RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13364
(285 letters)
>gnl|CDD|130053 TIGR00980, 3a0801so1tim17, mitochondrial import inner membrane
translocase subunit tim17. [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 170
Score = 183 bits (467), Expect = 2e-58
Identities = 73/122 (59%), Positives = 89/122 (72%), Gaps = 2/122 (1%)
Query: 155 LEEYAREPCPWRIVDDCGGAFTMGLIGGALFHGIKGFRNAPSGMNRRFLGMTTTIKQKSP 214
+EEY REPCP+RI+DD GGAF MG IGG++F KGFRN+P G G IK ++P
Sbjct: 1 MEEYTREPCPYRILDDFGGAFAMGTIGGSIFQAFKGFRNSPKGEKLV--GAMRAIKTRAP 58
Query: 215 ILAGNFAVWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNGVPAMAGSALIGG 274
+L GNFAVWG +FSTIDC++V +RKKEDPWNSIISG TG LA R G AM GSA++G
Sbjct: 59 VLGGNFAVWGGLFSTIDCAVVAIRKKEDPWNSIISGFLTGAALAVRGGPRAMRGSAILGA 118
Query: 275 KL 276
+
Sbjct: 119 CI 120
Score = 108 bits (272), Expect = 3e-29
Identities = 45/72 (62%), Positives = 54/72 (75%)
Query: 4 VGMTTTIKQKSPILAGNFAVWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNG 63
VG IK ++P+L GNFAVWG +FSTIDC++V +RKKEDPWNSIISG TG LA R G
Sbjct: 47 VGAMRAIKTRAPVLGGNFAVWGGLFSTIDCAVVAIRKKEDPWNSIISGFLTGAALAVRGG 106
Query: 64 VPAMAGSALIGG 75
AM GSA++G
Sbjct: 107 PRAMRGSAILGA 118
>gnl|CDD|173487 PTZ00236, PTZ00236, mitochondrial import inner membrane translocase
subunit tim17; Provisional.
Length = 164
Score = 165 bits (419), Expect = 3e-51
Identities = 62/116 (53%), Positives = 84/116 (72%), Gaps = 2/116 (1%)
Query: 159 AREPCPWRIVDDCGGAFTMGLIGGALFHGIKGFRNAPSGMNRRFLGMTTTIKQKSPILAG 218
+REPCP RI++D GGAF+MG IGG ++H +KG RN+P G RF G +++++PIL G
Sbjct: 7 SREPCPDRIIEDMGGAFSMGCIGGFIWHFLKGMRNSPKG--ERFSGGFYLLRKRAPILGG 64
Query: 219 NFAVWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNGVPAMAGSALIGG 274
NFA+WG +FST DC+L Y+R KED WN+I SG TGG+LA R G + +A+ GG
Sbjct: 65 NFAIWGGLFSTFDCTLQYLRGKEDHWNAIASGFFTGGVLAIRGGWRSAVRNAIFGG 120
Score = 99.3 bits (248), Expect = 9e-26
Identities = 36/71 (50%), Positives = 50/71 (70%)
Query: 5 GMTTTIKQKSPILAGNFAVWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNGV 64
G +++++PIL GNFA+WG +FST DC+L Y+R KED WN+I SG TGG+LA R G
Sbjct: 50 GGFYLLRKRAPILGGNFAIWGGLFSTFDCTLQYLRGKEDHWNAIASGFFTGGVLAIRGGW 109
Query: 65 PAMAGSALIGG 75
+ +A+ GG
Sbjct: 110 RSAVRNAIFGG 120
>gnl|CDD|217053 pfam02466, Tim17, Tim17/Tim22/Tim23/Pmp24 family. The pre-protein
translocase of the mitochondrial outer membrane (Tom)
allows the import of pre-proteins from the cytoplasm.
Tom forms a complex with a number of proteins, including
Tim17. Tim17 and Tim23 are thought to form the
translocation channel of the inner membrane. This family
includes Tim17, Tim22 and Tim23. This family also
includes Pmp24 a peroxisomal protein. The involvement of
this domain in the targeting of PMP24 remains to be
proved. PMP24 was known as Pmp27 in.
