RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15670
(420 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 = 172 bits (438), Expect = 1e-52
Identities = 69/151 (45%), Positives = 87/151 (57%), Gaps = 7/151 (4%)
Query: 129 KVEYPGNVSVNLGNTLTPTQVKEQPHVSWSA--NPKDHYVLCMTDPDAPSRDYPIAREWH 186
V Y + V GN LTP++ ++ P VS+S+ P Y L M DPDAPSRD P REW
Sbjct: 4 TVSYGSSGVVTPGNLLTPSETQKAPTVSFSSEDPPDKLYTLVMVDPDAPSRDDPKFREWL 63
Query: 187 HWLMGNIKGGNL-----EGADHLSRYIGAGPPKQTGPHRYAFLVYKQPNYTVFDEPRLMH 241
HWL+ NI G + + L Y+G GPPK TGPHRY FL++KQP F E +L
Sbjct: 64 HWLVTNIPGSDTTTGLVSKGEVLVPYLGPGPPKGTGPHRYVFLLFKQPGGLDFPESKLPP 123
Query: 242 NSIHGRANFSIAKFAKKYKLGDPIAVNYFLA 272
S GR F + +FAKK LG P+A N+F
Sbjct: 124 TSGLGRRGFDVREFAKKNGLGLPVAANFFQV 154
Score = 127 bits (322), Expect = 2e-35
Identities = 53/136 (38%), Positives = 72/136 (52%), Gaps = 25/136 (18%)
Query: 288 SVEYPDGVQVYLGNKLTPTQVKVEPNVTWSANPKDN--YVLAMIGSNPGCSLSEALLPIR 345
+V Y V GN LTP++ + P V++S+ + Y L M+
Sbjct: 4 TVSYGSSGVVTPGNLLTPSETQKAPTVSFSSEDPPDKLYTLVMV---------------- 47
Query: 346 KEDPDAPSRDNPTVKEWHHWLMGNIKGGDL-----EEADHLSRYIGAGPPKNTGLHRYVF 400
DPDAPSRD+P +EW HWL+ NI G D + + L Y+G GPPK TG HRYVF
Sbjct: 48 --DPDAPSRDDPKFREWLHWLVTNIPGSDTTTGLVSKGEVLVPYLGPGPPKGTGPHRYVF 105
Query: 401 LVYKQPKFIVFTEHRL 416
L++KQP + F E +L
Sbjct: 106 LLFKQPGGLDFPESKL 121
>gnl|CDD|216338 pfam01161, PBP, Phosphatidylethanolamine-binding protein.
Length = 147
Score = 99.5 bits (248), Expect = 5e-25
Identities = 51/155 (32%), Positives = 62/155 (40%), Gaps = 26/155 (16%)
Query: 129 KVEYPGNVSVNLGNTLTPTQ-VKEQPHVSWSANPKDHYVLCMTDPDAPSRDYPIAREWHH 187
VEY V GN L+P + P +S + Y L M DPDAPSR P E+ H
Sbjct: 5 PVEY-TGAFVCPGNNLSPPLSWSDAPTIS---DGTKSYALVMVDPDAPSRSDPKGSEFLH 60
Query: 188 WLMGNIKGGNLEGA-----------DHLSRYIGAGPPKQTGPHRYAFLVYKQPNYTVFDE 236
WL+ NI E L+ YIG PP TGPHRY FL+Y
Sbjct: 61 WLVTNIPASVTELPGGGVQGVNDFGQTLAGYIGPCPPPGTGPHRYVFLLYALDEKLDLPA 120
