RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032704
(135 letters)
>gnl|CDD|234566 PRK00004, rplX, 50S ribosomal protein L24; Reviewed.
Length = 105
Score = 79.0 bits (196), Expect = 3e-20
Identities = 28/60 (46%), Positives = 38/60 (63%)
Query: 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKV 126
M +K GDTV VIAG DKGK G++ KV + V+V+ +N+ KH K +E QG II+
Sbjct: 2 MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEK 61
>gnl|CDD|214374 CHL00141, rpl24, ribosomal protein L24; Validated.
Length = 83
Score = 77.8 bits (192), Expect = 5e-20
Identities = 33/59 (55%), Positives = 46/59 (77%)
Query: 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125
KMHVK GDTVK+I+G DKGKIGE+ K+ + ++ V+VK IN+K KH+K +E E G+I +
Sbjct: 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQ 64
>gnl|CDD|233263 TIGR01079, rplX_bact, ribosomal protein L24, bacterial/organelle.
This model recognizes bacterial and organellar forms of
ribosomal protein L24. It excludes eukaryotic and
archaeal forms, designated L26 in eukaryotes [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 104
Score = 74.2 bits (183), Expect = 2e-18
Identities = 29/60 (48%), Positives = 40/60 (66%), Gaps = 1/60 (1%)
Query: 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE-EEQGQIIK 125
KM +K GDTVKVI+G DKGK G++ KV + V+V+ +N+ KHVK + QG II+
Sbjct: 1 KMKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIE 60
>gnl|CDD|240513 cd06089, KOW_RPL26, KOW motif of Ribosomal Protein L26. RPL26 and
its bacterial paralogs RPL24 have a KOW motif at their N
terminal. KOW domain is known as an RNA-binding motif
that is shared so far among some families of ribosomal
proteins, the essential bacterial transcriptional
elongation factor NusG, the eukaryotic chromatin
elongation factor Spt5, the higher eukaryotic KIN17
proteins and Mtr4. RPL26 makes a very minor
contributions to the biogenesis, structure, and function
of 60s ribosomal subunits. However, RPL24 is essential
to generate the first intermediate during 50s ribosomal
subunits assembly. RPL26 have an extra-ribosomal
function to enhances p53 translation after DNA damage.
Length = 65
Score = 71.8 bits (177), Expect = 7e-18
Identities = 28/60 (46%), Positives = 39/60 (65%)
Query: 73 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY 132
GD V+VI G DKGK G++ KV R + V+V+ +N+ KHVK +E QG II+V + I
Sbjct: 1 GDEVQVIRGKDKGKQGKVLKVDRKKNRVIVEGVNVVKKHVKPSQENPQGGIIEVEAPIHI 60
>gnl|CDD|223276 COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal
structure and biogenesis].
Length = 104
Score = 62.7 bits (153), Expect = 6e-14
Identities = 30/59 (50%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125
KM VK GDTVKVIAG DKGK G++ KV V+V+ +N+ KH+K +E +G II
Sbjct: 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPK--KVVVEGVNVVKKHIKPSQENPEGGIIN 58
>gnl|CDD|183399 PRK12281, rplX, 50S ribosomal protein L24; Reviewed.
Length = 76
Score = 61.6 bits (150), Expect = 8e-14
Identities = 23/58 (39%), Positives = 34/58 (58%)
Query: 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124
K+ VK GD VKVIAG DKGK G++ V + V+V+ + + K +K ++ G I
Sbjct: 4 KLKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFI 61
>gnl|CDD|144165 pfam00467, KOW, KOW motif. This family has been extended to
coincide with ref. The KOW (Kyprides, Ouzounis, Woese)
motif is found in a variety of ribosomal proteins and
NusG.
Length = 32
Score = 41.3 bits (98), Expect = 2e-06
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 73 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103
GD V+VI+G KGK G++ +V + V V+
Sbjct: 2 GDVVRVISGPFKGKKGKVVEVDDSKARVHVE 32
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 35.4 bits (83), Expect = 3e-04
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 69 HVKAGDTVKVIAGCDKGKIGEITKVFRH 96
+ GDTV+VIAG KGK+G++ +V
Sbjct: 1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
>gnl|CDD|240504 cd00380, KOW, KOW: an acronym for the authors' surnames (Kyrpides,
Ouzounis and Woese). KOW domain is known as an
RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. The KOW motif contains an
invariants glycine residue and comprises alternating
blocks of hydrophilic and hydrophobic residues.
