RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780837|ref|YP_003065250.1| putative restriction
endonuclease S subunit [Candidatus Liberibacter asiaticus str. psy62]
(426 letters)
>gnl|CDD|31076 COG0732, HsdS, Restriction endonuclease S subunits [Defense
mechanisms].
Length = 391
Score = 70.5 bits (171), Expect = 9e-13
Identities = 75/407 (18%), Positives = 152/407 (37%), Gaps = 31/407 (7%)
Query: 25 WKVVPIKRFTKLNTGRTS------ESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTV 78
WK + + ++ G+T G DI + ++DV+ ++
Sbjct: 1 WKELKLGDIGEIIRGKTPSTESPLNYGSDIPILTVKDVKGRYSVKGNNGIIGKKLS---- 56
Query: 79 SIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIE 138
+ A L + L + + L L+PK P+ L +LL + ++
Sbjct: 57 YLIAGLGPLGELVRAGLGDVAYVNGKLSINQGCLSLRPKKKEPKSLFLYLLLKLELKLLK 116
Query: 139 AICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEK 198
+ G+T+ + + IP+P+PPL EQ + I +D LI + IELL+
Sbjct: 117 SGAGGSTIPNLSKSSLKEIPIPLPPLEEQ----QAIAKILSTLDDLIELLEKLIELLEAI 172
Query: 199 KQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNT--KLIESNI 256
KQ L + TKG +K +P+ W+V +V ++ L +
Sbjct: 173 KQKLFKELFTKGKYLLNNIKS--------IPEDWKVIKLKDIVEIISGGTKIKPLEKGVN 224
Query: 257 LSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGII 316
+S ++ E N + S I ++I L + ++ A + +
Sbjct: 225 VSYGKNPVLNGGEPNNGDIVKLSRIDNFIYGLKLSGGKYITLSSSGATIGIAIINNGTLK 284
Query: 317 TSAY-----MAVKPHGIDSTYLAWLMRSYDLCKVF-YAMGSGLRQSLKFEDVKRLPVLVP 370
+ ++ +L + + S K+ L + ++ +P+ +P
Sbjct: 285 FILSQGIGILRIENKVEGEKFLYYYLSSEFFKKIIKKVSKGSTIPRLNKKLLEEIPIPIP 344
Query: 371 PIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTG 417
P++EQ I +++ ID+L + + LK++ + +TG
Sbjct: 345 PLEEQQKIAEILSALDKLIDIL-NRKPAELEALKKQLDYLLNKLLTG 390
Score = 42.0 bits (97), Expect = 3e-04
Identities = 49/216 (22%), Positives = 89/216 (41%), Gaps = 10/216 (4%)
Query: 2 KHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTG 61
K +K + I +IP+ WKV+ +K ++ +G T +
Sbjct: 175 KLFKELFTKGKYLLNNIKSIPEDWKVIKLKDIVEIISGGTKIKPLEKGVNVSYGKNPVLN 234
Query: 62 KYLPKDGNSRQSDTSTVSIFAKGQ-----ILYGKLGPYLRKAIIAD--FDGICSTQFLVL 114
P +G+ + I+ I G + AII + I S +L
Sbjct: 235 GGEPNNGDIVKLSRIDNFIYGLKLSGGKYITLSSSGATIGIAIINNGTLKFILSQGIGIL 294
Query: 115 QPKD--VLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIRE 172
+ ++ + L +L S + I+ + +G+T+ + K + IP+PIPPL EQ I E
Sbjct: 295 RIENKVEGEKFLYYYLSSEFFKKIIKKVSKGSTIPRLNKKLLEEIPIPIPPLEEQQKIAE 354
Query: 173 KIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208
+ A ID L + +E LK++ L++ ++T
Sbjct: 355 ILSALDKLIDILNRKPAE-LEALKKQLDYLLNKLLT 389
>gnl|CDD|144860 pfam01420, Methylase_S, Type I restriction modification DNA
specificity domain. This domain is also known as the
target recognition domain (TRD).
Restriction-modification (R-M) systems protect a
bacterial cell against invasion of foreign DNA by
endonucleolytic cleavage of DNA that lacks a site
specific modification. The host genome is protected from
cleavage by methylation of specific nucleotides in the
target sites. In type I systems, both restriction and
modification activities are present in one heteromeric
enzyme complex composed of one DNA specificity subunit
(this family), two modification (M) subunits and two
restriction (R) subunits.
