RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780413|ref|YP_003064826.1| PAS/PAC sensor signal transduction histidine kinase [Candidatus Liberibacter asiaticus str. psy62] (820 letters) >gnl|CDD|30987 COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]. Length = 336 Score = 156 bits (393), Expect = 3e-38 Identities = 88/238 (36%), Positives = 129/238 (54%), Gaps = 13/238 (5%) Query: 574 AKKIAEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRS 633 +++ K +FLA +SHE+RTPLTAI G E++ P E I+ Sbjct: 104 LERLERLLRRAKREFLANISHELRTPLTAIRGLLELLLEGLLDPQR-----ELLEIIEEE 158 Query: 634 GNLVLDIVNDLLDISKIESG-KMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFAN 692 +L +VNDLLD+S++E+G K+ L E V L E + E + L+ A EK I + Sbjct: 159 AERLLRLVNDLLDLSRLEAGTKLKLLLELVDLAELLEEVVRLLAPLAQEKGIELAVDLPE 218 Query: 693 NIPRILADLRSVKQIALNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYE 752 +P +L D ++Q+ +N+LSNAI +TP GG+I IS +E+V + V DTG G+ E Sbjct: 219 -LPYVLGDPERLRQVLVNLLSNAIKYTP-GGEITISVRQD-DEQVTISVEDTGPGIPEEE 275 Query: 753 LEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810 LE+ +PF + S GTGLGL + K +V+ + G + S P KGT I PL Sbjct: 276 LERIFEPFFRTDKS----RSGTGLGLAIVKRIVELHGGTISVESEPGKGTTFTIRLPL 329 >gnl|CDD|32387 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]. Length = 890 Score = 137 bits (346), Expect = 1e-32 Identities = 73/240 (30%), Positives = 121/240 (50%), Gaps = 11/240 (4%) Query: 573 HAKKIAEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGP-LGNPRYIEYANYI- 630 A+ AE+E S LA +SH++RTPLTAI+G +E + G L E + I Sbjct: 649 QARLAAERERLR-SALLASISHDLRTPLTAIMGAAETLL--LDGEALSPEDRAELLSSIR 705 Query: 631 DRSGNLVLDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSF 690 + S L +V +LLD+++++SG +NL + V ++E V EA+ ++ + I S Sbjct: 706 EESERLTR-LVTNLLDMTRLQSGGVNLKLDWVLVEEVVGEALQRLRKRFTGHK--IVVSV 762 Query: 691 ANNIPRILADLRSVKQIALNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTN 750 ++P I D ++Q+ +N+L NA+ + P G +I I+ E V+ V D G G+ Sbjct: 763 PVDLPLIHVDSPLIEQVLINLLENALKYAPPGSEIRINAGVE-RENVVFSVIDEGPGIPE 821 Query: 751 YELEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810 ELE+ F + R G GLGL + + +V+A+ G + P G + P+ Sbjct: 822 GELERIFDKFYRGNKESATR--GVGLGLAICRGIVEAHGGTISAENNPGGGAIFVFTLPV 879 >gnl|CDD|34607 COG5002, VicK, Signal transduction histidine kinase [Signal transduction mechanisms]. Length = 459 Score = 135 bits (341), Expect = 5e-32 Identities = 96/371 (25%), Positives = 177/371 (47%), Gaps = 37/371 (9%) Query: 447 MEIEVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTP 506 E E +L S+L +DG+ +R G I+ N+ K+ G ED L + L+ Sbjct: 106 TEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLK---- 161 Query: 507 SVMNHYLTEILSL-DLRQTLEKITLGSTKEEKLLSLRI----IIKKLPFSSCYSLTMHDI 561 + + + DL + + + L S+ EE+ LR+ I ++ F S +HD+ Sbjct: 162 ------IEDTYTFEDLVEKNDSLLLDSSDEEEGYVLRVNFSVIQRESGFISGLIAVLHDV 215 Query: 562 SEWKQEKNKLSHAKKIAEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRF-GPLGN 620 +E EK + +F+A VSHE+RTPLT++ + E ++ + Sbjct: 216 TE--------------QEKVERERREFVANVSHELRTPLTSMKSYLEALEEGAWEDKEIA 261 Query: 621 PRYIEYANYIDRSGNLVLDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYAN 680 PR++ ++ +VNDLL +S++++ + L+ E ++ ++E I+ ++ Sbjct: 262 PRFLRVTL---NETERMIRLVNDLLQLSRMDNARYQLNKEWINFTAFLNEIINRFEMILK 