RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780801|ref|YP_003065214.1| hypothetical protein
CLIBASIA_03460 [Candidatus Liberibacter asiaticus str. psy62]
(222 letters)
>1ct5_A Protein (yeast hypothetical protein, selenoMet); TIM barrel,
pyridoxal-5'-phosphate, selenomethionine, MAD,
structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces
cerevisiae} SCOP: c.1.6.2 PDB: 1b54_A*
Length = 256
Score = 192 bits (490), Expect = 5e-50
Identities = 66/237 (27%), Positives = 101/237 (42%), Gaps = 22/237 (9%)
Query: 3 LGNKLQVFKQKIENSA--ILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60
L + + ++ + A + + L+ VSK+ + I++ G F EN +QE
Sbjct: 14 LIAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYDHGVREFGENYVQE 73
Query: 61 AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSL--FDVIETVSREKTASLLSLEMIK--- 115
+K L D++ FIG LQ+NK ++ + +ET+ K A L+ K
Sbjct: 74 LIEKAKLLPD--DIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQP 131
Query: 116 QSRFLPVYIQVNTGYEIQKSGIMPNQTKDFV---ILCRQKYQLNVEGLMCIP-----PAM 167
+ +Q+NT +E QKSG+ V L + + + GLM I
Sbjct: 132 DCNPILCNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGLMTIGSWNVSHED 191
Query: 168 GNPKPHFYLLSEIARECK-----LTKLSMGMTRDFELAIASGATSVRIGSGIFGERP 219
F L E ++ KLSMGM+ DF AI G VRIG+ IFG RP
Sbjct: 192 SKENRDFATLVEWKKKIDAKFGTSLKLSMGMSADFREAIRQGTAEVRIGTDIFGARP 248
>3cpg_A Uncharacterized protein; unknown protein, TIM barrel, monomer,
structural genomics, PSI-2, protein structure
initiative; 1.71A {Bifidobacterium adolescentis
ATCC15703}
Length = 282
Score = 176 bits (448), Expect = 3e-45
Identities = 67/243 (27%), Positives = 101/243 (41%), Gaps = 31/243 (12%)
Query: 7 LQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWI 66
+ +I + A R SV L+A +K D +I A+ G + EN+ QE K
Sbjct: 29 VHRVLDRIAAAEEQAGREAGSVRLLAATKTRDIGEIMAAIDAGVRMIGENRPQEVTAKAE 88
Query: 67 PLRK-------------------EWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTAS 107
L + + IG LQSNK+ +++ + D IE+V A
Sbjct: 89 GLARRCAERGFSLGVAGAAPDAAAEHIPFHLIGQLQSNKIGKVLPVVDTIESVDSIDLAE 148
Query: 108 LLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAM 167
+S + + + V ++VN E KSG P + ++GLM I +
Sbjct: 149 KISRRAVARGITVGVLLEVNESGEESKSGCDPAHAIRIAQKIGTLDGIELQGLMTIGAHV 208
Query: 168 GNP---KPHFYLLSEIARECK---------LTKLSMGMTRDFELAIASGATSVRIGSGIF 215
+ + F L + +LSMGMT D ELAIA G+T VR+G+ IF
Sbjct: 209 HDETVIRRGFSHLRKTRDLILASGEPGTDRCRELSMGMTGDMELAIAEGSTIVRVGTAIF 268
Query: 216 GER 218
GER
Sbjct: 269 GER 271
>1w8g_A YGGS, hypothetical UPF0001 protein YGGS; structural genomics,
hypothetical protein, putative enzyme with PLP-binding
domain; HET: PLP ICT; 2.0A {Escherichia coli}
Length = 234
Score = 146 bits (370), Expect = 3e-36
Identities = 72/229 (31%), Positives = 109/229 (47%), Gaps = 11/229 (4%)
Query: 1 MS-LGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQ 59
M+ + + L + KI +A R + ++L+AVSK + I A+ GQ F EN +Q
Sbjct: 1 MNDIAHNLAQVRDKISAAATRCGRSPEEITLLAVSKTKPASAIAEAIDAGQRQFGENYVQ 60
Query: 60 E--AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQS 117
E K + ++ FIG LQSNK + FD T+ R + A+ L+ + +
Sbjct: 61 EGVDKIRHFQELGVTGLEWHFIGPLQSNKSRLVAEHFDWCHTIDRLRIATRLNDQRPAEL 120
Query: 118 RFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLL 177
L V IQ+N E KSGI + + + +L + GLM IP F +
Sbjct: 121 PPLNVLIQINISDENSKSGIQLAELDELAAAVAELPRLRLRGLMAIPAPESEYVRQFEVA 180
