RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3174
(265 letters)
>gnl|CDD|218234 pfam04733, Coatomer_E, Coatomer epsilon subunit. This family
represents the epsilon subunit of the coatomer complex,
which is involved in the regulation of intracellular
protein trafficking between the endoplasmic reticulum
and the Golgi complex.
Length = 288
Score = 169 bits (429), Expect = 2e-51
Identities = 93/254 (36%), Positives = 131/254 (51%), Gaps = 47/254 (18%)
Query: 10 DELFDVRNSYYLGNYQQCIKEGQRLKATDPKVLLEKDFYVCRSYLAQKKYKVVLEE---K 66
DELF+VRN +YLGNYQ+ I E + + + L+E+D Y+ RSYLA Y++V+ E
Sbjct: 1 DELFNVRNYFYLGNYQKAINESD-VTSLSEEALVERDVYMYRSYLALGSYQIVISEIKES 59
Query: 67 LPEELSCIKVLAEYLSIPS---------------------------------KNGSSN-- 91
L +++LAEYL+ PS G +
Sbjct: 60 AATPLQAVRLLAEYLNSPSRKESILASLKEWVADSHIGSNSTLRLLAAIIFIHEGDFDDA 119
Query: 92 -----FGTHLEINALKIHTYLTMYRNDLALKELKVMQDKDEDHTLTQLCSAWVHIANNVD 146
G +LE AL + L M+R DLA ++LK MQ DED TLTQL +AWV +A +
Sbjct: 120 LKHLHKGENLEAMALNVQILLKMHRIDLAEQQLKKMQQIDEDATLTQLANAWVKLAVGGE 179
Query: 147 KLNEAFYTLQDLIDKYGSTPMLVNAQVAVLIAQDKYEEAWDLLQ---DTAGDSEDTLINN 203
K+ +A+Y Q+ +KY STP+L+N Q + +YEEA LL+ D +TLIN
Sbjct: 180 KIQDAYYIFQEFSEKYDSTPLLLNGQAVCCMCLGRYEEAESLLKEALDKDAKDPETLINL 239
Query: 204 MVTAGRLGKGNEMS 217
+V A LGK E+S
Sbjct: 240 VVCALHLGKPAEVS 253
>gnl|CDD|214781 smart00703, NRF, N-terminal domain in C. elegans NRF-6 (Nose
Resistant to Fluoxetine-4) and NDG-4 (resistant to
nordihydroguaiaretic acid-4). Also present in several
other worm and fly proteins.
Length = 110
Score = 28.5 bits (64), Expect = 1.5
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 6/57 (10%)
Query: 17 NSYYLGNYQQCIKEGQRLKATDPKVLLEKDFYVCRSYLAQKKYKVVLEEKLPEELSC 73
N+ +LG+Y++C++ +T + C L K + L L
Sbjct: 22 NNLWLGSYEECLRISGPGTSTKYQG------KYCYLPLVPGKNLNCSIKSLTSVLVL 72
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 30.1 bits (68), Expect = 1.6
Identities = 15/91 (16%), Positives = 28/91 (30%), Gaps = 2/91 (2%)
Query: 95 HLEINALKIHTYLTMYRNDLALKELKVMQDKDEDHTLTQLCSAWVHIANNVDKLNEAFYT 154
L Y M A+ LK + D+T Q+ A + + A
Sbjct: 634 SALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLA--QLLLAAKRTESAKKI 691
Query: 155 LQDLIDKYGSTPMLVNAQVAVLIAQDKYEEA 185
+ L ++ + + + + Q Y A
Sbjct: 692 AKSLQKQHPKAALGFELEGDLYLRQKDYPAA 722
>gnl|CDD|184782 PRK14661, acpS, 4'-phosphopantetheinyl transferase; Provisional.
