RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12776
(435 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 74.1 bits (183), Expect = 6e-17
Identities = 26/45 (57%), Positives = 33/45 (73%)
Query: 233 RRNRTTFSPSQLDELEKEFDKSHYPCVSTRERLAAKTSLSEARVQ 277
RR RTTF+P QL+ELEKEF+K+ YP RE LA K L+E +V+
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVK 45
Score = 35.9 bits (84), Expect = 0.002
Identities = 10/12 (83%), Positives = 11/12 (91%)
Query: 343 VWFSNRRAKWRR 354
VWF NRRAKW+R
Sbjct: 46 VWFQNRRAKWKR 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 67.7 bits (166), Expect = 1e-14
Identities = 26/45 (57%), Positives = 32/45 (71%)
Query: 233 RRNRTTFSPSQLDELEKEFDKSHYPCVSTRERLAAKTSLSEARVQ 277
RR RT+F+P QL+ELEKEF K+ YP RE LA K LSE +V+
Sbjct: 2 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVK 46
Score = 31.8 bits (73), Expect = 0.062
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 343 VWFSNRRAKWR 353
VWF NRRAKW+
Sbjct: 47 VWFQNRRAKWK 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 = 67.3 bits (165), Expect = 2e-14
Identities = 24/45 (53%), Positives = 32/45 (71%)
Query: 233 RRNRTTFSPSQLDELEKEFDKSHYPCVSTRERLAAKTSLSEARVQ 277
RR RT F+P QL+ELEKEF+K+ YP RE LA + L+E +V+
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45
Score = 34.5 bits (80), Expect = 0.006
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 343 VWFSNRRAKWRRHQ 356
+WF NRRAK +R +
Sbjct: 46 IWFQNRRAKLKRSE 59
>gnl|CDD|238076 cd00131, PAX, Paired Box domain.
Length = 128
Score = 45.1 bits (107), Expect = 6e-06
Identities = 17/23 (73%), Positives = 19/23 (82%)
Query: 91 EGVCTNATAPSVSSINRILRNRA 113
EGVC + PSVSSINRILRN+A
Sbjct: 106 EGVCDKSNVPSVSSINRILRNKA 128
>gnl|CDD|128645 smart00351, PAX, Paired Box domain.
Length = 125
Score = 41.9 bits (99), Expect = 8e-05
Identities = 15/22 (68%), Positives = 16/22 (72%)
Query: 89 IIEGVCTNATAPSVSSINRILR 110
+ EGVC PSVSSINRILR
Sbjct: 104 LSEGVCDKDNVPSVSSINRILR 125
>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain.
Length = 125
Score = 40.2 bits (94), Expect = 3e-04
Identities = 19/34 (55%), Positives = 21/34 (61%), Gaps = 5/34 (14%)
Query: 82 PHIFPMKI-----IEGVCTNATAPSVSSINRILR 110
P IF +I EGVC N PSVSSI+RILR
Sbjct: 92 PGIFAWEIRDRLLAEGVCDNDNVPSVSSISRILR 125
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 39.0 bits (91), Expect = 0.001
Identities = 14/55 (25%), Positives = 23/55 (41%)
Query: 223 SGSGSEQPKFRRNRTTFSPSQLDELEKEFDKSHYPCVSTRERLAAKTSLSEARVQ 277
+ R + QL LE+EF+ + YP TR +L+ ++ VQ
Sbjct: 42 ERKQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQ 96
>gnl|CDD|219398 pfam07394, DUF1501, Protein of unknown function (DUF1501). This
family contains a number of hypothetical bacterial
proteins of unknown function approximately 400 residues
long.
