RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780856|ref|YP_003065269.1| NADH-quinone oxidoreductase, E
subunit [Candidatus Liberibacter asiaticus str. psy62]
(218 letters)
>3i9v_2 NADH-quinone oxidoreductase subunit 2; electron transport,
respiratory chain, 4Fe- 4S, cell membrane, flavoprotein,
FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8}
PDB: 2fug_2* 3iam_2* 3ias_2*
Length = 181
Score = 156 bits (396), Expect = 3e-39
Identities = 51/179 (28%), Positives = 90/179 (50%), Gaps = 4/179 (2%)
Query: 17 SFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVL 76
F ++ ++ E ++YPP ++A++PLL R Q++EGW+ IE +A ++ V+
Sbjct: 2 GFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEVM 61
Query: 77 EIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWE 136
+A+FY+ +Q P + H+QVC T C L G E+L + + P DG S +
Sbjct: 62 GVASFYSYYQFVPT-GKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ 120
Query: 137 EVECQGACVNAPMVMIGKDTY-EDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPA 194
+VEC G+C AP++ + + Y E +T RLE ++ G+ + +
Sbjct: 121 KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGK--RLEEIELPGKCGHHVH 177
>2auv_A Potential NAD-reducing hydrogenase subunit; thioredoxin,
thiordoxin-like, oxidoreductase; NMR {Desulfovibrio
fructosovorans}
Length = 85
Score = 103 bits (257), Expect = 4e-23
Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 1/86 (1%)
Query: 87 LSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVN 146
+ P G + + VC T C ++G +K++ + ++ DG S + + C G C
Sbjct: 1 MVPKG-KYPISVCMGTACFVKGADKVVHAFKEQLKIDIGDVTPDGRFSIDTLRCVGGCAL 59
Query: 147 APMVMIGKDTYEDLTPERLEEIIDAF 172
AP+VM+G+ Y ++TP ++++I+ +
Sbjct: 60 APIVMVGEKVYGNVTPGQVKKILAEY 85
>1m2d_A [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2S] cluster,
Cys59Ser variant, electron transport; 1.05A {Aquifex
aeolicus} SCOP: c.47.1.11 PDB: 1m2a_A 1f37_A 1m2b_A
Length = 110
Score = 64.3 bits (156), Expect = 2e-11
Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 13/86 (15%)
Query: 95 HVQVCGTTP--------CMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVN 146
HV VC C RG ++ + KI P T C A +
Sbjct: 5 HVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQL---FMTTVITPTGCMNASMM 61
Query: 147 APMVMIGKD--TYEDLTPERLEEIID 170
P+V++ D Y + PE ++EI++
Sbjct: 62 GPVVVVYPDGVWYGQVKPEDVDEIVE 87
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 37.6 bits (87), Expect = 0.002
Identities = 41/284 (14%), Positives = 77/284 (27%), Gaps = 133/284 (46%)
Query: 18 FSEESAIWVNEVISRYPP------SRCQSAVIPLLMRAQEQE----------GWVSRAAI 61
F E + ++ Y + L+ + E W+ +
Sbjct: 170 FEE-----LRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPS- 223
Query: 62 EVVANILDMAY----------IRVLEIATFYTQFQ---LSPVGT-RAHVQVCGTTPCMLR 107
N D Y I V+++A + + +P G R++++ G T
Sbjct: 224 ----NTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP-GELRSYLK--GAT----- 271
Query: 108 GCEKLIEVCRNKIHQKPLHRNSDGTL---------SWEE----------------VECQ- 141
G H S G + SWE V C
Sbjct: 272 G-----------------H--SQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYE 312
