RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11040
(346 letters)
>gnl|CDD|176644 cd00866, PEBP_euk, PhosphatidylEthanolamine-Binding Protein (PEBP)
domain present in eukaryotes.
PhosphatidylEthanolamine-Binding Proteins (PEBPs) are
represented in all three major phylogenetic divisions
(eukaryotes, bacteria, archaea). The members in this
subgroup are present in eukaryotes. Members here
include those in plants such as Arabidopsis thaliana
FLOWERING LOCUS (FT) and TERMINAL FLOWER1 (FT1) which
function as a promoter and a repressor of the floral
transitions, respectively as well as the mammalian Raf
kinase inhibitory protein (RKIP) which inhibits MAP
kinase (Raf-MEK-ERK), G protein-coupled receptor (GPCR)
kinase and NFkappaB signaling cascades. Although their
overall structures are similar, the members of the PEBP
family have very different substrates and
oligomerization states (monomer/dimer/tetramer).
Length = 154
Score = 147 bits (373), Expect = 9e-44
Identities = 65/188 (34%), Positives = 86/188 (45%), Gaps = 46/188 (24%)
Query: 152 IVYPNNSKVSLGNELTPTSVKDEPTVTWDAEPAG--TYTLIMSGSDIHSGKVLAEYIGSG 209
+ Y ++ V+ GN LTP+ + PTV++ +E YTL+M
Sbjct: 5 VSYGSSGVVTPGNLLTPSETQKAPTVSFSSEDPPDKLYTLVM------------------ 46
Query: 210 PPLGTGLHRYIFYVFKQSGYIDFTEPYSSNTVKG-FLHWLVVNIQGSD-----IHSGKVL 263
+D P + +LHWLV NI GSD + G+VL
Sbjct: 47 --------------------VDPDAPSRDDPKFREWLHWLVTNIPGSDTTTGLVSKGEVL 86
Query: 264 AEYIGSGPPLGTGLHRYIFYVFKQTGYIDFTEPYSSNTSAEGRLGFSTQNFADKYKLGSP 323
Y+G GPP GTG HRY+F +FKQ G +DF E TS GR GF + FA K LG P
Sbjct: 87 VPYLGPGPPKGTGPHRYVFLLFKQPGGLDFPESKLPPTSGLGRRGFDVREFAKKNGLGLP 146
Query: 324 VAGNFYLA 331
VA NF+
Sbjct: 147 VAANFFQV 154
Score = 43.5 bits (103), Expect = 2e-05
Identities = 15/30 (50%), Positives = 17/30 (56%)
Query: 4 SAEGRLGFSTQNFADKYKLGSPVAGNFYLA 33
S GR GF + FA K LG PVA NF+
Sbjct: 125 SGLGRRGFDVREFAKKNGLGLPVAANFFQV 154
>gnl|CDD|216338 pfam01161, PBP, Phosphatidylethanolamine-binding protein.
Length = 147
Score = 79.1 bits (195), Expect = 6e-18
Identities = 51/188 (27%), Positives = 68/188 (36%), Gaps = 64/188 (34%)
Query: 156 NNSKVSLGNELTPT-SVKDEPTVTWDAEPAGTYTLIMSGSDIHSGKVLAEYIGSGPPLGT 214
+ V GN L+P S D PT+ ++ +Y L+M
Sbjct: 9 TGAFVCPGNNLSPPLSWSDAPTI---SDGTKSYALVM----------------------- 42
Query: 215 GLHRYIFYVFKQSGYIDFTEPYSSNTV-KGFLHWLVVNIQGS-----------DIHSGKV 262
+D P S+ FLHWLV NI S G+
Sbjct: 43 ---------------VDPDAPSRSDPKGSEFLHWLVTNIPASVTELPGGGVQGVNDFGQT 87
Query: 263 LAEYIGSGPPLGTGLHRYIFYVFKQTGYIDFTEPYSSNTSAEGRLGFSTQNFADKYKLGS 322
LA YIG PP GTG HRY+F ++ +D T AE R F + LG
Sbjct: 88 LAGYIGPCPPPGTGPHRYVFLLYALDEKLDLPAG---VTRAELREAFK------GHVLGP 138
Query: 323 P-VAGNFY 329
+AGNF+
Sbjct: 139 ATLAGNFF 146
>gnl|CDD|192278 pfam09384, UTP15_C, UTP15 C terminal. U3 snoRNA is ubiquitous in
eukaryotes and is required for nucleolar processing of
pre-18S ribosomal RNA. It is a component of the
ribosomal small subunit (SSU) processome. UTP15 is
needed for optimal pre-ribosomal RNA transcription by
RNA polymerase I, together with a subset of U3 proteins
required for transcription (t-UTPs). This entry
represents the C terminal of UTP15, and is found
adjacent to WD40 repeats (pfam00400).
