RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 002880
(871 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 = 182 bits (465), Expect = 7e-52
Identities = 73/283 (25%), Positives = 120/283 (42%), Gaps = 24/283 (8%)
Query: 591 QYVNQFPFESCLV----MKHHLAETVQKAHGSPEWLQPTYNLETHLPQLIGDYYVRKRDG 646
Q +N FP + + ++ ++L T+ L P + ++ D
Sbjct: 9 QALNHFPGSYEITRKDLLWKNIKRQPCDFGRKFDFLPRTFIL----PTDLAEFVDYFEDN 64
Query: 647 LNNLWILKPWNMARTIDTSVTDDLSAVIRLMETGPKICQKYIEFPALFQGRKFDLRYIVL 706
N WI+KP AR +T+DLS +++ +++ P + QKYIE P L GRKFD+R VL
Sbjct: 65 ERNTWIVKPSASARGRGIRITNDLSQILKQIQSRPLVVQKYIERPLLIDGRKFDIRLYVL 124
Query: 707 VRSMDPLEIFLSDVFWVRLANNPYSLDKHSFFEYETHFTVMNY-------GRRFNHMNTP 759
V S++PL +++ +R A+ YS + E H T + +N N
Sbjct: 125 VTSVNPLRVYVYREGLLRFASVKYSPSVSDLDDVEMHLTNYSIQKKSSSLNEDYNEPNGH 184
Query: 760 D-FVRGFEA-EHQVKWLEIHQRVKNTIRSVFEAAAVAHPEMHSSK---SRAMYGVDIMLD 814
+ F + EI +++ I AA V ++ +YG D M+D
Sbjct: 185 KWSLFNFWKYLEEKDKEEIWLEIESIIIKTILAAEVEASRLNVQPLYNCFELYGFDFMID 244
Query: 815 SSFQPKLLEVTYCPDCTRACKYDTEALVTGEVVKGADFFNYVF 857
+ +P LLEV P K D A + +++ D N V
Sbjct: 245 ENLKPWLLEVNASPSLHSTTKLD--ARLKEQLID--DVLNSVV 283
>gnl|CDD|238064 cd00116, LRR_RI, Leucine-rich repeats (LRRs), ribonuclease
inhibitor (RI)-like subfamily. LRRs are 20-29 residue
sequence motifs present in many proteins that
participate in protein-protein interactions and have
different functions and cellular locations. LRRs
correspond to structural units consisting of a beta
strand (LxxLxLxxN/CxL conserved pattern) and an alpha
helix. This alignment contains 12 strands corresponding
to 11 full repeats, consistent with the extent observed
in the subfamily acting as Ran GTPase Activating
Proteins (RanGAP1).
Length = 319
Score = 40.4 bits (95), Expect = 0.003
Identities = 38/172 (22%), Positives = 62/172 (36%), Gaps = 32/172 (18%)
Query: 172 LSLNLSSKFPDLQALSLCGNKL--ETVEIIVQEVTKLKNLRALWLNNNPVLKKCDHCMED 229
L+ L + DL+ L+L N + + + + + NL L LNNN + + + +
Sbjct: 157 LAKALRAN-RDLKELNLANNGIGDAGIRALAEGLKANCNLEVLDLNNNGLTDEGASALAE 215
Query: 230 AILQGCPKLEIYNSNFTINFGEWALGFCGEVYDKDNP-SSLCLRD------RPLQSVTSL 282
+ LE +N G DN + P S+ +L
Sbjct: 216 TLASLK-SLE------VLNLG-------------DNNLTDAGAAALASALLSPNISLLTL 255
Query: 283 DLSNRCIHNLVNKAFSP--AEMPSLSHLNIRGNPLEQNSVRELLEVLKGFPC 332
LS I + K + AE SL L++RGN + + L E L
Sbjct: 256 SLSCNDITDDGAKDLAEVLAEKESLLELDLRGNKFGEEGAQLLAESLLEPGN 307
>gnl|CDD|206026 pfam13855, LRR_8, Leucine rich repeat.
