RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7153
(131 letters)
>gnl|CDD|238955 cd01997, GMP_synthase_C, The C-terminal domain of GMP synthetase.
It contains two subdomains; the ATP pyrophosphatase
domain which closes to the N-termial and the
dimerization domain at C-terminal end. The ATP-PPase is
a twisted, five-stranded parallel beta-sheet sandwiched
between helical layers. It has a signature
nucleotide-binding motif, or P-loop, at the end of the
first-beta strand.The dimerization domain formed by the
C-terminal 115 amino acid for prokaryotic proteins. It
is adjacent to teh ATP-binding site of the ATP-PPase
subdomain. The largest difference between the primary
sequence of prokaryotic and eukaryotic GMP synthetase
map to the dimerization domain.Eukaryotic GMP synthetase
has several large insertions relative to prokaryotes.
Length = 295
Score = 146 bits (370), Expect = 2e-44
Identities = 51/102 (50%), Positives = 64/102 (62%), Gaps = 7/102 (6%)
Query: 1 MEELKLDPNQTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPL 60
++L L L QGTL PD+IES S S AD IK+HHN L + K+IEPL
Sbjct: 95 AKKLGLA---EYLAQGTLYPDVIESGSGKGS--ADTIKSHHNVGGLPE--DMKLKLIEPL 147
Query: 61 KDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGEER 102
+D KDEVR+LG +LGL E+V RHPFPGPGLA+R++
Sbjct: 148 RDLFKDEVRELGRELGLPEEIVERHPFPGPGLAVRILGEVTE 189
>gnl|CDD|234614 PRK00074, guaA, GMP synthase; Reviewed.
Length = 511
Score = 125 bits (316), Expect = 7e-35
Identities = 54/101 (53%), Positives = 67/101 (66%), Gaps = 10/101 (9%)
Query: 2 EELKLDPNQTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALRE--QGKVIEP 59
EE K L QGTL PD+IES + KA IK+HHN + L E + K++EP
Sbjct: 309 EEAKKLGGVKFLAQGTLYPDVIESGG---TKKAATIKSHHN----VGGLPEDMKLKLVEP 361
Query: 60 LKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGE 100
L++ KDEVRKLGL+LGL E+V RHPFPGPGLAIR++ GE
Sbjct: 362 LRELFKDEVRKLGLELGLPEEIVYRHPFPGPGLAIRIL-GE 401
>gnl|CDD|223593 COG0519, GuaA, GMP synthase, PP-ATPase domain/subunit [Nucleotide
transport and metabolism].
Length = 315
Score = 109 bits (276), Expect = 3e-30
Identities = 46/88 (52%), Positives = 62/88 (70%), Gaps = 7/88 (7%)
Query: 13 LCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLG 72
L QGT+ PD+IES + KA IK+HHN L + + K++EPL++ KDEVR+LG
Sbjct: 125 LAQGTIYPDVIESGT----GKAGTIKSHHNVGGLPEDM--KLKLVEPLRELFKDEVRELG 178
Query: 73 LDLGLTPEVVMRHPFPGPGLAIRVICGE 100
+LGL E+V RHPFPGPGLA+R++ GE
Sbjct: 179 RELGLPEEIVYRHPFPGPGLAVRIL-GE 205
>gnl|CDD|233169 TIGR00884, guaA_Cterm, GMP synthase (glutamine-hydrolyzing),
C-terminal domain or B subunit. This protein of purine
de novo biosynthesis is well-conserved. However, it
appears to split into two separate polypeptide chains in
most of the Archaea. This C-terminal region would be the
larger subunit [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 311
Score = 106 bits (267), Expect = 5e-29
Identities = 49/88 (55%), Positives = 63/88 (71%), Gaps = 7/88 (7%)
Query: 13 LCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEVRKLG 72
L QGT+ PD+IESA+ A VIK+HHN L ++ K++EPL++ KDEVRKLG
Sbjct: 121 LAQGTIYPDVIESAA----GTAHVIKSHHNVGGLPEDMKL--KLVEPLRELFKDEVRKLG 174
Query: 73 LDLGLTPEVVMRHPFPGPGLAIRVICGE 100
+LGL E+V RHPFPGPGLA+RV+ GE
Sbjct: 175 KELGLPEEIVWRHPFPGPGLAVRVL-GE 201
>gnl|CDD|215197 PLN02347, PLN02347, GMP synthetase.
