RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5916
(190 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 69.0 bits (170), Expect = 3e-16
Identities = 23/52 (44%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 86 RLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILM 137
R N RERRR +NDA +ELR ++P + +KLSK L LA YI
Sbjct: 2 RKAHNERERRRRDRINDAFEELRELLPTPPN---KKLSKAEILRLAIEYIKH 50
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 68.8 bits (169), Expect = 3e-16
Identities = 25/55 (45%), Positives = 33/55 (60%), Gaps = 2/55 (3%)
Query: 90 NARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALEE 144
NARERRR +N+A DELR+++P P +KLSK L LA YI L++
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTL--PKNKKLSKAEILRLAIEYIKSLQEELQK 53
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four helix
bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide sequences
such as N-box (5-CACGc/aG-3), those which have a COE
domain (Collier/Olf-1/EBF) which is involved in both in
dimerization and in DNA binding, and those which bind
pentanucleotides ACGTG or GCGTG and have a PAS domain
which allows the dimerization between PAS proteins, the
binding of small molecules (e.g., dioxin), and
interactions with non-PAS proteins.
Length = 60
Score = 67.6 bits (166), Expect = 1e-15
Identities = 25/58 (43%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 86 RLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLAKNYILMQANALE 143
R N RERRR +NDA DELR+++P P +KLSK L A +YI L+
Sbjct: 5 REAHNLRERRRRERINDAFDELRSLLPT--LPPSKKLSKAEILRKAVDYIKSLQELLQ 60
>gnl|CDD|132496 TIGR03455, HisG_C-term, ATP phosphoribosyltransferase, C-terminal
domain. This domain corresponds to the C-terminal third
of the HisG protein. It is absent in many lineages.
Length = 100
Score = 30.6 bits (70), Expect = 0.13
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 89 INARERRRMHDLN---DALDELRAVIPYAHSPSVRKLSK 124
+ AR + + +N D LDE+RA++P P+V L+
Sbjct: 24 LAARGKV-LLMMNVPRDNLDEVRALLPGLEGPTVSPLAD 61
>gnl|CDD|235270 PRK04286, PRK04286, hypothetical protein; Provisional.
Length = 298
Score = 29.9 bits (68), Expect = 0.63
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 53 HLSHNSRFQDPTHSGAMGSLQPLAKKNRQGKTV-----RLNINARERRRMHDLNDALDEL 107
H H++ F + + S + + K+ +GK V NIN +RRR A+ ++
Sbjct: 75 HYDHHTPFYEDPY---ELSDEEIPKEIYKGKIVLIKDPTENINWSQRRRAPRFLKAVKDI 131
Query: 108 RAVIPYA 114
I YA
Sbjct: 132 AKKIEYA 138
>gnl|CDD|132943 cd06612, STKc_MST1_2, Catalytic domain of the Protein
Serine/Threonine Kinases, Mammalian Ste20-like protein
kinase 1 and 2. Serine/threonine kinases (STKs),
mammalian Ste20-like protein kinase 1 (MST1) and MST2
subfamily, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
MST1/2 subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. This subfamily is composed of MST1, MST2, and
related proteins including Drosophila Hippo and
Dictyostelium discoideum Krs1 (kinase responsive to
stress 1). MST1/2 and Hippo are involved in a conserved
pathway that governs cell contact inhibition, organ size
control, and tumor development. MST1 activates the
mitogen-activated protein kinases (MAPKs) p38 and c-Jun
N-terminal kinase (JNK) through MKK7 (a MAPK kinase) and
MEKK1 (a MAPK kinase kinase) by acting as a MAPK kinase
kinase kinase (MAPKKKK). Activation of JNK by MST1 leads
to caspase activation and apoptosis. MST1 has also been
implicated in cell proliferation and differentiation.
Krs1 may regulate cell growth arrest and apoptosis in
response to cellular stress.
