RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2625
(396 letters)
>gnl|CDD|217380 pfam03133, TTL, Tubulin-tyrosine ligase family. Tubulins and
microtubules are subjected to several post-translational
modifications of which the reversible
detyrosination/tyrosination of the carboxy-terminal end
of most alpha-tubulins has been extensively analysed.
This modification cycle involves a specific
carboxypeptidase and the activity of the
tubulin-tyrosine ligase (TTL). The true physiological
function of TTL has so far not been established.
Tubulin-tyrosine ligase (TTL) catalyzes the
ATP-dependent post-translational addition of a tyrosine
to the carboxy terminal end of detyrosinated
alpha-tubulin. In normally cycling cells, the
tyrosinated form of tubulin predominates. However, in
breast cancer cells, the detyrosinated form frequently
predominates, with a correlation to tumour
aggressiveness. On the other hand, 3-nitrotyrosine has
been shown to be incorporated, by TTL, into the carboxy
terminal end of detyrosinated alpha-tubulin. This
reaction is not reversible by the carboxypeptidase
enzyme. Cells cultured in 3-nitrotyrosine rich medium
showed evidence of altered microtubule structure and
function, including altered cell morphology, epithelial
barrier dysfunction, and apoptosis. Bacterial homologs
of TTL are predicted to form peptide tags. Some of these
are fused to a 2-oxoglutarate Fe(II)-dependent
dioxygenase domain.
Length = 291
Score = 188 bits (480), Expect = 3e-57
Identities = 79/220 (35%), Positives = 125/220 (56%), Gaps = 11/220 (5%)
Query: 126 ILKPCDGCQGKGIKLAMKIDDITSTMEFDSMICQQYITNPLLWNGYKFDIRFYVLITSVK 185
I+KP +G+GI++ + I ++ ++ Q+YI PLL +G KFDIR YVL+TSV
Sbjct: 70 IVKPSASARGRGIRITNDLSQILKQIQSRPLVVQKYIERPLLIDGRKFDIRLYVLVTSVN 129
Query: 186 HLRIYIYNEGIVRLATEKYESPNETNIDNMYMHLTNYSINKNSENFNEDLSKQSLERMN- 244
LR+Y+Y EG++R A+ KY SP+ +++D++ MHLTNYSI K S + NED ++ +
Sbjct: 130 PLRVYVYREGLLRFASVKY-SPSVSDLDDVEMHLTNYSIQKKSSSLNEDYNEPN-GHKWS 187
Query: 245 --KFLRDVHNVDLNALYARIHDIIVKTVLTGYKPILREYLDTFKNYVYREACFQLLGFDI 302
F + + D ++ I II+KT+L R + CF+L GFD
Sbjct: 188 LFNFWKYLEEKDKEEIWLEIESIIIKTILAAEVEASRLNVQP------LYNCFELYGFDF 241
Query: 303 ILDSHCNPYLLEINKNASLKRPTSIDKIIKTNLTRDLFSI 342
++D + P+LLE+N + SL T +D +K L D+ +
Sbjct: 242 MIDENLKPWLLEVNASPSLHSTTKLDARLKEQLIDDVLNS 281
>gnl|CDD|224734 COG1821, COG1821, Predicted ATP-utilizing enzyme (ATP-grasp
superfamily) [General function prediction only].
Length = 307
Score = 34.0 bits (78), Expect = 0.10
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 115 TTEVEENTPIYILKPCDGCQGKGIKLAMKIDDITSTMEFDSMICQQYI 162
T E E Y++KP DGC G+GI DI I Q++I
Sbjct: 131 TREWAEEPKKYVIKPADGCGGEGILFGRDFPDI--------EIAQEFI 170
>gnl|CDD|234948 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
Length = 304
Score = 33.5 bits (78), Expect = 0.17
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 6/31 (19%)
Query: 292 EACFQLLG------FDIILDSHCNPYLLEIN 316
++ LG D +LD PYLLE+N
Sbjct: 237 LKAYRALGCRGWGRVDFMLDEDGKPYLLEVN 267
>gnl|CDD|233121 TIGR00768, rimK_fam, alpha-L-glutamate ligases, RimK family. This
family, related to bacterial glutathione synthetases,
contains at least two different alpha-L-glutamate
ligases. One is RimK, as in E. coli, which adds
additional Glu residues to the native Glu-Glu C-terminus
of ribosomal protein S6, but not to Lys-Glu mutants.
