RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780260|ref|YP_003064673.1| 50S ribosomal protein L4
[Candidatus Liberibacter asiaticus str. psy62]
(207 letters)
>gnl|CDD|144240 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family. This
family includes Ribosomal L4/L1 from eukaryotes and
archaebacteria and L4 from eubacteria. L4 from yeast has
been shown to bind rRNA.
Length = 190
Score = 201 bits (514), Expect = 1e-52
Identities = 78/191 (40%), Positives = 113/191 (59%), Gaps = 3/191 (1%)
Query: 17 ISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHS 76
+ + +F + + +L RV+ Q +R G + +K RSEV+ G K + QKGTGRAR
Sbjct: 1 VELPPAVFGAEIRPDLLHRVVVAQLANRRQGTASTKTRSEVSGGGKKPWRQKGTGRARAG 60
Query: 77 SKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKT 136
S +RGGG AFGP P + L KKVR LALR ALS K ++V+D+ + KT
Sbjct: 61 SIRSPLWRGGGVAFGPKPRDYSYKLNKKVRRLALRSALSAKAREGKLVVVDDFELEIPKT 120
Query: 137 KYLVTRFRALDLSN--ALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVL 194
K V + L L LI+ + D N L+ARN+P ++++ V G+NVYD+L K+V+
Sbjct: 121 KEAVKLLKNLGLKGKSVLIVVDEK-DENLYLSARNLPGVDVVTVDGLNVYDLLPADKVVI 179
Query: 195 SKSAIEALEDR 205
+KSA+E LE+R
Sbjct: 180 TKSALEKLEER 190
>gnl|CDD|30437 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 176 bits (449), Expect = 3e-45
Identities = 80/211 (37%), Positives = 116/211 (54%), Gaps = 4/211 (1%)
Query: 1 MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYT 60
M++L V +LDGE+ G + + ++F + + ++ R + Q +R G +K R EV+
Sbjct: 1 MMKLKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEVSGG 60
Query: 61 GSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVH-ALPKKVRSLALRHALSDKFC 119
G K + QKGTGRAR S Q+RGGG A GP P L KK R LALR ALS K
Sbjct: 61 GKKPWGQKGTGRARQGSIRSPQWRGGGVAHGPKPERDYSQKLNKKERRLALRSALSAKAR 120
Query: 120 SNDIMVIDNL-VSKECKTKYLVTRFRALDLSN-ALIIDGCQLDRNFQLAARNIPNIN-LL 176
+ ++V+ KTK LV + L L L+I + D N +L+ARN+ N+ +L
Sbjct: 121 AGKLVVVRGHVFEDAPKTKELVEFLKKLGLDVKRLLIVKGERDGNGKLSARNLKNVKVVL 180
Query: 177 PVQGINVYDILRCSKLVLSKSAIEALEDRFK 207
V G+ V D+LR KLV++K A +E+R
Sbjct: 181 VVGGLPVVDVLRADKLVITKLAPGKIEERLT 211
>gnl|CDD|36837 KOG1624, KOG1624, KOG1624, Mitochondrial/chloroplast ribosomal
protein L4 [Translation, ribosomal structure and
biogenesis].
Length = 290
Score = 164 bits (415), Expect = 2e-41
Identities = 80/207 (38%), Positives = 117/207 (56%), Gaps = 4/207 (1%)
Query: 4 LSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSK 63
+ + E G++ + D+FA P++ IL R + WQ +R+G + +K R+EV G K
Sbjct: 56 EPLDFFELEKVGLVDLHPDVFAEPPRRDILHRAVVWQLDNRRVGTASTKTRAEVRGGGRK 115
Query: 64 MYVQKGTGRARHSSKSVSQFRGGGKAFGP-VPIIGVHALPKKVRSLALRHALSDKFCSND 122
+ QKGTGRAR S Q RGGG A GP P + LP KVRSL L+ ALS K +D
Sbjct: 116 PWPQKGTGRARVGSLRSPQRRGGGVAHGPRGPRDYSYKLPSKVRSLGLKIALSAKLAQDD 175
Query: 123 IMVIDNLVSKECKTKYLVTRFRALDLS-NALIIDGC--QLDRNFQLAARNIPNINLLPVQ 179
+ ++D L K KYL+ + + L +D + D N LA+R + +NL+PV
Sbjct: 176 LHIVDELGLPTGKPKYLLNLLAQRNWGTSVLFVDEDHFEFDENLALASRRLGYLNLIPVG 235
Query: 180 GINVYDILRCSKLVLSKSAIEALEDRF 206
G+NV+ IL+ LVL++ A+E LE+R
Sbjct: 236 GLNVFSILKHDTLVLTREAVEFLEERL 262
>gnl|CDD|177068 CHL00147, rpl4, ribosomal protein L4; Validated.
