RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10242
(77 letters)
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 105 bits (263), Expect = 5e-31
Identities = 51/76 (67%), Positives = 61/76 (80%)
Query: 1 MDSFLTEDQVNDFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEG 60
M LTE+Q+ +F+EAFSLFDKDG GTIT K LG VMRSLG+NP+EAEL++MI EVD +G
Sbjct: 1 MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG 60
Query: 61 KGIIDFPHFLELMMKK 76
G IDFP FL LM +K
Sbjct: 61 NGTIDFPEFLTLMARK 76
Score = 61.7 bits (150), Expect = 6e-14
Identities = 30/69 (43%), Positives = 47/69 (68%)
Query: 8 DQVNDFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGIIDFP 67
D + +EAF +FD+DG+G I+A L VM +LG ++ E++EMIRE D +G G I++
Sbjct: 81 DSEEEIKEAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQINYE 140
Query: 68 HFLELMMKK 76
F+++MM K
Sbjct: 141 EFVKMMMSK 149
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 77.4 bits (191), Expect = 5e-20
Identities = 41/73 (56%), Positives = 52/73 (71%)
Query: 5 LTEDQVNDFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGII 64
LTEDQ + REAF LFD DGSGTI K L + MRSLG P + E+++MI +VD +G G I
Sbjct: 11 LTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGKI 70
Query: 65 DFPHFLELMMKKV 77
DF FL++M KK+
Sbjct: 71 DFEEFLDIMTKKL 83
Score = 55.1 bits (133), Expect = 3e-11
Identities = 26/61 (42%), Positives = 34/61 (55%)
Query: 16 AFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGIIDFPHFLELMMK 75
AF LFD D +G I+ K+L V + LG ++ EL+EMI E D G G I F +M K
Sbjct: 95 AFRLFDDDKTGKISLKNLKRVAKELGETITDEELQEMIDEADRNGDGEISEEEFYRIMKK 154
Query: 76 K 76
Sbjct: 155 T 155
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse
superfamily of calcium sensors and calcium signal
modulators; most examples in this alignment model have
2 active canonical EF hands. Ca2+ binding induces a
conformational change in the EF-hand motif, leading to
the activation or inactivation of target proteins.
EF-hands tend to occur in pairs or higher copy numbers.
Length = 63
Score = 68.7 bits (169), Expect = 1e-17
Identities = 38/63 (60%), Positives = 45/63 (71%)
Query: 12 DFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGIIDFPHFLE 71
+ REAF LFDKDG GTI+A L ++SLG SE E++EMIREVD +G G IDF FLE
Sbjct: 1 ELREAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLE 60
Query: 72 LMM 74
LM
Sbjct: 61 LMA 63
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 69.6 bits (171), Expect = 5e-17
Identities = 35/77 (45%), Positives = 50/77 (64%), Gaps = 1/77 (1%)
Query: 1 MDSFLTEDQVNDFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEG 60
+ LTE+Q+ + +EAF LFD+D G I LG ++RSLG NPSEAE+ ++ E+D G
Sbjct: 10 TFTQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEID-AG 68
Query: 61 KGIIDFPHFLELMMKKV 77
+DFP FL +M K+
Sbjct: 69 NETVDFPEFLTVMSVKL 85
Score = 56.5 bits (137), Expect = 7e-12
Identities = 27/66 (40%), Positives = 41/66 (62%)
Query: 11 NDFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGIIDFPHFL 70
+ REAF LFDKD G I+ L V++SLG S+ E+E++++E D +G G ID+ F
Sbjct: 92 EELREAFKLFDKDHDGYISIGELRRVLKSLGERLSDEEVEKLLKEYDEDGDGEIDYEEFK 151
Query: 71 ELMMKK 76
+L+
Sbjct: 152 KLIKDS 157
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 40.8 bits (96), Expect = 1e-06
Identities = 23/60 (38%), Positives = 34/60 (56%), Gaps = 4/60 (6%)
