RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 015658
(403 letters)
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 735 bits (1900), Expect = 0.0
Identities = 305/396 (77%), Positives = 332/396 (83%), Gaps = 11/396 (2%)
Query: 3 LSSHTQSGLSLSFHSTNSSPPSPTPPKTMIADDSISLQIDSSYCHSPNPMPSKPLQLLEE 62
LS QS LSL FHS PSP P IADDSI+LQIDSS+ S NPMP PLQLLE+
Sbjct: 1 LSRIAQSDLSLGFHS--HPSPSPAP----IADDSITLQIDSSFRSSSNPMPPIPLQLLEQ 54
Query: 63 RTEKLHSGNNDERVDKDDEQEEVEFSILGHPMCLKRQRD-----CQSLPFTKRFAVEPGL 117
+ EK + D++++ E+ FSILGHPMCLKR RD S +KR AV+ GL
Sbjct: 55 KEEKEEDAGEEGDEDEEEQGEDEHFSILGHPMCLKRPRDGDSSSSSSSSSSKRAAVDSGL 114
Query: 118 ESRRAGVRAWGNQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTN 177
ESRRA VRAWGNQ LP ADP+I ++MEKEKQRQFKGIELIASENFVCRAVMEALGSHLTN
Sbjct: 115 ESRRAAVRAWGNQPLPEADPDIHELMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTN 174
Query: 178 KYSEGYPGARYYTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGL 237
KYSEG PGARYYTGNQYIDQIE LC ERAL AF LDS+ WGVNVQPYSCTSANFAVYTGL
Sbjct: 175 KYSEGMPGARYYTGNQYIDQIERLCCERALAAFGLDSEKWGVNVQPYSCTSANFAVYTGL 234
Query: 238 LLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKA 297
LLPGDRIMGLDSPSGGH+SHGY+TPGGKKVS ASIFFES PYKVNPQTGYIDY+KLEEKA
Sbjct: 235 LLPGDRIMGLDSPSGGHMSHGYYTPGGKKVSGASIFFESLPYKVNPQTGYIDYDKLEEKA 294
Query: 298 MDYRPKILICGGSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDI 357
+D+RPKILICGGSSYPREWDY RFRQIADKCGAVLMCDMAHISGL+AAKE +PFDYCDI
Sbjct: 295 LDFRPKILICGGSSYPREWDYARFRQIADKCGAVLMCDMAHISGLVAAKECVNPFDYCDI 354
Query: 358 VTSTTHKSLRGPRGGIIFFRRGKKPRKQGIPLNHGD 393
VTSTTHKSLRGPRGGIIF+R+G K RKQG+ L+HGD
Sbjct: 355 VTSTTHKSLRGPRGGIIFYRKGPKLRKQGMLLSHGD 390
>gnl|CDD|215639 PLN03226, PLN03226, serine hydroxymethyltransferase; Provisional.
Length = 475
Score = 539 bits (1391), Expect = 0.0
Identities = 189/269 (70%), Positives = 219/269 (81%), Gaps = 1/269 (0%)
Query: 118 ESRRAGVRAWGNQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTN 177
E V WGN L DPEI DI+EKEK+RQ+KG+ELIASENF RAVMEALGS LTN
Sbjct: 1 EKSMVSVPKWGNAPLEEVDPEIADIIEKEKRRQWKGLELIASENFTSRAVMEALGSCLTN 60
Query: 178 KYSEGYPGARYYTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGL 237
KYSEG PGARYY GN+YIDQIE LC +RAL+AF LD + WGVNVQP S + ANFAVYT L
Sbjct: 61 KYSEGLPGARYYGGNEYIDQIETLCQKRALEAFRLDPEKWGVNVQPLSGSPANFAVYTAL 120
Query: 238 LLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKA 297
L P DRIMGLD P GGHLSHGY T GKK+SA SI+FES PY+++ TG IDY+KLE+KA
Sbjct: 121 LQPHDRIMGLDLPHGGHLSHGYQTD-GKKISATSIYFESMPYRLDESTGLIDYDKLEKKA 179
Query: 298 MDYRPKILICGGSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDI 357
M +RPK++I G S+YPR+WDY R R+IADK GA+LMCDMAHISGL+AA+E ASPF+YCD+
Sbjct: 180 MLFRPKLIIAGASAYPRDWDYARMRKIADKVGALLMCDMAHISGLVAAQEAASPFEYCDV 239
Query: 358 VTSTTHKSLRGPRGGIIFFRRGKKPRKQG 386
VT+TTHKSLRGPRGG+IFFR+G KP K
Sbjct: 240 VTTTTHKSLRGPRGGMIFFRKGPKPPKGQ 268
>gnl|CDD|240264 PTZ00094, PTZ00094, serine hydroxymethyltransferase; Provisional.
Length = 452
Score = 477 bits (1230), Expect = e-168
Identities = 166/255 (65%), Positives = 203/255 (79%), Gaps = 2/255 (0%)
Query: 128 GNQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGAR 187
NQSL ADPE+++++EKEK+RQ +G+ELIASENF RAV+E LGS TNKY+EG PG R
Sbjct: 11 LNQSLKEADPELYELIEKEKERQIEGLELIASENFTSRAVLECLGSCFTNKYAEGLPGNR 70
Query: 188 YYTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGL 247
YY GN+ +D+IENLC +RAL+AF LD + WGVNVQPYS + ANFAVYT LL P DRIMGL
Sbjct: 71 YYGGNEVVDKIENLCQKRALEAFGLDPEEWGVNVQPYSGSPANFAVYTALLQPHDRIMGL 130
Query: 248 DSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILIC 307
D PSGGHL+HG++T KKVSA SI+FES PY+VN + G IDY+KLEE A +RPK++I
Sbjct: 131 DLPSGGHLTHGFYT-AKKKVSATSIYFESLPYQVNEK-GLIDYDKLEELAKAFRPKLIIA 188
Query: 308 GGSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLR 367
G S+YPR+ DY RFR+I D GA LM D+AH SGL+AA L SPF Y D+VT+TTHKSLR
Sbjct: 189 GASAYPRDIDYKRFREICDSVGAYLMADIAHTSGLVAAGVLPSPFPYADVVTTTTHKSLR 248
Query: 368 GPRGGIIFFRRGKKP 382
GPR G+IF+R+ KP
Sbjct: 249 GPRSGLIFYRKKVKP 263
>gnl|CDD|189558 pfam00464, SHMT, Serine hydroxymethyltransferase.
