RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy840
(178 letters)
>gnl|CDD|217357 pfam03079, ARD, ARD/ARD' family. The two acireductone dioxygenase
enzymes (ARD and ARD', previously known as E-2 and E-2')
from Klebsiella pneumoniae share the same amino acid
sequence, but bind different metal ions: ARD binds Ni2+,
ARD' binds Fe2+. ARD and ARD' can be experimentally
interconverted by removal of the bound metal ion and
reconstitution with the appropriate metal ion. The two
enzymes share the same substrate,
1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield
different products. ARD' yields the alpha-keto precursor
of methionine (and formate), thus forming part of the
ubiquitous methionine salvage pathway that converts
5'-methylthioadenosine (MTA) to methionine. This pathway
is responsible for the tight control of the
concentration of MTA, which is a powerful inhibitor of
polyamine biosynthesis and transmethylation reactions.
ARD yields methylthiopropanoate, carbon monoxide and
formate, and thus prevents the conversion of MTA to
methionine. The role of the ARD catalyzed reaction is
unclear: methylthiopropanoate is cytotoxic, and carbon
monoxide can activate guanylyl cyclase, leading to
increased intracellular cGMP levels. This family also
contains other members, whose functions are not well
characterized.
Length = 157
Score = 167 bits (426), Expect = 7e-54
Identities = 77/157 (49%), Positives = 99/157 (63%), Gaps = 6/157 (3%)
Query: 3 RVWYMDTDVKSDQRLEHHRTPKEYLDLQTLNKLTGVEY-----FNVQDEVLTKLRKDRNY 57
+ W MD DQRL HH PKE + L KL + + E L ++RK ++Y
Sbjct: 1 QAWIMDDSPCGDQRLPHHTFPKEKAETDELAKLGVLYWKLDADDEETAEELLRIRKYKHY 60
Query: 58 NYEDEI-TCSKDCLPNYEEKLKSFYTEHLHTDEEIRLVLDGSGYFDVRDKFDDWIRIEVT 116
+ D T + PN++EKLK F+ EHLHTDEEIR +++G+GYFDVRDK D WIR+ V
Sbjct: 61 DDVDIDVTVCPETTPNFDEKLKKFFEEHLHTDEEIRYIVEGTGYFDVRDKDDVWIRVFVE 120
Query: 117 KGDLIIIPAGIYHRFTLDINNYVKAKRYFIGEPVWTP 153
KGDLI +PAGIYHRFT +NYVKA R F+ +P WT
Sbjct: 121 KGDLISLPAGIYHRFTTTPDNYVKALRLFVTKPGWTA 157
>gnl|CDD|224704 COG1791, COG1791, Uncharacterized conserved protein, contains
double-stranded beta-helix domain [Function unknown].
Length = 181
Score = 118 bits (297), Expect = 4e-34
Identities = 43/128 (33%), Positives = 61/128 (47%), Gaps = 1/128 (0%)
Query: 46 EVLTKLRKDRNYNYEDEITCSKDCLPNYEEKLKSFYTEHLHTDEEIRLVLDGSGYFDVRD 105
+ +L ++R Y D ++ S P +E F EHLHTD+E+R + G G FDV
Sbjct: 54 TEIDRLIRERGYKNRDVVSVSPSN-PKLDELRAKFLQEHLHTDDEVRYFVAGEGIFDVHS 112
Query: 106 KFDDWIRIEVTKGDLIIIPAGIYHRFTLDINNYVKAKRYFIGEPVWTPHNRPADDMECRL 165
+I KGDLI +P GIYH FTL + KA R F W D +
Sbjct: 113 PDGKVYQIRCEKGDLISVPPGIYHWFTLTESPNFKAVRLFTEPEGWVAIYTGDDIADRFP 172
Query: 166 EYLKKIQN 173
+Y+++I
Sbjct: 173 KYIEEINQ 180
>gnl|CDD|219618 pfam07883, Cupin_2, Cupin domain. This family represents the
conserved barrel domain of the 'cupin' superfamily
('cupa' is the Latin term for a small barrel).
