RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11344
(586 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 = 217 bits (556), Expect = 2e-66
Identities = 101/270 (37%), Positives = 147/270 (54%), Gaps = 23/270 (8%)
Query: 45 NHIPKASSICRKDQLTRYLKSMKKIFGSIYNFSPEAYNLPLEYTKLVAECSRQARNSTYE 104
NH P + I RKD L + +K FG ++F P + LP + + + +
Sbjct: 12 NHFPGSYEITRKDLLWKNIKRQPCDFGRKFDFLPRTFILPTDL--------AEFVDYFED 63
Query: 105 NPDNVWICKPVGQSQGRGILLFQRLSELVYESN---AVVQQYVKNPLLIGGYKFDLRLYV 161
N N WI KP ++GRGI + LS+++ + VVQ+Y++ PLLI G KFD+RLYV
Sbjct: 64 NERNTWIVKPSASARGRGIRITNDLSQILKQIQSRPLVVQKYIERPLLIDGRKFDIRLYV 123
Query: 162 CVPSFHPLTIFVYREGLARFGTDKFS--LANLDNPFAHLTNSSLNKLGPGYGTTKERVGS 219
V S +PL ++VYREGL RF + K+S +++LD+ HLTN S+ K +
Sbjct: 124 LVTSVNPLRVYVYREGLLRFASVKYSPSVSDLDDVEMHLTNYSIQKKSSSLNEDYNE-PN 182
Query: 220 GCKWSLSQLRQYLYQNNIQDWLLWQRISSIIVLTI-ASELSAIPQT----KNCFEFFGFD 274
G KWSL +YL + + ++ +W I SII+ TI A+E+ A NCFE +GFD
Sbjct: 183 GHKWSLFNFWKYLEEKDKEE--IWLEIESIIIKTILAAEVEASRLNVQPLYNCFELYGFD 240
Query: 275 ILVDSSLNPWLLE--SQPDTAPGTNKDLRL 302
++D +L PWLLE + P T D RL
Sbjct: 241 FMIDENLKPWLLEVNASPSLHSTTKLDARL 270
>gnl|CDD|197310 cd09076, L1-EN, Endonuclease domain (L1-EN) of the non-LTR
retrotransposon LINE-1 (L1), and related domains. This
family contains the endonuclease domain (L1-EN) of the
non-LTR retrotransposon LINE-1 (L1), and related
domains, including the endonuclease of Xenopus laevis
Tx1. These retrotranspons belong to the subtype 2,
L1-clade. LINES can be classified into two subtypes.
Subtype 2 has two ORFs: the second (ORF2) encodes a
modular protein consisting of an N-terminal
apurine/apyrimidine endonuclease domain (EN), a central
reverse transcriptase, and a zinc-finger-like domain at
the C-terminus. LINE-1/L1 elements (full length and
truncated) comprise about 17% of the human genome. This
endonuclease nicks the genomic DNA at the consensus
target sequence 5'TTTT-AA3' producing a ribose
3'-hydroxyl end as a primer for reverse transcription of
associated template RNA. This subgroup also includes the
endonuclease of Xenopus laevis Tx1, another member of
the L1-clade. This family belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 236
Score = 51.2 bits (123), Expect = 4e-07
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 302 LGTWNVQTLHKPGAFDNLIMEASRYNLDILAIQETRWIGTEQEQQTEEITPET 354
+GT NV+ L PG L+ E R LDIL +QET W T + + ++ T
Sbjct: 1 IGTLNVRGLRSPGKRAQLLEELKRKKLDILGLQETHW--TGEGELKKKREGGT 51
>gnl|CDD|177302 PHA00734, PHA00734, hypothetical protein.
