RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780438|ref|YP_003064851.1| pyridoxine 5'-phosphate
synthase [Candidatus Liberibacter asiaticus str. psy62]
(261 letters)
>gnl|CDD|58644 cd00003, PNPsynthase, Pyridoxine 5'-phosphate (PNP) synthase
domain; pyridoxal 5'-phosphate is the active form of
vitamin B6 that acts as an essential, ubiquitous
coenzyme in amino acid metabolism. In bacteria,
formation of pyridoxine 5'-phosphate is a step in the
biosynthesis of vitamin B6. PNP synthase, a
homooctameric enzyme, catalyzes the final step in PNP
biosynthesis, the condensation of 1-amino-acetone
3-phosphate and 1-deoxy-D-xylulose 5-phosphate. PNP
synthase adopts a TIM barrel topology, intersubunit
contacts are mediated by three ''extra'' helices,
generating a tetramer of symmetric dimers with shared
active sites; the open state has been proposed to accept
substrates and to release products, while most of the
catalytic events are likely to occur in the closed
state; a hydrophilic channel running through the center
of the barrel was identified as the essential structural
feature that enables PNP synthase to release water
molecules produced during the reaction from the closed,
solvent-shielded active site..
Length = 234
Score = 264 bits (677), Expect = 1e-71
Identities = 92/242 (38%), Positives = 142/242 (58%), Gaps = 9/242 (3%)
Query: 5 VSVNLNAVAVLRNRRNLPWPNLVHIGKIALQSGASGLTVHPRPDQRHIRYTDLPEIRRLI 64
+ VN++ VA LRN R +P+ V +A ++GA G+TVH R D+RHI+ D+ +R L+
Sbjct: 2 LGVNIDHVATLRNARGTNYPDPVEAALLAEKAGADGITVHLREDRRHIQDRDVRLLRELV 61
Query: 65 DEQFPKAELNIEGYPNETFLNLCERYKPEQITLVPDDPHQLTSDHGWDFLQNQALLTKTV 124
+ ELN+E P E L + KP Q+TLVP+ +LT++ G D L +
Sbjct: 62 -----RTELNLEMAPTEEMLEIALEVKPHQVTLVPEKREELTTEGGLDVAGQAEKLKPII 116
Query: 125 ARLHNLGSRISLFADGNGNEHSLQAAKLTGADCIELYTGPYGACYNNPQQERIFLNKLAI 184
RL + G R+SLF D + ++AAK GAD +EL+TGPY Y+ ++E L ++A
Sbjct: 117 ERLKDAGIRVSLFID--PDPEQIEAAKEVGADRVELHTGPYANAYDKAEREAE-LERIAK 173
Query: 185 TAQLAQKMDLQINAGHDLTIQNIPNLINAIPYISEISVGHAFAATALECGVKEAVFCFRR 244
A+LA+++ L +NAGH L +N+ I IP I+E+++GHA + AL G++EAV +
Sbjct: 174 AAKLARELGLGVNAGHGLNYENVK-PIAKIPGIAELNIGHAIISRALFVGLEEAVREMKD 232
Query: 245 AC 246
Sbjct: 233 LI 234
>gnl|CDD|31195 COG0854, PdxJ, Pyridoxal phosphate biosynthesis protein [Coenzyme
metabolism].
Length = 243
Score = 259 bits (663), Expect = 6e-70
Identities = 96/245 (39%), Positives = 142/245 (57%), Gaps = 10/245 (4%)
Query: 6 SVNLNAVAVLRNRRNLPWPNLVHIGKIALQSGASGLTVHPRPDQRHIRYTDLPEIRRLID 65
VN++ +A LRN R P+P+ V IA Q+GA G+TVH R D+RHI+ D+ +R LID
Sbjct: 4 GVNIDHIATLRNARGTPYPDPVEAAFIAEQAGADGITVHLREDRRHIQDRDVRILRALID 63
Query: 66 EQFPKAELNIEGYPNETFLNLCERYKPEQITLVPDDPHQLTSDHGWDFLQNQALLTKTVA 125
N+E P E L + + KP Q+TLVP+ ++T++ G D L V
Sbjct: 64 -----TRFNLEMAPTEEMLAIALKTKPHQVTLVPEKREEVTTEGGLDVAGQLDKLRDAVR 118
Query: 126 RLHNLGSRISLFADGNGNEHSLQAAKLTGADCIELYTGPYGACYNNPQQERIF--LNKLA 183
RL N G R+SLF D + ++AA GA IEL+TGPY ++ +Q R L +LA
Sbjct: 119 RLKNAGIRVSLFID--PDPEQIEAAAEVGAPRIELHTGPYADAHDAAEQARADAELERLA 176
Query: 184 ITAQLAQKMDLQINAGHDLTIQNIPNLINAIPYISEISVGHAFAATALECGVKEAVFCFR 243
A+LA ++ L++NAGH LT N+ L AIP ++E+++GH+ A A+ G++EAV +
Sbjct: 177 KAAKLAAELGLKVNAGHGLTYHNVKPLA-AIPPLAELNIGHSIIARAVFVGLEEAVREMK 235
Query: 244 RACGQ 248
R +
Sbjct: 236 RLMKR 240
>gnl|CDD|112550 pfam03740, PdxJ, Pyridoxal phosphate biosynthesis protein PdxJ.
