RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780955|ref|YP_003065368.1| hypothetical protein
CLIBASIA_04270 [Candidatus Liberibacter asiaticus str. psy62]
(204 letters)
>gnl|CDD|33607 COG3814, COG3814, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 157
Score = 182 bits (462), Expect = 7e-47
Identities = 100/180 (55%), Positives = 123/180 (68%), Gaps = 23/180 (12%)
Query: 25 MNYDHIRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNY 84
M DHIRYDILA+EALRG+VK VL++VA+ G LPG+HHFYITF T A GVRI L++ Y
Sbjct: 1 MGQDHIRYDILAQEALRGVVKKVLAKVAATG-LPGDHHFYITFLTGAPGVRIPSKLKQKY 59
Query: 85 PEKMTIVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFNAIKGFYDPSVNFELEFDVHI 144
PE+MTIV+Q+QFWDLKV D F V LSFS VPE+L IPF+A++GFYDPSVNFELEFDV
Sbjct: 60 PEQMTIVLQHQFWDLKVTDTGFSVTLSFSGVPEKLYIPFDALRGFYDPSVNFELEFDVS- 118
Query: 145 EHIEEKLEGGNTGKVLTSPDNFDKNQTNSVSQDSSKKKSTKKQNKNKMASVISLDNFRKK 204
+IEE+ E P+ N+ S + S+ +V+SLD FRKK
Sbjct: 119 LNIEEEAE----------PEAEPSNKAKSGATSDSEG-----------PNVVSLDAFRKK 157
>gnl|CDD|146826 pfam04386, SspB, Stringent starvation protein B. Escherichia coli
stringent starvation protein B (SspB), is thought to
enhance the specificity of degradation of tmRNA-tagged
proteins by the ClpXP protease. The tmRNA tag, also
known as ssrA, is an 11-aa peptide added to the C
terminus of proteins stalled during translation, targets
proteins for degradation by ClpXP and ClpAP. SspB a
cytoplasmic protein that specifically binds to residues
1-4 and 7 of the tag. Binding of SspB enhances
degradation of tagged proteins by ClpX, and masks
sequence elements important for ClpA interactions,
inhibiting degradation by ClpA. However, more recent
work has cast doubt on the importance of SspB in
wild-type cells. SspB is encoded in an operon whose
synthesis is stimulated by carbon, amino acid, and
phosphate starvation. SspB may play a special role
during nutrient stress, for example by ensuring rapid
degradation of the products of stalled translation,
without causing a global increase in degradation of all
ClpXP substrates.
Length = 152
Score = 172 bits (439), Expect = 5e-44
Identities = 56/167 (33%), Positives = 82/167 (49%), Gaps = 15/167 (8%)
Query: 30 IRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMT 89
I YD L ALR + + VL++VA G L +H YITF T A GV++ L + YP+ M
Sbjct: 1 ITYDSLRPYALRAVYRWVLTDVAKEG-LDNDHTPYITFDTTAPGVQVPDELVERYPQIML 59
Query: 90 IVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFNAIKGFYDPSVNFELEFDVHIEHIEE 149
V+Q+ FWDL+V ++ F L F VPERL +PF AI FYDP F L+F+ +E
Sbjct: 60 NVLQHAFWDLEVGNDGFSFNLRFGGVPERLYVPFAAILAFYDPENGFGLQFEPEEADEDE 119
Query: 150 KLEGGNTGKVLTSPDNFDKNQTNSVSQDSSKKKSTKKQNKNKMASVI 196
+ + ++ + + + K K V+
Sbjct: 120 --------------EEEEDDEADEEDDEDPEPKDPPKTKGRPSLKVV 152
>gnl|CDD|36420 KOG1206, KOG1206, KOG1206, Peroxisomal multifunctional
beta-oxidation protein and related enzymes [Lipid
transport and metabolism].
Length = 272
Score = 28.1 bits (62), Expect = 1.8
Identities = 21/85 (24%), Positives = 28/85 (32%), Gaps = 9/85 (10%)
Query: 112 FSNVPERLVIPFNAIKGFYDPSVNFELEFDVHIEH---IEEKLEGGNTGKVLTSP-DNFD 167
F +P VIP A + NF+ +H E + L T K L D D
Sbjct: 37 FQVLPTFAVIPATATLLMDNLVDNFDYAMLLHGEQYFELCTTLPSNGTLKTLAKVLDVLD 96
Query: 168 KNQ-----TNSVSQDSSKKKSTKKQ 187
K N + D + K Q
Sbjct: 97 KGSGALVVGNFETYDETGKLIAYNQ 121
>gnl|CDD|146138 pfam03348, Serinc, Serine incorporator (Serinc). This is a family
of eukaryotic membrane proteins which incorporate serine
into membranes and facilitate the synthesis of the
serine-derived lipids phosphatidylserine and
sphingolipid. Members of this family contain 11
transmembrane domains and form intracellular complexes
with key enzymes involved in serine and sphingolipid
biosynthesis.
Length = 426
Score = 27.2 bits (61), Expect = 3.4
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 63 FYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVL 102
F++ A GV+ S++ R IQN FW K+L
Sbjct: 85 FFLILALLMIGVKSSKDPRA--------AIQNGFWFFKIL 116
>gnl|CDD|32800 COG2981, CysZ, Uncharacterized protein involved in cysteine
biosynthesis [Amino acid transport and metabolism].
Length = 250
Score = 26.4 bits (58), Expect = 5.3
Identities = 10/29 (34%), Positives = 12/29 (41%), Gaps = 3/29 (10%)
Query: 2 VSLWNFFSSRWQWF-FIIKWIDTLMNYDH 29
+ LW W F + WIDTLM
Sbjct: 36 ILLW--GGLFWLLFSQALPWIDTLMPGIP 62
>gnl|CDD|32922 COG3108, COG3108, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 185
Score = 26.0 bits (57), Expect = 7.3
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 14/64 (21%)
Query: 75 RISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFNAIKGFYDPSV 134
R+ ++ R+N +M + + + LK L+ H P G+ P+
Sbjct: 71 RLLRDWRQNEVVRMDPRLFDLVYQLKTLEGHRR--------------PVQVTSGYRSPAT 116
Query: 135 NFEL 138
N L
Sbjct: 117 NRML 120
>gnl|CDD|143839 pfam00054, Laminin_G_1, Laminin G domain.
Length = 131
Score = 25.7 bits (57), Expect = 7.9
Identities = 9/52 (17%), Positives = 21/52 (40%)
Query: 146 HIEEKLEGGNTGKVLTSPDNFDKNQTNSVSQDSSKKKSTKKQNKNKMASVIS 197
+E + G+ V+ S D + + +SV + + + T + + S
Sbjct: 30 RLEVSYDLGSGPAVVRSGDKLNDGKWHSVELERNGRSGTLSVDGEARVTGES 81
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
0.319 0.135 0.402
Gapped
Lambda K H
0.267 0.0674 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,500,288
Number of extensions: 126736
Number of successful extensions: 288
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 14
Length of query: 204
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 115
Effective length of database: 4,340,536
Effective search space: 499161640
Effective search space used: 499161640
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: 55 (25.1 bits)