RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780847|ref|YP_003065260.1| hypothetical protein
CLIBASIA_03710 [Candidatus Liberibacter asiaticus str. psy62]
(282 letters)
>gnl|CDD|30992 COG0647, NagD, Predicted sugar phosphatases of the HAD superfamily
[Carbohydrate transport and metabolism].
Length = 269
Score = 195 bits (497), Expect = 1e-50
Identities = 79/248 (31%), Positives = 119/248 (47%), Gaps = 10/248 (4%)
Query: 8 LRTILPYYDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVIS-Q 66
L ++ YD L D+ GVL+ G + +PG ALK + G VI TN+ S V++ +
Sbjct: 1 LFDVMDKYDGFLFDLDGVLYRGNEAIPGAAEALKRLKAAGKPVIFLTNNSTRSREVVAAR 60
Query: 67 IQSLGSSSQFWDDIITSGDLTHHLLVEESHN--IFFIGPQRDYALLEKLNIKIVNEQHAE 124
+ SLG DDI+TSGD T L ++ ++ IG + LE ++V+E+
Sbjct: 61 LSSLGGVDVTPDDIVTSGDATADYLAKQKPGKKVYVIGEEGLKEELEGAGFELVDEEEPA 120
Query: 125 TILCTGLYDDEKDKTEDYRMLLERFAHRHIPLICANPDIVANRGNKIIPCAGALALIYQQ 184
+ + D E L A P I NPD+ + P AGA+A + +Q
Sbjct: 121 RVDAVVVGLDRTLTYEKLAEALLAIAAG-APFIATNPDLTVPTERGLRPGAGAIAALLEQ 179
Query: 185 LNGIV-KMIGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYV 243
G +IGKP IYE A +K+ ++ +L +GD +DTDI GA +G+D L V
Sbjct: 180 ATGREPTVIGKPSPAIYEAALEKL-----GLDRSEVLMVGDRLDTDILGAKAAGLDTLLV 234
Query: 244 SDGIHRHE 251
G+ E
Sbjct: 235 LTGVSSAE 242
>gnl|CDD|38093 KOG2882, KOG2882, KOG2882, p-Nitrophenyl phosphatase [Inorganic ion
transport and metabolism].
Length = 306
Score = 71.8 bits (176), Expect = 2e-13
Identities = 61/288 (21%), Positives = 109/288 (37%), Gaps = 32/288 (11%)
Query: 8 LRTILPYYDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTN-SPRPSASVISQ 66
R +L +D + D GVL G+K +PG+ AL + G ++I TN S + + +
Sbjct: 15 ARELLDSFDTFIFDCDGVLWLGEKPIPGSPEALNLLKSLGKQIIFVTNNSTKSREQYMKK 74
Query: 67 IQSLGSSSQFWDDIITSGD-----LTHHLLVEESHNIFFIGPQRDYALLEKLNIK----- 116
LG +S ++I +S L + ++ IG + L++ +
Sbjct: 75 FAKLGFNSVKEENIFSSAYAIADYLKKRKPFGKK--VYVIGEEGIREELDEAGFEYFGGG 132
Query: 117 ---IVNEQHAETILCTGLYDDEK------DKTEDYRMLLERFAHRHIP---LICANPD-I 163
+ +L GL D D+ Y L++ + P + N D
Sbjct: 133 PDGKDTDGAKSFVLSIGLDPDVGAVVVGYDEHFSYPKLMKALNYLQNPGCLFLATNRDAT 192
Query: 164 VANRGNKIIPCAGALALIYQQLNG-IVKMIGKPHLPIYEMAFKKISSLCNSFNKKRILAI 222
IP AG+ + G ++GKP ++E +K + + R +
Sbjct: 193 TPPTPGVEIPGAGSFVAAVKFATGRQPIVLGKPSTFMFEYLLEKFN-----IDPSRTCMV 247
Query: 223 GDGMDTDIKGALQSGIDALYVSDGIHRHEYLFNDNIDAQMLQNFFTKK 270
GD +DTDI G L V G+ E + D +M+ +++
Sbjct: 248 GDRLDTDILFGKNCGFKTLLVLSGVTTLEDILEAQGDNKMVPDYYADS 295
>gnl|CDD|119389 cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The
haloacid dehalogenase-like (HAD) superfamily includes
L-2-haloacid dehalogenase, epoxide hydrolase,
phosphoserine phosphatase, phosphomannomutase,
phosphoglycolate phosphatase, P-type ATPase, and many
others, all of which use a nucleophilic aspartate in
their phosphoryl transfer reaction. All members possess
a highly conserved alpha/beta core domain, and many also
possess a small cap domain, the fold and function of
which is variable. Members of this superfamily are
sometimes referred to as belonging to the DDDD
superfamily of phosphohydrolases..