Query: 18 SLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIRE----VDPEGKGIIDFPHFLELM 73
L DKDG G I + L ++++LG ++ E+EE+I +D +G G I F FLE M
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 37.9 bits (89), Expect = 2e-05
Identities = 18/50 (36%), Positives = 26/50 (52%)
Query: 24 GSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGIIDFPHFLELM 73
G IT + L + LG + SE E++ + RE D +G G I F F L+
Sbjct: 1 EKGLITREELKRALALLGISLSEEEVDILFREFDTDGDGKISFEEFCVLL 50
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 36.4 bits (85), Expect = 3e-05
Identities = 18/30 (60%), Positives = 22/30 (73%)
Query: 12 DFREAFSLFDKDGSGTITAKHLGIVMRSLG 41
+ REAF LFDKDG G I+A+ L +RSLG
Sbjct: 1 ELREAFKLFDKDGDGYISAEELRKALRSLG 30
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 33.5 bits (78), Expect = 5e-04
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 12 DFREAFSLFDKDGSGTITAKHLGIVMRSL 40
+ +EAF LFDKDG G I + ++++L
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLKAL 29
Score = 29.3 bits (67), Expect = 0.022
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 48 ELEEMIREVDPEGKGIIDFPHFLELMMKK 76
EL+E R D +G G IDF F +L+
Sbjct: 1 ELKEAFRLFDKDGDGKIDFEEFKDLLKAL 29
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not
undergo calcium dependent conformational changes.
Length = 29
Score = 32.0 bits (74), Expect = 0.002
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 12 DFREAFSLFDKDGSGTITAKHLGIVMRSL 40
+ +EAF FDKDG G I+ + +++ L
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLKKL 29
Score = 29.3 bits (67), Expect = 0.020
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 48 ELEEMIREVDPEGKGIIDFPHFLELMMK 75
EL+E +E D +G G I F F EL+ K
Sbjct: 1 ELKEAFKEFDKDGDGKISFEEFKELLKK 28
>gnl|CDD|197477 smart00027, EH, Eps15 homology domain. Pair of EF hand motifs
that recognise proteins containing Asn-Pro-Phe (NPF)
sequences.
Length = 96
Score = 33.4 bits (77), Expect = 0.002
Identities = 12/66 (18%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 4 FLTEDQVNDFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGI 63
++ + + + F DK+ GT+T ++ G + L ++ D + G
Sbjct: 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQT--LLAKIWNLADIDNDGE 60
Query: 64 IDFPHF 69
+D F
Sbjct: 61 LDKDEF 66
>gnl|CDD|238009 cd00052, EH, Eps15 homology domain; found in proteins implicated
in endocytosis, vesicle transport, and signal
transduction. The alignment contains a pair of EF-hand
motifs, typically one of them is canonical and binds to
Ca2+, while the other may not bind to Ca2+. A
hydrophobic binding pocket is formed by residues from
both EF-hand motifs. The EH domain binds to proteins
containing NPF (class I), [WF]W or SWG (class II), or
H[TS]F (class III) sequence motifs.
Length = 67
Score = 27.6 bits (62), Expect = 0.18
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 13 FREAFSLFDKDGSGTITAKHL-GIVMRSLGRNPSEAELEEMIREVDPEGKGIIDFPHF 69
+ + F D DG G I+ + +S + L ++ D + G +D F
Sbjct: 1 YDQIFRSLDPDGDGLISGDEARPFLGKS---GLPRSVLAQIWDLADTDKDGKLDKEEF 55
>gnl|CDD|221331 pfam11940, DUF3458, Domain of unknown function (DUF3458). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, archaea and eukaryotes.
This domain is typically between 402 to 419 amino acids
in length. This domain is found associated with
pfam01433. This domain has a conserved FSAPV sequence
motif.
