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= 0001.1559.p (480 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311016|ref|YP_003775108.1| MocR family transcription regul... 932 0.0 gi|300311074|ref|YP_003775166.1| transcription regulator protein... 358 e-100 gi|300311134|ref|YP_003775226.1| transcription regulator protein... 141 9e-35 gi|300313928|ref|YP_003778020.1| GntR family transcription regul... 139 4e-34 gi|300312133|ref|YP_003776225.1| transcription regulator protein... 137 2e-33 >gi|300311016|ref|YP_003775108.1| MocR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 480 Score = 932 bits (2408), Expect = 0.0, Method: Compositional matrix adjust. Identities = 451/480 (93%), Positives = 463/480 (96%) Query: 1 MAVTPLYKQFADQLAASIRDGVLRPGERIASVRIASQQHKVSVTTVVRAYELLESRGIIE 60 MAVTPLYKQFADQLAASIRDGVLRPGERIASVRIASQQHKVSVTTVVRAYELLESRGIIE Sbjct: 1 MAVTPLYKQFADQLAASIRDGVLRPGERIASVRIASQQHKVSVTTVVRAYELLESRGIIE 60 Query: 61 SQPQSGYFVRQQAETIARPTASPPVQADHPAWQQSTEVDVSRLVLATLKTIQQDGTVPLG 120 SQPQSGYFVR+Q E +P + DHPAWQ+STEVDVSRLVLATLKTIQQDGTVPLG Sbjct: 61 SQPQSGYFVREQPEAPPKPALRTTSREDHPAWQESTEVDVSRLVLATLKTIQQDGTVPLG 120 Query: 121 SPYPNPALFPSHRLAQYAGRIARHASQSSVFDDLPPGHPELLRQIARRYLENGLKVDPAE 180 SPYPNPALFPSHRLAQYAGRIARHASQSSVFDDLPPGHPELLRQIARRYLENGLKVDP E Sbjct: 121 SPYPNPALFPSHRLAQYAGRIARHASQSSVFDDLPPGHPELLRQIARRYLENGLKVDPEE 180 Query: 181 IVVTVGATEAINLCLQAVARPGDTIAVETPTFYAMLHAIERLGMRALEIPTDPRRGIDVA 240 IV+TVGATEAINLCLQAVARPGDTIAVETPTFYAMLHAIERLGMRALEIPTDP+RGIDV Sbjct: 181 IVITVGATEAINLCLQAVARPGDTIAVETPTFYAMLHAIERLGMRALEIPTDPQRGIDVG 240 Query: 241 ALEERLQTQAVAACMVMPNFQNPLGFQMPDSEKERLVRLAAQHQMPIIENAVYSELYYGN 300 ALEER++TQA+AACMVMPNFQNPLGFQMPDSEKERLVRLA QHQMP+IENAVYSELYYGN Sbjct: 241 ALEERMKTQAIAACMVMPNFQNPLGFQMPDSEKERLVRLAEQHQMPVIENAVYSELYYGN 300 Query: 301 AHPSSLKNYDRDGLVLHCSSFSKSLTSAHRIGWAMPGRYRAQVEKLKFLNTLATPTAPQR 360 AHPSSLKNYDRDGLVLHCSSFSKSLTSA+RIGWAMPGRYRAQVEKLKFLNTLATPTAPQR Sbjct: 301 AHPSSLKNYDRDGLVLHCSSFSKSLTSAYRIGWAMPGRYRAQVEKLKFLNTLATPTAPQR 360 Query: 361 AIAEYLTQGGYERHLRRVRRAFAQQRDMMRHFVLRFFPAGTQVSEPEGGYVLWVELPPQV 420 AIAEYLTQGGYERHLRRVRRAFAQQRDMMRHFVLRFFPAGTQVSEP+GGYVLWVELP V Sbjct: 361 AIAEYLTQGGYERHLRRVRRAFAQQRDMMRHFVLRFFPAGTQVSEPQGGYVLWVELPQGV 420 Query: 421 DAMELYRRSLALGITVAPGRIFAATNRYSHFIRLNYSYTWSKETEQALKLVGKLVEELAG 480 DAMELYRRSLALGITVAPGRIFAATNRYSHFIRLNYSY WSKETEQALKLVGKLVEELAG Sbjct: 421 DAMELYRRSLALGITVAPGRIFAATNRYSHFIRLNYSYAWSKETEQALKLVGKLVEELAG 480 >gi|300311074|ref|YP_003775166.