Length = 95
Score = 33.2 bits (76), Expect = 0.070
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 133 VYESNAVVQQYVKNPLLIGGYKFDLR-----LYVCVPSFHPLTIFVY 174
E+N + + ++KN + YKFDL L + +P+FH IF+
Sbjct: 27 AREANIIARLFMKNKWTLAIYKFDLATVALLLGLMLPTFHQTEIFLL 73
>gnl|CDD|197338 cd10283, MnuA_DNase1-like, Mycoplasma pulmonis MnuA nuclease-like.
This subfamily includes Mycoplasma pulmonis MnuA, a
membrane-associated nuclease related to
Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1).
The in vivo role of MnuA is as yet undetermined. This
subfamily belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 266
Score = 33.1 bits (76), Expect = 0.30
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 300 LRLGTWNVQTL--HKPGAFDNLIME-ASRYNLDILAIQE 335
LR+ +WN+ K + I E S ++LD++A+QE
Sbjct: 1 LRIASWNILNFGNSKGKEKNPAIAEIISAFDLDLIALQE 39
>gnl|CDD|197319 cd09085, Mth212-like_AP-endo, Methanothermobacter
thermautotrophicus Mth212-like subfamily of the ExoIII
family purinic/apyrimidinic (AP) endonucleases. This
subfamily includes the thermophilic archaeon
Methanothermobacter thermautotrophicus Mth212and related
proteins. These are Escherichia coli exonuclease III
(ExoIII)-like AP endonucleases and they belong to the
large EEP (exonuclease/endonuclease/phosphatase)
superfamily that contains functionally diverse enzymes
that share a common catalytic mechanism of cleaving
phosphodiester bonds. AP endonucleases participate in
the DNA base excision repair (BER) pathway. AP sites are
one of the most common lesions in cellular DNA. During
BER, the damaged DNA is first recognized by DNA
glycosylase. AP endonucleases then catalyze the
hydrolytic cleavage of the phosphodiester bond 5' to the
AP site, and this is followed by the coordinated actions
of DNA polymerase, deoxyribose phosphatase, and DNA
ligase. If left unrepaired, AP sites block DNA
replication, and have both mutagenic and cytotoxic
effects. AP endonucleases can carry out a variety of
excision and incision reactions on DNA, including 3'-5'
exonuclease, 3'-deoxyribose phosphodiesterase,
3'-phosphatase, and occasionally, nonspecific DNase
activities. Different AP endonuclease enzymes catalyze
the different reactions with different efficiences.
Mth212 is an AP endonuclease, and a DNA uridine
endonuclease (U-endo) that nicks double-stranded DNA at
the 5'-side of a 2'-d-uridine residue. After incision at
the 5'-side of a 2'-d-uridine residue by Mth212, DNA
polymerase B takes over the 3'-OH terminus and carries
out repair synthesis, generating a 5'-flap structure
that is resolved by a 5'-flap endonuclease. Finally, DNA
ligase seals the resulting nick. This U-endo activity
shares the same catalytic center as its AP-endo
activity, and is absent from other AP endonuclease
homologues.
Length = 252
Score = 31.5 bits (72), Expect = 1.00
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 10/55 (18%)
Query: 300 LRLGTWNVQTL---HKPGAFDNLIMEASRYNLDILAIQETRWIGTEQEQQTEEIT 351
+++ +WNV L HK G D E DIL +QET+ + EQ E++
Sbjct: 1 MKIISWNVNGLRAVHKKGFLD-WFKE---EKPDILCLQETK---AQPEQLPEDLR 48
>gnl|CDD|219434 pfam07501, G5, G5 domain. This domain is found in a wide range of
extracellular proteins. It is found tandemly repeated in
up to 8 copies. It is found in the N-terminus of
peptidases belonging to the M26 family which cleave
human IgA. The domain is also found in proteins involved
in metabolism of bacterial cell walls suggesting this
domain may have an adhesive function.
