RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 039298
(197 letters)
>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 = 200 bits (511), Expect = 5e-67
Identities = 104/147 (70%), Positives = 122/147 (82%), Gaps = 14/147 (9%)
Query: 51 PAVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAA 110
RD VFGVA I+ASFNDTF+HVTDLSG+ET+ R+TGGMKVKADRDESSPYAAMLAA
Sbjct: 5 VQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAMLAA 64
Query: 111 QDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDLEGLLILG 170
QDV+ +CKE+GITA+H+K+RATGG +TKTPGPG Q+ALRALARSG++IGRI
Sbjct: 65 QDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRI--------- 115
Query: 171 LYYISEDVTPIPTDSTRRKGGRRGRRL 197
EDVTP+P+DSTR+KGGRRGRRL
Sbjct: 116 -----EDVTPVPSDSTRKKGGRRGRRL 137
>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 = 198 bits (505), Expect = 7e-66
Identities = 115/165 (69%), Positives = 128/165 (77%), Gaps = 15/165 (9%)
Query: 34 MSRRKNREPKEENVTLGPA-VRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGM 92
M+ +K ++E ++ GP V E+VFGV HI A++NDTFIHVTDLSGRETLVR+TGGM
Sbjct: 1 MAPKKTAPVQKEVISYGPPNVGANENVFGVCHIMATWNDTFIHVTDLSGRETLVRVTGGM 60
Query: 93 KVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALA 152
KVKADR+ESSPYAAM AA DV RCKEL I ALHIKLRA GG +TK PGPGAQSALRALA
Sbjct: 61 KVKADREESSPYAAMQAAIDVVNRCKELKINALHIKLRAKGGVETKQPGPGAQSALRALA 120
Query: 153 RSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRRGRRL 197
RSGMKIGRI EDVTPIPTDSTRR+GGRRGRRL
Sbjct: 121 RSGMKIGRI--------------EDVTPIPTDSTRREGGRRGRRL 151
>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 = 9e-47
Identities = 48/133 (36%), Positives = 65/133 (48%), Gaps = 23/133 (17%)
Query: 61 GVAHIFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVSTRCKEL 120
GVAHI ASFN+T + +TD G GG + R +S+P+AA +AA+ + KE
Sbjct: 7 GVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSR-KSTPFAAQVAAERCADAVKEY 65
Query: 121 GITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDLEGLLILGLYYISEDVTP 180
GI L + + K PGPG +S +RAL +G +I I DVTP
Sbjct: 66 GIKNLEVMV--------KGPGPGRESTIRALNAAGFRITNI--------------TDVTP 103
Query: 181 IPTDSTRRKGGRR 193
IP + R RR
Sbjct: 104 IPHNGCRPPKKRR 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 = 138 bits (351), Expect = 1e-42
Identities = 41/162 (25%), Positives = 64/162 (39%), Gaps = 25/162 (15%)
Query: 34 MSRRKNREPKEENVTLGPAVRDGEHV--FGVAHIFASFNDTFIHVTDLSGRETLVRITGG 91
M++ + N + GV H+ ASFN+T + VTD+ G + + G
Sbjct: 1 MAKPIPKIGSRRNGRISSRKSASARKIPKGVIHVQASFNNTIVTVTDVRG-RVVSWASAG 59
Query: 92 MKVKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRAL 151
+P+AA AA + E G+ + + K PG G +ALRA+
Sbjct: 60 TCGFRGTKRGTPFAAQTAAGNAIRTVVEQGMQRAEVMI--------KGPGLGRDAALRAI 111
Query: 152 ARSGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRR 193
RSG+ + + DVTP+P + R RR
Sbjct: 112 RRSGILLSFV--------------RDVTPMPHNGCRPPKKRR 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 = 137 bits (347), Expect = 4e-42
