RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16684
(429 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 = 236 bits (605), Expect = 2e-75
Identities = 104/308 (33%), Positives = 152/308 (49%), Gaps = 38/308 (12%)
Query: 56 SSMKNHQKIAHYRNFYEISRKNYLARNLKRYRRQCVKNGNTEEAELSNAMPMTFEIPSET 115
HQ + H+ YEI+RK+ L +N+KR + +P TF +P++
Sbjct: 3 LDEPYHQALNHFPGSYEITRKDLLWKNIKRQPCD--------FGRKFDFLPRTFILPTDL 54
Query: 116 ALFLQEARRDSHNMWIVKPSGGSQGRGILLFKKLSEFEEWRENKDWSPKERKRSDDPNDI 175
A F+ + N WIVKPS ++GRGI + LS+ + +++
Sbjct: 55 AEFVDYFEDNERNTWIVKPSASARGRGIRITNDLSQILKQIQSRPL-------------- 100
Query: 176 ELIPEVYVAQKYITNPYLLEGRKFDMRMYVLVTSFSPLTVWIARDGFARIAGIKYCK--D 233
V QKYI P L++GRKFD+R+YVLVTS +PL V++ R+G R A +KY
Sbjct: 101 -------VVQKYIERPLLIDGRKFDIRLYVLVTSVNPLRVYVYREGLLRFASVKYSPSVS 153
Query: 234 NFADNCMHLTNTAIQ------LSGENLSQGRKWDIQNLRLFLTAMHGREIVDELFQKIAK 287
+ D MHLTN +IQ N G KW + N +L EI E+ I K
Sbjct: 154 DLDDVEMHLTNYSIQKKSSSLNEDYNEPNGHKWSLFNFWKYLEEKDKEEIWLEIESIIIK 213
Query: 288 VVITALKSVECIMMGN-KHCFELFGFDILLQDNLNVCLLEANAAPSMKATDDHDYKLKYN 346
++ A + + +CFEL+GFD ++ +NL LLE NA+PS+ +T D +LK
Sbjct: 214 TILAAEVEASRLNVQPLYNCFELYGFDFMIDENLKPWLLEVNASPSLHSTTKLDARLKEQ 273
Query: 347 LIQDALNV 354
LI D LN
Sbjct: 274 LIDDVLNS 281
>gnl|CDD|225190 COG2308, COG2308, Uncharacterized conserved protein [Function
unknown].
Length = 488
Score = 37.3 bits (87), Expect = 0.015
Identities = 25/103 (24%), Positives = 40/103 (38%), Gaps = 24/103 (23%)
Query: 131 IVKPSGGSQGRGILLFKKLSEFEEWRENKDWSPKERKRSDDPNDIELIPEVYVAQKYI-- 188
++KP GS G G+L+ S+ E ++ + + PE Y+AQ +
Sbjct: 369 VIKPVEGSGGYGMLVGPAASK----AELAAFAERIKAD----------PENYIAQPVLQL 414
Query: 189 -TNPYL----LEGRKFDMRMYVLVTSFSPLTVWIARDGFARIA 226
T P L R D+R + L V + G R+A
Sbjct: 415 STVPTFVDGGLAPRHVDLRPFALAD---RDGVQVMPGGLTRVA 454
>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 = 33.4 bits (77), Expect = 0.17
Identities = 50/209 (23%), Positives = 78/209 (37%), Gaps = 40/209 (19%)
Query: 131 IVKPSGGSQGRGILLFKKL--SEFEEWRENKDWSPKERKRSDDPNDIELIPEVYVAQKYI 188
+KP GS+G+GI+ KL +R++ + R S + I + +KYI
Sbjct: 59 YLKPINGSKGKGIIRLTKLEGRYIVRYRDDG--KNQTRTFSSLASLASWILKHLSTRKYI 116
Query: 189 TNPYL----LEGRKFDMRMYVLVTSFSPLTVW-IARDGFARIAGIKYCKDNFADNCMHLT 243
+ +GR D R V TV IA R+AG +T
Sbjct: 117 VQQGIDLIDFQGRPVDFRALVQKNGEGKWTVTGIA----VRVAGKG-----------SIT 161
Query: 244 NTAIQLSGENLSQGRKWDIQNLRLFLTAMHGREIVDELFQKIAKVVITALKSVECIMMGN 303
NLS G + L +L RE++ + ++ A + ++ +
Sbjct: 162 T--------NLSSG--GTAKTLDEYLADEEEREVLIKKLEEAA---LKIAHGLDKHIEA- 207
Query: 304 KHCFELFGFDILLQDNLNVCLLEANAAPS 332
EL G DI L + LLEAN+ P
Sbjct: 208 -RIGEL-GIDIGLDTQGRIWLLEANSKPG 234
>gnl|CDD|188036 TIGR00236, wecB, UDP-N-acetylglucosamine 2-epimerase. This
cytosolic enzyme converts UDP-N-acetyl-D-glucosamine to
UDP-N-acetyl-D-mannosamine. In E. coli, this is the
first step in the pathway of enterobacterial common
antigen biosynthesis.Members of this orthology group
have many gene symbols, often reflecting the overall
activity of the pathway and/or operon that includes it.
