RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8820
(234 letters)
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of
transcription factors; members include CAP (or cAMP
receptor protein (CRP)), which binds cAMP, FNR
(fumarate and nitrate reduction), which uses an
iron-sulfur cluster to sense oxygen) and CooA, a heme
containing CO sensor. In all cases binding of the
effector leads to conformational changes and the
ability to activate transcription. Cyclic
nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity
of the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits,
a catalytic chain and a regulatory chain, which
contains both copies of the domain; cGPK's are single
chain enzymes that include the two copies of the domain
in their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 62.3 bits (152), Expect = 1e-12
Identities = 25/64 (39%), Positives = 36/64 (56%)
Query: 3 DRSDSTYIVLTGRLRSVKTLESGKRKEEAEYSKGDLVGLIEMVTSTSRNTTVMAVRDSEL 62
D +DS YIVL+G + K E G+ + GDL G + ++ + R+ TV A+ DSEL
Sbjct: 33 DPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPRSATVRALTDSEL 92
Query: 63 AKLP 66
LP
Sbjct: 93 LVLP 96
Score = 45.4 bits (108), Expect = 2e-06
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 104 IRVEHIPGGTCLVRE-EVVEDNKLIYVIAGSLFITQKSSDGSNDVHLFTAFPGDMIGGLA 162
+ P G ++R+ + + L V++GS+ + + DG + + PGD+ G LA
Sbjct: 17 LEERRFPAGEVIIRQGDPA--DSLYIVLSGSVEVYKLDEDGR-EQIVGFLGPGDLFGELA 73
Query: 163 VLTGEASVFTIQSRLPATIAWLPQDD 188
+L T+++ + + LP+ D
Sbjct: 74 LLGNGPRSATVRALTDSELLVLPRSD 99
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 57.3 bits (139), Expect = 4e-11
Identities = 24/64 (37%), Positives = 38/64 (59%)
Query: 3 DRSDSTYIVLTGRLRSVKTLESGKRKEEAEYSKGDLVGLIEMVTSTSRNTTVMAVRDSEL 62
D +DS YIVL+G+++ K E G+ + A GD G + ++ R+ TV+A+ DSEL
Sbjct: 15 DPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFGELALLGGEPRSATVVALTDSEL 74
Query: 63 AKLP 66
+P
Sbjct: 75 LVIP 78
Score = 44.2 bits (105), Expect = 2e-06
Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 2/91 (2%)
Query: 106 VEHIPGGTCLVREEVVEDNKLIYVIAGSLFITQKSSDGSNDVHLFTAFPGDMIGGLAVLT 165
+ G + RE + L V++G + + + DG + L PGD G LA+L
Sbjct: 1 LRSFKKGEVIFREGD-PADSLYIVLSGKVKVYKLDEDG-REQILAFLGPGDFFGELALLG 58
Query: 166 GEASVFTIQSRLPATIAWLPQDDCSTLIDAD 196
GE T+ + + + +P++D L++ D
Sbjct: 59 GEPRSATVVALTDSELLVIPREDFLELLEQD 89
>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
Catabolite gene activator protein (CAP) is a prokaryotic
homologue of eukaryotic cNMP-binding domains, present in
ion channels, and cNMP-dependent kinases.
Length = 120
Score = 50.9 bits (122), Expect = 2e-08
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 3/78 (3%)
Query: 3 DRSDSTYIVLTGRLRSVKTLESGKRKEEAEYSKGDLVGLIEMVT--STSRNTTVMAVRDS 60
D DS YI+++G + K LE G+ + GD G + ++T + + +A+ +
Sbjct: 33 DVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRAASAAAVALELA 92
Query: 61 ELAKLP-EGLCDHLPRSP 77
L ++ LP P
Sbjct: 93 TLLRIDFRDFLQLLPELP 110
Score = 33.5 bits (77), Expect = 0.028
Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 5/86 (5%)
Query: 104 IRVEHIPGGTCLVREEVVEDNKLIYVI-AGSLFITQKSSDGSNDVHLFTAFPGDMIGGLA 162
+ P G ++R+ V D+ Y+I +G + + + DG + + T PGD G LA
Sbjct: 17 LEPVRYPAGEVIIRQGDVGDS--FYIIVSGEVEVYKVLEDG-EEQIVGTLGPGDFFGELA 73
Query: 163 VLTGEASVFTIQSRLPATIAWLPQDD 188
+LT + + + +A L + D
Sbjct: 74 LLTNSRRAASA-AAVALELATLLRID 98
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator and
regulatory subunit of cAMP-dependent protein kinases
[Signal transduction mechanisms].