Length = 380
Score = 414 bits (1066), Expect = e-144
Identities = 161/271 (59%), Positives = 196/271 (72%), Gaps = 21/271 (7%)
Query: 132 LPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARYYTG 191
L +DPEIFDI++KEK+RQ +GIELIASENF RAVMEALGS LTNKY+EGYPG RYY G
Sbjct: 1 LSDSDPEIFDIIKKEKERQREGIELIASENFTSRAVMEALGSVLTNKYAEGYPGKRYYGG 60
Query: 192 NQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDSPS 251
+Y+D++E L +RA + F LD GVNVQP S + AN AVYT LL PGDRIMGLD P
Sbjct: 61 CEYVDEVETLAQDRAKELFGLD----GVNVQPLSGSQANLAVYTALLNPGDRIMGLDLPH 116
Query: 252 GGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICGGSS 311
GGHL+HGY V+ + FFES PY V+P TG IDY++LE+ A ++PK+++ G S+
Sbjct: 117 GGHLTHGY------PVNFSGKFFESMPYGVDPDTGLIDYDQLEKNAKLFKPKLIVAGTSA 170
Query: 312 YPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRGPRG 371
Y R DY RFR+IAD+ GA LM DMAHI+GL+AA + SPF Y +VT+TTHK+LRGPRG
Sbjct: 171 YSRLIDYARFREIADEVGAYLMVDMAHIAGLVAAGVIPSPFPYAHVVTTTTHKTLRGPRG 230
Query: 372 GIIFFRRG-----KK------PRKQGIPLNH 391
G+IFFR KK P QG PLNH
Sbjct: 231 GMIFFREILYELEKKINSAVFPGLQGGPLNH 261
>gnl|CDD|99733 cd00378, SHMT, Serine-glycine hydroxymethyltransferase (SHMT). This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). SHMT
carries out interconversion of serine and glycine; it
catalyzes the transfer of hydroxymethyl group of N5,
N10-methylene tetrahydrofolate to glycine resulting in
the formation of serine and tetrahydrofolate. Both
eukaryotic and prokaryotic SHMT enzymes form tight
obligate homodimers; the mammalian enzyme forms a
homotetramer comprising four pyridoxal phosphate-bound
active sites.
Length = 402
Score = 406 bits (1046), Expect = e-141
Identities = 143/265 (53%), Positives = 185/265 (69%), Gaps = 17/265 (6%)
Query: 136 DPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARYYTGNQYI 195
DPEI +I++KE +RQ + +ELIASENF AVMEA+GS LTNKY+EGYPG RYY G +Y+
Sbjct: 4 DPEIAEIIKKENERQRETLELIASENFTSPAVMEAMGSDLTNKYAEGYPGKRYYGGCEYV 63
Query: 196 DQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDSPSGGHL 255
D+IE+L ERA K F + NVQP+S + AN AVY LL PGD IMGLD GGHL
Sbjct: 64 DEIEDLAIERAKKLFGAE----YANVQPHSGSQANLAVYFALLEPGDTIMGLDLSHGGHL 119
Query: 256 SHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICGGSSYPRE 315
+HG T KVSA+ FES PY V+P+TG IDY+ LE+ A++++PK+++ G S+YPR
Sbjct: 120 THGSFT----KVSASGKLFESVPYGVDPETGLIDYDALEKMALEFKPKLIVAGASAYPRP 175
Query: 316 WDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRGPRGGIIF 375
D+ RFR+IAD+ GA L+ DMAH++GL+A +P D+VT+TTHK+LRGPRGG+I
Sbjct: 176 IDFKRFREIADEVGAYLLVDMAHVAGLVAGGVFPNPLPGADVVTTTTHKTLRGPRGGLIL 235
Query: 376 FRRG---KK------PRKQGIPLNH 391
R+G KK P QG P H
Sbjct: 236 TRKGELAKKINSAVFPGLQGGPHLH 260
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 390 bits (1005), Expect = e-134
Identities = 134/272 (49%), Positives = 177/272 (65%), Gaps = 19/272 (6%)
Query: 129 NQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARY 188
+L DPEI D +E+E +RQ + IELIASENFV AVMEA GS LTNKY+EGYPG RY
Sbjct: 3 MDNLAEYDPEIADAIEQELKRQEEHIELIASENFVSPAVMEAQGSVLTNKYAEGYPGKRY 62
Query: 189 YTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLD 248
Y G +Y+D +E L +RA + F + NVQP+S + AN AVY LL PGD I+G+D
Sbjct: 63 YGGCEYVDVVEQLAIDRAKELFGAEY----ANVQPHSGSQANAAVYFALLKPGDTILGMD 118
Query: 249 SPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICG 308
GGHL+HG V+ + + Y V+ +TG IDY+++E+ A++++PK++I G
Sbjct: 119 LAHGGHLTHG------SPVNFSGKLYNVVSYGVDEETGLIDYDEVEKLALEHKPKLIIAG 172
Query: 309 GSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRG 368
S+Y R D+ RFR+IAD+ GA LM DMAHI+GL+AA SP + D+VT+TTHK+LRG
Sbjct: 173 ASAYSRPIDFKRFREIADEVGAYLMVDMAHIAGLVAAGVHPSPVPHADVVTTTTHKTLRG 232
Query: 369 PRGGIIFFRR---GKK------PRKQGIPLNH 391
PRGG+I KK P QG PL H
Sbjct: 233 PRGGLILTNDEELAKKINSAVFPGIQGGPLMH 264
>gnl|CDD|223190 COG0112, GlyA, Glycine/serine hydroxymethyltransferase [Amino acid
transport and metabolism].
