RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15129
(308 letters)
>gnl|CDD|238020 cd00063, FN3, Fibronectin type 3 domain; One of three types of
internal repeats found in the plasma protein
fibronectin. Its tenth fibronectin type III repeat
contains an RGD cell recognition sequence in a flexible
loop between 2 strands. Approximately 2% of all animal
proteins contain the FN3 repeat; including extracellular
and intracellular proteins, membrane spanning cytokine
receptors, growth hormone receptors, tyrosine
phosphatase receptors, and adhesion molecules. FN3-like
domains are also found in bacterial glycosyl hydrolases.
Length = 93
Score = 64.1 bits (156), Expect = 3e-13
Identities = 25/90 (27%), Positives = 33/90 (36%), Gaps = 2/90 (2%)
Query: 103 APEAMSAGVLNLTSAFVKWSPPPPQHHNGILLGYKIQVKAYNSTKILAQMSLNASTTSVL 162
P + + TS + W+PP G + GY ++ + S S TS
Sbjct: 3 PPTNLRVTDVTSTSVTLSWTPPE--DDGGPITGYVVEYREKGSGDWKEVEVTPGSETSYT 60
Query: 163 LNNLTSGAVYTARVVAYTRAGLGPYSAPVT 192
L L G Y RV A G P S VT
Sbjct: 61 LTGLKPGTEYEFRVRAVNGGGESPPSESVT 90
>gnl|CDD|200951 pfam00041, fn3, Fibronectin type III domain.
Length = 84
Score = 62.8 bits (153), Expect = 6e-13
Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 103 APEAMSAGVLNLTSAFVKWSPPPPQHHNGILLGYKIQVKAYNSTKILAQMSLNASTTSVL 162
AP ++ + TS + WSPPP NG + GY+++ + N + ++++ +TTS
Sbjct: 2 APTNLTVTDVTSTSLTLSWSPPPG---NGPITGYEVEYRPVNGGEEWKEITVPGTTTSYT 58
Query: 163 LNNLTSGAVYTARVVAYTRAGLGPYS 188
L L G Y RV A AG GP S
Sbjct: 59 LTGLKPGTEYEVRVQAVNGAGEGPPS 84
>gnl|CDD|214495 smart00060, FN3, Fibronectin type 3 domain. One of three types of
internal repeat within the plasma protein, fibronectin.
The tenth fibronectin type III repeat contains a RGD
cell recognition sequence in a flexible loop between 2
strands. Type III modules are present in both
extracellular and intracellular proteins.
Length = 83
Score = 52.6 bits (126), Expect = 4e-09
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 103 APEAMSAGVLNLTSAFVKWSPPPPQHHNGILLGYKIQVKAYNSTKILAQMSLNASTTSVL 162
P + + TS + W PPP G ++GY+++ + S ++++ S+TS
Sbjct: 3 PPSNLRVTDVTSTSVTLSWEPPPDDGITGYIVGYRVEYREEGSEWK--EVNVTPSSTSYT 60
Query: 163 LNNLTSGAVYTARVVAYTRAGLG 185
L L G Y RV A AG G
Sbjct: 61 LTGLKPGTEYEFRVRAVNGAGEG 83
>gnl|CDD|198170 smart01102, CRM1_C, CRM1 C terminal. CRM1 (also known as
Exportin1) mediates the nuclear export of proteins
bearing a leucine-rich nuclear export signal (NES). CRM1
forms a complex with the NES containing protein and the
small GTPase Ran. This region forms an alpha helical
structure formed by six helical hairpin motifs that are
structurally similar to the HEAT repeat, but share
little sequence similarity to the HEAT repeat.
Length = 321
Score = 32.3 bits (74), Expect = 0.23
Identities = 18/75 (24%), Positives = 26/75 (34%), Gaps = 16/75 (21%)
Query: 62 MGEINTKMGEVNT---------RIIEVVV-------GVIRQPSNSMLVQSLEDVPSAAPE 105
G I TK +V ++IE + V +L L D P+
Sbjct: 27 EGTIATKTPKVRGLRTIKREILKLIETYISKAEDLEFVAENFVPPLLEAVLGDYRRNVPD 86
Query: 106 AMSAGVLNLTSAFVK 120
A A VL+L + V
Sbjct: 87 AREAEVLSLMTTIVN 101
>gnl|CDD|227432 COG5101, CRM1, Importin beta-related nuclear transport receptor
[Nuclear structure / Intracellular trafficking and
secretion].
