RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8945
(219 letters)
>gnl|CDD|235000 PRK02106, PRK02106, choline dehydrogenase; Validated.
Length = 560
Score = 159 bits (404), Expect = 6e-46
Identities = 75/204 (36%), Positives = 102/204 (50%), Gaps = 22/204 (10%)
Query: 10 RLADSLDVPDIQFHHDPMSVRDWITNPVNASSTNMSPFAYYDGITVRPILLKPKSRGYIQ 69
R +D P+IQ+H P+++R +N V G ++ SRG ++
Sbjct: 350 RSRAGVDWPNIQYHFLPVAIRYDGSNAVKG-----------HGFQAHVGPMRSPSRGSVK 398
Query: 70 LNATDPLWGPPLIFPKFFTKKPDLDVFVAGMKLGASIVQTEAMQKIHARLVDVSP-PQCV 128
L + DP P I + + + D F ++L I+ A+ R ++SP
Sbjct: 399 LKSADPR-AHPSILFNYMSTEQDWREFRDAIRLTREIMAQPALDPYRGR--EISPGADVQ 455
Query: 129 FYKFGTWDYWACIAMQFTGTIYHPVGTCKMGPKDDPGSVVDARLRVHGVENLRVVDASIM 188
+ D + + T YHP TCKMG DP +VVD RVHGVE LRVVDASIM
Sbjct: 456 TDE--EIDAFV---REHAETAYHPSCTCKMGT--DPMAVVDPEGRVHGVEGLRVVDASIM 508
Query: 189 PKIVRGNTNAPTIMIAEKAADMIK 212
P I GN NAPTIMIAEKAAD+I+
Sbjct: 509 PTITNGNLNAPTIMIAEKAADLIR 532
>gnl|CDD|218493 pfam05199, GMC_oxred_C, GMC oxidoreductase. This domain found
associated with pfam00732.
Length = 139
Score = 139 bits (353), Expect = 2e-42
Identities = 51/146 (34%), Positives = 70/146 (47%), Gaps = 7/146 (4%)
Query: 62 PKSRGYIQLNATDPLWGPPLIFPKFFTKKPDLDVFVAGMKLGASIVQTEAMQKIHARLVD 121
P+SRG + L+++DP G P+I P + + DL A ++L I+ L
Sbjct: 1 PRSRGRVTLSSSDP-LGLPVIDPNYLSDPADLAALRAALRLARRILAAA-----LVELTP 54
Query: 122 VSPPQCVFYKFGTWDYWACIAMQFTGTIYHPVGTCKMGPKDDPGSVVDARLRVHGVENLR 181
+ D T +HP+GTC+MG D G VVD LRVHGV+NLR
Sbjct: 55 GPVEVVPGAAEASDDEILEYIRAAAVTSWHPMGTCRMGADPDDG-VVDPDLRVHGVDNLR 113
Query: 182 VVDASIMPKIVRGNTNAPTIMIAEKA 207
VVDAS+ P GN +AE+A
Sbjct: 114 VVDASVFPSSPSGNPTLTIYALAERA 139
>gnl|CDD|225186 COG2303, BetA, Choline dehydrogenase and related flavoproteins
[Amino acid transport and metabolism].
