RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4673
(171 letters)
>gnl|CDD|182449 PRK10425, PRK10425, DNase TatD; Provisional.
Length = 258
Score = 90.5 bits (225), Expect = 1e-22
Identities = 31/79 (39%), Positives = 52/79 (65%), Gaps = 1/79 (1%)
Query: 27 DVGANLTNRKFGRDLESVVQRAKDSGVQKIIAIGSSLKSSKEALRLARIYPGMVYSTAGI 86
D+G NLT+ +F +D + VV RA +GV ++ G++L+ S++A +LAR YP +STAG+
Sbjct: 3 DIGVNLTSSQFAKDRDDVVARAFAAGVNGMLITGTNLRESQQAQKLARQYPS-CWSTAGV 61
Query: 87 HPHEAKSWDEDYIDQLRDL 105
HPH++ W + + +L
Sbjct: 62 HPHDSSQWQAATEEAIIEL 80
>gnl|CDD|238635 cd01310, TatD_DNAse, TatD like proteins; E.coli TatD is a
cytoplasmic protein, shown to have magnesium dependent
DNase activity.
Length = 251
Score = 89.9 bits (224), Expect = 1e-22
Identities = 36/84 (42%), Positives = 53/84 (63%), Gaps = 1/84 (1%)
Query: 25 LIDVGANLTNRKFGRDLESVVQRAKDSGVQKIIAIGSSLKSSKEALRLARIYPGMVYSTA 84
LID +L +F D + V+ RA+++GV KII +G+ LKSSK AL LA+ Y VY+
Sbjct: 1 LIDTHCHLDFPQFDADRDDVLARAREAGVIKIIVVGTDLKSSKRALELAKKYD-NVYAAV 59
Query: 85 GIHPHEAKSWDEDYIDQLRDLVSN 108
G+HPH+A ++ +D L L +N
Sbjct: 60 GLHPHDADEHVDEDLDLLELLAAN 83
>gnl|CDD|223162 COG0084, TatD, Mg-dependent DNase [DNA replication, recombination,
and repair].
Length = 256
Score = 89.2 bits (222), Expect = 3e-22
Identities = 30/82 (36%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 25 LIDVGANLTNRKFGRDLESVVQRAKDSGVQKIIAIGSSLKSSKEALRLARIYPGMVYSTA 84
LID +L +F D + V+ RA+++GV+K++ +G+ L+ K AL LA YP VY+
Sbjct: 3 LIDTHCHLDFEEFDEDRDEVIARAREAGVKKMVVVGTDLEDFKRALELAEKYPN-VYAAV 61
Query: 85 GIHPHEAKSWDEDYIDQLRDLV 106
G+HP +A E+ +++L L
Sbjct: 62 GVHPLDADEHSEEDLEELEQLA 83
>gnl|CDD|216250 pfam01026, TatD_DNase, TatD related DNase. This family of proteins
are related to a large superfamily of metalloenzymes.
TatD, a member of this family has been shown
experimentally to be a DNase enzyme.
Length = 255
Score = 88.9 bits (221), Expect = 4e-22
Identities = 31/80 (38%), Positives = 49/80 (61%)
Query: 26 IDVGANLTNRKFGRDLESVVQRAKDSGVQKIIAIGSSLKSSKEALRLARIYPGMVYSTAG 85
ID +L + F D + V++RA+++GV ++ +G+ L+ AL LAR YPG VY+ G
Sbjct: 1 IDAHCHLDFKDFDEDRDEVIERAREAGVTAVVVVGTDLEDFLRALELARKYPGKVYAAVG 60
Query: 86 IHPHEAKSWDEDYIDQLRDL 105
+HPHEA E+ ++ L L
Sbjct: 61 VHPHEADEASEEVLEALEKL 80
>gnl|CDD|232780 TIGR00010, TIGR00010, hydrolase, TatD family. PSI-BLAST, starting
with a urease alpha subunit, finds a large superfamily
of proteins, including a number of different enzymes
that act as hydrolases at C-N bonds other than peptide
bonds (EC 3.5.-.-), many uncharacterized proteins, and
the members of this family. Several genomes have
multiple paralogs related to this family. However, a set
of 17 proteins can be found, one each from 17 of the
first 20 genomes, such that each member forms a
bidirectional best hit across genomes with all other
members of the set. This core set (and one other
near-perfect member), but not the other paralogs, form
the seed for this model. Additionally, members of the
seed alignment and all trusted hits, but not all
paralogs, have a conserved motif DxHxH near the amino
end. The member from E. coli was recently shown to have
DNase activity [Unknown function, Enzymes of unknown
specificity].