Length = 139
Score = 53.1 bits (128), Expect = 8e-08
Identities = 31/115 (26%), Positives = 45/115 (39%), Gaps = 18/115 (15%)
Query: 17 VILCDVWGVLHNGQKFL---------PGTIPALKEARENGLKVILFTNSPRPSASVISQI 67
+L D+ G L + + + PG ALKE +E G+K+ L TN R V+ +
Sbjct: 1 AVLFDLDGTLLDSEPGIAEIEELELYPGVKEALKELKEKGIKLALATNKSR--REVLELL 58
Query: 68 QSLGSSSQFWDDIITSGDLT----HHLLVEESHNIFFIGPQRD--YALLEKLNIK 116
+ LG F D +ITS L P D A L+ L +
Sbjct: 59 EELGLDDYF-DPVITSNGAAIYYPKEGLFLGGGPFDIGKPNPDKLLAALKLLGVD 112
>gnl|CDD|38250 KOG3040, KOG3040, KOG3040, Predicted sugar phosphatase (HAD
superfamily) [General function prediction only].
Length = 262
Score = 51.8 bits (124), Expect = 2e-07
Identities = 57/235 (24%), Positives = 93/235 (39%), Gaps = 16/235 (6%)
Query: 18 ILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPS-ASVISQIQSLGSSSQF 76
+L D+ G LH +PG + ALK R+ +KV TN+ + S ++ ++Q LG
Sbjct: 10 VLLDLSGTLHIEDAAVPGAVEALKRLRDQHVKVKFVTNTTKESKRNLHERLQRLGFDVS- 68
Query: 77 WDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKIVNEQHAETILCTGLYDDEK 136
++I TS L E + I D AL + I + L + ++
Sbjct: 69 EEEIFTSLPAARQYLEENQLRPYLI--VDDDALEDFDGIDTSDPNCVVIGLAPEGFSYQR 126
Query: 137 DKTEDYRMLLERFAHRHIPLICANPDIVANR--GNKIIPCAGALALIYQQLNGIVKMIGK 194
+R+LLE LI R G + P AL Y ++GK
Sbjct: 127 -LNRAFRVLLEMKKP---LLIAIGKGRYYKRVDGLCLGPGPFVAALEYAT-GCEATVVGK 181
Query: 195 PHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDGIHR 249
P +E A + + + + + IGD ++ D+ GA G+ + V G R
Sbjct: 182 PSPFFFESALQALG-----VDPEEAVMIGDDLNDDVGGAQACGMRGILVKTGKFR 231
>gnl|CDD|31215 COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General
function prediction only].
Length = 229
Score = 38.3 bits (88), Expect = 0.002
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 194 KPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDG 246
KP I+E A +K+ + L +GD ++ DI GA G+ ++++ G
Sbjct: 154 KPDPEIFEYALEKLG-----VPPEEALFVGDSLENDILGARALGMKTVWINRG 201
>gnl|CDD|30907 COG0561, Cof, Predicted hydrolases of the HAD superfamily [General
function prediction only].
Length = 264
Score = 35.5 bits (81), Expect = 0.018
Identities = 42/207 (20%), Positives = 70/207 (33%), Gaps = 40/207 (19%)
Query: 14 YYDVILCDVWG-VLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSL-- 70
++ D+ G +L + + P T AL RE G+KV+L T RP V+S ++ L
Sbjct: 2 MIKLLAFDLDGTLLDSNKTISPETKEALARLREKGVKVVLATG--RPLPDVLSILEELGL 59
Query: 71 --------GSSSQFWDDIITSGDLTHHL------LVEESHNIFFIGPQRDYALLEK---- 112
G+ +++ L+ L+E+ I + D L K
Sbjct: 60 DGPLITFNGALIYNGGELLFQKPLSREDVEELLELLEDFQGIALVLYTDDGIYLTKKRGT 119
Query: 113 ----------LNIKIVNEQHAETILCTGLYDDEKDKTEDYRMLLERFAHRHIPLICANP- 161
L+ E L D + E L +RF + + + P
Sbjct: 120 FAEARIGFANLSPVGREAAELEDNKIIALDKDHEILEELVEALRKRFPDLGLTVSSSGPI 179
Query: 162 --DIVANRGNKIIPCAGALALIYQQLN 186
DI +K AL + + L
Sbjct: 180 SLDITPKGVSK----GYALQRLAKLLG 202
>gnl|CDD|144342 pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase. This
family are structurally different from the alpha/ beta
hydrolase family (pfam00561). This family includes
L-2-haloacid dehalogenase, epoxide hydrolases and
phosphatases. The structure of the family consists of
two domains. One is an inserted four helix bundle, which
is the least well conserved region of the alignment,
between residues 16 and 96 of (S)-2-haloacid
dehalogenase from Pseudomonas sp. CBS3. The rest of the
fold is composed of the core alpha/beta domain.