Length = 215
Score = 99.3 bits (248), Expect = 6e-22
Identities = 68/214 (31%), Positives = 110/214 (51%), Gaps = 16/214 (7%)
Query: 2 IELSVRNLDGEDKGVISVSEDIFALKPQQG----ILARVLRWQSWRKRIGCSKSKGRSEV 57
+ V +L G++K L + +L R L Q+ +R G + +K RSEV
Sbjct: 7 LNYPVIDLTGKEKS----ETIKLKLNVLEKSGNYLLHRALVRQNNNQRQGTASTKTRSEV 62
Query: 58 AYTGSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDK 117
G K + QKGTGRAR S ++GGG FGP P + L KK R LALR L +K
Sbjct: 63 RGGGRKPWKQKGTGRARAGSNRSPLWKGGGVIFGPKPKTYSNKLNKKERRLALRTLLYNK 122
Query: 118 FCSNDIMVIDNLVS--KECKTKYLVTRFRALDLS---NALIIDGCQLDRNFQLAARNIPN 172
SN+I V++N S KTK + + L+++ LII + N L+ RN+ N
Sbjct: 123 --SNNITVVENFESSITNPKTKAFINLLKKLNINLDQKILIIVP-EKTENLYLSTRNLKN 179
Query: 173 INLLPVQGINVYDILRCSKLVLSKSAIEALEDRF 206
+ L+ +N+ +L+ +++++K A++ +E+ +
Sbjct: 180 VELISADTLNIKSLLKAKQIIITKEALKIIEEVY 213
>gnl|CDD|173842 cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to
fadE5. Putative acyl-CoA dehydrogenase (ACAD).
Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze
the alpha,beta dehydrogenation of the corresponding
trans-enoyl-CoA by FAD, which becomes reduced. The
reduced form of ACAD is reoxidized in the oxidative
half-reaction by electron-transferring flavoprotein
(ETF), from which the electrons are transferred to the
mitochondrial respiratory chain coupled with ATP
synthesis. The ACD family includes the eukaryotic
beta-oxidation, as well as amino acid catabolism
enzymes. These enzymes share high sequence similarity,
but differ in their substrate specificities. The
mitochondrial ACD's are generally homotetramers and have
an active site glutamate at a conserved position.
Length = 407
Score = 28.9 bits (65), Expect = 0.93
Identities = 20/72 (27%), Positives = 26/72 (36%), Gaps = 15/72 (20%)
Query: 43 RKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALP 102
R +G + G +E AY + Y +K Q KA V II H P
Sbjct: 249 RLGVGT-QGTGLAEAAYLNALAY-----------AKERKQGGDLIKAAPAVTII-HH--P 293
Query: 103 KKVRSLALRHAL 114
RSL + A
Sbjct: 294 DVRRSLMTQKAY 305
>gnl|CDD|163630 cd07387, MPP_PolD2_C, PolD2 (DNA polymerase delta, subunit 2),
C-terminal domain. PolD2 (DNA polymerase delta, subunit
2) is an auxiliary subunit of the eukaryotic DNA
polymerase delta (PolD) complex thought to play a
regulatory role and to serve as a scaffold for PolD
assembly by interacting simultaneously with all of the
other three subunits. PolD2 is catalytically inactive
and lacks the active site residues required for
phosphoesterase activity in other members of this
superfamily. PolD2 is also involved in the recruitment
of several proteins regulating DNA metabolism, including
p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists
of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3),
and p12(PolD4). PolD is one of three major replicases
in eukaryotes. PolD also plays an essential role in
translesion DNA synthesis, homologous recombination, and
DNA repair. Within the PolD complex, PolD2 tightly
associates with PolD3. PolD2 belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but share a conserved domain with
an active site consisting of two metal ions (usually
manganese, iron, or zinc) coordinated with octahedral
geometry by a cage of histidine, aspartate, and
asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 257
Score = 28.0 bits (63), Expect = 1.7
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 170 IPNINLLPVQGINVYDILRCSKLVLSKSAIEALE 203
I + +L G NV DIL+ S L +S ++ LE
Sbjct: 141 IDGVRVLGTSGQNVDDILKYSSL---ESRLDILE 171
>gnl|CDD|173952 cd08193, HVD, 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the
oxidation of 5-hydroxyvalerate to 5-oxovalerate with
NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase (HVD)
is an iron-containing (type III) NAD-dependent alcohol
dehydrogenase. It plays a role in the cyclopentanol
metabolism biochemical pathway. It catalyzes the
oxidation of 5-hydroxyvalerate to 5-oxovalerate with
NAD+ as cofactor. This cyclopentanol (cpn) degradation
pathway is present in some bacteria which can use
cyclopentanol as sole carbon source. In Comamonas sp.
strain NCIMB 9872, this enzyme is encoded by the CpnD
gene.
