RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13490
(138 letters)
>gnl|CDD|189018 cd09839, M1_TAF2, TATA binding protein (TBP) associated factor 2.
This family includes TATA binding protein (TBP)
associated factor 2 (TAF2, TBP-associated factor
TAFII150, transcription initiation factor TFIID subunit
2, RNA polymerase II TBP-associated factor subunit B),
and has homology to the aminopeptidase N (APN)
subfamily, belonging to the M1 gluzincin family. TAF2 is
part of the TFIID multidomain subunit complex essential
for transcription of most protein-encoded genes by RNA
polymerase II. TAF2 is known to interact with the
initiator element (Inr) found at the transcription start
site of many genes, thus possibly playing a key role in
promoter binding as well as start-site selection. Image
analysis has shown TAF2 to form a complex with TAF1 and
TBP, inferring its role in promoter recognition.
Peptidases in the M1 family bind a single catalytic zinc
ion which is tetrahedrally co-ordinated by three amino
acid ligands and a water molecule that forms the
nucleophile on activation during catalysis. TAF2,
however, does not seem to contain any of the active site
residues.
Length = 507
Score = 116 bits (293), Expect = 1e-31
Identities = 48/87 (55%), Positives = 59/87 (67%), Gaps = 3/87 (3%)
Query: 21 PHNIQILGGHRIPFDIYVDPFMHEVTHFCLPPLKDLLKVSVRHVHQMFEFFEETLSNRYP 80
NI + G PF+I VDP HE+THFCLP L LK + ++H+ FEFFEE LS R+P
Sbjct: 216 AQNIGLAVG---PFEILVDPHAHEITHFCLPGLLPELKNTTSYLHEAFEFFEEYLSCRFP 272
Query: 81 YPCYKQVFVDSTVTDVTAYASMSILSS 107
+ YKQVFVD DVT+YAS+SI SS
Sbjct: 273 FSSYKQVFVDEAAEDVTSYASLSIFSS 299
>gnl|CDD|189002 cd09595, M1, Peptidase M1 family contains aminopeptidase N and
leukotriene A4 hydrolase. M1 Peptidase family includes
aminopeptidase N (APN) and leukotriene A4 hydrolase
(LTA4H). All peptidases in this family bind a single
catalytic zinc ion which is tetrahedrally co-ordinated
by three amino acid ligands and a water molecule that
forms the nucleophile on activation during catalysis.
APN 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. APN expression is
dysregulated in many inflammatory diseases and is
enhanced in numerous tumor cells, making it a lead
target in the development of anti-cancer and
anti-inflammatory drugs. LTA4H is a bifunctional enzyme,
possessing an aminopeptidase as well as an epoxide
hydrolase activity. The two activities occupy different,
but overlapping sites. The activity and physiological
relevance of the aminopeptidase in LTA4H is as yet
unknown while the epoxide hydrolase converts leukotriene
A4 (LTA4) into leukotriene B4 (LTB4), a potent
chemotaxin that is fundamental to the inflammatory
response of mammals.
Length = 407
Score = 54.4 bits (131), Expect = 1e-09
Identities = 23/103 (22%), Positives = 37/103 (35%), Gaps = 2/103 (1%)
Query: 33 PFDIYVDPFMHEVTHFCLPPLKDLLKVSVRHVHQMFEFFEETLSNRYPYPCYKQVFVDST 92
+ V + L L L +V + F F+E L YPY Y V V
Sbjct: 180 DLEYPVREQTVQGIPLHLYFLTPLAVDTVLRLQSAFLFYETDLGGPYPYSEYDVVEVPEF 239
Query: 93 VTDVTAYASMSILSSDSPVLWIRLDPEMTIIRSVVIEQPDYQW 135
+ I S S +L +D ++ +V+ + +QW
Sbjct: 240 PS-GAMENPGLIFFSQSLLL-AMIDAGDELLENVIAHELAHQW 280
>gnl|CDD|189010 cd09603, M1_APN_4, Peptidase M1 family Aminopeptidase N. This
family contains mostly bacterial and some archaeal
aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease
belonging to the M1 gluzincin family. APN 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, in higher eukaryotes,
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 predominantly
expressed on stem cells and on cells of the granulocytic
and monocytic lineages at distinct stages of
differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as 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 have also been extensively studied
as 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 = 415
Score = 36.0 bits (84), Expect = 0.003
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 45 VTHFCLPPLKDLLKVSVRHVHQMFEFFEETLSNRYPYPCYKQVFVD 90
V ++ P L + + +M +FFEE YP+ Y QV VD
Sbjct: 195 VVYYVPPGLAADARRAFARTPEMLDFFEELFGP-YPFEKYGQVVVD 239
>gnl|CDD|233857 TIGR02412, pepN_strep_liv, aminopeptidase N, Streptomyces lividans
type. This family is a subset of the members of the
zinc metallopeptidase family M1 (pfam01433), with a
single member characterized in Streptomyces lividans 66
and designated aminopeptidase N. The spectrum of
activity may differ somewhat from the aminopeptidase N
clade of E. coli and most other Proteobacteria, well
separated phylogenetically within the M1 family. The M1
family also includes leukotriene A-4
hydrolase/aminopeptidase (with a bifunctional active
site).