Members of this family belong to the PdxJ family that
catalyses the condensation of
1-deoxy-d-xylulose-5-phosphate (DXP) and
1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form
pyridoxine 5'-phosphate (PNP). This reaction is involved
in de novo synthesis of pyridoxine (vitamin B6) and
pyridoxal phosphate.
Length = 239
Score = 248 bits (635), Expect = 1e-66
Identities = 95/243 (39%), Positives = 139/243 (57%), Gaps = 9/243 (3%)
Query: 6 SVNLNAVAVLRNRRNLPWPNLVHIGKIALQSGASGLTVHPRPDQRHIRYTDLPEIRRLID 65
VN++ +A LRN R P+P+ V IA ++GA G+TVH R D+RHI+ D+ ++ LI
Sbjct: 4 GVNIDHIATLRNARGTPYPDPVEAALIAERAGADGITVHLREDRRHIQDRDVEVLKELIR 63
Query: 66 EQFPKAELNIEGYPNETFLNLCERYKPEQITLVPDDPHQLTSDHGWDFLQNQALLTKTVA 125
NIE P E L L + KP Q+TLVP+ ++T++ G D + L +
Sbjct: 64 -----TRFNIEMAPTEEMLELALKTKPHQVTLVPEKREEITTEGGLDVVAQLEKLKPAIR 118
Query: 126 RLHNLGSRISLFADGNGNEHSLQAAKLTGADCIELYTGPYGACYNNPQQER-IFLNKLAI 184
RL N G R+SLF D + ++AAK+ GAD IEL+TGPY +N+ +Q R L +LA
Sbjct: 119 RLKNAGIRVSLFID--PDPEQIEAAKIVGADRIELHTGPYADAHNDAEQAREELLERLAA 176
Query: 185 TAQLAQKMDLQINAGHDLTIQNIPNLINAIPYISEISVGHAFAATALECGVKEAVFCFRR 244
A LA + L +NAGH LT N+ + IP I+E+++GH+ A AL G+ +AV +
Sbjct: 177 GAALAFDLGLVVNAGHGLTYHNVKPVA-KIPPIAELNIGHSLVAEALFVGLAKAVLEMKA 235
Query: 245 ACG 247
Sbjct: 236 LMK 238
>gnl|CDD|73368 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present..
Length = 231
Score = 32.4 bits (74), Expect = 0.14
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 25 NLVHIGKIALQSGASGLTVHPR-PDQRHIRYTDLPEIRRLID 65
+ + K +GAS LTVH R +QR+ D I + +
Sbjct: 139 ETLELAKALEDAGASALTVHGRTREQRYSGPADWDYIAEIKE 180
>gnl|CDD|110253 pfam01238, PMI_typeI, Phosphomannose isomerase type I. This is a
family of Phosphomannose isomerase type I enzymes (EC
5.3.1.8).
Length = 373
Score = 29.8 bits (67), Expect = 0.74
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 53 RYTDLPEIRRLIDEQFPKAELNIEGYPNETFLNLCERYKPEQITLVPDDPH 103
DLPE+ ++EQ+P + G FLN + E + L +DPH
Sbjct: 223 NVYDLPELIDRLNEQYP----DDIGLF-RLFLNHVKLNPGEAMFLKANDPH 268
>gnl|CDD|144707 pfam01207, Dus, Dihydrouridine synthase (Dus). Members of this
family catalyse the reduction of the 5,6-double bond of
a uridine residue on tRNA. Dihydrouridine modification
of tRNA is widely observed in prokaryotes and
eukaryotes, and also in some archae. Most
dihydrouridines are found in the D loop of t-RNAs. The
role of dihydrouridine in tRNA is currently unknown, but
may increase conformational flexibility of the tRNA. It
is likely that different family members have different
substrate specificities, which may overlap. Dus 1 from
Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus
2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active
as a single subunit, requiring NADPH or NADH, and is
stimulated by the presence of FAD. Some family members
may be targeted to the mitochondria and even have a role
in mitochondria.
