RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16096
(154 letters)
>gnl|CDD|215550 PLN03049, PLN03049, pyridoxine (pyridoxamine) 5'-phosphate oxidase;
Provisional.
Length = 462
Score = 148 bits (374), Expect = 3e-43
Identities = 75/159 (47%), Positives = 103/159 (64%), Gaps = 10/159 (6%)
Query: 2 FGYEPEIYYPKPPSKELYVNLLHQCKSLDIPV--SESLPAE-TSVFHLIVDAIFGFSYK- 57
FGY+P I YPK K LY L+ Q +SL +P E LP++ +S F ++VDA+FGFS+
Sbjct: 85 FGYKPSICYPKRTDKPLYNGLVTQLESLSVPFLSVEDLPSDLSSQFDIVVDAMFGFSFHG 144
Query: 58 ---PPLRELFVPVINLFKSTKIPVVSIDIPSGWNVEHGPVEHK-YQPHTLISLTAPKLCA 113
PP +L ++ P+VS+DIPSGW+VE G V + +P L+SLTAPKLCA
Sbjct: 145 APRPPFDDLIQKLVRAAGPP--PIVSVDIPSGWHVEEGDVNGEGLKPDMLVSLTAPKLCA 202
Query: 114 HKFEGKHHFLGGRFIPKQLEKEYDLNLPPYKGTDTYVKI 152
F+G HHFLGGRF+P + +++ L+LPPY GT V+I
Sbjct: 203 KMFKGPHHFLGGRFVPPAIVEKFKLHLPPYPGTSMCVRI 241
>gnl|CDD|215551 PLN03050, PLN03050, pyridoxine (pyridoxamine) 5'-phosphate oxidase;
Provisional.
Length = 246
Score = 141 bits (358), Expect = 7e-43
Identities = 66/163 (40%), Positives = 93/163 (57%), Gaps = 12/163 (7%)
Query: 1 MFGYEPEIYYPKPPSKELYVNLLHQCKSLDIPVSESLPAETS-------VFHLIVDAIFG 53
FGYE + YPK SK Y NL+ QC+ L IP +++ + +IVDAIFG
Sbjct: 85 HFGYEVTVCYPKQSSKPHYENLVTQCEDLGIPFVQAIGGTNDSSKPLETTYDVIVDAIFG 144
Query: 54 FSYKPPLRELFVPVINLFKSTK---IPVVSIDIPSGWNVEHGPVE-HKYQPHTLISLTAP 109
FS+ R F ++ + P+VS+D+PSGW+V+ G V +P L+SLTAP
Sbjct: 145 FSFHGAPRAPFDTLLAQMVQQQKSPPPIVSVDVPSGWDVDEGDVSGTGMRPDVLVSLTAP 204
Query: 110 KLCAHKFEGKHHFLGGRFIPKQLEKEYDLNLPPYKGTDTYVKI 152
KL A KFEG HF+GGRF+P + ++Y L PPY G +++
Sbjct: 205 KLSAKKFEG-RHFVGGRFLPPAIAEKYGLQKPPYPGVSQVMEV 246
>gnl|CDD|215496 PLN02918, PLN02918, pyridoxine (pyridoxamine) 5'-phosphate oxidase.
Length = 544
Score = 145 bits (367), Expect = 9e-42
Identities = 82/163 (50%), Positives = 107/163 (65%), Gaps = 12/163 (7%)
Query: 2 FGYEPEIYYPKPPSKELYVNLLHQCKSLDIPV--SESLPAETSV-FHLIVDAIFGFSY-- 56
FGY+P + YPK +K LY L+ Q +SL +P E LPA+ S F +IVDA+FGFS+
Sbjct: 161 FGYKPFVCYPKRTAKPLYTGLVTQLESLSVPFVSVEDLPADLSKDFDIIVDAMFGFSFHG 220
Query: 57 --KPPLREL---FVPVINLFKSTKIPV-VSIDIPSGWNVEHGPVEHK-YQPHTLISLTAP 109
+PP +L V + N ++ K PV VS+DIPSGW+VE G E +P L+SLTAP
Sbjct: 221 APRPPFDDLIRRLVSLQNYEQTLKHPVIVSVDIPSGWHVEEGDHEGGGIKPDMLVSLTAP 280
Query: 110 KLCAHKFEGKHHFLGGRFIPKQLEKEYDLNLPPYKGTDTYVKI 152
KLCA KF G HHFLGGRF+P + ++Y L+LPPY GT V+I
Sbjct: 281 KLCAKKFRGPHHFLGGRFVPPSIVEKYKLHLPPYPGTSMCVRI 323
>gnl|CDD|223140 COG0062, COG0062, Uncharacterized conserved protein [Function
unknown].
