RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780563|ref|YP_003064976.1| extracellular solute-binding
protein [Candidatus Liberibacter asiaticus str. psy62]
(195 letters)
>gnl|CDD|31069 COG0725, ModA, ABC-type molybdate transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 258
Score = 42.2 bits (99), Expect = 8e-05
Identities = 35/144 (24%), Positives = 58/144 (40%), Gaps = 5/144 (3%)
Query: 1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQN-QSVMLPIIHSFEERTGVKISPIY 59
M K L+LL A S +T++ + + I FE+ TGVK+ +
Sbjct: 4 MKKILALLLLVLLALGCAAGSAAQEAATITVFAAASLTDALEEIAKQFEKETGVKVEVEF 63
Query: 60 TSSIQ-RPPITQGSPVDVIITKDETSL--ALNEDLLHKLPAHLIKKNSFVLKNENKKLMR 116
S I QG+P D+ I+ D+ + ++ L++ + N VL +
Sbjct: 64 GGSGALARQIEQGAPADLFISADDAYMDKLEDKGLIYADSRIVFAGNRLVLAVPKGSKKK 123
Query: 117 ISFDTQVLAYSTKRIKIADLPKSV 140
I +L R+ I D PK+V
Sbjct: 124 IESLEDLLERPDVRLAIGD-PKTV 146
>gnl|CDD|31031 COG0687, PotD, Spermidine/putrescine-binding periplasmic protein
[Amino acid transport and metabolism].
Length = 363
Score = 36.6 bits (84), Expect = 0.005
Identities = 32/159 (20%), Positives = 53/159 (33%), Gaps = 22/159 (13%)
Query: 10 LLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPI- 68
L A + E T + + +L FE+ TG+K+ S +
Sbjct: 17 ALAALAGAAAAAAEGKTLNVYNWGGYIDPALLK---PFEKETGIKVVYDTFDSNEEMLAK 73
Query: 69 --TQGSPVDVII-TKDETSLALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFD----- 120
G DV++ + + + E LL L + + L FD
Sbjct: 74 LKAGGGGYDVVVPSGYFVARLIKEGLLQPLDKSKLPNWKNLDPE---FLNPPKFDPGNKY 130
Query: 121 -------TQVLAYSTKRIKIADLPKSVFDLTNAQWKKRL 152
T +AY+T ++K A P S DL + + L
Sbjct: 131 SVPYFWGTTGIAYNTDKVKDAPPPTSWADLFDPEKFPGL 169
>gnl|CDD|32025 COG1840, AfuA, ABC-type Fe3+ transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 299
Score = 35.8 bits (82), Expect = 0.007
Identities = 23/122 (18%), Positives = 44/122 (36%), Gaps = 9/122 (7%)
Query: 43 IIHSFEERTGVKISPIYTSSI-----QRPPITQGSPVDVIITKDETSL--ALNEDLLHKL 95
+I +FE++ G+K+ + S DV+ SL LL
Sbjct: 1 LIKAFEKKPGIKVEFVDAGSGELLARIIAEKGNPQAADVLWGGAPVSLDQLKEAGLLQPY 60
Query: 96 PAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIK--IADLPKSVFDLTNAQWKKRLS 153
+ + + + + V A +T K + +PKS DL ++K ++
Sbjct: 61 KSPELDEIPAWAPDPDGAYGGGYVGPLVFAVNTDYNKDLLKPVPKSWADLAKPEYKGKVQ 120
Query: 154 IA 155
+A
Sbjct: 121 MA 122
>gnl|CDD|37919 KOG2708, KOG2708, KOG2708, Predicted metalloprotease with chaperone
activity (RNAse H/HSP70 fold) [Posttranslational
modification, protein turnover, chaperones].
Length = 336
Score = 30.3 bits (68), Expect = 0.34
Identities = 26/108 (24%), Positives = 46/108 (42%), Gaps = 16/108 (14%)
Query: 35 QNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVIITKDETSLALNEDLLHK 94
+++ +L ++ E GV I + P G+P+ V+ +A LL
Sbjct: 48 HHRAWILGLVKQALEEAGVTSDDIDCICYTKGP-GMGAPLSVVAI-----VARTLSLLWN 101
Query: 95 LP--------AHLIKKNSFVLKNENKKLMRISF-DTQVLAYSTKRIKI 133
P H I+ + +N ++ +S +TQV+AYS KR +I
Sbjct: 102 KPLVGVNHCIGH-IEMGREITGAQNPVVLYVSGGNTQVIAYSEKRYRI 148
>gnl|CDD|28891 cd00007, 35EXOc, 3'-5' exonuclease. The 35EXOc domain is
responsible for the 3'-5' exonuclease proofreading
activity of prokaryotic DNA polymerase I (pol I) and
other enzymes, it catalyses the hydrolysis of unpaired
or mismatched nucleotides. This domain consists of the
amino-terminal half of the Klenow fragment in E. coli
pol I. 35EXOc is also found in the Werner syndrome
helicase (WRN), focus forming activity 1 protein (FFA-1)
and ribonuclease D (RNase D)..
