RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10290
(128 letters)
>gnl|CDD|216400 pfam01266, DAO, FAD dependent oxidoreductase. This family includes
various FAD dependent oxidoreductases:
Glycerol-3-phosphate dehydrogenase EC:1.1.99.5,
Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine
oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.
Length = 234
Score = 40.0 bits (94), Expect = 8e-05
Identities = 20/95 (21%), Positives = 31/95 (32%), Gaps = 10/95 (10%)
Query: 24 GGLRQQFSL---RENIEMSLFGAEFLRNIKHHCHVIGEDEPDVNFTPNGYLFCA-SQDGA 79
G L ++L + R +I E D +F G L A +
Sbjct: 43 GLLHPGLRKERAPLLARLALESRDLWR------ELIEELGIDCDFRRTGVLVLARDEAEL 96
Query: 80 ATLEKNHQLQKELGAKNVLLGPEQLKAKFPWLNTD 114
L + + LG LL E+L+ P L+
Sbjct: 97 DALRRLAAALRALGLPVELLDAEELRELEPGLSPG 131
>gnl|CDD|223737 COG0665, DadA, Glycine/D-amino acid oxidases (deaminating) [Amino
acid transport and metabolism].
Length = 387
Score = 31.8 bits (72), Expect = 0.067
Identities = 17/111 (15%), Positives = 32/111 (28%), Gaps = 15/111 (13%)
Query: 17 ASTTLSVGGLRQQFSLRENIEMSLFGAE-----FLRNIKHHCHVIGEDEPDVNFTPNGYL 71
+ + GG+ ++ A+ + + G G L
Sbjct: 41 GAAGRNAGGILAPWASPGGELEVRPLADLSLALWRELSEELGTGAG-------LRRRGLL 93
Query: 72 FCASQDG---AATLEKNHQLQKELGAKNVLLGPEQLKAKFPWLNTDDIALA 119
A+++G A LE+ + G LL + P L D +
Sbjct: 94 DLAAREGLKGLAQLERLAAELEAAGEDAELLDAAEAAELEPALGPDFVCGG 144
>gnl|CDD|132164 TIGR03120, one_C_mch, methenyltetrahydromethanopterin
cyclohydrolase. Members of this protein family are the
enzyme methenyltetrahydromethanopterin cyclohydrolase, a
key enzyme for tetrahydromethanopterin (H4MPT)-linked C1
transfer metabolism [Central intermediary metabolism,
One-carbon metabolism].
Length = 312
Score = 30.0 bits (68), Expect = 0.29
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 93 GAKNVLLGPEQLK-AKFPWLN--TDDIALACLGLEKEGW 128
G V + P + K+P + TD +ACLG +K GW
Sbjct: 57 GLAEVTIVPFPIDGLKWPAVQVTTDHPVIACLGSQKAGW 95
>gnl|CDD|133248 cd05148, PTKc_Srm_Brk, Catalytic domain of the Protein Tyrosine
Kinases, Srm and Brk. Protein Tyrosine Kinase (PTK)
family; Src-related kinase lacking C-terminal regulatory
tyrosine and N-terminal myristylation sites (Srm) and
breast tumor kinase (Brk, also called protein tyrosine
kinase 6); catalytic (c) domains. 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. Srm and
Brk are a member of the Src subfamily of proteins, which
are cytoplasmic (or non-receptor) tyr kinases. Src
kinases in general 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). Srm and
Brk however, lack the N-terminal myristylation sites.
Src proteins are involved in signaling pathways that
regulate cytokine and growth factor responses,
cytoskeleton dynamics, cell proliferation, survival, and
differentiation. Brk has been found to be overexpressed
in a majority of breast tumors.
Length = 261
Score = 28.9 bits (65), Expect = 0.65
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 70 YLFCASQDGAATLEKNHQLQKELGAKNVLLG 100
+ C +G A LE+ + + ++L A+N+L+G
Sbjct: 108 DMACQVAEGMAYLEEQNSIHRDLAARNILVG 138
>gnl|CDD|235020 PRK02264, PRK02264, N(5),N(10)-methenyltetrahydromethanopterin
cyclohydrolase; Provisional.
