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= 0003.0060.p (1149 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312866|ref|YP_003776958.1| DNA polymerase III subunit alph... 2044 0.0 gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alph... 303 5e-83 >gi|300312866|ref|YP_003776958.1| DNA polymerase III subunit alpha [Herbaspirillum seropedicae SmR1] Length = 1152 Score = 2044 bits (5296), Expect = 0.0, Method: Compositional matrix adjust. Identities = 976/1152 (84%), Positives = 1069/1152 (92%), Gaps = 3/1152 (0%) Query: 1 MTTPQFVHLRLHSEYSIVDGLVRIDDVVKAAAKDGQAALAITDLANLFGMVKFYKGARGK 60 MTTPQFVHLR+HSEYSIVDGLVRIDD+VKAAAKDGQAALA+TDLANLF MV+FYK ARGK Sbjct: 1 MTTPQFVHLRMHSEYSIVDGLVRIDDIVKAAAKDGQAALAVTDLANLFCMVRFYKEARGK 60 Query: 61 GVKPIAGCDVWISNDDDRDKPTRLLLLVKDHHGYLQLCDLLSRAWLTNLHRGRAELRPEW 120 GVKPIAGCD+WI+ND DR+KP RLL+L+K+ HGYLQLC++LS+AWL N ++GRAE+R EW Sbjct: 61 GVKPIAGCDLWITNDADREKPFRLLVLIKNRHGYLQLCEVLSQAWLNNQYKGRAEVRMEW 120 Query: 121 LEQLRHDEGGNGLIALSGAHFGDVGIAIENGNVAAAERAAQRWSEVFPGAFYVEIQRANQ 180 L+ LRH EGGNGLIALSGA GD+G AI+NGN+A AE A+RW+E+FPGAFY+E+QRA Q Sbjct: 121 LDALRHQEGGNGLIALSGAAMGDIGQAIDNGNLAQAEACARRWAEIFPGAFYLELQRAGQ 180 Query: 181 PNMEVQVRQSVALAARLALPVVATHPIQFLSQDEFVAHEARTCIAEGEILANARRVRRFN 240 NMEVQVRQSVAL A+L LP VATHPIQF S +EF+AHEARTCIAEGEI+ANARRVRRFN Sbjct: 181 ANMEVQVRQSVALGAKLGLPCVATHPIQFQSPEEFIAHEARTCIAEGEIMANARRVRRFN 240 Query: 241 EQQNFKTQAEMAALFADLPGAVQNTIEIAKRCNLMLTLGKPQLPNFPTPDGMTIDDFLVA 300 EQQ FK+QAEM LFADLPGAV NT+EIAKRCNL+L LGKPQLP+FPTPDGMTIDDFLVA Sbjct: 241 EQQYFKSQAEMVELFADLPGAVANTVEIAKRCNLVLQLGKPQLPDFPTPDGMTIDDFLVA 300 Query: 301 ETKIGLEARLKHLYPDEARREKERPRYEARLKFENDTIIKMKFPGYFLIVADFIQWAKNN 360 +TK GLE RLK L+P+EA REK+RPRYEARL+FEN+TIIKMKFPGYFLIVADFIQWAKNN Sbjct: 301 QTKAGLEVRLKELFPNEAEREKQRPRYEARLEFENNTIIKMKFPGYFLIVADFIQWAKNN 360 Query: 361 GVPVGPGRGSGAGSLVAYALSITDLDPLEYNLLFERFLNPERVSMPDFDIDFCQEGRDRV 420 GVPVGPGRGSGAGSLVAY L ITDLDPL YNLLFERFLNPERVSMPDFDIDFCQEGRDRV Sbjct: 361 GVPVGPGRGSGAGSLVAYCLLITDLDPLRYNLLFERFLNPERVSMPDFDIDFCQEGRDRV 420 Query: 421 IQYVKDRYGKEAVSQIATFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLA 480 IQYVKDRYGKEAVSQIATFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLA Sbjct: 421 IQYVKDRYGKEAVSQIATFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLA 480 Query: 481 DAIEEEPLLKERLENEEEVKQLMGLAQQVEGIARNIGMX---VLIAPGKLTDFCPLYTQG 537 DAIEEEPLLKERLENEEEVKQLMGLAQQVEGIARNIGM VLIAPGKLTDFCPLYTQG Sbjct: 481 DAIEEEPLLKERLENEEEVKQLMGLAQQVEGIARNIGMHAGGVLIAPGKLTDFCPLYTQG 540 Query: 538 GDAGVVSQYDKDDVEAVGLVKFDFLGLTTLTILDRAVRYIKQLDPAMADFDLARLPLTDR 597 GD+GVVSQYDKDDVEAVGLVKFDFLGLTTLTILDRAVRYI+ LDPAMADFDLA+LPL DR Sbjct: 541 GDSGVVSQYDKDDVEAVGLVKFDFLGLTTLTILDRAVRYIRMLDPAMADFDLAKLPLDDR 600 Query: 598 ASYDLLTKAKTVAVFQLESRGMQGMLKDARPDRFEDIIALVALYRPGPMDLIPDFCKRKH 657 SY+LLTKAKTVAVFQLESRGMQGMLKDARPDRFEDIIALVALYRPGPMDLIPDFCKRKH Sbjct: 601 PSYELLTKAKTVAVFQLESRGMQGMLKDARPDRFEDIIALVALYRPGPMDLIPDFCKRKH 660 Query: 658 GEKFDYPDPRTEGILSETYGIMVYQEQVMQMAQVVGGYSLGGADLLRRAMGKKKAEEMAE 717 GE FDYPDPRTEGILSETYGIMVYQEQVMQMAQV+GGYSLGGADLLRRAMGKKKAEEMA+ Sbjct: 661 GEAFDYPDPRTEGILSETYGIMVYQEQVMQMAQVIGGYSLGGADLLRRAMGKKKAEEMAK 720 Query: 718 HRNIFREGAAKDGLSQEKADEIFDLMEKFAGYGFNKSHAAAYALLSYHTAYLKAHHPAAF 777 HR +FREGAAK+GL Q KADEIFDLMEKFAGYGFNKSHAAAYALLSY+TAYLKAHHPAAF Sbjct: 721 HRELFREGAAKNGLDQAKADEIFDLMEKFAGYGFNKSHAAAYALLSYYTAYLKAHHPAAF 780 Query: 778 MAANLSLAMDDTEKIKILVEDSLDVCGLSLLPPDINLSDYRFIPVGEPGKKAVHIRYGLG 837 MAANLSLAM+DT+K+KIL+ED++D+C L++LPPDIN SDYRF+PVGEPGKKA IRYGLG Sbjct: 781 MAANLSLAMEDTDKVKILIEDAIDICKLAILPPDINKSDYRFMPVGEPGKKATQIRYGLG 840 Query: 838 AVKGSGQSAIEAIIAARQDGPFKDLFDFAKRVDKKQINRRTVDSLIRAGAFDCFGVDRAI 897 AVKG+GQ+AIEAI+ AR+ GPFKDLFDFAKRVDKKQINRRT+DSLIRAGAFDCF VDRA+ Sbjct: 841 AVKGAGQNAIEAILEARKSGPFKDLFDFAKRVDKKQINRRTIDSLIRAGAFDCFKVDRAV 900 Query: 898 LQATVGLAWENAEQMEASANQVSLFGGDDSDLETPLEYVQVRPWSDKQRLTEEKTALGFY 957 LQA+V LAWE+AEQ E SANQVSLFGGDDSDLE PLEYVQV PWSDKQRLTEEK ALGFY Sbjct: 901 LQASVNLAWESAEQAEKSANQVSLFGGDDSDLEAPLEYVQVPPWSDKQRLTEEKGALGFY 960 Query: 958 LSGHLFDAYEKEVRQFVRTKISSLEPSRDPRSLAGIITGIRVQMTQRGKLLIVSLDDGSG 1017 LSGHLF AYEKEVR+FVRTKI+SLEPS +PRSLAGIITG+RVQMTQRGKL+I +LDDG+G Sbjct: 961 LSGHLFSAYEKEVRRFVRTKIASLEPSWEPRSLAGIITGVRVQMTQRGKLVICTLDDGTG 1020 Query: 1018 TVDVTVYGELAEPNKAFFKEDELLIVQGKVSEDRFNGGLRISAEKVMDIGAARIQYGQRV 