RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781020|ref|YP_003065433.1| isopentenyl pyrophosphate isomerase [Candidatus Liberibacter asiaticus str. psy62] (337 letters) >gnl|CDD|180081 PRK05437, PRK05437, isopentenyl pyrophosphate isomerase; Provisional. Length = 352 Score = 434 bits (1119), Expect = e-122 Identities = 152/329 (46%), Positives = 212/329 (64%), Gaps = 4/329 (1%) Query: 1 MVNDRKIDHINIVCKDPGIDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLL 60 +++RK +HI I K+ + FDD LIH ALPE+ D++D S EFLGKKLS P L Sbjct: 5 QISNRKDEHIEIALKEDVEYKKTTGFDDVRLIHNALPELDLDDIDLSTEFLGKKLSAPFL 64 Query: 61 ISSMTGGNNKMIERINRNLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFEL-RQYAPHTVL 119 I++MTGG+ K + INR LA AAE+ +AM VGSQR D SF + R+ AP +L Sbjct: 65 INAMTGGSEKA-KEINRKLAEAAEELGIAMGVGSQRAALKDPELADSFSVVRKVAPDGLL 123 Query: 120 ISNLGAVQLNYDFGVQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFADLSSKIALLS 179 +NLGAVQL Y +GV++A +AV ++ AD L +HLNPLQE++QP G+ +F IA + Sbjct: 124 FANLGAVQL-YGYGVEEAQRAVEMIEADALQIHLNPLQELVQPEGDRDFRGWLDNIAEIV 182 Query: 180 SAMDVPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRGGTSWSRIESHRDLESDIGIVFQ 239 SA+ VP+++KEVG G+S + +G++ D+AG GGTSW+ IE++R + + F Sbjct: 183 SALPVPVIVKEVGFGISKETAKRLADAGVKAIDVAGAGGTSWAAIENYRARDDRLASYFA 242 Query: 240 DWGIPTPLSLEMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLKPAMDSS- 298 DWGIPT SL AR + IASGG+RNG+DI K++ LGA G+A PFLK A++ Sbjct: 243 DWGIPTAQSLLEARSLLPDLPIIASGGIRNGLDIAKALALGADAVGMAGPFLKAALEGGE 302 Query: 299 DAVVAAIESLRKEFIVSMFLLGTKRVQEL 327 +AV+ IE +E ++MFL G K + EL Sbjct: 303 EAVIELIEQWIEELKIAMFLTGAKNIAEL 331 >gnl|CDD|162733 TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase, type 2. Isopentenyl-diphosphate delta-isomerase (IPP isomerase) interconverts isopentenyl diphosphate and dimethylallyl diphosphate. This model represents the type 2 enzyme. FMN, NADPH, and Mg2+ are required by this form, which lacks homology to the type 1 enzyme (TIGR02150). IPP is precursor to many compounds, including enzyme cofactors, sterols, and isoprenoids. Length = 333 Score = 354 bits (910), Expect = 2e-98 Identities = 146/333 (43%), Positives = 206/333 (61%), Gaps = 4/333 (1%) Query: 5 RKIDHINIVCKDPGIDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSM 64 RK +HI + K FDD LIH ALPEI+ D++D + EFLGK+L P I++M Sbjct: 2 RKDEHIELCLKQNVEYGGSTGFDDITLIHNALPEINLDDIDLTTEFLGKRLKAPFYINAM 61 Query: 65 TGGNNKMIERINRNLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFE-LRQYAPHTVLISNL 123 TGG+ + +INRNLA AA + + M VGSQR D +FE +R+ AP+ LI+N+ Sbjct: 62 TGGSEEA-GKINRNLARAARELGIPMGVGSQRAALKDPETADTFEVVREEAPNGPLIANI 120 Query: 124 GAVQLNYDFGVQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFADLSSKIALLSSAMD 183 GA QL G ++A +A+ ++ AD L +HLN LQE++QP G+ NF KIA + S + Sbjct: 121 GAPQLVE-GGPEEAQEAIDMIEADALAIHLNVLQELVQPEGDRNFKGWLEKIAEICSQLS 179 Query: 184 VPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRGGTSWSRIESHRDLESDIGIVFQDWGI 243 VP+++KEVG G+S +L +G+ D+AG GGTSW+++E++R