Length = 203
Score = 90.0 bits (224), Expect = 3e-23
Identities = 33/131 (25%), Positives = 48/131 (36%), Gaps = 6/131 (4%)
Query: 2 FGYEPEIYYPKPPSKELYVNLLHQCKSLDIPVSESLPAETSV---FHLIVDAIFGFSYKP 58
GY + P K KSL I + +IVDA+FG
Sbjct: 75 AGYAVTVLLLGDPKKLKTEAARANLKSLGIGGVVKIKELEDEPESADVIVDALFGTGLSG 134
Query: 59 PLRELFVPVINLFKSTKIPVVSIDIPSGWNVEHGPVEHKY-QPHTLISLTAPKLCAHKFE 117
PLRE F +I ++ P+V++DIPSG + + G V + ++ A K
Sbjct: 135 PLREPFASLIEAINASGKPIVAVDIPSGLDADTGEVLGAAVKADLTVTFGALKPG-L-LT 192
Query: 118 GKHHFLGGRFI 128
G G
Sbjct: 193 GPARDYVGELH 203
>gnl|CDD|217763 pfam03853, YjeF_N, YjeF-related protein N-terminus. YjeF-N domain
is a novel version of the Rossmann fold with a set of
catalytic residues and structural features that are
different from the conventional dehydrogenases. YjeF-N
domain is fused to Ribokinases in bacteria (YjeF), where
they may be phosphatases, and to divergent Sm and the
FDF domain in eukaryotes (Dcp3p and FLJ21128), where
they may be involved in decapping and catalyze
hydrolytic RNA-processing reactions.
Length = 170
Score = 84.2 bits (209), Expect = 3e-21
Identities = 29/116 (25%), Positives = 54/116 (46%), Gaps = 6/116 (5%)
Query: 3 GYEPEIY--YPKPPSKEL---YVNLLHQCKSLDIPVSESLPAETSVFHLIVDAIFGFSYK 57
GY+ + P E +++L + + ++ E ++ LI+DA+FG
Sbjct: 55 GYKVTVLLLLPDEKLSEDARRALDILKKLGGKIVELNPDEDLEEAIADLIIDALFGTGLS 114
Query: 58 PPLRELFVPVINLFKSTKIPVVSIDIPSGWNVEHGPVEHKY-QPHTLISLTAPKLC 112
PLR + +I ++K PV+++DIPSG + + G V + ++ APK
Sbjct: 115 RPLRGEYAELIEWINASKAPVLAVDIPSGLDADTGAVLGAAVKADYTVTFGAPKPG 170
>gnl|CDD|232869 TIGR00197, yjeF_nterm, yjeF N-terminal region. The protein region
corresponding to This model shows no clear homology to
any protein of known function. This model is built on
yeast protein YNL200C and the N-terminal regions of E.
coli yjeF and its orthologs in various species. The
C-terminal region of yjeF and its orthologs shows
similarity to hydroxyethylthiazole kinase (thiM) and
other enzymes involved in thiamine biosynthesis. Yeast
YKL151C and B. subtilis yxkO match the yjeF C-terminal
domain but lack this region [Unknown function, General].