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 516 Score = 358 bits (918), Expect = e-100, Method: Compositional matrix adjust. Identities = 195/484 (40%), Positives = 295/484 (60%), Gaps = 19/484 (3%) Query: 5 PLYKQFADQLAASIRDGVLRPGERIASVRIASQQHKVSVTTVVRAYELLESRGIIESQPQ 64 PLY++ AD ++I+ G L G+R+ SVR +QH+VS++T ++ +E G +E++P+ Sbjct: 41 PLYRRLADHYQSAIQAGTLVAGDRMPSVRDLMRQHQVSLSTALQTLRHMEEGGWLEARPR 100 Query: 65 SGYFVRQQAETIARPTASPPVQADHPAWQQSTEVDVSRLV-----LATLKTIQQDGT--V 117 SGYFVRQ + RP P + +D + V ++ ++Q G + Sbjct: 101 SGYFVRQPRRSAIRPVQEP---------KSLLAIDAGQFVGIHERVSKYIALRQAGAPHI 151 Query: 118 PLGSPYPNPALFPSHRLAQYAGRIARHASQSSVFDDLPPGHPELLRQ-IARRYLENGLKV 176 L P L+ L Q A R R + + +P RQ +ARR L G+++ Sbjct: 152 DLSGMTCAPQLYAVETLKQAAMRALRERPEL-LTSAMPHNGNATFRQAVARRALNAGMRI 210 Query: 177 DPAEIVVTVGATEAINLCLQAVARPGDTIAVETPTFYAMLHAIERLGMRALEIPTDPRRG 236 D E+VVT G EA+NL ++AVA PGDTIAVE+PT++ +L A+E LGM+ALEIPT P G Sbjct: 211 DTEEVVVTHGCIEALNLAMRAVAGPGDTIAVESPTYFGLLQALENLGMKALEIPTSPHTG 270 Query: 237 IDVAALEERLQTQA-VAACMVMPNFQNPLGFQMPDSEKERLVRLAAQHQMPIIENAVYSE 295 I V ALE ++T + A +V+PN QNPLG MP+ K++LVRL Q ++P+IE+ Y+E Sbjct: 271 ISVEALELAVRTYGNIKAVVVVPNLQNPLGCIMPEDHKDQLVRLCDQLKLPLIEDDAYTE 330 Query: 296 LYYGNAHPSSLKNYDRDGLVLHCSSFSKSLTSAHRIGWAMPGRYRAQVEKLKFLNTLATP 355 L G+ PSSLK+ DR+G V++C+S +K L R+GW GR+ +V+ LKF +T A Sbjct: 331 LADGSVTPSSLKSRDRNGNVIYCASLNKVLAPGMRLGWMNGGRWHERVKMLKFTHTRANE 390 Query: 356 TAPQRAIAEYLTQGGYERHLRRVRRAFAQQRDMMRHFVLRFFPAGTQVSEPEGGYVLWVE 415 Q A+++ Y+RHLRR+R+ QQR+ M + +FP GT+++ P GG LWVE Sbjct: 391 EWTQVTAADFIASPAYDRHLRRLRQMLKQQRERMAESIAAYFPEGTRLNLPNGGVGLWVE 450 Query: 416 LPPQVDAMELYRRSLALGITVAPGRIFAATNRYSHFIRLNYSYTWSKETEQALKLVGKLV 475 LP QV + +L+ R+LA G+ V+PG IF+ ++RY HF+R+ + +++E +QAL+ +G LV Sbjct: 451 LPVQVCSQQLFERALAEGVGVSPGAIFSNSSRYGHFVRICCGHPFNRELDQALRRLGGLV 510 Query: 476 EELA 479 LA Sbjct: 511 HHLA 514 >gi|300311134|ref|YP_003775226.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 141 bits (356), Expect = 9e-35, Method: Compositional matrix adjust. Identities = 120/462 (25%), Positives = 215/462 (46%), Gaps = 28/462 (6%) Query: 6 LYKQFADQLAASIRDGVLRPGERIASVRIASQQHKVSVTTVVRAYELLESRGIIESQPQS 65 L +Q + A I D +LR G R+ S+R + +++S TVV AY+ L ++G +ES+ S Sbjct: 40 LVEQIVRGIRARIDDKLLRSGMRMPSIRQFADTNQISRFTVVEAYDRLVAQGYLESRRGS 99 Query: 66 GYFVRQQAETIARPTASPPVQADHPAWQQSTE------VDVSRLVLATLKTIQQDGTVPL 119 G++V+++A P+ + A Q + +DV LV + + +P Sbjct: 100 GFYVKERA----------PLGGSYGAAQAELDTEPGRGLDVVWLVRNMFRQMPP-AKMPG 148 Query: 120 GSPYPNPALFPSHRLAQYAGRIARHASQSSVFDDLPPGHPELLRQIARRYLENGLKVDPA 179 G P P +A ++R Q + P G L +Q+ + E + P Sbjct: 149 GGLLP-PDWLDGELIANALRAVSRDNPQLLLGYGTPQGFLPLRQQLQLKLAELEIAAAPE 207 