Length = 317
Score = 28.2 bits (64), Expect = 0.99
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 106 AKFPWLN--TDDIALACLGLEKEGW 128
A +P++ TD ALACLG +K GW
Sbjct: 73 APWPFVEVSTDHPALACLGSQKAGW 97
>gnl|CDD|216961 pfam02289, MCH, Cyclohydrolase (MCH). Methenyl
tetrahydromethanopterin cyclohydrolase EC:3.5.4.27 is
involved in methanogenesis in bacteria and archaea,
producing methane from carbon monoxide or carbon
dioxide.
Length = 312
Score = 28.2 bits (63), Expect = 1.1
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 100 GPEQLKAKFPWLNTDDIALACLGLEKEGW 128
P L + TD A+ACLG +K GW
Sbjct: 67 EPNGLWLPAVQVKTDHPAIACLGSQKAGW 95
>gnl|CDD|236968 PRK11750, gltB, glutamate synthase subunit alpha; Provisional.
Length = 1485
Score = 27.9 bits (63), Expect = 1.5
Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 14/36 (38%)
Query: 26 LRQQFS---------LRENIEMSL---FGAEFLRNI 49
RQQF+ LRE MSL G E N+
Sbjct: 509 FRQQFAQVTNPPIDPLREAHVMSLATCIGRE--MNV 542
>gnl|CDD|238305 cd00545, MCH, Methenyltetrahydromethanopterin (methenyl-H4MPT)
cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that
has been identified in methanogenic archaea, sulfate-
reducing archaea, and methylotrophic bacteria. It
catalyzes the reversible formation of N(5),
N(10)-methenyltetrahydromethanopterin (methenyl-H4MPT+)
from N(5)-formyltetrahydromethanopterin (formyl- H4MPT),
in the third step of the reaction to reduce CO2 to CH4.
The protein functions as a homodimer or homotrimer,
depending on the organism.
Length = 312
Score = 27.7 bits (62), Expect = 1.9
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 113 TDDIALACLGLEKEGW 128
TD+ +ACLG + GW
Sbjct: 80 TDNPVIACLGSQYAGW 95
>gnl|CDD|173633 cd05052, PTKc_Abl, Catalytic domain of the Protein Tyrosine Kinase,
Abelson kinase. Protein Tyrosine Kinase (PTK) family;
Abelson (Abl) 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. Abl (or
c-Abl) is a ubiquitously-expressed cytoplasmic (or
nonreceptor) tyr kinase that contains SH3, SH2, and tyr
kinase domains in its N-terminal region, as well as
nuclear localization motifs, a putative DNA-binding
domain, and F- and G-actin binding domains in its
C-terminal tail. It also contains a short autoinhibitory
cap region in its N-terminus. Abl is normally inactive
and requires phosphorylation and myristoylation for
activation. Abl function depends on its subcellular
localization. In the cytoplasm, Abl plays a role in cell
proliferation and survival. In response to DNA damage or
oxidative stress, Abl is transported to the nucleus
where it induces apoptosis. In chronic myelogenous
leukemia (CML) patients, an aberrant translocation
results in the replacement of the first exon of Abl with
the BCR (breakpoint cluster region) gene. The resulting
BCR-Abl fusion protein is constitutively active and
associates into tetramers, resulting in a hyperactive
kinase sending a continuous signal. This leads to
uncontrolled proliferation, morphological transformation
and anti-apoptotic effects. BCR-Abl is the target of
selective inhibitors, such as imatinib (Gleevec), used
in the treatment of CML. Abl2, also known as ARG
(Abelson-related gene), is thought to play a cooperative
role with Abl in the proper development of the nervous
system. The Tel-ARG fusion protein, resulting from
reciprocal translocation between chromosomes 1 and 12,
is associated with acute myeloid leukemia (AML). The TEL
gene is a frequent fusion partner of other tyr kinase
oncogenes, including Tel/Abl, Tel/PDGFRbeta, and
Tel/Jak2, found in patients with leukemia and
myeloproliferative disorders.