Length = 190
Score = 35.3 bits (81), Expect = 0.020
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 33 LPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGDLTHH 89
PG ALK +E G+KV + TN R +A + + L +D I+ S D+
Sbjct: 99 YPGAREALKALKERGIKVAILTNGDRANAEAVLEALGLAD---LFDVIVDSDDVGPV 152
Score = 31.5 bits (71), Expect = 0.29
Identities = 36/222 (16%), Positives = 65/222 (29%), Gaps = 38/222 (17%)
Query: 15 YDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSS 74
++ D G L +G+ + I L + + LG
Sbjct: 1 IKAVVFDKDGTLTDGEPPIAEAIVEAAAELGLPLL-----------LPLEEVEKLLGRGV 49
Query: 75 QFWDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKIVNEQHAETILCTGLYDD 134
+ + I+ G LT LL+E + AL ++ I
Sbjct: 50 EGIERILLEGGLTAELLLELEGELAAGKTAVLVALDGEVLGLIA---------------- 93
Query: 135 EKDKT-EDYRMLLERFAHRHIPLICA--NPDIVANRGNKIIPCAGALALIYQQLNGIVKM 191
DK R L+ R I + A + + A +I +
Sbjct: 94 LADKLYPGAREALKALKERGIKVAILTNGDRANAEAVLEALGLADLFDVIV---DSDDVG 150
Query: 192 IGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGA 233
KP I+ A +++ + +L +GDG++ A
Sbjct: 151 PVKPKPEIFLKALERLG-----VKPEEVLMVGDGVNDAPALA 187
>gnl|CDD|30982 COG0637, COG0637, Predicted phosphatase/phosphohexomutase [General
function prediction only].
Length = 221
Score = 33.9 bits (77), Expect = 0.045
Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 26 LHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGD 85
G K +PG + L++ + G+ + + ++SPR +A + L ++D I+T+ D
Sbjct: 81 ELEGLKPIPGVVELLEQLKARGIPLAVASSSPRRAAERVLARLGL---LDYFDVIVTADD 137
Query: 86 LTHH 89
+
Sbjct: 138 VARG 141
>gnl|CDD|38295 KOG3085, KOG3085, KOG3085, Predicted hydrolase (HAD superfamily)
[General function prediction only].
Length = 237
Score = 34.2 bits (78), Expect = 0.045
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 194 KPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDGIHRHEYL 253
KP I+++A +++ + + IGD ++ D +GA G A+ V + I + L
Sbjct: 168 KPDPRIFQLALERLGV-----KPEECVHIGDLLENDYEGARNLGWHAILVDNSITALKEL 222
Query: 254 FN 255
Sbjct: 223 EY 224
>gnl|CDD|36831 KOG1618, KOG1618, KOG1618, Predicted phosphatase [General function
prediction only].