Query: 237 PRLMHNSIHGRANFSIAKFAKKYKLGDP-IAVNYF 270
R F K + LG +A N+F
Sbjct: 121 GV---TRAELREAF------KGHVLGPATLAGNFF 146
Score = 88.3 bits (219), Expect = 6e-21
Identities = 43/132 (32%), Positives = 56/132 (42%), Gaps = 34/132 (25%)
Query: 288 SVEYPDGVQVYLGNKLTPTQ-VKVEPNVTWSANPKDNYVLAMIGSNPGCSLSEALLPIRK 346
VEY G V GN L+P P + ++ +Y L M+
Sbjct: 5 PVEYT-GAFVCPGNNLSPPLSWSDAPTI---SDGTKSYALVMV----------------- 43
Query: 347 EDPDAPSRDNPTVKEWHHWLMGNIKG-----------GDLEEADHLSRYIGAGPPKNTGL 395
DPDAPSR +P E+ HWL+ NI G + L+ YIG PP TG
Sbjct: 44 -DPDAPSRSDPKGSEFLHWLVTNIPASVTELPGGGVQGVNDFGQTLAGYIGPCPPPGTGP 102
Query: 396 HRYVFLVYKQPK 407
HRYVFL+Y +
Sbjct: 103 HRYVFLLYALDE 114
>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 = 86.3 bits (214), Expect = 5e-20
Identities = 49/153 (32%), Positives = 58/153 (37%), Gaps = 40/153 (26%)
Query: 139 NLGNTLTPTQVKEQ----PHVSWSANPKD--HYVLCMTDPDAPSRDYPIAREWHHWLMGN 192
G+ L P E P +SW P D YVL M DPDAP + R H L+
Sbjct: 9 PSGSVLPPEYSFEGVGRFPSLSWDGPPPDVKEYVLVMEDPDAP-----LGRPIVHGLVYG 63
Query: 193 IK----------------------GGNLEGAD-HLSRYIGAGPPKQTGPHRYAFLVYKQP 229
I GG G + + YIG PP GPHRY F VY
Sbjct: 64 IPANKTSLSNDDFVVTDNGKGGLQGGFKYGKNRGGTVYIGPRPPLGHGPHRYFFQVYAL- 122
Query: 230 NYTVFDEPRLMHNSIHGRANFSIAKFAKKYKLG 262
DEP GR F +A+FA+ LG
Sbjct: 123 -----DEPLDRSKLGDGRTKFEVARFAEGNVLG 150
Score = 66.7 bits (163), Expect = 3e-13
Identities = 33/138 (23%), Positives = 43/138 (31%), Gaps = 52/138 (37%)
Query: 299 LGNKLTP----TQVKVEPNVTWSANPKD--NYVLAMIGSNPGCSLSEALLPIRKEDPDAP 352
G+ L P V P+++W P D YVL M EDPDAP
Sbjct: 10 SGSVLPPEYSFEGVGRFPSLSWDGPPPDVKEYVLVM------------------EDPDAP 51
Query: 353 SRDNPTVKEWHHWLMGNIKGGDLEEAD-----------------------HLSRYIGAGP 389
+ H L+ I ++ + YIG P
Sbjct: 52 -----LGRPIVHGLVYGIPANKTSLSNDDFVVTDNGKGGLQGGFKYGKNRGGTVYIGPRP 106
Query: 390 PKNTGLHRYVFLVYKQPK 407
P G HRY F VY +
Sbjct: 107 PLGHGPHRYFFQVYALDE 124
>gnl|CDD|177765 PLN00169, PLN00169, CETS family protein; Provisional.