Symbols include epsC (exopolysaccharide C) in
Burkholderia solanacerum, cap8P (type 8 capsule P) in
Staphylococcus aureus, and nfrC in an older designation
based on the effects of deletion on phage N4 adsorption.
Epimerase activity was also demonstrated in a
bifunctional rat enzyme, for which the N-terminal domain
appears to be orthologous. The set of proteins found
above the suggested cutoff includes E. coli WecB in one
of two deeply branched clusters and the rat
UDP-N-acetylglucosamine 2-epimerase domain in the other
[Cell envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 365
Score = 33.6 bits (77), Expect = 0.18
Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 6/69 (8%)
Query: 225 IAGIKYCKDNFADNCMHLT-NTAIQLSGENLSQGRKWDI-----QNLRLFLTAMHGREIV 278
A ++N + + +T NT I N+ + ++ R L +H RE V
Sbjct: 151 QAKDNLLRENVKADSIFVTGNTVIDALLTNVEIAYSSPVLSEFGEDKRYILLTLHRRENV 210
Query: 279 DELFQKIAK 287
E + I K
Sbjct: 211 GEPLENIFK 219
>gnl|CDD|224102 COG1181, DdlA, D-alanine-D-alanine ligase and related ATP-grasp
enzymes [Cell envelope biogenesis, outer membrane].
Length = 317
Score = 31.5 bits (72), Expect = 0.81
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 279 DELFQKIAKVVITALKSVECIMMGNKHCFELFGFDILLQDNL-NVCLLEANAAPSMKATD 337
DE+ ++I ++ + A K++ C+ + D + D+ LLE N P M T
Sbjct: 241 DEIHEEIKELALRAYKALGCLGLA--------RVDFFVDDDEGEFVLLEVNTNPGM--TA 290
Query: 338 DHDY 341
+
Sbjct: 291 MSLF 294
>gnl|CDD|223087 COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 472
Score = 31.1 bits (71), Expect = 1.1
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 6 AIRFKTEGQTNNTVIEDVLRGRPGWMPVGSDDTN--WDIFW 44
+R K V D++RGR + P D +D +
Sbjct: 152 VVRLKIPMAHPGPVFRDLVRGRIVFAPKHPDFVILRYDGYP 192
>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 = 30.7 bits (70), Expect = 1.6
Identities = 17/57 (29%), Positives = 22/57 (38%), Gaps = 18/57 (31%)
Query: 131 IVKPSGGSQGRGILLFKKLS--EFEEWRENKDWSPKERKRSDDPNDIELIPEVYVAQ 185
++KP G G G + KLS E EE R +D N Y+AQ
Sbjct: 291 VIKPVAGYGGYGAYIGPKLSKAELEEVW--------ARILADPRN--------YIAQ 331
>gnl|CDD|130447 TIGR01380, glut_syn, glutathione synthetase, prokaryotic. This
model was built using glutathione synthetases found in
Gram-negative bacteria. This gene does not appear to be
present in genomes of Gram-positive bacteria.
Glutathione synthetase has an ATP-binding domain in the
COOH terminus and catalyzes the second step in the
glutathione biosynthesis pathway: ATP +
gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate
+ glutathione. Glutathione is a tripeptide that
functions as a reductant in many cellular reactions
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Glutathione and analogs].
