RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7735
(120 letters)
>gnl|CDD|215274 PLN02496, PLN02496, probable phosphopantothenoylcysteine
decarboxylase.
Length = 209
Score = 104 bits (261), Expect = 2e-29
Identities = 43/70 (61%), Positives = 52/70 (74%)
Query: 2 GLCDNLLTCILRAWDFSKPILFCPAMNTKMWNHPITKSHINTLKSWGYEEIPCVSKTLMC 61
GLCDNLLTCI+RAWD+SKP+ PAMNT MWN+P T+ H+ ++ G IP V+K L C
Sbjct: 116 GLCDNLLTCIVRAWDYSKPLFVAPAMNTFMWNNPFTERHLMSIDELGISLIPPVTKRLAC 175
Query: 62 GDTGLGAMAE 71
GD G GAMAE
Sbjct: 176 GDYGNGAMAE 185
>gnl|CDD|235513 PRK05579, PRK05579, bifunctional phosphopantothenoylcysteine
decarboxylase/phosphopantothenate synthase; Validated.
Length = 399
Score = 105 bits (264), Expect = 4e-28
Identities = 35/75 (46%), Positives = 46/75 (61%), Gaps = 2/75 (2%)
Query: 1 MGLCDNLLTCILRAWDFSKPILFCPAMNTKMWNHPITKSHINTLKSWGYEEIPCVSKTLM 60
G+ D+LLT L A + P+L PAMNT+MW +P T+ ++ TL+S G E I S L
Sbjct: 101 HGIADDLLTTTLLA--TTAPVLVAPAMNTQMWENPATQRNLATLRSRGVEIIGPASGRLA 158
Query: 61 CGDTGLGAMAEVDTI 75
CGD G G MAE + I
Sbjct: 159 CGDVGPGRMAEPEEI 173
>gnl|CDD|235986 PRK07313, PRK07313, phosphopantothenoylcysteine decarboxylase;
Validated.
Length = 182
Score = 98.5 bits (246), Expect = 3e-27
Identities = 32/74 (43%), Positives = 47/74 (63%)
Query: 2 GLCDNLLTCILRAWDFSKPILFCPAMNTKMWNHPITKSHINTLKSWGYEEIPCVSKTLMC 61
G+ D+L+T + A + P L PAMNTKM+ +P T+ ++ TLK G +EI L C
Sbjct: 97 GIADDLVTSVALALPATTPKLIAPAMNTKMYENPATQRNLKTLKEDGVQEIEPKEGLLAC 156
Query: 62 GDTGLGAMAEVDTI 75
GD G GA+A+++TI
Sbjct: 157 GDEGYGALADIETI 170
>gnl|CDD|131168 TIGR02113, coaC_strep, phosphopantothenoylcysteine decarboxylase,
streptococcal. In most bacteria, a single bifunctional
protein catalyses phosphopantothenoylcysteine
decarboxylase and phosphopantothenate--cysteine ligase
activities, sequential steps in coenzyme A biosynthesis
(see TIGR00521). These activities reside in separate
proteins encoded by tandem genes in some bacterial
lineages. This model describes proteins from the genera
Streptococcus and Enterococcus homologous to the
N-terminal region of TIGR00521, corresponding to
phosphopantothenoylcysteine decarboxylase activity
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pantothenate and coenzyme A].