Length = 147
Score = 66.4 bits (163), Expect = 3e-13
Identities = 30/92 (32%), Positives = 48/92 (52%), Gaps = 4/92 (4%)
Query: 61 RKGLHRAVIGLDEKFTKKLVAFIAKHIDVPQYFDVLSQTTYIIIDVLEEMIDSGLSPSGS 120
R L A+ G DE + L+ F+ K+I P+Y VL +++D+ +I S
Sbjct: 60 RGALRVALAGRDEVTLQPLLNFLLKNITDPRYTPVLMDVANVVLDIYASVIGK----SPV 115
Query: 121 LVSILQRLARRIKSEQESVRDLLELQGALQMI 152
L + QRL R++ E E ++ LELQG L ++
Sbjct: 116 LDKMFQRLRRKVGEELELQQEALELQGMLDLL 147
>gnl|CDD|176642 cd00457, PEBP, PhosphatidylEthanolamine-Binding Protein (PEBP)
domain. PhosphatidylEthanolamine-Binding Proteins
(PEBPs) are represented in all three major phylogenetic
divisions (eukaryotes, bacteria, archaea). A number of
biological roles for members of the PEBP family include
serine protease inhibition, membrane biogenesis,
regulation of flowering plant stem architecture, and
Raf-1 kinase inhibition. Although their overall
structures are similar, the members of the PEBP family
bind very different substrates including phospholipids,
opioids, and hydrophobic odorant molecules as well as
having different oligomerization states
(monomer/dimer/tetramer).
Length = 159
Score = 62.4 bits (152), Expect = 8e-12
Identities = 42/199 (21%), Positives = 56/199 (28%), Gaps = 78/199 (39%)
Query: 162 LGNELTPTSVKDE----PTVTWDAEPAGT--YTLIMSGSDIHSGKVLAEYIGSGPPLGTG 215
G+ L P + P+++WD P Y L+M D PLG
Sbjct: 10 SGSVLPPEYSFEGVGRFPSLSWDGPPPDVKEYVLVMEDPDA--------------PLGRP 55
Query: 216 LHRYIFYVFKQSGYIDFTEPYSSNTVKGFLHWLVVNIQGSDI------------------ 257
+H LV I +
Sbjct: 56 ----------------------------IVHGLVYGIPANKTSLSNDDFVVTDNGKGGLQ 87
Query: 258 ---HSGKVL--AEYIGSGPPLGTGLHRYIFYVFKQTGYIDFTEPYSSNTSAEGRLGFSTQ 312
GK YIG PPLG G HRY F V+ +D ++ +GR F
Sbjct: 88 GGFKYGKNRGGTVYIGPRPPLGHGPHRYFFQVYALDEPLDRSKL------GDGRTKFEVA 141
Query: 313 NFADKYKLGSPVAGNFYLA 331
FA+ LG V
Sbjct: 142 RFAEGNVLG-AVGEWVGQF 159
>gnl|CDD|177765 PLN00169, PLN00169, CETS family protein; Provisional.
Length = 175
Score = 57.5 bits (139), Expect = 5e-10
Identities = 50/183 (27%), Positives = 77/183 (42%), Gaps = 50/183 (27%)
Query: 156 NNSKVSLGNELTPTSVKDEPTVTWDAEPAGT-YTLIMSGSDIHSGKVLAEYIGSGPPLGT 214
+ +V+ G EL P+ V ++P V E T YTL+M D S S P L
Sbjct: 33 GSREVNNGCELKPSQVVNQPRVDIGGEDLRTFYTLVMVDPDAPSP--------SNPNL-- 82
Query: 215 GLHRYIFYVFKQSGYIDFTEPYSSNTVKGFLHWLVVNIQGSDIHS-GKVLAEYIGSGPPL 273
+ +LHWLV +I + + G+ + Y P
Sbjct: 83 ---------------------------REYLHWLVTDIPATTGATFGQEVVCYESPRPTA 115
Query: 274 GTGLHRYIFYVFKQTGYIDFTEPYSSNTSAEG-RLGFSTQNFADKYKLGSPVAGNFYLAQ 332
G +HR++F +F+Q G A G R F+T++FA+ Y LGSPVA ++ Q
Sbjct: 116 G--IHRFVFVLFRQLG--------RQTVYAPGWRQNFNTRDFAELYNLGSPVAAVYFNCQ 165
Query: 333 YDN 335
++
Sbjct: 166 RES 168
Score = 33.6 bits (77), Expect = 0.080
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 8 RLGFSTQNFADKYKLGSPVAGNFYLAQ 34
R F+T++FA+ Y LGSPVA ++ Q
Sbjct: 139 RQNFNTRDFAELYNLGSPVAAVYFNCQ 165
>gnl|CDD|224793 COG1881, COG1881, Phospholipid-binding protein [General function
prediction only].