Length = 393
Score = 30.4 bits (69), Expect = 2.1
Identities = 26/165 (15%), Positives = 49/165 (29%), Gaps = 29/165 (17%)
Query: 51 NLFTDYYPSTWRKHLGNFLKCNRT----LPVLETVPHIFPMKIIEGVCTNATAPSVSSIN 106
+ F D P K + + + E +PH+ ++ + +C + S+ +
Sbjct: 17 DTF-DPKPDLDYLGGKPLPKFIQHGESGIWISELLPHL--AQLADDLCLH---RSMHT-- 68
Query: 107 RILRNRAAERAAAEFARAAGYGIYHTAHPYASF-HWPNPGIWNPNN---PPVVSNQGPGT 162
A A + G S W G+ + N VVS+
Sbjct: 69 -----ELANHGPAAYVMNTGS----LPPGRPSMGSWVTYGLGSENQNLPAFVVSHFEERG 119
Query: 163 TPSSGAAGSPRGLMPRLFVPFGHCYSFSPTSDHVHINNEHTPITP 207
SG+ G +PR + + D V + +
Sbjct: 120 GAGSGSRNWGSGFLPRAYQGL----PLRSSGDPVLDLSPPAGLDR 160
>gnl|CDD|129711 TIGR00624, tag, DNA-3-methyladenine glycosylase I. All proteins in
this family are alkylation DNA glycosylases that
function in base excision repair 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 = 179
Score = 29.5 bits (66), Expect = 2.5
Identities = 24/95 (25%), Positives = 34/95 (35%), Gaps = 11/95 (11%)
Query: 108 ILRNRAAERAAAEFARAAGYGIYHTAHPYASFHWPNPGIWNPNNPPVVSNQGPGTTPSSG 167
I+RNR A ARAA + + F W ++ P +TP S
Sbjct: 84 IIRNRGKIEATIANARAA---LQLEQNDLVEFLWSFVNHQPQPRQRPTDSEIPSSTPESK 140
Query: 168 AAGSPRGLMPRLFVPFGH--CYSFSPTS----DHV 196
A + L R F G CY+ + DH+
Sbjct: 141 AMS--KELKKRGFRFVGPTICYALMQATGMVDDHI 173
>gnl|CDD|133160 cd06096, Plasmepsin_5, Plasmepsins are a class of aspartic
proteinases produced by the plasmodium parasite. The
family contains a group of aspartic proteinases
homologous to plasmepsin 5. Plasmepsins are a class of
at least 10 enzymes produced by the plasmodium parasite.
Through their haemoglobin-degrading activity, they are
an important cause of symptoms in malaria sufferers.
This family of enzymes is a potential target for
anti-malarial drugs. Plasmepsins are aspartic acid
proteases, which means their active site contains two
aspartic acid residues. These two aspartic acid residue
act respectively as proton donor and proton acceptor,
catalyzing the hydrolysis of peptide bond in proteins.
Aspartic proteinases are composed of two structurally
similar beta barrel lobes, each lobe contributing an
aspartic acid residue to form a catalytic dyad that acts
to cleave the substrate peptide bond. The catalytic Asp
residues are contained in an Asp-Thr-Gly-Ser/thr motif
in both N- and C-terminal lobes of the enzyme. There
are four types of plasmepsins, closely related but
varying in the specificity of cleavage site. The name
plasmepsin may come from plasmodium (the organism) and
pepsin (a common aspartic acid protease with similar
molecular structure). This family of aspartate proteases
is classified by MEROPS as the peptidase family A1
(pepsin A, clan AA).
Length = 326
Score = 29.7 bits (67), Expect = 2.8
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 9/37 (24%)
Query: 5 FVDFPEEQYWILRHLTLFNKLIVFIPTYNFIMDSDIN 41
FPE+ L+NK+ F PT I ++++
Sbjct: 242 LSHFPED---------LYNKINNFFPTITIIFENNLK 269
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 30.0 bits (67), Expect = 3.1
Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 142 PNPGIWNPNNPPVVSNQGPGTTP----SSGAAGSPRGLMP 177
N + P P V S GPG+ P S G SP LMP
Sbjct: 422 TNQSMPQPPQPSVPSPGGPGSQPPQSVSGGMIPSPPALMP 461
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation termination
are recognised and rapidly degraded by eukaryotic cells
through a pathway known as nonsense-mediated mRNA decay.
In Saccharomyces cerevisiae, three trans-acting factors
(Upf1 to Upf3) are required for nonsense-mediated mRNA
decay.
Length = 171
Score = 28.9 bits (65), Expect = 3.1
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 414 DDADQHYPSSDESEEINVT 432
D +Q S E E+I VT
Sbjct: 34 PDDEQDEESDSEEEQIFVT 52
>gnl|CDD|226444 COG3934, COG3934, Endo-beta-mannanase [Carbohydrate transport and
metabolism].
