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= 0001.3235.p (292 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312573|ref|YP_003776665.1| dihydrodipicolinate synthase [H... 578 e-166 gi|300310616|ref|YP_003774708.1| dihydrodipicolinate synthase/N-... 86 3e-18 gi|300310700|ref|YP_003774792.1| dihydrodipicolinate synthase/N-... 75 5e-15 gi|300312447|ref|YP_003776539.1| 5-dehydro-4-deoxyglucarate dehy... 75 7e-15 >gi|300312573|ref|YP_003776665.1| dihydrodipicolinate synthase [Herbaspirillum seropedicae SmR1] Length = 292 Score = 578 bits (1489), Expect = e-166, Method: Compositional matrix adjust. Identities = 281/292 (96%), Positives = 286/292 (97%) Query: 1 MIKGSIVAIVTPMHPDGSLDYDGLRKLIDWHIAEGTDSIVIVGTTGESPTVSMEEHCELI 60 MIKGSIVAIVTPMH DGSLDYDGLRKLIDWHIAEGTDSIVIVGTTGESPTVSMEEHCELI Sbjct: 1 MIKGSIVAIVTPMHQDGSLDYDGLRKLIDWHIAEGTDSIVIVGTTGESPTVSMEEHCELI 60 Query: 61 KVAVEHTAKRIPIIAGTGGNSTSEAIELTEFAKKVGADASLQVVPYYNRPTQEGMYLHFK 120 KVAVEHTAKRIPIIAGTGGNSTSEAIELTEFAKKVGADASLQVVPYYNRPTQEGMYLHFK Sbjct: 61 KVAVEHTAKRIPIIAGTGGNSTSEAIELTEFAKKVGADASLQVVPYYNRPTQEGMYLHFK 120 Query: 121 TIAEAVDLPVILYNVPGRTVADMSNETILRLAQVKGIVGVKDATGNIARGSDLIRLAPKS 180 IAE+VDLPVILYNVPGRTVADMSNETILRLAQVKGIVGVKDATGNIARG+DLIRLAPKS Sbjct: 121 KIAESVDLPVILYNVPGRTVADMSNETILRLAQVKGIVGVKDATGNIARGTDLIRLAPKS 180 Query: 181 FAVYSGDDATAFALMFYGGAGNISVTANVAPRDMHELCVAAMSGNIARAVELNNKLLPLH 240 FAVYSGDDATA ALM YGGAGNISVTANVAPRDMHELCVAAMSGNIARAVELNNKLLPLH Sbjct: 181 FAVYSGDDATAIALMLYGGAGNISVTANVAPRDMHELCVAAMSGNIARAVELNNKLLPLH 240 Query: 241 NKLFVEPNPVPVKWAMQEMGLIPTGMRLPLAPLGEAFHDTVRAALRESGVLN 292 NKLFVEPNPVP+KWAMQEMGLIP+GMRLPLAPLG A+HDTVRAALRESGVL Sbjct: 241 NKLFVEPNPVPLKWAMQEMGLIPSGMRLPLAPLGAAYHDTVRAALRESGVLK 292 >gi|300310616|ref|YP_003774708.1| dihydrodipicolinate synthase/N-acetylneuraminate lyase [Herbaspirillum seropedicae SmR1] Length = 305 Score = 86.3 bits (212), Expect = 3e-18, Method: Compositional matrix adjust. Identities = 81/300 (27%), Positives = 139/300 (46%), Gaps = 15/300 (5%) Query: 2 IKGSIVAIVTPMHPDGSLDYDGLRKLIDWHIA-EGTDSIVIVGTTGESPTVSMEEHCELI 60 ++G + A VTP DG++D+ + +L W + +G +V++G GE +S E +I Sbjct: 5 LRGLVPAPVTPFTRDGAVDHAAIMRLGKWLGSFDGVKGLVVLGHAGEGTFLSQSEQAAVI 64 Query: 61 KVAVEHTAKRIPIIAGTGGNSTSEAIELTEFAKKVGADASLQVVP---YYNRPTQEGM-Y 116 + V+ T R+P+IAG T A E + A K GA A L V P + Q+G Sbjct: 65 ESFVKSTDGRVPVIAGITLEGTQVAAEEAKRAVKAGAAAGL-VYPSHGWLRFGYQKGAPQ 123 Query: 117 LHFKTIAEAVDLPVILYNVPGRTVADMSNETILRLAQVKGIVGVKDATGNIARGSD---L 173 ++ I E LP+IL+ P T A + ET L +A + G+ +K+ N+ R + Sbjct: 124 DRYRAIYEESGLPLILFQYPDATKATYNLETQLDIAALPGVFAMKNGVRNMRRWDTEIPV 183 Query: 174 IRLAPKSFAVYSGDDATAFALMFYGGAGNISVTANVAPRDMHELCVAAMSGNIARAVELN 233 +R + + D MF G + ++AP + +L A + + +A ++ Sbjct: 184 VRRERPDLQILTCHDEYLLHTMF-DVDGALVGYGSIAPELLIDLIAAGKAKDYRKARAIH 