RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019319
(343 letters)
>gnl|CDD|215508 PLN02941, PLN02941, inositol-tetrakisphosphate 1-kinase.
Length = 328
Score = 555 bits (1433), Expect = 0.0
Identities = 216/295 (73%), Positives = 245/295 (83%), Gaps = 3/295 (1%)
Query: 19 SFPQTQQQSKLVVVGYALTSKKTKSFLQPKLEGLARNKGILFVAIDQNRPLSDQGPFDIV 78
+ + Q K VVGYALT KK KSFLQP LE LAR+KGI VAID +RPLS+QGPFD++
Sbjct: 11 APLSSSSQQKRFVVGYALTPKKVKSFLQPSLEALARSKGIDLVAIDPSRPLSEQGPFDVI 70
Query: 79 LHKLTGKEWRQILEEYRQTHPEVTVLDPPYAIQHLHNRQSMLQCVADMNLSNSYGKVDVP 138
LHKL GKEWRQ LEEYR+ HP+VTVLDPP AIQ LHNRQSMLQ VAD+ LS+ YG V VP
Sbjct: 71 LHKLYGKEWRQQLEEYREKHPDVTVLDPPDAIQRLHNRQSMLQVVADLKLSDGYGSVGVP 130
Query: 139 RQLVIERDASSIPDVVLKAGLTLPLVAKPLVADGSAKSHELSLAYDQYSLKKLEPPLVLQ 198
+QLV+ D SSIPD V AGL PLVAKPLVADGSAKSH++SLAYDQ L KLEPPLVLQ
Sbjct: 131 KQLVVYDDESSIPDAVALAGLKFPLVAKPLVADGSAKSHKMSLAYDQEGLSKLEPPLVLQ 190
Query: 199 EFVNHGGVLFKVYIVGEAIKVVRRFSLPDVTKQDLSTSAGVFRFPRVSCAAASADDAD-- 256
EFVNHGGVLFKVY+VG+ +K VRRFSLPDV++++LS++ GV FPRVS AAASADDAD
Sbjct: 191 EFVNHGGVLFKVYVVGDYVKCVRRFSLPDVSEEELSSAEGVLPFPRVSNAAASADDADNG 250
Query: 257 -LDPCVAELPPRPLLERLAKELRRQLGLRLFNLDIIREHGTRDQFYVIDINYFPG 310
LDP VAELPPRP LE LA+ELRR+LGLRLFN D+IREHGT D++YVIDINYFPG
Sbjct: 251 GLDPEVAELPPRPFLEDLARELRRRLGLRLFNFDMIREHGTGDRYYVIDINYFPG 305
>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 = 470 bits (1211), Expect = e-168
Identities = 188/291 (64%), Positives = 222/291 (76%), Gaps = 4/291 (1%)
Query: 22 QTQQQSKLVVVGYALTSKKTKSFLQPKLEGLARNKGILFVAIDQNRPLSDQGPFDIVLHK 81
T + LV GYAL KK KSF+QP L LAR +GI V +D +RPLS+QGPFDI++HK
Sbjct: 2 DTFLKRYLV--GYALAEKKIKSFIQPSLAELARKRGIDLVQLDPSRPLSEQGPFDIIIHK 59
Query: 82 LTGKEWRQILEEYRQTHPEVTVLDPPYAIQHLHNRQSMLQCVADMNLSNSYGKVDVPRQL 141
LT KEWR LEE+R+ HPEV VLDPP AI+ LHNRQSMLQ VAD+NLS G+ VP Q+
Sbjct: 60 LTDKEWRHRLEEFREAHPEVPVLDPPPAIRRLHNRQSMLQVVADLNLSMEDGRFGVPPQV 119
Query: 142 VIERDASSIPDVVLKAGLTLPLVAKPLVADGSAKSHELSLAYDQYSLKKLEPPLVLQEFV 201
V+ +DASS+ KAGLT PL+AKPLVADG+AKSHE+SL YDQ L KL+PPLVLQEFV
Sbjct: 120 VVMKDASSLSRAGAKAGLTFPLIAKPLVADGTAKSHEMSLVYDQEGLNKLQPPLVLQEFV 179
Query: 202 NHGGVLFKVYIVGEAIKVVRRFSLPDVTKQDLSTSAGVFRFPRVSCAAASADDADLD--P 259
NHGGVLFKVY+VGE + VV+R SLPDV+ L S+G FRF +VS ASADDA+LD
Sbjct: 180 NHGGVLFKVYVVGEHVTVVKRRSLPDVSAGTLDRSSGSFRFSQVSNLTASADDAELDKIL 239
Query: 260 CVAELPPRPLLERLAKELRRQLGLRLFNLDIIREHGTRDQFYVIDINYFPG 310
+AE+PP P LE LA+ LRR LGLRLFN DIIR+ GT D++ VIDINYFPG
Sbjct: 240 EIAEMPPDPFLEDLARALRRALGLRLFNFDIIRDAGTADRYLVIDINYFPG 290
>gnl|CDD|223267 COG0189, RimK, Glutathione synthase/Ribosomal protein S6
modification enzyme (glutaminyl transferase) [Coenzyme
metabolism / Translation, ribosomal structure and
biogenesis].
