RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780187|ref|YP_003064600.1| 30S ribosomal protein S4
[Candidatus Liberibacter asiaticus str. psy62]
(206 letters)
>gnl|CDD|180018 PRK05327, rpsD, 30S ribosomal protein S4; Validated.
Length = 203
Score = 291 bits (747), Expect = 1e-79
Identities = 101/208 (48%), Positives = 139/208 (66%), Gaps = 7/208 (3%)
Query: 1 MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQ-RRKSKPSYFGLQLRAKQKMK 59
M++ K K+ RR+G +L+ K + + Y PG HGQ RRK K S +GLQLR KQK++
Sbjct: 1 MARYTGPKCKLSRRLGVDLFKSGKRCLKRK-YPPGQHGQRRRKPKLSDYGLQLREKQKLR 59
Query: 60 KYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHR 119
+ YG + EK+FR FKEA R +G+T NL+ LESRLD +VYR F PT ARQ V+H
Sbjct: 60 RIYG-VLEKQFRRYFKEAARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSHG 118
Query: 120 HVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAE-RDVPEYISVNHDNMVAT 178
H+LVNG+ VNI SYR K GDVIEV++KSK+L + EA +LAE R VP+++ V+ + + T
Sbjct: 119 HILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKLEGT 178
Query: 179 FVRIPSSLKDVPYPVIMQPNLVVEFYSR 206
F R+P ++ PV + L+VE YS+
Sbjct: 179 FKRLP-EREE--IPVPINEQLIVELYSK 203
>gnl|CDD|130089 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle
type. This model finds organelle (chloroplast and
mitochondrial) ribosomal protein S4 as well as bacterial
ribosomal protein S4.
Length = 200
Score = 218 bits (557), Expect = 1e-57
Identities = 93/201 (46%), Positives = 134/201 (66%), Gaps = 6/201 (2%)
Query: 7 SKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDIS 66
K K+ RR+G NL+G+ + + R Y PG HGQRRK K S +GLQL+ KQK+K YG I+
Sbjct: 5 PKFKLSRRLGVNLFGKSRKLLLKRKYPPGQHGQRRK-KLSDYGLQLQEKQKLKFMYG-IT 62
Query: 67 EKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGR 126
EK+FR FKEA + +G+T NL+ LESRLD +VYR F PT FAARQ V+H H+LVNG+
Sbjct: 63 EKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGK 122
Query: 127 SVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLA-ERDVPEYISVNHDNMVATFVRIPSS 185
V+I SY+ + GD+I +K+KSK++ V E + +R++P ++ V+ + +R+P
Sbjct: 123 KVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVLRVPE- 181
Query: 186 LKDVPYPVIMQPNLVVEFYSR 206
P+ + +LVVE+YSR
Sbjct: 182 --RSQLPLPINESLVVEYYSR 200
>gnl|CDD|128657 smart00363, S4, S4 RNA-binding domain.
Length = 60
Score = 66.1 bits (162), Expect = 6e-12
Identities = 21/55 (38%), Positives = 27/55 (49%)
Query: 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148
RLD + R P+ AR+ + V VNG+ V SY K GDVI V+ K
Sbjct: 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKEL 55
>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated.
Length = 177
Score = 54.9 bits (133), Expect = 1e-08
Identities = 23/44 (52%), Positives = 25/44 (56%)
Query: 90 SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133
LE RL TIVYR T ARQF+ H H+ VNGR V SY
Sbjct: 99 DILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142
>gnl|CDD|130090 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal
type)/S9(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S9 as well as archaeal
ribosomal protein S4.
Length = 162
Score = 50.1 bits (120), Expect = 4e-07
Identities = 20/43 (46%), Positives = 25/43 (58%)
Query: 91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133
FLE RL T V++ TI ARQ + H H+ V+GR V SY
Sbjct: 101 FLERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSY 143
>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional.
Length = 194
Score = 42.4 bits (100), Expect = 9e-05
Identities = 16/44 (36%), Positives = 27/44 (61%)
Query: 90 SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133
+FLE RL T+V+++ +I AR + RH+ V + VN+ S+
Sbjct: 105 NFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSF 148
>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional.
Length = 181
Score = 37.8 bits (88), Expect = 0.002
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133
LE RL T V++ +I AR + RH+ V + V+I S+
Sbjct: 104 LLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 146
>gnl|CDD|165505 PHA03246, PHA03246, large tegument protein UL36; Provisional.