Length = 174
Score = 38.5 bits (90), Expect = 0.002
Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 18/62 (29%)
Query: 243 GFLHWLVVNI--------QGSDIHSGKVLAE---------YIGSGPPLGTGLHRYIFYVF 285
G++HW+V NI +GS S + + Y G PP G G HRY F V+
Sbjct: 77 GWVHWVVANIPADVTELPEGSGPKSKIGIVQGINDFGSRGYGGPCPPKGHG-HRYYFTVY 135
Query: 286 KQ 287
Sbjct: 136 AL 137
Score = 30.0 bits (68), Expect = 1.2
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 205 YIGSGPPLGTGLHRYIFYVFKQ 226
Y G PP G G HRY F V+
Sbjct: 117 YGGPCPPKGHG-HRYYFTVYAL 137
>gnl|CDD|176643 cd00865, PEBP_bact_arch, PhosphatidylEthanolamine-Binding Protein
(PEBP) domain present in bacteria and archaea.
PhosphatidylEthanolamine-Binding Proteins (PEBPs) are
represented in all three major phylogenetic divisions
(eukaryotes, bacteria, archaea). The members in this
subgroup are present in bacterial and archaea. Members
here include Escherichia coli YBHB and YBCL which are
thought to regulate protein phosphorylation as well as
Sulfolobus solfataricus SsCEI which inhibits serine
proteases alpha-chymotrypsin and elastase. Although
their overall structures are similar, the members of the
PEBP family have very different substrates and
oligomerization states (monomer/dimer/tetramer). In a
few of the bacterial members present here the
dimerization interface is proposed to form the ligand
binding site, unlike in other PEBP members.
Length = 150
Score = 35.3 bits (82), Expect = 0.015
Identities = 20/61 (32%), Positives = 25/61 (40%), Gaps = 19/61 (31%)
Query: 243 GFLHWLVVNIQGS------DIHSGKVLAE------------YIGSGPPLGTGLHRYIFYV 284
GF+HW+V NI G + A Y G PP G G HRY+F V
Sbjct: 56 GFVHWVVWNIPADTTELPEGASRGALPAGAVQGRNDFGEAGYGGPCPPDG-GPHRYVFTV 114
Query: 285 F 285
+
Sbjct: 115 Y 115
Score = 28.3 bits (64), Expect = 3.4
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 205 YIGSGPPLGTGLHRYIFYVF 224
Y G PP G G HRY+F V+
Sbjct: 97 YGGPCPPDG-GPHRYVFTVY 115
>gnl|CDD|129572 TIGR00481, TIGR00481, Raf kinase inhibitor-like protein, YbhB/YbcL
family. [Unknown function, General].
Length = 141
Score = 32.8 bits (75), Expect = 0.099
Identities = 21/67 (31%), Positives = 26/67 (38%), Gaps = 23/67 (34%)
Query: 240 TVKGFLHWLVVNI-------------QGSDIHSGKVLAE--------YIGSGPPLGTGLH 278
T G+ HW+VVNI + G L YIG PP G H
Sbjct: 41 TGCGWWHWVVVNIPADTTVLPENASSDDKRLPQGVPLQGRNDFGKSGYIGPCPP--KGDH 98
Query: 279 RYIFYVF 285
RY+F V+
Sbjct: 99 RYLFTVY 105
>gnl|CDD|213058 cd12089, Hef_ID, insert domain of Hef nuclease and similar archaeal
proteins. Archaeal Hef helicase/nuclease, originally
identified in the hyperthermophilic archaeon Pyrococcus
furiosus, contains an N-terminal SF2 helicase domain and
an C-terminal XPF/Mus81-type nuclease domain. Hef has
been shown to process flap- or fork-DNA structures, and
that both helicase and nuclease domain independently
recognize branched DNA, with a strong preference for the
forked DNA. The SF2 helicase domain is comprised of 3
structural domains, the 2 generally conserved helicase
domains and a helical domain inserted between the two
domains. This domain which is not present in all SF2
helicases, has been shown to play a important role in
branched structure processing.
Length = 119
Score = 31.8 bits (73), Expect = 0.17
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 103 IIDVLEEMIDSGLSPSGSLVSILQRLARRIKSEQESVRDLLELQGALQ 150
I +L+E ++ L L+ L + S S +DLLELQ +Q
Sbjct: 3 IRKLLKEALEDRLKE-------LKELGVIVSSSNVSKKDLLELQKRIQ 43
>gnl|CDD|182339 PRK10257, PRK10257, putative kinase inhibitor protein; Provisional.