Length = 175
Score = 76.4 bits (188), Expect = 2e-16
Identities = 51/144 (35%), Positives = 68/144 (47%), Gaps = 12/144 (8%)
Query: 129 KVEYPGNVSVNLGNTLTPTQVKEQPHVSWSANP-KDHYVLCMTDPDAPSRDYPIAREWHH 187
+V Y G+ VN G L P+QV QP V + Y L M DPDAPS P RE+ H
Sbjct: 29 RVTY-GSREVNNGCELKPSQVVNQPRVDIGGEDLRTFYTLVMVDPDAPSPSNPNLREYLH 87
Query: 188 WLMGNIKGGNLEGADHLSRYIGAGPPKQT-GPHRYAFLVYKQPNYTVFDEPRLMHNSIHG 246
WL+ +I GA + P+ T G HR+ F++++Q P
Sbjct: 88 WLVTDIPA--TTGATFGQEVVCYESPRPTAGIHRFVFVLFRQLGRQTVYAPGW------- 138
Query: 247 RANFSIAKFAKKYKLGDPIAVNYF 270
R NF+ FA+ Y LG P+A YF
Sbjct: 139 RQNFNTRDFAELYNLGSPVAAVYF 162
Score = 46.7 bits (111), Expect = 3e-06
Identities = 32/108 (29%), Positives = 49/108 (45%), Gaps = 22/108 (20%)
Query: 300 GNKLTPTQVKVEPNVTWSANPKDN-YVLAMIGSNPGCSLSEALLPIRKEDPDAPSRDNPT 358
G +L P+QV +P V Y L M+ DPDAPS NP
Sbjct: 40 GCELKPSQVVNQPRVDIGGEDLRTFYTLVMV------------------DPDAPSPSNPN 81
Query: 359 VKEWHHWLMGNIKGGDLEEADHLSRYIGAGPPKNT-GLHRYVFLVYKQ 405
++E+ HWL+ +I A + P+ T G+HR+VF++++Q
Sbjct: 82 LREYLHWLVTDIPA--TTGATFGQEVVCYESPRPTAGIHRFVFVLFRQ 127
>gnl|CDD|224793 COG1881, COG1881, Phospholipid-binding protein [General function
prediction only].
Length = 174
Score = 62.4 bits (152), Expect = 1e-11
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 25/96 (26%)
Query: 153 PHVSWSANPKD--HYVLCMTDPDAPSRDYPIAREWHHWLMGNIKGGN---LEGADHLS-- 205
P +SWS P+ + L + DPDAP+ W HW++ NI EG+ S
Sbjct: 49 PPLSWSGVPEGTKSFALTVDDPDAPTGG-----GWVHWVVANIPADVTELPEGSGPKSKI 103
Query: 206 ------------RYIGAGPPKQTGPHRYAFLVYKQP 229
Y G PPK G HRY F VY
Sbjct: 104 GIVQGINDFGSRGYGGPCPPKGHG-HRYYFTVYALD 138
Score = 52.4 bits (126), Expect = 4e-08
Identities = 23/78 (29%), Positives = 28/78 (35%), Gaps = 23/78 (29%)
Query: 347 EDPDAPSRDNPTVKEWHHWLMGNIKGGDLEEADHLS-----------------RYIGAGP 389
+DPDAP+ W HW++ NI E + Y G P
Sbjct: 68 DDPDAPTG-----GGWVHWVVANIPADVTELPEGSGPKSKIGIVQGINDFGSRGYGGPCP 122
Query: 390 PKNTGLHRYVFLVYKQPK 407
PK G HRY F VY
Sbjct: 123 PKGHG-HRYYFTVYALDV 139
>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 = 51.1 bits (123), Expect = 7e-08
Identities = 30/94 (31%), Positives = 37/94 (39%), Gaps = 26/94 (27%)
Query: 153 PHVSWSANPKD--HYVLCMTDPDAPSRDYPIAREWHHWLMGNIKGGNL---EGADHL--- 204
P +SWS P L + DPDAP+ + HW++ NI EGA
Sbjct: 28 PPLSWSGVPAGTKSLALIVEDPDAPTG-----GGFVHWVVWNIPADTTELPEGASRGALP 82
Query: 205 ------------SRYIGAGPPKQTGPHRYAFLVY 226
+ Y G PP GPHRY F VY
Sbjct: 83 AGAVQGRNDFGEAGYGGPCPPD-GGPHRYVFTVY 115
Score = 42.2 bits (100), Expect = 8e-05
Identities = 25/75 (33%), Positives = 30/75 (40%), Gaps = 24/75 (32%)
Query: 347 EDPDAPSRDNPTVKEWHHWLMGNIKGGDLEEADHLSR------------------YIGAG 388
EDPDAP+ + HW++ NI E + SR Y G
Sbjct: 47 EDPDAPTG-----GGFVHWVVWNIPADTTELPEGASRGALPAGAVQGRNDFGEAGYGGPC 101
Query: 389 PPKNTGLHRYVFLVY 403
PP G HRYVF VY
Sbjct: 102 PPD-GGPHRYVFTVY 115
>gnl|CDD|129572 TIGR00481, TIGR00481, Raf kinase inhibitor-like protein, YbhB/YbcL
family. [Unknown function, General].
