RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780775|ref|YP_003065188.1| undecaprenyl diphosphate
synthase [Candidatus Liberibacter asiaticus str. psy62]
(243 letters)
>1f75_A Undecaprenyl pyrophosphate synthetase; parallel beta sheet, NEW
fold for isoprenoid synthase, peptidoglycan synthesis,
transferase; 2.20A {Micrococcus luteus} SCOP: c.101.1.1
Length = 249
Score = 283 bits (726), Expect = 2e-77
Identities = 103/229 (44%), Positives = 147/229 (64%)
Query: 11 PDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRR 70
P HI IIMDGNGRWA + +PR GH +G++ +I A+++G+K LT++AFS NW R
Sbjct: 21 PKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASDLGVKYLTLYAFSTENWSR 80
Query: 71 PVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLNTGL 130
P E++ L+KL FL L + N+KV IG L D + EA+++T+ NTGL
Sbjct: 81 PKDEVNYLMKLPGDFLNTFLPELIEKNVKVETIGFIDDLPDHTKKAVLEAKEKTKHNTGL 140
Query: 131 NLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLIIRTGG 190
L A NY R EI A++ I + +SG + ++ + +YL T+++PDP+L+IRT G
Sbjct: 141 TLVFALNYGGRKEIISAVQLIAERYKSGEISLDEISETHFNEYLFTANMPDPELLIRTSG 200
Query: 191 EKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRRFGGL 239
E+RLS+FL+WQ +YSEFVFI E+WPDF+ E ++ Y R RRFGGL
Sbjct: 201 EERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQNRHRRFGGL 249
>1ueh_A Undecaprenyl pyrophosphate synthase; parallel alpha-beta,
rossmann-like fold, transferase; HET: OXN; 1.73A
{Escherichia coli} SCOP: c.101.1.1 PDB: 1jp3_A* 1v7u_A*
1x06_A* 1x07_A* 2e98_A* 2e99_A* 2e9a_A* 2e9c_A* 2e9d_A*
1x09_A* 1x08_A*
Length = 253
Score = 222 bits (566), Expect = 7e-59
Identities = 89/233 (38%), Positives = 141/233 (60%)
Query: 6 MSSSPPDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSI 65
+ + H+ IIMDGNGRWA +G R GH+ G + V+ AA GI+ LT++AFS
Sbjct: 13 LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSS 72
Query: 66 NNWRRPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTR 125
NW RP E+S L++L L SL ++N+++R+IG+ + + ++++E T
Sbjct: 73 ENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTA 132
Query: 126 LNTGLNLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLI 185
NTGL L IA NY R +I + ++ + + ++ G++ +D ++ +++ ++ DL+
Sbjct: 133 GNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLV 192
Query: 186 IRTGGEKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRRFGG 238
IRTGGE R+S+FLLWQ+AY+E F WPDF + F ALN + R+RRFGG
Sbjct: 193 IRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRERRFGG 245
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL
biogenesis/degradation, cell cycle, cell shape, cell
division; HET: GPP; 1.8A {Mycobacterium tuberculosis}
PDB: 2vg2_A* 2vg4_A
Length = 284
Score = 219 bits (558), Expect = 5e-58
Identities = 88/228 (38%), Positives = 138/228 (60%)
Query: 11 PDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRR 70
P+H+ I+MDGNGRWA RGL R GH+ G V +I A E+GIK L+++AFS NW+R
Sbjct: 56 PNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWKR 115
Query: 71 PVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLNTGL 130
E+ L+ + +++ +LKK +++R +G+R L ++ L AE+ T+ N +
Sbjct: 116 SPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGSRPRLWRSVINELAVAEEMTKSNDVI 175
Query: 131 NLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLIIRTGG 190
+ NY R EI+ A + I +++ +G + + S IA++L D+PD DL +RT G
