RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11043
(217 letters)
>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 = 65.0 bits (159), Expect = 2e-14
Identities = 19/55 (34%), Positives = 31/55 (56%)
Query: 149 QKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
+K F L + + ++PYP+ ++ ELA+ GLT QV WF+NRR + +
Sbjct: 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLK 56
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 60.0 bits (146), Expect = 2e-12
Identities = 17/50 (34%), Positives = 29/50 (58%)
Query: 154 FKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
F L + + ++PYP+ ++ ELA+ GL+ QV WF+NRR + +
Sbjct: 8 FTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 52.9 bits (128), Expect = 5e-10
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 141 PRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQ 200
RT + EQ L + + ++ YP+ ++ ELA+ GLT QV WF+NRR
Sbjct: 3 KRTTFTPEQ---------LEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRA 53
Query: 201 RDR 203
+ +
Sbjct: 54 KWK 56
>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 = 48.3 bits (116), Expect = 2e-08
Identities = 18/35 (51%), Positives = 25/35 (71%)
Query: 167 LQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQR 201
L +PYP+ +K ELA+ TGL+ Q+ NWF N R+R
Sbjct: 6 LHNPYPSEEEKSELARQTGLSRKQIDNWFINARRR 40
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 39.7 bits (93), Expect = 3e-04
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 151 THCFKERTR------SLLREWYLQDPYPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
+ +R R +L + +PYP+ + +L+ + P V WF+N+R +++
Sbjct: 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEK 107
>gnl|CDD|222133 pfam13443, HTH_26, Cro/C1-type HTH DNA-binding domain. This is a
helix-turn-helix domain that probably binds to DNA.
Length = 63
Score = 29.4 bits (67), Expect = 0.27
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 176 KKRELAQATGLTPTQVGNWFKNRRQR 201
K +LA+ATG++ + K +R
Sbjct: 12 SKTDLARATGISRATLSRLKKGEAKR 37
>gnl|CDD|218541 pfam05292, MCD, Malonyl-CoA decarboxylase (MCD). This family
consists of several eukaryotic malonyl-CoA decarboxylase
(MLYCD) proteins. Malonyl-CoA, in addition to being an
intermediate in the de novo synthesis of fatty acids, is
an inhibitor of carnitine palmitoyltransferase I, the
enzyme that regulates the transfer of long-chain fatty
acyl-CoA into mitochondria, where they are oxidized.
After exercise, malonyl-CoA decarboxylase participates
with acetyl-CoA carboxylase in regulating the
concentration of malonyl-CoA in liver and adipose
tissue, as well as in muscle. Malonyl-CoA decarboxylase
is regulated by AMP-activated protein kinase (AMPK).
Length = 354
Score = 30.8 bits (69), Expect = 0.50
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 109 MWLEAHYQEAEKLRGRPLGPVDKYRVRKKFPLPRTIWDGEQ 149
M L A Y EK RG+ L V + ++ L R W G++
Sbjct: 296 MRLCARYLLQEKKRGKALDSVANFHLQNGAMLERLNWMGDR 336
>gnl|CDD|215304 PLN02554, PLN02554, UDP-glycosyltransferase family protein.
Length = 481
Score = 30.9 bits (70), Expect = 0.53
Identities = 20/51 (39%), Positives = 23/51 (45%), Gaps = 10/51 (19%)
Query: 28 FTVSQVATVCETLEESGDIERLARFLWSLPVAHPNI-----GELNKNEAVL 73
F+ Q + LE SG RFLWSL A PNI GE E +L
Sbjct: 287 FSEEQAREIAIALERSGH-----RFLWSLRRASPNIMKEPPGEFTNLEEIL 332
>gnl|CDD|188624 cd09904, H3TH_XPG, H3TH domain of Xeroderma pigmentosum
complementation group G (XPG) nuclease, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease. The Xeroderma pigmentosum complementation
group G (XPG) nuclease plays a central role in
nucleotide excision repair (NER) in cleaving DNA bubble
structures or loops. XPG 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. Members of this subgroup include the
H3TH (helix-3-turn-helix) domains of XPG and other
similar eukaryotic 5' nucleases. These nucleases contain
a PIN (PilT N terminus) domain with a helical arch/clamp
region/I domain (not included here) and inserted within
the PIN domain is an atypical helix-hairpin-helix-2
(HhH2)-like region. This atypical HhH2 region, the H3TH
domain, has an extended loop with at least three turns
between the first two helices, and only three of the
four helices appear to be conserved. Both the H3TH
domain and the helical arch/clamp region are involved in
DNA binding. Studies suggest that a glycine-rich loop
in the H3TH domain contacts the phosphate backbone of
the template strand in the downstream DNA duplex. These
nucleases have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+ or Mn2+) required for nuclease activity.
The first metal binding site is composed entirely of
Asp/Glu residues from the PIN domain, whereas, the
second metal binding site is composed generally of two
Asp residues from the PIN domain and one Asp residue
from the H3TH domain. Together with the helical arch and
network of amino acids interacting with metal binding
ions, the H3TH region defines a positively charged
active-site DNA-binding groove in structure-specific 5'
nucleases.