Length = 214
Score = 51.0 bits (122), Expect = 7e-08
Identities = 16/64 (25%), Positives = 33/64 (51%)
Query: 3 DRSDSTYIVLTGRLRSVKTLESGKRKEEAEYSKGDLVGLIEMVTSTSRNTTVMAVRDSEL 62
+ +DS YI+L+G ++ E G+ GD G + ++ R+ + +A+ D E+
Sbjct: 39 EEADSLYIILSGIVKLYANTEDGREIILGFLGPGDFFGELALLGGDPRSASAVALTDVEV 98
Query: 63 AKLP 66
++P
Sbjct: 99 LEIP 102
Score = 42.5 bits (100), Expect = 5e-05
Identities = 30/134 (22%), Positives = 56/134 (41%), Gaps = 8/134 (5%)
Query: 79 EQELIHSSKREFMEQLGVKDFSGLDIRVEHIPGGTCLVREEVVEDNKLIYVIAGSLFITQ 138
E L++ E +E L L + V +P G L E E + L +++G + +
Sbjct: 4 ENPLLNLLPSELLELLA------LKLEVRKLPKGEVLFTE-GEEADSLYIILSGIVKLYA 56
Query: 139 KSSDGSNDVHLFTAFPGDMIGGLAVLTGEASVFTIQSRLPATIAWLPQDDCSTLIDADMN 198
+ DG + L PGD G LA+L G+ + + + +P+ D L+
Sbjct: 57 NTEDGREII-LGFLGPGDFFGELALLGGDPRSASAVALTDVEVLEIPRKDFLELLAESPK 115
Query: 199 VTLKIAHSVLKRMS 212
+ L + + +R+
Sbjct: 116 LALALLRLLARRLR 129
>gnl|CDD|236494 PRK09391, fixK, transcriptional regulator FixK; Provisional.
Length = 230
Score = 29.6 bits (67), Expect = 1.1
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 3 DRSDSTYIVLTGRLRSVKTLESGKRKEEAEYSKGDLVGLIEMVTSTSR-------NTTVM 55
+ +D Y V +G +R+ + L G+R+ A + GD+ GL E ST R +TTV
Sbjct: 54 EPADYVYQVESGAVRTYRLLSDGRRQIGAFHLPGDVFGL-ES-GSTHRFTAEAIVDTTVR 111
Query: 56 AVRDSELAKLPE 67
++ L +
Sbjct: 112 LIKRRSLEQAAA 123
>gnl|CDD|129923 TIGR00843, benE, benzoate transporter. The benzoate transporter
family contains only a single characterised member, the
benzoate transporter of Acinetobacter calcoaceticus,
which functions as a benzoate/proton symporter
[Transport and binding proteins, Carbohydrates, organic
alcohols, and acids].
Length = 395
Score = 29.5 bits (66), Expect = 1.4
Identities = 24/95 (25%), Positives = 36/95 (37%), Gaps = 9/95 (9%)
Query: 99 FSGLDIRVEHIPGGTCLVRE-EVVEDNKLIYVIAGSLFITQKSSDGSNDVHLFTAFPGD- 156
G+ I + I C+ ++ +D + I A +F LF A P +
Sbjct: 273 AGGISIGIAAITAAICMGKDAHEDKDKRWIAAAAAGIFYLLAGLFAGAITALFAALPKEL 332
Query: 157 --MIGGLAVLTGEASVFTI-----QSRLPATIAWL 184
+ GLA+L A I Q R A IA+L
Sbjct: 333 IAALAGLALLGAIAGNIKIALHEDQERDAALIAFL 367
>gnl|CDD|226993 COG4646, COG4646, DNA methylase [Transcription / DNA replication,
recombination, and repair].
