RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032476
(140 letters)
>gnl|CDD|185418 PTZ00054, PTZ00054, 60S ribosomal protein L23; Provisional.
Length = 139
Score = 256 bits (656), Expect = 1e-89
Identities = 115/139 (82%), Positives = 128/139 (92%)
Query: 2 SKRGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMV 61
KRGRGG GNKFR++LGLPV A VNCADN+GAKNLYII+VKGI GRLNRLPSA +GDMV
Sbjct: 1 MKRGRGGVGGNKFRVTLGLPVGAVVNCADNSGAKNLYIIAVKGIHGRLNRLPSASLGDMV 60
Query: 62 MATVKKGKPDLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPI 121
+ATVKKGKP+LRKKV+ AVI+RQRK WRRKDGVF+YFEDNAGVIVNPKGEMKGSAITGP+
Sbjct: 61 LATVKKGKPELRKKVLNAVIIRQRKAWRRKDGVFIYFEDNAGVIVNPKGEMKGSAITGPV 120
Query: 122 GKECADLWPRIASAANAIV 140
KECADLWP+I+SAA AIV
Sbjct: 121 AKECADLWPKISSAAPAIV 139
>gnl|CDD|181478 PRK08571, rpl14p, 50S ribosomal protein L14P; Reviewed.
Length = 132
Score = 178 bits (455), Expect = 3e-59
Identities = 75/130 (57%), Positives = 97/130 (74%)
Query: 11 GNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70
G + +++ GLPV A + CADNTGAK + IISVKG KG RLP A VGDMV+ +VKKG P
Sbjct: 3 GIRSKVTRGLPVGARLVCADNTGAKEVEIISVKGYKGVKRRLPKAGVGDMVVVSVKKGTP 62
Query: 71 DLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWP 130
++RK+V+ AV+VRQRK +RR DG + FEDNA VIV P+G KG+ I GP+ +E A+ WP
Sbjct: 63 EMRKQVLRAVVVRQRKEYRRPDGTRVKFEDNAAVIVTPEGTPKGTEIKGPVAREAAERWP 122
Query: 131 RIASAANAIV 140
+IAS A+ IV
Sbjct: 123 KIASIASIIV 132
>gnl|CDD|132712 TIGR03673, rpl14p_arch, 50S ribosomal protein L14P. Part of the
50S ribosomal subunit. Forms a cluster with proteins L3
and L24e, part of which may contact the 16S rRNA in 2
intersubunit bridges.
Length = 131
Score = 171 bits (435), Expect = 3e-56
Identities = 74/130 (56%), Positives = 94/130 (72%)
Query: 11 GNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP 70
G + ++ LPV A + CADNTGAK + +ISVKG KG RLP A VGDMV+ +VKKG P
Sbjct: 2 GIRAGITRALPVGALLVCADNTGAKEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTP 61
Query: 71 DLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWP 130
++RK+V AV+VRQRK +RR DG + FEDNA VIV P GE KG+ I GP+ +E A+ WP
Sbjct: 62 EMRKQVFKAVVVRQRKEYRRPDGTRVKFEDNAVVIVTPDGEPKGTEIKGPVAREAAERWP 121
Query: 131 RIASAANAIV 140
+IAS A+ IV
Sbjct: 122 KIASIASIIV 131
>gnl|CDD|223171 COG0093, RplN, Ribosomal protein L14 [Translation, ribosomal
structure and biogenesis].
Length = 122
Score = 145 bits (369), Expect = 3e-46
Identities = 52/126 (41%), Positives = 76/126 (60%), Gaps = 8/126 (6%)
Query: 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP-DLRKK-- 75
+ V +N ADN+GAK + I V G R A VGD+++ +VKK P + KK
Sbjct: 1 MIQVQTRLNVADNSGAKEVMCIKVLGGSRRR----YAGVGDIIVVSVKKAIPRGMVKKGD 56
Query: 76 VMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADL-WPRIAS 134
V+ AV+VR +K RR DG ++ F+DNA VI+NP GE +G+ I GP+ +E + + +IAS
Sbjct: 57 VVKAVVVRTKKEVRRPDGSYIKFDDNAAVIINPDGEPRGTRIFGPVARELRERGFMKIAS 116
Query: 135 AANAIV 140
A +V
Sbjct: 117 LAPEVV 122
>gnl|CDD|201105 pfam00238, Ribosomal_L14, Ribosomal protein L14p/L23e.
Length = 122
Score = 131 bits (331), Expect = 2e-40
Identities = 53/126 (42%), Positives = 77/126 (61%), Gaps = 8/126 (6%)
Query: 19 GLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKG--KPDLRK-K 75
+ V +N ADN+GAK + I V G R A VGD+++ +VKK K ++K
Sbjct: 1 MIQVGTRLNVADNSGAKKVKCIKVLGGS----RKKYAKVGDIIVVSVKKAIPKGKVKKGD 56
Query: 76 VMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKEC-ADLWPRIAS 134
V+ AVIVR +K RRKDG ++ F+DNA V++N KGE KG+ I GP+ +E A +P+I S
Sbjct: 57 VVKAVIVRTKKEVRRKDGSYIRFDDNAVVLINNKGEPKGTRIFGPVARELRAKKFPKILS 116
Query: 135 AANAIV 140
A ++
Sbjct: 117 LAPEVL 122
>gnl|CDD|180117 PRK05483, rplN, 50S ribosomal protein L14; Validated.
