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)