318 Query: 681 EKRI--LIRTSFANNIPRILADLRSVKQIALNILSNAIHFTPSGGQIIISTTHTSNEEVI 738 ++ I +R +I + D + Q+ NI+SNA+ ++P GG+I +S V Sbjct: 319 KETIARFVRDIPKQDI-WVEIDPDKMTQVLDNIISNALKYSPDGGRITVSVKQR-ETWVE 376 Query: 739 LRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTP 798 + + D G+G+ +LEK F ++ ++ + GTGLGL +AK +V A+ G+ + S Sbjct: 377 ISISDQGLGIPKEDLEKIFDRFYRVDKARSRKMGGTGLGLAIAKEIVQAHGGRIWAESEE 436 Query: 799 AKGTLIEIIFP 809 KGT P Sbjct: 437 GKGTTFSFTLP 447 >gnl|CDD|34605 COG5000, NtrY, Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]. Length = 712 Score = 101 bits (253), Expect = 9e-22 Identities = 77/378 (20%), Positives = 151/378 (39%), Gaps = 40/378 (10%) Query: 443 NKRKMEIEVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLE 502 K +E L ++L + G+ + G I + N + ++ G P + +L + + Sbjct: 361 AKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLSAIA- 419 Query: 503 QNTPSVMNHYLTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSSCYSLTMHDIS 562 + E + ++ L EE+ L+++ + + Y +T DI+ Sbjct: 420 ----PELEEVFAEAGAAARTDKRVEVKLAREGEERTLNVQATREPEDNGNGYVVTFDDIT 475 Query: 563 EWKQEKNKLSHAKKIAEKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPR 622 + L A++ S+ D R++HEI+ PLT I +E + ++ G + Sbjct: 476 D-------LVIAQR-----SAAWGDVARRIAHEIKNPLTPIQLSAERLL-RKLGKEIDED 522 Query: 623 YIEYANYIDRSGNLVLDI---VNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYA 679 + D V DI V++ +++ + K E L + E L ++ Sbjct: 523 REVFDRCTDTIIRQVEDIKRMVDEFRAFARMPAPK----LEKSDLRALLKEVSFLYEIGN 578 Query: 680 NEKRILIRTSFANNIPRILADLRSVKQIALNILSNAIH------FTPSGGQIIISTTHTS 733 + I+ F +AD + Q+ N+L NA +I + + Sbjct: 579 DH--IVFAAEFGGEPLIGMADATLLGQVFGNLLKNAAEAIEAVEAEERRTALIRVSLDDA 636 Query: 734 NEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFY 793 + +++ V D G G +A++P+ R +GTGLGL + K +V+ + G+ Sbjct: 637 DGRIVVDVIDNGKGFPRENRHRALEPY------VTTREKGTGLGLAIVKKIVEEHGGRLE 690 Query: 794 IFSTP-AKGTLIEIIFPL 810 + + P G +I I FPL Sbjct: 691 LHNAPDFDGAMIRIKFPL 708 >gnl|CDD|145582 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase. This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. Length = 111 Score = 90.1 bits (224), Expect = 2e-18 Identities = 33/112 (29%), Positives = 56/112 (50%), Gaps = 2/112 (1%) Query: 699 ADLRSVKQIALNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMK 758 D ++Q+ N+L NAI P+GG+I ++ + + V D G+G+ +L K + Sbjct: 1 GDEDRLRQVLSNLLDNAIKHAPAGGEIEVTLERD-GGRLRITVEDNGIGIPPEDLPKIFE 59 Query: 759 PFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810 PF + + + GTGLGL + + +V+ + G + S P GT PL Sbjct: 60 PFFRTDKDSR-KVGGTGLGLSIVRKLVELHGGTITVESEPGGGTTFTFTLPL 110 >gnl|CDD|33974 COG4251, COG4251, Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]. Length = 750 Score = 83.1 bits (205), Expect = 3e-16 Identities = 56/237 (23%), Positives = 110/237 (46%), Gaps = 14/237 (5%) Query: 571 LSHAKKIA------EKESSHKSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYI 624 L HA+++A E+ ++ F SH+++ PL I +++++ + L Sbjct: 504 LRHAEELAQLRRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEE-AK 562 Query: 625 EYANYIDRSGNLVLDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRI 684 E+ +I R +L+ +++DLL SK+ G +P + + V + + + + Sbjct: 563 EFITFISRLTSLMQQLIDDLLTYSKL--GLTEAPLQPTDVQKVVDKVLLELSQRIADTGA 620 Query: 685 