Most species with a member of this subfamily lack an S6
homolog ending in Glu-Glu, however. Members in
Methanococcus jannaschii act instead as a
tetrahydromethanopterin:alpha-l-glutamate ligase
(MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase
(MJ1001).
Length = 277
Score = 32.3 bits (74), Expect = 0.33
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 13/62 (20%)
Query: 126 ILKPCDGCQGKGIKLAMKIDDITSTME--------FDSMICQQYITNPLLWNGYKFDIRF 177
+LKP G G+ + LA + +E + Q+YI P G + DIR
Sbjct: 127 VLKPVFGSWGRLVSLARDKQAAETLLEHFEQLNGPQNLFYVQEYIKKP----GGR-DIRV 181
Query: 178 YV 179
+V
Sbjct: 182 FV 183
>gnl|CDD|217166 pfam02655, ATP-grasp_3, ATP-grasp domain. No functional
information or experimental verification of function is
known in this family. This family appears to be an
ATP-grasp domain (Pers. obs. A Bateman).
Length = 159
Score = 30.8 bits (70), Expect = 0.66
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 115 TTEVEENTPI---YILKPCDGCQGKGIKLAMKIDDITSTMEFDSMICQQYI 162
T EE T YI+KP DGC G+G++ + +E ++I Q++I
Sbjct: 20 TLSAEEPTEEEKKYIVKPRDGCGGEGVRFVENGREDEEFIE--NVIIQEFI 68
>gnl|CDD|223267 COG0189, RimK, Glutathione synthase/Ribosomal protein S6
modification enzyme (glutaminyl transferase) [Coenzyme
metabolism / Translation, ribosomal structure and
biogenesis].
Length = 318
Score = 31.2 bits (71), Expect = 0.84
Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 15/80 (18%)
Query: 126 ILKPCDGCQGKGIKLAMKID-DITSTMEF------DSMICQQYITNPLLWNGYKFDIRFY 178
+LKP DG G+G+ L D ++ S +E +I Q+YI D R
Sbjct: 159 VLKPLDGSGGRGVFLVEDADPELLSLLETLTQEGRKLIIVQEYIPKAKRD-----DRRVL 213
Query: 179 V---LITSVKHLRIYIYNEG 195
V + ++ L +
Sbjct: 214 VGGGEVVAIYALARIPASGD 233
>gnl|CDD|224236 COG1317, FliH, Flagellar biosynthesis/type III secretory pathway
protein [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 234
Score = 29.3 bits (66), Expect = 2.7
Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 10/87 (11%)
Query: 235 LSKQSLERMNKFLRDVHNVDLNALYARIHDIIVKTVLTGYKPILREYLDTFK----NYVY 290
+ LER+ K + + L AL + +V+ VL + ++ + L+ V
Sbjct: 89 EEGRVLERLAKLIAEFQAE-LEALKEVVEKQLVQLVLEIARKVIGKELELDPEALLAAV- 146
Query: 291 REACFQLLGF--DIILDSHCNPYLLEI 315
REA ++ F I L NP LEI
Sbjct: 147 REALEEVPLFAAAITL--RVNPDDLEI 171
>gnl|CDD|202916 pfam04174, CP_ATPgrasp_1, A circularly permuted ATPgrasp. An
ATP-grasp family that is present both as catalytically
active and inactive versions. Contextual analysis
suggests that it functions in a distinct peptide
synthesis/modification system that additionally contains
a transglutaminase, an NTN-hydrolase, the Alpha-E
domain, and a transglutaminase fused N-terminal to a
circularly permuted COOH-NH2 ligase. The inactive forms
are often fused N-terminal to the Alpha-E domain.