Length = 49
Score = 36.0 bits (84), Expect = 3e-04
Identities = 12/42 (28%), Positives = 17/42 (40%)
Query: 73 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKK 114
GD V+V+ G KG+ G + + V VK K
Sbjct: 1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKGAELK 42
>gnl|CDD|234915 PRK01191, rpl24p, 50S ribosomal protein L24P; Validated.
Length = 120
Score = 37.2 bits (87), Expect = 4e-04
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 54 RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKT 109
R++ SLPV + GDTVKV+ G KG+ G++ +V + V+ + +K
Sbjct: 36 REKYGIRSLPV------RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKK 85
>gnl|CDD|240515 cd06091, KOW_NusG, NusG contains an NGN domain at its N-terminus
and KOW motif at its C-terminus. KOW_NusG motif is one
of the two domains of N-Utilization Substance G (NusG) a
transcription elongation and Rho-termination factor in
bacteria and archaea. KOW domain is known as an
RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. The eukaryotic ortholog of NusG
is Spt5 with multiple KOW motifs at its C-terminus.
Length = 56
Score = 33.2 bits (77), Expect = 0.005
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102
+ GDTV++I+G G G++ ++ V V
Sbjct: 4 FEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKV 36
>gnl|CDD|150132 pfam09356, Phage_BR0599, Phage conserved hypothetical protein
BR0599. This entry describes a family of proteins
found almost exclusively in phage or in prophage
regions of bacterial genomes, including the phage-like
Rhodobacter capsulatus gene transfer agent, which
packages DNA. An apparent exception is Wolbachia
pipientis wMel, a bacterial endosymbiont of the fruit
fly, which has several candidate phage-related genes
physically separate from obvious prophage regions.
Length = 80
Score = 32.2 bits (74), Expect = 0.016
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 70 VKAGDTVKVIAGCDK 84
+ GD V++ AGCDK
Sbjct: 41 IAVGDAVRLTAGCDK 55
>gnl|CDD|240507 cd06083, KOW_Spt5_3, KOW domain of Spt5, repeat 3. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains
play critical roles in recruitment of multiple other
eukaryotic transcription elongation and RNA biogenesis
factors and additionally are involved in the binding of
the eukaryotic Spt5 proteins to RNA polymerases.
Length = 51
Score = 29.8 bits (68), Expect = 0.069
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101
H K GD VKVI+G +G+ G + KV TV
Sbjct: 1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVF 33
>gnl|CDD|227736 COG5449, COG5449, Uncharacterized conserved protein [Function
unknown].
Length = 225
Score = 29.9 bits (67), Expect = 0.33
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 61 SLPVLHKMHVKAGDTVKVIAGCDK 84
L + +V GD K+ AGCDK
Sbjct: 160 ILEDIIPDYVAPGDEFKITAGCDK 183
>gnl|CDD|240508 cd06084, KOW_Spt5_4, KOW domain of Spt5, repeat 4. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains
play critical roles in recruitment of multiple other
eukaryotic transcription elongation and RNA biogenesis
factors and additionally are involved in the binding of
the eukaryotic Spt5 proteins to RNA polymerases.
Length = 43
Score = 27.5 bits (62), Expect = 0.38
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 73 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104
GDTVKV+ G KG+ G + ++R T+ +
Sbjct: 1 GDTVKVVDGPYKGRQGTVLHIYR--GTLFLHS 30
>gnl|CDD|140250 PTZ00223, PTZ00223, 40S ribosomal protein S4; Provisional.
Length = 273
Score = 29.2 bits (65), Expect = 0.68
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 64 VLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRH 96
V+ + + G V V G ++G+IGEI + RH
Sbjct: 166 VVDLIKNRNGKVVMVTGGANRGRIGEIVSIERH 198
>gnl|CDD|130152 TIGR01080, rplX_A_E, ribosomal protein L24p/L26e,
archaeal/eukaryotic. This model represents the archaeal
and eukaryotic branch of the ribosomal protein L24p/L26e
family. Bacterial and organellar forms are represented
by related model TIGR01079 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 114
Score = 27.4 bits (61), Expect = 1.2
Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 54 RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLK 108
R++ +LPV + GD V+++ G KG G+++KV + V+ + +
Sbjct: 32 REKYGKRALPV------RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKE 80
>gnl|CDD|130335 TIGR01268, Phe4hydrox_tetr, phenylalanine-4-hydroxylase, tetrameric
form. This model describes the larger, tetrameric form
of phenylalanine-4-hydroxylase, as found in metazoans.
