RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12239
(785 letters)
>gnl|CDD|221288 pfam11882, DUF3402, Domain of unknown function (DUF3402). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 350 to 473 amino acids in length. This domain is
found associated with pfam07923.
Length = 402
Score = 448 bits (1155), Expect = e-152
Identities = 182/381 (47%), Positives = 237/381 (62%), Gaps = 13/381 (3%)
Query: 360 PIVVEKKVLPWSPKVRQKELDMFLEAIRMKFVGFALRGDRDSLIGLPHPIHESVKVLKQH 419
P + + +S KVR K L R KF+ + D +SL+G P I ESVK LK
Sbjct: 1 PYSIIEAGELFSKKVRMKLATKQLWEEREKFMKYERGWDTESLVGDPLDISESVKELKLE 60
Query: 420 IYTSLSEVHIQKEEEINRSPMSLGEEIIGSSPTEMLYQKMLPNLPQYMIALLKILLAAAP 479
+YTSL+E +KEE S S EEI E Y + LP+L +I LLK +LA P
Sbjct: 61 MYTSLAEDQPKKEEIERLSTDS--EEIPRLDRVESFYSEALPSLQSLVIVLLKTILANVP 118
Query: 480 --TSKAKTDSINILSDVLPEEMPMTILQSMKLGTDVNRHKEIIVKAISSILLLLLKHFKL 537
TSKA +SIN +D LP+EMP T +S++L D+NRHKEI +KA+S+ILLLLLK FKL
Sbjct: 119 SLTSKANGESINGFADGLPDEMPAT-EESLQLQLDINRHKEITLKAVSAILLLLLKWFKL 177
Query: 538 NHVYQFEFMSQHLVFANCIPLVLKFFN-QNISMYISAKSVIPILDFPACVIG---DQPEL 593
+HV +FE+++Q LV +N +PL+LKFF QNI+ +++K+ IP L F + + PEL
Sbjct: 178 SHVLKFEYLTQLLVDSNFLPLILKFFGLQNINRLVNSKNEIPNLSFFSECYLEARNPPEL 237
Query: 594 TSESFEIG----EGQTPHSWRNLVSCINLLRILNKLTKWKHSRIMMLVIFKSAPILKRTL 649
SF G E T SWRN S INLLRIL K+TK K RI++LV +KS+ ILK+ L
Sbjct: 238 DELSFPYGPLPKEPITVFSWRNFFSLINLLRILQKVTKKKTHRILLLVQYKSSTILKKLL 297
Query: 650 KVRHAMMQLYVLKLLKMQTKYLGRQWRKSNMKTISAIYAKVRHRLNDDWAYGNDLDARPW 709
KV ++LYVLKLLK Q Y GR+WR+SNM+ ISAIY R L DDW G+D+DA
Sbjct: 298 KVPQPDLRLYVLKLLKEQVPYCGRKWRQSNMRVISAIYLNCRLELRDDWLAGSDIDAEVE 357
Query: 710 DFQAEECALRASVDRFNSRRY 730
D +E ALRA + +N RRY
Sbjct: 358 DAYPQEQALRALLQFYNLRRY 378
>gnl|CDD|219645 pfam07923, N1221, N1221-like protein. The sequences featured in
this family are similar to a hypothetical protein
product of ORF N1221 in the CPT1-SPC98 intergenic region
of the yeast genome. This encodes an acidic polypeptide
with several possible transmembrane regions.
