RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780836|ref|YP_003065249.1| putative type I
restriction-modification system DNA methylase [Candidatus Liberibacter
asiaticus str. psy62]
(674 letters)
>gnl|CDD|30634 COG0286, HsdM, Type I restriction-modification system
methyltransferase subunit [Defense mechanisms].
Length = 489
Score = 197 bits (503), Expect = 7e-51
Identities = 128/469 (27%), Positives = 203/469 (43%), Gaps = 48/469 (10%)
Query: 9 ASLANFIWKNAEDLWGDFKHTDFGKVILPFTLLRRLECALEPTRSAVREKYLAFGGSNID 68
L++ +WK A+ L GD + + IL L+ L E A E+
Sbjct: 5 KELSDKLWKIADILRGDIDVSGYKDYILGLLFLKYLSDKFELEFEAELEEDNEAK-YAYP 63
Query: 69 LESFVKVAGYSFYNTSEYSLSTLGSTNTRNNLESYIASFSDNAKAIFEDFDFSSTIARLE 128
+ F Y F + + + LG +N I + + K +F D DF+ +
Sbjct: 64 AKGFFIPERYRFDDLKKNAEENLGDFL--DNALRKIEEKNPDLKGVFADLDFNDALKLGS 121
Query: 129 KAGLLYKICKNFSGIELHPDTVPDRVMSNIYEHLIRRFGSEVSEGAEDFMTPRDVVHLAT 188
LL K+ F I+ + + YE+L+R+F + A +F TPR+V L
Sbjct: 122 LLKLLNKVILKFDEIDGRALD--RDLFGDAYEYLLRKFAEAEGKEAGEFYTPREVSEL-I 178
Query: 189 ALLLDPDDALFKESPGMIRTLYDPTCGTGGFLTDAMNHVADCGSHHKIPPILVPHGQELE 248
LLDP+ ++YDP CG+GG L A ++ I +GQE+
Sbjct: 179 VELLDPEP---------RNSIYDPACGSGGMLLQAAKYLKRHQDEIFI------YGQEIN 223
Query: 249 PETHAVCVAGMLIRRLESDPRRDLSKNIQQGSTLSKDLFTGK----RFHYCLSNPPF-GK 303
T+ + +++ +E D NI+ G TLS K +F + ++NPPF GK
Sbjct: 224 DTTYRLAKMNLILHGIEGD------ANIRHGDTLSNPKHDDKDDKGKFDFVIANPPFSGK 277
Query: 304 KWEKDKDAVEKEHKNGELGRFGPGLPKISDGSMLFLMHLANKLELPPNGGGRAAIVLSSS 363
W D E++ + G F + + FL H+ KL GGRAAIVL
Sbjct: 278 GWGGDLLESEQDERFFFYGVFPTK----NSADLAFLQHILYKL----KPGGRAAIVLPDG 329
Query: 364 PLFNGRAGSGESEIRRWLLENDLIEAIVALPTDLFFRTNIATYLWILSNRKTEERRGKVQ 423
LF G E +IR+ LLE++L+EAI+ LPT LF+ T I T + L+ K ER V
Sbjct: 330 VLF---RGGAEKDIRKDLLEDNLLEAIIGLPTGLFYNTGIPTNILFLTKNKPAERN-DVL 385
Query: 424 LINATDLWTSIRNEGKKRRIINDDQRRQILDIYVSRENG-KFSRMLDYR 471
I+A+ + ++ + ++ +I+D Y + FS+ +
Sbjct: 386 FIDASKEHF---EKPLNKKRLTEENIEKIVDTYREFKEIEGFSKSVSLE 431
>gnl|CDD|111293 pfam02384, N6_Mtase, N-6 DNA Methylase. 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 R-M system is a
complex containing three polypeptides: M (this family),
S (pfam01420), and R. This family consists of N-6
adenine-specific DNA methylase EC:2.1.1.72 from Type I
and Type IC restriction systems. These methylases have
the same sequence specificity as their corresponding
restriction enzymes.
