RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1901
(205 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 99.5 bits (249), Expect = 5e-28
Identities = 33/57 (57%), Positives = 44/57 (77%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
RR RTTFT +QLEELE+ F++ +YP REELA+K LTE +V+VWF NRRA+ ++
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 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 = 91.2 bits (227), Expect = 1e-24
Identities = 31/58 (53%), Positives = 43/58 (74%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
RR RT FT +QLEELE+ F++ YP REELA++ LTE +V++WF NRRA+L++
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 90.0 bits (224), Expect = 3e-24
Identities = 32/57 (56%), Positives = 43/57 (75%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
+RR RT+FT +QLEELE+ FQ+ YP REELA+K L+E +V+VWF NRRA+ +
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 63.2 bits (154), Expect = 8e-13
Identities = 21/61 (34%), Positives = 32/61 (52%)
Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
+ R T +QL LER F+ YP TR +L+ + VQ+WF N+RA+ +K
Sbjct: 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKK 108
Query: 93 Q 93
+
Sbjct: 109 K 109
>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 = 35.2 bits (82), Expect = 0.001
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 59 YPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
YP + ELA++T L+ ++ WF N R R
Sbjct: 10 YPSEEEKSELARQTGLSRKQIDNWFINARRR 40
>gnl|CDD|178608 PLN03046, PLN03046, D-glycerate 3-kinase; Provisional.
Length = 460
Score = 30.7 bits (69), Expect = 0.47
Identities = 22/97 (22%), Positives = 36/97 (37%), Gaps = 10/97 (10%)
Query: 108 HHQYADSAANFSHQSHPTSWAQQAASYATAGAALTAGYNSHAYSSATP-------EFPVS 160
+ +A NF+ S+P + ++ S ++ + +Y S+ P
Sbjct: 29 IPCASAAAFNFNPISNPFNLKRRPYSPSSHKFNDRVAASCSSYPSSKLSSRKTHLSCPGC 88
Query: 161 GPGYHQTNQHCADS-TAAWS--RHHSSSTKSPVDVPS 194
G + Q N D T A + R S T SP V S
Sbjct: 89 GCSWIQDNSMVHDYATTAATSKRCSSLPTSSPALVSS 125
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 29.3 bits (66), Expect = 1.4
Identities = 12/82 (14%), Positives = 28/82 (34%), Gaps = 9/82 (10%)
Query: 23 TESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVW 82
+P K + + +LE+ F + + R+++ Q E +++
Sbjct: 238 NPLKPNYYYKDE--KYLDVVPLKAYADLEKLFNEA-LDEKFERDKIKQLASELEKKLE-- 292
Query: 83 FSNRRARLRKQLNSQ--QLNAF 102
+L +L Q +L
Sbjct: 293 --KELKKLENKLEKQEDELEEL 312
>gnl|CDD|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70
family. This model encompasses all varieties of the
sigma-70 type sigma factors including the ECF subfamily.
A number of sigma factors have names with a different
number than 70 (i.e. sigma-38), but in fact, all except
for the Sigma-54 family (TIGR02395) are included within
this family. Several PFAM models hit segments of these
sequences including Sigma-70 region 2 (pfam04542) and
Sigma-70, region 4 (pfam04545), but not always above
their respective trusted cutoffs.
Length = 158
Score = 28.5 bits (64), Expect = 1.5
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 45 DQLEELER-AFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94
++L E ER + + +E+A+ ++ V+ R +LR+ L
Sbjct: 109 EKLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
>gnl|CDD|234081 TIGR02989, Sig-70_gvs1, RNA polymerase sigma-70 factor,
Rhodopirellula/Verrucomicrobium family. This group of
sigma factors are members of the sigma-70 family
(TIGR02937) and are abundantly found in the species
Rhodopirellula baltica (11), and Verrucomicrobium
spinosum (16) and to a lesser extent in Gemmata
obscuriglobus (2).
Length = 159
Score = 27.2 bits (61), Expect = 4.2
Identities = 20/89 (22%), Positives = 25/89 (28%), Gaps = 29/89 (32%)
Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPD-------------------------VYTR-- 65
RK R R F + LE L + T+ Y R
Sbjct: 69 RKLGRDRLVFDDELLEALAAEAEATEADRSEDELEALEGCLEKLPERQRELLQLRYQRGV 128
Query: 66 --EELAQKTKLTEARVQVWFSNRRARLRK 92
LA++ T V S R RLR
Sbjct: 129 SLTALAEQLGRTVNAVYKALSRLRVRLRD 157
>gnl|CDD|219882 pfam08524, rRNA_processing, rRNA processing. This is a family of
proteins that are involved in rRNA processing. In a
localisation study they were found to localise to the
nucleus and nucleolus. The family also includes other
metazoa members from plants to mammals where the protein
has been named BR22 and is associated with TTF-1,
thyroid transcription factor 1. In the lungs, the family
binds TTF-1 to form a complex which influences the
expression of the key lung surfactant protein-B (SP-B)
and -C (SP-C), the small hydrophobic surfactant proteins
that maintain surface tension in alveoli.