242 Query: 234 NKLLPLHNKLFVE----PNPVPVKWAMQEMGLIPTG-MRLPLAPLGEAFHDTVRAALRES 288 +KLLP+ ++ V +K A+ G++ +R PL PL + ALR + Sbjct: 243 DKLLPVTKNVYHRGSHMEGTVALKHALVARGILEHATVRSPLLPLEPGADVEIAKALRSA 302 >gi|300310700|ref|YP_003774792.1| dihydrodipicolinate synthase/N-acetylneuraminate lyase [Herbaspirillum seropedicae SmR1] Length = 306 Score = 75.5 bits (184), Expect = 5e-15, Method: Compositional matrix adjust. Identities = 70/277 (25%), Positives = 131/277 (47%), Gaps = 13/277 (4%) Query: 16 DGSLDYDGLRKLIDWHIAEGTDSIVIVGTTGESPTVSMEEHCELIKVAVEHTAKRIPIIA 75 +G LD +G ++ ID+ I G++ + I+ E +S EE ++ +EH A R+P+I Sbjct: 20 NGKLDLEGQKRAIDFMIDAGSNGLCILANFSEQFVLSDEERVQVQNTVLEHVAGRVPVIV 79 Query: 76 GTGGNSTSEAIELTEFAKKVGADASLQVVPYYN---RPTQEGMYLHFKTIAEAVDLPVIL 132 T + E + A+ GA + + PY+ R ++ +Y +K +++A+D+P+++ Sbjct: 80 TTTHYGSQICAERSRAAQDAGAAMVMVMPPYHGATFRVPEKQIYEFYKHVSDAIDIPIMI 139 Query: 133 YNVPGRTVADMSNETILRLA-QVKGIVGVK-DATGNIARGSDLIRLAPKS-FAVYSGDDA 189 + P +S + R+A +++ + K + G ++ DLI L + + G++A Sbjct: 140 QDAPVAGTP-LSAPFLARMAKEIEQVSYFKIETAGAASKLRDLIELGGDAVVGPWDGEEA 198 Query: 190 TAFALMFYGGAGNISVTANVAPRDMHELCVAAMSGNIARAVELNNKLLPLHNKLFVEPNP 249 + ++T P + ++ A +G+I +A EL + LPL N + Sbjct: 199 ITL-IPDLDAGATGAMTGGGYPDGIRKIVDAYFAGDIEKAAELYMQWLPLINYENRQCGL 257 Query: 250 VPVKWAMQEMGLIPTGM-RLPLAPLGEAFHDTVRAAL 285 K M E G+I + M R P PL H VR L Sbjct: 258 SACKALMLEGGVIKSDMLRHPQPPL----HPKVREGL 290 >gi|300312447|ref|YP_003776539.1| 5-dehydro-4-deoxyglucarate dehydratase [Herbaspirillum seropedicae SmR1] Length = 306 Score = 75.1 bits (183), Expect = 7e-15, Method: Compositional matrix adjust. Identities = 44/141 (31%), Positives = 78/141 (55%), Gaps = 5/141 (3%) Query: 28 IDWHIAEGTDSIVIVGTTGESPTVSMEEHCELIKVAVEHTAKRIPIIAGTGGNSTSEAIE 87 ++W G ++ G TGE ++ E+ ++I+ AV+ ++PIIAG GG ST AI Sbjct: 40 LEWLAPYGASALFAAGGTGEFFSLVPGEYSDIIRTAVDTCRGKVPIIAGAGG-STRAAIA 98 Query: 88 LTEFAKKVGADASLQVVPYYNRPTQEGMYLHFKTIAEAVDLPVILYNVPGRTVADMSNET 147 + A+++GA L + Y +Q+G+ H + + ++V VI+YN R V ++ +T Sbjct: 99 YAQEAERLGAHGILLMPHYLTEASQDGIAAHVEAVCKSVKFGVIIYN---RAVCKLNADT 155 Query: 148 ILRLA-QVKGIVGVKDATGNI 167 + +LA + ++G KD G I Sbjct: 156 LQKLADRCPNLIGFKDGIGEI 176 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 0.135 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: 916,883 Number of extensions: 38035 Number of successful extensions: 146 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 142 Number of HSP's successfully gapped: 4 Length of query: 292 Length of database: 1,619,870 Length adjustment: 84 Effective length of query: 208 Effective length of database: 1,222,130 Effective search space: 254203040 Effective search space used: 254203040 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: 130 (54.7 bits)