RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780238|ref|YP_003064651.1| 30S ribosomal protein S11
[Candidatus Liberibacter asiaticus str. psy62]
(129 letters)
>gnl|CDD|30449 COG0100, RpsK, Ribosomal protein S11 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 149 bits (378), Expect = 2e-37
Identities = 69/129 (53%), Positives = 93/129 (72%)
Query: 1 MPKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSP 60
M K+ +R + + +KNI G AH+ ++FNNT +TITD GN I W+S +GF GSRK++P
Sbjct: 1 MAKAKARKKKKVKKNIADGVAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTP 60
Query: 61 FAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNG 120
+AAQ+A +D + KA+ HG+ S+EVKV G G GR++A+RAL A G I I DVT I HNG
Sbjct: 61 YAAQLAAEDAAKKAKEHGIKSVEVKVKGPGPGREAAIRALAAAGLKITRIEDVTPIPHNG 120
Query: 121 CRPRKRRRI 129
CRP KRRR+
Sbjct: 121 CRPPKRRRV 129
>gnl|CDD|144124 pfam00411, Ribosomal_S11, Ribosomal protein S11.
Length = 109
Score = 127 bits (321), Expect = 8e-31
Identities = 56/109 (51%), Positives = 75/109 (68%)
Query: 19 GRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHG 78
G AH+ ++FNNT +T+TD G ++WSS GF GSRK++P+AAQ A ++ + A+ G
Sbjct: 1 GIAHIQASFNNTIVTVTDVIGRVVSWSSAGGCGFKGSRKSTPYAAQTAAENAAKIAKEQG 60
Query: 79 MSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRR 127
+ +LEVK+ G G GR+SALRAL G I I DVT I HNGCRP K+R
Sbjct: 61 IKALEVKIKGPGPGRESALRALARSGLRIGRIRDVTPIPHNGCRPPKKR 109
>gnl|CDD|176982 CHL00041, rps11, ribosomal protein S11.
Length = 116
Score = 126 bits (318), Expect = 2e-30
Identities = 50/112 (44%), Positives = 69/112 (61%)
Query: 10 NRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDD 69
+ ++ I G H+ ++FNNT +T+TD G I+WSS GF G+RK +PFAAQ A ++
Sbjct: 5 RKSKRKIPKGVIHIQASFNNTIVTVTDVRGRVISWSSAGACGFKGARKGTPFAAQTAAEN 64
Query: 70 CSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGC 121
+ GM EV + G G GRD+ALRA+R G + SI DVT + HNGC
Sbjct: 65 AIRTVIDQGMKRAEVMIKGPGLGRDTALRAIRRSGLKLSSIRDVTPMPHNGC 116
>gnl|CDD|35629 KOG0408, KOG0408, KOG0408, Mitochondrial/chloroplast ribosomal
protein S11 [Translation, ribosomal structure and
biogenesis].
Length = 190
Score = 100 bits (251), Expect = 9e-23
Identities = 53/109 (48%), Positives = 71/109 (65%)
Query: 21 AHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMS 80
H+ ++FNNT +T+TD G I+WSS GF +RK +P AAQ A +A + GM
Sbjct: 82 IHIRASFNNTIVTVTDVKGEVISWSSCGTEGFRNTRKGTPIAAQTAAVAAIRRAVDQGMQ 141
Query: 81 SLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129
++ V+V GLG GR SAL+ LR G +VSI D T + HNGCRPRK+RR+
Sbjct: 142 TVRVRVKGLGPGRMSALKGLRMGGLLVVSITDNTPMPHNGCRPRKKRRL 190
>gnl|CDD|35628 KOG0407, KOG0407, KOG0407, 40S ribosomal protein S14 [Translation,
ribosomal structure and biogenesis].
