RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2355
(452 letters)
>gnl|CDD|240299 PTZ00164, PTZ00164, bifunctional dihydrofolate
reductase-thymidylate synthase; Provisional.
Length = 514
Score = 449 bits (1158), Expect = e-155
Identities = 150/216 (69%), Positives = 177/216 (81%), Gaps = 1/216 (0%)
Query: 74 EQQYLHLLDKIIKTGHKKSDRTGVGTLSLFGAQMRFDLTNGTFPLLTTKRVFWKGVVEEL 133
E QYL L+ IIK G+ K DRTGVGT+S FG QMRFDL +FPLLTTK+VF +G++EEL
Sbjct: 231 EFQYLDLIADIIKNGNVKEDRTGVGTISKFGYQMRFDLRE-SFPLLTTKKVFLRGIIEEL 289
Query: 134 LWFIKGSTNAKELSDKGVKIWDPNSTREYLDSIGLVDRKEGDLGPVYGFQWRHYGAEYKD 193
LWFI+G TN L DKGV+IW+ N +RE+LDS GL R+E DLGPVYGFQWRH+GAEYKD
Sbjct: 290 LWFIRGETNGNLLLDKGVRIWEGNGSREFLDSRGLTHREENDLGPVYGFQWRHFGAEYKD 349
Query: 194 MFTDYTDQGIDQLQNIINTIKTNPNDRRIIMCAWNPIDMPKMALPPCHCLAQFYVADGKL 253
M DYT QG+DQL+NII TIK NP+DRR+I+ AWNP + +MALPPCH L+QFYV DGKL
Sbjct: 350 MHDDYTGQGVDQLKNIIETIKNNPDDRRLILTAWNPSALDQMALPPCHLLSQFYVNDGKL 409
Query: 254 SCQLYQRSADMGLGVPFNIASYSLLTYMIAHVTGLQ 289
SC +YQRS DMGLGVPFNIASY+LLT+MIA V GL+
Sbjct: 410 SCMMYQRSCDMGLGVPFNIASYALLTHMIAQVCGLR 445
>gnl|CDD|215846 pfam00303, Thymidylat_synt, Thymidylate synthase.
Length = 262
Score = 351 bits (903), Expect = e-120
Identities = 139/216 (64%), Positives = 157/216 (72%), Gaps = 23/216 (10%)
Query: 74 EQQYLHLLDKIIKTGHKKSDRTGVGTLSLFGAQMRFDLTNGTFPLLTTKRVFWKGVVEEL 133
E+QYL LL I++ G K DRTG GT SLFG Q+RFDL G FPLLTTK+VFWK VVEEL
Sbjct: 1 EEQYLDLLRDILENGEFKEDRTGTGTKSLFGVQLRFDLRKG-FPLLTTKKVFWKSVVEEL 59
Query: 134 LWFIKGSTNAKELSDKGVKIWDPNSTREYLDSIGLVDRKEGDLGPVYGFQWRHYGAEYKD 193
LWF+ GSTN K LS+ GV IWD ++ E GDLGPVYGFQWRH+GAE
Sbjct: 60 LWFLSGSTNVKFLSEYGVHIWDEWASEE------------GDLGPVYGFQWRHWGAE--- 104
Query: 194 MFTDYTDQGIDQLQNIINTIKTNPNDRRIIMCAWNPIDMPKMALPPCHCLAQFYVADGKL 253
QG+DQL +I +K NP+ RRII+ AWNP D+PKMALPPCH L QFYV DGKL
Sbjct: 105 -------QGVDQLARVIEKLKNNPDSRRIIISAWNPADLPKMALPPCHTLFQFYVRDGKL 157
Query: 254 SCQLYQRSADMGLGVPFNIASYSLLTYMIAHVTGLQ 289
SCQLYQRS DM LGVPFNIASY+LLT MIA VTGL+
Sbjct: 158 SCQLYQRSNDMFLGVPFNIASYALLTEMIAQVTGLE 193
>gnl|CDD|234984 PRK01827, thyA, thymidylate synthase; Reviewed.