Length = 318
Score = 39.7 bits (93), Expect = 0.002
Identities = 48/221 (21%), Positives = 74/221 (33%), Gaps = 46/221 (20%)
Query: 101 VTVLDPPYAIQHLHNRQSMLQCVADMNLSNSYGKVDVPRQLVIERDASSIPDVVLKAGLT 160
V V++ P +I+ N+ Q +A + VP L+ + V L
Sbjct: 105 VPVINDPQSIRRCRNKLYTTQLLAKA-------GIPVPPTLITRDPDEAAEFV--AEHLG 155
Query: 161 LPLVAKPLVADGSAKSHELSLAYDQYSLKKLE-------PPLVLQEFVNHGGVLFKVYIV 213
P+V KPL G L D L LE +++QE++ + +V
Sbjct: 156 FPVVLKPLDGSGGRGVF-LVEDADPELLSLLETLTQEGRKLIIVQEYIPKAKRDDRRVLV 214
Query: 214 GE----AIKVVRRFSLPDVTKQDLSTSAGVFRFPRVSCAAASADDADLDPCVAELPPRPL 269
G AI + R + +L+ EL
Sbjct: 215 GGGEVVAIYALARIPASGDFRSNLARGGRAEPC--------------------ELTEE-- 252
Query: 270 LERLAKELRRQLGLRLFNLDIIREHGTRDQFYVIDINYFPG 310
E LA + LGL L +DII +D YV ++N P
Sbjct: 253 EEELAVKAAPALGLGLVGVDIIE---DKDGLYVTEVNVSPT 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 = 36.9 bits (86), Expect = 0.006
Identities = 34/187 (18%), Positives = 62/187 (33%), Gaps = 35/187 (18%)
Query: 135 VDVPRQLVIERDASSIPDVVLKAGLTLPLVAKPLVADGSAKSH------ELSLAYDQYSL 188
+ VP +++ D + + G P+V KP GS EL A +
Sbjct: 17 LPVPPFFLVD-DEEDLDAAAEEIGF--PVVLKPRDGAGSLGVFRVDSAAELEAALAALAA 73
Query: 189 KK-LEPPLVLQEFVNHGGVLFKV--YIVGEAIKVVRRFSLPDVTKQDLSTSAGVFRFPRV 245
+ +++E++ G + V + + + V
Sbjct: 74 EVEDTREYLVEEYI--DGDEYHVDGLVDDGELVFLGVS--------RYLGPPPPDFSEGV 123
Query: 246 SCAAASADDADLDPCVAELPPRPLLERLAKELRRQLGLR--LFNLDIIREHGTRDQFYVI 303
+ S E P L LA+ + + LGLR +F+L+ R ++
Sbjct: 124 ELGSVS---------PGEDPLPEALRELAERVLKALGLRNGVFHLEFFLTPDGR--PVLL 172
Query: 304 DINYFPG 310
+IN PG
Sbjct: 173 EINPRPG 179
>gnl|CDD|215001 smart01058, CarD_TRCF, CarD-like/TRCF domain. CarD is a
Myxococcus xanthus protein required for the activation
of light- and starvation-inducible genes. This family
includes the presumed N-terminal domain. CarD interacts
with the zinc-binding protein CarG, to form a complex
that regulates multiple processes in Myxococcus
xanthus. This family also includes a domain to the
N-terminal side of the DEAD helicase of TRCF proteins.
TRCF displaces RNA polymerase stalled at a lesion,
binds to the damage recognition protein UvrA, and
increases the template strand repair rate during
transcription. This domain is involved in binding to
the stalled RNA polymerase.