Length = 79
Score = 29.5 bits (67), Expect = 1.0
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 341 TEQEQQTEEITPETAEVEDEPPTMQEIENAIKRLKNNKTPGSDEITSELLKKGGSTI-KE 399
++E +TEEI ET ED P++ + E +++ PG +T + + G + +E
Sbjct: 4 EKEETETEEIPFETERKED--PSLPKGE---EKVVQEGKPGEKVVTYRVTYENGKEVSRE 58
Query: 400 ELHKLITKCWKEEII 414
+ + + K +I+
Sbjct: 59 LISEDVYKEPVNKIV 73
>gnl|CDD|197337 cd10282, DNase1, Deoxyribonuclease 1. Deoxyribonuclease 1 (DNase1,
EC 3.1.21.1), also known as DNase I, is a Ca2+,
Mg2+/Mn2+-dependent secretory endonuclease, first
isolated from bovine pancreas extracts. It cleaves DNA
preferentially at phosphodiester linkages next to a
pyrimidine nucleotide, producing 5'-phosphate terminated
polynucleotides with a free hydroxyl group on position
3'. It generally produces tetranucleotides. DNase1
substrates include single-stranded DNA, double-stranded
DNA, and chromatin. This enzyme may be responsible for
apoptotic DNA fragmentation. Other deoxyribonucleases in
this subfamily include human DNL1L (human DNase I
lysosomal-like, also known as DNASE1L1, Xib, and DNase X
), human DNASE1L2 (also known as DNAS1L2), and DNASE1L3
(also known as DNAS1L3, nhDNase, LS-DNase, DNase Y, and
DNase gamma) . DNASE1L3 is implicated in apoptotic DNA
fragmentation. DNase I is also a cytoskeletal protein
which binds actin. A recombinant form of human DNase1 is
used as a mucoactive therapy in patients with cystic
fibrosis; it hydrolyzes the extracellular DNA in sputum
and reduces its viscosity. Mutations in the gene
encoding DNase1 have been associated with Systemic Lupus
Erythematosus, a multifactorial autoimmune disease. This
subfamily belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 256
Score = 30.7 bits (70), Expect = 1.8
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 301 RLGTWNVQTLHKPGAFDNLIME-----ASRYNLDILAIQETR 337
R+ +N+Q + +M+ SRY DI+ IQE R
Sbjct: 1 RIAAFNIQVFGESKMSKPEVMDVLVKILSRY--DIVLIQEIR 40
>gnl|CDD|225397 COG2841, COG2841, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 72
Score = 28.1 bits (63), Expect = 2.1
Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 366 EIENAIKRLKNNKTPGSDEITSELLKKGGSTIKEELHKLITK 407
E+++ IKR + N+ PGSD S LKK +K+E+ ++ K
Sbjct: 28 ELDDRIKRAEGNRQPGSDAEVSN-LKKQKLQLKDEIASILQK 68
>gnl|CDD|165339 PHA03046, PHA03046, Hypothetical protein; Provisional.
Length = 142
Score = 29.7 bits (67), Expect = 2.3
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 352 PETAEVEDEPPTMQEIENAIKRLKNNKTPG---SDEITSELLK 391
+ +VE+E P + I N IK++ N K ++ S++LK
Sbjct: 33 KKRLDVEEEEPNLINIRNEIKKIINEKYSTFPIHEDDISDILK 75
>gnl|CDD|233585 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model
represents NtrC, a DNA-binding response regulator that
is phosphorylated by NtrB and interacts with sigma-54.
NtrC usually controls the expression of glutamine
synthase, GlnA, and may be called GlnL, GlnG, etc
[Central intermediary metabolism, Nitrogen metabolism,
Regulatory functions, DNA interactions, Signal
transduction, Two-component systems].
