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= 0001.0245.p (382 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309602|ref|YP_003773694.1| GGDEF domain-containing protein... 536 e-153 gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspi... 109 4e-25 gi|300313074|ref|YP_003777166.1| GGDEF domain-containing protein... 95 1e-20 gi|300312514|ref|YP_003776606.1| GGDEF domain-containing protein... 94 2e-20 gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodies... 93 4e-20 >gi|300309602|ref|YP_003773694.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 384 Score = 536 bits (1380), Expect = e-153, Method: Compositional matrix adjust. Identities = 305/382 (79%), Positives = 332/382 (86%) Query: 1 MALDPSTLLILTIALAASAACYLAVEWSVVRERSLLIWSSGFAIITLGSFLALLRSRGYL 60 MALDPSTLLILTIALAA+A+ YL VEWSVVRERSLL+WSSGFAIIT+GSFLALLRSRGYL Sbjct: 1 MALDPSTLLILTIALAAAASLYLTVEWSVVRERSLLLWSSGFAIITVGSFLALLRSRGYL 60 Query: 61 LVGIWFANGLLIAAHACFLTGVAWFTRRRLSHGWWLLAGLWLLMLLLPTHPWWSRVMLGI 120 LVGIWFANGLLIAAHACFL GVA F R R+S WWL+A LWLLMLLLPTH WWSRVMLG+ Sbjct: 61 LVGIWFANGLLIAAHACFLAGVAGFMRTRISRAWWLIALLWLLMLLLPTHAWWSRVMLGL 120 Query: 121 QSLMIAALTLRASSLLRPHGASLSVGAAQLRHVLLVHGLFYVAKAVSALALGAWVDLAAF 180 QSLMIA LTLRASSLLRPHGASLSVGA QLR+VLL+HGLFY+AKAVSALALGA VDLAAF Sbjct: 121 QSLMIAVLTLRASSLLRPHGASLSVGAVQLRYVLLIHGLFYLAKAVSALALGAVVDLAAF 180 Query: 181 GGTIIQVSLIEGSMAVMLIALSMTGTERQRREERIGQLAARDPLTGLLNRRALHARAPAL 240 GGT+IQ+SL+EGSMAVMLIALSMTGTER RREERIGQLAARDPLTGLLNRRAL ARAPAL Sbjct: 181 GGTLIQISLVEGSMAVMLIALSMTGTERHRREERIGQLAARDPLTGLLNRRALQARAPAL 240 Query: 241 LAQASAQHPTALLLIDIDNFKQVNDLHGHAAGDKLLEALSTLLRESLPEHALAARLGGDE 300 +AQAS HP ALLLIDIDNFKQVNDLHGHAAGDKLLEALSTLLRE LP+ ALAARLGGDE Sbjct: 241 IAQASQAHPGALLLIDIDNFKQVNDLHGHAAGDKLLEALSTLLREVLPDDALAARLGGDE 300 Query: 301 FVILLQDVRAEELMRSLEELRQAFSLMARNMFATPDVVSLSTGASLVEVPPLDLDSVIAI 360 F ILL D R ++ E+LRQAF + + ATP+ VSLS G SL LDL ++A Sbjct: 301 FAILLPDGRQAQVAHIGEQLRQAFVHVTQTAVATPEAVSLSVGVSLFSTAALDLAGLMAR 360 Query: 361 TDAALYEAKRKGRDRVVMTRSG 382 DAALYEAKR GR+++V+T S Sbjct: 361 ADAALYEAKRAGRNQIVITPSN 382 >gi|300313329|ref|YP_003777421.1| transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 501 Score = 109 bits (272), Expect = 4e-25, Method: Compositional matrix adjust. Identities = 73/179 (40%), Positives = 106/179 (59%), Gaps = 11/179 (6%) Query: 212 EERIGQLAARDPLTGLLNRRALHARAPALLA--QASAQHPTA---LLLIDIDNFKQVNDL 266 E+++ LA D LTGLLNRR+L ALLA Q S + PTA L ID+D FK+ ND Sbjct: 320 EKQLEDLARTDGLTGLLNRRSLDE---ALLAVWQRSQRSPTAGFSTLFIDVDYFKRYNDT 376 Query: 267 HGHAAGDKLLEALSTLLRESLP-EHALAARLGGDEFVILLQDVRAEELMRSLEELRQAFS 325 +GH GD +L+A++ +LRE L ++ LA R GG+EFV+LL+ +R ++L +A Sbjct: 377 YGHEMGDTVLQAVAAVLREHLQRQNDLAGRYGGEEFVVLLEQTDEHGALRMAQQLCEAIY 436 Query: 326 LMARNMFATP-DVVSLSTG-ASLVEVPPLDLDSVIAITDAALYEAKRKGRDRVVMTRSG 382 +P V+S+S G A++ P ++ V+ D ALY AKR+GR+RV + G Sbjct: 437 NRGIPHSGSPLGVISVSIGVATMNRAPHQRMEDVLNAADHALYIAKREGRNRVCVAHPG 495 >gi|300313074|ref|YP_003777166.