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= 0003.0095.p (454 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313123|ref|YP_003777215.1| D-lactate dehydrogenase [Herbas... 881 0.0 gi|300313121|ref|YP_003777213.1| glycolate oxidase (FAD-linked s... 199 5e-52 gi|300312605|ref|YP_003776697.1| FAD/FMN-containing dehydrogenas... 160 1e-40 gi|300313195|ref|YP_003777287.1| oxidoreductase [Herbaspirillum ... 72 8e-14 gi|300313120|ref|YP_003777212.1| glycolate oxidase iron-sulfur s... 65 8e-12 >gi|300313123|ref|YP_003777215.1| D-lactate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 471 Score = 881 bits (2277), Expect = 0.0, Method: Compositional matrix adjust. Identities = 425/434 (97%), Positives = 432/434 (99%) Query: 1 VPQALLDELKALFGERCSTTLAMREHHGRDESSYDPMLPDAVVFAHSTEEVAAFVKLCSQ 60 VPQALLDELKALFG+RCSTTLAMREHHGRDESSYDPMLPDAVVFAHSTEEVAAFVKLCSQ Sbjct: 14 VPQALLDELKALFGDRCSTTLAMREHHGRDESSYDPMLPDAVVFAHSTEEVAAFVKLCSQ 73 Query: 61 YDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLAVNAEDLTATVQAGVTRKQLNQEI 120 YDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLAV+AEDLTATVQAGVTRKQLNQEI Sbjct: 74 YDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLAVHAEDLTATVQAGVTRKQLNQEI 133 Query: 121 KDTGLFFPIDPGADASLGGMASTRASGTNAVRYGTMKENTLTLTVVTAQGEIIKTGTRAK 180 KDTGLFFPIDPGADASLGGMASTRASGTNAVRYGTMKENTLTLTVVTAQGEIIKTGTRAK Sbjct: 134 KDTGLFFPIDPGADASLGGMASTRASGTNAVRYGTMKENTLTLTVVTAQGEIIKTGTRAK 193 Query: 181 KSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAISAAICSFPSVADAVNTVIQTIQMG 240 KSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAISAAICSFP+VADAVNTVIQTIQMG Sbjct: 194 KSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAISAAICSFPTVADAVNTVIQTIQMG 253 Query: 241 VPLARVELLDENGVRAINAHDRLSLPVNPLLLFEFHGSENGVKEQAELVQDIAKEFHALG 300 VPLARVELLDENGVRAINAHD+LSLPVNPLLLFEFHGSENGVKEQAELVQDIAKEFHALG Sbjct: 254 VPLARVELLDENGVRAINAHDKLSLPVNPLLLFEFHGSENGVKEQAELVQDIAKEFHALG 313 Query: 301 FEWATRPEDRTRLWTARHNAYFALLQLRPGARAISTDCCVPISRLAECVLATKADCEEQG 360 FEWATRPEDRTRLWTARHNAYFALLQLRPGARAISTDCCVPISRLAECVLATKADCEEQG Sbjct: 314 FEWATRPEDRTRLWTARHNAYFALLQLRPGARAISTDCCVPISRLAECVLATKADCEEQG 373 Query: 361 LIHAIIGHVGDGNFHVQMMVDPNDPADIARAEGVNARMVARALGMDGTCTGEHGVGLHKM 420 L HAIIGHVGDGNFHVQMMVDPNDPADIARAEGVN RMVARA+GMDGTCTGEHGVGLHKM Sbjct: 374 LTHAIIGHVGDGNFHVQMMVDPNDPADIARAEGVNQRMVARAIGMDGTCTGEHGVGLHKM 433 Query: 421 DFLIQEHGDGAIAL 434 DFLIQEHG+GAIA+ Sbjct: 434 DFLIQEHGEGAIAV 447 >gi|300313121|ref|YP_003777213.1| glycolate oxidase (FAD-linked subunit) oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 495 Score = 199 bits (505), Expect = 5e-52, Method: Compositional matrix adjust. Identities = 122/388 (31%), Positives = 199/388 (51%), Gaps = 7/388 (1%) Query: 38 LPDAVVFAHSTEEVAAFVKLCSQYDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLA 97 LP VV + +V A +K C I+P GAGT L G + GV V ++ NQ+L Sbjct: 51 