Length = 97
Score = 28.0 bits (63), Expect = 1.3
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 15/64 (23%)
Query: 127 GPVDKYRVRKKFPLP------RTIWDGEQKTH---------CFKERTRSLLREWYLQDPY 171
GPV+ + +FP + W+ Q FK + ++ L+ L +
Sbjct: 22 GPVNAMEILSEFPGEEDLEKFKDWWENAQPEKSEDSDNDKQEFKRKHKNYLKNLILPPGF 81
Query: 172 PNPT 175
P+P
Sbjct: 82 PSPA 85
>gnl|CDD|200360 TIGR04109, heme_ox_HugZ, heme oxygenase, HugZ family. Members of
this protein family are HugZ, a class of heme oxygenase
that belongs to the PPOX family (pfam01243) and lacks
homology to the HmuO family (pfam01126). Characterized
members of this family include HP0318 from Helicobacter
pylori and CJ1613c from Campylobacter jejuni. This
enzyme releases iron during the conversion of heme to
biliverdin.
Length = 243
Score = 29.3 bits (66), Expect = 1.4
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 63 IGELNKNEAVLRARA-IVSFHSGNYREMYSILEHYKFTKDSHGKLQAMWLE 112
+ LN N V+ + A VS Y + + EH+ K++ K++ M+LE
Sbjct: 100 LSTLNANGEVVCSYAPFVSDGGDYYIYISEVSEHFANLKNNPNKVEVMFLE 150
>gnl|CDD|236727 PRK10625, tas, putative aldo-keto reductase; Provisional.
Length = 346
Score = 28.7 bits (64), Expect = 2.3
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 171 YPNPTKKRELAQATGLTPTQVGNWFKNRRQRDR 203
YP P + + GLT T +GNW R R++
Sbjct: 53 YPVPPR----PETQGLTETYIGNWLAKRGSREK 81
>gnl|CDD|197775 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Length = 56
Score = 26.3 bits (59), Expect = 2.5
Identities = 5/23 (21%), Positives = 12/23 (52%)
Query: 178 RELAQATGLTPTQVGNWFKNRRQ 200
ELA+ G++ + + +R+
Sbjct: 14 EELAEKLGVSRSTLSRIENGKRK 36
>gnl|CDD|238631 cd01306, PhnM, PhnM is believed to be a subunit of the membrane
associated C-P lyase complex. C-P lyase is thought to
catalyze the direct cleavage of inactivated C-P bonds to
yield inorganic phosphate and the corresponding
hydrocarbons. It is responsible for cleavage of
alkylphosphonates, which are utilized as sole phosphorus
sources by many bacteria.
Length = 325
Score = 28.4 bits (64), Expect = 2.7
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 168 QDPYPNPTKKRE-LAQATGLTPTQVGNWFKNRRQRDRAAAAKNRLEV 213
Q + + K RE A+ GL+ +V R+ R A A NR E+
Sbjct: 122 QRQFRDLEKYREYYAKKYGLSDEEVEEAILERKARAAAYAPANRSEL 168
>gnl|CDD|238045 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Prokaryotic DNA binding proteins belonging to the
xenobiotic response element family of transcriptional
regulators.
Length = 58
Score = 26.4 bits (59), Expect = 3.0
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 178 RELAQATGLTPTQVGNWFKNRR 199
ELA+ G++ + + +R
Sbjct: 16 EELAEKLGVSRSTISRIENGKR 37
>gnl|CDD|219000 pfam06367, Drf_FH3, Diaphanous FH3 Domain. This region is found in
the Formin-like and and diaphanous proteins.
Length = 197
Score = 28.0 bits (63), Expect = 3.2
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 82 HSGNYREMYSILEHYKFTKDSHGKLQAMW 110
+ SIL+H +D +L W
Sbjct: 133 DTEAEPHFLSILQHLLLIRDDEEELPQYW 161
>gnl|CDD|200443 cd11287, Sec23_C, C-terminal Actin depolymerization factor-homology
domain of Sec23. The C-terminal domain of the Sec23
subunit of the coat protein complex II (COPII) is
distantly related to gelsolin-like repeats and the actin
depolymerizing domains found in cofilin and similar
proteins. Sec23 forms a tight complex with Sec24. The
cytoplasmic Sec23/24 complex is recruited together with
Sar1-GTP and Sec13/31 to induce coat polymerization and
membrane deformation in the forming of COPII-coated
endoplasmic reticulum vesicles. The function of the
Sec23 C-terminal domain is unclear.
Length = 121
Score = 27.3 bits (61), Expect = 3.4
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 103 HGKLQAMWLEAHYQ---EAEKLRGRPLGPVDKYR--VRKKFPLPRTI 144
HG+ A W +A YQ E E + PVD + ++ +FP+PR I
Sbjct: 51 HGETIAQWRKAGYQDQPEYENFKDLLEAPVDDAQELLQDRFPMPRYI 97
>gnl|CDD|201759 pfam01381, HTH_3, Helix-turn-helix. This large family of DNA
binding helix-turn helix proteins includes Cro and CI.