Length = 536
Score = 96.7 bits (241), Expect = 2e-24
Identities = 48/97 (49%), Positives = 60/97 (61%), Gaps = 4/97 (4%)
Query: 3 ELKLDPNQTLLCQGTLRPDLIESASHLASNK--ADVIKTHHNDSPLIRALREQGKVIEPL 60
E KL L QGTL PD+IES S + + IK+HHN L + + + K+IEPL
Sbjct: 329 EQKLGKKPAFLVQGTLYPDVIESCPPPGSGRTHSHTIKSHHNVGGLPKDM--KLKLIEPL 386
Query: 61 KDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVI 97
K KDEVRKLG LG+ + RHPFPGPGLA+RV+
Sbjct: 387 KLLFKDEVRKLGRLLGVPEAFLKRHPFPGPGLAVRVL 423
>gnl|CDD|179167 PRK00919, PRK00919, GMP synthase subunit B; Validated.
Length = 307
Score = 89.2 bits (222), Expect = 2e-22
Identities = 45/101 (44%), Positives = 59/101 (58%), Gaps = 15/101 (14%)
Query: 2 EELKLDPNQTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALRE--QGKVIEP 59
EE+ + L QGT+ PD IES IK+HHN + L E K++EP
Sbjct: 112 EEVAKEIGAEYLVQGTIAPDWIESEGG--------IKSHHN----VGGLPEGMVLKIVEP 159
Query: 60 LKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGE 100
L+D +KDEVR++ LGL E+ R PFPGPGLA+R+I GE
Sbjct: 160 LRDLYKDEVREVARALGLPEEISERMPFPGPGLAVRII-GE 199
>gnl|CDD|218930 pfam06186, DUF992, Protein of unknown function (DUF992). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 147
Score = 29.5 bits (67), Expect = 0.31
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 67 EVRKLGLDLGLTPEVVMR 84
+RK GLDLG T E VM
Sbjct: 60 TIRKFGLDLGFTGETVMA 77
>gnl|CDD|224522 COG1606, COG1606, ATP-utilizing enzymes of the PP-loop superfamily
[General function prediction only].
Length = 269
Score = 29.6 bits (67), Expect = 0.36
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 41 HNDSPLIRALREQGKVIEPLKDFH--KDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVIC 98
+ P +RAL+E G + PL +F K E+R++ LGL LA R+
Sbjct: 127 FDYRPGLRALKELG-IRSPLAEFGITKKEIREIAKSLGLP----TWDKPSMACLASRIPY 181
Query: 99 GEERYIEK 106
GEE +E
Sbjct: 182 GEEITVED 189
>gnl|CDD|234664 PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed.
Length = 346
Score = 29.3 bits (67), Expect = 0.54
Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 51 REQ-GKVIEPLKDFHKDEVRKLGLDLGL 77
+EQ K++ PL + K EVR++ + GL
Sbjct: 153 QEQLAKLLFPLGELTKPEVREIAEEAGL 180
>gnl|CDD|185037 PRK15079, PRK15079, oligopeptide ABC transporter ATP-binding
protein OppF; Provisional.
Length = 331
Score = 29.3 bits (66), Expect = 0.56
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 9/42 (21%)
Query: 54 GKVI-EPLKDFH--------KDEVRKLGLDLGLTPEVVMRHP 86
G++I EPL+ +H KD V+ + L +GL P ++ R+P
Sbjct: 118 GEIIAEPLRTYHPKLSRQEVKDRVKAMMLKVGLLPNLINRYP 159
>gnl|CDD|238948 cd01990, Alpha_ANH_like_I, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily. Adenine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins probably binds ATP. This
domain is about 200 amino acids long with a strongly
conserved motif SGGKD at the N terminus.
Length = 202
Score = 28.4 bits (64), Expect = 0.89
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 43 DSPLIRALREQGKVIEPLKDF--HKDEVRKLGLDLGLT 78
P ++ALRE G V PL + K E+R+L +LGL
Sbjct: 111 YRPGLKALRELG-VRSPLAEAGLGKAEIRELARELGLP 147
>gnl|CDD|200373 TIGR04122, Xnuc_lig_assoc, putative exonuclease, DNA
ligase-associated. Members of this protein family
frequently are found annotated as a putative exonuclease
involved in mRNA processing. This protein is found,
exclusively in bacteria, associated with three other
proteins: an ATP-dependent DNA ligase, a helicase, and
putative phosphoesterase.
Length = 326
Score = 28.7 bits (65), Expect = 0.91
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 20 PDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDE 67
P L+ + + +V TH + L+R LREQG PL ++DE
Sbjct: 281 PGLLRTI--KETGAEEVWVTHGYEDALVRWLREQGIDARPLHTVYEDE 326
>gnl|CDD|238956 cd01998, tRNA_Me_trans, tRNA methyl transferase. This family
represents
tRNA(5-methylaminomethyl-2-thiouridine)-
methyltransferase which is involved in the biosynthesis
of the modified nucleoside
5-methylaminomethyl-2-thiouridine present in the wobble
position of some tRNAs. This family of enzyme only
presents in bacteria and eukaryote. The archaeal
counterpart of this enzyme performs same function, but
is completely unrelated in sequence.