Length = 128
Score = 125 bits (315), Expect = 5e-36
Identities = 50/115 (43%), Positives = 64/115 (55%), Gaps = 2/115 (1%)
Query: 162 PCPWRIVDDCGGAFTMGLIGGALFHGIKGFRNAP--SGMNRRFLGMTTTIKQKSPILAGN 219
PCP RIV D GG F MG + G F G NA + R G+ ++ P N
Sbjct: 1 PCPERIVYDTGGGFLMGAVYGGFFGAPHGLVNALRSGPLKLRLNGVLNATGRRGPSHGNN 60
Query: 220 FAVWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNGVPAMAGSALIGG 274
FAV+G ++S I+C+L +R KEDPWNSII+GA TG +L R G A A A +G
Sbjct: 61 FAVFGGLYSGIECALEKLRGKEDPWNSIIAGALTGAVLGLRGGPKAAAVGAAVGA 115
Score = 88.9 bits (221), Expect = 3e-22
Identities = 31/68 (45%), Positives = 42/68 (61%)
Query: 8 TTIKQKSPILAGNFAVWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNGVPAM 67
++ P NFAV+G ++S I+C+L +R KEDPWNSII+GA TG +L R G A
Sbjct: 48 NATGRRGPSHGNNFAVFGGLYSGIECALEKLRGKEDPWNSIIAGALTGAVLGLRGGPKAA 107
Query: 68 AGSALIGG 75
A A +G
Sbjct: 108 AVGAAVGA 115
>gnl|CDD|227883 COG5596, TIM22, Mitochondrial import inner membrane translocase,
subunit TIM22 [Posttranslational modification, protein
turnover, chaperones].
Length = 191
Score = 76.4 bits (188), Expect = 7e-17
Identities = 38/124 (30%), Positives = 51/124 (41%), Gaps = 3/124 (2%)
Query: 141 GENLVHVEATPEVELEEYAREPCPWRIVDDCGGAFTMGLIGGALFHGIKGFRNAPSGMNR 200
E L L R+PCP + D AF+ IG + G+KGFR G +
Sbjct: 8 LEQLSPPSPNAYNILSPEERDPCPLEKLADFMKAFSYSCIGKSALSGLKGFRL--GGPSG 65
Query: 201 RFLGMTTTIKQKSPILAGNFA-VWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAA 259
F +L NF VWG +FSTIDC+ ++ KE N+ G TG L
Sbjct: 66 GFSSSLAYGTGLVHLLGLNFGGVWGGLFSTIDCTPFRLQLKEQLNNAGKRGFFTGKNLGV 125
Query: 260 RNGV 263
+
Sbjct: 126 LGLI 129
Score = 45.2 bits (107), Expect = 7e-06
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 10 IKQKSPILAGNFA-VWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNGV 64
+L NF VWG +FSTIDC+ ++ KE N+ G TG L +
Sbjct: 74 GTGLVHLLGLNFGGVWGGLFSTIDCTPFRLQLKEQLNNAGKRGFFTGKNLGVLGLI 129
Score = 44.1 bits (104), Expect = 2e-05
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 13 KSPILAGNFAVWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNGVPAMA-GSA 71
+ N V G +++ I+ + +R K D N+I +GA TG LA+ G AM G A
Sbjct: 115 RGFFTGKNLGVLGLIYAGINSIITALRAKHDIANAIAAGAFTGAALASSAGPQAMPMGGA 174
Query: 72 LIG 74
Sbjct: 175 GFA 177
>gnl|CDD|130056 TIGR00983, 3a0801s02tim23, mitochondrial import inner membrane
translocase subunit tim23. [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 149
Score = 53.3 bits (128), Expect = 7e-09
Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 8/108 (7%)
Query: 172 GGAFTMGLIGGALFHGIKGFRNAPSG-----MNRRFLGMTTTIKQKSPILAGNFAVWGAM 226
G + GL GAL G + S + L M T ++ P + +
Sbjct: 39 GTCYLTGLAIGALNGLRLGLKETQSMPWTKLRLNQILNMVT---RRGPFWGNTLGILALV 95
Query: 227 FSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNGVPAMAGSALIGG 274
