RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2936
(174 letters)
>gnl|CDD|201647 pfam01187, MIF, Macrophage migration inhibitory factor (MIF).
Length = 114
Score = 126 bits (318), Expect = 3e-38
Identities = 53/113 (46%), Positives = 73/113 (64%)
Query: 2 PVFRIETNIPKEKIPANFGKETGALVAKTLGKPENYVAVIVVPDVNLVFGGSDAPAAIAS 61
P+F ++TN+P +P K +AK LGKPE +AV +VP +VFGGS P A+ S
Sbjct: 1 PMFEVDTNLPANSVPDGLEKRLTQQLAKALGKPEQRIAVHIVPGQAMVFGGSTEPCAVCS 60
Query: 62 LMSIGKLGTAENKKHSAVLFPHIEKTLGIPKDRMYISYIDSSTDVVGYNGTTF 114
L SIGK+G +N+ HSA+L + K L +PKDR+YI++ D VG+NGTTF
Sbjct: 61 LKSIGKVGAEQNRSHSALLCKFLTKELSLPKDRIYINFFDLEAANVGFNGTTF 113
>gnl|CDD|240401 PTZ00397, PTZ00397, macrophage migration inhibition factor-like
protein; Provisional.
Length = 116
Score = 64.5 bits (157), Expect = 6e-14
Identities = 30/115 (26%), Positives = 52/115 (45%), Gaps = 1/115 (0%)
Query: 1 MPVFRIETNIPKEKIPAN-FGKETGALVAKTLGKPENYVAVIVVPDVNLVFGGSDAPAAI 59
MP ++ TN+ A+ + +A LGKP +Y+ ++ FGGS
Sbjct: 1 MPCCQVSTNVNATDDQADAALSDIENAIADVLGKPLSYIMSGYDYQKHMRFGGSHDGCCF 60
Query: 60 ASLMSIGKLGTAENKKHSAVLFPHIEKTLGIPKDRMYISYIDSSTDVVGYNGTTF 114
+ SIG + + N +A + + L + +R+YI + D S +NG+TF
Sbjct: 61 VRVTSIGGISRSNNSSIAAAITKILASHLKVKSERVYIEFKDCSAQNWAFNGSTF 115
>gnl|CDD|185629 PTZ00450, PTZ00450, macrophage migration inhibitory factor-like
protein; Provisional.
Length = 113
Score = 60.4 bits (146), Expect = 2e-12
Identities = 34/115 (29%), Positives = 56/115 (48%), Gaps = 3/115 (2%)
Query: 1 MPVFRIETNIP-KEKIPANFGKETGALVAKTLGKPENYVAVIVVPDVNLVFGGSDAPAAI 59
MP + ++ ++ AN + + + LGKPE++V + F GS APAA
Sbjct: 1 MPFLQTIVSVSLDDQKRANLSQAYRMICREELGKPEDFVMTAFSDSTPMSFQGSTAPAAY 60
Query: 60 ASLMSIGKLGTAENKKHSAVLFPHIEKTLGIPKDRMYISYIDSSTDVVGYNGTTF 114
+ + G+ ++ K + + I K GIP +R+Y+ Y ST G+NGT F
Sbjct: 61 VRVEAWGEYAPSKPKMMTPRITAAITKECGIPAERIYVFYY--STKHCGWNGTNF 113
>gnl|CDD|224853 COG1942, COG1942, Uncharacterized protein, 4-oxalocrotonate
tautomerase homolog [General function prediction only].
Length = 69
Score = 29.5 bits (67), Expect = 0.18
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 1 MPVFRIETNIPK--EKIPANFGKETGALVAKTLGKPENYVAVIV--VPDVNLVFGG 52
MP I+ + E+ A E + +TLGK + + VI+ VP N GG
Sbjct: 1 MPFVNIKLFEGRLDEEQKAELAAEVTEVTVETLGKDPSAIHVIIEEVPPENWGVGG 56
>gnl|CDD|111033 pfam02091, tRNA-synt_2e, Glycyl-tRNA synthetase alpha subunit.
Length = 284
Score = 28.9 bits (65), Expect = 1.2
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 84 IEKTLGIPKDRMYISYIDSSTDVVGYNGTTFHEIFGGPVLNKRAMESIVLEFKNV 138
E T G+ + MY+ +DS D+V +G T+ +IF N+ + E NV
Sbjct: 153 GEITYGLERLAMYLQKVDSVYDLVWADGLTYGDIF---QQNEVEQSTYNFETANV 204
>gnl|CDD|219542 pfam07732, Cu-oxidase_3, Multicopper oxidase. This entry contains
many divergent copper oxidase-like domains that are not
recognised by the pfam00394 model.