Query: 178 SEIARECK--------LTKLSMGMTRDFELAIASGATSVRIGSGIFGER 218
++A + LS+GM+ D E AIA+G+T VRIG+ IFG R
Sbjct: 181 RQMAVAFAGLKTRYPHIDTLSLGMSDDMEAAIAAGSTMVRIGTAIFGAR 229
>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 = 43.0 bits (101), Expect = 6e-05
Identities = 42/218 (19%), Positives = 67/218 (30%), Gaps = 93/218 (42%)
Query: 12 QKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIF-----AENKLQEAKKKWI 66
K NSA+ + + LVA IF ++ +E
Sbjct: 138 DKKSNSALFRAVGEGNAQLVA-------------------IFGGQGNTDDYFEE------ 172
Query: 67 PLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQV 126
LR + +G D+I+ + E + L+ V+ Q
Sbjct: 173 -LRDLYQTYHVLVG--------------DLIKFSA-ETLSELIRTT----LDAEKVFTQ- 211
Query: 127 NTGYEIQK--SGIMPNQTKDFVILCRQKYQLNVEGLMCIP---PAMGNPKPHFYLLSEIA 181
G I + P+ T D + Y L+ IP P +G + ++A
Sbjct: 212 --GLNILEWLEN--PSNTPD------KDY------LLSIPISCPLIG--------VIQLA 247
Query: 182 R---ECKLTKLSMGMTRDFELAIASGATSVRIG-S-GI 214
KL + G R + L GAT G S G+
Sbjct: 248 HYVVTAKLLGFTPGELRSY-L---KGAT----GHSQGL 277
Score = 28.0 bits (62), Expect = 1.6
Identities = 33/158 (20%), Positives = 53/158 (33%), Gaps = 75/158 (47%)
Query: 28 VSLVAVSKMVDS---------KKIRVALSCG---QVIF-----AENKLQEAKK--KWIP- 67
V+ VA++ DS K I V G + + L+++ + + +P
Sbjct: 278 VTAVAIA-ETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS 336
Query: 68 -------LRKEWDVQLRFIG----SLQSNK-VSEIVSLFD-----VIETVSREKT---AS 107
L +E VQ ++ L + K V +SL + V+ + S
Sbjct: 337 PMLSISNLTQE-QVQ-DYVNKTNSHLPAGKQVE--ISLVNGAKNLVV-------SGPPQS 385
Query: 108 L----LSLEMIK------QSR-------------FLPV 122
L L+L K QSR FLPV
Sbjct: 386 LYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPV 423
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.8 bits (66), Expect = 0.46
Identities = 33/139 (23%), Positives = 57/139 (41%), Gaps = 47/139 (33%)
Query: 54 AENKLQEAKKKW-----------IPLRKEWDVQLRFIGSLQSN--KVSEI-VSLFDVIET 99
AE++L+ A+++W PLR G+L + + ++ V+ F T
Sbjct: 1298 AESQLRAAQQQWGNDFYKRDPRIAPLR----------GALATYGLTIDDLGVASFHGTST 1347
Query: 100 VSREKTASLLSLEMIKQ-------------SRFLPVYIQ-------VNTGYEIQKSGIMP 139
+ +K S EM+K +FL + + +N +I SGI+P
Sbjct: 1348 KANDKNESATINEMMKHLGRSEGNPVIGVFQKFLTGHPKGAAGAWMMNGALQILNSGIIP 1407
Query: 140 -NQTKDFV--ILCRQKYQL 155
N+ D V IL + +Y L
Sbjct: 1408 GNRNADNVDKILEQFEYVL 1426
>3cpr_A Dihydrodipicolinate synthetase; (beta/alpha)8-barrel fold with A
C-terminal alpha-helical segment, amino-acid
biosynthesis, cytoplasm; HET: MCL; 2.20A
{Corynebacterium glutamicum}
Length = 304
Score = 27.5 bits (60), Expect = 2.8
Identities = 10/67 (14%), Positives = 20/67 (29%), Gaps = 2/67 (2%)
Query: 106 ASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPP 165
+ + + L + +G+ N T+ V L +GL+ + P
Sbjct: 63 SPTTTAAEKLE--LLKAVREEVGDRAKLIAGVGTNNTRTSVELAEAAASAGADGLLVVTP 120
Query: 166 AMGNPKP 172
P
Sbjct: 121 YYSKPSQ 127
>3noe_A DAP-A, dihydrodipicolinate synthase; Lys biosynthesis pathway,
lyase; 2.95A {Pseudomonas aeruginosa}
Length = 292
Score = 26.8 bits (59), Expect = 3.9
Identities = 11/65 (16%), Positives = 22/65 (33%), Gaps = 2/65 (3%)
Query: 106 ASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPP 165
++ L +E Q + + G +G N T++ V L + + + P
Sbjct: 48 SATLDVEEHIQ--VVRRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTP 105
Query: 166 AMGNP 170
P
Sbjct: 106 YYNKP 110