The enzyme irreversibly converts phenylalanine to
tryosine and is known to be the rate-limiting step in
phenylalanine catabolism in some systems. It is closely
related to metazoan tyrosine 3-monooxygenase and
tryptophan 5-monoxygenase, and more distantly to
monomeric phenylalanine-4-hydroxylases of some
Gram-negative bacteria. The member of this family from
Drosophila has been described as having both
phenylalanine-4-hydroxylase and tryptophan
5-monoxygenase activity (PMID:1371286). However, a
Drosophila member of the tryptophan 5-monoxygenase clade
has subsequently been discovered.
Length = 436
Score = 28.3 bits (63), Expect = 1.3
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 80 AGCDKGKIGEITKVFRHNSTVMVKDINLKTK 110
K+ + + R + V V ++ K
Sbjct: 66 DEASDRKLEGVIEHLRQKAEVTVNILSRDNK 96
>gnl|CDD|180698 PRK06798, fliD, flagellar capping protein; Validated.
Length = 440
Score = 28.2 bits (63), Expect = 1.3
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 83 DKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYS 128
D+G IGE +K + V ++LK + + +++Q I+ Y
Sbjct: 373 DEGIIGERSK----SIDNRVSKLDLKITDIDTQNKQKQDNIVDKYQ 414
>gnl|CDD|226223 COG3700, AphA, Acid phosphatase (class B) [General function
prediction only].
Length = 237
Score = 27.5 bits (61), Expect = 2.0
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 16/88 (18%)
Query: 52 WER--KECKPNSLPV-----LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104
WE+ S+P L MH + GD + + G GK ++K + K+
Sbjct: 102 WEKVNNGWDEFSIPKEVARQLIDMHQRRGDAIYFVTGRTPGKTDTVSK-------TLAKN 154
Query: 105 INLKTKH--VKKREEEEQGQIIKVYSLI 130
++ + + ++ + GQ K +
Sbjct: 155 FHITNMNPVIFAGDKPKPGQYTKTQWIQ 182
>gnl|CDD|233522 TIGR01672, AphA, HAD superfamily (subfamily IIIB) phosphatase,
TIGR01672. This family of proteins is a member of the
IIIB subfamily (pfam02767) of the haloacid dehalogenase
(HAD) superfamily of hydrolases. All characterized
members of subfamily III and most characterized members
of the HAD superfamily are phosphatases. HAD superfamily
phosphatases contain active site residues in several
conserved catalytic motifs, all of which are found
conserved here. The AphA gene from E. coli has been
characterized and shown to be an active phosphatase
enzyme. This family has been previously described as the
"class B non-specific bacterial acid phosphatase"
(B-NSAP) family where it is noted that the enzyme is
secreted and has a broad substrate range. The
possibility exists, however, that the enzyme is specific
for an as yet undefined substrate. Supporting evidence
for the inclusion in the HAD superfamily, whose
phosphatase members are magnesium dependent, is the
inhibition by EDTA and calcium ions, and stimulation by
magnesium ion.
Length = 237
Score = 27.6 bits (61), Expect = 2.1
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 14/67 (20%)
Query: 52 WER--KECKPNSLPV-----LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104
WE+ S+P L MH + GD + + G GK ++K + K+
Sbjct: 102 WEKVNNGWDEFSIPKEVARQLIDMHQRRGDAIFFVTGRTPGKTDTVSK-------TLAKN 154
Query: 105 INLKTKH 111
++ +
Sbjct: 155 FHIPAMN 161
>gnl|CDD|240506 cd06082, KOW_Spt5_2, KOW domain of Spt5, repeat 2. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains
play critical roles in recruitment of multiple other
eukaryotic transcription elongation and RNA biogenesis
factors and additionally are involved in the binding of
the eukaryotic Spt5 proteins to RNA polymerases.
