RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8070
(173 letters)
>gnl|CDD|215366 PLN02681, PLN02681, proline dehydrogenase.
Length = 455
Score = 108 bits (272), Expect = 3e-28
Identities = 40/130 (30%), Positives = 64/130 (49%), Gaps = 1/130 (0%)
Query: 29 SATPAIKDPLDLSFANPEAAFKSKTTWEVLRAYIVYQLCSSSFLVDNNMKLMKVGKAILG 88
++T L F++ A F +T E+LR+ +V QLC+ LVD L+ +LG
Sbjct: 13 TSTTTPASDDVLDFSDHAALFAGLSTSELLRSLLVLQLCAIGPLVDLGEWLLTSPLMVLG 72
Query: 89 QKMFAQVMKLTFYGHFVAGEDQYKIVPVLKRLHSFGVKPILDYSVEEDISQEEAEKRELE 148
+ + ++K TFY HF AGED + ++RL G+ ILDY+ E+ + R LE
Sbjct: 73 RAIVLALVKATFYSHFCAGEDAEEAARTVRRLWELGLGGILDYAAEDAGDNAACD-RNLE 131
Query: 149 ASTSELEQTK 158
+ +
Sbjct: 132 KFLAAIRAAA 141
>gnl|CDD|183567 PRK12515, PRK12515, RNA polymerase sigma factor; Provisional.
Length = 189
Score = 28.5 bits (64), Expect = 1.3
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 22 QKKHA--SQSATPAIKDPLDLSFANPEAAFKSKTTWEVLRAYI 62
++KH A AI+D D PE A + T LRA +
Sbjct: 91 RRKHEEIDDEAAAAIEDGAD----TPEVALQKSDTSAALRACL 129
>gnl|CDD|219955 pfam08657, DASH_Spc34, DASH complex subunit Spc34. The DASH
complex is a ~10 subunit microtubule-binding complex
that is transferred to the kinetochore prior to mitosis.
In Saccharomyces cerevisiae DASH forms both rings and
spiral structures on microtubules in vitro. Components
of the DASH complex, including Dam1, Duo1, Spc34, Dad1
and Ask1, are essential and connect the centromere to
the plus end of spindle microtubules.
Length = 255
Score = 27.9 bits (62), Expect = 2.5
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 133 VEEDISQEEAEKRELEASTSELE 155
++E I +EE E RELE +LE
Sbjct: 233 IDELIRKEEEEIRELERQLRQLE 255
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 306
Score = 28.0 bits (63), Expect = 2.5
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 118 KRLHSFGVKPILDYSVEEDISQEEAEKRELE 148
KRL FG K ++ Y ++ AE+ LE
Sbjct: 155 KRLSGFGCK-VIAYDKYKNFGDAYAEQVSLE 184
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 27.9 bits (62), Expect = 2.9
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 128 ILDYSVEEDISQEEAEKRELEASTSELEQTKEAAA 162
IL Y V EDI E+ +K +L S S L + E+ A
Sbjct: 936 ILHYLVTEDILAEDVKKSDLYGSVSSLLKVNESKA 970
>gnl|CDD|238893 cd01912, proteasome_beta, proteasome beta subunit. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each.
Length = 189
Score = 27.0 bits (61), Expect = 3.9
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 122 SFGVKPILDYSVEEDISQEEAEK 144
S ILD + D++ EEA +
Sbjct: 133 SKYAYGILDRGYKPDMTLEEAVE 155
>gnl|CDD|133221 cd05090, PTKc_Ror1, Catalytic domain of the Protein Tyrosine
Kinase, Receptor tyrosine kinase-like Orphan Receptor 1.
Protein Tyrosine Kinase (PTK) family; Receptor tyrosine
kinase-like Orphan Receptor 1 (Ror1); catalytic (c)
domain. The PTKc family is part of a larger superfamily
that includes the catalytic domains of other kinases
such as protein serine/threonine kinases, RIO kinases,
and phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. Ror
proteins are orphan receptor tyr kinases (RTKs)
containing an extracellular region with
immunoglobulin-like, cysteine-rich, and kringle domains,
a transmembrane segment, and an intracellular catalytic
domain. Ror RTKs are unrelated to the nuclear receptor
subfamily called retinoid-related orphan receptors
(RORs). RTKs are usually activated through ligand
binding, which causes dimerization and
autophosphorylation of the intracellular tyr kinase
catalytic domain. Ror kinases are expressed in many
tissues during development. Avian Ror1 was found to be
involved in late limb development. Studies in mice
reveal that Ror1 is important in the regulation of
neurite growth in central neurons, as well as in
respiratory development. Loss of Ror1 also enhances the
heart and skeletal abnormalities found in Ror2-deficient
mice.
Length = 283
Score = 27.3 bits (60), Expect = 4.3
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 101 YGHFVAGEDQYKIVPVLKRLHSFGVKPILDYSVEEDISQEEAEKREL 147
YG F + D + VL + SFG++P +S +E I E KR+L
Sbjct: 200 YGKFSSDSDIWSFGVVLWEIFSFGLQPYYGFSNQEVI--EMVRKRQL 244
>gnl|CDD|218580 pfam05409, Peptidase_C30, Coronavirus endopeptidase C30.
Corresponds to Merops family C30. These peptidases are
involved in viral polyprotein processing in replication.
Length = 293
Score = 27.1 bits (60), Expect = 5.7
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 107 GEDQYKIVPVLKRLHS-FGVKPILDYSVEED 136
G D K++ ++ L+S FG K IL Y ED
Sbjct: 228 GVDVEKLLAAIQVLNSGFGGKQILGYYSLED 258
>gnl|CDD|237259 PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed.