>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.34.5.1 PDB: 1nwx_S* 1nwy_S* 1sm1_S*
1xbp_S* 2d3o_S 2zjp_R* 2zjq_R 1nkw_S 3cf5_R* 3dll_R*
1pnu_S 1pny_S 1vor_V 1vou_V 1vow_V 1voy_V 1vp0_V
Length = 115
Score = 26.6 bits (59), Expect = 4.3
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 35 KMVDSKKIRVALSCGQVI 52
++VD KK+RVA++ G+ I
Sbjct: 97 QIVDGKKVRVAVASGKTI 114
>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 191
Score = 26.4 bits (58), Expect = 4.8
Identities = 6/27 (22%), Positives = 16/27 (59%)
Query: 38 DSKKIRVALSCGQVIFAENKLQEAKKK 64
D +K+R + G+++ ++ +E + K
Sbjct: 154 DVRKVRYLIKTGEIVDTPDRWKEIQNK 180
>3bi8_A Dihydrodipicolinate synthase; TIM-barrel, amino-acid biosynthesis,
cytoplasm, diaminopimelate biosynthesis, lyase, lysine
biosynthesis; HET: MLT; 1.96A {Clostridium botulinum}
PDB: 3ird_A*
Length = 291
Score = 26.3 bits (57), Expect = 5.2
Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 8/56 (14%)
Query: 136 GIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKP-----HFYLLSEIARECKL 186
G N T + + + + V+GL+ I P HF ++
Sbjct: 76 GTGSNNTAASIAMSKWAESIGVDGLLVITPYYNKTTQKGLVKHF---KAVSDAVST 128
>1y0e_A Putative N-acetylmannosamine-6-phosphate 2- epimerase; mannac-6-P
epimerase, NANE, structural genomics, protein structure
initiative; 1.95A {Staphylococcus aureus subsp} SCOP:
c.1.2.5
Length = 223
Score = 26.4 bits (57), Expect = 5.6
Identities = 11/84 (13%), Positives = 24/84 (28%), Gaps = 5/84 (5%)
Query: 139 PNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTR--- 195
+ K+ L + G + F L ++ + ++ G
Sbjct: 129 VEEAKNAARLGFDYIGTTLHGYTSYTQGQLLYQNDFQFLKDVLQSVDAKVIAEGNVITPD 188
Query: 196 DFELAIASGATSVRIGSGIFGERP 219
++ + G +G I RP
Sbjct: 189 MYKRVMDLGVHCSVVGGAIT--RP 210
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.0 bits (56), Expect = 6.7
Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 32/95 (33%)
Query: 60 EAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRF 119
E+ +KW R+E Q ++ E+ + V+E REK L +QS
Sbjct: 85 ESIRKW---REE-----------QRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSE- 129
Query: 120 LPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQ 154
+++K+ I N+ D + YQ
Sbjct: 130 -----------QVEKNKI-NNRIAD-----KAFYQ 147
>3ofq_U 50S ribosomal protein L24; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, antibi EXIT, peptidyl, ribosomal
subunit, large; 3.10A {Escherichia coli} PDB: 2j28_U*
3fik_U 2wwq_U 3ofr_U* 3i1n_U 1vs8_U 1vs6_U 1vt2_U 3i1p_U
3i1r_U 3i1t_U 3i20_U 3i22_U 3kcr_U 3orb_U* 3e1b_O 3e1d_O
2qam_U* 1p85_S 1p86_S ...
Length = 102
Score = 25.8 bits (57), Expect = 7.6
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 35 KMVDSKKIRVALSCGQVI 52
+ D KK+R S + I
Sbjct: 85 RFEDGKKVRFFKSNSETI 102
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
0.320 0.134 0.378
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,758,281
Number of extensions: 75654
Number of successful extensions: 244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 234
Number of HSP's successfully gapped: 19
Length of query: 222
Length of database: 5,693,230
Length adjustment: 89
Effective length of query: 133
Effective length of database: 3,535,514
Effective search space: 470223362
Effective search space used: 470223362
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 (25.0 bits)