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= 0001.1279.p (313 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310700|ref|YP_003774792.1| dihydrodipicolinate synthase/N-... 132 3e-32 gi|300310616|ref|YP_003774708.1| dihydrodipicolinate synthase/N-... 77 1e-15 gi|300312573|ref|YP_003776665.1| dihydrodipicolinate synthase [H... 69 3e-13 >gi|300310700|ref|YP_003774792.1| dihydrodipicolinate synthase/N-acetylneuraminate lyase [Herbaspirillum seropedicae SmR1] Length = 306 Score = 132 bits (332), Expect = 3e-32, Method: Compositional matrix adjust. Identities = 99/293 (33%), Positives = 157/293 (53%), Gaps = 9/293 (3%) Query: 15 RGVYTICPTPFHADGTLDLGSIATLVEFQIEAGVSGLAILGFLGEAHKLSNAERRAVTST 74 RGV+ + PT F A+G LDL ++F I+AG +GL IL E LS+ ER V +T Sbjct: 7 RGVFPVAPTIFDANGKLDLEGQKRAIDFMIDAGSNGLCILANFSEQFVLSDEERVQVQNT 66 Query: 75 FVKCAAGRVPVWVGVRALGLAGAIEQATEAAEAGAAAVFAAPLDMAS-----DAVQFDYY 129 ++ AGRVPV V G E++ A +AGAA V P + + +++Y Sbjct: 67 VLEHVAGRVPVIVTTTHYGSQICAERSRAAQDAGAAMVMVMPPYHGATFRVPEKQIYEFY 126 Query: 130 KSLAAALAIPVVIHDFPDSFGTEIKAEVIARLGRE-GGVNFIKMEEPPVGQKISRIRDLA 188 K ++ A+ IP++I D P + GT + A +AR+ +E V++ K+E K+ + +L Sbjct: 127 KHVSDAIDIPIMIQDAPVA-GTPLSAPFLARMAKEIEQVSYFKIETAGAASKLRDLIELG 185 Query: 189 GESMR-IFGGLGGVYFLEELQRGAVGTMTGFAFPEILVRIYDQFAAGDLAGAAATFDQYC 247 G+++ + G + + +L GA G MTG +P+ + +I D + AGD+ AA + Q+ Sbjct: 186 GDAVVGPWDGEEAITLIPDLDAGATGAMTGGGYPDGIRKIVDAYFAGDIEKAAELYMQWL 245 Query: 248 PLIRYEFQPKIGLSLRKYVYRKRGVISSDAIRSPGMRIDPETERELEAVIARV 300 PLI YE + + GLS K + + GVI SD +R P + P+ L V R+ Sbjct: 246 PLINYENR-QCGLSACKALMLEGGVIKSDMLRHPQPPLHPKVREGLLRVARRL 297 >gi|300310616|ref|YP_003774708.1| dihydrodipicolinate synthase/N-acetylneuraminate lyase [Herbaspirillum seropedicae SmR1] Length = 305 Score = 77.4 bits (189), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 79/303 (26%), Positives = 134/303 (44%), Gaps = 37/303 (12%) Query: 15 RGVYTICPTPFHADGTLDLGSIATLVEFQIE-AGVSGLAILGFLGEAHKLSNAERRAVTS 73 RG+ TPF DG +D +I L ++ GV GL +LG GE LS +E+ AV Sbjct: 6 RGLVPAPVTPFTRDGAVDHAAIMRLGKWLGSFDGVKGLVVLGHAGEGTFLSQSEQAAVIE 65 Query: 74 TFVKCAAGRVPVWVGVRALGLAGAIEQATEAAEAGAAAVFAAPLDMASDAVQFDY----- 128 +FVK GRVPV G+ G A E+A A +AGAAA P + ++F Y Sbjct: 66 SFVKSTDGRVPVIAGITLEGTQVAAEEAKRAVKAGAAAGLVYP---SHGWLRFGYQKGAP 122 Query: 129 ---YKSLAAALAIPVVIHDFPD----SFGTEIKAEVIARLG---REGGVNFIK---MEEP 175 Y+++ +P+++ +PD ++ E + ++ A G + GV ++ E P Sbjct: 123 QDRYRAIYEESGLPLILFQYPDATKATYNLETQLDIAALPGVFAMKNGVRNMRRWDTEIP 182 Query: 176 PVGQKISRIRDLAGESMRIFGGLGGVYFLEELQRGAVGTMTGFAF--PEILVRIYDQFAA 233 V ++ ++ L + + V G + G+ PE+L+ + A Sbjct: 183 VVRRERPDLQILTCHDEYLLHTMFDVD----------GALVGYGSIAPELLIDLIAAGKA 232 Query: 234 GDLAGAAATFDQYCPLIRYEFQ---PKIGLSLRKYVYRKRGVISSDAIRSPGMRIDPETE 290 D A A D+ P+ + + G K+ RG++ +RSP + ++P + Sbjct: 233 KDYRKARAIHDKLLPVTKNVYHRGSHMEGTVALKHALVARGILEHATVRSPLLPLEPGAD 292 Query: 291 REL 293 E+ Sbjct: 293 VEI 295 >gi|300312573|ref|YP_003776665.1| dihydrodipicolinate synthase [Herbaspirillum seropedicae SmR1] Length = 292 Score = 69.3 bits (168), Expect = 3e-13, Method: Compositional matrix adjust. Identities = 65/266 (24%), Positives = 120/266 (45%), Gaps = 11/266 (4%) Query: 23 TPFHADGTLDLGSIATLVEFQIEAGVSGLAILGFLGEAHKLSNAERRAVTSTFVKCAAGR 82 TP H DG+LD + L+++ I G + I+G GE+ +S E + V+ A R Sbjct: 11 TPMHQDGSLDYDGLRKLIDWHIAEGTDSIVIVGTTGESPTVSMEEHCELIKVAVEHTAKR 70 Query: 83 VPVWVGVRALGLAGAIEQATEAAEAGA-AAVFAAP-LDMASDAVQFDYYKSLAAALAIPV 140 +P+ G + AIE A + GA A++ P + + + ++K +A ++ +PV Sbjct: 71 IPIIAGTGGNSTSEAIELTEFAKKVGADASLQVVPYYNRPTQEGMYLHFKKIAESVDLPV 130 Query: 141 VIHDFPDSFGTEIKAEVIARLGREGGVNFIKMEEPPVGQKISRIRDLAGESMRIFGGLGG 200 ++++ P ++ E I RL + G+ +K + + IR LA +S ++ G Sbjct: 131 ILYNVPGRTVADMSNETILRLAQVKGIVGVKDATGNIARGTDLIR-LAPKSFAVYSGDDA 189 Query: 201 VYFLEELQRGAVG-TMTGFAFPEILVRIYDQFAAGDLAGAAATFDQYCPLIRYEFQPKIG 259 L GA ++T P + + +G++A A ++ PL F Sbjct: 190 TAIALMLYGGAGNISVTANVAPRDMHELCVAAMSGNIARAVELNNKLLPLHNKLFVEPNP 249 Query: 260 LSLRKYVYRKRGVISSDAIRSPGMRI 285 + L K+ ++ G+I S GMR+ Sbjct: 250 VPL-KWAMQEMGLIPS------GMRL 268 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 0.322 0.138 0.396 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: 855,916 Number of extensions: 32403 Number of successful extensions: 115 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 109 Number of HSP's successfully gapped: 3 Length of query: 313 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 228 Effective length of database: 1,217,395 Effective search space: 277566060 Effective search space used: 277566060 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)