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= 0003.0139.p (316 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313156|ref|YP_003777248.1| D-2-hydroxyacid dehydrogenase [... 567 e-163 gi|300309865|ref|YP_003773957.1| D-isomer specific 2-hydroxyacid... 228 5e-61 gi|300311988|ref|YP_003776080.1| D-3-phosphoglycerate dehydrogen... 226 2e-60 gi|300310960|ref|YP_003775052.1| dehydrogenase oxidoreductase [H... 209 2e-55 gi|300310832|ref|YP_003774924.1| D-isomer specific 2-hydroxyacid... 192 3e-50 >gi|300313156|ref|YP_003777248.1| D-2-hydroxyacid dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 316 Score = 567 bits (1462), Expect = e-163, Method: Compositional matrix adjust. Identities = 277/316 (87%), Positives = 299/316 (94%) Query: 1 MTSSSRPVVLIVARLPQHLLDLLQQNFTCHNLILDPLTDEALAAIAPQVRGIAANGEAKV 60 MT+++RP VLIVARLPQHLLDLLQQ++TCHNLIL P ++ LAAIAPQ+RGIAANGEAKV Sbjct: 1 MTTNNRPHVLIVARLPQHLLDLLQQHYTCHNLILQPHSEAELAAIAPQIRGIAANGEAKV 60 Query: 61 GREFMARFPALEIVSVFGVGYDGVDVPAARERGIHVTHTPDVLTEDVADMAIALMLAVAR 120 REFMARFPALEIVSVFGVGYDGVDVPAARERGIHVTHTPDVL +DVAD+A+ALMLA AR Sbjct: 61 SREFMARFPALEIVSVFGVGYDGVDVPAARERGIHVTHTPDVLNDDVADLAMALMLATAR 120 Query: 121 NVVRADRFARSGEWKKGPFPFTTKVSGARLGIVGLGRIGQAIAQRAAAFDMQIAYHNRSR 180 NVVRADRFARSGEWKKGPFPFTTKVSGARLGIVGLGRIGQAIA+RAAAFDMQI+YHNRSR Sbjct: 121 NVVRADRFARSGEWKKGPFPFTTKVSGARLGIVGLGRIGQAIAKRAAAFDMQISYHNRSR 180 Query: 181 KDVPYTYVEDIVSLAREVDFLVMITPGGAGTRALVNAEVLEALGPKGFLINVARGSVVDE 240 KDVPYTYV+ I +LAREVDFLVMITPGGAGTRALVNAEVLEALGPKGFLINVARGSVVDE Sbjct: 181 KDVPYTYVDSITALAREVDFLVMITPGGAGTRALVNAEVLEALGPKGFLINVARGSVVDE 240 Query: 241 KALIAALQAGTIAGAGLDVFENEPNIPAELAALENVVLTPHMASGTLVTRTAMAELAFTN 300 ALIAAL+ G IAGAGLDVF +EPN+PAELAAL+NVVLTPHMASGTLVTRTAMA+LAF N Sbjct: 241 AALIAALKTGVIAGAGLDVFADEPNVPAELAALDNVVLTPHMASGTLVTRTAMADLAFNN 300 Query: 301 LQAHFSGKPVVTPVPD 316 LQAHFSG V++PVPD Sbjct: 301 LQAHFSGAGVISPVPD 316 >gi|300309865|ref|YP_003773957.1| D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein [Herbaspirillum seropedicae SmR1] Length = 348 Score = 228 bits (581), Expect = 5e-61, Method: Compositional matrix adjust. Identities = 125/293 (42%), Positives = 181/293 (61%), Gaps = 6/293 (2%) Query: 21 DLLQQNFTCHNLILDPLTDEALAAIAPQVRGIAANGEAKVGREFMARFPALEIVSVFGVG 80 D L+ + H L + +A + G+ G + M PAL++V+V GVG Sbjct: 49 DKLESLYHMHRLFEQEDKEAYIARHGAVIEGVITGGHTGISNALMDSLPALKVVAVNGVG 108 Query: 81 YDGVDVPAARERGIHVTHTPDVLTEDVADMAIALMLAVARNVVRADRFARSGEWKKGP-- 138 D VD+ AR +G+ VT T LTEDVAD+A+ LMLAV+R + F + G+W + P Sbjct: 109 TDAVDLNHARSKGLPVTGTFGALTEDVADLALGLMLAVSRQICPGHAFVQRGDWVRHPSP 