Length = 637
Score = 29.5 bits (66), Expect = 1.7
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 10/53 (18%)
Query: 96 VKDFSGLDIRVEHIPGGTCLVREEVVEDNKLIYVIAGSLFITQKSSDGSNDVH 148
V++ DIR+ H+P + VE +L ++ AG S G++ H
Sbjct: 352 VQETMSADIRIHHMPE----LASWTVEARQLGWLAAG------TSEWGTDRRH 394
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 29.5 bits (66), Expect = 2.0
Identities = 35/133 (26%), Positives = 62/133 (46%), Gaps = 23/133 (17%)
Query: 69 LCDHLPRSPSEQE--LIHSSKREFMEQLGVKDFSGLDIRVEHIPGGTCLVREEVVEDNKL 126
+C HL P ++ L RE + L K ++ E+IP RE+V+ N+
Sbjct: 367 ICQHL-FLPVVEKVYLFKGVSREILLLLVTK------MKAEYIPP-----REDVIMQNEA 414
Query: 127 ---IYVI-AGSLFITQKSSDGSNDVHLFTAFPGDMIGGLAVLTGEASVFTIQSRLPATIA 182
+Y++ +G + I S+G + + T GD+ G + L FT +++ T++
Sbjct: 415 PDDVYIVVSGEVEIID--SEGEKERVVGTLGCGDIFGEVGALCCRPQSFTFRTK---TLS 469
Query: 183 WLPQDDCSTLIDA 195
L + STLI+A
Sbjct: 470 QLLRLKTSTLIEA 482
>gnl|CDD|197296 cd09200, PLDc_pPLDbeta_2, Catalytic domain, repeat 2, of plant
beta-type phospholipase D. Catalytic domain, repeat 2,
of plant beta-type phospholipase D (PLDbeta, EC
3.1.4.4). Plant PLDbeta is a phosphatidylinositol
4,5-bisphosphate (PIP2)-dependent PLD that possesses a
regulatory calcium-dependent phospholipid-binding C2
domain in the N-terminus and requires nanomolar calcium
and cytosolic factors for optimal activity. The C2
domain is unique to plant PLDs and is not present in
animal or fungal PLDs. Sequence analysis shows that
plant PLDbeta is evolutionarily divergent from
alpha-type plant PLD, and plant PLDbeta is more closely
related to mammalian and yeast PLDs than to plant
PLDalpha. Like other PLD enzymes, the monomer of plant
PLDbeta consists of two catalytic domains, each of which
contains one copy of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue). Two HKD motifs from two domains form a single
active site. Plant PLDbeta may utilize a common two-step
ping-pong catalytic mechanism involving an
enzyme-substrate intermediate to cleave phosphodiester
bonds. The two histidine residues from the two HKD
motifs play key roles in the catalysis. Upon substrate
binding, a histidine residue from one HKD motif could
function as the nucleophile, attacking the
phosphodiester bond to create a covalent
phosphohistidine intermediate, while the other histidine
residue from the second HKD motif could serve as a
general acid, stabilizing the leaving group.
Length = 211
Score = 28.7 bits (64), Expect = 2.2
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 120 VVEDNKLIYVIAGSLFITQKSSDGSNDVHL 149
+V+D YVI GS I Q+S DGS D +
Sbjct: 171 IVDDE---YVIIGSANINQRSMDGSRDTEI 197
>gnl|CDD|143498 cd06825, PLPDE_III_VanT, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, VanT and similar proteins.
This subfamily is composed of Enterococcus gallinarum
VanT and similar proteins. VanT is a membrane-bound
serine racemase (EC 5.1.1.18) that is essential for
vancomycin resistance in Enterococcus gallinarum. It
converts L-serine into its D-enantiomer (D-serine) for
peptidoglycan synthesis. The C-terminal region of this
protein contains a PLP-binding TIM-barrel domain
followed by beta-sandwich domain, which is homologous to
the fold type III PLP-dependent enzyme, bacterial
alanine racemase (AR). AR exists as homodimers with
active sites that lie at the interface between the TIM
barrel domain of one subunit and the beta-sandwich
domain of the other subunit. On the basis of this
similarity, it has been suggested that dimer formation
of VanT is required for its catalytic activity, and that
it catalyzes the racemization of serine in a
mechanistically similar manner to that of alanine by
bacterial AR. Some biochemical evidence indicates that
VanT also exhibits alanine racemase activity and plays a
role in the racemization of L-alanine. VanT contains a
unique N-terminal transmembrane domain, which may
function as an L-serine transporter. VanT serine
racemases are not related to eukaryotic serine
racemases, which are fold type II PLP-dependent enzymes.
