RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9332
(148 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 = 94.3 bits (235), Expect = 3e-24
Identities = 36/84 (42%), Positives = 52/84 (61%), Gaps = 1/84 (1%)
Query: 17 RGKDITNKLFTNISWLIVHSLKSVSYI-MANDKHCFECYGYDIIIDNQLKPWLIEVNASP 75
++I ++ + I I+ + S + + +CFE YG+D +ID LKPWL+EVNASP
Sbjct: 199 DKEEIWLEIESIIIKTILAAEVEASRLNVQPLYNCFELYGFDFMIDENLKPWLLEVNASP 258
Query: 76 SLTCTTVNDRILKYKLIDNILNIV 99
SL TT D LK +LID++LN V
Sbjct: 259 SLHSTTKLDARLKEQLIDDVLNSV 282
>gnl|CDD|234948 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
Length = 304
Score = 35.1 bits (82), Expect = 0.008
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 53 CYGY---DIIIDNQLKPWLIEVNASPSLT 78
C G+ D ++D KP+L+EVN P +T
Sbjct: 245 CRGWGRVDFMLDEDGKPYLLEVNTQPGMT 273
>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 = 32.5 bits (74), Expect = 0.053
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 55 GYDIIIDNQLKPWLIEVNASPSLTCTTVNDRILKYKL 91
G D+++D + P ++E+NA P L N L +L
Sbjct: 250 GVDMVLDKEEGPLVLELNARPGLAIQIANGAGLLPRL 286
>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 = 32.3 bits (74), Expect = 0.064
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 55 GYDIIIDNQLKPWLIEVNASPS 76
G DI +D Q + WL+E N+ P
Sbjct: 213 GIDIGLDTQGRIWLLEANSKPG 234
>gnl|CDD|184875 PRK14875, PRK14875, acetoin dehydrogenase E2 subunit
dihydrolipoyllysine-residue acetyltransferase;
Provisional.
Length = 371
Score = 30.7 bits (70), Expect = 0.27
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 62 NQLKPWLIEVNASPSL-TCTTVNDRILKYKLID 93
+LKP L + A P+L T V D +LKYK +D
Sbjct: 252 RELKPVLELLFADPALVTRQMVED-LLKYKRLD 283
>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 = 0.38
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 54 YGYDIIIDNQLKPWLIEVNA-SPS 76
YG D++ + ++E N +PS
Sbjct: 71 YGADLVRGPDGRWRVLEDNTRAPS 94
>gnl|CDD|152556 pfam12121, DD_K, Dermaseptin. This protein is found in eukaryotes.
Proteins in this family are typically between 30 to 76
amino acids in length. This protein is found associated
with pfam03032. This domain is part of a dermaseptin
protein which is used as an antimicrobial agent. The
full protein is almost completely defined in an alpha
helical domain. It creates high levels of disorder at
the level of the phospholipid head group of bacterial
membranes suggesting that it partitions into the bilayer
where it severely disrupts membrane packing.
Length = 23
Score = 26.1 bits (58), Expect = 1.0
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 100 MWNKYKKADGGAAGGEALN 118
+W+ K G AAG ALN
Sbjct: 2 LWSTILKKVGKAAGKAALN 20
>gnl|CDD|234459 TIGR04082, rSAM_for_selen, selenobiotic family peptide radical SAM
maturase. Members of this protein family are radical
SAM (rSAM) enzymes similar in sequence to others with
known or postulated roles in peptide modification, and
regularly found adjacent to members of the GSU_1558
peptide family described by model TIGR04081. GSU_1558
and several other members of that family appear to be
selenoproteins, hence the term selenobiotic.
