQK 68
>2om6_A Probable phosphoserine phosphatase; rossmann fold, B-hairpin,
four-helix bundle, structural GENO NPPSFA; 2.20A
{Pyrococcus horikoshii}
Length = 235
Score = 25.2 bits (55), Expect = 10.0
Identities = 9/34 (26%), Positives = 14/34 (41%)
Query: 110 PGAQSALRALARSNMKIGRIEDVTPIPSDSTRRK 143
G + AL+ + +K I +V P TR
Sbjct: 102 EGTKEALQFVKERGLKTAVIGNVMFWPGSYTRLL 135
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
0.316 0.133 0.373
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,314,338
Number of extensions: 137105
Number of successful extensions: 432
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 37
Length of query: 151
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 66
Effective length of database: 4,328,508
Effective search space: 285681528
Effective search space used: 285681528
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: 41 (21.6 bits)
S2: 53 (24.2 bits)