Length = 331
Score = 29.5 bits (67), Expect = 2.8
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 296 QLLGFDIILDSHCNPYLLEINKNA 319
+ G D++ +LE N A
Sbjct: 69 HVYGADLVRGPDGRWRVLEDNTRA 92
>gnl|CDD|211427 cd11602, Ndc10, Ndc10 component of the yeast centromere-binding
factor 3. Ndc10 is a multidomain protein conserved in
Saccharomycotina that interacts with kinetochore
components. This model characterizes the majority of the
protein; some family members may have an additional
C-terminal domain that is homologous to transcriptional
activators (GCR1_C). Ndc10 is part of the
centromere-binding factor 3 (CBF3) complex in budding
yeast. The CBF3 complex contains four essential
proteins, Ndc10, Cep3, Ctf13, and Skp1. CBF3/Ndc10 is
essential for the recruitment of the centromeric
nucleosome and formation of the kinetochore. The
Kinetochore is the large, multiprotein assembly that
serves to connect condensed sister chromatids to the
mitotic spindle. Ndc10 forms a dimer and it has
non-sequence-specific DNA binding activity via the DNA
backbone. Ndc10 also plays an important role in the
coordination of cell division. It has been noted that
the protein bears resemblance to the tyrosine
recombinases (type IB topoisomerase/lambda-integrase).
Length = 413
Score = 29.7 bits (67), Expect = 3.2
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 4/63 (6%)
Query: 192 YNEGIVRLATEKYESPNETNIDNMYMHLTNYSIN---KNSENFNEDLSKQSLERMNKFLR 248
Y E I++L + Y N N L SIN ++ N +E K LE++ +FL
Sbjct: 108 YLESIIKLHSFWYSLLKNNNQSNTTPPLLKVSINLWNPHTTNLSEKYFKTCLEKL-RFLV 166
Query: 249 DVH 251
D H
Sbjct: 167 DFH 169
>gnl|CDD|237555 PRK13914, PRK13914, invasion associated secreted endopeptidase;
Provisional.
Length = 481
Score = 28.6 bits (63), Expect = 6.3
Identities = 15/66 (22%), Positives = 22/66 (33%)
Query: 34 NVKNMVMELNRLNHTNTTNDNATKANKTIRRNSPIEDNDNIKDKSSNQDSSNKTDVDIQR 93
N N + T+ + N N+ N N SSN +S++ I
Sbjct: 313 NANKTNTNTNTNTNNTNTSTPSKNTNTNTNSNTNTNSNTNANQGSSNNNSNSSASAIIAE 372
Query: 94 DDKHDG 99
KH G
Sbjct: 373 AQKHLG 378
>gnl|CDD|217059 pfam02480, Herpes_gE, Alphaherpesvirus glycoprotein E.
Glycoprotein E (gE) of Alphaherpesvirus forms a complex
with glycoprotein I (gI) (pfam01688), functioning as an
immunoglobulin G (IgG) Fc binding protein. gE is
involved in virus spread but is not essential for
propagation.
Length = 437
Score = 28.5 bits (64), Expect = 6.3
Identities = 14/65 (21%), Positives = 20/65 (30%), Gaps = 9/65 (13%)
Query: 291 REACFQLLGFDIILDSHCNPY-----LLEINKNASLKRPTSIDKIIKTNLTRDLFSILNL 345
R CF D++LD C L R I+ + +F L
Sbjct: 31 RGHCFH----DLVLDKACARKAREAPLALAEFYVRNGRLKRIEDVYFVGENPTVFPRLTA 86
Query: 346 NESRL 350
N+ L
Sbjct: 87 NKGGL 91
>gnl|CDD|153364 cd07680, F-BAR_PACSIN1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons 1 (PACSIN1). F-BAR
domains are dimerization modules that bind and bend
membranes and are found in proteins involved in membrane
dynamics and actin reorganization. Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins,
also called Synaptic dynamin-associated proteins
(Syndapins), act as regulators of cytoskeletal and
membrane dynamics. Vetebrates harbor three isoforms with
distinct expression patterns and specific functions.