Query: 180 EIVVTVGATEAINLCLQAVARPGDTIAVETPTFYAMLHAIERLGMRALEIPTDPRRGIDV 239 +IV+T G T+ ++ + RPGD I V+ P ++ M + LG + + IP G D+ Sbjct: 208 QIVLTTGVTQGLDTVARHFLRPGDVIFVDDPAWFLMFGSFAALGAKVVGIPR-LGDGPDI 266 Query: 240 AALEERLQTQAVAACMVMPNFQNPLGFQMPDSEKERLVRLAAQHQMPIIENAVYSELYYG 299 A L E ++ NP + ++ +++R+A +H I+E+ +Y +++ G Sbjct: 267 ARLRELAAVHKPKLYVINSVLHNPTSTSLSAAKAFQVLRIAEEHDFVIVEDDIYCDMHPG 326 Query: 300 NA-HPSS-LKNYDRDGLVLHCSSFSKSLTSAHRIGW-AMPGRYRAQVEKLKFLNTLATPT 356 +A P++ + D+ V++ FSK+L++ R+G+ A + K L+TL T Sbjct: 327 SAVQPATRIAALDQLQRVIYLGGFSKTLSANLRVGYIATSAELARSLADRKLLSTLTTGE 386 Query: 357 APQRAIAEYLTQGGYERHLRRVRRAFAQQRDMMRHFVLRFFPAGTQVSE-PEGGYVLWVE 415 +R + L++G Y +H RVR RD + + R G V E P G LWV+ Sbjct: 387 IGERVAYKVLSEGHYRKHAERVRARLNGARDKVMRQLERL---GMDVVEAPPCGMFLWVD 443 Query: 416 LPPQVDAMELYRRSLALGITVAPGRIFAATNRYSHFIRLNYS 457 + M ++ G +APG +F+ S ++R+N + Sbjct: 444 TGRDTNVMT--EAAMQEGFLLAPGSLFSPAQLPSTYMRINVA 483 >gi|300313928|ref|YP_003778020.1| GntR family transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 472 Score = 139 bits (351), Expect = 4e-34, Method: Compositional matrix adjust. Identities = 120/460 (26%), Positives = 208/460 (45%), Gaps = 28/460 (6%) Query: 6 LYKQFADQLAASIRDGVLRPGERIASVRIASQQHKVSVTTVVRAYELLESRGIIESQPQS 65 L +Q A+ LA I G LR GER+ SVR +Q H + +TVV AYE L +RG+++++ + Sbjct: 21 LVEQVANGLAGLIETGELRSGERLPSVRQFAQHHDIGSSTVVEAYEQLVARGMLQARRGA 80 Query: 66 GYFVRQQA-ETIARPTASPPVQADHPAWQQSTEVDVSRLVLATLKTIQQDGTVPL--GSP 122 G+FV +A ++ PP AW L + D VP+ G Sbjct: 81 GFFVAARAGQSGQHAVFVPPEPVIDSAW--------------LLSEMFADERVPIKAGCG 126 Query: 123 YPNPALFPSHRLAQYAGRIARHASQSSVFDDLPPGHPELLRQIARRYLEN-GLKVDPAEI 181 + L Q RI R V P G+ LRQ+ ++L + L++ ++ Sbjct: 127 WLPGKWLNDEGLHQAERRIIRSPGAQQVGYGHPYGYAP-LRQLITQFLGHWSLELGIEQV 185 Query: 182 VVTVGATEAINLCLQAVARPGDTIAVETPTFYAMLHAIERLGMRALEIPTDPRRGIDVAA 241 + T GAT+A++L ++ + +PGDT+ ++ P + ++ + G+ + +P P G+D Sbjct: 186 LTTHGATQALDLVIRTMTQPGDTVLIDDPGYCNLIAMLRLAGLNVIGVPRTP-GGVDTDV 244 Query: 242 LEERLQTQAVAACMVMPNFQNPLGFQMPDSEKERLVRLAAQHQMPIIENAVYSELYYGNA 301 LE +T QNP G + R+++ A +H ++E+ ++ EL G A Sbjct: 245 LETLARTHHPKMFFTTSVLQNPTGTSYTPACAMRVLQAAERHGFWVVEDDIFREL--GQA 302 Query: 302 HPSSLKNYDRDGLVLHCSSFSKSLTSAHRIGWAMPGRYRA-QVEKLKFLNTLATPTAPQR 360 L D V++ S+SK++ + R+G+ R A Q+ K + TL +R Sbjct: 303 TDPMLAALDGLQRVIYVGSYSKTIAPSLRVGYIACQRELARQIVHTKMVLTLTNSEINER 362 Query: 361 AIAEYLTQGGYERHLRRVRRAFAQQRDMMRHFVLRFFPAG-TQVSEPEGGYVLWVELPP- 418 + LT+G + RH++ + + + + G T + GG W + Sbjct: 363 LVHNVLTEGHHRRHVQTLNATLLSAQATLN---AKLSEVGLTPFTAARGGMFSWATIEGC 419 Query: 419 