Within the Neisseria gonorrhoeae phage associated
protein NGO0477, the full protein fold incorporates a
helix-turn-helix motif, but the function of this member
is unlikely to be that of a DNA-binding regulator, the
function of most other members, so is not necessarily
characteristic of the whole family.
Length = 55
Score = 25.6 bits (57), Expect = 4.1
Identities = 5/23 (21%), Positives = 12/23 (52%)
Query: 177 KRELAQATGLTPTQVGNWFKNRR 199
+ ELA+ G++ + + +R
Sbjct: 12 QEELAEKLGVSRSTISKIENGKR 34
>gnl|CDD|116948 pfam08367, M16C_assoc, Peptidase M16C associated. This domain
appears in eukaryotes as well as bacteria and tends to
be found near the C-terminus of the metalloprotease M16C
(pfam05193).
Length = 248
Score = 27.6 bits (62), Expect = 4.4
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 71 AVLRARAIVSFHSGNYREMYSILEHYKFTKD 101
A+ RA + +S +G E+ S L+ KF K+
Sbjct: 218 AMSRAASYLS-IAGAISELLSGLDQVKFIKE 247
>gnl|CDD|147776 pfam05804, KAP, Kinesin-associated protein (KAP). This family
consists of several eukaryotic kinesin-associated (KAP)
proteins. Kinesins are intracellular multimeric
transport motor proteins that move cellular cargo on
microtubule tracks. It has been shown that the sea
urchin KRP85/95 holoenzyme associates with a KAP115
non-motor protein, forming a heterotrimeric complex in
vitro, called the Kinesin-II.
Length = 708
Score = 27.9 bits (62), Expect = 4.4
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 19 PMFALPTLNFTVSQVATVCETL-EESGDIERLARFLWSLPVAHPNIGELNKNEAVLRARA 77
P PT++ ++ + E L E+S + R + + L N+ EL NE +L A A
Sbjct: 107 PPIEGPTIDANINDIDEYIELLYEDSPEKVRGSALILQLARNPDNLEELVNNETLLGALA 166
Query: 78 IV 79
V
Sbjct: 167 RV 168
>gnl|CDD|225194 COG2312, COG2312, Erythromycin esterase homolog [General function
prediction only].
Length = 405
Score = 27.4 bits (61), Expect = 6.2
Identities = 7/36 (19%), Positives = 13/36 (36%)
Query: 86 YREMYSILEHYKFTKDSHGKLQAMWLEAHYQEAEKL 121
YREM + +D+ + A +K+
Sbjct: 235 YREMPDAGDASWNLRDAAMAETLEAVLATDYPPDKI 270
>gnl|CDD|235907 PRK07004, PRK07004, replicative DNA helicase; Provisional.
Length = 460
Score = 27.6 bits (61), Expect = 6.4
Identities = 23/61 (37%), Positives = 27/61 (44%), Gaps = 14/61 (22%)
Query: 4 SLGEN-------ISR----LAPVIPCPMFALPTLNFTVSQVAT---VCETLEESGDIERL 49
S GEN ISR LA + P+ AL LN + Q V L ESG IE+
Sbjct: 340 SQGENRATEISEISRSLKSLAKELDVPVIALSQLNRGLEQRPNKRPVMSDLRESGAIEQD 399
Query: 50 A 50
A
Sbjct: 400 A 400
>gnl|CDD|226957 COG4591, LolE, ABC-type transport system, involved in lipoprotein
release, permease component [Cell envelope biogenesis,
outer membrane].
Length = 408
Score = 26.9 bits (60), Expect = 8.2
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 166 YLQDPYPNPTKKRELAQATGLTPTQVGNWF 195
L+DP+ KR+L + +W
Sbjct: 226 KLKDPFNAEELKRKLEIELLPQGLKAKDWR 255
>gnl|CDD|166842 PRK00183, PRK00183, hypothetical protein; Provisional.
Length = 157
Score = 26.3 bits (58), Expect = 9.4
Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 11/67 (16%)
Query: 106 LQAMWLEAHYQEAEKLRGRPLGPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRSLLRE- 164
Q+ WL + +E L G+P + R W H +ER+ + +
Sbjct: 71 AQSTWLGLEVESSEVLGGQPEHAFVTFTAR---------WHDADGEHSHRERSAFVQHQG 121
Query: 165 -WYLQDP 170
WY DP
Sbjct: 122 RWYFIDP 128
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 0.133 0.411
Gapped
Lambda K H
0.267 0.0825 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,327,880
Number of extensions: 1062507
Number of successful extensions: 968
Number of sequences better than 10.0: 1
Number of HSP's gapped: 968
Number of HSP's successfully gapped: 30
Length of query: 217
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 124
Effective length of database: 6,812,680
Effective search space: 844772320
Effective search space used: 844772320
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: 57 (25.6 bits)