Length = 542
Score = 140 bits (355), Expect = 5e-39
Identities = 69/207 (33%), Positives = 98/207 (47%), Gaps = 25/207 (12%)
Query: 10 RLADSLDVPDIQFHHDPMSVRDWITNPVNASSTNMSPFAYYDGITVRPILLKPKSRGYIQ 69
R + + PD Q+H P+ + G T+ ++PKSRG +
Sbjct: 353 RSGPAGEYPDGQYHFAPLPLAIR-------------AAGAEHGFTLHVGPMRPKSRGSVT 399
Query: 70 LNATDPLWGPPLIFPKFFTKKPDLDVFVAGMKLGASIVQTEAMQ-KIHARLVDVSPPQCV 128
L + DP P+I P + + + D +F AG++L I+ A+ + A L
Sbjct: 400 LRSPDPD-NRPVIDPNYLSAEGDRAIFRAGIRLTREIIGQPALDARRKAELAPGPRVT-- 456
Query: 129 FYKFGTWDYWACIAMQFTGTIYHPVGTCKMGPKDDPGSVVD-ARLRVHGVENLRVVDASI 187
T + + T YHP+GTC+MG DP +VVD LRVHG+ENLRVVDAS+
Sbjct: 457 -----TDEDISAAIRFLARTAYHPMGTCRMG--SDPAAVVDDPYLRVHGLENLRVVDASV 509
Query: 188 MPKIVRGNTNAPTIMIAEKAADMIKED 214
MP N N I +AE+AAD I D
Sbjct: 510 MPTSTGVNPNLTIIALAERAADHILGD 536
>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase. Choline dehydrogenase
catalyzes the conversion of exogenously supplied choline
into the intermediate glycine betaine aldehyde, as part
of a two-step oxidative reaction leading to the
formation of osmoprotectant betaine. This enzymatic
system can be found in both gram-positive and
gram-negative bacteria. As in Escherichia coli ,
Staphylococcus xylosus , and Sinorhizobium meliloti,
this enzyme is found associated in a transciptionally
co-induced gene cluster with betaine aldehyde
dehydrogenase, the second catalytic enzyme in this
reaction. Other gram-positive organisms have been shown
to employ a different enzymatic system, utlizing a
soluable choline oxidase or type III alcohol
dehydrogenase instead of choline dehydrogenase. This
enzyme is a member of the GMC oxidoreductase family
(pfam00732 and pfam05199), sharing a common
evoluntionary origin and enzymatic reaction with alcohol
dehydrogenase. Outgrouping from this model, Caulobacter
crescentus shares sequence homology with choline
dehydrogenase, yet other genes participating in this
enzymatic reaction have not currently been identified
[Cellular processes, Adaptations to atypical
conditions].
Length = 532
Score = 132 bits (333), Expect = 5e-36
Identities = 72/204 (35%), Positives = 107/204 (52%), Gaps = 20/204 (9%)
Query: 10 RLADSLDVPDIQFHHDPMSVRDWITNPVNASSTNMSPFAYYDGITVRPILLKPKSRGYIQ 69
R D +D P+IQ+H P+++R T A G V + SRG+++
Sbjct: 343 RSNDDVDYPNIQYHFLPVAIRYDGTKAPKAH-----------GFQVHVGPMYSNSRGHVK 391
Query: 70 LNATDPLWGPPLIFPKFFTKKPDLDVFVAGMKLGASIVQTEAMQKIHARLVDVSP-PQCV 128
+ + DP P ++F + + + D F +++ I++ +A+ ++SP P+
Sbjct: 392 IKSKDPFEKPEIVF-NYMSHEEDWREFREAIRVTREILKQKALDPYRGG--EISPGPEVQ 448
Query: 129 FYKFGTWDYWACIAMQFTGTIYHPVGTCKMGPKDDPGSVVDARLRVHGVENLRVVDASIM 188
