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= 0001.3477.p (1152 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... 2356 0.0 gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alph... 325 1e-89 >gi|300312866|ref|YP_003776958.1| DNA polymerase III subunit alpha [Herbaspirillum seropedicae SmR1] Length = 1152 Score = 2356 bits (6106), Expect = 0.0, Method: Compositional matrix adjust. Identities = 1142/1152 (99%), Positives = 1150/1152 (99%) Query: 1 MTTPQFVHLRMHSEYSIVDGLVRIDDIVKAAAKDGQAALAVTDLANLFCMVRFYKEARGK 60 MTTPQFVHLRMHSEYSIVDGLVRIDDIVKAAAKDGQAALAVTDLANLFCMVRFYKEARGK Sbjct: 1 MTTPQFVHLRMHSEYSIVDGLVRIDDIVKAAAKDGQAALAVTDLANLFCMVRFYKEARGK 60 Query: 61 GVKPIAGCDLWITNDADREKPFRLLVLIKNRHGYLQLCEVLSQAWLNNQYKGRAEVRMEW 120 GVKPIAGCDLWITNDADREKPFRLLVLIKNRHGYLQLCEVLSQAWLNNQYKGRAEVRMEW Sbjct: 61 GVKPIAGCDLWITNDADREKPFRLLVLIKNRHGYLQLCEVLSQAWLNNQYKGRAEVRMEW 120 Query: 121 LEALRHQEGGNGLIALSGAAMGDIGQAIDNGNLTQAEACARRWAEIFPGAFYLELQRAGQ 180 L+ALRHQEGGNGLIALSGAAMGDIGQAIDNGNL QAEACARRWAEIFPGAFYLELQRAGQ Sbjct: 121 LDALRHQEGGNGLIALSGAAMGDIGQAIDNGNLAQAEACARRWAEIFPGAFYLELQRAGQ 180 Query: 181 ANMELQVRQSVALGAKLGLPCVATHPIQFQSPEEFIAHEARTCIAEGEIMANARRVRRFN 240 ANME+QVRQSVALGAKLGLPCVATHPIQFQSPEEFIAHEARTCIAEGEIMANARRVRRFN Sbjct: 181 ANMEVQVRQSVALGAKLGLPCVATHPIQFQSPEEFIAHEARTCIAEGEIMANARRVRRFN 240 Query: 241 EQQYFKSQAEMAELFADLPGALANSVEIAKRCNLVLQLGKPQLPDFPTPDGMSIDDFLVA 300 EQQYFKSQAEM ELFADLPGA+AN+VEIAKRCNLVLQLGKPQLPDFPTPDGM+IDDFLVA Sbjct: 241 EQQYFKSQAEMVELFADLPGAVANTVEIAKRCNLVLQLGKPQLPDFPTPDGMTIDDFLVA 300 Query: 301 QTKAGLEVRLKELFPNEAEREKQRPRYEARLEFENNTIIKMKFPGYFLIVADFIQWAKNN 360 QTKAGLEVRLKELFPNEAEREKQRPRYEARLEFENNTIIKMKFPGYFLIVADFIQWAKNN Sbjct: 301 QTKAGLEVRLKELFPNEAEREKQRPRYEARLEFENNTIIKMKFPGYFLIVADFIQWAKNN 360 Query: 361 GVPVGPGRGSGAGSLVAYCLLITDLDPLRYNLLFERFLNPERVSMPDFDIDFCQEGRDRV 420 GVPVGPGRGSGAGSLVAYCLLITDLDPLRYNLLFERFLNPERVSMPDFDIDFCQEGRDRV Sbjct: 361 GVPVGPGRGSGAGSLVAYCLLITDLDPLRYNLLFERFLNPERVSMPDFDIDFCQEGRDRV 420 Query: 421 IQYVKDRYGKDAVSQIATFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLA 480 IQYVKDRYGK+AVSQIATFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLA