RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3351
(276 letters)
>gnl|CDD|214514 smart00094, TR_FER, Transferrin.
Length = 332
Score = 141 bits (358), Expect = 3e-40
Identities = 78/280 (27%), Positives = 110/280 (39%), Gaps = 81/280 (28%)
Query: 3 KNSLPDLTHISHLRGKKACFAGVGTQAGWVIPVDVLIRNGGMEVIDCNNHVKSVINYFGP 62
K T + LRGKK+C GVG AGW IP+ +L + +C K+V +F
Sbjct: 93 KKGSAIFT-WNQLRGKKSCHTGVGRTAGWNIPMGLLYNKLVIRPPNCPFE-KAVSKFFSA 150
Query: 63 SCAVNALINKYNPIGDNSDRLCELCIGRVPGEKCTTADPYAGFEGAFRCLVDKGEVAFLK 122
SCA A D + LC LC G +C E
Sbjct: 151 SCAPGA------DKPDPNSNLCALCA------------------GDNKCACSSHE----- 181
Query: 123 HTTVQEMIEGRIDACKYSFLGKELKMSFFYFLLLQYSGGLIEGTGAFRCLVD-KGEVAFL 181
Y G +GAFRCL + G+VAF+
Sbjct: 182 ----------------------------------PYYGY----SGAFRCLAEGAGDVAFV 203
Query: 182 KHTTVQEMIEGRID---AYGLTKENFELLCTDGTRQPVDNYQSCNWGQVPSNAVMTTSAK 238
KH+TV E +G+ A L ++++ELLC DGTR+PV Y++C+ +VPS+AV+ K
Sbjct: 204 KHSTVFENTDGKNGADWAKNLKRDDYELLCLDGTRKPVTEYKNCHLARVPSHAVVARKDK 263
Query: 239 STQIRRYYQQFLIKTVQLFGGPVPPQ----RTQGKNVILF 274
+ L+ Q FG P + +LF
Sbjct: 264 KEDVI----WELLNQQQKFGKDKPSLFQLFGSPTGKDLLF 299
>gnl|CDD|215903 pfam00405, Transferrin, Transferrin.
Length = 328
Score = 92.1 bits (229), Expect = 1e-21
Identities = 48/134 (35%), Positives = 70/134 (52%), Gaps = 10/134 (7%)
Query: 11 HISHLRGKKACFAGVGTQAGWVIPVDVLIRNGGMEVIDCNNHVKSVINYFGPSCAVNALI 70
++ L+GKK+C G+G AGW IP+ +L R I K+V +F SC A
Sbjct: 100 QLNQLQGKKSCHTGLGRSAGWNIPIGLL-RPQLPWAIPREPLEKAVSKFFSASCVPGA-- 156
Query: 71 NKYNPIGDNSDRLCELCIGRVPGE-KCTTADPYAGFEGAFRCLVD-KGEVAFLKHTTVQE 128
+LC+LC G + C+ +PY G+ GAF+CL D G+VAF+KH+TV E
Sbjct: 157 -----DEGAFPKLCQLCAGDGENKCACSNNEPYFGYSGAFKCLKDGAGDVAFVKHSTVFE 211
Query: 129 MIEGRIDACKYSFL 142
+ + D +Y L
Sbjct: 212 NLPDKADRDQYELL 225
Score = 91.0 bits (226), Expect = 3e-21
Identities = 42/104 (40%), Positives = 57/104 (54%), Gaps = 15/104 (14%)
Query: 167 GAFRCLVD-KGEVAFLKHTTVQEMIEGRIDAYGLTKENFELLCTDGTRQPVDNYQSCNWG 225
GAF+CL D G+VAF+KH+TV E + + D ++ +ELLC D TR+PVD Y+ C+
Sbjct: 189 GAFKCLKDGAGDVAFVKHSTVFENLPDKAD-----RDQYELLCPDNTRKPVDEYKDCHLA 243
Query: 226 QVPSNAVMTTS--AKSTQIRRYYQQ----FLIKTV---QLFGGP 260
+VPS+AV+ S K I Q F QLF P
Sbjct: 244 RVPSHAVVARSVDGKEDLIWELLNQAQEKFGKDKSSDFQLFSSP 287
>gnl|CDD|225762 COG3221, PhnD, ABC-type phosphate/phosphonate transport system,
periplasmic component [Inorganic ion transport and
metabolism].