Length = 252
Score = 73.8 bits (182), Expect = 2e-16
Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 25 LIDVGANLTNRKFGRDLESVVQRAKDSGVQKIIAIGSSLKSSKEALRLARIYPGMVYSTA 84
LID +L F D+E V++RAK +GV ++A+G+ L+ AL LA YP VY+
Sbjct: 1 LIDAHCHLDFLDFEEDVEEVIERAKAAGVTAVVAVGTDLEDFLRALELAEKYP-NVYAAV 59
Query: 85 GIHPHEAKSWDEDYIDQLRDLV 106
G+HP + ++ I +L L
Sbjct: 60 GVHPLDVDDDTKEDIKELERLA 81
>gnl|CDD|171118 PRK11449, PRK11449, putative deoxyribonuclease YjjV; Provisional.
Length = 258
Score = 41.9 bits (98), Expect = 5e-05
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 25 LIDVGANLTNRKFGRDLESVVQRAKDSGVQKIIAIGSSLKSSKEALRLARIYPGMVYSTA 84
ID + F D E+ +QRA +GV KII + ++ L LA Y + Y+
Sbjct: 5 FIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAERYQPL-YAAL 63
Query: 85 GIHPHEAKSWDEDYIDQLR 103
G+HP + + +DQL+
Sbjct: 64 GLHPGMLEKHSDVSLDQLQ 82
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 31.9 bits (73), Expect = 0.011
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 141 CEFCQKNFSRKEHLNRHL 158
C C K+FSRK +L RHL
Sbjct: 2 CPDCGKSFSRKSNLKRHL 19
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 31.5 bits (71), Expect = 0.017
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 141 CEFCQKNFSRKEHLNRHLWVHK 162
C C K+FS K+ L RHL H
Sbjct: 3 CPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|223353 COG0276, HemH, Protoheme ferro-lyase (ferrochelatase) [Coenzyme
metabolism].
Length = 320
Score = 31.8 bits (73), Expect = 0.14
Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 18/80 (22%)
Query: 41 LESVVQRAKDSGVQKIIAI-----------GSSLKSSKEALRLARIYPGMVYSTAGIHPH 89
+E V+ K GV++I+ + GS + AL+ R P + I +
Sbjct: 104 IEEAVEELKKDGVERIVVLPLYPQYSSSTTGSYVDELARALKELRGQPKIST----IPDY 159
Query: 90 EAKSWDEDYIDQLRDLVSNT 109
+ YI+ L D +
Sbjct: 160 YD---EPLYIEALADSIREK 176
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 28.6 bits (64), Expect = 0.15
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 141 CEFCQKNFSRKEHLNRHL 158
C C K F K L H+
Sbjct: 3 CPECGKVFKSKSALREHM 20
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 31.3 bits (71), Expect = 0.23
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 140 LCEFCQKNFSRKEHLNRHL 158
CEFC K RKE L RH+
Sbjct: 200 FCEFCLKFMKRKEQLQRHM 218
>gnl|CDD|223757 COG0685, MetF, 5,10-methylenetetrahydrofolate reductase [Amino acid
transport and metabolism].