Length = 264
Score = 339 bits (873), Expect = e-116
Identities = 126/216 (58%), Positives = 154/216 (71%), Gaps = 21/216 (9%)
Query: 74 EQQYLHLLDKIIKTGHKKSDRTGVGTLSLFGAQMRFDLTNGTFPLLTTKRVFWKGVVEEL 133
+QYL LL KI+ G KK+DRTG GTLS+FGAQMRFDL+ G FPLLTTK+V +K ++ EL
Sbjct: 1 MKQYLDLLRKILDEGTKKNDRTGTGTLSVFGAQMRFDLSKG-FPLLTTKKVHFKSIIHEL 59
Query: 134 LWFIKGSTNAKELSDKGVKIWDPNSTREYLDSIGLVDRKEGDLGPVYGFQWRHYGAEYKD 193
LWF++G TN L + GV IWD E+ D + GDLGPVYG QWR +
Sbjct: 60 LWFLRGDTNIAYLQENGVHIWD-----EWAD-------ENGDLGPVYGKQWRSWPT---- 103
Query: 194 MFTDYTDQGIDQLQNIINTIKTNPNDRRIIMCAWNPIDMPKMALPPCHCLAQFYVADGKL 253
+ IDQ+ +I +KTNP+ RR+I+ AWNP ++ KMALPPCH L QFYVADGKL
Sbjct: 104 ----PDGRHIDQISKVIEQLKTNPDSRRLIVSAWNPGELDKMALPPCHALFQFYVADGKL 159
Query: 254 SCQLYQRSADMGLGVPFNIASYSLLTYMIAHVTGLQ 289
SCQLYQRSAD+ LGVPFNIASY+LLT+MIA TGL+
Sbjct: 160 SCQLYQRSADVFLGVPFNIASYALLTHMIAQQTGLK 195
>gnl|CDD|238211 cd00351, TS_Pyrimidine_HMase, Thymidylate synthase and pyrimidine
hydroxymethylase: Thymidylate synthase (TS) and
deoxycytidylate hydroxymethylase (dCMP-HMase) are
homologs that catalyze analogous alkylation of C5 of
pyrimidine nucleotides. Both enzymes are involved in the
biosynthesis of DNA precursors and are active as
homodimers. However, they exhibit distinct pyrimidine
base specificities and differ in the details of their
catalyzed reactions. TS is biologically ubiquitous and
catalyzes the conversion of dUMP and
methylene-tetrahydrofolate (CH2THF) to dTMP and
dihydrofolate (DHF). It also acts as a regulator of its
own expression by binding and inactivating its own RNA.
Due to its key role in the de novo pathway for
thymidylate synthesis and, hence, DNA synthesis, it is
one of the most conserved enzymes across species and
phyla. TS is a well-recognized target for anticancer
chemotherapy, as well as a valuable new target against
infectious diseases. Interestingly, in several protozoa,
a single polypeptide chain codes for both, dihydrofolate
reductase (DHFR) and thymidylate synthase (TS), forming
a bifunctional enzyme (DHFR-TS), possibly through gene
fusion at a single evolutionary point. DHFR-TS is also
active as a dimer. Virus encoded dCMP-HMase catalyzes
the reversible conversion of dCMP and CH2THF to
hydroxymethyl-dCMP and THF. This family also includes
dUMP hydroxymethylase, which is encoded by several
bacteriophages that infect Bacillus subtilis, for their
own protection against the host restriction system, and
contain hydroxymethyl-dUMP instead of dTMP in their DNA.
Length = 215
Score = 308 bits (790), Expect = e-104
Identities = 124/215 (57%), Positives = 147/215 (68%), Gaps = 23/215 (10%)
Query: 76 QYLHLLDKIIKTG-HKKSDRTGVGTLSLFGAQMRFDLTNGTFPLLTTKRVFWKGVVEELL 134
QYL L KI++ G K DRTG GT SLFGAQ+RFDL+ G FPLLTTK+V WK +EELL
Sbjct: 1 QYLDLWRKILEEGYRKTDDRTGTGTRSLFGAQLRFDLSEG-FPLLTTKKVPWKSAIEELL 59
Query: 135 WFIKGSTNAKELSDKGVKIWDPNSTREYLDSIGLVDRKEGDLGPVYGFQWRHYGAEYKDM 194
WF++G TNA+ L + GV IWD + KEGDLG YGFQWRH+GA
Sbjct: 60 WFLRGDTNAERLKEYGVSIWDEWA------------SKEGDLGYTYGFQWRHWGAP---- 103
Query: 195 FTDYTDQGIDQLQNIINTIKTNPNDRRIIMCAWNPIDMPKMALPPCHCLAQFYVADGKLS 254
QG+DQ++ +I +K NP+ RR I+ AWNP D+ MALPPCH L QFYV +GKLS
Sbjct: 104 -----GQGVDQIEKVIEKLKNNPDSRRAIISAWNPADLDLMALPPCHTLIQFYVRNGKLS 158
Query: 255 CQLYQRSADMGLGVPFNIASYSLLTYMIAHVTGLQ 289
LYQRS D LGVPFNIASY+LLT MIA VTGL+
Sbjct: 159 LTLYQRSNDAFLGVPFNIASYALLTEMIARVTGLE 193
>gnl|CDD|213790 TIGR03284, thym_sym, thymidylate synthase. Members of this protein
family are thymidylate synthase, an enzyme that produces
dTMP from dUMP. In prokaryotes, its gene usually is
found close to that for dihydrofolate reductase, and in
some systems the two enzymes are found as a fusion
protein. This model excludes a set of related proteins
(TIGR03283) that appears to replace this family in
archaeal methanogens, where tetrahydrofolate is replaced
by tetrahydromethanopterin [Purines, pyrimidines,
nucleosides, and nucleotides, 2'-Deoxyribonucleotide
metabolism].