Length = 299
Score = 28.1 bits (63), Expect = 4.4
Identities = 11/53 (20%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 1 MKKNSLPDLTHISHLRGKKACFAGVGTQAGWVIPVDVLIRNGGMEVIDCNNHV 53
++ +S + + L+GK+ F + +G++ P+ L + GG++ V
Sbjct: 130 VRADS--PIKSLEDLKGKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGEV 180
>gnl|CDD|238929 cd01967, Nitrogenase_MoFe_alpha_like, Nitrogenase_MoFe_alpha_like:
Nitrogenase MoFe protein, alpha subunit_like. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. Three genetically distinct
types of nitrogenase systems are known to exist: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase). These
nitrogenase systems consist of component 1 (MoFe
protein, VFe protein or, FeFe protein respectively) and,
component 2 (Fe protein). This group contains the alpha
subunit of component 1 of all three different forms. The
most widespread and best characterized of these systems
is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer,
the alternative nitrogenases are alpha2beta2delta2
hexamers having alpha and beta subunits similar to the
alpha and beta subunits of MoFe. The role of the delta
subunit is unknown. For MoFe, each alphabeta pair of
subunits contains one P-cluster (located at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein is a homodimer which contains, a
single [4Fe-4S] cluster from which electrons are
transferred to the P-cluster of the MoFe and in turn,
to FeMoCo the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the Mo-
nitrogenase in that it produces free hydrazine, as a
minor product during dinitrogen reduction and, ethane
as a minor product during acetylene reduction.
Length = 406
Score = 28.3 bits (64), Expect = 5.0
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 14 HLRGKKACFAGVGTQAGWVIPVDVLIRNGGMEVIDC 49
L+GKK G ++ VI +R GMEV+
Sbjct: 283 RLKGKKVIIYTGGARSWHVI---AALRELGMEVVAA 315
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 28.3 bits (64), Expect = 5.6
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 10/35 (28%)
Query: 103 AGFEGAFRCLVDKGEVAFLKHTTVQEMIEGRIDAC 137
GF+ R L TTV+E+++ +DAC
Sbjct: 28 LGFDNPARALY----------TTVKELVDNSLDAC 52
>gnl|CDD|215485 PLN02895, PLN02895, phosphoacetylglucosamine mutase.
Length = 562
Score = 28.1 bits (63), Expect = 6.4
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 93 GEKCTTADPYAGFEGAFRCLVD 114
G K T +D + +FR L+D
Sbjct: 179 GMKATESDYFEQLSSSFRALLD 200
>gnl|CDD|132761 cd07076, NR_LBD_GR, Ligand binding domain of the glucocorticoid
receptor, a member of the nuclear receptor superfamily.
The ligand binding domain of the glucocorticoid receptor
(GR): GR is a ligand-activated transcription factor
belonging to the nuclear receptor superfamily. It binds
with high affinity to cortisol and other
glucocorticoids. GR is expressed in almost every cell in
the body and regulates genes controlling a wide variety
of processes including the development, metabolism, and
immune response of the organism. In the absence of
hormone, the glucocorticoid receptor (GR) is complexes
with a variety of heat shock proteins in the cytosol.
The binding of the glucocorticoids results in release of
the heat shock proteins and transforms it to its active
state. One mechanism of action of GR is by direct
activation of gene transcription. The activated form of
GR forms dimers, translocates into the nucleus, and
binds to specific hormone responsive elements,
activating gene transcription. GR can also function as a
repressor of other gene transcription activators, such
as NF-kappaB and AF-1 by directly binding to them, and
bloc king the expression of their activated genes. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, GR has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD). The LBD also
functions for dimerization and chaperone protein
association.