Length = 1053
Score = 31.1 bits (70), Expect = 0.85
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 16/74 (21%)
Query: 63 GEINTKMGEVN------TRIIEVVVGVIRQPSNSMLVQS----------LEDVPSAAPEA 106
G I TK V I+++V I + + VQ+ L D + P+A
Sbjct: 742 GLIATKTPAVRGLRTIKKEILKLVATYISKARDLKFVQNDLVNMLCEAVLFDYKNNVPDA 801
Query: 107 MSAGVLNLTSAFVK 120
A VLNL + V+
Sbjct: 802 RDAEVLNLGTTIVR 815
>gnl|CDD|239960 cd04587, CBS_pair_CAP-ED_DUF294_PBI_assoc, This cd contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domains associated with either the CAP_ED (cAMP
receptor protein effector domain) family of
transcription factors and the DUF294 domain or the PB1
(Phox and Bem1p) domain. Members of CAP_ED, include CAP
which binds cAMP, FNR (fumarate and nitrate reductase)
which uses an iron-sulfur cluster to sense oxygen, and
CooA a heme containing CO sensor. In all cases binding
of the effector leads to conformational changes and the
ability to activate transcription. DUF294 is a putative
nucleotidyltransferase with a conserved DxD motif. The
PB1 domain adopts a beta-grasp fold, similar to that
found in ubiquitin and Ras-binding domains. A motif,
variously termed OPR, PC and AID, represents the most
conserved region of the majority of PB1 domains, and is
necessary for PB1 domain function. This function is the
formation of PB1 domain heterodimers, although not all
PB1 domain pairs associate. CBS is a small domain
originally identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown.
Length = 113
Score = 29.5 bits (67), Expect = 0.91
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 173 TARVVAYTRAGLGPYSAPVTLVMDPHAPPHALPSDILITHLVLI 216
RVVA GL P S V VM P+ P SD + + +
Sbjct: 45 ALRVVA---QGLDPESTLVERVMTPN--PVCATSDTPVLEALHL 83
>gnl|CDD|236361 PRK08999, PRK08999, hypothetical protein; Provisional.
Length = 312
Score = 29.1 bits (66), Expect = 3.2
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 74 TRIIEVVVGVIRQPSNSMLV 93
+ I V GVIR +L+
Sbjct: 2 MKRIHVAAGVIRDADGRILL 21
>gnl|CDD|99862 cd06109, BsCS-I_like, Bacillus subtilis (Bs) citrate synthase
CS-I_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). 2MCS catalyzes the
condensation of propionyl-coenzyme A (PrCoA) and OAA to
form 2-methylcitrate and coenzyme A (CoA) during
propionate metabolism. The overall CS reaction is
thought to proceed through three partial reactions and
involves both closed and open conformational forms of
the enzyme: a) the carbanion or equivalent is generated
from AcCoA by base abstraction of a proton, b) the
nucleophilic attack of this carbanion on OAA to generate
citryl-CoA, and c) the hydrolysis of citryl-CoA to
produce citrate and CoA. This group contains proteins
similar to BsCS-I, one of two CS isozymes in the
gram-positive B. subtilis. The majority of CS activity
in B. subtilis is provided by the other isozyme, BsCS-II
(not included in this group). BsCS-I has a lower
catalytic activity than BsCS-II, and has a Glu in place
of a key catalytic Asp residue. This change is conserved
in other members of this group. For E. coli CS (not
included in this group), site directed mutagenesis of
the key Asp residue to a Glu converts the enzyme into
citryl-CoA lyase which cleaves citryl-CoA to AcCoA and
OAA. A null mutation in the gene encoding BsCS-I (citA)
had little effect on B. subtilis CS activity or on
sporulation. However, disruption of the citA gene in a
strain null for the gene encoding BsCS-II resulted in a
sporulation deficiency, a characteristic of strains
defective in the Krebs cycle. This group contains
proteins which functions exclusively as either a CS or a
2MCS, as well as those with relaxed specificity which
have dual functions as both a CS and a 2MCS. Many of the
gram-negative species represented in this group have a
second CS isozyme which is in another group.
Length = 349
Score = 28.4 bits (64), Expect = 4.4
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 13/31 (41%)
Query: 154 LNASTTSVLLNNLTSGAVYTARVVAYTRAGL 184
+NAST +TARV+A T A L
Sbjct: 171 MNAST-------------FTARVIASTEADL 188
>gnl|CDD|219865 pfam08493, AflR, Aflatoxin regulatory protein. This domain is
found in the aflatoxin regulatory protein (AflR) which
is involved in the regulation of the biosynthesis of
aflatoxin in the fungal genus Aspergillus. It occurs
together with the fungal Zn(2)-Cys(6) binuclear cluster
domain (pfam00172).