168 Query: 139 --FPFTTKVSGARLGIVGLGRIGQAIAQRAAAFDMQIAYHN-RSRKDVPYTYVEDIVSLA 195 P + ++SG R+GIVG+G++G+AIAQRAAAF I Y + R+ +D+PY + +++ LA Sbjct: 169 TAIPLSRRLSGKRVGIVGMGKVGRAIAQRAAAFGCPITYTDLRAMEDLPYAFQPELLQLA 228 Query: 196 REVDFLVMITPGGAGTRALVNAEVLEALGPKGFLINVARGSVVDEKALIAALQAGTIAGA 255 RE D LV+ + ++NA VL+ALG +G LIN+ARG +V E+ L+ ALQ G IAGA Sbjct: 229 RESDVLVLAAAADK-AQGIINAAVLDALGREGILINIARGKLVVEEDLVDALQRGVIAGA 287 Query: 256 GLDVFENEPNIPAELAALENVVLTPHMASGTLVTRTAMAELAFTNLQAHFSGK 308 GLDVF +EPN+PA L ++ VVL H AS T+ +RTAM E+ +L +G+ Sbjct: 288 GLDVFVDEPNVPAALLQMDQVVLQAHRASATVESRTAMGEMVLASLAQGLAGQ 340 >gi|300311988|ref|YP_003776080.1| D-3-phosphoglycerate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 310 Score = 226 bits (575), Expect = 2e-60, Method: Compositional matrix adjust. Identities = 125/275 (45%), Positives = 168/275 (61%), Gaps = 3/275 (1%) Query: 39 DEALAAIAPQVRGIAANGEAKVGREFMARFPALEIVSVFGVGYDGVDVPAARERGIHVTH 98 DE +A A +V + NG + E M P L++V G G++ VDV A GI + Sbjct: 35 DEMIAGPARKVAVVLTNGSTGLTAEEMRALPHLQLVCTLGAGFENVDVAHAEAHGIEIAT 94 Query: 99 TPDVLTEDVADMAIALMLAVARNVVRADRFARSGEWKKGPFPFTTKVSGARLGIVGLGRI 158 + VAD A+ L+LA+ RN+ DR+ R G W++ P +++G R+GIVG+G I Sbjct: 95 GAGTNEDCVADHALGLLLAILRNIPVLDRYTRDGGWRE-TIPLQPQLAGKRVGIVGMGNI 153 Query: 159 GQAIAQRAAAFDMQIAYHNRS-RKDVPYTYVEDIVSLAREVDFLVMITPGGAGTRALVNA 217 G+ IA+RAAAFD +IAY NR R DV Y Y D+ LA D L++ PGGA TR L+NA Sbjct: 154 GKKIARRAAAFDAEIAYCNRKKRDDVDYHYFPDVAQLAGWADCLIVAAPGGAQTRHLINA 213 Query: 218 EVLEALGPKGFLINVARGSVVDEKALIAALQAGTIAGAGLDVFENEPNIPAELAALENVV 277 VLE LGP+G+L+N+ RGS+VD AL AAL +G +AGAGLDV+E EP PA L AL NVV Sbjct: 214 RVLEELGPQGYLVNIGRGSIVDTDALGAALSSGRLAGAGLDVYEGEPQPPAALIALPNVV 273 Query: 278 LTPHMASGTLVTRTAMAELAFTNLQAHF-SGKPVV 311 LTPH+A + A N + HF + +PV+ Sbjct: 274 LTPHIAGWSPEAIRASVTQFLRNCEEHFAAAEPVL 308 >gi|300310960|ref|YP_003775052.1| dehydrogenase oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 326 Score = 209 bits (533), Expect = 2e-55, Method: Compositional matrix adjust. Identities = 126/315 (40%), Positives = 173/315 (54%), Gaps = 15/315 (4%) Query: 6 RPVVLIVARLPQHLLDLLQQNFTCHNLILDPLTDEA-LAAIAPQVRGIAANGEAKVGREF 64 +P + + + +L L+Q+F + D + A L A A G+ V Sbjct: 2 KPKIFVARAVFPEVLARLEQHFEVESNQDDRIYSAAELQAKAQGKDGLFTTPSEPVTAAL 61 Query: 65 MARFPALEIVSVFGVGYDGVDVPAARERGIHVTHTPDVLTEDVADMAIALMLAVARNVVR 124 A P L+ V VGY+ +DV AA + G+ T+TPDVL E AD ALM+A AR + Sbjct: 62 FAANPQLKAVCNMAVGYNNIDVAAATQAGVMATNTPDVLNETTADFGWALMMAAARRITE 121 Query: 125 ADRFARSGEWKKGPFP--FTTKVSGARLGIVGLGRIGQAIAQRAAAFDMQIAYHNRSR-- 