Length = 365
Score = 28.2 bits (64), Expect = 0.30
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 44 PSEAELEEMIREVDPE 59
PSEAEL E ++ VDP+
Sbjct: 157 PSEAELAEQMKVVDPD 172
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 26.1 bits (59), Expect = 0.39
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 13 FREAFSLFDKDGSGTITAK 31
++ F FD +G G I+ +
Sbjct: 1 LKDLFRQFDTNGDGKISKE 19
>gnl|CDD|237585 PRK14015, pepN, aminopeptidase N; Provisional.
Length = 875
Score = 27.8 bits (63), Expect = 0.51
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 44 PSEAELEEMIREVDPE 59
PSEAEL E + +DP+
Sbjct: 623 PSEAELAEQMEVIDPD 638
>gnl|CDD|112487 pfam03672, UPF0154, Uncharacterized protein family (UPF0154).
This family contains a set of short bacterial proteins
of unknown function.
Length = 64
Score = 26.7 bits (59), Expect = 0.52
Identities = 7/29 (24%), Positives = 17/29 (58%)
Query: 28 ITAKHLGIVMRSLGRNPSEAELEEMIREV 56
I + ++ +GR PSE ++ +++R +
Sbjct: 32 INEDMIRMMYMQMGRKPSEKQINQIMRAI 60
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 27.5 bits (61), Expect = 0.60
Identities = 10/52 (19%), Positives = 24/52 (46%)
Query: 14 REAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGIID 65
R ++ D D G ++ ++++ G + + EE+ + D G G++
Sbjct: 182 RRILAIVDYDEDGQLSFSEFSDLIKAFGNLVAANKKEELFKAADLNGDGVVT 233
>gnl|CDD|233350 TIGR01302, IMP_dehydrog, inosine-5'-monophosphate dehydrogenase.
This model describes IMP dehydrogenase, an enzyme of
GMP biosynthesis. This form contains two CBS domains.
This model describes a rather tightly conserved cluster
of IMP dehydrogenase sequences, many of which are
characterized. The model excludes two related families
of proteins proposed also to be IMP dehydrogenases, but
without characterized members. These are related
families are the subject of separate models [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 450
Score = 26.9 bits (60), Expect = 0.83
Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 6/50 (12%)
Query: 27 TITAKHLGIVMRSLG------RNPSEAELEEMIREVDPEGKGIIDFPHFL 70
T+T + I M G RN S E E ++ V GII P +
Sbjct: 44 TVTESRMAIAMAREGGIGVIHRNMSIEEQAEQVKRVKRAENGIISDPVTI 93
>gnl|CDD|226286 COG3763, COG3763, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 71
Score = 26.2 bits (58), Expect = 0.92
Identities = 7/27 (25%), Positives = 18/27 (66%)
Query: 28 ITAKHLGIVMRSLGRNPSEAELEEMIR 54
I + + ++M +G+ PSE ++ +++R
Sbjct: 39 INEEMIRMMMAQMGQKPSEKKINQVMR 65
>gnl|CDD|107253 cd01540, PBP1_arabinose_binding, Periplasmic L-arabinose-binding
protein (ABP), a member of a family of pentose/hexose
sugar-binding proteins of the type I periplasmic binding
protein superfamily. Periplasmic L-arabinose-binding
protein (ABP), a member of a family of pentose/hexose
sugar-binding proteins of the type I periplasmic binding
protein superfamily. ABP is only involved in transport
contrary to other related sugar-binding proteins such as
the glucose/galactose-binding protein (GGBP) and the
ribose-binding protein (RBP), both of which are involved
in chemotaxis as well as transport. The periplasmic ABP
consists of two alpha/beta globular domains connected by
a three-stranded hinge, a Venus flytrap-like domain,
which undergoes a transition from an open to a closed
conformational state upon ligand binding. Moreover, ABP
is homologous to the ligand-binding domain of eukaryotic
receptors such as metabotropic glutamate receptor
(mGluR) and DNA-binding transcriptional repressors such
as LacI and GalR.