Length = 169
Score = 28.4 bits (63), Expect = 2.6
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 6/59 (10%)
Query: 173 VAVLIAQDKYEEAWDLLQDTAGD-----SEDTLINNMVTAGRLGKGNEMSVS-PPFLFR 225
V ++ D++ A +L+ GD E L R +G E+ S PPF +
Sbjct: 91 AHVSLSHDRFAVALVVLEKRKGDIIVEGDESFLRKRFEVLERSVEGWEIETSLPPFTLK 149
>gnl|CDD|198196 cd09943, SH2_Nck_family, Src homology 2 (SH2) domain found in the
Nck family. Nck proteins are adaptors that modulate
actin cytoskeleton dynamics by linking proline-rich
effector molecules to tyrosine kinases or phosphorylated
signaling intermediates. There are two members known in
this family: Nck1 (Nckalpha) and Nck2 (Nckbeta and
Growth factor receptor-bound protein 4 (Grb4)). They
are characterized by having 3 SH3 domains and a
C-terminal SH2 domain. Nck1 and Nck2 have overlapping
functions as determined by gene knockouts. Both bind
receptor tyrosine kinases and other
tyrosine-phosphorylated proteins through their SH2
domains. In addition they also bind distinct targets.
Neuronal signaling proteins: EphrinB1, EphrinB2, and
Disabled-1 (Dab-1) all bind to Nck-2 exclusively. And in
the case of PDGFR, Tyr(P)751 binds to Nck1 while
Tyr(P)1009 binds to Nck2. Nck1 and Nck2 have a role in
the infection process of enteropathogenic Escherichia
coli (EPEC). Their SH3 domains are involved in
recruiting and activating the N-WASP/Arp2/3 complex
inducing actin polymerization resulting in the
production of pedestals, dynamic bacteria-presenting
protrusions of the plasma membrane. A similar thing
occurs in the vaccinia virus where motile plasma
membrane projections are formed beneath the virus.
Recently it has been shown that the SH2 domains of both
Nck1 and Nck2 bind the G-protein coupled receptor
kinase-interacting protein 1 (GIT1) in a
phosphorylation-dependent manner. In general SH2 domains
are involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 93
Score = 27.5 bits (61), Expect = 3.0
Identities = 9/36 (25%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 138 WVHIANNVDKL-NEAFYTLQDLIDKYGSTPMLVNAQ 172
V + +NV + F+T+ +L++ Y P+ + Q
Sbjct: 52 KVQVVDNVYCIGQRKFHTMDELVEHYKKAPIFTSEQ 87
>gnl|CDD|183140 PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional.
Length = 1157
Score = 28.9 bits (65), Expect = 3.2
Identities = 14/59 (23%), Positives = 23/59 (38%)
Query: 138 WVHIANNVDKLNEAFYTLQDLIDKYGSTPMLVNAQVAVLIAQDKYEEAWDLLQDTAGDS 196
W +A + EA LQ L Y L N +L + + +E + +L+ A
Sbjct: 153 WRLVAKLPAQRPEAINQLQRLNADYPGNTGLRNTLALLLFSSGRRDEGFAVLEQMAKSP 211
>gnl|CDD|129743 TIGR00658, orni_carb_tr, ornithine carbamoyltransferase. This
family of ornithine carbamoyltransferases (OTCase) is in
a superfamily with the related enzyme aspartate
carbamoyltransferase. Most known examples are anabolic,
playing a role in arginine biosynthesis, but some are
catabolic. Most OTCases are homotrimers, but the
homotrimers are organized into dodecamers built from
four trimers in at least two species; the catabolic
OTCase of Pseudomonas aeruginosa is allosterically
regulated, while OTCase of the extreme thermophile
Pyrococcus furiosus shows both allostery and thermophily
[Amino acid biosynthesis, Glutamate family].