Length = 51
Score = 25.5 bits (57), Expect = 2.6
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 73 GDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKT 109
GD V+VI G KG G++ V T+M K +LK
Sbjct: 4 GDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKE 40
>gnl|CDD|132172 TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. Members of
this protein family are 3-hexulose-6-phosphate synthase
(HPS), or the HPS domain of a fusion protein. This
enzyme is part of the ribulose monophosphate (RuMP)
pathway, which in one direction removes the toxic
metabolite formaldehyde by assimilation into
fructose-6-phosphate. In the other direction, in species
lacking a complete pentose phosphate pathway, the RuMP
pathway yields ribulose-5-phosphate, necessary for
nucleotide biosynthesis, at the cost of also yielding
formaldehyde. These latter species tend usually have a
formaldehyde-activating enzyme to attach formaldehyde to
the C1 carrier tetrahydromethanopterin. In these
species, the enzyme is viewed as a lyase rather than a
synthase and is called D-arabino 3-hexulose 6-phosphate
formaldehyde lyase. Note that there is some overlap in
specificity with the Escherichia coli enzyme
3-keto-L-gulonate 6-phosphate decarboxylase.
Length = 206
Score = 26.9 bits (60), Expect = 2.7
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 73 GDTVKVIAGCDKGKI-GEITKVFRHNSTVMVKDINLKTKHVKKREEEEQG-QIIKVY 127
D V V+ D I G + +H V V IN+K K + +E +E G I V+
Sbjct: 77 ADIVTVLGVADDATIKGAVKAAKKHGKEVQVDLINVKDKVKRAKELKELGADYIGVH 133
>gnl|CDD|223328 COG0250, NusG, Transcription antiterminator [Transcription].
Length = 178
Score = 26.9 bits (60), Expect = 2.9
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 8/67 (11%)
Query: 58 KPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVF--RHNSTVMVKDIN------LKT 109
+ P K+ + GD V++I G G ++ +V + V V L+
Sbjct: 112 EEEVAPKKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEF 171
Query: 110 KHVKKRE 116
V+K +
Sbjct: 172 DQVEKLK 178
>gnl|CDD|212039 cd10329, SLC5sbd_SGLT1-like, Na(+)/glucose cotransporter SGLT1 and
related proteins; solute binding domain. This subfamily
includes the solute-binding domain of SGLT proteins that
cotransport Na+ with various solutes. Its members
include: the human glucose (SGLT1, -2, -4, -5 ),
chiro-inositol (SGLT5), and myo-inositol (SMIT)
cotransporters. It also includes human SGLT3 which has
been characterized as a glucose sensor and not a
transporter. It belongs to the solute carrier 5 (SLC5)
transporter family.
Length = 564
Score = 27.3 bits (61), Expect = 3.1
Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 1 MAAM-AALQSSMTSLSISSNSFF 22
+A M AAL SS+TS+ SS++ F
Sbjct: 354 LAVMLAALMSSLTSIFNSSSTLF 376
>gnl|CDD|185508 PTZ00194, PTZ00194, 60S ribosomal protein L26; Provisional.
Length = 143
Score = 26.2 bits (58), Expect = 4.5
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 54 RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLK 108
R + S+PV + D V V+ G KG+ G++T V+R + ++ I +
Sbjct: 37 RAKYNVRSMPV------RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITRE 85
>gnl|CDD|220244 pfam09441, Abp2, ARS binding protein 2. This DNA-binding protein
binds to the autonomously replicating sequence (ARS)
binding element. It may play a role in regulating the
cell cycle response to stress signals.
