RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9339
(258 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 = 196 bits (500), Expect = 4e-62
Identities = 69/162 (42%), Positives = 100/162 (61%), Gaps = 5/162 (3%)
Query: 32 VGGKKFDLRLYVLVTSFRPLKCYLFKLGFCRFCTVKYDKNITELDNMYVHLTNVSVQKH- 90
+ G+KFD+RLYVLVTS PL+ Y+++ G RF +VKY ++++LD++ +HLTN S+QK
Sbjct: 112 IDGRKFDIRLYVLVTSVNPLRVYVYREGLLRFASVKYSPSVSDLDDVEMHLTNYSIQKKS 171
Query: 91 ---GADYNNIHGGKMNLQNLRLYLESTRGKDITNKLFTNISWLIVHSLKSVSYI-MANDK 146
DYN +G K +L N YLE ++I ++ + I I+ + S + +
Sbjct: 172 SSLNEDYNEPNGHKWSLFNFWKYLEEKDKEEIWLEIESIIIKTILAAEVEASRLNVQPLY 231
Query: 147 HCFECYGYDIIIDNQLKPWLIEVNASPSLTCTTVNDRILISP 188
+CFE YG+D +ID LKPWL+EVNASPSL TT D L
Sbjct: 232 NCFELYGFDFMIDENLKPWLLEVNASPSLHSTTKLDARLKEQ 273
>gnl|CDD|234948 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
Length = 304
Score = 33.9 bits (79), Expect = 0.059
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 151 CYGY---DIIIDNQLKPWLIEVNASPSLT 176
C G+ D ++D KP+L+EVN P +T
Sbjct: 245 CRGWGRVDFMLDEDGKPYLLEVNTQPGMT 273
>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 = 33.0 bits (76), Expect = 0.11
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 153 GYDIIIDNQLKPWLIEVNASPS 174
G DI +D Q + WL+E N+ P
Sbjct: 213 GIDIGLDTQGRIWLLEANSKPG 234
>gnl|CDD|233813 TIGR02291, rimK_rel_E_lig, alpha-L-glutamate ligase-related
protein. Members of this protein family contain a
region of homology to the RimK family of
alpha-L-glutamate ligases (TIGR00768), various members
of which modify the Glu-Glu C-terminus of ribosomal
protein S6, or tetrahydromethanopterin, or a form of
coenzyme F420 derivative. Members of this family are
found so far in various Vibrio and Pseudomonas species
and some other gamma and beta Proteobacteria. The
function is unknown.
Length = 317
Score = 31.4 bits (71), Expect = 0.40
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 153 GYDIIIDNQLKPWLIEVNASPSLTCTTVNDR 183
G D+++D + P ++E+NA P L N
Sbjct: 250 GVDMVLDKEEGPLVLELNARPGLAIQIANGA 280
>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 = 29.9 bits (68), Expect = 1.1
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 152 YGYDIIIDNQLKPWLIEVNA-SPS 174
YG D++ + ++E N +PS
Sbjct: 71 YGADLVRGPDGRWRVLEDNTRAPS 94
>gnl|CDD|190632 pfam03431, RNA_replicase_B, RNA replicase, beta-chain. This family
is of Leviviridae RNA replicases. The replicase is also
known as RNA dependent RNA polymerase.
Length = 540
Score = 30.2 bits (68), Expect = 1.2
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 7/71 (9%)
Query: 99 GGKMNLQNLRLYLESTRGKDITNKLFTNISWLIVHSLKSVSYIMANDKHCFECYGYDIII 158
GK+ S+ G T +L + I + S+ + +D YG DII+
Sbjct: 285 DGKV----HTYEKISSMGNGFTFELESLIFAALARSVCELLGGDTSD---VGIYGDDIIV 337
Query: 159 DNQLKPWLIEV 169
+ P L+EV
Sbjct: 338 PSCAVPPLMEV 348
>gnl|CDD|222774 PHA00028, rep, RNA replicase, beta subunit.
Length = 561
Score = 30.1 bits (68), Expect = 1.2
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 113 STRGKDITNKLFTNISWLIVHSLKSVSYIMANDKHCFECYGYDIIIDNQLKPWLIEV 169
S+ G T +L + I I S + YG DII+ ++ P LI V
Sbjct: 304 SSMGNGFTFELESLIFAAIARS---FCLLFGGPGTI-SVYGDDIIVPTEVAPPLINV 356
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 30.1 bits (69), Expect = 1.4
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 189 AEKLLATADDLYKNLEETVFKLNAELGPKVQEQLAEVVKKAKSSLEEMKKNLVDA 243
A + L + L K L + +EL +V+ L E +K+ + LE++K L A
Sbjct: 692 ALEYLNEQEALLKELAALLKAKPSELPERVEALLEE-LKELEKELEQLKAKLAAA 745
>gnl|CDD|172947 PRK14472, PRK14472, F0F1 ATP synthase subunit B; Provisional.