Length = 413
Score = 386 bits (995), Expect = e-133
Identities = 139/271 (51%), Positives = 177/271 (65%), Gaps = 19/271 (7%)
Query: 130 QSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARYY 189
SL DPEIF+ +++E +RQ + IELIASENF AVMEA GS LTNKY+EGYPG RYY
Sbjct: 5 ASLADYDPEIFEAIQQELERQREHIELIASENFTSPAVMEAQGSDLTNKYAEGYPGKRYY 64
Query: 190 TGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDS 249
G +Y+D++E L ERA K F + NVQP+S + AN AVY LL PGD IMGLD
Sbjct: 65 GGCEYVDEVEELAIERAKKLFGAE----YANVQPHSGSQANQAVYLALLQPGDTIMGLDL 120
Query: 250 PSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICGG 309
GGHL+HG V+ + F Y V+P+TG IDY+++E+ A + +PK++I GG
Sbjct: 121 SHGGHLTHGS------PVNFSGKLFNVVSYGVDPETGLIDYDEVEKLAKEVKPKLIIAGG 174
Query: 310 SSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRGP 369
S+Y R D+ RFR+IAD+ GA LM DMAH++GLIA +P + D+VT+TTHK+LRGP
Sbjct: 175 SAYSRPIDFKRFREIADEVGAYLMVDMAHVAGLIAGGVHPNPLPHADVVTTTTHKTLRGP 234
Query: 370 RGGIIFFRR---GKK------PRKQGIPLNH 391
RGGII KK P QG PL H
Sbjct: 235 RGGIILTNDEELAKKINSAVFPGLQGGPLMH 265
>gnl|CDD|237280 PRK13034, PRK13034, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 345 bits (886), Expect = e-116
Identities = 136/272 (50%), Positives = 179/272 (65%), Gaps = 19/272 (6%)
Query: 129 NQSLPLADPEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARY 188
+ SL D E+F + KE +RQ +ELIASENF AVMEA GS LTNKY+EGYPG RY
Sbjct: 6 SDSLEEYDDEVFAAINKELERQQDHLELIASENFTSPAVMEAQGSVLTNKYAEGYPGKRY 65
Query: 189 YTGNQYIDQIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLD 248
Y G +++D++E L ERA + F D NVQP+S + AN AVY LL PGD I+G+
Sbjct: 66 YGGCEFVDEVEALAIERAKQLFGCDY----ANVQPHSGSQANGAVYLALLKPGDTILGMS 121
Query: 249 SPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILICG 308
GGHL+HG KVS + ++ + Y V+ TG IDY+++EE A +++PK++I G
Sbjct: 122 LSHGGHLTHG------AKVSLSGKWYNAVQYGVDRLTGLIDYDEVEELAKEHKPKLIIAG 175
Query: 309 GSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRG 368
S+YPRE D+ RFR+IAD+ GA+LM DMAHI+GL+AA E +PF + +VT+TTHK+LRG
Sbjct: 176 FSAYPRELDFARFREIADEVGALLMVDMAHIAGLVAAGEHPNPFPHAHVVTTTTHKTLRG 235
Query: 369 PRGGIIFFRR---GKK------PRKQGIPLNH 391
PRGG+I KK P QG PL H
Sbjct: 236 PRGGMILTNDEEIAKKINSAVFPGLQGGPLMH 267
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 226 bits (579), Expect = 2e-69
Identities = 100/273 (36%), Positives = 145/273 (53%), Gaps = 46/273 (16%)
Query: 137 PEIFDIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGYPGARYYTGNQYID 196
P I + + +E Q ++LIASEN+ AV A+G+ LT+KY+EG PG R+Y G Q +D
Sbjct: 35 PRIAEAIRQELADQRSSLKLIASENYSSLAVQLAMGNLLTDKYAEGTPGHRFYAGCQNVD 94
Query: 197 QIENLCFERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLL------------------ 238
+E E A + F + VQP+S AN + +L
Sbjct: 95 TVEWEAAEHAKELFGAEH----AYVQPHSGADANLVAFWAILAHKVESPALEKLGAKTVN 150
Query: 239 -------------LPGDRIMGLDSPSGGHLSHGY-HTPGGKKVSAASIFFESFPYKVNPQ 284
L R++G+ SGGHL+HG+ GK F Y V+P
Sbjct: 151 DLTEEDWEALRAELGNQRLLGMSLDSGGHLTHGFRPNISGK-------MFHQRSYGVDPD 203
Query: 285 TGYIDYEKLEEKAMDYRPKILICGGSSYPREWDYGRFRQIADKCGAVLMCDMAHISGLIA 344
TG +DY+++ A +++P IL+ G S+YPR ++ + R+IAD+ GAVLM DMAH +GL+A
Sbjct: 204 TGLLDYDEIAALAREFKPLILVAGYSAYPRRVNFAKLREIADEVGAVLMVDMAHFAGLVA 263
Query: 345 AKELASPFD---YCDIVTSTTHKSLRGPRGGII 374
K D + DIVT+TTHK+LRGPRGG++
Sbjct: 264 GKVFTGDEDPVPHADIVTTTTHKTLRGPRGGLV 296
>gnl|CDD|99742 cd01494, AAT_I, Aspartate aminotransferase (AAT) superfamily (fold
type I) of pyridoxal phosphate (PLP)-dependent enzymes.
PLP combines with an alpha-amino acid to form a compound
called a Schiff base or aldimine intermediate, which
depending on the reaction, is the substrate in four
kinds of reactions (1) transamination (movement of amino
groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
Structure and sequence analysis has revealed that the
PLP dependent enzymes can be classified into four major
groups of different evolutionary origin: aspartate
aminotransferase superfamily (fold type I), tryptophan
synthase beta superfamily (fold type II), alanine
racemase superfamily (fold type III), and D-amino acid
superfamily (fold type IV) and Glycogen phophorylase
family (fold type V).