LPMVVVLPENEAQVVAIMKTCHALQVQIVPRGAGTGLSGGATPIADGVVVSTAKFNQILQ 110 Query: 98 VNAEDLTATVQAGVTRKQLNQEIKDTGLFFPIDPGAD--ASLGGMASTRASGTNAVRYGT 155 ++ TA VQ GV +++ GL++ DP + S+GG + + G + ++YG Sbjct: 111 MDKYSRTAVVQPGVRNLAISEAAAPHGLYYAPDPSSQIACSIGGNVAENSGGVHCLKYGL 170 Query: 156 MKENTLTLTVVTAQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEA 215 N L + +VT +GE+++ G+ A + G DL V++GSEG LG++TEVTV+L P+P+A Sbjct: 171 TVHNVLRVRMVTIEGEVVELGSGAL-DAPGLDLLAVFIGSEGMLGVVTEVTVKLVPKPQA 229 Query: 216 ISAAICSFPSVADAVNTVIQTIQMGVPLARVELLDENGVRAINAHDRLSLPVN--PLLLF 273 + SF V N V I G+ A +E++D+ R + + ++ +LL Sbjct: 230 ARVIMASFDDVVKGGNAVANVIAAGIIPAGLEMMDKTSSRMVEPFVKAGYDIDAEAILLC 289 Query: 274 EFHGSENGVKEQAELVQDIAKEFHALGFEWATRPEDRTRLWTARHNAYFALLQLRPGARA 333 E G+ V+E+ + D+ A + +R R W+ R NA+ A ++ P Sbjct: 290 ESDGTVEEVEEEIGRMTDVLNASGATAIACSQSEAERLRFWSGRKNAFPAAGRISPDYYC 349 Query: 334 ISTDCCVPISRLAECVLATKADCEEQGLIHAIIGHVGDGNFHVQMMVDPNDPADIARAEG 393 + D +P +LA+ +L ++ GL A + H GDGN H ++ D N + RAE Sbjct: 350 M--DGTIPRKKLAQVLLGIAEMEKKYGLRCANVFHAGDGNLHPLILFDANIADEFHRAEL 407 Query: 394 VNARMVARALGMDGTCTGEHGVGLHKMD 421 A ++ + + GT TGEHGVG+ K++ Sbjct: 408 FGAEILELCVEVGGTITGEHGVGIEKIN 435 >gi|300312605|ref|YP_003776697.1| FAD/FMN-containing dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 475 Score = 160 bits (406), Expect = 1e-40, Method: Compositional matrix adjust. Identities = 134/409 (32%), Positives = 199/409 (48%), Gaps = 42/409 (10%) Query: 41 AVVFAHSTEEVAAFVKLCSQYDTPIIPYGAGTSLE-GHVLALQG-GVTVDLSQMNQVLAV 98 AV+ + EVAA V+LC+Q+ P++P G T L G V QG V + L ++N++ AV Sbjct: 48 AVLRPADSAEVAAVVRLCAQFAVPLVPQGGNTGLVLGSVPDQQGNAVVLSLRRLNRIRAV 107 Query: 99 NAEDLTATVQAGVTRKQLNQEIKDTGLFFPIDPGADAS--LGGMASTRASGTNAVRYGTM 156 +A + T TV++G + L ++ G FP+ A+ S +GG ST A GT +RYG Sbjct: 108 DALNNTITVESGCVLQHLQEQAAAAGRLFPLSLAAEGSCTIGGNLSTNAGGTGVLRYGNT 167 Query: 157 KENTLTLTVVTAQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAI 216 +E L L VVTAQGEI+ + +K + GYDL +++G+EGTLG+IT ++L+PQP A Sbjct: 168 RELCLGLEVVTAQGEIMSSLKGLRKDNTGYDLRDLFIGAEGTLGVITAAVMKLFPQPRAQ 227 Query: 217 SAAICSFP-SVADAVNTVIQTIQMGVPLARVELLDENGVRAINAH---DRLSL--PVNPL 270 A+ + P + G L EL+ + ++ + H RL P Sbjct: 228 VTALAALPHPAQALQLLQLAQAHCGPALTGFELMSDFCLQLVRKHFPEQRLPFDRPHPQY 287 Query: 271 LLFEFHGSEN------------GVKEQAELVQDIAKEFHALGFEWATRPEDRTRLWTARH 318 +L E SE+ G + LV D A+ + R LW R Sbjct: 288 VLLELSDSESEEHARALFEGLIGTALEQGLVDD--------AVIAASLAQSRA-LWRLRE 338 Query: 319 NAYFALLQLRPGARAISTDCCVPISRLAECVLATKADCEEQ--GLIHAIIGHVGDGNFHV 376 + A Q G + I D VPISR+AE + AT ++ G GH+GDGN H Sbjct: 339 SISSA--QAHEG-KNIKHDISVPISRIAEFIAATDVLVQQAAPGCRMVTFGHLGDGNLHY 395 Query: 377 QMMVDPNDPAD---IARAEGVNARMVARALG-MDGTCTGEHGVGLHKMD 421 + P AD IAR +N R+V ++ G+ + EHG+G K + Sbjct: 396 NVS-PPEGVADRDFIARQAAIN-RVVHDSVDRFGGSISAEHGLGALKRE 442 >gi|300313195|ref|YP_003777287.1| oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 