Length = 175
Score = 29.0 bits (65), Expect = 1.7
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 182 DRILISPAEKLLATADDLYKNLEETVFKLNAELGPKVQEQLAEVVKKAKSSLEEMKKNLV 241
+R L++ A+ A AD + + +E KL AE+ K + +++ AK +E+ K+ +
Sbjct: 75 NRELLAKAD---AEADKIIREGKEYAEKLRAEITEKAHTEAKKMIASAKEEIEQEKRRAL 131
Query: 242 DAL 244
D L
Sbjct: 132 DVL 134
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 29.4 bits (67), Expect = 2.1
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 189 AEKLLATADDLYKNLEETVFKLNAELGPKVQEQ---LAEVVKKAKSSLEEMKKNL 240
AE LL A+ L + LEE KL E ++E + +K+AK +E+ K L
Sbjct: 539 AEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKEL 593
>gnl|CDD|226951 COG4585, COG4585, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 365
Score = 28.6 bits (64), Expect = 3.1
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 187 SPAEKLLATADDLYKNLEETVFKLNAELGPKVQEQLAEVVKKAKSSLEEMKKNLVDAL-P 245
S + L A + L + L E K QE+L E+ K + +L+E+ + LV L P
Sbjct: 181 SVGQSLTAISM-----LLALLLLLADEDAEKAQEELKEIEKLLREALQEV-RALVRDLRP 234
Query: 246 VVFE 249
V E
Sbjct: 235 VELE 238
>gnl|CDD|153272 cd07588, BAR_Amphiphysin, The Bin/Amphiphysin/Rvs (BAR) domain of
Amphiphysins. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions. Amphiphysins
function primarily in endocytosis and other membrane
remodeling events. They contain an N-terminal BAR domain
with an additional N-terminal amphipathic helix (an
N-BAR), a variable central domain, and a C-terminal SH3
domain. This subfamily is composed of different isoforms
of amphiphysin and Bridging integrator 2 (Bin2).
Amphiphysin I proteins, enriched in the brain and
nervous system, contain domains that bind clathrin,
Adaptor Protein complex 2 (AP2), dynamin and
synaptojanin. They function in synaptic vesicle
endocytosis. Some amphiphysin II isoforms, also called
Bridging integrator 1 (Bin1), are localized in many
different tissues and may function in intracellular
vesicle trafficking. In skeletal muscle, Bin1 plays a
role in the organization and maintenance of the T-tubule
network. Bin2 is mainly expressed in hematopoietic cells
and is upregulated during granulocyte differentiation.
The N-BAR domains of amphiphysins form a curved dimer
with a positively-charged concave face that can drive
membrane bending and curvature.
Length = 211
Score = 28.5 bits (64), Expect = 3.2
Identities = 10/35 (28%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 216 PKVQEQLAEVVKKAKSSLEEMKKNLVDALPVVFES 250
K+ + E +++AK EE+ L + LP +++S
Sbjct: 139 QKLT-KAEEELQQAKKVYEELNTELHEELPALYDS 172
>gnl|CDD|234437 TIGR03998, thiol_BshC, bacillithiol biosynthesis cysteine-adding
enzyme BshC. Members of this protein family are BshC,
an enzyme required for bacillithiol biosynthesis and
described as a cysteine-adding enzyme. Bacillithiol is a
low-molecular-weight thiol, an analog of glutathione and
mycothiol, and is found largely in the Firmicutes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Glutathione and analogs].
Length = 528
Score = 28.8 bits (65), Expect = 3.3
Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 12/76 (15%)
Query: 173 PSLTCTTVNDRILISPAEKLLA----TADDLYKNLEETVFKLNAELGPKVQEQLAEVVKK 228
P L+ T + R+ EKLL + D++ +E L + E + + ++
Sbjct: 368 PRLSATLIEPRV-----EKLLDKYQLSVADIFTGVEG---LKERFLERQDPEPIDALFEE 419
Query: 229 AKSSLEEMKKNLVDAL 244
AK + K L + L
Sbjct: 420 AKEQITAAHKPLREEL 435
>gnl|CDD|179658 PRK03830, PRK03830, small acid-soluble spore protein Tlp;
Provisional.
Length = 73
Score = 26.5 bits (59), Expect = 3.9
Identities = 12/54 (22%), Positives = 26/54 (48%)
Query: 189 AEKLLATADDLYKNLEETVFKLNAELGPKVQEQLAEVVKKAKSSLEEMKKNLVD 242
EKL + +N+EE + E K ++ + E ++ + S++ M+ + D
Sbjct: 11 VEKLQEMIQNTIENIEEAEETIAEEDSEKEKQAIEEKNERREESIDGMRSEIKD 64
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 28.7 bits (64), Expect = 4.3
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 189 AEKLLATADDLYKNLEETVFKLNAELGPKVQEQLAEVVKKAKSSLEEMKKNLVD 242
A ++ D+L +L+E V K+ E ++ +LA V+K + + K D
Sbjct: 588 ASSGASSGDELDDDLKEKVEKMKKE----IELELAGVLKSMGLEVIGVTKKNKD 637
>gnl|CDD|187806 cd09675, Csy1_I-F, CRISPR/Cas system-associated protein Csy1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins; Predicted subunit of the Cascade
complex; signature gene for I-F subtype; also known as
Csy1 family.