Length = 263
Score = 27.1 bits (60), Expect = 2.5
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 71 LFCASQ--DGAATLEKNHQLQKELGAKNVLLGPEQL 104
L+ A+Q LEK + + ++L A+N L+G L
Sbjct: 107 LYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHL 142
>gnl|CDD|225791 COG3252, COG3252, Methenyltetrahydromethanopterin cyclohydrolase
[Coenzyme metabolism].
Length = 314
Score = 26.6 bits (59), Expect = 4.3
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 106 AKFPWLN--TDDIALACLGLEKEGW 128
P + TD A+A LG +K GW
Sbjct: 72 ITLPAVQVATDHPAIATLGAQKAGW 96
>gnl|CDD|234196 TIGR03397, acid_phos_Burk, acid phosphatase, Burkholderia-type. A
member of this family, AcpA from Burkholderia mallei,
has been charactized as a surface-bound glycoprotein
with acid phosphatase activity, as can be shown with the
colorigenic substrate 5-bromo-4-chloro-3-indolyl
phosphate. This family shares regions of sequence
similarity with phosphocholine-preferring phospholipase
C enzymes (TIGR03396) from many of the same species.
Length = 483
Score = 26.3 bits (58), Expect = 5.8
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 14 YARASTTLSVGGLRQQFSLRENIEMSLFGAEFL 46
YA+ ++ L + L QQ++L +N M FG FL
Sbjct: 129 YAQDASKLPMWKLAQQYTLADNFFMGAFGGSFL 161
>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 = 26.3 bits (58), Expect = 5.9
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 11/66 (16%)
Query: 74 ASQDGAATLEKNHQLQKELGAKNVLLGPEQ-----LKAKFPWLNTD------DIALACLG 122
A+ D A NH + K+ AKN+L G E+ P+ + D D+ A
Sbjct: 261 ATSDLAVRQAINHAVNKQSIAKNILYGTEKPADTLFAKNVPYADIDLKPYKYDVKKANAL 320
Query: 123 LEKEGW 128
L++ GW
Sbjct: 321 LDEAGW 326
>gnl|CDD|217682 pfam03708, Avian_gp85, Avian retrovirus envelope protein, gp85.
Family of a vain specific viral glycoproteins that
forms a receptor-binding gp85 polypeptide that is
linked through disulfide to a membrane-spanning gp37
spike. Gp85 confers a high degree of subgroup
specificity for interaction with distinct cell
receptors.
Length = 254
Score = 26.1 bits (57), Expect = 6.0
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 34 ENIEMSLFGAEFLRNIKHHCHVIGEDEPDVNFTPN 68
E E+ L G++ L N+ + V G + F P
Sbjct: 8 EPQELQLLGSQSLPNVTNITQVTGVAGGCIGFAPY 42
>gnl|CDD|217211 pfam02743, Cache_1, Cache domain.
Length = 81
Score = 24.9 bits (55), Expect = 6.2
Identities = 8/36 (22%), Positives = 11/36 (30%)
Query: 61 PDVNFTPNGYLFCASQDGAATLEKNHQLQKELGAKN 96
+ GY F +G NHQ +L
Sbjct: 46 KSIKLGKTGYAFIVDNNGKVLAHPNHQPVTKLLGDW 81
>gnl|CDD|133199 cd05068, PTKc_Frk_like, Catalytic domain of Fyn-related kinase-like
Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK)
family; Human Fyn-related kinase (Frk) and similar
proteins; 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. Frk and
Srk are members 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. Frk, also known as Rak, is specifically
expressed in liver, lung, kidney, intestine, mammary
glands, and the islets of Langerhans. Rodent homologs
were previously referred to as GTK (gastrointestinal tyr
kinase), BSK (beta-cell Src-like kinase), or IYK
(intestinal tyr kinase). Studies in mice reveal that Frk
is not essential for viability. It plays a role in the
signaling that leads to cytokine-induced beta-cell death
in Type I diabetes. It also regulates beta-cell number
during embryogenesis and early in life.