Length = 177
Score = 86.8 bits (215), Expect = 1e-22
Identities = 34/74 (45%), Positives = 45/74 (60%)
Query: 2 GLCDNLLTCILRAWDFSKPILFCPAMNTKMWNHPITKSHINTLKSWGYEEIPCVSKTLMC 61
G DN++T + A P L PAMNTKM+ +PIT+ +I LK GY+EI L C
Sbjct: 96 GFADNIVTSVALALPPETPKLIAPAMNTKMYQNPITQRNIKILKKIGYQEIQPKESLLAC 155
Query: 62 GDTGLGAMAEVDTI 75
GD G GA+A++D I
Sbjct: 156 GDYGRGALADLDDI 169
>gnl|CDD|233006 TIGR00521, coaBC_dfp, phosphopantothenoylcysteine decarboxylase /
phosphopantothenate--cysteine ligase. This model
represents a bifunctional enzyme that catalyzes the
second and third steps (cysteine ligation, EC 6.3.2.5,
and decarboxylation, EC 4.1.1.36) in the biosynthesis of
coenzyme A (CoA) from pantothenate in bacteria. In early
descriptions of this flavoprotein, a ts mutation in one
region of the protein appeared to cause a defect in DNA
metaobolism rather than an increased need for the
pantothenate precursor beta-alanine. This protein was
then called dfp, for DNA/pantothenate metabolism
flavoprotein. The authors responsible for detecting
phosphopantothenate--cysteine ligase activity suggest
renaming this bifunctional protein coaBC for its role in
CoA biosynthesis. This enzyme contains the FMN cofactor,
but no FAD or pyruvoyl group. The amino-terminal region
contains the phosphopantothenoylcysteine decarboxylase
activity [Biosynthesis of cofactors, prosthetic groups,
and carriers, Pantothenate and coenzyme A].
Length = 390
Score = 80.9 bits (200), Expect = 4e-19
Identities = 31/74 (41%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 2 GLCDNLLTCILRAWDFSKPILFCPAMNTKMWNHPITKSHINTLKSWGYEEIPCVSKTLMC 61
G+ D+L++ A S PI+ PAMN M+N+P + +I LK GY I S L C
Sbjct: 98 GIADDLVSTTALA--ASAPIILAPAMNENMYNNPAVQENIKRLKDDGYIFIEPDSGLLAC 155
Query: 62 GDTGLGAMAEVDTI 75
GD G G +AE +TI
Sbjct: 156 GDEGKGRLAEPETI 169
>gnl|CDD|223529 COG0452, Dfp, Phosphopantothenoylcysteine synthetase/decarboxylase
[Coenzyme metabolism].
Length = 392
Score = 77.4 bits (191), Expect = 6e-18
Identities = 35/122 (28%), Positives = 51/122 (41%), Gaps = 20/122 (16%)
Query: 2 GLCDNLLTCILRAWDFSKPILFCPAMNTKMWNHPITKSHINTLKSWGYEEIPCVSKTLMC 61
G+ DNL T L A P++ PAMN M+ HP T+ ++ LKS G I + L
Sbjct: 99 GIADNLSTTTLLAA--KAPLVLAPAMNVIMYTHPATQENLQRLKSEGVLFIEPIEGEL-- 154
Query: 62 GDTGLGAMAEVDTIKYGFVPNTIRKST--------------EPQDPNNFVDNNA-GITEY 106
D G G +AE + I ++ E DP F+ N + G +
Sbjct: 155 ADVGDGRLAEPEEI-VEAALALLKTPDLKGKKVLITAGPTREYIDPVRFISNRSSGKMGF 213
Query: 107 SL 108
+L
Sbjct: 214 AL 215
>gnl|CDD|217035 pfam02441, Flavoprotein, Flavoprotein. This family contains
diverse flavoprotein enzymes. This family includes
epidermin biosynthesis protein, EpiD, which has been
shown to be a flavoprotein that binds FMN. This enzyme
catalyzes the removal of two reducing equivalents from
the cysteine residue of the C-terminal meso-lanthionine
of epidermin to form a --C==C-- double bond. This family
also includes the B chain of dipicolinate synthase a
small polar molecule that accumulates to high
concentrations in bacterial endospores, and is thought
to play a role in spore heat resistance, or the
maintenance of heat resistance. dipicolinate synthase
catalyzes the formation of dipicolinic acid from
dihydroxydipicolinic acid. This family also includes
phenyl-acrylic acid decarboxylase (EC:4.1.1.-).
Length = 132
Score = 62.6 bits (153), Expect = 8e-14
Identities = 18/37 (48%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 2 GLCDNLLTCILRAWD-FSKPILFCPAMNTKMWNHPIT 37
G+ DNLLT A KP++ PAMN MW +PIT
Sbjct: 96 GIADNLLTRAALAALKERKPLVLAPAMNPLMWENPIT 132
>gnl|CDD|172484 PRK13982, PRK13982, bifunctional
SbtC-like/phosphopantothenoylcysteine
decarboxylase/phosphopantothenate synthase; Provisional.
