RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 047754
(330 letters)
>gnl|CDD|215508 PLN02941, PLN02941, inositol-tetrakisphosphate 1-kinase.
Length = 328
Score = 449 bits (1157), Expect = e-160
Identities = 164/316 (51%), Positives = 221/316 (69%), Gaps = 5/316 (1%)
Query: 1 MSNHEGQPYCKIGYVFAPNKEQTVIQPSLITKATEQGIGLIRIDPDKPLTEQGPFDCIMH 60
+S+ Q +GY P K ++ +QPSL A +GI L+ IDP +PL+EQGPFD I+H
Sbjct: 13 LSSSSQQKRFVVGYALTPKKVKSFLQPSLEALARSKGIDLVAIDPSRPLSEQGPFDVILH 72
Query: 61 KLYGPDWTQQLQQFSSRNPDVRIIDPPESIERLHNRDSMLEVVSRLKIELNKEKVSVPNQ 120
KLYG +W QQL+++ ++PDV ++DPP++I+RLHNR SML+VV+ LK+ V VP Q
Sbjct: 73 KLYGKEWRQQLEEYREKHPDVTVLDPPDAIQRLHNRQSMLQVVADLKLSDGYGSVGVPKQ 132
Query: 121 AVVSETELVTRDMAIEELKLRFPLIAKPLEANGSDKSHQMYLIFDNEGLEVLEAPILLQE 180
VV + E D A+ L+FPL+AKPL A+GS KSH+M L +D EGL LE P++LQE
Sbjct: 133 LVVYDDESSIPD-AVALAGLKFPLVAKPLVADGSAKSHKMSLAYDQEGLSKLEPPLVLQE 191
Query: 181 FVNHGGIIFKVYVAGSSVKCVKRKSLPDISEEKMKSLKGFLPFSQISS--NSVDADEE-- 236
FVNHGG++FKVYV G VKCV+R SLPD+SEE++ S +G LPF ++S+ S D +
Sbjct: 192 FVNHGGVLFKVYVVGDYVKCVRRFSLPDVSEEELSSAEGVLPFPRVSNAAASADDADNGG 251
Query: 237 VDLEKTEMPREGFVVELSRALREALGLNLFNFDLIRDAGERDGYLVIDINYLPGYAKLPG 296
+D E E+P F+ +L+R LR LGL LFNFD+IR+ G D Y VIDINY PGYAK+PG
Sbjct: 252 LDPEVAELPPRPFLEDLARELRRRLGLRLFNFDMIREHGTGDRYYVIDINYFPGYAKMPG 311
Query: 297 YETLLMDFFLNVAKSK 312
YET+L DF L++ + K
Sbjct: 312 YETVLTDFLLSLVQKK 327
>gnl|CDD|114493 pfam05770, Ins134_P3_kin, Inositol 1, 3, 4-trisphosphate
5/6-kinase. This family consists of several inositol 1,
3, 4-trisphosphate 5/6-kinase proteins. Inositol
1,3,4-trisphosphate is at a branch point in inositol
phosphate metabolism. It is dephosphorylated by specific
phosphatases to either inositol 3,4-bisphosphate or
inositol 1,3-bisphosphate. Alternatively, it is
phosphorylated to inositol 1,3,4,6-tetrakisphosphate or
inositol 1,3,4,5-tetrakisphosphate by inositol
trisphosphate 5/6-kinase.
