RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy958
(137 letters)
>gnl|CDD|216956 pfam02274, Amidinotransf, Amidinotransferase. This family contains
glycine (EC:2.1.4.1) and inosamine (EC:2.1.4.2)
amidinotransferases, enzymes involved in creatine and
streptomycin biosynthesis respectively. This family also
includes arginine deiminases, EC:3.5.3.6. These enzymes
catalyze the reaction: arginine + H2O <=> citrulline +
NH3. Also found in this family is the Streptococcus anti
tumour glycoprotein.
Length = 286
Score = 38.0 bits (89), Expect = 6e-04
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 11/70 (15%)
Query: 35 VDTVRAIIKKELRPPQ-VLDI---EDEEAKLDGSDVLFT-------GISKWTNEKGARAV 83
I+ K Q VLDI EDE A L+G D++ G+S+ T+E+G +
Sbjct: 90 RRLDILILLKHPYKVQLVLDISELEDENAFLEGGDMVLDHKGVVAYGVSERTDEEGIEEL 149
Query: 84 ADSFPEYPCT 93
A + P
Sbjct: 150 ARTLGYEPVA 159
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 33.8 bits (78), Expect = 0.017
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 3 VPEYLGTRYSRSERFDDHFIEKCDKY---LGNFIYVDTVRAIIKKELRPPQVLDIED 56
V E+L R R+ R + + + D + I +D V+ I+K LR + + IED
Sbjct: 268 VLEFLAKRLDRNVRELEGALNRLDAFALFTKRAITIDLVKEILKDLLRAGEKITIED 324
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 29.3 bits (66), Expect = 0.54
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 15 ERFDDHFIEKCDKYLGNFIYVDTVRAIIK-KELRPPQVLDIEDE 57
ER D I +G +Y +++ +I L P + ++I+
Sbjct: 184 EREDGGRIGDLFDLIGPIVYEVSLKELIDEGYLAPYKYVEIKVT 227
>gnl|CDD|235323 PRK04960, PRK04960, universal stress protein UspB; Provisional.
Length = 111
Score = 28.4 bits (64), Expect = 0.69
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 10 RYSRSERFDDH----FIEKCDKYLGNFI 33
Y ++R+ DH FI +C++ FI
Sbjct: 64 WYIYAQRYLDHHDPEFIRRCERVRRQFI 91
>gnl|CDD|235621 PRK05842, flgD, flagellar basal body rod modification protein;
Reviewed.
Length = 295
Score = 27.7 bits (61), Expect = 1.8
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 96 KVKNKNPKAKMSTSTGIDQLLVRTQVEM 123
++KN++P A M T I Q TQVEM
Sbjct: 40 QLKNQDPTAPMETDKIITQTAQLTQVEM 67
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine. This
subgroup has the characteristic active site tetrad and
NAD-binding motif of the extended SDRs. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. 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. 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. 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 = 303
Score = 27.7 bits (62), Expect = 2.1
Identities = 12/56 (21%), Positives = 21/56 (37%), Gaps = 7/56 (12%)
Query: 32 FIYVDTVRAIIKKELRPPQVLDIEDEEAKLDGSDVLFTGISKWTNEKGARAVADSF 87
F+++ +V+ + + P D D A D G SK E+ + S
Sbjct: 105 FVFLSSVKVNGEGTVGAP--FDETDPPAPQDA-----YGRSKLEAERALLELGASD 153
>gnl|CDD|211363 cd09252, AP-3_Mu3_Cterm, C-terminal domain of medium Mu3 subunit
in adaptor protein (AP) complex AP-3. AP complexes
participate in the formation of intracellular coated
transport vesicles and select cargo molecules for
incorporation into the coated vesicles in the late
secretory and endocytic pathways. There are four AP
complexes, AP-1, AP-2, AP-3, and AP-4, described in
various eukaryotic organisms. Each AP complex consists
of four subunits: two large chains (one each of
gamma/alpha/delta/epsilon and beta1-4, respectively), a
medium mu chain (mu1-4), and a small sigma chain
(sigma1-4). Each of the four subunits from the
different AP complexes exhibits similarity with each
other. This family corresponds to the C-terminal domain
of heterotetrameric adaptor protein complex 3 (AP-3)
medium mu3 subunit, which includes two closely related
homologs, mu3A (P47A, encoded by ap3m1) and mu1B (P47B,
encoded by ap3m2). Mu3A is ubiquitously expressed, but
mu3B is specifically expressed in neurons and
neuroendocrine cells. AP-3 is particularly important
for targeting integral membrane proteins to lysosomes
and lysome-related organelles at trans-Golgi network
(TGN) and/or endosomes, such as the yeast vacuole, fly
pigment granules and mammalian melanosomes, platelet
dense bodies and the secretory lysosomes of cytotoxic T
lymphocytes. Unlike AP-1 and AP-2, which function in
conjunction with clathrin which is a scaffolding
protein participating in the formation of coated
vesicles, the nature of the outer shell of AP-3
containing coats remains to be elucidated.
Membrane-anchored cargo molecules interact with
adaptors through short sorting signals in their
cytosolic segments. Tyrosine-based endocytotic signals
are one of the most important sorting signals. They are
of the form Y-X-X-Phi, where Y is tyrosine, X is any
amino acid and Phi is a bulky hydrophobic residue that
can be Leu, Ile, Met, Phe, or Val. These kinds of
sorting signals can be recognized by the C-terminal
domain of AP-3 mu3 subunit, also known as Y-X-X-Phi
signal-binding domain that contains two hydrophobic
pockets, one for the tyrosine-binding and one for the
bulky hydrophobic residue-binding.