Length = 289
Score = 26.6 bits (59), Expect = 1.3
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 19 LFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEM-IREVDPEGKGII 64
L D DG H+G+ +G EA +EM R DP+ G +
Sbjct: 89 LVDADGKPMEDVPHVGMSATKIGEQVGEAIADEMKKRGWDPKEVGAL 135
>gnl|CDD|163638 cd07395, MPP_CSTP1, Homo sapiens CSTP1 and related proteins,
metallophosphatase domain. CSTP1 (complete
S-transactivated protein 1) is an uncharacterized Homo
sapiens protein with a metallophosphatase domain, that
is transactivated by the complete S protein of
hepatitis B virus. CSTP1 belongs to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all 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 = 262
Score = 26.5 bits (59), Expect = 1.3
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 7 EDQVNDFREAFSLFDKD 23
E QV+D ++ SL D D
Sbjct: 70 ERQVSDLKDVLSLLDPD 86
>gnl|CDD|233858 TIGR02414, pepN_proteo, aminopeptidase N, Escherichia coli type.
The M1 family of zinc metallopeptidases contains a
number of distinct, well-separated clades of proteins
with aminopeptidase activity. Several are designated
aminopeptidase N, EC 3.4.11.2, after the Escherichia
coli enzyme, suggesting a similar activity profile (see
SP|P04825 for a description of catalytic activity). This
family consists of all aminopeptidases closely related
to E. coli PepN and presumed to have similar (not
identical) function. Nearly all are found in
Proteobacteria, but members are found also in
Cyanobacteria, plants, and apicomplexan parasites. This
family differs greatly in sequence from the family of
aminopeptidases typified by Streptomyces lividans PepN
(TIGR02412), from the membrane bound aminopeptidase N
family in animals, etc [Protein fate, Degradation of
proteins, peptides, and glycopeptides].
Length = 863
Score = 26.5 bits (59), Expect = 1.3
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 44 PSEAELEEMIREVDPEG 60
PSEA L E++ +DP+
Sbjct: 613 PSEAYLAELMENIDPDA 629
>gnl|CDD|215491 PLN02906, PLN02906, xanthine dehydrogenase.
Length = 1319
Score = 25.8 bits (57), Expect = 2.3
Identities = 8/24 (33%), Positives = 12/24 (50%), Gaps = 6/24 (25%)
Query: 34 GIVM------RSLGRNPSEAELEE 51
G +M RS P+E ++EE
Sbjct: 96 GFIMSMYALLRSSKTPPTEEQIEE 119
>gnl|CDD|132870 cd07232, Pat_PLPL, Patain-like phospholipase. Patatin-like
phospholipase. This family consists of various patatin
glycoproteins from plants and fungi. The patatin protein
accounts for up to 40% of the total soluble protein in
potato tubers. Patatin is a storage protein, but it also
has the enzymatic activity of a lipid acyl hydrolase,
catalyzing the cleavage of fatty acids from membrane
lipids. Members of this family have been found also in
vertebrates.
Length = 407
Score = 25.7 bits (57), Expect = 2.4
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 19/67 (28%)
Query: 18 SLFDKDGSGTITAKHLGIVMRSLGR-------NPSEAELEEMIREVDPEGKGIIDFPH-- 68
+F +D SGTIT I RS +P+ +LE MI EG+ FP
Sbjct: 342 QIFLQDFSGTIT-----IWPRSTLSDFLRILSDPTPEDLERMIH----EGQ-QAAFPKLH 391
Query: 69 FLELMMK 75
F++ M+
Sbjct: 392 FIKNRMR 398
>gnl|CDD|189007 cd09600, M1_APN_1, Peptidase M1 family containing Aminopeptidase N.
This family contains aminopeptidase N (APN; CD13;
Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral
membrane protease belonging to the M1 gluzincin family.
