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= 0001.3733.p (471 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... 953 0.0 gi|300313121|ref|YP_003777213.1| glycolate oxidase (FAD-linked s... 213 2e-56 gi|300312605|ref|YP_003776697.1| FAD/FMN-containing dehydrogenas... 191 1e-49 gi|300313195|ref|YP_003777287.1| oxidoreductase [Herbaspirillum ... 76 6e-15 gi|300313120|ref|YP_003777212.1| glycolate oxidase iron-sulfur s... 66 6e-12 >gi|300313123|ref|YP_003777215.1| D-lactate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 471 Score = 953 bits (2463), Expect = 0.0, Method: Compositional matrix adjust. Identities = 459/471 (97%), Positives = 466/471 (98%) Query: 1 MNHLVDARKLKRPVPQALLDELKAVFGERCSTTLAMREHHGRDESSYDPMLPDAVVFAHS 60 MNHLVDARKLKRPVPQALLDELKA+FG+RCSTTLAMREHHGRDESSYDPMLPDAVVFAHS Sbjct: 1 MNHLVDARKLKRPVPQALLDELKALFGDRCSTTLAMREHHGRDESSYDPMLPDAVVFAHS 60 Query: 61 TEEVATFVKLCSQYDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLAVNAEDLTATV 120 TEEVA FVKLCSQYDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLAV+AEDLTATV Sbjct: 61 TEEVAAFVKLCSQYDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLAVHAEDLTATV 120 Query: 121 QAGVTRKQLNQEIKDTGLFFPIDPGADASLGGMASTRASGTNAVRYGTMKENTLTLTVVT 180 QAGVTRKQLNQEIKDTGLFFPIDPGADASLGGMASTRASGTNAVRYGTMKENTLTLTVVT Sbjct: 121 QAGVTRKQLNQEIKDTGLFFPIDPGADASLGGMASTRASGTNAVRYGTMKENTLTLTVVT 180 Query: 181 AQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAISAAICSFPSVA 240 AQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAISAAICSFP+VA Sbjct: 181 AQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAISAAICSFPTVA 240 Query: 241 DAVNTVIQTIQMGVPLARVELLDENGVRAINAHDKLSLPVNPLLLFEFHGSDNGVKEQAE 300 DAVNTVIQTIQMGVPLARVELLDENGVRAINAHDKLSLPVNPLLLFEFHGS+NGVKEQAE Sbjct: 241 DAVNTVIQTIQMGVPLARVELLDENGVRAINAHDKLSLPVNPLLLFEFHGSENGVKEQAE 300 Query: 301 LVQDIAHENHARGFEWATRPEDRSRLWTARHNAYFALLQLRPGARAISTDCCVPISRLAE 360 LVQDIA E HA GFEWATRPEDR+RLWTARHNAYFALLQLRPGARAISTDCCVPISRLAE Sbjct: 301 LVQDIAKEFHALGFEWATRPEDRTRLWTARHNAYFALLQLRPGARAISTDCCVPISRLAE 360 Query: 361 CVLATKADCEEQGLTHAIIGHVGDGNFHVQMMVDPNDPADIARAEGVNARMVARAIGMDG 420 CVLATKADCEEQGLTHAIIGHVGDGNFHVQMMVDPNDPADIARAEGVN RMVARAIGMDG Sbjct: 361 CVLATKADCEEQGLTHAIIGHVGDGNFHVQMMVDPNDPADIARAEGVNQRMVARAIGMDG 420 Query: 421 TCTGEHGVGLHKMDFLVQEHGEGAIAVMRAIKHALDPKNIMNPGKILRWEQ 471 TCTGEHGVGLHKMDFL+QEHGEGAIAVMRAIKHALDPKNIMNPGKILRWEQ Sbjct: 421 TCTGEHGVGLHKMDFLIQEHGEGAIAVMRAIKHALDPKNIMNPGKILRWEQ 471 >gi|300313121|ref|YP_003777213.1| glycolate oxidase (FAD-linked subunit) oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 495 Score = 213 bits (543), Expect = 2e-56, Method: Compositional matrix adjust. Identities = 129/421 (30%), Positives = 213/421 (50%), Gaps = 7/421 (1%) Query: 51 LPDAVVFAHSTEEVATFVKLCSQYDTPIIPYGAGTSLEGHVLALQGGVTVDLSQMNQVLA 110 LP VV + +V +K C I+P GAGT L G + GV V ++ NQ+L Sbjct: 51 LPMVVVLPENEAQVVAIMKTCHALQVQIVPRGAGTGLSGGATPIADGVVVSTAKFNQILQ 110 Query: 111 VNAEDLTATVQAGVTRKQLNQEIKDTGLFFPIDPGAD--ASLGGMASTRASGTNAVRYGT 168 ++ TA VQ GV +++ GL++ DP + S+GG + + G + ++YG