Length = 475
Score = 60.9 bits (148), Expect = 4e-12
Identities = 31/75 (41%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 2 GLCDNLLTCILRAWDFSKPILFCPAMNTKMWNHPITKSHINTLKSWGYEEI-PCVSKTLM 60
GL D+L + IL A + +PIL PAMN MWN+P T+ ++ LK G I P +
Sbjct: 166 GLADDLASAILLAAN--RPILLAPAMNPLMWNNPATRRNVAQLKRDGVHMIGPNAGEMAE 223
Query: 61 CGDTGLGAMAEVDTI 75
G+ G+G MAE I
Sbjct: 224 RGEAGVGRMAEPLEI 238
>gnl|CDD|226259 COG3736, VirB8, Type IV secretory pathway, component VirB8
[Intracellular trafficking and secretion].
Length = 239
Score = 27.3 bits (61), Expect = 1.7
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 74 TIKYGFVPNTIRKSTEPQDPNNFVDNNAGITEYSLT 109
TI+Y FVP I S+ +P F +T Y +
Sbjct: 200 TIRYEFVPTPISTSSRLINPLGFQ-----VTSYRVD 230
>gnl|CDD|213246 cd03279, ABC_sbcCD, ATP-binding cassette domain of sbcCD. SbcCD
and other Mre11/Rad50 (MR) complexes are implicated in
the metabolism of DNA ends. They cleave ends sealed by
hairpin structures and are thought to play a role in
removing protein bound to DNA termini.
Length = 213
Score = 26.8 bits (60), Expect = 2.3
Identities = 15/61 (24%), Positives = 21/61 (34%), Gaps = 5/61 (8%)
Query: 58 TLMCGDTGLGAMAEVDTIKYGFVPNTIRKSTEPQDPNNFVDNNAGITEYSLTGFLYFSLR 117
L+CG TG G +D I Y T R + + F G ++ F L
Sbjct: 31 FLICGPTGAGKSTILDAITYALYGKTPRYGRQENLRSVF---APGEDTAEVS--FTFQLG 85
Query: 118 D 118
Sbjct: 86 G 86
>gnl|CDD|237053 PRK12315, PRK12315, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 581
Score = 27.3 bits (61), Expect = 2.5
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 33 NHPITKSHINTLKSWGYE 50
+HPI HI+TLK GY+
Sbjct: 233 DHPIV-LHIHTLKGKGYQ 249
>gnl|CDD|218058 pfam04390, LptE, Lipopolysaccharide-assembly. LptE (formerly known
as RplB) is involved in lipopolysaccharide-assembly on
the outer membrane of Gram-negative organisms. The
lipopolysaccharide component of the outer bacterial
membrane is transported from its source of origin to the
outer membrane by a set of proteins constituting a
transport machinery that is made up of LptA, LptB, LptC,
LptD, LptE. LptD appears to be anchored in the outer
membrane, and LptE forms a complex with it. This part of
the machinery complex is involved in the assembly of
lipopolysaccharide in the outer leaflet of the outer
membrane.
Length = 142
Score = 26.6 bits (59), Expect = 2.5
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 97 VDNNAGITEYSLTGFLYFSLRD 118
D N + EY LT + + L D
Sbjct: 70 YDANGRVAEYRLTLTVNYRLTD 91
>gnl|CDD|220709 pfam10350, DUF2428, Putative death-receptor fusion protein
(DUF2428). This is a family of proteins conserved from
plants to humans. The function is not known. Several
members have been annotated as being HEAT
repeat-containing proteins while others are designated
as death-receptor interacting proteins, but neither of
these could be confirmed.
