RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9480
(395 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 = 242 bits (620), Expect = 4e-78
Identities = 100/290 (34%), Positives = 153/290 (52%), Gaps = 11/290 (3%)
Query: 73 MSKSMEVYHRINHFPGMANLESKAFLAYHLNRMRNHFPEDYDFYPRSWSLPYQQEDFLSY 132
+ + +NHFPG + K L ++ R F +DF PR++ LP +F+ Y
Sbjct: 1 ILLDEPYHQALNHFPGSYEITRKDLLWKNIKRQPCDFGRKFDFLPRTFILPTDLAEFVDY 60
Query: 133 VREHPHQVFISKPSRGAEGKGIKIFNTLEEARGIYTE--SVSQLYMSNLLLMDGFKFDLR 190
++ +I KPS A G+GI+I N L + V Q Y+ LL+DG KFD+R
Sbjct: 61 FEDNERNTWIVKPSASARGRGIRITNDLSQILKQIQSRPLVVQKYIERPLLIDGRKFDIR 120
Query: 191 VYVLITCIDPLRIFVYNNGLVRLATCQYTSPETGNLTNQYMHLTNYSVNKSSENYNKSPE 250
+YVL+T ++PLR++VY GL+R A+ +Y SP +L + MHLTNYS+ K S + N+
Sbjct: 121 LYVLVTSVNPLRVYVYREGLLRFASVKY-SPSVSDLDDVEMHLTNYSIQKKSSSLNEDYN 179
Query: 251 RGSKRDFTALNSWLLSQGLNSTKLWNDIDDIIIKTIISVYPILKEKYEDLLPEHYHHNVS 310
+ ++ N W + + ++W +I+ IIIKTI++ E +
Sbjct: 180 EPNGHKWSLFNFWKYLEEKDKEEIWLEIESIIIKTILAA--------EVEASRLNVQPLY 231
Query: 311 ASFEILGFDILIDSTMKPFLLEVNRSPSFNIAGIVDERVKRTLIYDTFKI 360
FE+ GFD +ID +KP+LLEVN SPS + +D R+K LI D
Sbjct: 232 NCFELYGFDFMIDENLKPWLLEVNASPSLHSTTKLDARLKEQLIDDVLNS 281
>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 = 36.5 bits (85), Expect = 0.014
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 301 LPEHYHHNVSASFEILGFDILIDSTMKPFLLEVNRSPSFNI 341
+ ++ A LG DI +D+ + +LLE N P +I
Sbjct: 197 IAHGLDKHIEARIGELGIDIGLDTQGRIWLLEANSKPGRSI 237
>gnl|CDD|201639 pfam01174, SNO, SNO glutamine amidotransferase family. This family
and its amidotransferase domain was first described in.
It is predicted that members of this family are involved
in the pyridoxine biosynthetic pathway, based on the
proximity and co-regulation of the corresponding genes
and physical interaction between the members of
pfam01174 and pfam01680.
Length = 188
Score = 35.2 bits (81), Expect = 0.027
Identities = 26/113 (23%), Positives = 40/113 (35%), Gaps = 19/113 (16%)
Query: 133 VREHPHQVFISKPSRGAEGKGIKIFNTLEEARGIYTESVSQLYMSNLLLMDGFKFDLRVY 192
V EH + GAE K +K L + + MS LL + F
Sbjct: 8 VEEHEEAI----KKCGAENKTVKRPEDLAQCDALIIPGGESTAMS--LLAKRYGF----- 56
Query: 193 VLITCIDPLRIFVYNNGLVRLATCQ---YTSPETGNLTNQYMHLTNYSVNKSS 242
+PL FV+N TC S + GN + + L +V +++
Sbjct: 57 -----YEPLYEFVHNPNKPIWGTCAGLILLSKQLGNELVKTLGLLKVTVKRNA 104
>gnl|CDD|216282 pfam01071, GARS_A, Phosphoribosylglycinamide synthetase, ATP-grasp
(A) domain. Phosphoribosylglycinamide synthetase
catalyzes the second step in the de novo biosynthesis of
purine. The reaction catalyzed by
Phosphoribosylglycinamide synthetase is the ATP-
dependent addition of 5-phosphoribosylamine to glycine
to form 5'phosphoribosylglycinamide. This domain is
related to the ATP-grasp domain of biotin
carboxylase/carbamoyl phosphate synthetase (see
pfam02786).