Sbjct: 176 TINYCVNYGGRTEITEATREIAREVAAGRLNPERITESTIARHLQRPDIPDVDLFLRTSG 235
Query: 191 EKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRRFGG 238
E+R S+F+LWQ AY+E++F + WPD+ R + A +Y R RRFG
Sbjct: 236 EQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYASRTRRFGS 283
>2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase; 1.88A
{Helicobacter pylori} PDB: 2dtn_A
Length = 245
Score = 213 bits (543), Expect = 3e-56
Identities = 88/245 (35%), Positives = 140/245 (57%), Gaps = 10/245 (4%)
Query: 5 MMSS---------SPPDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGI 55
M+S+ S H+ IIMDGNGRWA + R GH+KG++ +I A +
Sbjct: 1 MLSATQPLSEKLDSTLKHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKL 60
Query: 56 KNLTIFAFSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILC 115
+ LT++AFS NW+RP SE+ L+K++K +LK + NNI+ R IG+ ++
Sbjct: 61 ECLTLYAFSTENWKRPKSEVDFLMKMLKKYLKDERSTYLDNNIRFRAIGDLEGFSKELRD 120
Query: 116 VLKEAEDQTRLNTGLNLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLD 175
+ + E+ TR +A NY S++E+SRA K++ + S +++ + LD
Sbjct: 121 TILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPPSNISLLESLENEIS-NRLD 179
Query: 176 TSDVPDPDLIIRTGGEKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRR 235
T ++P+ DL++RTGGE RLS+FLLWQ +Y+E F P WPDF+ + + ++ + R R+
Sbjct: 180 TRNLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFYKRVRK 239
Query: 236 FGGLS 240
FG L
Sbjct: 240 FGELK 244
>2vg0_A Short-chain Z-isoprenyl diphosphate synthetase; peptidoglycan
synthesis, cell WALL biogenesis/degradation, secreted,
cell shape; HET: GPP; 1.7A {Mycobacterium tuberculosis}
PDB: 2vfw_A* 2vg1_A*
Length = 227
Score = 182 bits (463), Expect = 5e-47
Identities = 73/227 (32%), Positives = 113/227 (49%), Gaps = 7/227 (3%)
Query: 11 PDHIGIIMDGNGRWAAARGLPRCA-GHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWR 69
P HI ++ DGN RWA + G + G+R G E++ E GI+ T++ S N +
Sbjct: 3 PRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQ 62
Query: 70 RPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLNTG 129
R E++ L+++I +++ N+ VR +G+ + ++ L+ A + T
Sbjct: 63 RDPDELAALIEIITDVVEE--ICAPANHWSVRTVGDLGLIGEEPARRLRGAVESTPEVAS 120
Query: 130 LNLFIAFNYSSRDEISRAIKNIFQDIESG----SVCSHDVDSSLIAKYLDTSDVPDPDLI 185
++ +A Y R EI A++ + + V I++ L TS PDPDL+
Sbjct: 121 FHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLV 180
Query: 186 IRTGGEKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLR 232
IRT GE+RLS FLLWQ AYSE F +WP F F AL Y+ R
Sbjct: 181 IRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYSAR 227
>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 = 38.8 bits (90), Expect = 0.001
Identities = 50/274 (18%), Positives = 73/274 (26%), Gaps = 120/274 (43%)
Query: 7 SSSPPDHIGIIMD----GNGRWA---AARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLT 59
+S PP I+ D G + + L + + N + A +V I
Sbjct: 317 TSLPPS---ILEDSLENNEGVPSPMLSISNLTQEQVQ-DYVNKTNSHLPAGKQVEI---- 368
Query: 60 IFAFSINNWRR-------PVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDD 112
S+ N + P S L Y L N+ +R L
Sbjct: 369 ----SLVNGAKNLVVSGPPQS----L------------YGL---NLTLRKAKAPSGL--- 402
Query: 113 ILCVLKEAEDQTRLNTGLNLFIAFNYSSRD-EIS----------------RAIKNIFQDI 155
DQ+R I F S R + S A I +D+
Sbjct: 403 ---------DQSR--------IPF--SERKLKFSNRFLPVASPFHSHLLVPASDLINKDL 443
Query: 156 ESGSVCSHDVD---SSL-IAKYLDTSDVPDPDLIIRTGGEKRLSDFLLWQVAYSEFVFIP 211
