RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9333
(308 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 = 240 bits (615), Expect = 1e-78
Identities = 95/248 (38%), Positives = 137/248 (55%), Gaps = 32/248 (12%)
Query: 24 RMNDNQIINHFPNHYELTRKDLLVKNIKRYRKELEREGNPLAEKSNEVPGRYIHLDFIPI 83
+Q +NHFP YE+TRKDLL KNIKR + R+ DF+P
Sbjct: 4 DEPYHQALNHFPGSYEITRKDLLWKNIKRQPCDFGRK-----------------FDFLPR 46
Query: 84 TFILPADYNMFVEEYRKNPASTWIMKPCGKSQGNGIFLINKLSKLKKWSRESKTPFNPIL 143
TFILP D FV+ + N +TWI+KP ++G GI + N LS++ K +
Sbjct: 47 TFILPTDLAEFVDYFEDNERNTWIVKPSASARGRGIRITNDLSQILKQIQ---------- 96
Query: 144 VKESYVISKYIDNPLLIGGKKFDLRLYVLVTSFRPLKCYLFKLGFCRFCTVKYDKNITEL 203
V+ KYI+ PLLI G+KFD+RLYVLVTS PL+ Y+++ G RF +VKY ++++L
Sbjct: 97 -SRPLVVQKYIERPLLIDGRKFDIRLYVLVTSVNPLRVYVYREGLLRFASVKYSPSVSDL 155
Query: 204 DNMYVHLTNVSVQKH----GADYNNIHGGKMNLQNLRLYLESTRGKDITNKLFTNISWLI 259
D++ +HLTN S+QK DYN +G K +L N YLE ++I ++ + I I
Sbjct: 156 DDVEMHLTNYSIQKKSSSLNEDYNEPNGHKWSLFNFWKYLEEKDKEEIWLEIESIIIKTI 215
Query: 260 VHSLKSVS 267
+ + S
Sbjct: 216 LAAEVEAS 223
Score = 35.8 bits (83), Expect = 0.021
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 288 KESYVISKYIDNPLLIGGKKC 308
V+ KYI+ PLLI G+K
Sbjct: 97 SRPLVVQKYIERPLLIDGRKF 117
>gnl|CDD|117020 pfam08443, RimK, RimK-like ATP-grasp domain. This ATP-grasp domain
is found in the ribosomal S6 modification enzyme RimK.
Length = 190
Score = 33.2 bits (76), Expect = 0.083
Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 88 PADYNMFVEEYRKNPASTWIMKPCGKSQGNGIFLINKLSKLKKWSRESKTPFNPILVKES 147
P D F+E+ + P ++K SQG G+FL L++ K N ILV+E
Sbjct: 27 PEDAEKFIEQIKGFPV---VVKSVFGSQGIGVFLAEDEQSLEQLLEAFKWLKNQILVQE- 82
Query: 148 YVISKYIDNPLLIGGKKFDLRLYVL 172
+I G + D+R V+
Sbjct: 83 -----FIAEA---GNR--DIRCLVV 97
>gnl|CDD|183536 PRK12458, PRK12458, glutathione synthetase; Provisional.