Length = 150
Score = 27.2 bits (60), Expect = 4.3
Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK 73
KR+QR +LE++E + ++ + + R++L +KTK
Sbjct: 85 KREQREKELAKRQKELEKIELSKKKQKERE-RRRKKLTKKTK 125
>gnl|CDD|226046 COG3515, COG3515, Predicted component of the type VI protein
secretion system [Intracellular trafficking, secretion,
and vesicular transport].
Length = 346
Score = 27.8 bits (62), Expect = 4.5
Identities = 18/91 (19%), Positives = 28/91 (30%), Gaps = 3/91 (3%)
Query: 66 EELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQYADSAANFSHQSHPT 125
+L Q L +++ + RA L +QL S L A +
Sbjct: 133 LQLLQLLPLEAIDLELGYFLERALQLLGLLLRQLELKLSAELAALLAALQQTAARLETQA 192
Query: 126 SWAQQAASYATAGAALTAGYNSHAYSSATPE 156
+ +AA+ A L A S P
Sbjct: 193 ARDIKAAALTALRAGLLAA---EQVLSRLPG 220
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 27.2 bits (61), Expect = 7.0
Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 12/87 (13%)
Query: 29 IPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 88
+PL + +F + L E + Y R+ + QK E RV+ N
Sbjct: 257 LPLSHLSGYEKRSF--ESLSEALDEY----YSKKAERDRVKQKRSDLEKRVE----NELE 306
Query: 89 RLRKQLNSQ--QLNAFNSMSLHHQYAD 113
+L K+L +L + + Y +
Sbjct: 307 KLEKKLEKLEKELEEAENAENYRLYGE 333
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 27.2 bits (60), Expect = 8.2
Identities = 19/105 (18%), Positives = 28/105 (26%), Gaps = 24/105 (22%)
Query: 98 QLNAFNSMSLHHQYADSAANFSHQSHPTSWAQQAASYATAGAALTAGYNSHAYSSATPEF 157
SM L + + S S+ S ++ NS S++ P F
Sbjct: 183 PSLGSQSMQLPSPHFRQKFSSSDTSNGFS-----------YPSIR--KNSRHSSNSMPSF 229
Query: 158 PVSGPGY---HQTNQHCADSTAAWSRHHSSSTKSPVDVPSPWTST 199
P S + SS +P S ST
Sbjct: 230 PHSSTAVLLKRHSGSS--------GASLISSNITPSSSNSEAMST 266
>gnl|CDD|148617 pfam07111, HCR, Alpha helical coiled-coil rod protein (HCR). This
family consists of several mammalian alpha helical
coiled-coil rod HCR proteins. The function of HCR is
unknown but it has been implicated in psoriasis in
humans and is thought to affect keratinocyte
proliferation.
Length = 739
Score = 26.9 bits (59), Expect = 8.3
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 31 LKRKQRRSRTTF--TGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 88
L+R+ + S+ + G QLE Q + R+EL Q+ ++ +Q +
Sbjct: 526 LERELQESQESLASAGAQLEAARAGQQESTEEAASLRQELTQQQEVYGQALQEKVAEVET 585
Query: 89 RLRKQL 94
RLR+QL
Sbjct: 586 RLREQL 591
>gnl|CDD|99738 cd00614, CGS_like, CGS_like: Cystathionine gamma-synthase is a
PLP dependent enzyme and catalyzes the committed step
of methionine biosynthesis. This pathway is unique to
microorganisms and plants, rendering the enzyme an
attractive target for the development of antimicrobials
and herbicides. This subgroup also includes
cystathionine gamma-lyases (CGL), O-acetylhomoserine
sulfhydrylases and O-acetylhomoserine thiol lyases.
CGL's are very similar to CGS's. Members of this group
are widely distributed among all three forms of life.
Length = 369
Score = 26.8 bits (60), Expect = 8.5
Identities = 6/28 (21%), Positives = 10/28 (35%)
Query: 40 TTFTGDQLEELERAFQRTQYPDVYTREE 67
+TF E F + +Y+R
Sbjct: 11 STFVFPSPAEAADLFALREGGYIYSRIG 38
>gnl|CDD|221793 pfam12824, MRP-L20, Mitochondrial ribosomal protein subunit L20.
This family is the essential mitochondrial ribosomal
protein subunit L20 of fungi.
Length = 164
Score = 26.1 bits (58), Expect = 9.9
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 15 PSSGDESDTESEPGIPLKRKQRRSRT-TFTGDQLEELERAFQRTQYPDVYTREELAQK 71
S + P L+ K + + T + + E+ R R + P +TR++LA+K
Sbjct: 59 KQSTISPKSSDLP-PILRYKAEKEKKYHLTPEDIAEIRRL--RAEDPVKWTRKKLAKK 113
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
0.311 0.121 0.363
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,053,401
Number of extensions: 863244
Number of successful extensions: 739
Number of sequences better than 10.0: 1
Number of HSP's gapped: 735
Number of HSP's successfully gapped: 36
Length of query: 205
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 113
Effective length of database: 6,857,034
Effective search space: 774844842
Effective search space used: 774844842
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 (21.9 bits)
S2: 57 (25.7 bits)