Length = 60
Score = 36.0 bits (84), Expect = 0.005
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 276 LQSVTSLDLSNRCIHNLVNKAFSPAEMPSLSHLNIRGNPL 315
L ++ LDLS + ++ +AFS +PSL L++ GN L
Sbjct: 23 LPNLKVLDLSGNNLTSISPEAFS--GLPSLRSLDLSGNNL 60
Score = 28.3 bits (64), Expect = 2.2
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 278 SVTSLDLSNRCIHNLVNKAFSPAEMPSLSHLNIRGNPLEQNSVRELLEVLKGFPCLQSL 336
++ SLDLSN + + + AF +P+L L++ GN L S+ E G P L+SL
Sbjct: 1 NLKSLDLSNNRLTVIPDGAFKG--LPNLKVLDLSGNNLT--SISP--EAFSGLPSLRSL 53
Score = 27.9 bits (63), Expect = 3.3
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 165 DIGDDMLLSLNLSSKFPDLQALSLCGNKLETVEIIVQEVTKLKNLRALWLNNNP 218
I D L P+L+ L L GN L ++ + L +LR+L L+ N
Sbjct: 14 VIPDGAFKGL------PNLKVLDLSGNNLTSISPEA--FSGLPSLRSLDLSGNN 59
>gnl|CDD|205079 pfam12799, LRR_4, Leucine Rich repeats (2 copies). Leucine rich
repeats are short sequence motifs present in a number of
proteins with diverse functions and cellular locations.
These repeats are usually involved in protein-protein
interactions. Each Leucine Rich Repeat is composed of a
beta-alpha unit. These units form elongated non-globular
structures. Leucine Rich Repeats are often flanked by
cysteine rich domains.
Length = 43
Score = 34.0 bits (79), Expect = 0.016
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 183 LQALSLCGNKLETVEIIVQEVTKLKNLRALWLNNNPV 219
L+ L L N++ + ++ L NL L L+ N +
Sbjct: 3 LETLDLSNNQITDLP----PLSNLPNLETLDLSGNKI 35
Score = 27.5 bits (62), Expect = 3.6
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 277 QSVTSLDLSNRCIHNLVNKAFSP-AEMPSLSHLNIRGNPLEQNSV 320
++ +LDLSN I +L P + +P+L L++ GN + S
Sbjct: 1 TNLETLDLSNNQITDL-----PPLSNLPNLETLDLSGNKITDLSP 40
>gnl|CDD|187754 cd09293, AMN1, Antagonist of mitotic exit network protein 1. Amn1
has been functionally characterized in Saccharomyces
cerevisiae as a component of the Antagonist of MEN
pathway (AMEN). The AMEN network is activated by MEN
(mitotic exit network) via an active Cdc14, and in turn
switches off MEN. Amn1 constitutes one of the
alternative mechanisms by which MEN may be disrupted.
Specifically, Amn1 binds Tem1 (Termination of M-phase, a
GTPase that belongs to the RAS superfamily), and
disrupts its association with Cdc15, the primary
downstream target. Amn1 is a leucine-rich repeat (LRR)
protein, with 12 repeats in the S. cerevisiae ortholog.
As a negative regulator of the signal transduction
pathway MEN, overexpression of AMN1 slows the growth of
wild type cells. The function of the vertebrate members
of this family has not been determined experimentally,
they have fewer LRRs that determine the extent of this
model.
Length = 226
Score = 36.9 bits (86), Expect = 0.026
Identities = 58/231 (25%), Positives = 89/231 (38%), Gaps = 60/231 (25%)
Query: 127 VLHENGTKSNVEDILESEIHNATEKGDGTVKWLELEDADIGDDMLLSLNLSSKFPDLQAL 186
+LH + S++ G ++WLEL I D L L+ +K L+ L
Sbjct: 7 ILH---KLGQITQSNISQLLRILHSG---LEWLELYMCPISDPPLDQLSNCNK---LKKL 57
Query: 187 SLCGNKLETVEIIVQEVTKLKNLRALWLNNNPVLKKCDHCMEDAILQ---GCPKLEIYNS 243
L G+KL E ++ NL+ L L+ C++ + I+ CPKL+
Sbjct: 58 ILPGSKLIDDEGLIALAQSCPNLQVL------DLRACENITDSGIVALATNCPKLQ---- 107
Query: 244 NFTINFGEW----------------------ALGFCG-EVYDKDNPSSLCLRDRPLQSVT 280
TIN G +GF G +V DK + +
Sbjct: 108 --TINLGRHRNGHLITDVSLSALGKNCTFLQTVGFAGCDVTDK------GVWELASGCSK 159
Query: 281 SLD-LS-NRCIHNLVNKA----FSPAEMPSLSHLNIRGNPLEQNSVRELLE 325
SL+ LS N C NL +++ + P+LS L RG PL + R +L
Sbjct: 160 SLERLSLNNCR-NLTDQSIPAILASNYFPNLSVLEFRGCPLITDFSRIILF 209
>gnl|CDD|168663 PRK06756, PRK06756, flavodoxin; Provisional.