++ I+ + R K D +NS+ +GA TG + + G+ MA S +G
Sbjct: 96 YNGINSIIEATRGKHDDFNSVAAGALTGALYKSTRGLRGMARSGALGA 143
Score = 44.4 bits (105), Expect = 8e-06
Identities = 16/72 (22%), Positives = 33/72 (45%)
Query: 4 VGMTTTIKQKSPILAGNFAVWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGILAARNG 63
+ + ++ P + +++ I+ + R K D +NS+ +GA TG + + G
Sbjct: 72 NQILNMVTRRGPFWGNTLGILALVYNGINSIIEATRGKHDDFNSVAAGALTGALYKSTRG 131
Query: 64 VPAMAGSALIGG 75
+ MA S +G
Sbjct: 132 LRGMARSGALGA 143
>gnl|CDD|128752 smart00476, DNaseIc, deoxyribonuclease I. Deoxyribonuclease I
catalyzes the endonucleolytic cleavage of
double-stranded DNA. The enzyme is secreted outside the
cell and also involved in apoptosis in the nucleus.
Length = 276
Score = 30.5 bits (69), Expect = 0.90
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 111 YLRGHRPLTYGYNKSKELRSSPVMERYVN-YGENLVHVEAT------PEVELEEYAREP 162
L P TY Y S+ L + E+Y+ Y +LV V + E + ++REP
Sbjct: 71 QLNSDSPNTYSYVSSEPLGRNSYKEQYLFLYRSDLVSVLDSYLYDDGCECGNDVFSREP 129
>gnl|CDD|227426 COG5095, TAF6, Transcription initiation factor TFIID, subunit TAF6
(also component of histone acetyltransferase SAGA)
[Transcription].
Length = 450
Score = 30.3 bits (68), Expect = 1.1
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 5/48 (10%)
Query: 117 PLTYGYNKSKELRSSPVMERYVNYGENLVHVEATPEVELEEYAREPCP 164
PL YGY+ S+ L+ S V + G+++ +++ EV+ EEY P P
Sbjct: 74 PL-YGYDPSRPLQFSLV---FRGLGQSVYYLD-DEEVDFEEYINRPLP 116
>gnl|CDD|219269 pfam07021, MetW, Methionine biosynthesis protein MetW. This family
consists of several bacterial and one archaeal
methionine biosynthesis MetW proteins. Biosynthesis of
methionine from homoserine in Pseudomonas putida takes
place in three steps. The first step is the acylation of
homoserine to yield an acyl-L-homoserine. This reaction
is catalyzed by the products of the metXW genes and is
equivalent to the first step in enterobacteria,
gram-positive bacteria and fungi, except that in these
microorganisms the reaction is catalyzed by a single
polypeptide (the product of the metA gene in Escherichia
coli and the met5 gene product in Neurospora crassa). In
Pseudomonas putida, as in gram-positive bacteria and
certain fungi, the second and third steps are a direct
sulfhydrylation that converts the O-acyl-L-homoserine
into homocysteine and further methylation to yield
methionine. The latter reaction can be mediated by
either of the two methionine synthetases present in the
cells.
Length = 193
Score = 29.3 bits (66), Expect = 1.8
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 96 IISFYNFLTYRYRW-IYLRGHRPLT 119
I+SF NF +R RW + RG P+T
Sbjct: 106 IVSFPNFGHWRVRWSLLSRGRMPVT 130
>gnl|CDD|226941 COG4575, ElaB, Uncharacterized conserved protein [Function
unknown].