It includes bacterial-type alanyl aminopeptidases as
well as PfA-M1 aminopeptidase (Plasmodium
falciparum-type). APN consists of a small N-terminal
cytoplasmic domain, a single transmembrane domain and a
large extracellular ectodomain that contains the active
site. It preferentially cleaves neutral amino acids from
the N-terminus of oligopeptides and, in higher
eukaryotes, is present in a variety of human tissues and
cell types (leukocyte, fibroblast, endothelial and
epithelial cells). APN expression is dysregulated in
inflammatory diseases such as chronic pain, rheumatoid
arthritis, multiple sclerosis, systemic sclerosis,
systemic lupus erythematosus,
polymyositis/dermatomyosytis and pulmonary sarcoidosis,
and is enhanced in tumor cells such as melanoma, renal,
prostate, pancreas, colon, gastric and thyroid cancers.
It is predominantly expressed on stem cells and on cells
of the granulocytic and monocytic lineages at distinct
stages of differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 861
Score = 25.7 bits (57), Expect = 2.4
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 44 PSEAELEEMIREVDPEG 60
PSE E+ E + +DP+
Sbjct: 612 PSENEIAERMEVIDPDA 628
>gnl|CDD|200486 cd11348, AmyAc_2, Alpha amylase catalytic domain found in an
uncharacterized protein family. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The catalytic triad (DED) is not
present here. The family members are quite extensive and
include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 429
Score = 25.7 bits (57), Expect = 2.8
Identities = 7/30 (23%), Positives = 8/30 (26%)
Query: 1 MDSFLTEDQVNDFREAFSLFDKDGSGTITA 30
F + R FD G G I
Sbjct: 264 NSLFRNLNTDGGHRRDNCYFDASGKGDIKP 293
>gnl|CDD|181749 PRK09276, PRK09276, LL-diaminopimelate aminotransferase;
Provisional.
Length = 385
Score = 25.6 bits (57), Expect = 3.0
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 10/41 (24%)
Query: 47 AELEEMIREVDPEGKGIIDF----------PHFLELMMKKV 77
AE+++ E G +I H +E M K V
Sbjct: 17 AEIDKKKAEKIARGVDVISLGIGDPDLPTPDHIIEAMCKAV 57
>gnl|CDD|163566 TIGR03854, F420_MSMEG_3544, probable F420-dependent oxidoreductase,
MSMEG_3544 family. Coenzyme F420 has a limited
phylogenetic distribution, including methanogenic
archaea, Mycobacterium tuberculosis and related species,
Colwellia psychrerythraea 34H, Rhodopseudomonas
palustris HaA2, and others. Partial phylogenetic
profiling identifies protein subfamilies, within the
larger family called luciferase-like monooxygenanases
(pfam00296), that appear only in F420-positive genomes
and are likely to be F420-dependent. This model
describes a small family, closely related to other such
families in the putative F420-binding region,
exemplified by MSMEG_3544 in Mycobacterium smegmatis
[Unknown function, Enzymes of unknown specificity].
Length = 290
Score = 25.2 bits (55), Expect = 3.4
Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 5/61 (8%)
Query: 3 SFLTEDQVNDFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIR----EVDP 58
SF+T ++ R I H GI + + A + +R +VDP
Sbjct: 180 SFVTPEEARAGRRTIEAAAAAAGREIEPDHFGISLA-VADGDLPAPVIAALRRRRPDVDP 238
Query: 59 E 59
Sbjct: 239 A 239
>gnl|CDD|198372 cd07804, FGGY_XK_like_1, uncharacterized xylulose kinase-like
proteins; a subgroup of the FGGY family of carbohydrate
kinases. This subgroup is composed of uncharacterized
bacterial and archaeal xylulose kinases-like proteins
with similarity to bacterial D-xylulose kinases (XK,
also known as xylulokinase; EC 2.7.1.17), which catalyze
the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. The presence of Mg2+ or Mn2+
is required for catalytic activity. D-XK exists as a
dimer with an active site that lies at the interface
between the N- and C-terminal domains. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 492
Score = 25.2 bits (56), Expect = 3.5
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 41 GRNPSEAELEEMIREVDPEGKGIIDFPHFL 70
G + ELEE +V P G++ P+
Sbjct: 315 GGLDAYDELEEEAEKVPPGADGLLFLPYLA 344
>gnl|CDD|182853 PRK10939, PRK10939, autoinducer-2 (AI-2) kinase; Provisional.