Length = 248
Score = 26.8 bits (60), Expect = 4.1
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 27 KYLGNFIYVD---TVRAIIKKELRP 48
KY N IYVD + AI+ K +P
Sbjct: 9 KYTNNEIYVDVVEEIDAIVDKSGKP 33
>gnl|CDD|234757 PRK00421, murC, UDP-N-acetylmuramate--L-alanine ligase;
Provisional.
Length = 461
Score = 26.6 bits (60), Expect = 4.2
Identities = 6/32 (18%), Positives = 10/32 (31%), Gaps = 2/32 (6%)
Query: 19 DHFIEKCDKYLGNFIYVD--TVRAIIKKELRP 48
F Y D +R ++ + RP
Sbjct: 202 QEFAHNLPFYGALVACGDDPELRELLPRVSRP 233
>gnl|CDD|212048 cd11478, SLC5sbd_u2, Uncharacterized bacterial solute carrier 5
subfamily; putative solute-binding domain. SLC5 (also
called the sodium/glucose cotransporter family or solute
sodium symporter family) is a family of proteins that
co-transports Na+ with sugars, amino acids, inorganic
ions or vitamins. Prokaryotic members of this family
include Vibrio parahaemolyticus glucose/galactose
(vSGLT), and Escherichia coli proline (PutP) and
pantothenate (PutF) cotransporters. One member of the
SLC5 family, human SGLT3, has been characterized as a
glucose sensor and not a transporter. This subfamily
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 495
Score = 26.9 bits (60), Expect = 4.5
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 3 VPEYLGTRYSRSER 16
VPEYL R++ S R
Sbjct: 101 VPEYLKLRFNESTR 114
>gnl|CDD|238678 cd01382, MYSc_type_VI, Myosin motor domain, type VI myosins. Myosin
VI is a monomeric myosin, which moves towards the
minus-end of actin filaments, in contrast to most other
myosins. It has been implicated in endocytosis,
secretion, and cell migration. This catalytic (head)
domain has ATPase activity and belongs to the larger
group of P-loop NTPases. Myosins are actin-dependent
molecular motors that play important roles in muscle
contraction, cell motility, and organelle transport. The
head domain is a molecular motor, which utilizes ATP
hydrolysis to generate directed movement toward the
minus end along actin filaments. A cyclical interaction
between myosin and actin provides the driving force.
Rates of ATP hydrolysis and consequently the speed of
movement along actin filaments vary widely, from about
0.04 micrometer per second for myosin I to 4.5
micrometer per second for myosin II in skeletal muscle.
Myosin II moves in discrete steps about 5-10 nm long and
generates 1-5 piconewtons of force. Upon ATP binding,
the myosin head dissociates from an actin filament. ATP
hydrolysis causes the head to pivot and associate with a
new actin subunit. The release of Pi causes the head to
pivot and move the filament (power stroke). Release of
ADP completes the cycle.
Length = 717
Score = 26.7 bits (59), Expect = 5.2
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 34 YVDTVRAIIKKELRPPQVLDIEDEEAKL-DGSDVLFT 69
YVD I E + +LDI DEE +L SD FT
Sbjct: 455 YVDNQDCIDLIEAKLNGILDILDEENRLPQPSDQHFT 491
>gnl|CDD|119145 pfam10625, UspB, Universal stress protein B (UspB). UspB in
Escherichia coli is a 14kDa protein which is predicted
to be an integral membrane protein. Overexpression of
UspB results in cell death in stationary phase, and
mutants of uspB are sensitive to ethanol exposure
during stationary phase.
Length = 107
Score = 25.8 bits (57), Expect = 5.7
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 4/27 (14%)
Query: 11 YSRSERFDDH----FIEKCDKYLGNFI 33
Y RS+ + H F KC++ FI
Sbjct: 65 YIRSQEYLHHHDPVFTGKCERVRKLFI 91
>gnl|CDD|224747 COG1834, COG1834, N-Dimethylarginine dimethylaminohydrolase [Amino
acid transport and metabolism].
Length = 267
Score = 25.8 bits (57), Expect = 8.4
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 61 LDGSDVLFTGISKWTNEKGARAVADSFPE 89
+DG D ++ G S TN +G + E
Sbjct: 125 MDGGDTVYIGYSFRTNLEGIEQLQAWLEE 153
>gnl|CDD|215173 PLN02304, PLN02304, probable pectinesterase.
Length = 379
Score = 26.0 bits (57), Expect = 8.8
Identities = 16/40 (40%), Positives = 17/40 (42%), Gaps = 7/40 (17%)
Query: 89 EYPCTAIKVKNKNPKAKMSTSTGIDQLLVRTQVEMFLNDS 128
EY C+ P A MS Q L TQV FLN S
Sbjct: 334 EYNCSG-------PGANMSMRAPYVQKLNDTQVSPFLNTS 366
>gnl|CDD|181655 PRK09110, PRK09110, flagellar motor protein MotA; Validated.
Length = 283
Score = 25.5 bits (57), Expect = 9.9
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 18/68 (26%)
Query: 26 DKYLGNFIYVDTVRAIIKKELRPPQVLDIEDEEAKLDGSDVLFTGISKWTNEK--GARA- 82
D +L +FI D +R +I + P ++ + DEE I +E A A
Sbjct: 119 DHHLVDFI-CDYLRLMISGNMNPHEIEALMDEE------------IETHHHEAEVPAHAL 165
Query: 83 --VADSFP 88
VAD+ P
Sbjct: 166 QKVADALP 173
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
0.317 0.136 0.392
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,033,912
Number of extensions: 631387
Number of successful extensions: 533
Number of sequences better than 10.0: 1
Number of HSP's gapped: 531
Number of HSP's successfully gapped: 20
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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 (21.7 bits)
S2: 54 (24.6 bits)