Length = 70
Score = 51.5 bits (124), Expect = 1e-09
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 83 EHLHTDEEIRLVLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYHRF 131
H H EE VL+G G V + + + GD + PAG+ HRF
Sbjct: 13 PHRHPGEEFFYVLEGEGELTVDGE-----EVVLKAGDSVYFPAGVPHRF 56
>gnl|CDD|223734 COG0662, {ManC}, Mannose-6-phosphate isomerase [Carbohydrate
transport and metabolism].
Length = 127
Score = 40.1 bits (94), Expect = 9e-05
Identities = 25/77 (32%), Positives = 32/77 (41%), Gaps = 12/77 (15%)
Query: 84 HLHTDEEIRLVLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYHRFTLDINNYVKAKR 143
H H DE VL+G+G + + +EV GD + IPAG HR N K
Sbjct: 54 HHHRDE-HWYVLEGTGKVTIGGE-----EVEVKAGDSVYIPAGTPHRVR----NTGKIPL 103
Query: 144 YFIGEPVWTPHNRPADD 160
I V +P DD
Sbjct: 104 VLIE--VQSPPYLGEDD 118
>gnl|CDD|145456 pfam02311, AraC_binding, AraC-like ligand binding domain. This
family represents the arabinose-binding and dimerisation
domain of the bacterial gene regulatory protein AraC.
The domain is found in conjunction with the
helix-turn-helix (HTH) DNA-binding motif pfam00165. This
domain is distantly related to the Cupin domain
pfam00190.
Length = 134
Score = 39.7 bits (93), Expect = 1e-04
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 81 YTEHLHTDEEIRLVLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYHRFTLDINN 137
+ H+H I + G G + + + GDL ++P G H + + +
Sbjct: 16 FPPHVHDFYVIGYIERGVGRLRLNGR-----TYHLGPGDLFLLPPGEPHDYEPESED 67
>gnl|CDD|224829 COG1917, COG1917, Uncharacterized conserved protein, contains
double-stranded beta-helix domain [Function unknown].
Length = 131
Score = 36.4 bits (84), Expect = 0.002
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 83 EHLHTDEEIRL-VLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYHRF 131
H H E + VL+G G + + + E+ GD+IIIP G+ H
Sbjct: 58 WHTHPLGEQTIYVLEGEGTVQLEGE-----KKELKAGDVIIIPPGVVHGL 102
>gnl|CDD|225969 COG3435, COG3435, Gentisate 1,2-dioxygenase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 351
Score = 37.0 bits (86), Expect = 0.002
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 82 TEHLHTDEEIRLVLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYH 129
H H +R V++G G + V D R + GD I+ PA +H
Sbjct: 106 PSHRHNQSALRFVVEGKGAYTVVDGE----RTPMEAGDFILTPAWTWH 149
Score = 28.5 bits (64), Expect = 1.8
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 84 HLHTDEEIRLVLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYHRF 131
H HTD I V++GSGY + + DW + GD+ ++P+ +H
Sbjct: 277 HRHTDSTIYHVVEGSGYTIIGGERFDW-----SAGDIFVVPSWAWHEH 319
>gnl|CDD|215780 pfam00190, Cupin_1, Cupin. This family represents the conserved
barrel domain of the 'cupin' superfamily ('cupa' is the
Latin term for a small barrel). This family contains 11S
and 7S plant seed storage proteins, and germins. Plant
seed storage proteins provide the major nitrogen source
for the developing plant.
Length = 139
Score = 33.8 bits (78), Expect = 0.015
Identities = 23/95 (24%), Positives = 33/95 (34%), Gaps = 32/95 (33%)
Query: 84 HLHTD-EEIRLVLDGSGYF-------DVRDKFDDWIRIEVTKGDLIIIPAGIYHRFT--- 132
H H + EI VL G G R F ++ +GD+ ++PAG H
Sbjct: 50 HYHPNATEILYVLQGRGRVGFVVPGCGFRV-FHQ----KLREGDVFVVPAGFAHWQYNSG 104
Query: 133 --------LDINNY-------VKAKRYFI-GEPVW 151
D NN V A+ +F+ G
Sbjct: 105 DPGLELVAFDTNNPANQLPREVLARAFFLAGNEAR 139
>gnl|CDD|214845 smart00835, Cupin_1, Cupin. This family represents the conserved
barrel domain of the 'cupin' superfamily ('cupa' is the
Latin term for a small barrel). This family contains 11S
and 7S plant seed storage proteins, and germins. Plant
seed storage proteins provide the major nitrogen source
for the developing plant.