Length = 170
Score = 96.3 bits (240), Expect = 1e-23
Identities = 43/178 (24%), Positives = 63/178 (35%), Gaps = 15/178 (8%)
Query: 203 FERALKAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTP 262
E L L N P S T AN A LL PGD ++ + G
Sbjct: 5 LEEKLARL-LQPGNDKAVFVP-SGTGANEAALLALLGPGDEVIVDANGHGSRYW------ 56
Query: 263 GGKKVSAASIFFESFPYKVNPQTGYIDYEKLEEKAMDYRPKILIC---GGSSYPREWDYG 319
V+A + P V+ + E+ LI +S
Sbjct: 57 ----VAAELAGAKPVPVPVDDAGYGGLDVAILEELKAKPNVALIVITPNTTSGGVLVPLK 112
Query: 320 RFRQIADKCGAVLMCDMAHISGLIAAKELASPFDYCDIVTSTTHKSLRGPRGGIIFFR 377
R+IA + G +L+ D A G A + P D+VT + HK+L G GG++ +
Sbjct: 113 EIRKIAKEYGILLLVDAASAGGASPAPGVLIPEGGADVVTFSLHKNLGGEGGGVVIVK 170
>gnl|CDD|216367 pfam01212, Beta_elim_lyase, Beta-eliminating lyase.
Length = 288
Score = 46.1 bits (110), Expect = 2e-05
Identities = 41/193 (21%), Positives = 58/193 (30%), Gaps = 44/193 (22%)
Query: 227 TSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTG 286
T AN GD ++ G +H Y G P + G
Sbjct: 57 TMANQLALMAHCRRGDEVIC------GEPAHIYFDETGGHAELGGAQPVPLP---GAEAG 107
Query: 287 YIDYEKLE----EKAMDYRPKI-LIC--------GGSSYPREWDYGRFRQIADKCGAVLM 333
+D E LE + P LI GG E R IA + G L
Sbjct: 108 KLDLEDLEAAIRPVGDIHFPPTGLISLENTHNSAGGQVVSLEE-LREIRAIAREHGIPLH 166
Query: 334 CDMAHI-----SGLIAAKELASPFDYCDIVTSTTHKSLRGPRGGIIFFRR---------- 378
D A + + + KE+ S Y D V+ + K L P G ++
Sbjct: 167 LDGARLANAAVALGVIVKEITS---YADSVSMSLSKGLGAPVGSVLAGSDDFIAYARRQR 223
Query: 379 ---GKKPRKQGIP 388
G R+ G+
Sbjct: 224 KYLGGGMRQAGVL 236
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 43.5 bits (103), Expect = 1e-04
Identities = 41/208 (19%), Positives = 67/208 (32%), Gaps = 34/208 (16%)
Query: 190 TGNQYIDQIENLCFERALKAFDLDSDNWG----VNVQPYSCTSANFAVYTGLL--LPGDR 243
T N Y AL F S V S AN LL PGD
Sbjct: 33 TRNLYGPTDGLPELREALAKFLGRSPVLKLDREAAVVFGSGAGANIEALIFLLRLNPGDA 92
Query: 244 IMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQTGYIDYEKLEE--KAMDYR 301
I+ + +P+ + + A +P ++D++ LE K
Sbjct: 93 IL-VPAPT-----YPSYIRI---FRLAGGEVVRYPLYS-SNDFHLDFDALEAALKEATEG 142
Query: 302 PK-ILICG-----GSSYPREWDYGRFRQIADKCGAVLMCDMAHI------SGLIAAKELA 349
K +L G+ E + + +A + +L+ D A+ +A + L
Sbjct: 143 NKVVLHTSPHNPTGTVATLE-ELEKLLDLAKEHNILLLVDEAYAGFVFGSLDAVATRALL 201
Query: 350 SPFDYCDIVTSTTHKS--LRGPRGGIIF 375
+ +V + K+ L G R G I
Sbjct: 202 AEGPN-LLVVGSFSKAFGLAGWRVGYIL 228
>gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The major groups in this CD
corresponds to serine palmitoyltransferase (SPT),
5-aminolevulinate synthase (ALAS),
8-amino-7-oxononanoate synthase (AONS), and
2-amino-3-ketobutyrate CoA ligase (KBL). SPT is
responsible for the condensation of L-serine with
palmitoyl-CoA to produce 3-ketodihydrospingosine, the
reaction of the first step in sphingolipid biosynthesis.
ALAS is involved in heme biosynthesis; it catalyzes the
synthesis of 5-aminolevulinic acid from glycine and
succinyl-coenzyme A. AONS catalyses the decarboxylative
condensation of l-alanine and pimeloyl-CoA in the first
committed step of biotin biosynthesis. KBL catalyzes the
second reaction step of the metabolic degradation
pathway for threonine converting 2-amino-3-ketobutyrate,
to glycine and acetyl-CoA. The members of this CD are
widely found in all three forms of life.
Length = 349
Score = 42.2 bits (100), Expect = 3e-04
Identities = 44/162 (27%), Positives = 61/162 (37%), Gaps = 29/162 (17%)
Query: 225 SCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQ 284
S +AN V + L GD I+ S S H S G ++S A +K N
Sbjct: 69 SGYAANDGVLSTLAGKGDLII---SDSLNHAS----IIDGIRLSGAKK----RIFKHN-- 115
Query: 285 TGYIDYEKLEEKAMDYR---PKILICGGSSYPREWDYGRFRQI---ADKCGAVLMCDMAH 338
D E LE+ + R K LI Y + D ++ A K GA+L D AH
Sbjct: 116 ----DMEDLEKLLREARRPYGKKLIVTEGVYSMDGDIAPLPELVDLAKKYGAILFVDEAH 171
Query: 339 ISGLI--AAKELASPFDYC---DIVTSTTHKSLRGPRGGIIF 375
G+ + + DI+ T K+ G GG I
Sbjct: 172 SVGVYGPHGRGVEEFGGLTDDVDIIMGTLGKAF-GAVGGYIA 212
>gnl|CDD|130881 TIGR01822, 2am3keto_CoA, 2-amino-3-ketobutyrate coenzyme A ligase.