Length = 295
Score = 306 bits (786), Expect = e-102
Identities = 125/235 (53%), Positives = 153/235 (65%), Gaps = 30/235 (12%)
Query: 76 QYLHLLDKIIKTGHKKSDRTGVGTLSLFGAQMRFDLTNGTFPLLTTKRVFWKGVVEELLW 135
QYL LL I++ GH+K DRTG GT+S+FG QMRFDL+ G FPLLTTK+V ++ + ELLW
Sbjct: 1 QYLDLLRDILENGHQKGDRTGTGTISVFGYQMRFDLSKG-FPLLTTKKVPFRLIASELLW 59
Query: 136 FIKGSTNAKELSDKGVKIWD----------PNSTREYLDSIGL-----------VDRKEG 174
F+KG TN + L D V IWD + + G K G
Sbjct: 60 FLKGDTNIRYLLDHNVNIWDEWAFERWVKSDDYNGPDMTDFGHRAQDDPEEDDEFADKYG 119
Query: 175 DLGPVYGFQWRHYGAEYKDMFTDYTDQGIDQLQNIINTIKTNPNDRRIIMCAWNPIDMPK 234
DLGPVYG QWR + + IDQ++N+I IKTNP+ RR+I+ AWNP D+P
Sbjct: 120 DLGPVYGKQWRSWATPDGE--------TIDQIKNVIEMIKTNPDSRRLIVSAWNPEDVPT 171
Query: 235 MALPPCHCLAQFYVADGKLSCQLYQRSADMGLGVPFNIASYSLLTYMIAHVTGLQ 289
MALPPCH L QFYVADGKLSCQLYQRSAD+ LGVPFNIASY+LLT++IA TGL+
Sbjct: 172 MALPPCHTLFQFYVADGKLSCQLYQRSADVFLGVPFNIASYALLTHLIAQETGLE 226
>gnl|CDD|223285 COG0207, ThyA, Thymidylate synthase [Nucleotide transport and
metabolism].
Length = 268
Score = 296 bits (759), Expect = 1e-98
Identities = 116/216 (53%), Positives = 147/216 (68%), Gaps = 19/216 (8%)
Query: 74 EQQYLHLLDKIIKTGHKKSDRTGVGTLSLFGAQMRFDLTNGTFPLLTTKRVFWKGVVEEL 133
+QYL L++ I++ G +SDRTG GTLS+FG QMRFDL+ FPLLTTK+V K ++ EL
Sbjct: 3 MKQYLDLIEHILENGTSRSDRTGTGTLSVFGYQMRFDLSKSEFPLLTTKKVHLKSIIHEL 62
Query: 134 LWFIKGSTNAKELSDKGVKIWDPNSTREYLDSIGLVDRKEGDLGPVYGFQWRHYGAEYKD 193
LWF++G TN L + GVKIWD + Y GDLGPVYG+QWR +
Sbjct: 63 LWFLRGDTNIAYLKENGVKIWDEWADENY-----------GDLGPVYGYQWRKWLRP--- 108
Query: 194 MFTDYTDQGIDQLQNIINTIKTNPNDRRIIMCAWNPIDMPKMALPPCHCLAQFYVADGKL 253
+ IDQ+ +I +K NP+ RR I+ AWNP ++ +MALPPCH L QFYV DGKL
Sbjct: 109 -----DGEKIDQIDKVIEQLKENPDSRRAIVSAWNPGELDEMALPPCHILFQFYVRDGKL 163
Query: 254 SCQLYQRSADMGLGVPFNIASYSLLTYMIAHVTGLQ 289
SC LYQRS D+ LGVPFNIASY+LLT+M+A VTGL+
Sbjct: 164 SCTLYQRSNDVFLGVPFNIASYALLTHMVAQVTGLE 199
>gnl|CDD|240309 PTZ00189, PTZ00189, 60S ribosomal protein L21; Provisional.
Length = 160
Score = 246 bits (631), Expect = 6e-81
Identities = 95/160 (59%), Positives = 115/160 (71%), Gaps = 1/160 (0%)
Query: 294 MTNSKGYRRGTRDLFSRPFRRHGTIPLSVYMKVYKVGDIVDIKGHGAVQKGMPFKDYHGK 353
M +S GYR GTR F++PFR+HG LS Y+ +KVGD VDI AV KGMP+K YHG+
Sbjct: 1 MPHSYGYRAGTRHKFAKPFRKHGVPSLSTYLTTFKVGDYVDIVVDSAVHKGMPYKYYHGR 60
Query: 354 TGRVFNVTQHAVGVIVNKRVRTRIIPKRINVRIEHIKHSKCREDFLKRVKENELKRKEAK 413
TGRVFNVT AVGVIVNKRVR RI+ KRI+VRIEH++ S+CREDFLKRV N+ + EAK
Sbjct: 61 TGRVFNVTPRAVGVIVNKRVRGRIVRKRIHVRIEHVRKSRCREDFLKRVAANDAIKAEAK 120
Query: 414 EKGIKVNLKRQPAQPRPAHIVS-GRTAPVMLAPIPYEFIA 452
+KG + KRQPAQPRPA V T V + P+P+ I
Sbjct: 121 KKGELPSTKRQPAQPRPAGFVKPKPTEVVTVRPLPFVEIY 160
>gnl|CDD|177784 PLN00190, PLN00190, 60S ribosomal protein L21; Provisional.