Length = 139
Score = 53.5 bits (128), Expect = 2e-08
Identities = 41/122 (33%), Positives = 63/122 (51%), Gaps = 9/122 (7%)
Query: 16 IVSGRAHVVSTFNNTRITITDPHGN-TIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKA 74
V G AH+ ++FN+T + +TD G TI + + + ++SP+AA +A D +AK
Sbjct: 14 QVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKC 73
Query: 75 QNHGMSSLEVKVSG--------LGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126
+ G+++L +K+ G G SALRAL G I I DVT I + R +
Sbjct: 74 KELGITALHIKLRATGGTKTKTPGPGAQSALRALARSGMRIGRIEDVTPIPSDSTRRKGG 133
Query: 127 RR 128
RR
Sbjct: 134 RR 135
>gnl|CDD|133243 cd05112, PTKc_Itk, Catalytic domain of the Protein Tyrosine Kinase,
Interleukin-2-inducible T-cell Kinase. Protein Tyrosine
Kinase (PTK) family; Interleukin-2 (IL-2)-inducible
T-cell kinase (Itk); catalytic (c) domain. The PTKc
family is part of a larger superfamily that includes the
catalytic domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. Itk (also
known as Tsk or Emt) is a member of the Tec subfamily of
proteins, which are cytoplasmic (or nonreceptor) tyr
kinases with similarity to Src kinases in that they
contain Src homology protein interaction domains (SH3,
SH2) N-terminal to the catalytic tyr kinase domain.
Unlike Src kinases, most Tec subfamily members (except
Rlk) also contain an N-terminal pleckstrin homology (PH)
domain, which binds the products of PI3K and allows
membrane recruitment and activation. In addition, Itk
contains the Tec homology (TH) domain containing one
proline-rich region and a zinc-binding region. Tec
kinases are expressed mainly by haematopoietic cells.
Itk is expressed in T-cells and mast cells, and is
important in their development and differentiation. Of
the three Tec kinases expressed in T-cells, Itk plays
the predominant role in T-cell receptor (TCR) signaling.
It is activated by phosphorylation upon TCR crosslinking
and is involved in the pathway resulting in
phospholipase C-gamma1 activation and actin
polymerization. It also plays a role in the downstream
signaling of the T-cell costimulatory receptor CD28, the
T-cell surface receptor CD2, and the chemokine receptor
CXCR4. In addition, Itk is crucial for the development
of T-helper(Th)2 effector responses.
Length = 256
Score = 28.4 bits (63), Expect = 0.61
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 9 RNRERKNIVSGRAHVV--STFNNTRITITDPHGNT------IAWSSPKVVGFS 53
R+ +N + G VV S F TR + D + ++ + WSSP+V FS
Sbjct: 124 RDLAARNCLVGENQVVKVSDFGMTRFVLDDQYTSSTGTKFPVKWSSPEVFSFS 176
>gnl|CDD|36838 KOG1625, KOG1625, KOG1625, DNA polymerase alpha-primase complex,
polymerase-associated subunit B [Replication,
recombination and repair].
Length = 600
Score = 27.6 bits (61), Expect = 0.92
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 3/75 (4%)
Query: 2 PKSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRK-NSP 60
P SPS + K VV+TF ++ G+ + KV F ++K +
Sbjct: 145 PSSPSS--EKFEKRASVNPGEVVTTFGGEKLKDVSSKGSVGPSTQLKVTNFIDAKKPSYR 202
Query: 61 FAAQVATDDCSAKAQ 75
+ +D
Sbjct: 203 YMYDKLSDRSEVLRD 217
>gnl|CDD|145615 pfam02570, CbiC, Precorrin-8X methylmutase. This is a family
Precorrin-8X methylmutases also known as Precorrin
isomerase, CbiC/CobH, EC:5.4.1.2. This enzyme catalyses
the reaction: Precorrin-8X <=> hydrogenobyrinate. This
enzyme is part of the Cobalamin (vitamin B12)
biosynthetic pathway and catalyses a methyl
rearrangement.
