RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781016|ref|YP_003065429.1| diphosphomevalonate
decarboxylase/isopentenyl-diphosphate delta-isomerase [Candidatus
Liberibacter asiaticus str. psy62]
(355 letters)
>gnl|CDD|130307 TIGR01240, mevDPdecarb, diphosphomevalonate decarboxylase.
Alternate names: mevalonate diphosphate decarboxylase;
pyrophosphomevalonate decarboxylase.
Length = 305
Score = 265 bits (679), Expect = 1e-71
Identities = 118/301 (39%), Positives = 167/301 (55%), Gaps = 5/301 (1%)
Query: 25 SAFLPSNIALCKYWGKRDSKLNLPLNNSLSLSLGHLGTITHITVIDS-DADCIILNGQKI 83
S NIA KYWGKR++KLNLP N+S+SL+L L T+T + D + D LNG
Sbjct: 2 SVTAYVNIATIKYWGKRNTKLNLPTNSSISLTLSQLRTLTSVAFADEFERDTFYLNGTLQ 61
Query: 84 SSQSSFFKKTTQFCDLFRQFSKV--YFLIETSNNIPTKAGLASSASGFAALTLALFRIYS 141
S + +KT+ D FRQ K I + NN PT AGLASSASG AAL A ++Y
Sbjct: 62 HSIDN--EKTSNCLDDFRQLRKEQEKLHIVSQNNFPTAAGLASSASGLAALVSACAKLYQ 119
Query: 142 IPEKSESLSRVARLGSGSACRSFYRGFCEWICGTDQNGMDSFAVPFNNQWPDLRIGLLKI 201
+P + LSR+AR GSGSACRS + G+ W G D + + V ++ WP + +L +
Sbjct: 120 LPLDTSELSRIARKGSGSACRSLFGGYVAWEKGKDDHSSAAVQVADDSDWPQXAMCVLVV 179
Query: 202 IDREKKIGSREAMEITRHHSPFFTQWTQQISTDLAHIKQAIIDQDFIKLGEVAEKNALKM 261
D +K + SR+ M++T S F +W + + D ++AI +DF G+ E N+L M
Sbjct: 180 NDIKKDVSSRQGMQLTVATSELFKEWIEHVVPDFEVXRKAIKTKDFATFGKETEANSLSM 239
Query: 262 HATMIAASPPLLYWQKETIQGMERVWDARQQSIPIYFTLDAGPNLKLLFTHKIEETIKQF 321
HAT + A PP Y + + M V RQ YFT+DAGPN+K+L+ + + +F
Sbjct: 240 HATTLDAFPPFFYLNDTSKRAMSAVHTLRQGGTICYFTMDAGPNVKVLYLAENLSKLFEF 299
Query: 322 F 322
Sbjct: 300 I 300
>gnl|CDD|178029 PLN02407, PLN02407, diphosphomevalonate decarboxylase.
Length = 343
Score = 193 bits (492), Expect = 6e-50
Identities = 107/326 (32%), Positives = 173/326 (53%), Gaps = 32/326 (9%)
Query: 29 PSNIALCKYWGKRDSKLNLPLNNSLSLSL--GHLGTITHITVIDS-DADCIILNGQKISS 85
P+NIA+ KYWGKRD KL LP+N+S+S++L HL T + V S D D + LNG++IS
Sbjct: 9 PTNIAVIKYWGKRDEKLILPINSSISVTLDPDHLCATTTVAVSPSFDQDRLWLNGKEISL 68
Query: 86 QSSFFKKT-----TQFCDLF----------RQFSKVYFLIETSNNIPTKAGLASSASGFA 130
++ + D+ + + K++ I + NN PT AGLASSA+GFA
Sbjct: 69 SGGRYQNCLREIRARATDVEDEEKGIKITKKDWEKLHVHIASYNNFPTAAGLASSAAGFA 128
Query: 131 ALTLALFRIYSIPEKSES-LSRVARLGSGSACRSFYRGFCEWICGTDQNGMDSFAVPFNN 189
L AL ++ ++ E LS +AR GSGSACRS Y GF +W G ++G DS AV +
Sbjct: 129 CLVFALAKLMNVKEDFPGELSAIARQGSGSACRSLYGGFVKWNMGKKEDGSDSIAVQLAD 188
Query: 190 Q--WPDLRIGLLKIIDREKKIGSREAMEITRHHSPFFTQWTQQI-STDLAHIKQAIIDQD 246
+ W DL I + + R+K+ S M + SP +++ + +++AI ++D
Sbjct: 189 EKHWDDLVIIIAVVSSRQKETSSTSGMRESVETSPLLQHRAKEVVPKRILQMEEAIKNRD 248
Query: 247 FIKLGEVAEKNALKMHATMIAASPPLLYWQ---KETIQGMERVWDARQQSIPIYFTLDAG 303
F ++ ++ + HAT + SPP+ Y + I +E+ W+ + + + +T DAG
Sbjct: 249 FASFAKLTCADSNQFHATCLDTSPPIFYMNDTSRRIISLVEK-WNRSEGTPQVAYTFDAG 307
Query: 304 PNLKLLFTHK------IEETIKQFFP 323
PN L+ ++ ++ + F P
Sbjct: 308 PNAVLIALNRKVAAQLLQRLLYYFPP 333
>gnl|CDD|162602 TIGR01920, Shik_kin_archae, shikimate kinase. This model
represents the shikimate kinase (SK) gene found in
archaea which is only distantly related to homoserine
kinase (thrB) and not atr all to the bacterial SK
enzyme. The SK from M. janaschii has been overexpressed
in E. coli and characterized. SK catalyzes the fifth
step of the biosynthesis of chorismate from
D-erythrose-4-phosphate and phosphoenolpyruvate.