Length = 261
Score = 25.8 bits (57), Expect = 6.3
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 78 GAATLEKNHQLQKELGAKNVLLG 100
G A LE + + ++L A+NVL+G
Sbjct: 115 GMAYLEAQNYIHRDLAARNVLVG 137
>gnl|CDD|236167 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional
regulator; Reviewed.
Length = 309
Score = 26.1 bits (58), Expect = 6.8
Identities = 14/35 (40%), Positives = 17/35 (48%)
Query: 4 KHILASLVSLYARASTTLSVGGLRQQFSLRENIEM 38
+ ILAS LYARA + GL SL E+
Sbjct: 264 RRILASREPLYARADAVVDTSGLTVAQSLARLREL 298
>gnl|CDD|226185 COG3659, OprB, Carbohydrate-selective porin [Cell envelope
biogenesis, outer membrane].
Length = 439
Score = 26.0 bits (57), Expect = 7.7
Identities = 19/61 (31%), Positives = 25/61 (40%), Gaps = 10/61 (16%)
Query: 58 EDEPDVNFTPNGYLFCASQDGAATLEKNHQLQKELGAKNVLLGPEQLKAKFP---WLNTD 114
E PD TPNG+ F A L ELG + +G EQL ++ + T
Sbjct: 219 EANPDNLATPNGWDFSGDGTKGAL------LPLELGWQP-KVGAEQLPGEYRLGYYYYTA 271
Query: 115 D 115
D
Sbjct: 272 D 272
>gnl|CDD|173636 cd05057, PTKc_EGFR_like, Catalytic domain of Epidermal Growth
Factor Receptor-like Protein Tyrosine Kinases. Protein
Tyrosine Kinase (PTK) family; Epidermal Growth Factor
Receptor (EGFR) subfamily; catalytic (c) domain. EGFR
(HER, ErbB) subfamily members include EGFR (HER1,
ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and
similar proteins. 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.
The EGFR proteins are receptor tyr kinases (RTKs)
containing an extracellular EGF-related ligand-binding
region, a transmembrane helix, and a cytoplasmic region
with a tyr kinase domain and a regulatory C-terminal
tail. Unlike other tyr kinases, phosphorylation of the
activation loop of EGFR proteins is not critical to
their activation. Instead, they are activated by
ligand-induced dimerization, resulting in the
phosphorylation of tyr residues in the C-terminal tail,
which serve as binding sites for downstream signaling
molecules. Collectively, they can recognize a variety of
ligands including EGF, TGFalpha, and neuregulins, among
others. All four subfamily members can form homo- or
heterodimers. HER3 contains an impaired kinase domain
and depends on its heterodimerization partner for
activation. EGFR subfamily members are involved in
signaling pathways leading to a broad range of cellular
responses including cell proliferation, differentiation,
migration, growth inhibition, and apoptosis. Gain of
function alterations, through their overexpression,
deletions, or point mutations in their kinase domains,
have been implicated in various cancers. These receptors
are targets of many small molecule inhibitors and
monoclonal antibodies used in cancer therapy.
Length = 279
Score = 25.8 bits (57), Expect = 7.8
Identities = 10/30 (33%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 77 DGAATLEKNHQLQKELGAKNVLL-GPEQLK 105
G + LE+ + ++L A+NVL+ P+ +K
Sbjct: 120 KGMSYLEEKRLVHRDLAARNVLVKTPQHVK 149
>gnl|CDD|173654 cd05108, PTKc_EGFR, Catalytic domain of the Protein Tyrosine
Kinase, Epidermal Growth Factor Receptor. Protein
Tyrosine Kinase (PTK) family; Epidermal Growth Factor
Receptor (EGFR); 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. EGFR
(HER1, ErbB1) is a member of the EGFR (HER, ErbB)
subfamily of proteins, which are receptor tyr kinases
(RTKs) containing an extracellular EGF-related
ligand-binding region, a transmembrane helix, and a
cytoplasmic region with a tyr kinase domain and a
regulatory C-terminal tail. Unlike other tyr kinases,
phosphorylation of the activation loop of EGFR proteins
is not critical to their activation. Instead, they are
activated by ligand-induced dimerization, leading to the
phosphorylation of tyr residues in the C-terminal tail,
which serve as binding sites for downstream signaling
molecules. Ligands for EGFR include EGF, heparin binding
EGF-like growth factor (HBEGF), epiregulin,
amphiregulin, TGFalpha, and betacellulin. Upon ligand
binding, EGFR can form homo- or heterodimers with other
EGFR subfamily members. The EGFR signaling pathway is
one of the most important pathways regulating cell
proliferation, differentiation, survival, and growth.