Length = 463
Score = 30.5 bits (69), Expect = 2.8
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 314 GAFDNLIMEASRYNLDILAIQETRWIGTEQEQQTEEITP----ETAEVEDEPPTMQEIEN 369
GAF+ L ++LD R + QEQ ++AE+ E P MQE+
Sbjct: 92 GAFEYL---PKPFDLDEAVTLVERALAHAQEQVALPADAGEAEDSAELIGEAPAMQEVFR 148
Query: 370 AIKRL 374
AI RL
Sbjct: 149 AIGRL 153
>gnl|CDD|213272 cd05904, 4CL, 4-Coumarate-CoA Ligase (4CL). 4-Coumarate:coenzyme A
ligase is a key enzyme in the phenylpropanoid metabolic
pathway for monolignol and flavonoid biosynthesis. It
catalyzes the synthesis of hydroxycinnamate-CoA
thioesters in a two-step reaction, involving the
formation of hydroxycinnamate-AMP anhydride and the
nucleophilic substitution of AMP by CoA. The
phenylpropanoid pathway is one of the most important
secondary metabolism pathways in plants and
hydroxycinnamate-CoA thioesters are the precursors of
lignin and other important phenylpropanoids.
Length = 504
Score = 30.3 bits (69), Expect = 3.5
Identities = 9/28 (32%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 32 VSHYKQLKNNQYTNHIPKASS--ICRKD 57
V+ YK+++ + + IPK+ S I R++
Sbjct: 476 VAPYKKVRKVVFVDAIPKSPSGKILRRE 503
>gnl|CDD|204432 pfam10281, Ish1, Putative stress-responsive nuclear envelope
protein. This family of proteins found in fungi is a
putative stress-responsive nuclear envelope protein
Ish1.
Length = 38
Score = 26.7 bits (60), Expect = 3.8
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 223 WSLSQLRQYLYQNNIQ 238
WS S L+++L + I
Sbjct: 4 WSDSDLKEWLDSHGIP 19
>gnl|CDD|188708 cd08754, RGS_LARG, Regulator of G protein signaling (RGS) domain
found in the leukemia-associated Rho guanine nucleotide
exchange factor (RhoGEF) protein (LARG). The RGS domain
is an essential part of the leukemia-associated RhoGEF
protein (LARG), a member of the RhoGEF (Rho guanine
nucleotide exchange factor) subfamily of the RGS protein
family. The RhoGEFs are peripheral membrane proteins
that regulate essential cellular processes, including
cell shape, cell migration, cell cycle progression of
cells, and gene transcription by linking signals from
heterotrimeric G-alpha12/13 protein-coupled receptors to
Rho GTPase activation, leading to various cellular
responses, such as actin reorganization and gene
expression. The RhoGEF subfamily includes p115RhoGEF,
LARG, PDZ-RhoGEF, and its rat specific splice variant
GTRAP48. The RGS domain of RhoGEFs has very little
sequence similarity with the canonical RGS domain of the
RGS proteins and is often refered to as RH (RGS
Homology) domain. In addition to being a G-alpha13
effector, the LARG protein also functions as a
GTPase-activating protein (GAP) for G-alpha13. RGS
proteins play critical regulatory role as GTPase
activating proteins (GAPs) of the heterotrimeric
G-protein G-alpha-subunits. RGS proteins play critical
regulatory role as GTPase activating proteins (GAPs) of
the heterotrimeric G-protein G-alpha-subunits. RGS
proteins regulate many aspects of embryonic development
such as glial differentiation, embryonic axis formation,
skeletal and muscle development, cell migration during
early embryogenesis, as well as apoptosis, cell
proliferation, and modulation of cardiac development.
Length = 222
Score = 29.6 bits (66), Expect = 4.3
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 371 IKRLKNNKTPGSDEITSELLKKGGSTIKEELHKLITKCWKEEIIPN 416
+ R N K P DE++ +L K+ I EELH+ + +E + P
Sbjct: 82 LDRAANLKVPVPDEVSLDLEKRRPELIPEELHRHYIQTMQERVSPE 127
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''.
This family consists of the archaeal A'' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein
[Transcription, DNA-dependent RNA polymerase].
