RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1333
(79 letters)
>gnl|CDD|180276 PRK05820, deoA, thymidine phosphorylase; Reviewed.
Length = 440
Score = 105 bits (265), Expect = 7e-29
Identities = 38/66 (57%), Positives = 47/66 (71%), Gaps = 3/66 (4%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSW---GPEGIVVDKHSTGGVGDKVSIPLVP 69
A+ MA+F NG+T E +ALT +M DSGE L W G +VDKHSTGGVGDK+S+ L P
Sbjct: 41 ALAMAIFFNGMTRPERVALTLAMRDSGEVLDWSSLNLNGPIVDKHSTGGVGDKISLMLAP 100
Query: 70 ALAACG 75
+AACG
Sbjct: 101 MVAACG 106
>gnl|CDD|233961 TIGR02644, Y_phosphoryl, pyrimidine-nucleoside phosphorylase. In
general, members of this protein family are designated
pyrimidine-nucleoside phosphorylase, enzyme family EC
2.4.2.2, as in Bacillus subtilis, and more narrowly as
the enzyme family EC 2.4.2.4, thymidine phosphorylase
(alternate name: pyrimidine phosphorylase), as in
Escherichia coli. The set of proteins encompassed by
this model is designated subfamily rather than equivalog
for this reason; the protein name from this model should
be used when TIGR02643 does not score above trusted
cutoff [Purines, pyrimidines, nucleosides, and
nucleotides, Other].
Length = 405
Score = 103 bits (260), Expect = 3e-28
Identities = 41/66 (62%), Positives = 51/66 (77%), Gaps = 1/66 (1%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSW-GPEGIVVDKHSTGGVGDKVSIPLVPAL 71
A+LMA++ NG+T+EET LTK+M+DSGE L G VDKHSTGGVGDKVS+ L P +
Sbjct: 38 ALLMAIYFNGMTDEETAYLTKAMIDSGEVLDLSSLPGPKVDKHSTGGVGDKVSLVLGPIV 97
Query: 72 AACGLK 77
AACG+K
Sbjct: 98 AACGVK 103
>gnl|CDD|223291 COG0213, DeoA, Thymidine phosphorylase [Nucleotide transport and
metabolism].
Length = 435
Score = 101 bits (254), Expect = 3e-27
Identities = 40/65 (61%), Positives = 46/65 (70%), Gaps = 1/65 (1%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSW-GPEGIVVDKHSTGGVGDKVSIPLVPAL 71
A LMA+F G+T +E ALT +MVDSGE L G VVDKHSTGGVGDK S+ LVP +
Sbjct: 41 AFLMAIFFRGMTMDEIAALTMAMVDSGEVLDLSDIPGPVVDKHSTGGVGDKTSLILVPIV 100
Query: 72 AACGL 76
AA GL
Sbjct: 101 AAAGL 105
>gnl|CDD|235289 PRK04350, PRK04350, thymidine phosphorylase; Provisional.
Length = 490
Score = 82.9 bits (206), Expect = 2e-20
Identities = 33/66 (50%), Positives = 44/66 (66%), Gaps = 2/66 (3%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGIVVDKHSTGGV-GDKVSIPLVPAL 71
A L A INGL +E ALT++MV++GE L W VVDKHS GGV G++ ++ +VP +
Sbjct: 118 AFLTASAINGLDMDEIEALTRAMVETGERLDW-DRPPVVDKHSIGGVPGNRTTLIVVPIV 176
Query: 72 AACGLK 77
AA GL
Sbjct: 177 AAAGLT 182
>gnl|CDD|131691 TIGR02643, T_phosphoryl, thymidine phosphorylase. Thymidine
phosphorylase (alternate name: pyrimidine
phosphorylase), EC 2.4.2.4, is the designation for the
enzyme of E. coli and other Proteobacteria involved in
(deoxy)nucleotide degradation. It often occurs in an
operon with a deoxyribose-phosphate aldolase,
phosphopentomutase and a purine nucleoside
phosphorylase. In many other lineages, the corresponding
enzyme is designated pyrimidine-nucleoside phosphorylase
(EC 2.4.2.2); the naming convention imposed by this
model represents standard literature practice [Purines,
pyrimidines, nucleosides, and nucleotides, Other].
Length = 437
Score = 79.0 bits (195), Expect = 4e-19
Identities = 37/67 (55%), Positives = 45/67 (67%), Gaps = 3/67 (4%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPE---GIVVDKHSTGGVGDKVSIPLVP 69
A MA+F NG+ +E +ALT +M DSG+ L W G VVDKHSTGGVGD VS+ L P
Sbjct: 40 AFAMAVFFNGMNRDERVALTLAMRDSGDVLDWRSLDLNGPVVDKHSTGGVGDVVSLMLGP 99
Query: 70 ALAACGL 76
+AACG
Sbjct: 100 IVAACGG 106
>gnl|CDD|180387 PRK06078, PRK06078, pyrimidine-nucleoside phosphorylase; Reviewed.