Length = 293
Score = 215 bits (549), Expect = 6e-64
Identities = 81/280 (28%), Positives = 136/280 (48%), Gaps = 16/280 (5%)
Query: 31 PEVRYIYDDTDYHQNEISEIYSYTEQPEFQLNVKNFEDQMEAYGLIPCWQKLTPVEKNSV 90
P + Y D+D ++E+SE +SY++ +FE + + W ++
Sbjct: 2 PAYEFEYADSDSLEDELSEWFSYSDYSMLLGAKSSFEKKWRTFCGDQSWTDADFDQRRKF 61
Query: 91 IAKLLDQLEVSNKVVRMRSARCFLYLAQGCWGECQSDDEQYDTAVKNCIMLYKFGVFHAF 150
KL+DQLEV++ R+++ LY+AQG W E S EQ + +N ++L + G F
Sbjct: 62 AMKLVDQLEVTDLSRRLKALEALLYIAQGTWAETASKSEQLHSIRRNVLLLVECGGFEPL 121
Query: 151 IDLLNLEID--SSSNTTTVRKLAVSLHDSTDLRIILSVLCTIVEVVRHLEPNVRHSSVFE 208
++LLN+ + + + A S D T+L ++L++L IVEV R
Sbjct: 122 VELLNMFFEHAIACDDAATNLPAYSAADETELFLLLTILYLIVEVCREQR---DSDEENA 178
Query: 209 MLKNEISNPIGDELLAVKLFKMVTRFCSGATPHFPMKKVLILLWKVILVSLGGMKDLQEL 268
+++ I +G L V L K + R + P++K+++LLWKV+L+ GG L+E
Sbjct: 179 IVRKFILE-LGKPNLLVFLTKYIERLRWDSALSMPIRKIILLLWKVLLLQFGGSSHLKEA 237
Query: 269 KKEKRKQNGLKVLDEDTIEIAKTMRPSSPPASAVDIIEAQ 308
K+ R+ +GLK K MR SSPP ++ Q
Sbjct: 238 KEFLRELHGLK----------KNMRSSSPPKLTASPLDYQ 267
>gnl|CDD|213302 cd05936, FC-FACS_FadD_like, Prokaryotic long-chain fatty acid CoA
synthetases similar to Escherichia coli FadD. This
subfamily of the AMP-forming adenylation family contains
Escherichia coli FadD and similar prokaryotic fatty acid
CoA synthetases. FadD was characterized as a long-chain
fatty acid CoA synthetase. The gene fadD is regulated by
the fatty acid regulatory protein FadR. Fatty acid CoA
synthetase catalyzes the formation of fatty acyl-CoA in
a two-step reaction: the formation of a fatty acyl-AMP
molecule as an intermediate, followed by the formation
of a fatty acyl-CoA. This is a required step before free
fatty acids can participate in most catabolic and
anabolic reactions.
Length = 468
Score = 33.6 bits (78), Expect = 0.37
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 459 MLPNLPQYMIALLKILLAAA 478
MLPN PQ+ IA IL A A
Sbjct: 55 MLPNCPQFPIAYFGILKAGA 74
>gnl|CDD|153072 cd03602, CLECT_1, C-type lectin (CTL)/C-type lectin-like (CTLD)
domain subgroup 1; a subgroup of protein domains
homologous to the carbohydrate-recognition domains
(CRDs) of the C-type lectins. CLECT_1: C-type lectin
(CTL)/C-type lectin-like (CTLD) domain subgroup 1; a
subgroup of protein domains homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. Many CTLDs are calcium-dependent carbohydrate
binding modules; other CTLDs bind protein ligands,
lipids, and inorganic surfaces including CaCO3 and ice.
Animal C-type lectins are involved in such functions as
extracellular matrix organization, endocytosis,
complement activation, pathogen recognition, and
cell-cell interactions. CTLDs may bind a variety of
carbohydrate ligands including mannose,
N-acetylglucosamine, galactose, N-acetylgalactosamine,
and fucose. CTLDs associate with each other through
several different surfaces to form dimers, trimers, or
tetramers from which ligand-binding sites project in
different orientations. In some CTLDs a loop extends to
the adjoining domain to form a loop-swapped dimer.
Length = 108
Score = 30.8 bits (70), Expect = 0.70
Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 8/47 (17%)
Query: 697 DWAYGNDLDARPWD----FQAEECALRASVDRFNSRRYNSTCFDPDY 739
W+ G++ R W+ F +CA + R Y + C
Sbjct: 61 RWSDGSESSFRNWNTFQPFGQGDCA----TMYSSGRWYAALCSALKP 103
>gnl|CDD|239783 cd04250, AAK_NAGK-C, AAK_NAGK-C: N-Acetyl-L-glutamate kinase -
cyclic (NAGK-C) catalyzes the phosphorylation of the
gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in
the second step of arginine biosynthesis found in some
bacteria and photosynthetic organisms using the
non-acetylated, cyclic route of ornithine biosynthesis.
