RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14049
(93 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 67.9 bits (167), Expect = 5e-17
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
R++RT+FTP+ LE L FE+N +PS E LA +LG +++WF N+R K
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 63.8 bits (156), Expect = 2e-15
Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
KR++RTSFTP+ LE L F++N +PS E LA +LG +++WF N+R K
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 62.6 bits (153), Expect = 5e-15
Identities = 26/58 (44%), Positives = 36/58 (62%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
R++RT FTP+ LE L FE+N +PS E LA +LG ++IWF N+R LK +
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 45.5 bits (108), Expect = 2e-07
Identities = 20/67 (29%), Positives = 29/67 (43%)
Query: 16 TEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFC 75
E S + +R T + L +L FE N +PS L+ L + ++IWF
Sbjct: 41 LERKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQ 100
Query: 76 NKRQALK 82
NKR K
Sbjct: 101 NKRAKEK 107
>gnl|CDD|197854 smart00745, MIT, Microtubule Interacting and Trafficking molecule
domain.
Length = 77
Score = 26.9 bits (60), Expect = 0.70
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 8 YKSGQNHLTEFIGMEPSKKRK 28
YK +L E I +E KR+
Sbjct: 31 YKKAIEYLLEGIKVESDSKRR 51
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain. This is a homeobox
transcription factor KN domain conserved from fungi to
human and plants.
Length = 40
Score = 24.8 bits (55), Expect = 2.1
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 41 LNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
L H N +PS E + LA Q G R+ I WF N R
Sbjct: 2 LLEHLH-NPYPSEEEKSELARQTGLSRKQIDNWFINAR 38
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 26.2 bits (59), Expect = 2.4
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 23 PSKKRKRRTSFTPQALELLN-AHF-ERN-THPSGTE 55
K+ R+ ++ PQALELL AH +R SG E
Sbjct: 67 SPKELARKIAYVPQALELLGLAHLADRPFNELSGGE 102
>gnl|CDD|173271 PRK14810, PRK14810, formamidopyrimidine-DNA glycosylase;
Provisional.
Length = 272
Score = 25.6 bits (56), Expect = 3.7
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 3/43 (6%)
Query: 51 PSGTEITTLA---HQLGYEREVIRIWFCNKRQALKNTVRMMSK 90
P E+ T+A R + F N R K +M+
Sbjct: 2 PELPEVETVARGLAPRAAGRRIATAEFRNLRIPRKGDPDLMAA 44
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 25.5 bits (57), Expect = 4.1
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 17 EFIGMEPSKKRKRRTSFTPQALELLNAHFERN 48
E I M + + + +P LE + ER
Sbjct: 335 EIIDMRELLRGENGSFLSPPLLEAIKQRLERG 366
>gnl|CDD|149793 pfam08847, DUF1817, Domain of unknown function (DUF1817). Members
of this family are functionally uncharacterized.
Length = 150
Score = 25.3 bits (56), Expect = 4.6
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 33 FTPQALEL--------LNAHFERNTHPSGTEITTLAHQLGYE 66
F P+ALEL L+ ++ S + +A LGYE
Sbjct: 100 FNPEALELFVMHKLFVLDDWLKQQGLSSRGRLKQMAAMLGYE 141
>gnl|CDD|214467 smart00005, DEATH, DEATH domain, found in proteins involved in
cell death (apoptosis). Alpha-helical domain present
in a variety of proteins with apoptotic functions. Some
(but not all) of these domains form homotypic and
heterotypic dimers.
Length = 88
Score = 24.7 bits (54), Expect = 6.1
Identities = 9/39 (23%), Positives = 13/39 (33%)
Query: 50 HPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88
HP G + LA +LG I + L +
Sbjct: 14 HPLGLDWRELARKLGLSEADIDQIRTEAPRDLAEQSVQL 52
>gnl|CDD|221204 pfam11749, DUF3305, Protein of unknown function (DUF3305). Several
members of this family are annotated as being
molybdopterin-guanine dinucleotide biosynthesis protein
A; however, this could not be confirmed. The family is
found in proteobacteria.
Length = 140
Score = 24.9 bits (55), Expect = 6.5
Identities = 9/20 (45%), Positives = 10/20 (50%), Gaps = 4/20 (20%)
Query: 15 LTEFIGM----EPSKKRKRR 30
L F+ EP KKRKR
Sbjct: 121 LEAFVERHHEEEPFKKRKRD 140
>gnl|CDD|99860 cd06107, EcCS_AthCS-per_like, Escherichia coli (Ec) citrate
synthase (CS) gltA and Arabidopsis thaliana (Ath)
peroxisomal (Per) CS_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). 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.
There are two types of CSs: type I CS and type II CSs.
Type I CSs are found in eukarya, gram-positive bacteria,
archaea, and in some gram-negative bacteria and are
homodimers with both subunits participating in the
active site. Type II CSs are unique to gram-negative
bacteria and are homohexamers of identical subunits
(approximated as a trimer of dimers). Some type II CSs,
including EcCS, are strongly and specifically inhibited
by NADH through an allosteric mechanism. Included in
this group is an NADH-insensitive type II Acetobacter
acetii CS which has retained many of the residues used
by EcCS for NADH binding. C. aurantiacus is a
gram-negative thermophilic green gliding bacterium; its
CS belonging to this group may be a type I CS. It is
not inhibited by NADH or 2-oxoglutarate and is inhibited
by ATP. Both gram-positive and gram-negative bacteria
are found in this group. This group also contains three
Arabidopsis peroxisomal CS proteins, CYS-1, -2, and -3
which participate in the glyoxylate cycle. AthCYS1, in
addition to a peroxisomal targeting sequence, has a
predicted secretory signal peptide; it may be targeted
to both the secretory pathway and the peroxisomes and
perhaps is located in the extracellular matrix. AthCSY1
is expressed only in siliques and specifically in
developing seeds. AthCSY2 and 3 are active during seed
germination and seedling development and are thought to
participate in the beta-oxidation of fatty acids.
Length = 382
Score = 24.7 bits (54), Expect = 8.3
Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 12/83 (14%)
Query: 20 GMEPSKKRKRRTSFT-------PQALELLNAHFERNTHPSGTEITTLAHQLGYEREVI-- 70
G P++++ P+++ L F R+ HP G L+ + E I
Sbjct: 55 GELPTQEQYDEFQRRLSEHMMVPESVHRLIQTFPRDAHPMGILCAGLSALSAFYPEAIPA 114
Query: 71 ---RIWFCNKRQALKNTVRMMSK 90
++ N K +R ++K
Sbjct: 115 HTGDLYQNNPEVRDKQIIRTLAK 137
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
0.321 0.131 0.391
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,499,819
Number of extensions: 350180
Number of successful extensions: 308
Number of sequences better than 10.0: 1
Number of HSP's gapped: 308
Number of HSP's successfully gapped: 19
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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 (21.9 bits)
S2: 53 (24.2 bits)