Length = 158
Score = 30.9 bits (70), Expect = 0.55
Identities = 24/67 (35%), Positives = 28/67 (41%), Gaps = 25/67 (37%)
Query: 240 TVKGFLHWLVVNI--------QGSDIHSGKV--------------LAEYIGSGPPLGTGL 277
T G+ HW+VVN+ QG SG V A Y G+ PP G
Sbjct: 57 TGSGWWHWVVVNLPADTRVLPQGFG--SGLVALPDGVLQTRTDFGKAGYGGAAPPKGET- 113
Query: 278 HRYIFYV 284
HRYIF V
Sbjct: 114 HRYIFTV 120
>gnl|CDD|223407 COG0330, HflC, Membrane protease subunits, stomatin/prohibitin
homologs [Posttranslational modification, protein
turnover, chaperones].
Length = 291
Score = 31.3 bits (71), Expect = 0.59
Identities = 12/69 (17%), Positives = 30/69 (43%), Gaps = 12/69 (17%)
Query: 94 DVLSQTTYIIIDVLEEMIDSGLSPSGSLV------------SILQRLARRIKSEQESVRD 141
++L++ I + E++D P G V + + +++ +E++ +
Sbjct: 133 ELLTERRAEINAKIREILDEAADPWGIKVVDVEIKDIDPPEEVQAAMEKQMAAERDKRAE 192
Query: 142 LLELQGALQ 150
+LE +G Q
Sbjct: 193 ILEAEGEAQ 201
>gnl|CDD|145556 pfam02478, Pneumo_phosprot, Pneumovirus phosphoprotein. This
family represents the phosphoprotein of Paramyxoviridae,
a putative RNA polymerase alpha subunit that may
function in template binding.
Length = 266
Score = 31.0 bits (70), Expect = 0.75
Identities = 13/58 (22%), Positives = 24/58 (41%)
Query: 131 RIKSEQESVRDLLELQGALQMIVYPNNSKVSLGNELTPTSVKDEPTVTWDAEPAGTYT 188
IK E SV + +++ + V P + + + T K + V++ G YT
Sbjct: 61 CIKDEIISVNKVKDIESIYEKPVTPTSDGKTPTEKSDDTPTKKKKKVSFKEPEPGKYT 118
>gnl|CDD|176165 cd08476, PBP2_CrgA_like_7, The C-terminal substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator CrgA-like, contains the type 2 periplasmic
binding fold. This CD represents the substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator (LTTR) CrgA-like 7. The LTTRs are acting as
both auto-repressors and activators of target
promoters, controlling operons involved in a wide
variety of cellular processes such as amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to name a few. In contrast to the tetrameric
form of other LTTRs, CrgA from Neisseria meningitides
assembles into an octameric ring, which can bind up to
four 63-bp DNA oligonucleotides. Phylogenetic cluster
analysis showed that the CrgA-like regulators form a
subclass of the LTTRs that function as octamers. The
CrgA is an auto-repressor of its own gene and activates
the expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is
increased by MBL (alpha-methylene-gamma-butyrolactone),
an inducer of NADPH-quinone oxidoreductase. The
structural topology of this substrate-binding domain is
most similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake
of a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 197
Score = 30.7 bits (70), Expect = 0.81
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 9/51 (17%)
Query: 39 VPILHRQFMPVLVDHQSTYKQQRKGLHRAVIGLDEKFTKKLVAFIAKHIDV 89
+P++ +PVL Y + I LD F+ +LV I + D
Sbjct: 7 LPLVGGLLLPVLAAFMQRYPE---------IELDLDFSDRLVDVIDEGFDA 48
>gnl|CDD|177990 PLN02361, PLN02361, alpha-amylase.
Length = 401
Score = 30.6 bits (69), Expect = 1.1
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 230 IDFTEPYSSNTVKGFLHWLVVNIQGSDI-------HSGKVLAEYIGSGPPL 273
ID T+ + + G+L WL ++ D +S K + EYI + PL
Sbjct: 149 IDHTQHFVRKDIIGWLIWLRNDVGFQDFRFDFAKGYSAKFVKEYIEAAKPL 199
>gnl|CDD|224285 COG1366, SpoIIAA, Anti-anti-sigma regulatory factor (antagonist of
anti-sigma factor) [Signal transduction mechanisms].