Length = 520
Score = 25.4 bits (56), Expect = 3.5
Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 15/61 (24%)
Query: 13 FREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGIIDFPHFLEL 72
FR+AF +K + A+ LGI SL LEEM V GII P F ++
Sbjct: 311 FRDAFCAEEK-----LLAERLGIDAYSL--------LEEMASRVPVGSHGII--PIFSDV 355
Query: 73 M 73
M
Sbjct: 356 M 356
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate
Dehydrogenases, NAD-binding and catalytic domains.
Phosphoglycerate dehydrogenases (PGDHs) catalyze the
initial step in the biosynthesis of L-serine from
D-3-phosphoglycerate. PGDHs come in 3 distinct
structural forms, with this first group being related
to 2-hydroxy acid dehydrogenases, sharing structural
similarity to formate and glycerate dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily,
which also include groups such as L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2
similar subdomains of the alpha/beta Rossmann fold NAD+
binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence. Many,
not all, members of this family are dimeric.
Length = 306
Score = 25.1 bits (56), Expect = 3.6
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 17 FSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVDPEGKGII 64
FS + ++ + A +V+ LGR +E EL E++++ D G+I
Sbjct: 9 FSKYSEEAKELLEAAGFEVVLNPLGRPLTEEELIELLKDAD----GVI 52
>gnl|CDD|233750 TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase,
type 2. Isopentenyl-diphosphate delta-isomerase (IPP
isomerase) interconverts isopentenyl diphosphate and
dimethylallyl diphosphate. This model represents the
type 2 enzyme. FMN, NADPH, and Mg2+ are required by this
form, which lacks homology to the type 1 enzyme
(TIGR02150). IPP is precursor to many compounds,
including enzyme cofactors, sterols, and isoprenoids
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 333
Score = 25.3 bits (56), Expect = 3.7
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 30 AKHLGIVM-----RSLGRNPSEAELEEMIREVDPEGKGI--IDFPHFLELMMKKV 77
A+ LGI M R+ ++P A+ E++RE P G I I P +E ++
Sbjct: 79 ARELGIPMGVGSQRAALKDPETADTFEVVREEAPNGPLIANIGAPQLVEGGPEEA 133
>gnl|CDD|219479 pfam07587, PSD1, Protein of unknown function (DUF1553). A family
of proteins found in Rhodopirellula baltica.
Length = 258
Score = 25.0 bits (55), Expect = 4.6
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 35 IVMRSLGRNPSEAELEEMIREVD 57
+R L R P++ E EE++ +
Sbjct: 235 AFLRVLSRPPTDEEREELVTFLS 257
>gnl|CDD|116538 pfam07928, Vps54, Vps54-like protein. This family contains
various proteins that are homologs of the yeast Vps54
protein, such as the rat homolog , the human homolog,
and the mouse homolog. In yeast, Vps54 associates with
Vps52 and Vps53 proteins to form a trimolecular complex
that is involved in protein transport between Golgi,
endosomal, and vacuolar compartments. All Vps54
homologs contain a coiled coil region (not found in the
region featured in this family) and multiple dileucine
motifs.
Length = 133
Score = 24.6 bits (54), Expect = 5.1
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 27 TITAKHLGIVMRSLG 41
TIT KHL + +SL
Sbjct: 67 TITTKHLALASQSLA 81
>gnl|CDD|233530 TIGR01686, FkbH, FkbH-like domain. This model describes a domain
of a family of proteins of unknown overall function. One
of these, however, is a modular polyketide synthase 4800
amino acids in length from Streptomyces avermilitis in
which this domain is the C-terminal segment. By
contrast, the FkbH protein from Streptomyces
hygroscopicus aparently contains only this domain. The
remaining members of the family all contain an
additional N-terminal domain of between 200 and 275
amino acids which show less than 20% identity to one
another. It seems likely then that these proteins are
involved in disparate functions, probably the
biosynthesis of different natural products. For
instance, the FkbH gene is found in a gene cluster
believed to be responsible for the biosynthesis of
unususal "PKS extender units" in the ascomycin pathway.