This model represents a narrowly defined clade of animal
and bacterial (almost exclusively Proteobacterial)
2-amino-3-ketobutyrate--CoA ligase. This enzyme can act
in threonine catabolism. The closest homolog from
Bacillus subtilis, and sequences like it, may be
functionally equivalent but were not included in the
model because of difficulty in finding reports of
function [Energy metabolism, Amino acids and amines].
Length = 393
Score = 38.6 bits (90), Expect = 0.004
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 322 RQIADKCGAVLMCDMAHISGLIAAK-----ELASPFDYCDIVTSTTHKSLRGPRGGIIFF 376
+ADK A++M D H +G + EL DI+T T K+L G GG F
Sbjct: 193 CDLADKYDALVMVDECHATGFLGPTGRGSHELCGVMGRVDIITGTLGKALGGASGG---F 249
Query: 377 RRGKKP 382
+K
Sbjct: 250 TTARKE 255
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 37.7 bits (88), Expect = 0.010
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 15/65 (23%)
Query: 322 RQIADKC---GAVLMCDMAHISGLIAAKELASPFD----YCDIVTSTTHKSLRGPRG-GI 373
++IA+ GA+++ D A +G + P D CD + + HK L GP G G+
Sbjct: 182 KEIAELAHEHGALVLVDAAQAAGHL-------PIDVQELGCDFLAFSGHKWLLGPTGIGV 234
Query: 374 IFFRR 378
++ R+
Sbjct: 235 LYVRK 239
>gnl|CDD|235893 PRK06939, PRK06939, 2-amino-3-ketobutyrate coenzyme A ligase;
Provisional.
Length = 397
Score = 35.6 bits (83), Expect = 0.042
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 324 IADKCGAVLMCDMAHISGLIAAKELASPFDYC------DIVTSTTHKSLRGPRGGIIFFR 377
+ADK A++M D +H G + + ++ DI+T T K+L G GG +
Sbjct: 199 LADKYDALVMVDDSHAVGFVGENGRGTV-EHFGVMDRVDIITGTLGKALGGASGG---YT 254
Query: 378 RGKKP 382
G+K
Sbjct: 255 AGRKE 259
>gnl|CDD|215829 pfam00266, Aminotran_5, Aminotransferase class-V. This domain is
found in amino transferases, and other enzymes including
cysteine desulphurase EC:4.4.1.-.
Length = 370
Score = 35.3 bits (82), Expect = 0.046
Identities = 29/106 (27%), Positives = 48/106 (45%), Gaps = 17/106 (16%)
Query: 280 KVNPQTGYIDYEKLEEKAMDYRPKIL-ICGGSS-YPREWDYGRFRQIADKCGAVLMCDMA 337
V+P G +D + LE K + R K++ I S+ ++A + GA+++ D A
Sbjct: 120 PVDPN-GLLDLDALE-KLLTPRTKLVAITHVSNVTGTVNPVEEIGKLAHEYGALVVVDAA 177
Query: 338 ----HISGLIAAKELASPFDYCDIVTSTTHKSLRGPRG-GIIFFRR 378
H I + L D + + HK L GP G G+++ RR
Sbjct: 178 QAVGHRP--IDVQALG-----VDFLAFSGHK-LYGPTGIGVLYGRR 215
>gnl|CDD|237957 PRK15401, PRK15401, alpha-ketoglutarate-dependent dioxygenase AlkB;
Provisional.
Length = 213
Score = 33.3 bits (77), Expect = 0.13
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 5/26 (19%)
Query: 371 GGIIFFRRGKKPRKQGIPLNHGDVVV 396
GG +R ++ I L HGDVVV
Sbjct: 158 GG---LKRSDPLQR--ILLEHGDVVV 178
>gnl|CDD|224832 COG1921, SelA, Selenocysteine synthase [seryl-tRNASer selenium
transferase] [Amino acid transport and metabolism].
Length = 395
Score = 33.1 bits (76), Expect = 0.25
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 14/67 (20%)
Query: 321 FRQIADKCGAVLMCDMAHISGLIAAKE------LASPFDYCDIVTSTTHKSLRGPRGGII 374
+IA + G ++ D+A SG + KE LA D+V+ + K L GP+ GII
Sbjct: 179 LVEIAHEKGLPVIVDLA--SGALVDKEPDLREALALG---ADLVSFSGDKLLGGPQAGII 233
Query: 375 FFRRGKK 381
GKK
Sbjct: 234 V---GKK 237
>gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Pyridoxal
phosphate combines with an alpha-amino acid to form a
compound called a Schiff base or aldimine intermediate,
which depending on the reaction, is the substrate in
four kinds of reactions (1) transamination (movement of
amino groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
The major groups in this CD corresponds to Aspartate
aminotransferase a, b and c, Tyrosine, Alanine,
Aromatic-amino-acid, Glutamine phenylpyruvate,
1-Aminocyclopropane-1-carboxylate synthase,
Histidinol-phosphate, gene products of malY and cobC,
Valine-pyruvate aminotransferase and Rhizopine
catabolism regulatory protein.
Length = 350
Score = 32.3 bits (74), Expect = 0.36
Identities = 23/124 (18%), Positives = 47/124 (37%), Gaps = 26/124 (20%)
Query: 226 CTSANFAVYTGLLLPGDRIMGLDSPS-GGHLSHGYHTPGGKKVSAASIFFESFPYKVNPQ 284
A + LL PGD ++ + P+ G+ + +A E P ++ +
Sbjct: 68 AQEALSLLLRALLNPGDEVL-VPDPTYPGYEA-----------AARLAGAEVVPVPLDEE 115
Query: 285 TGYIDYEKLEEKAMDYRPKILICG------GSSYPREWDYGRFRQIADKC---GAVLMCD 335
G++ +L E A + K+L G+ E ++A+ G +++ D
Sbjct: 116 GGFLLDLELLEAAKTPKTKLLYLNNPNNPTGAVLSEE----ELEELAELAKKHGILIISD 171
Query: 336 MAHI 339
A+
Sbjct: 172 EAYA 175
>gnl|CDD|182180 PRK09981, PRK09981, hypothetical protein; Provisional.