LIRTSFANNIPRILADLRSVKQIALNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDT 744 IR + +P + AD + Q+ N+++NAI F I + +E VRD Sbjct: 621 EIRIA---PLPVVAADATQLGQVFQNLIANAIKFGGPENPDIEISAERQEDEWTFSVRDN 677 Query: 745 GVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKG 801 G+G+ E+ F ++ + GTGLGL + K + + + G+ ++ STP +G Sbjct: 678 GIGIDPAYFERIFVIFQRL--HSRDEYLGTGLGLAICKKIAERHQGRIWVESTPGEG 732 >gnl|CDD|33642 COG3852, NtrB, Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]. Length = 363 Score = 80.3 bits (198), Expect = 2e-15 Identities = 80/370 (21%), Positives = 148/370 (40%), Gaps = 43/370 (11%) Query: 457 ILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTEI 516 IL + + +++ E I N A +L + + L S++ L ++ Sbjct: 12 ILNNLINPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLSELLPF--GSLLLSLLDQV 69 Query: 517 LSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSS-CYSLTMHDISEW-KQEKNKLSHA 574 L T ++TL ++ L + +P L H + ++ + HA Sbjct: 70 LERGQPVTEYEVTLVILGRSHIVDL--TVAPVPEEPGSVLLEFHPRDMQRRLDREQTQHA 127 Query: 575 KKIAEKESSHKSDFLAR-VSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRS 633 ++ A K L R ++HEI+ PL I G +++++ L + E I Sbjct: 128 QQRAVKG-------LVRGLAHEIKNPLGGIRGAAQLLERA----LPDEALRELTQLIIEE 176 Query: 634 GNLVLDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANN 693 D + +L+D ++ + PV++ E + +LV+ + LIR + + Sbjct: 177 ----ADRLRNLVDRLEVLGPQRPGDRVPVNIHEVLERVRALVEAEFADNVRLIR-DYDPS 231 Query: 694 IPRILADLRSVKQIALNILSNAIH----FTPSGGQIIIST-------THTSNEEVILR-- 740 +P +L D + Q+ LN++ NA GG+II+ T + + L Sbjct: 232 LPEVLGDRDQLIQVFLNLVRNAAQALGGRADEGGEIILRTRTGIQLTIAGTRYRLALPLE 291 Query: 741 VRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAK 800 V D G G+ + P R GTGLGL LA+ ++D + GK S P + Sbjct: 292 VIDNGPGVPPDLQDHLFYPM------VSGREGGTGLGLALAQNLIDQHGGKIEFDSWPGR 345 Query: 801 GTLIEIIFPL 810 T+ ++ P+ Sbjct: 346 -TVFRVLLPI 354 >gnl|CDD|28956 cd00075, HATPase_c, Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins. Length = 103 Score = 80.4 bits (198), Expect = 2e-15 Identities = 37/105 (35%), Positives = 57/105 (54%), Gaps = 2/105 (1%) Query: 704 VKQIALNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQI 763 ++Q+ LN+LSNAI TP GG I + + + +RV D G G+ +LE+ + F Sbjct: 1 LQQVLLNLLSNAIKHTPEGGGRITISVERDGDHLEIRVEDNGPGIPEEDLERIFERFSDG 60 Query: 764 PNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIF 808 S++ G GTGLGL + K +V+ + G+ + S P GT I Sbjct: 61 SRSRK--GGGTGLGLSIVKKLVELHGGRIEVESEPGGGTTFTITL 103 >gnl|CDD|33926 COG4191, COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]. Length = 603 Score = 78.0 bits (192), Expect = 9e-15 Identities = 50/228 (21%), Positives = 93/228 (40%), Gaps = 22/228 (9%) Query: 590 ARVSHEIRTPLTAIIGFSE----VIKNQRFGPL-GNPRYIEYANYIDRSGNLVLDIVNDL 644 A ++HE+ PL AI +++ +++ R N I + +R I L Sbjct: 389 AGIAHELNQPLAAIRTYADNARLLLERGRTEEARENLERI--SALTERMAA----ITAHL 442 Query: 645 LDISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSV 704 K + K PVSL EA+ A+ L++ + + + ++A+ + Sbjct: 443 ----KSFARKSRDAAGPVSLREAIEGALELLRGRLRAAGVELELDLPDAPLWVMANEIRL 498 Query: 705 KQIALNILSNAIHFT--PSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQ 762 +Q+ +N+L NA+ ++ I +V+L VRD G G+ L +PF Sbjct: 499 EQVLVNLLQNALDAMAGQEDRRLSIRAQ-REGGQVVLTVRDNGPGIAPEALPHLFEPF-- 555 Query: 763 IPNSQQIRGEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810 + + G+G GLGL +++ + G + + P G I Sbjct: 556 --FTTKPVGKGLGLGLAISQNIARDLGGSLEVANHPEGGASFTIELRR 601 >gnl|CDD|144196 pfam00512, HisKA, His Kinase A (phosphoacceptor) domain. dimerization and phosphoacceptor domain of histidine kinases. Length = 66 Score = 71.0 bits (175), Expect = 1e-12 Identities = 32/69 (46%), Positives = 45/69 (65%), Gaps = 4/69 (5%) Query: 585 KSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDL 644 KS+FLA +SHE+RTPLTAI G+ E++ + EY I RS +L ++NDL Sbjct: 2 KSEFLANLSHELRTPLTAIRGYLELLLDTELSEEQR----EYLETILRSAERLLRLINDL 57 Query: 645 LDISKIESG 653 LD+S+IE+G Sbjct: 58 LDLSRIEAG 66 >gnl|CDD|119399 cd00082, HisKA, Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.. Length = 65 Score = 70.7 bits (174), Expect = 1e-12 Identities = 28/65 (43%), Positives = 40/65 (61%), Gaps = 3/65 (4%) Query: 585 KSDFLARVSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDL 644 K +FLA VSHE+RTPLTAI G E+++ + L + EY I +L ++NDL Sbjct: 4 KGEFLANVSHELRTPLTAIRGALELLEEE---LLDDEEQREYLERIREEAERLLRLINDL 60 Query: 645 LDISK 649 LD+S+ Sbjct: 61 LDLSR 65 >gnl|CDD|33927 COG4192, COG4192, Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]. Length = 673 Score = 63.9 bits (155), Expect = 2e-10 Identities = 60/262 (22%), Positives = 117/262 (44%), Gaps = 37/262 (14%) Query: 565 KQEKNKLSHAKKIAEKESSHKSDFLARVSHEIRTPLTAIIGF----SEVIKNQRFGPLGN 620 K+ + +L A K+A + + ++HEI PL A+ + ++ Sbjct: 436 KKTQGELIQAAKLAVVGQT-----MTSLAHEINQPLNAMSAYLFSARLALEEAPSAQA-- 488 Query: 621 PRYIEYANYIDRSGNLV---LDIVNDLLDISKIESGKMNLHFEPVSLDEAVSEAISLVQL 677 A +D+ NL IVN L ++ S +L +PV L+ V +A L+Q Sbjct: 489 ------ATSLDKIENLTERMGKIVNSLRQFARKNSSDESL--QPVRLNSVVEQAWELLQT 540 Query: 678 YANEKRILIRTSFANNIPRILADLRSVKQIALNILSNAI----HFTPSGGQIIISTTHTS 733 KR I+ + ++ D S++Q+ +N++ NA+ HF P I + T Sbjct: 541 KH--KRRQIKLINPTDDLMVMGDAVSIEQVLVNLIVNALDASTHFAP---WIKLIALGTE 595 Query: 734 NEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGKFY 793 E + + + D G G + ++K + PF S+++ G GLGL +++++++ G+ Sbjct: 596 QEMLRIAIIDNGQGWPHELVDKLLTPF---TTSKEV---GLGLGLSISQSLMEQMQGRLA 649 Query: 794 IFSTPAKGTLIEIIFPLYDTSH 815 + ST K ++ + F + + Sbjct: 650 LASTLTKNAMVILEFQVDEKYR 671 >gnl|CDD|33099 COG3290, CitA, Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]. Length = 537 Score = 58.3 bits (141), Expect = 8e-09 Identities = 72/390 (18%), Positives = 150/390 (38%), Gaps = 75/390 (19%) Query: 432 GIEPEDVDTRINKRKMEIEVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGY--PV 489 G+EPE++ T + +R+ ++L++ +G+ ++++G+I N+A KL G P Sbjct: 204 GLEPEEIATLLEERQ---------AMLQSIKEGVIAVDKKGVITLINQAAQKLLGLRQPS 254 Query: 490 EDILRKPFTVFLEQNTPSVMNHYLTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLP 549 D + + L ++ DL + LE +E ++ ++ ++P Sbjct: 255 GDPIGRSIVEVLPPDS--------------DLPEVLETGKPQHDEEIRINGRLLVANRVP 300 Query: 550 FSS-----CYSLTMHDISEWKQEKNKLSHAKKIAEKESSHKSDFLARVSHEIRTPLTAII 604 S +T D +E K+ +L+ ++ AE L SHE L I+ Sbjct: 301 IRSGGQIVGAIITFRDKTEIKKLTEQLTGVRQYAEA--------LRAQSHEFMNKLHTIL 352 Query: 605 GFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDLLDISKIESGKMNLHFEPVSL 664 G + D + + + + I+S + Sbjct: 353 GLLQ------------------LGEYDDALDYIQQESEE--QQELIDSLSEKIK------ 386 Query: 665 