++V + I Y DT D D +R ++ + V
Sbjct: 444 V-----KNNVSFNAKDIQIPVY-DTFDGSD----LRVLSGSISER-IVDCII-RLPVK-- 489
Query: 212 EYWPDFSRELFF---HALNQYNLRDRRF--GGLS 240
W F H L D F GG S
Sbjct: 490 --WE---TTTQFKATHIL------D--FGPGGAS 510
Score = 36.1 bits (83), Expect = 0.008
Identities = 33/183 (18%), Positives = 58/183 (31%), Gaps = 37/183 (20%)
Query: 73 SEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDIL-CVLKEAEDQTRLNTGLN 131
E + +L+ FL G+ + V +++ D +L L E E+ ++
Sbjct: 52 DEPTTPAELVGKFL--GY-------VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIH 102
Query: 132 LFIAFNYSSRD----EISRAIKNIFQDIE-SGSVCSHDVDSSLIAKYLDTSDVPDPDLII 186
A D + IKN + +S+L V + + +
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF------RAVGEGNAQL 156
Query: 187 RT--GGEKRLSDFL-----LWQVAYSEFV--FIPEYWPDFSRELFFHALNQYNLRDRRFG 237
GG+ D+ L+Q Y V I FS E + ++ F
Sbjct: 157 VAIFGGQGNTDDYFEELRDLYQT-YHVLVGDLI-----KFSAETLSELIRTTLDAEKVFT 210
Query: 238 -GL 239
GL
Sbjct: 211 QGL 213
>2hj0_A Putative citrate lyase, ALFA subunit; alpha beta protein.,
structural genomics, PSI-2, protein structure
initiative; HET: CIT; 2.70A {Streptococcus mutans UA159}
Length = 519
Score = 36.0 bits (83), Expect = 0.009
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 37 RKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRRPVSEISE---LVKLIKSFL 86
R+G V N ++ A++GIK+++I SI N P+ + + + + S L
Sbjct: 74 REGDYVMNMVLDEIAKMGIKDISIAPSSIANVHEPLIDHIKNGVVTNITSSGL 126
>1xr4_A Putative citrate lyase alpha chain/citrate-ACP transferase; the
midwest center for structural genomics, MCSG, structural
genomics; 2.37A {Salmonella typhimurium LT2} SCOP:
c.124.1.2 c.124.1.2
Length = 509
Score = 34.1 bits (78), Expect = 0.028
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 37 RKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRRPVSEISELVKLIKS 84
R G +V N ++A AE+G ++LT+ + S+ + L++ IK+
Sbjct: 71 RGGDKVVNMVMAKLAEMGFRDLTLASSSLID------AHWPLIEHIKN 112
>1yj5_A 5' polynucleotide kinase-3' phosphatase catalytic domain; beta
sandwich, P-loop, transferase; 2.80A {Mus musculus}
SCOP: c.108.1.9 c.37.1.1
Length = 383
Score = 30.8 bits (69), Expect = 0.31
Identities = 21/168 (12%), Positives = 51/168 (30%), Gaps = 10/168 (5%)
Query: 40 IEVFNEIVAA-AAEVGIKNLTIFAFSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNI 98
EVF V A ++G+ + A R+P + + ++ + +
Sbjct: 89 AEVFKGKVEAVLEKLGVPFQVLVATHAGLNRKP------VSGMWDHLQEQANEGIPISVE 142
Query: 99 KVRVIGNRLS-LDDDILCVLKEAEDQTRLNTGLNLFIAFNYSSRDEISRAIKNIFQDIES 157
+G+ L + K+ LN+ + F +E ++ +
Sbjct: 143 DSVFVGDAAGRLANWAPGRKKKDFSCADRLFALNVGLPFATP--EEFFLKWPAARFELPA 200
Query: 158 GSVCSHDVDSSLIAKYLDTSDVPDPDLIIRTGGEKRLSDFLLWQVAYS 205
+ L + P+P++++ G + + S
Sbjct: 201 FDPRTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFIQEHLVS 248
>3h4p_a Proteasome subunit beta; core particle, cytoplasm, hydrolase,
protease, threonine protease; 4.10A {Methanocaldococcus
jannaschii}
Length = 219
Score = 28.8 bits (64), Expect = 1.2
Identities = 0/80 (0%), Positives = 0/80 (0%), Gaps = 8/80 (10%)
Query: 50 AAEVGIKNLTIFAFSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGN---- 105
A E + + ++
Sbjct: 166 AMERDTFSGNGISLAVITKDGVKIF- 224
Query: 106 --RLSLDDDILCVLKEAEDQ 123
Sbjct: 225 - 243
>1h0b_A Cellulase; endoglucanase, hydrolase; HET: EPE; 1.8A {Rhodothermus