Length = 831
Score = 32.1 bits (73), Expect = 0.076
Identities = 12/63 (19%), Positives = 20/63 (31%), Gaps = 11/63 (17%)
Query: 28 GGHRIPFDIYVDPFMHE-VTHFCLPPLKDLLKVSVRHVHQMFEFFEETLSNRYPYPCYKQ 86
P IY + + + + ++ Q FF YP+ Y Q
Sbjct: 201 ESRSYPLGIYARRSLAQYLDA------DAIFTIT----RQGLAFFHRKFGYPYPFKKYDQ 250
Query: 87 VFV 89
+FV
Sbjct: 251 IFV 253
>gnl|CDD|216501 pfam01433, Peptidase_M1, Peptidase family M1. Members of this
family are aminopeptidases. The members differ widely in
specificity, hydrolysing acidic, basic or neutral
N-terminal residues. This family includes leukotriene-A4
hydrolase, this enzyme also has an aminopeptidase
activity.
Length = 390
Score = 29.2 bits (66), Expect = 0.61
Identities = 13/59 (22%), Positives = 19/59 (32%), Gaps = 11/59 (18%)
Query: 33 PFDIYVDPFMHEVTHFCLPPLKDLLKVSVRHVHQMFEFFEETLSNRYPYPCYKQVFVDS 91
P +Y P + L ++ EFFE+ YP P QV +
Sbjct: 214 PVRVYARPGAINAGQYAL-----------EVTQKLLEFFEDYFGFPYPLPKLDQVALPD 261
>gnl|CDD|227222 COG4885, COG4885, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 312
Score = 28.8 bits (64), Expect = 0.86
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 7/47 (14%)
Query: 93 VTDVTAYASMSILSSDSPVL----WIRLD---PEMTIIRSVVIEQPD 132
V A + + +DS VL W + P+ T++ + E PD
Sbjct: 173 VKSYDVVARIKVRQADSNVLAGESWKNVTLQKPKTTVVSNAEFEVPD 219
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 27.3 bits (60), Expect = 2.8
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 4/38 (10%)
Query: 5 KANPKFQHSD-HQVCFFPHNIQILGGHRIPFDIYVDPF 41
KA+P+F S +Q+ F +++ +IPF I V+PF
Sbjct: 649 KADPRFLKSTLYQIPLFSETLKL---SQIPFGIIVNPF 683
>gnl|CDD|223385 COG0308, PepN, Aminopeptidase N [Amino acid transport and
metabolism].
Length = 859
Score = 27.4 bits (61), Expect = 3.1
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 12/61 (19%)
Query: 31 RIPFDIYVDPFMHEVTHFCLPPLKDLLKVSVRHVHQMFEFFEETLSNRYPYPCYKQVFVD 90
+P +IYV P + D K ++ + EF+EE Y P V V
Sbjct: 225 DVPLEIYVPPGV-----------LDRAKYALDETKRSIEFYEEYFGLPYALP-IDIVAVP 272
Query: 91 S 91
Sbjct: 273 D 273
>gnl|CDD|189009 cd09602, M1_APN_3, Peptidase M1 family containing Aminopeptidase N.
This family contains bacterial and eukaryotic
aminopeptidase N (APN; CD13; Alanyl aminopeptidase; EC
3.4.11.2), a Type II integral membrane protease
belonging to the M1 gluzincin family. APN 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, in higher eukaryotes,
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 predominantly
expressed on stem cells and on cells of the granulocytic
and monocytic lineages at distinct stages of
differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as 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 have also been extensively studied
as 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 = 438
Score = 27.2 bits (61), Expect = 3.6
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 68 FEFFEETLSNRYPYPCYKQVFV 89
+FFEE YP+ Y QVFV
Sbjct: 227 LDFFEEYFGIPYPFGKYDQVFV 248
>gnl|CDD|225755 COG3214, COG3214, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 400
Score = 26.6 bits (59), Expect = 5.1
Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 14/69 (20%)
Query: 4 LKANPKFQHSDHQVCFFPHNIQILGGHRI--PFDI----YVDPFMHEVTHFCLPPLKDLL 57
L+ F++ H+ F P L HR+ Y + E +
Sbjct: 75 LRRGELFEYWAHEASFLPRETFPLIRHRMLRAEKGGRWKYRAAWGEE--------HAAEI 126
Query: 58 KVSVRHVHQ 66
+ +RH+ +
Sbjct: 127 EQLLRHIAE 135
>gnl|CDD|178532 PLN02946, PLN02946, cysteine-tRNA ligase.
Length = 557
Score = 26.0 bits (57), Expect = 7.2
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 37 YVDPFMHEVTHF-CLPPLKDLLKVSVRHVHQMFEFFEETLSNRYPY 81
Y + F+ ++ + CLPP + +VS H+ Q+ + ++ L N Y
Sbjct: 150 YCEEFLSDMAYLHCLPPSVEP-RVS-DHIPQIIDMIKQILDNGCAY 193
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
0.327 0.140 0.457
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,070,320
Number of extensions: 602966
Number of successful extensions: 677
Number of sequences better than 10.0: 1
Number of HSP's gapped: 676
Number of HSP's successfully gapped: 19
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (24.6 bits)