RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780914|ref|YP_003065327.1| hypothetical protein
CLIBASIA_04065 [Candidatus Liberibacter asiaticus str. psy62]
(408 letters)
>gnl|CDD|177239 MTH00191, CYTB, cytochrome b; Provisional.
Length = 365
Score = 29.5 bits (67), Expect = 1.8
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 10/46 (21%)
Query: 210 TLVKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREY 255
T++ N LS IPY ++ W G +SVDN T TR +
Sbjct: 141 TVITNLLSAIPYIG--------DDLVQWLWGG--FSVDNATLTRFF 176
>gnl|CDD|35313 KOG0090, KOG0090, KOG0090, Signal recognition particle receptor,
beta subunit (small G protein superfamily)
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 238
Score = 29.1 bits (65), Expect = 2.4
Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 11/93 (11%)
Query: 31 SSFVAIVDVVVDQVTVMQKTAWLQEVLDHVIYRTSPK----------NLYDLREAGRDNF 80
+ + VVD T ++ + E L ++ + K N DL A
Sbjct: 106 NYSAKAIVFVVDSATFLKNVRDVAEFLYDILLDSRVKKNKPPVLIACNKQDLFTAKTAEK 165
Query: 81 IRHQIEKALNTYN-SRDLSNIGSIESIVKDAVI 112
IR Q+EK ++ SR S E I KD +
Sbjct: 166 IRQQLEKEIHKLRESRSALRSISDEDIAKDFTL 198
>gnl|CDD|39700 KOG4500, KOG4500, KOG4500, Rho/Rac GTPase guanine nucleotide
exchange factor smgGDS/Vimar [Signal transduction
mechanisms].
Length = 604
Score = 28.5 bits (63), Expect = 3.7
Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 5/53 (9%)
Query: 283 FGDGQVLTNTNHCFPHGASQNKYMLMLAIGNQLSRSS-----VEKEKIEKVLQ 330
D Q L F S M LAIGN R V+K+ + K++
Sbjct: 311 HADPQFLDFLESWFRSDDSNLITMGSLAIGNFARRDDICIQLVQKDFLNKLIS 363
>gnl|CDD|133316 cd04116, Rab9, Rab9 subfamily. Rab9 is found in late endosomes,
together with mannose 6-phosphate receptors (MPRs) and
the tail-interacting protein of 47 kD (TIP47). Rab9 is
a key mediator of vesicular transport from late
endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it a
potential target for inhibiting a variety of viruses.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 27.9 bits (62), Expect = 4.7
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 242 LTYSVDNKTTTREY--YKDP--YYA---TWDHFPYSFIKNVFDMTSNQFG--DGQVLTNT 292
LT++VD+ + + +K YYA + FP+ + N D+ Q + Q
Sbjct: 83 LTFAVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVVLGNKNDIPERQVSTEEAQAWCRE 142
Query: 293 NHCFPH 298
N +P+
Sbjct: 143 NGDYPY 148
>gnl|CDD|177109 MTH00034, CYTB, cytochrome b; Validated.
Length = 379
Score = 27.7 bits (62), Expect = 5.3
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 18/63 (28%)
Query: 210 TLVKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREYYKDPYYATWDHFPY 269
T++ N +S +PY + I+ W G +SVDN T TR ++A HF +
Sbjct: 144 TVITNLVSAVPYIG--------TDIVQWIWGG--FSVDNATLTR------FFAF--HFLF 185
Query: 270 SFI 272
FI
Sbjct: 186 PFI 188
>gnl|CDD|35436 KOG0215, KOG0215, KOG0215, RNA polymerase III, second largest
subunit [Transcription].
Length = 1153
Score = 27.2 bits (60), Expect = 7.4
Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 16/77 (20%)
Query: 331 DCHYMHKRHRTGRDAITIFSVGFSP-------------DQDTRYTLRQCASDPSKYYEIN 377
D Y R + + I G P D++ L +C DP Y+ +
Sbjct: 137 DIEYTRGRQIIAKRDVII---GRMPIMLRSSKCVLRGKDEEELARLNECPLDPGGYFIVK 193
Query: 378 SDENVMPIAKSLARNVI 394
E V+ I + L++N I
Sbjct: 194 GTEKVILIQEQLSKNRI 210
>gnl|CDD|35549 KOG0328, KOG0328, KOG0328, Predicted ATP-dependent RNA helicase
FAL1, involved in rRNA maturation, DEAD-box superfamily
[Translation, ribosomal structure and biogenesis].
Length = 400
Score = 27.2 bits (60), Expect = 9.4
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 334 YMHKRHRTGRDAITIFSVGFSPDQDTRYTLRQCASDPSKYYEINSDENVMPIAKSL 389
Y+H+ R+GR ++ F D R D +YY DE M +A +
Sbjct: 350 YIHRIGRSGRFGRKGVAINFVKSDDLRILR-----DIEQYYSTQIDEMPMNVADLI 400
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 0.134 0.402
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,909,533
Number of extensions: 256460
Number of successful extensions: 560
Number of sequences better than 10.0: 1
Number of HSP's gapped: 553
Number of HSP's successfully gapped: 17
Length of query: 408
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 312
Effective length of database: 4,189,273
Effective search space: 1307053176
Effective search space used: 1307053176
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: 59 (26.5 bits)