This domain is composed of two parts, the first of which
is a member of subfamily IIIC (TIGR01681) of the
haloacid dehalogenase (HAD) superfamily of
aspartate-nucleophile hydrolases. All of the
characterized enzymes within subfamily III are
phosphatases, and all of the active site residues
characteristic of HAD-superfamily phosphatases are
present in this domain. The C-terminal portion of this
domain is unique to this family (by BLAST).
Length = 320
Score = 24.4 bits (53), Expect = 6.2
Identities = 9/47 (19%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 11 NDFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVD 57
ND +A +F++ + A+ RS+ P L ++ ++++
Sbjct: 56 NDEDDAKKVFERRKDFILQAEDF--DARSINWGPKSESLRKIAKKLN 100
>gnl|CDD|183522 PRK12426, PRK12426, elongation factor P; Provisional.
Length = 185
Score = 24.4 bits (53), Expect = 6.3
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 64 IDFPHFLELMMKK 76
++ PHFLELM+ K
Sbjct: 123 VELPHFLELMVSK 135
>gnl|CDD|223668 COG0595, COG0595, mRNA degradation ribonucleases J1/J2
(metallo-beta-lactamase superfamily) [Translation,
ribosomal structure and biogenesis; Replication,
recombination and repair].
Length = 555
Score = 24.5 bits (54), Expect = 6.8
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 41 GRNPSEAELEEMIREVDPEGKG--IIDFPH 68
G PSE+E+ E + ++ KG I+
Sbjct: 206 GFTPSESEVGENLEDIIRNAKGRVIVTTFA 235
>gnl|CDD|237434 PRK13578, PRK13578, ornithine decarboxylase; Provisional.
Length = 720
Score = 24.5 bits (54), Expect = 6.9
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 46 EAELEEMIREVDPE 59
E L E IREV PE
Sbjct: 262 EEYLREQIREVAPE 275
>gnl|CDD|221230 pfam11800, RP-C_C, Replication protein C C-terminal region.
Replication protein C is involved in the early stages
of viral DNA replication.
Length = 208
Score = 24.5 bits (54), Expect = 7.1
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 32 HLGIVMRSLGRNPSEAELEEMIRE 55
++R L R + A+LE ++ E
Sbjct: 9 RFRAIVRRLPRKATLADLEALLDE 32
>gnl|CDD|232973 TIGR00433, bioB, biotin synthase. Catalyzes the last step of the
biotin biosynthesis pathway. All members of the seed
alignment are in the immediate gene neighborhood of a
bioA gene [Biosynthesis of cofactors, prosthetic groups,
and carriers, Biotin].
Length = 296
Score = 24.3 bits (54), Expect = 7.2
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 5/30 (16%)
Query: 30 AKHLGIVMRSLGRNPSEAELE---EMIREV 56
A +V GR PS+ E E E IRE+
Sbjct: 80 ASRFCMVTS--GRGPSDREFEKVLEAIREI 107
>gnl|CDD|215290 PLN02531, PLN02531, GTP cyclohydrolase I.
Length = 469
Score = 24.3 bits (53), Expect = 7.6
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 36 VMRSLGRNPSEAEL 49
++RSLG +P EL
Sbjct: 276 ILRSLGEDPLRKEL 289
>gnl|CDD|238622 cd01297, D-aminoacylase, D-aminoacylases (N-acyl-D-Amino acid
amidohydrolases) catalyze the hydrolysis of
N-acyl-D-amino acids to produce the corresponding
D-amino acids, which are used as intermediates in the
synthesis of pesticides, bioactive peptides, and
antibiotics.
