RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781213|ref|YP_003065626.1| head-to-tail joining protein, putative [Candidatus Liberibacter asiaticus str. psy62] (556 letters) >gnl|CDD|106978 PHA00670, PHA00670, hypothetical protein. Length = 540 Score = 241 bits (617), Expect = 3e-64 Identities = 158/559 (28%), Positives = 253/559 (45%), Gaps = 51/559 (9%) Query: 1 MNQRSAKDIQDRFNYLKNQRGELNYWMEELTGFLYPYKNNAQLR---MWDTTGSEACIKL 57 + +R + +R + + +Y M + F +N + R ++D+TG++A L Sbjct: 6 LLKRLGQLKTERQSVESHWDEISDYIMPRRSRFFSDDRNRGENRNRKIFDSTGTDALRTL 65 Query: 58 SSLLSSLITPPGQKWHGLAESFSAYQAFLYKEDARSKKVREWCDQVTDTLFGFRERSRSG 117 SS + S IT P + W LA E +V+ W + VT ++ +S Sbjct: 66 SSGMMSGITSPARPWFRLA--------TRDPELNEDAEVKAWLENVTRDMYSAF--QKSN 115 Query: 118 FVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRYISVPLSNVYMSVNHQNVVDSVYR 177 F L Y S+ FGT +E D DE + + S P+ + Y + +++ VD+ YR Sbjct: 116 FYLELNETYISLGGFGTAAMVVEEDEDE-----VVVFQSSPIGDYYFAEDNRGQVDTFYR 170 Query: 178 EFTFTVDQIVSKWGDKVLSSKMKSALARNENERF-TIIHAVYPKSLTDKKK-DKGNKGFH 235 +F +TV Q+V ++GD+ S ++S NE + ++HAV P++ D K D N F Sbjct: 171 QFRWTVAQMVQEFGDENTSESVQSKAEEGSNEAWVEVVHAVEPRADRDPSKLDPRNMPFK 230 Query: 236 SKFVSV--DENRFFEEKQIATFPYIVGRYRVRADEIYGRSPAMEALPTIRRLNETVNELA 293 S + DE R E FP + R+RV ++YG SPAM AL +R L A Sbjct: 231 SVYFEKGGDEVRLLRESGYREFPALAPRWRVSGGDVYGFSPAMLALGDVRTLQREQKRKA 290 Query: 294 QFGRLSLHPPTIAVSEAKQRNFDLKPGYMNIGALSREGRSLFQPVQFGNPLPYH--EELN 351 Q ++PP +A K ++ L PG + E + N ++ Sbjct: 291 QSIDKVINPPLMAPESGKNQDISLGPGGLTYVDDM-ESNGGIRKAFEVNARFDVLLADIQ 349 Query: 352 RLKESIRSLFLLDLFQVLDDKASRS--AAESMEKTREKGAFVGPLIGGLQSEFIGAMISR 409 +++I ++ +DLFQ+L +K S + A E E+ EK +GP++ L++EF+ +I R Sbjct: 350 DTRQTINRIYYVDLFQMLANKDSPAMTATEVQERYEEKLLMLGPVLERLENEFLSPLIQR 409 Query: 410 ELDILDSQGNLPECEGADNPPVSL----LKVEYTSPLFKYQQAESVASALQGVNTVVELG 465 +I+ LPE PP L L VEYTSPL + Q+A AS + V ++ +L Sbjct: 410 TFNIMVRANKLPE------PPQELQGADLDVEYTSPLAQAQKAIQAASIERWVGSLGQLA 463 Query: 466 VKTGDPSCMDHMDTDRVSRFSLWATNTPAVLIRDTAEVEDIRQQREVQRRVMEEQHLQQQ 525 P +D D DR++ P LI +V+ IR+QR QQ Sbjct: 464 --QIKPEVLDKPDWDRMADMLADMLGVPPTLIVPKEQVQSIRKQR------------AQQ 509 Query: 526 LQQTSQDIGAKAAGRAMEK 544 Q Q A+AA A + Sbjct: 510 QQAAQQAAIAEAAANAAKA 528 >gnl|CDD|152671 pfam12236, Head-tail_con, Bacteriophage head to tail connecting protein. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 516 and 555 amino acids in length. The head-tail connector, a dodecamer of gp10, is embedded within a unique five-fold vertex of the head. The connector serves as the site of assembly of the transient DNA packaging motor that translocates the dsDNA genome into a precursor head shell, or prohead. Length = 480 Score = 223 bits (570), Expect = 1e-58 Identities = 130/470 (27%), Positives = 202/470 (42%), Gaps = 42/470 (8%) Query: 44 RMWDTTGSEACIKLSSLLSSLITPPGQKWHGLAESFSAYQAFLYKEDARSKKVREWCDQV 103 ++D+TG+ A L++ L S +TPPG+ W L + +V+ W D V Sbjct: 42 NIFDSTGARALRNLAAKLMSGLTPPGRPWFRL----ELRDDEDNEAAD---EVKAWLDAV 94 Query: 104 