Length = 117
Score = 29.3 bits (66), Expect = 1.2
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 11/76 (14%)
Query: 97 SQTTYIIIDVLE-EMIDS-GLSPSGSLVSILQRLARR-----IKSEQESVRDLLELQGAL 149
S ++ID+ + +DS GL G LV++L+ R + Q V LEL G
Sbjct: 42 SGARGLVIDLSGVDFMDSAGL---GVLVALLKSARLRGVELVLVGIQPEVARTLELTGLD 98
Query: 150 Q-MIVYPNNSKVSLGN 164
+ I+ P + +L
Sbjct: 99 KSFIITPTELEAALAL 114
>gnl|CDD|143585 cd07316, terB_like_DjlA, N-terminal tellurium resistance protein
terB-like domain of heat shock DnaJ-like proteins.
Tellurium resistance terB-like domain of the DnaJ-like
DjlA proteins. This family represents the terB-like
domain of DjlA-like proteins, a subgroup of heat shock
DnaJ-like proteins. Escherichia coli DjlA is a type III
membrane protein with a small N-terminal transmembrane
region and DnaJ-like domain on the extreme C-terminus.
Overproduction has been shown to activate the RcsC
pathway, which regulates the production of the capsular
exopolysaccharide colanic acid. The specific function
of this domain is unknown.
Length = 106
Score = 28.6 bits (65), Expect = 1.5
Identities = 14/80 (17%), Positives = 21/80 (26%), Gaps = 16/80 (20%)
Query: 79 LVAFIAK--------HID-VPQYFDVLSQTT---YIIIDVLEEMIDSGLSPSGSLVSILQ 126
L+ +AK I D + I + E G L +
Sbjct: 5 LMGKLAKADGRVSEAEIQAARALMDQMGLDAEARREAIRLFNE----GKESDFGLEEYAR 60
Query: 127 RLARRIKSEQESVRDLLELQ 146
+ R E + LLE
Sbjct: 61 QFRRACGGRPELLLQLLEFL 80
>gnl|CDD|191103 pfam04821, TIMELESS, Timeless protein. The timeless gene in
Drosophila melanogaster and its homologues in a number
of other insects and mammals (including human) are
involved in circadian rhythm control. This family
includes a related proteins from a number of fungal
species.
Length = 266
Score = 29.9 bits (68), Expect = 1.6
Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 9/54 (16%)
Query: 38 YVPILHRQFMPVLVDHQSTYKQQRKGLHRAVIGLDEKFTKKLVAFIAKHIDVPQ 91
+ R+ +P L + YK A LD K K LV + + VP
Sbjct: 82 PKTVNGRRHIPELQEALQGYK-------EAF--LDAKVLKALVRILLPSLAVPW 126
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.4 bits (68), Expect = 1.8
Identities = 16/81 (19%), Positives = 32/81 (39%)
Query: 63 GLHRAVIGLDEKFTKKLVAFIAKHIDVPQYFDVLSQTTYIIIDVLEEMIDSGLSPSGSLV 122
L++ + + ++ + L + + I DV++ M G S SG L+
Sbjct: 2208 YFLFIERCLNDPLNMFQEGLVVEMNELEEKSLSLFVSAHAIHDVMKHMYKYGKSNSGYLL 2267
Query: 123 SILQRLARRIKSEQESVRDLL 143
++ R IK + +RD
Sbjct: 2268 ESVEDYERGIKEYKIKIRDSE 2288
>gnl|CDD|236886 PRK11249, katE, hydroperoxidase II; Provisional.
Length = 752
Score = 29.6 bits (67), Expect = 2.9
Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 18/86 (20%)
Query: 113 SGLSPSGSLVSILQRLARRIKSEQ--------------ESVRDLLELQGALQMIVYPNNS 158
+GL +L S+ IK + ++ L+ +G ++YP
Sbjct: 577 NGLKKDPAL-SLYAIPDGDIKGRKVAILLNDGVDAADLLAILKALKAKGVHAKLLYPRMG 635
Query: 159 KV--SLGNELTP-TSVKDEPTVTWDA 181
+V G L + P++T+DA
Sbjct: 636 EVTADDGTVLPIAATFAGAPSLTFDA 661
>gnl|CDD|236931 PRK11563, PRK11563, bifunctional aldehyde dehydrogenase/enoyl-CoA
hydratase; Provisional.
