RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12243
(278 letters)
>gnl|CDD|132995 cd00218, GlcAT-I, Beta1,3-glucuronyltransferase I (GlcAT-I) is
involved in the initial steps of proteoglycan synthesis.
Beta1,3-glucuronyltransferase I (GlcAT-I) domain;
GlcAT-I is a Key enzyme involved in the initial steps of
proteoglycan synthesis. GlcAT-I catalyzes the transfer
of a glucuronic acid moiety from the uridine
diphosphate-glucuronic acid (UDP-GlcUA) to the common
linkage region of trisaccharide
Gal-beta-(1-3)-Gal-beta-(1-4)-Xyl of proteoglycans. The
enzyme has two subdomains that bind the donor and
acceptor substrate separately. The active site is
located at the cleft between both subdomains in which
the trisaccharide molecule is oriented perpendicular to
the UDP. This family has been classified as
Glycosyltransferase family 43 (GT-43).
Length = 223
Score = 284 bits (729), Expect = 3e-97
Identities = 99/217 (45%), Positives = 137/217 (63%), Gaps = 8/217 (3%)
Query: 34 PIIYFITPTYPRREQVAELTRLGQTLMHIPNLHWIVADDTLQCSPMISALLPKFGIPYTH 93
P IY +TPTY R Q AELTRL TL +P LHWIV +D+ + +P+++ LL + G+ YTH
Sbjct: 1 PTIYVVTPTYARPVQKAELTRLAHTLRLVPPLHWIVVEDSEEKTPLVAELLRRSGLMYTH 60
Query: 94 IASPMPPVYRTNNAVPPRGVANRRAALAWIRSYV---KSGVVYFGDDDNTFDLKLFDEIR 150
+ + P + PRGV R AL WIR ++ GVVYF DDDNT+DL+LF+E+R
Sbjct: 61 LNAKTP---SDPTWLKPRGVEQRNLALRWIREHLSAKLDGVVYFADDDNTYDLELFEEMR 117
Query: 151 DTKKISMFPVGLIGSYGISSPVLRKGNVIGFFDSWPAKRKFPVDMAGFAVNVDLILKHPN 210
K++ ++PVGL+G + PV G V+G+ +W +R FP+DMAGFA N L+ P
Sbjct: 118 KIKRVGVWPVGLVGGLRVEGPVCENGKVVGWHTAWKPERPFPIDMAGFAFNSKLLWDPPR 177
Query: 211 ATMPY--KAGYEEDRFISSLGVKLSDIEPKANNCSEV 245
A PY K GY+E F+ L + ++EP ANNCS+V
Sbjct: 178 AVFPYSAKRGYQESSFLEQLVLDRKELEPLANNCSKV 214
>gnl|CDD|217513 pfam03360, Glyco_transf_43, Glycosyltransferase family 43.
Length = 206
Score = 264 bits (678), Expect = 8e-90
Identities = 93/197 (47%), Positives = 128/197 (64%), Gaps = 6/197 (3%)
Query: 55 LGQTLMHIPNLHWIVADDTLQCSPMISALLPKFGIPYTHIASPMPPVYRTNNAVPPRGVA 114
L TL +PNLHWIV +D +P++S +L + G+PYTH+ P Y+ + PRGV
Sbjct: 1 LANTLRLVPNLHWIVVEDGEATTPLVSNILRRTGLPYTHLVVKTPSGYKDPTWLKPRGVE 60
Query: 115 NRRAALAWIRSYV---KSGVVYFGDDDNTFDLKLFDEIRDTKKISMFPVGLIGSYGISSP 171
R AL WIR GVVYF DDDNT+DL+LF+E+R+ KK+ ++PVGL+G + P
Sbjct: 61 QRNLALRWIRQNGEHKLEGVVYFADDDNTYDLELFEEMRNVKKVGVWPVGLVGGLRVEGP 120
Query: 172 VLRKGNVIGFFDSWPAKRKFPVDMAGFAVNVDLILKHPNATMPYKA---GYEEDRFISSL 228
V+ G V+G+ W KR FP+DMAGFAVN+ LIL PNA +K GY+E F+ L
Sbjct: 121 VVNNGKVVGWHTVWKPKRPFPIDMAGFAVNLKLILDRPNAVFGFKCLRGGYQESSFLEQL 180
Query: 229 GVKLSDIEPKANNCSEV 245
G+ L+D+EP ANNC+++
Sbjct: 181 GLDLNDLEPLANNCTKI 197
>gnl|CDD|215252 PLN02458, PLN02458, transferase, transferring glycosyl groups.
