RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781175|ref|YP_003065588.1| UDP-3-O-[3-hydroxymyristoyl]
N-acetylglucosamine deacetylase [Candidatus Liberibacter asiaticus
str. psy62]
(296 letters)
>gnl|CDD|31117 COG0774, LpxC, UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell
envelope biogenesis, outer membrane].
Length = 300
Score = 331 bits (850), Expect = 1e-91
Identities = 136/287 (47%), Positives = 188/287 (65%), Gaps = 6/287 (2%)
Query: 8 RLQHTIADSITITGIGIHSGKRANLKLCPAPEGVGILFKCTQSGGITDSLSALWSNVLRT 67
Q T+ +++TG+G+HSGK+ L L PAP GI+F+ T + + A NV T
Sbjct: 2 MKQRTLKRIVSLTGVGLHSGKKVTLTLRPAPANTGIVFRRTDLNPPVE-IPADAENVRDT 60
Query: 68 TLSTTIG-SSSCQVRTIEHLMAALYAYGIDNVIIEIDSTEVPIMDGSAKAFVEVIERIGI 126
LSTT+G ++ T+EHLMAAL GIDN+IIE+D E+PIMDGSA FVE+I+ GI
Sbjct: 61 MLSTTLGNDHGVRISTVEHLMAALAGLGIDNLIIEVDGPEIPIMDGSAAPFVELIDEAGI 120
Query: 127 KTLTAKRRYLRIIKSVRITSGESWAEFSPHCSMRFEISIEFKNSIIG--FQKWAGDLTQT 184
K AK++++RI K VR+ G+ WAEF+P+ R +I+F + IG +Q + D +
Sbjct: 121 KEQNAKKKFIRIKKPVRVEDGDKWAEFTPYDGFRLSYTIDFDHPAIGRQWQSFEFDFSAE 180
Query: 185 VFRNEIYAARTFGFLRDVERYRKAGCALGASLENSVVISEDDQVMNHGGLRYSGEEFVRH 244
FR EI ARTFGF+RDVE R G ALG SLEN++VI DD+V+N GLR+ +EFVRH
Sbjct: 181 SFRKEIARARTFGFMRDVEYLRSKGLALGGSLENAIVID-DDRVLNPEGLRF-EDEFVRH 238
Query: 245 KTLDAIGDIALAGYPVIGCYRSCRGSHEINHMALCTLFADKDSYEIV 291
K LDAIGD+ L G+P+IG + + + H +N+ L + AD+ +YEIV
Sbjct: 239 KILDAIGDLYLLGHPIIGAFTAYKSGHALNNALLKAILADQTAYEIV 285
>gnl|CDD|146126 pfam03331, LpxC, UDP-3-O-acyl N-acetylglycosamine deacetylase. The
enzymes in this family catalyse the second step in the
biosynthetic pathway for lipid A.
Length = 276
Score = 270 bits (693), Expect = 3e-73
Identities = 114/277 (41%), Positives = 174/277 (62%), Gaps = 4/277 (1%)
Query: 10 QHTIADSITITGIGIHSGKRANLKLCPAPEGVGILFKCTQSGGITDSLSALWSNVLRTTL 69
Q T+ ++++G+G+H+GK++ L L PA E GI+F+ T + A NV T L
Sbjct: 3 QRTLKRPVSVSGVGLHTGKKSTLTLEPAKENTGIVFQRTDLSPYPI-IPARPENVRDTML 61
Query: 70 STTIGSSSCQVRTIEHLMAALYAYGIDNVIIEIDSTEVPIMDGSAKAFVEVIERIGIKTL 129
STT+G+ ++ T+EHL+AAL GIDN+IIE+D E+PIMDGSA FVE+I++ GIK
Sbjct: 62 STTLGNDGARISTVEHLLAALAGLGIDNLIIEVDGPEIPIMDGSALPFVELIDQAGIKEQ 121
Query: 130 TAKRRYLRIIKSVRITSGESWAEFSPHCSMRFEISIEFKN-SIIGFQKWAGDLTQTVFRN 188
A ++ +RI + V + G+ + P ++ +I+FK+ +I Q ++ +Q FR
Sbjct: 122 EAAKKIIRIKEPVYVQDGDKFLAAFPSDGLKISYTIDFKHPAIGKSQWYSFVFSQESFRK 181
Query: 189 EIYAARTFGFLRDVERYRKAGCALGASLENSVVISEDDQVMNHGGLRYSGEEFVRHKTLD 248
EI ARTFGF+R++E R G G SLEN++V +DD+V+N GLR+ +E VRHK LD
Sbjct: 182 EIAPARTFGFMREIEYLRSKGLIKGGSLENAIVF-DDDKVLNPPGLRFE-DEPVRHKILD 239
Query: 249 AIGDIALAGYPVIGCYRSCRGSHEINHMALCTLFADK 285
IGD+ L G PVIG + + + H +N+ + + AD+
Sbjct: 240 LIGDLYLLGVPVIGHFIAYKSGHSLNNQLVQKILADQ 276
>gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 27.4 bits (61), Expect = 5.3
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 90 LYAYGIDNVIIEIDSTEVPIMDGSAKAFVEVIERIGIKTLTAKRRYLRI 138
LY G I++I + + DG+ K VE ++R+ I L+ + +
Sbjct: 68 LYEVGTLAKILQI----LKLPDGTVKVLVEGLQRVRISKLSDEEEFFEA 112
>gnl|CDD|37043 KOG1832, KOG1832, KOG1832, HIV-1 Vpr-binding protein [Cell cycle
control, cell division, chromosome partitioning].