Length = 434
Score = 71.7 bits (176), Expect = 1e-16
Identities = 31/64 (48%), Positives = 43/64 (67%), Gaps = 1/64 (1%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGP-EGIVVDKHSTGGVGDKVSIPLVPAL 71
A+ MA++ +T+ E LT +MV+SG+T+ EGI VDKHSTGGVGD ++ L P +
Sbjct: 40 ALAMAIYFKDMTDRERADLTMAMVNSGDTIDLSAIEGIKVDKHSTGGVGDTTTLVLAPLV 99
Query: 72 AACG 75
AA G
Sbjct: 100 AAFG 103
>gnl|CDD|132370 TIGR03327, AMP_phos, AMP phosphorylase. This enzyme family is
found, so far, strictly in the Archaea, and only in
those with a type III Rubisco enzyme. Most of the
members previously were annotated as thymidine
phosphorylase, or DeoA. The AMP metabolized by this
enzyme may be produced by ADP-dependent sugar kinases.
Length = 500
Score = 69.3 bits (170), Expect = 1e-15
Identities = 28/66 (42%), Positives = 45/66 (68%), Gaps = 2/66 (3%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGIVVDKHSTGGV-GDKVSIPLVPAL 71
A + A +ING+ +E LT++M ++G+ LS+ ++DKHS GGV G+K+S+ +VP +
Sbjct: 124 AFVTASYINGMDMDEIEWLTRAMAETGDMLSF-DRHPIMDKHSIGGVPGNKISLLVVPIV 182
Query: 72 AACGLK 77
AA GL
Sbjct: 183 AAAGLT 188
>gnl|CDD|233962 TIGR02645, ARCH_P_rylase, putative thymidine phosphorylase.
Members of this family are closely related to
characterized examples of thymidine phosphorylase (EC
2.4.2.4) and pyrimidine nucleoside phosphorylase (RC
2.4.2.2). Most examples are found in the archaea, but
other examples in Legionella pneumophila str. Paris and
Rhodopseudomonas palustris CGA009.
Length = 493
Score = 68.3 bits (167), Expect = 3e-15
Identities = 33/66 (50%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGIVVDKHSTGGV-GDKVSIPLVPAL 71
A L A ING+T +E ALT +M D+GE L W ++DKHS GGV G+K S+ +VP +
Sbjct: 123 AFLTASAINGMTMDEIEALTIAMADTGEMLEW-DREPIMDKHSIGGVPGNKTSLIVVPIV 181
Query: 72 AACGLK 77
AA GL
Sbjct: 182 AAAGLL 187
>gnl|CDD|145834 pfam02885, Glycos_trans_3N, Glycosyl transferase family, helical
bundle domain. This family includes anthranilate
phosphoribosyltransferase (TrpD), thymidine
phosphorylase. All these proteins can transfer a
phosphorylated ribose substrate.
Length = 66
Score = 39.8 bits (94), Expect = 4e-06
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGE 40
A LMA+ I G T EE K+M +S
Sbjct: 39 AFLMALRIKGETPEEIAGAAKAMRESAT 66
>gnl|CDD|216013 pfam00591, Glycos_transf_3, Glycosyl transferase family, a/b
domain. This family includes anthranilate
phosphoribosyltransferase (TrpD), thymidine
phosphorylase. All these proteins can transfer a
phosphorylated ribose substrate.
Length = 254
Score = 39.2 bits (92), Expect = 4e-05
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 47 EGIVVDKHSTGGVGDK---VSIPLVPALAACGLK 77
G +VD TGG GD +S AACG+K
Sbjct: 1 LGDIVDIVGTGGDGDNTFNISTAAAFVAAACGVK 34
>gnl|CDD|233329 TIGR01245, trpD, anthranilate phosphoribosyltransferase. In many
widely different species, including E. coli, Thermotoga
maritima, and Archaeoglobus fulgidus, this enzymatic
domain (anthranilate phosphoribosyltransferase) is found
C-terminal to glutamine amidotransferase; the fusion
protein is designated anthranilate synthase component II
(EC 4.1.3.27) [Amino acid biosynthesis, Aromatic amino
acid family].