DEAVSEAISLVQLYANEKRILIRTSFANNIPRILADLRSVKQIAL--NILSNAIHFT--- 719 D ++ + A E + + + +P++ ++L+ + + N++ NA+ Sbjct: 387 DPVLAGFLLGKISRARELGVSLIIDPNSQLPQLPSELQPHDLVTILGNLIDNALEALLAP 446 Query: 720 PSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGLP 779 +I +S + + E+++ V DTG G+ + + S + G G+GL Sbjct: 447 EENKEIELSLSDRGD-ELVIEVADTGPGIP----PEVRDKIFEKGVSTK-NTGGRGIGLY 500 Query: 780 LAKAMVDANMGKFYIFSTPAKGTLIEIIFP 809 L K +V+ G + S +GT I P Sbjct: 501 LVKQLVERLGGSIEVESEKGQGTRFSIYIP 530 >gnl|CDD|35739 KOG0519, KOG0519, KOG0519, Sensory transduction histidine kinase [Signal transduction mechanisms]. Length = 786 Score = 50.4 bits (120), Expect = 2e-06 Identities = 51/185 (27%), Positives = 86/185 (46%), Gaps = 16/185 (8%) Query: 588 FLARVSHEIRTPLTA--IIGFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDLL 645 FLA +SHEIRTPL + G S+ + N S +L ++ND+L Sbjct: 224 FLATLSHEIRTPLNGGMLGGLSDTDLD--------SDQRLILNTDRVSAKSLLSLLNDIL 275 Query: 646 DISKIESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTSFANNIPRILA-DLRSV 704 D+SK+ESGK L + L ++ ISL+ + K ++ ++ +PR + D + Sbjct: 276 DLSKVESGKGELVAKRFDLRTLLNFVISLLSELSQAKYAILVLDLSSGVPRNVRGDEARL 335 Query: 705 KQIALNILSNAIHFTPSGGQI---IISTTHTSNEEVILRVR--DTGVGMTNYELEKAMKP 759 +Q+ N++SNAI FT +G I + + +V+LR + G + + M Sbjct: 336 RQVIANLVSNAIKFTHAGHLEESVIAREELSESNDVLLRAKEEAHMAGKARIDFLQKMSH 395 Query: 760 FGQIP 764 + P Sbjct: 396 AMRAP 400 >gnl|CDD|32384 COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction mechanisms]. Length = 232 Score = 46.1 bits (106), Expect = 4e-05 Identities = 39/239 (16%), Positives = 74/239 (30%), Gaps = 14/239 (5%) Query: 333 FFVYSHGNLFYANPSFLLLTKYKSVDDIEIAGGLSTLLDAPKLSDNNAIKPVMLYRSDRT 392 + G + YAN + L Y + + + GL L + +L + Sbjct: 3 LVLDRDGRIIYANEAAEELLGYSAEELL----GLLLALHPEDRDRLRELLRRLLAGEELL 58 Query: 393 CIAASARLHTIQWNRENSLAMTFIPFEKANQFPENMPQNGIEPEDVDTRINKRKMEIEVM 452 + A E + + + + + + Sbjct: 59 SEELRLVRKDGEERWVELSAAPLRDGE------GRVLGLLGLRDITERKRAEEALRESEE 112 Query: 453 QLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHY 512 +L ++LEA+ DGI +++ +G IL N A +L GY E+ L + + + Sbjct: 113 RLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELE 172 Query: 513 LTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPFSS----CYSLTMHDISEWKQE 567 L L+ LE K+ + + + DI+E KQ Sbjct: 173 LARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRDDGEIVGVVGIARDITERKQA 231 >gnl|CDD|144544 pfam00989, PAS, PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. Length = 112 Score = 45.5 bits (108), Expect = 6e-05 Identities = 15/54 (27%), Positives = 28/54 (51%) Query: 457 ILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMN 510 ILE+ DGI +++ +G IL N A +L G E+++ K + + + + Sbjct: 6 ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVA 59 >gnl|CDD|33622 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]. Length = 560 Score = 43.0 bits (101), Expect = 4e-04 Identities = 17/59 (28%), Positives = 31/59 (52%) Query: 457 ILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTE 515 IL++ DG+ +++ +GII+ N+A +KL G E++L K + S + L Sbjct: 122 ILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGEDSTLLEVLRT 180 >gnl|CDD|34223 COG4585, COG4585, Signal transduction histidine kinase [Signal transduction mechanisms]. Length = 365 Score = 41.7 bits (97), Expect = 0.001 