1077 ++ T+Y EL EP K KEDELL+V GKVSEDRFNGGLR++A+KVMD+GAARIQYG R+ Sbjct: 1021 VIEATIYNELFEPFKHLIKEDELLVVSGKVSEDRFNGGLRVAADKVMDLGAARIQYGVRM 1080 Query: 1078 VVSLNKSVDPVHLRDTLSSYRQPQGLPFVMKYVQSGVGCEVMLGDAWRVVPSDGLQVSLR 1137 VVS+NK++DP HLRDTLS++RQ QGLPFVM+Y Q+ CEV+LGDAWR+ PSD LQ +L Sbjct: 1081 VVSINKAIDPNHLRDTLSAHRQEQGLPFVMRYQQADAACEVVLGDAWRINPSDSLQSTLV 1140 Query: 1138 ESFGQEAVVVEY 1149 SFG+EAVVVEY Sbjct: 1141 ASFGKEAVVVEY 1152 >gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alpha [Herbaspirillum seropedicae SmR1] Length = 942 Score = 303 bits (776), Expect = 5e-83, Method: Compositional matrix adjust. Identities = 263/906 (29%), Positives = 419/906 (46%), Gaps = 74/906 (8%) Query: 2 TTPQFVHLRLHSEYSIVDGLVRIDDVVKAAAKDGQAALAITDLANLFGMVKFYKG----- 56 T P++ L S +S + G ++V+ A ALAITD L G+V+ Y Sbjct: 4 TLPEYAELYCRSNFSFLQGASHAHELVQRAIALDYRALAITDECTLAGVVRAYAAWKEQF 63 Query: 57 --ARGKGVKPIAG-CDVWISNDDDRDKPTRLLLLV---KDHHGYLQLCDLLSRAWLTNLH 110 R + K I G C + +D+ P L LV ++ GY L +L++ A T Sbjct: 64 DKGRTQDFKLIIGSCFRFTGLEDEPAHPLAALTLVALARNREGYGNLSELITLA-RTRAA 122 Query: 111 RGRAELRPEWLEQLRHDEGGNGLIALSGAHFGDVGIAIENGNVAAAER--AAQRW-SEVF 167 +G L PE D G D + + A E A RW + + Sbjct: 123 KGSYLLHPE-------DLSGPPPALSHLRALPDCQLILVPDYPADEETLDAQLRWFAPLA 175 Query: 168 PGAFYVEIQRANQPNMEVQVRQSVALAARLALPVVATHPIQFLSQDEFVAHEARTCIAEG 227 PG +V I R +P ++ A R LP+ A +Q + + T I G Sbjct: 176 PGRSWVGITRLYRPLDDLHRAALEAATRRHGLPLAAVGDVQMHQRSRKYLQDVVTAIRLG 235 Query: 228 EILANARRVRRFNEQQNFKTQAEMAALFADLPGAVQNTIEIAKRCNLMLTLGKPQLPNFP 287 + + N +Q+ +++ + + P + T+ IA C L + + P+ Sbjct: 236 QPVQECGHALAPNAEQHLRSRVRLGMVHT--PATLAQTLAIAADCRFSLAELRYEYPDEL 293 Query: 288 TPDGMTIDDFLVAETKIGLEARLKHLYPDEARREKERPRYEARLKFENDTIIKMKFPGYF 347 P GM+ D+L +T G R P R + EA L I + ++ YF Sbjct: 294 VPLGMSAADYLRQQTLAGAAKRYPQGLPGGVREQ-----IEAELAL----IAQKEYEAYF 344 Query: 348 LIVADFIQWAKNNGVPVGPGRGSGAGSLVAYALSITDLDPLEYNLLFERFLNPERVSMPD 407 L V D +Q+A++ G+ + GRGS A S V Y L +T++DP LLF RF++ +R PD Sbjct: 345 LTVYDLVQFARSRGI-LCQGRGSAANSAVCYCLGVTEVDPTSTRLLFARFISEKREEPPD 403 Query: 408 FDIDFCQEGRDRVIQYVKDRYGKEAVSQIATFGTMAAKGAVRDVGRVLDLGYNFCDGISK 