RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12534
(343 letters)
>gnl|CDD|221257 pfam11838, DUF3358, Domain of unknown function (DUF3358). This
domain is functionally uncharacterized. This domain is
found in eukaryotes and bacteria. This domain is found
to the C-terminus of an aminopeptidase domain.
Length = 323
Score = 66.9 bits (164), Expect = 2e-12
Identities = 31/90 (34%), Positives = 43/90 (47%), Gaps = 5/90 (5%)
Query: 251 WIIFNIQQTGYYRVLYDEKNWYLIIATLRNSTTYNTIHLLNRAQLIDDAMNLARAGLLDY 310
++ N GYYRV YD ++ ATL + + L+RA L DA L R G L
Sbjct: 1 LVLLNDDDLGYYRVRYDPESL----ATLGEALARLKLDPLDRAGLWADAWALVRDGELPT 56
Query: 311 KIALD-VTAYLQYETELVPWRSAMQALGYI 339
+ LD V A+L ET+ V + LG +
Sbjct: 57 RDFLDLVLAFLPNETDYVVLSEILAQLGTL 86
>gnl|CDD|189008 cd09601, M1_APN_2, Peptidase M1 Aminopeptidase N family incudes
tricorn interacting factor F3, Endoplasmic reticulum
aminopeptidase 1 (ERAP1), Aminopeptidase Q (APQ). This
M1 peptidase family includes eukaryotic and bacterial
members: aminopeptidase N (APN), aminopeptidase Q (APQ,
laeverin), endoplasmic reticulum aminopeptidase 1
(ERAP1) as well as tricorn interacting factor F3.
Aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease,
consists of a small N-terminal cytoplasmic domain, a
single transmembrane domain and a large extracellular
ectodomain that contains the active site. It
preferentially cleaves neutral amino acids from the
N-terminus of oligopeptides and is present in a variety
of human tissues and cell types (leukocyte, fibroblast,
endothelial and epithelial cells). APN expression is
dysregulated in inflammatory diseases such as chronic
pain, rheumatoid arthritis, multiple sclerosis, systemic
sclerosis, systemic lupus erythematosus,
polymyositis/dermatomyosytis and pulmonary sarcoidosis,
and is enhanced in tumor cells such as melanoma, renal,
prostate, pancreas, colon, gastric and thyroid cancers.
It is considered a marker of differentiation since it is
predominantly expressed on stem cells and on cells of
the granulocytic and monocytic lineages at distinct
stages of differentiation. Thus, APN inhibition may lead
to the development of anti-cancer and anti-inflammatory
drugs. ERAP1 also known as endoplasmic reticulum
aminopeptidase associated with antigen processing
(ERAAP), adipocyte derived leucine aminopeptidase
(A-LAP) or aminopeptidase regulating tumor necrosis
factor receptor I (THFRI) shedding (ARTS-1), associates
with the closely related ER aminopeptidase ERAP2, for
the final trimming of peptides within the ER for
presentation by MHC class I molecules. ERAP1 is
associated with ankylosing spondylitis (AS), an
inflammatory arthritis that predominantly affects the
spine. ERAP1 also aids in the shedding of membrane-bound
cytokine receptors. The tricorn interacting factor F3,
together with factors F1 and F2, degrades the tricorn
protease products, producing free amino acids, thus
completing the proteasomal degradation pathway. F3 is
homologous to F2, but not F1, and shows a strong
preference for glutamate in the P1' position. APQ, also
known as laeverin, is specifically expressed in human
embryo-derived extravillous trophoblasts (EVTs) that
invade the uterus during early placentation. It cleaves
the N-terminal amino acid of various peptides such as
angiotensin III, endokinin C, and kisspeptin-10, all
expressed in the placenta in large quantities. APN is a
receptor for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs are also putative Cry toxin
receptors. Cry1 proteins are pore-forming toxins that
bind to the midgut epithelial cell membrane of
susceptible insect larvae, causing extensive damage.
Several different toxins, including Cry1Aa, Cry1Ab,
Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have been shown to
bind to APNs; however, a direct role of APN in
cytotoxicity has been yet to be firmly established.
Length = 446
Score = 55.6 bits (135), Expect = 1e-08
Identities = 24/57 (42%), Positives = 34/57 (59%), Gaps = 6/57 (10%)
Query: 54 VLKLGLQKYIKKKAMGSSTQAELWAFLTNAGHEMRTLPEKMDVETIMNTWTLQTGFP 110
V + GL+ Y+KK A G++T +LW L+ A DV+ IM+TWTLQ G+P
Sbjct: 396 VFRKGLRNYLKKHAYGNATTDDLWEALSEA------SKLGKDVKEIMDTWTLQPGYP 446
>gnl|CDD|223385 COG0308, PepN, Aminopeptidase N [Amino acid transport and
metabolism].