Length = 146
Score = 32.3 bits (74), Expect = 0.060
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 10/52 (19%)
Query: 84 HLHTD-EEIRLVLDGSGYFDVRD-----KFDDWIRIEVTKGDLIIIPAGIYH 129
H H E+ V+ G G V D +D + +GD+ ++P G H
Sbjct: 46 HYHPRATELLYVVRGEGRVGVVDPNGNKVYDA----RLREGDVFVVPQGHPH 93
>gnl|CDD|226747 COG4297, COG4297, Uncharacterized protein containing
double-stranded beta helix domain [Function unknown].
Length = 163
Score = 31.0 bits (70), Expect = 0.18
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 113 IEVTKGDLIIIPAGIYHR 130
+EV +GD+++IPAG+ H
Sbjct: 87 LEVGEGDVLLIPAGVGHC 104
>gnl|CDD|182362 PRK10296, PRK10296, DNA-binding transcriptional regulator ChbR;
Provisional.
Length = 278
Score = 30.9 bits (70), Expect = 0.29
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 84 HLHTDEEIRLVLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYHRFTLD-----INNY 138
H H E LVL G Y ++ K R+ + +GD + IP G +H+ + I N
Sbjct: 39 HQHDYYEFTLVLTGRYYQEINGK-----RVLLERGDFVFIPLGSHHQSFYEFGATRILNV 93
Query: 139 VKAKRYF 145
+KR+F
Sbjct: 94 GISKRFF 100
>gnl|CDD|225051 COG2140, COG2140, Thermophilic glucose-6-phosphate isomerase and
related metalloenzymes [Carbohydrate transport and
metabolism / General function prediction only].
Length = 209
Score = 30.1 bits (68), Expect = 0.50
Identities = 19/50 (38%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 84 HLH--TDE-EIRLVLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYHR 130
H H DE EI VL G G V+ + I V GD+I +P G H
Sbjct: 96 HYHPNADEPEIYYVLKGEGRMLVQKPEGEARVIAVRAGDVIYVPPGYGHY 145
>gnl|CDD|131325 TIGR02272, gentisate_1_2, gentisate 1,2-dioxygenase. This family
consists of gentisate 1,2-dioxygenases. This
ring-opening enzyme acts in salicylate degradation that
goes via gentisate rather than via catechol. It converts
gentisate to maleylpyruvate. Some putative gentisate
1,2-dioxygenases are excluded by a relatively high
trusted cutoff score because they are too closely
related to known examples of 1-hydroxy-2-naphthoate
dioxygenase. Therefore some homologs may be bona fide
gentisate 1,2-dioxygenases even if they score below the
given cutoffs.
Length = 335
Score = 29.7 bits (67), Expect = 0.66
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 84 HLHTDEEIRLVLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYH 129
H HT +R +++G G F D R + GD II P+ +H
Sbjct: 97 HRHTQSALRFIVEGKGAFTAVDG----ERTTMHPGDFIITPSWTWH 138
>gnl|CDD|223750 COG0678, AHP1, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 165
Score = 28.9 bits (65), Expect = 0.98
Identities = 13/59 (22%), Positives = 19/59 (32%), Gaps = 21/59 (35%)
Query: 64 TCSKDCLPNYEEKLKSF---------------------YTEHLHTDEEIRLVLDGSGYF 101
TCS LP Y E F + + + I+ + DG+G F
Sbjct: 52 TCSSSHLPGYLELADEFKAKGVDEIYCVSVNDAFVMNAWAKSQGGEGNIKFIPDGNGEF 110
>gnl|CDD|221809 pfam12852, Cupin_6, Cupin. This is a family of bacterial and
eukaryotic proteins that belong to the Cupin
superfamily. Some of the proteins in this family are
annotated as being members of the AraC family of
transcription factors, in which case this domain
corresponds to the ligand binding domain.
