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= 0001.3335.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|300312667|ref|YP_003776759.1| anti-restriction protein ArdA [... 533 e-153 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 108 8e-25 gi|300310865|ref|YP_003774957.1| response regulator containing a... 107 2e-24 gi|300313918|ref|YP_003778010.1| transmembrane protein [Herbaspi... 106 2e-24 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 99 6e-22 >gi|300312667|ref|YP_003776759.1| anti-restriction protein ArdA [Herbaspirillum seropedicae SmR1] Length = 354 Score = 533 bits (1373), Expect = e-153, Method: Compositional matrix adjust. Identities = 268/351 (76%), Positives = 301/351 (85%), Gaps = 2/351 (0%) Query: 1 VRFVQRIFRLRLIGLGIGFFCVAAGFLQQPVAWPLWLLLAAHGYLWPHLARYWALKSTIP 60 +RFV+RI+ LR IGLG+GFFCVAA F+QQPVAWPLW LL HGYLWP +AR WAL S IP Sbjct: 1 MRFVKRIYLLRTIGLGVGFFCVAAAFVQQPVAWPLWALLVFHGYLWPQVARAWALASRIP 60 Query: 61 YRAERRNLIIDAAFGGFWIAALNGNLVPSTVIISMLSMDNIAAGGLRLFMRGLYASLATA 120 YRAERRNL+IDAAFGGFWIAA+ GNLVPS VI+SMLSMDNIAAGGLRLFMRGLYAS+A Sbjct: 61 YRAERRNLVIDAAFGGFWIAAMQGNLVPSAVILSMLSMDNIAAGGLRLFMRGLYASIAAC 120 Query: 121 ILAWWLLEAQFQPQSDLVTILACLPMMALYPLALGQSTYAMSKKLAERSRQFEIVSQLDG 180 L WWLL+A + PQSDL TILACLPMMALYPLALG+STY MSKKLAERSRQFE+VSQ+DG Sbjct: 121 ALGWWLLDAHWSPQSDLPTILACLPMMALYPLALGKSTYEMSKKLAERSRQFEVVSQMDG 180 Query: 181 LTLLFNRRYWENLLAAEF-ERRRQERAPTHQAFLLLLDLDHFKSINDTHGHLIGDEVLRN 239 LT LFNRRYWE+LL EF +RR+ A ++FLLLLDLDHFK INDTHGHL+GDEVLRN Sbjct: 181 LTHLFNRRYWESLLIEEFSQRRKAPGAQQKESFLLLLDLDHFKRINDTHGHLVGDEVLRN 240 Query: 240 FSRLLRANLREDDLIGRYGGEEFVVILRDIQPGEALALSQRLVEAARAANDE-NNLYGCT 298 F++LLR +LR++DLIGRYGGEEFVVILR+I +AL LSQRLVE ARA+ D N LYGCT Sbjct: 241 FAQLLRIHLRKEDLIGRYGGEEFVVILRNIAHADALHLSQRLVERARASQDGVNKLYGCT 300 Query: 299 VSAGLVPFSTDMEAYFVWLQRADHAMYCAKESGRDRLVVWNERLERKVRAA 349 VSAGLVPF++DMEA+FVWLQRADHAMYCAK +GRDRLVVW L R A Sbjct: 301 VSAGLVPFTSDMEAHFVWLQRADHAMYCAKANGRDRLVVWEATLVRNAEPA 351 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 108 bits (269), Expect = 8e-25, Method: Compositional matrix adjust. Identities = 70/173 (40%), Positives = 102/173 (58%), Gaps = 7/173 (4%) Query: 170 RQFEIVSQLDGLTLLFNRRYWENLLAAEFERRRQERAPTHQAFLLLLDLDHFKSINDTHG 229 +Q E +++ DGLT L NRR + L A ++R +R+PT L +D+D+FK NDT+G Sbjct: 321 KQLEDLARTDGLTGLLNRRSLDEALLAVWQR--SQRSPTAGFSTLFIDVDYFKRYNDTYG 378 Query: 230 HLIGDEVLRNFSRLLRANL-REDDLIGRYGGEEFVVILRDIQPGEALALSQRLVEA--AR 286 H +GD VL+ + +LR +L R++DL GRYGGEEFVV+L AL ++Q+L EA R Sbjct: 379 HEMGDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQTDEHGALRMAQQLCEAIYNR 438 Query: 287 AANDENNLYGC-TVSAGLVPFS-TDMEAYFVWLQRADHAMYCAKESGRDRLVV 337 + G +VS G+ + + L ADHA+Y AK GR+R+ V Sbjct: 439 GIPHSGSPLGVISVSIGVATMNRAPHQRMEDVLNAADHALYIAKREGRNRVCV 491 >gi|300310865|ref|YP_003774957.1| response regulator containing a CheY-like receiver domain and a GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 554 Score = 107 bits (267), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 72/185 (38%), Positives = 104/185 (56%), Gaps = 12/185 (6%) Query: 160 AMSKKLAERSRQFEIVSQLDGLTLLFNRRYWENLLAAEFERRRQERAPTHQAF-LLLLDL 218 A ++L R E SQ DGLT +FNRRY++ LAAE R + T ++ L+++D+ Sbjct: 337 AARQELESLYRTLEAQSQKDGLTDVFNRRYFDAALAAELARLNR----TGESLSLMMIDV 392 Query: 219 DHFKSINDTHGHLIGDEVLRNFSRLLRA-NLREDDLIGRYGGEEFVVILRDIQPGEALAL 277 DHFK NDT+GH GD LR + + R+ D++ RYGGEEF VIL + PG A L Sbjct: 393 DHFKQFNDTYGHAAGDVCLRQVAAAISTVARRQGDIVARYGGEEFAVILPNCHPGSAQGL 452 Query: 278 SQRLVEAARA---ANDENNLYGCTVSAGLVPFSTDMEAYF---VWLQRADHAMYCAKESG 331 + R+V+A R A++ + + T+S G+ ++ + AD A+Y AKE G Sbjct: 453 AHRVVQAVRGLEIAHERSPMGVVTISVGVASLASGKSLLIEPRELIDSADGALYRAKEEG 512 Query: 332 RDRLV 336 RDR V Sbjct: 513 RDRAV 517 >gi|300313918|ref|YP_003778010.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 515 Score = 106 bits (265), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 68/171 (39%), Positives = 97/171 (56%), Gaps = 7/171 (4%) Query: 170 RQFEIVSQLDGLTLLFNRRYWENLLAAEFERRRQERAPTHQAFLLLLDLDHFKSINDTHG 229 RQ E +++ DGLT L NRR + L A +ER ++ + +L +D+D+FK+ NDT+G Sbjct: 341 RQLEALARTDGLTDLLNRRALDEALQATWERCQRNLGASFS--VLFIDVDYFKAYNDTYG 398 Query: 230 HLIGDEVLRNFSRLLRANL-REDDLIGRYGGEEFVVILRDIQPGEALALSQRLVEAARA- 287 H +GD VL+ + L A L R D GRYGGEEFVV+L A ++QRL +A R Sbjct: 399 HKLGDTVLKEVAATLTARLPRHTDCAGRYGGEEFVVLLEQTDLQGAQMMAQRLCDAVRER 458 Query: 288 --ANDENNLYGCTVSAGLVPFSTDMEAYFV-WLQRADHAMYCAKESGRDRL 335 A+ + L T+S G+ D L AD A+Y AK++GRDR+ Sbjct: 459 HIAHTSSPLAVVTISVGVATLERDHHRRVEDVLNAADAALYRAKQAGRDRV 509 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 98.6 bits (244), Expect = 6e-22, Method: Compositional matrix adjust. Identities = 66/184 (35%), Positives = 106/184 (57%), Gaps = 8/184 (4%) Query: 162 SKKLAERSRQFEIVSQLDGLTLLFNRRYWENLLAAEFERRRQERAPTHQAFLLLLDLDHF 221 +++L +R+ E +S DGLT + NRR ++ LA E RR R+ A LL+LD+D+F Sbjct: 388 TRELERANRKLEALSATDGLTGVANRRRFDEALANEM--RRAVRSGQSLA-LLMLDVDYF 444 Query: 222 KSINDTHGHLIGDEVLRNFSRLL-RANLREDDLIGRYGGEEFVVILRDIQPGEALALSQR 280 K ND +GHL GDE LR +R+L +++ R DL+ RYGGEEF VI+ + +AL ++ Sbjct: 445 KKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAEN 504 Query: 281 LVEAA---RAANDENNLYGCTVSAGLVPFSTDMEAYFVWLQR-ADHAMYCAKESGRDRLV 336 + +A + + ++ + S G+ D + R AD A+Y AK GR+R+V Sbjct: 505 ICQAIFELKLPHADSPFGYISASIGVAVLLPDEHTAPEQMVRIADQALYHAKYQGRNRVV 564 Query: 337 VWNE 340 + ++ Sbjct: 565 LGSD 568 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 0.327 0.140 0.435 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: 1,003,591 Number of extensions: 37711 Number of successful extensions: 239 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 191 Number of HSP's successfully gapped: 39 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: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 131 (55.1 bits)