Length = 312
Score = 30.0 bits (68), Expect = 2.4
Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 8/86 (9%)
Query: 115 TALFLQEARRDSHNMWIVKPSGGSQGRGILLFKKLSEFEEWRENKDWSPKERKRSDDPND 174
T ++EA++ H ++ +P S G +F + +DW K +
Sbjct: 20 TFALMEEAQKRGHELFFYEPGDLSVVNG-EVFARARPVRVGPNKQDWYTLGEKVRLSLGE 78
Query: 175 IELI-----PEVYVAQKYITNPYLLE 195
++ + P + YI YLLE
Sbjct: 79 LDAVLMRKDPPFDME--YIYATYLLE 102
>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 = 3.9
Identities = 41/208 (19%), Positives = 69/208 (33%), Gaps = 73/208 (35%)
Query: 131 IVKPSGGSQGRGILLFKKLSEFEEWRENKDWSPKERKRSDDPNDIELIPEVYVAQKYITN 190
++KP GS GR + L + E E+ + + ++ Q+YI
Sbjct: 127 VLKPVFGSWGRLVSLARDKQAAETLLEHFEQLNGPQN-------------LFYVQEYIKK 173
Query: 191 PYLLEGRKFDMRMYVLVTSFSPLTVWIARDGFARIAGIKYCKD-NFADNCMHLTNTAIQL 249
P GR D+R++V+ G IA I ++ N
Sbjct: 174 P---GGR--DIRVFVV--------------GDEVIAAIYRITSGHWRTNL---------- 204
Query: 250 SGENLSQGRKWDIQNLRLFLTAMHGREIVDELFQKIAKVVITALKSVECIMMGNKHCFEL 309
++G K + LT E ++EL K AK +G
Sbjct: 205 -----ARGGKAE----PCPLT-----EEIEELAIKAAKA------------LGLDVV--- 235
Query: 310 FGFDILLQDNLNVCLLEANAAPSMKATD 337
G D+L ++ + + E N P K +
Sbjct: 236 -GIDLLESEDRGLLVNEVNPNPEFKNSV 262
>gnl|CDD|223267 COG0189, RimK, Glutathione synthase/Ribosomal protein S6
modification enzyme (glutaminyl transferase) [Coenzyme
metabolism / Translation, ribosomal structure and
biogenesis].
Length = 318
Score = 28.9 bits (65), Expect = 4.9
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 24/67 (35%)
Query: 131 IVKPSGGSQGRGILLFKK-----LSEFEEWRENKDWSPKERKRSDDPNDIELIPEVYVAQ 185
++KP GS GRG+ L + LS E + ++ + Q
Sbjct: 159 VLKPLDGSGGRGVFLVEDADPELLSLLETLTQEGR-------------------KLIIVQ 199
Query: 186 KYITNPY 192
+YI
Sbjct: 200 EYIPKAK 206
>gnl|CDD|223516 COG0439, AccC, Biotin carboxylase [Lipid metabolism].
Length = 449
Score = 28.8 bits (65), Expect = 6.4
Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 20/70 (28%)
Query: 131 IVKPSGGSQGRGILLFKKLSEFEE-----WRENKDWSPKERKRSDDPNDIELIPEVYVAQ 185
IVK + G GRG+ + + E E E E + P VY+ +
Sbjct: 156 IVKAAAGGGGRGMRVVRNEEELEAAFEAARGE------AEAAFGN--------PRVYL-E 200
Query: 186 KYITNPYLLE 195
K+I P +E
Sbjct: 201 KFIEGPRHIE 210
>gnl|CDD|169452 PRK08463, PRK08463, acetyl-CoA carboxylase subunit A; Validated.
Length = 478
Score = 28.6 bits (64), Expect = 6.5
Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 10/65 (15%)
Query: 131 IVKPSGGSQGRGILLFKKLSEFEEWRENKDWSPKERKRSDDPNDIELIPEVYVAQKYITN 190
I+K SGG GRGI + K + E E S K + ND EV++ +KY+ N
Sbjct: 156 ILKASGGGGGRGIRVVHKEEDLENAFE----SCKREALAYFNND-----EVFM-EKYVVN 205
Query: 191 PYLLE 195
P +E
Sbjct: 206 PRHIE 210
>gnl|CDD|178151 PLN02536, PLN02536, diaminopimelate epimerase.
Length = 267
Score = 28.6 bits (64), Expect = 6.7
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 296 VECIMMGNKHCFELFGFDILLQDNLNV 322
V C+ MGN HC FG L D+L +
Sbjct: 140 VTCVSMGNPHCV-TFGEKELKVDDLPL 165
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
0.320 0.136 0.418
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: 21,974,998
Number of extensions: 2126066
Number of successful extensions: 1776
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1770
Number of HSP's successfully gapped: 24
Length of query: 429
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 329
Effective length of database: 6,502,202
Effective search space: 2139224458
Effective search space used: 2139224458
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: 60 (26.9 bits)