Length = 158
Score = 215 bits (549), Expect = 1e-68
Identities = 87/155 (56%), Positives = 112/155 (72%), Gaps = 1/155 (0%)
Query: 294 MTNSKGYRRGTRDLFSRPFRRHGTIPLSVYMKVYKVGDIVDIKGHGAVQKGMPFKDYHGK 353
M G R TRDLF+RPFR+ G IPL+ Y++ +KVGD VDIK +GA+ KGMP K YHG+
Sbjct: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLTTYLRTFKVGDYVDIKVNGAIHKGMPHKFYHGR 60
Query: 354 TGRVFNVTQHAVGVIVNKRVRTRIIPKRINVRIEHIKHSKCREDFLKRVKENELKRKEAK 413
TG V+NVT+ AVGV VNK+V RII KRI+VR+EH++ S+CRE+FL R K N+ + EAK
Sbjct: 61 TGIVWNVTKRAVGVEVNKQVGNRIIRKRIHVRVEHVQPSRCREEFLLRKKSNDEAKAEAK 120
Query: 414 EKGIKVNLKRQPAQPRPAHIVSGRTAPVMLAPIPY 448
KG K++ KRQP P+P +V G T + PIPY
Sbjct: 121 AKGEKISTKRQPKGPKPGFMVEGATLET-VTPIPY 154
>gnl|CDD|184347 PRK13821, thyA, thymidylate synthase; Provisional.
Length = 323
Score = 181 bits (461), Expect = 2e-53
Identities = 87/246 (35%), Positives = 130/246 (52%), Gaps = 39/246 (15%)
Query: 75 QQYLHLLDKIIKTGHKKSDRTGVGTLSLFGAQMRFDLTNGTFPLLTTKRVFWKGVVEELL 134
+QYL L+ I+ TG + +RTG+ T+S+ GA +RFDL G FP +TTK++ +K + EL+
Sbjct: 2 KQYLDLVRTILDTGTWQENRTGIRTISIPGAMLRFDLQQG-FPAVTTKKLAFKSAIGELV 60
Query: 135 WFIKGSTNAKELSDKGVKIWDPNSTR--EYLDSIGLVDRKEG--DLGPVYGFQWRHYGAE 190
F++ S +A + G K+WD N+ ++L + ++G DLG VYG QWR +
Sbjct: 61 GFLRASRSAADFRALGCKVWDQNANENAQWLAN----PYRQGVDDLGDVYGVQWRQWPG- 115
Query: 191 YKDMFTDYTDQ---------------------------GIDQLQNIINTIKTNPNDRRII 223
YK + Q IDQL+ ++TI NP RRI+
Sbjct: 116 YKVLDASADAQIADATSRGFRIVARFDEDGAPKVLLYKAIDQLRQCLDTIMNNPGSRRIL 175
Query: 224 MCAWNPIDMPKMALPPCHCLAQFY--VADGKLSCQLYQRSADMGLGVPFNIASYSLLTYM 281
WNP + ++ALP CH L QF V ++S LY RS D+GLG PFN+ + L +
Sbjct: 176 FHGWNPAVLDEIALPACHLLYQFLPNVETREISLCLYIRSNDVGLGTPFNLTEGAALLSL 235
Query: 282 IAHVTG 287
+ +TG
Sbjct: 236 VGRLTG 241
>gnl|CDD|110179 pfam01157, Ribosomal_L21e, Ribosomal protein L21e.
Length = 99
Score = 157 bits (398), Expect = 4e-47
Identities = 67/99 (67%), Positives = 78/99 (78%)
Query: 295 TNSKGYRRGTRDLFSRPFRRHGTIPLSVYMKVYKVGDIVDIKGHGAVQKGMPFKDYHGKT 354
NS G RRGTR +F RPFR+HG PLS Y++ YKVGD VDIK +G+VQKGMP K +HGKT
Sbjct: 1 PNSNGPRRGTRYMFKRPFRKHGLSPLSTYLREYKVGDYVDIKINGSVQKGMPHKRFHGKT 60
Query: 355 GRVFNVTQHAVGVIVNKRVRTRIIPKRINVRIEHIKHSK 393
GRV+NVT AVGV VNK+VR I+ KRINVR EHI+ SK
Sbjct: 61 GRVYNVTPGAVGVAVNKKVRDGILEKRINVRPEHIRPSK 99
>gnl|CDD|225050 COG2139, RPL21A, Ribosomal protein L21E [Translation, ribosomal
structure and biogenesis].