Length = 256
Score = 29.2 bits (66), Expect = 1.1
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 149 ITYIQ-AQGTMTMPPGFDLQATMLPVQQPDTPPPSTSDPSNVS 190
IT I+ A+G PP D+ P+ PPP+ SDP S
Sbjct: 187 ITAIEMAEGK---PPYSDIHPMRAIFMIPNKPPPTLSDPEKWS 226
>gnl|CDD|223118 COG0040, HisG, ATP phosphoribosyltransferase [Amino acid transport
and metabolism].
Length = 290
Score = 28.7 bits (65), Expect = 1.7
Identities = 10/37 (27%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 89 INARERR--RMHDLNDALDELRAVIPYAHSPSVRKLS 123
I AR + ++ + LDE+ A++P P++ L+
Sbjct: 213 IEARGSKYIMLNAPRERLDEVTALLPGMEGPTILPLA 249
>gnl|CDD|131880 TIGR02833, spore_III_AB, stage III sporulation protein AB. A
comparative genome analysis of all sequenced genomes of
shows a number of proteins conserved strictly among the
endospore-forming subset of the Firmicutes. This
protein, a member of this panel, is designated stage III
sporulation protein AB [Cellular processes, Sporulation
and germination].
Length = 170
Score = 28.4 bits (64), Expect = 1.7
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 92 RERRR-MHDLNDALDELRAVIPYAHSPSVRKLSKIA 126
+ER R + L +AL L A I Y H+P KIA
Sbjct: 24 KERPRQLRQLINALQSLEAEIVYGHTPLPEAFKKIA 59
>gnl|CDD|234781 PRK00489, hisG, ATP phosphoribosyltransferase; Reviewed.
Length = 287
Score = 28.5 bits (65), Expect = 1.8
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 89 INARERRRMHDLN---DALDELRAVIPYAHSPSVRKLSK 124
+ ARE + +N + LD + A++P SP+V L
Sbjct: 210 LRARESK-YLMMNAPKEKLDAVIALLPGLESPTVSPLGD 247
>gnl|CDD|176187 cd05284, arabinose_DH_like, D-arabinose dehydrogenase. This group
contains arabinose dehydrogenase (AraDH) and related
alcohol dehydrogenases. AraDH is a member of the medium
chain dehydrogenase/reductase family and catalyzes the
NAD(P)-dependent oxidation of D-arabinose and other
pentoses, the initial step in the metabolism of
d-arabinose into 2-oxoglutarate. Like the alcohol
dehydrogenases, AraDH binds a zinc in the catalytic
cleft as well as a distal structural zinc. AraDH forms
homotetramers as a dimer of dimers. AraDH replaces a
conserved catalytic His with replace with Arg, compared
to the canonical ADH site. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 340
Score = 28.3 bits (64), Expect = 2.8
Identities = 25/113 (22%), Positives = 36/113 (31%), Gaps = 30/113 (26%)
Query: 10 SNETSQVPGRRT-PLGN---VGLGGFYFPPSVSAVSAGPPSDENCPEHLSHNSRFQDPTH 65
S+ET + + G VG GG P+ V
Sbjct: 245 SDETLALAAKLLAKGGRYVIVGYGGHGRLPTSDLVPTE--------------ISVIGS-L 289
Query: 66 SGAMGSLQPLAKKNRQGKTVRLNINARERRRMHDLNDALDEL-------RAVI 111
G L + GK V++ I + + D N+ALD L RAV+
Sbjct: 290 WGTRAELVEVVALAESGK-VKVEI---TKFPLEDANEALDRLREGRVTGRAVL 338
>gnl|CDD|151234 pfam10768, FliX, Class II flagellar assembly regulator. The FliX
protein is possibly a transient component of the
flagellum that is required for the assembly process.
FliX may contribute to the targeting or assembly of the
P- and L-ring protein monomers at the cell pole. The
family carries a potential N-terminal signal sequence
and at least one transmembrane domain indicating that it
might function either in or in association with the cell
membrane.