Length = 167
Score = 53.9 bits (130), Expect = 9e-08
Identities = 37/187 (19%), Positives = 67/187 (35%), Gaps = 28/187 (14%)
Query: 22 PKHWKVVPIKRFTKLNTGRT------SESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDT 75
P W+ + ++ G+T E+G YI D+ +G +
Sbjct: 1 PVDWEEFKLGEIFEIKKGKTLSKKELRENG-KYPYITAGDLNNGVIGGVGYIKKK----- 54
Query: 76 STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQ 135
IF IL + D + VL PK+ +L + +
Sbjct: 55 ----IFPGNSILIS-SNGSIGYVFYRDKPFFANQDVKVLIPKNNELLNKFLYLFLKTILK 109
Query: 136 RIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195
+++ + G+ + K + + +P+PPL EQ + IA+ ++ L IEL
Sbjct: 110 KLKKLKFGSGQPKLNKKRLKELKIPLPPLEEQ-----QKIAD--ILEQL----DATIELE 158
Query: 196 KEKKQAL 202
K+K L
Sbjct: 159 KKKLAEL 165
>gnl|CDD|34136 COG4457, SrfB, Uncharacterized protein conserved in bacteria,
putative virulence factor [Function unknown].
Length = 1014
Score = 28.4 bits (63), Expect = 3.7
Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 5/72 (6%)
Query: 105 GICSTQFLVLQ-PKDVLPELLQGWLLSI--DVTQRIEAICEGATMSHADWKGIGNIPMPI 161
+ + QF +L P + L LS D+T +A+CE D + P +
Sbjct: 732 ELPAGQFSILDVPLAIDLSQLHECFLSGDYDITGVFDALCEAINHYDCDVLLLTGRPSRL 791
Query: 162 PPLAEQVLIREK 173
P + Q L R
Sbjct: 792 PGV--QALFRHL 801
>gnl|CDD|38525 KOG3315, KOG3315, KOG3315, Transport protein particle (TRAPP)
complex subunit [Intracellular trafficking, secretion,
and vesicular transport].
Length = 191
Score = 28.4 bits (63), Expect = 4.2
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 12/85 (14%)
Query: 244 LNRKNTKL------IESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFID 297
++ TK+ I S + +G KLE N + TY I+D +V FI
Sbjct: 78 GQKRETKILGILQFIHSTVWKYLFGKEADKLEKAN-----DDDRTYMIIDKEPLVNTFIS 132
Query: 298 LQNDKRSLRSAQVMERGIITSAYMA 322
+ + +L A + GII +
Sbjct: 133 VPKENGTLNCAAFVA-GIIEAVLDN 156
>gnl|CDD|35289 KOG0066, KOG0066, KOG0066, eIF2-interacting protein ABC50 (ABC
superfamily) [Translation, ribosomal structure and
biogenesis].
Length = 807
Score = 28.1 bits (62), Expect = 4.8
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 152 KGIGNIPMPIPPLAEQVLIREKIIA-ETVRIDTLITERIRFIELLKEKKQALVSYIVTKG 210
K I + IPP + +L ++++A T IDT++ + + LL+E+ + L+S I
Sbjct: 308 KHIAARALAIPPNIDVLLCEQEVVADSTSAIDTVLKADKKRLALLEEEAK-LMSQIEEGD 366
Query: 211 LNPDVKMKDSGIE 223
++K+ E
Sbjct: 367 TTAAERLKEVADE 379
>gnl|CDD|38899 KOG3695, KOG3695, KOG3695, Uncharacterized conserved protein
[Function unknown].
Length = 825
Score = 27.3 bits (60), Expect = 8.8
Identities = 21/65 (32%), Positives = 26/65 (40%), Gaps = 9/65 (13%)
Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
AE I I ER F +L AL S + + G +W L+PD W
Sbjct: 225 AENKSIGEYIAERTSFCPVLTTGLSALYS---------SLPREILGDDWHRLLPDDWLEI 275
Query: 236 PFFAL 240
PF AL
Sbjct: 276 PFLAL 280
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.138 0.400
Gapped
Lambda K H
0.267 0.0664 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,203,076
Number of extensions: 278079
Number of successful extensions: 519
Number of sequences better than 10.0: 1
Number of HSP's gapped: 515
Number of HSP's successfully gapped: 10
Length of query: 426
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 330
Effective length of database: 4,189,273
Effective search space: 1382460090
Effective search space used: 1382460090
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: 59 (26.6 bits)