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= 0012.0020.p (1135 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... 2328 0.0 gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alph... 312 1e-85 >gi|300312866|ref|YP_003776958.1| DNA polymerase III subunit alpha [Herbaspirillum seropedicae SmR1] Length = 1152 Score = 2328 bits (6032), Expect = 0.0, Method: Compositional matrix adjust. Identities = 1134/1135 (99%), Positives = 1135/1135 (100%) Query: 1 VDGLVRIDDIVKAAAKDGQAALAVTDLANLFCMVRFYKEARGKGVKPIAGCDLWITNDAD 60 VDGLVRIDDIVKAAAKDGQAALAVTDLANLFCMVRFYKEARGKGVKPIAGCDLWITNDAD Sbjct: 18 VDGLVRIDDIVKAAAKDGQAALAVTDLANLFCMVRFYKEARGKGVKPIAGCDLWITNDAD 77 Query: 61 REKPFRLLVLIKNRHGYLQLCEVLSQAWLNNQYKGRAEVRMEWLDALRHQEGGNGLIALS 120 REKPFRLLVLIKNRHGYLQLCEVLSQAWLNNQYKGRAEVRMEWLDALRHQEGGNGLIALS Sbjct: 78 REKPFRLLVLIKNRHGYLQLCEVLSQAWLNNQYKGRAEVRMEWLDALRHQEGGNGLIALS 137 Query: 121 GAAMGDIGQAIDNGNLAQAEACARRWAEIFPGAFYLELQRAGQANMEVQVRQSVALGAKL 180 GAAMGDIGQAIDNGNLAQAEACARRWAEIFPGAFYLELQRAGQANMEVQVRQSVALGAKL Sbjct: 138 GAAMGDIGQAIDNGNLAQAEACARRWAEIFPGAFYLELQRAGQANMEVQVRQSVALGAKL 197 Query: 181 GLPCVATHPIQFQSPEEFIAHEARTCIAEGEIMANARRVRRFNEQQYFKSQAEMVELFAD 240 GLPCVATHPIQFQSPEEFIAHEARTCIAEGEIMANARRVRRFNEQQYFKSQAEMVELFAD Sbjct: 198 GLPCVATHPIQFQSPEEFIAHEARTCIAEGEIMANARRVRRFNEQQYFKSQAEMVELFAD 257 Query: 241 LPGAVANTVEIAKRCNLVLQLGKPQLPDFPTPDGMTIDDFLVAQTKAGLEVRLKELFPNE 300 LPGAVANTVEIAKRCNLVLQLGKPQLPDFPTPDGMTIDDFLVAQTKAGLEVRLKELFPNE Sbjct: 258 LPGAVANTVEIAKRCNLVLQLGKPQLPDFPTPDGMTIDDFLVAQTKAGLEVRLKELFPNE 317 Query: 301 AEREKQRPRYEARLEFENNTIIKMKFPGYFLIVADFIQWAKNNGVPVGPGRGSGAGSLVA 360 AEREKQRPRYEARLEFENNTIIKMKFPGYFLIVADFIQWAKNNGVPVGPGRGSGAGSLVA Sbjct: 318 AEREKQRPRYEARLEFENNTIIKMKFPGYFLIVADFIQWAKNNGVPVGPGRGSGAGSLVA 377 Query: 361 YCLLITDLDPLRYNLLFERFLNPERVSMPDFDIDFCQEGRDRVIQYVKDRYGKEAVSQIA 420 YCLLITDLDPLRYNLLFERFLNPERVSMPDFDIDFCQEGRDRVIQYVKDRYGKEAVSQIA Sbjct: 378 YCLLITDLDPLRYNLLFERFLNPERVSMPDFDIDFCQEGRDRVIQYVKDRYGKEAVSQIA 437 Query: 421 TFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLADAIEEEPLLKERLENEE 480 TFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLADAIEEEPLLKERLENEE Sbjct: 438 TFGTMAAKGAVRDVGRVLDLGYNFCDGISKLIPFKPGKLVTLADAIEEEPLLKERLENEE 497 Query: 481 EVKQLMGLAQQVEGIARNIGMHAGGVLIAPGKLTDFCPLYTQGGDSGVVSQYDKDDVEAV 540 EVKQLMGLAQQVEGIARNIGMHAGGVLIAPGKLTDFCPLYTQGGDSGVVSQYDKDDVEAV Sbjct: 498 EVKQLMGLAQQVEGIARNIGMHAGGVLIAPGKLTDFCPLYTQGGDSGVVSQYDKDDVEAV 557 Query: 541 GLVKFDFLGLTTLTILDRAVRYIRMLDPAMADFDLAKLPLDDRPSYELLTKAKTVAVFQL 600 GLVKFDFLGLTTLTILDRAVRYIRMLDPAMADFDLAKLPLDDRPSYELLTKAKTVAVFQL Sbjct: 558 