Length = 99
Score = 30.3 bits (68), Expect = 0.50
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 101 DCQSLPFTKRFAVEPGLESRRAGVRAWGNQSLPLADPEI--FDIMEKEKQRQFKGIELIA 158
+C S F++ FA ES ++ + + + I + E Q +EL A
Sbjct: 25 NCTSK-FSRFFATREEAESFMTKLKELAAAASSADEGASVAYKIKDLEGQ-----VELDA 78
Query: 159 SENFVCRAVM 168
+ F C+A M
Sbjct: 79 AFTFSCQAEM 88
>gnl|CDD|132318 TIGR03275, methan_mark_8, putative methanogenesis marker protein 8.
Members of this protein family, to date, are found in a
completed prokaryotic genome if and only if the species
is one of the archaeal methanogens. The exact function
is unknown, but likely is linked to methanogenesis or a
process closely connected to it.
Length = 259
Score = 31.6 bits (72), Expect = 0.67
Identities = 28/111 (25%), Positives = 47/111 (42%), Gaps = 13/111 (11%)
Query: 281 VNPQTGYIDYEKLEEKA--MDYRPKILICGGSSYPREWDYGRFRQIADKCGAVLMCDMAH 338
++P T ID K EKA + Y+ KI + + E D R++ + G ++ H
Sbjct: 142 LDPDTATIDQIKGVEKAIELGYK-KIAV---TVADAE-DAKAIRELESESGIDIIIFAVH 196
Query: 339 ISGLIAAKELASPFDYCDIVTSTTHKSLRGPRGGIIFFRRGKKPRKQGIPL 389
+G I ++ Y DIVTS K++R + G +P+
Sbjct: 197 TTG-IDREDAEEVVQYADIVTSCASKNIREIAKPRALLQVGS-----AVPV 241
>gnl|CDD|100122 cd06225, HAMP, Histidine kinase, Adenylyl cyclase,
Methyl-accepting protein, and Phosphatase (HAMP)
domain. HAMP is a signaling domain which occurs in a
wide variety of signaling proteins, many of which are
bacterial. The HAMP domain consists of two alpha
helices connected by an extended linker. The structure
of the HAMP dimer from Archaeoglobus fulgidus has been
solved using nuclear magnetic resonance, revealing a
parallel four-helix bundle; this structure has been
confirmed by cross-linking analysis of HAMP domains
from the Escherichia coli aerotaxis receptor Aer. It
has been suggested that the four-helix arrangement can
rotate between the unusually packed conformation
observed in the NMR structure and a canonical
coiled-coil arrangement. Such rotation may coincide
with signal transduction, but a common mechanism by
which HAMP domains relay a variety of input signals has
yet to be established.
Length = 48
Score = 28.4 bits (64), Expect = 0.81
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 54 SKPLQLLEERTEKLHSGNNDERVDKDDEQE 83
+PL+ L E +++ +G+ D R+ E
Sbjct: 2 LRPLRRLAEAAQRIAAGDLDVRLPVTGRDE 31
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 31.1 bits (71), Expect = 1.1
Identities = 41/170 (24%), Positives = 62/170 (36%), Gaps = 45/170 (26%)
Query: 225 SCTSANFAVYTGLLLPGDRIMGLDSPSGGHLSHGYHTPGGKKVSAASIFF-------ESF 277
S AN + + LL GD I S +++ ASI E
Sbjct: 107 SGFVANLGLLSALLKKGDLI----------FSD--------ELNHASIIDGIRLSRAEVR 148
Query: 278 PYKVNPQTGYIDYEKLEEKAMDYR-----PKILICGG--SSYPREWDYGRFRQIADKCGA 330
+K N D + LE + R K+++ G S ++A+K GA
Sbjct: 149 RFKHN------DLDHLEALLEEARENGARRKLIVTEGVFSMDGDIAPLPELVELAEKYGA 202
Query: 331 VLMCDMAHISGLIA------AKELASPFDYCDIVTSTTHKSLRGPRGGII 374
+L D AH G++ A+ + DI+ T K+L G GG I
Sbjct: 203 LLYVDEAHAVGVLGPNGRGLAEHFGLEPEEVDIIVGTLGKAL-GSSGGYI 251
>gnl|CDD|131032 TIGR01977, am_tr_V_EF2568, cysteine desulfurase family protein.
This model describes a subfamily of probable pyridoxal
phosphate-dependent enzymes in the aminotransferase
class V family. Related families contain members active
as cysteine desulfurases, selenocysteine lyases, or
both. The members of this family form a distinct clade
and all are shorter at the N-terminus. The function of
this subfamily is unknown [Unknown function, Enzymes of
unknown specificity].
Length = 376
Score = 30.4 bits (69), Expect = 1.5
Identities = 28/107 (26%), Positives = 46/107 (42%), Gaps = 19/107 (17%)
Query: 284 QTGYIDYEKLEEKAMDYRPKILICG------GSSYPREWDYGRFRQIADKCGAVLMCDMA 337
G I E+++ K+++ G+ P E ++A + G + D A
Sbjct: 121 NEGLISPERIKRAIKT-NTKLIVVSHASNVTGTILPIE----EIGELAQENGIFFILDAA 175
Query: 338 HISGL--IAAKELASPFDYCDIVTSTTHKSLRGPRG-GIIFFRRGKK 381
+G+ I ELA D++ T HK L GP+G G ++ R G K
Sbjct: 176 QTAGVIPIDMTELA-----IDMLAFTGHKGLLGPQGTGGLYIREGIK 217
>gnl|CDD|99964 cd03789, GT1_LPS_heptosyltransferase, Lipopolysaccharide
heptosyltransferase is involved in the biosynthesis of
lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a
major component of the outer membrane of gram-negative
bacteria. LPS heptosyltransferase transfers heptose
molecules from ADP-heptose to
3-deoxy-D-manno-octulosonic acid (KDO), a part of the
inner core component of LPS. This family belongs to the
GT-B structural superfamily of glycoslytransferases,
which have characteristic N- and C-terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two
domains includes the catalytic center and permits a high
degree of flexibility.