Query: 142 ------------------GACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRPG 183
V +PM+ I +LT E++++ ++ ++ +
Sbjct: 313 AYPNTSLPPSILEDSLENNEGVPSPMLSI-----SNLTQEQVQDYVNKTNS----HL--- 360
Query: 184 PQIDRISSA----P-----AGGLTSLLDNNSKKRGKKKKDDKIS 218
P ++ + +G SL N R K K +
Sbjct: 361 PAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLR-KAKAPSGLD 403
Score = 29.1 bits (65), Expect = 0.80
Identities = 35/156 (22%), Positives = 54/156 (34%), Gaps = 57/156 (36%)
Query: 1 MSVRRLAEEEFQ---------P-SSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQ 50
MS+ L E F P S I +N R S Q A+ ++ R
Sbjct: 1777 MSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINP--GRVAASFSQEALQYVVERVG 1834
Query: 51 EQEGWVSRAAIEVVA-NILDMAYI-----RVLEIATFYTQF-QLSPVGTRAHVQVCGTTP 103
++ GW+ +E+V N+ + Y+ R L+ T F +L +
Sbjct: 1835 KRTGWL----VEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKI------------- 1877
Query: 104 CMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVE 139
+IE+ QK +LS EEVE
Sbjct: 1878 -------DIIEL------QK--------SLSLEEVE 1892
Score = 28.0 bits (62), Expect = 1.5
Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 10/82 (12%)
Query: 17 SFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRA---AIEVVANILDMAYI 73
SFS+E+ +V E + + ++ ++ E + +V+ A++ V N+L+ +I
Sbjct: 1820 SFSQEALQYVVERVGKR-----TGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLN--FI 1872
Query: 74 RVLEIATFYTQFQLSPVGTRAH 95
++ +I Q LS H
Sbjct: 1873 KLQKIDIIELQKSLSLEEVEGH 1894
>1uyl_A HSP 86, heat shock protein HSP 90-alpha; ATPase, chaperone,
ATP-binding; 1.4A {Homo sapiens} SCOP: d.122.1.1 PDB:
1uy7_A* 1uy8_A* 1uy9_A* 1uyc_A* 1uyd_A* 1uye_A* 1uyf_A*
1uyg_A* 1uyh_A* 1uyk_A* 1uy6_A 2cdd_A* 2uwd_A* 2vci_A*
2vcj_A* 2wi1_A* 2wi2_A* 2wi3_A* 2wi4_A* 2wi5_A* ...
Length = 236
Score = 31.2 bits (70), Expect = 0.17
Identities = 17/103 (16%), Positives = 36/103 (34%), Gaps = 8/103 (7%)
Query: 78 IATFYTQFQLSPVGTRAHVQVCGTTPCMLR----GCEKLIEVCRNKIHQKPLHRNSDGTL 133
IA T+ + + A + + G EK+ + ++ ++ S
Sbjct: 110 IAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQY-AWESSAGG 168
Query: 134 SWEEVECQGACVNAPM---VMIGKDTYEDLTPERLEEIIDAFS 173
S+ G + + + +D E L R++EI+ S
Sbjct: 169 SFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHS 211
>3evu_A Myosin light chain kinase, green fluorescent protein, calmodulin
chimera; gcamp2,calcium sensor, GFP, calmodulin,M13,
signaling protein; HET: CRO; 1.75A {Aequorea victoria}
PDB: 3ek4_A* 3ek7_A* 3evv_A* 3ek8_A* 3ekh_A* 3ekj_A*
3evr_A*
Length = 449
Score = 29.5 bits (66), Expect = 0.68
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 8/57 (14%)
Query: 125 LHRNSDGTLSWE----EVECQGAC----VNAPMVMIGKDTYEDLTPERLEEIIDAFS 173
++ + +E +G N + +T + LT E++ E +AFS
Sbjct: 262 YKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNTRDQLTEEQIAEFKEAFS 318
>2gqp_A Endoplasmin; GRP94, HSP82, HSP90, HTPG, chaperone, ligand, NECA,
NPCA, adenosine; HET: PA7 PG4 1PE; 1.50A {Canis lupus
familiaris} SCOP: d.122.1.1 PDB: 1tc0_A* 1tbw_A* 1u0z_A*