Length = 376
Score = 27.5 bits (62), Expect = 2.8
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 86 GGKAFGPVPIIGVHAL 101
G+AF P+ VHAL
Sbjct: 245 AGQAFANAPVAAVHAL 260
>gnl|CDD|36161 KOG0943, KOG0943, KOG0943, Predicted ubiquitin-protein
ligase/hyperplastic discs protein, HECT superfamily
[Posttranslational modification, protein turnover,
chaperones].
Length = 3015
Score = 27.1 bits (59), Expect = 3.9
Identities = 11/71 (15%), Positives = 18/71 (25%), Gaps = 9/71 (12%)
Query: 35 RVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVP 94
Q+ G S S A + + GR S P
Sbjct: 131 LAAAGQAGVGGSGGGNSGRSSAGARDSRRATRRIRGGRDLGEGLLGSL---------GAP 181
Query: 95 IIGVHALPKKV 105
I +P+++
Sbjct: 182 RIPASNIPEEL 192
>gnl|CDD|153203 cd04931, ACT_PAH, ACT domain of the nonheme iron-dependent
aromatic amino acid hydroxylase, phenylalanine
hydroxylases (PAH). ACT domain of the nonheme
iron-dependent aromatic amino acid hydroxylase,
phenylalanine hydroxylases (PAH). PAH catalyzes the
hydroxylation of L-Phe to L-Tyr, the first step in the
catabolic degradation of L-Phe. In PAH, an
autoregulatory sequence, N-terminal of the ACT domain,
extends across the catalytic domain active site and
regulates the enzyme by intrasteric regulation. It
appears that the activation by L-Phe induces a
conformational change that converts the enzyme to a
high-affinity and high-activity state. Modulation of
activity is achieved through inhibition by BH4 and
activation by phosphorylation of serine residues of the
autoregulatory region. The molecular basis for the
cooperative activation process is not fully understood
yet. Members of this CD belong to the superfamily of
ACT regulatory domains.
Length = 90
Score = 26.3 bits (58), Expect = 6.7
Identities = 14/24 (58%), Positives = 18/24 (75%), Gaps = 3/24 (12%)
Query: 15 GVISVSEDIFALKPQQGILARVLR 38
GVIS+ IF+LK + G LA+VLR
Sbjct: 13 GVISL---IFSLKEEVGALAKVLR 33
>gnl|CDD|48434 cd00728, malate_synt_G, Malate synthase G (MSG), monomeric enzyme
present in some bacteria. In general, malate synthase
catalyzes the Claisen condensation of glyoxylate and
acetyl-CoA to malyl-CoA , which hydrolyzes to malate and
CoA. This reaction is part of the glyoxylate cycle,
which allows certain organisms to derive their carbon
requirements from two-carbon compounds, by bypassing the
two carboxylation steps of the citric acid cycle..
Length = 712
Score = 26.0 bits (57), Expect = 7.0
Identities = 12/21 (57%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 30 QGILARVLRWQSWRKRIGCSK 50
QGIL V+RW + IGCSK
Sbjct: 593 QGILGYVVRWVD--QGIGCSK 611
>gnl|CDD|37454 KOG2243, KOG2243, KOG2243, Ca2+ release channel (ryanodine receptor)
[Signal transduction mechanisms].
Length = 5019
Score = 25.8 bits (56), Expect = 9.0
Identities = 14/45 (31%), Positives = 20/45 (44%)
Query: 156 GCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIE 200
GC L L A+ P+I P++G D LR + +S E
Sbjct: 2283 GCGLQSCPMLLAKGYPDIGWNPIEGERYLDFLRFAVFCNGESVEE 2327
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.321 0.137 0.397
Gapped
Lambda K H
0.267 0.0746 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,382,109
Number of extensions: 116408
Number of successful extensions: 234
Number of sequences better than 10.0: 1
Number of HSP's gapped: 223
Number of HSP's successfully gapped: 14
Length of query: 207
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 118
Effective length of database: 4,340,536
Effective search space: 512183248
Effective search space used: 512183248
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 (21.9 bits)
S2: 55 (24.9 bits)