Length = 312
Score = 180 bits (459), Expect = 1e-45
Identities = 98/319 (30%), Positives = 156/319 (48%), Gaps = 39/319 (12%)
Query: 154 VMSNIYEHLIRRFGSEVSEGAEDFMTPRDVVHLATALLLDPDDALFKESPGMIRTLYDPT 213
+ + YE+L+ +F +E + +F TPR+V L LL+P ++YDP
Sbjct: 5 LFGDAYEYLLGKFANEEGKSGGEFYTPREVSKL-IVELLEPKPG---------ESIYDPA 54
Query: 214 CGTGGFLTDAMNHVADCGSHHKIPPILVPHGQELEPETHAVCVAGMLIRRLESDPRRDLS 273
CG+GGFL A V SH + +GQEL P T+ + M++ +E +
Sbjct: 55 CGSGGFLIQADKFV---KSHDGDTNDISIYGQELNPTTYRLARMNMILHGIEYN-----D 106
Query: 274 KNIQQGSTLSKDLFTG-KRFHYCLSNPPFGKKWEKDKDAVEKEHKNGELGRFGPGLPKIS 332
I+ G TL F K+F ++NPPF +KW+ + + +N R G+P S
Sbjct: 107 FGIRHGDTLLSPKFEEDKKFDVVVANPPFNQKWDANDNL-----ENDPRFRAY-GVPPKS 160
Query: 333 DGSMLFLMHLANKLELPPNGGGRAAIVLSSSPLFNGRAGSGESEIRRWLLENDLIEAIVA 392
+ FL H+ L GRAA+VL + LF G E +IR+ L+E DLIEA++A
Sbjct: 161 NADFAFLQHIIYHLS----PNGRAAVVLPNGVLF---RGGAEGDIRKALVEKDLIEAVIA 213
Query: 393 LPTDLFFRTNIATYLWILSNRKTEERRGKVQLINATDLWTSIRNEGKKRRIINDDQRRQI 452
LP +LF+ T I T + L K + R+G V I+A++ + +G+K + D+ +I
Sbjct: 214 LPPNLFYNTGIPTCILFL--TKNKARKGDVLFIDASNEFEK---KGRKLNPLTDEHIEKI 268
Query: 453 LDIYVSRENG--KFSRMLD 469
+D Y F+++
Sbjct: 269 VDTYGEWPEDVAGFAKVAT 287
>gnl|CDD|31243 COG1041, COG1041, Predicted DNA modification methylase [DNA
replication, recombination, and repair].
Length = 347
Score = 32.2 bits (73), Expect = 0.51
Identities = 28/144 (19%), Positives = 46/144 (31%), Gaps = 21/144 (14%)
Query: 95 NTRNNLESYIASFSDNAKAIFEDFDFSSTIARLEKAG-------LLYKICKNFSGIELHP 147
+ + D ++ FE+ I R E+ + I + L
Sbjct: 78 DINEFTVLVLGEAVDWSEYKFEEEKGRVRIRRKEQDVDKGLEKAIGGAIPSEGLRVSL-- 135
Query: 148 DTVPDRVMSNIYEHLIRRFGSEVSEGAEDFMTPRD-----VVHLATALLLDPDDALFKES 202
+ PD V+ + G V E RD + +DP A +
Sbjct: 136 -SKPDEVVRVVVTEDKVYLGLTVRERDRKAFEKRDPEKRPFFRPGS---MDPRLARAMVN 191
Query: 203 PGMIR---TLYDPTCGTGGFLTDA 223
++ + DP CGTGG L +A
Sbjct: 192 LARVKRGELVLDPFCGTGGILIEA 215
>gnl|CDD|36757 KOG1544, KOG1544, KOG1544, Predicted cysteine proteinase TIN-ag
[General function prediction only].
Length = 470
Score = 30.0 bits (67), Expect = 2.4
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 350 PNGGGRAAIVLSSSPLFNGRAGSGESEIRRWLLENDLIEAIVALPTDLF-FRTNIATYLW 408
PN + + +P + R S E EI + L+EN ++A++ + D F ++ I ++
Sbjct: 331 PNSYVNSNDIYQVTPPY--RVSSNEKEIMKELMENGPVQALMEVHEDFFLYKGGIYSHT- 387
Query: 409 ILSNRKTEERR 419
+S + E R
Sbjct: 388 PVSLGRPERYR 398
>gnl|CDD|110191 pfam01170, UPF0020, Putative RNA methylase family UPF0020. This
domain is probably a methylase. It is associated with
the THUMP domain that also occurs with RNA modification
domains.