In this pathway, glutamate is first N-acetylated and
then phosphorylated by NAGK to give phosphoryl NAG,
which is converted to NAG-ornithine. There are two
variants of this pathway. In one, typified by the
pathway in Thermotoga maritima and Pseudomonas
aeruginosa, the acetyl group is recycled by reversible
transacetylation from acetylornithine to glutamate. The
phosphorylation of NAG by NAGK is feedback inhibited by
arginine. In photosynthetic organisms, NAGK is the
target of the nitrogen-signaling protein PII. Hexameric
formation of NAGK domains appears to be essential to
both arginine inhibition and NAGK-PII complex formation.
NAGK-C are members of the Amino Acid Kinase Superfamily
(AAK).
Length = 279
Score = 30.9 bits (71), Expect = 2.1
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 244 MKKVLILLWKVILVSLGG---MKDLQELKKEKRKQNGLKVLDEDTIEIAKTM 292
+K V I ++V GG + L++L E NGL+V DE+T+EI + +
Sbjct: 42 LKYVGI---NPVVVHGGGPEINEMLKKLGIESEFVNGLRVTDEETMEIVEMV 90
>gnl|CDD|178621 PLN03072, PLN03072, 60S ribosomal protein L12; Provisional.
Length = 166
Score = 30.2 bits (68), Expect = 2.3
Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 4/39 (10%)
Query: 262 MKDLQELKKEKRKQNGLK----VLDEDTIEIAKTMRPSS 296
+K L+E +++++K +K + +D IEIAK MRP S
Sbjct: 83 IKALKEPERDRKKVKNIKHNGNISLDDVIEIAKIMRPRS 121
>gnl|CDD|239771 cd04238, AAK_NAGK-like, AAK_NAGK-like: N-Acetyl-L-glutamate kinase
(NAGK)-like . Included in this CD are the Escherichia
coli and Pseudomonas aeruginosa type NAGKs which
catalyze the phosphorylation of N-acetyl-L-glutamate
(NAG) by ATP in the second step of arginine biosynthesis
found in bacteria and photosynthetic organisms using
either the acetylated, noncyclic (NC), or
non-acetylated, cyclic (C) route of ornithine
biosynthesis. Also included in this CD is a distinct
group of uncharacterized (UC) bacterial and archeal
NAGKs. Members of this CD belong to the Amino Acid
Kinase Superfamily (AAK).
Length = 256
Score = 30.2 bits (69), Expect = 3.8
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 13/55 (23%)
Query: 246 KVLILLW----KVILVSLGG------MKDLQELKKEKRKQNGLKVLDEDTIEIAK 290
++LL ++V GG +K L E NGL+V D++T+EI +
Sbjct: 21 DDIVLLKQVGINPVIVHGGGPEINELLKRLG---IESEFVNGLRVTDKETMEIVE 72
>gnl|CDD|234869 PRK00942, PRK00942, acetylglutamate kinase; Provisional.
Length = 283
Score = 30.1 bits (69), Expect = 4.0
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 12/52 (23%)
Query: 249 ILLWK-----VILVSLGG-----MKDLQELKKEKRKQNGLKVLDEDTIEIAK 290
I+L K ++V GG + L++L E NGL+V D +T+E+ +
Sbjct: 48 IVLLKQVGINPVVVHGGGPQIDEL--LKKLGIESEFVNGLRVTDAETMEVVE 97
>gnl|CDD|237479 PRK13719, PRK13719, conjugal transfer transcriptional regulator
TraJ; Provisional.
Length = 217
Score = 29.7 bits (67), Expect = 5.3
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 124 CQSDDEQYDTAVKNCIMLYKFGVFHAFI-DLLNLEIDSSSNTTTVRKLAVSLHDSTDLRI 182
+ Q D +LY FG H +I LLN+ + SS N + + +L I
Sbjct: 142 NKVTKYQNDV-----FILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFGISSRDELLI 196
Query: 183 IL 184
IL
Sbjct: 197 IL 198
>gnl|CDD|181507 PRK08626, PRK08626, fumarate reductase flavoprotein subunit;
Provisional.