Length = 384
Score = 28.3 bits (63), Expect = 4.6
Identities = 19/109 (17%), Positives = 29/109 (26%), Gaps = 34/109 (31%)
Query: 80 VHLTNVSVQKHGADYNN---IHGGKMNLQNLRLYLESTRGKDITNKLFTNISWLI----- 131
+V QK ADY + G QN+ L S+R S+L+
Sbjct: 180 ARRKSVWHQKRYADYLDLAVQKLGGTKPQNIS-QLNSSRK---------GRSYLLPSLPP 229
Query: 132 ---------VHSLKSVSYIMANDKHCFECYGYDIIIDNQLKPWLIEVNA 171
+ + + QLK L+ V
Sbjct: 230 VWKNIDKPPIKFSSILESRFFSKSLARRTLD-------QLKILLLVVKP 271
>gnl|CDD|233930 TIGR02564, cas_Csy1, CRISPR type I-F/YPEST-associated protein Csy1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family, typified by YPO2465 of Yersinia pestis, is a
CRISPR-associated (Cas) family strictly associated with
the Ypest subtype of CRISPR/Cas locus. This family is
designated Csy1, for CRISPR/Cas Subtype Ypest protein 1
[Mobile and extrachromosomal element functions, Other].
Length = 384
Score = 28.3 bits (63), Expect = 4.6
Identities = 19/109 (17%), Positives = 29/109 (26%), Gaps = 34/109 (31%)
Query: 80 VHLTNVSVQKHGADYNN---IHGGKMNLQNLRLYLESTRGKDITNKLFTNISWLI----- 131
+V QK ADY + G QN+ L S+R S+L+
Sbjct: 181 ARRKSVWHQKRYADYLDLAVQKLGGTKPQNIS-QLNSSRK---------GRSYLLPSLPP 230
Query: 132 ---------VHSLKSVSYIMANDKHCFECYGYDIIIDNQLKPWLIEVNA 171
+ + + QLK L+ V
Sbjct: 231 VWKNIDKPPIKFSSILESRFFSKSLARRTLD-------QLKILLLVVKP 272
>gnl|CDD|218852 pfam06008, Laminin_I, Laminin Domain I. coiled-coil structure. It
has been suggested that the domains I and II from
laminin A, B1 and B2 may come together to form a triple
helical coiled-coil structure.
Length = 263
Score = 27.7 bits (62), Expect = 5.9
Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 191 KLLATADDLYKNLEETVFKLNAELGPKVQEQLAEVVKKAKSSLEEMKKNLVD 242
K+L ++L + L + ++A ++ E ++KA S L + +NL
Sbjct: 20 KILYNIENLTQQLSGRLSPISA------TKRQLEDLEKALSKLAQDAENLQK 65
>gnl|CDD|223281 COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal
structure and biogenesis].
Length = 116
Score = 26.8 bits (60), Expect = 6.2
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 103 NLQNLRLYLESTRGKDITNKLFTNIS 128
+L N RL R KD KLF I+
Sbjct: 59 DLANRRLAFARLRDKDAVKKLFDEIA 84
>gnl|CDD|220103 pfam09074, Mer2, Mer2. Mer2 (Rec107) forms part of a complex that
is required for meiotic double strand DNA break
formation. Mer2 increases in abundance and is
phosphorylated during the prophase phase of cell
division. Blocking double strand break formation results
in delayed dephosphorylation and dissociation of Mer2
from the chromosome.
Length = 190
Score = 27.2 bits (60), Expect = 8.3
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 188 PAEKLLATADDLYKNLEETVFKLNAELGP---KVQEQLAEVVKKAKSSLEEMKKNLVDAL 244
AEKL+ ++ K L +T ++LN L V E++ ++ + + L + +V AL
Sbjct: 45 KAEKLINILNNNSKELNKTNYQLNELLNSCEASVNEEIKTLIYQLGAQLNNQLEEVVIAL 104
>gnl|CDD|215236 PLN02428, PLN02428, lipoic acid synthase.
Length = 349
Score = 27.0 bits (60), Expect = 9.8
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 61 CRFCTVKYDKNITELDNMYVHLTNVSVQKHGADY 94
CRFC VK + D ++ G DY
Sbjct: 116 CRFCAVKTSRTPPPPDPDEPENVAEAIASWGVDY 149
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
0.319 0.135 0.389
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,785,385
Number of extensions: 1201566
Number of successful extensions: 1393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1389
Number of HSP's successfully gapped: 48
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
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: 58 (26.2 bits)