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= 0016.0006.p (338 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B0YJD7.1 B0YJD7_PAEPO tRNA-dihydrouridine synthase 593 e-167 B3K915.1 B3K915_9BACI TIM-barrel protein, nifR3 family 569 e-160 B1DIC9.1 B1DIC9_9BACL TIM-barrel protein, nifR3 family 558 e-157 Q9KGG5.1 Q9KGG5_BACHD Transcriptional regulator involved in nitr... 499 e-139 Q5WLU6.1 Q5WLU6_BACSK tRNA-dihydrouridine synthase 496 e-138 >B0YJD7.1 B0YJD7_PAEPO tRNA-dihydrouridine synthase Length = 342 Score = 593 bits (1528), Expect = e-167, Method: Compositional matrix adjust. Identities = 284/337 (84%), Positives = 311/337 (92%), Gaps = 3/337 (0%) Query: 1 MLKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTREMLF 60 MLKIG IEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAI+HGN RTREMLF Sbjct: 1 MLKIGDIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAIIHGNKRTREMLF 60 Query: 61 VDEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNP 120 VDEREKPLSLQIFGGDRKSLVEAAKVV++ETNADIIDINMGCPVPKVTKCDAGARWLL+P Sbjct: 61 VDEREKPLSLQIFGGDRKSLVEAAKVVNQETNADIIDINMGCPVPKVTKCDAGARWLLDP 120 Query: 121 DKIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYT 180 +KIYEMVSAVV++V KPVTVKMRIGWDSEHI+ +NARAVERAGGQAVSVHGRTREQLYT Sbjct: 121 NKIYEMVSAVVESVSKPVTVKMRIGWDSEHIYAVENARAVERAGGQAVSVHGRTREQLYT 180 Query: 181 GHADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTI 240 GHA+W I+ KEAVSIPVIGNGDV +PEDAR MLD T CDGVMIGRGALGNPWMLYRTI Sbjct: 181 GHANWDIIKEVKEAVSIPVIGNGDVASPEDARRMLDLTNCDGVMIGRGALGNPWMLYRTI 240 Query: 241 QYLNTGELMPEPGPEEKIKVAILHMDRLISLKGEAVAVREMRKHMAWYLKGMKAAARVKD 300 +YL TGEL+P+P PEEKI++AILHMDRL++LKGEAVAVREMRKH+AWYLKG K +AR+KD Sbjct: 241 EYLQTGELLPDPSPEEKIRIAILHMDRLVALKGEAVAVREMRKHLAWYLKGFKGSARIKD 300 Query: 301 VIMEETKRDEMVRILNQFVTQLKEEEEQEGLNPSLTA 337 VIMEETKRD+MVRIL+QFV+QL + E PS +A Sbjct: 301 VIMEETKRDDMVRILDQFVSQLHMVDNDE---PSTSA 334 >B3K915.1 B3K915_9BACI TIM-barrel protein, nifR3 family Length = 343 Score = 569 bits (1467), Expect = e-160, Method: Compositional matrix adjust. Identities = 266/327 (81%), Positives = 300/327 (91%) Query: 2 LKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTREMLFV 61 LKIG +EMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVS KAI+HGN RT+EMLFV Sbjct: 4 LKIGNVEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSGKAIVHGNKRTQEMLFV 63 Query: 62 DEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNPD 121 DEREKPLSLQIFGGDR SLVEAAKVVD++TNADIIDINMGCP PKVTK DAGARWLL+ + Sbjct: 64 DEREKPLSLQIFGGDRVSLVEAAKVVDQQTNADIIDINMGCPAPKVTKMDAGARWLLDSN 123 Query: 122 KIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYTG 181 KIYEMV+AVVDAV+KPVTVKMR GWDS+HI+ +NA+AVERAGGQAVSVHGRTR+QLYTG Sbjct: 