Sbjct: 421 IQYVKDRYGKEAVSQIATFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLA 480 Query: 481 DAIEEEPLLKERLENEEEVKQLMGLAQQVEGIARNIGMHAGGVLIAPGKLTDFCPLYTQG 540 DAIEEEPLLKERLENEEEVKQLMGLAQQVEGIARNIGMHAGGVLIAPGKLTDFCPLYTQG Sbjct: 481 DAIEEEPLLKERLENEEEVKQLMGLAQQVEGIARNIGMHAGGVLIAPGKLTDFCPLYTQG 540 Query: 541 GDSGVVSQYDKDDVEAVGLVKFDFLGLTTLTILDRAVRYIRMLDPAMADFDLAKLPLDDR 600 GDSGVVSQYDKDDVEAVGLVKFDFLGLTTLTILDRAVRYIRMLDPAMADFDLAKLPLDDR Sbjct: 541 GDSGVVSQYDKDDVEAVGLVKFDFLGLTTLTILDRAVRYIRMLDPAMADFDLAKLPLDDR 600 Query: 601 PSYELLTKAKTVAVFQLESRGMQGMLKDARPDRFEDIIALVALYRPGPMDLIPDFCKRKH 660 PSYELLTKAKTVAVFQLESRGMQGMLKDARPDRFEDIIALVALYRPGPMDLIPDFCKRKH Sbjct: 601 PSYELLTKAKTVAVFQLESRGMQGMLKDARPDRFEDIIALVALYRPGPMDLIPDFCKRKH 660 Query: 661 GEAFDYPDPRTEGILSETYGIMVYQEQVMQMAQVIGGYSLGGADLLRRAMGKKKAEEMAK 720 GEAFDYPDPRTEGILSETYGIMVYQEQVMQMAQVIGGYSLGGADLLRRAMGKKKAEEMAK Sbjct: 661 GEAFDYPDPRTEGILSETYGIMVYQEQVMQMAQVIGGYSLGGADLLRRAMGKKKAEEMAK 720 Query: 721 HRELFREGAAKNGLDQAKADEIFDLMEKFAGYGFNKSHAAAYALLSYYTAYLKAHHPAAF 780 HRELFREGAAKNGLDQAKADEIFDLMEKFAGYGFNKSHAAAYALLSYYTAYLKAHHPAAF Sbjct: 721 HRELFREGAAKNGLDQAKADEIFDLMEKFAGYGFNKSHAAAYALLSYYTAYLKAHHPAAF 780 Query: 781 MAANLSLAMEDTDKVKILIEDSIDICKLAILPPDINKSDYRFMPVGEPGKKATQIRYGLG 840 MAANLSLAMEDTDKVKILIED+IDICKLAILPPDINKSDYRFMPVGEPGKKATQIRYGLG Sbjct: 781 MAANLSLAMEDTDKVKILIEDAIDICKLAILPPDINKSDYRFMPVGEPGKKATQIRYGLG 840 Query: 841 AVKGAGQNAIEAILEARKSGPFKDLFDFAKRVDKKQINRRTIDSLIRAGAFDCFKVDRAI 900 AVKGAGQNAIEAILEARKSGPFKDLFDFAKRVDKKQINRRTIDSLIRAGAFDCFKVDRA+ Sbjct: 841 AVKGAGQNAIEAILEARKSGPFKDLFDFAKRVDKKQINRRTIDSLIRAGAFDCFKVDRAV 900 Query: 901 LQASVNLAWESAEQAEKSANQVSLFGGDDSDLEAPLEYVQVPPWSDKQRLTEEKGALGFY 960 LQASVNLAWESAEQAEKSANQVSLFGGDDSDLEAPLEYVQVPPWSDKQRLTEEKGALGFY Sbjct: 901 LQASVNLAWESAEQAEKSANQVSLFGGDDSDLEAPLEYVQVPPWSDKQRLTEEKGALGFY 960 Query: 961 LSGHLFSAYEKEVRRFVRTKIASLEPSWEPRSLAGIITGVRVQMTQRGKLVICTLDDGTG 1020 LSGHLFSAYEKEVRRFVRTKIASLEPSWEPRSLAGIITGVRVQMTQRGKLVICTLDDGTG Sbjct: 961 LSGHLFSAYEKEVRRFVRTKIASLEPSWEPRSLAGIITGVRVQMTQRGKLVICTLDDGTG 1020 Query: 1021 VIEATIYNELFEPFKHLIKEDELLVVSGKVSEDRFNGGLRVAADKVMDLGAARIQYGVRM 1080 