Length = 389
Score = 31.5 bits (71), Expect = 0.27
Identities = 26/106 (24%), Positives = 45/106 (42%), Gaps = 12/106 (11%)
Query: 153 HIPLICANPDIV---ANRGNKIIPCAGALAL--IYQQLNGI---VKMIGKPHLPIYEMA- 203
HIP+ +N D++ + + A L L IYQ+L G +GKP Y+ A
Sbjct: 222 HIPIYASNMDLLWMAEYKLPRFGHGAFRLCLESIYQKLTGKPLRYTTLGKPTKLTYDYAE 281
Query: 204 ---FKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDG 246
++ + K++ +GD +D++GA A + G
Sbjct: 282 DVLRRQAKRRGGAAPIKKLYMVGDNPMSDVRGANLFHQYAPELGAG 327
>gnl|CDD|107313 cd06318, PBP1_ABC_sugar_binding_like_9, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 282
Score = 31.3 bits (71), Expect = 0.34
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 35 GTIPALKEARENGLKVILFTNSPRPSASVISQIQS 69
G +PA+ A+ G+ V++ +S A V++Q+QS
Sbjct: 68 GLVPAVAAAKAAGVPVVVVDSSINLEAGVVTQVQS 102
>gnl|CDD|36583 KOG1369, KOG1369, KOG1369, Hexokinase [Carbohydrate transport and
metabolism].
Length = 474
Score = 31.0 bits (70), Expect = 0.35
Identities = 27/185 (14%), Positives = 56/185 (30%), Gaps = 27/185 (14%)
Query: 2 TKEITSLRTILPYYDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSA 61
+ I + + + WG + LP T V++ S P
Sbjct: 250 MRNIEKVEGDAGRGPMCINTEWGAFGDNSLDLPRTE----------YDVVVDEESLNPGK 299
Query: 62 SVISQIQSLGSSSQFWDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKIVNEQ 121
+ ++ S G + G++ +L++ G Q K V+
Sbjct: 300 QLFEKMIS-G---------MYLGEIVRLVLLDLLEEGLLFGGQSTKLTPFIFETKYVSAI 349
Query: 122 HAETILCTGLYDDEKDKTEDYRMLLERFAHRHIPLICANPDIVANRGNKIIPCAGALALI 181
+ TG + + + + R L+ D+V+ R ++ A +A I
Sbjct: 350 EED---DTGALQETEKILDLLGLETTTTEDRK--LVREVCDVVSRRAARL--AAAGIAAI 402
Query: 182 YQQLN 186
+
Sbjct: 403 LNKTG 407
>gnl|CDD|34199 COG4555, NatA, ABC-type Na+ transport system, ATPase component
[Energy production and conversion / Inorganic ion
transport and metabolism].
Length = 245
Score = 31.0 bits (70), Expect = 0.35
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 19 LCDVWGVLHNGQKFLPGTIPALKEA-RENGLKVILFT 54
LCD VLH G+ L G+I AL L+ I
Sbjct: 199 LCDRVIVLHKGEVVLEGSIEALDARTVLRNLEEIFAF 235
>gnl|CDD|147746 pfam05761, 5_nucleotid, 5' nucleotidase family. This family of
eukaryotic proteins includes 5' nucleotidase enzymes,
such as purine 5'-nucleotidase EC:3.1.3.5.
Length = 448
Score = 31.1 bits (71), Expect = 0.37
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 25 VLHNGQKFL---PGTIPALKEARENGLKVILFTNSP 57
VL + +K++ P PAL RE+G K+ L TNSP
Sbjct: 174 VLKDLEKYVIKDPELPPALSRLRESGKKLFLLTNSP 209
>gnl|CDD|88408 cd05013, SIS_RpiR, RpiR-like protein. RpiR contains a SIS (Sugar
ISomerase) domain, which is found in many phosphosugar
isomerases and phosphosugar binding proteins. In E.
coli, rpiR negatively regulates the expression of rpiB
gene. Both rpiB and rpiA are ribose phosphate isomerases
that catalyze the reversible reactions of ribose
5-phosphate into ribulose 5-phosphate..
Length = 139
Score = 30.3 bits (68), Expect = 0.65
Identities = 15/57 (26%), Positives = 24/57 (42%)
Query: 36 TIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGDLTHHLLV 92
T+ A + A+E G KVI T+S + ++ I L SS + L +
Sbjct: 76 TVEAAEIAKERGAKVIAITDSANSPLAKLADIVLLVSSEEGDFRSSAFSSRIAQLAL 132
>gnl|CDD|31923 COG1737, RpiR, Transcriptional regulators [Transcription].
Length = 281
Score = 29.9 bits (67), Expect = 0.77
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 36 TIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQ--FWDDIITS 83
+ A + A+E G KVI T+S + ++ I L ++ F+ I+S
Sbjct: 193 IVEAAELAKERGAKVIAITDSADSPLAKLADIVLLVPVAEESFFRSPISS 242
>gnl|CDD|30590 COG0241, HisB, Histidinol phosphatase and related phosphatases
[Amino acid transport and metabolism].
