RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780329|ref|YP_003064742.1| 30S ribosomal protein S6
[Candidatus Liberibacter asiaticus str. psy62]
(135 letters)
>gnl|CDD|144734 pfam01250, Ribosomal_S6, Ribosomal protein S6.
Length = 92
Score = 111 bits (281), Expect = 5e-26
Identities = 43/90 (47%), Positives = 66/90 (73%)
Query: 2 KLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYV 61
+ YE +F+LR D+S +++K I +Y+ LI+ENGGEV V + G R +AY I+K R+ YYV
Sbjct: 1 RKYETMFILRPDLSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYV 60
Query: 62 FMNIASPPAAIHEMKRKMRIDENVLRSLTL 91
+N + P AI E++R++RI+E+VLR LT+
Sbjct: 61 LINFEAEPEAIAELERRLRINEDVLRFLTV 90
>gnl|CDD|30709 COG0360, RpsF, Ribosomal protein S6 [Translation, ribosomal
structure and biogenesis].
Length = 112
Score = 100 bits (250), Expect = 1e-22
Identities = 40/106 (37%), Positives = 71/106 (66%)
Query: 4 YEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFM 63
YE VF++R D+S +Q+ + +Y+ ++ NGGE+ V + G R +AY I+K R+ +YV M
Sbjct: 3 YEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYVLM 62
Query: 64 NIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDR 109
N + PAAI E++R +RI+E+VLR L + V+ ++ + +++ D+
Sbjct: 63 NFEAEPAAIAELERLLRINEDVLRHLIIKVEKAKEELSPMLKKKDQ 108
>gnl|CDD|177046 CHL00123, rps6, ribosomal protein S6; Validated.
Length = 97
Score = 58.5 bits (142), Expect = 6e-10
Identities = 26/90 (28%), Positives = 52/90 (57%)
Query: 2 KLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYV 61
YE ++LL+ D++ +++ I Y+ L+++ G + V G R ++Y+I K Y+
Sbjct: 6 NKYETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRGKRKLSYKINKYEDGIYI 65
Query: 62 FMNIASPPAAIHEMKRKMRIDENVLRSLTL 91
MN + ++ +++ +++DENVLR LT
Sbjct: 66 QMNYSGNGKLVNSLEKALKLDENVLRYLTF 95
>gnl|CDD|39906 KOG4708, KOG4708, KOG4708, Mitochondrial ribosomal protein MRP17
[Translation, ribosomal structure and biogenesis].
Length = 141
Score = 42.6 bits (100), Expect = 3e-05
Identities = 32/98 (32%), Positives = 46/98 (46%), Gaps = 5/98 (5%)
Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRK----NR 56
M LYE + R + K LI NG VR V LG R + Y+I+K +
Sbjct: 3 MPLYELALITRSLSRPELAKLLARTGGHLIDRNG-VVRDVESLGKRELPYKIKKLDQRHY 61
Query: 57 KAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVD 94
+ + M S PA E+KR ++ D +V+R L + VD
Sbjct: 62 RGQHFLMTFYSSPAVQSEIKRILKRDPDVIRWLIVKVD 99
>gnl|CDD|36043 KOG0825, KOG0825, KOG0825, PHD Zn-finger protein [General function
prediction only].
Length = 1134
Score = 26.0 bits (56), Expect = 3.1
Identities = 23/110 (20%), Positives = 40/110 (36%), Gaps = 6/110 (5%)
Query: 27 QSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAI--HEMKRKMRIDEN 84
QS+ Q +R V +R IA + F NI + + K ++N
Sbjct: 301 QSVKQPEVQLLRHVETERVRAIATC---DTFGSEDFNNIQDSENNLLKNTKLEKSLEEKN 357
Query: 85 VLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRD-RNVDRKQHVSEEKP 133
+ + IQ+H +D N+ P + + Q+ SE +P
Sbjct: 358 ESLTEHPRSTELPKRHVQQIQKHFSEDNNEMIPMECDSFCSDQNESEVEP 407
>gnl|CDD|185751 cd09238, V_Alix_like_1, Protein-interacting V-domain of an
uncharacterized family of the V_Alix_like superfamily.
This domain family is comprised of uncharacterized plant
proteins. It belongs to the V_Alix_like superfamily
which includes the V-shaped (V) domains of Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, mammalian Alix (apoptosis-linked gene-2
interacting protein X), (His-Domain) type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23), and
related domains. Alix, also known as apoptosis-linked
gene-2 interacting protein 1 (AIP1), participates in
membrane remodeling processes during the budding of
enveloped viruses, vesicle budding inside late endosomal
multivesicular bodies (MVBs), and the abscission
reactions of mammalian cell division. It also functions
in apoptosis. HD-PTP functions in cell migration and
endosomal trafficking, Bro1 in endosomal trafficking,
and Rim20 in the response to the external pH via the
Rim101 pathway. Alix, HD-PTP, Bro1, and Rim20 all
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. The mammalian Alix
V-domain (belonging to a different family) contains a
binding site, partially conserved in the superfamily,
for the retroviral late assembly (L) domain YPXnL motif.
The Alix V-domain is also a dimerization domain. In
addition to this V-domain, members of the
V_Alix_Rim20_Bro1_like superfamily also have an
N-terminal Bro1-like domain, which binds components of
the ESCRT-III complex. The Bro1-like domains of Alix and
HD-PTP can also bind to human immunodeficiency virus
type 1 (HIV-1) nucleocapsid. Many members of the
V_Alix_like superfamily also have a proline-rich region
(PRR).
Length = 339
Score = 25.9 bits (57), Expect = 3.9
Identities = 6/34 (17%), Positives = 18/34 (52%)
Query: 64 NIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHE 97
+ + A I +M + ++ ++N+L + S++
Sbjct: 206 ALGNERAGIEDMMKALKRNDNILAKVMATTGSYD 239
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 0.135 0.375
Gapped
Lambda K H
0.267 0.0767 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,567,581
Number of extensions: 72757
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 177
Number of HSP's successfully gapped: 15
Length of query: 135
Length of database: 6,263,737
Length adjustment: 84
Effective length of query: 51
Effective length of database: 4,448,581
Effective search space: 226877631
Effective search space used: 226877631
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: 52 (23.7 bits)