GLVKFDFLGLTTLTILDRAVRYIRMLDPAMADFDLAKLPLDDRPSYELLTKAKTVAVFQL 617 Query: 601 ESRGMQGMLKDARPDRFEDIIALVALYRPGPMDLIPDFCKRKHGEAFDYPDPRTEGILSE 660 ESRGMQGMLKDARPDRFEDIIALVALYRPGPMDLIPDFCKRKHGEAFDYPDPRTEGILSE Sbjct: 618 ESRGMQGMLKDARPDRFEDIIALVALYRPGPMDLIPDFCKRKHGEAFDYPDPRTEGILSE 677 Query: 661 TYGIMVYQEQVMQMAQVIGGYSLGGADLLRRAMGKKKAEEMAKHRELFREGAAKNGLDQA 720 TYGIMVYQEQVMQMAQVIGGYSLGGADLLRRAMGKKKAEEMAKHRELFREGAAKNGLDQA Sbjct: 678 TYGIMVYQEQVMQMAQVIGGYSLGGADLLRRAMGKKKAEEMAKHRELFREGAAKNGLDQA 737 Query: 721 KADEIFDLMEKFAGYGFNKSHAAAYALLSYYTAYLKAHHPAAFMAANLSLAMEDTDKVKI 780 KADEIFDLMEKFAGYGFNKSHAAAYALLSYYTAYLKAHHPAAFMAANLSLAMEDTDKVKI Sbjct: 738 KADEIFDLMEKFAGYGFNKSHAAAYALLSYYTAYLKAHHPAAFMAANLSLAMEDTDKVKI 797 Query: 781 LIEDAIDICKLAILPPDINKSDYRFMPVGEPGKKATQIRYGLGAVKGAGQNAIEAILEAR 840 LIEDAIDICKLAILPPDINKSDYRFMPVGEPGKKATQIRYGLGAVKGAGQNAIEAILEAR Sbjct: 798 LIEDAIDICKLAILPPDINKSDYRFMPVGEPGKKATQIRYGLGAVKGAGQNAIEAILEAR 857 Query: 841 KSGPFKDLFDFAKRVDKKQINRRTIDSLIRAGAFDCFKVDRAVLQASVNLAWESAEQAEK 900 KSGPFKDLFDFAKRVDKKQINRRTIDSLIRAGAFDCFKVDRAVLQASVNLAWESAEQAEK Sbjct: 858 KSGPFKDLFDFAKRVDKKQINRRTIDSLIRAGAFDCFKVDRAVLQASVNLAWESAEQAEK 917 Query: 901 SANQVSLFGGDDSDLEAPLEYVQVPPWSDKQRLTEEKGALGFYLSGHLFSAYEKEVRRFV 960 SANQVSLFGGDDSDLEAPLEYVQVPPWSDKQRLTEEKGALGFYLSGHLFSAYEKEVRRFV Sbjct: 918 SANQVSLFGGDDSDLEAPLEYVQVPPWSDKQRLTEEKGALGFYLSGHLFSAYEKEVRRFV 977 Query: 961 RTKIASLEPSWEPRSLAGIITGVRVQMTQRGKLVICTLDDGTGVIEATIYNELFEPFKHI 1020 RTKIASLEPSWEPRSLAGIITGVRVQMTQRGKLVICTLDDGTGVIEATIYNELFEPFKH+ Sbjct: 978 RTKIASLEPSWEPRSLAGIITGVRVQMTQRGKLVICTLDDGTGVIEATIYNELFEPFKHL 1037 Query: 1021 IKEDELLVVSGKVSEDRFNGGLRVAADKVMDLGAARIQYGVRMVVSINKAIDPNHLRDTL 1080 IKEDELLVVSGKVSEDRFNGGLRVAADKVMDLGAARIQYGVRMVVSINKAIDPNHLRDTL Sbjct: 1038 IKEDELLVVSGKVSEDRFNGGLRVAADKVMDLGAARIQYGVRMVVSINKAIDPNHLRDTL 1097 Query: 1081 SAHRQEQGLPFVMRYQQADAACEVVLGDAWRINPSDSLQSTLVASFGKEAVVVEY 1135 SAHRQEQGLPFVMRYQQADAACEVVLGDAWRINPSDSLQSTLVASFGKEAVVVEY Sbjct: 1098 SAHRQEQGLPFVMRYQQADAACEVVLGDAWRINPSDSLQSTLVASFGKEAVVVEY 1152 >gi|300311573|ref|YP_003775665.1| DNA polymerase III subunit alpha [Herbaspirillum seropedicae SmR1] Length = 942 Score = 312 bits (799), Expect = 1e-85, Method: Compositional matrix adjust. Identities = 223/732 (30%), Positives = 358/732 (48%), Gaps = 48/732 (6%) Query: 145 RW-AEIFPGAFYLELQRAGQANMEVQVRQSVALGAKLGLPCVATHPIQFQSPEEFIAHEA 203 RW A + PG ++ + R + ++ A + GLP A +Q + Sbjct: 169 RWFAPLAPGRSWVGITRLYRPLDDLHRAALEAATRRHGLPLAAVGDVQMHQRSRKYLQDV 228 Query: 204 RTCIAEGEIMANARRVRRFNEQQYFKSQAEMVELFADLPGAVANTVEIAKRCNLVLQLGK 263 T I G+ + N +Q+ +S+ + P +A T+ IA C L + Sbjct: 229 VTAIRLGQPVQECGHALAPNAEQHLRSRVRLG--MVHTPATLAQTLAIAADCRFSLAELR 