1u2o_A* 1ysz_A* 1yt0_A* 1yt1_A* 2exl_A* 2fyp_A* 2gfd_A*
1tc6_A* 2h8m_A* 2hch_A* 2hg1_A* 2esa_A*
Length = 236
Score = 28.5 bits (63), Expect = 1.0
Identities = 6/67 (8%), Positives = 22/67 (32%), Gaps = 3/67 (4%)
Query: 110 EKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVM---IGKDTYEDLTPERLE 166
+ V + SD + +G + + + ++ + L + ++
Sbjct: 142 ADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIK 201
Query: 167 EIIDAFS 173
++ +S
Sbjct: 202 NLVKKYS 208
>1a32_A Ribosomal protein S15; multiwavelength anomalous diffraction,
protein-RNA, ribosomal protein interactions, ribosome,
RNA-binding; 2.10A {Bacillus stearothermophilus} SCOP:
a.16.1.2 PDB: 1qd7_H
Length = 88
Score = 28.5 bits (64), Expect = 1.1
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 13/62 (20%)
Query: 160 LTPERLEEIIDAFSTGQGDTIRPGPQI----DRISSAPAGGLTSLLDNNSK----KRGKK 211
LT ER EII+ F + DT P QI ++I++ L L + K +RG
Sbjct: 2 LTQERKREIIEQFKVHENDTGSPEVQIAILTEQINN-----LNEHLRVHKKDHHSRRGLL 56
Query: 212 KK 213
K
Sbjct: 57 KM 58
>3ofo_O 30S ribosomal protein S15; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_O
1p87_O 3ofp_O 3i1m_O 2qan_O* 2qb9_O* 2qbb_O* 2qbd_O
2qbf_O 2qbh_O* 2qbj_O* 2qou_O* 2qow_O* 2qoy_O* 2qp0_O*
2vaz_F 2z4k_O* 2z4m_O* 2qal_O 3i1o_O ...
Length = 88
Score = 28.1 bits (63), Expect = 1.7
Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 13/62 (20%)
Query: 160 LTPERLEEIIDAFSTGQGDTIRPGPQI----DRISSAPAGGLTSLLDNNSK----KRGKK 211
L+ E +I+ F DT Q+ +I+ L + K +RG
Sbjct: 2 LSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINH-----LQGHFAEHKKDHHSRRGLL 56
Query: 212 KK 213
+
Sbjct: 57 RM 58
>2wer_A ATP-dependent molecular chaperone HSP82; ATPase, cytoplasm,
ATP-binding, phosphoprotein, stress response,
nucleotide-binding; HET: RDC; 1.60A {Saccharomyces
cerevisiae} PDB: 2weq_A* 2wep_A* 1zwh_A* 1zw9_A* 2fxs_A*
3c11_A* 3c0e_A* 2akp_A
Length = 220
Score = 27.7 bits (61), Expect = 2.3
Identities = 17/106 (16%), Positives = 44/106 (41%), Gaps = 7/106 (6%)
Query: 75 VLEIATFYTQFQLSPVGTRAHVQVCGTTPC----MLRGCEKLIEVCRNKIHQKPLHRNSD 130
+ IA T+ + + A V + G + +++ + ++ ++ + ++
Sbjct: 93 LGTIAKSGTKAFMEALSAGADVSMIGQFGVGFYSLFLVADRVQVISKSNDDEQYIWESNA 152
Query: 131 G---TLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFS 173
G T++ +EV + + + D E L +R++E+I S
Sbjct: 153 GGSFTVTLDEVNERIGRGTILRLFLKDDQLEYLEEKRIKEVIKRHS 198
>1te4_A Conserved protein MTH187; methanobacterium thermoautotrophicum,
structural proteomics, heat-like repeat; NMR
{Methanothermobacterthermautotrophicus} SCOP:
a.118.1.16
Length = 131
Score = 27.5 bits (60), Expect = 2.7
Identities = 9/38 (23%), Positives = 18/38 (47%)
Query: 40 SAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLE 77
S ++P ++ WV R ++ + D A+ +LE
Sbjct: 12 SGLVPRGSHMADENKWVRRDVSTALSRMGDEAFEPLLE 49
>3i1m_O 30S ribosomal protein S15; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 2qan_O* 2qb9_O* 2qbb_O* 2qbd_O 2qbf_O
2qbh_O* 2qbj_O* 2qou_O* 2qow_O* 2qoy_O* 2qp0_O* 2vaz_F
2z4k_O* 2z4m_O* 2qal_O 3i1o_O 3i1q_O 3i1s_O 3i1z_O
3i21_O ...
