RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781003|ref|YP_003065416.1| hypothetical protein
CLIBASIA_04520 [Candidatus Liberibacter asiaticus str. psy62]
(304 letters)
>gnl|CDD|146159 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase
family. This large family of proteins includes
magnesium dependent endonucleases and a large number of
phosphatases involved in intracellular signalling. This
family includes: AP endonuclease proteins EC:4.2.99.18,
DNase I proteins EC:3.1.21.1, Synaptojanin an
inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56,
Sphingomyelinase EC:3.1.4.12 and Nocturnin.
Length = 255
Score = 58.5 bits (141), Expect = 2e-09
Identities = 43/295 (14%), Positives = 88/295 (29%), Gaps = 56/295 (18%)
Query: 24 VRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQE--MGSYNAVA 81
+++++WN+N LS + + LL + K D D++ LQE + + +
Sbjct: 1 LKILTWNVNGLSAALKLLWAR-----------LLLELLKLEDPDVICLQETKLSPESLIL 49
Query: 82 KVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAG 141
+ + + T + AI ++ V V+ +
Sbjct: 50 LLLLLLGY-VSPLTSSVYTGFGGGGGGKGGVAILSKEPLVEVILGIFSE----------N 98
Query: 142 NRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKKES 201
+ + + NGK V++ H L L+Q A+ L +
Sbjct: 99 EKDFIRRRILANGKSFVVVNTH---------LPAGGENLDERLAQLAELLDFLSDLRIPK 149
Query: 202 LVPFVIAGDFNRKINYLGNND---------DFWKTIDPNDSLIRFPKEKD-----SRCNA 247
P ++ GDFN + + + D S N+
Sbjct: 150 SDPVILCGDFNARPDSWDSALLKSIGKSTLFLLLERDLVFDGFDELPIGFPPTWWSYRNS 209
Query: 248 NKNLRNKIPIDYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDY 302
++ +D ++ + L + +L SDH P+
Sbjct: 210 SEKKNTGSRLDRILVSGS---LLRRVVILSLLLLVI------FTGSDHRPVLATL 255
>gnl|CDD|33370 COG3568, ElsH, Metal-dependent hydrolase [General function
prediction only].
Length = 259
Score = 31.9 bits (72), Expect = 0.20
Identities = 36/201 (17%), Positives = 67/201 (33%), Gaps = 50/201 (24%)
Query: 25 RLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQE----MGS---- 76
+++++NI+ + + R + + + + ADIV LQE G
Sbjct: 11 KVLTYNIHKGFGAFD---RRFDLPR-------IAEVIREVGADIVALQEVDGAFGRHRDG 60
Query: 77 ----YNAVAKVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLG 132
+ + ++ W + + + N I + + +R L L
Sbjct: 61 LLDLPHLLGRLGLAPYW--WSGAAFGAVYGEGQHGNAILSRLPIRDVENLALPDPTGLEP 118
Query: 133 AKDSFSRAGNRRAVELLVEIN-GKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWL 191
R A+ +E+ GK + V++ HL S L +QA L
Sbjct: 119 ----------RGALLAEIELPGGKPLRVINAHL-----------GLSEESRL--RQAAAL 155
Query: 192 KDWITQKKESLVPFVIAGDFN 212
+ P V+ GDFN
Sbjct: 156 LALAGLPALN--PTVLMGDFN 174
>gnl|CDD|31052 COG0708, XthA, Exonuclease III [DNA replication, recombination, and
repair].