Length = 587
Score = 29.9 bits (67), Expect = 3.6
Identities = 11/89 (12%), Positives = 25/89 (28%), Gaps = 16/89 (17%)
Query: 106 NRILRNRAAERAAAEFARAAGYGIYHTAHPYASFHWPNPGIWNP--NNPPVVSNQGPGTT 163
+L+ + F++ P S+H W + ++ G
Sbjct: 411 AWLLKGVVNQVPDVWFSK-----------PDTSYHGSPTHEWQGLFGVFDIDASGSAGIK 459
Query: 164 PSSGAAGSPRGLMPRLFVPFGHCYSFSPT 192
+ + L + + YSF +
Sbjct: 460 AHAANV---KLLGKSDWEEVRYAYSFERS 485
>gnl|CDD|200089 TIGR01289, LPOR, light-dependent protochlorophyllide reductase.
This model represents the light-dependent,
NADPH-dependent form of protochlorophyllide reductase.
It belongs to the short chain alcohol dehydrogenase
family, in contrast to the nitrogenase-related
light-independent form [Biosynthesis of cofactors,
prosthetic groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 314
Score = 29.4 bits (66), Expect = 3.7
Identities = 16/44 (36%), Positives = 20/44 (45%)
Query: 55 DYYPSTWRKHLGNFLKCNRTLPVLETVPHIFPMKIIEGVCTNAT 98
+ S HLG+FL CN L L+ P+ II G T T
Sbjct: 105 GFELSVGTNHLGHFLLCNLLLDDLKNSPNKDKRLIIVGSITGNT 148
>gnl|CDD|222366 pfam13764, E3_UbLigase_R4, E3 ubiquitin-protein ligase UBR4. This
is a family of E## ubiquitin ligase enzymes.
Length = 794
Score = 29.6 bits (67), Expect = 3.9
Identities = 24/113 (21%), Positives = 35/113 (30%), Gaps = 14/113 (12%)
Query: 294 ERNSTFMYFIFYLILVLFTTHCGK------FLTIIPTPSHTWDLRIGRTDG-HFKSV--W 344
E N + ++ + L L L + PS W D + V
Sbjct: 613 ESNMRLLPYLIQMALHLLDQSRQTQREEKTLLAFLSAPSEKWIESEYEEDNPQYMLVLSL 672
Query: 345 FSNRRAKWRRHQRMNLLKSRRANAANVSGQGQVTSDSSSPSTPS-LW---RHM 393
+W H R LK A+A + TS +S T L+ R M
Sbjct: 673 LVESYEQWNEH-RRAFLKRLIAHAHTRHVSPRTTSRASPSDTSEKLFSIYRPM 724
>gnl|CDD|131795 TIGR02748, GerC3_HepT, heptaprenyl diphosphate synthase component
II. Members of this family are component II of the
heterodimeric heptaprenyl diphosphate synthase. The
trusted cutoff was set such that all members identified
are encoded near to a recognizable gene for component I
(in Pfam family pfam07307). This enzyme acts in
menaquinone-7 isoprenoid side chain biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 319
Score = 29.3 bits (66), Expect = 4.0
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 66 GNFLKCNRTLPVLETVPHIFPMKIIEGVCTNATAPSVSS-INRILRNRAAERAAA 119
G+ L+ N TLPVL + F K IE V TA + I + ++ A E A A
Sbjct: 228 GDLLQGNVTLPVLYAMEDPFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYA 282
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 29.1 bits (65), Expect = 4.3
Identities = 18/95 (18%), Positives = 24/95 (25%), Gaps = 13/95 (13%)
Query: 135 PYASFHWPNPGIWNPNNPPVVSNQGPGTTPSSGAAGSPRGLMPRLFVPFGHCYSFSPTSD 194
++P PG +NQG G G G P V G S P
Sbjct: 14 QMGGGNYPAPGQPAQQG---YANQGMGGPVGGGGGPGAGGGAPGGPVGGGGGGSGGPPGG 70
Query: 195 HVHINNEHTPITPCFVSDGDAKDDDSVGSGSGSEQ 229
++ + D S S E
Sbjct: 71 GEVAGE----------AEDAMSEFDDYSSSSIEEG 95
>gnl|CDD|107350 cd06355, PBP1_FmdD_like, Periplasmic component (FmdD) of an active
transport system for short-chain amides and urea
(FmdDEF). This group includes the periplasmic component
(FmdD) of an active transport system for short-chain
amides and urea (FmdDEF), found in Methylophilus
methylotrophus, and its homologs from other bacteria.
FmdD, a type I periplasmic binding protein, is induced
by short-chain amides and urea and repressed by excess
ammonia, while FmdE and FmdF are hydrophobic
transmembrane proteins. FmdDEF is predicted to be an
ATP-dependent transporter and closely resembles the
periplasmic binding protein and the two transmembrane
proteins present in various hydrophobic amino
acid-binding transport systems.