Length = 98
Score = 120 bits (302), Expect = 4e-33
Identities = 43/102 (42%), Positives = 51/102 (50%), Gaps = 4/102 (3%)
Query: 295 TNSKGYRRGTRDLFSRPFRRHGTIPLSVYMKVYKVGDIVDIKGHGAVQKGMPFKDYHGKT 354
S GYR TR + R G PLS Y++ YKVGD V I +V KGMP + GKT
Sbjct: 1 KRSHGYRSRTRYKLQKDPRERGLSPLSRYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKT 60
Query: 355 GRVFNVTQHAVGVIVNKRVRTRIIPKRINVRIEHIKHSKCRE 396
G V V A V V + K + VR EH+K KCRE
Sbjct: 61 GTVVGVRGRAYKVEVYDGNKE----KTLIVRPEHLKPQKCRE 98
>gnl|CDD|235275 PRK04306, PRK04306, 50S ribosomal protein L21e; Reviewed.
Length = 98
Score = 75.3 bits (186), Expect = 9e-17
Identities = 27/64 (42%), Positives = 35/64 (54%)
Query: 294 MTNSKGYRRGTRDLFSRPFRRHGTIPLSVYMKVYKVGDIVDIKGHGAVQKGMPFKDYHGK 353
M S G+R TR S+ R G PLS ++ ++ GD V I +V KGMP +HGK
Sbjct: 2 MKKSHGFRSKTRKKLSKSPRERGLSPLSRALQEFEEGDKVHIVIDPSVHKGMPHPRFHGK 61
Query: 354 TGRV 357
TG V
Sbjct: 62 TGTV 65
>gnl|CDD|132326 TIGR03283, thy_syn_methano, thymidylate synthase, methanogen type.
Thymidylate synthase makes dTMP for DNA synthesis, and
is among the most widely distributed of all enzymes.
Members of this protein family are encoded within a
completed genome sequence if and only if that species is
one of the methanogenenic archaea. In these species,
tetrahydromethanopterin replaces tetrahydrofolate, The
member from Methanobacterium thermoautotrophicum was
shown to behave as a thymidylate synthase based on
similar side reactions (the exchange of a characteristic
proton with water), although the full reaction was not
reconstituted. Partial sequence data showed no
similarity to known thymidylate synthases simply because
the region sequenced was from a distinctive N-terminal
region not found in other thymidylate synthases. Members
of this protein family appear, therefore, to a novel,
tetrahydromethanopterin-dependent thymidylate synthase
[Purines, pyrimidines, nucleosides, and nucleotides,
2'-Deoxyribonucleotide metabolism].
Length = 199
Score = 65.1 bits (159), Expect = 2e-12
Identities = 39/136 (28%), Positives = 53/136 (38%), Gaps = 15/136 (11%)
Query: 154 WDPNSTREYLDSIGLVDRKEGDLGPVYGFQWRHYGAEYKDMFTDYTDQGIDQLQNIINTI 213
D EY L+D + YG + R Y GIDQ+ II +
Sbjct: 58 LDEEKLEEYEKQ--LLDPERQGFVYTYGNRLRRYF-------------GIDQIDYIIERL 102
Query: 214 KTNPNDRRIIMCAWNPIDMPKMALPPCHCLAQFYVADGKLSCQLYQRSADMGLGVPFNIA 273
+PN RR I W+P K+ PC L QF + D KL + RS D+G N
Sbjct: 103 NQSPNSRRAIAITWDPPQDIKVDEVPCLQLVQFLIRDNKLYLTAFFRSNDVGGAWVANAI 162
Query: 274 SYSLLTYMIAHVTGLQ 289
L +A G++
Sbjct: 163 GLRRLQEYVAEKVGVE 178
>gnl|CDD|179181 PRK00956, thyA, thymidylate synthase; Provisional.
Length = 208
Score = 51.9 bits (125), Expect = 1e-07
Identities = 29/87 (33%), Positives = 38/87 (43%)
Query: 203 IDQLQNIINTIKTNPNDRRIIMCAWNPIDMPKMALPPCHCLAQFYVADGKLSCQLYQRSA 262
+DQ+ II +K N N RR WNP K+ PC L F + DGKL + RS
Sbjct: 95 VDQIDYIIEKLKENKNSRRATAVTWNPYIDTKVDEVPCLQLVDFLIRDGKLYLTVLFRSN 154
Query: 263 DMGLGVPFNIASYSLLTYMIAHVTGLQ 289
D G N L +A G++
Sbjct: 155 DAGGAFHANAIGLIKLGEYVAEKVGVE 181
>gnl|CDD|235777 PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl carrier
protein subunit; Validated.