Length = 185
Score = 28.0 bits (63), Expect = 2.4
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 9/48 (18%)
Query: 84 HLHTDEEIRLVLDGSGYFDVRDKFDDWIRIEVTKGDLIIIPAGIYHRF 131
H LVL GS + + + +R+E GDL+++P G H
Sbjct: 37 TFH------LVLRGSCWLRLPGG-GEPVRLEA--GDLVLLPRGDAHVL 75
>gnl|CDD|222269 pfam13621, Cupin_8, Cupin-like domain. This cupin like domain
shares similarity to the JmjC domain.
Length = 247
Score = 27.7 bits (62), Expect = 3.3
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 110 WIRIEVTKGDLIIIPAGIYHR 130
+ E+ GD + IPAG +H
Sbjct: 206 ALVAELEPGDALYIPAGWWHH 226
>gnl|CDD|225647 COG3105, COG3105, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 138
Score = 27.1 bits (60), Expect = 4.0
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 38 VEYFNVQDEVLTKLRKDRNYNYEDEITCSKDCLPNYEEKLKSFYTEHLHTDEE 90
V++F E+L L +D Y+ S LP E K +L +EE
Sbjct: 58 VKHFARSAELLKTLAQDYQKLYQHMAKSSTSLLP--ELSAKDNPFRNLLAEEE 108
>gnl|CDD|219088 pfam06560, GPI, Glucose-6-phosphate isomerase (GPI). This family
consists of several bacterial and archaeal
glucose-6-phosphate isomerase (GPI) proteins
(EC:5.3.1.9).
Length = 181
Score = 26.4 bits (58), Expect = 7.1
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 4/45 (8%)
Query: 90 EIRLVLDGSGYFDVR----DKFDDWIRIEVTKGDLIIIPAGIYHR 130
E+ VL G ++ DD IE+ KG ++ +P HR
Sbjct: 84 EVYQVLKGKALMLLQKPEGGAVDDVRVIEMEKGTVVYVPPYYGHR 128
>gnl|CDD|131081 TIGR02026, BchE, magnesium-protoporphyrin IX monomethyl ester
anaerobic oxidative cyclase. This model respresents the
cobalamin-dependent oxidative cyclase responsible for
forming the distinctive E-ring of the chlorin ring
system under anaerobic conditions. This step is
essential in the biosynthesis of both
bacteriochlorophyll and chlorophyll under anaerobic
conditions (a separate enzyme, AcsF, acts under aerobic
conditions). This model identifies two clades of
sequences, one from photosynthetic, non-cyanobacterial
bacteria and another including Synechocystis and several
non-photosynthetic bacteria. The function of the
Synechocystis gene is supported by gene clustering with
other photosynthetic genes, so the purpose of the gene
in the non-photosynthetic bacteria is uncertain. Note
that homologs of this gene are not found in plants which
rely solely on the aerobic cyclase.
Length = 497
Score = 26.4 bits (58), Expect = 8.9
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 20 HRTPKEYLD-LQTLNKLTGVEYFNVQDEVLTKLRK 53
HR PK+++D ++ L + GV +F + DE T RK
Sbjct: 221 HRDPKKFVDEIEWLVRTHGVGFFILADEEPTINRK 255
>gnl|CDD|237468 PRK13684, PRK13684, Ycf48-like protein; Provisional.
Length = 334
Score = 26.5 bits (59), Expect = 9.2
Identities = 6/10 (60%), Positives = 7/10 (70%)
Query: 147 GEPVWTPHNR 156
G+ WTPH R
Sbjct: 202 GQTAWTPHQR 211
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
0.320 0.139 0.425
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,517,357
Number of extensions: 908078
Number of successful extensions: 878
Number of sequences better than 10.0: 1
Number of HSP's gapped: 872
Number of HSP's successfully gapped: 40
Length of query: 178
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 87
Effective length of database: 6,901,388
Effective search space: 600420756
Effective search space used: 600420756
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: 56 (25.3 bits)