Length = 205
Score = 84.0 bits (208), Expect = 6e-21
Identities = 38/138 (27%), Positives = 58/138 (42%), Gaps = 12/138 (8%)
Query: 3 GYEPEIYYPKPPSK-ELYVNLLHQ---CKSLDIPVSES-LPAETSVFHLIVDAIFGFSYK 57
G+ E++ K + E + K I + E L +I+DAI G K
Sbjct: 70 GFGVEVFLLKKEERIEFTEQAVVNLKALKVGGISIDEGNLVKPEDC-DVIIDAILGTGVK 128
Query: 58 PPLRELFVPVINLFKSTKIPVVSIDIPSGWNVEHGPVEH-KYQPHTLISLTAPKLCA--- 113
PLRE F ++ P+VS+D+PSG +V+ G +E I+ APK
Sbjct: 129 GPLREPFKTIVEEINELPAPIVSVDVPSGLDVDTGAIEGPAVNADLTITFHAPKPGLLHD 188
Query: 114 -HKFEGKHHFLGGRFIPK 130
+ G+ + GG IP
Sbjct: 189 RAEVTGELYV-GGIGIPP 205
>gnl|CDD|182554 PRK10565, PRK10565, putative carbohydrate kinase; Provisional.
Length = 508
Score = 35.8 bits (83), Expect = 0.006
Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 46 LIVDAIFGFSYKPPLRELFVPVINLFKSTKIPVVSIDIPSGWNVEHG 92
LIVDA+ G + RE + +I+ + PVV++DIPSG E G
Sbjct: 132 LIVDALLGTGLRQAPREPYAALIDQANAHPAPVVALDIPSGLLAETG 178
>gnl|CDD|239162 cd02761, MopB_FmdB-FwdB, The MopB_FmdB-FwdB CD contains the
molybdenum/tungsten formylmethanofuran dehydrogenases,
subunit B (FmdB/FwdB), and other related proteins.
Formylmethanofuran dehydrogenase catalyzes the first
step in methane formation from CO2 in methanogenic
archaea and some eubacteria. Members of this CD belong
to the molybdopterin_binding (MopB) superfamily of
proteins.
Length = 415
Score = 27.7 bits (62), Expect = 2.8
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 7/51 (13%)
Query: 38 PAETSVFHLI----VDAIFGFSYKPPLRELFVPVINLFKSTKIPVVSIDIP 84
P E + L+ DA+ + PP P + +IPV+ ID P
Sbjct: 311 PGEFTAVDLLAEGEADALLIIASDPPAH---FPQSAVKHLAEIPVIVIDPP 358
>gnl|CDD|217644 pfam03621, MbtH, MbtH-like protein. This domain is found in the
MbtH protein, as well as at the N terminus of the
antibiotic synthesis protein NIKP1. MbtH and its
homologues were first noted in gene clusters involved
in non-ribosomal peptides and other secondary
metabolites by Quadri et al. This domain is about 70
amino acids long and contains 3 fully conserved
tryptophan residues. The structure of the PA2412
protein shows it adopts a beta-beta-beta-alpha-alpha
topology with the short C-terminal helix forming the
tip of an overall arrowhead shape.
Length = 53
Score = 25.6 bits (57), Expect = 3.1
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 82 DIPSGWNVEHGP 93
+P+GW V GP
Sbjct: 31 PVPAGWRVVFGP 42
>gnl|CDD|132138 TIGR03094, sulfo_cyanin, sulfocyanin. Members of this family are
blue-copper redox proteins designated sulfocyanin, from
the archaeal genera Sulfolobus, Ferroplasma, and
Picrophilus. The most closely related proteins
characterized as functionally different are the
rustacyanins [Energy metabolism, Electron transport].
Length = 195
Score = 26.8 bits (59), Expect = 5.1
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 71 FKSTKIPVVSIDIPSGWNVEHGPVEHKYQPHTLISL 106
F T ++I +P+GWNV ++ PH L L
Sbjct: 77 FNGTSYGAMTIYLPAGWNVYVTFTNYESLPHNLKLL 112
>gnl|CDD|236002 PRK07369, PRK07369, dihydroorotase; Provisional.