Length = 330
Score = 34.9 bits (81), Expect = 0.001
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGIVVDKHSTGGVGDK---VSIPLVP 69
A+L A+ I G T EE K+M + + P +VD TGG G +S
Sbjct: 34 AILAALRIKGETPEEITGFAKAMREHAVKVPGRPVEDLVDIVGTGGDGANTINISTASAF 93
Query: 70 ALAACGLK 77
AA G+K
Sbjct: 94 VAAAAGVK 101
>gnl|CDD|223621 COG0547, TrpD, Anthranilate phosphoribosyltransferase [Amino acid
transport and metabolism].
Length = 338
Score = 29.5 bits (67), Expect = 0.11
Identities = 22/69 (31%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 13 AMLMAMFINGLTNEETIALTKSMVDSGETLSWGPEGIVVDKHSTGGVGDKVSIPLVPA-- 70
A L A+ I G T EE ++M + L P VD TGG G +I + A
Sbjct: 41 AFLTALRIKGETPEEIAGFAEAMREHAPKLP-VPAADPVDIVGTGGDGAN-TINISTAAA 98
Query: 71 --LAACGLK 77
AA G+
Sbjct: 99 IVAAAAGVP 107
>gnl|CDD|182810 PRK10885, cca, multifunctional tRNA nucleotidyl
transferase/2'3'-cyclic
phosphodiesterase/2'nucleotidase/phosphatase; Reviewed.
Length = 409
Score = 28.3 bits (64), Expect = 0.31
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 26 EETIALTKSMVDSGETLSWGPE 47
ET+AL + MV SGE + PE
Sbjct: 154 PETLALMREMVASGELDALTPE 175
>gnl|CDD|235279 PRK04319, PRK04319, acetyl-CoA synthetase; Provisional.
Length = 570
Score = 26.8 bits (60), Expect = 1.2
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 6/30 (20%)
Query: 42 LSWGPEGIV------VDKHSTGGVGDKVSI 65
SW G V +D+H+ GG DKV++
Sbjct: 34 FSWLETGKVNIAYEAIDRHADGGRKDKVAL 63
>gnl|CDD|236643 PRK10044, PRK10044, ferrichrome outer membrane transporter;
Provisional.
Length = 727
Score = 26.6 bits (59), Expect = 1.2
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 11/66 (16%)
Query: 13 AMLMAMFINGLT---------NEETIALTKSMVDSGETLSWGPEGIVVDKHSTGGVGDKV 63
A+++A ++G++ EETI +T + + +WGP + K S G
Sbjct: 17 AVVVATAVSGMSVYAQAAVEPKEETITVTAAPA--PQESAWGPAATIAAKRSATGTKTDT 74
Query: 64 SIPLVP 69
I P
Sbjct: 75 PIEKTP 80
>gnl|CDD|223474 COG0397, COG0397, Uncharacterized conserved protein [Function
unknown].
Length = 488
Score = 25.4 bits (56), Expect = 3.1
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 6/28 (21%)
Query: 19 FINGLTNEETIALTKSMVDSGETLSWGP 46
F++G+ N T +M +GET +GP
Sbjct: 246 FVHGVLN------TDNMSITGETFDYGP 267
>gnl|CDD|163656 cd07413, MPP_PA3087, Pseudomonas aeruginosa PA3087 and related
proteins, metallophosphatase domain. PA3087 is an
uncharacterized protein from Pseudomonas aeruginosa
with a metallophosphatase domain that belongs to the
phosphoprotein phosphatase (PPP) family. The PPP
family also includes: PP1, PP2A, PP2B (calcineurin),
PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and
ApA4 hydrolase. The PPP catalytic domain is defined by
three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-).
The PPP enzyme family is ancient with members found in
all eukaryotes, and in most bacterial and archeal
genomes. Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes.
PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and
acid sphingomyelinases (ASMases). The conserved domain
is a double beta-sheet sandwich with a di-metal active
site made up of residues located at the C-terminal side
of the sheets. This domain is thought to allow for
productive metal coordination.
Length = 222
Score = 25.3 bits (56), Expect = 3.4
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 12 RAMLMAMFI-NGLTNEETIALTKSMVDSGETL 42
+ + + I G E + + KSMVD+G L
Sbjct: 36 QVVFLGDLIDRGPEIRELLEIVKSMVDAGHAL 67
>gnl|CDD|143406 cd07087, ALDH_F3-13-14_CALDH-like, ALDH subfamily: Coniferyl
aldehyde dehydrogenase, ALDH families 3, 13, and 14, and
other related proteins. ALDH subfamily which includes
NAD(P)+-dependent, aldehyde dehydrogenase, family 3
member A1 and B1 (ALDH3A1, ALDH3B1, EC=1.2.1.5) and
fatty aldehyde dehydrogenase, family 3 member A2
(ALDH3A2, EC=1.2.1.3), and also plant ALDH family
members ALDH3F1, ALDH3H1, and ALDH3I1, fungal ALDH14
(YMR110C) and the protozoan family 13 member (ALDH13),
as well as coniferyl aldehyde dehydrogenases (CALDH,
EC=1.2.1.68), and other similar sequences, such as the
Pseudomonas putida benzaldehyde dehydrogenase I that is
involved in the metabolism of mandelate.