Length = 368
Score = 28.9 bits (65), Expect = 2.3
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 56 AVRDSELAKLPEGLCDHLPRSPSEQE---LIHSSKREF-----MEQLGVKDFSGLD 103
A R + +A + G D PRS S Q+ LI+ + M+QL V D + +
Sbjct: 266 ASRTTRIATVSIGYADGYPRSLSNQKAYVLINGKRAPIIGNICMDQLMV-DVTDIP 320
>gnl|CDD|239139 cd02674, Peptidase_C19R, A subfamily of peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 230
Score = 28.0 bits (63), Expect = 3.4
Identities = 8/44 (18%), Positives = 17/44 (38%)
Query: 32 EYSKGDLVGLIEMVTSTSRNTTVMAVRDSELAKLPEGLCDHLPR 75
++K + + A + +++LP+ L HL R
Sbjct: 92 LFTKEETLDGDNAWKCPKCKKKRKATKKLTISRLPKVLIIHLKR 135
>gnl|CDD|109247 pfam00181, Ribosomal_L2, Ribosomal Proteins L2, RNA binding domain.
Length = 77
Score = 26.4 bits (59), Expect = 3.7
Identities = 8/35 (22%), Positives = 16/35 (45%)
Query: 97 KDFSGLDIRVEHIPGGTCLVREEVVEDNKLIYVIA 131
+ G I +E+ P + + ED + Y++A
Sbjct: 31 GNIKGKVIDIEYDPNRSAPIALVKYEDGEKRYILA 65
>gnl|CDD|217054 pfam02469, Fasciclin, Fasciclin domain. This extracellular domain
is found repeated four times in grasshopper fasciclin I
as well as in proteins from mammals, sea urchins,
plants, yeast and bacteria.
Length = 123
Score = 26.8 bits (60), Expect = 5.5
Identities = 25/105 (23%), Positives = 42/105 (40%), Gaps = 13/105 (12%)
Query: 39 VGLIEMVTSTSRNTTVMAVRDSELAKLPEGLCDHLPRSPSEQELI---H-SSKREFMEQL 94
GL++ + + TV A D AKLP G + L + + + + H R L
Sbjct: 13 AGLVDTLNGSQGPFTVFAPTDEAFAKLPAGTLNFLLKDKEQLKNLLKYHVVPGRLTSSDL 72
Query: 95 G----VKDFSGLDIRVEHIPG-----GTCLVREEVVEDNKLIYVI 130
+ G +RV G G +V+ ++ N +I+VI
Sbjct: 73 KNGGTLATLQGSKLRVNVTGGTVTVNGARVVQSDIEATNGVIHVI 117
>gnl|CDD|180982 PRK07452, PRK07452, DNA polymerase III subunit delta; Validated.
Length = 326
Score = 27.6 bits (62), Expect = 6.1
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 15/56 (26%)
Query: 6 DSTYIVLT------GRLRSVKTLESGKRKEEAEYS-----KGDLVGLIEMVTSTSR 50
++T+++LT GRL+S K L+ K EE E+S + GL ++V T++
Sbjct: 93 ENTHLLLTNTKKPDGRLKSTKLLQ--KLAEEKEFSLIPPWDTE--GLKQLVERTAQ 144
>gnl|CDD|233891 TIGR02487, NrdD, anaerobic ribonucleoside-triphosphate reductase.
This model represents the oxygen-sensitive (anaerobic,
class III) ribonucleotide reductase. The mechanism of
the enzyme involves a glycine-centered radical , a
C-terminal zinc binding site , and a set of conserved
active site cysteines and asparagines. This enzyme
requires an activating component, NrdG, a radical-SAM
domain containing enzyme (TIGR02491). Together the two
form an alpha-2/beta-2 heterodimer [Purines,
pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 579
Score = 26.9 bits (60), Expect = 9.8
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 12 LTGRLRSVKTLESGKRKEEAE 32
+TG L V+ GK+ E +
Sbjct: 555 ITGYLGPVENWNDGKQAEFKD 575
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
0.318 0.135 0.386
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,782,608
Number of extensions: 1095375
Number of successful extensions: 904
Number of sequences better than 10.0: 1
Number of HSP's gapped: 904
Number of HSP's successfully gapped: 26
Length of query: 234
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 140
Effective length of database: 6,768,326
Effective search space: 947565640
Effective search space used: 947565640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.8 bits)