Length = 830
Score = 27.0 bits (61), Expect = 5.7
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 89 QKMFAQVMKLTFYGHFVAG--EDQYKIVPVLKRLHS-FGVKPILDYSVEEDISQEEAEKR 145
M V++ + G E+ + + + + L + FG++ ++ +EE + +EE +R
Sbjct: 659 LDMREDVIEDLVDAYIPPGSYEEDWDLEGLEEALKTDFGLELPIEEWLEEGLDEEELRER 718
Query: 146 ELEASTSELEQTKEAA 161
LEA+ E+ KE
Sbjct: 719 ILEAAEEAYEE-KEEE 733
>gnl|CDD|237418 PRK13534, PRK13534, 7-cyano-7-deazaguanine tRNA-ribosyltransferase;
Provisional.
Length = 639
Score = 26.9 bits (60), Expect = 7.5
Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 4/42 (9%)
Query: 128 ILDYSVEEDISQEEAEKRELEASTSELEQTKEAAAITEDVAL 169
ILD D+S+E+AE+ +LE + LE+ KEA I E +AL
Sbjct: 120 ILDIPTPPDVSREKAEE-DLEET---LERAKEAIEIKEKLAL 157
>gnl|CDD|182289 PRK10179, PRK10179, formate dehydrogenase-N subunit gamma;
Provisional.
Length = 217
Score = 26.4 bits (58), Expect = 8.2
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 72 LVDNNMKLMKVGKAILGQK-MFAQVMKLTF 100
L N K+ VGK GQK MF +M + F
Sbjct: 96 LKGNEHKVADVGKYNAGQKMMFWSIMSMIF 125
>gnl|CDD|189020 cd00128, PIN_FEN1_EXO1-like, PIN domains of Flap Endonuclease-1
(FEN1)-like and Exonuclease-1 (EXO1)-like nucleases,
structure-specific, divalent-metal-ion dependent, 5'
nucleases. PIN (PilT N terminus) domain of Flap
Endonuclease-1 (FEN1) and Exonuclease-1 (EXO1)-like
nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1)
and Xeroderma pigmentosum complementation group G (XPG)
nuclease are members 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 domain with a helical arch/clamp region (I
domain) of variable length (approximately 30 to 800
residues) 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. Most
nucleases within this family also have a carboxylate
rich active site that is involved in binding essential
divalent metal ion cofactors (Mg2+/Mn2+). Some nucleases
in this family have C-terminal extensions that act as
interaction sites for other proteins.
Length = 209
Score = 26.4 bits (58), Expect = 8.4
Identities = 11/45 (24%), Positives = 18/45 (40%)
Query: 119 RLHSFGVKPILDYSVEEDISQEEAEKRELEASTSELEQTKEAAAI 163
+L G+ PI + + EA + EA + EA+ I
Sbjct: 62 KLFENGITPIFVFDGGPPYLKSEASGKRTEARAEAEISSTEASYI 106
>gnl|CDD|197231 cd09133, PLDc_unchar5, Putative catalytic domain of uncharacterized
hypothetical proteins with one or two copies of the HKD
motif. Putative catalytic domain of uncharacterized
hypothetical proteins with similarity to phospholipase D
(PLD, EC 3.1.4.4). PLD enzymes hydrolyze phospholipid
phosphodiester bonds to yield phosphatidic acid and a
free polar head group. They can also catalyze
transphosphatidylation of phospholipids to acceptor
alcohols. Members of this subfamily contain one or two
copies of the HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the PLD superfamily.
Length = 127
Score = 25.8 bits (57), Expect = 8.4
Identities = 7/63 (11%), Positives = 22/63 (34%)
Query: 101 YGHFVAGEDQYKIVPVLKRLHSFGVKPILDYSVEEDISQEEAEKRELEASTSELEQTKEA 160
+ ++ ++ L++ GVK + + + D +E+ E+ +
Sbjct: 20 HSPWLGNAVFENLLEALEKAAERGVKIDILWGISSDEEKEKKALSEIAEKLLADRGLRGG 79
Query: 161 AAI 163
+
Sbjct: 80 VNV 82
>gnl|CDD|224188 COG1269, NtpI, Archaeal/vacuolar-type H+-ATPase subunit I [Energy
production and conversion].
Length = 660
Score = 26.6 bits (59), Expect = 9.2
Identities = 9/39 (23%), Positives = 13/39 (33%)
Query: 129 LDYSVEEDISQEEAEKRELEASTSELEQTKEAAAITEDV 167
VEE + E EL+ +LE E +
Sbjct: 107 FSSEVEELTRKLEERLSELDEELEDLEDLLEELEPLAYL 145
>gnl|CDD|224006 COG1080, PtsA, Phosphoenolpyruvate-protein kinase (PTS system EI
component in bacteria) [Carbohydrate transport and
metabolism].
Length = 574
Score = 26.4 bits (59), Expect = 9.5
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 134 EEDISQEEAEKRELEASTSELEQTKEAAAITED 166
E + + A++ A +EL Q K+ A T D
Sbjct: 234 EAVLQEYRAKQAAYAAEKAELAQLKDLPARTRD 266
>gnl|CDD|191033 pfam04576, Zein-binding, Zein-binding. This domain binds to zein
proteins, pfam01559. Zein proteins are seed storage
proteins.
Length = 94
Score = 25.3 bits (56), Expect = 9.8
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 141 EAEKRELEASTSELEQTKEAAAITEDVALK 170
EAE++ L A ELE+ + AAA A+
Sbjct: 9 EAERKALAALYKELEEERSAAASAASEAMA 38
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
0.316 0.129 0.359
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,486,994
Number of extensions: 760058
Number of successful extensions: 1059
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1056
Number of HSP's successfully gapped: 44
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (24.8 bits)