Length = 181
Score = 29.5 bits (66), Expect = 0.98
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 31 KFLPGTIPALKEARENGLKVILFTN 55
+F+PG IPAL + + G K+++ TN
Sbjct: 31 QFIPGVIPALLKLQRAGYKLVVVTN 55
>gnl|CDD|73387 cd04725, OMP_decarboxylase_like, Orotidine 5'-phosphate
decarboxylase (ODCase) is a dimeric enzyme that
decarboxylates orotidine 5'-monophosphate (OMP) to form
uridine 5'-phosphate (UMP), an essential step in the
pyrimidine biosynthetic pathway. In mammals, UMP
synthase contains two domains: the orotate
phosphoribosyltransferase (OPRTase) domain that
catalyzes the transfer of phosphoribosyl
5'-pyrophosphate (PRPP) to orotate to form OMP, and the
orotidine-5'-phosphate decarboxylase (ODCase) domain
that decarboxylates OMP to form UMP..
Length = 216
Score = 28.6 bits (64), Expect = 1.9
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 7/73 (9%)
Query: 177 ALALIYQQLNGIVKMIGKPHLPIYEMAFKKISSLCNSFNKKRIL-----AIGDGMDTDIK 231
ALALI L V + K L ++E A +I L I + + +
Sbjct: 13 ALALI-DALGPYVCAV-KVGLELFEAAGPEIVKELRELGFLVFLDLKLGDIPNTVAAAAE 70
Query: 232 GALQSGIDALYVS 244
L G DA+ V
Sbjct: 71 ALLGLGADAVTVH 83
>gnl|CDD|100118 cd06167, LabA_like, LabA_like proteins. A well conserved group of
bacterial proteins with no defined function. LabA, a
member from Synechococcus elongatus PCC 7942, has been
shown to play a role in cyanobacterial circadian timing.
It is required for negative feedback regulation of the
autokinase/autophosphatase KaiC, a central component of
the circadian clock system. In particular, LabA seems
necessary for KaiC-dependent repression of gene
expression..
Length = 149
Score = 28.4 bits (64), Expect = 2.1
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 37 IPALKEARENGLKVILFTNSPRPSASVI 64
+P ++ RE G +VI+ + S +
Sbjct: 113 VPLVERLRELGKRVIVVGFEAKTSRELR 140
>gnl|CDD|173729 cd06617, PKc_MKK3_6, Catalytic domain of the dual-specificity
Protein Kinases, MAP kinase kinases 3 and 6. Protein
kinases (PKs), MAP kinase kinase 3 (MKK3) and MKK6
subfamily, catalytic (c) domain. PKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine or tyrosine residues on protein
substrates. The MKK3 and MKK6 subfamily is part of a
larger superfamily that includes the catalytic domains
of other protein serine/threonine kinases, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. The mitogen-activated protein (MAP) kinase
signaling pathways are important mediators of cellular
responses to extracellular signals. The pathways involve
a triple kinase core cascade comprising the MAP kinase
(MAPK), which is phosphorylated and activated by a MAPK
kinase (MAPKK or MKK), which itself is phosphorylated
and activated by a MAPK kinase kinase (MAPKKK or MKKK).
MKK3 and MKK6 are dual-specificity PKs that
phosphorylate and activate their downstream target, p38
MAPK, on specific threonine and tyrosine residues.
MKK3/6 plays roles in the regulation of cell cycle
progression, cytokine- and stress-induced apoptosis,
oncogenic transformation, and adult tissue regeneration.
In addition, MKK6 plays a critical role in osteoclast
survival in inflammatory disease while MKK3 is
associated with tumor invasion, progression, and poor
patient survival in glioma.
Length = 283
Score = 28.2 bits (63), Expect = 2.5
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 187 GIV-KMIGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDI 230
G+V KM P I MA K+I + NS +KR+L MD DI
Sbjct: 15 GVVDKMRHVPTGTI--MAVKRIRATVNSQEQKRLL-----MDLDI 52
>gnl|CDD|88404 cd05007, SIS_Etherase, N-acetylmuramic acid 6-phosphate etherase.
Members of this family contain the SIS (Sugar ISomerase)
domain. The SIS domain is found in many phosphosugar
isomerases and phosphosugar binding proteins. The
bacterial cell wall sugar N-acetylmuramic acid carries a
unique D-lactyl ether substituent at the C3 position.