Length = 675
Score = 29.5 bits (67), Expect = 3.0
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 68 VIGLDEKFTKKLVAFIAKHIDVPQYFDVLSQTTYIIIDVLEEMIDSGLSPSGSL 121
V G+ EK AF+A VP + T Y+ V+ +++SGL P G+L
Sbjct: 162 VWGMLEKLAP---AFLA---GVPAIVKPATATAYLTEAVVRLIVESGLLPEGAL 209
>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 29.1 bits (65), Expect = 3.9
Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 7/88 (7%)
Query: 219 YIFYVFKQSGYID-FTEPYSSN-TVKGFLHWLVVNIQG---SDIHSGKVLAEYIGSGPPL 273
Y F GY D F + N + WL I G D+ + KV A+ + L
Sbjct: 1076 YGFRFKPLPGYADGFPYFFDINLSAAEAQTWLDYMIYGLMIDDVKTRKVTAQVVVYNAEL 1135
Query: 274 GTGLHRYIFYVFKQTGYIDFTEPYSSNT 301
G + +F+ F G I+ T + NT
Sbjct: 1136 GYFGNVMVFFEFTDGGKIEVT--HRLNT 1161
>gnl|CDD|182092 PRK09818, PRK09818, putative kinase inhibitor; Provisional.
Length = 183
Score = 28.4 bits (63), Expect = 4.7
Identities = 26/99 (26%), Positives = 37/99 (37%), Gaps = 33/99 (33%)
Query: 208 SGPPLGTGLHRYIFYVFKQSGYIDFTEPYSSNTVKGFLHWLVVNI--------------Q 253
SG P GT +S + +P + T G+ HW V NI
Sbjct: 58 SGAPEGT-----------KSFAVTVYDP-DAPTGSGWWHWTVANIPATVTYLPADAGRRD 105
Query: 254 GSDIHSGKV-------LAEYIGSGPPLGTGLHRYIFYVF 285
G+ + +G V A + G+ PP G H Y F V+
Sbjct: 106 GTKLPTGAVQGRNDFGYAGFGGACPPKGDKPHHYQFKVW 144
>gnl|CDD|236247 PRK08345, PRK08345, cytochrome-c3 hydrogenase subunit gamma;
Provisional.
Length = 289
Score = 28.6 bits (64), Expect = 5.2
Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 14/73 (19%)
Query: 69 IGLDEKFTKKLVAFIAKHIDVPQYFDVLSQTTYIII--------DVLEEMIDSGLSPSGS 120
GL + F +++ + + D + TY I V +E+I+ G P
Sbjct: 184 HGLPQGFIERVCKGVVTDLFREANTDP--KNTYAAICGPPVMYKFVFKELINRGYRPE-- 239
Query: 121 LVSILQRLARRIK 133
I L RR++
Sbjct: 240 --RIYVTLERRMR 250
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 28.6 bits (64), Expect = 5.6
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 113 SGLSPSGSLVSILQRLARRIKSEQESVRDLLELQGALQMI 152
GL P V L+RLA R+ RDL L+ +L+ +
Sbjct: 321 EGLRPLLKEVGDLERLAARVALGNARPRDLARLRTSLEQL 360
>gnl|CDD|216895 pfam02137, A_deamin, Adenosine-deaminase (editase) domain.
Adenosine deaminases acting on RNA (ADARs) can deaminate
adenosine to form inosine. In long double-stranded RNA,
this process is non-specific; it occurs
site-specifically in RNA transcripts. The former is
important in defence against viruses, whereas the latter
may affect splicing or untranslated regions. They are
primarily nuclear proteins, but a longer isoform of
ADAR1 is found predominantly in the cytoplasm. ADARs are
derived from the Tad1-like tRNA deaminases that are
present across eukaryotes. These in turn belong to the
nucleotide/nucleic acid deaminase superfamily and are
characterized by a distinct insert between the two
conserved cysteines that are involved in binding zinc.
Length = 329
Score = 28.1 bits (63), Expect = 6.5
Identities = 12/41 (29%), Positives = 14/41 (34%)
Query: 155 PNNSKVSLGNELTPTSVKDEPTVTWDAEPAGTYTLIMSGSD 195
+K+ G P D T G TL MS SD
Sbjct: 111 QLRTKIERGRGTIPVKGSDGVVRTKPGRLDGERTLSMSCSD 151
>gnl|CDD|215939 pfam00482, T2SF, Type II secretion system (T2SS), protein F. The
original family covered both the regions found by the
current model. The splitting of the family has allowed
the related FlaJ_arch (archaeal FlaJ family) to be
merged with it. Proteins with this domain in form a
platform for the machiney of the Type II secretion
system, as well as the Type 4 pili and the archaeal
flagella. This domain seems to show some similarity to
PF00664 but this may just be due to similarities in the
TM helices (personal obs: C Yeats).
Length = 124
Score = 27.3 bits (61), Expect = 6.6
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 94 DVLSQTTYIIIDVLEEMIDSGLSPSGSLVSILQRLARRIKSEQESVRDLL 143
+ L++T D+L +I +G S G+L +L+RLA ++ +E R +L
Sbjct: 50 EALARTPSEFPDLLVALIAAGES-GGNLAEVLERLADYLEERRELRRKIL 98
>gnl|CDD|227699 COG5412, COG5412, Phage-related protein [Function unknown].