Length = 99
Score = 30.9 bits (71), Expect = 0.23
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 54 RNKGILFVAIDQ----NRPLSDQGPFDIVLHKLTGKEWRQ 89
L+V +D +R + +G + VL KL G W +
Sbjct: 39 AGGDKLYVPVDNLDLGSRYVGSEGEVEPVLDKLGGGSWSK 78
>gnl|CDD|130780 TIGR01719, euk_UDPppase, uridine phosphorylase. This model
represents a clade of mainly eucaryotic uridine
phosphorylases. Genes from human and mouse have been
characterized. This enzyme is a member of the PHP/UDP
subfamily (pfam01048) and is closely related to the
bacterial uridine (TIGR01718) and inosine (TIGR00107)
phosphorylase equivalogs. In addition to the eukaryotes,
a gene from Mycobacterium leprae is included in this
equivalog and may have resulted from lateral gene
transfer [Purines, pyrimidines, nucleosides, and
nucleotides, Salvage of nucleosides and nucleotides].
Length = 287
Score = 30.9 bits (70), Expect = 0.78
Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 5/97 (5%)
Query: 164 VAKPLVADGSAKSHELSLAYDQYSLKKLEPPLVLQEFVNHGGVLFKVYIV-GEAIKVVRR 222
V L +S D++++ K+ P L V+HG + + I+ E IK++
Sbjct: 50 VGAELGLSCGRDYPNISERGDRFAMYKVGPVL----CVSHGMGIPSISIMLHELIKLLYY 105
Query: 223 FSLPDVTKQDLSTSAGVFRFPRVSCAAASADDADLDP 259
+ T + TS G+ P ++ A DA L P
Sbjct: 106 ARCKNPTFIRIGTSGGIGVPPGTVVVSSEAVDACLKP 142
>gnl|CDD|181458 PRK08527, PRK08527, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 563
Score = 30.8 bits (70), Expect = 1.2
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 85 KEWRQILEEYRQTHP-----EVTVLDPPYAIQHL 113
KEWR+IL+ Y + HP VL P + I+ +
Sbjct: 341 KEWREILKRYNELHPLSYEDSDEVLKPQWVIERV 374
>gnl|CDD|221300 pfam11898, DUF3418, Domain of unknown function (DUF3418). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria. This domain is typically
between 582 to 594 amino acids in length. This domain is
found associated with pfam07717, pfam00271, pfam04408.
Length = 586
Score = 30.6 bits (70), Expect = 1.4
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 7/51 (13%)
Query: 260 CVAELPPR--PLLERLAKELRRQLGLRL----FNLDIIREHGTRDQFYVID 304
+ L P PLL+ LA+ELRR G+R+ ++L+ + H R F V+D
Sbjct: 218 FLEALEPGEGPLLDALARELRRMTGVRIPPDDWDLEALPPH-LRMNFRVVD 267
>gnl|CDD|179554 PRK03204, PRK03204, haloalkane dehalogenase; Provisional.
Length = 286
Score = 29.1 bits (65), Expect = 2.9
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 5/27 (18%)
Query: 261 VAELP-----PRPLLERLAKELRRQLG 282
VAE+P RPLL RLA+E+ LG
Sbjct: 200 VAEMPKQILAARPLLARLAREVPATLG 226
>gnl|CDD|176121 cd08430, PBP2_IlvY, The C-terminal substrate binding of LysR-type
transcriptional regulator IlvY, which activates the
expression of ilvC gene that encoding acetohydroxy acid
isomeroreductase for the biosynthesis of branched amino
acids; contains the type 2 periplasmic binding fold. In
Escherichia coli, IlvY is required for the regulation of
ilvC gene expression that encodes acetohydroxy acid
isomeroreductase (AHIR), a key enzyme in the
biosynthesis of branched-chain amino acids (isoleucine,
valine, and leucine). The ilvGMEDA operon genes encode
remaining enzyme activities required for the
biosynthesis of these amino acids. Activation of ilvC
transcription by IlvY requires the additional binding of
a co-inducer molecule (either alpha-acetolactate or
alpha-acetohydoxybutyrate, the substrates for AHIR) to a
preformed complex of IlvY protein-DNA. Like many other
LysR-family members, IlvY negatively auto-regulates the
transcription of its own divergently transcribed ilvY
gene in an inducer-independent manner. This
substrate-binding domain has significant homology to 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.