Length = 348
Score = 28.8 bits (65), Expect = 6.0
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 318 FLTIIPTPSHTWD-LRIGR--TDGHFKSVWFS 346
+T+ P H W +RIGR DG F+ VW S
Sbjct: 317 PVTVDPANHHLWKPVRIGRIQADGQFEIVWSS 348
>gnl|CDD|185402 PTZ00026, PTZ00026, 60S ribosomal protein L15; Provisional.
Length = 204
Score = 28.1 bits (63), Expect = 6.4
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 335 RTDGHFKSVWFSNRRAKWRRHQRMNLLKSR 364
R GH S +RRA W+R R+ L + R
Sbjct: 175 RVKGHRASKLRPSRRANWKRRNRIVLRRYR 204
>gnl|CDD|215530 PLN02980, PLN02980, 2-oxoglutarate decarboxylase/ hydro-lyase/
magnesium ion binding / thiamin pyrophosphate binding.
Length = 1655
Score = 29.1 bits (65), Expect = 6.7
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 340 FKSVWFSNRRAK-WRRHQRMNLLKSRRANAANVSGQGQVTSDSSSPSTPSLW 390
F W+S K R H N + + R +V ++ SD S PSLW
Sbjct: 1510 FLENWYSGELWKSLRNHPHFNKIVASRLLHKDVPSLAKLLSDLSIGRQPSLW 1561
>gnl|CDD|189040 cd09870, PIN_YEN1, PIN domain of Yeast Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and fungal homologs. Yeast Endonuclease 1
(YEN1) is a Holliday junction resolvase which promotes
reciprocal exchange during mitotic recombination to
maintain genome integrity in budding yeast. YEN1 is a
member of the structure-specific, 5' nuclease family
that catalyzes hydrolysis of DNA duplex-containing
nucleic acid structures during DNA replication, repair,
and recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 15 - 50
residues in YEN1 PIN domains) and a H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 239
Score = 28.4 bits (64), Expect = 6.9
Identities = 13/50 (26%), Positives = 17/50 (34%), Gaps = 13/50 (26%)
Query: 202 HTPITPCFVSDGDAKDDDSVGSGSGSEQPKFRRNRTTFSPSQLDELEKEF 251
PITP FV DG +P F+R + + L K
Sbjct: 79 ALPITPVFVFDGP-------------NRPSFKRGKRVGLKKKEHWLIKLV 115
>gnl|CDD|173801 cd07475, Peptidases_S8_C5a_Peptidase, Peptidase S8 family domain in
Streptococcal C5a peptidases. Streptococcal C5a
peptidase (SCP), is a highly specific protease and
adhesin/invasin. The subtilisin-like protease domain is
located at the N-terminus and contains a
protease-associated domain inserted into a loop. There
are three fibronectin type III (Fn) domains at the
C-terminus. SCP binds to integrins with the help of
Arg-Gly-Asp motifs which are thought to stabilize
conformational changes required for substrate binding.
Peptidases S8 or Subtilases are a serine endo- and
exo-peptidase clan. They have an Asp/His/Ser catalytic
triad similar to that found in trypsin-like proteases,
but do not share their three-dimensional structure and
are not homologous to trypsin. The stability of
subtilases may be enhanced by calcium, some members have
been shown to bind up to 4 ions via binding sites with
different affinity. Some members of this clan contain
disulfide bonds. These enzymes can be intra- and
extracellular, some function at extreme temperatures and
pH values.
Length = 346
Score = 28.4 bits (64), Expect = 8.4
Identities = 14/65 (21%), Positives = 20/65 (30%)
Query: 113 AAERAAAEFARAAGYGIYHTAHPYASFHWPNPGIWNPNNPPVVSNQGPGTTPSSGAAGSP 172
E+ A + AR AG + A + NNP + P T S
Sbjct: 163 DPEQQAIKRAREAGVVVVVAAGNDGNSGSGTSKPLATNNPDTGTVGSPATADDVLTVASA 222
Query: 173 RGLMP 177
+P
Sbjct: 223 NKKVP 227
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
0.320 0.134 0.427
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: 22,661,956
Number of extensions: 2164319
Number of successful extensions: 2160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2159
Number of HSP's successfully gapped: 35
Length of query: 435
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 335
Effective length of database: 6,502,202
Effective search space: 2178237670
Effective search space used: 2178237670
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 (21.8 bits)
S2: 60 (26.8 bits)