Length = 171
Score = 29.6 bits (67), Expect = 3.2
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 207 RTLYDPTCGTGGFLTDA 223
L DP CG+G L +A
Sbjct: 30 DPLLDPFCGSGTILIEA 46
>gnl|CDD|177098 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 29.3 bits (66), Expect = 3.6
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 437 EGKKRRIINDDQRRQILDIYVSRENGKFSRMLDYRTFGYR 476
EGK R I ++ + + D + NG + R++ F
Sbjct: 748 EGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS 787
>gnl|CDD|133345 cd04145, M_R_Ras_like, M-Ras/R-Ras-like subfamily. This subfamily
contains R-Ras2/TC21, M-Ras/R-Ras3, and related members
of the Ras family. M-Ras is expressed in
lympho-hematopoetic cells. It interacts with some of
the known Ras effectors, but appears to also have its
own effectors. Expression of mutated M-Ras leads to
transformation of several types of cell lines, including
hematopoietic cells, mammary epithelial cells, and
fibroblasts. Overexpression of M-Ras is observed in
carcinomas from breast, uterus, thyroid, stomach, colon,
kidney, lung, and rectum. In addition, expression of a
constitutively active M-Ras mutant in murine bone marrow
induces a malignant mast cell leukemia that is distinct
from the monocytic leukemia induced by H-Ras. TC21,
along with H-Ras, has been shown to regulate the
branching morphogenesis of ureteric bud cell branching
in mice. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 29.3 bits (66), Expect = 3.6
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 599 IQDYFVREVSPHVPDAYIDKIFIDEK 624
IQ YFV + P + D+Y + ID +
Sbjct: 23 IQSYFVTDYDPTIEDSYTKQCEIDGQ 48
>gnl|CDD|37143 KOG1932, KOG1932, KOG1932, TATA binding protein associated factor
[Transcription].
Length = 1180
Score = 28.8 bits (64), Expect = 5.0
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 3/61 (4%)
Query: 568 DPRADPVTDVNGEWIPDTNLTEYENVPYLESIQDYFVREVSPHVPDAYIDKIFIDEKDKE 627
+P +T +P YL +++ E+S P + +F+DE E
Sbjct: 258 EPSMIDITHF---CLPGLEPLVKNTTVYLHKAIEFYEEELSSRYPFSCYKTVFVDEAAVE 314
Query: 628 I 628
I
Sbjct: 315 I 315
>gnl|CDD|35956 KOG0737, KOG0737, KOG0737, AAA+-type ATPase [Posttranslational
modification, protein turnover, chaperones].
Length = 386
Score = 28.3 bits (63), Expect = 6.8
Identities = 31/150 (20%), Positives = 55/150 (36%), Gaps = 22/150 (14%)
Query: 419 RGKVQLINAT----DLWTSIRNEGKKRRII---NDDQRRQILDIYVSRENGKFSRMLDYR 471
+V ++ AT DL +I +R + + +QRR+IL + + +E K +D
Sbjct: 229 SERVLVLGATNRPFDLDEAIIRRLPRRFHVGLPDAEQRRKILKVILKKE--KLEDDVDLD 286
Query: 472 -----TFGYR--------RIKVLRPLRMSFILDKTGLARLEADITWRKLSPLHQSFWLDI 518
T GY R+ LRP+R + + L +A + S L
Sbjct: 287 EIAQMTEGYSGSDLKELCRLAALRPIRELLVSETGLLDLDKAIADLKPTQAAASSCLLRP 346
Query: 519 LKPMMQQIYPYGWAESFVKESIKSNEAKTL 548
L+ + S ++ + N K
Sbjct: 347 LEQEDFPKAINRVSASVAMDATRMNALKQW 376
>gnl|CDD|73189 cd00309, chaperonin_type_I_II, chaperonin families, type I and type
II. Chaperonins are involved in productive folding of
proteins. They share a common general morphology, a
double toroid of 2 stacked rings, each composed of 7-9
subunits. There are 2 main chaperonin groups. The
symmetry of type I is seven-fold and they are found in
eubacteria (GroEL) and in organelles of eubacterial
descent (hsp60 and RBP). The symmetry of type II is
eight- or nine-fold and they are found in archea
(thermosome), thermophilic bacteria (TF55) and in the
eukaryotic cytosol (CTT). Their common function is to
sequester nonnative proteins inside their central cavity
and promote folding by using energy derived from ATP
hydrolysis..