Length = 291
Score = 30.8 bits (70), Expect = 0.27
Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 14/73 (19%)
Query: 39 RDLESVVQRAKDSGVQKIIAI----------GSSLKSSKEALRLARIY-PGMVYSTAGIH 87
++ S+++ A G++ I+A+ G S + + L + G+ +
Sbjct: 92 IEIISILKGAAALGIRNILALRGDPPAGDKPGGKDLYSVDLVELIKKMRGGIFDIGVAAY 151
Query: 88 P---HEAKSWDED 97
P E+K ED
Sbjct: 152 PEGHPESKDVKED 164
>gnl|CDD|216106 pfam00762, Ferrochelatase, Ferrochelatase.
Length = 311
Score = 30.2 bits (69), Expect = 0.41
Identities = 16/79 (20%), Positives = 27/79 (34%), Gaps = 22/79 (27%)
Query: 41 LESVVQRAKDSGVQKIIAI-----------GSSLKSSKEALRLARIYPGMVYSTAGIHPH 89
+E ++ K GV +I+ + GS L AL+ R P
Sbjct: 100 IEDALEELKADGVDRIVVLPLYPQYSASTTGSYLDELARALKKGRPAP---------EVR 150
Query: 90 EAKSW--DEDYIDQLRDLV 106
+ + YI+ L D +
Sbjct: 151 VIRRYYDHPGYIEALADSI 169
>gnl|CDD|217269 pfam02887, PK_C, Pyruvate kinase, alpha/beta domain. As well as
being found in pyruvate kinase this family is found as
an isolated domain in some bacterial proteins.
Length = 117
Score = 29.4 bits (67), Expect = 0.47
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 42 ESVVQRAKDSGVQKIIAIGSSLKSSKEALRLARIYPGM 79
S V+ AK+ G + I+ + S + A +++ PG
Sbjct: 6 RSAVEAAKELGAKAIVVLTESGST---ARLVSKYRPGA 40
>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 = 29.8 bits (68), Expect = 0.67
Identities = 9/30 (30%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 40 DLESVVQRAKDSGVQKIIAI--GSSLKSSK 67
+E+ V+ A+ +G +I GSS+ +K
Sbjct: 71 VVEAAVEAARAAGADGVIGFGGGSSMDVAK 100
>gnl|CDD|107336 cd06341, PBP1_ABC_ligand_binding_like_7, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. Members of this group are
sequence-similar to members of the family of ABC-type
hydrophobic amino acid transporters such as
leucine-isoleucine-valine-binding protein (LIVBP);
however their ligand specificity has not been determined
experimentally.
Length = 341
Score = 29.2 bits (66), Expect = 1.0
Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 9/50 (18%)
Query: 40 DLESVVQRAKDSGVQKIIAIGSSLKSSKEALRLARIYPGMVYSTAGIHPH 89
D Q+A +G II + A A + + AG+ P
Sbjct: 176 DPTPQAQQAAAAGADAIITVLD-------AAVCASVLKAV--RAAGLTPK 216
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 29.4 bits (66), Expect = 1.0
Identities = 11/63 (17%), Positives = 25/63 (39%)
Query: 12 ELTKLTNCFDNYVLIDVGANLTNRKFGRDLESVVQRAKDSGVQKIIAIGSSLKSSKEALR 71
L V ++ A +T G D+ ++V+ A +++ +L +AL+
Sbjct: 422 HLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREARRREVTLDDFLDALK 481
Query: 72 LAR 74
+
Sbjct: 482 KIK 484
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a zinc-finger
domain with the CxxCx(12)Hx(6)H motif, found in multiple
copies in a wide range of proteins from plants to
metazoans. Some member proteins, particularly those from
plants, are annotated as being RNA-binding.
Length = 25
Score = 26.3 bits (59), Expect = 1.1
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 141 CEFCQKNFSRKEHLNRHL 158
CE C F+ + L HL
Sbjct: 3 CELCNVTFTSESQLKSHL 20
>gnl|CDD|236872 PRK11183, PRK11183, D-lactate dehydrogenase; Provisional.