The etherase catalyzes the cleavage of the lactyl ether
bond of N-acetylmuramic acid 6-phosphate..
Length = 257
Score = 28.2 bits (63), Expect = 2.8
Identities = 9/34 (26%), Positives = 14/34 (41%)
Query: 34 PGTIPALKEARENGLKVILFTNSPRPSASVISQI 67
P + AL+ AR G I +P ++ I
Sbjct: 132 PYVLGALRYARARGALTIGIACNPGSPLLQLADI 165
>gnl|CDD|107305 cd06310, PBP1_ABC_sugar_binding_like_2, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 273
Score = 28.0 bits (63), Expect = 3.3
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 36 TIPALKEARENGLKVILF---TNSPRPSASV 63
+P LKEA++ G+ V+L NS + V
Sbjct: 71 LVPPLKEAKDAGIPVVLIDSGLNSDIAVSFV 101
>gnl|CDD|88405 cd05008, SIS_GlmS_GlmD_1, SIS (Sugar ISomerase) domain repeat 1
found in Glucosamine 6-phosphate synthase (GlmS) and
Glucosamine-6-phosphate deaminase (GlmD). The SIS
domain is found in many phosphosugar isomerases and
phosphosugar binding proteins. GlmS contains a
N-terminal glutaminase domain and two C-terminal SIS
domains and catalyzes the first step in hexosamine
metabolism, converting fructose 6-phosphate into
glucosamine 6-phosphate using glutamine as nitrogen
source. The glutaminase domain hydrolyzes glutamine to
glutamate and ammonia. Ammonia is transferred through a
channel to the isomerase domain for glucosamine
6-phosphate synthesis. The end product of the pathway
is N-acetylglucosamine, which plays multiple roles in
eukaryotic cells including being a building block of
bacterial and fungal cell walls. In the absence of
glutamine, GlmS catalyzes the isomerization of fructose
6-phosphate into glucose 6- phosphate (PGI-like
activity). Glucosamine-6-phosphate deaminase (GlmD)
contains two SIS domains and catalyzes the deamination
and isomerization of glucosamine-6-phosphate into
fructose-6-phosphate with the release of ammonia; in
presence of high ammonia concentration, GlmD can
catalyze the reverse reaction..
Length = 126
Score = 27.8 bits (62), Expect = 3.6
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 34 PGTIPALKEARENGLKVILFTNSP 57
T+ AL+ A+E G K + TN
Sbjct: 60 ADTLAALRLAKEKGAKTVAITNVV 83
>gnl|CDD|144475 pfam00890, FAD_binding_2, FAD binding domain. This family
includes members that bind FAD. This family includes
the flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 27.7 bits (62), Expect = 4.3
Identities = 17/65 (26%), Positives = 21/65 (32%), Gaps = 13/65 (20%)
Query: 42 EARENGLKVILFTNSPR-PSASVISQ---------IQSLGSSS---QFWDDIITSGDLTH 88
EA E GLKV + A+ S Q G S D + +L
Sbjct: 17 EAAEAGLKVAVVEKGQPFGGATAWSSGGIDALGTPPQGAGIDSPDLHPTDTLKGLDELAD 76
Query: 89 HLLVE 93
H VE
Sbjct: 77 HPYVE 81
>gnl|CDD|30798 COG0449, GlmS, Glucosamine 6-phosphate synthetase, contains
amidotransferase and phosphosugar isomerase domains
[Cell envelope biogenesis, outer membrane].