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 738 Score = 94.7 bits (234), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 73/242 (30%), Positives = 126/242 (52%), Gaps = 22/242 (9%) Query: 157 HGLFYVAKAVSALALGAWVDLAAF--GGTIIQVSLIEGSMAV----MLIALSMTGTERQR 210 HG+ K +++ + ++L A G + V + G + + IA TER Sbjct: 501 HGMAQFLKDGTSVVINNRIELQALHRDGHELPVEITVGHVKRQSGHLFIAFLHDITERLA 560 Query: 211 REERIGQLAARDPLTGLLNRRALHARAPALLAQASAQHPT-ALLLIDIDNFKQVNDLHGH 269 +++ +LA D LT L NRRA R P + +A H AL +D+D FK +ND +GH Sbjct: 561 FRDQMRELALTDVLTSLPNRRAFSDRLPEGMMRARRAHQLLALFFMDLDGFKGINDRYGH 620 Query: 270 AAGDKLLEALSTLLRESLPEHALAARLGGDEFVILLQDVRAEE-----LMRSLEELRQAF 324 AGD+LL + L+ S+ + ARL GDEFV++L+++++++ + L +R+ F Sbjct: 621 EAGDELLVEFARRLQASVRDVDTVARLAGDEFVVILENLQSQQDAIMVAEKILHAIREPF 680 Query: 325 SLMARNMFATPDVVSLSTGASLVEVPPLD----LDSVIAITDAALYEAKRKGRDRVVMTR 380 L + +S S G ++ + P LD + ++++ D A+Y AKR G++R+ + R Sbjct: 681 ELTHSTVH-----ISSSIGVAVYQ-PDLDGEIGPEELLSMADKAMYAAKRLGKNRIELGR 734 Query: 381 SG 382 G Sbjct: 735 VG 736 >gi|300312514|ref|YP_003776606.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 346 Score = 93.6 bits (231), Expect = 2e-20, Method: Compositional matrix adjust. Identities = 64/178 (35%), Positives = 98/178 (55%), Gaps = 15/178 (8%) Query: 206 TERQRREERIGQLAARDPLTGLLNRRALHARAPALLAQASAQHPTALLLIDIDNFKQVND 265 E R + + +A +DPLTG+ NRR + P +L QA L+IDIDNFK++ND Sbjct: 179 VESLRLRKELEFIAFKDPLTGIDNRRRFMQQLPIIL-QAGQPSDACFLMIDIDNFKKIND 237 Query: 266 LHGHAAGDKLLEALSTLLRESLPEHALAARLGGDEFVILLQD---VRAEEL-MRSLEELR 321 GHA+GD+ L + ++ +L E AL R+GG+EF I L AE++ + L+E+R Sbjct: 238 DFGHASGDEALILTARAMQSALSEGAL-GRMGGEEFGIALSGGGLAHAEQVAAKLLQEVR 296 Query: 322 QAFSLMARNMFATPDVVSLSTGASLVEVPPLDLDSVIAITDAALYEAKRKGRDRVVMT 379 Q ++ A P VS+ + + V++ D ALY+AKR G+DR V++ Sbjct: 297 QI------HIHARPLTVSIGIARATDHS---SVSKVLSAADQALYQAKRAGKDRYVVS 345 >gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodiesterase A protein [Herbaspirillum seropedicae SmR1] Length = 1002 Score = 92.8 bits (229), Expect = 4e-20, Method: Compositional matrix adjust. Identities = 61/170 (35%), Positives = 92/170 (54%), Gaps = 2/170 (1%) Query: 207 ERQRREERIGQLAARDPLTGLLNRRALHARAPALLAQASAQHPT-ALLLIDIDNFKQVND 265 ER+ RI QLA D LTGL NR L +A +A A T A++ ID+D FKQVND Sbjct: 546 EREDARARIHQLAFYDSLTGLPNRSLLLVQAGQAIAAAERNCSTVAVMFIDLDRFKQVND 605 Query: 266 LHGHAAGDKLLEALSTLLRESLPEHALAARLGGDEFVILLQDVRAEELMRSLEELRQAFS 325 GH AGD+LL ++T L+ + RL GDEFV++L + L ++ +++ + Sbjct: 606 SLGHQAGDELLRTVATRLQSQARRSDIVGRLSGDEFVVVLTQYDTQHLTEVVKRIQERLA 665 Query: 326 LMARNMFATPDVVSLSTGASLVEVPPLDLDSVIAITDAALYEAKRKGRDR 375 M ++ TP S S G ++ D+++++ D A+Y+AK R R Sbjct: 666 -MPCHINGTPLNPSASIGVAIFPDNGNDIETLLHRADIAMYQAKAVNRGR 714 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 0.325 0.136 0.404 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: 922,382 Number of extensions: 32441 Number of successful extensions: 268 Number of sequences better than 1.0e-08: 39 Number of HSP's gapped: 214 Number of HSP's successfully gapped: 39 Length of query: 382 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 295 Effective length of database: 1,207,925 Effective search space: 356337875 Effective search space used: 356337875 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 131 (55.1 bits)