Length = 564
Score = 28.7 bits (65), Expect = 1.7
Identities = 7/39 (17%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 81 YSTAGIHPHEAKSWDEDYIDQLRDLVSNTGNSTMNRYNS 119
+ + + D +Y +++RD+ ++T R+N+
Sbjct: 204 FDDEDVRHDGRHASDHEYAERVRDVDADTP----ARFNA 238
>gnl|CDD|218323 pfam04910, Tcf25, Transcriptional repressor TCF25. Members of this
family are transcriptional repressors. They may act by
increasing histone deacetylase activity at promoter
regions.
Length = 342
Score = 28.4 bits (64), Expect = 1.7
Identities = 10/59 (16%), Positives = 22/59 (37%), Gaps = 9/59 (15%)
Query: 121 QWITEIKQTLFTTFVDITALCEFCQKNFSRKEH---------LNRHLWVHKDSSMMKEL 170
W+ ++ + L + E ++ L RH+ + ++SS+M L
Sbjct: 267 LWLEDVLRVLSNVIHSKPSDAEDAGALLVKESLAYIPEIPLNLLRHVILSEESSLMALL 325
>gnl|CDD|178777 PLN03239, PLN03239, histone acetyltransferase; Provisional.
Length = 351
Score = 28.5 bits (63), Expect = 1.7
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 106 VSNTGNSTMNRYNSSQW-ITEIKQTLFTT--FVDITALCEFCQKNFSRKEHLNRH 157
V N + Y W + + + LF F+D+ +CEF F+RK L R
Sbjct: 71 VKNVAFLELGPYQMDTWYFSPLPKELFKAGGFIDVLYVCEFSFGFFARKSELLRF 125
>gnl|CDD|233980 TIGR02712, urea_carbox, urea carboxylase. Members of this family
are ATP-dependent urea carboxylase, including
characterized members from Oleomonas sagaranensis (alpha
class Proteobacterium) and yeasts such as Saccharomyces
cerevisiae. The allophanate hydrolase domain of the
yeast enzyme is not included in this model and is
represented by an adjacent gene in Oleomonas
sagaranensis. The fusion of urea carboxylase and
allophanate hydrolase is designated urea amidolyase. The
enzyme from Oleomonas sagaranensis was shown to be
highly active on acetamide and formamide as well as urea
[Central intermediary metabolism, Nitrogen metabolism].
Length = 1201
Score = 28.5 bits (64), Expect = 1.9
Identities = 24/59 (40%), Positives = 30/59 (50%), Gaps = 16/59 (27%)
Query: 35 RKFG-----RDLESVVQRAKDSGVQKIIAIGSSL-KSSKEALRLA-RI-YPGMVYSTAG 85
RKFG R+L A+ +GV + G+ L S EAL A I YP M+ STAG
Sbjct: 110 RKFGLKHTAREL------AEAAGVP--LLPGTGLLSSLDEALEAAKEIGYPVMLKSTAG 160
>gnl|CDD|132301 TIGR03257, met_CoM_red_bet, methyl-coenzyme M reductase, beta
subunit. Members of this protein family are the beta
subunit of methyl coenzyme M reductase, also called
coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This
enzyme, with alpha, beta, and gamma subunits, catalyzes
the last step in methanogenesis. Several methanogens
have encode two such enzymes, designated I and II; this
model does not separate the isozymes [Energy metabolism,
Methanogenesis].