Length = 199
Score = 28.7 bits (65), Expect = 3.6
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 89 QILEEYRQTHPEVTVL----DPPYAIQHLHNRQ 117
ILE +R HP+V + DP AI + N +
Sbjct: 17 PILERFRAQHPQVEIKLHTGDPADAIDKVLNGE 49
>gnl|CDD|211907 TIGR04184, ATPgraspMvdD, ATP-grasp ribosomal peptide maturase, MvdD
family. The pair of ATP-grasp proteins MvdD and MvdC
(microviridin D and C), as well as an acetyltransferase,
produce microviridin K, an example of a RiPP
(ribosomally synthesized and posttranslationally
modified peptide). Microviridins are peptidase
inhibitors.
Length = 321
Score = 28.5 bits (64), Expect = 5.1
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 7/38 (18%)
Query: 104 LDPPYAIQHLHNRQSMLQCVADMNLSNSYGKVDVPRQL 141
LDP ++ N+Q LQ + L D+PR L
Sbjct: 112 LDPISNVRRAENKQLQLQIARKLGL-------DIPRTL 142
>gnl|CDD|235550 PRK05660, PRK05660, HemN family oxidoreductase; Provisional.
Length = 378
Score = 28.3 bits (64), Expect = 5.7
Identities = 14/26 (53%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 274 AKELRRQLGLRLFNLDIIREHGTRDQ 299
A +L + LGLR FNLD++ HG DQ
Sbjct: 148 AAKLAQGLGLRSFNLDLM--HGLPDQ 171
>gnl|CDD|163574 TIGR03862, flavo_PP4765, uncharacterized flavoprotein, PP_4765
family. This model describes a sharply distinctive
clade of proteins within the larger family of
flavoproteins described by pfam03486 and TIGRFAMs model
TIGR00275. The function is unknown.
Length = 376
Score = 28.2 bits (63), Expect = 7.0
Identities = 22/87 (25%), Positives = 31/87 (35%), Gaps = 15/87 (17%)
Query: 254 DADLDPCVAELPPRPLLERLAKELRRQLGLRLFNLDIIREHGTRDQFYVIDINYFPGEVW 313
D L+ L + L+ LR+ LGL ++RE FP W
Sbjct: 243 DLSLEQVTKRLAAPRGKQSLSNHLRKALGLDGVKRALLREV-------------FPKAAW 289
Query: 314 ENAGVRAH-IYRLPIKPD-TEPVQEKV 338
A I LP+ D T P+ E +
Sbjct: 290 SQPETLAQTIKALPLPLDGTRPIDEAI 316
>gnl|CDD|240024 cd04666, Nudix_Hydrolase_9, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 122
Score = 26.8 bits (60), Expect = 8.5
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 311 EVWENAGVRAHIYRLPI 327
E WE AGVR I + P+
Sbjct: 48 EAWEEAGVRGKIGKRPL 64
>gnl|CDD|224102 COG1181, DdlA, D-alanine-D-alanine ligase and related ATP-grasp
enzymes [Cell envelope biogenesis, outer membrane].
Length = 317
Score = 27.6 bits (62), Expect = 8.7
Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 15/90 (16%)
Query: 251 SADDADLDPCVAELPP--RPLLERLAKELRRQLGLR-LFNLDIIREHGTRDQFYVIDINY 307
S A D A L ++ LA + LG L +D + +F ++++N
Sbjct: 227 STGGAQYD-IPAGLTDEIHEEIKELALRAYKALGCLGLARVDFFVDDDE-GEFVLLEVNT 284
Query: 308 FPG--------EVWENAGVRAH--IYRLPI 327
PG + AG+ + R
Sbjct: 285 NPGMTAMSLFPKAAAAAGISFAILVLRFVE 314
>gnl|CDD|182281 PRK10170, PRK10170, hydrogenase 1 large subunit; Provisional.
Length = 597
Score = 28.1 bits (62), Expect = 9.5
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 120 LQCVADMNLSNSYGKVDVPR----QLVIERDASSIPDVVLKAGLTLPLVAKPLVADGSAK 175
+ C +++ S + G V++ R Q +I R A I +V++ L + KP G+
Sbjct: 237 MPCAINIDESGAVGAVNMERLNLVQSIITRTADFINNVMIPDALAIGQFNKPWSEIGTGL 296
Query: 176 SHELSLAYDQY 186
S + L+Y +
Sbjct: 297 SDKCVLSYGAF 307
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
0.319 0.137 0.397
Gapped
Lambda K H
0.267 0.0863 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,111,272
Number of extensions: 1798091
Number of successful extensions: 1835
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1832
Number of HSP's successfully gapped: 29
Length of query: 343
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 245
Effective length of database: 6,590,910
Effective search space: 1614772950
Effective search space used: 1614772950
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: 59 (26.3 bits)