Length = 141
Score = 41.7 bits (98), Expect = 1e-04
Identities = 29/97 (29%), Positives = 36/97 (37%), Gaps = 30/97 (30%)
Query: 153 PHVSWSANPKD--HYVLCMTDPDAPSRDYPIAREWHHWLMGNIKGGNLEGADHLSR---- 206
P +SW P+ L DPDAP+ W HW++ NI ++ S
Sbjct: 16 PPLSWDGVPEGAKSLALTCIDPDAPT-----GCGWWHWVVVNIPADTTVLPENASSDDKR 70
Query: 207 -----------------YIGAGPPKQTGPHRYAFLVY 226
YIG PPK G HRY F VY
Sbjct: 71 LPQGVPLQGRNDFGKSGYIGPCPPK--GDHRYLFTVY 105
Score = 37.5 bits (87), Expect = 0.004
Identities = 25/78 (32%), Positives = 30/78 (38%), Gaps = 28/78 (35%)
Query: 347 EDPDAPSRDNPTVKEWHHWLMGNIKGGDLEEADHLSR---------------------YI 385
DPDAP T W HW++ NI ++ S YI
Sbjct: 35 IDPDAP-----TGCGWWHWVVVNIPADTTVLPENASSDDKRLPQGVPLQGRNDFGKSGYI 89
Query: 386 GAGPPKNTGLHRYVFLVY 403
G PPK G HRY+F VY
Sbjct: 90 GPCPPK--GDHRYLFTVY 105
>gnl|CDD|182092 PRK09818, PRK09818, putative kinase inhibitor; Provisional.
Length = 183
Score = 41.9 bits (98), Expect = 2e-04
Identities = 31/118 (26%), Positives = 44/118 (37%), Gaps = 37/118 (31%)
Query: 141 GNTLTPTQV---------KEQPHVSWSANPKDHYVLCMT--DPDAPSRDYPIAREWHHWL 189
G LT + V P ++WS P+ +T DPDAP+ W HW
Sbjct: 32 GEQLTTSHVFSGFGCEGGNTSPSLTWSGAPEGTKSFAVTVYDPDAPT-----GSGWWHWT 86
Query: 190 MGNIKG-------------------GNLEGADHL--SRYIGAGPPKQTGPHRYAFLVY 226
+ NI G ++G + + + GA PPK PH Y F V+
Sbjct: 87 VANIPATVTYLPADAGRRDGTKLPTGAVQGRNDFGYAGFGGACPPKGDKPHHYQFKVW 144
Score = 33.4 bits (76), Expect = 0.13
Identities = 31/134 (23%), Positives = 42/134 (31%), Gaps = 51/134 (38%)
Query: 300 GNKLTPTQV---------KVEPNVTWSANPKDNYVLAMIGSNPGCSLSEALLPIRKEDPD 350
G +LT + V P++TWS P+ A + DPD
Sbjct: 32 GEQLTTSHVFSGFGCEGGNTSPSLTWSGAPEGTKSFA----------------VTVYDPD 75
Query: 351 APSRDNPTVKEWHHWLMGNI--------KGGDLEEADHL-------------SRYIGAGP 389
AP T W HW + NI + L + + GA P
Sbjct: 76 AP-----TGSGWWHWTVANIPATVTYLPADAGRRDGTKLPTGAVQGRNDFGYAGFGGACP 130
Query: 390 PKNTGLHRYVFLVY 403
PK H Y F V+
Sbjct: 131 PKGDKPHHYQFKVW 144
>gnl|CDD|182339 PRK10257, PRK10257, putative kinase inhibitor protein; Provisional.