Length = 367
Score = 29.6 bits (67), Expect = 4.5
Identities = 15/58 (25%), Positives = 27/58 (46%)
Query: 350 ITPETAEVEDEPPTMQEIENAIKRLKNNKTPGSDEITSELLKKGGSTIKEELHKLITK 407
I + ++++ T+ ++E AIK+ K K D + + K +EL KL K
Sbjct: 144 IELDEEQLKERGITVDDVEKAIKKAKLGKVIEIDMDGNTITIKPPKPSLKELRKLKEK 201
>gnl|CDD|239457 cd03341, TCP1_theta, TCP-1 (CTT or eukaryotic type II) chaperonin
family, theta subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. The best studied in
vivo substrates of CTT are actin and tubulin.
Length = 472
Score = 29.5 bits (67), Expect = 5.6
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 15/67 (22%)
Query: 56 KDQLTRYLKS--MKKIFGSIYNFSPEAYNLPLEYTKLVAECSRQA--RNSTYENPDNVWI 111
K+++++ LK+ K +G+ SP LVAE N N DN+ +
Sbjct: 138 KEEVSKALKTAIASKQYGNEDFLSP-----------LVAEACISVLPENIGNFNVDNIRV 186
Query: 112 CKPVGQS 118
K +G S
Sbjct: 187 VKILGGS 193
>gnl|CDD|217962 pfam04201, TPD52, Tumour protein D52 family. The hD52 gene was
originally identified through its elevated expression
level in human breast carcinoma. Cloning of D52
homologues from other species has indicated that D52 may
play roles in calcium-mediated signal transduction and
cell proliferation. Two human homologues of hD52, hD53
and hD54, have also been identified, demonstrating the
existence of a novel gene/protein family. These proteins
have an amino terminal coiled-coil that allows members
to form homo- and heterodimers with each other.
Length = 162
Score = 28.8 bits (64), Expect = 5.9
Identities = 30/116 (25%), Positives = 53/116 (45%), Gaps = 18/116 (15%)
Query: 341 TEQEQQTEEITPETAEVEDEPPTMQEIENAI-KRLKNNKTPGSDEITSELLKKGGSTIKE 399
+E E+ EE+ E A++E+E T++++ A K L +EL +K G T
Sbjct: 27 SEAEK--EELRTELAKLEEEISTLRQVLAAKEKHL------------AELKRKLGLTPLS 72
Query: 400 ELHKLITKCWKEEIIPNKWKERKPLFHNTARTFRSSKQSNKWGNGKDWSKIEPNEG 455
EL + I+K W + + +K +K + A S K G+ ++ S + E
Sbjct: 73 ELKQNISKSWHDVTATSAYKGQKT---SAAAASVGSAIKKKLGDMRNSSTFKSFEE 125
>gnl|CDD|240413 PTZ00423, PTZ00423, glideosome-associated protein 45; Provisional.