Length = 309
Score = 29.6 bits (67), Expect = 0.83
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 25 NLVHIGKIALQSGASGLTVHPR-PDQRHIRYTDLPEIRRLID 65
N V I + +GA LTVH R Q + D I+++
Sbjct: 139 NAVEIARRVEDAGAQALTVHGRTRAQNYEGPADWDAIKQVKQ 180
>gnl|CDD|30391 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 28.8 bits (64), Expect = 1.5
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 25 NLVHIGKIALQSGASGLTVHPR-PDQRHIRYTDLPEIRRLIDE 66
+ I +I +GA LTVH R Q ++ D I+ L +
Sbjct: 153 LALEIARILEDAGADALTVHGRTRAQGYLGPADWDYIKELKEA 195
>gnl|CDD|176084 cd08534, SAM_PNT-GABP-alpha, Sterile alpha motif (SAM)/Pointed
domain of GA-binding protein alpha chain. SAM Pointed
domain of GABP-alpha subfamily of ETS transcriptional
regulators is a putative protein-protein interaction
domain. This type of transcriptional regulators forms
heterotetramers containing two alpha and two beta
subunits. It interacts with GA repeats (purine rich
repeats). GABP transcriptional factors control gene
expression in cell cycle control, apoptosis, and
cellular respiration. GABP participates in regulation of
transmembrane receptors and key hormones especially in
myeloid cells and at the neuromuscular junction.
Length = 89
Score = 28.1 bits (63), Expect = 2.3
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 86 LCERYKPEQITL-VPDDPHQLTSDH 109
+ Y+ EQ L +P DP + T D
Sbjct: 2 VDSNYRKEQERLKIPYDPMEWTEDQ 26
>gnl|CDD|133235 cd05104, PTKc_Kit, Catalytic domain of the Protein Tyrosine Kinase,
Kit. Protein Tyrosine Kinase (PTK) family; Kit (or
c-Kit); catalytic (c) domain. The PTKc family is part of
a larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Kit is a member of the
Platelet Derived Growth Factor Receptor (PDGFR)
subfamily of proteins, which are receptor tyr kinases
(RTKs) containing an extracellular ligand-binding region
with five immunoglobulin-like domains, a transmembrane
segment, and an intracellular catalytic domain. The
binding of Kit to its ligand, the stem-cell factor
(SCF), leads to receptor dimerization, trans
phosphorylation and activation, and intracellular
signaling. Kit is important in the development of
melanocytes, germ cells, mast cells, hematopoietic stem
cells, the interstitial cells of Cajal, and the
pacemaker cells of the GI tract. Kit signaling is
involved in major cellular functions including cell
survival, proliferation, differentiation, adhesion, and
chemotaxis. Mutations in Kit, which result in
constitutive ligand-independent activation, are found in
human cancers such as gastrointestinal stromal tumor
(GIST) and testicular germ cell tumor (TGCT). The
aberrant expression of Kit and/or SCF is associated with
other tumor types such as systemic mastocytosis and
cancers of the breast, neurons, lung, prostate, colon,
and rectum. Although the structure of the human Kit
catalytic domain is known, it is excluded from this
specific alignment model because it contains a deletion
in its sequence.
Length = 375
Score = 27.9 bits (62), Expect = 3.0
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 101 DPHQLTSDHGWDFLQNQALLTKTV 124
DP QL DH W+F +N+ KT+
Sbjct: 20 DPTQLPYDHKWEFPRNRLSFGKTL 43
>gnl|CDD|144742 pfam01261, AP_endonuc_2, Xylose isomerase-like TIM barrel. This
TIM alpha/beta barrel structure is found in xylose
isomerase and in endonuclease IV (EC:3.1.21.2). This
domain is also found in the N termini of bacterial
myo-inositol catabolism proteins. These are involved in
the myo-inositol catabolism pathway, and is required for
growth on myo-inositol in Rhizobium leguminosarum bv.
viciae.
Length = 201
Score = 27.3 bits (61), Expect = 4.7
Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 147 LQAAKLTGADCIELYTGPYGACYNNPQQERIFLNKLAITAQLAQKMDLQINAGH 200
L+ A G D +EL+ + + E + L ++ L+I + +
Sbjct: 1 LELAAELGFDGVELFFDDPRPASDKLEIEEL--------KALLKEYGLEITSLN 46
>gnl|CDD|173691 cd05600, STKc_Sid2p_Dbf2p, Catalytic domain of Fungal Sid2p- and
Dbf2p-like Protein Serine/Threonine Kinases.