Length = 307
Score = 366 bits (941), Expect = e-127
Identities = 153/298 (51%), Positives = 206/298 (69%), Gaps = 4/298 (1%)
Query: 12 IGYVFAPNKEQTVIQPSLITKATEQGIGLIRIDPDKPLTEQGPFDCIMHKLYGPDWTQQL 71
+GY A K ++ IQPSL A ++GI L+++DP +PL+EQGPFD I+HKL +W +L
Sbjct: 10 VGYALAEKKIKSFIQPSLAELARKRGIDLVQLDPSRPLSEQGPFDIIIHKLTDKEWRHRL 69
Query: 72 QQFSSRNPDVRIIDPPESIERLHNRDSMLEVVSRLKIELNKEKVSVPNQAVVSETELVTR 131
++F +P+V ++DPP +I RLHNR SML+VV+ L + + + VP Q VV +
Sbjct: 70 EEFREAHPEVPVLDPPPAIRRLHNRQSMLQVVADLNLSMEDGRFGVPPQVVVMKDASSLS 129
Query: 132 DMAIEELKLRFPLIAKPLEANGSDKSHQMYLIFDNEGLEVLEAPILLQEFVNHGGIIFKV 191
A + L FPLIAKPL A+G+ KSH+M L++D EGL L+ P++LQEFVNHGG++FKV
Sbjct: 130 R-AGAKAGLTFPLIAKPLVADGTAKSHEMSLVYDQEGLNKLQPPLVLQEFVNHGGVLFKV 188
Query: 192 YVAGSSVKCVKRKSLPDISEEKMKSLKGFLPFSQIS---SNSVDADEEVDLEKTEMPREG 248
YV G V VKR+SLPD+S + G FSQ+S +++ DA+ + LE EMP +
Sbjct: 189 YVVGEHVTVVKRRSLPDVSAGTLDRSSGSFRFSQVSNLTASADDAELDKILEIAEMPPDP 248
Query: 249 FVVELSRALREALGLNLFNFDLIRDAGERDGYLVIDINYLPGYAKLPGYETLLMDFFL 306
F+ +L+RALR ALGL LFNFD+IRDAG D YLVIDINY PGYAK+P YET+L DFF
Sbjct: 249 FLEDLARALRRALGLRLFNFDIIRDAGTADRYLVIDINYFPGYAKMPEYETVLTDFFW 306
>gnl|CDD|223267 COG0189, RimK, Glutathione synthase/Ribosomal protein S6
modification enzyme (glutaminyl transferase) [Coenzyme
metabolism / Translation, ribosomal structure and
biogenesis].
Length = 318
Score = 38.5 bits (90), Expect = 0.003
Identities = 57/230 (24%), Positives = 86/230 (37%), Gaps = 64/230 (27%)
Query: 81 VRIIDPPESIERLHNRDSMLEVVSRLKIELNKEKVSVPNQAVVSETELVTRDM--AIEEL 138
V +I+ P+SI R N+ L L K + VP L+TRD A E +
Sbjct: 105 VPVINDPQSIRRCRNK---LYTTQLLA----KAGIPVPP-------TLITRDPDEAAEFV 150
Query: 139 K--LRFPLIAKPLEANGSDKSHQMYLIFDNEG--LEVLEA-------PILLQEFVNHGG- 186
L FP++ KPL+ +G L+ D + L +LE I++QE++
Sbjct: 151 AEHLGFPVVLKPLDGSGGRGVF---LVEDADPELLSLLETLTQEGRKLIIVQEYIPKAKR 207
Query: 187 ------IIFKVYVAGSSVKCVKRKSLPDISEEKMKSLKGFLPFSQISSNSVDADEEVDLE 240
+ VA + + R P + + SN + E
Sbjct: 208 DDRRVLVGGGEVVA---IYALARI--PASGDFR--------------SN-LARGGRA--E 245
Query: 241 KTEMPREGFVVELSRALREALGLNLFNFDLIRDAGERDGYLVIDINYLPG 290
E+ E EL+ ALGL L D+I D DG V ++N P
Sbjct: 246 PCELTEE--EEELAVKAAPALGLGLVGVDIIEDK---DGLYVTEVNVSPT 290
>gnl|CDD|222206 pfam13535, ATP-grasp_4, ATP-grasp domain. This family includes a
diverse set of enzymes that possess ATP-dependent
carboxylate-amine ligase activity.
Length = 183
Score = 37.6 bits (88), Expect = 0.004
Identities = 38/205 (18%), Positives = 67/205 (32%), Gaps = 61/205 (29%)
Query: 110 LNKEKVSVPNQAVVSETELVTRDMAIEELKLRFPLIAKPLEANGSDKSHQMYLIFDNEGL 169
L + VP +V + E + ++ FP++ KP + G S ++ + L
Sbjct: 12 LRAAGLPVPPFFLVDDEEDLDAAAE----EIGFPVVLKPRDGAG---SLGVFRVDSAAEL 64
Query: 170 E----------VLEAPILLQEF-----------VNHGGIIFKVYVAGSSVKCVKRKSLPD 208
E L++E+ V+ G ++ G S PD
Sbjct: 65 EAALAALAAEVEDTREYLVEEYIDGDEYHVDGLVDDG----ELVFLGVSRY--LGPPPPD 118
Query: 209 ISEEKMKSLKGFLPFSQISSNSVDADEEVDLEKTEMPREGFVVELSRALREALGLN--LF 266
SE L + + + EL+ + +ALGL +F
Sbjct: 119 FSEGV------ELGSVSPGEDPLPEA---------------LRELAERVLKALGLRNGVF 157
Query: 267 NFDLIRDAGERDGYLV-IDINYLPG 290
+ + DG V ++IN PG
Sbjct: 158 HLEFFLTP---DGRPVLLEINPRPG 179
>gnl|CDD|226433 COG3919, COG3919, Predicted ATP-grasp enzyme [General function
prediction only].