467 D+DF + R+ VIQ++ +YG+ + A + +GA+R+VG+ L + D ++K Sbjct: 404 IDVDFEHQRREEVIQHIYRKYGRRRAALAAAVHSYRPRGALREVGKALGVDAAIVDAVAK 463 Query: 468 LIPFKPGKLVTLADAIEEEPLLKERLEN--EEEVKQLMGLAQQVEG--------IARNIG 517 + D+ EE LL E + E+ Q+ GL + G ++++ G Sbjct: 464 SQHW--------FDSREE--LLARFAEAGLDPELPQI-GLWASITGKLLRFPRHLSQHTG 512 Query: 518 MXVLIAPGKLTDFCPLYTQGGDAGVVSQYDKDDVEAVGLVKFDFLGLTTLTILDRAVRYI 577 V IA G+L+ P+ V ++DKDD+E++ L+K D L L LT L R + + Sbjct: 513 GFV-IARGQLSRLVPIQNAAMPERCVIEWDKDDLESLKLLKVDVLALGMLTALRRTLELV 571 Query: 578 KQLDPAMADFDLARLPLTDRASYDLLTKAKTVAVFQLESRGMQGMLKDARPDRFEDIIAL 637 + +P D A+++++ KA T+ VFQ+ESR ML +P D++ Sbjct: 572 SLRRGLPEVMQMHAIPREDPATFEMICKADTIGVFQIESRAQMSMLPRMQPRTQYDLVVQ 631 Query: 638 VALYRPGPMD--LIPDFCKR----KHGEKFDYPDPRTEG-----ILSETYGIMVYQEQVM 686 VA+ RPGP+ ++ + +R + G FDYPD ++ +L T GI ++QEQVM Sbjct: 632 VAIVRPGPIQGGMVHPYLRRRELVREGGSFDYPDNTSKSGKIKKVLERTLGIPIFQEQVM 691 Query: 687 QMAQVVGGYSLGGADLLRRAMGK-KKAEEMAEHRNIFREGAAKDGLSQEKADEIFDLMEK 745 +A GYS AD LRR+M K+ M H G +G S+E A+ IF +E Sbjct: 692 DVAIEAAGYSPSEADDLRRSMAAWKRKGGMGPHYERLVLGMTDNGYSREFAESIFKQIEG 751 Query: 746 FAGYGFNKSHAAAYALLSYHTAYLKAHHPAAFMAANLSLAMDDTEKIKILVEDSLDVCGL 805 F YGF +SHAA++ALL+Y +++LK H P AF+ L+ L++D+ G+ Sbjct: 752 FGEYGFPESHAASFALLTYFSSWLKCHEPEAFLCGLLNSQPMGFYSPSQLIQDARRH-GV 810 Query: 806 SLLPPDINLSDYRF---IPVGEPGKKAVHIRYGLGAVKGSGQSAIEAIIAARQDGPFKDL 862 +LP ++ S + +P + AV R GL ++ A + I AR PF D+ Sbjct: 811 QVLPANVVRSRWESTLELPSSAGARPAV--RLGLSLLRSMPAEAAQRIEQARAQRPFADV 868 Query: 863 FDFAKR 868 D A+R Sbjct: 869 DDLARR 874 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 0.138 0.401 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: 3,558,063 Number of extensions: 153448 Number of successful extensions: 426 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 419 Number of HSP's successfully gapped: 2 Length of query: 1149 Length of database: 1,619,870 Length adjustment: 96 Effective length of query: 1053 Effective length of database: 1,165,310 Effective search space: 1227071430 Effective search space used: 1227071430 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: 136 (57.0 bits)