RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046142
(132 letters)
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type. [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 113 bits (286), Expect = 4e-33
Identities = 43/96 (44%), Positives = 61/96 (63%), Gaps = 2/96 (2%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHR 93
F + L+IVGVGY RA+ +G+ L L LGY H VE +P + + K + G+DK
Sbjct: 82 FEKKLEIVGVGY--RAQLQGKKLNLSLGYSHPVEYEIPEGITVEVPKPTEIVVKGIDKQL 139
Query: 94 VHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGKK 129
V Q AA +R+ + P+P+KGKGI A EV+++K GKK
Sbjct: 140 VGQVAAEIRAFRKPEPYKGKGIRYAGEVVRRKEGKK 175
>gnl|CDD|235495 PRK05498, rplF, 50S ribosomal protein L6; Validated.
Length = 178
Score = 110 bits (279), Expect = 6e-32
Identities = 46/98 (46%), Positives = 63/98 (64%), Gaps = 2/98 (2%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHR 93
F + L+IVGVGY RA+ +G+ L L LGY H VE +P + + K + G+DK
Sbjct: 83 FEKKLEIVGVGY--RAQVKGKKLNLSLGYSHPVEYEIPEGITVEVPKPTEIVVKGIDKQL 140
Query: 94 VHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGKKKS 131
V Q AA +RS +PP+P+KGKGI A EV+++K GKKK
Sbjct: 141 VGQVAAEIRSYRPPEPYKGKGIRYAGEVVRRKEGKKKK 178
>gnl|CDD|177062 CHL00140, rpl6, ribosomal protein L6; Validated.
Length = 178
Score = 91.5 bits (228), Expect = 2e-24
Identities = 42/96 (43%), Positives = 61/96 (63%), Gaps = 2/96 (2%)
Query: 33 KFLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKH 92
F + L++ GVGY RA+ +G+ L L LGY H V++ +P + + N + G+DK
Sbjct: 82 GFEKKLELQGVGY--RAQVQGKDLILNLGYSHPVKIKIPPGISVEVENNTNITIKGIDKE 139
Query: 93 RVHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGK 128
V QFAA +RS +PP+P+KGKGI EVI++K GK
Sbjct: 140 LVGQFAAKIRSVRPPEPYKGKGIRYKGEVIRRKAGK 175
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 89.9 bits (224), Expect = 9e-24
Identities = 39/96 (40%), Positives = 56/96 (58%), Gaps = 2/96 (2%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHR 93
F + L+IVGVGY RA+ G L L LGY H V + +P + + + G+DK
Sbjct: 83 FEKKLEIVGVGY--RAQVVGGNLELFLGYSHPVVIEIPEGITVEVPGPTEIVVEGIDKEL 140
Query: 94 VHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGKK 129
V Q AA++R+ + P+P+KGKGI E I++K GK
Sbjct: 141 VGQVAANIRAARKPEPYKGKGIRYDGEYIRRKEGKT 176
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 64.9 bits (159), Expect = 5e-15
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 41 VGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHRVHQFAAS 100
+ VG R +G L L LG ++ +P V + K V+ G+DK +V QFAA
Sbjct: 1 IPVGV--RVSIDGVNLVLVLGPKGELTREIPPGVTVKVEKITVIIVSGIDKEKVGQFAAL 58
Query: 101 VRSRKPPDPFKGKGIM 116
+ + + P P GKG+
Sbjct: 59 IGTYRAPIPNMGKGVS 74
>gnl|CDD|165398 PHA03126, PHA03126, dUTPase; Provisional.
Length = 326
Score = 28.8 bits (64), Expect = 0.68
Identities = 15/28 (53%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 42 GVGYKARAEAEGRLLYLKLGYVHDVELT 69
G ++ARAEA GRLL L H VEL+
Sbjct: 17 GNRWRARAEAAGRLLVLINN--HTVELS 42
>gnl|CDD|223545 COG0469, PykF, Pyruvate kinase [Carbohydrate transport and
metabolism].
Length = 477
Score = 26.7 bits (60), Expect = 4.1
Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 23 DKFTLTWMEAKFLRFLKIVGVGYKARAEA--EGRLLYLKLGYVH-DVELTVPSAVR 75
+KFTLT + + V V YK A+ G + L G + V AV
Sbjct: 91 EKFTLTTDDKVGEGDEERVSVDYKDLAKDVKPGDRILLDDGKIELRVVEVDGDAVI 146
>gnl|CDD|234593 PRK00046, murB, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 334
Score = 26.3 bits (59), Expect = 5.3
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 22/74 (29%)
Query: 36 RFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHRVH 95
R+ I VG++ + + L Y G + ++ +A +F + VC
Sbjct: 175 RYA-ITAVGFRLPKQWQPVLDY---GDLARLDPDTVTAQDVF----DAVC---------- 216
Query: 96 QFAASVRSRKPPDP 109
++R K PDP
Sbjct: 217 ----AIRRSKLPDP 226
>gnl|CDD|173738 cd07835, STKc_CDK1_like, Catalytic domain of Cyclin-Dependent
protein Kinase 1-like Serine/Threonine Kinases.