Length = 158
Score = 38.6 bits (90), Expect = 0.002
Identities = 29/97 (29%), Positives = 39/97 (40%), Gaps = 30/97 (30%)
Query: 153 PHVSWSANPK--DHYVLCMTDPDAPSRDYPIAREWHHWLMGNI-------KGGNLEGADH 203
PH++W P +V+ DPDAP+ W HW++ N+ G G
Sbjct: 32 PHLAWDDVPAGTKSFVVTCYDPDAPT-----GSGWWHWVVVNLPADTRVLPQGFGSGLVA 86
Query: 204 L-------------SRYIGAGPPKQTGP-HRYAFLVY 226
L + Y GA PPK G HRY F V+
Sbjct: 87 LPDGVLQTRTDFGKAGYGGAAPPK--GETHRYIFTVH 121
Score = 34.8 bits (80), Expect = 0.031
Identities = 23/76 (30%), Positives = 30/76 (39%), Gaps = 26/76 (34%)
Query: 348 DPDAPSRDNPTVKEWHHWLMGNIK-------------GGDLEEADHLSR-------YIGA 387
DPDAP T W HW++ N+ L + +R Y GA
Sbjct: 52 DPDAP-----TGSGWWHWVVVNLPADTRVLPQGFGSGLVALPDGVLQTRTDFGKAGYGGA 106
Query: 388 GPPKNTGLHRYVFLVY 403
PPK HRY+F V+
Sbjct: 107 APPKGET-HRYIFTVH 121
>gnl|CDD|149273 pfam08123, DOT1, Histone methylation protein DOT1. The DOT1 domain
regulates gene expression by methylating histone H3. H3
methylation by DOT1 has been shown to be required for
the DNA damage checkpoint in yeast.
Length = 205
Score = 31.9 bits (73), Expect = 0.44
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 105 QNVDKLLQDLKINTGQALSSREICKVEYPGNVSVNLGNTLTPTQVKEQP----HVSWSAN 160
+ ++LQDLK + +S + + Y N NL + +V+E VSW++
Sbjct: 139 LQLKEMLQDLKDGC-KIISLKSFVPLNYRIN-FRNLSDIFNILKVEELKLPEGSVSWTSR 196
Query: 161 PKDHYV 166
++Y+
Sbjct: 197 GVEYYI 202
>gnl|CDD|234495 TIGR04192, GRASP_w_spasm, ATP-GRASP peptide maturase,
grasp-with-spasm system. Members of this protein family
are ATP-GRASP proteins that occur in a peptide
maturation cassette with a SPASM domain protein. SPASM
(TIGR04085) usually occurs as a C-terminal extension to
radical SAM enzymes that act as peptide maturases,
although it can occur independently.
Length = 318
Score = 30.5 bits (69), Expect = 1.7
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 48 KGIRFELPPHHHEEQNVDKLLQDLKINTG 76
+ + ++LP H E +DKL+ +L +N G
Sbjct: 250 RNVPYKLP--AHVEHKIDKLMNELDLNCG 276
Score = 30.5 bits (69), Expect = 1.7
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 91 KGIRFELPPHHHEEQNVDKLLQDLKINTG 119
+ + ++LP H E +DKL+ +L +N G
Sbjct: 250 RNVPYKLP--AHVEHKIDKLMNELDLNCG 276
>gnl|CDD|143594 cd07570, GAT_Gln-NAD-synth, Glutamine aminotransferase (GAT,
glutaminase) domain of glutamine-dependent NAD
synthetases (class 7 and 8 nitrilases).
Glutamine-dependent NAD synthetases are bifunctional
enzymes, which have an N-terminal GAT domain and a
C-terminal NAD+ synthetase domain. The GAT domain is a
glutaminase (EC 3.5.1.2) which hydrolyses L-glutamine to
L-glutamate and ammonia. The ammonia is used by the NAD+
synthetase domain in the ATP-dependent amidation of
nicotinic acid adenine dinucleotide. Glutamine
aminotransferases are categorized depending on their
active site residues into different unrelated classes.