Serine/Threonine Kinases (STKs), ROCK- and NDR-like
subfamily, fungal Sid2p- and Dbf2p-like proteins,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The Sid2p- and
Dbf2p-like group is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. This group contains fungal kinases including
Schizosaccharomyces pombe Sid2p and Saccharomyces
cerevisiae Dbf2p. Group members show similarity to NDR
kinases in that they contain an N-terminal regulatory
(NTR) domain and an insert within the catalytic domain
that contains an auto-inhibitory sequence. Sid2p plays a
crucial role in the septum initiation network (SIN) and
in the initiation of cytokinesis. Dbf2p is important in
regulating the mitotic exit network (MEN) and in
cytokinesis.
Length = 333
Score = 27.0 bits (60), Expect = 5.4
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 79 PNETFLNLCERYKPEQITLVPDDPHQLTSDHGWDFLQNQALLTKTVARLHNL 130
PNET+ NL + +K V DDP SD WD + L+ R +L
Sbjct: 203 PNETWENL-KYWKETLQRPVYDDPRFNLSDEAWDLITK--LINDPSRRFGSL 251
>gnl|CDD|32798 COG2979, COG2979, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 225
Score = 26.5 bits (58), Expect = 6.8
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 2/62 (3%)
Query: 147 LQAAKLTGADCIELYTGPYGACYNNPQQERIFLNKLAITAQLAQKMDLQINAGHDLTIQN 206
+ AA +ELY A ++ + ER +LN LA L + + +
Sbjct: 165 IAAAARNEEQALELYLASRLAIDDDSRMERSYLNALAGALGLPDALVDHLER--QVGQAK 222
Query: 207 IP 208
+
Sbjct: 223 VT 224
>gnl|CDD|31617 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport and
metabolism].
Length = 216
Score = 26.4 bits (58), Expect = 8.1
Identities = 16/94 (17%), Positives = 29/94 (30%), Gaps = 1/94 (1%)
Query: 44 HPRPDQRHIRYTDLPEIRRLIDEQFPKAELNIEGYPNETFLNLCERYKPEQITLVPDDPH 103
RPD L + R I ++ E++ + +L RY P
Sbjct: 124 PGRPDLLIYLDASLETLLRRIAKRGRPFEIDNFDENKDYLKDLHRRYDDWFEN-YDACPV 182
Query: 104 QLTSDHGWDFLQNQALLTKTVARLHNLGSRISLF 137
DF+ N+ L K + ++ +
Sbjct: 183 LGIDGDSIDFVNNEQDLEKVLDQILAKLKLLPKL 216
>gnl|CDD|31260 COG1060, ThiH, Thiamine biosynthesis enzyme ThiH and related
uncharacterized enzymes [Coenzyme metabolism / General
function prediction only].
Length = 370
Score = 26.4 bits (58), Expect = 9.1
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 22 PWPNL-VHIGKIALQSGASGL-------TVHPRPDQRHIRYTDLPEIRRLIDEQ 67
W V + + AL SGA+ L V+P + + E+ LI E
Sbjct: 296 SWLRDGVILAQAALLSGANDLGGTGYEEKVNPAAGAFSGDWRSVEELAALIKEA 349
>gnl|CDD|30409 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 26.3 bits (58), Expect = 9.7
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 57 LPEIRRLIDEQFPKAELNIEGYPNETFLNLCERYKPEQI 95
LP I ++++ + +IE + E F C + EQ+
Sbjct: 100 LP-IELKVEKKLGIGKKDIESFGVEEFREKCREFALEQV 137
>gnl|CDD|37546 KOG2335, KOG2335, KOG2335, tRNA-dihydrouridine synthase
[Translation, ribosomal structure and biogenesis].
Length = 358
Score = 26.0 bits (57), Expect = 10.0
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 1 MSTSVSVNLNAVAVLRNRRNLPWPNLVHIGKIALQSGASGLTVHPR-PDQRHIRY--TDL 57
M ++V NLN ++ R + V K+ +G S LTVH R +Q+ ++ D
Sbjct: 132 MVSAVRANLNVPVSVKIRIFVDLEKTVDYAKMLEDAGVSLLTVHGRTREQKGLKTGPADW 191
Query: 58 PEIRRLID 65
I+ + +
Sbjct: 192 EAIKAVRE 199
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.136 0.412
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,130,662
Number of extensions: 159909
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 412
Number of HSP's successfully gapped: 20
Length of query: 261
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 169
Effective length of database: 4,275,709
Effective search space: 722594821
Effective search space used: 722594821
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: 56 (25.4 bits)