S++ F DWGI Sbjct: 180 VPVIVKEVGFGISKEVAKLLADAGVSAIDVAGAGGTSWAQVENYRAKGSNLASFFNDWGI 239 Query: 244 PTPLSLEMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLKPAMDSS-DAVV 302 PT SL R +A IASGGLR G+D+ K+I LGA G+A PFLK A+D +AV+ Sbjct: 240 PTAASLLEVRSDAPDAPIIASGGLRTGLDVAKAIALGADAVGMARPFLKAALDEGEEAVI 299 Query: 303 AAIESLRKEFIVSMFLLGTKRVQELYLNTALIR 335 IE + +E V+MFL G K + EL +I Sbjct: 300 EEIELIIEELKVAMFLTGAKTIAELKKVPLVIS 332 >gnl|CDD|166620 PLN02979, PLN02979, glycolate oxidase. Length = 366 Score = 38.5 bits (89), Expect = 0.003 Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 1/67 (1%) Query: 265 GGLRNGVDILKSIILGASLGGLASPFL-KPAMDSSDAVVAAIESLRKEFIVSMFLLGTKR 323 GG+R G D+ K++ LGAS + P + A + V ++ LR EF ++M L G + Sbjct: 285 GGVRRGTDVFKALALGASGIFIGRPVVFSLAAEGEAGVRKVLQMLRDEFELTMALSGCRS 344 Query: 324 VQELYLN 330 ++E+ N Sbjct: 345 LKEISRN 351 >gnl|CDD|183033 PRK11197, lldD, L-lactate dehydrogenase; Provisional. Length = 381 Score = 38.1 bits (89), Expect = 0.003 Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 1/67 (1%) Query: 262 IASGGLRNGVDILKSIILGASLGGLASPFLKP-AMDSSDAVVAAIESLRKEFIVSMFLLG 320 +A G+RNG+D+++ I LGA L F+ A V ++ + KE V+M L G Sbjct: 304 LADSGIRNGLDVVRMIALGADTVLLGRAFVYALAAAGQAGVANLLDLIEKEMRVAMTLTG 363 Query: 321 TKRVQEL 327 K + E+ Sbjct: 364 AKSISEI 370 >gnl|CDD|166134 PLN02493, PLN02493, probable peroxisomal (S)-2-hydroxy-acid oxidase. Length = 367 Score = 37.8 bits (87), Expect = 0.004 Identities = 36/159 (22%), Positives = 68/159 (42%), Gaps = 25/159 (15%) Query: 175 IALLSSAMDVPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRGGTSWSRIESHRDLESDI 234 + L + +P+L+K V L+ D + +++G ++ G R L+ Sbjct: 216 VQWLQTITKLPILVKGV---LTGEDARIAIQAGAAGIIVSNHGA---------RQLDY-- 261 Query: 235 GIVFQDWGIPTPLSL--EMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFL- 291 +P +S E+ + GG+R G D+ K++ LGAS + P + Sbjct: 262 --------VPATISALEEVVKATQGRIPVFLDGGVRRGTDVFKALALGASGIFIGRPVVF 313 Query: 292 KPAMDSSDAVVAAIESLRKEFIVSMFLLGTKRVQELYLN 330 A + V ++ LR EF ++M L G + ++E+ N Sbjct: 314 SLAAEGEAGVRKVLQMLRDEFELTMALSGCRSLKEISRN 352 >gnl|CDD|178150 PLN02535, PLN02535, glycolate oxidase. Length = 364 Score = 33.3 bits (76), Expect = 0.099 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 1/64 (1%) Query: 265 GGLRNGVDILKSIILGASLGGLASPFLKP-AMDSSDAVVAAIESLRKEFIVSMFLLGTKR 323 GG+R G D+ K++ LGA + P + A D V IE L+ E ++M L G Sbjct: 285 GGVRRGTDVFKALALGAQAVLVGRPVIYGLAAKGEDGVRKVIEMLKDELEITMALSGCPS 344 Query: 324 VQEL 327 V+++ Sbjct: 345 VKDI 348 >gnl|CDD|162293 TIGR01302, IMP_dehydrog, inosine-5'-monophosphate dehydrogenase. This model describes a rather tightly conserved cluster of IMP dehydrogenase sequences, many of which are characterized. The model excludes two related families of proteins proposed also to be IMP dehydrogenases, but without characterized members. These are related families are the subject of separate models. Length = 450 Score = 31.9 bits (73), Expect = 0.21 Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 