RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3631
(184 letters)
>gnl|CDD|201070 pfam00191, Annexin, Annexin. This family of annexins also includes
giardin that has been shown to function as an annexin.
Length = 66
Score = 87.1 bits (217), Expect = 3e-23
Identities = 39/97 (40%), Positives = 50/97 (51%), Gaps = 32/97 (32%)
Query: 39 DAEVLRAAMKGFGTDEQSIIDVLAKRSNQQRQEIADAFKTLFGKEESFDPAVTTKLLYHN 98
DAE+LRAAMKG GTDE ++I +LA RSN Q Q I +A+K L+GK
Sbjct: 2 DAELLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKKLYGK---------------- 45
Query: 99 VIRHLFQCSIHCLPHQDLIDDLKSELGGNFEDAIVAL 135
DL D+KSE G+FE ++AL
Sbjct: 46 ----------------DLEKDIKSETSGDFEKLLLAL 66
Score = 52.4 bits (127), Expect = 7e-10
Identities = 17/39 (43%), Positives = 26/39 (66%)
Query: 144 AKELHDAMSGVGTDEEAIVEILSTLSNYGIRTIAEVYEN 182
A+ L AM G+GTDE+ ++ IL+T SN ++ I E Y+
Sbjct: 3 AELLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKK 41
>gnl|CDD|197661 smart00335, ANX, Annexin repeats.
Length = 53
Score = 72.8 bits (180), Expect = 9e-18
Identities = 29/85 (34%), Positives = 40/85 (47%), Gaps = 32/85 (37%)
Query: 51 GTDEQSIIDVLAKRSNQQRQEIADAFKTLFGKEESFDPAVTTKLLYHNVIRHLFQCSIHC 110
GTDE+++I++LA RSN Q Q I A+K +GK
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGK---------------------------- 32
Query: 111 LPHQDLIDDLKSELGGNFEDAIVAL 135
DL DD+KSE G+FE ++AL
Sbjct: 33 ----DLEDDIKSETSGDFEKLLLAL 53
Score = 36.6 bits (86), Expect = 3e-04
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 155 GTDEEAIVEILSTLSNYGIRTIAEVYEN 182
GTDE+ ++EIL++ SN ++ I + Y+
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKK 28
>gnl|CDD|221138 pfam11573, Med23, Mediator complex subunit 23. Med23 is one of the
subunits of the Tail portion of the Mediator complex that
regulates RNA polymerase II activity. Med23 is required
for heat-shock-specific gene expression, and has been
shown to mediate transcriptional activation of E1A in
mice.
Length = 1341
Score = 29.1 bits (65), Expect = 1.6
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 127 NFEDAIVALMTPLPELYAKELHDAMSGV 154
N+ +AI +M LPE Y K LHD + V
Sbjct: 1174 NWFNAIGLIMAALPEAYWKVLHDRIIEV 1201
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 29.2 bits (65), Expect = 1.6
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 2/76 (2%)
Query: 4 QQYCRFDSSLGSTYRCLFQQCLPTVVPADPFDPNGDAEVLRAAMKGFGTDEQSIIDVLAK 63
+ CRF + S + + D +P E + GT+E +++D +++
Sbjct: 946 DEVCRFVDTENSRVYGMLVAGKGRIY--DGTEPRSRIEAGPICEEERGTEESALLDEISR 1003
Query: 64 RSNQQRQEIADAFKTL 79
+D F+ L
Sbjct: 1004 TILVDEYLNSDEFRML 1019
>gnl|CDD|235076 PRK02842, PRK02842, light-independent protochlorophyllide reductase
subunit N; Provisional.
Length = 427
Score = 28.3 bits (64), Expect = 2.2
Identities = 14/50 (28%), Positives = 20/50 (40%)
Query: 33 PFDPNGDAEVLRAAMKGFGTDEQSIIDVLAKRSNQQRQEIADAFKTLFGK 82
P P G L AA FG D + + A + R+ + + L GK
Sbjct: 242 PLGPEGTRAWLEAAAAAFGIDPDGLEEREAPAWERARKALEPYRELLRGK 291
>gnl|CDD|176503 cd08560, GDPD_EcGlpQ_like_1, Glycerophosphodiester
phosphodiesterase domain similar to Escherichia coli
periplasmic phosphodiesterase (GlpQ) include
uncharacterized proteins. This subfamily corresponds to
the glycerophosphodiester phosphodiesterase domain
(GDPD) present in a group of uncharacterized
glycerophosphodiester phosphodiesterases (GP-GDE, EC
3.1.4.46) and their hypothetical homologs. Members in
this subfamily show high sequence similarity to
Escherichia coli periplasmic phosphodiesterase GlpQ,
which catalyzes the Ca2+-dependent degradation of
periplasmic glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols.