Length = 426
Score = 25.2 bits (56), Expect = 3.8
Identities = 9/17 (52%), Positives = 11/17 (64%), Gaps = 3/17 (17%)
Query: 66 PLVPALAA---CGLKPS 79
PL+ A+AA LKPS
Sbjct: 120 PLIGAIAAGNTVVLKPS 136
>gnl|CDD|178400 PLN02803, PLN02803, beta-amylase.
Length = 548
Score = 24.8 bits (54), Expect = 5.2
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 49 IVVDKHSTGG-VGDKVSIPLVP 69
+V+ H GG VGD SIPL P
Sbjct: 162 VVMSFHQCGGNVGDSCSIPLPP 183
>gnl|CDD|132290 TIGR03246, arg_catab_astC, succinylornithine transaminase family.
Members of the seed alignment for this protein family
are the enzyme succinylornithine transaminase (EC
2.6.1.81), which catalyzes the third of five steps in
arginine succinyltransferase (AST) pathway, an
ammonia-releasing pathway of arginine degradation. All
seed alignment sequences are found within arginine
succinyltransferase operons, and all proteins that
score above 820.0 bits should function as
succinylornithine transaminase. However, a number of
sequences extremely closely related in sequence, found
in different genomic contexts, are likely to act in
different biological processes and may act on different
substrates. This model is desigated subfamily rather
than equivalog, pending further consideration, for this
reason [Energy metabolism, Amino acids and amines].
Length = 397
Score = 24.7 bits (54), Expect = 5.2
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 21 NGLTNEETIALTKSMVDS 38
NG TNE + L K +VD+
Sbjct: 72 NGYTNEPVLRLAKKLVDA 89
>gnl|CDD|216462 pfam01373, Glyco_hydro_14, Glycosyl hydrolase family 14. This
family are beta amylases.
Length = 399
Score = 24.8 bits (54), Expect = 5.5
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 42 LSWGPEGIVVDKHSTGG-VGDKVSIPLVP 69
L W P ++ H GG VGD +IPL
Sbjct: 64 LKWVP---IISTHQCGGNVGDDCNIPLPS 89
>gnl|CDD|173004 PRK14538, PRK14538, putative bifunctional signaling protein/50S
ribosomal protein L9; Provisional.
Length = 838
Score = 24.8 bits (54), Expect = 7.0
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 32 TKSMVDSGETLSWGPEGIVVDKHST 56
TK +V+S E LS IV+D H
Sbjct: 456 TKDIVNSPELLSLTNNIIVIDHHRA 480
>gnl|CDD|183486 PRK12381, PRK12381, bifunctional succinylornithine
transaminase/acetylornithine transaminase; Provisional.
Length = 406
Score = 24.3 bits (53), Expect = 8.2
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 21 NGLTNEETIALTKSMVDS 38
NG TNE + L K ++D+
Sbjct: 76 NGYTNEPVLRLAKKLIDA 93
>gnl|CDD|221666 pfam12617, LdpA_C, Iron-Sulfur binding protein C terminal. This
domain family is found in bacteria and eukaryotes, and
is typically between 179 and 201 amino acids in length.
The family is found in association with pfam00037. LdpA
(light-dependent period) plays a role in controlling the
redox state in cyanobacteria to modulate its. circadian
clock. LdpA is a protein with Iron-Sulfur
cluster-binding motifs.
Length = 182
Score = 24.1 bits (53), Expect = 9.5
Identities = 7/28 (25%), Positives = 11/28 (39%)
Query: 22 GLTNEETIALTKSMVDSGETLSWGPEGI 49
G TN T+ K + + S G+
Sbjct: 110 GGTNAHTVEKLKQLGLLKPSSSVFIAGV 137
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
0.313 0.130 0.374
Gapped
Lambda K H
0.267 0.0790 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,803,148
Number of extensions: 286528
Number of successful extensions: 245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 233
Number of HSP's successfully gapped: 29
Length of query: 79
Length of database: 10,937,602
Length adjustment: 48
Effective length of query: 31
Effective length of database: 8,808,610
Effective search space: 273066910
Effective search space used: 273066910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)