Length = 516
Score = 28.5 bits (64), Expect = 1.3
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 93 DNILNIVMWNKYKKADGGAAG---GEALNLGNFQLLLDEE 129
DN+LNIV + + GG G G A N LL D E
Sbjct: 409 DNLLNIVREERGQPLFGGCTGFGCGAAFNF--VALLPDGE 446
>gnl|CDD|119353 cd02874, GH18_CFLE_spore_hydrolase, Cortical fragment-lytic
enzyme (CFLE) is a peptidoglycan hydrolase involved in
bacterial endospore germination. CFLE is expressed as
an inactive preprotein (called SleB) in the forespore
compartment of sporulating cells. SleB translocates
across the forespore inner membrane and is deposited as
a mature enzyme in the cortex layer of the spore. As
part of a sensory mechanism capable of initiating
germination, CFLE degrades a spore-specific
peptidoglycan constituent called muramic-acid
delta-lactam that comprises the outer cortex. CFLE has
a C-terminal glycosyl hydrolase family 18 (GH18)
catalytic domain as well as two N-terminal LysM
peptidoglycan-binding domains. In addition to SleB,
this family includes YaaH, YdhD, and YvbX from Bacillus
subtilis.
Length = 313
Score = 28.4 bits (64), Expect = 1.5
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 61 DNQLKPWLIEVNA-----SPSLTCTTVNDRILKYKLIDNILNIV 99
+KP L+ N L +++ + +LI+NIL +
Sbjct: 56 RRGVKPLLVITNLTNGNFDSELAHAVLSNPEARQRLINNILALA 99
>gnl|CDD|224102 COG1181, DdlA, D-alanine-D-alanine ligase and related ATP-grasp
enzymes [Cell envelope biogenesis, outer membrane].
Length = 317
Score = 27.6 bits (62), Expect = 2.5
Identities = 8/23 (34%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 57 DIII-DNQLKPWLIEVNASPSLT 78
D + D++ + L+EVN +P +T
Sbjct: 267 DFFVDDDEGEFVLLEVNTNPGMT 289
>gnl|CDD|213334 cd05132, RasGAP_GAPA, Ras-GTPase Activating Domain of GAPA. GAPA
is an IQGAP-related protein and is predicted to bind to
small GTPases, which are yet to be identified. IQGAP
proteins are integral components of cytoskeletal
regulation. Results from truncated GAPAs indicated that
almost the entire region of GAPA homologous to IQGAP is
required for cytokinesis in Dictyostelium. More members
of the IQGAP family are emerging, and evidence suggests
that there are both similarities and differences in
their function.
Length = 352
Score = 26.9 bits (60), Expect = 3.9
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 10/45 (22%)
Query: 92 IDNILNIVMW----NKYKKADGGAAGGEALNLGNFQLLLDEEYDE 132
ID++L VM+ N+Y+ + E L L FQ +L E+DE
Sbjct: 2 IDSLLQTVMFTLYGNQYESRE------EHLLLSMFQSVLTYEFDE 40
>gnl|CDD|173594 PTZ00403, PTZ00403, phosphatidylserine decarboxylase; Provisional.
Length = 353
Score = 27.1 bits (60), Expect = 3.9
Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 89 YKLIDNILNI----VMWNKYKKADGGAAGGEALNLGNFQLLLDEEYDENNVKQNIS 140
+K+I+N+ NI ++ ++K + A A N+GN +++ DEE NN++ +S
Sbjct: 222 FKIINNLFNINERVILSGEWKGGNVYYAAISAYNVGNIKIINDEELVTNNLRTQLS 277
>gnl|CDD|222774 PHA00028, rep, RNA replicase, beta subunit.
Length = 561
Score = 27.1 bits (60), Expect = 5.0
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 18 GKDITNKLFTNISWLIVHSLKSVSYIMANDKHCFECYGYDIIIDNQLKPWLIEV 71
G T +L + I I S + YG DII+ ++ P LI V
Sbjct: 307 GNGFTFELESLIFAAIARS---FCLLFGGPGTI-SVYGDDIIVPTEVAPPLINV 356
>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 = 26.0 bits (57), Expect = 9.8
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 18 GKDITNKLFTNISWLIVHSLKSVSYIMANDKHCFECYGYDIIIDNQLKPWLIEV 71
G T +L + I + S+ + +D YG DII+ + P L+EV
Sbjct: 298 GNGFTFELESLIFAALARSVCELLGGDTSD---VGIYGDDIIVPSCAVPPLMEV 348
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 0.136 0.416
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: 7,482,948
Number of extensions: 654707
Number of successful extensions: 431
Number of sequences better than 10.0: 1
Number of HSP's gapped: 430
Number of HSP's successfully gapped: 22
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
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: 54 (24.6 bits)