Serine/Threonine Kinases (STKs), Cyclin-Dependent
protein Kinase 1 (CDK1)-like subfamily, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The CDK1 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. CDKs belong to a large
family of STKs that are regulated by their cognate
cyclins. Together, they are involved in the control of
cell-cycle progression, transcription, and neuronal
function. This subfamily is composed of CDK1 from
higher eukaryotes, plants, and yeasts, as well as CDK2
and CDK3. CDK1 is also called Cell division control
protein 2 (Cdc2) or p34 protein kinase, and is
regulated by cyclins A, B, and E. The CDK1/cyclin A
complex controls G2 phase entry and progression while
the CDK1/cyclin B complex is critical for G2 to M phase
transition. CDK2 is regulated by cyclin E or cyclin A.
Upon activation by cyclin E, it phosphorylates the
retinoblastoma (pRb) protein which activates E2F
mediated transcription and allows cells to move into S
phase. The CDK2/cyclin A complex plays a role in
regulating DNA replication. Studies in knockout mice
revealed that CDK1 can compensate for the loss of the
cdk2 gene as it can also bind cyclin E and drive G1 to
S phase transition. CDK3 is regulated by cyclin C and
it phosphorylates pRB specifically during the G0/G1
transition. This phosphorylation is required for cells
to exit G0 efficiently and enter the G1 phase.
Length = 283
Score = 26.1 bits (58), Expect = 6.1
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 42 GVGYKARAEAEGRLLYLKLGYVHDVELTVPS-AVR-IFCLKN----NVVC 85
GV YKAR + G ++ LK + + VPS A+R I LK N+V
Sbjct: 13 GVVYKARDKLTGEIVALKKIRLETEDEGVPSTAIREISLLKELNHPNIVR 62
>gnl|CDD|143395 cd06534, ALDH-SF, NAD(P)+-dependent aldehyde dehydrogenase
superfamily. The aldehyde dehydrogenase superfamily
(ALDH-SF) of NAD(P)+-dependent enzymes, in general,
oxidize a wide range of endogenous and exogenous
aliphatic and aromatic aldehydes to their corresponding
carboxylic acids and play an important role in
detoxification. Besides aldehyde detoxification, many
ALDH isozymes possess multiple additional catalytic and
non-catalytic functions such as participating in
metabolic pathways, or as binding proteins, or
osmoregulants, to mention a few. The enzyme has three
domains, a NAD(P)+ cofactor-binding domain, a catalytic
domain, and a bridging domain; and the active enzyme is
generally either homodimeric or homotetrameric. The
catalytic mechanism is proposed to involve cofactor
binding, resulting in a conformational change and
activation of an invariant catalytic cysteine
nucleophile. The cysteine and aldehyde substrate form an
oxyanion thiohemiacetal intermediate resulting in
hydride transfer to the cofactor and formation of a
thioacylenzyme intermediate. Hydrolysis of the
thioacylenzyme and release of the carboxylic acid
product occurs, and in most cases, the reduced cofactor
dissociates from the enzyme. The evolutionary
phylogenetic tree of ALDHs appears to have an initial
bifurcation between what has been characterized as the
classical aldehyde dehydrogenases, the ALDH family
(ALDH) and extended family members or aldehyde
dehydrogenase-like (ALDH-L) proteins. The ALDH proteins
are represented by enzymes which share a number of
highly conserved residues necessary for catalysis and
cofactor binding and they include such proteins as
retinal dehydrogenase, 10-formyltetrahydrofolate
dehydrogenase, non-phosphorylating glyceraldehyde
3-phosphate dehydrogenase,
delta(1)-pyrroline-5-carboxylate dehydrogenases,
alpha-ketoglutaric semialdehyde dehydrogenase,
alpha-aminoadipic semialdehyde dehydrogenase, coniferyl
aldehyde dehydrogenase and succinate-semialdehyde
dehydrogenase. Included in this larger group are all
human, Arabidopsis, Tortula, fungal, protozoan, and
Drosophila ALDHs identified in families ALDH1 through
ALDH22 with the exception of families ALDH18, ALDH19,
and ALDH20 which are present in the ALDH-like group. The
ALDH-like group is represented by such proteins as
gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA
reductase, and coenzyme A acylating aldehyde
dehydrogenase. All of these proteins have a conserved
cysteine that aligns with the catalytic cysteine of the
ALDH group.
Length = 367
Score = 26.0 bits (58), Expect = 7.4
Identities = 13/58 (22%), Positives = 18/58 (31%), Gaps = 10/58 (17%)
Query: 41 VGVGYKARAEAEGRL--LYLKLG-----YVH---DVELTVPSAVRIFCLKNNVVCCCG 88
VG A L + L+LG V D++ V AV +C
Sbjct: 181 TAVGKAIMKAAAENLKPVTLELGGKSPVIVDEDADLDAAVEGAVFGAFFNAGQICTAA 238
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
0.324 0.138 0.433
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,537,398
Number of extensions: 561578
Number of successful extensions: 539
Number of sequences better than 10.0: 1
Number of HSP's gapped: 533
Number of HSP's successfully gapped: 11
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)