Overexpression and mutation in the kinase domain of EGFR
have been implicated in the development and progression
of a variety of cancers. A number of monoclonal
antibodies and small molecule inhibitors have been
developed that target EGFR, including the antibodies
Cetuximab and Panitumumab, which are used in combination
with other therapies for the treatment of colorectal
cancer and non-small cell lung carcinoma (NSCLC). The
small molecule inhibitors Gefitinib (Iressa) and
Erlotinib (Tarceva), already used for NSCLC, are
undergoing clinical trials for other types of cancer
including gastrointestinal, breast, head and neck, and
bladder.
Length = 316
Score = 25.7 bits (56), Expect = 8.8
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 78 GAATLEKNHQLQKELGAKNVLL-GPEQLK 105
G LE+ + ++L A+NVL+ P+ +K
Sbjct: 121 GMNYLEERRLVHRDLAARNVLVKTPQHVK 149
>gnl|CDD|241390 cd13236, PH2_FGD1-4, FYVE, RhoGEF and PH domain
containing/faciogenital dysplasia proteins pleckstrin
homology (PH) domain, C-terminus. In general, FGDs
have a RhoGEF (DH) domain, followed by an N-terminal PH
domain, a FYVE domain and a C-terminal PH domain. All
FGDs are guanine nucleotide exchange factors that
activates the Rho GTPase Cdc42, an important regulator
of membrane trafficking. The RhoGEF domain is
responsible for GEF catalytic activity, while the
N-terminal PH domain is involved in intracellular
targeting of the DH domain. Not much is known about
FGD2. FGD1 is the best characterized member of the
group with mutations here leading to the X-linked
disorder known as faciogenital dysplasia (FGDY). Both
FGD1 and FGD3 are targeted by the ubiquitin ligase
SCF(FWD1/beta-TrCP) upon phosphorylation of two serine
residues in its DSGIDS motif and subsequently degraded
by the proteasome. However, FGD1 and FGD3 induced
significantly different morphological changes in HeLa
Tet-Off cells and while FGD1 induced long finger-like
protrusions, FGD3 induced broad sheet-like protrusions
when the level of GTP-bound Cdc42 was significantly
increased by the inducible expression of FGD3. They
also reciprocally regulated cell motility in inducibly
expressed in HeLa Tet-Off cells, FGD1 stimulated cell
migration while FGD3 inhibited it. FGD1 and FGD3
therefore play different roles to regulate cellular
functions, even though their intracellular levels are
tightly controlled by the same destruction pathway
through SCF(FWD1/beta-TrCP). FGD4 is one of the genes
associated with Charcot-Marie-Tooth neuropathy type 4
(CMT4), a group of progressive motor and sensory axonal
and demyelinating neuropathies that are distinguished
from other forms of CMT by autosomal recessive
inheritance. Those affected have distal muscle weakness
and atrophy associated with sensory loss and,
frequently, pes cavus foot deformity. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They
share little sequence conservation, but all have a
common fold, which is electrostatically polarized. Less
than 10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 105
Score = 25.0 bits (55), Expect = 9.7
Identities = 11/26 (42%), Positives = 12/26 (46%), Gaps = 5/26 (19%)
Query: 55 VIGEDEPDVNFTPNGYLFCASQDGAA 80
VI EP V YL+ A QD A
Sbjct: 29 VIPRTEPLV-----LYLYGAPQDVRA 49
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 0.135 0.410
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,430,511
Number of extensions: 558432
Number of successful extensions: 484
Number of sequences better than 10.0: 1
Number of HSP's gapped: 484
Number of HSP's successfully gapped: 31
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
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: 53 (24.1 bits)