Length = 415
Score = 33.8 bits (77), Expect = 0.11
Identities = 41/197 (20%), Positives = 69/197 (35%), Gaps = 47/197 (23%)
Query: 123 VSETELVTRDMAIEELKLRFPLIAKPLE--ANGSDKSHQMYLIFDNEGL---------EV 171
+T LV ++ +L FP+I KP + + + + DNE + E+
Sbjct: 129 YPKTYLVNSEIDTLVDELTFPVILKPGMGGSVHFEARAKAFTAADNEEMKLALHRAYEEI 188
Query: 172 LEAPILLQEFVNHGGIIFKVYVA----GSSV-KCVKRKSLPDISEEKMKSLKGFLPFSQI 226
+++QEF+ GG Y A G V + R+ F
Sbjct: 189 GPDNVVVQEFIPGGGENQFSYAALWDKGHPVAEFTARRLRQYPV-----------DFGYT 237
Query: 227 SSNSVDADEEVDLEKTEMPREGFVVELSRALREALGLN-LFNFDLIRDAGERDG-YLVID 284
S+ E+ V++ +R E++ L + D RDG Y ++D
Sbjct: 238 ST------------VVEVVDNQQVIQAARDFLESIEHTGLVEVEFKYDP--RDGSYKLLD 283
Query: 285 INYLP----GYAKLPGY 297
+N P G GY
Sbjct: 284 VNPRPWRWFGLVTAAGY 300
>gnl|CDD|241419 cd13265, PH_evt, Evectin Pleckstrin homology (PH) domain. There
are 2 members of the evectin family (also called
pleckstrin homology domain containing, family B): evt-1
(also called PLEKHB1) and evt-2 (also called PLEKHB2).
evt-1 is specific to the nervous system, where it is
expressed in photoreceptors and myelinating glia. evt-2
is widely expressed in both neural and nonneural
tissues. Evectins possess a single N-terminal PH domain
and a C-terminal hydrophobic region. evt-1 is thought to
function as a mediator of post-Golgi trafficking in
cells that produce large membrane-rich organelles. It is
a candidate gene for the inherited human retinopathy
autosomal dominant familial exudative vitreoretinopathy
and a susceptibility gene for multiple sclerosis. evt-2
is essential for retrograde endosomal membrane transport
from the plasma membrane (PM) to the Golgi. Two membrane
trafficking pathways pass through recycling endosomes: a
recycling pathway and a retrograde pathway that links
the PM to the Golgi/ER. Its PH domain that is unique in
that it specifically recognizes phosphatidylserine (PS),
but not polyphosphoinositides. PS is an anionic
phospholipid class in eukaryotic biomembranes, is highly
enriched in the PM, and plays key roles in various
physiological processes such as the coagulation cascade,
recruitment and activation of signaling molecules, and
clearance of apoptotic cells. PH domains are only found
in eukaryotes. They share little sequence conservation,
but all have a common fold, which is electrostatically
polarized. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 108
Score = 29.2 bits (66), Expect = 1.00
Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 80 DVRIIDPPESIERLHNRDSMLEVVSR 105
+ R + PPE +RD +L++V+R
Sbjct: 61 ECRDVQPPEG----RSRDCLLQIVTR 82
>gnl|CDD|117020 pfam08443, RimK, RimK-like ATP-grasp domain. This ATP-grasp domain
is found in the ribosomal S6 modification enzyme RimK.