Length = 155
Score = 29.2 bits (65), Expect = 0.81
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 4/53 (7%)
Query: 98 HLIKKNSFVLKNENKKLMRISFDTQVLAY----STKRIKIADLPKSVFDLTNA 146
H K + VL + +L FDT + AY + DL K +
Sbjct: 60 HDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIELD 112
>gnl|CDD|176649 cd06128, DNA_polA_exo, DEDDy 3'-5' exonuclease domain of family-A
DNA polymerases. The 3'-5' exonuclease domain of
family-A DNA polymerases has a fundamental role in
reducing polymerase errors and is involved in
proofreading activity. Family-A DNA polymerases contain
a DnaQ-like exonuclease domain in the same polypeptide
chain as the polymerase domain, similar to family-B DNA
polymerases. The exonuclease domain contains three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
which are clustered around the active site and contain
four invariant acidic residues that serve as ligands for
the two metal ions required for catalysis. The Klenow
fragment (KF) of Escherichia coli Pol I, the Thermus
aquaticus (Taq) Pol I, and Bacillus stearothermophilus
(BF) Pol I are examples of family-A DNA polymerases.
They are involved in nucleotide excision repair and in
the processing of Okazaki fragments that are generated
during lagging strand synthesis. The N-terminal domains
of BF Pol I and Taq Pol I resemble the fold of the 3'-5'
exonuclease domain of KF without the proofreading
activity of KF. The four critical metal-binding residues
are not conserved in BF Pol I and Taq Pol I, and they
are unable to bind metals necessary for exonuclease
activity.
Length = 151
Score = 28.9 bits (64), Expect = 0.85
Identities = 14/46 (30%), Positives = 20/46 (43%)
Query: 81 DETSLALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAY 126
E L ED +K + +L N +L I+FDT + AY
Sbjct: 42 LELLKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAY 87
>gnl|CDD|133047 cd06425, M1P_guanylylT_B_like_N, N-terminal domain of the
M1P-guanylyltransferase B-isoform like proteins.
GDP-mannose pyrophosphorylase (GTP:
alpha-d-mannose-1-phosphate guanyltransferase) catalyzes
the formation of GDP-d-mannose from GTP and
alpha-d-mannose-1-Phosphate. It contains an N-terminal
catalytic domain and a C-terminal Lefthanded-beta-Helix
fold domain. GDP-d-mannose is the activated form of
mannose for formation of cell wall lipoarabinomannan and
various mannose-containing glycolipids and
polysaccharides. The function of GDP-mannose
pyrophosphorylase is essential for cell wall integrity,
morphogenesis and viability. Repression of GDP-mannose
pyrophosphorylase in yeast leads to phenotypes, such as
cell lysis, defective cell wall, and failure of
polarized growth and cell separation.
Length = 233
Score = 27.2 bits (61), Expect = 3.2
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 37 QSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPV----DVIITKDETSLALNEDLL 92
M+P + +E++ G+KI+ SI+ P+ P+ D++ DE LN D++
Sbjct: 57 PEDMVPFLKEYEKKLGIKITF----SIETEPLGTAGPLALARDLLGDDDEPFFVLNSDVI 112
Query: 93 HKLP 96
P
Sbjct: 113 CDFP 116
>gnl|CDD|146401 pfam03743, TrbI, Bacterial conjugation TrbI-like protein. Although
not essential for conjugation, the TrbI protein greatly
increase the conjugational efficiency.
Length = 186
Score = 27.1 bits (61), Expect = 3.3
Identities = 13/74 (17%), Positives = 30/74 (40%), Gaps = 9/74 (12%)
Query: 12 LLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTS-SIQRPP--- 67
LL G +A + ++ T ++ + + +++ Y +I PP
Sbjct: 115 LLSGGGQAAAASASS---TSGNGNTSTLQAGDSGA--GQAASQLAQQYLERAINIPPTIE 169
Query: 68 ITQGSPVDVIITKD 81
I G V++++ +D
Sbjct: 170 INPGRRVNIVVARD 183
>gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5'
exonuclease domain of Bacillus stearothermophilus DNA
polymerase I and similar family-A DNA polymerases.
Bacillus stearothermophilus-like Polymerase I (Pol I), a
subgroup of the family-A DNA polymerases, contains an
inactive DnaQ-like 3'-5' exonuclease domain in the same
polypeptide chain as the polymerase region. The
exonuclease-like domain of these proteins possess the
same fold as the Klenow fragment (KF) of Escherichia
coli Pol I, but does not contain the four critical
metal-binding residues necessary for activity. The
function of this domain is unknown. It might act as a
spacer between the polymerase and the 5'-3' exonuclease
domains. Some members of this subgroup, such as those
from Bacillus sphaericus and Thermus aquaticus, are
thermostable DNA polymerases.