This class of GAT domain belongs to a larger nitrilase
superfamily comprised of nitrile- or amide-hydrolyzing
enzymes and amide-condensing enzymes, which depend on a
Glu-Lys-Cys catalytic triad. This superfamily has been
classified in the literature based on global and
structure based sequence analysis into thirteen
different enzyme classes (referred to as 1-13), this
subgroup corresponds to classes 7 and 8. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Mycobacterium tuberculosis glutamine-dependent NAD+
synthetase forms a homooctamer.
Length = 261
Score = 29.7 bits (68), Expect = 2.7
Identities = 11/16 (68%), Positives = 11/16 (68%), Gaps = 2/16 (12%)
Query: 225 VYKQ--PNYTVFDEPR 238
V KQ PNY VFDE R
Sbjct: 107 VPKQLLPNYGVFDEKR 122
>gnl|CDD|183983 PRK13339, PRK13339, malate:quinone oxidoreductase; Reviewed.
Length = 497
Score = 30.0 bits (68), Expect = 2.7
Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 7/82 (8%)
Query: 319 NPKDNYVLAMIGSNPGCS--LSEALLPIRKEDPDAPSRDNPTVKEWHHWLMGNIKGGDLE 376
N +D+ V+A++G +PG S +S AL + + P+ P +KE M G L
Sbjct: 419 NSQDHSVIALLGESPGASTSVSVALEVLERNFPEYAKEWAPKLKE-----MIPSYGKSLI 473
Query: 377 EADHLSRYIGAGPPKNTGLHRY 398
E L R I K+ L Y
Sbjct: 474 EDAKLMRKIRKQTSKDLELGYY 495
>gnl|CDD|200468 cd11329, AmyAc_maltase-like, Alpha amylase catalytic domain family
found in maltase. Maltase (EC 3.2.1.20) hydrolyzes the
terminal, non-reducing (1->4)-linked alpha-D-glucose
residues in maltose, releasing alpha-D-glucose. The
catalytic triad (DED) which is highly conserved in the
other maltase group is not present in this subfamily.
The Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 477
Score = 29.7 bits (67), Expect = 3.0
Identities = 18/89 (20%), Positives = 28/89 (31%), Gaps = 13/89 (14%)
Query: 156 SWSANPKDHYVLCMTDPDAPSRDY--PIARE-----WHHWLMGNIKGGNLEGADHL---- 204
+W Y L PD P + P + HWL ++G L A +L
Sbjct: 183 AWKWVEDRQYYLHQFGPDQPDLNLNNPAVVDELKDVLKHWLDLGVRGFRLANAKYLLEDP 242
Query: 205 --SRYIGAGPPKQTGPHRYAFLVYKQPNY 231
+ K P+ Y F + +
Sbjct: 243 NLKDEEISSNTKGVTPNDYGFYTHIKTTN 271
>gnl|CDD|153443 cd08041, OBF_kDNA_ligase_like, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain of kDNA ligase-like
ATP-dependent DNA ligases is a DNA-binding module that
is part of the catalytic core unit. ATP-dependent
polynucleotide ligases catalyze phosphodiester bond
formation using nicked nucleic acid substrates with the
high energy nucleotide of ATP as a cofactor in a three
step reaction mechanism. DNA ligases play a vital role
in the diverse processes of DNA replication,
recombination and repair. ATP-dependent ligases are
present in many organisms such as viruses,
bacteriohages, eukarya, archaea and bacteria. The
mitochondrial DNA of parasitic protozoan is highly
unusual. It is termed the kinetoplast DNA (kDNA) and
consists of circular DNA molecules (maxicircles) and
several thousand smaller circular molecules
(minicircles). This group is composed of kDNA ligase,
Chlorella virus DNA ligase, and similar proteins. kDNA
ligase and Chlorella virus DNA ligase are the smallest
known ATP-dependent ligases. They are involved in DNA
replication or repair. ATP dependent DNA ligases have a
highly modular architecture consisting of a unique
arrangement of two or more discrete domains. The
adenylation and oligonucleotide/oligosaccharide binding
(OB)-fold domains comprise a catalytic core unit that is
common to most members of the ATP-dependent DNA ligase
family. The catalytic core unit contains six conserved
sequence motifs (I, III, IIIa, IV, V and VI) that define
this family of related nucleotidyltransferases. The
OB-fold domain contacts the nicked DNA substrate and is
required for the ATP-dependent DNA ligase
nucleotidylation step. The RxDK motif (motif VI), which
is essential for ATP hydrolysis, is located in the
OB-fold domain.