marinus} SCOP: b.29.1.11
Length = 256
Score = 28.7 bits (64), Expect = 1.3
Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 6/54 (11%)
Query: 24 WAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIF------AFSINNWRRP 71
A ARG R + +E E+ A + + ++ A I +P
Sbjct: 186 DAVARGYIRPEWYLHAVETGFELWEGGAGLRSADFSVTVQKLAAALEIKRASQP 239
>1i60_A IOLI protein; beta barrel, structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; 1.60A {Bacillus subtilis} SCOP: c.1.15.4
PDB: 1i6n_A
Length = 278
Score = 28.2 bits (62), Expect = 1.8
Identities = 9/59 (15%), Positives = 21/59 (35%), Gaps = 7/59 (11%)
Query: 34 AGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSIN-------NWRRPVSEISELVKLIKSF 85
GH + I F ++ +G+K + + V ++EL + + +
Sbjct: 77 KGHNEIITEFKGMMETCKTLGVKYVVAVPLVTEQKIVKEEIKKSSVDVLTELSDIAEPY 135
>2g8y_A Malate/L-lactate dehydrogenases; NAD, E.coli, structural genomics,
PSI, protein structure initiative, midwest center for
structural genomics; HET: NAD 1PE; 2.15A {Escherichia
coli K12}
Length = 385
Score = 27.4 bits (60), Expect = 2.7
Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 9/68 (13%)
Query: 1 MVASMMSSSPPDHIGIIMDGNGRWAAARGLPRCAGHRKGI----EVFNEIVAAAAEVGIK 56
+ +S D I++ G R ++GI + I AA ++G+
Sbjct: 316 FAEWVKASPHDDDKPILLPGEWEVNTRR-----ERQKQGIPLDAGSWQAICDAARQIGMP 370
Query: 57 NLTIFAFS 64
T+ AF
Sbjct: 371 EETLQAFC 378
>2v1l_A Hypothetical protein; pathogenicity island, unknown function; 2.13A
{Vibrio cholerae}
Length = 148
Score = 27.4 bits (61), Expect = 3.3
Identities = 7/32 (21%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 199 LWQVAY-SEFVFIPEYWPDFSRELFFHALNQY 229
W + Y ++F ++ ++P+ R L F
Sbjct: 71 QWCIEYITDFAYVGNHFPELERCLDFDFQRGD 102
>2w56_A VC0508; unknown function; 1.90A {Vibrio cholerae} PDB: 2w56_B
Length = 147
Score = 27.2 bits (60), Expect = 3.5
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 200 WQVAY-SEFVFIPEYWPDFSRELFFHALNQY 229
W + Y ++F ++ Y+P+ R L F
Sbjct: 72 WSIEYITDFAYMGNYYPELERNLDFDFRVGQ 102
>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 = 27.3 bits (59), Expect = 3.6
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 13/34 (38%)
Query: 121 EDQT--RLNTGLNLFIAFNYSSRDEISR---AIK 149
E Q +L L L Y+ D+ S AIK
Sbjct: 18 EKQALKKLQASLKL-----YA--DD-SAPALAIK 43
>3krb_A Aldose reductase; ssgcid, SBRI, emerald biostructures, university
of washington, NIH, niaid, oxidoreductase, structural
genomics; HET: NAP; 1.75A {Giardia lamblia atcc 50803}
Length = 334
Score = 26.5 bits (57), Expect = 6.1
Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 3/48 (6%)
Query: 118 KEAEDQTR--LNTGLNLF-IAFNYSSRDEISRAIKNIFQDIESGSVCS 162
+ + L TG A+ Y + + I RA IF+D SG
Sbjct: 38 EAVQTAVETALMTGYRHIDCAYVYQNEEAIGRAFGKIFKDASSGIKRE 85
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
0.322 0.139 0.413
Gapped
Lambda K H
0.267 0.0442 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,214,894
Number of extensions: 104551
Number of successful extensions: 345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 342
Number of HSP's successfully gapped: 29
Length of query: 243
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 153
Effective length of database: 3,511,270
Effective search space: 537224310
Effective search space used: 537224310
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 (21.9 bits)
S2: 55 (25.7 bits)