Length = 104
Score = 27.7 bits (62), Expect = 2.5
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 31 IDCSLVYVRKKEDPWNSIISGAATG---GILAAR 61
D + YVR E+PW + AA G G+L +R
Sbjct: 72 ADATDDYVR--ENPWQGVGVAAAVGLLLGLLLSR 103
Score = 27.7 bits (62), Expect = 2.5
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 230 IDCSLVYVRKKEDPWNSIISGAATG---GILAAR 260
D + YVR E+PW + AA G G+L +R
Sbjct: 72 ADATDDYVR--ENPWQGVGVAAAVGLLLGLLLSR 103
>gnl|CDD|233713 TIGR02081, metW, methionine biosynthesis protein MetW. This
protein is found alongside MetX, of the enzyme that
acylates homoserine as a first step toward methionine
biosynthesis, in many species. It appears to act in
methionine biosynthesis but is not fully characterized
[Amino acid biosynthesis, Aspartate family].
Length = 194
Score = 28.9 bits (65), Expect = 2.7
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 96 IISFYNFLTYRYRWIYLRGHR-PLT 119
I+SF NF +R RW L R P+T
Sbjct: 106 IVSFPNFGYWRVRWSILTKGRMPVT 130
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 27.7 bits (62), Expect = 4.3
Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 7/88 (7%)
Query: 101 NFLTYRYRWIYL---RGHRPLTYGYNKS----KELRSSPVMERYVNYGENLVHVEATPEV 153
+ L+ R I + ++ L NK+ KE+ V E YG + AT
Sbjct: 11 DPLSSRNPDIEVLINEKNKKLIMVLNKADLVPKEVLRKWVAELSELYGTKTFFISATNGQ 70
Query: 154 ELEEYAREPCPWRIVDDCGGAFTMGLIG 181
+ + E ++ +G++G
Sbjct: 71 GILKLKAEITKQKLKLKYKKGIRVGVVG 98
>gnl|CDD|215441 PLN02825, PLN02825, amino-acid N-acetyltransferase.
Length = 515
Score = 28.6 bits (64), Expect = 4.5
Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 15/80 (18%)
Query: 105 YRYRWIYLRGHRPLTYGYNKSKELRSSPVMERYVN-------YGENLVHVEATPEVE--- 154
+R W Y++GHR T+ S E+ + P ++ + G V V T V+
Sbjct: 5 FREAWPYIQGHRGSTFVVVISGEVVAGPHLDNILQDISLLHGLGIKFVLVPGT-HVQIDK 63
Query: 155 -LEEYAREPC---PWRIVDD 170
L E REP +RI D
Sbjct: 64 LLAERGREPKYVGAYRITDS 83
>gnl|CDD|184405 PRK13931, PRK13931, stationary phase survival protein SurE;
Provisional.
Length = 261
Score = 28.2 bits (63), Expect = 5.0
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 46 NSIISGAATGGILAARNGVPAMAGSALIGGKVRTLELVLLFEPAPNQGTSII 97
N + SG G + AA G+PA+A S G + L+ FE A G ++
Sbjct: 104 NVLYSGTVGGAMEAALQGLPAIALSQYYGPRNEGLDDP--FEAARTHGARVV 153
>gnl|CDD|238716 cd01436, Dipth_tox_like, Mono-ADP-ribosylating toxins catalyze the
transfer of ADP_ribose from NAD+ to eukaryotic
Elongation Factor 2, halting protein synthesis. A single
molecule of delivered toxin is sufficient to kill a
cell. These toxins share mono-ADP-ribosylating activity
with a variety of bacterial toxins, such as cholera
toxin and pertussis toxin. The structural core is
homologous to the poly-ADP ribosylating enzymes such as
the PARP enzymes and Tankyrase. Diphtheria toxin is
encoded by a lysogenic bacteriophage. Both diphtheria
toxin and Pseudomonas aeruginosa exotoxin A are
multi-domain proteins. These domains provide a EF2
ADP_ribosylating, receptor-binding, and intracellular
trafficking/transmembrane functions .
