RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3119
(187 letters)
>gnl|CDD|220399 pfam09783, Vac_ImportDeg, Vacuolar import and degradation protein.
Members of this family are involved in the negative
regulation of gluconeogenesis. They are required for
both proteosome-dependent and vacuolar catabolite
degradation of fructose-1,6-bisphosphatase (FBPase),
where they probably regulate FBPase targeting from the
FBPase-containing vesicles to the vacuole.
Length = 176
Score = 237 bits (606), Expect = 8e-81
Identities = 93/175 (53%), Positives = 120/175 (68%), Gaps = 6/175 (3%)
Query: 11 LLYNGSRFQGHQKSKGNSYEIEVV--HVDEENSYLCGYLKIKGLTEEYPTLTTFFDGEII 68
L GSRF+G Q SK Y++EV VD +S+LCGYL+IKGLT+++P LTTFF+GEII
Sbjct: 2 YLRPGSRFRGTQLSKYEKYQVEVTIKTVDLPDSHLCGYLEIKGLTDQHPELTTFFEGEII 61
Query: 69 SKKYPFLTRKWDADEDVDRKHWGKFSSFYDYSK----TFNSDSFDYDSLKDTDFVFMRWK 124
KY FLT KW A E++D +HW +F +F +K S + + L + DF+FMRWK
Sbjct: 62 GNKYTFLTEKWGASEEIDLEHWKRFPAFKPLTKQTMRNLISRDYKHYDLLNQDFIFMRWK 121
Query: 125 EHFLVPDHTIKDINGASFAGFYYICFQKSAATIEGYYFHRSSEWFQSLTLCHVPD 179
E FLVPDH +K I+GASF GFYYICF +S +I+GYY+H +SE FQ L L V D
Sbjct: 122 EQFLVPDHRVKSISGASFEGFYYICFDQSTGSIQGYYYHPNSEKFQQLELTPVED 176
>gnl|CDD|227405 COG5073, VID24, Vacuolar import and degradation protein
[Intracellular trafficking and secretion].
Length = 272
Score = 133 bits (335), Expect = 1e-38
Identities = 71/193 (36%), Positives = 94/193 (48%), Gaps = 17/193 (8%)
Query: 12 LYNGSRFQGHQKSKGNSYEIEV--------VHVDEENSYLCGYLKIKGLTEEYPTLTTFF 63
L NG++F G Q S +EV D +LCG L I+ LT+ TLTT+F
Sbjct: 79 LRNGAQFGGVQISGYPPLTVEVNIDTVDLPKKDDYSLPHLCGTLNIQNLTDPSSTLTTYF 138
Query: 64 DGEIIS-KKYPFLTRKW---DADEDVDRKHWGKFSSFYDYSKTFNSDSF---DYDSLKDT 116
+GEII K PF T KW A E++D HW +F F + TF F D +
Sbjct: 139 EGEIIGFNKLPFATEKWSMAPASEEIDVCHWKRFPPFRMDNGTFIERIFNQKSKDYKINQ 198
Query: 117 DFVFMRWKEHFLVPD-HTIKDINGASFAGFYYICFQKSAATIEGYYFHRSS-EWFQSLTL 174
+++M+WKE FL+PD + I+GAS GFYY C + I+GYY+H E Q L L
Sbjct: 199 RYIYMKWKELFLLPDPLQLDTISGASIDGFYYCCLDQETGYIQGYYYHPKHAEKSQQLEL 258
Query: 175 CHVPDHSLQIYEF 187
Y F
Sbjct: 259 VPEQPRKSPSYSF 271
>gnl|CDD|218338 pfam04940, BLUF, Sensors of blue-light using FAD. The BLUF
domain has been shown to bind FAD in the AppA protein.
AppA is involved in the repression of photosynthesis
genes in response to blue-light.
Length = 93
Score = 27.1 bits (61), Expect = 2.3
Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 1 NSKQPGVTGTLLYNGSRF 18
N++ G+TG LLY+G RF
Sbjct: 30 NARL-GITGVLLYDGGRF 46
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 27.9 bits (62), Expect = 3.7
Identities = 10/43 (23%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 77 RKWDADEDVDRKHWGKFSSFYDYSKT---FNSDSFDYDSLKDT 116
R D DR + S+ + S+ DS SL+ +
Sbjct: 27 RSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYS 69
>gnl|CDD|235313 PRK04813, PRK04813, D-alanine--poly(phosphoribitol) ligase subunit
1; Provisional.