Length = 155
Score = 32.1 bits (74), Expect = 0.24
Identities = 17/62 (27%), Positives = 22/62 (35%), Gaps = 6/62 (9%)
Query: 386 IEHIKHSKCREDFLKRVKENELKRKEAKEKGIKVNLKRQPAQPRPAHIVSGRTAPVMLAP 445
I IK ++ V E+ + E KE V + R A P APV AP
Sbjct: 3 IRKIK------KLIELVDESGISEFEIKEGEESVRISRAAAAPVAPVAQQAAAAPVAAAP 56
Query: 446 IP 447
Sbjct: 57 AA 58
>gnl|CDD|203706 pfam07647, SAM_2, SAM domain (Sterile alpha motif).
Length = 66
Score = 29.6 bits (67), Expect = 0.49
Identities = 19/81 (23%), Positives = 28/81 (34%), Gaps = 25/81 (30%)
Query: 151 VKIWDPNSTREYLDSIGLVDRKEGDLGPVYGFQWRHYGAEYKDMFTDYTDQGIDQLQNI- 209
V+ W P E+L SIGL +Y D F D G + L +
Sbjct: 1 VESWSPEDVAEWLRSIGL--------------------PQYADNFRDQGITGGELLLRLT 40
Query: 210 INTIK----TNPNDRRIIMCA 226
+K T+ R+ I+
Sbjct: 41 EEDLKALGITSVGHRKKILKK 61
>gnl|CDD|241363 cd13209, PH-GRAM_MTMR3_MTMR4, Myotubularian (MTM) related 3 and 4
proteins (MTMR3 and MTMR4) Pleckstrin
Homology-Glucosyltransferases, Rab-like GTPase
activators and Myotubularins (PH-GRAM) domain. MTMR3 is
a member of the myotubularin dual specificity protein
phosphatase gene family. MTMR3 binds to phosphoinositide
lipids through its PH-GRAM domain, and can hydrolyze
phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro. The
protein can self-associate and also form heteromers with
MTMR4. MTMR4, a member of the myotubularin dual
specificity protein phosphatase gene family. MTMR4 binds
to phosphoinositide lipids through its PH-GRAM domain,
and can hydrolyze phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro. The
protein form heteromers with MTMR3. Both MTMR3 and MTMR4
contain a N-terminal PH-GRAM domain, a Rac-induced
recruitment domain (RID) domain, an active PTP domain, a
SET-interaction domain, a coiled-coil region, and a
C-terminal lipid-binding FYVE domain which binds
phosphotidylinositol-3-phosphate. Myotubularin-related
proteins are a subfamily of protein tyrosine
phosphatases (PTPs) that dephosphorylate
D3-phosphorylated inositol lipids. Mutations in this
family cause the human neuromuscular disorders
myotubular myopathy and type 4B Charcot-Marie-Tooth
syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain
naturally occurring substitutions of residues required
for catalysis by PTP family enzymes. Although these
proteins are predicted to be enzymatically inactive,
they are thought to function as antagonists of
endogenous phosphatase activity or interaction modules.
Most MTMRs contain a N-terminal PH-GRAM domain, a
Rac-induced recruitment domain (RID) domain, a PTP
domain (which may be active or inactive), a
SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is part
of a larger motif with a pleckstrin homology (PH) domain
fold. The PH domain family possesses multiple functions
including the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date.
Length = 121
Score = 30.0 bits (67), Expect = 0.95
Identities = 14/54 (25%), Positives = 23/54 (42%)
Query: 345 MPFKDYHGKTGRVFNVTQHAVGVIVNKRVRTRIIPKRINVRIEHIKHSKCREDF 398
+PF G+ AV I N R+ + INV + ++ +CR+ F
Sbjct: 25 VPFTVLQGEGVEYLGHANDAVIAISNYRLHIKFKDSVINVPLRMMESVECRDMF 78
>gnl|CDD|241495 cd13341, PH-GRAM_MTMR3, Myotubularian (MTM) related 3 protein
(MTMR3) Pleckstrin Homology-Glucosyltransferases,
Rab-like GTPase activators and Myotubularins (PH-GRAM)
domain. MTMR3 is a member of the myotubularin dual
specificity protein phosphatase gene family. MTMR3 binds
to phosphoinositide lipids through its PH-GRAM domain,
and can hydrolyze phosphatidylinositol(3)-phosphate and
phosphatidylinositol(3,5)-biphosphate in vitro. The
protein can self-associate and also form heteromers with
MTMR4. Both MTMR3 and MTMR4 contain a N-terminal PH-GRAM
domain, a Rac-induced recruitment domain (RID) domain,
an active PTP domain, a SET-interaction domain, a
coiled-coil region, and a C-terminal lipid-binding FYVE
domain which binds phosphotidylinositol-3-phosphate.