Length = 3095
Score = 29.9 bits (67), Expect = 0.44
Identities = 24/85 (28%), Positives = 34/85 (40%), Gaps = 12/85 (14%)
Query: 2 SKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKY 61
S+ +S+HK RR W P S N S GP R+ S+ S L L
Sbjct: 456 SRGSNSRHK--RR--RPSWTPPSSSENVSSDGPTFSQSRKPSRKSKRALDLD-------- 503
Query: 62 YGDISEKKFRSIFKEADRSRGDTSH 86
YG +S + + +D G S+
Sbjct: 504 YGHLSNEPSDVDGENSDSPAGAISN 528
>gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 29.9 bits (67), Expect = 0.49
Identities = 13/21 (61%), Positives = 17/21 (80%), Gaps = 1/21 (4%)
Query: 58 MKKYYGDISEKKFRSIFKEAD 78
M KYYG+ SE++ R IFKEA+
Sbjct: 249 MSKYYGE-SEERLREIFKEAE 268
>gnl|CDD|162487 TIGR01687, moaD_arch, MoaD family protein, archaeal. Members of
this family appear to be archaeal versions of MoaD,
subunit 1 of molybdopterin converting factor. This model
has been split from the bacterial/eukaryotic equivalog
model TIGR01682 because the presence of two members of
this family in a substantial number of archaeal species
suggests that roles might not be interchangeable.
Length = 88
Score = 29.7 bits (67), Expect = 0.52
Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 10/86 (11%)
Query: 60 KYYGDISEKKFRSIFK-EADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNH 118
KY+ + + + + E + G T +L++ L +R Y +F V +
Sbjct: 4 KYFATLRDITGKKSEEIEIE---GKTVGDLLNELMAR-----YPKEFSELFKEGLGLVPN 55
Query: 119 RHVLVNGRSVNIG-SYRCKEGDVIEV 143
+LVNGR+V+ G K+GDV+ +
Sbjct: 56 VIILVNGRNVDWGLGTELKDGDVVAI 81
>gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein;
Provisional.
Length = 267
Score = 27.4 bits (61), Expect = 2.8
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 13/60 (21%)
Query: 95 RLDTI------VYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148
RLD + + R+K V I + V VN R V K GDV+ V K +
Sbjct: 193 RLDALASAGFRMSRSKLVDLISSG-------DVRVNWREVTKNGTTLKTGDVVSVSGKGR 245
>gnl|CDD|184784 PRK14667, uvrC, excinuclease ABC subunit C; Provisional.
Length = 567
Score = 27.4 bits (61), Expect = 2.9
Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 34 PGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDI-SEKKFRSIFKEAD 78
PG++ ++K + Y G K ++ ++Y ++ K R+IF E+
Sbjct: 17 PGVYLFKKKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESS 62
>gnl|CDD|165244 PHA02933, PHA02933, unchracterized protein; Provisional.
Length = 149
Score = 26.5 bits (58), Expect = 4.5
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 62 YGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLD 97
Y ISE +F+S+ D D + LI FLE +L+
Sbjct: 114 YKKISESRFQSLGNITDLMTDDNINILILFLEKKLN 149
>gnl|CDD|180858 PRK07139, PRK07139, amidase; Provisional.
Length = 439
Score = 26.6 bits (59), Expect = 4.8
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 28 NTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKE 76
NTRS G G Q+R SYF ++ +KY+ + KK R + K
Sbjct: 304 NTRSEGFGKMVQKRLILGSYF----LEEENQEKYF--LKAKKVRRVIKN 346
>gnl|CDD|132113 TIGR03069, PS_II_S4, photosystem II S4 domain protein. Members of
this protein family are about 265 residues long and each
contains an S4 RNA-binding domain of about 48 residues.
The member from the Cyanobacterium, Synechocystis sp.
PCC 6803, was detected as a novel polypeptide in a
highly purified preparation of active photosystem II
(Kashino, et al., 2002). The phylogenetic distribution,
including Cyanobacteria and Arabidopsis, supports a role
in photosystem II, although the high bit score cutoffs
for this model reflect similar sequences in
non-photosynthetic organisms such as Carboxydothermus
hydrogenoformans, a Gram-positive bacterium.
Length = 257
Score = 26.1 bits (58), Expect = 6.5
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 13/58 (22%)
Query: 95 RLDTI------VYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146
R+D I + R+K V I A R + +N ++V S K GD ++++ K
Sbjct: 185 RIDAIASAGFGLSRSKIVDQIKAGR-------LRLNWKTVTQPSRELKVGDRLQLRGK 235
>gnl|CDD|179455 PRK02645, ppnK, inorganic polyphosphate/ATP-NAD kinase;
Provisional.
Length = 305
Score = 25.6 bits (57), Expect = 9.6
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 5/27 (18%)
Query: 180 VRIPSSLKDVPYPVIM-----QPNLVV 201
+ PS KD PYPV + +L +
Sbjct: 36 LMGPSGPKDNPYPVFLASASELIDLAI 62
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.134 0.384
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,269,490
Number of extensions: 193724
Number of successful extensions: 417
Number of sequences better than 10.0: 1
Number of HSP's gapped: 407
Number of HSP's successfully gapped: 21
Length of query: 206
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 117
Effective length of database: 4,071,361
Effective search space: 476349237
Effective search space used: 476349237
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 (21.7 bits)
S2: 55 (25.0 bits)