Length = 503
Score = 27.9 bits (63), Expect = 3.7
Identities = 9/19 (47%), Positives = 10/19 (52%), Gaps = 1/19 (5%)
Query: 54 EEYPTLTTF-FDGEIISKK 71
E P LT F F GE + K
Sbjct: 257 EHLPNLTHFLFCGEELPHK 275
>gnl|CDD|225228 COG2353, COG2353, Uncharacterized conserved protein [Function
unknown].
Length = 192
Score = 27.3 bits (61), Expect = 4.3
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 1/47 (2%)
Query: 45 GYLKIKGLTEEYPTLTTFFDGEIISKKYPFLTRKWDADEDVDRKHWG 91
G L I+G+T+ TL G + A ++R +G
Sbjct: 122 GNLTIRGVTKPV-TLDVELIGCGRDPMGGKEVIGFSATGKINRSDFG 167
>gnl|CDD|198102 smart01034, BLUF, Sensors of blue-light using FAD. The BLUF
domain has been shown to bind FAD in the AppA protein.
AppA is involved in the repression of photosynthesis
genes in response to blue-light.
Length = 92
Score = 26.0 bits (58), Expect = 4.9
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 1 NSKQPGVTGTLLYNGSRF 18
N+ + G+TG LLYNG F
Sbjct: 29 NNARLGITGVLLYNGGHF 46
>gnl|CDD|213312 cd05959, BCL_4HBCL, Benzoate CoA ligase (BCL) and
4-Hydroxybenzoate-Coenzyme A Ligase (4-HBA-CoA ligase).
Benzoate CoA ligase and 4-hydroxybenzoate-coenzyme A
ligase catalyze the first activating step for benzoate
and 4-hydroxybenzoate catabolic pathways, respectively.
Although these two enzymes share very high sequence
homology, they have their own substrate preference. The
reaction proceeds via a two-step process; the first
ATP-dependent step forms the substrate-AMP intermediate,
while the second step forms the acyl-CoA ester,
releasing the AMP. Aromatic compounds represent the
second most abundant class of organic carbon compounds
after carbohydrates. Some bacteria can use benzoic acid
or benzenoid compounds as the sole source of carbon and
energy through degradation. Benzoate CoA ligase and
4-hydroxybenzoate-Coenzyme A ligase are key enzymes of
this process.
Length = 506
Score = 26.9 bits (60), Expect = 7.7
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 129 VPDHTIKD--INGASFAGFYYICFQKSAATIEGYYFH 163
V D I + + G S A Y+ +K+ T G +
Sbjct: 351 VADGEIGELWVRGDSSAAGYWNRREKTRETFVGEWTR 387
>gnl|CDD|239255 cd02957, Phd_like, Phosducin (Phd)-like family; composed of Phd
and Phd-like proteins (PhLP), characterized as
cytosolic regulators of G protein functions. Phd and
PhLPs specifically bind G protein betagamma
(Gbg)-subunits with high affinity, resulting in the
solubilization of Gbg from the plasma membrane and
impeding G protein-mediated signal transduction by
inhibiting the formation of a functional G protein
trimer (G protein alphabetagamma). Phd also inhibits
the GTPase activity of G protein alpha. Phd can be
phosphorylated by protein kinase A and G
protein-coupled receptor kinase 2, leading to its
inactivation. Phd was originally isolated from the
retina, where it is highly expressed and has been
implicated to play an important role in light
adaptation. It is also found in the pineal gland,
liver, spleen, striated muscle and the brain. The
C-terminal domain of Phd adopts a thioredoxin fold, but
it does not contain a CXXC motif. Phd interacts with G
protein beta mostly through the N-terminal helical
domain. Also included in this family is a PhLP
characterized as a viral inhibitor of apoptosis
(IAP)-associated factor, named VIAF, that functions in
caspase activation during apoptosis.
Length = 113
Score = 26.0 bits (58), Expect = 7.7
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 30 EIEVVHVDEENSYLCGYLKIKGLTEEYPTLTTFFDGEIISK 70
E + V ++ E ++L YL IK L PTL + +GE+I
Sbjct: 55 ETKFVKINAEKAFLVNYLDIKVL----PTLLVYKNGELIDN 91
>gnl|CDD|233551 TIGR01734, D-ala-DACP-lig, D-alanine--poly(phosphoribitol) ligase,
subunit 1. This model represents the enzyme (also
called D-alanine-D-alanyl carrier protein ligase) which
activates D-alanine as an adenylate via the reaction
D-ala + ATP -> D-ala-AMP + PPi, and further catalyzes
the condensation of the amino acid adenylate with the
D-alanyl carrier protein (D-ala-ACP). The D-alanine is
then further transferred to teichoic acid in the
biosynthesis of lipoteichoic acid (LTA) and wall
teichoic acid (WTA) in gram positive bacteria, both
polysacchatides [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan].