Length = 279
Score = 30.3 bits (69), Expect = 1.8
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 9/64 (14%)
Query: 301 RPKILICGGSSYP-REWDYGRFRQIADKCGA-----VLMC---DMAHISGLIAAKELASP 351
+P +++ G+S P + W RF +AD+ A VL + + AA
Sbjct: 121 KPVVVLPPGASGPAKRWPAERFAALADRLLARGARVVLTGGPAERELAEEIAAALGGPRV 180
Query: 352 FDYC 355
+
Sbjct: 181 VNLA 184
>gnl|CDD|224919 COG2008, GLY1, Threonine aldolase [Amino acid transport and
metabolism].
Length = 342
Score = 30.3 bits (69), Expect = 1.9
Identities = 26/110 (23%), Positives = 40/110 (36%), Gaps = 20/110 (18%)
Query: 285 TGYIDYEKLEEKAM----DYRPKILIC-------GGSSYPREWDYGRFRQIADKCGAVLM 333
G + E +E + P L GG+ YP + + + + G L
Sbjct: 109 DGKLTPEDVEAAIRPDDIHHAPTPLAVLENTATEGGTVYPLD-ELEAISAVCKEHGLPLH 167
Query: 334 CDMAHI-SGLIA----AKELASPFDYCDIVTSTTHKSLRGPRGGIIFFRR 378
D A + + L+A K + S Y D V+ K P G I+F R
Sbjct: 168 MDGARLANALVALGVALKTIKS---YVDSVSFCLTKGGGAPVGAIVFGNR 214
>gnl|CDD|130884 TIGR01825, gly_Cac_T_rel, pyridoxal phosphate-dependent
acyltransferase, putative. This model represents an
enzyme subfamily related to three known enzymes; it
appears closest to glycine C-acteyltransferase, shows no
overlap with it in species distribution, and may share
that function. The three closely related enzymes are
glycine C-acetyltransferase (2-amino-3-ketobutyrate
coenzyme A ligase), 5-aminolevulinic acid synthase, and
8-amino-7-oxononanoate synthase. All transfer the
R-group (acetyl, succinyl, or 6-carboxyhexanoyl) from
coenzyme A to an amino acid (Gly, Gly, Ala,
respectively), with release of CO2 for the latter two
reactions.
Length = 385
Score = 29.8 bits (67), Expect = 2.9
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 289 DYEKLEEKAMDYRPKILICGGSSYPREWDYGRFRQI---ADKCGAVLMCDMAHISGLIAA 345
D +++ + Y K+++ G + + D +I A++ GAV D AH SG++
Sbjct: 151 DLDRVLRENPSYGKKLIVTDGV-FSMDGDVAPLPEIVELAERYGAVTYVDDAHGSGVMGE 209
Query: 346 K 346
Sbjct: 210 A 210
>gnl|CDD|217931 pfam04153, NOT2_3_5, NOT2 / NOT3 / NOT5 family. NOT1, NOT2,
NOT3, NOT4 and NOT5 form a nuclear complex that
negatively regulates the basal and activated
transcription of many genes. This family includes NOT2,
NOT3 and NOT5.
Length = 131
Score = 28.5 bits (64), Expect = 3.1
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 8/57 (14%)
Query: 11 LSLSFHSTNSSPPSPTPPKTMIADDSISLQIDSSYCHSPNPMPSKPLQLLEERTEKL 67
L SF S PPSP+ + I Y ++P+ P P L + +K
Sbjct: 1 LHPSFAS----PPSPSDA----RERPPQYDIPECYLNTPSSYPQNPPPLSPSKFQKF 49
>gnl|CDD|233705 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin is
an insoluble storage polymer for carbon, nitrogen, and
energy, found in most Cyanobacteria. The polymer has a
backbone of L-aspartic acid, with most Asp side chain
carboxyl groups attached to L-arginine. The polymer is
made by this enzyme, cyanophycin synthetase, and
degraded by cyanophycinase. Heterologously expressed
cyanophycin synthetase in E. coli produces a closely
related, water-soluble polymer with some Arg replaced by
Lys. It is unclear whether enzymes that produce soluble
cyanophycin-like polymers in vivo in non-Cyanobacterial
species should be designated as cyanophycin synthetase
itself or as a related enzyme. This model makes the
designation as cyanophycin synthetase. Cyanophycin
synthesis is analogous to polyhydroxyalkanoic acid (PHA)
biosynthesis, except that PHA polymers lack nitrogen and
may be made under nitrogen-limiting conditions [Cellular
processes, Biosynthesis of natural products].
Length = 864
Score = 29.7 bits (67), Expect = 3.3
Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 7/50 (14%)
Query: 356 DIVTSTTHKSLRGPRGGII------FFRRGKKPRKQGIPLNHGDVVVIMI 399
DIVT + LR G I+ R P QG P N +V M+
Sbjct: 422 DIVTEDISRPLRDTDGAIVEVNAAPGLRMHLAP-SQGKPRNVARAIVDML 470
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 27.2 bits (61), Expect = 3.9
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 312 YPREWDYGRFRQIADKCGAVLMC 334
P E+ +FR++ GAV C
Sbjct: 7 LPLEFTDEQFRELVSPFGAVERC 29
>gnl|CDD|218332 pfam04929, Herpes_DNAp_acc, Herpes DNA replication accessory
factor. Replicative DNA polymerases are capable of
polymerising tens of thousands of nucleotides without
dissociating from their DNA templates. The high
processivity of these polymerases is dependent upon
accessory proteins that bind to the catalytic subunit of
the polymerase or to the substrate. The Epstein-Barr
virus (EBV) BMRF1 protein is an essential component of
the viral DNA polymerase and is absolutely required for
lytic virus replication. BMRF1 is also a transactivator.
