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= 0001.4004.p (372 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 676 0.0 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 130 2e-31 gi|300312318|ref|YP_003776410.1| diguanylate cyclase with PAS/PA... 124 1e-29 gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein... 121 8e-29 gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil... 121 1e-28 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 676 bits (1744), Expect = 0.0, Method: Compositional matrix adjust. Identities = 331/372 (88%), Positives = 350/372 (94%) Query: 1 MRSTIEMESLIADNEQLRSELQDLLQQAHINQSIIERHQAFDLKLIGASQFRELIEVMLT 60 MRS I+ E+LIADNEQLR+ELQDLLQQAHINQSIIERHQAFDLKLIGAS+FRELIEVMLT Sbjct: 1 MRSAIDSEALIADNEQLRAELQDLLQQAHINQSIIERHQAFDLKLIGASEFRELIEVMLT 60 Query: 61 VMPGVFSLETVTLSLIDHDHGIQHILRDLQIGVNEFPKLLFLKDPLHFIDDEDALESEKP 120 VMPGVFSLETVTLSLID D+ IQ ILRDLQIG+NEFPKLLFLK L F DD+ EKP Sbjct: 61 VMPGVFSLETVTLSLIDGDYAIQRILRDLQIGINEFPKLLFLKQALAFPDDDLTRADEKP 120 Query: 121 RLGEYVSALHGPLFPHYEPVSVAVLPLVRQHRLLGYLSLGSAYQERFTRTLATDFIERLA 180 RLG YV+ALHGPLFPHYEPVSVAVLPLVRQHRLLGYL+LGSAY ERFTR+LATDFIERLA Sbjct: 121 RLGPYVAALHGPLFPHYEPVSVAVLPLVRQHRLLGYLALGSAYGERFTRSLATDFIERLA 180 Query: 181 TVAAICLENVINNERLKHIGLTDPLTGVNNRRYIEQRMAEEVARSQRDRSALSCLFIDID 240 T+AA+CLENVINNERLKHIGLTDPLTGVNNRRYIEQRM EEVARSQRDRSALSCLFIDID Sbjct: 181 TIAAVCLENVINNERLKHIGLTDPLTGVNNRRYIEQRMQEEVARSQRDRSALSCLFIDID 240 Query: 241 HFKRVNDQFGHQSGDDVLREVAARIKKELRLSDALGRYGGEEFVVLLTHATRDDAVRIAE 300 HFKRVNDQFGHQSGDDVLREVAARIKKELRLSDALGR+GGEEFVVLLTHATR+DA RIAE Sbjct: 241 HFKRVNDQFGHQSGDDVLREVAARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIAE 300 Query: 301 RIRAGICSRGVMIEGSRDPLKITASIGAASLSPPDRGRPAVDVKQAMLKAADQALYQAKE 360 RIRAG+CSRGVMIEGSRDPLKITASIGAA+L+PPDR RPA +VKQAMLKAADQALYQAKE Sbjct: 301 RIRAGVCSRGVMIEGSRDPLKITASIGAAALTPPDRSRPAAEVKQAMLKAADQALYQAKE 360 Query: 361 AGRNRVVQAASD 372 AGRNRV+ AA D Sbjct: 361 AGRNRVMLAAGD 372 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 130 bits (326), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 82/186 (44%), Positives = 115/186 (61%), Gaps = 10/186 (5%) Query: 187 LENVINNERLKHIGLTDPLTGVNNRRYIEQRMAEEVARSQRDRSA-LSCLFIDIDHFKRV 245 L+ V ++L+ + TD LTG+ NRR +++ + RSQR +A S LFID+D+FKR Sbjct: 314 LKRVAAEKQLEDLARTDGLTGLLNRRSLDEALLAVWQRSQRSPTAGFSTLFIDVDYFKRY 373 Query: 246 NDQFGHQSGDDVLREVAARIKKEL-RLSDALGRYGGEEFVVLLTHATRDDAVRIAERIRA 304 ND +GH+ GD VL+ VAA +++ L R +D GRYGGEEFVVLL A+R+A+++ Sbjct: 374 NDTYGHEMGDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQTDEHGALRMAQQLCE 433 Query: 305 GICSRGVMIEGSRDPLK-ITASIGAASLSPPDRGRPAVDVKQAMLKAADQALYQAKEAGR 363 I +RG+ GS PL I+ SIG A+++ R + +L AAD ALY AK GR Sbjct: 434 AIYNRGIPHSGS--PLGVISVSIGVATMNRAPHQR-----MEDVLNAADHALYIAKREGR 486 Query: 364 NRVVQA 369 NRV A Sbjct: 487 NRVCVA 492 >gi|300312318|ref|YP_003776410.1| diguanylate cyclase with PAS/PAC sensor protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 124 bits (310), Expect = 1e-29, Method: Compositional matrix adjust. Identities = 84/198 (42%), Positives = 113/198 (57%), Gaps = 16/198 (8%) Query: 170 TLATDFIERLATVAAICLENVINNERLKHIGLTDPLTGVNNRRYIEQRMAEEVARSQRDR 229 TL FI ++ AI LE L+ LTD LT + NRRY QR+ EE +R QR Sbjct: 418 TLWHGFISDISQSKAIELE-------LQEFALTDYLTQLPNRRYFMQRLQEEYSRIQRSV 470 Query: 230 SA-LSCLFIDIDHFKRVNDQFGHQSGDDVLREVAARIKKELRLSDALGRYGGEEFVVLLT 288 +A + L D+DHFKR+ND GH GD VLR A +K +LR SD GR GGEEF ++LT Sbjct: 471 TAGAAVLMCDLDHFKRINDSLGHAVGDLVLRHFATVLKSQLRRSDTAGRLGGEEFAIILT 530 Query: 289 HATRDDAVRIAERIRAGICSRGVMIEGSRDPLKITASIGAASLSPPDRGRPAVDVKQAML 348 A + A A R++ + +I R+ +K+T SIG A + G ++ +L Sbjct: 531 GADQQAAADFAARLQNRFAGQ-PLIHDERE-VKVTLSIGVALMQADSAG------QEQVL 582 Query: 349 KAADQALYQAKEAGRNRV 366 +A+D ALY+AKE GRNRV Sbjct: 583 RASDDALYRAKEKGRNRV 600 >gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 585 Score = 121 bits (304), Expect = 8e-29, Method: Compositional matrix adjust. Identities = 68/165 (41%), Positives = 103/165 (62%), Gaps = 8/165 (4%) Query: 202 TDPLTGVNNRRYIEQRMAEEVARSQRDRSALSCLFIDIDHFKRVNDQFGHQSGDDVLREV 261 TD LTGV NRR +++ ++R L+ + DIDHFK++ND +GHQ+GD +LR V Sbjct: 415 TDFLTGVLNRRAFFTHGQQQMTVAKRYGRELAVVLFDIDHFKQINDSYGHQAGDAILRGV 474 Query: 262 AARIKKELRLSDALGRYGGEEFVVLLTHATRDDAVRIAERIRAGICSRGVMIEGSRDPLK 321 A + + LR D L RYGGEEF++LL ++ A +E++RA + + I+G R ++ Sbjct: 475 AQSVSQLLRKVDVLARYGGEEFIILLPESSLLQAAAASEKLRAALAAGEFEIDGGRR-IR 533 Query: 322 ITASIGAASLSPPDRGRPAVDVKQAMLKAADQALYQAKEAGRNRV 366 +TAS G A+ + G P ++ ++K AD ALY+AK+ GRNRV Sbjct: 534 VTASFGVAA----ENGGPGLE---HLIKQADIALYRAKKLGRNRV 571 >gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 369 Score = 121 bits (303), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 71/178 (39%), Positives = 104/178 (58%), Gaps = 6/178 (3%) Query: 193 NERLKHIGLTDPLTGVNNRRYIEQRMAEEVARSQRDRSALSCLFIDIDHFKRVNDQFGHQ 252 NE+L+ + LTD LTG+ NRR ++ + +E RS R + L FID+D FK ND +GH Sbjct: 190 NEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFKPYNDHYGHL 249 Query: 253 SGDDVLREVAARIKKEL-RLSDALGRYGGEEFVVLLTHATRDDAVRIAERIRAGICSRGV 311 +GD VLR+VA +++ + R+ D + RYGGEEF ++ + R+ + + + Sbjct: 250 AGDAVLRQVAQTLRQSIARVGDTVARYGGEEFAIIAADTDGQAGADMLRRMCDAVHALAI 309 Query: 312 MIEGSRDPLKITASIGAASLSPPDRGRPAVDVKQAMLKAADQALYQAKEAGRNRVVQA 369 GS +IT S G AS +P G+P + +L+AAD ALY+AK GRNRVV A Sbjct: 310 AHAGSAMG-RITISAGVASCNP---GQPGAGL-DGLLQAADAALYRAKMEGRNRVVLA 362 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 0.321 0.137 0.384 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: 1,105,385 Number of extensions: 46574 Number of successful extensions: 248 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 199 Number of HSP's successfully gapped: 39 Length of query: 372 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 285 Effective length of database: 1,207,925 Effective search space: 344258625 Effective search space used: 344258625 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: 131 (55.1 bits)