3/28 (10%) Query: 262 IASGGLRNGVDILKSIILGAS---LGGL 286 IA GG+R DI+K++ GA LG L Sbjct: 331 IADGGIRYSGDIVKALAAGADAVMLGSL 358 >gnl|CDD|185550 PTZ00314, PTZ00314, inosine-5'-monophosphate dehydrogenase; Provisional. Length = 495 Score = 31.5 bits (72), Expect = 0.35 Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 5/38 (13%) Query: 254 PYCNEAQF--IASGGLRNGVDILKSIILGAS---LGGL 286 Y E IA GG++N DI K++ LGA LG L Sbjct: 338 RYARERGVPCIADGGIKNSGDICKALALGADCVMLGSL 375 >gnl|CDD|180097 PRK05458, PRK05458, guanosine 5'-monophosphate oxidoreductase; Provisional. Length = 326 Score = 30.7 bits (70), Expect = 0.51 Identities = 12/22 (54%), Positives = 15/22 (68%) Query: 262 IASGGLRNGVDILKSIILGASL 283 IA GG+R DI KSI GA++ Sbjct: 205 IADGGIRTHGDIAKSIRFGATM 226 >gnl|CDD|183297 PRK11750, gltB, glutamate synthase subunit alpha; Provisional. Length = 1485 Score = 30.2 bits (69), Expect = 0.81 Identities = 12/21 (57%), Positives = 17/21 (80%), Gaps = 1/21 (4%) Query: 265 GGLRNGVDILKSIILGA-SLG 284 GGL+ G+D++K+ ILGA S G Sbjct: 1074 GGLKTGLDVIKAAILGAESFG 1094 >gnl|CDD|130373 TIGR01306, GMP_reduct_2, guanosine monophosphate reductase, bacterial. A deep split separates two families of GMP reductase. The other (TIGR01305) is found in eukaryotic and some proteobacterial lineages, including E. coli, while this family is found in a variety of bacterial lineages. Length = 321 Score = 29.1 bits (65), Expect = 1.7 Identities = 15/29 (51%), Positives = 18/29 (62%) Query: 262 IASGGLRNGVDILKSIILGASLGGLASPF 290 IA GG+R DI KSI GAS+ + S F Sbjct: 202 IADGGIRTHGDIAKSIRFGASMVMIGSLF 230 >gnl|CDD|183666 PRK12666, PRK12666, putative monovalent cation/H+ antiporter subunit D; Reviewed. Length = 528 Score = 27.9 bits (63), Expect = 3.7 Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 3/32 (9%) Query: 164 GNTNFADLSSKIALLSSAMDVPLLLKEVGCGL 195 G N ADL+ +IA L +A D LL E G L Sbjct: 187 GTLNMADLAQRIAQLPAA-DRALL--EAGAAL 215 >gnl|CDD|181521 PRK08649, PRK08649, inosine 5-monophosphate dehydrogenase; Validated. Length = 368 Score = 27.9 bits (63), Expect = 4.3 Identities = 13/29 (44%), Positives = 15/29 (51%) Query: 262 IASGGLRNGVDILKSIILGASLGGLASPF 290 IA GG+ DI K+I GA L SP Sbjct: 260 IADGGIGTSGDIAKAIACGADAVMLGSPL 288 >gnl|CDD|181033 PRK07565, PRK07565, dihydroorotate dehydrogenase 2; Reviewed. Length = 334 Score = 27.5 bits (62), Expect = 4.5 Identities = 10/35 (28%), Positives = 20/35 (57%) Query: 258 EAQFIASGGLRNGVDILKSIILGASLGGLASPFLK 292 A A+ G+ + D++K ++ GA + +AS L+ Sbjct: 239 GADLAATTGVHDAEDVIKMLLAGADVVMIASALLR 273 >gnl|CDD|172978 PRK14507, PRK14507, putative bifunctional 4-alpha-glucanotransferase/malto-oligosyltrehalose synthase; Provisional. Length = 1693 Score = 27.4 bits (61), Expect = 5.5 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 17/71 (23%) Query: 196 SSMDIELGLKSGIRYFDIA---GRGGT-SWSRIESHR---------DLESDIGIVFQDWG 242 LG++ G+ Y D+A RGG+ +WS E D + G QDWG Sbjct: 392 GERAQALGMRLGL-YRDLAVGVDRGGSETWSHPELFANGASIGAPPDELNPKG---QDWG 447 Query: 243 