Length = 464
Score = 28.1 bits (63), Expect = 7.1
Identities = 22/122 (18%), Positives = 43/122 (35%), Gaps = 11/122 (9%)
Query: 42 RRLECALEPTRSAVREKYLAFGGSNIDLESFVKVAGYSFYNTSEYSLSTLGSTNTRNNLE 101
R L AL R+AV + + GG ++E + + + LG + LE
Sbjct: 330 RSLHDALCAVRAAVEDGGIVPGGGAAEIELSKALEELA---KTLPGKEQLGIEAFADALE 386
Query: 102 SYIASFSDNAKAIFEDFDFSSTIARLEKAGLLYKICKNFSGIELHPDTVPDRVMSNIYEH 161
+ ++NA D + +L + +G ++ + D + I +
Sbjct: 387 VIPRTLAENAG-----LDPIEVVTKLRAK---HAEGGGNAGGDVETGEIVDMKEAGIIDP 438
Query: 162 LI 163
L
Sbjct: 439 LK 440
>gnl|CDD|34113 COG4412, COG4412, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 760
Score = 28.1 bits (62), Expect = 7.3
Identities = 20/71 (28%), Positives = 27/71 (38%), Gaps = 13/71 (18%)
Query: 562 NAFGRKDPRADPVTDVNGEWIPDTNLTEYENVPYL---------ESIQDYFVREVSPHVP 612
N K P P T +GE + D NLT N P L +++ S H
Sbjct: 114 NNDKWKVPSTGPNTAADGEKVYDKNLTNLINFPDLPLVMNPLTAPDTGMLYLQYKSSH-- 171
Query: 613 DAYIDKIFIDE 623
Y D +F+ E
Sbjct: 172 --YQDYVFVPE 180
>gnl|CDD|113851 pfam05096, Glu_cyclase_2, Glutamine cyclotransferase. This family
of enzymes EC:2.3.2.5 catalyse the cyclization of free
L-glutamine and N-terminal glutaminyl residues in
proteins to pyroglutamate (5-oxoproline) and
pyroglutamyl residues respectively. This family includes
plant and bacterial enzymes and seems unrelated to the
mammalian enzymes.
Length = 264
Score = 28.0 bits (62), Expect = 7.9
Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 373 GESEIRRWLLENDLIEAIVALPTDLFFR--TNIATYLWILS 411
G S++R + L ++ +A P +F T + Y+++L+
Sbjct: 66 GFSKVRVYDLTQEIFSEKIAFPDTVFGEGLTVVEDYVYLLT 106
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 27.8 bits (62), Expect = 9.2
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 599 IQDYFVREVSPHVPDAYIDKIFIDE 623
IQ++FV E P + D+Y ++ ID
Sbjct: 22 IQNHFVDEYDPTIEDSYRKQVVIDG 46
>gnl|CDD|32766 COG2943, MdoH, Membrane glycosyltransferase [Cell envelope
biogenesis, outer membrane].
Length = 736
Score = 28.0 bits (62), Expect = 9.3
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 163 IRRFGSEVSE----GAEDFMTPRDVVHLATALLLDPDDALFKESPGMI--RTLY 210
RR+GS S A+ MT +V L + +PD L + SP TLY
Sbjct: 234 CRRWGSAYSYMLVLDADSVMTGDCLVRLVRLMEANPDAGLIQTSPKASGGDTLY 287
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
0.320 0.137 0.409
Gapped
Lambda K H
0.267 0.0586 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 8,568,408
Number of extensions: 477210
Number of successful extensions: 1116
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1103
Number of HSP's successfully gapped: 20
Length of query: 674
Length of database: 6,263,737
Length adjustment: 100
Effective length of query: 574
Effective length of database: 4,102,837
Effective search space: 2355028438
Effective search space used: 2355028438
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: 61 (27.6 bits)