Length = 637
Score = 28.2 bits (63), Expect = 6.8
Identities = 45/230 (19%), Positives = 89/230 (38%), Gaps = 43/230 (18%)
Query: 64 LHRAVIGLDEKFTKKLVAFIAKHIDVPQYFDVLSQTTYIIIDVLEEMIDSGLSPSGSLVS 123
H A IGL K T +++QT I+I VL + + S G+++S
Sbjct: 316 AHSAFIGLITKIT-----------------GLVNQTFDIVIPVLSWISEIWNSIIGNIIS 358
Query: 124 ILQRLARRIKSEQESVRDLL--------ELQGALQMIVYPNNSKVSLGNELTPTSVKDEP 175
I+ R+ +++ ++ D++ ++ + V P + + L + V
Sbjct: 359 IITRIIDFVRTIIGTIIDVIGPIISTIADVIKIIFDGVKPIINFLKNIFSLIGSKVGMAI 418
Query: 176 TVTWDAEPAGTYTLIMSG--SDIHSGKVLAEYIGSG-----PPLGTGLHRYIFYVF--KQ 226
G T +M+ S I +G + + + + + G+ I VF +
Sbjct: 419 IPV-----LGIITTVMNTIKSTISNGSIAIKSVATRIFSGRSSIFNGVRNLITIVFDGIR 473
Query: 227 SGYIDFTEPYSS--NTVKGFLHWLVVNIQG--SDIHSGKVLAEYIGSGPP 272
+ T S + V F+ +V N++ I G+ +A+ IG+ P
Sbjct: 474 GAWGGLTSAVSPIFSKVGNFVQTIVNNVKSFVGFIIRGRNMAKDIGNKIP 523
>gnl|CDD|213358 cd12824, ZntB-like, Salmonella typhimurium Zn2+ transporter
ZntB-like subfamily. A bacterial subfamily belonging to
the Escherichia coli CorA-Salmonella typhimurium
ZntB_like family (EcCorA_ZntB-like) family of the MIT
superfamily of essential membrane proteins involved in
transporting divalent cations (uptake or efflux) across
membranes. This subfamily includes the Zn2+ transporter
Salmonella typhimurium ZntB which mediates the efflux of
Zn2+ (and Cd2+). Structures of the intracellular domain
of Vibrio parahaemolyticus and Salmonella typhimurium
ZntB form funnel-shaped homopentamers, the tip of the
funnel is formed from two C-terminal transmembrane (TM)
helices from each monomer, and the large opening of the
funnel from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA, and
Mrs2p. Natural variants such as GVN and GIN, which occur
in proteins belonging to this subfamily, may be
associated with the transport of different divalent
cations, such as zinc and cadmium. The functional
diversity of MIT transporters may also be due to minor
structural differences regulating gating, substrate
selection, and transport.
Length = 290
Score = 27.9 bits (62), Expect = 7.1
Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 79 LVAFIAKHIDVPQYFDVLSQTTYIIIDVLEEMIDSGLSPS----GSLVSILQRLARRIKS 134
L+A + + + V+ T + +V + ++D G +P +L L R+ R+I+
Sbjct: 108 LLAQMISGM-TKRLELVIFDLTETLDEVEDNLLDGGTAPPPYALIALQRRLFRIRRQIRP 166
Query: 135 EQESVRDLLE 144
+Q+++R L+
Sbjct: 167 QQQALRPLIT 176
>gnl|CDD|214617 smart00323, RasGAP, GTPase-activator protein for Ras-like GTPases.
All alpha-helical domain that accelerates the GTPase
activity of Ras, thereby "switching" it into an "off"
position. Improved domain limits from structure.
Length = 344
Score = 28.0 bits (63), Expect = 7.4
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 73 EKFTKKLVAFIAKHID-VPQYFDVLSQTTYIIIDVLEEMIDSGLSPSGSLVSILQRLARR 131
E + + L F+ H D V + D LS I++D + + + SG +S+L L
Sbjct: 253 EPWMEPLNDFLLSHKDRVKDFLDELSSVPEILVDKVSD----STTISGRELSLLHSL--- 305
Query: 132 IKSEQESVRDLLE 144
+ ++++ L
Sbjct: 306 LLENGDALKRELN 318
>gnl|CDD|200580 cd10956, CE4_BH1302_like, Putative catalytic NodB homology domain
of uncharacterized BH1302 protein from Bacillus
halodurans and its bacterial homologs. This family is
represented by a putative polysaccharide deacetylase
BH1302 from Bacillus halodurans. Although its biological
function is unknown, BH1302 shows high sequence homology
to the catalytic NodB homology domain of Streptococcus
pneumoniae polysaccharide deacetylase PgdA (SpPgdA),
which is an extracellular metal-dependent polysaccharide
deacetylase with de-N-acetylase activity toward a
hexamer of chitooligosaccharide N-acetylglucosamine, but
not shorter chitooligosaccharides or a synthetic
peptidoglycan tetrasaccharide. Both BH1302 and SpPgdA
belong to the carbohydrate esterase 4 (CE4) superfamily.