124 KIYEMVAAVVDAVNKPVTVKMRTGWDSDHIYAVENAQAVERAGGQAVSVHGRTRDQLYTG 183 Query: 182 HADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTIQ 241 HADW IR KEAVSIPVIGNGDV TPEDAR MLD TGCDGVMIGRGALGNPWMLYRT++ Sbjct: 184 HADWDIIRQVKEAVSIPVIGNGDVVTPEDARRMLDTTGCDGVMIGRGALGNPWMLYRTVE 243 Query: 242 YLNTGELMPEPGPEEKIKVAILHMDRLISLKGEAVAVREMRKHMAWYLKGMKAAARVKDV 301 YL TG+L+ +P P+EKI++AILHMDRLI+L+GEAVAVREMRKH++WYLKG+K +AR+KD+ Sbjct: 244 YLKTGQLLSDPSPQEKIRIAILHMDRLIALRGEAVAVREMRKHLSWYLKGLKGSARIKDI 303 Query: 302 IMEETKRDEMVRILNQFVTQLKEEEEQ 328 IMEETKRDE+V +LN FV L++ EE Sbjct: 304 IMEETKRDELVSLLNNFVNNLEDHEES 330 >B1DIC9.1 B1DIC9_9BACL TIM-barrel protein, nifR3 family Length = 338 Score = 558 bits (1438), Expect = e-157, Method: Compositional matrix adjust. Identities = 266/325 (81%), Positives = 293/325 (90%) Query: 1 MLKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTREMLF 60 MLKIG IEMKN+VVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGN RT EMLF Sbjct: 1 MLKIGDIEMKNKVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNKRTMEMLF 60 Query: 61 VDEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNP 120 VDEREKPLSLQIFGGDR+SLVEAAKVVD++TNADIIDINMGCPVPKVTKCDAGARWLL+P Sbjct: 61 VDEREKPLSLQIFGGDRESLVEAAKVVDQQTNADIIDINMGCPVPKVTKCDAGARWLLDP 120 Query: 121 DKIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYT 180 +KIYEMVSAV AV KPVTVKMRIGWD EHI+ DNA+AVE AGG+AVSVHGRTREQ YT Sbjct: 121 NKIYEMVSAVTAAVSKPVTVKMRIGWDDEHIYAVDNAKAVESAGGKAVSVHGRTREQQYT 180 Query: 181 GHADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTI 240 G A+W IR K+AVSIPVIGNGDV +PEDAR MLD TGCDGVMIGRGALGNPWMLYRTI Sbjct: 181 GKANWDIIRDVKQAVSIPVIGNGDVFSPEDARRMLDHTGCDGVMIGRGALGNPWMLYRTI 240 Query: 241 QYLNTGELMPEPGPEEKIKVAILHMDRLISLKGEAVAVREMRKHMAWYLKGMKAAARVKD 300 QYL +GEL+P+P P EK++VAILHMDRL++L+GEA AVREMRKHMAWYLKG+ AARVKD Sbjct: 241 QYLESGELLPDPLPREKLEVAILHMDRLVALRGEAAAVREMRKHMAWYLKGLPGAARVKD 300 Query: 301 VIMEETKRDEMVRILNQFVTQLKEE 325 VIMEET RD++V ++ ++ L EE Sbjct: 301 VIMEETGRDKLVEVMENYIASLDEE 325 >Q9KGG5.1 Q9KGG5_BACHD Transcriptional regulator involved in nitrogen regulation (NifR3/Smm1 family) Length = 334 Score = 499 bits (1285), Expect = e-139, Method: Compositional matrix adjust. Identities = 235/323 (72%), Positives = 274/323 (84%) Query: 1 MLKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTREMLF 60 MLKIG IEMKNQVVLAPMAGVCNPAFRLIAKEFG GLVCAEMVSDKAILH N ++ ML+ Sbjct: 1 MLKIGPIEMKNQVVLAPMAGVCNPAFRLIAKEFGAGLVCAEMVSDKAILHKNEKSLSMLY 60 Query: 61 VDEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNP 120 VDEREKPLSLQIFGG++++LVEAAK VDK TNADIIDINMGCPVPK+TKCDAGARWLL+P Sbjct: 61 VDEREKPLSLQIFGGEKETLVEAAKFVDKNTNADIIDINMGCPVPKITKCDAGARWLLDP 120 Query: 121 DKIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYT 180 +KIY+MVSAVVD VDKPVTVKMRIGWD EHI+ +NA+AVERAGG AV+VHGRTR Q+Y Sbjct: 121 NKIYDMVSAVVDEVDKPVTVKMRIGWDEEHIYAVENAQAVERAGGAAVAVHGRTRVQMYE 180 Query: 181 GHADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTI 240 G ADW IR K+AV IPVIGNGDV TP+DA+ MLD+ G DGVMIGR ALGNPWMLYRTI Sbjct: 181 GTADWNIIREVKQAVGIPVIGNGDVKTPQDAKRMLDEIGVDGVMIGRAALGNPWMLYRTI 240 Query: 241 QYLNTGELMPEPGPEEKIKVAILHMDRLISLKGEAVAVREMRKHMAWYLKGMKAAARVKD 300 YL TGEL+P+P P EK+ V ++H+DRLI LKGE VAVREMRKH AWYLKG++ +++D Sbjct: 241 HYLETGELLPDPTPREKMDVCMIHLDRLIKLKGENVAVREMRKHAAWYLKGLRGNGKIRD 300 Query: 301 VIMEETKRDEMVRILNQFVTQLK 323 I + R+++ L ++ +L+ Sbjct: 301 QINQFETREDVSSTLYAYIEELE 323 >Q5WLU6.1 Q5WLU6_BACSK tRNA-dihydrouridine synthase Length = 333 Score = 496 bits (1277), Expect = e-138, Method: Compositional matrix adjust. Identities = 236/329 (71%), Positives = 278/329 (84%) Query: 1 MLKIGGIEMKNQVVLAPMAGVCNPAFRLIAKEFGTGLVCAEMVSDKAILHGNLRTREMLF 60 MLKIG IEMKNQVVLAPMAGVCNPAFRLIAKEFG GLVCAEMVSDKAILH N ++ +ML+ Sbjct: 1 MLKIGDIEMKNQVVLAPMAGVCNPAFRLIAKEFGAGLVCAEMVSDKAILHKNEKSLQMLY 60 Query: 61 VDEREKPLSLQIFGGDRKSLVEAAKVVDKETNADIIDINMGCPVPKVTKCDAGARWLLNP 120 VDEREKPLSLQIFGG++ +LVEAA+ VD+ TNADIIDINMGCPVPK+TKCDAGARWLL+P Sbjct: 61 VDEREKPLSLQIFGGEKDTLVEAARFVDQNTNADIIDINMGCPVPKITKCDAGARWLLDP 120 Query: 121 DKIYEMVSAVVDAVDKPVTVKMRIGWDSEHIFVEDNARAVERAGGQAVSVHGRTREQLYT 180 KIYEMV+AVVDAV KPVTVKMRIGWD +HI+ +NARAVERAGG AV+VHGRTR Q+Y Sbjct: 121 KKIYEMVAAVVDAVKKPVTVKMRIGWDEDHIYAIENARAVERAGGSAVAVHGRTRVQMYE 180 Query: 181 GHADWKYIRMAKEAVSIPVIGNGDVNTPEDARAMLDQTGCDGVMIGRGALGNPWMLYRTI 240 G ADW I K+AV+IPVIGNGDV TP+DA+ MLD+ G DGVMIGR ALGNPWMLYRTI Sbjct: 181 GVADWNIIGDVKKAVNIPVIGNGDVATPQDAKRMLDEYGVDGVMIGRAALGNPWMLYRTI 240 Query: 241 QYLNTGELMPEPGPEEKIKVAILHMDRLISLKGEAVAVREMRKHMAWYLKGMKAAARVKD 300 QYL G L PEP P EKI+V ++H+DRL++LKGE VAVREMRKH AWY+KG++ A+++D Sbjct: 241 QYLENGTLPPEPTPREKIEVCLIHLDRLVALKGERVAVREMRKHTAWYIKGLRGKAKIRD 300 Query: 301 VIMEETKRDEMVRILNQFVTQLKEEEEQE 329 + + RD++V+ L ++V L+ E E Sbjct: 301 KVNQFETRDDVVKALYEYVDFLEGRELAE 329 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.319 0.135 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 1,995,187,590 Number of extensions: 83499034 Number of successful extensions: 235573 Number of sequences better than 1.0e-05: 3099 Number of HSP's gapped: 229789 Number of HSP's successfully gapped: 3099 Length of query: 338 Length of database: 3,060,696,203 Length adjustment: 136 Effective length of query: 202 Effective length of database: 1,779,438,163 Effective search space: 359446508926 Effective search space used: 359446508926 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 (21.7 bits) S2: 131 (55.1 bits)