Length = 304
Score = 28.5 bits (64), Expect = 3.6
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 19/72 (26%)
Query: 74 IKVLAEYLSIPSKNGSSNFGTHLEINALKIHTYLTMYRNDLALKELKVMQDKDEDHTLTQ 133
++ LA+Y S+P NG ++ + A LT+ + LK +KV
Sbjct: 108 VEELAKYASVPVINGLTDLFHPCQALA----DLLTIIEHFGKLKGVKV------------ 151
Query: 134 LCSAWVHIANNV 145
+V NNV
Sbjct: 152 ---VYVGDGNNV 160
>gnl|CDD|217642 pfam03618, Kinase-PPPase, Kinase/pyrophosphorylase. This family of
regulatory proteins has ADP-dependent kinase and
inorganic phosphate-dependent pyrophosphorylase
activity.
Length = 255
Score = 28.2 bits (64), Expect = 4.6
Identities = 13/24 (54%), Positives = 13/24 (54%), Gaps = 5/24 (20%)
Query: 53 YLAQKKYKV-----VLEEKLPEEL 71
YLA K KV V E LPEEL
Sbjct: 156 YLANKGIKVANYPLVPEVPLPEEL 179
>gnl|CDD|100054 cd04649, LbH_THP_succinylT_putative, Putative
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP)
N-succinyltransferase (THP succinyltransferase),
C-terminal left-handed parallel alpha-helix (LbH)
domain: This group is composed of mostly uncharacterized
proteins containing an N-terminal domain of unknown
function and a C-terminal LbH domain with similarity to
THP succinyltransferase LbH. THP succinyltransferase
catalyzes the conversion of tetrahydrodipicolinate and
succinyl-CoA to N-succinyltetrahydrodipicolinate and
CoA. It is the committed step in the succinylase pathway
by which bacteria synthesize L-lysine and
meso-diaminopimelate, a component of peptidoglycan. The
enzyme is trimeric and displays the left-handed parallel
alpha-helix (LbH) structural motif encoded by the
hexapeptide repeat motif.
Length = 147
Score = 27.4 bits (61), Expect = 5.5
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 192 TAGDSEDTLINNMVTAGRLGKGNEMSVSPPFLFRSDETTATLDA 235
TAG ++ TL +N + K E+S LFR + + ++A
Sbjct: 105 TAG-TKVTLPDNEEFEKNVVKARELSGKNGLLFRRNSQSGKVEA 147
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I. All proteins in this family for
which functions are known are DNA polymerases Many also
have an exonuclease motif. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 887
Score = 28.1 bits (63), Expect = 6.3
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 124 DKDEDHTLTQLCSAWVHIANNVDKLNEAFYTLQDLIDKYGSTP 166
DKD L QL S V + K + T + +++KYG TP
Sbjct: 132 DKD----LLQLVSDNVKVLIPKGKTSFTEITPEYVVEKYGVTP 170
>gnl|CDD|226198 COG3672, COG3672, Predicted transglutaminase-like cysteine
proteinase [General function prediction only].
Length = 191
Score = 26.9 bits (60), Expect = 8.4
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 169 VNAQVAVLIAQDKY--EEAWDLLQDTAGDSED 198
VN + + + Y E+ W AGD ED
Sbjct: 81 VNTSIKPMTDMEIYGKEDYWAYPVTGAGDCED 112
>gnl|CDD|237026 PRK11930, PRK11930, putative bifunctional
UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine
ligase/alanine racemase; Provisional.
Length = 822
Score = 27.2 bits (61), Expect = 9.6
Identities = 8/45 (17%), Positives = 22/45 (48%)
Query: 55 AQKKYKVVLEEKLPEELSCIKVLAEYLSIPSKNGSSNFGTHLEIN 99
+ +++ KL E+ ++L ++ K G + + H++I+
Sbjct: 540 EPTSFDTIIDYKLEPEIYSFRLLDAFIKAAQKKGITGYPIHIKID 584
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 0.368
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,112,382
Number of extensions: 1225703
Number of successful extensions: 693
Number of sequences better than 10.0: 1
Number of HSP's gapped: 690
Number of HSP's successfully gapped: 20
Length of query: 265
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 170
Effective length of database: 6,723,972
Effective search space: 1143075240
Effective search space used: 1143075240
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: 58 (26.2 bits)