Length = 198
Score = 27.0 bits (61), Expect = 1.7
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 94 DSALRALRAIGFTIVSICDVTMIAH 118
++ AL+A G I+ DVTM+A
Sbjct: 51 EAGRAALKA-GAPIL--TDVTMVAA 72
>gnl|CDD|33151 COG3342, COG3342, Uncharacterized conserved protein [Function
unknown].
Length = 265
Score = 26.1 bits (57), Expect = 3.1
Identities = 14/74 (18%), Positives = 26/74 (35%), Gaps = 8/74 (10%)
Query: 31 RITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQ--VATDDCSAKAQNHGMSSLEVKVSG 88
++ + D G A++ + ++G R + Q + +A M+ G
Sbjct: 82 QVGVVDQKGRAAAFTGRECYEYAGHRAGENYTVQGNLLAGPEVVEA----MAKAFESAKG 137
Query: 89 LGAGRDSALRALRA 102
R L AL A
Sbjct: 138 WLVER--LLAALAA 149
>gnl|CDD|31205 COG1001, AdeC, Adenine deaminase [Nucleotide transport and
metabolism].
Length = 584
Score = 26.0 bits (57), Expect = 3.3
Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 2/62 (3%)
Query: 8 IRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVAT 67
+ V V + +I + + HG T + V GF K A+ VA
Sbjct: 414 TEELRERLPVEDGKVVPLERDILKIAVLERHGKTGNVGNGFVKGF--GLKEGAIASTVAH 471
Query: 68 DD 69
D
Sbjct: 472 DS 473
>gnl|CDD|58177 cd03511, Rhizopine-oxygenase-like, This CD includes the putative
hydrocarbon oxygenase, MocD, a bacterial rhizopine
(3-O-methyl-scyllo-inosamine, 3-O-MSI) oxygenase, and
other related proteins. It has been proposed that MocD,
MocE (Rieske-like ferredoxin), and MocF (ferredoxin
reductase) under the regulation of MocR, act in concert
to form a ferredoxin oxygenase system that demethylates
3-O-MSI to form scyllo-inosamine. 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, HXXHH, 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 = 285
Score = 25.6 bits (56), Expect = 4.1
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 18 SGRAHVVSTFNNTRITITDPHGNTIAWSSP 47
G + NTR T+T+P + W+ P
Sbjct: 217 GGCPEDANDLRNTRTTLTNPPLRFLYWNMP 246
>gnl|CDD|112483 pfam03668, ATP_bind_2, P-loop ATPase protein family. This family
contains an ATP-binding site and could be an ATPase
(personal obs:C Yeats).
Length = 284
Score = 25.5 bits (56), Expect = 4.1
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 84 VKVSGL-GAGRDSALRALRAIGFTIV 108
V ++G GAG+ ALRAL +G+ V
Sbjct: 4 VIITGRSGAGKSVALRALEDLGYYCV 29
>gnl|CDD|133321 cd04121, Rab40, Rab40 subfamily. This subfamily contains Rab40a,
Rab40b, and Rab40c, which are all highly homologous. In
rat, Rab40c is localized to the perinuclear recycling
compartment (PRC), and is distributed in a
tissue-specific manor, with high expression in brain,
heart, kidney, and testis, low expression in lung and
liver, and no expression in spleen and skeletal muscle.
Rab40c is highly expressed in differentiated
oligodendrocytes but minimally expressed in
oligodendrocyte progenitors, suggesting a role in the
vesicular transport of myelin components. Unlike most
other Ras-superfamily proteins, Rab40c was shown to have
a much lower affinity for GTP, and an affinity for GDP
that is lower than for GTP. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 189
Score = 25.3 bits (55), Expect = 4.6
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 47 PKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEV 84
PK++ G+R + F QVAT+ A A+ +GM+ EV
Sbjct: 112 PKIL--VGNRLHLAFKRQVATEQAQAYAERNGMTFFEV 147
>gnl|CDD|133271 cd01868, Rab11_like, Rab11-like. Rab11a, Rab11b, and Rab25 are
closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 25.2 bits (56), Expect = 5.3
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 64 QVATDDCSAKAQNHGMSSLE 83
V T++ A A+ +G+S +E
Sbjct: 125 AVPTEEAKAFAEKNGLSFIE 144
>gnl|CDD|31846 COG1660, COG1660, Predicted P-loop-containing kinase [General
function prediction only].