Length = 349
Score = 28.6 bits (65), Expect = 0.97
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 55 KVIEPLKDFHKDEVRKLGLDLGL 77
++I PL D K EVR++ +LGL
Sbjct: 159 RLIFPLGDLTKPEVREIAKELGL 181
>gnl|CDD|236111 PRK07843, PRK07843, 3-ketosteroid-delta-1-dehydrogenase; Reviewed.
Length = 557
Score = 28.5 bits (64), Expect = 1.1
Identities = 16/47 (34%), Positives = 18/47 (38%), Gaps = 12/47 (25%)
Query: 48 RALREQGKVIEPLKDFHKDEVRKLGLDLGLTPEVVMRHPFPGPGLAI 94
R LR+ G VIE L G VM H + GPG I
Sbjct: 505 RVLRDDGSVIEGL------------YAAGNVSAPVMGHTYAGPGATI 539
>gnl|CDD|217339 pfam03054, tRNA_Me_trans, tRNA methyl transferase. This family
represents
tRNA(5-methylaminomethyl-2-thiouridine)-
methyltransferase which is involved in the biosynthesis
of the modified nucleoside
5-methylaminomethyl-2-thiouridine present in the wobble
position of some tRNAs.
Length = 355
Score = 27.2 bits (61), Expect = 2.4
Identities = 12/28 (42%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 51 REQ-GKVIEPLKDFHKDEVRKLGLDLGL 77
+EQ K++ PL + K+EVRK+ + GL
Sbjct: 157 QEQLAKLLFPLGELTKEEVRKIAKEAGL 184
>gnl|CDD|215325 PLN02605, PLN02605, monogalactosyldiacylglycerol synthase.
Length = 382
Score = 27.2 bits (61), Expect = 2.8
Identities = 31/101 (30%), Positives = 37/101 (36%), Gaps = 37/101 (36%)
Query: 24 ESASHLASNKADVIKTHHNDSPL-----IRALREQGK----------VIEPLKD-----F 63
E A L K D+I + H PL +R LR QGK V+ L F
Sbjct: 91 EVAKGLMKYKPDIIVSVH---PLMQHVPLRVLRWQGKELGKKIPFTTVVTDLGTCHPTWF 147
Query: 64 HKD---------EVRKLGLDLGLTPEVVMRHPFPGPGLAIR 95
HK EV K L GL P + + GL IR
Sbjct: 148 HKGVTRCFCPSEEVAKRALKRGLEPSQIRVY-----GLPIR 183
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 26.9 bits (59), Expect = 4.0
Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 10/72 (13%)
Query: 21 DLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLKDFHKDEV-----RKLGLDL 75
+L++ S+ + ++T PL L E+ I ++ F +EV R +GL
Sbjct: 75 ELLKQKSYTEPERKKTLQTL---KPLSERLEEKESAIYEIESFELEEVITEPERPVGLS- 130
Query: 76 GLTPEVVMRHPF 87
E+ ++ F
Sbjct: 131 -FEKELFEKNSF 141
>gnl|CDD|216697 pfam01784, NIF3, NIF3 (NGG1p interacting factor 3). This family
contains several NIF3 (NGG1p interacting factor 3)
protein homologues. NIF3 interacts with the yeast
transcriptional coactivator NGG1p which is part of the
ADA complex, the exact function of this interaction is
unknown.
Length = 237
Score = 26.5 bits (59), Expect = 4.1
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 7/49 (14%)
Query: 17 TLRPDLIESASHLASNKADVIKTHH----NDSPLIRALREQGKVIEPLK 61
++IE A N AD+I THH I +G+ I L
Sbjct: 40 DATEEVIEEA---IENGADLIITHHPLIFKPLKRITGDDPKGRRILKLI 85
>gnl|CDD|211966 TIGR04243, nodulat_NodB, chitooligosaccharide deacetylase NodB.
Nodulation factors are lipooligosaccharide signalling
molecules produced by rhizobia, the symbiotic
nitrogen-fixing bacteria that form nodules in plants.
These Nod factor sustems have the NodABC genes in common
but differ subtly in what they produce, which affects
host range. NodB is a chitooligosaccharide deacetylase.
Length = 197
Score = 26.2 bits (58), Expect = 5.2
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 46 LIRALREQGKVIEPL 60
LI AL E+G VI L
Sbjct: 182 LIPALHERGFVIRSL 196
>gnl|CDD|176106 cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding
domain of LysR-type transcriptional regulators involved
in the catabolism of aromatic compounds and that of
other related regulators, contains type 2 periplasmic
binding fold. This CD includes the C-terminal substrate
binding domain of LTTRs involved in degradation of
aromatic compounds, such as CbnR, BenM, CatM, ClcR and
TfdR, as well as that of other transcriptional
regulators clustered together in phylogenetic trees,
including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and
OccR. The structural topology of this substrate-binding
domain 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 substrate-binding domains from
ionotropic glutamate receptors, LysR-like
transcriptional regulators, and unorthodox sensor
proteins involved in signal transduction.