QVDAMELYRRSLALGITVAPGRIFAATNRYSHFIRLNYSY 458 ++ A E+ R+ GI +APG F + + R N Y Sbjct: 420 ELSAREIADRARQKGIWLAPGDFFHLSAPHQTSFRFNVGY 459 >gi|300312133|ref|YP_003776225.1| transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 491 Score = 137 bits (345), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 127/489 (25%), Positives = 228/489 (46%), Gaps = 46/489 (9%) Query: 8 KQFADQLAASIRDGV----LRPGERIASVRIASQQHKVSVTTVVRAYELLESRGIIESQP 63 + D++ ++ +GV L G+++ S+R+ ++ +VS TV RAYE L + G + ++P Sbjct: 30 RLLVDRIFTAVLEGVRTRRLAHGDKLPSLRVVAESAQVSRDTVARAYEKLVAHGHVYTRP 89 Query: 64 QSGYFVR--QQAETIARPTASPPVQADHPAWQQSTEVDVSRLVLATLKTIQQDGTVPLGS 121 +G+FVR Q TA P+ + W+Q L +T+ G LGS Sbjct: 90 GAGFFVRVDNQVANAQTQTAPAPLLTN---WRQR---------LLDPRTLLHRG---LGS 134 Query: 122 PYPNPALFPSHRLAQYAGRIARHASQSSVFDDLPPGHPELLRQIARRYLENGLKVDPAEI 181 +LA ++R + G+ L +Q+ R+ + G+ V P ++ Sbjct: 135 GDLPAEWINVPQLAAALRAVSRSNINWAAGYGDAQGYLPLRQQLQRKLADIGVDVTPPQV 194 Query: 182 VVTVGATEAINLCLQAVAR-PGDTIAVETPTFYAMLHAIERLGMRALEIPTDPRRGIDVA 240 + T+GAT+AINL + + R PG T+ V+ P + ++ + GM + + D G D+ Sbjct: 195 LTTLGATDAINLIVMSYLRQPGMTVLVDDPGSFLLMERLLASGMHIVGVARDAD-GPDIT 253 Query: 241 ALEERLQTQAVAACMVMPNFQNPLGFQMPDSEKERLVRLAAQHQMPIIENAVYSELY--Y 298 AL+ + +P + +++RLA + I+E+ Y +L + Sbjct: 254 ALQNACEQHGPTFYFCQSLLHSPGYTGLSPQRAFQILRLAERFNFTIVEDDTYGDLAPAH 313 Query: 299 GNAHPSSLKNYDRDGLVLHCSSFSKSLTSAHRIGWAMPGRYRAQVEKL---KFLNTLATP 355 + H + L + D+ VL+ SFSK+L + R G+ + G + Q+E L K ++ + Sbjct: 314 RSPHATRLASLDQLQHVLYVGSFSKTLGAGMRAGF-IAGNPQ-QIEWLLLYKLVSRASNG 371 Query: 356 TAPQRAIAEYLTQGGYERHLRRVRRAFAQQRDMMRHFVLRFFPAGTQVS-----EPEGGY 410 + +RAI L++GGY RH ++R Q R R A + P+ G Sbjct: 372 SLAERAIYRLLSEGGYRRHCEQLRTRLDQARP-------RLMAALEALGIVLPHRPDAGL 424 Query: 411 VLWVELPPQVDAMELYRRSLALGITVAPGRIFAATNRYSHFIRLNYSYTWSKETEQALKL 470 LW +LP ++AME+ R LA G APG +F++ ++R N + ++AL+ Sbjct: 425 YLWGKLPGDLNAMEVAERMLANGYLTAPGPVFSSGQAARSYMRFNV----ASSDDEALRA 480 Query: 471 VGKLVEELA 479 + ++E A Sbjct: 481 LSNVLERSA 489 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 0.320 0.134 0.391 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: 1,574,210 Number of extensions: 66960 Number of successful extensions: 270 Number of sequences better than 1.0e-08: 14 Number of HSP's gapped: 246 Number of HSP's successfully gapped: 14 Length of query: 480 Length of database: 1,619,870 Length adjustment: 89 Effective length of query: 391 Effective length of database: 1,198,455 Effective search space: 468595905 Effective search space used: 468595905 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: 132 (55.5 bits)