Length = 261
Score = 32.1 bits (73), Expect = 0.21
Identities = 54/320 (16%), Positives = 100/320 (31%), Gaps = 100/320 (31%)
Query: 25 RLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNAVAKVF 84
++ SWN+N L R L + + D++ LQE A + F
Sbjct: 2 KIASWNVNGL--------------RARLKK--LLDWLEEEQPDVLCLQET---KAQDEQF 42
Query: 85 PKNTW-CIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAGNR 143
P+ + Y + NH ++ + AI +K ++ G
Sbjct: 43 PREELEALGY--HHVFNHGQKGYSG---VAILSKKP----PDDVRRGFPGEEEDDEEG-- 91
Query: 144 RAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCS-----LLSQQAQWLKD---WI 195
R +E E +G ++ N Y P+ S + ++L ++
Sbjct: 92 RVIEA--EFDGFRVI----------------NLYFPNGSSIGLEKFDYKLRFLDALRNYL 133
Query: 196 TQKKESLVPFVIAGDFNR----------KINYLGNND--------------------DFW 225
+ + P V+ GDFN K +L + D +
Sbjct: 134 EELLKKGKPVVLCGDFNIAPEEIDVANPKKRWLNEGNSGFLPEERAWFRRLLNAGFVDTF 193
Query: 226 KTIDPNDSLIRFPKEKDSRCNANKNLRNKIPIDYFVMDQNAYKFLIQESFSEILYNEDDI 285
+ P + + + N+ R IDY ++ L + I
Sbjct: 194 RLFHPEPEKYTWWDYRANAARRNRGWR----IDYILVSPALADRLKD---AGIDREV--- 243
Query: 286 KSRG-KRLSDHCPISIDYDF 304
RG ++ SDH P+ ++ D
Sbjct: 244 --RGWEKPSDHAPVWVELDL 261
>gnl|CDD|37967 KOG2756, KOG2756, KOG2756, Predicted Mg2+-dependent
phosphodiesterase TTRAP [Signal transduction
mechanisms].
Length = 349
Score = 31.6 bits (71), Expect = 0.26
Identities = 56/291 (19%), Positives = 107/291 (36%), Gaps = 53/291 (18%)
Query: 24 VRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGS--YNAVA 81
L++WNI +G+ L N +R + + Y D++FLQE+ Y+ +
Sbjct: 100 FSLITWNI------DGLDL-NNLSERMRA----VCHYLALYSPDVIFLQEVIPPYYSYLK 148
Query: 82 KVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSRAG 141
K + + I E TAI ++K V+V Q F +
Sbjct: 149 KR--SSNYEIITGHEEGY-----------FTAIMLKKSRVKVKSQEII------PFPNSK 189
Query: 142 NRRAVELL-VEINGKKIWVLDIHLKSFCFLDSLENTYSPS-CSLLSQQAQWLKDWITQKK 199
R + ++ V ++G K+ ++ HL+S ++P + + +++ I
Sbjct: 190 MMRNLLIVEVNVSGNKLCLMTSHLESTR-------GHAPERMNQFKMVLKKMQEAIESLP 242
Query: 200 ESLVPFVIAGDFN---RKINYLGNND---DFWKTI-DPNDSLIRFPKEKDSRCNANKNLR 252
+ V F GD N R++ G D D W+ + P + + +S +
Sbjct: 243 NATVIF--GGDTNLRDREVTRCGLPDNIVDVWEFLGKPKHCQFTWDTQMNSNLGGTAACK 300
Query: 253 NKIPIDYFVMDQNAYKFLIQESFSEILYNEDDIKSRGKRLSDHCPISIDYD 303
+ +F +I S L + ++ G+ SDH + D
Sbjct: 301 LRFDRIFFRAAAEEGH-IIPRSLD--LLGLEKLRGCGRFPSDHWGLLCTLD 348
>gnl|CDD|112008 pfam03173, CHB_HEX, Putative carbohydrate binding domain. This
domain represents the N terminal domain in chitobiases
and beta-hexosaminidases EC:3.2.1.52. It is composed of
a beta sandwich structure that is similar in structure
to the cellulose binding domain of cellulase from
Cellulomonas fimi. This suggests that this may be a
carbohydrate binding domain.