Length = 193
Score = 28.5 bits (63), Expect = 6.5
Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 318 NLIMEASRYNLDILAIQETRWIGTEQ--EQQTEEITPETAEVEDEPPTMQEIENAIKRLK 375
N E R ++D LA +E E+ EQ+ E+I E + +EPP +E K +
Sbjct: 8 NKAKEPKRRDIDELAEREKLKKEVEEIPEQKPEDIVEELEDQPEEPPEQEEENEEQKPKE 67
Query: 376 NNKTP-----GSDEITSELLKKGGSTIKEELHK 403
P DE + L++ S I E HK
Sbjct: 68 EIDYPIQENKSFDEKNLDDLERSNSDIYSESHK 100
>gnl|CDD|197311 cd09077, R1-I-EN, Endonuclease domain encoded by various R1- and
I-clade non-long terminal repeat retrotransposons. This
family contains the endonuclease (EN) domain of various
non-long terminal repeat (non-LTR) retrotransposons,
long interspersed nuclear elements (LINEs) which belong
to the subtype 2, R1- and I-clade. LINES can be
classified into two subtypes. Subtype 2 has two ORFs:
the second (ORF2) encodes a modular protein consisting
of an N-terminal apurine/apyrimidine endonuclease domain
(EN), a central reverse transcriptase, and a
zinc-finger-like domain at the C-terminus. Most non-LTR
retrotransposons are inserted throughout the host
genome; however, many retrotransposons of the R1 clade
exhibit target-specific retrotransposition. This family
includes the endonucleases of SART1 and R1bm, from the
silkworm Bombyx mori, which belong to the R1-clade. It
also includes the endonuclease of snail (Biomphalaria
glabrata) Nimbus/Bgl and mosquito Aedes aegypti
(MosquI), both which belong to the I-clade. This family
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 205
Score = 28.4 bits (64), Expect = 8.4
Identities = 13/56 (23%), Positives = 19/56 (33%), Gaps = 2/56 (3%)
Query: 300 LRLGTWNVQTLHKPGAFDNLIMEASRYNLDILAIQETRWIGTEQEQQTEEITPETA 355
LR+ N+ A D L+ A DI IQE + + + A
Sbjct: 1 LRILQINLN--RCKAAQDLLLQTAREEGADIALIQEPYLVPVNNPNWVTDESGRAA 54
>gnl|CDD|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional.
Length = 193
Score = 28.3 bits (64), Expect = 8.5
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 341 TEQEQQTEEITPE--TAEVEDEPPTMQEIENAIKR 373
T QEQ +EEI E E DE E++ A R
Sbjct: 8 TPQEQVSEEIEAEVEQQEEADEAELEDELDEADAR 42
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 28.9 bits (64), Expect = 9.0
Identities = 26/107 (24%), Positives = 48/107 (44%), Gaps = 5/107 (4%)
Query: 287 ESQPDTAPGTNKDLRLGTWNVQTLHKPGAFDNLIMEA-SRYNLDILAIQETRWIGTEQEQ 345
E +P+ P N+DL + N L G ++ E S D + + E + + + E
Sbjct: 435 EPEPEPEPQPNQDLMVFDPNHHEL--IGLESAVVQETVSVLEEDFIPVPEQKLVQVQAET 492
Query: 346 QTEEITPETAEVEDEPPTMQEIENAIKRLKNNKTPGSDEITSELLKK 392
Q ++I PE A EP + E +A L + T D ++ ++++
Sbjct: 493 QVKQIEPEPASTA-EPIGLFEASSAEFSLAQD-TSAYDLVSEPVIEQ 537
>gnl|CDD|129242 TIGR00136, gidA, glucose-inhibited division protein A. GidA, the
longer of two forms of GidA-related proteins, appears to
be present in all complete eubacterial genomes so far,
as well as Saccharomyces cerevisiae. A subset of these
organisms have a closely related protein. GidA is absent
in the Archaea. It appears to act with MnmE, in an
alpha2/beta2 heterotetramer, in the
5-carboxymethylaminomethyl modification of uridine 34 in
certain tRNAs. The shorter, related protein, previously
called gid or gidA(S), is now called TrmFO (see model
TIGR00137) [Protein synthesis, tRNA and rRNA base
modification].
Length = 617
Score = 28.9 bits (65), Expect = 9.0
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 364 MQEIENAIKRLKNNKTPGSDEITSELLKKGGSTIKEE 400
+ IE I+RLK+ S E+ EL S +K E
Sbjct: 465 KENIEEEIQRLKSTWLTPSKEVKEELKNHLQSPLKRE 501
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 0.133 0.410
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: 29,612,206
Number of extensions: 2843039
Number of successful extensions: 2744
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2734
Number of HSP's successfully gapped: 35
Length of query: 586
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 484
Effective length of database: 6,413,494
Effective search space: 3104131096
Effective search space used: 3104131096
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: 62 (27.6 bits)