+ D + + T HP GTCKMGP D SVVD RVHG+E LRVVDASIM
Sbjct: 449 TDE--EIDEFV---RRHGETALHPCGTCKMGPASDEMSVVDPETRVHGMEGLRVVDASIM 503
Query: 189 PKIVRGNTNAPTIMIAEKAADMIK 212
P+I GN NAP IM+ EKAAD+I+
Sbjct: 504 PRITNGNLNAPVIMMGEKAADIIR 527
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 94.5 bits (235), Expect = 1e-22
Identities = 63/207 (30%), Positives = 93/207 (44%), Gaps = 24/207 (11%)
Query: 10 RLADSLDVPDIQFHHDP-----MSVRDWITNPVNASSTNMSPFAYYDGITVRPILLKPKS 64
R + D PD P ++ D P A T + P + D + L++P S
Sbjct: 299 RWRPTHDRPD----TSPVLETVLNTADIEIRPYTAGFTALVPGSPRDDPHLGVALMRPHS 354
Query: 65 RGYIQLNATDPLWGPPLIFPKFFTKKPDLDVFVAGMKLGASIVQTEAMQKIHARLVDVSP 124
RG I+L + DP PP I ++ + D AG L ++ + + + V
Sbjct: 355 RGRIRLASADPA-DPPRIEHRYDSSAADRAALRAGAALAHELLGSPELGPLLEPAVREGE 413
Query: 125 PQCVFYKFGTWDYWACIAMQFTGTIYHPVGTCKMGPKDDPGSVVDARLRVHGVENLRVVD 184
W + T H G+C+MG +DDPG+VVDAR RV GVE L VVD
Sbjct: 414 -----------ASWVLARL---ATSQHLCGSCRMGGRDDPGAVVDARCRVRGVEGLWVVD 459
Query: 185 ASIMPKIVRGNTNAPTIMIAEKAADMI 211
SI+P I +A +M+AE+AA+ +
Sbjct: 460 GSILPVIPSRGPHATAVMVAERAAEFL 486
>gnl|CDD|215420 PLN02785, PLN02785, Protein HOTHEAD.
Length = 587
Score = 36.7 bits (85), Expect = 0.008
Identities = 42/161 (26%), Positives = 62/161 (38%), Gaps = 35/161 (21%)
Query: 62 PKSRGYIQLNATDPLWGPPLIFPKFFTKKPDLDVFVAGMKLGASIVQTE--------AMQ 113
P S G++ L T+ P + F +F DL V G++ IV+T Q
Sbjct: 424 PISTGHLSLINTNVDDNPSVTF-NYFKHPQDLQRCVYGIRTIEKIVKTNHFTNFTQCDKQ 482
Query: 114 KIHARL-------VDVSPPQCVFYKFGTWDYWACIAMQFTG----TIYHPVGTCKMGPKD 162
+ L +++ P T D + QF TI+H G C +G
Sbjct: 483 TMEKVLNMSVKANINLIPKH-------TNDTKS--LEQFCKDTVITIWHYHGGCHVG--- 530
Query: 163 DPGSVVDARLRVHGVENLRVVDASIMPKIVRGNTNAPTIMI 203
VVD +V GV LRV+D S + N A +M+
Sbjct: 531 ---KVVDQNYKVLGVSRLRVIDGSTFDESPGTNPQATVMMM 568
>gnl|CDD|131515 TIGR02462, pyranose_ox, pyranose oxidase. Pyranose oxidase (also
called glucose 2-oxidase) converts D-glucose and
molecular oxygen to 2-dehydro-D-glucose and hydrogen
peroxide. Peroxide production is believed to be
important to the wood rot fungi in which this enzyme is
found for lignin degradation.
Length = 544
Score = 30.2 bits (68), Expect = 0.91
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 147 GTIYHPVGTCKMGPKDDPGSVVDARLRVHGVENLRVVDASIMPKIVRGNTNAPTIMIAEK 206
G H GT ++G D+ +V + +VH +NL V +P N ++ A K
Sbjct: 476 GLALHLAGTTRIG-FDEQTTVANTDSKVHNFKNLYVGGNGNIPTAFGANPTLTSMCYAIK 534
Query: 207 AADMIK 212
+A+ I
Sbjct: 535 SAEYII 540
>gnl|CDD|148326 pfam06656, Tenui_PVC2, Tenuivirus PVC2 protein. This family
consists of several Tenuivirus PVC2 proteins from Rice
grassy stunt virus, Maize stripe virus and Rice hoja
blanca virus. The function of this family is unknown.