VIEATIYNELFEPFKHLIKEDELLVVSGKVSEDRFNGGLRVAADKVMDLGAARIQYGVRM Sbjct: 1021 VIEATIYNELFEPFKHLIKEDELLVVSGKVSEDRFNGGLRVAADKVMDLGAARIQYGVRM 1080 Query: 1081 VVSINKAIDPNHLRDTLSAHRQEQGLPFVMRYQQADAACEVVLGDAWRINPSDSLQSTLV 1140 VVSINKAIDPNHLRDTLSAHRQEQGLPFVMRYQQADAACEVVLGDAWRINPSDSLQSTLV Sbjct: 1081 VVSINKAIDPNHLRDTLSAHRQEQGLPFVMRYQQADAACEVVLGDAWRINPSDSLQSTLV 1140 Query: 1141 ASFGKEAVVVEY 1152 ASFGKEAVVVEY Sbjct: 1141 ASFGKEAVVVEY 1152 >gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alpha [Herbaspirillum seropedicae SmR1] Length = 942 Score = 325 bits (833), Expect = 1e-89, Method: Compositional matrix adjust. Identities = 267/907 (29%), Positives = 422/907 (46%), Gaps = 73/907 (8%) Query: 2 TTPQFVHLRMHSEYSIVDGLVRIDDIVKAAAKDGQAALAVTDLANLFCMVRFYK------ 55 T P++ L S +S + G ++V+ A ALA+TD L +VR Y Sbjct: 4 TLPEYAELYCRSNFSFLQGASHAHELVQRAIALDYRALAITDECTLAGVVRAYAAWKEQF 63 Query: 56 -EARGKGVKPIAGCDLWITNDADR----EKPFRLLVLIKNRHGYLQLCEVLSQAWLNNQY 110 + R + K I G T D L+ L +NR GY L E+++ A Sbjct: 64 DKGRTQDFKLIIGSCFRFTGLEDEPAHPLAALTLVALARNREGYGNLSELITLA-RTRAA 122 Query: 111 KGRAEVRMEWLE----ALRHQEGGNGLIALSGAAMGDIGQAIDNGNLTQAEACARRW-AE 165 KG + E L AL H L AL + + + A+ RW A Sbjct: 123 KGSYLLHPEDLSGPPPALSH------LRALPDCQLILVPDYPADEETLDAQL---RWFAP 173 Query: 166 IFPGAFYLELQRAGQANMELQVRQSVALGAKLGLPCVATHPIQFQSPEEFIAHEARTCIA 225 + PG ++ + R + +L A + GLP A +Q + T I Sbjct: 174 LAPGRSWVGITRLYRPLDDLHRAALEAATRRHGLPLAAVGDVQMHQRSRKYLQDVVTAIR 233 Query: 226 EGEIMANARRVRRFNEQQYFKSQAEMAELFADLPGALANSVEIAKRCNLVLQLGKPQLPD 285 G+ + N +Q+ +S+ + P LA ++ IA C L + + PD Sbjct: 234 LGQPVQECGHALAPNAEQHLRSRVRLG--MVHTPATLAQTLAIAADCRFSLAELRYEYPD 291 Query: 286 FPTPDGMSIDDFLVAQTKAGLEVRLKELFPNEAEREKQRPRYEARLEFENNTIIKMKFPG 345 P GMS D+L QT AG R + P + +E E I + ++ Sbjct: 292 ELVPLGMSAADYLRQQTLAGAAKRYPQGLPGGVREQ---------IEAELALIAQKEYEA 342 Query: 346 YFLIVADFIQWAKNNGVPVGPGRGSGAGSLVAYCLLITDLDPLRYNLLFERFLNPERVSM 405 YFL V D +Q+A++ G+ + GRGS A S V YCL +T++DP LLF RF++ +R Sbjct: 343 YFLTVYDLVQFARSRGI-LCQGRGSAANSAVCYCLGVTEVDPTSTRLLFARFISEKREEP 401 Query: 406 PDFDIDFCQEGRDRVIQYVKDRYGKDAVSQIATFGTMAAKGAVRDVGRVLDLGYNFCDGI 465 PD D+DF + R+ VIQ++ +YG+ + A + +GA+R+VG+ L + D + Sbjct: 402 PDIDVDFEHQRREEVIQHIYRKYGRRRAALAAAVHSYRPRGALREVGKALGVDAAIVDAV 461 Query: 466 SKLIPFKPGKLVTLADAIEEEPLLKERLEN--EEEVKQLMGLAQQVEG----IARNIGMH 519 +K + D+ EE LL E + E+ Q+ GL + G R++ H Sbjct: 462 AKSQHW--------FDSREE--LLARFAEAGLDPELPQI-GLWASITGKLLRFPRHLSQH 510 Query: 520 AGGVLIAPGKLTDFCPLYTQGGDSGVVSQYDKDDVEAVGLVKFDFLGLTTLTILDRAVRY 579 GG +IA G+L+ P+ V ++DKDD+E++ L+K D L L LT L R + Sbjct: 511 TGGFVIARGQLSRLVPIQNAAMPERCVIEWDKDDLESLKLLKVDVLALGMLTALRRTLEL 570 Query: 580 IRMLDPAMADFDLAKLPLDDRPSYELLTKAKTVAVFQLESRGMQGMLKDARPDRFEDIIA 639 + + + +P +D ++E++ KA T+ VFQ+ESR ML +P D++ Sbjct: 571 VSLRRGLPEVMQMHAIPREDPATFEMICKADTIGVFQIESRAQMSMLPRMQPRTQYDLVV 630 Query: 640 LVALYRPGPMD--LIPDFCKR----KHGEAFDYPDPRTEG-----ILSETYGIMVYQEQV 688 VA+ RPGP+ ++ + +R + G +FDYPD ++ +L T GI ++QEQV Sbjct: 631 QVAIVRPGPIQGGMVHPYLRRRELVREGGSFDYPDNTSKSGKIKKVLERTLGIPIFQEQV 690 Query: 689 MQMAQVIGGYSLGGADLLRRAMGK-KKAEEMAKHRELFREGAAKNGLDQAKADEIFDLME 747 M +A GYS AD LRR+M K+ M H E G NG + A+ IF +E Sbjct: 691 MDVAIEAAGYSPSEADDLRRSMAAWKRKGGMGPHYERLVLGMTDNGYSREFAESIFKQIE 750 Query: 748 KFAGYGFNKSHAAAYALLSYYTAYLKAHHPAAFMAANLSLAMEDTDKVKILIEDSIDICK 807 F YGF +SHAA++ALL+Y++++LK H P AF+ L+ LI+D+ Sbjct: 751 GFGEYGFPESHAASFALLTYFSSWLKCHEPEAFLCGLLNSQPMGFYSPSQLIQDARRH-G 809 Query: 808 LAILPPDINKSDYRF---MPVGEPGKKATQIRYGLGAVKGAGQNAIEAILEARKSGPFKD 864 + +LP ++ +S + +P + A +R GL ++ A + I +AR PF D Sbjct: 810 VQVLPANVVRSRWESTLELPSSAGARPA--VRLGLSLLRSMPAEAAQRIEQARAQRPFAD 867 Query: 865 LFDFAKR 871 + D A+R Sbjct: 868 VDDLARR 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 0.321 0.138 0.403 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: 3,507,508 Number of extensions: 148682 Number of successful extensions: 381 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 375 Number of HSP's successfully gapped: 2 Length of query: 1152 Length of database: 1,619,870 Length adjustment: 96 Effective length of query: 1056 Effective length of database: 1,165,310 Effective search space: 1230567360 Effective search space used: 1230567360 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)