Length = 1516
Score = 27.4 bits (60), Expect = 5.4
Identities = 21/109 (19%), Positives = 39/109 (35%), Gaps = 5/109 (4%)
Query: 182 TQTVFRNEIYAARTFGFLRDVERYRKAGCALGASLENSVVISEDDQVMNHGGL---RYSG 238
+ + +EI+ RTF L V + CA+ + V+ + + + R
Sbjct: 1279 NEVIINSEIWDMRTFKLLHSVPSLDQ--CAVTFNSTGDVMYAMLNIEDVMSDVHTRRVKH 1336
Query: 239 EEFVRHKTLDAIGDIALAGYPVIGCYRSCRGSHEINHMALCTLFADKDS 287
F +T DAI +A PV C + + + + +D
Sbjct: 1337 PLFSSFRTFDAIDYSDIATIPVDRCLLDLCTEPTDSFLGVIEMEDQEDM 1385
>gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor
2). eIF2 is a heterotrimeric translation initiation
factor that consists of alpha, beta, and gamma subunits.
The GTP-bound gamma subunit also binds initiator
methionyl-tRNA and delivers it to the 40S ribosomal
subunit. Following hydrolysis of GTP to GDP, eIF2:GDP
is released from the ribosome. The gamma subunit has no
intrinsic GTPase activity, but is stimulated by the
GTPase activating protein (GAP) eIF5, and GDP/GTP
exchange is stimulated by the guanine nucleotide
exchange factor (GEF) eIF2B. eIF2B is a heteropentamer,
and the epsilon chain binds eIF2. Both eIF5 and
eIF2B-epsilon are known to bind strongly to eIF2-beta,
but have also been shown to bind directly to eIF2-gamma.
It is possible that eIF2-beta serves simply as a
high-affinity docking site for eIF5 and eIF2B-epsilon,
or that eIF2-beta serves a regulatory role. eIF2-gamma
is found only in eukaryotes and archaea. It is closely
related to SelB, the selenocysteine-specific elongation
factor from eubacteria. The translational factor
components of the ternary complex, IF2 in eubacteria and
eIF2 in eukaryotes are not the same protein (despite
their unfortunately similar names). Both factors are
GTPases; however, eubacterial IF-2 is a single
polypeptide, while eIF2 is heterotrimeric. eIF2-gamma
is a member of the same family as eubacterial IF2, but
the two proteins are only distantly related. This
family includes translation initiation, elongation, and
release factors.
Length = 203
Score = 27.2 bits (61), Expect = 6.1
Identities = 21/80 (26%), Positives = 31/80 (38%), Gaps = 26/80 (32%)
Query: 74 GSSSC-QVRTIEHLMAALYAYGIDNVII---EIDSTEVPIMDGSAKAFVEVIERIGIKTL 129
+ C Q +T EHL AL G+ ++II +ID +K
Sbjct: 116 ANEPCPQPQTSEHLA-ALEIMGLKHIIIVQNKIDL---------------------VKEE 153
Query: 130 TAKRRYLRIIKSVRITSGES 149
A Y +I K V+ T E+
Sbjct: 154 QALENYEQIKKFVKGTIAEN 173
>gnl|CDD|34243 COG4623, COG4623, Predicted soluble lytic transglycosylase fused to
an ABC-type amino acid-binding protein [Cell envelope
biogenesis, outer membrane].
Length = 473
Score = 27.2 bits (60), Expect = 6.1
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 1 MEMLQIGRLQHTIADSITI 19
+EM+ G+L +TIADS+ I
Sbjct: 169 LEMVAEGKLDYTIADSVEI 187
>gnl|CDD|34398 COG4787, FlgF, Flagellar basal body rod protein [Cell motility and
secretion].
Length = 251
Score = 26.8 bits (59), Expect = 6.6
Identities = 24/104 (23%), Positives = 38/104 (36%), Gaps = 24/104 (23%)
Query: 183 QTVFRNEIYAARTFGFLRDVERYRKAGCALGASLENSVVISEDDQV-MNHGGLRYSG--- 238
Q V N + A T GF + R + + V++ M+ G L Y+G
Sbjct: 19 QAVTANNLANASTTGFRAQLNAARAVQVHGDSLPTRTFVMASTPGTDMSPGSLDYTGRPL 78
Query: 239 ------------------EEFVR--HKTLDAIGDIALAGYPVIG 262
E + R + +DA G + + G+PVIG
Sbjct: 79 DVAIQGDGWLAVQDADGSEAYTRNGNIQIDATGQLTIQGHPVIG 122
>gnl|CDD|33033 COG3220, COG3220, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 282
Score = 26.8 bits (59), Expect = 7.8
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 10/61 (16%)
Query: 198 FLRDVERYRKAGCALGASLENSVVISEDDQVMNHGGLRYSGEEFVRHKTLDAIGDIALAG 257
FL + R+AGC L + N V + +NHG + EE++ ++ +G+I LAG
Sbjct: 157 FLNAL--AREAGCGLLLDVNNIYVNA-----VNHG---FDPEEYLAALPVERVGEIHLAG 206
Query: 258 Y 258
+
Sbjct: 207 H 207
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
0.322 0.137 0.404
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,532,979
Number of extensions: 183889
Number of successful extensions: 370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 361
Number of HSP's successfully gapped: 12
Length of query: 296
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 203
Effective length of database: 4,254,100
Effective search space: 863582300
Effective search space used: 863582300
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 (25.7 bits)