PACSIN 1 or Syndapin I is expressed specifically in the
brain and is localized in neurites and synaptic boutons.
It binds the brain-specific proteins dynamin I,
synaptojanin, synapsin I, and neural Wiskott-Aldrich
syndrome protein (nWASP), and functions as a link
between the cytoskeletal machinery and synaptic vesicle
endocytosis. PACSIN 1 interacts with huntingtin and may
be implicated in the neuropathology of Huntington's
disease. It contains an N-terminal F-BAR domain and a
C-terminal SH3 domain. F-BAR domains form banana-shaped
dimers with a positively-charged concave surface that
binds to negatively-charged lipid membranes. They can
induce membrane deformation in the form of long tubules.
Length = 258
Score = 28.5 bits (63), Expect = 6.7
Identities = 13/52 (25%), Positives = 23/52 (44%)
Query: 75 KDKSSNQDSSNKTDVDIQRDDKHDGHKNKADKENERKPNVTTEVEENTPIYI 126
++ +S + S + + DK D K K E+ V +V + TP Y+
Sbjct: 155 REANSKAEQSVTPEQQKKLQDKVDKCKQDVQKTQEKYEKVLDDVGKTTPQYM 206
>gnl|CDD|216616 pfam01628, HrcA, HrcA protein C terminal domain. HrcA is found to
negatively regulate the transcription of heat shock
genes. HrcA contains an amino terminal helix-turn-helix
domain, however this corresponds to the carboxy terminal
domain.
Length = 224
Score = 28.3 bits (64), Expect = 6.8
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 230 NFNEDLSKQSLERMNKFLRD-VHNVDLNALYARIHDIIVKTVLTGYKPILREYLDTFKN 287
ED+S++ LE+++ FL + + + L+ + ++ + L Y +L E LD +
Sbjct: 62 TLPEDISEEDLEKLSNFLNERLVGLTLSEIREKLRAEL-PQELQEYDELLDEVLDLLEA 119
>gnl|CDD|222735 pfam14398, ATPgrasp_YheCD, YheC/D like ATP-grasp. A member of the
ATP-grasp fold predicted to be involved in the
modification/biosynthesis of spore-wall and capsular
proteins.
Length = 262
Score = 28.0 bits (63), Expect = 7.1
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 298 LGFDIILDSHCNPYLLEIN 316
LG DI LD+ +LLE N
Sbjct: 212 LGIDIGLDTQGRIWLLEAN 230
>gnl|CDD|219293 pfam07093, SGT1, SGT1 protein. This family consists of several
eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known
to suppress GCR2 and is highly expressed in the muscle
and heart. The function of this family is unknown
although it has been speculated that SGT1 may be
functionally analogous to the Gcr2p protein of
Saccharomyces cerevisiae which is known to be a
regulatory factor of glycolytic gene expression.
Length = 557
Score = 28.1 bits (63), Expect = 9.1
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 222 YSINKNSENFNEDLSKQSLERMNKFLRDVHNVD 254
NK N +DL + M +FL V + +
Sbjct: 401 LKSNKEDANEVDDLEEVV-SSMEEFLNKVSSFE 432
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
0.316 0.134 0.385
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,535,598
Number of extensions: 1879356
Number of successful extensions: 1797
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1787
Number of HSP's successfully gapped: 56
Length of query: 396
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 297
Effective length of database: 6,546,556
Effective search space: 1944327132
Effective search space used: 1944327132
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 (21.6 bits)
S2: 60 (26.9 bits)