Length = 190
Score = 30.1 bits (68), Expect = 1.00
Identities = 25/100 (25%), Positives = 39/100 (39%), Gaps = 20/100 (20%)
Query: 110 LNKEKVSVPNQAVV-SETELVTRDMAIEELKLRFPLIAKPLE---------ANGSDKSHQ 159
L K + VPN + S + IE++K FP++ K + A Q
Sbjct: 11 LAKHGIPVPNTGLAWSPEDAEK---FIEQIK-GFPVVVKSVFGSQGIGVFLAEDEQSLEQ 66
Query: 160 MYLIFDNEGLEVLEAPILLQEFVNH-GGIIFKVYVAGSSV 198
+ E + L+ IL+QEF+ G + V G V
Sbjct: 67 LL-----EAFKWLKNQILVQEFIAEAGNRDIRCLVVGGEV 101
>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin
like protein family. The third LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 27.7 bits (62), Expect = 1.1
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 3 NHEGQPYCKIGY 14
HEG PYC+ Y
Sbjct: 41 EHEGLPYCETHY 52
>gnl|CDD|233301 TIGR01175, pilM, type IV pilus assembly protein PilM. This protein
is required for the assembly of the type IV fimbria in
Pseudomonas aeruginosa responsible for twitching
motility, and for a similar pilus-like structure in
Synechocystis. It is also found in species such as
Deinococcus described as having natural transformation
(for which a type IV pilus-like structure is proposed)
but not fimbria.
Length = 348
Score = 30.5 bits (69), Expect = 1.3
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 80 DVRIIDPPESIERLHNRDSMLEVVSRLKIELNKEKVSVPNQAVVSETELVTRDMAIEELK 139
+ I++ E L E++S L I K +VP AV+++ V + EL+
Sbjct: 44 EGHIVEYQAVAEALK------ELLSELGINTKKAATAVPGSAVITKVIPVPAGLDERELE 97
>gnl|CDD|237195 PRK12767, PRK12767, carbamoyl phosphate synthase-like protein;
Provisional.
Length = 326
Score = 29.9 bits (68), Expect = 1.9
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 6/55 (10%)
Query: 134 AIEELKLRFPLIAKPLEANGSDKSHQMYLIFDNEGLEVLEA---PILLQEFVNHG 185
A+ + +L+FPL KP +GS S ++ + D E LE L +++QEF+
Sbjct: 141 ALAKGELQFPLFVKPR--DGS-ASIGVFKVNDKEELEFLLEYVPNLIIQEFIEGQ 192
>gnl|CDD|131199 TIGR02144, LysX_arch, Lysine biosynthesis enzyme LysX. The family
of proteins found in this equivalog include the
characterized LysX from Thermus thermophilus which is
part of a well-organized lysine biosynthesis gene
cluster. LysX is believed to carry out an ATP-dependent
acylation of the amino group of alpha-aminoadipate in
the prokaryotic version of the fungal AAA lysine
biosynthesis pathway. No species having a sequence in
this equivalog contains the elements of the more common
diaminopimelate lysine biosythesis pathway, and none has
been shown to be a lysine auxotroph. These sequences
have mainly recieved the name of the related enzyme,
"ribosomal protein S6 modification protein RimK". RimK
has been characterized in E. coli, and acts by
ATP-dependent condensation of S6 with glutamate
residues.
Length = 280
Score = 29.7 bits (67), Expect = 2.0
Identities = 50/225 (22%), Positives = 87/225 (38%), Gaps = 55/225 (24%)
Query: 81 VRIIDPPESIERLHNRDSMLEVVSRLKIELNKEKVSVPNQAVVSETELVTRDMAIEELKL 140
V +I+ IE ++ + + LK L K V P + + E + E L
Sbjct: 73 VPVINSSHVIEACGDK-----IFTYLK--LAKAGVPTPRTYLAFDREAALK--LAEALG- 122
Query: 141 RFPLIAKPLEANGS---------DKSHQMYLIFDNEGLEVLEAPIL----LQEFVNHGGI 187
+P++ KP+ GS DK L+ E EVL +QE++N G
Sbjct: 123 -YPVVLKPVI--GSWGRLVALIRDKDELESLL---EHKEVLGGSQHKLFYIQEYINKPGR 176
Query: 188 IFKVYVAG-SSVKCVKRKSLPDISEEKMKSLKGFLPFSQISSNSVDADEEVDLEKTEMPR 246
+V+V G ++ + R S + + + +G DEEV+
Sbjct: 177 DIRVFVIGDEAIAAIYRYS----NHWRTNTARGGKA------EPCPLDEEVE-------- 218
Query: 247 EGFVVELSRALREALGLNLFNFDLIRDAGERDGYLVIDINYLPGY 291
EL+ EA+G + D+ + G LV ++N++P +
Sbjct: 219 -----ELAVKAAEAVGGGVVAIDIFES--KERGLLVNEVNHVPEF 256
>gnl|CDD|173870 cd08505, PBP2_NikA_DppA_OppA_like_18, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 528
Score = 29.6 bits (67), Expect = 2.7
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 215 KSLKGFLPFSQISSNSVDADEEVDLEKT-----EMPREGFVVELSRALREALGLNLFNFD 269
K L+G+ S ISS++ D V E+ ++G + LSRA+ ++ FN
Sbjct: 237 KFLQGYYDVSGISSDAFDQALRVSAGGEPELTPELAKKG--IRLSRAVEPSIFYIGFNML 294
>gnl|CDD|218843 pfam05988, DUF899, Bacterial protein of unknown function (DUF899).
