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= 0001.2111.p (393 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311572|ref|YP_003775664.1| transmembrane protein [Herbaspi... 588 e-169 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 108 6e-25 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 103 3e-23 gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 102 5e-23 gi|300310865|ref|YP_003774957.1| response regulator containing a... 100 3e-22 >gi|300311572|ref|YP_003775664.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 395 Score = 588 bits (1517), Expect = e-169, Method: Compositional matrix adjust. Identities = 290/392 (73%), Positives = 325/392 (82%) Query: 1 MNAATASIALALVQFCGGVVMAGLFLNMPREHCTRQWALSGGLSASGICIMVAGYAGLGG 60 MNAATASIALALVQFCGG++MAGLF+NMP+EHCTR WALSG A+GIC+M+ GY +G Sbjct: 1 MNAATASIALALVQFCGGLIMAGLFMNMPKEHCTRLWALSGLCGAAGICLMLVGYNHMGD 60 Query: 61 AWNPLLLLMGNTSLFAGCLTAWSGLRSFYQRRTGRWPVLMVGVYAFLFSLLLLYRVSFTN 120 WNPL LL GNT LF+ CL AW+GLRSFYQRRTG WP L+VG YAFLFSLLLLY+VSFT Sbjct: 61 VWNPLALLAGNTGLFSCCLLAWAGLRSFYQRRTGWWPWLLVGFYAFLFSLLLLYQVSFTQ 120 Query: 121 RAYLAMFALQVVFWLVLIEFVRGMSGPGGRRYGGWTFGRCIGIFSLFIFITTHLVRFVLS 180 R+YLA+ ALQ+ FWL L EF RGMSGP +RY W+FGRCIGI SL IFI+TH+ RFVLS Sbjct: 121 RSYLALVALQLTFWLALGEFARGMSGPHAQRYARWSFGRCIGIVSLLIFISTHVARFVLS 180 Query: 181 FSQPELFIPPAMSTIGVALIYMIPLCGSLLFSVSLMMIYFERLLADKQRLATEDELTGTL 240 FS PELFIPPAMS IGVALIY+IPL GSLLFSVSLMMIYFERLLAD+QRLATED+LTG L Sbjct: 181 FSHPELFIPPAMSNIGVALIYLIPLSGSLLFSVSLMMIYFERLLADRQRLATEDQLTGAL 240 Query: 241 NRRELVRCGELALAQAVQTRQRLTLAFIDVDHFKLINDTHGHLAGDRVLADIGILLRKHC 300 NRRELVRCGEL LA+AV+ + L LAFIDVDHFK IND HGHLAGDRVLA IG L + C Sbjct: 241 NRRELVRCGELLLARAVERKSVLALAFIDVDHFKQINDRHGHLAGDRVLAGIGATLAQSC 300 Query: 301 AQGGLIGRYGGEEFCAVFPGWSEEQARASAQHLLETVRNHVFVHGQEVTISVGLAVLQPG 360 G ++GRYGGEEFCAVFPG +QA Q LLE+VR F HG VTISVGLAVLQPG Sbjct: 301 RPGDVLGRYGGEEFCAVFPGVDHDQACQIGQRLLESVRTQRFEHGHPVTISVGLAVLQPG 360 Query: 361 QVMSWDQLVHEADQALYRAKSEGRNAFRMALA 392 SWD+LVHEAD ALYRAK+EGRNA+RMA++ Sbjct: 361 NQRSWDELVHEADLALYRAKNEGRNAYRMAMS 392 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 108 bits (271), Expect = 6e-25, Method: Compositional matrix adjust. Identities = 79/199 (39%), Positives = 102/199 (51%), Gaps = 18/199 (9%) Query: 199 LIYMIPLCGSLLFSVSLMMIYFERLLADKQ--RLATEDELTGTLNRRELVRCGELALAQA 256 LI L G LL V ++ +R+ A+KQ LA D LTG LNRR L + AL Sbjct: 295 LIIFTALAGVLLMLVRRELL--KRVAAEKQLEDLARTDGLTGLLNRRSL----DEALLAV 348 Query: 257 VQTRQRLTLA-----FIDVDHFKLINDTHGHLAGDRVLADIGILLRKHCA-QGGLIGRYG 310 Q QR A FIDVD+FK NDT+GH GD VL + +LR+H Q L GRYG Sbjct: 349 WQRSQRSPTAGFSTLFIDVDYFKRYNDTYGHEMGDTVLQAVAAVLREHLQRQNDLAGRYG 408 Query: 311 GEEFCAVFPGWSEEQARASAQHLLETVRNHVFVHGQE----VTISVGLAVLQPGQVMSWD 366 GEEF + E A AQ L E + N H +++S+G+A + + Sbjct: 409 GEEFVVLLEQTDEHGALRMAQQLCEAIYNRGIPHSGSPLGVISVSIGVATMNRAPHQRME 468 Query: 367 QLVHEADQALYRAKSEGRN 385 +++ AD ALY AK EGRN Sbjct: 469 DVLNAADHALYIAKREGRN 487 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 103 bits (256), Expect = 3e-23, Method: Compositional matrix adjust. Identities = 64/178 (35%), Positives = 93/178 (52%), Gaps = 5/178 (2%) Query: 213 VSLMMIYFERLLADKQRLATEDELTGTLNRRELVRCGELALAQAVQTRQRLTLAFIDVDH 272 V L ER + L+ D LTG NRR + +AV++ Q L L +DVD+ Sbjct: 384 VRLRTRELERANRKLEALSATDGLTGVANRRRFDEALANEMRRAVRSGQSLALLMLDVDY 443 Query: 273 FKLINDTHGHLAGDRVLADIGILLRKHCAQG-GLIGRYGGEEFCAVFPGWSEEQARASAQ 331 FK ND +GHLAGD L + +L+K + L+ RYGGEEF + QA A+ Sbjct: 444 FKKYNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAE 503 Query: 332 HLLETVRNHVFVHGQE----VTISVGLAVLQPGQVMSWDQLVHEADQALYRAKSEGRN 385 ++ + + H ++ S+G+AVL P + + +Q+V ADQALY AK +GRN Sbjct: 504 NICQAIFELKLPHADSPFGYISASIGVAVLLPDEHTAPEQMVRIADQALYHAKYQGRN 561 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 102 bits (254), Expect = 5e-23, Method: Compositional matrix adjust. Identities = 58/159 (36%), Positives = 90/159 (56%), Gaps = 5/159 (3%) Query: 230 LATEDELTGTLNRRELVRCGELALAQAVQTRQRLTLAFIDVDHFKLINDTHGHLAGDRVL 289 L ED+LTG+LNRR + + + A++ L +A +D+D FK INDTHGH GD VL Sbjct: 363 LVREDQLTGSLNRRGMDESLDREITNALRRDTPLCVALLDLDDFKRINDTHGHATGDEVL 422 Query: 290 ADIGILLRKHCAQGGLIGRYGGEEFCAVFPGWSEEQARASAQHLLETVRNHVFVHGQE-- 347 + ++R+ + +I R+GGEEF + P + + A + + +F+H + Sbjct: 423 VHMVQVIRETLRKLDVIARFGGEEFLVLMPETAPQDAVQIITRVQRELTKRIFMHESQRL 482 Query: 348 -VTISVGLAVLQPGQVMSWDQLVHEADQALYRAKSEGRN 385 +T S G+AV PG+ S L+ AD ALY+AK+ G+N Sbjct: 483 LITFSAGVAVYHPGE--SQADLLKRADVALYKAKNAGKN 519 >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 = 99.8 bits (247), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 66/165 (40%), Positives = 91/165 (55%), Gaps = 13/165 (7%) Query: 231 ATEDELTGTLNRRELVRCGELALAQAVQTRQRLTLAFIDVDHFKLINDTHGHLAGD---- 286 + +D LT NRR LA+ +T + L+L IDVDHFK NDT+GH AGD Sbjct: 353 SQKDGLTDVFNRRYFDAALAAELARLNRTGESLSLMMIDVDHFKQFNDTYGHAAGDVCLR 412 Query: 287 RVLADIGILLRKHCAQGGLIGRYGGEEFCAVFPGWSEEQARASAQHLLETVRNHVFVHGQ 346 +V A I + R+ QG ++ RYGGEEF + P A+ A +++ VR H + Sbjct: 413 QVAAAISTVARR---QGDIVARYGGEEFAVILPNCHPGSAQGLAHRVVQAVRGLEIAHER 469 Query: 347 E----VTISVGLAVLQPGQ--VMSWDQLVHEADQALYRAKSEGRN 385 VTISVG+A L G+ ++ +L+ AD ALYRAK EGR+ Sbjct: 470 SPMGVVTISVGVASLASGKSLLIEPRELIDSADGALYRAKEEGRD 514 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 0.329 0.141 0.443 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: 1,149,678 Number of extensions: 46800 Number of successful extensions: 262 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 206 Number of HSP's successfully gapped: 39 Length of query: 393 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 306 Effective length of database: 1,207,925 Effective search space: 369625050 Effective search space used: 369625050 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 (21.8 bits) S2: 131 (55.1 bits)