Myotubularin-related proteins are a subfamily of protein
tyrosine phosphatases (PTPs) that dephosphorylate
D3-phosphorylated inositol lipids. Mutations in this
family cause the human neuromuscular disorders
myotubular myopathy and type 4B Charcot-Marie-Tooth
syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain
naturally occurring substitutions of residues required
for catalysis by PTP family enzymes. Although these
proteins are predicted to be enzymatically inactive,
they are thought to function as antagonists of
endogenous phosphatase activity or interaction modules.
Most MTMRs contain a N-terminal PH-GRAM domain, a
Rac-induced recruitment domain (RID) domain, a PTP
domain (which may be active or inactive), a
SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is part
of a larger motif with a pleckstrin homology (PH) domain
fold. The PH domain family possesses multiple functions
including the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date.
Length = 148
Score = 30.0 bits (67), Expect = 1.5
Identities = 13/54 (24%), Positives = 28/54 (51%)
Query: 345 MPFKDYHGKTGRVFNVTQHAVGVIVNKRVRTRIIPKRINVRIEHIKHSKCREDF 398
+PF + HG++ + A+ + N R+ + +NV ++ I+ +CR+ F
Sbjct: 32 VPFPELHGESTEYVGRAEDAIIALSNYRLHIKFKESVVNVPLQLIESVECRDIF 85
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal. This
domain is found to the N-terminus of bacterial signal
peptidases of the S49 family (pfam01343).
Length = 154
Score = 29.8 bits (68), Expect = 1.5
Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 365 VGVIVNKRVRTRIIPKRINVR---------IEHIKHSKCREDFLKRVKENELKRKEAKEK 415
VG+IV + + + + E ++ + + LK ++ E K ++AK K
Sbjct: 25 VGLIVALAQKKKGKKGELEITDLNEEYKDLKESLEAALLDKKELKAWEKAEKKAEKAKAK 84
Query: 416 GIKVNLKRQPAQPR 429
K K++ +PR
Sbjct: 85 AEKKKAKKEEPKPR 98
>gnl|CDD|234555 TIGR04344, ovoA_Nterm, 5-histidylcysteine sulfoxide synthase.
Ovothiol A is N1-methyl-4-mercaptohistidine. In the
absence of S-adenosylmethione, a methyl donor, the
intermediate produced is 4-mercaptohistidine. In both
Erwinia tasmaniensis and Trypanosoma cruzi, a protein
occurs with 5-histidylcysteine sulfoxide synthase
activity, but these two enzymes and most homologs share
an additional C-terminal methyltransferase domain. Thus
OvoA may be a bifunctional enzyme with
5-histidylcysteine sulfoxide synthase and
4-mercaptohistidine N1-methyltranferase activity. This
model describes the 5-histidylcysteine sulfoxide
synthase domain, a homolog of the ergothioneine
biosynthesis protein EgtB [Biosynthesis of cofactors,
prosthetic groups, and carriers, Glutathione and
analogs].
Length = 442
Score = 30.7 bits (70), Expect = 1.7
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 363 HAVGVIVNKRVRTRIIPKRINVRIEHI 389
H +NK V +I +RIN R E I
Sbjct: 58 HTATFYINKLVLAGLIDERINPRFESI 84
>gnl|CDD|147693 pfam05676, NDUF_B7, NADH-ubiquinone oxidoreductase B18 subunit
(NDUFB7). This family consists of several
NADH-ubiquinone oxidoreductase B18 subunit proteins from
different eukaryotic organisms. Oxidative
phosphorylation is the well-characterized process in
which ATP, the principal carrier of chemical energy of
individual cells, is produced due to a mitochondrial
proton gradient formed by the transfer of electrons from
NADH and FADH2 to molecular oxygen. The oxidative
phosphorylation (OXPHOS) system is located in the
mitochondrial inner membrane and consists of five
multi-subunit enzyme complexes and two small electron
carriers: coenzyme Q10 and cytochrome C. At least 70
structural proteins involved in the formation of the
whole OXPHOS system are encoded by nuclear genes,
whereas 13 structural proteins are encoded by the
mitochondrial genome. Deficiency of NADH ubiquinone
oxidoreductase, the first enzyme complex of the
mitochondrial respiratory chain, is one of the most
frequent causes of human mitochondrial
encephalomyopathies.
Length = 66
Score = 27.7 bits (62), Expect = 2.2
Identities = 11/23 (47%), Positives = 16/23 (69%), Gaps = 3/23 (13%)
Query: 387 EHIKHS--KC-REDFLKRVKENE 406
EH +HS KC +D++ R+KE E
Sbjct: 44 EHERHSYEKCQYDDYVLRMKEYE 66
>gnl|CDD|144565 pfam01024, Colicin, Colicin pore forming domain.