Length = 193
Score = 33.8 bits (78), Expect = 0.083
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 127 EDFLSYVREHPHQVFISKPSRGAEGKGIKIFNTLEEAR 164
E+ SY+RE + K A GKG+ + EEA
Sbjct: 27 EEAKSYIREAGFPAVV-KADGLAAGKGVIVAMDNEEAI 63
>gnl|CDD|222206 pfam13535, ATP-grasp_4, ATP-grasp domain. This family includes a
diverse set of enzymes that possess ATP-dependent
carboxylate-amine ligase activity.
Length = 183
Score = 33.4 bits (77), Expect = 0.096
Identities = 13/66 (19%), Positives = 21/66 (31%), Gaps = 2/66 (3%)
Query: 104 RMRNHFPEDYDFYPRSWSLPYQQEDFLSYVREHPHQVFISKPSRGAEGKGIKIFNTLEEA 163
MR P + + +ED + E V + KP GA G+ ++ E
Sbjct: 7 LMRELLRAAGLPVPPFFLVD-DEEDLDAAAEEIGFPVVL-KPRDGAGSLGVFRVDSAAEL 64
Query: 164 RGIYTE 169
Sbjct: 65 EAALAA 70
>gnl|CDD|224386 COG1469, COG1469, Uncharacterized conserved protein [Function
unknown].
Length = 289
Score = 32.3 bits (74), Expect = 0.35
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 10/76 (13%)
Query: 12 ENEAGTSTQALRPRPKEATINLKRCMY-KIVEDVATLMGMGIVRDDEEPWDVYWSDFSVS 70
E+ A + L RP E + K K VEDV + +V E+ D +
Sbjct: 211 ESSASSPLYTLLKRPDEKAVTEKAYENPKFVEDVVREIARRLV---EDFPD------AAF 261
Query: 71 TVMSKSMEVYHRINHF 86
TV ++ E H + F
Sbjct: 262 TVEVENEESIHPHDAF 277
>gnl|CDD|233164 TIGR00877, purD, phosphoribosylamine--glycine ligase. Alternate
name: glycinamide ribonucleotide synthetase (GARS). This
enzyme appears as a monofunctional protein in
prokaryotes but as part of a larger, multidomain protein
in eukaryotes [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 422
Score = 32.3 bits (74), Expect = 0.42
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 10/85 (11%)
Query: 90 ANLE-SKAFLAYHLNRMRNHFPEDYDFYPRSWSLPYQQEDFLSYVREHPHQVFISKPSRG 148
A LE SKAF ++ F + Y + + E+ SY++E + + K
Sbjct: 99 AQLEGSKAF-------AKD-FMKRYGIPTAEYEVFTDPEEAKSYIQEKGAPIVV-KADGL 149
Query: 149 AEGKGIKIFNTLEEARGIYTESVSQ 173
A GKG+ + T EEA + + Q
Sbjct: 150 AAGKGVIVAKTNEEAIKAVEDILEQ 174
>gnl|CDD|223229 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
transport and metabolism].
Length = 428
Score = 31.4 bits (72), Expect = 0.90
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 127 EDFLSYVREHPHQVFISKPSRGAEGKGIKIFNTLEEAR 164
E+ +Y+ E + + K A GKG+ + TLEEA
Sbjct: 128 EEAKAYIDEKGAPIVV-KADGLAAGKGVIVAMTLEEAE 164
>gnl|CDD|214654 smart00415, HSF, heat shock factor.