Length = 346
Score = 58.8 bits (142), Expect = 5e-10
Identities = 56/181 (30%), Positives = 84/181 (46%), Gaps = 25/181 (13%)
Query: 35 IIYFITPTYPR-REQVAELTRLGQTLMHIPN-LHWIVADDTLQCSPMISALLPKFGIPYT 92
++ +TP + R Q L RL TL +P L WIV + S +S +L K GI Y
Sbjct: 113 LVIIVTPISTKDRYQGVLLRRLANTLRLVPPPLLWIVVEGQSD-SEEVSEMLRKTGIMYR 171
Query: 93 HIASPMPPVYRTNNAVPPRGVANRR-AALAWIRSYVKSGVVYFGDDDNTFDLKLFDEIRD 151
H+ V++ N P + ++R AL I + SG+V+F N +DL FDEIRD
Sbjct: 172 HL------VFKENFTDPEAELDHQRNLALRHIEHHKLSGIVHFAGLSNVYDLDFFDEIRD 225
Query: 152 TKKISMFPVGLIGSYG----ISSPVLRKGNVIGFFDSWPAKR-------KFPVDMAGFAV 200
+ +P+ L+ + I PV VIG W K+ + P+ ++ FA
Sbjct: 226 IEVFGTWPMALLSANRNKVIIEGPVCDSSQVIG----WHLKKMNNETETRPPIHISSFAF 281
Query: 201 N 201
N
Sbjct: 282 N 282
>gnl|CDD|187562 cd05252, CDP_GD_SDR_e, CDP-D-glucose 4,6-dehydratase, extended (e)
SDRs. This subgroup contains CDP-D-glucose
4,6-dehydratase, an extended SDR, which catalyzes the
conversion of CDP-D-glucose to
CDP-4-keto-6-deoxy-D-glucose. 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 = 336
Score = 40.4 bits (95), Expect = 6e-04
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 156 SMFPVGLIGSYGISSPVLRKGNVIGFFDSWPAKRKFPVDMAGFAVNVDLILKHPNATMPY 215
S F G +GI+ R GNVIG D W R P + F +I+++PNA P+
Sbjct: 169 SFFNPENYGKHGIAIASARAGNVIGGGD-WAEDRIVPDCIRAFEAGERVIIRNPNAIRPW 227
Query: 216 K------AGY 219
+ +GY
Sbjct: 228 QHVLEPLSGY 237
>gnl|CDD|218465 pfam05144, Phage_CRI, Phage replication protein CRI. The phage
replication protein CRI, is also known as Gene II, is
essential for DNA replication.
Length = 235
Score = 30.8 bits (70), Expect = 0.61
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 17/59 (28%)
Query: 113 VANRRAALAWIRS--------------YVKSGVVYFGDDDNTFDLKLF---DEIRDTKK 154
+ +R LAW+RS K +YFG + + LK++ DEI+ K
Sbjct: 131 LPSRDIVLAWLRSLERVSNTYHRGRRQGDKESTLYFGKNSRRWSLKIYSKGDEIQHQLK 189
>gnl|CDD|233954 TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase. Members of
this protein family are CDP-glucose 4,6-dehydratase from
a variety of Gram-negative and Gram-positive bacteria.
Members typically are encoded next to a gene that
encodes a glucose-1-phosphate cytidylyltransferase,
which produces the substrate, CDP-D-glucose, used by
this enzyme to produce CDP-4-keto-6-deoxyglucose [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 349
Score = 29.6 bits (67), Expect = 1.6
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 174 RKGNVIGFFDSWPAKRKFPVDMAGFAVNVDLILKHPNATMPYK------AGY 219
R GNVIG D W R P + F+ N +I+++P+AT P++ +GY
Sbjct: 185 RAGNVIGGGD-WAEDRLIPDVIRAFSSNKIVIIRNPDATRPWQHVLEPLSGY 235
>gnl|CDD|225060 COG2149, COG2149, Predicted membrane protein [Function unknown].
Length = 120
Score = 28.6 bits (64), Expect = 1.8
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 99 PPVYRTNNAVPPR-GVANRRAALAWIRS 125
P + R R +AN R LAWIR+
Sbjct: 5 PKISRAGEEPDYRFTLANERTFLAWIRT 32
>gnl|CDD|219795 pfam08324, PUL, PUL domain. The PUL (PLAP, Ufd3p and Lub1p) domain
is a novel alpha-helical Ub-associated domain. It
directly binds to Cdc48, a chaperone-like AAA ATPase
that collects ubiquitylated substrates.