Length = 433
Score = 28.3 bits (63), Expect = 1.9
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 21 DNYVLIDVGANLTNRKFGRDLESVVQRAKDSGVQKI 56
DN + V AN + G +ESVV+RA + GV +
Sbjct: 245 DNLLYDLVKANGKDGTVGSVVESVVERAIEDGVISV 280
>gnl|CDD|187577 cd05267, SDR_a6, atypical (a) SDRs, subgroup 6. These atypical SDR
family members of unknown function have only a partial
match to a prototypical glycine-rich NAD(P)-binding
motif consensus, GXXG, which conserves part of the motif
of extended SDR. Furthermore, they lack the
characteristic active site residues of the SDRs. This
subgroup is related to phenylcoumaran benzylic ether
reductase, an NADPH-dependent aromatic alcohol
reductase. One member is identified as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 27.3 bits (61), Expect = 3.1
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 28 VGANLTNRKFGRDLESVVQRAKDSGVQKIIAIGS 61
V ANL + E+VVQ K GV+++I S
Sbjct: 69 VYANLGGTDLDQQAENVVQAMKAVGVKRLIWTTS 102
>gnl|CDD|212663 cd07782, FGGY_YpCarbK_like, Yersinia Pseudotuberculosis
carbohydrate kinase-like subgroup; belongs to the FGGY
family of carbohydrate kinases. This subgroup is
composed of the uncharacterized Yersinia
Pseudotuberculosis carbohydrate kinase that has been
named glyerol/xylulose kinase and similar
uncharacterized proteins from bacteria and eukaryota.
Carbohydrate kinases catalyze the ATP-dependent
phosphorylation of their carbohydrate substrate to
produce phosphorylated sugar and ADP. The presence of
Mg2+ is required for catalytic activity. This subgroup
shows high homology to characterized ribulokinases and
belongs to the FGGY family of carbohydrate kinases, the
monomers of which contain two large domains, which are
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain.
Length = 536
Score = 27.9 bits (63), Expect = 3.2
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 88 PHEAKSWDEDYIDQ--LRDLVSN 108
HE K WD+D+++ L DLV
Sbjct: 190 AHEKKGWDDDFLEAIGLEDLVEE 212
>gnl|CDD|234585 PRK00035, hemH, ferrochelatase; Reviewed.
Length = 333
Score = 27.5 bits (62), Expect = 3.4
Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 18/78 (23%)
Query: 41 LESVVQRAKDSGVQKIIAI-----------GSSLKSSKEALRLARIYPGMVYSTAGIHPH 89
+E ++ K GV +I+ + S + AL R+ P + + I +
Sbjct: 107 IEEALEALKADGVDRIVVLPLYPQYSYSTTASYFEDLARALAKLRLQPEIRF----IRSY 162
Query: 90 EAKSWDEDYIDQLRDLVS 107
YI+ L + +
Sbjct: 163 YD---HPGYIEALAESIR 177
>gnl|CDD|143495 cd06821, PLPDE_III_D-TA, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme D-Threonine Aldolase.
D-threonine aldolase (D-TA, EC 4.3.1.18) reversibly
catalyzes the aldol cleavage of D-threonine into glycine
and acetaldehyde, and the synthesis of D-threonine from
glycine and acetaldehyde. Its activity is present in
several genera of bacteria but not in fungi. It requires
PLP and a divalent cation such as Co2+, Ni2+, Mn2+, or
Mg2+ as cofactors for catalytic activity and thermal
stability. Members of this subfamily show similarity to
bacterial alanine racemase (AR), a fold type III
PLP-dependent enzyme which contains an N-terminal
PLP-binding TIM-barrel domain and a C-terminal
beta-sandwich domain. AR exists as homodimers with
active sites that lie at the interface between the TIM
barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Based on its similarity to
AR, it is possible that low specificity D-TAs also form
dimers in solution. Experimental data show that the
monomeric form of low specificity D-TAs exhibit full
catalytic activity.