Length = 338
Score = 31.9 bits (73), Expect = 0.34
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 21/83 (25%)
Query: 94 FVEEYRKNPASTWIMKPCGKSQGNGIFLINKLSKLKKWSRESKTPFNPIL---VKESYVI 150
F+EE + I+KP S G G+FLI K +++ N IL + YVI
Sbjct: 156 FLEESPGDKM---ILKPLQGSGGQGVFLIEK---------SAQSNLNQILEFYSGDGYVI 203
Query: 151 SK-YIDNPLLIGGKKFDLRLYVL 172
++ Y+ G ++ D+R+ +L
Sbjct: 204 AQEYLP-----GAEEGDVRILLL 221
>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 = 0.71
Identities = 22/98 (22%), Positives = 39/98 (39%), Gaps = 23/98 (23%)
Query: 80 FIPITFIL--PADYNMFVEEYRKNPASTWIMKPCGKSQGNGIFLINK----LSKLKKWSR 133
+P T I P + FV E+ P ++KP S G G+FL+ L L +
Sbjct: 133 PVPPTLITRDPDEAAEFVAEHLGFPV---VLKPLDGSGGRGVFLVEDADPELLSLLETLT 189
Query: 134 ESKTPFNPILVKESYVISKYIDNP------LLIGGKKF 165
+ ++ ++ +YI +L+GG +
Sbjct: 190 Q--------EGRKLIIVQEYIPKAKRDDRRVLVGGGEV 219
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 302
Score = 29.6 bits (67), Expect = 1.9
Identities = 6/28 (21%), Positives = 10/28 (35%), Gaps = 4/28 (14%)
Query: 33 HFPNHYELTRKDLLVKNIKRYRKELERE 60
H P +T ++L I + R
Sbjct: 217 HLPGAGAITTREL----IAIAARAAGRP 240
>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 = 29.2 bits (66), Expect = 2.3
Identities = 21/93 (22%), Positives = 35/93 (37%), Gaps = 14/93 (15%)
Query: 81 IPITFIL--PADYNMFVEEYRKNPASTWIMKPCGKSQGNGIFLINKLSKLKKWSRESKTP 138
P T + P + +EE P ++KP S G + L + E
Sbjct: 103 QPRTGLAGSPEEALKLIEEI-GFPV---VLKPVFGSWGRLVSLARDKQAAETLL-EHFEQ 157
Query: 139 FNPILVKESYVISKYIDNPLLIGGKKFDLRLYV 171
N + + +YI P GG+ D+R++V
Sbjct: 158 LNGPQ--NLFYVQEYIKKP---GGR--DIRVFV 183
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 28.5 bits (64), Expect = 5.2
Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 1/66 (1%)
Query: 91 YNMFVEEYRKNPASTWIMKPCGKSQGNGIFLINKLSKLKKWSRESKTPFNPILVKESYVI 150
Y F +NP +I K + +G I +L + KW+ + K +KE VI
Sbjct: 859 YRGFKGTIERNPKGKFISKGIYEKVPDGTVEITELP-IGKWTEDYKEFLESETLKEKDVI 917
Query: 151 SKYIDN 156
Y D
Sbjct: 918 VDYRDY 923
>gnl|CDD|202486 pfam02955, GSH-S_ATP, Prokaryotic glutathione synthetase, ATP-grasp
domain.
Length = 173
Score = 27.5 bits (62), Expect = 5.8
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 79 DFIPITFIL--PADYNMFVEEYRKNPASTWIMKPCGKSQGNGIFLINK 124
+ IP T + + F+EE+ I+KP G G+F I K
Sbjct: 10 ELIPPTLVTRDKEEIRAFLEEHGD-----IILKPLDGMGGAGVFRIKK 52
>gnl|CDD|215536 PLN02991, PLN02991, oxidoreductase.
Length = 543
Score = 27.7 bits (61), Expect = 9.0
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 11/77 (14%)
Query: 67 KSNEVPGRYIHLDFIPITFILPADYNMFVE---EYRKNPASTWIMKPCGKSQGNGIFLIN 123
+P + + P+T ++ DY FVE E ++ TW + G +++
Sbjct: 392 NPGSIPDQPTNGAIFPVTSVMQTDYKAFVEIVFENWEDIVQTWHL------DGYSFYVVG 445
Query: 124 KLSKLKKWSRESKTPFN 140
+L KWS S+ +N
Sbjct: 446 M--ELGKWSAASRKVYN 460
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
0.322 0.140 0.428
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,750,728
Number of extensions: 1493766
Number of successful extensions: 1277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1274
Number of HSP's successfully gapped: 20
Length of query: 308
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 211
Effective length of database: 6,635,264
Effective search space: 1400040704
Effective search space used: 1400040704
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 (21.9 bits)
S2: 59 (26.6 bits)