Length = 263
Score = 29.3 bits (66), Expect = 2.0
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 11/62 (17%)
Query: 182 FDSWPAKRKFPVDMAGFAVNVDL---ILKHPNATMPYKAGYEEDRFISSLGVKLSDIEPK 238
SWP +FP +DL ++ +P A +E IS+L + S+ +
Sbjct: 71 LKSWPEANRFPA--------LDLLRLLVLNPPAAALLCDAFEIADLISTLILLGSNSKNP 122
Query: 239 AN 240
A
Sbjct: 123 AL 124
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 28.8 bits (65), Expect = 3.4
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 45 RREQVAELTRLGQTLMHIPNLHWIVADDTLQCSPMISALL 84
R + +L L L + W+VAD L A+L
Sbjct: 37 RNAE--KLEALAARLPYPGRHRWVVAD--LTSEAGREAVL 72
>gnl|CDD|216231 pfam00995, Sec1, Sec1 family.
Length = 554
Score = 28.7 bits (65), Expect = 3.9
Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 14/49 (28%)
Query: 7 LDQ-THDPITCTTSFKDLRLFHNVV------------KDLPIIYFITPT 42
LD+ T ++ + DL H V DLP IYFI PT
Sbjct: 6 LDKETTKILSSVLTVSDLLE-HGVTLVENIENKREPLPDLPAIYFIRPT 53
>gnl|CDD|224744 COG1831, COG1831, Predicted metal-dependent hydrolase (urease
superfamily) [General function prediction only].
Length = 285
Score = 28.5 bits (64), Expect = 4.0
Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 8/90 (8%)
Query: 169 SSPVLRKGNVIGFFDSWPAKRKFPVDMAG----FAVNVDLI--LKHPNATMPYKAGYEED 222
+ P++ K +G F S PA RK D A F + D I + P A + K
Sbjct: 195 APPLVLKCEEVGIFPSVPASRKNVEDAAELGPRFMMETDYIDDPRRPGAVLGPKTVPRRT 254
Query: 223 RFISSLGVKLSDIEPKANNCSEVSENIFKV 252
R I G + + + E E ++ +
Sbjct: 255 REILEKGDLTEEDVYRIHV--ENPERVYGI 282
>gnl|CDD|235522 PRK05591, rplQ, 50S ribosomal protein L17; Validated.
Length = 113
Score = 27.0 bits (61), Expect = 5.1
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 13/37 (35%)
Query: 113 VANRRAALAWIRSYVKSGVVYFGDDDNTFDLKLFDEI 149
+ RR A A +R D + KLFDEI
Sbjct: 57 LHARRQAFARLR-----------DKEAVH--KLFDEI 80
>gnl|CDD|223281 COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal
structure and biogenesis].
Length = 116
Score = 27.1 bits (61), Expect = 5.2
Identities = 14/37 (37%), Positives = 16/37 (43%), Gaps = 13/37 (35%)
Query: 113 VANRRAALAWIRSYVKSGVVYFGDDDNTFDLKLFDEI 149
+ANRR A A +R D KLFDEI
Sbjct: 60 LANRRLAFARLR-------------DKDAVKKLFDEI 83
>gnl|CDD|225246 COG2371, UreE, Urease accessory protein UreE [Posttranslational
modification, protein turnover, chaperones].
Length = 155
Score = 27.3 bits (61), Expect = 5.5
Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 17/64 (26%)
Query: 49 VAELTRLGQTLMHIPNLHW---------IVADDTLQCSPMISALLPKFGIPYTHIASPMP 99
EL + H+ N H V D + + A+L G+ T + P
Sbjct: 87 PLELAKAAH---HLGNRHLPAQVEEDELRVPYDHV-----LRAMLEGLGVTVTRVELPFE 138
Query: 100 PVYR 103
P +
Sbjct: 139 PEFG 142
>gnl|CDD|217143 pfam02614, UxaC, Glucuronate isomerase. This is a family of
Glucuronate isomerases also known as D-glucuronate
isomerase, uronic isomerase, uronate isomerase, or
uronic acid isomerase, EC:5.3.1.12. This enzyme
catalyzes the reactions: D-glucuronate <=>
D-fructuronate and D-galacturonate <=> D-tagaturonate.
It is not however clear where the experimental evidence
for this functional assignment came from and thus this
family has no literature reference.