Length = 361
Score = 27.6 bits (62), Expect = 3.6
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 69 ALRLARIYPGMVYSTAGIHPHEAKSWDE------DYIDQLRDLVSNTGNSTMNR 116
L LA+ YPG +S A++ + L D+ NTG MNR
Sbjct: 93 FLELAKKYPGTRFSALVDDLEAAEALSAAAGSAGLTLSVLLDV--NTG---MNR 141
>gnl|CDD|233815 TIGR02294, nickel_nikA, nickel ABC transporter, nickel/metallophore
periplasmic binding protein. Members of this family are
periplasmic nickel-binding proteins of nickel ABC
transporters. Most appear to be lipoproteins. This
protein was previously (circa 2003) thought to mediate
binding to nickel through water molecules, but is now
thought to involve a chelating organic molecule, perhaps
butane-1,2,4-tricarboxylate, acting as a metallophore
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 500
Score = 27.5 bits (61), Expect = 3.8
Identities = 17/39 (43%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 75 IYPGMVYSTAG--IHPHEAKSWD--ED---YIDQLRDLV 106
+Y +V TA I P AKSW ED Y +LRD V
Sbjct: 35 VYEPLVRYTADGKIEPWLAKSWTVSEDGKTYTFKLRDDV 73
>gnl|CDD|239504 cd03411, Ferrochelatase_N, Ferrochelatase, N-terminal domain:
Ferrochelatase (protoheme ferrolyase or HemH) is the
terminal enzyme of the heme biosynthetic pathway. It
catalyzes the insertion of ferrous iron into the
protoporphyrin IX ring yielding protoheme. This enzyme
is ubiquitous in nature and widely distributed in
bacteria and eukaryotes. Recently, some archaeal members
have been identified. The oligomeric state of these
enzymes varies depending on the presence of a
dimerization motif at the C-terminus.
Length = 159
Score = 27.1 bits (61), Expect = 3.8
Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 11/52 (21%)
Query: 41 LESVVQRAKDSGVQKIIAI-----------GSSLKSSKEALRLARIYPGMVY 81
+E ++ K GV +I+ + GS L + AL+ R P +
Sbjct: 101 IEEALEELKADGVDRIVVLPLYPQYSASTTGSYLDEVERALKKLRPAPELRV 152
>gnl|CDD|234297 TIGR03656, IsdC, heme uptake protein IsdC. Isd proteins are
iron-regulated surface proteins found in Bacillus,
Staphylococcus and Listeria species and are responsible
for heme scavenging from hemoproteins. The IsdC protein
consists of an N-terminal hydrophobic signal sequence, a
central NEAT (NEAr Transporter, pfam05031) domain which
confers the ability to bind heme and a C-terminal SrtB
processing signal which targets the protein to the cell
wall. IsdC is believed to make a direct contact with,
and transfer heme to, the heme-binding component (IsdE)
of an ABC transporter in the cytoplasmic membrane, and
to receive heme from other NEAT-containing heme-binding
proteins also localized in the cell wall.
Length = 217
Score = 26.4 bits (58), Expect = 7.4
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 97 DYIDQLRDLVSNTGNSTMN-RYNSSQWITEIK 127
DY ++ L+ G T+ N S WIT K
Sbjct: 53 DYFEKPAKLIVKNGKMTVQITVNHSHWITGFK 84
>gnl|CDD|239155 cd02754, MopB_Nitrate-R-NapA-like, Nitrate reductases, NapA
(Nitrate-R-NapA), NasA, and NarB catalyze the reduction
of nitrate to nitrite. Monomeric Nas is located in the
cytoplasm and participates in nitrogen assimilation.
Dimeric Nap is located in the periplasm and is coupled
to quinol oxidation via a membrane-anchored tetraheme
cytochrome. Members of the MopB_Nitrate-R-NapA CD belong
to the molybdopterin_binding (MopB) superfamily of
proteins.
Length = 565
Score = 26.4 bits (59), Expect = 8.5
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 93 SWDE--DYI-DQLRDLVSNTGNSTMNRYNSSQWITE 125
SWDE D I ++ + + + G ++ Y S Q +TE
Sbjct: 71 SWDEALDLIAERFKAIQAEYGPDSVAFYGSGQLLTE 106
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
0.315 0.128 0.373
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,233,565
Number of extensions: 719003
Number of successful extensions: 940
Number of sequences better than 10.0: 1
Number of HSP's gapped: 936
Number of HSP's successfully gapped: 40
Length of query: 171
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 81
Effective length of database: 6,945,742
Effective search space: 562605102
Effective search space used: 562605102
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.1 bits)