Length = 176
Score = 26.3 bits (58), Expect = 4.7
Identities = 11/27 (40%), Positives = 12/27 (44%), Gaps = 12/27 (44%)
Query: 46 VVRLKRWERKECKPNSLPVLHKMHVKA 72
VRLKRW +H MHV A
Sbjct: 100 AVRLKRW------------MHSMHVDA 114
>gnl|CDD|173641 cd05072, PTKc_Lyn, Catalytic domain of the Protein Tyrosine Kinase,
Lyn. Protein Tyrosine Kinase (PTK) family; Lyn kinase;
catalytic (c) domain. The PTKc family is part of a
larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Lyn is a member of the
Src subfamily of proteins, which are cytoplasmic (or
non-receptor) tyr kinases. Src kinases contain an
N-terminal SH4 domain with a myristoylation site,
followed by SH3 and SH2 domains, a tyr kinase domain,
and a regulatory C-terminal region containing a
conserved tyr. They are activated by autophosphorylation
at the tyr kinase domain, but are negatively regulated
by phosphorylation at the C-terminal tyr by Csk
(C-terminal Src Kinase). Src proteins are involved in
signaling pathways that regulate cytokine and growth
factor responses, cytoskeleton dynamics, cell
proliferation, survival, and differentiation. Lyn is
expressed in B lymphocytes and myeloid cells. It
exhibits both positive and negative regulatory roles in
B cell receptor (BCR) signaling. Lyn, as well as Fyn and
Blk, promotes B cell activation by phosphorylating ITAMs
(immunoreceptor tyr activation motifs) in CD19 and in Ig
components of BCR. It negatively regulates signaling by
its unique ability to phosphorylate ITIMs
(immunoreceptor tyr inhibition motifs) in cell surface
receptors like CD22 and CD5. Lyn also plays an important
role in G-CSF receptor signaling by phosphorylating a
variety of adaptor molecules.
Length = 261
Score = 26.5 bits (58), Expect = 4.9
Identities = 15/65 (23%), Positives = 35/65 (53%), Gaps = 8/65 (12%)
Query: 74 DTVKVIAGCDKGKIGEITKVFRHNST-VMVKDINLKTKHVKKREEE-------EQGQIIK 125
+++K++ G+ GE+ + +NST V VK + T V+ EE + ++++
Sbjct: 6 ESIKLVKKLGAGQFGEVWMGYYNNSTKVAVKTLKPGTMSVQAFLEEANLMKTLQHDKLVR 65
Query: 126 VYSLI 130
+Y+++
Sbjct: 66 LYAVV 70
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 363
Score = 26.4 bits (59), Expect = 5.0
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 64 VLHKMHVKAGDTVKVIAGCDKGKIG 88
V++ V+ GDTV VI GC G +G
Sbjct: 174 VVNTARVRPGDTVAVI-GC--GGVG 195
>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also
called TypA) having homology to domain II of the
elongation factors (EFs) EF-G and EF-Tu. BipA is a
highly conserved protein with global regulatory
properties in Escherichia coli. BipA is phosphorylated
on a tyrosine residue under some cellular conditions.
Mutants show altered regulation of some pathways. BipA
functions as a translation factor that is required
specifically for the expression of the transcriptional
modulator Fis. BipA binds to ribosomes at a site that
coincides with that of EF-G and has a GTPase activity
that is sensitive to high GDP:GTP ratios and, is
stimulated by 70S ribosomes programmed with mRNA and
aminoacylated tRNAs. The growth rate-dependent
induction of BipA allows the efficient expression of
Fis, thereby modulating a range of downstream
processes, including DNA metabolism and type III
secretion.
Length = 86
Score = 25.1 bits (56), Expect = 5.5
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 70 VKAGDTVKVIAGCDKGKIGEITKVFRH 96
VK G V V+ K + +ITK+F
Sbjct: 27 VKVGQQVAVVKRDGKIEKAKITKLFGF 53
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 26.3 bits (58), Expect = 5.7
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 1/75 (1%)
Query: 53 ERKECKPNSLPVLHKMHV-KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKH 111
+ KE K K GD V++ KGKI +I + N TV + +
Sbjct: 607 KLKETKQKIPQKPTNFQADKIGDKVRIRYFGQKGKIVQILGGNKWNVTVGGMRMKVHGSE 666
Query: 112 VKKREEEEQGQIIKV 126
++K + + KV
Sbjct: 667 LEKINKAPPPKKFKV 681
>gnl|CDD|212058 cd11489, SLC5sbd_SGLT5, Na(+)/glucose cotransporter SGLT5 and
related proteins; solute-binding domain. Human SGLT5 is
a glucose transporter, which also transports galactose.
It is encoded by the SLC5A10 gene, and is exclusively
expressed in the renal cortex. This subgroup belongs to
the solute carrier 5 (SLC5) transporter family.