Length = 187
Score = 29.6 bits (67), Expect = 2.5
Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 13/64 (20%)
Query: 186 HYGAEYKDMFTDYTDQ-------GIDQLQNIINTIKTNPN------DRRIIMCAWNPIDM 232
+YG +YK + + D +D+ K NPN DR I A ++
Sbjct: 29 YYGEKYKKLARELADDAKGKKIRSVDEALASFEKYKANPNKKINKADRDAIANALKSVNA 88
Query: 233 PKMA 236
MA
Sbjct: 89 QDMA 92
>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 30.0 bits (68), Expect = 2.6
Identities = 21/97 (21%), Positives = 43/97 (44%), Gaps = 18/97 (18%)
Query: 329 VGDIVDIKGHGAVQKGMPFKDYHG-------KTGRVFNVTQHAVGVIVNKRVRTRIIPKR 381
VG + + +GA + + G +G V N+ + V ++V +++ R
Sbjct: 16 VGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDY---VKEGQKVVAKVL--R 70
Query: 382 INVRIEHIKHSKCREDFLKRVKENELKRKEAKEKGIK 418
++ + HI S LKRV E++ ++K + K +
Sbjct: 71 VDPKRGHIDLS------LKRVTEHQRRKKIQEWKKEQ 101
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 30.1 bits (68), Expect = 2.8
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 123 RVFWKGVVEELLWFIKGSTNAKELSDK-GVKIWDPNSTREYLDSI 166
R +W V+ E+L KG+ + KELSD +K D ST + L+ I
Sbjct: 357 RGYWTRVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSLNLI 401
>gnl|CDD|202017 pfam01868, UPF0086, Domain of unknown function UPF0086. This
family consists of several archaeal and eukaryotic
proteins. The archaeal proteins are found to be
expressed within ribosomal operons and several of the
sequences are described as ribonuclease P protein
subunit p29 proteins.
Length = 89
Score = 27.2 bits (61), Expect = 5.3
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 348 KDYHGKTGRVFNVTQHAVGVIVNKRVRTRIIPKRINV 384
G GRV + T++ + VI ++ R + IPK +V
Sbjct: 25 PSLVGIKGRVVDETRNTL-VIETEKGREKTIPKDGSV 60
>gnl|CDD|217651 pfam03635, Vps35, Vacuolar protein sorting-associated protein 35.
Vacuolar protein sorting-associated protein (Vps) 35 is
one of around 50 proteins involved in protein
trafficking. In particular, Vps35 assembles into a
retromer complex with at least four other proteins Vps5,
Vps17, Vps26 and Vps29. Vps35 contains a central region
of weaker sequence similarity, thought to indicate the
presence of at least three domains.
Length = 741
Score = 28.7 bits (65), Expect = 7.7
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 14/79 (17%)
Query: 16 TSVQTDEQQ---YLHLLDKIIK--TIIRYQKTLHHSHTMFNLL-PIFSPQGDNPDQNGTS 69
S + L ++D I+K T+I TL +F L+ P+ Q D P +
Sbjct: 417 LSSLDYSTRKSVALAIIDNILKNNTLIT---TLDDVERLFELISPLIKDQPDQPSDELET 473
Query: 70 VQTDEQQY-----LHLLDK 83
+ E+Q +HL+
Sbjct: 474 EEFAEEQEKVARLIHLIRS 492
>gnl|CDD|197735 smart00454, SAM, Sterile alpha motif. Widespread domain in
signalling and nuclear proteins. In EPH-related tyrosine
kinases, appears to mediate cell-cell initiated signal
transduction via the binding of SH2-containing proteins
to a conserved tyrosine that is phosphorylated. In many
cases mediates homodimerisation.
Length = 68
Score = 26.1 bits (58), Expect = 8.6
Identities = 15/54 (27%), Positives = 19/54 (35%), Gaps = 23/54 (42%)
Query: 151 VKIWDPNSTREYLDSIGLVDRKEGDLGPVYGFQWRHYGAEYKDMFTDYTDQGID 204
V W P S ++L+SIGL +Y D F GID
Sbjct: 1 VSQWSPESVADWLESIGL--------------------EQYADNF---RKNGID 31
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 28.4 bits (64), Expect = 9.9
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 1/39 (2%)
Query: 184 WRHYGAEYKDMFTDYTDQGIDQLQNIINTIKTNPNDRRI 222
W H AE K+ Y + L+ IN+++
Sbjct: 399 WLHLVAELKEDIDAYQKE-KKGLEKAINSLEKEIKQLEA 436
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
0.321 0.138 0.418
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,372,760
Number of extensions: 2269045
Number of successful extensions: 2288
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2265
Number of HSP's successfully gapped: 38
Length of query: 452
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 352
Effective length of database: 6,502,202
Effective search space: 2288775104
Effective search space used: 2288775104
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 (21.8 bits)
S2: 61 (27.3 bits)