Length = 261
Score = 37.4 bits (87), Expect = 0.006
Identities = 25/99 (25%), Positives = 37/99 (37%), Gaps = 17/99 (17%)
Query: 94 TQFCDLFRQFSKVYFLIETSNNIPTKAGLASSASGFAALTLALFRIYS-------IPEKS 146
T F + +E+ IP +GL SS++ AL A+ + I
Sbjct: 53 TAIRSKFGIVDGLEVEVESE--IPAGSGLKSSSALVNALVEAVLKAKGVEIDDIDILRLG 110
Query: 147 ESLSRVARLG-SGS---ACRSFYRGFCEWICGTDQNGMD 181
LS+ A L +G+ A S+ G I TD M
Sbjct: 111 ARLSKDAGLSVTGAFDDAAASYLGG----IVITDNRRMK 145
>gnl|CDD|179230 PRK01123, PRK01123, shikimate kinase; Provisional.
Length = 282
Score = 36.8 bits (86), Expect = 0.009
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 21/76 (27%)
Query: 110 IETSNNIPTKAGLASSASGFAALTLALFRIYSIPEKSESLSR--VARLG----------- 156
+ T + IP +GL SS++ A LA E L + RLG
Sbjct: 78 VRTKSEIPLASGLKSSSAAANATVLATLDA-----LGEDLDDLDILRLGVKASRDAGVTV 132
Query: 157 SGS---ACRSFYRGFC 169
+G+ AC S++ G
Sbjct: 133 TGAFDDACASYFGGVT 148
>gnl|CDD|161922 TIGR00549, mevalon_kin, mevalonate kinase. Paracoccus exhibits two
genes within the phosphomevalonate/mevalonate kinase
family, one of which falls between trusted and noise
cutoffs of this model. The degree of divergence is high,
but if the trees created from this model are correct,
the proper names of these genes have been swapped.
Length = 273
Score = 36.5 bits (85), Expect = 0.012
Identities = 36/167 (21%), Positives = 57/167 (34%), Gaps = 36/167 (21%)
Query: 110 IETSNNIPTKAGLASSASGFAALTLALFRIYSIPEKSESLSRVARLGSGSACRSFYRGFC 169
IE + IP GL SSA+ AL AL + E L+++A
Sbjct: 81 IEIDSEIPPGRGLGSSAAVAVALIRALADYFGSELSKEELAKLANEA------------- 127
Query: 170 EWICGTDQNGMDSFAVPFNNQW------------PDLRIGLLKIIDREKKIGSREAMEIT 217
E I +G+D+ + L + I D ++EA+
Sbjct: 128 EKIAHGKPSGIDTATSTYGGPVYFEKGEGEFTKLISLDGYFV-IADTGVSGSTKEAVARV 186
Query: 218 RHHSPFFTQWTQQISTDLAHI-------KQAIIDQDFIKLGEVAEKN 257
R ++ + I + + I K A+ D D LGE+ N
Sbjct: 187 RQ---LLERFPELIDSIMDAIGELTLEAKAALQDGDVESLGELMNIN 230
>gnl|CDD|178136 PLN02521, PLN02521, galactokinase.