Length = 105
Score = 29.6 bits (67), Expect = 1.0
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 8/50 (16%)
Query: 272 TKLWNDIDDIIIKTIIS--------VYPILKEKYEDLLPEHYHHNVSASF 313
TKL+ ++D IIS V +E ++LLP ++ HN +SF
Sbjct: 7 TKLYLLVEDPSTDKIISWSPSGKSFVIWDPEEFAKNLLPRYFKHNNFSSF 56
>gnl|CDD|234948 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
Length = 304
Score = 29.7 bits (68), Expect = 2.3
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 319 DILIDSTMKPFLLEVNRSP 337
D ++D KP+LLEVN P
Sbjct: 252 DFMLDEDGKPYLLEVNTQP 270
>gnl|CDD|235828 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase;
Validated.
Length = 953
Score = 29.9 bits (68), Expect = 2.5
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 5/31 (16%)
Query: 219 TSPETG--NLTN---QYMHLTNYSVNKSSEN 244
T PE+G N +N +YM L N S N +S N
Sbjct: 345 TCPESGRINASNPCSEYMFLDNSSCNLASLN 375
>gnl|CDD|225617 COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino
acid transport and metabolism].
Length = 421
Score = 29.7 bits (67), Expect = 3.1
Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 10/84 (11%)
Query: 295 EKYEDLLPEHYHHNVSASFEILGFDILIDSTMKPFLLEVNRSP----SFNIAGIVDERVK 350
E D P+ +A+ G + P L + + + NIA ++D
Sbjct: 147 EGLHDFQPQL----AAANLRQAGLPVTTAELNLPELDVLRDNATEFRAVNIARLLDNEEA 202
Query: 351 RTLIYDTFKILNLNQNRKSILFPS 374
+ D +++ + + +L P+
Sbjct: 203 WPALAD--ELIPVANTAEMVLMPA 224
>gnl|CDD|234483 TIGR04150, pseudo_rSAM_GG, pseudo-rSAM protein, GG-Bacteroidales
system. Many peptide-modifying radical SAM enzymes have
two 4Fe4S-binding regions, an N-terminal one recognized
by Pfam radical SAM domain-defining model pfam04055 and
a C-terminal one recognized by TIGR04085. Members of
this protein family occur in cassettes with such a
radical SAM family (TIGR04148) and with a peptide
modification target (TIGR04149). Surprisingly, members
of this family show full-length homology to each other,
with several scoring at least borderline hits to both
pfam04055 and TIGR04085, and yet differ in the
presence/absence of a signature CX(3)CX(2)CX(9)C motif.
Instead, members are best-conserved in the
TIGR04085-like C-terminal region. Therefore, this
protein family is designated a pseudo-radical-SAM
protein, which likely works in partnership with a
TIGR04148 family protein.
Length = 407
Score = 29.2 bits (66), Expect = 3.7
Identities = 20/132 (15%), Positives = 46/132 (34%), Gaps = 10/132 (7%)
Query: 266 SQGLNSTKLWNDIDDIIIKTIISVYPI-----LKEKYEDLLPEHYHHNVSASFEILGFDI 320
+Q L+ KL + +D + I + +LL ++ L +
Sbjct: 153 NQVLSIDKLKSILDQLSYNNIYRINLFGGNIFKYPYLRELLSLLEQYSGKKQI-YLDYKN 211
Query: 321 LIDSTMKPFLLEVNRSPSFNIAGIVDERVKRTLIYDTFKILNLNQNRKSILFPSNDDSEN 380
+S +K L P+F+I +V V L+ +L + I ++++
Sbjct: 212 FYESDLKKLLNN----PNFSIKILVHFPVDEELLNSLIALLKDRDPVEWIFIVTSENEYE 267
Query: 381 QSSNSDHQASTL 392
++ + +
Sbjct: 268 EAEKIIEKYNID 279
>gnl|CDD|183437 PRK12322, PRK12322, NADH dehydrogenase subunit D; Provisional.