Length = 356
Score = 28.2 bits (63), Expect = 2.4
Identities = 23/95 (24%), Positives = 38/95 (40%), Gaps = 12/95 (12%)
Query: 76 FKTLFGKEESFDPAVTTKLLYHNVI----RHLFQCSIHCLPHQDLIDDLKSELGGNFEDA 131
FK+L GK ++ +P+ TT Y N L+ + H++ I L LG
Sbjct: 112 FKSLCGKMDASNPSATTPEEYQNGTPDWRTDLYATCGTLMTHKESI-ALFKSLGVKMTPE 170
Query: 132 IVALMTPLP-------ELYAKELHDAMSGVGTDEE 159
+ + P+P E YA+++ D G
Sbjct: 171 LKSPSVPMPFDGNYTQEDYAQQMIDEYKEAGVPPS 205
>gnl|CDD|153165 cd04893, ACT_GcvR_1, ACT domains that comprise the Glycine
Cleavage System Transcriptional Repressor (GcvR)
protein, and other related domains. This CD includes
the first of the two ACT domains that comprise the
Glycine Cleavage System Transcriptional Repressor
(GcvR) protein, and other related domains. The glycine
cleavage enzyme system in Escherichia coli provides
one-carbon units for cellular methylation reactions.
This enzyme system, encoded by the gcvTHP operon and
lpd gene, catalyzes the cleavage of glycine into CO2 +
NH3 and transfers a one-carbon unit to
tetrahydrofolate, producing
5,10-methylenetetrahydrofolate. The gcvTHP operon is
activated by the GcvA protein in response to glycine
and repressed by a GcvA/GcvR interaction in the absence
of glycine. It has been proposed that the co-activator
glycine acts through a mechanism of de-repression by
binding to GcvR and preventing GcvR from interacting
with GcvA to block GcvA's activator function. Evidence
also suggests that GcvR interacts directly with GcvA
rather than binding to DNA to cause repression. Members
of this CD belong to the superfamily of ACT regulatory
domains.
Length = 77
Score = 26.5 bits (59), Expect = 2.6
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 51 GTDEQSIIDVLAKRSNQQRQEIADAFKTLFGKEESF 86
GTD I++ L + ++ I D+ + G E +
Sbjct: 8 GTDRPGILNELTRAVSESGCNILDSRMAILGTEFAL 43
>gnl|CDD|215550 PLN03049, PLN03049, pyridoxine (pyridoxamine) 5'-phosphate oxidase;
Provisional.
Length = 462
Score = 28.3 bits (63), Expect = 2.7
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 88 PAVTTKLLYHNVIRHLFQCSIHCLPHQDLIDDLKSE 123
P T K LY+ ++ L S+ L +DL DL S+
Sbjct: 94 PKRTDKPLYNGLVTQLESLSVPFLSVEDLPSDLSSQ 129
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 28.4 bits (63), Expect = 3.0
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 37 NGDAEVLRAAMKGFGTDEQSIID-----VLAKRSNQQRQEIADAFKTLFGKEESFDP 88
+ D +LR+ K DE++++ VL KR +Q ++ + + K ++ DP
Sbjct: 256 HFDVRILRSYTKENKKDEKNVVSGIRSSVLLKRKSQCLRKDSYVYSNHQKKAKTGDP 312
>gnl|CDD|132927 cd07016, S14_ClpP_1, Caseinolytic protease (ClpP) is an
ATP-dependent, highly conserved serine protease. Clp
protease (caseinolytic protease; ClpP; Peptidase S14) is
a highly conserved serine protease present throughout in
bacteria and eukaryota, but seems to be absent in
archaea, mollicutes and some fungi. This subfamily only
contains bacterial sequences. Clp proteases are involved
in a number of cellular processes such as degradation of
misfolded proteins, regulation of short-lived proteins
and housekeeping removal of dysfunctional proteins. They
are also implicated in the control of cell growth,
targeting DNA-binding protein from starved cells. ClpP
has also been linked to the tight regulation of
virulence genes in the pathogens Listeria monocytogenes
and Salmonella typhimurium. This enzyme belong to the
family of ATP-dependent proteases; the functional Clp
protease is comprised of two components: a proteolytic
component and one of several regulatory ATPase
components, both of which are required for effective
levels of protease activity in the presence of ATP,
although the proteolytic subunit alone does possess some
catalytic activity. Active site consists of the triad
Ser, His and Asp; some members have lost all of these
active site residues and are therefore inactive, while
others may have one or two large insertions. ClpP seems
to prefer hydrophobic or non-polar residues at P1 or P1'
positions in its substrate. The protease exists as a
tetradecamer made up of two heptameric rings stacked
back-to-back such that the catalytic triad of each
subunit is located at the interface between three
monomers, thus making oligomerization essential for
function.