Length = 604
Score = 26.4 bits (58), Expect = 6.1
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 4 MAALQSSMTSLSISSNSFF 22
MAAL SS+TS+ SS++ F
Sbjct: 358 MAALMSSLTSIFNSSSTLF 376
>gnl|CDD|133458 cd06849, lipoyl_domain, Lipoyl domain of the dihydrolipoyl
acyltransferase component (E2) of 2-oxo acid
dehydrogenases. 2-oxo acid dehydrogenase multienzyme
complexes, like pyruvate dehydrogenase (PDH),
2-oxoglutarate dehydrogenase (OGDH) and branched-chain
2-oxo acid dehydrogenase (BCDH), contain at least three
different enzymes, 2-oxo acid dehydrogenase (E1),
dihydrolipoyl acyltransferase (E2) and dihydrolipoamide
dehydrogenase (E3) and play a key role in redox
regulation. E2, the central component of the complex,
catalyzes the transfer of the acyl group of CoA from E1
to E3 via reductive acetylation of a lipoyl group
covalently attached to a lysine residue.
Length = 74
Score = 25.1 bits (56), Expect = 6.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 64 VLHKMHVKAGDTVKV 78
VL K+ V+ GDTV V
Sbjct: 53 VLAKILVEEGDTVPV 67
>gnl|CDD|217879 pfam04081, DNA_pol_delta_4, DNA polymerase delta, subunit 4.
Length = 124
Score = 25.8 bits (56), Expect = 6.5
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 42 PCLIVVRLKRWERKE 56
PC+ + RL+RW+R +
Sbjct: 79 PCIGITRLQRWQRAK 93
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 26.3 bits (59), Expect = 6.8
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 8/45 (17%)
Query: 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKK 114
+K GD VKV +G + T F + + +DIN + KH ++
Sbjct: 289 IKKGDWVKV-----RGSVQNDT--FTRDLVMNAQDIN-EIKHPER 325
>gnl|CDD|236305 PRK08582, PRK08582, hypothetical protein; Provisional.
Length = 139
Score = 25.4 bits (56), Expect = 8.1
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 69 HVKAGD--TVKVIAGCDKGKIG 88
H+K GD VKV+ D GKIG
Sbjct: 49 HLKVGDEVEVKVLNVEDDGKIG 70
>gnl|CDD|236818 PRK11009, aphA, acid phosphatase/phosphotransferase; Provisional.
Length = 237
Score = 25.7 bits (57), Expect = 8.2
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 65 LHKMHVKAGDTVKVIAGCDKGKIGEITKV 93
L MHVK GD++ I G K ++K
Sbjct: 122 LIDMHVKRGDSIYFITGRTATKTETVSKT 150
>gnl|CDD|212057 cd11488, SLC5sbd_SGLT4, Na(+)/glucose cotransporter SGLT4 and
related proteins; solute-binding domain. Human SGLT4
(hSGLT4) has been reported to be a low-affinity glucose
transporter with unusual sugar selectivity: it
transports D-mannose but not galactose or
3-O-methyl-D-glucoside. It is encoded by the SLC5A9 gene
and is expressed in intestine, kidney, liver, brain,
lung, trachea, uterus, and pancreas. hSLGT4 is predicted
to contain 14 membrane-spanning regions. This subgroup
belongs to the solute carrier 5 (SLC5 )transporter
family.
Length = 605
Score = 26.0 bits (57), Expect = 8.7
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 4 MAALQSSMTSLSISSNSFF 22
MAAL SS+TS+ SS++ F
Sbjct: 355 MAALMSSLTSIFNSSSTLF 373
>gnl|CDD|165287 PHA02984, PHA02984, hypothetical protein; Provisional.
Length = 286
Score = 25.9 bits (57), Expect = 8.7
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 105 INLKTKHVKKREEEEQGQIIKVYSLICYFIH 135
+NLKTK+V +++ + Y+ C FIH
Sbjct: 127 LNLKTKYVTTTKDKNLHLAVITYTSNCPFIH 157
>gnl|CDD|109527 pfam00474, SSF, Sodium:solute symporter family. Membership of this
family is supported by a significant blast score.
Length = 406
Score = 25.8 bits (57), Expect = 10.0
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 2 AAMAALQSSMTSLSISSNSFF 22
+AA+ S++TS +SS+S F
Sbjct: 300 VMLAAIMSTLTSQLLSSSSAF 320
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 0.133 0.388
Gapped
Lambda K H
0.267 0.0941 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,511,611
Number of extensions: 550242
Number of successful extensions: 632
Number of sequences better than 10.0: 1
Number of HSP's gapped: 630
Number of HSP's successfully gapped: 59
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
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: 53 (23.8 bits)