Sbjct: 111 MDKYSRTAVVQPGVRNLAISEAAAPHGLYYAPDPSSQIACSIGGNVAENSGGVHCLKYGL 170 Query: 169 MKENTLTLTVVTAQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEA 228 N L + +VT +GE+++ G+ A + G DL V++GSEG LG++TEVTV+L P+P+A Sbjct: 171 TVHNVLRVRMVTIEGEVVELGSGALDAP-GLDLLAVFIGSEGMLGVVTEVTVKLVPKPQA 229 Query: 229 ISAAICSFPSVADAVNTVIQTIQMGVPLARVELLDENGVRAINAHDKLSLPVNP--LLLF 286 + SF V N V I G+ A +E++D+ R + K ++ +LL Sbjct: 230 ARVIMASFDDVVKGGNAVANVIAAGIIPAGLEMMDKTSSRMVEPFVKAGYDIDAEAILLC 289 Query: 287 EFHGSDNGVKEQAELVQDIAHENHARGFEWATRPEDRSRLWTARHNAYFALLQLRPGARA 346 E G+ V+E+ + D+ + + A + +R R W+ R NA+ A ++ P Sbjct: 290 ESDGTVEEVEEEIGRMTDVLNASGATAIACSQSEAERLRFWSGRKNAFPAAGRISPDYYC 349 Query: 347 ISTDCCVPISRLAECVLATKADCEEQGLTHAIIGHVGDGNFHVQMMVDPNDPADIARAEG 406 + D +P +LA+ +L ++ GL A + H GDGN H ++ D N + RAE Sbjct: 350 M--DGTIPRKKLAQVLLGIAEMEKKYGLRCANVFHAGDGNLHPLILFDANIADEFHRAEL 407 Query: 407 VNARMVARAIGMDGTCTGEHGVGLHKMDFLVQEHGEGAIAVMRAIKHALDPKNIMNPGKI 466 A ++ + + GT TGEHGVG+ K++ + + +K A DP ++NP K Sbjct: 408 FGAEILELCVEVGGTITGEHGVGIEKINSMCVQFSPAERETFFKLKRAFDPAFLLNPDKA 467 Query: 467 L 467 + Sbjct: 468 I 468 >gi|300312605|ref|YP_003776697.1| FAD/FMN-containing dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 475 Score = 191 bits (484), Expect = 1e-49, Method: Compositional matrix adjust. Identities = 147/436 (33%), Positives = 225/436 (51%), Gaps = 30/436 (6%) Query: 54 AVVFAHSTEEVATFVKLCSQYDTPIIPYGAGTSLE-GHVLALQG-GVTVDLSQMNQVLAV 111 AV+ + EVA V+LC+Q+ P++P G T L G V QG V + L ++N++ AV Sbjct: 48 AVLRPADSAEVAAVVRLCAQFAVPLVPQGGNTGLVLGSVPDQQGNAVVLSLRRLNRIRAV 107 Query: 112 NAEDLTATVQAGVTRKQLNQEIKDTGLFFPIDPGADAS--LGGMASTRASGTNAVRYGTM 169 +A + T TV++G + L ++ G FP+ A+ S +GG ST A GT +RYG Sbjct: 108 DALNNTITVESGCVLQHLQEQAAAAGRLFPLSLAAEGSCTIGGNLSTNAGGTGVLRYGNT 167 Query: 170 KENTLTLTVVTAQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLGIITEVTVRLYPQPEAI 229 +E L L VVTAQGEI+ + +K + GYDL +++G+EGTLG+IT ++L+PQP A Sbjct: 168 RELCLGLEVVTAQGEIMSSLKGLRKDNTGYDLRDLFIGAEGTLGVITAAVMKLFPQPRAQ 227 Query: 230 SAAICSFP-SVADAVNTVIQTIQMGVPLARVELLDENGVRAINAH-DKLSLPVN----PL 283 A+ + P + G L EL+ + ++ + H + LP + Sbjct: 228 VTALAALPHPAQALQLLQLAQAHCGPALTGFELMSDFCLQLVRKHFPEQRLPFDRPHPQY 287 Query: 284 LLFEFHGSDNGVKEQAE-LVQDIAHENHARGFE-----WATRPEDRSRLWTARHNAYFAL 337 +L E SD+ +E A L + + +G A+ + R+ LW R + A Sbjct: 288 VLLEL--SDSESEEHARALFEGLIGTALEQGLVDDAVIAASLAQSRA-LWRLRESISSA- 343 Query: 338 LQLRPGARAISTDCCVPISRLAECVLATKADCEEQ--GLTHAIIGHVGDGNFHVQMMVDP 395 Q G + I D VPISR+AE + AT ++ G GH+GDGN H + P Sbjct: 344 -QAHEG-KNIKHDISVPISRIAEFIAATDVLVQQAAPGCRMVTFGHLGDGNLHYNVS-PP 400 Query: 396 NDPAD---IARAEGVNARMVARAIG-MDGTCTGEHGVGLHKMDFLVQEHGEGAIAVMRAI 451 AD IAR +N R+V ++ G+ + EHG+G K + + + + +MRAI Sbjct: 401 EGVADRDFIARQAAIN-RVVHDSVDRFGGSISAEHGLGALKREEITRYKSPVELQLMRAI 459 Query: 452 KHALDPKNIMNPGKIL 467 K ALDP+ +MNPGK+L Sbjct: 460 KLALDPQQLMNPGKVL 475 >gi|300313195|ref|YP_003777287.1| oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 1333 Score = 75.9 bits (185), Expect = 6e-15, Method: Compositional matrix adjust. Identities = 104/396 (26%), Positives = 159/396 (40%), Gaps = 75/396 (18%) Query: 37 REHHGRDESSYDPMLPDAVVFAHSTEEVATFVKLCSQYDTPIIPYGAGTSLEGHVLALQG 96 R H D + + P V+ + +E+A VK C + IIP G GT G + L Sbjct: 180 RVSHVTDATDWRVEYPFVVLTPDTEDEMAGLVKACIELGLTIIPRGGGTGYTGGAIPLTP 239 Query: 97 -GVTVDLSQMNQVLAVNAEDL------TATVQ--AGVTRKQLNQEIKDTGLFFPIDP-GA 146 ++ ++ Q+ AV E L AT+ AGV K+++ + G F +DP A Sbjct: 240 MSAVINTEKLEQLGAVEMEILPGLDKPYATIYSGAGVVTKRVSDAAEKAGFVFAVDPTSA 299 Query: 147 DAS-LGGMASTRASGTNAVRYGTMKENTLTLTVVTAQG---------------------- 183 +AS +GG + A G AV +GT +N + +V QG Sbjct: 300 EASCIGGNVAMNAGGKKAVLWGTALDNLASWRMVDPQGDWLEVTRLDHNLGKIHDVEVAR 359 Query: 184 ---------------EIIKT------GTRAKKSSAGYDLTRVY------VGSEGTLGIIT 216 E+ KT G + +K G D+T + V EG G+IT Sbjct: 360 FKLEWSHPGEKGQKTEVFKTEILEISGKKFRKEGLGKDVTDKFLSGLPGVQKEGCDGLIT 419 Query: 217 EVTVRLYPQPEAISAAICSFPSVA-DAVNTVI--------QTIQMGVPLARVELLDENGV 267 L+ P+ F A DA+ +++ +T + G LA +E LDE + Sbjct: 420 SARWILHKMPKQTRTVCLEFFGQARDAIPSIVEIKDYLDAETKKGGAILAGLEHLDERYL 479 Query: 268 RAINAHDKLSLPVNP--LLLFEFHGSD-NGVKEQAELVQDIAHENHARGFEWATRPEDRS 324 RA+ K V P +L+ + G D N V A V +A+ GF A PE R Sbjct: 480 RAVGYATKSKRGVLPKMVLIGDIVGDDENAVAAAASEVIRMANNRVGEGFV-AVSPEARK 538 Query: 325 RLWTARHNAYFALLQLRPGARAISTDCCVPISRLAE 360 + W R A + A I+ D +P++R+ E Sbjct: 539 KFWLDRSRT--AAIAKHTNAFKINEDVVIPLNRMGE 572 Score = 56.2 bits (134), Expect = 5e-09, Method: Compositional matrix adjust. Identities = 29/87 (33%), Positives = 47/87 (54%), Gaps = 4/87 (4%) Query: 381 HVGDGNFHVQMMVDPNDPADIARAEGVNARMVARAIGMDGTCTGEHGVGLHKMDFLVQEH 440 H GDGN H + V+ + + A AR++ A ++G +GEHG+G+ K++FL ++ Sbjct: 740 HAGDGNVHTNIPVNSDHYEMLQDAHVAVARIMKLARSLNGVISGEHGIGITKLEFLTEDE 799 Query: 441 GEGAIAVMRAIKHALDPKNIMNPGKIL 467 I R K +DP+ N GK+L Sbjct: 800 ----IGEFREYKKRVDPEGRFNKGKLL 822 >gi|300313120|ref|YP_003777212.1| glycolate oxidase iron-sulfur subunit oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 359 Score = 65.9 bits (159), Expect = 6e-12, Method: Compositional matrix adjust. Identities = 39/140 (27%), Positives = 71/140 (50%), Gaps = 3/140 (2%) Query: 97 GVTVDLSQMNQVLAVNAEDLTATVQAGVTRKQLNQEIKDTGLFFPIDP---GADASLGGM 153 G +D + ++ +L T + G +++ + +P G A++GGM Sbjct: 43 GELLDTRAYSGIIDYEPTELVITARCGTPLSEIDAALAQHNQMLAWEPPSFGGAATVGGM 102 Query: 154 ASTRASGTNAVRYGTMKENTLTLTVVTAQGEIIKTGTRAKKSSAGYDLTRVYVGSEGTLG 213 + SG G +++ L ++ AQGE + G + K+ AGYD++R+ GS GTLG Sbjct: 103 VAAGLSGPARASAGAVRDFVLGAVLMDAQGEPLHFGGQVMKNVAGYDISRLLAGSLGTLG 162 Query: 214 IITEVTVRLYPQPEAISAAI 233 +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 0.391 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: 1,494,975 Number of extensions: 61934 Number of successful extensions: 189 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 177 Number of HSP's successfully gapped: 6 Length of query: 471 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 382 Effective length of database: 1,198,455 Effective search space: 457809810 Effective search space used: 457809810 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)