Length = 160
Score = 26.7 bits (60), Expect = 4.9
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 38 GDAEVLRAAMKGFGTDEQSIIDVLAKRSNQQRQEIAD 74
G+A+ LR A ++SI + A+++ +EI+
Sbjct: 102 GNADDLRKAADLLDKIDESIANAYAEKTGLSEEEISA 138
>gnl|CDD|211396 cd11558, W2_eIF2B_epsilon, C-terminal W2 domain of eukaryotic
translation initiation factor 2B epsilon. eIF2B is a
heteropentameric complex which functions as a guanine
nucleotide exchange factor in the recycling of eIF-2
during the initiation of translation in eukaryotes. The
epsilon and gamma subunits are sequence similar and both
are essential in yeast. Epsilon appears to be the
catalytically active subunit, with gamma enhancing its
activity. The C-terminal domain of the eIF2B epsilon
subunit contains bipartite motifs rich in acidic and
aromatic residues, which are responsible for the
interaction with eIF2. The structure of the domain
resembles that of a set of concatenated HEAT repeats.
Length = 169
Score = 26.8 bits (60), Expect = 5.3
Identities = 22/110 (20%), Positives = 40/110 (36%), Gaps = 31/110 (28%)
Query: 39 DAEVLRAAMKGFGTDEQSIIDVLAKRSNQQRQEIADAFKTLFGK---------EESFDP- 88
D +V RA +K ++++ + S+ E+ +A K L K + D
Sbjct: 42 DHDVRRAVVKAL-------LELILEVSSTSTAELLEALKKLLSKWGPLLENYVKSQDDQV 94
Query: 89 ----AVTTKLLYHNVIRHLFQCSIHCLPHQDLIDDLKSELGGNFEDAIVA 134
A+ L LF +H L D+++ E+AI+
Sbjct: 95 ELLLALEEFCLESEEGGPLFAKLLHALYDLDILE----------EEAILE 134
>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 = 5.4
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 32 DPFDPNGDAEVLRAAMKGFGTDEQSIIDVLAKRSNQQRQEIADAFKTLFGK 82
+P LR + FG E+ + +V+A+ + +AD + L GK
Sbjct: 231 NPIGLEATDAFLRKLAELFG-IEKEVPEVIARERARLLDALADYHEYLGGK 280
>gnl|CDD|168170 PRK05677, PRK05677, long-chain-fatty-acid--CoA ligase; Validated.
Length = 562
Score = 27.0 bits (60), Expect = 6.2
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 111 LPHQDLIDDL---KSELGGNFEDAIVALMTPLP--ELYAKELH 148
L H++L+ ++ ++ +G N + L+ PLP +YA H
Sbjct: 227 LTHRNLVANMLQCRALMGSNLNEGCEILIAPLPLYHIYAFTFH 269
>gnl|CDD|213970 TIGR04357, CofD_rel_GAK, CofD-related protein, GAK system.
Members of this family are distantly related to CofD,
the enzyme LPPG:FO 2-phospho-L-lactate transferase,
involved in coenzyme F420 biosynthesis. This family
appears to belong to a biosynthesis cassette of unknown
function.
Length = 368
Score = 26.8 bits (60), Expect = 6.5
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 33 PFDPNGDAEVLRAA--MKGFGTDEQSIIDVLAKRSNQQRQEIADAFKTLFGKEES 85
PFD G + VLR A M G D ++ + LA R+ EI F K+ S
Sbjct: 33 PFDSGGSSAVLRRAFAMPAVG-DLRNRLMALADRTVLGNPEIYRLFNYRLPKDAS 86
>gnl|CDD|223924 COG0855, Ppk, Polyphosphate kinase [Inorganic ion transport and
metabolism].
Length = 696
Score = 26.9 bits (60), Expect = 7.4
Identities = 11/47 (23%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 94 LLYHNVIRHLF-QCSIHCLPHQDLIDDLKSELGGNFEDAIVALMTPL 139
L++ ++ L + I + +++L + K L F++ I ++TPL
Sbjct: 99 RLFNELLLPLLAKEGIFIVNYRELSEAQKKWLRTYFKEQIFPVLTPL 145
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 27.0 bits (59), Expect = 7.9
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 90 VTTKLLYHNVIRHLFQCSI--HCL 111
VT K+ + I++LF CSI HC+
Sbjct: 219 VTKKMGFPEKIKNLFDCSIYSHCI 242
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
0.319 0.136 0.395
Gapped
Lambda K H
0.267 0.0891 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,506,279
Number of extensions: 895239
Number of successful extensions: 1038
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1038
Number of HSP's successfully gapped: 29
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
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 (21.7 bits)
S2: 56 (25.1 bits)