180 ++ F R+G+WKK + + GA LGI+G+GRIGQAIA+R+ FDMQ+ YHNRSR Sbjct: 122 SEHFLRAGKWKKWSYDSFVGPDIHGATLGIIGMGRIGQAIARRSLGFDMQVLYHNRSRLA 181 Query: 181 -------KDVPYTYVEDIVSLAREVDFLVMITPGGAGTRALVNAEVLEALGPKGFLINVA 233 Y E+++ R+ D ++++ P T + A L + P L N+A Sbjct: 182 PELEARANHARYVSKEELL---RQADHVILVLPYSKDTHHTIAAAELALMKPTATLTNIA 238 Query: 234 RGSVVDEKALIAALQAGTIAGAGLDVFENEPNIPAELAALENVVLTPHMASGTLVTRTAM 293 RG +VD+ ALIAAL+ G IA AG+DVFENEP E L NVVLTPH+AS + TR AM Sbjct: 239 RGGIVDDAALIAALREGRIAAAGVDVFENEPAFKPEFLDLSNVVLTPHIASASTPTRLAM 298 Query: 294 AELAFTNLQAHFSGK 308 A A NL A SG+ Sbjct: 299 ANCAADNLIAALSGQ 313 >gi|300310832|ref|YP_003774924.1| D-isomer specific 2-hydroxyacid dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 319 Score = 192 bits (488), Expect = 3e-50, Method: Compositional matrix adjust. Identities = 130/318 (40%), Positives = 176/318 (55%), Gaps = 18/318 (5%) Query: 6 RPVVLIVARLPQHLLDLLQQNF--TCHNLILDPLTDEALAAIAPQVRGIAANGEAKVGRE 63 +P V++ +LP+HL+ LQ F T + I D + +AA+A I A+ + Sbjct: 2 KPHVVVYKKLPEHLVQRLQAEFDLTLFDRITDDNRADFIAALATAHGMIGAS--LPITNA 59 Query: 64 FMARFPALEIVSVFGVGYDGVDVPAARERGIHVTHTPDVLTEDVADMAIALMLAVARNVV 123 + P L+IVS VG D D+ R+RG+ + HTP VLTE AD AL+LA AR VV Sbjct: 60 MLEAAPQLKIVSTISVGVDNFDLDYFRQRGLMLAHTPGVLTEATADTIFALILASARRVV 119 Query: 124 RADRFARSGEWKK--GPFPFTTKVSGARLGIVGLGRIGQAIAQRA-AAFDMQIAYHNR-- 178 + ++G WK G F V G LG++G+GRIG A+A+RA F M I YHNR Sbjct: 120 ELAEYVKAGRWKGSIGEAQFGVNVHGKTLGLIGMGRIGSAVARRAHHGFGMPILYHNRRP 179 Query: 179 ---SRKDVPYTYV--EDIVSLAREVDFLVMITPGGAGTRALVNAEVLEALGPKGFLINVA 233 + +++ YV ED+++ + DF+ ++ P T + A + IN + Sbjct: 180 DPEAERELGARYVSKEDLLA---QADFVCVMLPLTPQTERMFGAPEFALMKRSAIFINAS 236 Query: 234 RGSVVDEKALIAALQAGTIAGAGLDVFENEP-NIPAELAALENVVLTPHMASGTLVTRTA 292 RG +VDE ALIAALQ TI GAGLDVFE EP + + L L NVV PH+ S T TR A Sbjct: 237 RGRIVDEAALIAALQDKTIHGAGLDVFEVEPLPLQSPLLKLPNVVALPHIGSATHETRLA 296 Query: 293 MAELAFTNLQAHFSGKPV 310 MAELA TNL A G+PV Sbjct: 297 MAELAVTNLIAGLRGEPV 314 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 0.321 0.136 0.388 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: 954,721 Number of extensions: 39306 Number of successful extensions: 170 Number of sequences better than 1.0e-08: 11 Number of HSP's gapped: 148 Number of HSP's successfully gapped: 11 Length of query: 316 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 231 Effective length of database: 1,217,395 Effective search space: 281218245 Effective search space used: 281218245 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: 130 (54.7 bits)