Length = 597
Score = 27.5 bits (61), Expect = 4.5
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 84 GDLTH--HLLVEESHNIFFIGPQRDYALLEKL--NIKIVNEQHAETILCTGLYDDEKD 137
G+L H L++E+ + I P+ D L EK NI+ V + + I+ D +D
Sbjct: 491 GELKHGPIALIDENTPVIAIAPKPD--LFEKTKSNIQEVRARGGKIIVIADEGDVAED 546
Score = 27.1 bits (60), Expect = 5.1
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 36 TIPALKEARENGLKVILFTNSP 57
T+ AL+ A+E G K + TN P
Sbjct: 346 TLAALRLAKEQGAKTLAITNVP 367
>gnl|CDD|107388 cd06393, PBP1_iGluR_Kainate_GluR5_7, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR5-7 subunits of Kainate receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR5-7 subunits of Kainate
receptor. While this N-terminal domain belongs to the
periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. There are five types of
kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2,
which are structurally similar to AMPA and NMDA subunits
of ionotropic glutamate receptors. KA1 and KA2 subunits
can only form functional receptors with one of the
GluR5-7 subunits. Moreover, GluR5-7 can also form
functional homomeric receptor channels activated by
kainate and glutamate when expressed in heterologous
systems. Kainate receptors are involved in excitatory
neurotransmission by activating postsynaptic receptors
and in inhibitory neurotransmission by modulating
release of the inhibitory neurotransmitter GABA through
a presynaptic mechanism. Kainate receptors are closely
related to AMAP receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 384
Score = 27.3 bits (60), Expect = 4.6
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 38 PALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGDL 86
P LKE + I+F S + +A ++ Q ++G ++++ I T+ DL
Sbjct: 183 PLLKEMKRGREFRIIFDCSHQMAAQILKQAMAMGMMTEYYHFIFTTLDL 231
>gnl|CDD|107297 cd06302, PBP1_LsrB_Quorum_Sensing, Periplasmic binding domain of
autoinducer-2 (AI-2) receptor LsrB from Salmonella
typhimurium and its close homologs. Periplasmic
binding domain of autoinducer-2 (AI-2) receptor LsrB
from Salmonella typhimurium and its close homologs from
other bacteria. The members of this group are
homologous to a family of periplasmic pentose/hexose
sugar-binding proteins that function as the primary
receptors for chemotaxis and transporters of many sugar
based solutes in bacteria and archaea and that are a
member of the type I periplasmic binding protein
superfamily. LsrB binds a chemically distinct form of
the AI-2 signal that lacks boron, in contrast to the
Vibrio harveyi AI-2 signaling molecule that has an
unusual furanosyl borate diester. Hence, many bacteria
coordinate their gene expression according to the local
density of their population by producing species
specific AI-2. This process of quorum sensing allows
LsrB to function as a periplasmic AI-2 binding protein
in interspecies signaling.
Length = 298
Score = 27.2 bits (61), Expect = 4.8
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 38 PALKEARENGLKVI 51
P LK+ARE G+KV+
Sbjct: 72 PVLKKAREAGIKVV 85
>gnl|CDD|32362 COG2179, COG2179, Predicted hydrolase of the HAD superfamily
[General function prediction only].
Length = 175
Score = 27.1 bits (60), Expect = 5.1
Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 9/68 (13%)
Query: 214 FNKKRILAIGDGMDTDIKGALQSGIDALYV-----SDGIHRHEYLFNDNIDAQMLQNFFT 268
+ ++ +GD + TD+ G ++G+ + V DG N + ++L+
Sbjct: 108 LPPEEVVMVGDQLFTDVLGGNRAGMRTILVEPLVAPDGWITK---INRWRERRVLKK-LG 163
Query: 269 KKNLYPHW 276
KK HW
Sbjct: 164 KKYGPIHW 171
>gnl|CDD|30475 COG0126, Pgk, 3-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 395
Score = 27.0 bits (60), Expect = 5.7
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 13/56 (23%)
Query: 37 IPALKEARENGLKVILFT-----------NSPRPSASVISQIQSLGSSSQFWDDII 81
+P +K E G KV+L + S P A +S++ LG +F DD +
Sbjct: 42 LPTIKYLLEKGAKVVLLSHLGRPKEYSDKTSLEPVAKRLSEL--LGKEVKFVDDCV 95
>gnl|CDD|144433 pfam00834, Ribul_P_3_epim, Ribulose-phosphate 3 epimerase family.
This enzyme catalyses the conversion of D-ribulose
5-phosphate into D-xylulose 5-phosphate.