Length = 119
Score = 28.0 bits (63), Expect = 1.3
Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 94 RMYISYIDSSTDVVGYNGTTFHEIFGGPVLNKRAMESIVLEFKNVLIKNQSTT 146
++ + + V+G NG F GP + R +++V+ N L ++ TT
Sbjct: 4 YGTVTPLGGTRQVIGVNGQ-----FPGPTIRVREGDTVVVNVTNNL--DEPTT 49
>gnl|CDD|193496 cd03874, M28_PMSA_TfR_like, M28 Zn-peptidase Transferrin
Receptor-like family. Peptidase M28 family; Transferrin
Receptor (TfR) and prostate-specific membrane antigen
(PSMA, also called glutamate carboxypeptidase or GCP-II)
subfamily. TfR and PSMA are homodimeric type II
transmembrane proteins containing three distinct
domains: protease-like, apical or protease-associated
(PA) and helical domains. The protease-like domain is a
large extracellular portion (ectodomain). In TfR, it
contains a binding site for the transferrin molecule and
has 28% identity to membrane glutamate carboxypeptidase
II (mGCP-II or PSMA). The PA domain is inserted between
the first and second strands of the central beta sheet
in the protease-like domain. TfR1 is widely expressed,
and is a key player in the uptake of iron-loaded
transferrin (Tf) into cells. The TfR1 homodimer binds
two molecules of Tf and the complex is then
internalized. TfR1 may also participate in cell growth
and proliferation. TfR2 binds Tf but with a
significantly lower affinity than TfR1. It is expressed
chiefly in hepatocytes, hematopoietic cells, and
duodenal crypt cells; its expression overlaps with that
of hereditary hemochromatosis protein (HFE). TfR2 is
involved in iron homeostasis; in humans, mutations in
TfR2 are associated with a form of hemochromatosis
(HFE3). PSMA is over-expressed predominantly in prostate
cancer (PCa) as well as neovasculature of most solid
tumors, but not in the vasculature of normal tissues.
PSMA is considered a biomarker for PCa and possibly for
use as an imaging and therapeutic target. The
extracellular domain of PSMA possesses two unique
enzymatic functions: N-acetylated, alpha-linked acidic
dipeptidase (NAALADase) which cleaves terminal glutamate
from the neurodipeptide N-acetyl-aspartyl-glutamate
(NAAG), and folate hydrolase (FOLH) which cleaves the
terminal glutamates from gamma-linked polyglutamates
(carboxypeptidase). A mutation in this gene may be
associated with impaired intestinal absorption of
dietary folates, resulting in low blood folate levels
and consequent hyperhomocysteinemia. Expression of this
protein in the brain may be involved in a number of
pathological conditions associated with glutamate
excitotoxicity. This gene likely arose from a
duplication event of a nearby chromosomal region.
Alternative splicing gives rise to multiple transcript
variants. While related in sequence to peptidase M28
GCP-II, TfR lacks the metal ion coordination centers and
protease activity.
Length = 279
Score = 28.4 bits (64), Expect = 2.0
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 83 HIEKTLGIPKDRMYISYIDSSTDVVGYNGTTFHEIFGGPVLNK---RAMESI 131
+E +D Y +YI+ V G+ F + P+L RA++ +
Sbjct: 136 LVEDNKDSLRDEAY-AYINLDQAVS---GSEFR-VDAHPLLKSLLLRALKRV 182
>gnl|CDD|225565 COG3021, COG3021, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 309
Score = 28.2 bits (63), Expect = 2.1
Identities = 8/40 (20%), Positives = 12/40 (30%), Gaps = 3/40 (7%)
Query: 78 AVLFPHIEKTLGIPKDRMYISYIDSS---TDVVGYNGTTF 114
E L +PK + +Y VV + F
Sbjct: 161 CCPLTEAEPWLRLPKSALATAYPLPDGTELTVVALHAVNF 200
>gnl|CDD|217210 pfam02738, Ald_Xan_dh_C2, Molybdopterin-binding domain of aldehyde
dehydrogenase.
Length = 543
Score = 27.2 bits (61), Expect = 4.6
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 7/43 (16%)
Query: 26 LVAKTLGKPENYVAVIVVPDVNLVFGGS------DAPAAIASL 62
+VA+ LG PE+ V VI VP V FG AA+A+L
Sbjct: 77 MVARVLGIPEHKVRVI-VPRVGGGFGKKVFSLPLAVIAALAAL 118
>gnl|CDD|201747 pfam01361, Tautomerase, Tautomerase enzyme. This family includes
the enzyme 4-oxalocrotonate tautomerase that catalyzes
the ketonisation of 2-hydroxymuconate to
2-oxo-3-hexenedioate.