Length = 241
Score = 26.5 bits (59), Expect = 3.5
Identities = 5/20 (25%), Positives = 12/20 (60%)
Query: 3 LCDNLLTCILRAWDFSKPIL 22
+ L++ +R W+ KP++
Sbjct: 4 IVSRLVSLCIRIWEAVKPVV 23
>gnl|CDD|182183 PRK09986, PRK09986, DNA-binding transcriptional activator XapR;
Provisional.
Length = 294
Score = 26.6 bits (59), Expect = 3.6
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 78 GFVPNTIRKSTEPQDPNNFVDNNAGIT 104
GF P IR+ EPQ V GIT
Sbjct: 221 GFSPQIIRQVNEPQTVLAMVSMGIGIT 247
>gnl|CDD|234684 PRK00192, PRK00192, mannosyl-3-phosphoglycerate phosphatase;
Reviewed.
Length = 273
Score = 26.1 bits (58), Expect = 4.7
Identities = 21/64 (32%), Positives = 25/64 (39%), Gaps = 22/64 (34%)
Query: 41 INTLKSWGYEEIPCVSKTLMCGDTGLGAMAEVDTIKYGFVPNTIRKSTEPQDPNNF-VDN 99
+ LK G IPC SKT AEV +RK +DP F V+N
Sbjct: 30 LKALKEKGIPVIPCTSKTA----------AEV---------EVLRKELGLEDP--FIVEN 68
Query: 100 NAGI 103
A I
Sbjct: 69 GAAI 72
>gnl|CDD|234913 PRK01175, PRK01175, phosphoribosylformylglycinamidine synthase I;
Provisional.
Length = 261
Score = 26.3 bits (58), Expect = 5.0
Identities = 13/48 (27%), Positives = 22/48 (45%)
Query: 57 KTLMCGDTGLGAMAEVDTIKYGFVPNTIRKSTEPQDPNNFVDNNAGIT 104
+ + + L + E D I + +V + P +PN + N AGIT
Sbjct: 165 RVVFSEEEILERLIENDQIVFRYVDENGNYAGYPWNPNGSIYNIAGIT 212
>gnl|CDD|215575 PLN03100, PLN03100, Permease subunit of ER-derived-lipid
transporter; Provisional.
Length = 292
Score = 25.9 bits (57), Expect = 5.5
Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 58 TLMCGDTGLGAMAEVDTIKYGFVPNTI----RKSTEPQD 92
TLMC G+ A A + YG N I ++ P D
Sbjct: 192 TLMCFTVGMAASALLADSVYGVSANIILDSAARALRPWD 230
>gnl|CDD|128866 smart00603, LCCL, LCCL domain.
Length = 85
Score = 24.7 bits (54), Expect = 7.8
Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 4/23 (17%)
Query: 8 LTCILRAWDFSKPI----LFCPA 26
+TC R D KP+ + CPA
Sbjct: 3 VTCDTRGLDLCKPVTDNRVLCPA 25
>gnl|CDD|176140 cd08449, PBP2_XapR, The C-terminal substrate binding domain of
LysR-type transcriptional regulator XapR involved in
xanthosine catabolism, contains the type 2 periplasmic
binding fold. In Escherichia coli, XapR is a positive
regulator for the expression of xapA gene, encoding
xanthosine phosphorylase, and xapB gene, encoding a
polypeptide similar to the nucleotide transport protein
NupG. As an operon, the expression of both xapA and xapB
is fully dependent on the presence of both XapR and the
inducer xanthosine. Expression of the xapR is
constitutive but not auto-regulated, unlike many other
LysR family proteins. This substrate-binding domain
shows significant homology to 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.
Length = 197
Score = 25.3 bits (56), Expect = 8.5
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 75 IKYGFVPNTIRKSTEPQDPNNFVDNNAGIT 104
++ GF P ++ EPQ V G+
Sbjct: 121 LQAGFTPQITQEVVEPQTLMALVAAGFGVA 150
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
0.321 0.138 0.450
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,950,874
Number of extensions: 479721
Number of successful extensions: 332
Number of sequences better than 10.0: 1
Number of HSP's gapped: 328
Number of HSP's successfully gapped: 20
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
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: 53 (24.3 bits)