BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0001.3505.p (308 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310460|ref|YP_003774552.1| D-3-phosphoglycerate dehydrogen... 320 1e-88 gi|300311801|ref|YP_003775893.1| D-isomer specific 2-hydroxyacid... 123 2e-29 gi|300313156|ref|YP_003777248.1| D-2-hydroxyacid dehydrogenase [... 90 2e-19 gi|300310832|ref|YP_003774924.1| D-isomer specific 2-hydroxyacid... 86 3e-18 gi|300310960|ref|YP_003775052.1| dehydrogenase oxidoreductase [H... 86 3e-18 >gi|300310460|ref|YP_003774552.1| D-3-phosphoglycerate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 308 Score = 320 bits (819), Expect = 1e-88, Method: Compositional matrix adjust. Identities = 153/308 (49%), Positives = 210/308 (68%) Query: 1 MKVLYRSDVARGSAWQKMFAQLAPDVDFRVWPDAGNLEEIEYLIAWQVPPEFLAALPRLK 60 M LY++D RG+ W ++FAQ AP++ F++WP G+ + YL AW P + P+L+ Sbjct: 1 MTFLYKADPVRGAEWAQLFAQKAPELPFQIWPHDGDGASVRYLAAWTPPDDIAERFPKLE 60 Query: 61 VLFSSGAGVDHIDMTVVPPHVAIVRMVEPGIINGMLEYVTMSVLALHRHLFEYQEFQRQG 120 +LFS GAG+D DM+ +PP + +VRM EPGI GM++YVT +VL LHR Y QR Sbjct: 61 ILFSVGAGIDQFDMSTLPPALPVVRMTEPGIAAGMVQYVTHAVLGLHRDSRVYARQQRDQ 120 Query: 121 LWQPIEVYPPSTCSVGVMGLGVLGQAVLERLGVFGYRRLGWNRSPRSLPDVRCFEGEKAL 180 +W+ V P S C VGV+GLG+LG+AVL++L G+ GW+RS + + C+ G L Sbjct: 121 VWRAHRVRPASACRVGVLGLGMLGRAVLQQLHGLGFPCAGWSRSAHQMDGIDCYSGSAGL 180 Query: 181 NEFLRQCDILICLLPLTDATRGILGKRLFATLPAGSSLLHVGRGGHLDQDALLDALDRGQ 240 FL + D+L+CL+PLT+ TRG+L + LFA LP G++L++VGRGGHL +D LL AL+ GQ Sbjct: 181 RAFLARTDVLVCLVPLTEETRGLLCRDLFAQLPRGAALINVGRGGHLVEDDLLAALNDGQ 240 Query: 241 LGRAVLDVCDPEPLPVDHPLWRHPRVVLTPHVASMTQPETAIPILIHNLRRHQRGDALLD 300 L AVLDVC+ EPLP HP W HP +VLTPH+ASMTQP+ A+ ++ NLRR++ G LL Sbjct: 241 LSAAVLDVCEVEPLPPGHPFWTHPDIVLTPHIASMTQPDGAVDAVLENLRRYREGLPLLG 300 Query: 301 EIDRNTGY 308 IDR GY Sbjct: 301 LIDRQRGY 308 >gi|300311801|ref|YP_003775893.1| D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein [Herbaspirillum seropedicae SmR1] Length = 319 Score = 123 bits (308), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 98/276 (35%), Positives = 136/276 (49%) Query: 33 DAGNLEEIEYLIAWQVPPEFLAALPRLKVLFSSGAGVDHIDMTVVPPHVAIVRMVEPGII 92 DA L + I P L +P L + S AGV+ + + + + R+V+P + Sbjct: 44 DADQLAQCRVAIVANPDPAQLKRMPNLLWVHSVWAGVERLVADLGQSDLQLTRLVDPRLA 103 Query: 