Length = 147
Score = 27.6 bits (60), Expect = 5.1
Identities = 8/103 (7%), Positives = 29/103 (28%), Gaps = 5/103 (4%)
Query: 107 YRWIYLRGHRPLTYGYNKSKE----LRSSPVMERYVNYGENLVHVEATPEVELEEYAREP 162
++ Y ++ GY+ E ++ V++ ++ ++ +++
Sbjct: 33 WKGFYSTDNKYDAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLS 92
Query: 163 CPWRIVDDCGGAFTMGLIGGAL-FHGIKGFRNAPSGMNRRFLG 204
+++ G + G + S
Sbjct: 93 LTEPLMEQVGTEEFIKRFGDGASRVVLSLPFAEGSSSVEYINN 135
>gnl|CDD|117486 pfam08919, F_actin_bind, F-actin binding. The F-actin binding
domain forms a compact bundle of four antiparallel
alpha-helices, which are arranged in a left-handed
topology. Binding of F-actin to the F-actin binding
domain may result in cytoplasmic retention and
subcellular distribution of the protein, as well as
possible inhibition of protein function.
Length = 179
Score = 27.7 bits (61), Expect = 5.6
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 2 PPVGMTTTIKQKSPILAGNFAVWGAMFSTIDCSLVYVRKKEDPWNSIISGAATGGIL 58
PV + +T S + G A F + + V +RK P I SG T G++
Sbjct: 26 SPVPLPSTSPSPSKMANGT-QPSSAAFIPLISTRVSLRKTRQPPERIASGKITKGVV 81
>gnl|CDD|182323 PRK10236, PRK10236, hypothetical protein; Provisional.
Length = 237
Score = 28.0 bits (62), Expect = 5.7
Identities = 13/25 (52%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 48 IISGAATGGIL-AARNGVPAMAGSA 71
++ GA GG + AA NGV A++GSA
Sbjct: 190 LLRGAGLGGPVGAALNGVKAVSGSA 214
Score = 28.0 bits (62), Expect = 5.7
Identities = 13/25 (52%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 247 IISGAATGGIL-AARNGVPAMAGSA 270
++ GA GG + AA NGV A++GSA
Sbjct: 190 LLRGAGLGGPVGAALNGVKAVSGSA 214
>gnl|CDD|239580 cd03500, SQR_TypeA_SdhD_like, Succinate:quinone oxidoreductase
(SQR) Type A subfamily, Succinate dehydrogenase D
(SdhD)-like subunit; SQR catalyzes the oxidation of
succinate to fumarate coupled to the reduction of
quinone to quinol. Members of this subfamily reduce low
potential quinones such as menaquinone and
thermoplasmaquinone. SQR is also called succinate
dehydrogenase or Complex II, and is part of the citric
acid cycle and the aerobic respiratory chain. SQR is
composed of a flavoprotein catalytic subunit, an
iron-sulfur protein and one or two hydrophobic
transmembrane subunits. Members of this subfamily are
similar to the Thermoplasma acidophilum SQR and are
classified as Type A because they contain two
transmembrane subunits as well as two heme groups.
Although there are no structures available for this
subfamily, the presence of two hemes has been proven
spectroscopically for T. acidophilum. The two membrane
anchor subunits are similar to the SdhD and SdhC
subunits of bacterial SQRs, which contain heme and
quinone binding sites. The two-electron oxidation of
succinate in the flavoprotein active site is coupled to
the two-electron reduction of quinone in the membrane
anchor subunits via electron transport through FAD and
three iron-sulfur centers. The reversible reduction of
quinone is an essential feature of respiration, allowing
transfer of electrons between respiratory complexes.
Length = 106
Score = 26.5 bits (59), Expect = 6.6
Identities = 9/32 (28%), Positives = 11/32 (34%), Gaps = 5/32 (15%)
Query: 183 ALFHGIKGFRNA-----PSGMNRRFLGMTTTI 209
AL HG G RN RR + +
Sbjct: 60 ALLHGGNGLRNILLDYVRRPRLRRAVKGLLYV 91
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
0.321 0.138 0.430
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,093,585
Number of extensions: 1480074
Number of successful extensions: 1348
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1343
Number of HSP's successfully gapped: 39
Length of query: 285
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 189
Effective length of database: 6,679,618
Effective search space: 1262447802
Effective search space used: 1262447802
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: 58 (26.4 bits)