Length = 497
Score = 30.8 bits (70), Expect = 0.52
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 13/66 (19%)
Query: 116 IPTKAGLASSASGFAALTLALFRIYSIPEKSESLSRVARLGSGSACRSFYRGFCEWICGT 175
+PT +GL+SSA+ + +A I + + + VA+ C+ CE GT
Sbjct: 158 VPTGSGLSSSAALVCSAAIA---IMAALGLNFTKKEVAQF----TCK------CERHIGT 204
Query: 176 DQNGMD 181
GMD
Sbjct: 205 QSGGMD 210
>gnl|CDD|180144 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 29.4 bits (67), Expect = 1.5
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 12/42 (28%)
Query: 311 THKIEETIKQFFPE--ITIIDPLDSPDLWSTKDSLSQKNSIE 350
T ++EE + + FPE I ID +D+ +K ++E
Sbjct: 439 TERLEEELAELFPEARILRID----------RDTTRRKGALE 470
>gnl|CDD|178942 PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed.
Length = 297
Score = 29.0 bits (66), Expect = 2.2
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 126 ASGFAALTLALFRIYSIPEKSESLSR--VAR-LGSGSACRSFYR 166
S L A R + + + LS +AR L SA RSFYR
Sbjct: 47 ISSLQDLDAADLRSFLARRRRQGLSARSLARRL---SALRSFYR 87
>gnl|CDD|129295 TIGR00191, thrB, homoserine kinase. P.aeruginosa homoserine kinase
seems not to be homologous (see PROSITE:PDOC0054).
Length = 302
Score = 28.5 bits (64), Expect = 2.7
Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 9/98 (9%)
Query: 53 LSLSLGHLGTITHITVIDSDADCIILNGQKISSQSSFFKKT--TQ----FCDLF-RQFSK 105
+LSL T+T + +SD I G+ + + Q F D +
Sbjct: 21 AALSLYLGLTVTDVVAQESDDTEIEAEGEGVEKIPTEPTDNLIYQVAKRFLDQLGIRMPP 80
Query: 106 VYFLIETSNNIPTKAGLASSASGFAALTLALFRIYSIP 143
V +E NIP GL SSA+ A A + +P
Sbjct: 81 VKVTLE--KNIPLGRGLGSSAAAIVAALAAANELCGLP 116
>gnl|CDD|180014 PRK05322, PRK05322, galactokinase; Provisional.
Length = 387
Score = 27.9 bits (63), Expect = 3.9
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 115 NIPTKAGLASSAS 127
NIP AGL+SSAS
Sbjct: 120 NIPNGAGLSSSAS 132
>gnl|CDD|179653 PRK03817, PRK03817, galactokinase; Provisional.
Length = 351
Score = 28.0 bits (63), Expect = 4.0
Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 12/80 (15%)
Query: 108 FLIETSNNIPTKAGLASSASGFAALTLALFRIYSIPEKSESLSRVARLGSGSACRSFYRG 167
+ S+N+P AGL+SSAS A+ AL Y++ L+ +AR
Sbjct: 87 VKGKVSSNLPIGAGLSSSASLEVAVAYALNEAYNLNLSKLELALLAREAE--------NE 138
Query: 168 FCEWICGTDQNGMDSFAVPF 187
F CG MD FAV F
Sbjct: 139 FVGVPCGI----MDQFAVAF 154
>gnl|CDD|184766 PRK14610, PRK14610, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 283
Score = 27.8 bits (62), Expect = 4.1
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 115 NIPTKAGLASSASGFAALTLALFRIYSIPEKSESLSRVA-RLGSG-SAC----RSFYRGF 168
NIP AGLA ++ AA+ L +++ I E+ L+ +A +GS AC F RG
Sbjct: 92 NIPVSAGLAGGSADAAAVIRLLGKLWGIDEQ--ILNELALSVGSDVPACLDSKTLFVRGI 149
Query: 169 CEWIC 173
E I
Sbjct: 150 GEDIL 154
>gnl|CDD|130386 TIGR01319, glmL_fam, conserved hypothetical protein. This small
family includes, so far, an uncharacterized protein from
E. coli O157:H7 and GlmL from Clostridium tetanomorphum
and Clostridium cochlearium. GlmL is located between the
genes for the two subunits, epsilon (GlmE) and sigma
(GlmS), of the coenzyme-B12-dependent glutamate mutase
(methylaspartate mutase), the first enzyme in a pathway
of glutamate fermentation. Members shows significant
sequence similarity to the hydantoinase branch of the
hydantoinase/oxoprolinase family (pfam01968).