This family consists of several uncharacterized
bacterial proteins of unknown function.
Length = 211
Score = 29.1 bits (66), Expect = 2.8
Identities = 17/83 (20%), Positives = 21/83 (25%), Gaps = 31/83 (37%)
Query: 42 RIDPDKPL-TEQGP------FD-----CIMHKLYGPDWTQQ-------LQQFSSRNPDVR 82
+D D GP F + H ++GP W F
Sbjct: 44 EVDKDYRFDGPDGPVTLADLFGGRSQLIVYHFMFGPGWEAGCPGCSFLADHFDGALAH-- 101
Query: 83 IIDPPESIERLHNRDSMLEVVSR 105
L RD L VSR
Sbjct: 102 ----------LAARDVALAAVSR 114
>gnl|CDD|227306 COG4972, PilM, Tfp pilus assembly protein, ATPase PilM [Cell
motility and secretion / Intracellular trafficking and
secretion].
Length = 354
Score = 28.9 bits (65), Expect = 3.6
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 6/59 (10%)
Query: 80 DVRIIDPPESIERLHNRDSMLEVVSRLKIELNKEKVSVPNQAVVSETELVTRDMAIEEL 138
D +I+D L +++L I+ +VP A +++T V ++ +EL
Sbjct: 51 DGKIVDYDAVASALK------RALAKLGIKSKNAATAVPGSAAITKTIPVPDELDEKEL 103
>gnl|CDD|214497 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
bacterial proteins, eukaryotic ones are in PBPe.
Length = 219
Score = 28.1 bits (63), Expect = 5.0
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 18/60 (30%)
Query: 219 GFLPFSQISSNSVDADEEVDLEKTEMPREGFVVELSRALREALGLNL----FNFDLIRDA 274
+ PFS D D E+ GF V+L++A+ + LGL + +FD + A
Sbjct: 9 DYPPFS-----FADEDGEL---------TGFDVDLAKAIAKELGLKVEFVEVSFDSLLTA 54
>gnl|CDD|239911 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
(HMBPP reductase) domain.While RPS1 is found primarily
in bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 2 of the Escherichia coli and Homo sapiens
RPS1 (ec2 and hs2, respectively). Autoantibodies to
double-stranded DNA from patients with systemic lupus
erythematosus cross-react with the human RPS1 homolog.
Length = 67
Score = 25.9 bits (58), Expect = 7.5
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 215 KSLKGFLPFSQISSNSVDADEE 236
+ ++ FLP SQ+ V+ +E
Sbjct: 21 EGVRAFLPASQVDLRPVEDLDE 42
>gnl|CDD|132871 cd07044, CofD_YvcK, Family of CofD-like proteins and proteins
related to YvcK. CofD is a 2-phospho-L-lactate
transferase that catalyzes the last step in the
biosynthesis of coenzyme F(420)-0 (F(420) without
polyglutamate) by transferring the lactyl phosphate
moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to
7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0).