IPTPLSLEMAR 253 +P LE+ R Sbjct: 448 LPPFDPLELER 458 >gnl|CDD|163184 TIGR03211, catechol_2_3, catechol 2,3 dioxygenase. Members of this family all are enzymes active as catechol 2,3 dioxygenase (1.13.11.2), although some members have highly significant activity on catechol derivatives such as 3-methylcatechol, 3-chlorocatechol, and 4-chlorocatechol (see Mars, et al.). This enzyme is also called metapyrocatechase, as it performs a meta-cleavage (an extradiol ring cleavage), in contrast to the ortho-cleavage (intradiol ring cleavage)performed by catechol 1,2-dioxygenase (EC 1.13.11.1), also called pyrocatechase. Length = 303 Score = 27.2 bits (61), Expect = 5.9 Identities = 8/27 (29%), Positives = 15/27 (55%), Gaps = 2/27 (7%) Query: 2 VNDRKIDHINIVCKDPGIDRNKKFFDD 28 V R++DH + +D + N +FF + Sbjct: 141 VGARRLDHCLLYGED--VAENTRFFTE 165 >gnl|CDD|185115 PRK15193, PRK15193, outer membrane usher protein; Provisional. Length = 876 Score = 27.2 bits (60), Expect = 6.2 Identities = 28/101 (27%), Positives = 33/101 (32%), Gaps = 11/101 (10%) Query: 56 SFPLLISSMTGGNNKMIERINRNLAIAAEKTKVAMAVGSQRVMFS-DHNAIKSFELRQYA 114 +FP G LA V QR+ S AIKS R Y Sbjct: 121 AFPAFKQLAKGAC--------PPLASIIPDASVTFDFNKQRLDISVPQIAIKS-SARGYI 171 Query: 115 PHTVLISNLGAVQLNYDF-GVQKAHQAVHVLGADGLFLHLN 154 P + A+ LNY F G H + D FL LN Sbjct: 172 PPERWDEGINALLLNYSFSGANSIHSSADSDSGDSYFLGLN 212 >gnl|CDD|184075 PRK13478, PRK13478, phosphonoacetaldehyde hydrolase; Provisional. Length = 267 Score = 27.1 bits (61), Expect = 7.3 Identities = 9/32 (28%), Positives = 12/32 (37%), Gaps = 6/32 (18%) Query: 6 KIDHINIVCKDPGIDRNKKFFDDWHLIHRALP 37 K DHI + K P + W + LP Sbjct: 51 KWDHIRALLKMPRVAA------RWQAVFGRLP 76 >gnl|CDD|179435 PRK02506, PRK02506, dihydroorotate dehydrogenase 1A; Reviewed. Length = 310 Score = 26.8 bits (60), Expect = 8.0 Identities = 10/26 (38%), Positives = 16/26 (61%) Query: 258 EAQFIASGGLRNGVDILKSIILGASL 283 Q I +GG++ G D + I+ GAS+ Sbjct: 241 SIQIIGTGGVKTGRDAFEHILCGASM 266 >gnl|CDD|130495 TIGR01428, HAD_type_II, 2-haloalkanoic acid dehalogenase, type II. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related. Length = 198 Score = 26.5 bits (59), Expect = 9.0 Identities = 5/31 (16%), Positives = 16/31 (51%), Gaps = 2/31 (6%) Query: 53 KKLSFPLLISSMTGGNNKMIERINRNLAIAA 83 K+ + L I ++ G+ M++ + ++ + Sbjct: 105 KERGYRLAI--LSNGSPAMLKSLVKHAGLDD 133 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 0.321 0.138 0.400 Gapped Lambda K H 0.267 0.0762 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 5,580,153 Number of extensions: 367894 Number of successful extensions: 716 Number of sequences better than 10.0: 1 Number of HSP's gapped: 707 Number of HSP's successfully gapped: 33 Length of query: 337 Length of database: 5,994,473 Length adjustment: 94 Effective length of query: 243 Effective length of database: 3,963,321 Effective search space: 963087003 Effective search space used: 963087003 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: 57 (25.7 bits)