Identities = 42/160 (26%), Positives = 60/160 (37%), Gaps = 30/160 (18%) Query: 657 LHFEPVSLDEAVSEAISLVQLYAN-EKRILIRTSFANNIPRILADLRSVKQIAL-----N 710 PV L+ +L L A+ E+R I ++ L L + AL Sbjct: 230 RDLRPVELEGL-GLVEALRALLADFEERTGITVDL--SLGSELERLPPEAEDALFRIVQE 286 Query: 711 ILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIR 770 L+NAI + + T +++E+ L V D GVG F Sbjct: 287 ALTNAIRH--AQATEVRVTLERTDDELRLEVIDNGVG------------FDPDK------ 326 Query: 771 GEGTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810 EG G GL + V+A G I S P +GT + I PL Sbjct: 327 -EGGGFGLLGMRERVEALGGTLTIDSAPGQGTTVTITLPL 365 >gnl|CDD|29035 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.. Length = 103 Score = 38.7 bits (89), Expect = 0.006 Identities = 24/103 (23%), Positives = 39/103 (37%), Gaps = 2/103 (1%) Query: 461 TSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKPFTVFLEQNTPSVMNHYLTEILSLD 520 DG+ +++ +G IL N A +L GY E+++ K + + L +LS Sbjct: 1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGG 60 Query: 521 LRQTLEKITLGSTKEEK--LLSLRIIIKKLPFSSCYSLTMHDI 561 TLE L+SL I + + DI Sbjct: 61 EPVTLEVRLRRKDGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 >gnl|CDD|30988 COG0643, CheA, Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]. Length = 716 Score = 38.0 bits (88), Expect = 0.010 Identities = 28/115 (24%), Positives = 45/115 (39%), Gaps = 26/115 (22%) Query: 720 PSGGQIIISTTHTSNEEVILRVRDTGVGMTNYE--LEKAM-KPFGQIPNSQQIRGE---- 772 P G I +S H N +++ V D G G+ + E EKA+ + ++ + E Sbjct: 461 PEEGTITLSAYHEGNN-IVIEVSDDGAGI-DREKIREKAIERGLITEEEAETLSDEEILN 518 Query: 773 -----------------GTGLGLPLAKAMVDANMGKFYIFSTPAKGTLIEIIFPL 810 G G+G+ + K ++ G + S P KGT I PL Sbjct: 519 LIFAPGFSTAEQVTDVSGRGVGMDVVKTNIEQLGGSISVSSEPGKGTTFTIRLPL 573 >gnl|CDD|33093 COG3283, TyrR, Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]. Length = 511 Score = 36.1 bits (83), Expect = 0.043 Identities = 44/235 (18%), Positives = 91/235 (38%), Gaps = 43/235 (18%) Query: 448 EIEVMQLCSILEATSDGIAIINREGIILSTNRAVSKLFGYPVEDILRKP---------FT 498 E E + L ++LEA + + ++ +G + N A +LFG + + F Sbjct: 76 EREHLALSALLEALPEPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAAQLINGFNFL 135 Query: 499 VFLEQNTPSVMNHYLTEILSLDLRQTLEKITLGSTKEEKLLSLRIIIKKLPF---SSCYS 555 +LE N ++ I + + + L +E +L+ +++ + + Sbjct: 136 RWLEGEPQRSHNEHVV-INGQNFLMEITPVYLQDENDEHVLAGAVVMLRSTNRMGEQLQN 194 Query: 556 LTMHDISEWKQ-------EKNKLSHAKKIA--------EKESSHKSDFLARVSHEI---- 596 + D+S ++Q K+ + A+K+A E+ D LA+ H Sbjct: 195 VAAQDVSGFEQIVAVSPKMKHVVEQAQKLAMLDAPLLITGETGTGKDLLAKACHLASPRH 254 Query: 597 RTPLTAIIGFS---EVIKNQRFG----PLGNPRYIEYANYIDRSGNLVLDIVNDL 644 P A+ S + +++ FG G + E AN G ++LD + ++ Sbjct: 255 SKPFLALNCASLPEDAAESELFGHAPGDEGKKGFFEQAN----GGTVLLDEIGEM 305 >gnl|CDD|32791 COG2972, COG2972, Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]. Length = 456 Score = 32.8 bits (74), Expect = 0.44 Identities = 35/140 (25%), Positives = 52/140 (37%), Gaps = 17/140 (12%) Query: 677 LYANEKRILIRTSFANNIPRILADLRSVKQIALNILSNAIHF----TPSGGQIIISTTHT 732 L + RI R I L L K + ++ NAI GG I IS Sbjct: 324 LEIQKLRIGDRLEVPLPIDEELEPLIDPKLVLQPLVENAIEHGIEPKRPGGSIAISAK-K 382 Query: 733 SNEEVILRVRDTGVGMTNYELEKAMKPFGQIPNSQQIRGEGTGLGLPLAKAMVDANMGK- 791 ++ + + + D G G+ +LE +G+GL K + G+ Sbjct: 383 