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= 0018.0027.p (349 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312623|ref|YP_003776715.1| chaperone activity ATPase [Herb... 722 0.0 gi|300312956|ref|YP_003777048.1| CDP-6-deoxy-L-threo-D-glycero-4... 280 1e-76 gi|300310642|ref|YP_003774734.1| electron transfer component of ... 155 4e-39 gi|300314077|ref|YP_003778169.1| ferredoxin [2Fe-2S]-type protei... 59 4e-10 gi|300313415|ref|YP_003777507.1| phenylacetic acid degradation N... 59 9e-10 >gi|300312623|ref|YP_003776715.1| chaperone activity ATPase [Herbaspirillum seropedicae SmR1] Length = 349 Score = 722 bits (1864), Expect = 0.0, Method: Compositional matrix adjust. Identities = 348/349 (99%), Positives = 349/349 (100%) Query: 1 MSFQVTVQPSGRQFTCDADESILTAAIRAGVGLPYGCKNGACSSCKGKLVSGQVEHGPHQ 60 MSFQVTVQPSGRQFTCDADESILTAAIRAGVGLPYGCKNGACSSCKGKLVSGQVEHGPHQ Sbjct: 1 MSFQVTVQPSGRQFTCDADESILTAAIRAGVGLPYGCKNGACSSCKGKLVSGQVEHGPHQ 60 Query: 61 ERALSAHEQQLGMALFCVAKPQSDVTIEAREVAGAGDIPVRKLPVRVAKLDKVADDVIVL 120 ERALSAHEQQLGMALFCVAKPQSDVTIEAREVAGAGDIPVRKLPVRVAKLDKVADDVIVL Sbjct: 61 ERALSAHEQQLGMALFCVAKPQSDVTIEAREVAGAGDIPVRKLPVRVAKLDKVADDVIVL 120 Query: 121 SLQLPANDRLQYKAGQYVEFLLRDGKRRSYSMATAPHKDEHMSLHIRHLPGGLFTDQVFT 180 SLQLPANDRLQYKAGQYVEFLLRDGKRRSYSMATAPHKDEHMSLHIRHLPGGLFTDQVFT Sbjct: 121 SLQLPANDRLQYKAGQYVEFLLRDGKRRSYSMATAPHKDEHMSLHIRHLPGGLFTDQVFT 180 Query: 181 TLKERDILRIEGPLGTFFLREDSDKPIILLASGTGFAPIKAIVEQLEHAGSKRPITLYWG 240 TLKERDILRIEGPLGTFFLREDSDKPIILLASGTGFAPIKAIVEQLEHAGSKRP+TLYWG Sbjct: 181 TLKERDILRIEGPLGTFFLREDSDKPIILLASGTGFAPIKAIVEQLEHAGSKRPVTLYWG 240 Query: 241 GRRPQDLYMDALCQQWEQTLPNFKYVPVVSNAQAEDNWSGRTGFVHRAVMEDFPDLSGHQ 300 GRRPQDLYMDALCQQWEQTLPNFKYVPVVSNAQAEDNWSGRTGFVHRAVMEDFPDLSGHQ Sbjct: 241 GRRPQDLYMDALCQQWEQTLPNFKYVPVVSNAQAEDNWSGRTGFVHRAVMEDFPDLSGHQ 300 Query: 301 VYACGAPIVVESAQRDFSAQCGLPQDEFYADSFTSEADLAKPVADSPAA 349 VYACGAPIVVESAQRDFSAQCGLPQDEFYADSFTSEADLAKPVADSPAA Sbjct: 301 VYACGAPIVVESAQRDFSAQCGLPQDEFYADSFTSEADLAKPVADSPAA 349 >gi|300312956|ref|YP_003777048.1| CDP-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase reductase [Herbaspirillum seropedicae SmR1] Length = 360 Score = 280 bits (715), Expect = 1e-76, Method: Compositional matrix adjust. Identities = 134/234 (57%), Positives = 172/234 (73%), Gaps = 4/234 (1%) Query: 109 KLDKVADDVIVLSLQLPANDRLQYKAGQYVEFLLRDGKRRSYSMAT-APHKDEHMSLHIR 167 L + A DV +L L+ A L Y+AGQY++ LL DG+RRSYSMAT A + + LH+R Sbjct: 130 SLTRAAPDVAILRLRCAAP--LSYRAGQYIDLLLEDGQRRSYSMATYAKDGSDLLELHVR 187 Query: 168 HLPGGLFTDQVFTTLKERDILRIEGPLGTFFLREDSDKPIILLASGTGFAPIKAIVEQLE 227 HLPGGLFTD++F ++ +EGP G+FF+RE + +P+ILLASGTGFAP+KA+VE+ Sbjct: 188 HLPGGLFTDRLFNGMQPGQQFSLEGPAGSFFMREGT-QPLILLASGTGFAPVKALVEEAI 246 Query: 228 HAGSKRPITLYWGGRRPQDLYMDALCQQWEQTLPNFKYVPVVSNAQAEDNWSGRTGFVHR 287 +GS R + LYWGGRR DLY+DALC+ W +LP F YVPV+S A A WSGRTG VHR Sbjct: 247 ASGSTRAMRLYWGGRRAADLYLDALCRDWAASLPWFDYVPVLSEADATSGWSGRTGLVHR 306 Query: 288 AVMEDFPDLSGHQVYACGAPIVVESAQRDFSAQCGLPQDEFYADSFTSEADLAK 341 AVM+D P + +QVYACGAP+VVESA+RDF+A CGL + F+AD+F S ADL K Sbjct: 307 AVMQDVPAMQQYQVYACGAPVVVESARRDFTAACGLSETAFFADAFVSRADLRK 360 >gi|300310642|ref|YP_003774734.1| electron transfer component of chlorobenzoate 1,2-dioxygenase [Herbaspirillum seropedicae SmR1] Length = 351 Score = 155 bits (393), Expect = 4e-39, Method: Compositional matrix adjust. Identities = 109/328 (33%), Positives = 159/328 (48%), Gaps = 18/328 (5%) Query: 12 RQFTCDADESILTAAIRAGVGLPYGCKNGACSSCKGKLVSGQVEHGP-HQERALSAHEQQ 70 R C A E +L AA R + LP C +G C +CK + SG + G + + ALS+ E Sbjct: 16 RIIDCGAKEKVLDAAFRNRINLPMDCSDGVCGTCKCRAESGLYDLGDDYIDDALSSDEAG 75 Query: 71 LGMALFCVAKPQSDVTIEAREVAGAGDIPVRKLPVRVAKLDKVADDVIVLSLQLPANDRL 130 GM L C PQSD I + A +VA L + L L+ PAN Sbjct: 76 AGMVLTCQMVPQSDCVIAVPVASTACKTGTASFTGKVAGLSDLGGAAFELVLEAPANAP- 134 Query: 131 QYKAGQYVEF-LLRDGKRRSYSMATAPHKDEHMSLHIRHLPGGLFTDQVFTTLKERDILR 189 + GQYV + G+ RSYS ++ P MS I+++PGGL ++ + E L Sbjct: 135 AFLPGQYVNIGVPGSGQHRSYSFSS-PSGASRMSFLIKNVPGGLMSNWL-AGASEGATLE 192 Query: 190 IEGPLGTFFLREDSDKPIILLASGTGFAPIKAIVEQLEHAGSKRPITLYWGGRRPQDLYM 249 + GPLG+F+LR +P+++LA GTG AP +++E+L G +P+ L +G R QDL + Sbjct: 193 LTGPLGSFYLRP-VKRPVLMLAGGTGLAPFLSMLEELAQQGLDQPVHLIYGVTRDQDLVL 251 Query: 250 DALCQQWEQTLPNFKYVPVVSNAQAEDNWSGRTGFVHR----AVMEDFPDLSGHQVYACG 305 Q LP F + V++ R G+V + AV+ D VY CG Sbjct: 252 VERLQALADRLPGFSFTTCVADPATTH---ARQGYVTQHMPAAVLHD----GNVDVYLCG 304 Query: 306 APIVVESAQRDFSAQCGLPQDEFYADSF 333 P +VE+ Q+ F A G+ FY + F Sbjct: 305 PPPMVEAVQKHFQAT-GMQPASFYYEKF 331 >gi|300314077|ref|YP_003778169.1| ferredoxin [2Fe-2S]-type protein [Herbaspirillum seropedicae SmR1] Length = 100 Score = 59.3 bits (142), Expect = 4e-10, Method: Compositional matrix adjust. Identities = 31/87 (35%), Positives = 49/87 (56%), Gaps = 1/87 (1%) Query: 1 MSFQVTVQPSGRQFTCDADESILTAAIRAGVGLPYGCKNGACSSCKGKLVSGQVEHGPHQ 60 + F V +QPSG QF S+L +A+ A + LP C+NG C +C KL +G++++ Sbjct: 5 IRFLVRIQPSGLQFEQVPGRSVLLSALSASIRLPNSCRNGTCRTCMCKLSTGRIDYQIEW 64 Query: 61 ERALSAHEQQLGMALFCVAKPQSDVTI 87 L+ E+ G L CVA+ SD+ + Sbjct: 65 P-GLTREEKAEGWILPCVAEAASDLEL 90 >gi|300313415|ref|YP_003777507.1| phenylacetic acid degradation NADH oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 356 Score = 58.5 bits (140), Expect = 9e-10, Method: Compositional matrix adjust. Identities = 58/246 (23%), Positives = 112/246 (45%), Gaps = 19/246 (7%) Query: 104 PVRVAKLDKVADDVIVLSLQLPAN--DRLQYKAGQYVEF---LLRDGKRRSYSMATAPHK 158 P+ ++ + + D IV+S +PA D Y+ GQ++ + + RRSYS+ +A + Sbjct: 6 PLTISDVKQETRDTIVVSFAVPAELQDTFSYQQGQHLTLRSEINGEDLRRSYSICSAV-Q 64 Query: 159 DEHMSLHIRHLPGGLFTDQVFTTLKERDILRIEGPLGTFF--LREDSDKPIILLASGTGF 216 + + + I+ PGGLF++ + + + P+G F L + K + A+G+G Sbjct: 65 ERQLRVAIKRAPGGLFSNWANESFVPGQRIDVMPPMGHFNVPLEAGNRKHYLAFAAGSGI 124 Query: 217 APIKAIVEQLEHAGSKRPITLYWGGRRPQD-LYMDALCQQWEQTLPNFKYVPVVSNAQAE 275 P+ +I++ + TL + R ++ + L + L F V V+S Q + Sbjct: 125 TPMMSIIKTTLLSEPHSHFTLVYANRASSSVIFKEELTDLKDAYLERFNVVYVMSREQQD 184 Query: 276 -DNWSGRTGFVHRAVMEDF----PDLSG-HQVYACGAPIVVESAQRDFSAQCGLPQDEFY 329 + ++GR + RA + F DL + CG +V++ A GLP+ + Sbjct: 185 VELFNGR---IDRAKCDAFFASWIDLKDVDAAFLCGPEEMVQAVAASLQAH-GLPKTQIK 240 Query: 330 ADSFTS 335 + F + Sbjct: 241 TELFAA 246 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 0.319 0.135 0.408 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: 1,178,669 Number of extensions: 52335 Number of successful extensions: 144 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 136 Number of HSP's successfully gapped: 5 Length of query: 349 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 263 Effective length of database: 1,212,660 Effective search space: 318929580 Effective search space used: 318929580 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 (21.8 bits) S2: 131 (55.1 bits)