Length = 201
Score = 26.9 bits (60), Expect = 6.2
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 7/43 (16%)
Query: 10 TILPYYDVILCDVWGVL-------HNGQKFLPGTIPALKEARE 45
T L + +L D+ VL GQ F+P +P +++ R+
Sbjct: 116 TPLDAIEYLLDDLDLVLLMSVNPGFGGQSFIPSVLPKIRKVRK 158
>gnl|CDD|133291 cd01891, TypA_BipA, TypA (tyrosine phosphorylated protein A)/BipA
subfamily. BipA is a protein belonging to the
ribosome-binding family of GTPases and is widely
distributed in bacteria and plants. BipA was originally
described as a protein that is induced in Salmonella
typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The
properties thus far described for BipA are related to
its role in the process of pathogenesis by
enteropathogenic E. coli. It appears to be involved in
the regulation of several processes important for
infection, including rearrangements of the cytoskeleton
of the host, bacterial resistance to host defense
peptides, flagellum-mediated cell motility, and
expression of K5 capsular genes. It has been proposed
that BipA may utilize a novel mechanism to regulate the
expression of target genes. In addition, BipA from
enteropathogenic E. coli has been shown to be
phosphorylated on a tyrosine residue, while BipA from
Salmonella and from E. coli K12 strains is not
phosphorylated under the conditions assayed. The
phosphorylation apparently modifies the rate of
nucleotide hydrolysis, with the phosphorylated form
showing greatly increased GTPase activity.
Length = 194
Score = 26.7 bits (60), Expect = 6.8
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 33 LPGTIPALKEARENGLKVILFTNS-PRPSAS---VISQIQSL 70
+P T LK+A E GLK I+ N RP A V+ ++ L
Sbjct: 103 MPQTRFVLKKALELGLKPIVVINKIDRPDARPEEVVDEVFDL 144
>gnl|CDD|32049 COG1864, NUC1, DNA/RNA endonuclease G, NUC1 [Nucleotide transport
and metabolism].
Length = 281
Score = 26.5 bits (58), Expect = 7.5
Identities = 7/36 (19%), Positives = 15/36 (41%)
Query: 104 QRDYALLEKLNIKIVNEQHAETILCTGLYDDEKDKT 139
++ + LE + + + I+ TG Y + D
Sbjct: 157 RKIWLELEDYCRNLARKYGSVVIVFTGPYFRKDDTF 192
>gnl|CDD|36000 KOG0781, KOG0781, KOG0781, Signal recognition particle receptor,
alpha subunit [Intracellular trafficking, secretion, and
vesicular transport].
Length = 587
Score = 26.5 bits (58), Expect = 7.6
Identities = 29/118 (24%), Positives = 47/118 (39%), Gaps = 17/118 (14%)
Query: 15 YDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSL---- 70
+DV+L D G +HN + K + N +ILF + Q++
Sbjct: 467 FDVVLIDTAGRMHNNAPLMT---SLAKLIKVNKPDLILFVGEALVGNDSVDQLKKFNRAL 523
Query: 71 --GSSSQFWDDII-----TSGDLTHHLL--VEESHN-IFFIGPQRDYALLEKLNIKIV 118
S+ + D I+ T D + V + I F+G + Y+ L KLN+K V
Sbjct: 524 ADHSTPRLIDGILLTKFDTVDDKVGAAVSMVYITGKPILFVGVGQTYSDLRKLNVKAV 581
>gnl|CDD|119353 cd02874, GH18_CFLE_spore_hydrolase, Cortical fragment-lytic
enzyme (CFLE) is a peptidoglycan hydrolase involved in
bacterial endospore germination. CFLE is expressed as
an inactive preprotein (called SleB) in the forespore
compartment of sporulating cells. SleB translocates
across the forespore inner membrane and is deposited as
a mature enzyme in the cortex layer of the spore. As
part of a sensory mechanism capable of initiating
germination, CFLE degrades a spore-specific
peptidoglycan constituent called muramic-acid
delta-lactam that comprises the outer cortex. CFLE has
a C-terminal glycosyl hydrolase family 18 (GH18)
catalytic domain as well as two N-terminal LysM
peptidoglycan-binding domains. In addition to SleB,
this family includes YaaH, YdhD, and YvbX from Bacillus
subtilis..
Length = 313
Score = 26.8 bits (60), Expect = 7.6
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 5 ITSLRTILPYYDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVIL-FTN 55
SLR PY I +GV +G ++ A+ G+K +L TN
Sbjct: 16 YESLRANAPYLTYIAPFWYGVDADGTLTGLPDERLIEAAKRRGVKPLLVITN 67
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.322 0.140 0.425
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,549,850
Number of extensions: 187343
Number of successful extensions: 590
Number of sequences better than 10.0: 1
Number of HSP's gapped: 581
Number of HSP's successfully gapped: 46
Length of query: 282
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 189
Effective length of database: 4,254,100
Effective search space: 804024900
Effective search space used: 804024900
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: 57 (25.7 bits)