Length = 463
Score = 27.7 bits (61), Expect = 4.6
Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 5/104 (4%)
Query: 62 TITHITVIDSDADCIILNGQKISSQSSFFKKTTQFCDLFRQFSKVYFLIETSNNIPTKAG 121
T T D + D I+ I+ S F + ++ E ++ K
Sbjct: 6 TWTKAAAFDIEGDAILATAHDITPIESDHLAGGFFNKANEKLNEDLAGKELNSGEVAKKA 65
Query: 122 LASSASGFAALTLALFRIYSIPEKSESLSRVARLGSGSACRSFY 165
+S+A G A + L +PE + ++ A G+G+ + Y
Sbjct: 66 CSSAAGGLAMAAIGL-----VPEITAEAAKRAAHGAGAKIANVY 104
>gnl|CDD|129258 TIGR00154, ispE, 4-diphosphocytidyl-2C-methyl-D-erythritol kinase.
Members of this family of GHMP kinases were previously
designated as conserved hypothetical protein YchB or as
isopentenyl monophosphate kinase. It is now known, in
tomato and E. coli, to encode
4-diphosphocytidyl-2C-methyl-D-erythritol kinase, an
enzyme of the deoxyxylulose phosphate pathway of
terpenoid biosynthesis.
Length = 293
Score = 27.5 bits (61), Expect = 5.1
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 110 IETSNNIPTKAGLASSASGFAALTLALFRIY----SIPEKSE 147
IE NIP AGL +S A + + L +++ S+ E +E
Sbjct: 89 IEIDKNIPMGAGLGGGSSDAATVLVGLNQLWQLGLSLEELAE 130
>gnl|CDD|129517 TIGR00423, TIGR00423, radical SAM domain protein, CofH subfamily.
This protein family includes the CofH protein of
coenzyme F(420) biosynthesis from Methanocaldococcus
jannaschii, but appears to hit genomes more broadly than
just the subset that make coenzyme F(420), so that
narrower group is being built as a separate family.
Length = 309
Score = 27.4 bits (61), Expect = 6.1
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 304 PNLKLLFTHKIEETIKQFFPEITI 327
P L + + ++ IKQ FP++ I
Sbjct: 64 PQLDIEYYEELFRAIKQEFPDVHI 87
>gnl|CDD|161727 TIGR00131, gal_kin, galactokinase. The galactokinases found by
this model are divided into two sets. Prokaryotic forms
are generally shorter. The eukaryotic forms are longer
because of additional central regions and in some cases
are known to be bifunctional, with regulatory activities
that are independent of galactokinase activity.
Length = 386
Score = 27.5 bits (61), Expect = 6.2
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 113 SNNIPTKAGLASSAS 127
S N+PT +GL+SSA+
Sbjct: 116 SGNVPTGSGLSSSAA 130
>gnl|CDD|140319 PTZ00298, PTZ00298, mevalonate kinase; Provisional.
Length = 328
Score = 27.1 bits (60), Expect = 6.9
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 116 IPTKAGLASSASGFAALTLALFRIYSIPEKSESLSRVARLGSG 158
+P+ +G+ +SAS +L+ AL +Y + E ++ A +G G
Sbjct: 104 VPS-SGIGASASDVVSLSRALSELYQLNLTEEEVNLSAFVGEG 145
>gnl|CDD|179937 PRK05101, PRK05101, galactokinase; Provisional.
Length = 382
Score = 27.2 bits (61), Expect = 7.0
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 113 SNNIPTKAGLASSAS 127
S N+P AGL+SSAS
Sbjct: 118 SGNVPQGAGLSSSAS 132
>gnl|CDD|181199 PRK08020, ubiF, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
hydroxylase; Reviewed.
Length = 391
Score = 26.9 bits (60), Expect = 8.3
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 177 QNGMDSFAVPFNNQWPDLRI 196
Q+GMD F F+N P LR
Sbjct: 346 QSGMDLFYAGFSNNLPPLRF 365
>gnl|CDD|178649 PLN03102, PLN03102, acyl-activating enzyme; Provisional.
Length = 579
Score = 26.9 bits (59), Expect = 8.6
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 260 KMHATMIAASPPLLYWQKETIQGMERVWDA-RQQSIPIYFTLDAGPNLKLLFTHKIEETI 318
++ AT IAA +L K I ++R ++ ++ + + + D+ NL ++F H+I+
Sbjct: 97 RLDATSIAA---ILRHAKPKILFVDRSFEPLAREVLHLLSSEDSNLNLPVIFIHEIDFPK 153
Query: 319 KQFFPEI 325
+ E+
Sbjct: 154 RPSSEEL 160
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.320 0.135 0.405
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,622,553
Number of extensions: 347466
Number of successful extensions: 697
Number of sequences better than 10.0: 1
Number of HSP's gapped: 689
Number of HSP's successfully gapped: 22
Length of query: 355
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 261
Effective length of database: 3,963,321
Effective search space: 1034426781
Effective search space used: 1034426781
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: 58 (26.2 bits)