Length = 140
Score = 27.3 bits (61), Expect = 3.2
Identities = 24/102 (23%), Positives = 33/102 (32%), Gaps = 17/102 (16%)
Query: 8 YYSNETSQVPGRRTPLGNVGLGGFYFPPSVSAVSAGPPSDENCPEHLSHNSRFQDPTHSG 67
T+ V G G GF P + AG S+ + P
Sbjct: 4 SGPRGTTAVGGAGAKTRRSGGSGF-ALPLAAG--AGSTSE---------TAAASAPAAVA 51
Query: 68 AMGSLQPLAKKNRQGKTVRLNINARERRRMHDLNDALDELRA 109
+ +L L QG + R RR DL D LD+L+
Sbjct: 52 GVDALLAL-----QGVDDPVERRRRAVRRGEDLLDVLDDLKI 88
>gnl|CDD|238366 cd00714, GFAT, Glutamine amidotransferases class-II
(Gn-AT)_GFAT-type. This domain is found at the
N-terminus of glucosamine-6P synthase (GlmS, or GFAT in
humans). The glutaminase domain catalyzes amide
nitrogen transfer from glutamine to the appropriate
substrate. In this process, glutamine is hydrolyzed to
glutamic acid and ammonia. In humans, GFAT catalyzes
the first and rate-limiting step of hexosamine
metabolism, the conversion of D-fructose-6P (Fru6P)
into D-glucosamine-6P using L-glutamine as a nitrogen
source. The end product of this pathway, UDP-N-acetyl
glucosamine, is a major building block of the bacterial
peptidoglycan and fungal chitin.
Length = 215
Score = 27.0 bits (61), Expect = 5.0
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 43 GPPSDENCPEHLSHNSRF 60
G P+D N H S +
Sbjct: 77 GEPTDVNAHPHRSCDGEI 94
>gnl|CDD|227778 COG5491, VPS24, Conserved protein implicated in secretion [Cell
motility and secretion].
Length = 204
Score = 26.7 bits (59), Expect = 7.4
Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 6/86 (6%)
Query: 72 LQPLAKKNRQGKTVRLNINARERRRMHDLNDALDELRAVIPYAHSPSVRKLSKIATLLLA 131
Q L + + R A E ++ LD + + S K+ ++
Sbjct: 23 GQVLLNEIAKKAPNR-RRLAEELYKLRKARSRLDASISRL---QSLDTMLFEKVVMRQVS 78
Query: 132 KNYIL--MQANALEELRRIITYIQAQ 155
+ M N LE +RRI+ + Q
Sbjct: 79 GDMAKAAMYMNELESIRRIMQLFETQ 104
>gnl|CDD|100073 cd02644, R3H_jag, R3H domain found in proteins homologous to
Bacillus subtilus Jag, which is associated with SpoIIIJ.
SpoIIIJ is necessary for the third stage of sporulation.
The name of the R3H domain comes from the characteristic
spacing of the most conserved arginine and histidine
residues. The function of the domain is predicted to
bind ssDNA or ssRNA in a sequence-specific manner.
Length = 67
Score = 25.1 bits (56), Expect = 8.2
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 73 QPLAKKNRQ-GKTVRLN-INARERRRMHDL 100
+ A+K R+ GK V+L +NA ERR +HD
Sbjct: 13 ERAAEKVRRTGKPVKLEPMNAYERRIIHDA 42
>gnl|CDD|149228 pfam08029, HisG_C, HisG, C-terminal domain.
Length = 73
Score = 24.8 bits (55), Expect = 9.3
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 96 RMHDLN---DALDELRAVIPYAHSPSVRKLSK 124
+ N + LDE+ A++P +P+V LS
Sbjct: 4 VLVMYNAPREKLDEVLALLPGLEAPTVSPLSD 35
>gnl|CDD|215321 PLN02592, PLN02592, ent-copalyl diphosphate synthase.
Length = 800
Score = 26.8 bits (59), Expect = 9.6
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 29 GGFYFPPSVSAVSAGPPSDENCPEHL 54
G F F PS +A + DENC E+L
Sbjct: 266 GSFLFSPSSTAFALMQTKDENCLEYL 291
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
0.313 0.130 0.376
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,812,703
Number of extensions: 903096
Number of successful extensions: 747
Number of sequences better than 10.0: 1
Number of HSP's gapped: 743
Number of HSP's successfully gapped: 24
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
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: 56 (25.3 bits)