Identities = 40/160 (25%), Positives = 71/160 (44%), Gaps = 34/160 (21%)
Query: 34 MSRRKNREPKEENVTLGPAVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMK 93
M+++ +++ + V G A+I AS+N+T + +TD G + +GG+
Sbjct: 1 MAKKPSKKKVKRQVA-----------SGRAYIHASYNNTIVTITDPDG-NPITWSSGGVI 48
Query: 94 VKADRDESSPYAAMLAAQDVSTRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALAR 153
+ +PYAA LAA D + + G+ ++ + +R G G + A+RAL
Sbjct: 49 GYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRG--------TGAGREQAIRALQA 100
Query: 154 SGMKIGRIDLEGLLILGLYYISEDVTPIPTDSTRRKGGRR 193
SG+++ I D TP+P + R K R
Sbjct: 101 SGLQVKSI--------------VDDTPVPHNGCRPKKKFR 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 = 44.3 bits (104), Expect = 1e-05
Identities = 44/241 (18%), Positives = 74/241 (30%), Gaps = 84/241 (34%)
Query: 2 TECISLLFRVFTFSFRLGTN------PSLLNPSRV------------FAGMSRRKNREPK 43
+ ++L F + L N LL + K K
Sbjct: 81 DQVLNLCLTEFENCY-LEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDK 139
Query: 44 EENVTLGPAVRDGEHVFGVAHIFASF------NDTF-----IH------VTDL--SGRET 84
+ N L AV +G A + A F +D F ++ V DL ET
Sbjct: 140 KSNSALFRAVGEGN-----AQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAET 194
Query: 85 LVRI-----------TGGMKVKA--DRDESSPYAAMLAAQDVSTRCKELGITAL-H--IK 128
L + T G+ + + ++P L + +S C +G+ L H +
Sbjct: 195 LSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS--CPLIGVIQLAHYVVT 252
Query: 129 LRATGGNKTKTPG-------------PGAQSALRALARSG-----MKIGRIDLEGLLILG 170
+ G TPG G +A+ A+A + R + L +G
Sbjct: 253 AKLLG----FTPGELRSYLKGATGHSQGLVTAV-AIAETDSWESFFVSVRKAITVLFFIG 307
Query: 171 L 171
+
Sbjct: 308 V 308
Score = 41.2 bits (96), Expect = 1e-04
Identities = 41/244 (16%), Positives = 71/244 (29%), Gaps = 102/244 (41%)
Query: 3 ECISLLFRV-----FTFSFRLGTNPSLL---------NPSRVFA--GMSRRK-NREPKEE 45
+ I++LF + + PS+L PS + + +++ + +
Sbjct: 298 KAITVLFFIGVRCYEAYP-NTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKT 356
Query: 46 NVTLGPAVRDGEHVFGVAHIFASFN--DTFIHVT----DLSGRETLVRITGGMKVKADRD 99
N L PA G+ V I + N + V+ L G +R K + D
Sbjct: 357 NSHL-PA---GKQV----EI-SLVNGAKNLV-VSGPPQSLYGLNLTLR---KAKAPSGLD 403
Query: 100 ES-----------------------SPY--AAM------LAAQDVSTRCKELGITALHIK 128
+S S A L +VS K++ I
Sbjct: 404 QSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTF 463
Query: 129 ----LRATGGNKTKT--------P-----------------GPGAQSAL-----RALARS 154
LR G+ ++ P GPG S L R +
Sbjct: 464 DGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGT 523
Query: 155 GMKI 158
G+++
Sbjct: 524 GVRV 527
Score = 40.0 bits (93), Expect = 3e-04
Identities = 33/193 (17%), Positives = 53/193 (27%), Gaps = 83/193 (43%)
Query: 11 VFTFS---FRLGTNPSLLNPSRVFAGMSRRKNREPKEENVTLGPAVRDGEHVF----GVA 63
+ F + L+ FAG S L GE + +A
Sbjct: 1736 LTLMEKAAFEDLKSKGLIPADATFAGHS-------------L------GE--YAALASLA 1774
Query: 64 HIFASFNDTFIHVTDLSGRETLVRITGG-MKVKADRDE--SSPYAAMLA----------- 109
+ S +V G M+V RDE S Y M+A
Sbjct: 1775 DVM-SIESLV----------EVVFYRGMTMQVAVPRDELGRSNY-GMIAINPGRVAASFS 1822