Length = 164
Score = 29.8 bits (67), Expect = 0.98
Identities = 10/39 (25%), Positives = 18/39 (46%)
Query: 73 EMGSYNAVAKVFPKNTWCIFYSTERLINHSKRDSNNDIH 111
E+ N A V ++ W I++ + R+I + D H
Sbjct: 35 ELSLVNPGAAVLGESDWAIYFHSIRIILQVESDEFAIEH 73
>gnl|CDD|48147 cd03312, CIMS_N_terminal_like, CIMS - Cobalamine-independent
methonine synthase, or MetE, N-terminal domain_like.
Many members have been characterized as
5-methyltetrahydropteroyltriglutamate-homocysteine
methyltransferases, EC:2.1.1.14, mostly from bacteria
and plants. This enzyme catalyses the last step in the
production of methionine by transferring a methyl group
from 5-methyltetrahydrofolate to L-homocysteine without
using an intermediate methyl carrier. The active enzyme
has a dual (beta-alpha)8-barrel structure, and this
model covers the N-terminal barrel, and a few
single-barrel sequences most similar to the N-terminal
barrel. It is assumed that the homologous N-terminal
barrel has evolved from the C-terminus via gene
duplication and has subsequently lost binding sites, and
it seems as if the two barrels forming the active enzyme
may sometimes reside on different polypeptides. The
C-terminal domain incorporates the Zinc ion, which binds
and activates homocysteine. Side chains from both
barrels contribute to the binding of the folate
substrate..
Length = 360
Score = 28.2 bits (63), Expect = 3.3
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 152 INGKKIWVLDIHLKSFCFLDSLENTY------SPSCSLL 184
++G+ IW D+ S L++L SPSCSLL
Sbjct: 287 VDGRNIWRADLA-ASLALLETLAAILGDRLVVSPSCSLL 324
>gnl|CDD|39900 KOG4702, KOG4702, KOG4702, Uncharacterized conserved protein
[Function unknown].
Length = 77
Score = 27.7 bits (61), Expect = 3.8
Identities = 5/21 (23%), Positives = 10/21 (47%)
Query: 184 LSQQAQWLKDWITQKKESLVP 204
L Q + ++++ K L P
Sbjct: 24 LFNQPEIFEEFVRGYKRELSP 44
>gnl|CDD|88569 cd05129, RasGAP_RAP6, Rab5-activating protein 6 (RAP6) is an
endosomal protein with a role in the regulation of
receptor-mediated endocytosis. RAP6 contains a Vps9
domain, which is involved in the activation of Rab5, and
a Ras GAP domain (RGD). Rab5 is a small GTPase required
for the control of the endocystic route, and its
activity is regulated by guanine nucleotide exchange
factor, such as Rabex5, and GAPs, such as RN-tre. Human
Rap6 protein is localized on the plasma membrane and on
the endosome. RAP6 binds to Rab5 and Ras through the
Vps9 and RGD domains, respectively..
Length = 353
Score = 27.2 bits (60), Expect = 5.5
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 221 NDDFWKTIDPNDSLIRFP---KEKDSRCNANKNLRNKIP 256
D+FW IDP+ + RF +EK K ++
Sbjct: 117 EDEFWLDIDPDKLMERFSPDEREKRFGEKGTKEYERRVQ 155
>gnl|CDD|113374 pfam04601, DUF569, Protein of unknown function (DUF569). Family of
hypothetical proteins. Some family members contain a two
copies of the region.
Length = 142
Score = 26.7 bits (59), Expect = 8.0
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 23 KVRLVSWNINTLSEQEGVSLWKNSV 47
+V+L + N L G+ W+NSV
Sbjct: 102 QVKLKTRYGNYLRANGGLPPWRNSV 126
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
0.321 0.135 0.408
Gapped
Lambda K H
0.267 0.0636 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,689,804
Number of extensions: 188697
Number of successful extensions: 445
Number of sequences better than 10.0: 1
Number of HSP's gapped: 440
Number of HSP's successfully gapped: 14
Length of query: 304
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 211
Effective length of database: 4,254,100
Effective search space: 897615100
Effective search space used: 897615100
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 (21.9 bits)
S2: 57 (25.9 bits)