Length = 469
Score = 28.0 bits (63), Expect = 6.9
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 24 RLFHNVVKDLPII 36
RL+H+ KDLPII
Sbjct: 18 RLYHDHAKDLPII 30
>gnl|CDD|129022 smart00786, SHR3_chaperone, ER membrane protein SH3. This family
of proteins are membrane localised chaperones that are
required for correct plasma membrane localisation of
amino acid permeases (AAPs). Shr3 prevents AAPs
proteins from aggregating and assists in their correct
folding. In the absence of Shr3, AAPs are retained in
the ER.
Length = 196
Score = 27.3 bits (61), Expect = 7.1
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 14 ITCTTSFKDLRLFHNVVKDLPIIYFITPTYPRRE-QVAELTRLGQTLMHIPNLHWIVA 70
I +TSF LF N D P+++ PT + + L + + + + IV
Sbjct: 12 IIGSTSFFLGILFANFPYDYPLLWSPDPTPSAFDAALRHYQFLHASPLLVLYILHIVI 69
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 27.4 bits (61), Expect = 7.2
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 12/50 (24%)
Query: 58 TLMHIPNLHWIVADDTLQCSP----------MISALLPKFGIPYTHIASP 97
TL+ PN W+ D L+ ++ +L + IP+ I
Sbjct: 118 TLLLEPNTPWV--ADGLRSLGSSVQRQEFQNLLEQMLEENNIPFVVIEGE 165
>gnl|CDD|213328 cd04519, RasGAP, Ras GTPase Activating Domain. RasGAP functions as
an enhancer of the hydrolysis of GTP that is bound to
Ras-GTPases. Proteins having a RasGAP domain include
p120GAP, IQGAP, Rab5-activating protein 6, and
Neurofibromin, among others. Although the Rho (Ras
homolog) GTPases are most closely related to members of
the Ras family, RhoGAP and RasGAP exhibit no similarity
at their amino acid sequence level. RasGTPases function
as molecular switches in a large number of signaling
pathways. They are in the on state when bound to GTP,
and in the off state when bound to GDP. The RasGAP
domain speeds up the hydrolysis of GTP in Ras-like
proteins acting as a negative regulator.
Length = 256
Score = 27.5 bits (61), Expect = 7.4
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 8 DQTHDPITCTTSFKDLRLFHNVVKDLPIIYFITPTYPRREQVAELTRLGQTLMHIPNL 65
++ + + F LR + P ++ + P P + LT + + L + N
Sbjct: 167 EEPDEAYQAVSGFLFLRFICPAI-VSPELFGLVPDEPSEQARRNLTLISKVLQSLANG 223
>gnl|CDD|219294 pfam07095, IgaA, Intracellular growth attenuator protein IgaA.
This family consists of several bacterial intracellular
growth attenuator (IgaA) proteins. IgaA is involved in
negative control of bacterial proliferation within
fibroblasts. IgaA is homologous to the E. coli YrfF and
P. mirabilis UmoB proteins. Whereas the biological
function of YrfF is currently unknown, UmoB has been
shown elsewhere to act as a positive regulator of FlhDC,
the master regulator of flagella and swarming. FlhDC has
been shown to repress cell division during P. mirabilis
swarming, suggesting that UmoB could repress cell
division via FlhDC. This biological function, if
maintained in S. enterica, could sustain a putative
negative control of cell division and growth exerted by
IgaA in intracellular bacteria.
Length = 705
Score = 27.7 bits (62), Expect = 8.8
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 43 YPRREQVAELTRLGQTLMHIP 63
YP EQ EL RL L+H P
Sbjct: 600 YPALEQWRELQRLSDMLLHTP 620
>gnl|CDD|115718 pfam07082, DUF1350, Protein of unknown function (DUF1350). This
family consists of several hypothetical proteins from
both cyanobacteria and plants. Members of this family
are typically around 250 residues in length. The
function of this family is unknown but the species
distribution indicates that the family may be involved
in photosynthesis.
Length = 250
Score = 27.1 bits (60), Expect = 10.0
Identities = 17/43 (39%), Positives = 27/43 (62%), Gaps = 4/43 (9%)
Query: 162 LIGSYGISSPVLRKGNVIGFFDSWPAKRKFP-VDMAGFAVNVD 203
LIGS V R GN++ F+++PAK+ P +D G A++V+
Sbjct: 106 LIGSL---YDVERAGNILMAFNNYPAKQAIPWMDNFGTALSVE 145
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
0.322 0.138 0.423
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,523,344
Number of extensions: 1399098
Number of successful extensions: 1081
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1073
Number of HSP's successfully gapped: 25
Length of query: 278
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 182
Effective length of database: 6,679,618
Effective search space: 1215690476
Effective search space used: 1215690476
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: 58 (26.2 bits)