Length = 197
Score = 25.9 bits (58), Expect = 5.4
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 73 LDLGLTPEVVMRHPFPGPGLAIRVICGEERYI 104
LD+G +R P PGLA R + E +
Sbjct: 50 LDVGF-----VRPPPDPPGLASRPL-LREPLV 75
>gnl|CDD|238625 cd01300, YtcJ_like, YtcJ_like metal dependent amidohydrolases. YtcJ
is a Bacillus subtilis ORF of unknown function. The
Arabidopsis homolog LAF3 has been identified as a factor
required for photochrome A signalling.
Length = 479
Score = 26.1 bits (58), Expect = 7.4
Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 64 HKDEVRKLGLDLGLTPEVVMRHPFPGPGLAIRVICGEERY 103
D++ + LG+ V H + A GEER
Sbjct: 351 SPDDIPRFA-KLGVIASVQPNHLYSDGDAAEDRRLGEERA 389
>gnl|CDD|237144 PRK12582, PRK12582, acyl-CoA synthetase; Provisional.
Length = 624
Score = 25.8 bits (57), Expect = 8.1
Identities = 24/85 (28%), Positives = 34/85 (40%), Gaps = 15/85 (17%)
Query: 2 EELKLDPNQTLLCQGTLRPDLIESASHLASNKADVIKTHHNDSPLIRALREQGKVIEPLK 61
E+ KL T + GTLRPD + + S + D + D I L P
Sbjct: 480 EDFKLS-TGTWVSVGTLRPDAVAACSPVIH---DAVVAGQ-DRAFIGLL------AWP-- 526
Query: 62 DFHKDEVRKLGLDLGLTPEVVMRHP 86
+ R+L D PE V++HP
Sbjct: 527 NPA--ACRQLAGDPDAAPEDVVKHP 549
>gnl|CDD|240355 PTZ00314, PTZ00314, inosine-5'-monophosphate dehydrogenase;
Provisional.
Length = 495
Score = 25.7 bits (57), Expect = 8.3
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 6 LDPNQTLLCQGTL--RPDLIESASHLASNKADVI 37
LD N LL + RP+ IE A+ L DV+
Sbjct: 224 LDSNGQLLVGAAISTRPEDIERAAALIEAGVDVL 257
>gnl|CDD|201652 pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6. Rpb6 is an
essential subunit in the eukaryotic polymerases Pol I,
II and III. This family also contains the bacterial
equivalent to Rpb6, the omega subunit. Rpb6 and omega
are structurally conserved and both function in
polymerase assembly.
Length = 57
Score = 24.2 bits (53), Expect = 8.8
Identities = 5/24 (20%), Positives = 10/24 (41%)
Query: 29 LASNKADVIKTHHNDSPLIRALRE 52
L+ ++ P++ AL E
Sbjct: 24 LSYGAPPLVDEESEIKPVVIALEE 47
>gnl|CDD|237675 PRK14328, PRK14328, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 439
Score = 25.7 bits (57), Expect = 9.3
Identities = 16/33 (48%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 99 GEERYIEKDYSETQVLVKIIVEYDQMFKKIYPK 131
GE E+D+ ET LVK V YD F IY K
Sbjct: 310 GET---EEDFEETLDLVKE-VRYDSAFTFIYSK 338
>gnl|CDD|223558 COG0482, TrmU, Predicted tRNA(5-methylaminomethyl-2-thiouridylate)
methyltransferase, contains the PP-loop ATPase domain
[Translation, ribosomal structure and biogenesis].
Length = 356
Score = 25.7 bits (57), Expect = 9.7
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 54 GKVIEPLKDFHKDEVRKLGLDLGLTP 79
+++ PL D K EVR + + GL
Sbjct: 160 ERLLFPLGDLEKLEVRPIAAEKGLPT 185
>gnl|CDD|217093 pfam02540, NAD_synthase, NAD synthase. NAD synthase (EC:6.3.5.1)
is involved in the de novo synthesis of NAD and is
induced by stress factors such as heat shock and glucose
limitation.
Length = 242
Score = 25.4 bits (56), Expect = 10.0
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 57 IEPLKDFHKDEVRKLGLDLGLTPEVVMRHP----FPG 89
I P+ D +K +V +L L + ++ + P +PG
Sbjct: 148 IAPIGDLYKTQVYELAKRLNVPERIIKKPPSADLWPG 184
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 0.139 0.404
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,952,515
Number of extensions: 640310
Number of successful extensions: 718
Number of sequences better than 10.0: 1
Number of HSP's gapped: 705
Number of HSP's successfully gapped: 50
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
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 (21.7 bits)
S2: 53 (24.4 bits)