Length = 122
Score = 86.3 bits (215), Expect = 7e-23
Identities = 41/101 (40%), Positives = 62/101 (61%), Gaps = 7/101 (6%)
Query: 27 NCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKK---VMPAVIVR 83
N ADN+GAK + I V G R A +GD+++ +VK+ P + K V+ AV+VR
Sbjct: 9 NVADNSGAKEVMCIKVLGGSKRR----YASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVR 64
Query: 84 QRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKE 124
+K RR DG ++ F+DNA V++N GE +G+ I GP+ +E
Sbjct: 65 TKKGVRRPDGSYIRFDDNAAVLLNNDGEPRGTRIFGPVARE 105
>gnl|CDD|176997 CHL00057, rpl14, ribosomal protein L14.
Length = 122
Score = 80.3 bits (199), Expect = 1e-20
Identities = 40/105 (38%), Positives = 64/105 (60%), Gaps = 7/105 (6%)
Query: 27 NCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDL---RKKVMPAVIVR 83
N ADN+GA+ L I V G R A +GD+++A VK+ P++ R +V+ AVIVR
Sbjct: 9 NVADNSGARKLMCIRVLGASNR----KYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVR 64
Query: 84 QRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADL 128
K +R +G+ + F+DNA V+++ +G KG+ + GPI +E +
Sbjct: 65 TCKELKRDNGMIIRFDDNAAVVIDQEGNPKGTRVFGPIARELREK 109
>gnl|CDD|130139 TIGR01067, rplN_bact, ribosomal protein L14, bacterial/organelle.
This model distinguishes bacterial and most organellar
examples of ribosomal protein L14 from all archaeal and
eukaryotic forms [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 122
Score = 77.7 bits (192), Expect = 2e-19
Identities = 44/104 (42%), Positives = 62/104 (59%), Gaps = 7/104 (6%)
Query: 27 NCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPDLRKK---VMPAVIVR 83
N ADN+GAK + I V G R A VGD+++ VK P+ + K V+ AVIVR
Sbjct: 9 NVADNSGAKKVQCIKVLGGSRR----RYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVR 64
Query: 84 QRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECAD 127
+K RRKDG ++ F+DNA V++N E +G+ I GP+ +E D
Sbjct: 65 TKKGVRRKDGSYIRFDDNACVLINKNKEPRGTRIFGPVARELRD 108
>gnl|CDD|225387 COG2831, FhaC, Hemolysin activation/secretion protein
[Intracellular trafficking and secretion].
Length = 554
Score = 28.1 bits (63), Expect = 1.6
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 11/55 (20%)
Query: 49 LNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAG 103
LNRLP ++ + G+ DL + V+Q KPWR V DN G
Sbjct: 190 LNRLPGVQADAELVPGSEPGESDLV------IKVQQGKPWR----VSASA-DNYG 233
>gnl|CDD|143589 cd07565, aliphatic_amidase, aliphatic amidases (class 2
nitrilases). Aliphatic amidases catalyze the hydrolysis
of short-chain aliphatic amides to form ammonia and the
corresponding organic acid. This group includes
Pseudomonas aeruginosa (Pa) AmiE, the amidase from
Geobacillus pallidus RAPc8 (RAPc8 amidase), and
Helicobacter pylori (Hp) AmiE and AmiF. PaAimE and
HpAmiE hydrolyze various very short aliphatic amides,
including propionamide, acetamide and acrylamide. HpAmiF
is a formamidase which specifically hydrolyzes
formamide. These proteins belong to a larger nitrilase
superfamily comprised of nitrile- or amide-hydrolyzing
enzymes and amide-condensing enzymes, which depend on a
Glu-Lys-Cys catalytic triad. This superfamily has been
classified in the literature based on global and
structure based sequence analysis into thirteen
different enzyme classes (referred to as 1-13), this
subgroup corresponds to class 2. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer. HpAmiE ,
HpAmiF, and RAPc8 amidase, and PaAimE appear to be
homohexameric enzymes, trimer of dimers.
Length = 291
Score = 27.6 bits (62), Expect = 2.4
Identities = 16/45 (35%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 92 DGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECADLWPRIASAA 136
DGVF YF +IVN G G P A+L P + A
Sbjct: 211 DGVFSYF--GESMIVNFDGRTLGEGGREPDEIVTAELSPSLVRDA 253
>gnl|CDD|236958 PRK11709, PRK11709, putative L-ascorbate 6-phosphate lactonase;
Provisional.