Length = 418
Score = 26.1 bits (58), Expect = 8.8
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 20 VNLLHQCKSLDIPVSESLPAETSVFHLIVDAIFGFSYKPPLR 61
V L+ Q K+ +P++ A T+ HL++D SY P LR
Sbjct: 241 VELIAQAKARGLPIT----ASTTWMHLLLDTEALASYDPNLR 278
>gnl|CDD|153378 cd07366, 3MGA_Dioxygenase, Subunit B of the Class III Extradiol
ring-cleavage dioxygenase, 3-O-Methylgallate
Dioxygenase, which catalyzes the oxidization and
subsequent ring-opening of 3-O-Methylgallate.
3-O-Methylgallate Dioxygenase catalyzes the oxidization
and subsequent ring-opening of 3-O-Methylgallate (3MGA)
between carbons 2 and 3. 3-O-Methylgallate Dioxygenase
is a key enzyme in the syringate degradation pathway, in
which the syringate is first converted to
3-O-Methylgallate by O-demethylase. This enzyme is a
member of the class III extradiol dioxygenase family, a
group of enzymes which uses a non-heme Fe(II) to cleave
aromatic rings between a hydroxylated carbon and an
adjacent non-hydroxylated carbon. LigAB-like enzymes are
usually composed of two subunits, designated A and B,
which form a tetramer composed of two copies of each
subunit. This model represents the catalytic subunit, B.
Length = 328
Score = 26.2 bits (58), Expect = 8.8
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 1 MFGYEPEIYYPKPPSKELYVNLL-HQCKS-LDIPVSESLPAETSVFHLIVDAIFGFSYKP 58
GY P+ P EL +L+ H D+ + LP + H FGF Y+
Sbjct: 136 AAGYAPDEARTYPCHPELARHLIKHTVADGFDVAALDHLPDTVGIPH-----AFGFIYRR 190
Query: 59 PLRELFVPVINLFKSTKIPV 78
+ +L +PV+ + +T P
Sbjct: 191 IMGDLVIPVVPVLINTFYPP 210
>gnl|CDD|213282 cd05914, FACL_like_3, Uncharacterized subfamily of fatty acid CoA
ligase (FACL). Fatty acyl-CoA ligases catalyze the
ATP-dependent activation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. This is a
required step before free fatty acids can participate in
most catabolic and anabolic reactions.
Length = 448
Score = 26.1 bits (58), Expect = 8.9
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 14/62 (22%)
Query: 96 HKYQPHTLI-------SLTAPKLCAHKFE--GKHHFL---GGRFIPKQLEKEYDLNLPPY 143
++QPH+LI +L A F+ G R P L++ L LP Y
Sbjct: 208 SRWQPHSLILVPQLLMALVA--AVEQGPLPPESLRFVAVGGARVSPSLLQRARALGLPVY 265
Query: 144 KG 145
+G
Sbjct: 266 EG 267
>gnl|CDD|239909 cd04462, S1_RNAPII_Rpb7, S1_RNAPII_Rpb7: Eukaryotic RNA polymerase
II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is
composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a
heterodimer that associate with the RNAPII core. Rpb7 is
a homolog of the Rpc25 of RNA polymerase III, RpoE of
the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA
polymerase I. Rpb7 has two domains, an N-terminal
ribonucleoprotein (RNP) domain and a C-terminal S1
domain, both of which bind single-stranded RNA. It is
possible that the S1 domain interacts with the nascent
RNA transcript, assisted by the RNP domain. In yeast,
Rpb4/Rpb7 is necessary for promoter-directed
transcription initiation. They also play a role in
regulating transcription-coupled repair in the
Rad26-dependent pathway, in efficient mRNA export, and
in transcription termination.
Length = 88
Score = 24.9 bits (55), Expect = 9.5
Identities = 8/34 (23%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 122 FLGGRFIPKQLEKEYDLNLPPYKGTDTYV-KIDD 154
F+ IP +E + + + P + + V K D
Sbjct: 27 FISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDT 60
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
0.320 0.142 0.444
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,166,082
Number of extensions: 726942
Number of successful extensions: 573
Number of sequences better than 10.0: 1
Number of HSP's gapped: 561
Number of HSP's successfully gapped: 25
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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: 55 (24.9 bits)