Length = 275
Score = 28.4 bits (63), Expect = 4.8
Identities = 20/85 (23%), Positives = 22/85 (25%), Gaps = 17/85 (20%)
Query: 165 NLTSGAVYTARVVAYTRAGLGPYSAPVTLVMDPHAPPHALPSDILITHLV----LIHSPI 220
N S A A T + P PV PP A P T SP
Sbjct: 6 NTASSPTIPANTTANTTSSSHP-QPPVQSGPSSIQPPVATPHTPNGTSSPSPKFSHQSPP 64
Query: 221 QVP------------GSDRSTQSSL 233
P D+ SSL
Sbjct: 65 AEPELWGSILSPNASNQDQGDLSSL 89
>gnl|CDD|237070 PRK12350, PRK12350, citrate synthase 2; Provisional.
Length = 353
Score = 28.4 bits (64), Expect = 5.5
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 13/31 (41%)
Query: 154 LNASTTSVLLNNLTSGAVYTARVVAYTRAGL 184
+NAST +TARV+A T A +
Sbjct: 170 MNAST-------------FTARVIASTGADV 187
>gnl|CDD|236543 PRK09505, malS, alpha-amylase; Reviewed.
Length = 683
Score = 28.5 bits (64), Expect = 5.7
Identities = 11/30 (36%), Positives = 12/30 (40%)
Query: 229 TQSSLPHNQYHSGTRQDWINEDARMRYEES 258
T+ PH YH DW DA M E
Sbjct: 264 TKGDFPHYAYHGYYTLDWTKLDANMGTEAD 293
>gnl|CDD|99863 cd06110, BSuCS-II_like, Bacillus subtilis (Bs) citrate synthase
(CS)-II_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). 2MCS catalyzes the
condensation of propionyl-coenzyme A (PrCoA) and OAA to
form 2-methylcitrate and CoA during propionate
metabolism. The overall CS reaction is thought to
proceed through three partial reactions: a) the
carbanion or equivalent is generated from AcCoA by base
abstraction of a proton, b) the nucleophilic attack of
this carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
This group contains proteins similar to BsCS-II, the
major CS of the gram-positive bacterium Bacillus
subtilis. A mutation in the gene which encodes BsCS-II
(citZ gene) has been described which resulted in a
significant loss of CS activity, partial glutamate
auxotrophy, and a sporulation deficiency, all of which
are characteristic of strains defective in the Krebs
cycle. Streptococcus mutans CS, found in this group, may
participate in a pathway for the anaerobic biosynthesis
of glutamate. This group also contains functionally
uncharacterized CSs of various gram-negative bacteria.
Some of the gram-negative species represented in this
group have a second CS isozyme found in another group.
This group contains proteins which functions exclusively
as either a CS or a 2MCS, as well as those with relaxed
specificity which have dual functions as both a CS and a
2MCS.
Length = 356
Score = 28.4 bits (64), Expect = 5.7
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 16/54 (29%)
Query: 137 KIQVKAYNSTKIL-AQMSLNASTTSVLLNNLTSGAVYTARVVAYTRAGLGPYSA 189
+ +A++ IL A LNAST + ARVVA T + + YSA
Sbjct: 164 EEAARAFDVALILHADHELNAST-------------FAARVVASTLSDM--YSA 202
>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2). All proteins in this
superfamily for which functions are known are DNA
polymerases.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1172
Score = 28.1 bits (62), Expect = 7.4
Identities = 16/60 (26%), Positives = 21/60 (35%), Gaps = 6/60 (10%)
Query: 245 DWINEDARMRYEESRGQ-YEDSRNYEDGRGNYEDGRGKYEDGRNKYEDGRTFGAAIKERG 303
D+I ED R Q + +DG G EDGR + D K+ G
Sbjct: 6 DYIYEDVDEEEYSKRVQEKPIDDIFVK-----DDGEGYVEDGREFFPDEDDILDLDKDDG 60
>gnl|CDD|223526 COG0449, GlmS, Glucosamine 6-phosphate synthetase, contains
amidotransferase and phosphosugar isomerase domains
[Cell envelope biogenesis, outer membrane].
Length = 597
Score = 27.5 bits (62), Expect = 9.3
Identities = 8/49 (16%), Positives = 18/49 (36%), Gaps = 5/49 (10%)
Query: 92 LVQSLEDVPSAAPEAMSAGVLNLTSAFVKWSPPPPQHHNGILLGYKIQV 140
L++ L+ +P+ P+ VL + + + LG +
Sbjct: 424 LIKELQKLPNHIPK-----VLAAEEKIKELAKRLADAKDFFFLGRGVLY 467
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
0.312 0.131 0.381
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,684,899
Number of extensions: 1474888
Number of successful extensions: 879
Number of sequences better than 10.0: 1
Number of HSP's gapped: 873
Number of HSP's successfully gapped: 26
Length of query: 308
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 211
Effective length of database: 6,635,264
Effective search space: 1400040704
Effective search space used: 1400040704
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 59 (26.6 bits)