93 NGMLEYVTMSVLALHRHLFEYQEFQRQGLWQPIEVYPPSTCSVGVMGLGVLGQAVLERLG 152 M E V L LHR + Y QR+ W+ P V ++GLG LG+A L Sbjct: 104 ATMAEAVLAWTLYLHRDMPLYARRQREHHWEAQPYVLPEQRRVSLLGLGALGEAAAAALR 163 Query: 153 VFGYRRLGWNRSPRSLPDVRCFEGEKALNEFLRQCDILICLLPLTDATRGILGKRLFATL 212 + GW+RS R V+ F G L + L Q DIL+CLLPLT TRG++ A L Sbjct: 164 QARFAVNGWSRSAREAEGVQTFHGPAGLAQMLAQTDILVCLLPLTAETRGLIDAAHLAML 223 Query: 213 PAGSSLLHVGRGGHLDQDALLDALDRGQLGRAVLDVCDPEPLPVDHPLWRHPRVVLTPHV 272 P + L++ RG +D AL ALD GQL AVLDV EPLP W HP V + PH Sbjct: 224 PPQAQLINFARGPIIDDAALKAALDAGQLRHAVLDVFAVEPLPPAAWPWSHPAVTVLPHC 283 Query: 273 ASMTQPETAIPILIHNLRRHQRGDALLDEIDRNTGY 308 ++ T +TA I+ N+RR++ + +D GY Sbjct: 284 SAPTDRQTASAIVAANIRRYRHSGEIAANVDLRRGY 319 >gi|300313156|ref|YP_003777248.1| D-2-hydroxyacid dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 316 Score = 90.1 bits (222), Expect = 2e-19, Method: Compositional matrix adjust. Identities = 77/263 (29%), Positives = 126/263 (47%), Gaps = 14/263 (5%) Query: 47 QVPPEFLAALPRLKVLFSSGAGVDHIDMTVVPPHVAIVRMVEPGIINGMLEYVTMS-VLA 105 +V EF+A P L+++ G G D +D+ I P ++N + + M+ +LA Sbjct: 59 KVSREFMARFPALEIVSVFGVGYDGVDVPAARER-GIHVTHTPDVLNDDVADLAMALMLA 117 Query: 106 LHRHLFEYQEFQRQGLWQPIEVYPPST----CSVGVMGLGVLGQAVLERLGVFGYRRLGW 161 R++ F R G W+ +P +T +G++GLG +GQA+ +R F + Sbjct: 118 TARNVVRADRFARSGEWKK-GPFPFTTKVSGARLGIVGLGRIGQAIAKRAAAFDMQISYH 176 Query: 162 NRSPRSLPDVRCFEGEKALNEFLRQCDILICLLPLTDATRGILGKRLFATLPAGSSLLHV 221 NRS + +P + ++ R+ D L+ + P TR ++ + L L++V Sbjct: 177 NRSRKDVP----YTYVDSITALAREVDFLVMITPGGAGTRALVNAEVLEALGPKGFLINV 232 Query: 222 GRGGHLDQDALLDALDRGQLGRAVLDVCDPEPLPVDHPLWRHPRVVLTPHVASMT-QPET 280 RG +D+ AL+ AL G + A LDV EP V L VVLTPH+AS T T Sbjct: 233 ARGSVVDEAALIAALKTGVIAGAGLDVFADEP-NVPAELAALDNVVLTPHMASGTLVTRT 291 Query: 281 AIPIL-IHNLRRHQRGDALLDEI 302 A+ L +NL+ H G ++ + Sbjct: 292 AMADLAFNNLQAHFSGAGVISPV 314 >gi|300310832|ref|YP_003774924.1| D-isomer specific 2-hydroxyacid dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 319 Score = 86.3 bits (212), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 73/255 (28%), Positives = 117/255 (45%), Gaps = 20/255 (7%) Query: 52 FLAALPRLKVLFSSGAGVDHIDMTVVPPHVAIVRMVEPGIIN-GMLEYVTMSVLALHRHL 110 L A P+LK++ + GVD+ D+ ++ PG++ + + +LA R + Sbjct: 60 MLEAAPQLKIVSTISVGVDNFDLDYFRQR-GLMLAHTPGVLTEATADTIFALILASARRV 