Query: 110 AQDVSTRCKELGITALHIKLRATGG-------NKTKTPGPGAQ-------SALRALAR-- 153
+ + + +G + TG N Q AL +
Sbjct: 1823 QEALQYVVERVG--------KRTGWLVEIVNYNV-----ENQQYVAAGDLRALDTVTNVL 1869
Query: 154 SGMKIGRIDLEGL 166
+ +K+ +ID+ L
Sbjct: 1870 NFIKLQKIDIIEL 1882
Score = 33.1 bits (75), Expect = 0.062
Identities = 16/70 (22%), Positives = 23/70 (32%), Gaps = 25/70 (35%)
Query: 143 GAQSALRALARSGMKIG---------------RIDLEGLLILGLYYISEDVTPIPTDSTR 187
G+Q GM G R D G + I + V P + T
Sbjct: 1625 GSQEQ-------GM--GMDLYKTSKAAQDVWNRADNHFKDTYG-FSILDIVINNPVNLTI 1674
Query: 188 RKGGRRGRRL 197
GG +G+R+
Sbjct: 1675 HFGGEKGKRI 1684
>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 = 33.4 bits (75), Expect = 0.020
Identities = 8/29 (27%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 82 RETLVRITGGMKVKADRDESSPYAAMLAA 110
++ L ++ +K+ AD +S+P A+ A
Sbjct: 19 KQALKKLQASLKLYAD--DSAPALAIKAT 45
>3s3l_A CERJ; acyltransferase, FABH homologue, KS III homologue, dimethyl
transfer, transferase; 2.00A {Streptomyces tendae} PDB:
3t5y_A* 3t6s_A* 3t8e_A 3t5y_B*
Length = 357
Score = 30.3 bits (69), Expect = 0.35
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 121 GITALHIKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIDL 163
GI ++ + A+ + P A++A AL R + + L
Sbjct: 39 GIESVTV---ASDAEEDAPPRMAARAARAALGRGDVDPADVSL 78
>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 = 30.2 bits (67), Expect = 0.56
Identities = 28/166 (16%), Positives = 50/166 (30%), Gaps = 53/166 (31%)
Query: 1 ETECISLLFRVFTFSFR------LGTNPSLLNPSRVFA-----GMSRRKN-REPKEENVT 48
E SLL + + L TNP L+ + A G++ N + + +T
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS---IIAESIRDGLATWDNWKHVNCDKLT 356
Query: 49 ---------LGPAVRDGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGMK------ 93
L PA + +F + F + H+ L I +
Sbjct: 357 TIIESSLNVLEPA--EYRKMF---DRLSVFPPS-AHIP----TILLSLIWFDVIKSDVMV 406
Query: 94 ----------VKADRDESSPYAAMLAAQDVSTRCKELGITALHIKL 129
V+ ES+ + + + + K ALH +
Sbjct: 407 VVNKLHKYSLVEKQPKESTIS---IPSIYLELKVKLENEYALHRSI 449
>3svk_A Acetyl-COA acetyltransferase; ssgcid, NIH, niaid, SBRI, UW, emerald
biostructures, structu genomics; 2.20A {Mycobacterium
avium}
Length = 407
Score = 27.1 bits (61), Expect = 4.3
Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 3/24 (12%)
Query: 140 PGPGAQSALRALARSGMKIGRIDL 163
P P + + L R+G+ I IDL
Sbjct: 307 PTPATR---KVLDRAGLTIDDIDL 327
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
0.320 0.137 0.394
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,006,634
Number of extensions: 176321
Number of successful extensions: 511
Number of sequences better than 10.0: 1
Number of HSP's gapped: 498
Number of HSP's successfully gapped: 28
Length of query: 197
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 108
Effective length of database: 4,216,824
Effective search space: 455416992
Effective search space used: 455416992
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: 55 (24.8 bits)