Length = 859
Score = 37.5 bits (87), Expect = 0.012
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 58 GLQKYIKKKAMGSSTQAELWAFLTNAGHEMRTLPEKMDVETIMNTWTLQTGFPVIRVARD 117
GL Y K+ A G++T +LW L +A D+ +W Q G+PV+ V+
Sbjct: 422 GLSLYFKRHAGGNATTMDLWKALEDA--------SGKDLSAFFESWLSQAGYPVLTVSVR 473
Query: 118 YDA 120
YD
Sbjct: 474 YDD 476
>gnl|CDD|204973 pfam12587, DUF3761, Protein of unknown function (DUF3761). This
family of proteins is found in bacteria. Proteins in
this family are typically between 100 and 157 amino
acids in length.
Length = 87
Score = 30.4 bits (68), Expect = 0.35
Identities = 11/41 (26%), Positives = 13/41 (31%)
Query: 154 PAVGYHYYGAQELRRDLTTRNRPNFRVTKPSHWLRAEPNLT 194
PA +L R T RNR V P+ T
Sbjct: 19 PAFAQTAGDEADLDRHDTYRNRDGATVHAPARSKSVPAGAT 59
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 310
Score = 28.3 bits (64), Expect = 6.0
Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 27/63 (42%)
Query: 286 TIHLLNRAQLIDDAM-------NLARAGLLDY----------KI---ALDVTAYLQYETE 325
T ++ + M N ARAGL+D KI ALDV + E
Sbjct: 215 TRGMIGAEEF--ALMKPTAYFINTARAGLVDEDALIEALEEGKIGGAALDV-----FPEE 267
Query: 326 LVP 328
+P
Sbjct: 268 PLP 270
>gnl|CDD|130919 TIGR01860, VNFD, nitrogenase vanadium-iron protein, alpha chain.
This model represents the alpha chain of the
vanadium-containing component of the vanadium-iron
nitrogenase compound I. The complex also includes a
second alpha chain, two beta chains and two delta
chains. Compount I interacts with compound II also known
as the iron-protein which transfers electrons to
compound I where the catalysis occurs [Central
intermediary metabolism, Nitrogen fixation].
Length = 461
Score = 28.4 bits (63), Expect = 6.7
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 254 FNIQQTGYYRVLYDEKNWYLIIATLRNSTTYNTIHLLNRAQLIDDAMNLARA 305
+NIQ Y +K +IA + TY+ + ++RAQL + +N AR+
Sbjct: 210 YNIQGDTQVLQKYWDKMGIQVIAHFTGNGTYDDLRCMHRAQL--NVVNCARS 259
>gnl|CDD|223494 COG0417, PolB, DNA polymerase elongation subunit (family B) [DNA
replication, recombination, and repair].
Length = 792
Score = 28.2 bits (63), Expect = 7.5
Identities = 43/257 (16%), Positives = 83/257 (32%), Gaps = 37/257 (14%)
Query: 108 GFPVIRVARDYDAGSAVVKQVRGLGFTLIIIVLINTARTELKGPFTPAVGYHYYGAQELR 167
GFP++R+ D D+G +VVK V F V ++ +R E + ++
Sbjct: 7 GFPLVRIFGDTDSGKSVVKLVA--TFRPYFYVTLDNSRPE---DYVLK--ILNRRLDDVL 59
Query: 168 RDLTTRNRPNFRVTKPSHWLRAEPNLTIKQEDL-----NAESDDWIIFNIQVATRNRPNF 222
N P+ + + L+ L IF + R +
Sbjct: 60 ELEEVENVPDPYLGREVEVLKIYARDPQAVRKLREKVKRELEGVVDIFEADIPFAMR--Y 117
Query: 223 RVTK---PFHWLRAE-------PNLTIKQEDLNAESDDWIIFNIQQTGYYRVLYD-EKNW 271
+ K P W+ + +L ++ + + F+I+ D EK+
Sbjct: 118 LIDKGIRPMVWVSVDVEDIGSIHSLFLEHREDVRPPLRVLAFDIETLSEPGKFPDGEKDP 177
Query: 272 YLIIA-------TLRNSTTYNTIHLLNRAQLIDDAMNLARAGLLDYKIALDVTAYLQYET 324
++I+ L Y + + +I +A L R ++ D + Y
Sbjct: 178 IIMISYAIEAEGGLIEVFIYTSGEGFSVEVVISEAELLER--FVELIREYDPDVIVGYNG 235
Query: 325 ELVPWR---SAMQALGY 338
+ W + LG
Sbjct: 236 DNFDWPYLAERAERLGI 252
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
0.321 0.135 0.413
Gapped
Lambda K H
0.267 0.0552 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,607,905
Number of extensions: 1681268
Number of successful extensions: 1259
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1256
Number of HSP's successfully gapped: 11
Length of query: 343
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 245
Effective length of database: 6,590,910
Effective search space: 1614772950
Effective search space used: 1614772950
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 (21.9 bits)
S2: 59 (26.9 bits)