Length = 178
Score = 26.5 bits (59), Expect = 5.0
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 97 AHLIKKNSFVLKNENKKLMRISFDTQVLAY---STKRI-KIADL 136
H K+ LK +L ++FDT + AY T+ +ADL
Sbjct: 61 GHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADL 104
>gnl|CDD|111923 pfam03082, MAGSP, Male accessory gland secretory protein. The
accessory gland of male insects is a genital tissue that
secretes many components of the ejaculatory fluid, some
of which affect the female's receptivity to courtship
and her rate of oviposition. This protein is expressed
exclusively in the male accessory glands of adult
Drosophila melanogaster. The proteins are transferred to
the female fly during copulation and are rapidly altered
in the female genital tract.
Length = 267
Score = 26.3 bits (57), Expect = 5.1
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 131 IKIADLPKSVFDLTNAQWKKRLSIAPNNISFHRLLN 166
I I+DLP + + N++ K SI NNI F++ L+
Sbjct: 75 IDISDLPLDDYPINNSKSLKNSSIDLNNIPFNKGLD 110
>gnl|CDD|38225 KOG3015, KOG3015, KOG3015, F1-ATP synthase assembly protein [Energy
production and conversion].
Length = 283
Score = 26.5 bits (58), Expect = 5.3
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 20 FSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQ 70
FS E+ + L D P+I FE R GVK+ P + +I +
Sbjct: 144 FSPES--EDLGRLRDLQVEEWDPLIEWFENRLGVKLQP--SDNILGGKQAE 190
>gnl|CDD|176651 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain
of Escherichia coli DNA polymerase I and similar
bacterial family-A DNA polymerases. Escherichia
coli-like Polymerase I (Pol I), a subgroup of family-A
DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5'
exonuclease domain in the same polypeptide chain as the
polymerase domain. The exonuclease domain contains three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific YX(3)D pattern at ExoIII. These motifs
are clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. The 3'-5'
exonuclease domain of DNA polymerases has a fundamental
role in reducing polymerase errors and is involved in
proofreading activity. E. coli DNA Pol I is involved in
genome replication but is not the main replicating
enzyme. It is also implicated in DNA repair.
Length = 193
Score = 25.9 bits (58), Expect = 7.1
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 106 VLKNENKKLMRISFDTQVLAY 126
VL N +L +FDT + +Y
Sbjct: 81 VLANHGIELRGPAFDTMLASY 101
>gnl|CDD|58176 cd03510, Rhizobitoxine-FADS-like, This CD includes the
dihydrorhizobitoxine fatty acid desaturase (RtxC)
characterized in Bradyrhizobium japonicum USDA110, and
other related proteins. Dihydrorhizobitoxine desaturase
is reported to be involved in the final step of
rhizobitoxine biosynthesis. This domain family appears
to be structurally related to the membrane fatty acid
desaturases and the alkane hydroxylases. They all share
in common extensive hydrophobic regions that would be
capable of spanning the membrane bilayer at least twice.
Comparison of sequences also reveals the existence of
three regions of conserved histidine cluster motifs that
contain eight histidine residues: HXXXH, HXX(X)HH, and
HXXHH. These histidine residues are reported to be
catalytically essential and proposed to be the ligands
for the iron atoms contained within homologs, stearoyl
CoA desaturase and alkane hydroxylase..
Length = 175
Score = 25.6 bits (56), Expect = 8.6
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 144 TNAQWKKRLSIAPNNISFH 162
T W +RL AP+NI++H
Sbjct: 136 TFGGWIERLLFAPHNINYH 154
>gnl|CDD|37008 KOG1797, KOG1797, KOG1797, Uncharacterized conserved protein
(Neuroblastoma-amplified protein) [Function unknown].
Length = 1660
Score = 25.5 bits (55), Expect = 9.5
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 20 FSTENTTKYLTLYTDQNQSVMLPIIHSFEER 50
E+ L L T+ + M+ I FEE
Sbjct: 1017 LDAEDAALELGLCTNCGCADMMNIAIKFEEH 1047
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 0.133 0.371
Gapped
Lambda K H
0.267 0.0631 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,191,613
Number of extensions: 105908
Number of successful extensions: 280
Number of sequences better than 10.0: 1
Number of HSP's gapped: 278
Number of HSP's successfully gapped: 25
Length of query: 195
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 106
Effective length of database: 4,340,536
Effective search space: 460096816
Effective search space used: 460096816
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 (25.2 bits)