Length = 286
Score = 25.1 bits (55), Expect = 5.4
Identities = 13/26 (50%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 84 VKVSGL-GAGRDSALRALRAIGFTIV 108
V V+GL GAG+ ALR L +G+ V
Sbjct: 4 VIVTGLSGAGKSVALRVLEDLGYYCV 29
>gnl|CDD|145912 pfam03014, SP2, Structural protein 2. This family represents
structural protein 2 of the hepatitis E virus. The high
basic amino acid content of this protein has lead to the
suggestion of a role in viral genomic RNA encapsidation.
Length = 639
Score = 25.1 bits (54), Expect = 5.6
Identities = 14/39 (35%), Positives = 16/39 (41%)
Query: 90 GAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRR 128
G RDS AL I T DV + G RP + R
Sbjct: 3 GDRRDSQPFALPYIHPTNPFAADVFSQSGAGARPGQPPR 41
>gnl|CDD|73031 cd03272, ABC_SMC3_euk, Eukaryotic SMC3 proteins; SMC proteins are
large (approximately 110 to 170 kDa), and each is
arranged into five recognizable domains. Amino-acid
sequence homology of SMC proteins between species is
largely confined to the amino- and carboxy-terminal
globular domains. The amino-terminal domain contains a
'Walker A' nucleotide-binding domain (GxxGxGKS/T, in
the single-letter amino-acid code), which by mutational
studies has been shown to be essential in several
proteins. The carboxy-terminal domain contains a
sequence (the DA-box) that resembles a 'Walker B'
motif, and a motif with homology to the signature
sequence of the ATP-binding cassette (ABC) family of
ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18)..
Length = 243
Score = 24.8 bits (54), Expect = 7.9
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 7/36 (19%)
Query: 28 NNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAA 63
+ T I P N + VG +GS K++ FAA
Sbjct: 14 DQTVIEPFSPKHNVV-------VGRNGSGKSNFFAA 42
>gnl|CDD|145559 pfam02481, DNA_processg_A, DNA recombination-mediator protein A.
The SMF family, of DNA processing chain A, dprA, are a
group of bacterial proteins. In H. pylori, dprA is
required for natural chromosomal and plasmid
transformation. It has now been shown that DprA is found
to bind cooperatively to single-stranded DNA (ssDNA) and
to interact with RecA. In the process, DprA-RecA-ssDNA
filaments are produced and these filaments catalyse the
homology-dependent formation of joint molecules. While
the E.coli SSB protein limits access of RecA to ssDNA,
DprA alleviates this barrier. It is proposed that DprA
is a new member of the recombination-mediator protein
family, dedicated to natural bacterial transformation.
Length = 210
Score = 24.4 bits (54), Expect = 9.0
Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 15/60 (25%)
Query: 54 GSRKNSP----FAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDS-ALR-ALRAIGFTI 107
G+RK S A ++A + VSGL G D+ A R AL A G TI
Sbjct: 49 GTRKPSAYGLRVARKLAAELAERGI---------TIVSGLARGIDTAAHRAALEAGGRTI 99
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 0.130 0.385
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,491,713
Number of extensions: 66018
Number of successful extensions: 176
Number of sequences better than 10.0: 1
Number of HSP's gapped: 174
Number of HSP's successfully gapped: 20
Length of query: 129
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,470,190
Effective search space: 205628740
Effective search space used: 205628740
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 (24.0 bits)