Length = 415
Score = 24.2 bits (53), Expect = 7.6
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 36 VMRSLGRNPSEAELEEMIREVD 57
VM R +E EL +M +
Sbjct: 153 VMGLDAREATEEELAKMRELLR 174
>gnl|CDD|179056 PRK00523, PRK00523, hypothetical protein; Provisional.
Length = 72
Score = 23.5 bits (51), Expect = 7.7
Identities = 9/29 (31%), Positives = 19/29 (65%)
Query: 28 ITAKHLGIVMRSLGRNPSEAELEEMIREV 56
IT + + +GR PSE+++++++R V
Sbjct: 40 ITENMIRAMYMQMGRKPSESQIKQVMRSV 68
>gnl|CDD|215936 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain. This
family is involved in biosynthesis of guanosine
nucleotide. Members of this family contain a TIM barrel
structure. In the inosine monophosphate dehydrogenases
2 CBS domains pfam00571 are inserted in the TIM barrel.
This family is a member of the common phosphate binding
site TIM barrel family.
Length = 467
Score = 24.1 bits (53), Expect = 7.8
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 6/50 (12%)
Query: 27 TITAKHLGIVMRSLG------RNPSEAELEEMIREVDPEGKGIIDFPHFL 70
T+T + I M G +N S E E +R+V G I P +
Sbjct: 46 TVTESRMAIAMAREGGIGVIHKNMSIEEQAEEVRKVKRFESGFITDPVTV 95
>gnl|CDD|177875 PLN02230, PLN02230, phosphoinositide phospholipase C 4.
Length = 598
Score = 24.3 bits (52), Expect = 8.4
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 10 VNDFREAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAELEEMIREVD 57
V D R+ F + DG ++ + L +M G E LEE R VD
Sbjct: 28 VADVRDLFEKY-ADGDAHMSPEQLQKLMAEEGGGEGETSLEEAERIVD 74
>gnl|CDD|130109 TIGR01037, pyrD_sub1_fam, dihydroorotate dehydrogenase (subfamily
1) family protein. This family includes subfamily 1
dihydroorotate dehydrogenases while excluding the
closely related subfamily 2 (TIGR01036). This family
also includes a number of uncharacterized proteins and
a domain of dihydropyrimidine dehydrogenase. The
uncharacterized proteins might all be dihydroorotate
dehydrogenase.
Length = 300
Score = 24.3 bits (53), Expect = 8.6
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 15 EAFSLFDKDGSGTITAKHLGIVMRSLGRNPSEAEL 49
E+ D+ G+G + K +G+ R RNP+ E
Sbjct: 26 ESLRRIDRSGAGAVVTKSIGLEPRPGYRNPTIVET 60
>gnl|CDD|184499 PRK14090, PRK14090, phosphoribosylformylglycinamidine synthase
II; Provisional.
Length = 601
Score = 24.0 bits (52), Expect = 9.3
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 31 KHLGIVMRSLGRNPSEAELE 50
++L I+ LGR P+ EL+
Sbjct: 2 RYLNILEEKLGREPTFVELQ 21
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family
of proteins is universal in the archaea and consistsof
an N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 24.1 bits (53), Expect = 9.4
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 7/36 (19%)
Query: 35 IVMRSLGRNPS----EAELEEMIREVDPEGKGIIDF 66
IV+R +PS E E I+E+ PE GI D
Sbjct: 56 IVIRP---DPSVLLPPEEAIEKIKEIVPEEAGITDI 88
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 0.139 0.390
Gapped
Lambda K H
0.267 0.0908 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,229,058
Number of extensions: 350038
Number of successful extensions: 641
Number of sequences better than 10.0: 1
Number of HSP's gapped: 636
Number of HSP's successfully gapped: 64
Length of query: 77
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 31
Effective length of database: 8,897,318
Effective search space: 275816858
Effective search space used: 275816858
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 (21.7 bits)
S2: 53 (23.9 bits)