TDTLFGFRERSRSGFVGCLQSFYTSVVEFGTGCFYMEADVDEKGLEEGIRYISVPLSNVY 163 L E S F L + ++ G Y+E D + IR+ +VPL + Sbjct: 95 ERRLMSVLEAS--NFYVALHEAFKDLLVAGNALLYIEEDR-----KGVIRFEAVPLGSYV 147 Query: 164 M-SVNHQNVVDSVYREFTFTVDQIVSKWGDKVLSSKMKSALARNE--NERFTIIHAVYPK 220 + + NVVD V+R F+ TV QIV ++G LS +++ AL E ++ I HAV P+ Sbjct: 148 VARDANGNVVDIVFRRFSLTVRQIVQRFGLDALSEEIRKALEDGEKPEDKVEIYHAVEPR 207 Query: 221 SLTDKKKDKGNKGFHSKFVSVDENRFFEEK-QIATFPYIVGRYRVRADEIYGRSPAMEAL 279 + K F S ++ + FPY+V R+ E YGRSP +AL Sbjct: 208 ADDAKNMP-----FASYQEDAGKDVGVLSESGYDEFPYLVPRWEKIDGEAYGRSPVEDAL 262 Query: 280 PTIRRLNETVNELAQFGRLSLHPPTIAVSEAKQRNFDLKPGYMNIGALSREGRSLFQPVQ 339 P ++ LN+ L + + PP + + DL PG G +P++ Sbjct: 263 PDVKSLNKLSEALLKAAAKASKPPWLVPPSGVTQPRDLVPGGTGYVVTGVAGDIGIKPLE 322 Query: 340 FGNPLPY-HEELNRLKESIRSLFLLDLFQVLDDKASRSAAESMEKTREKGAFVGPLIGGL 398 + +++ IR F++DLFQ+ D +A E E+ EK +GP+ L Sbjct: 323 KYADFQVAQAVIQDIRQRIREAFMVDLFQMR-DAERVTATEVRERAEEKEQLLGPVYSRL 381 Query: 399 QSEFIGAMISRELDILDSQGNLPECEGADNPPVSL---LKVEYTSPL---FKYQQAESVA 452 Q EF+ +I R +IL G LP PP L +KVEY + L + S+ Sbjct: 382 QEEFLSPLIERTFNILQRAGMLPP------PPDELGVAVKVEYVTGLAAAQRAIDLASLE 435 Query: 453 SALQGVNTVVELGVKTGDPSCMDHMDTDRVSRFSLWATNTPAVLIRDTAE 502 LQ + + +L P +D +D D A PA L+R E Sbjct: 436 RFLQAIGQLAQL-----KPEVLDKIDWDEAVDRLADALGVPAGLLRSEEE 480 >gnl|CDD|132370 TIGR03327, AMP_phos, AMP phosphorylase. This enzyme family is found, so far, strictly in the Archaea, and only in those with a type III Rubisco enzyme. Most of the members previously were annotated as thymidine phosphorylase, or DeoA. The AMP metabolized by this enzyme may be produced by ADP-dependent sugar kinases. Length = 500 Score = 33.9 bits (78), Expect = 0.12 Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 15/94 (15%) Query: 140 EADVDEKGLEEGIRYISVPLSNVYMSVNHQNVVDSVYREFTFTVDQIVSKWGDKVLSSKM 199 E D E G+ G R V + ++VV V + D +V K G+ LS ++ Sbjct: 20 EEDAKELGVHPGDR--------VRIESGGKSVVGIVD-----STDTLVEK-GEIGLSHEV 65 Query: 200 KSALARNENERFTIIHAVYPKSLTD-KKKDKGNK 232 L +E E + A P+S+ KKK G K Sbjct: 66 LEELGISEGEVVEVTPAEKPESVEYIKKKMDGEK 99 >gnl|CDD|152472 pfam12037, DUF3523, Domain of unknown function (DUF3523). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with pfam00004. This domain has a conserved LER sequence motif. Length = 272 Score = 30.1 bits (68), Expect = 1.4 Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 3/46 (6%) Query: 501 AEVEDIRQQREVQRRVMEEQHLQQQLQQTSQDIGAKAAGRAMEKKL 546 A++E R + E +R+ ++EQ QQ QQ +Q + A + + +L Sbjct: 78 AKLERQRVEAEERRKTLQEQ--TQQEQQRAQ-YKDELARKRYQTEL 120 >gnl|CDD|179798 PRK04239, PRK04239, hypothetical protein; Provisional. Length = 110 Score = 29.5 bits (67), Expect = 2.3 Identities = 10/37 (27%), Positives = 24/37 (64%), Gaps = 2/37 (5%) Query: 502 EVEDIRQQR--EVQRRVMEEQHLQQQLQQTSQDIGAK 536 E+E+IR+++ E+Q++ E+Q Q++ ++ A+ Sbjct: 2 ELEEIRRRKLEELQKQAQEQQQAQEEQEEAQAQAEAQ 38 >gnl|CDD|163014 TIGR02778, ligD_pol, DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain. Length = 245 Score = 29.2 bits (66), Expect = 2.7 Identities = 23/85 (27%), Positives = 30/85 (35%), Gaps = 15/85 (17%) Query: 241 VDENRFFEEKQIATF--PYIVGRYRVRADEIYGRSPAMEALPTIRRLNETVNELAQFGRL 298 + FF+ K + P++V +E G E I E + L Q G L Sbjct: 50 IGGECFFQ-KHLPQGAPPFVV---SAEVEESDG-----ETYLVINDA-EGLLWLVQQGAL 99 Query: 299 SLHPP--TIAVSEAKQR-NFDLKPG 320 H I E R FDL PG Sbjct: 100 EFHIWGARIDAPEKPDRIVFDLDPG 124 >gnl|CDD|178622 PLN03073, PLN03073, ABC transporter F family; Provisional. Length = 718 Score = 29.1 bits (65), Expect = 3.0 Identities = 14/48 (29%), Positives = 25/48 (52%) Query: 475 DHMDTDRVSRFSLWATNTPAVLIRDTAEVEDIRQQREVQRRVMEEQHL 522 D MD V++ + P + RD A++E +++ E QR V + H+ Sbjct: 102 DGMDDSEVAKKKPEPDDGPLLSERDLAKIERRKRKEERQREVQYQAHV 149 >gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed. Length = 333 Score = 28.2 bits (63), Expect = 5.0 Identities = 11/28 (39%), Positives = 18/28 (64%) Query: 475 DHMDTDRVSRFSLWATNTPAVLIRDTAE 502 D++D + +R ++ TNTP VL TA+ Sbjct: 79 DNIDVEEATRRGIYVTNTPGVLTEATAD 106 >gnl|CDD|184965 PRK15003, PRK15003, cytochrome d ubiquinol oxidase subunit 2; Provisional. Length = 379 Score = 27.6 bits (61), Expect = 8.5 Identities = 9/28 (32%), Positives = 17/28 (60%) Query: 40 NAQLRMWDTTGSEACIKLSSLLSSLITP 67 NA L MWD T S+ + + + ++ ++ P Sbjct: 322 NASLTMWDATSSQLTLNVMTWVAVVLVP 349 >gnl|CDD|161832 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR family. Members of this family are assumed to differ from each other in DNA site specificity. Length = 667 Score = 27.8 bits (62), Expect = 8.5 Identities = 9/37 (24%), Positives = 18/37 (48%) Query: 305 IAVSEAKQRNFDLKPGYMNIGALSREGRSLFQPVQFG 341 + + E K+R+ ++ + I +E LF+ VQ Sbjct: 132 LVIIELKKRSVTIREAFNQIKRYEKEIPELFKYVQIF 168 >gnl|CDD|115219 pfam06548, Kinesin-related, Kinesin-related. This family represents a region within kinesin-related proteins from higher plants. Many family members also contain the pfam00225 domain. Kinesins are ATP-driven microtubule motor proteins that produce directed force. Some family members are associated with the phragmoplast, a structure composed mainly of microtubules that executes cytokinesis in higher plants. Length = 469 Score = 27.5 bits (61), Expect = 9.7 Identities = 15/41 (36%), Positives = 29/41 (70%), Gaps = 4/41 (9%) Query: 501 AEVEDIRQQREVQRRVMEEQH--LQQQLQQTSQDIGAKAAG 539 AE+ +R +RE +RR +++++ LQ QL+ T++ + +AAG Sbjct: 373 AELSALRVEREKERRYLKDENKSLQIQLRDTAEAV--QAAG 411 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.317 0.133 0.384 Gapped Lambda K H 0.267 0.0693 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 8,975,582 Number of extensions: 583053 Number of successful extensions: 1229 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1211 Number of HSP's successfully gapped: 21 Length of query: 556 Length of database: 5,994,473 Length adjustment: 98 Effective length of query: 458 Effective length of database: 3,876,889 Effective search space: 1775615162 Effective search space used: 1775615162 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 (21.7 bits) S2: 60 (27.0 bits)