Length = 657
Score = 29.6 bits (67), Expect = 7.5
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 331 PAGAEFEPEEDYEDPQVMEVTMP 353
P G EP +YE VM++ +P
Sbjct: 570 PEGEALEPTLEYEPLDVMKMELP 592
>gnl|CDD|236359 PRK08974, PRK08974, long-chain-fatty-acid--CoA ligase; Validated.
Length = 560
Score = 29.6 bits (67), Expect = 8.1
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 459 MLPNLPQYMIALLKILLA 476
M+PNL QY IAL IL A
Sbjct: 80 MMPNLLQYPIALFGILRA 97
>gnl|CDD|132173 TIGR03129, one_C_dehyd_B, formylmethanofuran dehydrogenase subunit
B. Members of this largely archaeal protein family are
subunit B of the formylmethanofuran dehydrogenase.
Nomenclature in some bacteria may reflect inclusion of
the formyltransferase described by TIGR03119 as part of
the complex, and therefore call this protein
formyltransferase/hydrolase complex Fhc subunit C. Note
that this model does not distinguish tungsten (FwdB)
from molybdenum-containing (FmdB) forms of this enzyme.
Length = 421
Score = 29.6 bits (67), Expect = 8.2
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 597 SFEIGEGQTPHSWRNLVSCINLLRILNKLTKW 628
F +G + RN+ I L++ LNK TK+
Sbjct: 247 FFGLGLTSSLGKHRNVEIAIELVKDLNKYTKF 278
>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed.
Length = 356
Score = 29.3 bits (65), Expect = 8.9
Identities = 22/97 (22%), Positives = 40/97 (41%), Gaps = 9/97 (9%)
Query: 290 KTMRPSSPPASAVDIIEAQNQKRNSRPLKRLALMKQSSLDEPAGAEFEPEEDYEDPQVME 349
+T + P + + A ++ S+P + +Q SL+ A + E+ +
Sbjct: 72 RTPKLEKAPNTNEEKTSASKIEKISQPKQE----EQKSLNISATPAPKQEQSQTTTESTT 127
Query: 350 VT--MPRPPS---PTPIVVEKKVLPWSPKVRQKELDM 381
+ PPS P P+ K P SP ++Q + DM
Sbjct: 128 PKTKVTTPPSTNTPQPMQSTKSDTPQSPTIKQAQTDM 164
>gnl|CDD|215413 PLN02770, PLN02770, haloacid dehalogenase-like hydrolase family
protein.
Length = 248
Score = 29.0 bits (65), Expect = 9.2
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 539 HVYQFEFMSQHLVFANCIPLVLKFFNQNIS 568
H Y F M Q + F +P+ +FF +NI+
Sbjct: 40 HYYAFREMLQEINFNGGVPITEEFFVENIA 69
>gnl|CDD|232864 TIGR00187, ribE, riboflavin synthase, alpha subunit. This protein
family consists almost entirely of two lumazine-binding
domains, described in the Lum_binding model from PFAM.
The model generates lower scores against other proteins
that also have two lumazine-binding domains, including
some involved in bioluminescence.The name ribE was
selected, from among alternatives including ribB and
ribC, to match the usage in EcoCyc [Biosynthesis of
cofactors, prosthetic groups, and carriers, Riboflavin,
FMN, and FAD].
Length = 200
Score = 28.5 bits (64), Expect = 9.9
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 494 VLPEEMPMTILQSMKLGTDVNRHKEIIVKAISSILLLLL 532
++P + TIL KLG VN +++ KA++ L L
Sbjct: 161 LIPHTLENTILGLKKLGDRVNIEIDMLGKAVADTLERTL 199
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 0.398
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 39,962,544
Number of extensions: 3948408
Number of successful extensions: 3211
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3204
Number of HSP's successfully gapped: 28
Length of query: 785
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 680
Effective length of database: 6,280,432
Effective search space: 4270693760
Effective search space used: 4270693760
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 (28.1 bits)