1333 Score = 72.4 bits (176), Expect = 8e-14, Method: Compositional matrix adjust. Identities = 103/396 (26%), Positives = 158/396 (39%), Gaps = 75/396 (18%) Query: 24 REHHGRDESSYDPMLPDAVVFAHSTEEVAAFVKLCSQYDTPIIPYGAGTSLEGHVLALQG 83 R H D + + P V+ + +E+A VK C + IIP G GT G + L Sbjct: 180 RVSHVTDATDWRVEYPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTP 239 Query: 84 -GVTVDLSQMNQVLAVNAEDL------TATVQ--AGVTRKQLNQEIKDTGLFFPIDP-GA 133 ++ ++ Q+ AV E L AT+ AGV K+++ + G F +DP A Sbjct: 240 MSAVINTEKLEQLGAVEMEILPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSA 299 Query: 134 DAS-LGGMASTRASGTNAVRYGTMKENTLTLTVVTAQG---------------------- 170 +AS +GG + A G AV +GT +N + +V QG Sbjct: 300 EASCIGGNVAMNAGGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVAR 359 Query: 171 ---------------EIIKT------GTRAKKSSAGYDLTRVY------VGSEGTLGIIT 203 E+ KT G + +K G D+T + V EG G+IT Sbjct: 360 FKLEWSHPGEKGQKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLIT 419 Query: 204 EVTVRLYPQPEAISAAICSFPSVA-DAVNTVI--------QTIQMGVPLARVELLDENGV 254 L+ P+ F A DA+ +++ +T + G LA +E LDE + Sbjct: 420 SARWILHKMPKQTRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYL 479 Query: 255 RAINAHDRLSLPVNP--LLLFEFHG-SENGVKEQAELVQDIAKEFHALGFEWATRPEDRT 311 RA+ + V P +L+ + G EN V A V +A GF A PE R Sbjct: 480 RAVGYATKSKRGVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFV-AVSPEARK 538 Query: 312 RLWTARHNAYFALLQLRPGARAISTDCCVPISRLAE 347 + W R A + A I+ D +P++R+ E Sbjct: 539 KFWLDRSRT--AAIAKHTNAFKINEDVVIPLNRMGE 572 >gi|300313120|ref|YP_003777212.1| glycolate oxidase iron-sulfur subunit oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 359 Score = 65.5 bits (158), Expect = 8e-12, Method: Compositional matrix adjust. Identities = 39/140 (27%), Positives = 71/140 (50%), Gaps = 3/140 (2%) Query: 84 GVTVDLSQMNQVLAVNAEDLTATVQAGVTRKQLNQEIKDTGLFFPIDP---GADASLGGM 140 G +D + ++ +L T + G +++ + +P G A++GGM Sbjct: 43 GELLDTRAYSGIIDYEPTELVITARCGTPLSEIDAALAQHNQMLAWEPPSFGGAATVGGM 102 Query: 141 ASTRASGTNAVRYGTMKENTLTLTVVTAQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLG 200 + SG G +++ L ++ AQGE + G + K+ AGYD++R+ GS GTLG Sbjct: 103 VAAGLSGPARASAGAVRDFVLGAVLMDAQGEPLHFGGQVMKNVAGYDISRLLAGSLGTLG 162 Query: 201 IITEVTVRLYPQPEAISAAI 220 +I EV++++ P+P A S + Sbjct: 163 LILEVSLKVLPRPIASSTRV 182 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 0.318 0.133 0.387 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: 1,365,055 Number of extensions: 56026 Number of successful extensions: 176 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 166 Number of HSP's successfully gapped: 5 Length of query: 454 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 366 Effective length of database: 1,203,190 Effective search space: 440367540 Effective search space used: 440367540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 132 (55.5 bits)