Length = 785
Score = 29.0 bits (65), Expect = 2.4
Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 7/56 (12%)
Query: 149 IYHPVGTCKMGPKDDPGSVVDARLRV--HGVENLRVVDASIMPKIVRGNTNAPTIM 202
+Y G C PK V + +RV E L + SI P N+N P +
Sbjct: 262 LYAIAGLCHRRPKLYEVEVDMSTVRVVQDEDEGLLADEDSIAP-----NSNVPDTV 312
>gnl|CDD|153437 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain of ATP-dependent DNA ligase IV
is a DNA-binding module that is part of the catalytic
core unit. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction mechanism.
DNA ligases play a vital role in the diverse processes
of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriohages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
IV is required for DNA non-homologous end joining
pathways, including recombination of the V(D)J
immunoglobulin gene segments in cells of the mammalian
immune system. DNA ligase IV is stabilized by forming a
complex with XRCC4, a nuclear phosphoprotein, which is
phosphorylated by DNA-dependent protein kinase. DNA
ligases have a highly modular architecture consisting of
a unique arrangement of two or more discrete domains.
The adenylation and C-terminal
oligouncleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
most members of the ATP-dependent DNA ligase family. The
catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is required
for the ATP-dependent DNA ligase nucleotidylation step.
The RxDK motif (motif VI), which is essential for ATP
hydrolysis, is located in the OB-fold domain.
Length = 140
Score = 27.5 bits (62), Expect = 3.0
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 12/49 (24%)
Query: 73 TDPLW------GPPLIFPKFFTKKPDL-----DVFVAGMKLGASIVQTE 110
P W PP KF +KPD+ D V +K A IV ++
Sbjct: 65 LKPHWKPFDKKAPPSSLLKFGKEKPDVWIEPKDSVVLEVK-AAEIVPSD 112
>gnl|CDD|235808 PRK06462, PRK06462, asparagine synthetase A; Reviewed.
Length = 335
Score = 28.1 bits (63), Expect = 3.4
Identities = 21/111 (18%), Positives = 44/111 (39%), Gaps = 19/111 (17%)
Query: 26 PMSVRDWITNPVNASSTNMSPFAYYDGITVRPILLKP-----KSRGYIQLNA------TD 74
P ++ + S ++S Y + V+ +L+ RG++++ TD
Sbjct: 7 PKEYEEF----LRMSWKHISSEKYRKVLKVQSSILRYTREFLDGRGFVEVLPPIISPSTD 62
Query: 75 PLWGPPLIFPKFFTKKPDLDVFVAGMKLGAS-IVQTEAMQKIHARLVDVSP 124
PL G P K+ +D + L S I+ + ++ ++ +SP
Sbjct: 63 PLMGLGSDLP---VKQISIDFYGVEYYLADSMILHKQLALRMLGKIFYLSP 110
>gnl|CDD|178621 PLN03072, PLN03072, 60S ribosomal protein L12; Provisional.
Length = 166
Score = 26.3 bits (58), Expect = 8.9
Identities = 23/59 (38%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 158 MGPKDDPGSVVDARLRVHGVENLRVVDASIM-PKIVRGNTNAPTIMIAEKAADMIKEDW 215
M PK DP VV+ +RV G E V AS + PKI G I E A +DW
Sbjct: 1 MPPKLDPSQVVEVYVRVTGGE---VGAASSLAPKI--GPLGLSPKKIGEDIAKETAKDW 54
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
0.323 0.139 0.442
Gapped
Lambda K H
0.267 0.0640 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,368,240
Number of extensions: 1046122
Number of successful extensions: 785
Number of sequences better than 10.0: 1
Number of HSP's gapped: 772
Number of HSP's successfully gapped: 19
Length of query: 219
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 126
Effective length of database: 6,812,680
Effective search space: 858397680
Effective search space used: 858397680
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 (21.9 bits)
S2: 57 (25.9 bits)