QDDVIQISISDNGPGIDEEKLEGL----------STKGENRSGIGLSNVKERLKLYFGEP 432 Query: 792 -FYIFSTPAKGTLIEIIFPL 810 I S P KGT ++II P Sbjct: 433 GLSIDSQPGKGTFVQIIIPK 452 >gnl|CDD|35838 KOG0618, KOG0618, KOG0618, Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]. Length = 1081 Score = 31.9 bits (72), Expect = 0.78 Identities = 18/69 (26%), Positives = 24/69 (34%), Gaps = 2/69 (2%) Query: 292 LQNNSKESFEYLSHRNHPSLSAYFDEGENLT--PETVDKCPIPFFVYSHGNLFYANPSFL 349 L N SF R L G LT P+TV + +H N + P Sbjct: 390 LSYNRLNSFPASKLRKLEELEELNLSGNKLTTLPDTVANLGRLHTLRAHSNQLLSFPELA 449 Query: 350 LLTKYKSVD 358 L + K +D Sbjct: 450 QLPQLKVLD 458 >gnl|CDD|185751 cd09238, V_Alix_like_1, Protein-interacting V-domain of an uncharacterized family of the V_Alix_like superfamily. This domain family is comprised of uncharacterized plant proteins. It belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), (His-Domain) type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. In addition to this V-domain, members of the V_Alix_Rim20_Bro1_like superfamily also have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind to human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members of the V_Alix_like superfamily also have a proline-rich region (PRR). Length = 339 Score = 30.5 bits (69), Expect = 2.1 Identities = 28/124 (22%), Positives = 48/124 (38%), Gaps = 23/124 (18%) Query: 357 VDDIEIAGGLSTLLDAPK----LSDNNAIKPVMLYRS---DRTCIAASARLHTIQWNREN 409 V+ ++I+GGL+ L L S + T +A+ + W R Sbjct: 65 VEAVQISGGLAALEGELPRLRELRRVCTELLAAAQESLEAEATEDSAARTQYGTAWTRPP 124 Query: 410 SLAMTFIPFEKANQFPENMPQNGIEPEDVDTRINKRKMEIEVMQLCSILEATSDGIAIIN 469 S +T +E+ N+F N+ Q G D D + +R +E DG+ I++ Sbjct: 125 SATLTKNLWERLNRFRVNLEQAG----DSDESLRRR------------IEDAMDGMLILD 168 Query: 470 REGI 473 E Sbjct: 169 DEPA 172 >gnl|CDD|32403 COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]. Length = 317 Score = 30.2 bits (68), Expect = 2.3 Identities = 12/46 (26%), Positives = 19/46 (41%) Query: 700 DLRSVKQIALNILSNAIHFTPSGGQIIISTTHTSNEEVILRVRDTG 745 LR + IA IH T G I + ++V+ +R+ G Sbjct: 46 TLRKIADIAEKYGDGLIHITSRQGLEIPGISPEDADDVVEELREIG 91 >gnl|CDD|33243 COG3437, COG3437, Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]. Length = 360 Score = 30.3 bits (68), Expect = 2.3 Identities = 21/112 (18%), Positives = 39/112 (34%), Gaps = 9/112 (8%) Query: 631 DRSGNLVLDIVNDLLDISK-IESGKMNLHFEPVSLDEAVSEAISLVQLYANEKRILIRTS 689 R ++L D D + +E+G + +P+S E V+ S +QL NE +L + Sbjct: 88 RRIPVILLTAYADSEDRQRALEAGADDYLSKPISPKELVARVSSHLQLKRNEDFLLDQNL 147 Query: 690 FANNIPRILADLRSVKQIALN-------ILSNAIHFTPSGGQIIISTTHTSN 734 + + + QI N + + G + S Sbjct: 148 YLEL-QELRRRTEELAQIEDNLDETLEELAALLEVRDYETGDHLERVAQYSE 198 >gnl|CDD|35367 KOG0145, KOG0145, KOG0145, RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]. Length = 360 Score = 29.2 bits (65), Expect = 4.2 Identities = 13/29 (44%), Positives = 18/29 (62%) Query: 748 MTNYELEKAMKPFGQIPNSQQIRGEGTGL 776 MT ELE+ PFG+I S+ + + TGL Sbjct: 139 MTQKELEQIFSPFGRIITSRILVDQVTGL 167 >gnl|CDD|37358 KOG2147, KOG2147, KOG2147, Nucleolar protein involved in 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]. Length = 823 Score = 29.2 bits (65), Expect = 5.0 Identities = 29/113 (25%), Positives = 43/113 (38%), Gaps = 14/113 (12%) Query: 491 