Length = 366
Score = 29.3 bits (66), Expect = 3.9
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 305 YHHNVSASFEILGFDILIDSTMKPFLLEVNRSPSFNIAGIVDERVKRTLIYDTFKIL 361
+ + + +G I D KP+ L+ R PSF I+ + +K I + IL
Sbjct: 299 AYVRIESPRGEIGCYIASDGKKKPYRLKF-RRPSFYNLQILPKLLKGENIANLIAIL 354
>gnl|CDD|233815 TIGR02294, nickel_nikA, nickel ABC transporter, nickel/metallophore
periplasmic binding protein. Members of this family are
periplasmic nickel-binding proteins of nickel ABC
transporters. Most appear to be lipoproteins. This
protein was previously (circa 2003) thought to mediate
binding to nickel through water molecules, but is now
thought to involve a chelating organic molecule, perhaps
butane-1,2,4-tricarboxylate, acting as a metallophore
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 500
Score = 29.0 bits (65), Expect = 5.6
Identities = 27/112 (24%), Positives = 47/112 (41%), Gaps = 9/112 (8%)
Query: 112 DYDF-YPRSWSLPYQQEDFLSYVREHPHQVFISKPSRGAEGKGIKIFNTLEEARGIYTES 170
D+D + +W PY F+S +R H ++ G K +I ++ +A E+
Sbjct: 391 DFDMMFNYTWGAPYDPHSFISAMRAKGHGDESAQ--SGLANKD-EIDKSIGDALASTDET 447
Query: 171 -VSQLYMSNLLLMDGFKFDLRVYVLITCIDPLRIFVYNNGLVRLATCQYTSP 221
+LY + L + D VY+ I+ I ++ + V A QY P
Sbjct: 448 ERQELYKNILTTLH----DEAVYIPISYISMTVVYRKDLEKVSFAPSQYELP 495
>gnl|CDD|223267 COG0189, RimK, Glutathione synthase/Ribosomal protein S6
modification enzyme (glutaminyl transferase) [Coenzyme
metabolism / Translation, ribosomal structure and
biogenesis].
Length = 318
Score = 28.5 bits (64), Expect = 7.1
Identities = 19/134 (14%), Positives = 43/134 (32%), Gaps = 15/134 (11%)
Query: 83 INHFPGMANLESKAFLAYHLNRMRNHFPEDYDFYPRSWSLPYQQEDFLSYVREHPHQVFI 142
IN + +K + L + P + ++ +V EH +
Sbjct: 108 INDPQSIRRCRNKLYTTQLLAKAGIPVPP--------TLITRDPDEAAEFVAEHLGFPVV 159
Query: 143 SKPSRGAEGKGIKIFNTLEEARGIYTESVSQLYMSNLLLMDGFKF---DLRVYVLI---- 195
KP G+ G+G+ + + E+++Q +++ + D R ++
Sbjct: 160 LKPLDGSGGRGVFLVEDADPELLSLLETLTQEGRKLIIVQEYIPKAKRDDRRVLVGGGEV 219
Query: 196 TCIDPLRIFVYNNG 209
I L +
Sbjct: 220 VAIYALARIPASGD 233
>gnl|CDD|233729 TIGR02103, pullul_strch, alpha-1,6-glucosidases, pullulanase-type.
Members of this protein family include secreted (or
membrane-anchored) pullulanases of Gram-negative
bacteria and pullulanase-type starch debranching enzymes
of plants. Both enzymes hydrolyze alpha-1,6 glycosidic
linkages. Pullulan is an unusual, industrially important
polysaccharide in which short alpha-1,4 chains
(maltotriose) are connected in alpha-1,6 linkages.