Length = 60
Score = 25.3 bits (56), Expect = 4.7
Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 2/44 (4%)
Query: 17 ANFGKETGALVAKTLGKPENYVAVIV--VPDVNLVFGGSDAPAA 58
A + + + LG P + V++ VP N GG
Sbjct: 17 AALIRRVTEAIVEALGAPREAIVVVIEEVPPENWGVGGESLGDR 60
>gnl|CDD|238375 cd00733, GlyRS_alpha_core, Class II Glycyl-tRNA synthetase (GlyRS)
alpha subunit core catalytic domain. GlyRS functions as
a homodimer in eukaryotes, archaea and some bacteria and
as a heterotetramer in the remainder of prokaryotes and
in arabidopsis. It is responsible for the attachment of
glycine to the 3' OH group of ribose of the appropriate
tRNA. This domain is primarily responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. This alignment contains only
sequences from the GlyRS form which heterotetramerizes.
The homodimer form of GlyRS is in a different family of
class II aaRS. Class II assignment is based upon
structure and the presence of three characteristic
sequence motifs.
Length = 279
Score = 26.5 bits (59), Expect = 7.2
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 84 IEKTLGIPKDRMYISYIDSSTDVVGYNGTTFHEIFGGPVLNKRAMESIVLEFKNV 138
+E T G+ + MY+ +D+ D+ T+ ++F + N+ E+ NV
Sbjct: 154 VEITYGLERIAMYLQGVDNVYDIEWNKKITYGDVF---LQNEIEQSVYNFEYANV 205
>gnl|CDD|223073 PHA03394, lef-8, DNA-directed RNA polymerase subunit beta-like
protein; Provisional.
Length = 865
Score = 26.8 bits (60), Expect = 8.0
Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 73 NKKHSAVLFPHIEKTLGIPKDRMYISY-IDSSTDVVGYNGTTFHEIFGGPVLNKRAMESI 131
+K S L I++ + + I+Y IDS ++ + Y + E+ P+L K
Sbjct: 191 DKGQSIQLVDQIKRIMSVD-----INYSIDSLSNKIIYKHSYLLELTYKPLLKKYQNMLA 245
Query: 132 VLEFKNVLIKNQSTTTVAF 150
IK + T+ F
Sbjct: 246 KDPDAQSAIKRKKNQTILF 264
>gnl|CDD|173776 cd01026, TOPRIM_OLD, TOPRIM_OLD: topoisomerase-primase (TOPRIM)
nucleotidyl transferase/hydrolase domain of the type
found in bacterial and archaeal nucleases of the OLD
(overcome lysogenization defect) family. The
bacteriophage P2 OLD protein, which has DNase as well as
RNase activity, consists of an N-terminal ABC-type
ATPase domain and a C-terminal Toprim domain; the
nuclease activity of OLD is stimulated by ATP, though
the ATPase activity is not DNA-dependent. Functional
details on OLD are scant and further experimentation is
required to define the relationship between the ATPase
and Toprim nuclease domains. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). The conserved glutamate may act as a general
acid in strand cleavage by nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 97
Score = 25.3 bits (56), Expect = 9.0
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 9/52 (17%)
Query: 69 GTAENKKHSAVLFPHIEKTLGIPKDRMYISYIDSSTDVVGYNGTTFHEIFGG 120
G +E +L P + K LG+ D IS I V G N F ++
Sbjct: 11 GDSE-----EILLPALAKKLGLDLDEAGISII----PVGGKNFKPFIKLLNA 53
>gnl|CDD|223214 COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid
transport and metabolism].
Length = 334
Score = 26.4 bits (59), Expect = 9.1
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 20 GKETGALVAKTLGKPENYVAVIVVPDVNLVF--GGSDAPAAIA 60
GK+ K++G PE+ V DV++VF G +
Sbjct: 41 GKKYIEFGGKSIGVPEDAADEFVFSDVDIVFFAAGGSVSKEVE 83
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
0.318 0.137 0.390
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,921,010
Number of extensions: 825467
Number of successful extensions: 686
Number of sequences better than 10.0: 1
Number of HSP's gapped: 686
Number of HSP's successfully gapped: 24
Length of query: 174
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 84
Effective length of database: 6,945,742
Effective search space: 583442328
Effective search space used: 583442328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.3 bits)