286 Query: 264 PQLPDFPTPDGMTIDDFLVAQTKAGLEVRLKELFPNEAEREKQRPRYEARLEFENNTIIK 323 + PD P GM+ D+L QT AG R + P + +E E I + Sbjct: 287 YEYPDELVPLGMSAADYLRQQTLAGAAKRYPQGLPGGVREQ---------IEAELALIAQ 337 Query: 324 MKFPGYFLIVADFIQWAKNNGVPVGPGRGSGAGSLVAYCLLITDLDPLRYNLLFERFLNP 383 ++ YFL V D +Q+A++ G+ + GRGS A S V YCL +T++DP LLF RF++ Sbjct: 338 KEYEAYFLTVYDLVQFARSRGI-LCQGRGSAANSAVCYCLGVTEVDPTSTRLLFARFISE 396 Query: 384 ERVSMPDFDIDFCQEGRDRVIQYVKDRYGKEAVSQIATFGTMAAKGAVRDVGRVLDLGYN 443 +R PD D+DF + R+ VIQ++ +YG+ + A + +GA+R+VG+ L + Sbjct: 397 KREEPPDIDVDFEHQRREEVIQHIYRKYGRRRAALAAAVHSYRPRGALREVGKALGVDAA 456 Query: 444 FCDGISKLIPFKPGKLVTLADAIEEEPLLKERLEN--EEEVKQLMGLAQQVEG----IAR 497 D ++K + D+ EE LL E + E+ Q+ GL + G R Sbjct: 457 IVDAVAKSQHW--------FDSREE--LLARFAEAGLDPELPQI-GLWASITGKLLRFPR 505 Query: 498 NIGMHAGGVLIAPGKLTDFCPLYTQGGDSGVVSQYDKDDVEAVGLVKFDFLGLTTLTILD 557 ++ H GG +IA G+L+ P+ V ++DKDD+E++ L+K D L L LT L Sbjct: 506 HLSQHTGGFVIARGQLSRLVPIQNAAMPERCVIEWDKDDLESLKLLKVDVLALGMLTALR 565 Query: 558 RAVRYIRMLDPAMADFDLAKLPLDDRPSYELLTKAKTVAVFQLESRGMQGMLKDARPDRF 617 R + + + + +P +D ++E++ KA T+ VFQ+ESR ML +P Sbjct: 566 RTLELVSLRRGLPEVMQMHAIPREDPATFEMICKADTIGVFQIESRAQMSMLPRMQPRTQ 625 Query: 618 EDIIALVALYRPGPMD--LIPDFCKR----KHGEAFDYPDPRTEG-----ILSETYGIMV 666 D++ VA+ RPGP+ ++ + +R + G +FDYPD ++ +L T GI + Sbjct: 626 YDLVVQVAIVRPGPIQGGMVHPYLRRRELVREGGSFDYPDNTSKSGKIKKVLERTLGIPI 685 Query: 667 YQEQVMQMAQVIGGYSLGGADLLRRAMGK-KKAEEMAKHRELFREGAAKNGLDQAKADEI 725 +QEQVM +A GYS AD LRR+M K+ M H E G NG + A+ I Sbjct: 686 FQEQVMDVAIEAAGYSPSEADDLRRSMAAWKRKGGMGPHYERLVLGMTDNGYSREFAESI 745 Query: 726 FDLMEKFAGYGFNKSHAAAYALLSYYTAYLKAHHPAAFMAANLSLAMEDTDKVKILIEDA 785 F +E F YGF +SHAA++ALL+Y++++LK H P AF+ L+ LI+DA Sbjct: 746 FKQIEGFGEYGFPESHAASFALLTYFSSWLKCHEPEAFLCGLLNSQPMGFYSPSQLIQDA 805 Query: 786 IDICKLAILPPDINKSDYRF---MPVGEPGKKATQIRYGLGAVKGAGQNAIEAILEARKS 842 + +LP ++ +S + +P + A +R GL ++ A + I +AR Sbjct: 806 RRH-GVQVLPANVVRSRWESTLELPSSAGARPA--VRLGLSLLRSMPAEAAQRIEQARAQ 862 Query: 843 GPFKDLFDFAKR 854 PF D+ D A+R Sbjct: 863 RPFADVDDLARR 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: 3,448,577 Number of extensions: 146921 Number of successful extensions: 369 Number of sequences better than 1.0e-08: 2 Number of HSP's gapped: 364 Number of HSP's successfully gapped: 2 Length of query: 1135 Length of database: 1,619,870 Length adjustment: 96 Effective length of query: 1039 Effective length of database: 1,165,310 Effective search space: 1210757090 Effective search space used: 1210757090 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)