Length = 148
Score = 31.0 bits (70), Expect = 1.4
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 104 MASLMCVDTDLDTDIEEV-DAVKGVLHENGTKSNVEDILESEIHNATEKGDGTV----KW 158
M+ L+ + + + EE+ D + GV+ E + V DI++S + E+ DG + W
Sbjct: 1 MSKLVMIFASMSGNTEEMADHIAGVIRETENEIEVIDIMDSPEASILEQYDGIILGAYTW 60
Query: 159 LELEDADIGDDML 171
D D+ DD L
Sbjct: 61 ---GDGDLPDDFL 70
>gnl|CDD|226414 COG3898, COG3898, Uncharacterized membrane-bound protein [Function
unknown].
Length = 531
Score = 31.4 bits (71), Expect = 2.2
Identities = 17/86 (19%), Positives = 26/86 (30%), Gaps = 20/86 (23%)
Query: 383 PRLPEWSADQPLADRVLSAMWLYL--MTYRLANEEKIDETSVWYV-MDELGSAVRHSDEP 439
PR P W+AD +++ W + +T RL E W +L +
Sbjct: 393 PRDPAWTADGVVSEA-----WAPVSPVTGRLDAFE-------WKAPTGQLAHP-IEDRDE 439
Query: 440 NFRVAPFLFMPEGKLSSAVSFSILWP 465
PE SA+
Sbjct: 440 AIMAPL----PEAPAKSAIEEPADEL 461
>gnl|CDD|234993 PRK01966, ddl, D-alanyl-alanine synthetase A; Reviewed.
Length = 333
Score = 30.9 bits (71), Expect = 3.4
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 834 CKYDTEALVTGEVVKGADFFNY 855
D +A V GE+VK DF++Y
Sbjct: 217 LGNDPKASVPGEIVKPDDFYDY 238
>gnl|CDD|215174 PLN02305, PLN02305, lipoxygenase.
Length = 918
Score = 30.7 bits (69), Expect = 4.2
Identities = 24/65 (36%), Positives = 33/65 (50%), Gaps = 11/65 (16%)
Query: 324 LEVLKGFPCLQSLGVDIPGPLGESAI--EILESLPTLCTLNGVTASKILEEGKHVI---D 378
+E+LK FP L L + GP ESA+ E++E L G+T K +EE + I
Sbjct: 436 IEILKEFPILSKLDPAVYGP-PESALTEELIER-----ELEGMTVEKAIEEKRLFILDYH 489
Query: 379 SMLQP 383
ML P
Sbjct: 490 DMLLP 494
>gnl|CDD|204206 pfam09349, OHCU_decarbox, OHCU decarboxylase. The proteins in this
family are OHCU decarboxylase - enzymes of the purine
catabolism that catalyze the conversion of OHCU into
S(+)-allantoin. This is the third step of the conversion
of uric acid (a purine derivative) to allantoin. Step
one is catalyzed by urate oxidase (pfam01014) and step
two is catalyzed by HIUases (pfam00576).
Length = 159
Score = 29.4 bits (67), Expect = 4.6
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 698 KFDLRYIVLVRSMDPLEIFLSDVFWVRLANNP 729
KF +I+ VR EI RL N+P
Sbjct: 109 KFGFPFIIAVRGRSRAEIL--AALERRLRNDP 138
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
DNA-binding domain. The plasmid conjugative coupling
protein TrwB forms hexamers from six structurally very
similar protomers. This hexamer contains a central
channel running from the cytosolic pole (made up by the
AADs) to the membrane pole ending at the transmembrane
pore shaped by 12 transmembrane helices, rendering an
overall mushroom-like structure. The TrwB_AAD (all-alpha
domain) domain appears to be the DNA-binding domain of
the structure. TrwB, a basic integral inner-membrane
nucleoside-triphosphate-binding protein, is the
structural prototype for the type IV secretion system
coupling proteins, a family of proteins essential for
macromolecular transport between cells and export.