Enzymes that cleave alpha-1,6 linkages in pullulan and
release maltotriose are called pullulanases although
pullulan itself may not be the natural substrate. This
family is closely homologous to, but architecturally
different from, the Gram-positive pullulanases of
Gram-positive bacteria (TIGR02102) [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 898
Score = 28.6 bits (64), Expect = 7.1
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 337 PSFNIAGIVDERVKRTLIYDTF-KILNLNQNRKSILFPSNDDSENQSSNSDHQAS 390
P+F+IA + +E+ K I F K+ LN + KS F DS +Q +D + +
Sbjct: 307 PTFDIATVNEEKEKVADIQQPFSKLCELNPDSKSSEFAGYCDSGSQLKQNDSKDN 361
>gnl|CDD|206571 pfam14403, CP_ATPgrasp_2, Circularly permuted ATP-grasp type 2.
Circularly permuted ATP-grasp prototyped by Roseiflexus
RoseRS_2616 that is associated in gene neighborhoods
with a GCS2-like COOH-NH2 ligase, alpha/beta hydrolase
fold peptidase, GAT-II -like amidohydrolase, and M20
peptidase. Members of this family are predicted to be
involved in the biosynthesis of small peptides.
Length = 445
Score = 28.6 bits (64), Expect = 7.2
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 105 MRNHFPEDYDFYPRSWSLPYQQEDFLSYVREHPHQVFISKPSRGAEGKGIKI 156
+ H P P + D + + + ++ + KP+ GKG+ I
Sbjct: 306 IHAHVPWTRLVRPGKTTYQGATIDLVEFAVANRERLVL-KPNDEYAGKGVLI 356
>gnl|CDD|232806 TIGR00067, glut_race, glutamate racemase. This family consists of
glutamate racemase, a protein required for making the
UDP-N-acetylmuramoyl-pentapeptide used as a precursor in
bacterial peptidoglycan biosynthesis. The most closely
related proteins differing in function are aspartate
racemases [Cell envelope, Biosynthesis and degradation
of murein sacculus and peptidoglycan].
Length = 251
Score = 28.1 bits (63), Expect = 8.2
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 6/33 (18%)
Query: 290 YPILKEKYEDLLPEHYH------HNVSASFEIL 316
+P+LKE+ E LPEH H + +L
Sbjct: 183 FPLLKEEIEQYLPEHVRLVDSGVHTARRTAWLL 215
>gnl|CDD|188998 cd06460, M32_Taq, Peptidase family M32 includes thermostable
carboxypeptidases TaqCP and PfuCP. Peptidase family M32
is a subclass of metallocarboxypeptidases which are
distributed mainly in bacteria and archaea, and contain
a HEXXH motif that coordinates a divalent cation such as
Zn2+ or Co2+, so far only observed in the active site of
neutral metallopeptidases but not in carboxypeptidases.
M32 includes the thermostable carboxypeptidases (E.C.
3.4.17.19) from Thermus aquaticus (TaqCP) and Pyrococcus
furiosus (PfuCP), which have broad specificities toward
a wide range of C-terminal substrates that include
basic, aromatic, neutral and polar amino acids. These
enzymes have a similar fold to the M3 peptidases such as
neurolysin and the M2 angiotensin converting enzyme
(ACE). Novel peptidases from protozoa Trypanosoma cruzi,
a causative agent of Chagas' disease, and Leishmania
major, a parasite that causes leishmaniasis, are the
first eukaryotic M32 enzymes identified so far, thus
making these enzymes an attractive potential target for
drug development against these organisms.
Length = 484
Score = 28.2 bits (64), Expect = 8.6
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 6/29 (20%)
Query: 94 SKAFLAYHLNRMRNHFPEDY------DFY 116
S+AF + +++ HFPE +FY
Sbjct: 296 SRAFWEFLYPKLQEHFPEQLGDVSLEEFY 324
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 0.400
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,148,541
Number of extensions: 1958336
Number of successful extensions: 1623
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1619
Number of HSP's successfully gapped: 28
Length of query: 395
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 296
Effective length of database: 6,546,556
Effective search space: 1937780576
Effective search space used: 1937780576
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 (21.7 bits)
S2: 60 (26.9 bits)