F420 is a hydride carrier, important for energy
metabolism of methanogenic archaea, as well as for the
biosynthesis of other natural products, like
tetracycline in Streptomyces. F420 and some of its
precursors are also utilized as cofactors for enzymes,
like DNA photolyase in Mycobacterium tuberculosis. YvcK
from Bacillus subtilis is a member of a family of mostly
uncharacterized proteins and has been proposed to play a
role in carbon metabolism, since its function is
essential for growth on intermediates of the Krebs cycle
and pentose phosphate pathway. Both families appear to
have a conserved phosphate binding site, but have
different substrate binding residues conserved within
each family.
Length = 309
Score = 27.9 bits (62), Expect = 7.9
Identities = 41/238 (17%), Positives = 81/238 (34%), Gaps = 34/238 (14%)
Query: 75 SSRNPDVRIIDPPESIER----LHNRDSMLEVVSRLKIELNKEKV---SVPNQAVVSETE 127
S + + I PP + L +++ LE + + + E + S+ N A+ T
Sbjct: 37 SGELRNXQDIPPPGDLRNVLVALSDQEDRLEQLFQYRKEEGINEGLGHSLGNLAIAGXTS 96
Query: 128 LVTRDM-AIEELKLRFPLIAKPLEANGSDKSHQMYLIFDNEGLEVLEAPILLQEFVNHGG 186
+ AI EL F + L + SD ++ ++ + E+ I
Sbjct: 97 ITGDFTDAIVELSKVFNIKGNILPS--SDDPVSLHAEXEDGTIVHGESFI-----PKGEK 149
Query: 187 IIFKVYVAGSSVKCVKRKSLPDISEEKMKSLKGFLPFSQISSNSVDADEEVDLEKTEMPR 246
I +V++ R+ L I + + ++ I N
Sbjct: 150 KIDRVFLTPVDEASPSREVLEAIEKADNIVIGPGSLYTSILPNIS--------------- 194
Query: 247 EGFVVELSRALREALGLNLFNFDLIRDAGERDGYLVID-INYLPGYAKLPGYETLLMD 303
V + AL++ ++ ++ GE D Y D L + P + +L+D
Sbjct: 195 ---VPGIREALKKTXAKKVYVSNIXTQPGETDEYTSSDHAEALQRHLGRPFIDVVLVD 249
>gnl|CDD|213969 TIGR04356, grasp_GAK, ATP-grasp enzyme, GAK system. Members of
this family are ATP-grasp family enzymes related to a
number of characterized glutamate ligases, including the
ribosomal protein S6 modification enzyme RimK. This
group belongs to a conserved gene neighborhood that also
features an HPr kinase-related protein (see TIGR04355).
We assign this system the initial designation GAK, for
Grasp (this ATP-grasp family enzyme), Amphipathic (for
the member of family TIGR04354, designated Amphi-Trp),
and Kinase, for the HPr-kinase homolog TIGR04355.
Length = 287
Score = 27.7 bits (62), Expect = 9.7
Identities = 34/113 (30%), Positives = 50/113 (44%), Gaps = 22/113 (19%)
Query: 81 VRIIDPPESIERLHNRDSMLEVVSRLKIELNKEKVSVPNQAVVSETELVTRDMAIEELKL 140
V I PESI RL +R S + L + + +P VV+E D A+E ++
Sbjct: 85 VPIFSRPESIIRLIDRLS-------CTVSLRQGDIPMP-PTVVTE----DLDAALEAVER 132
Query: 141 RFPLIAKPLEANGSDKSHQMYLIFDNEGL-EVLEA-----PIL-LQEFVNHGG 186
+ KPL S K+ M ++ GL LEA P + +Q+ VN G
Sbjct: 133 YGKAVFKPLY---STKARGMEVLEPGPGLRAALEAFRQGNPFMYIQQKVNLPG 182
>gnl|CDD|184207 PRK13648, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 269
Score = 27.4 bits (61), Expect = 9.8
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 78 NPDVRIIDPPESIERLHNRDSMLEVVSRLKIELNKEKVSV 117
NP V I+D S+ R ++L++V ++K E N +S+
Sbjct: 160 NPSVIILDEATSMLDPDARQNLLDLVRKVKSEHNITIISI 199
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.136 0.386
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,954,648
Number of extensions: 1672977
Number of successful extensions: 1659
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1654
Number of HSP's successfully gapped: 30
Length of query: 330
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 233
Effective length of database: 6,635,264
Effective search space: 1546016512
Effective search space used: 1546016512
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.5 bits)