118 Query: 111 FEYQEFQRQGLWQP--------IEVYPPSTCSVGVMGLGVLGQAVLERLG-VFGYRRLGW 161 E E+ + G W+ + V+ + +G++G+G +G AV R FG L Sbjct: 119 VELAEYVKAGRWKGSIGEAQFGVNVHGKT---LGLIGMGRIGSAVARRAHHGFGMPILYH 175 Query: 162 NRSPRSLPDVRCFEGEKALNEFLRQCDILICLLPLTDATRGILGKRLFATLPAGSSLLHV 221 NR P + + + L Q D + +LPLT T + G FA + + ++ Sbjct: 176 NRRPDPEAERELGARYVSKEDLLAQADFVCVMLPLTPQTERMFGAPEFALMKRSAIFINA 235 Query: 222 GRGGHLDQDALLDALDRGQLGRAVLDVCDPEPLPVDHPLWRHPRVVLTPHVASMTQ---- 277 RG +D+ AL+ AL + A LDV + EPLP+ PL + P VV PH+ S T Sbjct: 236 SRGRIVDEAALIAALQDKTIHGAGLDVFEVEPLPLQSPLLKLPNVVALPHIGSATHETRL 295 Query: 278 --PETAIPILIHNLR 290 E A+ LI LR Sbjct: 296 AMAELAVTNLIAGLR 310 >gi|300310960|ref|YP_003775052.1| dehydrogenase oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 326 Score = 86.3 bits (212), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 68/240 (28%), Positives = 113/240 (47%), Gaps = 12/240 (5%) Query: 48 VPPEFLAALPRLKVLFSSGAGVDHIDMTVVPPHVAIVRMVEPGIIN-GMLEYVTMSVLAL 106 V AA P+LK + + G ++ID+ ++ P ++N ++ ++A Sbjct: 57 VTAALFAANPQLKAVCNMAVGYNNIDVAAAT-QAGVMATNTPDVLNETTADFGWALMMAA 115 Query: 107 HRHLFEYQEFQRQGLWQPIE----VYPP-STCSVGVMGLGVLGQAVLERLGVFGYRRLGW 161 R + E + F R G W+ V P ++G++G+G +GQA+ R F + L Sbjct: 116 ARRITESEHFLRAGKWKKWSYDSFVGPDIHGATLGIIGMGRIGQAIARRSLGFDMQVLYH 175 Query: 162 NRSPRSLPDVRCFEGEK---ALNEFLRQCDILICLLPLTDATRGILGKRLFATLPAGSSL 218 NRS R P++ + E LRQ D +I +LP + T + A + ++L Sbjct: 176 NRS-RLAPELEARANHARYVSKEELLRQADHVILVLPYSKDTHHTIAAAELALMKPTATL 234 Query: 219 LHVGRGGHLDQDALLDALDRGQLGRAVLDVCDPEPLPVDHPLWRHPRVVLTPHVASMTQP 278 ++ RGG +D AL+ AL G++ A +DV + EP VVLTPH+AS + P Sbjct: 235 TNIARGGIVDDAALIAALREGRIAAAGVDVFENEP-AFKPEFLDLSNVVLTPHIASASTP 293 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.325 0.142 0.451 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,038,844 Number of extensions: 44091 Number of successful extensions: 183 Number of sequences better than 1.0e-08: 10 Number of HSP's gapped: 170 Number of HSP's successfully gapped: 10 Length of query: 308 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 223 Effective length of database: 1,217,395 Effective search space: 271479085 Effective search space used: 271479085 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 130 (54.7 bits)