Length = 386
Score = 29.9 bits (68), Expect = 5.6
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 388 WSADQPLADRVLSAMWLYLMTYRLANEEKIDETSVWYVMDELGS 431
DQ A R L ++WL + L + + +W+ +DEL S
Sbjct: 211 SREDQRAALRPLISLWLDIAIRALLSLPPNRDRRLWFFLDELPS 254
>gnl|CDD|133453 cd05311, NAD_bind_2_malic_enz, NAD(P) binding domain of malic
enzyme (ME), subgroup 2. Malic enzyme (ME), a member of
the amino acid dehydrogenase (DH)-like domain family,
catalyzes the oxidative decarboxylation of L-malate to
pyruvate in the presence of cations (typically Mg++ or
Mn++) with the concomitant reduction of cofactor NAD+ or
NADP+. ME has been found in all organisms, and plays
important roles in diverse metabolic pathways such as
photosynthesis and lipogenesis. This enzyme generally
forms homotetramers. The conversion of malate to
pyruvate by ME typically involves oxidation of malate to
produce oxaloacetate, followed by decarboxylation of
oxaloacetate to produce pyruvate and CO2. This
subfamily consists primarily of archaeal and bacterial
ME. Amino acid DH-like NAD(P)-binding domains are
members of the Rossmann fold superfamily and include
glutamate, leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 226
Score = 29.5 bits (67), Expect = 6.0
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 5/50 (10%)
Query: 125 KGVLHENGTKSNVEDILESEIHNATEKGDGTVKWLELEDADIGDDMLLSL 174
KGV++E D E EK GT L++A G D+ + +
Sbjct: 60 KGVIYEGREDDLNPDKNEIAKETNPEKTGGT-----LKEALKGADVFIGV 104
>gnl|CDD|222841 PHA01971, PHA01971, hypothetical protein.
Length = 123
Score = 28.7 bits (64), Expect = 6.6
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 115 DTDIEEVDAVKGVLHENGTKSNVEDILESEIHNATEKG-DGTVKWLELEDADIGDDMLLS 173
D IE+ KG+ T ++E I+ SE + G +G + D + + L +
Sbjct: 3 DKQIEKEIQAKGLTAPRITPQHIESIIASEHYFTAADGVEGANLYCTHADGETTNGPLEA 62
Query: 174 LNL 176
L+L
Sbjct: 63 LSL 65
>gnl|CDD|215851 pfam00310, GATase_2, Glutamine amidotransferases class-II.
Length = 223
Score = 29.2 bits (66), Expect = 8.3
Identities = 22/92 (23%), Positives = 33/92 (35%), Gaps = 11/92 (11%)
Query: 587 ITDQQYVNQFPFESCLVMKHHLAETVQKAHGSPEWLQPTYNLETHLPQLIGDYYVRKRDG 646
I + Y+ F+S L + H T +G P W H P + +
Sbjct: 72 IVAEFYLQDERFKSALAIVH----TRFSTNGFPSW------ENAH-PFRREGWVLAHNGE 120
Query: 647 LNNLWILKPWNMARTIDTSVTDDLSAVIRLME 678
+N L L+ W AR + D A L+E
Sbjct: 121 INTLRGLRNWMRAREGVFNSGSDSEAFDNLLE 152
>gnl|CDD|227223 COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function
unknown].
Length = 394
Score = 29.6 bits (66), Expect = 8.5
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 169 DMLLSLNLSSKFPDLQALSLCGNKLETVEIIVQEVTKLKNLRALWLNNN 217
++ L+ S +L L L NKLE + + + L NL L L+NN
Sbjct: 220 SIIELLSSLSNLKNLSGLELSNNKLED---LPESIGNLSNLETLDLSNN 265
>gnl|CDD|238547 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding
domain. TrwB is a homohexamer encoded by conjugative
plasmids in Gram-negative bacteria. TrwB also has an all
alpha domain which has been hypothesized to be
responsible for DNA binding. TrwB is a component of Type
IV secretion and is responsible for the horizontal
transfer of DNA between bacteria.
Length = 410
Score = 29.2 bits (66), Expect = 9.3
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 388 WSADQPLADRVLSAMWLYLMTYRLANEEKIDETSVWYVMDELGS 431
+AD + R L + WL + L + E +W+ +DEL S
Sbjct: 238 SNADMRASLRPLISTWLDVAVNTLLGLPENRERRLWFFIDELPS 281
>gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling
protein TraD. The TraD protein performs an essential
coupling function in conjugative type IV secretion
systems. This protein sits at the inner membrane in
contact with the assembled pilus and its scaffold as
well as the relaxosome-plasmid DNA complex (through
TraM).
Length = 566
Score = 29.3 bits (66), Expect = 9.6
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 390 ADQPLADRVLSAMWLYLMTYRLANEEKIDETSVWYVMDELGS 431
A Q + + L +MWL + + L + D+ +W++MDEL S
Sbjct: 377 AQQHASLKPLISMWLSIASRGLLSLPPNDDRRIWFIMDELPS 418
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 0.135 0.409
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 44,153,608
Number of extensions: 4300781
Number of successful extensions: 3132
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3120
Number of HSP's successfully gapped: 29
Length of query: 871
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 766
Effective length of database: 6,280,432
Effective search space: 4810810912
Effective search space used: 4810810912
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: 63 (27.9 bits)