This family is predicted to have a UL42 like structure.
Length = 381
Score = 29.3 bits (66), Expect = 4.5
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 19 NSSPPSPTPPKTMIADDSISLQIDSSYCHSPNPMPSKPLQLLEER 63
SS SP+PP T +D S +S HSP +PL L +R
Sbjct: 313 LSSDSSPSPPDTSDSDPSTETPPPASLSHSPPAAFERPLALSPKR 357
>gnl|CDD|240359 PTZ00324, PTZ00324, glutamate dehydrogenase 2; Provisional.
Length = 1002
Score = 29.0 bits (65), Expect = 5.4
Identities = 21/93 (22%), Positives = 32/93 (34%), Gaps = 3/93 (3%)
Query: 149 RQFKGIELIAS-ENFVCRAVMEALGSHLTNKYSEGYPGARYYTGNQYIDQIENLCFERAL 207
E+IA + + A GS + E A Y ++ CF R+
Sbjct: 81 FNTSQAEMIAHNQGSLTAAKRLREGSG-FEYFHENDGTAFYICRASPQKRLRMQCF-RST 138
Query: 208 KAFDLDSDNWGVNVQPYSCTSANFAVYTGLLLP 240
D GV ++ Y FA+YT + P
Sbjct: 139 FVSFNDDPKLGVRLRLYFLQDPVFAIYTASIEP 171
>gnl|CDD|130393 TIGR01326, OAH_OAS_sulfhy, OAH/OAS sulfhydrylase. This model
describes a distinct clade of the Cys/Met metabolism
pyridoxal phosphate-dependent enzyme superfamily.
Members include examples of OAH/OAS sulfhydrylase, an
enzyme with activity both as O-acetylhomoserine (OAH)
sulfhydrylase (EC 2.5.1.49) and O-acetylserine (OAS)
sulphydrylase (EC 2.5.1.47). An alternate name for OAH
sulfhydrylase is homocysteine synthase. This model is
designated subfamily because it may or may not have both
activities [Amino acid biosynthesis, Aspartate family,
Amino acid biosynthesis, Serine family].
Length = 418
Score = 28.9 bits (65), Expect = 5.5
Identities = 23/86 (26%), Positives = 32/86 (37%), Gaps = 11/86 (12%)
Query: 295 EKAMDYRPKILICGGSSYPRE--WDYGRFRQIADKCGAVLMCDMAHISGLIAAKELASPF 352
EKA+D K + P D ++A G L+ D A L P
Sbjct: 136 EKAIDENTKAVFAETIGNPAINVPDIEAIAEVAHAHGVPLIVD-----NTFATPYLCRPI 190
Query: 353 DY-CDIVTSTTHKSLRG---PRGGII 374
D+ DIV + K + G GG+I
Sbjct: 191 DHGADIVVHSATKYIGGHGTAIGGVI 216
>gnl|CDD|178697 PLN03152, PLN03152, hypothetical protein; Provisional.
Length = 241
Score = 28.7 bits (64), Expect = 5.6
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 11 LSLSFHSTNSSPPSPTPPKTMIA 33
LSLS H N P+P PK +
Sbjct: 6 LSLSPHPPNPQNPNPRKPKPLSR 28
>gnl|CDD|216285 pfam01075, Glyco_transf_9, Glycosyltransferase family 9
(heptosyltransferase). Members of this family belong to
glycosyltransferase family 9. Lipopolysaccharide is a
major component of the outer leaflet of the outer
membrane in Gram-negative bacteria. It is composed of
three domains; lipid A, Core oligosaccharide and the
O-antigen. All of these enzymes transfer heptose to the
lipopolysaccharide core.
Length = 249
Score = 28.4 bits (64), Expect = 5.9
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 6/40 (15%)
Query: 301 RPKILICGGSSYPRE-WDYGRFRQIADK-----CGAVLMC 334
RP I C G+S P + W F ++A VL
Sbjct: 107 RPYIAFCPGASRPAKRWPAEHFAELAQALQERGWQVVLFG 146
>gnl|CDD|150532 pfam09872, DUF2099, Uncharacterized protein conserved in archaea
(DUF2099). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 257
Score = 28.0 bits (63), Expect = 7.8
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 337 AHISGLIAAKELASPFDYCDIVTSTTHKSLRG 368
H +G I+ +E Y DIVT+ K +R
Sbjct: 194 VHTTG-ISREEAERLVKYADIVTACASKYIRE 224
>gnl|CDD|223476 COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme
apparently involved in regulation of cell wall
biogenesis [Cell envelope biogenesis, outer membrane].
Length = 374
Score = 28.4 bits (64), Expect = 8.0
Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 10/62 (16%)
Query: 281 VNPQTGYIDYEKLEEKAMDYRPKILIC----GGSSYPREWDYGRFRQIADKCGAVLMCDM 336
++P T ID + +E R K +I G D +A + G ++ D
Sbjct: 103 IDPDTLNIDPDLIEAAITP-RTKAIIPVHLAGQPC-----DMDAIMALAKRHGLPVIEDA 156
Query: 337 AH 338
A
Sbjct: 157 AQ 158
>gnl|CDD|222549 pfam14111, DUF4283, Domain of unknown function (DUF4283). This
domain family is found in plants, and is approximately
100 amino acids in length. Considering the very diverse
range of other domains it is associated with it is
possible that this domain is a binding/guiding region.
There are two highly conserved tryptophan residues.
Length = 153
Score = 27.6 bits (62), Expect = 8.4
Identities = 5/21 (23%), Positives = 8/21 (38%)
Query: 316 WDYGRFRQIADKCGAVLMCDM 336
W ++I CG + D
Sbjct: 117 WSEEILKRIGSACGGFVAVDE 137
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 0.136 0.414
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,981,162
Number of extensions: 2041591
Number of successful extensions: 1818
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1797
Number of HSP's successfully gapped: 47
Length of query: 403
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 304
Effective length of database: 6,546,556
Effective search space: 1990153024
Effective search space used: 1990153024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.8 bits)