Length = 77
Score = 27.5 bits (62), Expect = 3.6
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 282 YEKLFGS--VEYPDGVQVYLGNKLTPTQVKVEPNV 314
YE + G+ VE DG++ +G+ + Q + P +
Sbjct: 17 YEGMLGALVVETKDGIRFKIGSGFSDEQRRNPPPI 51
>gnl|CDD|226479 COG3970, COG3970, Fumarylacetoacetate (FAA) hydrolase family
protein [General function prediction only].
Length = 379
Score = 28.6 bits (64), Expect = 7.1
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 290 EYPDGVQVYLGNKLTPTQVKVEPNVTWSANPKD 322
+YPDG ++LG P + + + ++ D
Sbjct: 305 QYPDGFALFLGTMFAPGKDRGLKGLGFTHEVGD 337
>gnl|CDD|130674 TIGR01613, primase_Cterm, phage/plasmid primase, P4 family,
C-terminal domain. This model represents a clade within
a larger family of proteins from viruses of bacteria and
animals. Members of this family are found in phage and
plasmids of bacteria and archaea only. The model
describes a domain of about 300 residues, found
generally toward the protein C-terminus [DNA metabolism,
DNA replication, recombination, and repair, Mobile and
extrachromosomal element functions, Prophage functions].
Length = 304
Score = 28.5 bits (64), Expect = 7.2
Identities = 16/55 (29%), Positives = 20/55 (36%), Gaps = 7/55 (12%)
Query: 348 DPDAPSRDNPTVKEWHHWLMGNIKGGDLEEADHLSRYIGAGPPKNTGLHRYVFLV 402
DP A PT + G GD E ++L R IG N + FL
Sbjct: 35 DPKADC---PTWNGFLLETFG----GDNELIEYLQRVIGYSLTGNYTEQKLFFLY 82
>gnl|CDD|205225 pfam13044, DUF3904, Protein of unknown function (DUF3904). This
family of proteins is functionally uncharacterized. This
family of proteins is found in viruses. Proteins in this
family are typically between 437 and 448 amino acids in
length.
Length = 436
Score = 28.5 bits (63), Expect = 7.7
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 64 VDKLLQDLKINTGQALSSREICKAH-CTKGIRFELP 98
V+K +I TG+ L C H CTKGIR E+P
Sbjct: 173 VEKGFTTDRIKTGK-LDIDSCCTQHGCTKGIRVEVP 207
>gnl|CDD|237577 PRK13981, PRK13981, NAD synthetase; Provisional.
Length = 540
Score = 28.2 bits (64), Expect = 9.0
Identities = 10/16 (62%), Positives = 10/16 (62%), Gaps = 2/16 (12%)
Query: 226 YKQ--PNYTVFDEPRL 239
KQ PNY VFDE R
Sbjct: 108 RKQDLPNYGVFDEKRY 123
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
0.318 0.138 0.435
Gapped
Lambda K H
0.267 0.0542 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,168,698
Number of extensions: 2152897
Number of successful extensions: 1654
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1624
Number of HSP's successfully gapped: 34
Length of query: 420
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 321
Effective length of database: 6,546,556
Effective search space: 2101444476
Effective search space used: 2101444476
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: 60 (27.3 bits)