Length = 247
Score = 27.2 bits (60), Expect = 8.6
Identities = 7/26 (26%), Positives = 16/26 (61%)
Query: 125 TVQEMIEGRIDACKYSFLGKELKMSF 150
++ E++E ++ C +FL K + + F
Sbjct: 194 SMHEVVENLLNFCFQTFLDKTMSIEF 219
>gnl|CDD|234225 TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter
like protein HpnN. The genomes containing members of
this family share the machinery for the biosynthesis of
hopanoid lipids. Furthermore, the genes of this family
are usually located proximal to other components of this
biological process. The proteins appear to be related to
the RND family of export proteins, particularly the
hydrophobe/amphiphile efflux-3 (HAE3) family represented
by TIGR00921.
Length = 862
Score = 27.7 bits (62), Expect = 9.1
Identities = 13/29 (44%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 149 SFFYFLLLQYSG----GLIEGTGAFRCLV 173
FF FL Y G G+I GTG F L
Sbjct: 382 GFFAFLPTDYKGVSELGIIAGTGMFIALF 410
>gnl|CDD|238193 cd00316, Oxidoreductase_nitrogenase, The nitrogenase enzyme system
catalyzes the ATP-dependent reduction of dinitrogen to
ammonia. This group contains both alpha and beta
subunits of component 1 of the three known genetically
distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase) and, both
subunits of Protochlorophyllide (Pchlide) reductase and
chlorophyllide (chlide) reductase. The nitrogenase
systems consist of component 1 (MoFe protein, VFe
protein or, FeFe protein respectively) and, component 2
(Fe protein). The most widespread and best characterized
nitrogenase is the Mo-nitrogenase. MoFe is an
alpha2beta2 tetramer, the alternative nitrogenases are
alpha2beta2delta2 hexamers whose alpha and beta subunits
are similar to the alpha and beta subunits of MoFe. For
MoFe, each alphabeta pair contains one P-cluster (at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein contains a single [4Fe-4S]
cluster from which, electrons are transferred to the
P-cluster of the MoFe and in turn, to FeMoCo at the site
of substrate reduction. The V-nitrogenase requires an
iron-vanadium cofactor (FeVco), the iron
only-nitrogenase an iron only cofactor (FeFeco). These
cofactors are analogous to the FeMoco. The V-nitrogenase
has P clusters identical to those of MoFe. Pchlide
reductase and chlide reductase participate in the
Mg-branch of the tetrapyrrole biosynthetic pathway.
Pchlide reductase catalyzes the reduction of the D-ring
of Pchlide during the synthesis of chlorophylls (Chl)
and bacteriochlorophylls (BChl). Chlide-a reductase
catalyzes the reduction of the B-ring of Chlide-a during
the synthesis of BChl-a. The Pchlide reductase NB
complex is a an N2B2 heterotetramer resembling
nitrogenase FeMo, N and B proteins are homologous to the
FeMo alpha and beta subunits respectively. The NB
complex may serve as a catalytic site for Pchlide
reduction and, the ZY complex as a site of chlide
reduction, similar to MoFe for nitrogen reduction.
Length = 399
Score = 27.2 bits (61), Expect = 9.7
Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 3/36 (8%)
Query: 14 HLRGKKACFAGVGTQAGWVIPVDVLIRNGGMEVIDC 49
+L GKK G G + + GMEV+
Sbjct: 276 YLGGKKVAIFGDGDLLLALA---RFLLELGMEVVAA 308
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
0.323 0.140 0.434
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,922,873
Number of extensions: 1287518
Number of successful extensions: 895
Number of sequences better than 10.0: 1
Number of HSP's gapped: 884
Number of HSP's successfully gapped: 16
Length of query: 276
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 180
Effective length of database: 6,679,618
Effective search space: 1202331240
Effective search space used: 1202331240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.1 bits)