Length = 89
Score = 27.0 bits (60), Expect = 3.8
Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 13/62 (20%)
Query: 160 LTPERLEEIIDAFSTGQGDTIRPGPQI----DRISSAPAGGLTSLLDNNSK----KRGKK 211
L+ E +I+ F DT Q+ +I+ L + K +RG
Sbjct: 3 LSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINH-----LQGHFAEHKKDHHSRRGLL 57
Query: 212 KK 213
+
Sbjct: 58 RM 59
>2cs2_A Poly [ADP-ribose] polymerase-1; DNA BIND, DNA repair, necrosis,
apoptosis, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 134
Score = 26.9 bits (59), Expect = 4.2
Identities = 15/94 (15%), Positives = 25/94 (26%), Gaps = 8/94 (8%)
Query: 107 RGCEKLIE--VCR-NKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDT-----YE 158
+GC + IE R +K P W C +
Sbjct: 31 KGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVKNREELGFRPEYSASQLKGFS 90
Query: 159 DLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSA 192
L E E + + + R G ++D +
Sbjct: 91 LLATEDKEALKKQLPGVKSEGKRKGDEVDGVDEV 124
>2vqe_O 30S ribosomal protein S15; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: i.1.1.1 PDB: 1eg0_F*
1gix_R* 1hnw_O* 1hnx_O* 1hnz_O* 1hr0_O 1ibk_O* 1ibl_O*
1ibm_O 1jgo_R* 1jgp_R* 1jgq_R* 1ml5_R* 1xmo_O* 1xmq_O*
1xnq_O* 1xnr_O* 1yl4_R 2b64_O* 2b9m_O* ...
Length = 89
Score = 26.6 bits (59), Expect = 4.7
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 13/62 (20%)
Query: 160 LTPERLEEIIDAFSTGQGDTIRPGPQI----DRISSAPAGGLTSLLDNNSK----KRGKK 211
+T E +++I F+ GDT Q+ RI+ L+ L + K RG
Sbjct: 3 ITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINR-----LSEHLKVHKKDHHSHRGLL 57
Query: 212 KK 213
Sbjct: 58 MM 59
>2uva_G Fatty acid synthase beta subunits; fungal, dehydratase, enoyl
reductase, ketoacyl synthase, ketoacyl reductase; HET:
FMN; 3.10A {Thermomyces lanuginosus} PDB: 2uvc_G*
Length = 2060
Score = 26.0 bits (57), Expect = 7.8
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 148 PMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRP 182
PM+ I DLT ++E IDA + +
Sbjct: 331 PMLSI-----RDLTRSAVQEHIDATNQHLPEDRHI 360
>1j2q_H Proteasome beta subunit; ubiquitin, CP, hydrolase; HET: CIB; 2.83A
{Archaeoglobus fulgidus} SCOP: d.153.1.4
Length = 202
Score = 25.8 bits (56), Expect = 8.2
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 149 MVMIGKDTYEDLTPERLEEIIDAF 172
+V I +D + +PE +E+I+ F
Sbjct: 177 VVKITEDEFYQYSPEEVEQILAKF 200
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.317 0.132 0.393
Gapped
Lambda K H
0.267 0.0567 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,921,958
Number of extensions: 87833
Number of successful extensions: 367
Number of sequences better than 10.0: 1
Number of HSP's gapped: 363
Number of HSP's successfully gapped: 22
Length of query: 218
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 129
Effective length of database: 3,535,514
Effective search space: 456081306
Effective search space used: 456081306
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 (21.7 bits)
S2: 55 (25.3 bits)