This family also includes many uncharacterized bacterial
polysaccharide deacetylases.
Length = 194
Score = 27.7 bits (62), Expect = 8.0
Identities = 8/24 (33%), Positives = 9/24 (37%)
Query: 173 DEPTVTWDAEPAGTYTLIMSGSDI 196
+ TV WD EP DI
Sbjct: 119 NRTTVMWDVEPETFPDKAQDADDI 142
>gnl|CDD|143446 cd07128, ALDH_MaoC-N, N-terminal domain of the monoamine oxidase C
dehydratase. The N-terminal domain of the MaoC
dehydratase, a monoamine oxidase regulatory protein.
Orthologs of MaoC include PaaZ (Escherichia coli) and
PaaN (Pseudomonas putida), which are putative
ring-opening enzymes of the aerobic phenylacetic acid
(PA) catabolic pathway. The C-terminal domain of MaoC
has sequence similarity to enoyl-CoA hydratase. Also
included in this CD is a novel Burkholderia xenovorans
LB400 ALDH of the aerobic benzoate oxidation (box)
pathway. This pathway involves first the synthesis of a
CoA thio-esterified aromatic acid, with subsequent
dihydroxylation and cleavage steps, yielding the CoA
thio-esterified aliphatic aldehyde,
3,4-dehydroadipyl-CoA semialdehyde, which is further
converted into its corresponding CoA acid by the
Burkholderia LB400 ALDH.
Length = 513
Score = 28.0 bits (63), Expect = 8.1
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 12/55 (21%)
Query: 70 GLDEKFTKKLVA---FIAKHIDVPQYFDVLSQTTYIIIDVLEEMIDSGLSPSGSL 121
G+ EKF L+A I K P + T Y+ V++++++SGL P G+L
Sbjct: 160 GMLEKFAPALLAGVPVIVK----PA-----TATAYLTEAVVKDIVESGLLPEGAL 205
>gnl|CDD|221732 pfam12719, Cnd3, Nuclear condensing complex subunits, C-term
domain. The Cnd1-3 proteins are the three non-SMC
(structural maintenance of chromosomes) proteins that go
to make up the mitotic condensation complex along with
the two SMC protein families, XCAP-C and XCAP-E, (or in
the case of fission yeast, Cut3 and Cut14). The
five-member complex seems to be conserved from yeasts to
vertebrates. This domain is the C-terminal,
cysteine-rich domain of Cnd3. The complex shuttles
between the nucleus, during mitosis, and the cytoplasm
during the rest of the cycle. Thus this family is made
up of the C-termini of XCAP-Gs, Ycg1 and Ycs5 members.
Length = 302
Score = 28.0 bits (63), Expect = 8.4
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 101 YIIIDVLEEMIDSGLSPSGSLVSILQRLARR-IKSEQESVRDL 142
I+ +LE + LSP+ SL S+L L ++S +R+L
Sbjct: 5 TILQYMLENVSVGSLSPNISLESLLDTLILPAVRSHDADIREL 47
>gnl|CDD|216110 pfam00771, FHIPEP, FHIPEP family.
Length = 658
Score = 28.2 bits (64), Expect = 8.6
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 5/38 (13%)
Query: 105 DVLEEMIDSGLSPSGSLVSILQRLARRIKSEQESVRDL 142
++EE++ L G + +LQ L + E+ S+RDL
Sbjct: 492 KLVEELVPKLLPL-GRIQKVLQNLLK----ERVSIRDL 524
>gnl|CDD|237603 PRK14083, PRK14083, HSP90 family protein; Provisional.
Length = 601
Score = 28.0 bits (63), Expect = 8.7
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 169 TSVKDEPTVTWDAEPAGTYTL 189
S KD P V W + GTY++
Sbjct: 126 RSAKDGPAVEWRGKADGTYSV 146
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 0.138 0.405
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,116,612
Number of extensions: 1788404
Number of successful extensions: 1534
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1520
Number of HSP's successfully gapped: 49
Length of query: 346
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 248
Effective length of database: 6,590,910
Effective search space: 1634545680
Effective search space used: 1634545680
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 (21.7 bits)
S2: 59 (26.5 bits)