Length = 355
Score = 26.9 bits (60), Expect = 3.6
Identities = 25/90 (27%), Positives = 34/90 (37%), Gaps = 28/90 (31%)
Query: 57 VGDMV-------MATVKKGKPDLRKKVMPAVIVRQRKPW--RRKDGVFM--YFEDN---- 101
M MA V+K +P+LR P V+ P+ R D V D+
Sbjct: 73 NPLMKRGHQMARMAGVRKLQPNLR--TQPFVL----DPFAIREIDAVLATHDHSDHIDVN 126
Query: 102 --AGVIVNPKGEMKGSAITGPIGKECADLW 129
A V+ N +K GP + C DLW
Sbjct: 127 VAAAVLQNCADHVK---FIGP--QACVDLW 151
>gnl|CDD|211356 cd08346, PcpA_N_like, N-terminal domain of Sphingobium
chlorophenolicum 2,6-dichloro-p-hydroquinone
1,2-dioxygenase (PcpA), and similar proteins. The
N-terminal domain of Sphingobium chlorophenolicum
(formerly Sphingomonas chlorophenolica)
2,6-dichloro-p-hydroquinone1,2-dioxygenase (PcpA), and
similar proteins. PcpA is a key enzyme in the
pentachlorophenol (PCP) degradation pathway, catalyzing
the conversion of 2,6-dichloro-p-hydroquinone to
2-chloromaleylacetate. This domain belongs to a
conserved domain superfamily that is found in a variety
of structurally related metalloproteins, including the
bleomycin resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases.
Length = 126
Score = 26.4 bits (59), Expect = 3.9
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 18 LGLP-VAATVNCADNTGAKNLYIISVKGIKGRL 49
LGL V TVN D+ G +L+ G G L
Sbjct: 23 LGLRLVKKTVN-QDDPGTYHLFFGDGLGSPGTL 54
>gnl|CDD|181933 PRK09532, PRK09532, DNA polymerase III subunit alpha; Reviewed.
Length = 874
Score = 27.0 bits (60), Expect = 4.2
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 23/71 (32%)
Query: 29 ADNT-GAKNLY----IISVKGIKGR-------LNR-----------LPSACVGDMVMATV 65
A NT G KNL I ++G++G+ +N+ + SAC+G + +
Sbjct: 89 AKNTQGYKNLVKLTTISHLQGVQGKGIFARPCINKELLEQYHEGLIVTSACLGGEIPQAI 148
Query: 66 KKGKPDLRKKV 76
G+PD +KV
Sbjct: 149 LSGRPDAARKV 159
>gnl|CDD|176171 cd08482, PBP2_TrpI, The C-terminal substrate binding domain of
LysR-type transcriptional regulator TrpI, which is
involved in control of tryptophan synthesis, contains
type 2 periplasmic binding fold. TrpI and
indoleglycerol phosphate (InGP), are required to
activate transcription of the trpBA, the genes for
tryptophan synthase. The trpBA is induced by the InGp
substrate, rather than by tryptophan, but the exact
mechanism of the activation event is not known. This
substrate-binding domain of TrpI shows significant
homology to the type 2 periplasmic binding proteins
(PBP2), which are responsible for the uptake of a
variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 195
Score = 26.6 bits (59), Expect = 4.7
Identities = 13/61 (21%), Positives = 21/61 (34%)
Query: 48 RLNRLPSACVGDMVMATVKKGKPDLRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVN 107
RL +A + + G D + + A I PW V F + G + +
Sbjct: 18 RLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWPAGMQVIELFPERVGPVCS 77
Query: 108 P 108
P
Sbjct: 78 P 78
>gnl|CDD|140341 PTZ00320, PTZ00320, ribosomal protein L14; Provisional.
Length = 188
Score = 25.8 bits (56), Expect = 8.2
Identities = 27/114 (23%), Positives = 50/114 (43%), Gaps = 9/114 (7%)
Query: 2 SKRGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLN--RLPSACVGD 59
S R R G+ + + ++C DNT K++ +IS K R R+ A
Sbjct: 42 SYRSRWGTGAEGYGTGVPFSDQVKLHCVDNTNCKHVRLIS-KATAERFAHCRVFPAVAHR 100
Query: 60 MVMATVKKGKPDL-RKKVMPAVI-----VRQRKPWRRKDGVFMYFEDNAGVIVN 107
+ + K G+ ++ R +V P I + +R+ R G+ F+ N +++N
Sbjct: 101 VSVQRFKSGRGEVSRHRVKPGNIYWVCLLSRRQTNTRMSGLQTNFDRNTCILMN 154
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 0.136 0.409
Gapped
Lambda K H
0.267 0.0784 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,029,503
Number of extensions: 626243
Number of successful extensions: 479
Number of sequences better than 10.0: 1
Number of HSP's gapped: 466
Number of HSP's successfully gapped: 19
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 54 (24.5 bits)