DILRKPFTVFLEQNTPSVMNHYLTEILSLDLRQTLEKITLGSTKEEKLLSLR------II 544 +I F + LE + L E L D +EK+T E K L+L+ I Sbjct: 669 EIFFPIFLLLLEYLQAESLPQELQEKL-EDTLALVEKLT--GFAERKPLALQKHKPVAIR 725 Query: 545 IKKLPFSSCYSLTM-HDISEWKQEKNKLSH----AKKIAEKESSHKSDFLARV 592 +K F + D + + E KL +K A +E + FLAR Sbjct: 726 LKMPKFEENFDPDKKRDPDKERSELKKLKAKLKRERKGAIRELRKDAAFLARK 778 >gnl|CDD|36016 KOG0797, KOG0797, KOG0797, Actin-related protein [Cytoskeleton]. Length = 618 Score = 29.2 bits (65), Expect = 5.3 Identities = 21/106 (19%), Positives = 37/106 (34%), Gaps = 15/106 (14%) Query: 196 LGKRLDKKFSHLHEIKKGHSSVEKEKYDIFSQQSPPPHLRMKNKVSS------LTEYYAH 249 L +L +KF HL + + + ++ PP L+ K+ L +Y Sbjct: 340 LLNQLKEKFCHLRA-----AELGVQLTVFSYREPNPPTLKYTFKLGDEVMLAPLALFYP- 393 Query: 250 KDDVLKTEKYPLLTSEESSLPEQEDFHTINLNQYT-KKQYFGTLQN 294 ++ E ++ P++ED KQ FG N Sbjct: 394 --NLFVIEGTKSHKNQSFPQPDREDLFDYEYLLEDTWKQDFGGGGN 437 >gnl|CDD|111641 pfam02768, DNA_pol3_beta_3, DNA polymerase III beta subunit, C-terminal domain. A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. Length = 121 Score = 28.4 bits (64), Expect = 8.7 Identities = 11/31 (35%), Positives = 18/31 (58%) Query: 670 EAISLVQLYANEKRILIRTSFANNIPRILAD 700 +A++ V L ANEK +R SF ++ A+ Sbjct: 21 KALARVALLANEKNRGVRLSFEEGQLKLTAN 51 >gnl|CDD|33706 COG3920, COG3920, Signal transduction histidine kinase [Signal transduction mechanisms]. Length = 221 Score = 28.3 bits (63), Expect = 9.6 Identities = 23/110 (20%), Positives = 40/110 (36%), Gaps = 25/110 (22%) Query: 707 IALN-ILSNAI-HFTPSG--GQIIIS-TTHTSNEEVILRVRDTGVGMTNYELEKAMKPFG 761 + ++ +++NA+ H S G+I I+ + +L V D G G Sbjct: 125 LIVHELVTNALKHAFLSRPGGEIRITLSREGDGGRFLLTVWDEGGGP------------- 171 Query: 762 QIPNSQQIRGEGTGLGLPLAKAMVDANM-GKFYIFSTPAKGTLIEIIFPL 810 + G GL L + +V + G+ GT + FPL Sbjct: 172 ----PVEAPLSRGGFGLQLVERLVPEQLGGELEDER--PDGTEFRLRFPL 215 >gnl|CDD|143985 pfam00232, Glyco_hydro_1, Glycosyl hydrolase family 1. Length = 454 Score = 28.1 bits (63), Expect = 9.8 Identities = 8/24 (33%), Positives = 12/24 (50%), Gaps = 4/24 (16%) Query: 175 FSGFRG----FGIVHVNRVDNDPR 194 F G FG+V+V+R + R Sbjct: 413 FEWANGYSKRFGLVYVDRYETQER 436 >gnl|CDD|30660 COG0312, TldD, Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]. Length = 454 Score = 28.0 bits (62), Expect = 9.9 Identities = 17/98 (17%), Positives = 34/98 (34%), Gaps = 4/98 (4%) Query: 592 VSHEIRTPLTAIIGFSEVIKNQRFGPLGNPRYIEYANYIDRSGNLVLDIVNDLLDISKIE 651 + ++ I G + + G+ + E + LL+ + Sbjct: 166 ERTRVSLSVSVIAGEGGRGEERSGRGGGSRGFEELLEEPEEVAEEAARRALSLLEARPVP 225 Query: 652 SGKMNLHFEP----VSLDEAVSEAISLVQLYANEKRIL 685 SG+ + P V L EA+ A+ ++Y E +L Sbjct: 226 SGRYPVILSPEAAGVLLHEALGHALEGDRVYKGESSLL 263 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.316 0.134 0.387 Gapped Lambda K H 0.267 0.0680 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 9,881,608 Number of extensions: 534510 Number of successful extensions: 1282 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1253 Number of HSP's successfully gapped: 42 Length of query: 820 Length of database: 6,263,737 Length adjustment: 102 Effective length of query: 718 Effective length of database: 4,059,619 Effective search space: 2914806442 Effective search space used: 2914806442 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 62 (27.8 bits)