Length = 502
Score = 27.0 bits (60), Expect = 7.9
Identities = 10/19 (52%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 54 EEYPTLTTF-FDGEIISKK 71
E YP LT F F GE + K
Sbjct: 255 ENYPHLTHFLFCGEELPVK 273
>gnl|CDD|213667 TIGR01928, menC_lowGC/arch, o-succinylbenzoate synthase. This
model describes the enzyme o-succinylbenzoic acid
synthetase (menC) that is involved in one of the steps
of the menaquinone biosynthesis pathway. It takes SHCHC
and makes it into 2-succinylbenzoate. Included in this
model are low GC gram positive bacteria and archaea.
Also included in the seed and in the model are enzymes
with the com-name of N-acylamino acid racemase (or the
more general term, racemase / racemase family), which
refers to the enzyme's industrial application as
racemases, and not to its biological function as
o-succinylbenzoic acid synthetase [Biosynthesis of
cofactors, prosthetic groups, and carriers, Menaquinone
and ubiquinone].
Length = 324
Score = 26.7 bits (59), Expect = 8.5
Identities = 13/76 (17%), Positives = 29/76 (38%), Gaps = 7/76 (9%)
Query: 68 ISKKYPFLTRKWDADEDVDRKHWGKFSSFYDYSKTFNSDSFDYDSLKDTDFVFMRWKEHF 127
++P + DA+E D + + + Y + + F D + D + +
Sbjct: 167 RRLRFPQIPLVIDANESYDLQDFPRLKELDRYQLLYIEEPFKIDDISMLDEL----AKGT 222
Query: 128 LVP---DHTIKDINGA 140
+ P D +I ++ A
Sbjct: 223 ITPICLDESITSLDDA 238
>gnl|CDD|176981 CHL00040, rbcL, ribulose-1,5-bisphosphate carboxylase/oxygenase
large subunit.
Length = 475
Score = 26.6 bits (59), Expect = 9.2
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 111 DSLKDTDFV----FMRWKEHFL 128
D KD + V FMRW++ FL
Sbjct: 198 DFTKDDENVNSQPFMRWRDRFL 219
>gnl|CDD|211422 cd11609, MCT1_N, N-terminal domain of multiple copies T cell
malignancies 1 and related proteins. This N-terminal
domain of MCT-1 (multiple copies T cell malignancies
1), also known as MCTS-1 (malignant T cell-amplified
sequence 1), co-occurs with a PUA domain. MCT-1,
together with DENR (density regulated protein), has
been shown to have similar function as eIF2D
translation initiation factor (also known as ligatin),
which is involved in the recruitment and delivery of
aminoacyl-tRNAs to the P-site of the eukaryotic
ribosome in a GTP-independent manner.
Length = 77
Score = 24.8 bits (55), Expect = 9.8
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 48 KIKG-LTEEYPTLTTFFDGEIISKKYPFLTRK 78
I+ L E+YP L + D EI+ KK P + K
Sbjct: 21 GIRAKLLEQYPLLEPYID-EILPKKEPLVLVK 51
>gnl|CDD|175982 cd04015, C2_plant_PLD, C2 domain present in plant phospholipase D
(PLD). PLD hydrolyzes terminal phosphodiester bonds in
diester glycerophospholipids resulting in the
degradation of phospholipids. In vitro PLD transfers
phosphatidic acid to primary alcohols. In plants PLD
plays a role in germination, seedling growth,
phosphatidylinositol metabolism, and changes in
phospholipid composition. There is a single
Ca(2+)/phospholipid-binding C2 domain in PLD. C2 domains
fold into an 8-standed beta-sandwich that can adopt 2
structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions.
Length = 158
Score = 26.1 bits (58), Expect = 10.0
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 12/52 (23%)
Query: 122 RWKEHFLVP-DH-------TIKDIN--GASFAGFYYICFQK--SAATIEGYY 161
W E F + H T+KD + GA G YI + S +EG+
Sbjct: 84 VWNESFHIYCAHYASHVEFTVKDNDVVGAQLIGRAYIPVEDLLSGEPVEGWL 135
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 0.138 0.437
Gapped
Lambda K H
0.267 0.0794 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,634,976
Number of extensions: 886924
Number of successful extensions: 725
Number of sequences better than 10.0: 1
Number of HSP's gapped: 717
Number of HSP's successfully gapped: 28
Length of query: 187
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 96
Effective length of database: 6,901,388
Effective search space: 662533248
Effective search space used: 662533248
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 (25.2 bits)